Human Evil, Music, Logic, and Himalayan Dung Heaps

_{Gil Dodgen

July 6, 2011

Intelligent Design}

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When I was in college I studied classical piano with Istvan Nadas who was a Hungarian concert pianist and a student of Bela Bartok. Istvan was a miraculous survivor of one of Hitler’s death camps. The stories he told me still haunt me to this day.

The commandant of the death camp liked to play Bach over the loudspeaker system while he had random inmates shot or hung, just for fun and entertainment. Nadas told me about the horror of listening to Bach while he watched his fellow inmates being machine-gunned to death in front of him. Nadas told me, “I knew every note of that music and could play it on the piano, but I also knew that if they discovered I was a concert pianist they would break all my fingers so I could never play the piano again.”

Nadas’s death camp was eventually “liberated” by the Russians. Istvan was one of only 150 survivors from a camp of thousands. He weighed 90 pounds and was suffering from dysentery and other diseases. While the Russians were transporting him on a train to what he knew would be a Russian internment camp he managed to jump out of the train as it slowed in the mountains. Under machine-gun fire he fled into the trees, was helped my local residents, and was eventually smuggled by an African American GI under a tarp in the back of a jeep through Check Point Charlie.

Nadas eventually discovered that every member of his extended family had either been gassed or otherwise tortured and exterminated by the Nazis, or shot by the Russians, with one exception: his mother, whom he eventually tracked down in Italy after the war.

One evening, after a concert at the university while I was studying piano with Nadas, which was conducted by a guest “contemporary composer” — it was just a bunch of random cacophony, very painful to listen to, but sold as legitimate music — I asked Nadas what he thought.

“It is a Himalayan dung heap,” he replied. (Nadas spoke six languages fluently, and had a way with words.) This phrase stuck in my mind, and it’s the perfect description of something so obviously stupid that it represents a pile of crap of Himalayan proportions.

The students and faculty applauded the Himalayan-dung-heap “music” because no one had the courage to point out the obvious, except for Nadas.

This is a perfect metaphor for Darwinism. Very few people in academia have the courage to point out the cacophony and illogic of Darwinian speculation.

It takes the courage of someone like Nadas, who was willing to jump off a train in the mountains under machine-gun fire, to tell the obvious truth.

Comments

Please forgive my somewhat tangential, and belated, comment. I found your article as part of a search for information about Istvan Nadas. I met Istvan Nadas when I was a teenager attending a small-town high school in the Willamette Valley of Oregon. His wife at the time was one of my English teachers, and she took a small group of us home to meet her husband. He told stories of the Holocaust and played for us a very haunting piano work he had composed in response to his experiences. It strikes me now how unlikely and rich a blessing it was for a rural child such as myself to meet such a great man. Subsequently, I attended a portion of a series of recitals he played at George Fox College which comprised a complete Beethoven Piano Sonata cycle. Thank you for sharing your own experiences with Mr. Nadas. It comforts me to know that he is well remembered by others. As for the primary subject matter of your writings here, I regard the subject of Evolution as a theoretical process in general to be an interesting subject of inquiry, but do not share the certainty many have in the conclusions they have drawn from it. Evidence of adaptation through natural selection is by no means a conclusive repudiation of either an initial intelligent design nor does it prove that observed adaptations are not part of the ongoing manifestation of that design. Michael Kepler

I wanted to continue some thoughts on my post at #244 by explaining in more depth why I belive that in order to determine that CSI has been generated by a blind process either naturally or via simulation, that multiple systems need to be represented. The below is a little lengthy, and I'll split it up into more than one post. It rambles a bit. In my defense, it would have taken me much longer to clean it up and condense it than it will take anyone to read it. I think it conveys my thoughts pretty welll and is fairly intelligble as it stands, but I expect it'll need some revision too. Quoting myself above:
Ending point: a self-replicating virtual cell, containing at least each of these: an information storage medium, and an information processing system which operates on the medium, into which the systems themselves are encoded. These items are needed because without an abstraction between information storage and functional implementation, we couldn’t do anything but violence to the concept of information, which needs some sort of encryption and decryption protocol between two sets of elements that can have nothing but an abstract link between them — and this protocol must represent a link between an inert symbolic medium and a functional element into which it translates. In other words, we need one language which describes the element being operated on, and another language which directly represents the element being operated on. This element must be functional, and the system which does the translating from one to the other must itself be encoded in both languages.
I want to define how I'm using some key terms in case my usage differes some from an alternate or more orthodox usage. Specified Complexity: the presence of both specification and complexity. Specification: a sequence of symbols which conforms to an independently given pattern or function. Complexity: contingent arrangements of matter exceeding 500 bits. This is often set even higher, but 500 bits seems to account for every atom in the universe multiplied by every Planck-time quantum state that's ever occured in its history. Information: the presence of specified complexity. Chance: randomly contingent but otherwise inexplicable events, such as replication errors. Necessity:That which must occur with specific arrangements of matter under a specific set of circumstances. Law: That which governs necessity as expressed in the laws of physics and chemistry. Protocol: A specification which describes a mapping between two compatible languages, OR an entity which preforms the function of translation between the two. Mission.Imposible

EL: I am completely convinced by substantial evidence (including my own work!) that self-replication with variance in a fitness landscape results in entities with the appearance of well-engineered design!
Nobody disagrees. Genetic algorithms are used in engineering. I've written GAs myself. Finding solutions that were not readily foreseeable is the whole point of them. But, of course, GAs are designed to evolve with intelligently designed targets and terms. Was biological evolution designed to evolve towards certain goals? Science cannot presently answer that question. mike1962

EL: So people’s priors (in a Bayesian sense) are low, whereas they are considerably higher for a mechanism that we know works in principle
That's like saying since a car can get you from L.A. to New York that, in principle, it can get you to London, without considering any additional hurdles beyond pavement and dirt roads that may be encountered. While it is understandable why biologists and atheists would be motivated to place their hopes in this huge gap, the fact is, the known biological mechanisms have not been shown, either empirically or in principle, to be sufficient to produce novel cell types, tissue types, organs or body plans. And, of course, OOL remains virtually uncharted. So what can the science actually offer us at this point? Only that a gap-laden evolution of life seems to have occurred, there seems to be a sort of messy hierarchy to it, and that small random variations and natural selection can effect small phenotype changes. That's all. It cannot tell us the degree that intelligent intervention was required for large scale evolution and to what degree "blind" (atelic) mechanisms were sufficient. This is the point of contention. mike1962

Elizabeth Liddle @138:
I have no quarrel at all with the idea that the genome contains information; nor have I any quarrel with Nirenberg’s methodology – he and his team systematically figured out which codons coded (hence the name) for which amino acids, and noted that the sequence of the codons in the DNA molecule, corresponded to the sequence of the amino acids in the protein. We are in complete agreement with this I think. What I need to do, however, is to abstract from that specific example (of codons amino acids, etc) a criterion by which any candidate for the category “information” can be so categorised. Clearly not all information is mediated by codons; not all messages are “about” proteins. It’s not that I have any doubt that Nirenberg was finding “information” in the genome, nor about his methods for doing so – figuring out what mapped to what. The problem is defining what constitues a “mapping”.
So now if we could just develop a set of operations ... let's see ... identify a code ... figure out what maps to what... Upright BiPed:
Nirenberg et al discovered the information in the genome by demonstrating it. They isolated the representations, deciphered the protocols, and documented the effects; the same way that all other recorded information has been discovered.
Isolate the representations. Decipher the protocols. Document the effects. Mung

Nirenberg Elizabeth Liddle:
It’s not that I have any doubt that Nirenberg was finding “information” in the genome, nor about his methods for doing so – figuring out what mapped to what.
Mung:
How did they find it?
Elizabeth Liddle:
It doesn’t matter how they did it.
Well, that pretty much makes it clear what's going on here. The manner in which the presence of information was demonstrated to exist in the genome is irrelevant. Mung

material.infantacy: Your post looks interesting, but I haven't had time to read it properly yet. I will try to respond later today. Elizabeth Liddle

"Elizabeth has asserted that Shannon information is a measure of reduction in uncertainty. ..." One might almost forgive her her misunderstanding, if one were not aware of how long you have been conversationalizing with her on the matter. For, after all, that is how most treatments of S.I. describe it. And your further analysis of the "uncertainty" issue is spot-on. But, getting back to the 60mHz "message" ... its 'Shannon Information' is far greater than 0 bits. At a minimum, the S.I. requires however many bits are necessary to specify the tone and however many to specify the duration. If one cares about *when* the "message" was first received, one needs however many bits are required to record that. Was the "message" received multiple time? What is the time lapse between one and the next? During observation, is this time lapse invariant? And so on. Ilion

Likewise, she appears to think that if I do all the heavy lifting we are doing an equal amount of work and this amounts to a "real conversation." Mung

I think Lizzie is waiting for pixels to have an effect on her brain. Mung

Elizabeth has asserted that Shannon information is a measure of reduction in uncertainty. In order for a reduction in uncertainty to be measurable there must be an expectation. That expectation must be changed by the measurement. That expectation must be an expectation about what one believes to be the case and the reduction in uncertainty changes what one believes to be the case. It follows that, contrary to Elizabeth's claims, Shannon information is not information devoid of meaning. Mung

Has she forgotten already that 'Shannon Information' is totally agnostic about any information "in" the message? Ilion

Elizabeth has asserted that Shannon information can measure 0 bits of information in a message and can therefore tell us that there is no information present in a message and that therefore information can be devoid of meaning. We're still awaiting the demonstration. Mung

For the record. Elizabeth Liddle:
My original claim was that, contrary to ID claims, that Chance and Necessity could produce Information. Not “information in the genome”. Not “information at any place or time”. But “information”. For all definitions of information I was aware of, that claim stands, although what I had in mind was CSI.
Mung

Shannon Information 1. Does Shannon information give us an operational definition of information? 2. Does Shannon information give us a definition of information? Now we must keep in mind that an operational definition of information does not tell us what information is. So with regard to Shannon information Elizabeth has made two fundamental errors. 1.) She has conflated an operational definition with a definition of what a thing is. 2.) She has reasoned that because Shannon information provides a measure of information, and because operational definitions are a way to "measure" something, Shannon information is an operational definition of information. Mung

Continuing the Charade
It [one definition of information from Webster's dictionary] also includes this post, which is an arrangement of pixels on your screen, and produces specific effects in your brain, and, possibly, on your blood pressure.
The pixels on the screen are inherently meaningless. But even if they had meaning, they can produce no effect unless they are received. Pixels on a screen may be used to convey information when they are arranged in such a manner so as to take on certain shapes, more specifically, the shapes of symbols. There's that nasty nasty word again. Let's pretend we didn't say it. We certainly would not want to include the concept of a symbol in our operational definition. The pixels themselves, of course, have no effect on my brain, unless perhaps I decide to ram my head through the monitor in frustration. How carefully she must avoid actually talking about information and reduce it to pixels. Mere matter. Yet is it not the case that the pixels have a specific effect on the screen? So there you have it. Information! No brain required.
This [definition of information] is adroit, because it rules out, for example, a rock falling off a cliff, which might well produce “specific effects” but what is doing the producing is a material object, the rock, not an “arrangement of something”.
Pixels are not material objects? I can arrange some rocks and drop them into a pond and assert that due to the specific effect they produced I have demonstrated the presence of information. Or I can arrange some small pebbles on a plate into a semblance of a smiley face, place the plate on a scale, and since they will in fact have a quite specific and observable effect and even a measurable effect on the scale, I can declare, INFORMATION! Can we get a reality check? So to me at least it appears that Lizzie is asking too much from her definition of information. Far less is required. Or is it perhaps the case that Lizzie has left out an important ingredient. Upright BiPed, bless his soul:
I know you’re a stickler for precision Dr Liddle, but how does one object “communicate” with another object?
I think he's still awaiting a response from Elizabeth on that one. So let's have another look at that Webster's definition, as a sort of sanity check.
1: the communication or reception of knowledge or intelligence 2b : the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (as nucleotides in DNA or binary digits in a computer program) that produce specific effects
Rocks? Pixels? These are mere bits of matter than can be arranged. What, specifically, must material entities such as rocks and pixels be arranged into in order that they might acquire some attribute inherent in that arrangement which is just one of two or more alternative sequences or arrangements whereby whatever that is that inheres in that arrangement [let's call it information if] it is communicated by that arrangement in order that it might bring about a specific effect? Rocks in a pond are not enough. Pixels on a screen are not enough. Those pixels must be arranged, into symbols, those symbols must be arranged, into sequences, those sequences must be communicated, that which is communicated must bring about a specific effect. Now. An operational definition please, Lizzie. What are the entities that must be observed? What are the steps that define what operations must be executed, what observations must be made, by which we might declare the presence of information? Mung

It may be a bestseller: 'Defining the Functionally Operationalized Mung' Ilion

Ilion, I shall promptly get to work defining a set of discrete steps according to which anyone might be able to say that they do in fact understand what I say even if it is fact the case that they have not understood a single word. Mung

"function A -> transcribes/copies -> symbol a" should be "function A -> transcribes/copies -> symbols a and b" material.infantacy

You know, Mung, your problem is that you haven't learned to use words like "operationalize"; it's no wonder no one (including yourself) can understand anything you say. Ilion

After gleanings from this and other threads, I'm trying to understanding some issues relating to generating complex specified information from scratch (bootstrapping an information generation and storage system) and understand the minimum requirement of a system which would demonstrate that such has been accomplished. I'd appreciate criticism, as harsh and unruly as one sees fit. Starting point: a virtual self-replicating molecule of, say, 50-100 bits, with some latitude given to stability after any replication which produces an error. Ending point: a self-replicating virtual cell, containing at least each of these: an information storage medium, and an information processing system which operates on the medium, into which the systems themselves are encoded. These items are needed because without an abstraction between information storage and functional implementation, we couldn't do anything but violence to the concept of information, which needs some sort of encryption and decryption protocol between two sets of elements that can have nothing but an abstract link between them -- and this protocol must represent a link between an inert symbolic medium and a functional element into which it translates. In other words, we need one language which describes the element being operated on, and another language which directly represents the element being operated on. This element must be functional, and the system which does the translating from one to the other must itself be encoded in both languages. The protocol should be readily decipherable. A persistent observer should be able to decipher the protocol and hence translate in either direction between the storage system and the processing system. A sample image of symbols and their corresponding functions: symbol a -> encodes -> function A symbol b -> encodes -> function B ... function A -> is encoded into -> symbol a function B -> is encoded into -> symbol b ... function A -> transcribes/copies -> symbol a function B -> translates symbol a or b into -> function A or B ... I have some other notes but that's a good naive start. Tell me what's wrong with it. I can take it. UB, Mung, EL, anyone else? Does what I'm proposing make any sense, or am I stuck in a la la land of my own? material.infantacy

Elizabeth Liddle:
Please try to understand what an operational definition is
Indeed. I'm always up for learning something new. First and foremost, an operational definition is not in fact a definition. Rather it is a description. An operational definition is a process or procedure, a set of "operations," that can be followed in order to determine whether some thing of interest is present, for example, information. It is in defining this process or procedure, these operations, that we have created an operational definition. How am I doing so far? It's really not that complicated. And yes, even I can understand it. What's more, I am capable of communicating it to others in my own words, words simple and plain enough for others to understand. And this just goes to show how confused you are about Shannon information, but that's a topic for a different post. Mung

Mung, I'm sorry, but you are confused. I don't blame you, because it's confusing, but it is, I submit, you who are confused:
Let me see if I can state this another way. You, Elizabeth, are attempting to develop an operational definition of information according to what your proposed simulation will do.
No. I'm sorry, Mung, but you still haven't understood the purpose of an operational definition. I'm not sure why, but you haven't. You seem to think that I decide what my sim will do, and then define "information" to match the output. That would be circular. It is not what I am doing.
And then you accuse Upright BiPid of circularity! Oh. my. Gosh.
I don't accuse anyone of anything. I merely point out that the use of high-level terms like "symbol" or "representation" in a conceptual definition leads to potential circularity, which the Merriam-Webster definition avoids.
What you need to do, what you ought to do, is develop an operational definition that is independent of your simulation.
Well, as I said, Mung, that is actually a nonsense. Please try to understand what an operational definition is; until you do, perhaps stay out of the kitchen?
Preferably one that reflects known reality. And then, after you have built your simulation, we can use the operational definition you have developed to measure whether or not your simulation has met the independently developed operational definition. No scientist would approach this the way you are doing.
lol. Elizabeth Liddle

Liz: get real. Information: a sender, a receiver. DNA. Ribosomes making proteins. That's the real world example. How did it happen? You got no clue and nobody else does. Heading out to the pool now. It's hotter than hell outside. Enjoy! mike1962

Mung, we are going around in the most absurd circles here. Let's summarise: My original claim was that, contrary to ID claims, that Chance and Necessity could produce Information. Not "information in the genome". Not "information at any place or time". But "information". For all definitions of information I was aware of, that claim stands, although what I had in mind was CSI. But to demonstrate my claim to Upright BiPed, I needed a a conceptual definition of information in which meaning was intrinsic (fair enough) plus another requirement, which has proved more problematic. So we have been trying to get that conceptual definition sorted out, so that it can be operationalised for my demonstration, which will take the form of a computer simulation. Actually, it's not really a "simulation" in the sense that actual information will be generated by actual chance and actual necessity, but I will cast it in the form of a virtual OOL scenario, so I'll call it a sim. But you can only operationalise a conceptual definition once you have ironed out any ambiguities in the definition. And that is where we hit a snag, and, as I tried to show, potential circularities. And we hit a bit of an impasse. So, to try to break the log jam I turned to the definition cited by Meyer (who seems to think it works for him) which is the Merriam-Webster one. Being a good dictionary, they give an excellent conceptual definition which is non-circular. None of the terms used in the definition need by defined in terms of the defined words. In particular, words like "symbol" and "representation" are not included in the definition. Nonetheless, they are intrinsic to the definition because the definition firstly specifies that the information is present in an arrangement of something, and that it must produce specific effects. This is adroit, because it rules out, for example, a rock falling off a cliff, which might well produce "specific effects" but what is doing the producing is a material object, the rock, not an "arrangement of something". Similarly it rules out a message consisting of white noise that lacks any meaning, which might contain Shannon entropy, but the arrangement has no "specific effects". What it includes, of course, and gives an example, is a DNA sequence, which is an arrangement of something (nucleotides) that produces specific effects, for instance a protein. It also includes this post, which is an arrangement of pixels on your screen, and produces specific effects in your brain, and, possibly, on your blood pressure. So it looks good to me. But I added a further constraint: that the "specific effects" must be "functional". That rules out a splatter of paint on a Jackson Pollock canvas that doesn't do anything much except make people go "ahhhhh!", but it does include a lab report on a throat swab that enables an effective antibiotic to be prescribed. Finally UBP would like the definition to include an intermediary step in which an intermediary object serves to link the arrangement to the effect, without itself being involved "physically" in the translation. That's a bit tricky to operationalise for a computer sim, but I think I've done a reasonable job. As for the rest, I have utilised the Merriam-Webster definition to eliminate words like "representation" from UPD's conceptual definition, in order to produce an operational definition that can be applied to my sim. If you don't like this approach, then I suggest you raise your complaint with whoever designed the scientific method, because thassthewayitworks. If UBP is happy, I'll get going, though it may take a while (weeks, at least, possibly months). If not, I am happy to wait for more tweaks. But I am not going to demonstrate that there is information in the genome - I've already done that using at least two definitions. And I'm certainly not going to demonstrate that it got there through Chance or Necessity. A Nobel prize would look nice on the mantelpiece, but I'll make do with my grandmother's clock thanks. Elizabeth Liddle

Let me see if I can state this another way. You, Elizabeth, are attempting to develop an operational definition of information according to what your proposed simulation will do. And then you accuse Upright BiPid of circularity! Oh. my. Gosh. What you need to do, what you ought to do, is develop an operational definition that is independent of your simulation. Preferably one that reflects known reality. And then, after you have built your simulation, we can use the operational definition you have developed to measure whether or not your simulation has met the independently developed operational definition. No scientist would approach this the way you are doing. Mung

Oh, right. So now I'm all ready to build my sim, the goal posts change. Ah well. I might have known there'd be a snag. Elizabeth Liddle

Well, we need an operational definition. UPD’s wasn’t.
So what? You’re off in la la land, the land of virtual reality, and UPB is asking you to come back to reality and saying that if you’re going to develop an operational definition develop one that reflects reality. wow. deja vu.
Mung, um, I’m not sure how to break this to you – but – it depends how you are defining information. So take your proposed definition of information and operationalize it based upon something real, something that actually exists. The genome, for example.
Mung

Elizabeth is not attempting to operationalize anything that exists in reality. Er yes, I am. So you've already built your computer simulation? It's a reality now? What I am saying is that your attempt at an operational definition does not correspond to anything real. Why not develop an operational definition that corresponds to what we know to exist, in reality, in the genome? Mung

Mung: What a shame. We had the start of a real conversation last night. Oh, well, it was nice while it lasted. But it looks like there’s a heap of strawmen I’d better sweep up.
I’m sure it sounds crazy, but one might expect that at some point your response would include some of the language used in the description of the reality being operationalized…
Elizabeth is not attempting to operationalize anything that exists in reality.
Er yes, I am.
First Lizzie complains that the concepts are not abstract though, they need to be more abstract so they can be applied to other instances.
No, I don’t.
Then she argues that the concepts are too abstract to serve as an operational definition, that operational definitions cannot be general, they must be specific to one single instance of a measurement.
No, I don’t.
We cannot develop an operational definition of a peanut butter sandwich that can identify multiple instances of a peanut butter sandwich. The operational definition must be specific to a particular peanut butter sandwich.
No, it need not be. It would be useless if it were.
So if we have wheat bread, instead of white bread, that would require a different operational definition for a peanut butter sandwich.
No, it would not.
Totally bizarre.
Yes it is. Totally bizarre. I am at a loss to account for it.
So let’s take a closer look at Elizabeth’s own sources: Operationalization occurs when we take a hypothesis, e.g. aggression causes further aggression, and develop a procedure, or operation, for identifying instances of the critical terms, here, aggression. http://www.newfoundations.com/EGR/Oper.html Instances, is plural. We should be able to identify aggression, for example, in not just one subject, and not just in one scenario, but in multiple instances. Operationalization occurs when we take a hypothesis, e.g. violence causes further violence, and develop a procedure, or operation, for identifying instances of the critical terms, here, violence. http://web.jjay.cuny.edu/~pzap.....estion.htm Now this is too funny. It looks like one of Lizzie’s sources has plagiarized the other! Or perhaps they both plagiarized a common source. Design detection in action!
Probably. I expect they both plagiarized it from Wikipedia. I just googled a couple that seemed to save me the trouble of explaining it again myself.
Instances, is plural. We should be able to identify violence, for example, in not just one subject, and not just in one scenario, but in multiple instances. So Upright BiPed’s point is completely valid, as is mine. Elizabeth, could you please develop an operational definition that is based on reality?
I will, and have, developed an operational definition base d on a conceptual definition. I chose Webster Merriam as Meyer cited it, and it seemed to me to pretty well fit UPD’s with a couple of additions (one actually of my own).

Look I realises this is frustrating for you, UPD, but you must understand that the frustration is mutual! Your 1) and 2) are NOT operational definitions!!!!!!
So what? You’re off in la la land, the land of virtual reality, and UPB is asking you to come back to reality and saying that if you’re going to develop an operational definition develop one that reflects reality.
Well, we need an operational definition. UPD’s wasn’t.
As your own sources point out, reality is the place to start! Background for research consists of everything a researcher knows about a topic: 1) How well grounded the question is in the current knowledge base (the problem must have a basis in theory, research, or practice (we need to know what is already known so that we can judge how much it can add to the knowledge base; gives us an anchor) What do we already know about information and where did we obtain this knowledge? Why do you, Elizabeth, believe there is information in the genome? What do we already know about how information is communicated and where did we obtain this knowledge? How does the information in the genome get communicated?
Mung, um, I’m not sure how to break this to you – but – it depends how you are defining information. Still, I'm hopeful. I think I managed to operationalise UPD's version with a bit of help from Merriam-Webster, and when he gets a chance, I hope he'll give it the all-clear. Elizabeth Liddle

Look I realises this is frustrating for you, UPD, but you must understand that the frustration is mutual! Your 1) and 2) are NOT operational definitions!!!!!!
So what? You're off in la la land, the land of virtual reality, and UPB is asking you to come back to reality and saying that if you're going to develop an operational definition develop one that reflects reality. As your own sources point out, reality is the place to start!
Background for research consists of everything a researcher knows about a topic: 1) How well grounded the question is in the current knowledge base (the problem must have a basis in theory, research, or practice (we need to know what is already known so that we can judge how much it can add to the knowledge base; gives us an anchor)
What do we already know about information and where did we obtain this knowledge? Why do you, Elizabeth, believe there is information in the genome? What do we already know about how information is communicated and where did we obtain this knowledge? How does the information in the genome get communicated? Mung

I’m sure it sounds crazy, but one might expect that at some point your response would include some of the language used in the description of the reality being operationalized...
Elizabeth is not attempting to operationalize anything that exists in reality. This would be hilarious if it weren't so utterly pathetic. First Lizzie complains that the concepts are not abstract though, they need to be more abstract so they can be applied to other instances. Then she argues that the concepts are too abstract to serve as an operational definition, that operational definitions cannot be general, they must be specific to one single instance of a measurement. We cannot develop an operational definition of a peanut butter sandwich that can identify multiple instances of a peanut butter sandwich. The operational definition must be specific to a particular peanut butter sandwich. So if we have wheat bread, instead of white bread, that would require a different operational definition for a peanut butter sandwich. Totally bizarre. So let's take a closer look at Elizabeth's own sources:
Operationalization occurs when we take a hypothesis, e.g. aggression causes further aggression, and develop a procedure, or operation, for identifying instances of the critical terms, here, aggression. http://www.newfoundations.com/EGR/Oper.html
Instances, is plural. We should be able to identify aggression, for example, in not just one subject, and not just in one scenario, but in multiple instances.
Operationalization occurs when we take a hypothesis, e.g. violence causes further violence, and develop a procedure, or operation, for identifying instances of the critical terms, here, violence. http://web.jjay.cuny.edu/~pzapf/classes/CRJ70000/Formulating%20the%20research%20question.htm
Now this is too funny. It looks like one of Lizzie's sources has plagiarized the other! Or perhaps they both plagiarized a common source. Design detection in action! Instances, is plural. We should be able to identify violence, for example, in not just one subject, and not just in one scenario, but in multiple instances. So Upright BiPed's point is completely valid, as is mine. Elizabeth, could you please develop an operational definition that is based on reality? Mung

Mung:
Elizabeth, what is the purpose of having an operational definition?
The purpose of an operational definition is to allow a hypothesis to be tested in a manner that objective observers can agree on whether or not the hypothesis is supported by the results.
How broadly applicable should an operational definition be?
It is usually very narrow. Generalisability is the price of precision.
Can your operational definition tell us whether there is information present on, say, a computer hard disk?
No. It would have to be operationalised for that hypothesis. The reason it is called an "operational definition" is that it is specific to an operation within a hypothesis testing protocol.
Can it detect whether there is information in the genome of a cell?
Only if operationalised within a hypothesis aimed to demonstrate this.
Or is your operational definition applicable only to your own little virtual world?
The operational definition is applicable only to the hypothesis-testing operation for which it is defined. However, all operational definitions should be consistent with the conceptual definition at issue. So if, for example, we take the Merriam-Webster definition of information, that can be operationalised to any specific instantiation. And because the Merriam-Webster definition is so clear, it would be pretty easy to operationalise for any given hypothesis: Within a genome: Does the genome contain arrangements of nucleotides that correlate with any measures of cell behaviour? Within a computer: Does the computer contain binary strings that correlate with the output of the computer? Or something. But for present purposes, the operationalisation has to be a bit more complicated, because my entities are not a given (I start with no DNA, no computer, no cells), and therefore more specific (or the thing would be explosively complicated). Also, UPD wants this bit about intermediary objects in there. Which is fair enough, I guess. Elizabeth Liddle

Upright BiPed:
Dr Liddle, In response to the question I asked, your comment was a rather tragic disappointment. I asked for concrete examples of what variables you intended to measure, and you gave me sidesteps in return. I’m sure it sounds crazy, but one might expect that at some point your response would include some of the language used in the description of the reality being operationalized – but no, apparently that won’t be useful. I think back on my career and I try to remember a time when the critical issues described in discovery, are left absent from the study. Research cost money, so we typically don’t do business like that. Perhaps that’s just another one of those British/American thingies you were admiring earlier.
No Upright BiPed, I did not give you sidesteps, and I told you exactly what I intended to measure, and how I intended to measure them. I'll tell you again, and try to make it even clearer: Here is the conceptual definition of information I was using (from Merriam-Webster):
Information: the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something that produce specific effects
My "arrangments of something" will be strings of "virtual polymers". I will categorise them by their arrangements, as they will be categorical variables. I will measure their "specific effects" either as longevity (in terms of iterations) or reproductive fidelity (by comparison to "organisms" with different parentage. If the arrangement is a statistically significant predictor of "specific [functional] effects" I will consider my claim demonstrated.
If I had only known. After weeks of describing the various objects/dynamics involved in the existence of information, my conversation partner has chosen to rollover and play dead. Forever gone are those critical details which separate the existence of information from the formation of rust. I would have saved both of us the time, and just given a definition that ignores the details.
No, I have not UPD, as I think must be pretty clear to anyone reading this conversation.
Let’s look at your pitch:
Conceptual hypothesis: That chance and law alone can give rise to information, where “information” is defined conceptually, according to Merriam-Webster, as “the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something that produce specific effects.”
There is a problem with this.
Right. So you do have a problem with Merriam-Webster. OK. Well, that's a shame because it seemed to me to capture the essence of your definition, without the problematic terms.
It doesn’t cover anything of our observations; which is generally acknowledged as the “first mistake you made” in any study where you do it. The required physical objects, and their dynamic relationships to one another, are simply ignored. I know you’re a stickler for precision Dr Liddle, but how does one object “communicate” with another object?
And it's because I'm a stickler for precision, UPD that I needed a definition that did not use such terms. That is the beauty of the Merriam-Webster definition - it requires that an "arrangement of something" - which may be objects - "produces specific effects". We have agreed, I think, that if it was merely a physical object that caused specific effects (hydrogen burning in oxygen, for instance) we would not call that "information". What makes it information, I think we agreed, is when it is not the objects themselves,but a arrangement of those objects that produces the specific effects. As, for example, when a codon produces an amino acid, not because the nucleotides themselvesproduce this effect, but because the arrangement of the nucleotides produce this effect. Right?

Operational hypothesis: That, starting only with non-self-replicating entities with a physics-and-chemistry plus random kinetics, self-replicating “virtual organisms” can emerge that contain patterns of “virtual matter” whose arrangement determines the fidelity of its self replication (measured in terms of similarity to its “parent” as compared with a randomly substituted pattern).
There is a problem here as well. This supposed operationalization is based upon the definition above which ignores the required physical objects, and their dynamic relationships to one another. It also includes a mis-statement of what the final output must be.
No, it doesn't. I've actually specified "virtual matter" (we agree we are talking about virtual reality here, right, not an actual wet lab experiment?), and I've specified the dynamic relationship - the arrangement of the "virtual matter" must determine, at a future time (no backward causality!), i.e. dynamically, specific effects, namely either longevity or fidelity.
Here, let’s try this. Let us spill the last vesicles of illusion.
Starting only with non-self-replicating entities in a physics-and-chemistry (plus random kinetics) environment, self-replicating “virtual organisms” can emerge that contain dissociated representations embedded in the arrangement(s) of matter. These arrangements represent the system that created them, and will determine the output of that system by means of an intermediary “virtual object”. Without becoming incorporated, this object may interact with either the representation or output, or both, but where the two remain whole and physically separated. 1) Dissociated= having no physical relationship to that which it represents 2) Intermediary= serves the dynamic purpose of allowing the input representations to determine the output while they each remain discrete, a facilitator
Aaarrrghhhh! Look I realises this is frustrating for you, UPD, but you must understand that the frustration is mutual! Your 1) and 2) are NOT operational definitions!!!!!! "Representations" is NOT operationalised! Which seems really odd, because the Merriam-Webster definition manages to convey the essence of meaning without even using the word "representation", which would be circular (you can't just provide a near-synonym in a dictionary definition). Look UPD: forget (if you can bear it) for a moment your own conceptual definition for a moment and look at the Merriam-Webster one. It seems to me to encapsulate yours, but is considerably simpler, and does not use terms that themselves depend on the thing being defined (It's pretty hard to define "representation" or "meaning" without referencing "information"). It's a good dictionary. That dictionary definition, which Meyer, for example, approves, and so do I, captures the both immaterial nature of information ("arrangement of something" not "something"), the causal dynamic ("produces ...effects"), and the content ("specific effects"). I've made it even more rigorous by specifying "specific functional effects". It seems to fit your concept, without the burden of introducing potentially circular terms. It only lacks your requirement of a "virtual intermediary". Which I will try to add.
Which one of these observed requirements would you like to have removed? If there are none, then I wish you the very best of luck. If you succeed, things are likely to start moving real fast, so remember to mention me in your acceptance speech.
None, but they need clarification. Let me try:
Starting only with non-self-replicating entities in a physics-and-chemistry (plus random kinetics) environment, self-replicating “virtual organisms” can emerge that contain ~~dissociated representations embedded in the~~ arrangement(s) of virtual matter represented as strings that ~~These arrangements represent the system that created them~~ cause the virtual organism to self-replicate with fidelity, and ~~will~~thus determine the output of that system namely a copy of that system.
So far I don't think I have done too much damage to yours, and we aren't a million miles from Merriam-Webster. However, you include an additional requirement:
The arrangment must produce its output by means of an intermediary “virtual object”. ~~Without becoming incorporated, this object may interact with either the representation or output, or both, but where the two remain whole and physically separated.~~. This "virtual object" must take the form of a second arrangement of "virtual matter" that may interact with the strings and with some other "virtual object" that affect the fidelity of the self-replication of the "virtual organisms" without either permanently altering, or being altered by, the interaction.
I'm less confident I can pull off this second requirement, but I'm happy to give it a go. ********************************************************** What about the rest of your long post to me, to which I responded in detail? Do you have any response to mine? Because I spent quite a bit of time thinking about it, and wondering what you meant. Did you find my responses satisfactory? In which case do you agree that categorical variables are variables? It seems important, because my demonstration will involve categorical variables (the arrangements in my strings). Elizabeth Liddle

The Digital Code of DNA http://www.nature.com/nature/journal/v421/n6921/full/nature01410.html junkdnaforlife

Elizabeth, what is the purpose of having an operational definition? How broadly applicable should an operational definition be? Can your operational definition tell us whether there is information present on, say, a computer hard disk? Can it detect whether there is information in the genome of a cell? Or is your operational definition applicable only to your own little virtual world? Mung

I know you’re a stickler for precision Dr Liddle, but how does one object “communicate” with another object?
I know! I know! Mung

kf:
Dr Liddle: Pardon. Digital simply means discrete as opposed to continuous state. The alphabet is digital. GEM of TKI
And if that is all that is meant by it, I have no problem with it. But then any molecule is digital by that definition! Atoms are discrete. But I take your point. Elizabeth Liddle

Dr Liddle, In response to the question I asked, your comment was a rather tragic disappointment. I asked for concrete examples of what variables you intended to measure, and you gave me sidesteps in return. I’m sure it sounds crazy, but one might expect that at some point your response would include some of the language used in the description of the reality being operationalized - but no, apparently that won’t be useful. I think back on my career and I try to remember a time when the critical issues described in discovery, are left absent from the study. Research cost money, so we typically don’t do business like that. Perhaps that’s just another one of those British/American thingies you were admiring earlier. If I had only known. After weeks of describing the various objects/dynamics involved in the existence of information, my conversation partner has chosen to rollover and play dead. Forever gone are those critical details which separate the existence of information from the formation of rust. I would have saved both of us the time, and just given a definition that ignores the details. Let’s look at your pitch:
Conceptual hypothesis: That chance and law alone can give rise to information, where “information” is defined conceptually, according to Merriam-Webster, as “the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something that produce specific effects.”
There is a problem with this. It doesn’t cover anything of our observations; which is generally acknowledged as the “first mistake you made” in any study where you do it. The required physical objects, and their dynamic relationships to one another, are simply ignored. I know you're a stickler for precision Dr Liddle, but how does one object “communicate” with another object?
Operational hypothesis: That, starting only with non-self-replicating entities with a physics-and-chemistry plus random kinetics, self-replicating “virtual organisms” can emerge that contain patterns of “virtual matter” whose arrangement determines the fidelity of its self replication (measured in terms of similarity to its “parent” as compared with a randomly substituted pattern).
There is a problem here as well. This supposed operationalization is based upon the definition above which ignores the required physical objects, and their dynamic relationships to one another. It also includes a mis-statement of what the final output must be. Here, let’s try this. Let us spill the last vesicles of illusion.
Starting only with non-self-replicating entities in a physics-and-chemistry (plus random kinetics) environment, self-replicating “virtual organisms” can emerge that contain dissociated representations embedded in the arrangement(s) of matter. These arrangements represent the system that created them, and will determine the output of that system by means of an intermediary “virtual object”. Without becoming incorporated, this object may interact with either the representation or output, or both, but where the two remain whole and physically separated. 1) Dissociated= having no physical relationship to that which it represents 2) Intermediary= serves the dynamic purpose of allowing the input representations to determine the output while they each remain discrete, a facilitator
Which one of these observed requirements would you like to have removed? If there are none, then I wish you the very best of luck. If you succeed, things are likely to start moving real fast, so remember to mention me in your acceptance speech. Upright BiPed

Actually, Ilion, I'm not tossing any. I'm asking for them. And I'm happy with Merriam Webster, as long as you all are. Elizabeth Liddle

Mung: "How many different definitions of information do you plan to toss our way?" As many as it takes until one of them to stick to the wall? As many as it takes until you to decide that the "argument" isn't worth your time? Ilion

Mung:
Hi Lizzie, ok, so let’s see if we can clarify a couple points. Please read the entire post and think on it before responding. You, personally, believe that Chance + Necessity can create meaningless information. Is that correct?
Yes. Using Shannon's definition, which allows us something called "information" which can be meaningless.
Do you also think believe that Chance + Necessity can create meaningful information?
Yes. And that is what I intend to try to demonstrate.
I don’t understand the following:
…no ID proponent is proposing that Chance and Necessity can’t create meaningless information.
Is that what you meant to say, or did you mean to say something different? Because it really makes no sense, to me. I know that I personally deny that Chance + Necessity can create meaningless information. Perhaps you meant to say that no ID proponent accepts that information can be meaningless? [But is that true?]
You can put it either way. If information is defined in such a way as to include meaningless information (as in Shannon Entropy) then I would expect that ID proponents would agree that Chance and Necessity could produce it. Meyer and Dembski, for instance, quantify information in Shannon terms, and agree that it can be produced by Chance (and Necessity, sometimes, for Dembski). What they dispute is that Specified Information can be produced by Chance and Necessity. Other ID proponents, I now understand, more sensibly IMO, contend that meaningless information is an oxymoron, and take no stand on whether it can be created by Chance and Necessity alone or not. What they (in the person of Upright BiPed, inasmuch I understand him) contends is that meaningful information cannot be created by Chance and Necessity. It is that claim that I hope to falsify.
Or, stated another way, ID proponents believe information must have meaning. [Again, questionable.]
Well, I don't suppose either of us can speak for all ID proponents.
Or that no ID proponent accepts that Chance can generate information. [iirc, Debmski wrote that it can.]
Yes, but not Complex Specified Information, and AFAICT, he defines plain ole information in Shannon terms.
Or finally, that ID proponents themselves are confused about information and some believe that there are different kinds of information, including information that can have no meaning and produce no effect, but that’s not the kind of information that needs to be demonstrated in order to falsify ID.
Well, they need not be confused. Each one might be perfectly clear. But they do appear to differ. As I said, I regard this as healthy.
lol. [Laughing at the situation, not you.]
Well, that's something :)
Look, In some respects I don’t blame you. There is a lack of clarity in some authors and that can be confusing. But what I do doubt is that in your conversations with Upright BiPed, myself, and kf that any of us has engaged in that sort of lack of clarity. I think we’ve been clear and consistent from the beginning of this subject.
I'm not actually accusing any of you of lack of clarity, except in the sense that the definitions offered have not proved easy to operationalise. Which I guess does mean that things weren't clear. Certainly the essential thing in an operational definition is to remove ambiguity. That, as those links I gave pointed out, often means that the operational definition lacks generalisability - it's the price one pays for lack of ambiguity. But it buys something very worthwhile IMO, which is the ability to actually subject claims to rigorous testing. If I succeed, I will not have demonstrated that life wasn't designed (lack of generalisability). I will, however, have demonstrated that a fairly fundamental ID claim is not always true.
I once again think back to your coin tossing example, way back when, when Upright BiPed asked you what that 100 bits of Shannon information that you thought you had generated by tossing a coin was about. So what I think you are saying is that we are requesting that in your demonstration any information you generate must have meaning or be meaningful. And so you are attempting to come up with a definition of information that incorporates the concept of meaning.
Yes.
How am I doing so far?
A perfect 10. Well, 9.99.

Shannon information is not an appropriate measure of information for this purpose because it doesn’t incorporate the concept of meaning
Now assuming we are on the same page so far, and what a minor miracle that would be, how is it that you think that Shannon information cannot measure the information in a message that has meaning?
I think it cannot distinguish between meaningful information and non-meaningful information. Which is the point, essentially, made by both Dembski and Meyer, who do use Shannon information, but have to add this extra criterion of Specification. I think Upright BiPed's approach is better, although it wasn't the approach I had in mind when I made my original claim. But then my original claim was intended to cover any definition of information (unless it's a Humpty Dumpty one).
Surely that cannot be true. And yet you seem to think that Shannon information can only measure information in a message in which there is no meaningful information. How odd.
No. See above. Use your lawyer skills. Or just think in terms of Specificity and Sensitivity (in the Signal Detection Theory sense). The Shannon criterion is has Sensitivity (few false negatives) but not Specificity (lots of false positives). What I hope we can do using the Webster Merriam definition is get a definition that has both Sensitivity (no false negatives, which is obviously of importance to me as I want to demonstrate my claim) and Sensitivity (no false positives, which is obviously of importance to you, as you want to make sure my claim is sound).
Just because Shannon information does not concern itself with the meaning in a message, how is it thereby invalidated as a measure?
See above. More specifically (pun un-intended but apt) we need criteria that allow us to say that meaning is present, i.e. specificity for meaningful information. I think that Merriam-Webster covers that, but for good measure, I have added an additional criterion, which is that the "arrangement of [virtual] matter" has not only to have "specific effects" but "specific functional effects", which I operationalise as producing greater reproductive fidelity and/or greater longevity of my virtual critters (if they form in the first place, which they may not :))
If you in fact demonstrate that your messages have meaning, why can’t Shannon information measure that information?
It could. But it wouldn't be terribly relevant, because may claim is only that Chance and Necessity can create [meaningful] information,not a specific quantity of it. But sure, quantifying the information in the meaningful strings (if there were any) might a cool extra.
Shannon information is not an appropriate measure of information for this purpose because it doesn’t incorporate the concept of meaning
All this would indicate is that we need to have some other way to determine meaning. Correct?
Yes. Right now, I'd really like to go with Webster, especially as it has Meyer's imprimatur.
e.g., It [information] changes what someone believes to be the case. (How’s that for an operational definition!)
Yup :) But operational definitions are operation-specific, and that isn't the operation I intend to perform. However, as an epiphenomenon it would be very welcome :)
It does not mean we cannot use Shannon information to measure the information in the message. Right?
Right. It's just that we cannot use Shannon information to determine whether the information is meaningful. And if we can determine that my critters contain meaningful information, we won't need to quantify it because my job will already be done. But if you want to pay me per bit, I won't refuse. Cheers Mung. I needed a constructive conversation today :) Hope that was one. Lizzie Elizabeth Liddle

KF, RE 213, Was it you that referenced a proposed functional target ratio of 1 in 10^74 (or something similar) for proteins in another thread? I can't find the reference. material.infantacy

Dr Liddle: Pardon. Digital simply means discrete as opposed to continuous state. The alphabet is digital. GEM of TKI kairosfocus

Hi Lizzie, ok, so let's see if we can clarify a couple points. Please read the entire post and think on it before responding. You, personally, believe that Chance + Necessity can create meaningless information. Is that correct? Do you also think believe that Chance + Necessity can create meaningful information? I don't understand the following:
...no ID proponent is proposing that Chance and Necessity can’t create meaningless information.
Is that what you meant to say, or did you mean to say something different? Because it really makes no sense, to me. I know that I personally deny that Chance + Necessity can create meaningless information. Perhaps you meant to say that no ID proponent accepts that information can be meaningless? [But is that true?] Or, stated another way, ID proponents believe information must have meaning. [Again, questionable.] Or that no ID proponent accepts that Chance can generate information. [iirc, Debmski wrote that it can.] Or finally, that ID proponents themselves are confused about information and some believe that there are different kinds of information, including information that can have no meaning and produce no effect, but that's not the kind of information that needs to be demonstrated in order to falsify ID. lol. [Laughing at the situation, not you.] Look, In some respects I don't blame you. There is a lack of clarity in some authors and that can be confusing. But what I do doubt is that in your conversations with Upright BiPed, myself, and kf that any of us has engaged in that sort of lack of clarity. I think we've been clear and consistent from the beginning of this subject. I once again think back to your coin tossing example, way back when, when Upright BiPed asked you what that 100 bits of Shannon information that you thought you had generated by tossing a coin was about. So what I think you are saying is that we are requesting that in your demonstration any information you generate must have meaning or be meaningful. And so you are attempting to come up with a definition of information that incorporates the concept of meaning. How am I doing so far?
Shannon information is not an appropriate measure of information for this purpose because it doesn’t incorporate the concept of meaning
Now assuming we are on the same page so far, and what a minor miracle that would be, how is it that you think that Shannon information cannot measure the information in a message that has meaning? Surely that cannot be true. And yet you seem to think that Shannon information can only measure information in a message in which there is no meaningful information. How odd. Just because Shannon information does not concern itself with the meaning in a message, how is it thereby invalidated as a measure? If you in fact demonstrate that your messages have meaning, why can't Shannon information measure that information?
Shannon information is not an appropriate measure of information for this purpose because it doesn’t incorporate the concept of meaning
All this would indicate is that we need to have some other way to determine meaning. Correct? e.g., It [information] changes what someone believes to be the case. (How's that for an operational definition!) It does not mean we cannot use Shannon information to measure the information in the message. Right? Mung

UPD: Thanks. I'm going off to bed shortly, but will check in tomorrow. Elizabeth Liddle

Mung:
Elizabeth Liddle:
If we define information as an arrangement of matter that has specific effects…
How does tossing a coin generate information?
It doesn't, by that definition.
How many different definitions of information do you plan to toss our way?
I'm hoping we can agree on one. Elizabeth Liddle

Dr Liddle at 214 I see your response now. I will return this evening to comment on it. Upright BiPed

Elizabeth Liddle:
If we define information as an arrangement of matter that has specific effects...
How does tossing a coin generate information? How many different definitions of information do you plan to toss our way? Mung

Mung #209
Mung: Please describe the message and the measurement and explain how the measurement demonstrates that there is 0 bits of information in the message. Elizabeth Liddle: OK, let’s take a channel that is dominated by noise at a frequency of 50 hertz. We listen to this channel. We fail to detect any departure from the 50 Hz tone. We therefore receive 0 bits of information. In one sentence the 50Hz is noise. In the next sentence the 50Hz is a tone.
Yes, noise can be a tone. It’s why we use notch filters.
So if all that is present is a 50Hz tone, it’s the noise that’s being dominated, not the tone. But where’s the message? Well, you say we cannot detect the message, because we have not detected any departure from the 50 Hz tone. Yet you appear to argue that from this line of reasoning we can conclude that we’ve measured the message and found no information in it. We therefore receive 0 bits of information. We haven’t received any message. So we haven’t measured a message that contains 0 bits of information. Try again, please.
A message with 0 information isn’t a message, is it? But no, I won’t try again. It is utterly irrelevant. Mung #210
I suppose that I just imagined that someone suggested that we could use Shannon information because it [Shannon information] can tell us whether information is present or not. Elizabeth Liddle @168: An operational definition can also give criteria for establishing whether some categorical variable is present or absent. As I said. One that allows you to measure the variable will of course also allow you to say whether it is present or absent. Shannon’s definition does that – if there are 0 bits in the message, there is no information present, and if there are >0 bits in the message, there is information present.
That would be Shannon information duh. Which we have agreed we are not interested in. So let’s move on. Mung #211
Lizzie has constructed a box which information must fit into regardless of what information actually is and regardless of whether information can actually fit into the box she has created. This is the the problem, in a nutshell.
Um, no, it isn’t, and saying so doesn’t make it so. Mung #212
And Her name is Elizabeth Liddle (Lizzie). kairosfocus: Is there a serious objection to this, if so, what is it, why? The objection arises because someone thinks that because this measure cannot tell us the meaning of a message, that it follows by force of deductive logic that information can exist which is completely devoid of meaning. Therefore this person thinks she can generate 100 bits of information simply by flipping a two-sided coin 100 times. It follows that if she were to write a coin-flipping program consisting of necessity (two-sided coin, must come up either heads or tails) and chance (some probability that either heads or tails will appear) then she will have demonstrated that chance + necessity can generate information and will have falsified ID. So why has she not flat-out suggested that she can falsify ID by just such a computer simulation?
Um, I did, ages back, to demonstrate that we needed a definition of information that ID proponents actually called information. And that Shannon information wasn’t it. Obviously. For the precisely the reasons you give above. So we aren’t using Shannon information, right?
Probably because she knows it’s absurd and she would be laughed at and possibly even mocked. Now this same person will put forth a definition of information according to which information brings about a reduction in uncertainty. And then, when asked asked whence this uncertainty arises, and what is it uncertainty about she will say that she must have an operational definition of about. And yet we persist in attempts to carry on a rational conversation with this person.
I’m not at all sure why I persist in trying to carry on a conversation with someone who insists that I am saying the very opposite of the thing I have been trying to say since the beginning of the conversation. But let me try one more time: Shannon information is not an appropriate measure of information for this purpose because it doesn’t incorporate the concept of meaning and we all agree that no ID proponent is proposing that Chance and Necessity can’t create meaningless information. We agreed it about three months ago. So let’s stop talking about it right? We agree. There is no argument. It is a ex-subject. It is pushing up daisies. Nail it the perch right now. The Webster-Merriam definition, as quoted by Meyer seems good to me. Elizabeth Liddle

Upright BiPed:

That is what I need you to tell me, in sufficiently unambiguous terms that I can derive a set of measurable variables from it.
/ Dr Liddle, before this goes any further, would you please clarify your thought for me. In statistical research, a variable is often a measurement of the relationship between at least two different characteristics. For instance, a researcher might want to know the relationship between the number of persons in a population who are mothers of children under the age of five years, and those who are also over the age of 40. The researcher might then take that relationship and compare it over different cultures to gain an insight into those various cultures. That is an example of one such variable in statistical research. Another example would be a variable such as the asking for the amount of physical exercise within a given population. The variable comes into play in the form of defining what constitutes exercise: is it working out in a gym or is it also riding a bike to the grocery store. Such variables have to be established in order to either include or exclude them from a measurement.
Indeed.
Even so, these examples can be categorically different than asking for the presence of a particular characteristic within a population – where measuring the presence of the characteristic constitutes no more than simply finding that particular distinction. In that sense, there is no variable except the distinction between ‘yes’ and ‘no’.
Yes. But that does not absolve one from providing criteria. With some categories it is pretty easy (sex,for instance, although not gender), others easy-ish (handedness - we usually use a questionnaire with a cut-off score), and others much more arbitary (diagnosis, for instance, again, using a cut-off score on a screening instrument, or a decision from a "consensus diagnostic conference"). But sure. I am familiar with categorical variables.
An example of this would be to ask someone if their age is over 50, or if maximum circumference of their head is less than 60 centimeters, or if they currently possess a valid pilot’s license. These are three such examples of queries that have no variables.
Well, I guess this might be a US/Brit thing (but in which case it's also a US/Canadian thing) but here we call categorical variables "variables" even if they only vary between 0 and 1 (i.e. absent or present). And, as I said, the fact that you code a variable as a categorical variable doesn't absolve one from operationally defining it.
There are also others which have virtually no variable – meaning the variable is so small as to be statistically meaningless – such as ‘are you a male’ or “have you ever broken your tibia’. Even though these types of queries have no variation, or no statistically-viable variation, they are each completely valid queries within a sample. They are measured in research all the time, just as they are.
I'm sorry, you've lost me. By "variable" do you mean "variance"? Assuming you do, and that you are saying "the variance is so small as to be statistically meaningless" - it is quite untrue that the variable has "no statistically-viable variation" if by that you mean no quantifiable variance. Obviously if every subject in your sample had broken their tibia (or none), you would have no variance, and you would exclude the variable from your analysis, or, if very few had broken their tibia, you might find yourself with cell sizes so small that your results would be unreliable, but that isn't the same as having "no variance". In a typical population sample, half your sample will be male and half female. If you dummy code male as 0 and female as 1, the standard deviation of your variable will be .5. If the variable is a predictor,that's all you need to do - you get your regression coefficients, and then your predicted values will include the beta for the variable if your dummy is 1 and not if the dummy is 0 (ie. beta * 0 = 0). If the variable is a dependent variable, then you'd run it as a logistic regression, and your betas will sum in the exponent of the denominator to give you a probability, given your predictors, rather than a predicted value. If you don't mean this, can you explain what you do mean?
Thus far, you have said several times that the conceptual definition we developed is satisfactory, but simply needed to be operationalized.
Well, it's satisfactory if it is operationalisable! I hope it is.
In that process we may find the need to query for characteristics that do not have variation – in other words, they either exist or they do not. And if that is the case, such a situation does not invalidate the query by anyone’s conceptualization of research.
Well, as I said, characteristics that either exist or do not still have variation! Statistically speaking, they have variance. More to the point, if you are going to code them as present or absence you need a criterion by which to decide whether they are present or absent. I have provided one such criterion, using the Merriam-Webster definition, above.
In that vein, what exactly (in concrete terms) is the variable you are expecting to measure in the presence of information?
Well, I've given it above, but I'll give it again. If we define information as an arrangement of matter that has specific effects, we need to operationalise "arrangement of matter" which shouldn't be too hard for my sim as they will be strings of virtual matter; and "specific effects", which again isn't too hard. To ensure that the effects are "functional" ie. "useful" to the virtual organisms, I've specified that they must contribute to reproductive fidelity (i.e. not just create pretty patterns). What is important however (for me), is to make sure that the effects are correlate with the arrangement, and don't just happen haphazardly. Otherwise you win :) We could even set it up as a logistic linear regression, with the arrangements coded categorically, and the effects (reproductive fidelity) coded as continuous variable, and look for a significant beta. So we can be even more specific: If I succeed, my virtual organisms will contain "arrangements of matter" (strings representing "polymers") that affect reproductive fidelity. If certain strings result in greater reproductive fidelity than others, then I will have demonstrated that the strings embody information, because the arrangement will not just have "specific effects" but "specific functional effects" in that they increase reproductive fidelity. Or we could use longevity, I guess, measured in iterations. Look forward to your response. Cheers Lizzie Elizabeth Liddle

If information is a prearranged subset P of a larger set S consisting of all permutations of a configuration space of size N, then the only part that should really trip anyone up is the prearranged subset P. From what I gather, any permutation in S is considered potential information by those who have a problem accepting a definition of information that includes P. However the set P in a peptide chain is merely the selection of permutations that equate to functional sequences in set S. We can define set U to be all the arrangements which do not equate to functional sequences. Until there is some sort of agreement on the size of both P and thus U, I'm certain the equivocations will continue. S needs to be the same set as that formed by a union of P and U. Determining the size of P relative to S will likely continue to be controversial. KF provided a reference to an estimate of something like 10^-74 in another thread, but I can't find it at the moment. material.infantacy

And Her name is Elizabeth Liddle (Lizzie). kairosfocus:
Is there a serious objection to this, if so, what is it, why?
The objection arises because someone thinks that because this measure cannot tell us the meaning of a message, that it follows by force of deductive logic that information can exist which is completely devoid of meaning. Therefore this person thinks she can generate 100 bits of information simply by flipping a two-sided coin 100 times. It follows that if she were to write a coin-flipping program consisting of necessity (two-sided coin, must come up either heads or tails) and chance (some probability that either heads or tails will appear) then she will have demonstrated that chance + necessity can generate information and will have falsified ID. So why has she not flat-out suggested that she can falsify ID by just such a computer simulation? Probably because she knows it's absurd and she would be laughed at and possibly even mocked. Now this same person will put forth a definition of information according to which information brings about a reduction in uncertainty. And then, when asked asked whence this uncertainty arises, and what is it uncertainty about she will say that she must have an operational definition of about. And yet we persist in attempts to carry on a rational conversation with this person. Mung

Lizzie has constructed a box which information must fit into regardless of what information actually is and regardless of whether information can actually fit into the box she has created. This is the the problem, in a nutshell. Mung

I suppose that I just imagined that someone suggested that we could use Shannon information because it [Shannon information] can tell us whether information is present or not. Elizabeth Liddle @168:
An operational definition can also give criteria for establishing whether some categorical variable is present or absent. As I said. One that allows you to measure the variable will of course also allow you to say whether it is present or absent. Shannon’s definition does that – if there are 0 bits in the message, there is no information present, and if there are >0 bits in the message, there is information present.
Mung

Mung:
Please describe the message and the measurement and explain how the measurement demonstrates that there is 0 bits of information in the message.
Elizabeth Liddle:
OK, let’s take a channel that is dominated by noise at a frequency of 50 hertz. We listen to this channel. We fail to detect any departure from the 50 Hz tone. We therefore receive 0 bits of information.
In one sentence the 50Hz is noise. In the next sentence the 50Hz is a tone. So if all that is present is a 50Hz tone, it's the noise that's being dominated, not the tone. But where's the message? Well, you say we cannot detect the message, because we have not detected any departure from the 50 Hz tone. Yet you appear to argue that from this line of reasoning we can conclude that we've measured the message and found no information in it.
We therefore receive 0 bits of information.
We haven't received any message. So we haven't measured a message that contains 0 bits of information. Try again, please. Mung

That is what I need you to tell me, in sufficiently unambiguous terms that I can derive a set of measurable variables from it.
Dr Liddle, before this goes any further, would you please clarify your thought for me. In statistical research, a variable is often a measurement of the relationship between at least two different characteristics. For instance, a researcher might want to know the relationship between the number of persons in a population who are mothers of children under the age of five years, and those who are also over the age of 40. The researcher might then take that relationship and compare it over different cultures to gain an insight into those various cultures. That is an example of one such variable in statistical research. Another example would be a variable such as the asking for the amount of physical exercise within a given population. The variable comes into play in the form of defining what constitutes exercise: is it working out in a gym or is it also riding a bike to the grocery store. Such variables have to be established in order to either include or exclude them from a measurement. Even so, these examples can be categorically different than asking for the presence of a particular characteristic within a population – where measuring the presence of the characteristic constitutes no more than simply finding that particular distinction. In that sense, there is no variable except the distinction between ‘yes’ and ‘no’. An example of this would be to ask someone if their age is over 50, or if maximum circumference of their head is less than 60 centimeters, or if they currently possess a valid pilot’s license. These are three such examples of queries that have no variables. There are also others which have virtually no variable – meaning the variable is so small as to be statistically meaningless – such as ‘are you a male’ or “have you ever broken your tibia’. Even though these types of queries have no variation, or no statistically-viable variation, they are each completely valid queries within a sample. They are measured in research all the time, just as they are. Thus far, you have said several times that the conceptual definition we developed is satisfactory, but simply needed to be operationalized. In that process we may find the need to query for characteristics that do not have variation – in other words, they either exist or they do not. And if that is the case, such a situation does not invalidate the query by anyone’s conceptualization of research. In that vein, what exactly (in concrete terms) is the variable you are expecting to measure in the presence of information? Upright BiPed

Dr Bot: The big problem with it, that I have, is that if you make the nucleotides of DNA, the "digital" part of a "computer", the "computer" itself is the whole population over time, because it is at the level of replication that the "switches" (nucleotide) are reset, and the output is different phenotypes. And if you include the environment in the analogy, it is the environment that sets the switches (or at least the mean switch positions) in the population and the output is an adapted population. However, if you regard the organism as the computer, then the "digital" part is the genes, which are switched on and off according to incoming chemical and electro-chemical signals, and the output is the right protein at the right time. Of course sometimes the nucleotides are reset within the organism itself, but that usually means bad news! Elizabeth Liddle

I just don’t find it a very useful metaphor. But regarding the information content – of course. I fully agree that DNA has information content.
I believe - cynic that I am ;) that it is useful in helping with the argument from analogy - 'It is digital, which is like a computer, computers are designed.' DrBot

kf: I'll have to get back to your posts later, but meanwhile, you ask:
If not,then why do you seem so reluctant to accept that DNA is digital information bearing based on string data structures?
I completely accept that DNA contains information. I just wouldn't describe it as digital - it seems alphabetic to me (aka a "string" as you say"). But I guess in the sense that alphabetic characters can be demonstrated by ascii code then you could describe it as digital, and the tRNA as the translator from digital to ascii. I just don't find it a very useful metaphor. But regarding the information content - of course. I fully agree that DNA has information content. In fact I think "database" is a good description. Also a "library". Elizabeth Liddle

F/N: "Definitionitis" is in full blown form, it seems. But, don't we in fact have definitions adequately and reasonably reducible to empirical operations already; indeed long since? Let's clip Mung on Tuckman in 199 [noting that his onward linked at the foot gives . . . examples that look very familiar relative to what we have been using]:
A type A operational definition can be constructed in terms of the operations performed to cause the phenomenon to occur. [Fear - state produced by exposing an individual to an object highest in his or her hierarchy of objects to be avoided. Conflict - state produced by placing two or more individuals in a situation where each has the same goal but only one can obtain it.] A type B operational definition can be constructed in terms of how the particular object or thing operates. [Motor activity - excursions by a student from his or her seat. Motivation - persistent attendance of students in a school (as measured by number of days attended).] A type C operational definition can be constructed in terms of what an object or phenomenon looks like. [Introversion - the tendency or characteristic of an individual to prefer to engage in solitary rather than group activities. Team teaching - utilization of two or more teachers to develop lesson plans and teach in one or more subject matter areas to a fixed group of students.]
1 --> Type A does not seem particularly relevant [save in the trivial sense of describing how complex, specifically functional info -- like a post in this thread -- is say composed by an intelligent agent, typed in as ascii code and transferred to the site that stores the page info thence retransmitted to browsers], but B and C are already clearly and long since repeatedly represented. 2 --> To wit, we first have and/or have access to descriptions of how info operates as a meaningful, specific, rules based configuration of elements that communicates meaning in a comms system: source, encoder, transmission unit, channel and/or storage, receiver unit, decoder, sink, all in the face of noise, interference etc. 3 --> In addition, as I have outlined at 192 above, we have a metric that can be applied to give numerical results on a widely used symbol frequency metric and is itself the application of a well known, well tested and -- despite a lot of ill founded dismissals -- quite successful detection procedure, the explanatory filter. 4 --> As is well known, Mathgrrl et al have challenged the rigour of the definition of CSI, but this has been answered step by step, May 12, months ago now, here. (No cogent response has ever come to my notice, just repetitions of the assertions corrected.) 5 --> Let us note the Type C def'n, which is in effect saying that one can view an ostensive definition or a description of/pointing to examples, as a way to operationally define. So, the type of description plus key examples pattern that we have been repeatedly using is relevant. 6 --> And, it is long since the case that we have a metric that is operational and known to be relevant to biological cases, indeed since April 18 or thereabouts this has been put up for all to see -- and roundly ignored or dismissed by MG et al on grounds that seem to lack any significant merits. 7 --> All of this -- per the UB comment at 200 just above -- fits quite well with the definition apparently composed by Dr Liddle herself on various dictionary etc discussions in exchanges with UB:
Information is a representation of a discrete object/thing embedded in an arrangement of matter or energy, where the object/thing represented is entirely dissociated from the representation
8 --> We can compare this with the definition that has been there in the UD glossary all along, in turn clipped and re-arranged from Wiki by way of inadvertent testimony against interest:
“ . . that which would be communicated by a message if it were sent from a sender to a receiver capable of understanding the message . . . . In terms of data, it can be defined as a collection of facts [i.e. as represented or sensed in some format] from which conclusions may be drawn [and on which decisions and actions may be taken].”
9 --> And with say dictionary definitions accessible online:
1. Facts, data, or instructions in any medium or form. 2. The meaning that a human assigns to data by means of the known conventions used in their representation. [Dictionary of Military and Associated Terms. US Department of Defense 2005.] 6. (Electronics & Computer Science / Computer Science) Computing a. the meaning given to data by the way in which it is interpreted b. another word for data [2] [Collins English Dictionary – Complete and Unabridged © HarperCollins Publishers 1991, 1994, 1998, 2000, 2003] 2b) the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (as nucleotides in DNA or binary digits in a computer program) that produce specific effects . . . d) a quantitative measure of the content of information; specifically: a numerical quantity that measures the uncertainty in the outcome of a specific experiment to be performed. [Merriam-Webster]
10 --> On fair comment, all of this has long been adequately on the table, and easily explains the annoyance being expressed by several commenters, including the recent speculation on willful misdirection or distraction and worse. __________ Frankly, Dr Liddle, I feel quite annoyed at this point, as in I find myself seriously tempred tot hink I am being dragged in an endless loop of going over the same issues long since adequately addressed, and tha this -- whether or not it is your intent -- is serving as a distraction from far more important points of consequence. (Not to mention, in the usual fever swamps it is occasion for drumbeat repetition of the usual already adequately answered twisty talking points.) Can you show me that there is anything of significance on the table today that was not adequately there months ago, and/or that could not have been rapidly and almost trivially been agreed as a reasonable step forward? As someone who first met the crucial understanding of information in the technical sense decades ago, to with I = - log P, used it in my own work, and actually taught it at college level myself in the context of information systems and the classic ISO layercake model and Shannon's model [I prefer to use my own adaptation of that model, emphasising encoders and decoders], I find the tendency to dismiss -- from Schneider on -- it as selectively hyperskeptical. Let me clip, yet again, from my favourite Taub and Schilling, Comms Syss, Ch 5:
Let us consider a communication system in which the allowable messages are m1, m2, . . ., with probabilities of occurrence p1, p2 [generally, detected through statistical studies of messages, e/g E is about 1/8 of typical English text], . . . . Of course p1 + p2 + . . . = 1. Let the transmitter select message mk of probability pk; let us further assume that the receiver has correctly identified the message [My nb: i.e. the a posteriori probability in my online discussion is 1]. Then we shall say, by way of definition of the term information, that the system has communicated an amount of information Ik given by Ik = (def) log2 1/pk (13.2-1) [i.e. Ik = - log2 pk, in bits]
Is there a serious objection to this, if so, what is it, why? (And, kindly note that symbol frequency patterns in typical messages have been used ever since Shannon, to estimate the p values, never mind the pathological cases; we are dealing with real world highly successful praxis here.) If not, know that the H-metric boils down -- as I learned from F R Conner decades ago -- is in effect the average info in the Harley sense just clipped, per symbol. I trust that we may now move forward with something constuctive. GEM of TKI kairosfocus

Upright BiPed
Dr Liddle, First, what a funny thing that your resource link pointed to a site dealing with the operationalization of hypotheses in statistical population research, a social science, which has been my professional specialty of many years. Your problem then becomes obvious. Despite my best efforts over the past eight weeks, you still don’t know what information is. Or, perhaps you understand the individual observations, but lack the imagination to put them together and grasp what it all means. In any case, your post certainly shines some light on why you think a method is not a method. It also makes clear why you think it’s circular to demonstrate something in order to confirm its presence. Let’s go to this comment for a clue: It’s like saying: demonstrate the presence of water by demonstrating the presence of water. No Dr Liddle, it’s nothing like that at all. To demonstrate the presence of water is to show a molecule with two hydrogen atoms bonded to a single oxygen atom. The last time I checked, these substances were all very material, each proudly listed on the Periodic Table. Then it all stands to reason; in order to demonstrate water, all one needs is to find a particular physical substance with two hydrogen atoms bonded to a single oxygen atom. That exercise however, has nothing whatsoever to do with finding information. Nowhere in the course of this conversation has anyone suggested that information exists as a material substance – or that it could be treated as one. In fact, quite to the contrary, we have always been very clear that the exact opposite is true. It is not the mere presence of the physical substance known as DNA that causes information to exist in the genome, Dr Liddle. It is not the mere presence of air that causes information to exist in speech. It is not the mere presence of iron oxide that causes information to exist on a recording tape. It is not the mere presence of wood pulp and dye that causes information to exist in a book. I have no idea where you got that idea, but it would be immediately challenged in this conversation, and would be falsified by the physical evidence. Information is an immaterial phenomenon embedded in the arrangement of a material carrier, a physical medium. But the information is not the medium itself, and the medium did not cause it to exist. It requires a mechanism beyond the material medium in order to come into existence. As has already happened over and over, your objections are already answered in the definition you crafted when we walked through the observations. Here is the relevant part: “Information is a representation of a discrete object/thing embedded in an arrangement of matter or energy, where the object/thing represented is entirely dissociated from the representation”
Right. And all that remained was to operationalise that.
If information is a discrete representation, and that representation is embedded in an arrangement of matter, then the existence of information simply cannot be confirmed in the same way as demonstrating the mere presence of any material object, like water. Its existence is not confirmed by the existence of the material, but by the arrangement.
Exactly.
Therefore, in fact, demonstrating the existence of information and the existence of water have nothing whatsoever in common. One is a matter of finding a substance; the other is finding an arrangement within a substance.
Well, I see a lot in common myself, but OK. That’s fine. In my field we mainly detect arrangements, not the-thing-itself.
Nowhere in the description you produced can you come to the conclusion that the presence of matter (a material object) is an indicator of information. Therefore as a logical consequence, to confirm the existence of information requires something more.
Certainly I agree that we are not interested in “the presence of matter” but the presence of an arrangement of matter, or, in the case of my proposal, virtual matter.
So let’s not stop the observation there, because this plays directly into a correction of your other issue – ‘why do I have to demonstrate information’ in order to know it exist, or ‘why is it that a demonstration of information is the only way to confirm its existence? The answer is in the definition already on the table, and is a logical deduction made from the evidence. If you found a material object that you suspected of carrying information in its arrangement, how would you confirm it? Remember, you can’t confirm that information exist in an object by just looking at it.
Well, Dembski claims you can, of course, so did Paley. But I’m on your side here.
The only way to confirm the existence of information is to demonstrate its effect.
Abso-bloomin’-lutely.
This should come as no surprise to someone following this conversation. Any material object that you suspect of having information in its arrangement would by definition have representations of discrete objects/things embedded in that arrangement. The only way to know it does is to demonstrate the effect of those representations, and to do that they’ll have to be demonstrated. That is not circular Dr Liddle; it’s as straight a line of reasoning as it can possibly be. It also happens to be the same method used to establish any other instance of information ever known to exist.
That’s why I liked Meyer’s definition from Webster. The crucial thing is to demonstrate the effects of the arrangement of matter. That’s easy enough to operationalise. Where I struck a difficulty was where you bring in “representations of discrete objects or things”. I’d suggest is simply cutting that part out. If the arrangement of a set of material objects can be demonstrated to “cause specific effects” then I don’t think we need the “representations” part at all, because if the output of something depends on the arrangement of the materials that form the input, then we’ve satisfied the Webster definition. We could, post hoc, say that in that case, the arrangement of materials (a codon, say) “represented” the output, but that would simply be a manner of speaking (a reasonable manner of speaking). Operationally, we would demonstrate that information was present by the simple observation that the arrangement of input material resulted in specific output.
This is why the demonstration is the only viable method, Dr Liddle. It’s mandatory to the exercise. You have to demonstrate that a discrete representation is a discrete representation, and for it to actually be a discrete representation it will require something to create the mapping between itself and that which it is to represent. And as in all other cases of information known to exist, those representations will have a physical protocol to establish that mapping.
Well, I would then need operationalisations of “discrete representation” and “physical protocol” then. But I don’t see that they are necessary. If the output (say an amino acid) maps to an arrangement of nucleotides, then obviously there must be a physical mechanism to do so. But all we need to do to say that information has been created is to demonstrate the mapping, surely? We do not have to say – “oh, and that mapping has to have been created by a physical protocol”. And we certainly do not have to say, surely, that the mapping has to have been created by a non-physical protocol, or a “break in the causal chain”!
Your claim is that both the creation and coordination of those representations and their protocols can arise in a system by chance and law, and that the output of those representations will be the system that created them.
My claim is that chance and law alone can give rise to information. I am more than happy to define, following Webster, “information” as the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something that produce specific effects. I don’t see that we need the word “representations” or “protocols” in there, in addition, although you might want to use them to describe what my sim actually does (if it succeeds).
If you are asking to push the methods question down to the level of describing the exact operation of keystrokes necessary to cause the required demonstrate in your simulation, then I want you to know that those decisions are entirely your own responsibility. And with these final misunderstandings out of the way, we eagerly await your results.
No, we don’t need specify the exact keystrokes. And if we go with Webster, as I hope we do, that makes things a lot simpler. Here we go, then:
Conceptual hypothesis: That chance and law alone can give rise to information, where “information” is defined conceptually, according to Merriam-Webster, as “the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something that produce specific effects.” Operational hypothesis: That, starting only with non-self-replicating entities with a physics-and-chemistry plus random kinetics, self-replicating “virtual organisms” can emerge that contain patterns of “virtual matter” whose arrangement determines the fidelity of its self replication (measured in terms of similarity to its “parent” as compared with a randomly substituted pattern).
If you approve that, I am ready to start, I think. Elizabeth Liddle

Mung:
Elizabeth Liddle:
As I said. One that allows you to measure the variable will of course also allow you to say whether it is present or absent. Shannon’s definition does that – if there are 0 bits in the message, there is no information present, and if there are >0 bits in the message, there is information present.
Upright BiPed has provided a definition according to which you may say that information is present or absent. And yet you have denied that he has given you an operational definition according to which you may say that information is present or absent.
Because he hasn't.
Why did you do that?
Because he hasn't.
Can you please explain to me how, according to Shannon’s measure, there can be 0 bits of information in a message?
In a message in which there is no reduction of uncertainty.

Please describe the message and the measurement and explain how the measurement demonstrates that there is 0 bits of information in the message.
You cannot. You will not. Please stop with the incessant inanity, I beg you.
OK, let's take a channel that is dominated by noise at a frequency of 50 hertz. We listen to this channel. We fail to detect any departure from the 50 Hz tone. We therefore receive 0 bits of information. But, as we all agree, it's a totally irrelevant measure of information because it leaves out meaning. So we can stop talking about it, as you request. Nobody is suggesting we use this measure.
If you cannot, then I think it is entirely reasonable on our part to deny that Shannon information suffices as an operational definition, for it will be the case that you have given no reason to think that Shannon’s measure can identify when there is no information present in a message.
Of course it is entirely reasonable. That is why I am not suggesting it. It measures something that corresponds to no-one's conceptual definition of information. So. We. Won't. Use. It. Right?
It can tell you how much information is in a message, but it cannot tell you whether information is present or absent (it can only say it is present, not that it is absent).
Well, see above. But this is totally irrelevant anyway. As we both agree.
Again, I appeal to anyone else, other than Elizabeth, to take up the cause on her behalf and explain why I am mistaken. p.s. Why is it Elizabeth, that you continue to assert that Shannon provided a definition? What did Shannon give a definition of?
Of something that no-one in their right minds would regard as a conceptual definition of information that corresponds to common English usage, which was Meyer's absolutely correct point. Which is why we will not use it. OK? Elizabeth Liddle

UBP You write:
Despite my best efforts over the past eight weeks, you still don’t know what information is.
That is indeed the problem Upright BiPed. That is what I need you to tell me, in sufficiently unambiguous terms that I can derive a set of measurable variables from it. Until you do that, I cannot proceed. And until you see that, I guess we are stuck. I will try to address your long post in detail later. Elizabeth Liddle

Dr Liddle, First, what a funny thing that your resource link pointed to a site dealing with the operationalization of hypotheses in statistical population research, a social science, which has been my professional specialty of many years. Your problem then becomes obvious. Despite my best efforts over the past eight weeks, you still don’t know what information is. Or, perhaps you understand the individual observations, but lack the imagination to put them together and grasp what it all means. In any case, your post certainly shines some light on why you think a method is not a method. It also makes clear why you think it’s circular to demonstrate something in order to confirm its presence. Let’s go to this comment for a clue:
It’s like saying: demonstrate the presence of water by demonstrating the presence of water.
No Dr Liddle, it’s nothing like that at all. To demonstrate the presence of water is to show a molecule with two hydrogen atoms bonded to a single oxygen atom. The last time I checked, these substances were all very material, each proudly listed on the Periodic Table. Then it all stands to reason; in order to demonstrate water, all one needs is to find a particular physical substance with two hydrogen atoms bonded to a single oxygen atom. That exercise however, has nothing whatsoever to do with finding information. Nowhere in the course of this conversation has anyone suggested that information exists as a material substance – or that it could be treated as one. In fact, quite to the contrary, we have always been very clear that the exact opposite is true. It is not the mere presence of the physical substance known as DNA that causes information to exist in the genome, Dr Liddle. It is not the mere presence of air that causes information to exist in speech. It is not the mere presence of iron oxide that causes information to exist on a recording tape. It is not the mere presence of wood pulp and dye that causes information to exist in a book. I have no idea where you got that idea, but it would be immediately challenged in this conversation, and would be falsified by the physical evidence. Information is an immaterial phenomenon embedded in the arrangement of a material carrier, a physical medium. But the information is not the medium itself, and the medium did not cause it to exist. It requires a mechanism beyond the material medium in order to come into existence. As has already happened over and over, your objections are already answered in the definition you crafted when we walked through the observations. Here is the relevant part: “Information is a representation of a discrete object/thing embedded in an arrangement of matter or energy, where the object/thing represented is entirely dissociated from the representation” If information is a discrete representation, and that representation is embedded in an arrangement of matter, then the existence of information simply cannot be confirmed in the same way as demonstrating the mere presence of any material object, like water. Its existence is not confirmed by the existence of the material, but by the arrangement. Therefore, in fact, demonstrating the existence of information and the existence of water have nothing whatsoever in common. One is a matter of finding a substance; the other is finding an arrangement within a substance. Nowhere in the description you produced can you come to the conclusion that the presence of matter (a material object) is an indicator of information. Therefore as a logical consequence, to confirm the existence of information requires something more. So let’s not stop the observation there, because this plays directly into a correction of your other issue – ‘why do I have to demonstrate information’ in order to know it exist, or ‘why is it that a demonstration of information is the only way to confirm its existence? The answer is in the definition already on the table, and is a logical deduction made from the evidence. If you found a material object that you suspected of carrying information in its arrangement, how would you confirm it? Remember, you can’t confirm that information exist in an object by just looking at it. The only way to confirm the existence of information is to demonstrate its effect. This should come as no surprise to someone following this conversation. Any material object that you suspect of having information in its arrangement would by definition have representations of discrete objects/things embedded in that arrangement. The only way to know it does is to demonstrate the effect of those representations, and to do that they’ll have to be demonstrated. That is not circular Dr Liddle; it’s as straight a line of reasoning as it can possibly be. It also happens to be the same method used to establish any other instance of information ever known to exist. This is why the demonstration is the only viable method, Dr Liddle. It’s mandatory to the exercise. You have to demonstrate that a discrete representation is a discrete representation, and for it to actually be a discrete representation it will require something to create the mapping between itself and that which it is to represent. And as in all other cases of information known to exist, those representations will have a physical protocol to establish that mapping. Your claim is that both the creation and coordination of those representations and their protocols can arise in a system by chance and law, and that the output of those representations will be the system that created them. If you are asking to push the methods question down to the level of describing the exact operation of keystrokes necessary to cause the required demonstrate in your simulation, then I want you to know that those decisions are entirely your own responsibility. And with these final misunderstandings out of the way, we eagerly await your results. Upright BiPed

Down the Rabbit Hole aka Operational Definitions I think this site provides a fair insight into where Elizabeth is coming from: Research Methods Workshops: Operational Definitions Not that I agree with the approach she has taken. But further:
Tuckman (1978) identifies three types of operational definitions. A type A operational definition can be constructed in terms of the operations performed to cause the phenomenon to occur. A type B operational definition can be constructed in terms of how the particular object or thing operates. A type C operational definition can be constructed in terms of what an object or phenomenon looks like. here
Mung

Elizabeth, please see my post at 176 and respond. In particular, please answer how you propose to obtain a measure of 0 bits of information in a message. I am really looking forward to that. Mung

F/N 2: Kindly provide an operational definition of an operational definition, and another one that justifies the claim that only operationally defined entities are workable in scientific contexts. In fact, the concept information is defined in the first instance on known examples, labelled to identify something recognised as a common feature of entities like messages in this thread as opposed to gibberish. The use of symbols is then highlighted and the relative frequency of such in meaningful messages is identified as a means of quantifying on a frequency based probability metric. Taking negative logs simply gives us an additive measure. The whole ICT industry stands on that foundation. And when we look at DNA, we find it is the same class of symbolic, coned, rule-based meaningful entity. Indeed, routinely, we represent DNA strands on the symbols GCAT, for the relevant bases, and for RNA, GCAU. We even have worked out code tables. Against that backdrop, I begin to seriously wonder about your salvos of objections, whether they are simply selectively hyperskeptical. Do you object to the way PCs work and ASCII codes used to send text work? If not,then why do you seem so reluctant to accept that DNA is digital information bearing based on string data structures? kairosfocus

F/N: Ever since 1928, an operational definition of information has been on the table, I = - log p, in a context where messages can be distinguished form noise so that signal to noise ratios can be defined, one that is routinely used in entire disciplines. Please do not go down the road the manufactured character Mathgrrl went. kairosfocus

Liddle at 191 LOL Finally the problem rears its ugly head. I will return in a short while to give a response to your post. And there won't be an ounce of ambiguity in my response. Upright BiPed

Dr Liddle: Pardon me but I find your objections tha the likes of the above -- which you by now have been seen dozens of times -- are not "operationalised" to be selectively hyperskeptical. For reasons that should be quite evident, from the just above. If you objection is to I, you are objecting to well established approaches used in whole disciplines. If to S, that is to something that we have cases in hand that are operationally identifiable, and are open to reasonable identification of further cases. If it is to the 500 or 1000 bit complexity threshold, it is your challenge to show us practically or on analysis that the inference on FSCI at such levels is undermined by credible counter-examples. Remember, cases well within this limit we hold will be findable by chance. Of course maybe you can show us the equivalent of a path from See Spot run to a tome on mathematics, where one or a few steps are changed each stage and on blind trial and error progress is made, or a way to transform a Hello word into an operating system, or the like. Please, let us move on to something serious. GEM of TKI kairosfocus

PS: And since some still insist on trying to claim that there are no biologically relevant values of Chi_500 or the like, kindly note the values given as examples here, based on I values from Durston et al. And Durston's H calculations and use of observed patterns of distribution are reasonable extensions to well known approaches. kairosfocus

Ah well, It looks like this molehill has been inflated into a mountain yet once again. 1 --> Let's look again at the log-reduced Chi metric:
Chi_500 = I*S - 500, functionally specific bits beyond the solar system threshold
2 --> I is a well known quantity from info theory, usually measured on some version of I = - log p as suggested by hartley, p being a version on a symbol frequency metric interpreted as a probability. 3 --> Or, as Shannon also did in his original paper and as we routinely do, if we know how things are stored we may directly count up bits. (File size so many bits, good enough for govt work.) 4 --> This is well established commonplace praxis, so I will only be challenged by selective hyperskepticism. 5 --> We can lay I to one side as a well understood commonplace type of thing. 6 --> The RHS has a fixed number 500, which is more or less a threshold of complexity, beyond which it is unreasonable that a random walk on the gamut of our solar system would be able to find a sufficiently specific zone, T, as 10^102 PTQS's is 1 in 10^48 of the more than 10^150 states possible for 500 bits. 7 --> That leaves only S to be discussed, as Chi_500 is simply the name for the value beyond the threshold, of [functionally] specific bits. 8 --> It being inferred that if Chi_500 goes positive, no reasonable random walk or comparable process on the gamut of the solar system can sample more than 1 in 10^48 of the configs once we are beyond 500 bits, and so specific, unrepresentative zones T are not credibly going to be found that way. (It is only when you are in the zone T that something like a hill climbing algor based on existing function can then kick in to reward superior function.) 9 --> S, as has been repeatedly noted, is a dummy variable that stands in for, on some method or observation to be justified in the relevant case, identify the information in I as specific, coming from a zone T. 10 --> For instance, we can look at codes that must fulfill certain rules of meaning and take things form a specific vocabulary, etc. Or, we could start with something in T and see if significant perturbation caused function to vanish, etc. (In short we list certain operations and say if you can justify another it would be accepted.) 11 --> from this it is inferred that for I beyond 500 bits and S 1, then Chi_500 will be positive. 12 --> For instance, this post is more than 73 ASCII characters, it comes form English vocab and rules, and if you were to inject random variables into the code, it would vanish into a hash. 13 --> Chi_500 is positive and the inference is that this is a product of design, which is also directly known. 14 --> There are billions of similar test cases, all well affirmed, and there are no credible counter examples. GAs start in islands of function and proceed by hill climbing, for instance. 15 --> So, by analysis and by induction the expression is meaningful, it has procedures that can be used successfully, we know how to extend the methods, and we know its tested success. 16 -> It is also a metric, giving values of specific bits beyond a threshold, associated with design as the best explanation. 17 --> So, why -- apart from selective hyperskepticism -- is there a long drawn out debate as though the above were not well established and easy enough to refute if you could? __________ I think the matter is quite simple at this point: Dr Liddle needs to put up soehting which is inrformational, specific by some reasonable argument, and has been produced credibly by chance and necessity without intelligent direction. Failing such a decisive ounterexample we have every epsistemic right to trust the induction and analysis that has brought us to this point. So, Dr Liddle the ball is in your court. Your credible counter-instance on the gamut of our solar system [our "practical" universe] is __________, as documented by _________ and published in _________ . Failing a clear answer to the just above, we have every right to infer that you are unhappy with the implications of the expression, as opposed to its foundations. For, plainly, the expression implies that cell based life as we observe it is riddled with designed entities. Well, what's new about such a view, the co-founder of modern evolutionary theory thought much the same. (Along with many others.) We are jut putting he line of thought on a more specific, metric based footing. GEM of TKI kairosfocus

Upright Biped: Can you not see the circularity in your question? You ask me to assent to using "the one and only method of confirming the presence of recorded information that has ever been known to exist". then you say that that method is: "by demonstrating the information". In other words, I am to "demonstrate [confirm the presence of] [recorded] information by demonstrating the presence of information"! So my answer to the reason why I cannot use that method is because it isn't actually a method! It's like saying: demonstrate the presence of water by demonstrating the presence of water! What I need, as I think I have made pretty clear, is an operational definition of information. I have provided two further links to resources to make it clear why this is needed. You simply cannot do emprical science without operationalizing your hypothesis, and you cannot do that without operational definitions of all your variables. I have attempted to do this for your conceptual definition. I can try it again for Meyer's. But first I'd like you to look at the one I did for yours and to tell me whether it is acceptable. Then, by all means, I will attempt to confirm the presence of information - by measuring it to see if I've got it! And by offering the output to you to check, using the exact same criteria! Elizabeth Liddle

Dr Liddle, there is a very straighforward question you continue to avoid answering. I am wondering if it will, or will not, be possible for you to make a constrete statement about the issue raised. I will re-post it here for your convenience, and then perhaps after you address the issue in earnest providing a comprehensive statement that first recognizes the issue raised by the question, and then provides a clear and logically detailed response, then we will be in a much better position to move past this problem. Here is the question yet again: "I am willing to rely on the one and only method of confirming the presence of recorded information that ever been known to exist. That is, by demonstrating the information. The question you must answer is why you think your simulation should be held to any other standard. Specifically, in strong concrete terms, why can we not use the only method anyone has ever used?" Upright BiPed

This resource is even better, as it discusses measurement types for different kinds of variables (categorical/nominal; ordinal; interval; ratio): http://web.jjay.cuny.edu/~pzapf/classes/CRJ70000/Formulating%20the%20research%20question.htm Elizabeth Liddle

This is what I am after: http://www.newfoundations.com/EGR/Oper.html Hypothesis 6: Chance and Necessity can create Information.
Specify: a. the variables b. the identity criteria for each variable. c. a measurement procedure for each variable d. what would count as evidence for or against the hypothesis.
Elizabeth Liddle

Upright BiPed - sorry I missed this post:
Dr Liddle, what is false is that you need anything else, from anyone else, before you can demonstrate your claim. You want to falsify ID? Then get after it.
No, it isn't false, UPD. In order to falsify a claim, you need an operationalisation of that claim. You have not provided me with an operationalisation. As I said, that doesn't matter, as long as you give me a clear set of conceptual definitions which I can operationalise. As I have said, what you gave me turned out to be problematic. Nonetheless, I have made the attempt. I'd be grateful if you would review that attempt. If it is unsatisfactory, let me know in what respects, and I will try again. Alternatively I will use Meyer's conceptual definition, as that seems relatively easy to operationalise. But I will post the operationalisation here first, to make sure that at least one ID proponent accepts it! Otherwise there isn't a lot of point. No point in demonstrating something nobody questions is true! Hope things are better with you and yours. Elizabeth Liddle

Ah - Upright BiPed: Any comment on my operationalisation? Elizabeth Liddle

In the face of actually having to display the humilty you talk about... babble instead. Upright BiPed

Mung, it would depend entirely on the operation you wish to perform. Sheesh. If the operation is supplying packs of prepared peanut butter sandwiches, then it probably will include the bread thickness, ingredients of the peanut butter, quantity of peanut butter, and possibly the calorific value of the whole thing. And if you are a sharp operator (heh) you might want to make sure the criterion values are as low as possible for the expensive ingredients and as high as possible for the cheap ones. Did you know that British ice cream manufacturers failed to satisfy the EU operational definition for ice cream at one time? They couldn't call it "ice cream" because it didn't have enough (any?) cream. They had to call it something like "frozen dairy dessert" instead. And write "contains non-milk fat" on the label. They tried not to call attention to the fact that their other main product line was sausages. Still, it improved the standard of British Ice cream no end. Try Mackie's if you are ever over here. Elizabeth Liddle

Hi Elizabeth, What is the variable that we want to measure when it comes to creating an operational definition of a peanut butter sandwich? http://en.wikipedia.org/wiki/Operational_definition Mung

Dr Liddle, what is false is that you need anything else, from anyone else, before you can demonstrate your claim. You want to falsify ID? Then get after it. Upright BiPed

No, it isn't false Mung. UPD's definition remains to be operationalised, i.e. expressed in a manner in which an objective observer can measure the variables and ascertain whether the criteria given for their presence has been met. This is not a criticism of UPD's definition - a conceptual definition is also essential. And I am happy to do the operationalisation, which can be highly specific with respect to a particular demonstration (as mine was), or more general. But, as I said, as currently stated, it contains a problem. I have attempted to solve that problem, and still await UPD's response to my solution. If it is not acceptable, I suggest we use Meyer's conceptual definition from Webster (quoted above) and I try to operationalise that. Unless UPD has any issues with the Webster definition. Elizabeth Liddle

Upright BiPed:
Isolating the representations, deciphering the protocols, and documenting the effects is the only process that demonstrates the existence of information.
Perhaps it is the case that Elizabeth disagrees that this is in fact "the only process that demonstrates the existence of information." Perhaps she can offer an alternative operational definition. But her assertion that you failed to provide an operational definition is clearly false. Mung

#177 I don't really understand a "protocol that included symbols" and I certainly dont think I presented it by that wording. But I wouldn't read too much into it. I think she said it at a time when she was discovering that the existence of information has actual entailemnts which can be observed. The fact is there are representations, protocols, and effects. Each plays a specific and necssary role. Each must exist for the reasons we've discussed. Each is materially observable. Isolating the representations, deciphering the protocols, and documenting the effects is the only process that demonstrates the existence of information. If Dr Liddle's simulation is to be judged by a process that confirms the existence of information, then that is the process we'll be using. Upright BiPed

Upright BiPed:
The definition you offered says nothing whatsoever about codons or amino acids. Instead, it describes the dynamic role these physical objects play in the existence of information – any information. That gives you everything you need to properly operationalize it.
BINGO! The definition had already been abstracted. What more is required? Mung

Upright BiPed, please comment. Elizabeth Liddle wrote:
Upright Biped said that it [information] had to arise from some kind of protocol that included symbols.
I asserted that the above claim was a lie. That you had never said any such thing. Did you in fact ever say that information had to arise from some kind of protocol that included symbols, as Lizzie claims? Or was it in fact the case that you maintained that symbols and protocols were the means by which to determine whether or not information was present? Mung

Elizabeth Liddle:
As I said. One that allows you to measure the variable will of course also allow you to say whether it is present or absent. Shannon’s definition does that – if there are 0 bits in the message, there is no information present, and if there are >0 bits in the message, there is information present.
Upright BiPed has provided a definition according to which you may say that information is present or absent. And yet you have denied that he has given you an operational definition according to which you may say that information is present or absent. Why did you do that? Can you please explain to me how, according to Shannon's measure, there can be 0 bits of information in a message? Please describe the message and the measurement and explain how the measurement demonstrates that there is 0 bits of information in the message. You cannot. You will not. Please stop with the incessant inanity, I beg you. If you cannot, then I think it is entirely reasonable on our part to deny that Shannon information suffices as an operational definition, for it will be the case that you have given no reason to think that Shannon's measure can identify when there is no information present in a message. It can tell you how much information is in a message, but it cannot tell you whether information is present or absent (it can only say it is present, not that it is absent). Again, I appeal to anyone else, other than Elizabeth, to take up the cause on her behalf and explain why I am mistaken. p.s. Why is it Elizabeth, that you continue to assert that Shannon provided a definition? What did Shannon give a definition of? Mung

Dr Liddle,
I readily acknowledge the gulf that communication (information? ) barrier that exists between us. We are clearly coming at this issue from very different backgrounds, traditions, methodologies and even lexicons.
We are not experiencing a communication barrier Dr Liddle, that’s a positioning statement coming from a valiant defense. If the observations had gone in your direction, then you’d be on offense. The fact is, we understand the meaning of each other’s words completely, as well as their contexts. What is happening is that you came into this conversation thinking one thing, and found out something entirely different. But, the gulf you mentioned is not between the arguments I’ve made here versus others being made elsewhere, the gulf exists between your (almost complete) misunderstanding of information and what information really is. Incredibly, after this entire conversation, you actually went to another thread and claimed that - by any definition of information - the state of an object certainly contains it. Suddenly, this entire conversation over multiple threads and tens of thousands of words simply vanished into thin air. That is the vast saddening gulf Dr Liddle, both in what you said, and the fact that it was you saying it. - - - - - - - - - - - - -
I am not at all clear what you mean by rejecting “the one proven method of finding the very thing she claims to be looking for”.
This statement is literally divorced from reality: - - BIPED: “We are attempting to simulate the rise of information in the genome, and the central question at this point is “how will we know it’s there?” To me, it seems like the shortest path to that answer would be the least subject to error, and in fact, it’s already been proven to be entirely reliable. The question to be answered is “how did we find it in the genome in the first place?”” - - LIDDLE: “no, that isn’t the question to be answered!” - - LIDDLE: “we need an operational definition of information, so that we can both, independently, use that criterion to decide whether or not I have succeeded.” You want independent verification? So do I, Dr Liddle. I want it so badly that I am willing to rely on the one and only method of confirming the presence of recorded information that ever been known to exist. That is, by demonstrating the information. The question you must answer is why you think your simulation should be held to any other standard. Specifically, in strong concrete terms, why can we not use the only method anyone has ever used? - - BIPED: “Nirenberg et al discovered the information in the genome by demonstrating it. They isolated the representations, deciphered the protocols, and documented the effects; the same way that all other recorded information has been discovered.” LIDDLE: “I am not at all clear what you mean by rejecting “the one proven method of finding the very thing she claims to be looking for” This is not sloppiness, or forgetfulness – and it certainly isn’t a misunderstanding. This is the mark of a failed argument. One in which you’ve described yourself as willing to rush in to correct. This view of yourself has now been tested, and it appears to be false. - - - - - - - - - - - -
I’m sorry, UBP, but this is circular…
Dr Liddle, I am concerned that you might not be able to recognize a circular argument. Nirenberg and his colleagues confirmed the presence of information recorded in the genome by the same means that anyone at any other time has ever (in the history of life on earth) documented the presence of recorded information. They did it by isolating the representations, deciphering the protocols, and documenting the effects. To point out that this is what they did, and this how they did it, does not constitute a circular argument. It’s simply the recognition of a historical fact. It’s a historical fact that you first ignore, then acknowledge, then ignore. - - - - - - - - - - - -
What I need to do, however, is to abstract from that specific example (of codons amino acids, etc) a criterion by which any candidate for the category “information” can be so categorised. Clearly not all information is mediated by codons; not all messages are “about” proteins. So we need a general criterion by which we can look at either a process, or an object, and say: this is information transfer/this contains information.
You’ve already done this, but apparently fail to see it. The definition you offered says nothing whatsoever about codons or amino acids. Instead, it describes the dynamic role these physical objects play in the existence of information – any information. That gives you everything you need to properly operationalize it. We’ve spent tens of thousands of words on a granular observation of information, Dr Liddle. And yet we already knew how to detect information. Your request has therefore been thoroughly satisfied Elizabeth, and has grown sour. No one can actually tell you that you already have everything you need. Thus far, your response has been to completely ignore the fact. You prefer instead to repeat what you need, as if anyone questions it. The fact remains that you yourself already developed a valid definition of information from the observations, and on top of that, you already know how information is demonstrated to exist. You now need to deal with this fact, straight up.
Now, unlike Dembski, you have chosen to define information in terms of process, rather than product. I actually think this is sensible – it seems to me that information is only as good as the use that is made of it,
It’s nothing more than a logical demonstration of the evidence. And right now it’s a live demonstration that your claim (that ID hasn’t made a valid case) is not only false, but obviously false. Or should I say – it’s obvious to anyone who thinks you wouldn’t have to demonstrate a falsification of ID if their case was already invalid, even before that demonstration. The demonstration is necessary because their argument is valid, and yet that demonstration is still to be done, by anyone, anywhere.
I hit a snag – the word “protocol”, which I hoped we had already operationalised, seemed to acquire something I had not anticipated – ~~your~~ the “break in the causal chain” or “break in the physical chain”.
I have nothing to do with the fact that the observations are what they are. It is not because of me that protocols in the cell are discrete objects that allow discrete representations to enter and affect the discrete output of a system. Microbiologists made those observations, and I’ve already told you that you are free to describe them in your own terms. You did, and I then accepted those terms. Yet, here you are, still talking about it as if it’s an impediment to you.
… because I assumed that by those phrases you meant some process that could not be attributed to Chance or Necessity.
I do not attribute them to chance, Dr Liddle - you do. That is the point of your simulation.
This is why I pointed out that tRNA is, essentially, a catalyst – it is an inert facilator of a chemical process
Personally I don’t think ‘catalyst’ is the proper term. I think it’s more appropriate to see the ribosome as the catalyst, being facilitated by ribosomal RNA. However, if you would like to view the protocol as a catalyst, then that is fine - as long as this catalyst in your system remains a discrete structure that transfers the representations within the input, to the structure of the output, without becoming a part of either one of them, while keeping them separate. That is the dynamic structure of information as we know it to exist. The word ‘apple’ is not an apple, and the pattern in our neural activity which establishes the relationship (between the fruit and the word) isn’t a part of either one. A bee’s dance is not the same as the direction of food, and the observation of this dance by the other bees, is not the same as flying off in a particular direction. Everywhere you look in the existence and transfer of information you find this repeated evidence of a separation from pure physicality, yet something established and coordinated these relationships. That is the point of your simulation – to show that random contingency and physical law can accomplish the observed result. The system you are trying to simulate, has already accomplished it, and has become a part of the observable evidence.
But UBP – if I don’t have an operational definition of information, then we can’t confirm its presence, and if we can’t confirm its presence, then I can’t support my claim!
Dr Liddle, you have now gone over the top on this. The definition you developed already faithfully describes the dynamic structure required for any and all recorded information to exist. You will confirm the existence of information in your simulation by not contradicting that description, and most importantly, by demonstrating the information just like all other instances of recorded information have been demonstrated to exist.
It’s not that I have any doubt that Nirenberg was finding “information” in the genome, nor about his methods for doing so – figuring out what mapped to what. The problem is defining what constitues a “mapping”.
Nirenberg demonstrated it. That’s how we know its there. With all due respect, if this concept is beyond your ability to comprehend, then I don’t know what else to say. I have no recourse but to repeat the historical fact, which you apparently already understand.
After all, a footprint maps to a foot, a meteor maps to a crater, but we do not necessarily say that what we have, in a footprint, or a meteor creator, is “information”
Dr Liddle, please stop. Let us look at the first lines of your definition of information: “Information is a representation of a discrete object/thing embedded in an arrangement of matter or energy, where the object/thing represented is entirely dissociated from the representation” You perceive a footprint - caused by direct physical contact with a foot – to be an “entirely dissociated representation” of a foot? Come’on. A footprint is nothing more than the state of the ground after being stepped on. A footprint doesn’t become information until it is perceived by some living thing which causes a physical representation within that living thing, leading it to be in-formed by the representation.
So what I am trying to do is define a clear criterion, or set of criteria, tht can be applied to any system, and which will tell us not what the relevant protocols are, but whether they are can be considered part of information transfer system.
Without the protocols Dr Liddle, a discrete representation of something would not be possible. How would one thing represent something else, without something to establish the relationship, which otherwise wouldn’t exist? No representation, no information, no information transfer. This criterion has already been covered in your definition.
… a good way of looking at what I am trying to do here: establish quality control criteria such that you can look at my simulation and say: yes, the protocols here pass the criteria required
Please remember, I am the one here saying you already have all you need to do just that. I described the observations of information; you created a working definition based upon those observations. I affirmed it as being completely satisfactory. And am now asking you to get off of the pot, and demonstrate your mechanism can create the phenomena, because it is the demonstration itself that will confirm your success. Quite frankly, languishing on this objection is beginning to look a lot more like the pursuit of a means to skirt the edges of a definition, than it is the pursuit to demonstrate the rise of information in earnest - as we find it. You do realize don’t you, you are expected to operate in good faith?
No, it is not nonsense.
“It’s nonsense” - Elizabeth Liddle
But it is not operationalised. I have tried to operationalise it above. I am still waiting for your response!
The operation you are referring to is (and has always been) a demonstration of the effect of the recorded information itself. It’s a demonstration whereby discrete objects are represented in an arrangement of matter or energy, yet are entirely dissociated from those representations. The re-association of those representations (to the objects they represent) is established by means of physical protocols which allow the discrete representations to affect the discrete output of a system. And since your claim was about the rise of information from chance and law, then the output of that system will represent (and result in) the system itself. Is this not yet obvious?
What matters is what constitutes a “mapping”. This really does seem to be at the root of the problem between us. Not so much an Apples and Oranges problem as an Apples and Appletrees problem. I do not deny that those mappings exist. What I want to know is what, in your view, makes the mapping between a codon and an amino acid “information”, and the mapping between a foot and a footprint not “information”.
As already established by your definition; one mapping is completely disassociated while the other requires a direct physical interaction. In the instance of the relationship of codon to amino acid (with the codon/anticodon being a representation and the amino acid being the effect) they never directly interact. In the case of a foot and a footprint (the foot being the object and the footprint being the effect) the two must directly interact. There is no representation between them, and therefore no mapping. You as an observer say there is a mapping between them, but that’s only because that (for you) the footprint has become the representation instead of the effect, and its effect is your association of it to the foot that created it.
This seems confused to me. And unnecessarily complicated. It is often said, by ID proponents, that Chance and Necessity cannot generate Information (or, at least, Information of a certain kind, or degree). My counter-claim is that they can.
The observations I’ve made about information was not done to confuse you, Dr Liddle, but to clarify what (by the evidence itself) can be said of information. You came into this conversation with a concept of information that cannot in any way be justified by the evidence. You come from the school of thought where information is contained in all things everywhere. That is factually and demonstrably false. Moreover, it shows an absolute disregard for what information really is – for the evidence itself. What you’ve since found is that if you dissolve away the misunderstandings and assumptions, and rely on that observable evidence, the problems for your thesis are that it faces virtually intractable issues throughout the entire phenomenon. One problem atop another. You’ve claimed that these apparent problems are only illusions claimed to exist by ID proponents who fail to see the validity of your claim. But you still have yet to actually demonstrate the validity of your claim. I, for one, am ready for you to take a stab at it. If this constant definition derby is intended to demonstrate an ability to define something so precisely that no one from either side can ever argue over it, then you know nothing of humanity, and are a fool wasting her time. But you needn’t worry, if your simulation causes the rise of recorded information, then all the observations we’ve made will be there, and your ability to demonstrate them will be there as well.
I’m willing to take on any. It may be that someone here has a conceptual definition of information for which my claim is false.
The one taken directly from the observations is just such a case Dr Liddle. All that remains is for you to acknowledge it, while also acknowledging it has never been falsified – as evidenced by the fact that you are currently trying to do so.
Ah. If by “made their case” you mean “put a case forward”, then I readily retract my claim. Of course I agree that a case has been made, and should have worded that in a more bulletproof manner. I meant it in the sense of “I do not believe you have made your case” rather than “You have not attempted to make a case”. Of course the case has been “made” in the sense that it has been put forward. I do not believe it holds water.
That is insulting to the evidence, Dr Liddle – to me, to the recording of this conversation, and to those who might have followed along. Nowhere in this conversation have you been able to invalidate the observations being made, and at no time has “made their case” referred to an invalid case. If it were invalid, we wouldn’t need your simulation to invalidate it, which would seem rather obvious. If your words were an attempt to quietly retract your claim, then please allow me to read between the lines: Your claim is completely false. And your attempt to cover up that fact in a smoke screen of “I didn’t mean you hadn’t tried” is just plain ole’ unvarnished bullshit. Upright BiPed

A faucet that goes drip drip drip is a boon to a man dying of thirst. Mung

Elizabeth Liddle:
Have it your way Mung. Your argument is with people who call Shannon Entropy a measure of information, not with me.
At the very least, you could accept responsibility for your own arguments and not try to fob them off on some unspecified other people. My argument plainly is with you, in spite of your claim to the contrary. You are the one who is attempting to use Shannon's measure as a definition of information which you think then allows you to assert that there can be information which is devoid of any meaning, in spite of Shannon/Weaver's clear warning to the contrary. You and you alone are responsible for your actions, arguments and beliefs. Now if you were to come forth with a quote, or cite, saying that person x argues that Shannon information demonstrates that there can be information that is without meaning, you might have a point. But you have not done that. And the fact remains that I have repeatedly invited you to present a definition of information according to which information can be devoid of meaning. You have failed to do so. You said that I was "clearly wrong":
Both of us reject as relevant to this discussion any definition of information that does not include meaning. For some reason you are insisting that no-one has ever given such a definition. I’d say you are clearly wrong.
Who gave a definition of information according to which information so defined is devoid of meaning? Where is that definition published? Cites and quotes please. Again I raise the question of how it is logically possible to have two different definitions of information according to which in one case information has meaning and in the other case information has no meaning? What then, is information? Mung

Elizabeth Liddle:
An operational definition can also give criteria for establishing whether some categorical variable is present or absent.
What is the variable that we want to measure when it comes to creating an operational definition of a peanut butter sandwich? Mung

A nagging wife is like a faucet that goes drip, drip, drip. allanius

Ilion:
… that silly phrase, “The whole is greater than the sum of its parts” is both false and thought-stultifying. So, naturally, DarwinDefenders are all over it. When people say and think that stupid phrase, they are overlooking or ignoring parts of the whole, generally the immaterial parts, such as information and work and development-over-time and so forth.
Well, I'm not. It's exactly what I'm referring to. Elizabeth Liddle

Mung:
“The attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something … that produce specific effects.” http://www.merriam-webster.com.....nformation Now I ask you Elizabeth, does that sound like information that is devoid of meaning to you?
Of course it doesn't! It's why I offered it!
Information, to be information, must have meaning. It must be meaningful. There is no other kind of information.
Have it your way Mung. Your argument is with people who call Shannon Entropy a measure of information, not with me. Elizabeth Liddle

An operational definition can also give criteria for establishing whether some categorical variable is present or absent. As I said. One that allows you to measure the variable will of course also allow you to say whether it is present or absent. Shannon's definition does that - if there are 0 bits in the message, there is no information present, and if there are >0 bits in the message, there is information present. Elizabeth Liddle

Elizabeth Liddle:
Bear in mind that an operational definition is one that allows you to measure the item in question.
Meaning what? What does it mean to have a measure of something? You were the one who referred me to the wikipedia entry. Does the following operational definition of a peanut butter sandwich give us a way to measure a peanut butter sandwich?
The operational definition of a peanut butter sandwich might be simply "the result of putting peanut butter on a slice of bread with a butter knife and laying a second equally sized slice of bread on top"
I think you have only one thing in mind when you say "operational definition" and an operational definition is not that restrictive. More later. Mung

“The attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something ... that produce specific effects.” http://www.merriam-webster.com/dictionary/information Now I ask you Elizabeth, does that sound like information that is devoid of meaning to you? Information, to be information, must have meaning. It must be meaningful. There is no other kind of information. Mung

Anyone have any problems with that one?
As long as you don't make the same mistake Meyer made and confuse the symbols or the sequence of symbols with information itself. :) Also, the effect is not produced by the symbols or sequence, the effect is produced by the information which is communicated. Mung

... that silly phrase, "The whole is greater than the sum of its parts" is both false and thought-stultifying. So, naturally, DarwinDefenders are all over it. When people say and think that stupid phrase, they are overlooking or ignoring parts of the whole, generally the immaterial parts, such as information and work and development-over-time and so forth. Ilion

What you said in @162, Mung, is what my point was in introducing the house. Ilion

Ilion:
Rather, ‘Shannon Information’ is a measure-by-proxy (*) of the information necessary to reconstruct the message, regardless of whether the message itself represents information.
I like the way you put that. That's sort of what I was getting at with my talk in a previous thread about your house and what happens to the information in it if we tear it down. The information is not in the house. Information would be what it took to reconstruct the house. So when you build something, it takes information to do so, but that information does not get transferred into the thing constructed. But looking at a thing might possible provide some indication of the amount of information required to construct it. Mung

So, how about we go with Webster's (b) as suggested by Meyer? "The attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something ... that produce specific effects." Anyone have any problems with that one? Elizabeth Liddle

Mung: "Shannon information is not a definition of information. God. It is a way to measure the amount of information in a message." Not exactly. True, it's not a definition of information; but it's also not "a way to measure the amount of information in a message." Rather, 'Shannon Information' is a measure-by-proxy (*) of the information necessary to reconstruct the message, regardless of whether the message itself represents information. (*) the proxy being the symbols necessary to represent the information being measured-by-proxy. Ilion

Mung, I'm going to wait until UPD has time and energy to take a look at my operationalisation of his criteria. You might take a look at it too, and see if you see a problem with it. Bear in mind that an operational definition is one that allows you to measure the item in question. Just like Shannon's definition does. But we aren't going to use that one, because none of us are very interested in a definition that doesn't incorporate the concept of meaning. OK? Elizabeth Liddle

Mung: "Shannon information is not a definition of information, it is a measure of information. Is that concept so difficult to grasp?" Specifically, as formulated, it's a measure of the symbolic representation of some information about a message, which message may or may not represent some other information. Ilion

Elizabeth Liddle:
Both of us reject as relevant to this discussion any definition of information that does not include meaning.
Well, now I'm confused. I would like to agree with you, but at the same time that you say this you've also been saying that there is such a thing as information devoid of any meaning. And you say there is information in the genome "“according to most definitions that I am aware of. But certainly according to the its meaning in general English usage.” And if there is in fact a definition of information in general English usage in which information can be devoid of any meaning then you are saying just that there can be information in the genome that is meaningless. So can you see the source of my confusion? I seem to be demanding that information in the genome have meaning, you don't.
For some reason you are insisting that no-one has ever given such a definition. I’d say you are clearly wrong.
I'm asking that you provide a definition of information from any English dictionary according to which definition of information, information can be seen to be devoid of any meaning. Until you do so, how can you assert that I am wrong?
Shannon information does not measure meaning. It does not care whether the message has meaning or not.
And yet you are arguing that Shannon information can tell you that a message is devoid of meaning. It cannot tell you that any more than it can tell you that a message has meaning. You cannot have it both ways.
See Meyer’s quote from Weaver above: “The word information in this theory is used in a special mathematical sense that must not be confused with meaning”. But this argument is silly.
The argument seems silly to you because you are doing exactly what that quote says you cannot do. Shannon information does not and cannot tell you that information is meaningless. And yet here you are arguing that you can have a meaningless string of characters and you can measure it using Shannon's measure and then reasoning that therefore there can be such a thing as information devoid of meaning. I have seen some bizarre arguments in my time and this one is right up there. If I am clearly wrong, if it is fact that case that information can exist which is devoid of any meaning, you should easliy be able to demonstrate that this is the case. All I ask is that you provide a dictionary reference. A definition of information, in which information, according to that dictionary definition, can be devoid of meaning. If you won't, then you have no reasonable basis upon which to assert that I am clearly wrong.
But it doesn’t matter because even if I am hallucinating Meyer’s cite of Weaver, or, possibly, Meyer was, or possibly we are all hallucinating Shannon, we aren’t going to use that definition here. OK?
Shannon information is not a definition of information. God. It is a way to measure the amount of information in a message. How could it possibly be a definiton of information if it can be used to define information as both having meaning and as being devoid of meaning? What kind of definition allows that? Particularly when we are told explicitly that "the word information in this theory is used in a special mathematical sense that must not be confused with meaning”. So why are you confusing it with meaning? Do you really even know what you are saying? Let's recap your argument, it is as follows: Shannon information demonstrates that information can be devoid of meaning. Shannon information is a definition of information according to which information may be devoid of any meaning. That's what you are claiming, and it is absolutely irrational and without basis in fact. Mung

Mung: "I ask again, are you aware of any definition of information which allows for the possibility that information may be devoid of meaning?" Elizabeth Liddle:
Shannon’s measure of information, as Meyer points out, has nothing to do with meaning.
Shannon information is not a definition of information, it is a measure of information. Is that concept so difficult to grasp? So I ask again yet, are you aware of any definition of information which allows for the possibility that information may be devoid of meaning?
Um, yes, it [Shannon information] does “measure meaningless information”. See above.
And from this you reason that information can be devoid of meaning and you don't see the fallacy in that line of reasoning? If you know the "information" is devoid of meaning, you do not know that because you measured it using Shannon's measure of information and found it to be devoid of meaning based upon that measure, right? But you're avoiding the question. The question was: [Keeping in mind that Shannon information does not define information but is rather a measure] are you aware of any DEFINITION OF INFORMATION which allows for the possibility that information may be devoid of meaning? Haul out your dictionary please, and go to work. Mung

Mung: "What definition of information, according to the its meaning in general English usage, best exemplifies the information you think is present in the genome?" Elizabeth Liddle:
As I said, I can’t think of a definition that doesn’t. As I have also said, repeatedly, I agree that information is present in the genome, by any definition in English usage you care to give.
And I asked you to pick one. One that you thought best exemplifies the information that you think is present in the genome. Here's what I wrote: What definition of information, according to the its meaning in general English usage, best exemplifies the information you think is present in the genome? Just pick one. The one you think best applies. Please. Mung

Mung @ 142
Elizabeth Liddle:
And for examples of general English usage I would give: “a repository of information such as a database”; “on the basis of that information, I have changed my course of action”; “thank you for your useful information”.
I don’t recall anyone asking you for examples. I think you were asked to provide a definition.
Here was the question: Elizabeth, what is the meaning of information according to general English usage? When someone asks, what does this word [information] mean, the typical response is to provide a definition. Another response is to give examples of usage. Indeed, dictionary definitions frequently do precisely this. So it’s what I did. If you want more dictionary definitions, look them up. Dictionaries record usage, they do not prescribe it.
Let’s review. Elizabeth Liddle: “I simply don’t think that the source of the information in the genome (and I agree there is information in the genome) is a great mystery.” Mung: “And what does she [Elizabeth Liddle] mean by information? Elizabeth Liddle: “According to most definitions that I am aware of. But certainly according to the its meaning in general English usage.” Mung: Elizabeth, what is the meaning of information according to general English usage? And your answer is? What definition of information, according to the its meaning in general English usage, best exemplifies the information you think is present in the genome?
As I said, I can’t think of a definition that doesn’t. As I have also said, repeatedly, I agree that information is present in the genome, by any definition in English usage you care to give. Mung @ 143
Meaningless Information Some people here seem to think that there can be information devoid of meaning. How someone can think this is a mystery to me, the very idea seems absurd. Elizabeth Liddle: Others say it [information] has to have meaning. As would any sane person. I ask again, are you aware of any definition of information which allows for the possibility that information may be devoid of meaning? Do tell.
I already told you, ages back. Shannon’s measure of information, as Meyer points out, has nothing to do with meaning. You even corrected me, IIRC on a typo, but I’ll type out Meyer’s example again:
As one of Shannon’s collaborators, Warren Weaver, explained in 1949, “The word information in this theory is used in a special mathematical sense that must not be confused with meaning”. Consider two sequences of characters: “Four score and seven years ago” “nenen ytawoi jll sn mekhdx nnx” Both these sequences have an equal number of characters. Since both are composed of the same 26-letter English alphabet, the amount of uncertainty eliminated by each letter (or space) is identical. The probability of producing each of those two sequences at random is identical. Therefore, both sequences have an equal amount of information according to Shannon’s theory.
You wrote:
Elizabeth Liddle:
Well, Shannon information can be meaningless. That is why I think it is a poor metric for the kind of information we are interested in.
You’re confused. Shannon information is a measure of information. It is not itself meaningless, nor does it measure “meaningless information,” for there is no such thing as information devoid of meaning.
Um, yes, it does "measure meaningless information". See above.
Shannon information, as a measure of information, is distinct from the meaning of a given message and does not concern itself with the meaning of the message, but this is not the same as saying it is a measure of information devoid of meaning.
Yes it is. A string can have plenty of Shannon information, but be meaningless. Shannon information does not measure meaning. It does not care whether the message has meaning or not. See Meyer's quote from Weaver above: “The word information in this theory is used in a special mathematical sense that must not be confused with meaning”. But this argument is silly. Both of us reject as relevant to this discussion any definition of information that does not include meaning. For some reason you are insisting that no-one has ever given such a definition. I'd say you are clearly wrong. But it doesn't matter because even if I am hallucinating Meyer's cite of Weaver, or, possibly, Meyer was, or possibly we are all hallucinating Shannon, we aren't going to use that definition here. OK? Mung @ 144
Elizabeth Liddle:
Until then, I can only conclude that the original claim, to which I made my counter claim, is untestable.
So your counter-claim was nonsense?
No, because I think it remains true for any definition of information.
You made your claim without knowing what you meant by information and without knowing how it could be generated by chance and necessity sans intelligence? And you want to blame us for your over-reach? Here are the facts. You made an absurd claim which you had no means to demonstrate.
No. My claim applies to all definitions of information IMO. So if you want to refute it, then supply the definition you want to refute.
Since that point, you have been engaged in nothing but coming up with excuses why you could not do what you claimed you could do.
This is not true.
Now, let us not also forget that the reason you felt the original claim was false was because you thought you could demonstrate the truth of your counter-claim. So now what is your reason for believing the original claim was false?
Well, I thought it referred to Dembski's Complex Specified Information, which is quite an interesting definition, and, again, no matter how you operationalise it, I think the claim is false. But obviously to demonstrate this to the satisfaction of the person making the original claim we have to agree on that operationalisation.
Is it because you cannot demonstrate the truth of your counter-claim?
No. But I'm not going to demonstrate it for non-agreed definitions of information, because then the counter-counter-claim could then be "well, that's not what we meant by information". My, the logic that must take. Well, for some reason it seems to be beyond you, which is odd, because you seem quite smart. Mung @145
Elizabeth Liddle:
The method I am attempting to use is what is usually called the “scientific method”, in which a crucial step is finding a way of measuring the thing-to-be-found or otherwise ascertaining its presence or absence. To do that we need what is called an “operational definition”.
And you think that all the material UPB has given you so far does not suffice? Why not?
Because serious ambiguities remain. UPB has not operationalised his definition. That isn't necessarily too serious as long as he gives enough conceptual clarity to allow me to write an operationalised definition of his conceptual definition. As I've said, I thought we were nearly there, then we hit a snag.

I am not at all clear what you mean by rejecting “the one proven method of finding the very thing she claims to be looking for”.
Another way to state that might be, “rejecting the one proven method of ascertaining the presence of the very thing she claims to be looking for.”
Gee thanks.
So we need a general criterion by which we can look at either a process, or an object, and say: this is information transfer/this contains information. Now, unlike Dembski, you have chosen to define information in terms of process, rather than product. I actually think this is sensible –
UPB has not given you that general criterion? You two have not worked it out together? Or did you do that, and you just didn’t like what it led to? So you rejected it.
It's kind of frustrating that you don't actually read my posts. Or don't seem to, anyway. Yes, he gave a criterion but it was variously expressed as "a break in the causal chain"; "a break in the physical chain" which was majorly problematic! However, I did have a shot anyway. As I've said a few times. I'm still waiting for Upright BiPed to comment on it, but obviously he has far more important concerns right now.
It’s not that I have any doubt that Nirenberg was finding “information” in the genome, nor about his methods for doing so – figuring out what mapped to what.
So there is a way to ascertain the presence of information?
Yes, I 'm sure there is, but what Nirenberg did was figure out what the information was.
It’s not that there is anything “admirable” about an operational definition, it’s just that if you are trying to detect the presence or absence of something, you need one.
Apparently not. Or you’re contradicting yourself.
No, I'm not.
ok, this post is getting too long. continuing later…
But UBP – if I don’t have an operational definition of information, then we can’t confirm its presence, and if we can’t confirm its presence, then I can’t support my claim! Nor can you consider it unsupported! Of course it’s not “irrelevant” – it’s absolutely vital!
If she cannot support her claim, you cannot consider her claim unsupported! Yes, she really did just say that!!! I am just flabbergasted. (Well, not really.)
I mean: I can't support my claim to your satisfaction, ya numpty! Mung @146
Upright BiPed:
You have thus far refused to acknowledge that one cannot logically be testing a falsification of an ID argument, while simultaneously claiming it doesn’t exist.
Elizabeth Liddle:
It’s a fair cop. In mitigation, I plead that I did not understand the charge. I do now. I did not mean what you thought I was saying, but as I now understand what you thought I was saying, I willingly clarify that I did not mean what you thought I meant.
ok, that had me rolling.
Cool. Sometimes I awe myself. Mung @147
Elizabeth Liddle:
It may be that someone here has a conceptual definition of information for which my claim is false.
It just keeps getting better and better.
It does doesn't it? Or are you failing to follow the logic again? Mung @148
Elizabeth Liddle:
Dembski does not deny that information (measured as Shannon Information, in bits) can be generated by Chance – his claim is that Complex Specified information cannot be (or is vanishingly unlikely to be).
How do you know that Dembski does not deny that information can be generated by Chance? Has he some where stated that to be the case? Please provide a cite or reference. Please. Thank you.
lol. Mung @149
Operational Definitions So let’s set a couple simple things on the table and see where it gets us. Lizzie agrees there is information present in the genome or in the process that takes place during the reading of DNA and the subsequent generation of a protein. It would be nice to figure out just where she thinks the information exists but I think we can leave that for later. In support of this observation I offer the following quote:
I simply don’t think that the source of the information in the genome (and I agree there is information in the genome) is a great mystery.
So this I think leads to a some very obvious questions. Elizabeth, why do you think there is information in the genome? What leads you to hold that belief?
OK. Well, let's take what I think is a pretty good conceptual definition from Webster, cited by Meyer: "The attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (as nucleotides in DNA or binary digits in a computer program) that produce specific effects." http://www.merriam-webster.com/dictionary/information?show=0&t=1311364153 Now, leaving aside the fact that Webster's actually mentions DNA, DNA clearly satisfies the definition - the arrangement of nucleotides produces specific effects - the production of a protein, for instance. However, we would not have to know which patterns produced which proteins to know that DNA contains information by that definition, because we also know that different alleles are associated with different phenotypes. We also knew, from Mendel, that something heritable contained information, because of his observed patterns of inheritance.
You’re not clear at all what you mean by information. Which definition of information do you have in mind?
As I've said, I think my claim holds for any.
You don’t have an operational definition of information yet you still think information exists in the genome. Why?
Mung, I could operationalise any conceptual definition and show that it exists in the genome. That's my point. But I'm not going to bother until I've agreed with at least one person here, that their definition has been satisfactorily operationalised. Obviously. Or I could just use Shannon and be done already.
It’s not that I have any doubt that Nirenberg was finding “information” in the genome, nor about his methods for doing so – figuring out what mapped to what.
How did they find it?
I don't know. I think they used radio tracers. It doesn't matter how they did it.
Either they had an operational definition or they did not need one. Which is it?
They were trying to find out what DNA coded for. AFAICT they started from the assumption that it coded for something, i.e. that it contained information. They set out to find out what it was and how it did it. They succeeded. Decoding a message is not the same thing as figuring out whether the thing is a message. They would certainly have required an operational definition of an amino acid. Mung @150
Elizabeth Liddle:
Dembski does not deny that information (measured as Shannon Information, in bits) can be generated by Chance – his claim is that Complex Specified information cannot be (or is vanishingly unlikely to be).
Febble (aka Elizabeth Liddle: His [Dembski's] reasoning appears to be as follows: he [Dembski] states: “Natural causes comprise chance and necessity” (citing Monod), and proceeds to rule out both chance and necessity as a source of information. HERE Why, Elizabeth, do you now believe that Dembski allows that information can be generated by Chance?
I should have said "Complex Specified Information". I think that is pretty clear from the context. If not, allow me to clarify now.
What have you read in the intervening period between then and now that makes you think he changed his mind (if anything)?
I don't think he's changed his mind very radically, although he does seem to have dropped much mention of Necessity. His 2005 talks only of Chance, and he has said that the EF (which has two filters - Chance and Necessity) is subsumed under his 2005 definition of CSI. Mung @151
Febble (aka Elizabeth Liddle): I have read a fair number of Dr. Dembski’s monographs and writings, although I have not read the book “No Free Lunch”. However, I have read his piece: Intelligent Design as a Theory of Information http://www.arn.org/docs/dembski/wd_idtheory.htm several times… Then surely you must have come across the following bit: Chance can generate complex unspecified information, and chance can generate non-complex specified information. What chance cannot generate is information that is jointly complex and specified. And yet you then go on to say: [Dembski] proceeds to rule out both chance and necessity as a source of information. You read it several times? Wow.
I should have said complex specified information. The kind he ruled out chance and necessity for. Elizabeth Liddle

Mung re 152 Great book by one of my favorite authors. Nothing is No Thing and chance is nothing ( no thing). No thing (nothing) cannot be the cause of anything :) Vivid vividbleau

William A. Dembski:
Chance can generate complex unspecified information, and chance can generate non-complex specified information. What chance cannot generate is information that is jointly complex and specified. - here
Sorry Bill, I have to disagree. The concept of unspecified information is incoherent. And chance cannot generate information. That's tantamount to saying noise can generate information, or chaos can generate information, except that chance is not a cause of anything and thus cannot be a cause of information. Not a Chance: The Myth of Chance in Modern Science and Cosmology I realize that piece is a bit dated so I'd like to know if you've changed your mind since then. Mung

Febble (aka Elizabeth Liddle):
I have read a fair number of Dr. Dembski’s monographs and writings, although I have not read the book “No Free Lunch”. However, I have read his piece: Intelligent Design as a Theory of Information http://www.arn.org/docs/dembski/wd_idtheory.htm several times...
Then surely you must have come across the following bit: Chance can generate complex unspecified information, and chance can generate non-complex specified information. What chance cannot generate is information that is jointly complex and specified. And yet you then go on to say:
[Dembski] proceeds to rule out both chance and necessity as a source of information.
You read it several times? Wow. Mung

Elizabeth Liddle:
Dembski does not deny that information (measured as Shannon Information, in bits) can be generated by Chance – his claim is that Complex Specified information cannot be (or is vanishingly unlikely to be).
Febble (aka Elizabeth Liddle:
His [Dembski's] reasoning appears to be as follows: he [Dembski] states: "Natural causes comprise chance and necessity" (citing Monod), and proceeds to rule out both chance and necessity as a source of information. HERE
Why, Elizabeth, do you now believe that Dembski allows that information can be generated by Chance? What have you read in the intervening period between then and now that makes you think he changed his mind (if anything)? Mung

Operational Definitions So let's set a couple simple things on the table and see where it gets us. Lizzie agrees there is information present in the genome or in the process that takes place during the reading of DNA and the subsequent generation of a protein. It would be nice to figure out just where she thinks the information exists but I think we can leave that for later. In support of this observation I offer the following quote:
I simply don’t think that the source of the information in the genome (and I agree there is information in the genome) is a great mystery.
So this I think leads to a some very obvious questions. Elizabeth, why do you think there is information in the genome? What leads you to hold that belief? You're not clear at all what you mean by information. Which definition of information do you have in mind? You don't have an operational definition of information yet you still think information exists in the genome. Why?
It’s not that I have any doubt that Nirenberg was finding “information” in the genome, nor about his methods for doing so – figuring out what mapped to what.
How did they find it? Either they had an operational definition or they did not need one. Which is it? Mung

Elizabeth Liddle:
Dembski does not deny that information (measured as Shannon Information, in bits) can be generated by Chance – his claim is that Complex Specified information cannot be (or is vanishingly unlikely to be).
How do you know that Dembski does not deny that information can be generated by Chance? Has he some where stated that to be the case? Please provide a cite or reference. Please. Thank you. Mung

Elizabeth Liddle:
It may be that someone here has a conceptual definition of information for which my claim is false.
It just keeps getting better and better. Mung

Upright BiPed:
You have thus far refused to acknowledge that one cannot logically be testing a falsification of an ID argument, while simultaneously claiming it doesn’t exist.
Elizabeth Liddle:
It’s a fair cop. In mitigation, I plead that I did not understand the charge. I do now. I did not mean what you thought I was saying, but as I now understand what you thought I was saying, I willingly clarify that I did not mean what you thought I meant.
ok, that had me rolling. Mung

Elizabeth Liddle:
The method I am attempting to use is what is usually called the “scientific method”, in which a crucial step is finding a way of measuring the thing-to-be-found or otherwise ascertaining its presence or absence. To do that we need what is called an “operational definition”.
And you think that all the material UPB has given you so far does not suffice? Why not?
I am not at all clear what you mean by rejecting “the one proven method of finding the very thing she claims to be looking for”.
Another way to state that might be, "rejecting the one proven method of ascertaining the presence of the very thing she claims to be looking for."
So we need a general criterion by which we can look at either a process, or an object, and say: this is information transfer/this contains information. Now, unlike Dembski, you have chosen to define information in terms of process, rather than product. I actually think this is sensible –
UPB has not given you that general criterion? You two have not worked it out together? Or did you do that, and you just didn't like what it led to? So you rejected it.
It’s not that I have any doubt that Nirenberg was finding “information” in the genome, nor about his methods for doing so – figuring out what mapped to what.
So there is a way to ascertain the presence of information?
It’s not that there is anything “admirable” about an operational definition, it’s just that if you are trying to detect the presence or absence of something, you need one.
Apparently not. Or you're contradicting yourself. ok, this post is getting too long. continuing later...
But UBP – if I don’t have an operational definition of information, then we can’t confirm its presence, and if we can’t confirm its presence, then I can’t support my claim! Nor can you consider it unsupported! Of course it’s not “irrelevant” – it’s absolutely vital!
If she cannot support her claim, you cannot consider her claim unsupported! Yes, she really did just say that!!! I am just flabbergasted. (Well, not really.) UPB, I applaud your patience. Wow. Continuing to remember you and your family. Mung

Elizabeth Liddle:
Until then, I can only conclude that the original claim, to which I made my counter claim, is untestable.
So your counter-claim was nonsense? You made your claim without knowing what you meant by information and without knowing how it could be generated by chance and necessity sans intelligence? And you want to blame us for your over-reach? Here are the facts. You made an absurd claim which you had no means to demonstrate. Since that point, you have been engaged in nothing but coming up with excuses why you could not do what you claimed you could do. Now, let us not also forget that the reason you felt the original claim was false was because you thought you could demonstrate the truth of your counter-claim. So now what is your reason for believing the original claim was false? Is it because you cannot demonstrate the truth of your counter-claim? My, the logic that must take. Mung

Meaningless Information Some people here seem to think that there can be information devoid of meaning. How someone can think this is a mystery to me, the very idea seems absurd. Elizabeth Liddle:
Others say it [information] has to have meaning.
As would any sane person. I ask again, are you aware of any definition of information which allows for the possibility that information may be devoid of meaning? Do tell. Elizabeth Liddle:
Well, Shannon information can be meaningless. That is why I think it is a poor metric for the kind of information we are interested in.
You're confused. Shannon information is a measure of information. It is not itself meaningless, nor does it measure "meaningless information," for there is no such thing as information devoid of meaning. Shannon information, as a measure of information, is distinct from the meaning of a given message and does not concern itself with the meaning of the message, but this is not the same as saying it is a measure of information devoid of meaning. Mung

Elizabeth Liddle:
And for examples of general English usage I would give: “a repository of information such as a database”; “on the basis of that information, I have changed my course of action”; “thank you for your useful information”.
I don't recall anyone asking you for examples. I think you were asked to provide a definition. Here was the question: Elizabeth, what is the meaning of information according to general English usage? When someone asks, what does this word [information] mean, the typical response is to provide a definition. Let's review. Elizabeth Liddle: "I simply don’t think that the source of the information in the genome (and I agree there is information in the genome) is a great mystery." Mung: "And what does she [Elizabeth Liddle] mean by information? Elizabeth Liddle: "According to most definitions that I am aware of. But certainly according to the its meaning in general English usage." Mung: Elizabeth, what is the meaning of information according to general English usage? And your answer is? What definition of information, according to the its meaning in general English usage, best exemplifies the information you think is present in the genome? Mung

Dr Liddle: Please read the discussion here, noting the onward references. GEM of TKI kairosfocus

kf: I have no problem, as I said, with the idea that cells contain information transfer technology. What I need is a minimal description of what could be said to be information transfer technology. In other words, what is the essence of information transfer? We have excluded the imprint of an object on another object. I need a complete set of clear inclusion and exclusion criteria. Elizabeth Liddle

Dr Liddle: What is your technical experience in designing and developing digital information and communication technology? It seems to me that many of your objections would at once be resolved if you took such an experience base seriously. When I look at DNA, mRNA, tRNA etc in action, the patterns are at once very familiar. Familiar from what I have done with digital info systems. The specific technology is different, and the number of states used in the elements is different, but binary -- two state -- is not a defining characteristic of "digital." (Think about the high impedance state that is so often used in bus interfaces for just one instance of the utility of a third state. I loved the old 74LS245 for just that reason. An eight-line bidirectional bus interface chip, with easy enable/disable in a nice narrow DIL/DIP package. Used them by the handful.) And, digital information is being instantiated into the sequence of bases in DNA and RNA, and in the case of mRNA, it is being used as a control tape to drive an assembly line process, protein manufacture. I have already long since repeatedly pointed out how the tRNA coupler to hold the AAs is a standard CCA end, and that it locks to the carboxylic acid end of the AA, COOH. The AA is loaded by a special enzyme that conforms to the specific tRNA and loads it with the required AA. Experiments have already been done to reprogram some of the tRNAs to make them hold novel AAs and chain them into proteins. It is the side-branch that carries the key performance aspects of the AA, and it is coupled to the tRNA at the opposite end from the anticodon that key-lock fits the codon in the mRNA in sequence. This is a digital information system instantly recognisable from the materially similar ones we use in industry or for that matter in your cell phone. For operationalisation, we are looking at discrete state technologies, codes and action that transfers code into meaningful or functional output. All of these are observable or directly infer-able from observation, and all of these have been done to the point where the functioning of protein manufacture in the cell is now a standard bit of biology edu even at high school level. It is all over Youtube, for crying out loud. There is no reasonable question that we are dealing with an information system based on digital technology and using a code, the genetic code with its variants. Associated are control and regulatory codes that trigger the relevant action steps. Nor, that this is directly and materially comparable to similar processes in say a robot factory. As a matter of fact, I have a friend EP who has been using factory robot process flow and control diagrams to summarise and represent the processes in this context. Usefully so, too. In that context, when I see the sort of making mountains out of molehill objections that have been going on for quite a while now, I am not too amused. Especially, when the root of the ongoing exchanges here has been the fraudulent attack by the manufactured Internet personality MG, which has been repeatedly corrected but never acknowledged as reasonably responded to. Yes, it is possible to make up all sorts of objections to what informaiton is, to what codes and artificial computer languages are, to what an algorithm is, to what digital tech is, to what it means for info to be instantiated into specific and functional, complex patterns in matter and energy. But when we see the people who do this using PCs, cell phones, calculators and the like the bottom-line is that we never see them objecting to these technologies that rest on the selfsame ideas, definitions, metrics and approaches etc. So, the question is really: are we looking at selective hyperskepticism that objects because of a worldview level objection to this case, while exerting a double standard in accepting and using things that work in the very same way and are measured and warranted in the same way? If the real objection is a worldview objection, deal with it at that level. Start with the evident self referential incoherence of evolutionary materialism -- and please note the issue of mind and brain in the same context. GEM of TKI kairosfocus

Upright BiPed:
Dr Liddle, In my previous post to you, the issue in front of me was not knowing what else to say to you. I have that same problem still. What can be said to someone who simply refuses the observations? What can be said to someone who summarily rejects the one proven method of finding the very thing she claims to be looking for? Honestly, what else can be said?
UBD: I readily acknowledge the gulf that communication (information? :)) barrier that exists between us. We are clearly coming at this issue from very different backgrounds, traditions, methodologies and even lexicons. But I appreciate your response, and am more than willing to keep trying to reach common ground. I am not at all clear what you mean by rejecting "the one proven method of finding the very thing she claims to be looking for". The method I am attempting to use is what is usually called the "scientific method", in which a crucial step is finding a way of measuring the thing-to-be-found or otherwise ascertaining its presence or absence. To do that we need what is called an "operational definition". And to derive such a thing, we need as clear a conceptual definition as possible, from which we systematically exclude all potential ambiguities. This is what I have been attempting to do - to operationalise your conceptual definition of information.
Nirenberg et al discovered the information in the genome by demonstrating it. They isolated the representations, deciphered the protocols, and documented the effects; the same way that all other recorded information has been discovered.
I'm sorry, UBP, but this is circular. But let me first say: I have no quarrel at all with the idea that the genome contains information; nor have I any quarrel with Nirenberg's methodology - he and his team systematically figured out which codons coded (hence the name) for which amino acids, and noted that the sequence of the codons in the DNA molecule, corresponded to the sequence of the amino acids in the protein. We are in complete agreement with this I think. What I need to do, however, is to abstract from that specific example (of codons amino acids, etc) a criterion by which any candidate for the category "information" can be so categorised. Clearly not all information is mediated by codons; not all messages are "about" proteins. So we need a general criterion by which we can look at either a process, or an object, and say: this is information transfer/this contains information. Now, unlike Dembski, you have chosen to define information in terms of process, rather than product. I actually think this is sensible - it seems to me that information is only as good as the use that is made of it, and I think Dembski's attempt to define information (or at least "complex specified information" in terms of a subset of patterns is deeply flawed (for a number of reasons). So while this was the kind of definition I originally had in mind when I made my counter-claim (indeed I assumed it whas the kind of definition the original claimant hadn in mind), I think that in many ways your conceptualisation is better - nearer to the common English usage of the word. And at one stage we seemed very close to getting that process operationalised. Then, as I have said a few times, I hit a snag - the word "protocol", which I hoped we had already operationalised, seemed to acquire something I had not anticipated - your "break in the causal chain" or "break in the physical chain". This requirement seemed to me to render your definition circular, because I assumed that by those phrases you meant some process that could not be attributed to Chance or Necessity. This is why I pointed out that tRNA is, essentially, a catalyst - it is an inert facilator of a chemical process. And I would characterise a catalyst neither as acausal nor as non-physical! However, if all you mean is "inert", or, more interestingly, "arbitrarily" (hence my discussion about the subset of possible tRNA molecules we actually find in living cells), then we are back on track. And I have tried to incorporate that concept into my latest operationalisation.
Rather than dealing with these apparently unsophisticated facts, you’ve declared them irrelevant to your simulation, and have gone off on a debatefest on how to confirm the presence of information. You then wonder why I won’t join in, and if I throw up my hands, you suggest that the appropriate view of the situation is that I have lost interest in the issues – and oh yes, of course – you still don’t have an operational definition of information.
But UBP - if I don't have an operational definition of information, then we can't confirm its presence, and if we can't confirm its presence, then I can't support my claim! Nor can you consider it unsupported! Of course it's not "irrelevant" - it's absolutely vital! But perhaps that will be clearer in light of what I have written above. I do hope so. I'm certainly glad that you have not lost interest (though you'd have every reason to, given your other present concerns) but I certainly wonder why you won't "join in" with the project of operationalising my claim (and, by inversion, the counter-claim). It's not that I have any doubt that Nirenberg was finding "information" in the genome, nor about his methods for doing so - figuring out what mapped to what. The problem is defining what constitues a "mapping". After all, a footprint maps to a foot, a meteor maps to a crater, but we do not necessarily say that what we have, in a footprint, or a meteor creator, is "information" (although we could, and in many cases we do). And the second, at least, is created by Chance and Necessity. And so clearly, it should be excluded from the definition, or my claim is supported now. So what I am trying to do is define a clear criterion, or set of criteria, tht can be applied to any system, and which will tell us not what the relevant protocols are, but whether they are can be considered part of information transfer system.
In my field of research, the people at my level have been watching output for years (over 30 years for me) and we typically don’t stand around wondering what we are doing. Items such as sample integrity and retrieval methodology are far more important than wondering what we are looking for. But, I wouldn’t want you to think we don’t admire a good operational definition when we see one. Everyone at UD knows and appreciates the value of definitions. When they are not being legitimately used as a tool in understanding, they can always get a job as an impediment to that very same end.
I think we are still at cross-purposes! It's not that there is anything "admirable" about an operational definition, it's just that if you are trying to detect the presence or absence of something, you need one. You obvioiusly don't need one for things you aren't trying to detect. for example, in quality control, you don't need an operational definition of your product - you can see it's there, on the assembly line! But you do need an operational definition of quality - what the rejection criteria are. Perhaps that's a good way of looking at what I am trying to do here: establish quality control criteria such that you can look at my simulation and say: y"es, the protocols here pass the criteria required for an adequate product. I declare this certified Information TM" (oops don't seem to have superscript tags).
I’d hate for there to be any lingering impediments in this conversation, so please allow me to take a stab at it. The following is the definition we had both contributed to right before the train left the track. Even though you agreed to the observations along the way, I see you now claim the definition is nonsense. But since its two-thirds your willing contribution, perhaps you’ll know best how to fix it:
Information is a representation of a discrete object/thing embedded in an arrangement of matter or energy, where the object/thing represented is entirely dissociated from the representation, but where the association of the two can be established by means of a protocol instantiated in the receiver of the information.
No, it is not nonsense. But it is not operationalised. I have tried to operationalise it above. I am still waiting for your response!
Allow me to make a couple of suggestions, and then you can tell me if you think it makes sense from the observations.
Information is a representation of a discrete object/thing embedded in an arrangement of matter or energy, where the object/thing represented is entirely dissociated from the representation, but where the association of the two can be established by means of a protocol instantiated in [or accessed by] the receiver of the information. Information can be demonstrated to exist if these discrete representations and discrete protocols interact to cause a discrete output constrained by that interaction. If the rise of this phenomenon is observed to be the product of random contingency + natural law, then the representations stated above will output a system which reproduces those representations. Since I already know you have some issues with what a protocol is/does, let me just add that a protocol is what allows a discrete representation to be a discrete representation. It allows a bridge (a relationship to exist) over the observed physical gap found in all forms of recorded information. It’s what makes information possible by allowing dissociated things to have an association with one another; something to represent something else. In the cell, it provides a means for a dissociated representation to constrain the output of the system, while remaining dissociated. In other words, an apple doesn’t have to be called an apple, so something has to establish that relationship. If this phenomenon is as you say it is, ie the product of physical law, then it will be physical law that establishes these relationships, and it will provide the representations and protocols required for the information to have an effect.
Again, this is a helpful clarification of the concept at issue. It is not, however, operationalised. But thank you for it. I would still like your comments on my attempted operationalisation. It seems to me that it conforms pretty well to your conceptual definitions above, but, of course, applied specifically to my proposal.
There is one other thing I’d like to comment on. You seem to want to characterize these observations as my own personal conceptualization. That seems rather odd since you yourself walked through the observations with me, and remained in general agreement throughout.
Only because there are many definitions of information in regular use, including some in less regular use, and I want to make sure that I am not merely producing information by some trivial one. For example, Dembski does not deny that information (measured as Shannon Information, in bits) can be generated by Chance - his claim is that Complex Specified information cannot be (or is vanishingly unlikely to be). That is why I want to ensure that you, as the one who challenged my claim, sign off on the definition of information you have in mind. The issue is not whether I agree with your definition (you can define Information as "anything at a temperature of more than 100 degrees Kelvin" if you like, or "made of rubber and shaped like a chicken". What matters is what it is, and whether, knowing what it is, my claim that it can be generated by Chance and Necessity only still stands. As for the "observations" - I'm not sure what you mean by "observations" in this context - we are talking about definitions. We cannot deduce a definition from an observation! Perhaps that is the root of the difficulty here.
In any case, it is not my personal conceptualization that the code is a code; Francis Crick, James Watson, Rosalind Franklin, and the physical evidence had a role to play in that. It’s not my idea that a mapping exists between nucleic acids and amino acids; Nirenberg, Khorana, Holley, the NIH, and New York University Medical School came up with that one.
Of course not. What matters is what constitutes a "mapping". This really does seem to be at the root of the problem between us. Not so much an Apples and Oranges problem as an Apples and Appletrees problem. I do not deny that those mappings exist. What I want to know is what, in your view, makes the mapping between a codon and an amino acid "information", and the mapping between a foot and a footprint not "information". We are getting there with the idea of an inert, and arbitrary mediator of the mapping. But do you see why we have been at cross-purposes?
Three of them shared the Nobel prize for their work, and I had nothing to do with it. I’m not the one who noticed there are no bonds between the nucleotides that determine their order. I’m sure some under-appreciated practitioner somewhere figured that out long before I would have – so it wasn’t me. The same can be said for whomever discovered that the mRNA input does not directly interact with the amino acid output, and also to those who demonstated how the system accomplishes that fact.
Indeed, but see above.
I didn’t apply the chicken and egg paradox to biology first either, and I don’t know who did. I didn’t coin the phrase semiosis, or the epistemic cut or cybernetic cut. It wasn’t me who compared the patterns in genetic information with those from chance and law, observing nothing in common between them – as in there being a a fundamental distinction. That was Trevors an Abel. It also certainly wasn’t me who said there are boundary conditions within mechanisms which are irreducible to pure physical law; that was Polanyi’s conclusion. So it seems to me that your characterization is easily a waste of time if given too much credence. All I have done is observe the observations that exist, but I have nothing to do with the fact that they are the observations that exist.
This seems confused to me. And unnecessarily complicated. It is often said, by ID proponents, that Chance and Necessity cannot generate Information (or, at least, Information of a certain kind, or degree). My counter-claim is that they can. However, whether to demonstrate the ID claim, or my counter-claim, we need a clear operational definition of Information, as it is used in the ID claim,, or failing that, in any one ID proponent's claim. I originally took Dembski's, as I figured that was what people were talking about here (even though, IMO, it is insufficiently operationalised). I've now found out that not every one here accepts Dembski's definition, conceptual or operational, and some have their own. That's fine. I'm willing to take on any. It may be that someone here has a conceptual definition of information for which my claim is false. But we can make a start with the one you suggest. As long as we can operationalise it!
This all brings us back to where we started, except this time you have the answers required by the questions you asked. If the foundation of the argumnent has been given to you in a way that you can understand (and it has) and if you are beginning to grasp the issues you face, then this phase should be near complete. You should have every opportunity to prove your case. From the observations, you now know what information is, and you know how to demonstrate its existence.
Not until we have an agreed operational definition :) I hope we are nearly there.
This point in the exchange also gives you another opportunity. One to finally address your false claim that ID proponents had not made their case. If ID proponents had not made their case, then you would have no need to prove yours to them. The fact that you’re having to set out to prove your case, should be a clear indication of how willing you are to integrate your terms.
Ah. If by "made their case" you mean "put a case forward", then I readily retract my claim. Of course I agree that a case has been made, and should have worded that in a more bulletproof manner. I meant it in the sense of "I do not believe you have made your case" rather than "You have not attempted to make a case". Of course the case has been "made" in the sense that it has been put forward. I do not believe it holds water. I hope that is now clear. Because of course, it is that very case that I propose to dismantle. If it didn't exist at all, there would be nothing to dismantle! On the other hand, if it were what I'd call a "made case", I wouldn't be able to dismantle it! And I think I can. But I hope that has cleared that up. Though I confess to being surprised that anyone could possibly have interpreted my words to mean that I thought that no case had been attempted! Still, I guess it's possible that you might have thoguht that I considered all ID claims mere assertions unsupported by any attempt at producing evidence or making an argument. Well, let the record show: I don't think this. And I apologise if I inadvertently gave the impression I did.

I happen to be someone who finds it pretty easy to admit error, and do, frequently. If I find myself making an error, I am quick to correct it – if someone points out an error, or an inconsistency (apparent or real) I am quick to sort it out, and if someone convinces me I am in error (and it happpens) I am quick to acknowledge it.
You have thus far refused to acknowledge that one cannot logically be testing a falsification of an ID argument, while simultaneously claiming it doesn’t exist.
It's a fair cop. In mitigation, I plead that I did not understand the charge. I do now. I did not mean what you thought I was saying, but as I now understand what you thought I was saying, I willingly clarify that I did not mean what you thought I meant. Yes, there is an ID argument. It's why I'm interested in discussing it. I think it is fallacious. Thank you, Upright BiPed, for being willing to continue with this. I appreciate it, and the fact that you do so in the face of frustration and grave family concerns. Take your time, and all the best to you and your family. Lizzie Elizabeth Liddle

UPD: we seem to have cross-posted. I will look at your new post now. Elizabeth Liddle

Upright BiPed: I note that you still have not responded to my operationalisation of what I think is your conceptual definition. I have no idea what you mean by: "the search for an operational definition is just as fallible as any other of man’s good ideas." I can only conclude that you still do not understand what an operational definition is, and why it is critically important to supporting a claim empirically. My original claim was a counter-claim to the claim that natural processes (Chance and Necessity as operationalised earlier) cannot generate information. For that claim to be upheld, and for my counter-claim to be tested, we need to agree on an operational definition of "information". I have tried to operationalise the conceptual definitions you have offered, despite fairly intractable concepts like "break in the causal chain" and unpacked concepts like "protocol". I have now done so, and you have refused to comment on it, despite the fact that it has been here on this thread for quite a while, and you have noted the post, and made comments about the post. But about that operational definition you have not ventured so much as a footnote. It took me a while to understand what you were on about with your oblique references to Nirenberg. I took it for granted that we both understood that each possible DNA/RNA triplet has a corresponding amino acid, and that the correspondence is mediated by set of tRNA molecules with a codon binding site at one end and an amino binding site at the other. My difficulty was trying to abstract the relationship between this fact to your concept of a "break in the causal chain". However, I think I managed it in the end. I guess I'll keep this thread bookmarked in the hope that at some stage you will look at my operationalization and tell me whether or not it corresponds to your conceptualisation, and if not, why not. Until then, I can only conclude that the original claim, to which I made my counter claim, is untestable. Because you can't test a claim without first operationalising it. But there is no hurry. My best wishes to you and your family. I do hope your daughter is recovering. My own son is 17, and the thought of anything bad happening to him is like ice in the soul. I try not to go there. My heart goes out to anyone who has to. In peace. Lizzie Elizabeth Liddle

Dr Liddle, In my previous post to you, the issue in front of me was not knowing what else to say to you. I have that same problem still. What can be said to someone who simply refuses the observations? What can be said to someone who summarily rejects the one proven method of finding the very thing she claims to be looking for? Honestly, what else can be said? Nirenberg et al discovered the information in the genome by demonstrating it. They isolated the representations, deciphered the protocols, and documented the effects; the same way that all other recorded information has been discovered. Rather than dealing with these apparently unsophisticated facts, you’ve declared them irrelevant to your simulation, and have gone off on a debatefest on how to confirm the presence of information. You then wonder why I won’t join in, and if I throw up my hands, you suggest that the appropriate view of the situation is that I have lost interest in the issues – and oh yes, of course – you still don’t have an operational definition of information. In my field of research, the people at my level have been watching output for years (over 30 years for me) and we typically don’t stand around wondering what we are doing. Items such as sample integrity and retrieval methodology are far more important than wondering what we are looking for. But, I wouldn’t want you to think we don’t admire a good operational definition when we see one. Everyone at UD knows and appreciates the value of definitions. When they are not being legitimately used as a tool in understanding, they can always get a job as an impediment to that very same end. I’d hate for there to be any lingering impediments in this conversation, so please allow me to take a stab at it. The following is the definition we had both contributed to right before the train left the track. Even though you agreed to the observations along the way, I see you now claim the definition is nonsense. But since its two-thirds your willing contribution, perhaps you’ll know best how to fix it:
Information is a representation of a discrete object/thing embedded in an arrangement of matter or energy, where the object/thing represented is entirely dissociated from the representation, but where the association of the two can be established by means of a protocol instantiated in the receiver of the information.
Allow me to make a couple of suggestions, and then you can tell me if you think it makes sense from the observations.
Information is a representation of a discrete object/thing embedded in an arrangement of matter or energy, where the object/thing represented is entirely dissociated from the representation, but where the association of the two can be established by means of a protocol instantiated in [or accessed by] the receiver of the information. Information can be demonstrated to exist if these discrete representations and discrete protocols interact to cause a discrete output constrained by that interaction. If the rise of this phenomenon is observed to be the product of random contingency + natural law, then the representations stated above will output a system which reproduces those representations.
Since I already know you have some issues with what a protocol is/does, let me just add that a protocol is what allows a discrete representation to be a discrete representation. It allows a bridge (a relationship to exist) over the observed physical gap found in all forms of recorded information. It’s what makes information possible by allowing dissociated things to have an association with one another; something to represent something else. In the cell, it provides a means for a dissociated representation to constrain the output of the system, while remaining dissociated. In other words, an apple doesn’t have to be called an apple, so something has to establish that relationship. If this phenomenon is as you say it is, ie the product of physical law, then it will be physical law that establishes these relationships, and it will provide the representations and protocols required for the information to have an effect. There is one other thing I’d like to comment on. You seem to want to characterize these observations as my own personal conceptualization. That seems rather odd since you yourself walked through the observations with me, and remained in general agreement throughout. In any case, it is not my personal conceptualization that the code is a code; Francis Crick, James Watson, Rosalind Franklin, and the physical evidence had a role to play in that. It’s not my idea that a mapping exists between nucleic acids and amino acids; Nirenberg, Khorana, Holley, the NIH, and New York University Medical School came up with that one. Three of them shared the Nobel prize for their work, and I had nothing to do with it. I’m not the one who noticed there are no bonds between the nucleotides that determine their order. I’m sure some under-appreciated practitioner somewhere figured that out long before I would have – so it wasn’t me. The same can be said for whomever discovered that the mRNA input does not directly interact with the amino acid output, and also to those who demonstated how the system accomplishes that fact. I didn’t apply the chicken and egg paradox to biology first either, and I don’t know who did. I didn’t coin the phrase semiosis, or the epistemic cut or cybernetic cut. It wasn’t me who compared the patterns in genetic information with those from chance and law, observing nothing in common between them - as in there being a a fundamental distinction. That was Trevors an Abel. It also certainly wasn’t me who said there are boundary conditions within mechanisms which are irreducible to pure physical law; that was Polanyi’s conclusion. So it seems to me that your characterization is easily a waste of time if given too much credence. All I have done is observe the observations that exist, but I have nothing to do with the fact that they are the observations that exist. This all brings us back to where we started, except this time you have the answers required by the questions you asked. If the foundation of the argumnent has been given to you in a way that you can understand (and it has) and if you are beginning to grasp the issues you face, then this phase should be near complete. You should have every opportunity to prove your case. From the observations, you now know what information is, and you know how to demonstrate its existence. This point in the exchange also gives you another opportunity. One to finally address your false claim that ID proponents had not made their case. If ID proponents had not made their case, then you would have no need to prove yours to them. The fact that you’re having to set out to prove your case, should be a clear indication of how willing you are to integrate your terms.
I happen to be someone who finds it pretty easy to admit error, and do, frequently. If I find myself making an error, I am quick to correct it – if someone points out an error, or an inconsistency (apparent or real) I am quick to sort it out, and if someone convinces me I am in error (and it happpens) I am quick to acknowledge it.
You have thus far refused to acknowledge that one cannot logically be testing a falsification of an ID argument, while simultaneously claiming it doesn’t exist. Upright BiPed

In my post on 7/14 I forgot to properly thank Kairosfocus and Mung for their involvement in the conversation; KF for his precision, and Mung for keeping a defiant eye on the ball. Thank you to both. - - - - - - - - - Mung to Liddle:
I’d bet that if we were to go back and look at the history of this entire discussion we would discover that Upright BiPed never did have in mind a “pattern” being transmitted from one generation to the next. That was something entirely of your own making. I think we’ll also find it very clear what Upright BiPed did in fact have in mind. Let me give one huge hint: http://en.wikipedia.org/wiki/M....._Nirenberg
Very perceptive, Mung. To the number of times I have brought it up (going back deep into this conversation) Dr Liddle’s responses have ranged from ignoring the relevance (#77) to outright dismissal (#88) if I should bring it up again. In response to her dismissal I typed out the following response, but never posted it:
Nirenberg on his way to Moscow to present his results, talking on the phone to Matthaei back at the laboratory… Nirenberg: “Johann, I have decided not to present our results yet”. Matthaei: “What?! Are you nuts - we’ve begun to crack the language of life! This is what we’ve been working for, Marshal, it’s genetic information for crying out loud!! In fact, we just finished up with new results, and guess what – CCC is mapped to Proline.” Nirenberg: “Wow that’s fantastic…but still, how will anyone know what we are talking about? I mean, c’mon Johann, we don’t even have an operational definition of what it means for one thing to be mapped to another” Matthaei: “What tha-- Nirengerg: “What if someone wants to repeat the experiment? They can’t do it without an operational definition of information … we’ll be made fools! … Or what about the percentage of reproductive fidelity … what’s the fidelity threshold!!! … and what about the probabilities that the pattern will replicate itself … or what abou-- Matthaei: “Marshall, you are not hearing me, man. CCC is mapped to Proline, in the same way that UUU was mapped to phenylalanine!?!?! The pattern of bases is a signal mapped to the addition of specific amino acids … IT’S A CODE. Nirenberg: “a signal ?!? ... you don’t even know what a ‘signal’ is … a mapping ?!? ... a code ?!?
At the very start of this conversation, I made the remark that the search for an operational definition is just as fallible as any other of man’s good ideas. Dr Liddle wondered at the time what I meant by that. Apparently it never occurred to her that asking the questions might not be the problem. In any case, it should not go un-noticed that the person who is struggling against all odds to find a way to detect recorded information is the same Dr Liddle who ignores how it has been found before - every time it’s been found before. Upright BiPed

Mung:
Elizabeth Liddle:
I simply don’t think that the source of the information in the genome (and I agree there is information in the genome) is a great mystery.
And what does she mean by “information”? Elizabeth Liddle:
According to most definitions that I am aware of. But certainly according to the its meaning in general English usage.
By which she means? Elizabeth, what is the meaning of information according to general English usage? Unless that’s not really what you meant. (I always have to now keep in mind that you didn’t really mean what you say.)
Yes, I meant what I said. And for examples of general English usage I would give: “a repository of information such as a database”; “on the basis of that information, I have changed my course of action”; “thank you for your useful information”.

My claim is that information can rise from Chance and Necessity only, which would infirm the claim of ID.
Indeed, that is your claim. You still have not provided the demonstration. You blame that failure on us.
I don’t blame it on anyone. I’m ready to begin my project once we have operationalised the claim so that it reflects your (or anyone here’s ) conception definition of information.
You say that it is our fault because we have not told you what you mean by information.
Nope. I did not say that.
How bizarre is that?
Totally, because I did not say it.
Tell us what you mean by information.
I’ve told you. My claim is, I believe, robust to a number of definitions.
Why don’t you provide an operational definition? It was, after all, your claim.
Because there is no point in my operationalising a definition that does not correspond to the conceptual definition any of you guys are using. It is your counter-claim (that mine is false) that I want to infirm. So, clearly, the conceptual definition I need to operationalise is the one that corresponds to your counter claim.
Here, let me help: My operational definition of information is….
Mung, it seems that you do not know what an operational definition is. That’s fine. But please find out.
Elizabeth Liddle:
I will, however, say that my inference that you had “lost interest” in this conversation was not derived from your short absence from the board, but from the content of your last post, which did not even address my operationalisation…
This is just incredibly dishonest.
No, it is not.
Upright BiPed has repeatedly addressed your “operationalization” in numerous previous posts.
Upright BiPed has repeatedly given me conceptual definitions to try to operationalise. At one stage, I thought I was pretty close. Then when we got to a key concept, we hit a difficulty.
Has it in some way changed from when you first introduced it?
This makes no sense. Upright BiPed has never given me an operational definition. I did not even ask for one (that’s my job). What he did give me was a conceptual definition to operationalize. However, as I said, when I was nearly there, I hit a difficulty. I hope that that is now resolved.
Upright Biped, my prayers are with you and your wife, daughter, and family. May His love be with you all.
Mine too, UPD.
Elizabeth Liddle:
I perceive no agreement at all among the posters on this site as to what information is, or on what particularly type of information is postulated to be the signature of intelligent processes.
Another lie.
No, it is not a lie. My perception may be wrong, but it is true that that is my perception.
Elizabeth Liddle:
Upright Biped said that it [information] had to arise from some kind of protocol that included symbols.
A lie.
No, it is not a lie. Possibly it may be a misunderstanding, but that is exactly what I have been trying to resolve.
Elizabeth Liddle:
Dembski says it [information] has to be both complex and specified.
A lie.
No, not a lie. Mung, I do not lie. I have told you this. It may be a mistake, in which case, I’d appreciate correction, but it is not a lie.
Elizabeth Liddle:
Others say it [information] has to have meaning.
FINALLY! You’re aware of meaningless information? Do tell. According to what definition of information?
Well, Shannon information can be meaningless. That is why I think it is a poor metric for the kind of information we are interested in. Mung, I tolerate most things, but one thing, as I think I’ve said, I find personally hard to tolerate, is accusations of dishonesty. I am not dishonest, and I do not lie. If you think I have lied, then I appreciate being asked for clarification. I do not appreciate simply being told I am a liar. I am not. I do not accuse others of lying, and I do not expect to be so accused myself. I assume that everyone here is posting in good faith, as am I. Elizabeth Liddle

Elizabeth Liddle:
Upright Biped said that it [information] had to arise from some kind of protocol that included symbols.
A lie. Elizabeth Liddle:
Dembski says it [information] has to be both complex and specified.
A lie. Elizabeth Liddle:
Others say it [information] has to have meaning.
FINALLY! You're aware of meaningless information? Do tell. According to what definition of information? Mung

Elizabeth Liddle: I perceive no agreement at all among the posters on this site as to what information is, or on what particularly type of information is postulated to be the signature of intelligent processes. Another lie. Mung

Elizabeth Liddle:
I will, however, say that my inference that you had “lost interest” in this conversation was not derived from your short absence from the board, but from the content of your last post, which did not even address my operationalisation...
This is just incredibly dishonest. Upright BiPed has repeatedly addressed your "operationalization" in numerous previous posts. Has it in some way changed from when you first introduced it? Upright Biped, my prayers are with you and your wife, daughter, and family. May His love be with you all. Mung

Elizabeth Liddle:
I simply don’t think that the source of the information in the genome (and I agree there is information in the genome) is a great mystery.
And what does she mean by "information"? Elizabeth Liddle:
According to most definitions that I am aware of. But certainly according to the its meaning in general English usage.
By which she means? Elizabeth, what is the meaning of information according to general English usage? Unless that's not really what you meant. (I always have to now keep in mind that you didn't really mean what you say.)
My claim is that information can rise from Chance and Necessity only, which would infirm the claim of ID.
Indeed, that is your claim. You still have not provided the demonstration. You blame that failure on us. You say that it is our fault because we have not told you what you mean by information. How bizarre is that? Tell us what you mean by information. Why don't you provide an operational definition? It was, after all, your claim. Here, let me help: My operational definition of information is.... Mung

Ah, but was it a "neutral mutation" or a "beneficial mutation" which has lead to the total replacement of the population of non-italicized symbols by a population of italicized symbols? Ilion

Can the italics be ended? If they reproduce more than the non-italics, well, that's just evolution. Mung

Elizabeth Liddle:
Oh, and yes, I was talking about protein coding.
And how was anyone here supposed to know that? Mung

Dr Liddle, your characterization of my involvement in this conversation as “having lost interest” is not only patently opportunistic, it is also intellectually repugnant. It is exactly the kind of output from Darwinian ideologues that has been documented at UD for years on end, even if those putting it up are nice little old ladies practicing neuroscience in the United Kingdom. In truth, my wife and I have had a medical emergency with our 21 year old daughter for the past two days, and is it happens, concerning myself with some tomography and a spinal tap was slightly higher on my list than debating with you. I am traveling home today and will perhaps have an opportunity to respond later.
Upright BiPed: I am very sorry to hear this news; my best wishes to your daughter and your family. I will, however, say that my inference that you had "lost interest" in this conversation was not derived from your short absence from the board, but from the content of your last post, which did not even address my operationalisation, and in which you said:
If this conversation should move past this stage and return to something productive, then I may elect to rejoin. As clearly evidenced by your participation here, at this point no one has ever demonstrated the rise of information from physical law, and it is that information that makes life possible and is the backbone of biology. With that said, I thank you for the talk and bid you farewell.
I will be delighted if you decide to give my operationalisation a second look. Your response above seemed to me to be a clear decline.
By the way, GP is without exception my favorite contributor to UD, yet he and I often disagree. (So much for UD being the echo chamber that your colleagues constantly allude to. That accusation coming from the Darwinian orthodoxy is what Freud might have seen similar to being the ‘return of the repressed’).
Yes, gpuccio is one of my favorite contributors as well :) And I am delighted to find that UD is not an echo chamber. I am sure who "my colleagues" are supposed to be in this context, but I would agree that disagreement is a sign of life. Indeed, I regard it as a healthy sign that I myself am still here :) Elizabeth Liddle

Dr Liddle, your characterization of my involvement in this conversation as "having lost interest" is not only patently opportunistic, it is also intellectually repugnant. It is exactly the kind of output from Darwinian ideologues that has been documented at UD for years on end, even if those putting it up are nice little old ladies practicing neuroscience in the United Kingdom. In truth, my wife and I have had a medical emergency with our 21 year old daughter for the past two days, and is it happens, concerning myself with some tomography and a spinal tap was slightly higher on my list than debating with you. I am traveling home today and will perhaps have an opportunity to respond later. - - - - - - - - - - - - - By the way, GP is without exception my favorite contributor to UD, yet he and I often disagree. (So much for UD being the echo chamber that your colleagues constantly allude to. That accusation coming from the Darwinian orthodoxy is what Freud might have seen similar to being the ‘return of the repressed’). Upright BiPed

gpuccio, I spent a couple of months with Upright Biped, trying to operationalise his conceptual definition of information. The above is my attempt to do so. He has not commented. If it does not cover your conceptual definition, then we could start again, I guess. But this raises a much larger point: ID is a theory that depends, crucially, on a claim about information, and the processes that can generate it. I perceive no agreement at all among the posters on this site as to what information is, or on what particularly type of information is postulated to be the signature of intelligent processes. Upright Biped said that it had to arise from some kind of protocol that included symbols. Dembski says it has to be both complex and specified. Others say it has to have meaning. All these are conceptually different, but potentially lead to testable hypotheses, as long as they can be operationalised. I have attempted to operationalise Upright Biped's, but he's vanished, apparently because he thinks I haven't understood his definition. But that is the whole point - if you can't cast your operationalise your definition, then you can't make it part of a scientific claim. And to operationalise your definition, it has to be couched in totally unambiguous terms. i.e. so that it cannot be misunderstood. Elizabeth Liddle

Elizabeth: I disagree. The point is not that "information" can arise in your system. Maybe it can. We can see. The point is not even that functional information can arise in your system. Maybe it can. We can see. The point of ID is that functional complex information cannot arise in that system, unless enough active information has been added to it. But to understand the difference, we must understand the detail of the definitions. If you want, we can proceed. gpuccio

Well, as Upright BiPed has lost interest, is anyone else interested in taking up my challenge? My claim is that information can rise from Chance and Necessity only, which would infirm the claim of ID. I propose to demonstrate this using a simulation in which the starting conditions comprise no more than a set of rules of necessity (if this, then that), plus random input from a flat probability distribution. My claim is that an appropriate set of rules of necessity, coupled with chance input, can result in a population of self-replicating virtual organisms in which information is systematically transferred from parent to daughter organism. I have conceptualised and operationalised the hypothesis as follows: Conceptual Hypothesis: that information can arise from Chance and Necessity only. Operationalised hypothesis: That, starting only with non-self-replicating entities and a physics-and-chemistry plus random kinetics, self-replicating “virtual organisms” can emerge that satisfy the following criteria: 1. The daughter entities must resemble the parent entities with a significant degree of fidelity (measure and threshold to be determined). In other words the pattern embodied in my “virtual organisms” must be transmitted from generation with some measurable degree of fidelity 2. The nature of the pattern itself must contribute to the efficient maintenance and reproduction of the “virtual organism” (i.e. be more effective than some randomly substituted pattern), 3. The process of replication must involve transfer of information from some pattern embodied in the “organism” (e.g. a polymer-like string) via an inert intermediate product of the organism to a secondary product that serves some kind of self-maintenance or self-replication function for the virtual organism. I propose that if I succeed, I have supported my conceptual hypothesis and thus infirmed ID. If anyone disagrees, perhaps they would like to articulate the grounds on which they do so. Thanks. Elizabeth Liddle

Oh, and yes, I was talking about protein coding. Elizabeth Liddle

Yes, Mung, and those "rules" are in fact, a set of tRNA molecules. Right? A set in which each has a codon site at one end and an amino acid site at the other, right? Elizabeth Liddle

That’s interesting – do you have a cite?
wow. just wow.
The genetic code is the set of rules by which information encoded in genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines how sequences of three nucleotides, called codons, specify which amino acid will be added next during protein synthesis. With some exceptions,[1] a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. Because the vast majority of genes are encoded with exactly the same code (see the RNA codon table), this particular code is often referred to as the canonical or standard genetic code, or simply the genetic code, though in fact there are many variant codes. For example, protein synthesis in human mitochondria relies on a genetic code that differs from the standard genetic code. Not all genetic information is stored using the genetic code. All organisms' DNA contains regulatory sequences, intergenic segments, chromosomal structural areas, and other non-coding DNA that can contribute greatly to phenotype. Those elements operate under sets of rules that are distinct from the codon-to-amino acid paradigm underlying the genetic code. http://en.wikipedia.org/wiki/Genetic_code
Mung

Mung:

I simply don’t think that the source of the information in the genome (and I agree there is information in the genome) is a great mystery.
According to what definition of information?
According to most definitions that I am aware of. But certainly according to the its meaning in general English usage. In many ways, DNA can be regarded as a database, which the cell accesses as needed. Elizabeth Liddle

Ilion:
“But my point, I guess, is that these are not arbitrary/symbolic mappings. You can’t just make one codon code for different amino acid by declaring it so in some look-up dictionary – in that sense, DNA is more like a jig, or a template than a code. The mapping arises directly from the physical chemistry.” This isn’t actually true. In reality, there are some organisms for the biochemistry of which some codon that “means” ‘X’ in most other oganisms “means” ‘Y’.
That's interesting - do you have a cite? Presumably that means that in those organisms, there is a different tRNA molecule coded in the DNA. Which sort of supports the point that I made recently in some other thread that there will be selective pressure for the set of available tRNA molecules to have no duplicates at the amino acid end - the mapping has to be one amino acid to one or more codons. But which subset, of the possible set of 1280 tRNA molecules goes into that set, doesn't actually matter, as long as there only one of each for each amino acid. So, thinking further about it, the statement of mine you quote about it is indeed incorrect. It's not so much that the mapping arises directly from the chemistry, but that the set tRNA molecules that form that chemistry are themselves are an optimised subset from a larger possible set, of which several optimised subsets are possible. However, given such an optimised subset, the mapping is executed via a jig system. Elizabeth Liddle

"But my point, I guess, is that these are not arbitrary/symbolic mappings. You can’t just make one codon code for different amino acid by declaring it so in some look-up dictionary – in that sense, DNA is more like a jig, or a template than a code. The mapping arises directly from the physical chemistry." This isn't actually true. In reality, there are some organisms for the biochemistry of which some codon that "means" 'X' in most other oganisms "means" 'Y'. Ilion

I simply don’t think that the source of the information in the genome (and I agree there is information in the genome) is a great mystery. Elizabeth Liddle
According to what definition of information? Mung

The mapping of nucleic triplets to amino acids is an observable reality. Both modern biology and evolutionary theory are themselves based upon the reality that these mappings between discrete objects exist. Upright BiPed

But my point, I guess, is that these are not arbitrary/symbolic mappings. You can’t just make one codon code for different amino acid by declaring it so in some look-up dictionary – in that sense, DNA is more like a jig, or a template than a code. The mapping arises directly from the physical chemistry. Elizabeth Liddle
Mung

(I'm looking at this page's "HTML source") I see what's causing the problem: Mrs Liddle seems to have typed "<i />" when she meant to type "<i>" This apparenly codes for an "open global italics" that seems to have no equivalent "turn it off, already!" Ilion

I don’t think that “an abstraction of a discrete object” “embed[ded] into a medium by the implementation of a chemical code” is a good description of what DNA does. - Elizabeth Liddle

You are welcome to make your case, but I think Marshal Nirenberg would be out of luck if the facts were otherwise. Upright BiPed
Mung

Can the italics be ended? I put a great mass of "</i>" within that question, hoping that the problem is due to too many "<i>" upstream. Ilion

"can the italics be ended?" What do you have against italics? I have a lot of italic friends and they're really nice people. CannuckianYankee

Well, my position is that IDists have failed to demonstrate that what they consider the signature of intentional design is not also the signature of Darwinian evolutionary processes. Elizabeth Liddle
Mung

can the italics be ended? Probably not. But they're better than when we had all bold in one thread. Mung

junkdnaforlife
The irony of this two month long coding proposal dying in an italic graveyard of broken code by the proposed coder has not escaped me.
The irony that this is an Intelligent Design site is equally delicious. Elizabeth Liddle

Upright BiPed: I am deeply disappointed in your response, in which, I notice, you do not even bother to quote the text of the criteria I went to considerable trouble to propose to you. And of course my own perception of our conversation is very different to yours (it happens). Let me comment on your latest post to me below:
Hello Dr Liddle, I have taken some time to think about it, and quite frankly I am at the point where I just don’t know what else to say to you. This conversation began in late May and has run to the middle of July.
tbh, less than a couple of months isn't long to develop a proposal from first conception to detailed operationalised hypothesis, working on it part time, in a somewhat difficult discussion format, over several threads, when the two principals start with very different conceptual understandings of the problem.
It has had literally tens of thousands of words exchanged and has taken over five separate threads. Throughout the whole time I have felt like I was talking to someone who always had something slightly else in mind, almost condescendingly so at times, as if they thought they already knew the material and were just politely pacing their time.
Well, obviously that is your perception, and for my part in it I apologise. But as we are speaking frankly, I have to say that I have found much of your contributions to have a flavour of condescension as well. In fact, if you compare our exchanges, I think you will find far more personal criticism and expressions of skepticism about my motives and commitment in your posts than you will find about you in mine. I have consistently posted in good faith, and yet you have consistently questioned my good faith. In contrast, I have never, until the last day or so, questioned yours. I am, I confess, now starting to have my doubts. I happen to be someone who finds it pretty easy to admit error, and do, frequently. If I find myself making an error, I am quick to correct it - if someone points out an error, or an inconsistency (apparent or real) I am quick to sort it out, and if someone convinces me I am in error (and it happpens) I am quick to acknowledge it. When I find myself in a conversation that has become mired in mutual misunderstandings, I try to go the extra mile and find out why I might have misunderstood, or been misunderstood. I am very aware that when communication breaks down, the fault may at least partly be mine, and that at least some of the "fault" is due to circumstance - two people with very different habits of thought, patterns of language use, cultural hinterland, unquestioned premises.
This of course was interspersed with runs of “Great!”, and “Perfect!”, and “I like it”. I do not know the degree to which that accurately describes the events, but given the breadth of your misconceptions made obvious by the exchange, I would not say that it is not completely without merit.
I note your assumption that the misconceptions are all mine, which is a bit rich for someone who just accused me of being condescending! There have been times indeed, UPD, when I thought we were "nearly there" and that if we could just operationalise terms like "protocols" to our mutual satisfaction, then we'd be away. Unfortunately, as often happens in these conditions, once we started to unpack the remaining pieces of baggage, more evidence of differences in our understanding emerged. As I've said a few times, I have the hunch that if we could get to the stage of being absolutely clear what the other meant, we probably wouldn't need to go any further - the answer would be obvious. But we haven't succeeded in reaching that stage.
In any case, I have come to the end of my contributions in trying to describe the phenomena of information. Information is the dynamic outcome of a system that is unlike any other phenomenon in the cosmos. I have told you of the discrete entities/objects that are required for information to exist, and described their dynamic relation to one another. To the best of my knowledge, these descriptions hold true for the cell, the earthworm, the elephant, or the astronaut. Contrary to your claims of circularity, I never said that a mind was necessary to bring information into existence; I said a mechanism was required, and was willing to help establish the grounds to falsify the mechanism I believed to be responsible by a simulation of your mechanism accomplishing the same task. I have now already said everything at least a half dozen times so that you might break from your preconceptions, and at this point I am only repeating the repetitions.
What you have been doing, Upright BiPed, is indeed repeating your repetitions. Which no doubt has been frustrating for you, but even more frustating for me, because you have largely ignored my very pertinent queries! From my point of view there was a big unpacked bundle (often called "protocol") in your replies, but every time I tried to get you to unpack it, all I got was repackaging! I think I now see why - your post on the other thread about the UUU mapping to phenylalanine was the clue.
Other than our initial walk through the observations of information, the bulk of what I can say was said in post #50 and my clarifications at #85. Your preference to call the “break in the causal chain” a “dissociated link” would have been fine by me, as evidenced by my asking to use my phrase in the first place. The Popper in me says that the descriptors are far less important that the understanding anyway.
And the scientist in me says that the description is absolutely critical, which is precisely why I was trying to extract it from you. Upright BiPed, you no doubt know a lot about information but you do not know how to operationalise a hypothesis. Neither "break in the causal chain" nor "dissociated link" are operationalized. Neither give clear criteria by which an objective observer can determine whether the condition has been met. That is why the work was not finished. That was why I offered an operationalisation above. Which you have completely ignored.
If I thought factual integrity mattered, I would once again ask you to recant your comment that “IDists have failed to demonstrate that what they consider the signature of intentional design is not also the signature of Darwinian evolutionary processes”. Clearly that claim is demonstrably false, as indicated by the fact that you are attempting to design a simulation to refute the claim. Sideshow dismissals about meaning CSI or other measure are meaningless. If information doesn’t exist itself, then its subcategories don’t either, surely you understand that much by now.
No, the claim is not "demonstrably false". In fact it's not demonstrable at all until we have an agreed operational definition of information! Unfortunately we don't seem to have got even to the stage where you understand why this is an absolutely fundamental requirement before any claim about information can be tested. However, when I made the claim, I meant, by "the signature of intentional design": CSI. Or, as Dembsi puts it: Specification: the pattern that signifies intelligence. http://www.designinference.com/documents/2005.06.Specification.pdf My claim is that it does not - that it is also the signature of Darwinian evolutionary processes. That is what I said I would demonstrate. However, it seemed that you had something different in mind, which I have tried to accommodate. But, unlike Dembski, who at least provides an equation (though the variables are somewhat short of operationalised IMO), you have provided only conceptual definitions, and it is precisely those concepts that I have taken such pains to try to operationalise. In the face, of a great deal of the kind of condescension you display below!
If this conversation should move past this stage and return to something productive, then I may elect to rejoin. As clearly evidenced by your participation here, at this point no one has ever demonstrated the rise of information from physical law, and it is that information that makes life possible and is the backbone of biology. With that said, I thank you for the talk and bid you farewell.
Right. Well, I will offer, as "something productive", a refined version of the operationalised hypothesis I offered above, and which, unfortunately, you ignored. Here we go: Hypothesis: that information can arise from Chance and Necessity only. Operationalised hypothesis: That, starting only with non-self-replicating entities and a physics-and-chemistry plus random kinetics, self-replicating “virtual organisms” can emerge that satisfy the following criteria: 1. The daughter entities must resemble the parent entities with a significant degree of fidelity (measure and threshold to be determined). In other words the pattern embodied in my “virtual organisms” must be transmitted from generation with some measurable degree of fidelity 2. The nature of the pattern itself must contribute to the efficient maintenance and reproduction of the “virtual organism” (i.e. be more effective than some randomly substituted pattern), 3. The process of replication must involve transfer of information from some pattern embodied in the “organism” (e.g. a polymer-like string) via an inert intermediate product of the organism to a secondary product that serves some kind of self-maintenance or self-replication function for the virtual organism. I have thought very carefully about that last condition. I would like to know whether it satisfies your criteria for information. Elizabeth Liddle

can the italics be ended? Ilion

The irony of this two month long coding proposal dying in an italic graveyard of broken code by the proposed coder has not escaped me. junkdnaforlife

Hello Dr Liddle, I have taken some time to think about it, and quite frankly I am at the point where I just don’t know what else to say to you. This conversation began in late May and has run to the middle of July. It has had literally tens of thousands of words exchanged and has taken over five separate threads. Throughout the whole time I have felt like I was talking to someone who always had something slightly else in mind, almost condescendingly so at times, as if they thought they already knew the material and were just politely pacing their time. This of course was interspersed with runs of “Great!”, and “Perfect!”, and “I like it”. I do not know the degree to which that accurately describes the events, but given the breadth of your misconceptions made obvious by the exchange, I would not say that it is not completely without merit. In any case, I have come to the end of my contributions in trying to describe the phenomena of information. Information is the dynamic outcome of a system that is unlike any other phenomenon in the cosmos. I have told you of the discrete entities/objects that are required for information to exist, and described their dynamic relation to one another. To the best of my knowledge, these descriptions hold true for the cell, the earthworm, the elephant, or the astronaut. Contrary to your claims of circularity, I never said that a mind was necessary to bring information into existence; I said a mechanism was required, and was willing to help establish the grounds to falsify the mechanism I believed to be responsible by a simulation of your mechanism accomplishing the same task. I have now already said everything at least a half dozen times so that you might break from your preconceptions, and at this point I am only repeating the repetitions. Other than our initial walk through the observations of information, the bulk of what I can say was said in post #50 and my clarifications at #85. Your preference to call the “break in the causal chain” a “dissociated link” would have been fine by me, as evidenced by my asking to use my phrase in the first place. The Popper in me says that the descriptors are far less important that the understanding anyway. If I thought factual integrity mattered, I would once again ask you to recant your comment that “IDists have failed to demonstrate that what they consider the signature of intentional design is not also the signature of Darwinian evolutionary processes”. Clearly that claim is demonstrably false, as indicated by the fact that you are attempting to design a simulation to refute the claim. Sideshow dismissals about meaning CSI or other measure are meaningless. If information doesn’t exist itself, then its subcategories don’t either, surely you understand that much by now. If this conversation should move past this stage and return to something productive, then I may elect to rejoin. As clearly evidenced by your participation here, at this point no one has ever demonstrated the rise of information from physical law, and it is that information that makes life possible and is the backbone of biology. With that said, I thank you for the talk and bid you farewell. Upright BiPed

Hiya Lizzie! I can see you've had some rather unpleasant exchanges on another thread today, which is a shame. I understand why people are getting frustrated but I think it would be better for them to take some time out to calm down rather than repeatedly expressing their frustrations. Attack the position, not the person. I feel like I need to keep reminding you that that is my approach here. I greatly admire your patience and restraint, Lizzie! Okay, pour yourself another G + T, I'll get myself a wee stubby bottle of beer! We keep returning to the same fundamental disagreement: the one where, first of all, I’m just trying to establish whether the cell made itself or was made, while you’re not interested in that: you’d much rather nail down the Designer first. So far, I can only conclude that this is because you want to rule out the existence of a Designer that might be the Creator. Therefore the cell must have made itself, no matter how strong the evidence for Design is. At the very beginning of any design detection, we have no candidate designers. At that very early point, we immediately eliminate naturalistic causes and “infer Designers Unknown”. We do this all the time: especially for things like Stonehenge, the Sphinx and the Easter Island statues where the designers really are unknown, even to archaeologists. If we find a fresh corpse with severed limbs and missing bits, we quickly eliminate naturalistic causes and “infer Designers Unknown”. The very next step would be to assume a human killer. But this might be wrong as it could just be an animal attack. It is even possible that a demon appeared out of thin air and did the grisly deed before vanishing again: at the very outset, we can’t rule this out. Notice though that initial doubts about whether the cause of death was human, animal or demon does not in any way prevent us from eliminating naturalistic causes. We are certain that someone or something did this on purpose: ‘Designers Unknown’. Agreed? That just leaves self-replication as the last remaining reason to doubt design: so even though the cell is perhaps the most mind-bogglingly functional, sophisticated and complex things in existence you appeal to its ability to self-replicate as a reason to believe that it made itself. But, 1. No-one has any idea where the cell came from. 2. No-one has any idea where the first self-replicating molecule came from. 3. Every single experiment we’ve ever performed to try and re-create the first self-replicating molecule by purely naturalistic means has failed. Given these three indisputable facts, which reflect the impenetrable barriers that lie between naturalistic causes and the first self-replicating molecule (let alone, the cell), don’t you think it’s possible, Lizzie, that the cell didn’t make itself after all? There is certainly no scientific basis to believe otherwise. Which leaves us with that recurring need to reject the existence of any Designer which might be the Creator. If I showed you a 'smart' phone that had the ability to self-replicate, you wouldn't be much, much less likely to conclude that the 'smart' phone made itself, than if it lacked that ability. And yet, the cell is far more sophisticated, functional and complex than any 'smart' phone. The ability to self-replicate does not make the overwhelming evidence for Intelligent Design disappear. It merely enhances it. Finally, if “All evolution is limited to ‘sub-specific variety’!” then that just means nothing has ever really evolved in the first place. After all, the whole point of sub-specific variety is that there are well established limits as to what we can achieve with it, artificially. Those limits are even more restrictive when it’s just nature doing the selecting. That’s why Chihuahuas and Great Danes didn’t appear until humans literally designed them. Sub-specific variety – along with its clear limits – is all that we see in extant species, especially in all the living fossils. And extinct species obviously didn’t leave any offspring that surpassed these limits: that’s what made them extinct in the first place! Furthermore, beyond sub-specific variation, all we ever see is discontinuity. If there was one word to describe the entire fossil record, it could be “discontinuous”. And biological classification would only be possible if there was discontinuity between species. So I don’t see how we can square these indisputable, observable facts with your claim that “micro-evolution can become “macro” without any discontinuity”. Chris Doyle

Mung: re this:
I think it might be safe to say that if a communications system is present that might be a good indicator of information.
I would agree. Which was exactly why I thought that simply being able to show that self-replicators (who necessarily transfer information from themselves to their offspring) could emerge from non-self replicators with no inputs other than a physics-chemistry and random movements, I'd be there. I'm not sure I can even do that, mind, but I'd like to try. But if I'm going to, I'd like to go for the Big One. Hence my attempt to get UPD to sign off on my latest set of criteria. Elizabeth Liddle

Mung, it may well have been of my own making. I certainly came with preconceived ideas about what would be regarded as a definition information at UD (CSI and friends, basically) - namely a pattern indicative of design (a watch on a heath? SETI signals?) without any further information as to what or who had produced it. However, I have made great efforts to understand what UPD is getting at, and I await his comments on my suggested criteria with eager anticipation. I think I have incorporated everything he requires, apart, of course, for his requirement of a "break in the causal chain". I've done the next best thing, I think though. Elizabeth Liddle

Elizabeth Liddle:
However, what has emerged is that what you had in mind was not so much an INFORMATION-BEARING PATTERN, transmitted from generation to generation...
I'd bet that if we were to go back and look at the history of this entire discussion we would discover that Upright BiPed never did have in mind a "pattern" being transmitted from one generation to the next. That was something entirely of your own making. I think we'll also find it very clear what Upright BiPed did in fact have in mind. Let me give one one huge hint: http://en.wikipedia.org/wiki/Marshall_Warren_Nirenberg And then look at your own posts for tRNA or ribosome. There is within the cell a system. That system is incredibly similar to the one sketched by Shannon in his famous paper. Do you understand the distinction between an "information-bearing pattern" (your own words) and INFORMATION itself? I think it might be safe to say that if a communications system is present that might be a good indicator of information. Mung

Upright BiPed: thinking further on my bike (as I do!) I think I have perhaps put my finger on where things have come adrift. I had envisaged that what we both had in mind when defining information was that we would have a set of criteria by which we could look at a pattern, transmitted from parent to offspring, and say whether it contained information, of the type alleged by IDists to be highly unlikely to result without input from an Intelligent Designer), which I envisaged would, at the minimum, have to embody information that promoted the effective transmission of the pattern. This would rule out my Duplo Chemistry, but would include, for example, a pattern that was better able than other possible patterns to be transmitted faithfully from generation to generation. However, what has emerged is that what you had in mind was not so much an INFORMATION-BEARING PATTERN, transmitted from generation to generation, and which bore the hallmarks of Design (to be determined), but rather, but a kind INFORMATION TRANSFER PROTOCOL that bore the hallmark of a designer. That's fair enough I think. So what I need to get from you (or confirm that I already have), some minimal description of such a protocol - what criteria must be satisfied. And I certainly do not accept "a break in the causal chain" as a criteria! However, what I am willing to accept, is the following criteria for the output of my simulation, which should consist of self-replicating "virtual organisms": 1. The daughter entities must resemble the parent entities with a significant degree of fidelity (measure and threshold to be determined). In other words the pattern embodied in my "virtual organisms" must be transmitted from generation with some measurable degree of fidelity 2. The nature of the pattern itself must contribute to the efficient maintenance and reproduction of the "virtual organism" (i.e. be more effective than some randomly substituted pattern), 3. The process of replication must involve transfer of information from some pattern embodied in the "organism" (e.g. a polymer-like string) via an inert intermediate product of the organism to a secondary product that serves some kind of self-maintenance or self-replication function for the virtual organism. I was pretty well set to try to fulfill 1 and 2. I have now added 3. If my simulation, starting only with non-self-replicating entities and a physics-and-chemistry plus random kinetics, resulted in "virtual organisms" displaying the above characteristics, would you consider my claim fulfilled? Elizabeth Liddle

Upright BiPed: Your post below is obviously disappointing (as clearly my response to you was disappointing), but let me address it anyway:
Dr Liddle, Overall, I find your last response to be just short of a free-wheeling swing-fest; a politely-worded tirade against almost the entirety of the conversation that went before it. It seems as though you asked for an operational definition, then got one, then later found out what kind of dynamic structure would be required for such a phenomenon to exist, and have since gone on a rant to eviscerate yourself from the position you are in. It seems that either I have moved the goalpost, or you were thinking of a different thing, or I don’t give satisfactory definitions, or you were talking about somebody else’s something else, or suddenly the observations are circular, or whatever else is within a hand’s reach.
No, obviously I don't think this is a fair summary at all. Firstly, yes indeed, I said that in order fulfil my claim to your satisfaction I would need an operational definition from you of information. Now, clearly, if my original claim referenced, as it did, a different conceptual definition than yours, that is a potential problem. I was thinking of a CSI- type definition, as I have now made clear. However, I'm quite prepared to extend my claim to your own conceptual definition, which, in many ways, I prefer. But we need to operationalise it. And the two key properties an operationalised hypothesis must have is that it must render it possible for independent investigators to measure the key variables and get the same answer (e.g. input and output values) and it must be unambiguous. So any potentially ambiguous words must be clearly unpacked, so that we are all clear what they are intended to mean in the context of the investigation. But then you did, indeed "move the goal posts". We were trying to define information in such a way we could both examine the output of my simulation, and determine whether that output consisted of information. But then, instead of defining information in terms of what the output would look like, you started to try to define it in terms of what the process between input and output must look like! Moreover, you insisted that that process must involve a "break in the causal chain"! Well, obviously I can't do that, because my claim is that no such break is required in order to produce information! Do you really not see the circularity here? Nonetheless, I went to great efforts to derive an operational hypothesis that might satisfy your criteria. I repost it here:
That, starting from a population of non-self-replicators, and using only a set of rules governing their interaction and stochastic processes governing their movement, a set of self-replicators can emerge that incorporate patterned sequences (S) that directly initiate processes that result in products (P) that increases the probability that the S itself, and the whole of which it is a part, will be replicated with a fidelity of x%, and that moreover, this process will involve catalysis by intermediate products that form neither part of P nor part of S.
The part beginning "and moreover..." is my attempt to include your condition that some kind of inert intermediary product is involved in the transfer of information embodied in the patterned sequence to the functional product - the dynamic protocol, if you will, that connects the two. If you think this is inadequate, please explain precisely why.
This strikes me as odd, given the fact that there is one wholly-unmentioned possibility which seems to be immediately confirmed by the text of your own comments. It’s the possibility where you fully understood the observations as they were being made, and indeed, you yourself provided much of the operational definition which rose from those observations, but have since discovered the intractable problem within your position, and are now openly reacting to the simple fact that the problem is virtually impossible to solve by the means you’ve prescribed to it.
Well, I didn't mention it because it isn't actually true. I've been struggling to get from you a clear conceptual definition of information that we could operationalise. We seemed to be nearly there, but then you seemed to me to go off on a tangent about protocols. Can I remind you that the operational definition I was seeking was for INFORMATION (excuse caps but we seem to be stuck on italics in this thread), so that I could demonstrate my claim that it could be created by Chance and Necessity alone (and we have I think satisfactorily agreed on operational definitions of those). I was not, obviously, seeking an operational requirement regarding the PROCESSES by which that information must be generated in my simulation. It was precisely the claim that those processes NEED NOT include anything other than Chance and Necessity that I made!
In light of this, I would have every right to simply walk away from this conversation. I would have every justification to write it off as just another highly-trained but self-deluded ideologue who (by direct fault of their very own) truly had no fundamental idea what they were talking about when it comes to the case for design.
Well, no. If you want to walk away, fine, but do not do so under the impression that it is I who have done the evading here. I made a fairly straightforward claim, which you rightly challenged. I accepted your challenge, with the provise that we agree an operational definition of "information" so that we can independently verify whether I meet your challenge. You have sidestepped this requirement, substituting in place of a definition of information, a requirement that the method by which that information is created must include a "break in the causal chain", the very thing that I claimed was unnecessary to create information! Clearly you do not see it this way. Therefore, the right thing to do is to clarify what you do mean, rather than simply "walk away". But of course it is your choice.
I think our meeting demonstrates the dynamic rather well. On the one hand we have a specialist whose focus is perpetually misdirected by their faulty view of the issues, and on the other hand we have a generalist who has spent an enormous amount of time studying the physical properties of information. One spits off to the other “I can make information rise up” and the ensuing result is certain.
Well, obviously I dispute the characterisation of myself as "a specialist whose focus is perpetually misdirected by their faulty view of the issues" which seems to me to be begging the question ( whether my view of the issues is faulty). Nor, in fact, would I describe myself as a "specialist" really. But, whatever. But I'm delighted to hear that you have "spent an enormous amount of time studying the physical properties of information". My claim is that Chance and Necessity alone can create information. Please, therefore, give me a straightforward operationalised definition of information such that an independent observer can tell us both whether the output from a simulation in which the only inputs are Chance and Necessity satisfies it.
In any case, I will decide this evening if I want to try and detangle your last post.
Hope to see you later. Lizzie Elizabeth Liddle

Dr Liddle, Overall, I find your last response to be just short of a free-wheeling swing-fest; a politely-worded tirade against almost the entirety of the conversation that went before it. It seems as though you asked for an operational definition, then got one, then later found out what kind of dynamic structure would be required for such a phenomenon to exist, and have since gone on a rant to eviscerate yourself from the position you are in. It seems that either I have moved the goalpost, or you were thinking of a different thing, or I don’t give satisfactory definitions, or you were talking about somebody else’s something else, or suddenly the observations are circular, or whatever else is within a hand’s reach. This strikes me as odd, given the fact that there is one wholly-unmentioned possibility which seems to be immediately confirmed by the text of your own comments. It’s the possibility where you fully understood the observations as they were being made, and indeed, you yourself provided much of the operational definition which rose from those observations, but have since discovered the intractable problem within your position, and are now openly reacting to the simple fact that the problem is virtually impossible to solve by the means you’ve prescribed to it. In light of this, I would have every right to simply walk away from this conversation. I would have every justification to write it off as just another highly-trained but self-deluded ideologue who (by direct fault of their very own) truly had no fundamental idea what they were talking about when it comes to the case for design. I think our meeting demonstrates the dynamic rather well. On the one hand we have a specialist whose focus is perpetually misdirected by their faulty view of the issues, and on the other hand we have a generalist who has spent an enormous amount of time studying the physical properties of information. One spits off to the other “I can make information rise up” and the ensuing result is certain. In any case, I will decide this evening if I want to try and detangle your last post. Upright BiPed

Apologies for my 'smart' phone duplicating entries too. Duplications just clutter up data, rather than create it! Chris Doyle

Random errors just destroy order, Lizzie, that's why! Thanks for your reply, certainly worth waiting for. I continue to enjoy our discussions and am proud that you're a fellow Brit! I will respond more fully tomorrow (while I'm supposed to be working). Chris Doyle

Random errors destroy just order, Lizzie, that's why! Thanks for your reply, certainly worth waiting for. I continue to enjoy our discussions and am proud that you're a fellow Brit! I will respond more fully tomorrow (while I'm supposed to be working). Chris Doyle

Blimey I seem to have infested the thread with italics! Sorry! Don't know what's happened there! Elizabeth Liddle

Chris:
Good Afternoon Lizzie, Remember when you said that there was no “prejudice against a Creator God” at play when people reject Intelligent Design theory? I think your last response to me shows numerous examples of such a prejudice. In other words, design detection is perfectly rational, intuitive and empirically sound, unless the Designer in question might be the Creator. While you concede that you no longer need to know the identity of the Designer, you still insist that we must postulate a specific kind of Designer. Why?
Because otherwise we can go no further - we don't know whether the designer was an alien from another world, or a demon, or a Creator god. It doesn't get us anywhere. Nor does it offer any differential predictions that we can use to test it against an alternative hypothesis, such as Darwinian evolution.
Your next step is to postulate “an omnipotent God who could do anything s/he felt like at any time”. Again, why? Such a step is extremely illogical: it doesn’t follow from your previous step. It is also unscientific: what does science even have to say about things that possess omnipotence? Such muddled thinking is a clear sign that you are approaching Intelligent Design theory with a prejudice against any Designer who might be the Creator.
Not at all! I'm simply saying that science can only work with a hypothesis that makes differential predictions! A creator God isn't going to make any differential predictions, is it?
You also claim that it is unlikely that the Designer “was able to transfer solutions from one lineage to another” and that the Designer “preferred retrofitting to “going back to the drawing board” where possible”. Again, these are prejudicial comments given that all we are trying to do is establish whether or not actual Design has taken place. It’s almost as if you’re saying: “Well, the Designer is not capable of transferring solutions from one lineage to another and prefers retrofitting. If I was the Designer, that’s not how I would do it. So there can’t possibly be a Designer: it must have all made itself!”
Well, that's why I said - we can infer certain things about the postulated Designer - we can rule out certain attributes. But that isn't going to get us very far, just squish the designer into a slightly smaller gap. If you want actually to compare a Designer hypothesis with an evolutionary hypothesis you need a differential prediction.
At one point, you even suggested that we have to know that the Designer(s) “lived around these parts” before entertaining the possibility that something didn’t make itself. Why would you insist on such an odd requirement if you are not bringing prejudicial baggage to the table (ie. there is no Creator around these parts so don’t even go there with the cell)?
No, Chris I'm not saying that - I'm saying that when you compare the issue of biology to archaeology you are ommiting a couple of absolutely crucial differences - that archaelogists make their inferences in the light of knowledge about possible designers, and that archaeological artefacts don't self-replicate. If we had no candidate designers, AND no self-replication - yes, one might infer Designers Unknown, which would be quite exciting (obvious artefacts on Mars, for instance). But if the thing was self-replicating, we'd have good alternative hypothesis.
No doubt your opponents bring their own prejudices to the debate, Lizzie: Biblical Literalists being an extreme (and rare) example. But most of us put science ahead of those prejudices. Most of us can take or leave evolution, for example. You’ve got theistic evolutionists on one end of the scale and then creationists on the other. Personally, I don’t see any scientific evidence whatsoever to support the belief that a single-celled common ancestor evolved into human beings. I don’t even accept common ancestry. Again, this is on purely scientific grounds. If the evidence led to evolutionist explanations then I’d simply become a theistic evolutionist. Even front-loaded deism would be relatively easy to accommodate (including the implications for abiogenesis).
Excellent :) That's probably why I enjoy talking to you :) But I do think you've overlooked a lot important evidence. Still, I think theism is completely compatible with evolutionary theory. I certainly didn't become an atheist because of Darwinian evolutionary theory!
But atheists have got no room for manoeuvre. They can’t take or leave a Designer that might be the Creator. The universe and everything in it MUST have made itself, through purely naturalistic processes or else their entire worldview collapses and it really is back to the drawing board. I put it to you, Lizzie, that you are placing your worldview, and therefore prejudices against a Designer who might be the Creator, ahead of what are otherwise plainly obvious and entirely straightforward means of Design detection in the cell.
No, I'm not Chris, seriously. I'm not an atheist because I'm a Darwinist, nor am I a Darwinist because I'm an atheist. The two are entirely unconnected. And your point is only valid for those atheists who have an emotional vested interest in a firm belief that there is no God. I know of very few of those. Actually, I know of none, though I am sure they exist.
You’ve already conceded that you’ve got absolutely no idea where the first self-replicator came from. As I’ve already pointed out: things that self-replicate are more difficult to explain than the same things that don’t self-replicate. It is impossible that non self-replicating artifacts such as Stonehenge or the Sphinx made themselves. Crazy appeals to science fiction aside, it is all the more impossible that a self-replicating version of these things made themselves! It is not their inability to self-replicate that leads you to the certain and immediate conviction of design. Throwing self-replication into the mix only strengthens that conviction. And the cell is vastly more functional, sophisticated and complicated than Stonehenge and the Sphinx even before it self-replicates…
No, I don't have "absolutely no idea where the first self-replicator came from". Obviously it's a long way from my field, but there are lots of interesting candidate hypotheses. I guess I should entertain the possiblity that a supernatural force placed the first self-replicators capable of Darwinian evolution on earth, but my priors would be low compared with some of the candidate theories.
However, you “consider the evidence overwhelming, as well as supported by elementary logic, that things that reproduce themselves with variance tend to end up evolving into ever-more-efficient self-reproducing things”. Surely, then, you can briefly summarise an important part of this ‘elementary logic’ as well as briefly identifying some of this ‘overwhelming’ evidence because most of us just don’t see it. Just remember, artificial selection is much more powerful than natural selection. As kairosfocus pointed out back in May: “[Natural] selection, contrary to popular opinion, is not a source of information, but patently a culler — a remover — of information. The variants that do not find niches do not survive to pass on genes. That which subtracts does not add. We have to look at that which supposedly adds, before we can see how subtraction may lead to survivors. By repeating the mantra “natural selection” one does not escape the need for engines of variation, and for specifically non-foresighted engines of variation, for darwinian type evolution.”
I think this is flawed. Removal of stuff can be as informative as addition of stuff. If I present you with five pairs of shoes, all different sizes, and you reject all but one of them, the pair that is left will tell me your shoe size. The selection process has created information. However, what I would certainly agree with is that rejecting shoes won't create shoes. As for artificial selection - yes, it may well be faster than natural selection, though not necessarily. It will have an upper bound placed by the rate of "shoe creation" - new alleles that extend the range in a given phenotypic direction. Same with natural selection. Natural selection may be slower (or, in some cases, faster), but again, it will have an upper bound in any one dimension on the rate of new allele creation (or even, rarely, new gene creation). Still, I don't think this is the thread for presenting to you the full argument for evolutionary theory from First True Cell to now! Maybe sometime though :) I'm very glad to hear that it wouldn't destroy your faith.
Artificial selection offers more than Natural Selection, but it is still limited to mere sub-specific variety: something that has been happening to all extant species for their entire known existence without any significant alteration whatsoever. Just offering evidence of sub-specific variety would therefore be completely underwhelming because any increased efficiency it generates is merely a product of a pre-existing gene pool.
All evolution is limited to "sub-specific variety"! That's a really important point - ask me if you don't understand what I mean! As for "pre-existing gene pool": I think it's a mistake (made by evolutionists as well as antis) to imagine that evolution proceeds mainly by brand new alleles. For a start most alleles have tiny phenotypic effects, and most selectable phenotypic traits are likely to be polygeneic, and those poly-genes are likely to include interactions. So it's better, IMO, to think of the gene pool as a big reservoir into which new, near-neutral alleles drip quite slowly, and drip out quite slowly, with the provise that newer drips have a greater probability of dropping out than older drips. In other words, the longer an allele hangs around, the longer it is likely to hang around! So we have a constantly feed of potentially useful alleles into the gene pool. And what happens, as a population continuously adapts to its environment, is that constituents of the "best allele cocktail" at any given time become more prevalent, and non-constuents become rarer, and may even drop out completely. That's the sense in which micro-evolution can become "macro" without any discontinuity - there isn't a jump between "micro-evolution using pre-existing alleles" and "macro-evolution using new alleles" - all evolution uses "pre-existing alleles" (with rare exceptions - the nylon-eating bug being possibly one) but the pool of pre-existing alleles is being constantly fed, and purged, so that there is always some phenotypic dimension along which a population can move in order to better adapt. As for speciation - that's different, because it involves a population splitting. Nonetheless, it's just a special case in which two subpopulations from an ancestral population adapt (by "microevolution"!) independently to different environments, and eventually cease to interbreed. Hope that paints a more realistic picture than the one perhaps you have been entertaining (and the one which, tbh, is often painted by "my" side!) Elizabeth Liddle

oops that's weird - I checked the italic tags. Don't know what happened. Sorry. Elizabeth Liddle

Upright BiPed:
Dr Liddle,
Well, we certainly agree that in order to demonstrate my claim I need an operational definition of information, and that, clearly will have requirements.
Yes, and as the result of a long conversation about various observations, there seemed to be a fair amount of agreement. You yourself provided two thirds of the following working definition. Information is a representation of a discrete object/thing embedded in an arrangement of matter or energy, where the object/thing represented is entirely dissociated from the representation, but where the association of the two can be established by means of a protocol instantiated in the receiver of the information. At which point the conversation generally turned more to the topic of what specific observations we might like to see in order to verify the claim. Which I think is where we are now; I have given you my thoughts and you have responded to them.
Yes, I agree that that is where we are.
We are attempting to simulate the rise of information in the genome, and the central question at this point is “how will we know it’s there?” To me, it seems like the shortest path to that answer would be the least subject to error, and in fact, it’s already been proven to be entirely reliable. The question to be answered is “how did we find it in the genome in the first place?”
Well, no, that isn’t the question to be answered! The question to be answered is: have I succeeded in creating information from a starting population of non-self-replicators? And to do that, we need an operational definition of information, so that we can both, independently , use that criterion to decide whether or not I have succeeded.
This has been the whole point of making these observations, exactly for the purpose of finding it again in your simulation. Researchers witnessed a mapping (a relation) between two discrete things: the patterns within nucleic sequences and specific actions taken in the assembly of amino acids into proteins. This process passed through the transcription of an initial sequence into a second medium, and then that second medium was transported elsewhere to be decoded by the use of protocols, and onward to the end result. It was also observed that there are no bonds associated within the sequence itself which would determine the order of nucleotides. It was observed that the constituents of the sequence did not directly interact with the resulting protein chain; the sequence in the parent chain is a discrete object. We manipulated the system at the input, and then observed the end result, thereby decoding the protocols. Those protocols were found to be the physical bridge across the two causal chains – were the information is inserted and the output is constrained by it – and they themselves are a product of that constraint. The information paradigm, even in its infancy, has since become the centerpiece of biological understanding. The method to observe the presence of information is therefore already known to us. Your simulation won’t be biological, but the dynamics of information must still be present.
Well, we still have a problem. You are defining the required output from my simulation in terms of what procedures are used to produce that output. In other words, you are not providing an operational definition of my output (information), but of the process from which that output must emerge. This is circular. I said that natural processes could produce information, and asked you to define information. Now you are saying that information is stuff that is output from a specific observed process! So are not asking me to demonstrate my original claim, but quite another one – that something like the ribosome can emerge by from a starting population of non-self replicators. I think it’s probably true, but it’s not what I claimed. It is a frequent claim made by IDists that information (more often “complex specified information”) can be detected in patterns (i.e. you can look at a pattern, and say whether it contains complex specified information) and that such patterns cannot be produced by Chance and/or Necessity alone – that they require a Designer. I dispute this claim. This is why I wanted a clear definition of information, which was why I went off on what you considered a tangent, trying to get a good operational definition of CSI that we could apply to the output of my simulation). However, you said the CSI definition was irrelevant to our conversation, and that we were in the process of developing our own definition. That’s fine, in principle, although, depending on what it is, it may not correspond to the kind of thing I had in mind when I made my claim, which was something like CSI (seeing as I’ve read quite a lot of ID literature :)) So we got to: Information is a representation of a discrete object/thing embedded in an arrangement of matter or energy, where the object/thing represented is entirely dissociated from the representation, but where the association of the two can be established by means of a protocol instantiated in the receiver of the information. But it’s still a bit conceptual. We still need to unpack some of those words, especially “representation” and “entirely dissociated”. The trouble is that rather than unpacking these words so that they can used as objective criterion for my end product, you have tried to specify the process I must use to produce that end product, and thus moved the goal posts (almost literally – the goal anyway) from producing information to producing something like a biological DNA-to-protein by way of mRNA, tRNA and ribosome in simulation. That is simply not what I claimed to be able to do! It would be awesome, but I’m simply not competent to do that! So, where to go from here? Let me look at what you say below:

However, if it turns out that your requirements (your operational definition) goes well beyond the conceptual definition I had in mind, I may have to retract.
Well as far as the operational definition goes, we seem to have some general agreement. It doesn’t seem that understanding the observations (those that shaped the definition) presents any difficulty for you, as well it shouldn’t. The problem lies in simulating the dynamic structure required for it to exist and come into being – without having it there, and only by chance and necessity from your initial conditions.
Well, we still have to do some operationalising. What we don’t have to do (or you don’t have to do) is figure out the simulation. That’s my job. Ideally, what should be possible is that you look at my inputs (non-self-replicators only, with some Laws and some Chance), and examine my outputs, and tell me whether they contain of information. That criterion must not depend on how I did it, or we have a quite different claim for me to defend from the one I made.
As far as what conceptions you had about information, and the claims you make about it, I can only recount what you’ve said: In an ongoing conversation on June 2nd, you made a comment about gene duplication: I simply do not accept the tenet that replication with modification + natural selection cannot introduce “new information” into the genome. It demonstrably can, IMO, on any definition of information I am aware of. I took mild exception to that remark, for no other reason than it rest on a flawed understanding of what information is.
Well, I don’t think it was “flawed” though it may have been information by a different definition from the one you think I could have been using. I was using something like CSI.
Materialist come here all the time to beat the evolution drum, as if they are faithfully defending their theory against ID. They seem to think that ID somehow denies change-over-time, or violates observed facts. They seem to think that by constantly recounting the already-observed regularities in biology, this will be detrimental to the case for design. It isn’t, because it’s conceptually misdirected by misrepresentations. And as always, it’s the fact that the system even exist at all that is most taken for granted. In other words, the conclusion against design is simply assumed to be true. So I replied: ”It demonstrably can, IMO, on any definition of information I am aware of.” Neo-Darwinism doesn’t have a mechanism to bring information into existence in the first place. To speak freely of what it can do with information once it exist, is to ignore the 600lbs assumption in the room. To which you replied: Well, tell me what definition of information you are using, and I’ll see if I can demonstrate that it can That is how we arrived where we are. - – - – - – - – - – - – - – -
Right – so you agreed that once you have a self-replicator, further information can be generated OK? But that the crucial part is how a self-replicator can emerge from non-self-replicators? Right. And while that was not my original claim, that is what I’m interested in demonstrating. My view was that if I succeeded in that, I would, by definition, have provided evidence that information–generators (i.e. self-replicators) could emerge from a population of non-selfreplicators. But you probably rightly rejected a couple of fairly simple self-replicator that I originally proposed (my “Duplo Chemistry” for instance) because my self-replicating sequences did not do anything apart from self-replicate. The sequence didn’t matter except that it was the sequence that was replicated. So I promised to include another layer of information – that the sequence itself would contribute to the efficiency with which the thing self-replicated. In other words that that the sequence would embody functional information - information that contributed to the maintenance and persistence, over time, of its own pattern. I submit that a system that did that would fulfil the conceptual definition of information we agreed : Information is a representation of a discrete object/thing embedded in an arrangement of matter or energy, where the object/thing represented is entirely dissociated from the representation, but where the association of the two can be established by means of a protocol instantiated in the receiver of the information. Because I’d have a pattern (a sequence) that caused the formation of something else (a molecule for instance) that then increased the probability that the whole (including the original pattern) would be self-replicated. In other words, my sequence would represent the molecule, from which it would differ, but the two would be associated because the production of the latter would enhance the probability that the former would be replicated. So my suggested operational definition of information for the purpose of my simulation is: A pattern that directly initiates a process that results in a product that increases the probability that the pattern itself, and the whole of which it is a part, will be replicated with a fidelity of x% where x is an agreed threshold (90%?) Alternatively we could express the fidelity threshold as something like the probability that something resembling the replicated individual would have emerged spontaneously from the starting conditions. That would be more elegant, but trickier to define. I’d have to think about that.
As for recanting, I have no desire whatsoever for you to recant. Well, that is not entirely true, I very much think you should recant your comment that ”IDists have failed to demonstrate that what they consider ”the signature of intentional design” is not also the signature of Darwinian evolutionary processes”. ” That accusation is demonstrably without merit at this point, even if you thought it had merit when you made it. You yourself have demonstrated why this is so. You’ve set yourself up to defend a position which quite literally flies in the face of the fact that you’re trying to design a simulation to refute what you say doesn’t exist. Quit frankly, I shouldn’t even have to ask you to recant, but you’ve made your position clear.
Well, I meant CSI. You thought I meant Meyer. I hadn’t read Meyer at that point.
As far as the simulation itself, I have no desire for you to quit.
Yes, except that I need to know a little more about what you would regard as the minimum for the “symbolic” requirement. This is not part Dembski’s definition, and, as I think I said, when I made the claim, I was thinking in those terms.
Firstly, I think we should be clear about this now. The requirement for a symbolic relationship between discrete objects is not my requirement. I have nothing to do with it. It’s an observation coming directly from the evidence itself. It’s how we discovered the genetic code in the first place. Modern biology is based upon it.
But, as we have seen, this lands us in difficulties, because we then need an operational definition of symbolic, and that has proved problematic (see above). We can’t just say: well, a ribosome operates with symbolic information, so let’s define symbolic information as the as the kind that emerges from something like a ribosome, or we are back in circles again. I did not claim to be able to simulate the emergence of a ribosome from non-self-replicators. What I said I’d demonstrate was that something that could produce information (functional, i.e. useful, meaningful, information) could emerge from non-self-replicators. And information that furthers the efficiency with which a self-replicator self-replicates is clearly useful to the self-replicator, and therefore functional.
Secondly, Dr. Dembski’s definition of information was never on your list of points. If you will recall, you spent a great deal of time repeating your need for my operational definition of information, not anyone else’s. I then gave it to you by going through the observations so that we might agree to them, which we did. It is those observations, and their entailments, which will allow us to verify your claim.
Well, as I said, I took it for granted when I made my claim. I assumed that we were talking information as defined in Dembski’s work, seeing as Dembski is at the forefront of the ID movement, not to mention the owner of this blog, and we were talking about ID claims. So I didn’t at that point expect any operational definition arising from your own concept to be radically different. But it turns out to be. That’s fine, to some extent my claim also applies to yours. But it was not my original claim (though you may have assumed it was).
The second structural item has to do with a necessity that the output of information transfer must be dynamic, based upon the input of that information. If the output is not dynamically driven by the representations being given at the input, then the input cannot be seen as informative to the output.
I’d like that unpacked with some ferinstances if possible
The receiver of the information must be able to access discrete protocols it in order for the information to have an effect. (example; GGC= glysine, CCA= proline) It’s part of the operational definition.
Who is the “receiver” in this scenario? And no, it is not (yet) part of the “operational definition” because we don’t yet have one, though I hope we are getting there.
Thirdly, to facilitate this dynamic property, there must be a necessary break in the causal chain. This break is exemplified within the cell by the simple fact that proteins are not created from nucleotides. In other words, if you plucked the ribosome from the cell’s protein synthesis machinery, and put yourself in its place, in one direction you would see sequences of nucleotides coming in for translation, and in the other direction you would see sequenced amino acids floating off into the distance to be folded into proteins. One of these marks the input of information (representations instantiated in matter) and the other is the output (a process being dynamically altered by the input). But these are two entirely separate causal chains (if I may use that word). Ah. A problem. No, I cannot incorporate a “necessary break in the causal chain”! To insist I do so is to make the criteria for my success the refutation of my claim! … I am essentially saying “a miracle occurs here” which is precisely what I am claiming to demonstrate need not occur!
Again, it is not at my insistence that the entailment be simulated, it’s a requirement coming from the evidence itself – but there is no miracle there. The tRNA – a physical object subject to physical law – is the protocol that (by its physical configuration) allows the information to be transferred into the output, and thereby constraining it. If there is an unbroken line between the information and its final effect, then no discrete representation could exist, and no protocol either. Neither would even be necessary. This would violate your own operational definition, as well as the dynamic structure that the definition entails. Your simulation would be a failure by virtue of not demonstrating two of the observed and confirmed requirements of information; representations and their protocols. The transfer of information would be out the window as well. It would be a mere chemical reaction with a probability of 1, none of which has any supporting observations whatsoever in the phenomena you are attempting to simulate. To simulate the rise of information without being obligated to demonstrate the very nature of information is obviously unacceptable; it’s not a simulation of information. If you are not going to accept that obligation, then what is the justification for proceeding?
Oh boy. I think it’s time to go back to the drawing board. Look: obviously in order to demonstrate the rise of information, to your satisfaction, I need a clear definition of information, such that you can look at what my simulation has produced and say: yes, that is information, or, no that is not information. That’s what an operational definition is. It doesn’t terribly matter to me what that definition is, but if it is an operationalisation of a conceptual definition that I did not have in mind when I made the claim, obviously I need to make that clear. But right now, I’m not at all sure even what your conceptual definition is, so I certainly can’t attempt to operationalise it! But let me go through your paragraph above and see whether I can tease it out:
1. The tRNA – a physical object subject to physical law – is the protocol that (by its physical configuration) allows the information to be transferred into the output, and thereby constraining it.
OK, but remember I do not intend to simulate tRNA. I’m looking for an operational criterion here. But yes, let’s say that, at least in a modern living cell an intermediate object (tRNA) maps the information instantiated in the mRNA sequence (derived by direct template mapping from the DNA) to a given amino acid. So if mRNA is the input, and the amino acid the output, tRNA connects the two, physically (i.e. by physical law).
2. If there is an unbroken line between the information and its final effect, then no discrete representation could exist, and no protocol either.
I simply don’t understand this. Are you saying that the intermediate (the tRNA) is the break in the line? If so, then fine. But what is the principle here? There is no break in chemical cause-and-effect. Various tRNA molecules exist, and each one binds at one end to certain codons and at the other end to certain amino acids. It’s a chemical property of those molecules, and subject to just the same laws as govern the binding of RNA to DNA, and indeed of nucleotide to nucleotide. You might ask why those particularly tRNA molecules are present in cells, and not others, but again, that’s a circular question. It’s perfectly possible that on some other planet, life might have evolved with the same kind of DNA, but with a different set of tRNA molecules. So in one sense the set we have is arbitrary. But that doesn’t make it symbolic – it’s still just chemistry, with additional intermediate reaction. What makes this one a “break” in the chain?
3. Neither would even be necessary. This would violate your own operational definition, as well as the dynamic structure that the definition entails.
But we don’t yet have an operational definition! And when we do, it will be agreed between us, it won’t be “mine”. This is exactly what I am trying to get from you – what are your criteria for determining whether a “break” in the “line” has occurred? What line are you talking about? There is no break in the chemical line in a cell – it’s all chemistry. tRNA molecules are created from DNA in just the same way as mRNA molecules are. They bind to the amino acids they do because of the DNA sequence that serves as their template. It’s all chemistry. There is no break in the chemistry.
4. Your simulation would be a failure by virtue of not demonstrating two of the observed and confirmed requirements of information; representations and their protocols.
And that’s exactly why we need to figure out what you mean by “representation” and “protocols”. Protocols is pretty clear – I’m interpreting as a set of events contingent on some pattern (probably a polymeric sequence), but “representation” is the difficulty. When does something causes something else in a physical/chemical causal chain, start to become “symbolic”? And if you are somehow claiming that tRNA isn’t part of a physical/chemical causal chain, then I’m not sure what you are claiming! And obviously I can’t incorporate non-physical/chemical causation in a demonstration that is a priori confined to physical/chemical causation!
5. The transfer of information would be out the window as well. It would be a mere chemical reaction with a probability of 1, none of which has any supporting observations whatsoever in the phenomena you are attempting to simulate.
No, it need not have a “probability of 1”. No chemical reaction has a “probability of 1”. Stochastic events (“Chance”) affect all physical/chemical interactions, whether at the quantum level or above. What you seem to be saying is that if a message is transferred with 100% fidelity (probability of transmission of each bit=1) then no information has been transferred! Now, obviously you don’t mean that, but, in that case, what do you mean?
Again, I genuinely hope that you do proceed, and I fully understand the conceptual problem you face by way of the evidence (welcome to a refutation of your comment above). But it would be useless to intend from the start to not demonstrate the very observations that must be demonstrated.
Indeed. But nor can I be expected to demonstrate something that is defined, a priori, as something that cannot be demonstrated! I said, a while back, Upright BiPed, that it was possible that if we really managed to establish an operational definition of information that would satisfy both of us, I probably wouldn’t have to do the demonstration. It would be obvious to both of us that one of us was wrong (and we would agree as to which of us it was!) I have a sense that this might be where we end up (though I hope not, because I do think that demonstrating that a self-replicator could emerge from non-self replicators would be pretty cool, especially if those self-replicators incorporated sequenced information that itself increased their probability of self-replication). But it seems to me we have hit a fundamental problem. Let’s see if it is resolved here, where you summarise very nicely your reasoning. I hope I can make it clear where I think your reasoning is fundamentally flawed:. I will number your points:
1. The first causal chain is the sequence of representations, which I say is the product of design, and you contend is the result of chance/necessity. It is made up of nucleic acids. 2. The second causal chain is the bonding within the resulting polypeptide. It is made up of amino acids. 3. The amino acids and the nucleic acids do not interact. They are connected at this dynamic break only by the protocol itself, which I say is the product of design, and you say is the result of chance/necessity. Regardless of who is correct, this dynamic break in the causal chain must be represented in the simulation
My response: 1. You seem to be equivocating with the word “chain” here. I am not clear whether your “causal chain” is the same as your DNA chain of nucleic acids. A chain of nucleic acids is not a “causal chain”. It’s just a polymer. However, I agree that it must have had a cause. I also agree that as yet we do not know how DNA formed spontaneously outside a non-self-replicator, or whether it did (it could have followed RNA-based self-replictors, or even protein-based self-replicators). But that’s OK, because as part of my demonstration I will have my polymers form spontaneously. So this is fine. Let’s call this the “input”. And its immediate output is mRNA. That then forms the input to the next stage. 2. Again, you seem to be equivocating with “chain”. But I agree that the output from the system is a sequence of amino acids that we call a polypeptide. Let’s call this the “output”. 3. You say that the input is connected only to the output by means of a “protocol”. And that this means that there is a break in the “causal chain” OK, and this is where I fundamentally disagree. Your point seems to be that the input (mRNA) and the output (polypeptide) “do not interact”. I assume you mean that they do not chemically interact. This true. But this is trivial. What we have here is a catalyst – a compound (or series of compounds) that facilitate a chemical reaction (the bonding of amino acid to amino acid without themselves taking part in the reaction. Yes, a ribosome is a very complex catalyst, but essentially that is what it is. And we do not normally consider that a catalysed reaction is necessarily “designed”. If I recall my inorganic chemistry correctly, rust itself catalyses the oxidation of iron, which is why it’s important not to let rust get a hold on your car, because once it gets started, it will accelerate. Indeed, you can even get a stainless steel knife to rust if you put it in contact with a rusty carbon steel one (as I have found to my cost). And we certainly do not claim that there is a “break in the causal chain”. Indeed, when I found my damaged stainless steel knife, I immediately realised that the cause of its rust was the catalytic effect of the rust on the carbon steel one.
My challenge to you is to rewrite this paragraph in such a way that it is clear to me that it is not circular. I am not saying that it is – there may be something important that I am missing. But to me, you seem to be saying that my simulation must involve a pairing of symbol with meaning (cf DNA sequence with amino acid) that does not arise from either Chance or Necessity, which seems to me to be the same as saying, “that is not causal”.
No, that is not what I am saying, at all. In fact, this probably goes to the “problem statement” that you were flirting with earlier in the conversation. What I am saying is that the cause of this very well-recorded fact is the input of design, and you say it can be created by chance and necessity. This is the very purpose of the simulation – to show that the claim of design is not necessary, and that chance and law alone can establish these relationships.
What “very well-recorded fact”? You haven’t clarified the circularity all! What I need (see above) is a definition of “symbol” that is independent of its cause. Because if you define a symbol by a certain chain of causation, and that chain of causation includes the very thing I am seeking to exclude, then obviously, my task is impossible! However, you now (see above) seem to have included in your category “symbol” any chemical catalyst – any compound that facilitates a chemical reaction without actually taking part in it (or at least remaining unchanged at the end of the reaction. That’s fine, but is that really what you mean?
The sequences of nucleotides in DNA, and the order of amino acids in proteins, are two discrete objects. They are separated by both space and direct interaction. They are bridged by transcription and translation machinery which includes a physical object which converts one sequence into the other while they remain separate. It responds to the representation at the input, and transfers that representation to a second sequence which is entirely disassociated from the first. This fulfills the operational definition you put forth. And it does so by coding for the objects within the system which make it all work. As I said before, this is NOT (of course) where your simulation must start. But it does have to end up here; because that’s the way we found it.
OK, let’s see if I can produce a phoenix from these ashes. Proposed operationalisation of my claim: That, starting from a population of non-self-replicators, and using only a set of rules governing their interaction and stochastic processes governing their movement, a set of self-replicators can emerge that incorporate patterned sequences (S) that directly initiate processes that result in products (P) that increases the probability that the S itself, and the whole of which it is a part, will be replicated with a fidelity of x%, and that moreover, this process will involve catalysis by intermediate products that form neither part of P nor part of S. Howzat? Not sure I can pull off that last part, but it would be sort of cool if I could. Elizabeth Liddle

Thank you as well Dr Liddle, I look forward to your response. Upright BiPed

Thanks, Upright BiPed! Really gottagoto work now, but will try to respond this evening. Cheers Lizzie Elizabeth Liddle

Dr Liddle,
Well, we certainly agree that in order to demonstrate my claim I need an operational definition of information, and that, clearly will have requirements.
Yes, and as the result of a long conversation about various observations, there seemed to be a fair amount of agreement. You yourself provided two thirds of the following working definition. Information is a representation of a discrete object/thing embedded in an arrangement of matter or energy, where the object/thing represented is entirely dissociated from the representation, but where the association of the two can be established by means of a protocol instantiated in the receiver of the information. At which point the conversation generally turned more to the topic of what specific observations we might like to see in order to verify the claim. Which I think is where we are now; I have given you my thoughts and you have responded to them. We are attempting to simulate the rise of information in the genome, and the central question at this point is “how will we know it’s there?” To me, it seems like the shortest path to that answer would be the least subject to error, and in fact, it’s already been proven to be entirely reliable. The question to be answered is “how did we find it in the genome in the first place?” This has been the whole point of making these observations, exactly for the purpose of finding it again in your simulation. Researchers witnessed a mapping (a relation) between two discrete things: the patterns within nucleic sequences and specific actions taken in the assembly of amino acids into proteins. This process passed through the transcription of an initial sequence into a second medium, and then that second medium was transported elsewhere to be decoded by the use of protocols, and onward to the end result. It was also observed that there are no bonds associated within the sequence itself which would determine the order of nucleotides. It was observed that the constituents of the sequence did not directly interact with the resulting protein chain; the sequence in the parent chain is a discrete object. We manipulated the system at the input, and then observed the end result, thereby decoding the protocols. Those protocols were found to be the physical bridge across the two causal chains - were the information is inserted and the output is constrained by it - and they themselves are a product of that constraint. The information paradigm, even in its infancy, has since become the centerpiece of biological understanding. The method to observe the presence of information is therefore already known to us. Your simulation won’t be biological, but the dynamics of information must still be present.
However, if it turns out that your requirements (your operational definition) goes well beyond the conceptual definition I had in mind, I may have to retract.
Well as far as the operational definition goes, we seem to have some general agreement. It doesn’t seem that understanding the observations (those that shaped the definition) presents any difficulty for you, as well it shouldn’t. The problem lies in simulating the dynamic structure required for it to exist and come into being – without having it there, and only by chance and necessity from your initial conditions. As far as what conceptions you had about information, and the claims you make about it, I can only recount what you’ve said: In an ongoing conversation on June 2nd, you made a comment about gene duplication:
I simply do not accept the tenet that replication with modification + natural selection cannot introduce “new information” into the genome. It demonstrably can, IMO, on any definition of information I am aware of.
I took mild exception to that remark, for no other reason than it rest on a flawed understanding of what information is. Materialist come here all the time to beat the evolution drum, as if they are faithfully defending their theory against ID. They seem to think that ID somehow denies change-over-time, or violates observed facts. They seem to think that by constantly recounting the already-observed regularities in biology, this will be detrimental to the case for design. It isn’t, because it’s conceptually misdirected by misrepresentations. And as always, it’s the fact that the system even exist at all that is most taken for granted. In other words, the conclusion against design is simply assumed to be true. So I replied:
”It demonstrably can, IMO, on any definition of information I am aware of.”
Neo-Darwinism doesn’t have a mechanism to bring information into existence in the first place. To speak freely of what it can do with information once it exist, is to ignore the 600lbs assumption in the room.
To which you replied:
Well, tell me what definition of information you are using, and I’ll see if I can demonstrate that it can
That is how we arrived where we are. - - - - - - - - - - - - - - - As for recanting, I have no desire whatsoever for you to recant. Well, that is not entirely true, I very much think you should recant your comment that ”IDists have failed to demonstrate that what they consider the signature of intentional design is not also the signature of Darwinian evolutionary processes”. That accusation is demonstrably without merit at this point, even if you thought it had merit when you made it. You yourself have demonstrated why this is so. You’ve set yourself up to defend a position which quite literally flies in the face of the fact that you’re trying to design a simulation to refute what you say doesn’t exist. Quit frankly, I shouldn’t even have to ask you to recant, but you’ve made your position clear. As far as the simulation itself, I have no desire for you to quit.
Yes, except that I need to know a little more about what you would regard as the minimum for the “symbolic” requirement. This is not part Dembski’s definition, and, as I think I said, when I made the claim, I was thinking in those terms.
Firstly, I think we should be clear about this now. The requirement for a symbolic relationship between discrete objects is not my requirement. I have nothing to do with it. It’s an observation coming directly from the evidence itself. It’s how we discovered the genetic code in the first place. Modern biology is based upon it. Secondly, Dr. Dembski’s definition of information was never on your list of points. If you will recall, you spent a great deal of time repeating your need for my operational definition of information, not anyone else’s. I then gave it to you by going through the observations so that we might agree to them, which we did. It is those observations, and their entailments, which will allow us to verify your claim.
The second structural item has to do with a necessity that the output of information transfer must be dynamic, based upon the input of that information. If the output is not dynamically driven by the representations being given at the input, then the input cannot be seen as informative to the output.
I’d like that unpacked with some ferinstances if possible
The receiver of the information must be able to access discrete protocols it in order for the information to have an effect. (example; GGC= glysine, CCA= proline) It’s part of the operational definition.
Thirdly, to facilitate this dynamic property, there must be a necessary break in the causal chain. This break is exemplified within the cell by the simple fact that proteins are not created from nucleotides. In other words, if you plucked the ribosome from the cell’s protein synthesis machinery, and put yourself in its place, in one direction you would see sequences of nucleotides coming in for translation, and in the other direction you would see sequenced amino acids floating off into the distance to be folded into proteins. One of these marks the input of information (representations instantiated in matter) and the other is the output (a process being dynamically altered by the input). But these are two entirely separate causal chains (if I may use that word).
Ah. A problem. No, I cannot incorporate a “necessary break in the causal chain”! To insist I do so is to make the criteria for my success the refutation of my claim! … I am essentially saying “a miracle occurs here” which is precisely what I am claiming to demonstrate need not occur!
Again, it is not at my insistence that the entailment be simulated, it’s a requirement coming from the evidence itself – but there is no miracle there. The tRNA – a physical object subject to physical law – is the protocol that (by its physical configuration) allows the information to be transferred into the output, and thereby constraining it. If there is an unbroken line between the information and its final effect, then no discrete representation could exist, and no protocol either. Neither would even be necessary. This would violate your own operational definition, as well as the dynamic structure that the definition entails. Your simulation would be a failure by virtue of not demonstrating two of the observed and confirmed requirements of information; representations and their protocols. The transfer of information would be out the window as well. It would be a mere chemical reaction with a probability of 1, none of which has any supporting observations whatsoever in the phenomena you are attempting to simulate. To simulate the rise of information without being obligated to demonstrate the very nature of information is obviously unacceptable; it’s not a simulation of information. If you are not going to accept that obligation, then what is the justification for proceeding? Again, I genuinely hope that you do proceed, and I fully understand the conceptual problem you face by way of the evidence (welcome to a refutation of your comment above). But it would be useless to intend from the start to not demonstrate the very observations that must be demonstrated.
The first causal chain is the sequence of representations, which I say is the product of design, and you contend is the result of chance/necessity. It is made up of nucleic acids. The second causal chain is the bonding within the resulting polypeptide. It is made up of amino acids. The amino acids and the nucleic acids do not interact. They are connected at this dynamic break only by the protocol itself, which I say is the product of design, and you say is the result of chance/necessity. Regardless of who is correct, this dynamic break in the causal chain must be represented in the simulation.
My challenge to you is to rewrite this paragraph in such a way that it is clear to me that it is not circular. I am not saying that it is – there may be something important that I am missing. But to me, you seem to be saying that my simulation must involve a pairing of symbol with meaning (cf DNA sequence with amino acid) that does not arise from either Chance or Necessity, which seems to me to be the same as saying, “that is not causal”.
No, that is not what I am saying, at all. In fact, this probably goes to the “problem statement” that you were flirting with earlier in the conversation. What I am saying is that the cause of this very well-recorded fact is the input of design, and you say it can be created by chance and necessity. This is the very purpose of the simulation – to show that the claim of design is not necessary, and that chance and law alone can establish these relationships. The sequences of nucleotides in DNA, and the order of amino acids in proteins, are two discrete objects. They are separated by both space and direct interaction. They are bridged by transcription and translation machinery which includes a physical object which converts one sequence into the other while they remain separate. It responds to the representation at the input, and transfers that representation to a second sequence which is entirely disassociated from the first. This fulfills the operational definition you put forth. And it does so by coding for the objects within the system which make it all work. As I said before, this is NOT (of course) where your simulation must start. But it does have to end up here; because that’s the way we found it. Upright BiPed

Mung:
Elizabeth Liddle:
I am completely convinced by substantial evidence (including my own work!) that self-replication with variance in a fitness landscape results in entities with the appearance of well-engineered design!
You keep talking about reams and reams of evidence. Please, show it so us. Just one.
I already have. GAs. Ask DrBot - if you set up self-replication with variance in a fitness landscape, you end up with virtual organisms that do a job with great efficiency, often using tricks that the person who set up the GA hadn't even thought of. DrBot had a good example. Sometimes it takes a while for the people who set up the GA even to work out how the solution actually works! And often the code (if code is what is evolving) is exceptionally efficient. Now I know you have raised objections to this example, but I think your objections are ill-founded, as I have tried to explain. So we may have to continue to differ on that. But from my own PoV, the principle is extremely well established, to the extent that if I want to solve a difficult problem (a pattern classification problem for instance) I figure out some learning algorithm (i.e. one based on Darwinian principles) to figure it out, rather than do it myself. That's a pretty good example, actually, as pattern classifiers are an important aspect of biological vision.
But first. Where did the replicator and fitness landscape come from?
The fitness landscape is dead easy. It's the environment. The replicator is of course more tricky, and, as of writing, remains unsolved. However, what I was quite excited about doing was devising a simulation in which a self-replicator would emerge from non-self-replicators. I'm hoping still to have a shot at that. It might even be publishable if I succeed :)
IOW, don’t we have the appearance of well-engineered design before we had those things you assert are capable of generating the appearance of well-engineered design?
Well, the very simplest self-replicators can be pretty crude. It's getting in the variance that's the tricky part - variance in self-replication efficiency. Elizabeth Liddle

Mung:
Are you serious? A footprint in cement is information? To whom?
To someone looking at it.
You need to explain the arrival of information prior to the presence of any mind to pronounce meaning.
Not if what I am trying to do is determine the depth of symbolism in the medium in which the message is encoded, which I was. I wasn't discussing sender or receiver, but the format of the message. Context is important.
Please, come up with a better example than one that requires a mind to assign the meaning.
Upright BiPed have already agreed that no mind is require to assign the meaning. That is not at issue. Elizabeth Liddle

Elizabeth Liddle:
I am completely convinced by substantial evidence (including my own work!) that self-replication with variance in a fitness landscape results in entities with the appearance of well-engineered design!
You keep talking about reams and reams of evidence. Please, show it so us. Just one. But first. Where did the replicator and fitness landscape come from? IOW, don't we have the appearance of well-engineered design before we had those things you assert are capable of generating the appearance of well-engineered design? Mung

Elizabeth Liddle:
Let say that a footprint is recorded in a wet cement pavement. In a sense that footprint is information (it has meaning – it informs us that someone stepped in the cement while it was wet).
Are you serious? A footprint in cement is information? To whom? You need to explain the arrival of information prior to the presence of any mind to pronounce meaning. Please, come up with a better example than one that requires a mind to assign the meaning. Mung

Hello Dr LIddle, Sorry for the delay by not being able to respond yesterday. I will post my repsonse later today. Upright BiPed

Good Afternoon Lizzie, Remember when you said that there was no “prejudice against a Creator God” at play when people reject Intelligent Design theory? I think your last response to me shows numerous examples of such a prejudice. In other words, design detection is perfectly rational, intuitive and empirically sound, unless the Designer in question might be the Creator. While you concede that you no longer need to know the identity of the Designer, you still insist that we must postulate a specific kind of Designer. Why? Your next step is to postulate “an omnipotent God who could do anything s/he felt like at any time”. Again, why? Such a step is extremely illogical: it doesn’t follow from your previous step. It is also unscientific: what does science even have to say about things that possess omnipotence? Such muddled thinking is a clear sign that you are approaching Intelligent Design theory with a prejudice against any Designer who might be the Creator. You also claim that it is unlikely that the Designer “was able to transfer solutions from one lineage to another” and that the Designer “preferred retrofitting to “going back to the drawing board” where possible”. Again, these are prejudicial comments given that all we are trying to do is establish whether or not actual Design has taken place. It’s almost as if you’re saying: “Well, the Designer is not capable of transferring solutions from one lineage to another and prefers retrofitting. If I was the Designer, that’s not how I would do it. So there can’t possibly be a Designer: it must have all made itself!” At one point, you even suggested that we have to know that the Designer(s) “lived around these parts” before entertaining the possibility that something didn’t make itself. Why would you insist on such an odd requirement if you are not bringing prejudicial baggage to the table (ie. there is no Creator around these parts so don’t even go there with the cell)? No doubt your opponents bring their own prejudices to the debate, Lizzie: Biblical Literalists being an extreme (and rare) example. But most of us put science ahead of those prejudices. Most of us can take or leave evolution, for example. You’ve got theistic evolutionists on one end of the scale and then creationists on the other. Personally, I don’t see any scientific evidence whatsoever to support the belief that a single-celled common ancestor evolved into human beings. I don’t even accept common ancestry. Again, this is on purely scientific grounds. If the evidence led to evolutionist explanations then I’d simply become a theistic evolutionist. Even front-loaded deism would be relatively easy to accommodate (including the implications for abiogenesis). But atheists have got no room for manoeuvre. They can’t take or leave a Designer that might be the Creator. The universe and everything in it MUST have made itself, through purely naturalistic processes or else their entire worldview collapses and it really is back to the drawing board. I put it to you, Lizzie, that you are placing your worldview, and therefore prejudices against a Designer who might be the Creator, ahead of what are otherwise plainly obvious and entirely straightforward means of Design detection in the cell. You’ve already conceded that you’ve got absolutely no idea where the first self-replicator came from. As I’ve already pointed out: things that self-replicate are more difficult to explain than the same things that don’t self-replicate. It is impossible that non self-replicating artifacts such as Stonehenge or the Sphinx made themselves. Crazy appeals to science fiction aside, it is all the more impossible that a self-replicating version of these things made themselves! It is not their inability to self-replicate that leads you to the certain and immediate conviction of design. Throwing self-replication into the mix only strengthens that conviction. And the cell is vastly more functional, sophisticated and complicated than Stonehenge and the Sphinx even before it self-replicates… However, you “consider the evidence overwhelming, as well as supported by elementary logic, that things that reproduce themselves with variance tend to end up evolving into ever-more-efficient self-reproducing things”. Surely, then, you can briefly summarise an important part of this ‘elementary logic’ as well as briefly identifying some of this ‘overwhelming’ evidence because most of us just don’t see it. Just remember, artificial selection is much more powerful than natural selection. As kairosfocus pointed out back in May: “[Natural] selection, contrary to popular opinion, is not a source of information, but patently a culler — a remover — of information. The variants that do not find niches do not survive to pass on genes. That which subtracts does not add. We have to look at that which supposedly adds, before we can see how subtraction may lead to survivors. By repeating the mantra “natural selection” one does not escape the need for engines of variation, and for specifically non-foresighted engines of variation, for darwinian type evolution.” Artificial selection offers more than Natural Selection, but it is still limited to mere sub-specific variety: something that has been happening to all extant species for their entire known existence without any significant alteration whatsoever. Just offering evidence of sub-specific variety would therefore be completely underwhelming because any increased efficiency it generates is merely a product of a pre-existing gene pool. Chris Doyle

Hi Chris! No apology required for persisting, Chris, it's a good thing not a bad, IMO :)
Sorry to persist, Lizzie, but you definitely are getting “way ahead of yourself”! We identified the same problem over on the “extraterrestrials-could-have-started-life-on-earth” thread: You won’t even consider the possibility of murder until I give you the identity and motive of the murderer so natural causes MUST be the explanation no matter what I say! In the real world, we do not require the identity and motive of the murderer in order to establish that murder has taken place.
That is true. But it does not contradict my point. We do not have to know the identity of the axehead maker to infer that the axehead was made by an axehead maker. But we do have to know that axehead makers lived around these parts, in order to draw the conclusion with any degree of confidence. That was my point.
The same applies in many other fields of knowledge, including archaeology and biochemistry. Instead of dealing with at least one of the three examples I listed, you decided to bring up dodgy axeheads (made out of straw, not rock). I repeat, you do not need to know anything whatsoever about the Designer(s) of Stonehenge, the Sphinx or the Easter Island statues to know that these things did NOT make themselves: they must have been made.
I agree. And I specifically addressed the Stonehenge example.
This is all the more true of the cell.
Well, no, because in the case of the cell we have something very different, which is a self-replicator! And we know that self-replicators have certain pertinent properties. At least it is my claim that they do.
I strongly deny “the undeniable fact that unlike most human artefacts, living things reproduce themselves with variance, and we know that things that reproduce themselves with variance tend to end up evolving into ever-more-efficient self-reproducing things.”
Right. :)
This is 100% wishful thinking and 0% fact. It is also highly misleading: if Stonehenge or the Sphinx reproduced themselves tomorrow we wouldn’t all of a sudden conclude “oh well, they weren’t made after all, they must have just made themselves.” No, creating something that has the ability to reproduce itself is vastly more difficult than creating something that lacks this ability.
Yes, we might well do precisely that. Well, I mean obviously this is a fantastical example, but if we were in some sci fi movie perhaps, to observe the stones moving around and reproducing, and their seeds flying off and burrowing into some green plain elsewhere, leaving no surface trace, we might well think: "aha! Perhaps this is why we have found no answer to how the stones were erected! They are not stones at all! They are self-reproducing organisms! And we have witnessed a rare event - the self-seeding of a new stone circle - an Avebury for the future!" So no, it's not 100% wishful thinking at all. I am completely convinced by substantial evidence (including my own work!) that self-replication with variance in a fitness landscape results in entities with the appearance of well-engineered design! But I do accept that you are not :)
Confusingly, you’ve used the term ‘know’ in the “undeniable” statement above when surely what you meant was ‘must believe’: “…and we must believe that things that reproduce themselves with variance tend to end up evolving into ever-more-efficient self-reproducing things.”
Fair enough. But I tend to consider that things I've seen with my own eyes are probably true! However, both illusions and delusions are possible, as I should know. I'll rephrase: I consider the evidence overwhelming, as well as supported by elementary logic, that things that reproduce themselves with variance tend to end up evolving into ever-more-efficient self-reproducing things". Better?
If we correct the statement in that way, I can understand your position as it is now less unrealistic. In the absence of an empirical basis, belief in this is necessary because without it, neo-darwinism fails. By the way, evidence for sub-specific variety doesn’t count (just in case you were going to bring up peppered moths, finches or e-coli again).
The first two do count! - e-coli, not so much, as e-coli don't speciate, whereas finches may, and indeed do. I simply dispute that this inference has no "empirical basis". It has as much, if not more, empirical basis than much science we simply take for granted. Remember that we don't do "proof" in science - we fit models to data. The evolutionary model fits the data extremely well.
As for misunderstanding the Null Hypothesis, it seems like you’ve identified a misunderstanding that is shared by all atheistic evolutionists. ID opponents have criticised ID proponents precisely for articulating the null, then rejecting it (apparently, that approach is too negative)!
No, it isn't too negative at all. The reason I think ID proponents are wrong is not because they articulate non-Design as the null (that's the best way of doing it) but because their rejection criteria are incorrect.
Furthermore, we could substitute “Stonehenge” for “the cell” and quickly discover that the vast majority of atheists do not proceed on that basis.
Not sure what you mean.
“So if you wanted to demonstrate that Stonehenge was NOT designed, your null would have to be:Stonehenge was designed.”
So if you wanted to demonstrate the the cell was NOT designed, you null would have to be: the cell was designed.
Yes. But to do that you'd have to postulate a specific kind of Designer. If the postulated designer was an omnipotent God who could do anything s/he felt like at any time, it wouldn't work, because the null would cover every possible and every impossible observation. That's why proving that the cell was not designed is not actually feasible. The best we can do is show that we have a good model of the emergence and evolution of the cell that is compatible with non-design. Then you either use a Bayesian approach, or Occam's Razor to decide which alternative you prefer. However, we can demonstrate that living things were not likely to be designed by any entity that was able to transfer solutions from one lineage to another, as human designers do, and, if they were designed, were designed by someone who preferred retrofitting to "going back to the drawing board" where possible. This pattern of design fits will with Darwin's theory, but is rather unlike the pattern of human design lineages. Elizabeth Liddle

Upright BiPed: Responding to your response to my belated response to you, aware that it may now be out of date (that’s why I responded to your other post first).
Dr Liddle, Below is my response to your post at 46. I hesitate to post it yet, given that I don’t want to cover up your response to my post at 50. - – - – - – - – - – -
My own view – or perhaps “hunch”- is that the reason that IDsts regard evolutionary scientists as missing a Glaringly Obvious Fact (and therefore assume at best stupidity and/or ignorance, and at worst deliberate dishonesty) while conversely evolutionary scientists regard IDists as Completely Missing The Point (and therefore assume ditto) is not because they disagree on some level at which the disagreement can be resolved in favour of one or other to the satisfaction of both, but because they have very different “problem statements”.
I’m not interested in political statements at this juncture. If your point is that people who are competing with ideas argue about them, then thanks for pointing that out, but it’s irrelevant to the content of the conversation we were having.
No, that’s not my point. My point is that you can’t even start to argue constructively until you have a shared problem statement. That’s what I’m trying to get to.
Unfortunately, the converse is probably true as well – that we don’t manage to agree on the problem statement, or, worse (for me!) we appear to agree with it, and I produce a demonstration that I think supports my view, and then we find that actually we didn’t actually agree in the first place!
You have my apologies if you cannot tell it, but I am trying to be clear and descriptive of the observations. When I say something and you reply “Yes!” or “Right!” or “Cool, I like it” then I assume you understand what I am saying. If you make that same reply several times in a row to several interrelated comments, then I assume you understand a whole class of interrelated comments. Beyond that, I have asked you for a reasonable preliminary overview of how you plan to integrate the observations we’ve agreed upon into your simulation. I think it’s reasonable to expect at some point that overview might include such words are “representation” and “protocol” and the like – given that is what the conversation is about. Conversely, it would seem odd to acknowledge the observations of a phenomenon on the front side, then to attempt a simulation of that phenomenon without addressing those observations.
Well, I do understand that you are trying to be clear and descriptive, and yes, when I say I like something, it does mean that I think I understand it – and that I agree with it! However, it is no guarantee that I understand it, because words are tricksy things. , “Protocol” I was interpreting as a set of procedures that are initiated in response to incoming information, for instance, the assembly of a protein from the information arriving in the form of messenger RNA from the DNA. I’m fairly clear about that I think. “Representation” however, opens a potential can of worms, but I’ve already flagged that up.
For that we needed an operational definition of both “information” and “Darwinian processes”. For the latter, I have operationalized “Darwinian processes “ as comprising of no more than Chance and Necessity. I haven’t done this formally, but I’ll do so now: “Chance” processes will be generated by a random number generator with a flat distribution, and will govern the movement of elements in my model, in a manner analogous to Brownian Motion. “Necessity” processes will govern the conditions under which the basic elements of my model bind and/or repel each other. These will be laid out at the start, and will not be changed during the running of the model – the “chemistry” of the system.
No problem.
Excellent!
Meyer’s account of Shannon information is … … So it seems that Shannon information supplies us with… …and is what Dembski calls… … Dembski, talks about … … But Meyer talks about…
Again, these things may be interesting on their own merit, but they have nothing to do with the conversation we have been having. These concepts were not required by Nirenberg, and they aren’t a requirement for us.
Nirenberg? OK, well, now I know we aren’t talking about Shannon information, or Dembski information or Meyer information, but Nirenberg! But my original claim was about those first things, because I, obviously naively as it turns out, assumed that on Dembski’s own site, that was probably what people regarded as information! But OK.
Two things were missing …
I have not seen this exchange between you and KF – but to my understanding of them, I agree with both points. To my mind, they speak to the same structural problem. If such a structure somehow existed in the genome, we would have never discovered the genetic code. There would have been no observations in which to discern it as we did. At the same time, we are not looking for a new way in which information can exist; we are looking for it as it does exist.
In my original plan, I was not going to attempt …
When recorded information is transferred from a medium it goes through protocol to its e. See my comment #50
Not sure which comment you mean. Nor what this means. Let say that a footprint is recorded in a wet cement pavement. In a sense that footprint is information (it has meaning – it informs us that someone stepped in the cement while it was wet). If we then drop a load of latex on the pavement, and let it set, we can then use that latex mould to make a replica of the original pavement. We can, in other words, transfer the information to a new piece of cement, using the medium of the latex. But I think you would, rightly, say that this medium was not “symbolic”, even though there is a clear “protocol” for the transfer of information (pouring the latex, taking it elsewhere, using it as cement shuttering). But let’s say the footprints were those of a great dancer, and the purpose of making replicas was to help train new dancers in the same style, by showing them how to place their feet. Now that information is being translated into something quite different – a dance. We still don’t have a true symbol though, more what Saussure (Saussure? My semiotics is rusty, it might have been Peirce) called an index - a pointer. So let’s say that instead, a choreographer interprets the footprints and notates them. Now (if I recall my memories of a choreologist friend!) we have an iconic representation of the original dance – signifiers derived from the way the original looks. Finally, we might simply describe the footprints in words – true symbols, and transmit the dance steps that way to the dancer. So there are layers and layers of abstraction between a direct template or mould, to a fully symbolic system. In my view tRNA is not much more than a template. But I’d like to know just how remote the information format has to be from the transmission medium format for it to qualify as a symbolic representation.
This is what I meant when I said DNA is not “inert” – its state at the beginning and end of the process is unchanged, but it undergoes a state change during the process.
We can talk about the backbone of DNA if you wish; it’s an extremely rare object that allows any of the four nucleotides to occupy any position along its length without influencing their order. But as interesting as it is, the sequence of nucleotides seems more interesting, given that it is where the information is. And that sequence doesn’t change as an observable effect of being unzipped for transcription.
I entirely agree that the nucleotide sequence does not change. I didn’t mean to imply that it did. I simply meant that as a molecule it actually takes part in the process, and changes state during the process, while reverting to its original state afterward. That’s as long as we regard the DNA molecule as not including the methyl groups periodically bonded to it. If we do, then it most certainly is not inert. Elizabeth Liddle

Sorry to persist, Lizzie, but you definitely are getting “way ahead of yourself”! We identified the same problem over on the “extraterrestrials-could-have-started-life-on-earth” thread: You won’t even consider the possibility of murder until I give you the identity and motive of the murderer so natural causes MUST be the explanation no matter what I say! In the real world, we do not require the identity and motive of the murderer in order to establish that murder has taken place. The same applies in many other fields of knowledge, including archaeology and biochemistry. Instead of dealing with at least one of the three examples I listed, you decided to bring up dodgy axeheads (made out of straw, not rock). I repeat, you do not need to know anything whatsoever about the Designer(s) of Stonehenge, the Sphinx or the Easter Island statues to know that these things did NOT make themselves: they must have been made. This is all the more true of the cell. I strongly deny “the undeniable fact that unlike most human artefacts, living things reproduce themselves with variance, and we know that things that reproduce themselves with variance tend to end up evolving into ever-more-efficient self-reproducing things.” This is 100% wishful thinking and 0% fact. It is also highly misleading: if Stonehenge or the Sphinx reproduced themselves tomorrow we wouldn’t all of a sudden conclude “oh well, they weren’t made after all, they must have just made themselves.” No, creating something that has the ability to reproduce itself is vastly more difficult than creating something that lacks this ability. Confusingly, you’ve used the term ‘know’ in the "undeniable" statement above when surely what you meant was ‘must believe’: "...and we must believe that things that reproduce themselves with variance tend to end up evolving into ever-more-efficient self-reproducing things." If we correct the statement in that way, I can understand your position as it is now less unrealistic. In the absence of an empirical basis, belief in this is necessary because without it, neo-darwinism fails. By the way, evidence for sub-specific variety doesn’t count (just in case you were going to bring up peppered moths, finches or e-coli again). As for misunderstanding the Null Hypothesis, it seems like you’ve identified a misunderstanding that is shared by all atheistic evolutionists. ID opponents have criticised ID proponents precisely for articulating the null, then rejecting it (apparently, that approach is too negative)! Furthermore, we could substitute “Stonehenge” for “the cell” and quickly discover that the vast majority of atheists do not proceed on that basis. “So if you wanted to demonstrate that Stonehenge was NOT designed, your null would have to be:Stonehenge was designed.” So if you wanted to demonstrate the the cell was NOT designed, you null would have to be: the cell was designed. Wouldn’t that be refreshing? Chris Doyle

Dr Liddle, I have just read your response. I thank you for it, and will respond later today. Upright BiPed

Chris: Chris:
Morning Lizzie, There is a big problem with this statement that you made: “A-theism is surely the default in the absense of evidence for a theos? I mean, I know you disagree about evidence, but the burden of proof is usually to those making the claim for the existence of something, rather than on those who do not accept the claim.” I think identifying this problem gets us closer to the question that we need to answer: if the basis for the atheistic worldview is neither rational, nor empirical, then what is it? You get way ahead of yourself Lizzie when you get preoccupied with questions about HOW Intelligent Design was implemented and by WHO. Front-loading, tinkering, aliens, the Creator: all interesting technical details but utterly irrelevant until you admit that Intelligent Design is the best, and only, scientific explanation for existence. After all, we are in complete agreement that everywhere we look and anything we look at is giving us the overwhelming impression of design. The only disagreement lies in the fact that atheists and evolutionists claim that this appearance of design is not real, it is only an illusion.
Well, I disagree, Chris, that I get “way ahead of myself”. That would only be true if it were true that we can distinguish, without a shadow of a doubt, between natural phenomena and artefacts, without any knowledge of the characteristics of likely designers. Archaeologists often struggle to distinguish between axe-heads and naturally chipped stones, and the way they do so is not only by exhaustive examination of the object in question, but also by using other information such as the proximity of known camps; known styles of axehead; the technology known to be contemporaneous with the object etc. In other words, it’s an iterative process of hypothesis testing, and very substantially Bayesian: given two identical candidate axe heads, one found in a region known to be inhabited by axehead makers and the other on Mars, the reason we would infer that the first was probably designed, and the second probably wasn’t is by computing the conjoint probability that it’s an axehead based on its morphology and the probability based on the likelihood of an axehead Designer at that time in that location (namely 1-(1-p(axehead morphology)*1-p(axehead designer)).
Yet, atheists only ever employ this rather absurd line of argument when it comes to one thing: the Creator. In all other walks of life, they wouldn’t entertain it for a minute. Take three examples: 1. Stonehenge 2. The Sphinx 3. Easter Island Atheists never, ever say that the null hypothesis is that these things just made themselves. Atheists never say that the default position is that these things were put together by Chance and Necessity and that the burden of proof is on those who claim that these things required Intelligent Design. Atheists never say that people who reject purely naturalistic explanations for these things are Completely Missing The Point.
Here we come up against (I think) a misunderstanding of the nature of a Null Hypothesis (again!) Yes, “atheists” might present “these things just made themselves” as the null in these examples, because casting that as the null is the best way to test the hypothesis that they did not. And it’s a hypothesis that can be readily rejected. That’s the whole point of articulating the null – so that you have a chance of rejecting it. If you want to demonstrate design, in fact, that’s exactly the null you have to cast, which is exactly what Dembski does in the Explanatory Filter, and in the concept of CSI. You cast as the null, in other words, the hypothesiss you seek to reject. And if you fail to reject it, you are not entitled to conclude the null, merely to “retain it”. Your alternative hypothesis remains undemonstrated, not rejected. So if you wanted to demonstrate that Stonehenge was NOT designed, your null would have to be: Stonehenge was designed. To reject that hypothesis, you’d have to find evidence that a non-design mechanism was unlikely under the null hypothesis that it was designed. Which would be very difficult. In fact, you wouldn’t use null hypothesis testing at all, probably, you’d use some kind of Bayesian method: you’d say (as above) : is a non-design mechanism possible? If so, how probable are the conditions that would make possible? And how does this probability compare with the probability that the conditions existed for stone-age designers to have erected such vast stones? And you’d probably conclude that while a freak set of geological catastrophes just might have left the henge as we find it, they are vanishingly unlikely, while the probability that a stone-age civilisation just might have figured out how to erect the stones is more likely, even though we still have no clue how they did it.
Atheists would be the first to agree that the burden of proof lies COMPLETELY with anyone who claimed that Stonehenge built itself, that the Sphinx carved itself and that the Easter Island statues buried themselves. Atheists would have no doubt that anyone who advanced such absurd claims would have entirely irrational and non-empirical reasons for rejecting that which is plainly obvious. And yet, it is far more probable that Stonehenge made itself than that the cell made itself. It is much more obvious that the cell requires Intelligent Design than Stonehenge. There is no logic, no reason and no evidence to support the belief that Stonehenge made itself and that is even more true of the cell. It seems that atheists only ever reject arguments for Intelligent Design if there is a possibility that the Intelligent Designer might be the Creator (a point previously hammered home by Cannuckian Yankee). So it all comes back to, what is really going on with atheists? Why do they ignore science whenever science points to the Creator? Something emotional or cultural perhaps? If we can identify the true (no doubt, very personal) motivation behind atheism, we need not concern ourselves with trying to define our disagreement in the most acceptable terms: or even quibbling over the meaning of the term “information”.
Well, as I explain above, I think you have a straw man here. “Atheists” (scare quotes because they include lots of non-atheists) do not reject a Designer as the best explanation for the complexity of the cell because of some prejudice against a Creator God, but because there is a plausible alternative (or one they consider plausible) that is more likely. In particular is the undeniable fact that unlike most human artefacts, living things reproduce themselves with variance, and we know that things that reproduce themselves with variance tend to end up evolving into ever-more-efficient self-reproducing things. So we have a candidate mechanism, that makes predictions that are in fact borne out by evidence, some of which are rather different to the predictions made by the hypothesis of an Intentional Designer. In addition, there isn’t much really credible independent evidence for an Interventionist Designer God, whatever the logical arguments might be for a Light-Touch-Paper-And-Retire one, and the hypothesis requires an Interventionist Designer (or, if not, I haven’t seen a convincing one that doesn’t). So people’s priors (in a Bayesian sense) are low, whereas they are considerably higher for a mechanism that we know works in principle, and makes testable differential predictions. We are still stuck, of course, on the problem of how self-replicators emerged from non-self-replicators, but it isn’t as though even there we have some promising candidate explanation that again do not require a high prior for something (an Interventionist Designer God) that doesn’t seem to be much in evidence. As usual, not asking you to agree with me, just trying to explain my position :) Cheers Lizzie Elizabeth Liddle

Dr Liddle, From my previous post to you, I have assumed that we came to some valuable agreements, based upon your responses. For instance we agreed that the presence of information has specific requirements. To my mind, these requirements are the primary agreement needed in demonstrating that information did in fact arise from your simulation. Those requirements consist of the presence of discrete representations, as well as the discrete protocols needed to decode them.
Well, we certainly agree that in order to demonstrate my claim I need an operational definition of information, and that, clearly will have requirements. However, if it turns out that your requirements (your operational definition) goes well beyond the conceptual definition I had in mind, I may have to retract. But I’m not there yet :)
I make the above assumption from the following exchange: BIPED: In retrospect, when I stated that recorded information requires symbols in order to exist, it would have been more correct to say that recorded information requires both symbols and the discrete protocols that actualize them. Without symbols, recorded information cannot exist, and without protocols it cannot be transferred. Yet, we know in the cell that information both exists and is transferred. LIDDLE: Yes. And I like that you refer to “the cell” and not simply “the DNA”. BIPED: This goes to the very heart of the claim that ID makes regarding the necessity of a living agent in the causal chain leading to the origin of biological information. LIDDLE: Let me be clear here: by “living agent”, are you referring to the postulated Intelligent Designer[s]? Or am I misunderstanding you? BIPED: ID views these symbols and their discrete protocols as formal, abstract, and with their origins associated only with the living kingdom (never with the remaining inanimate world). Their very presence reflects a break in the causal chain, where on one side is pure physicality (chance contingency + physical law) and on the other side is formalism (choice contingency + physical law). Your simulation should be an attempt to cause the rise of symbols and their discrete protocols (two of the fundamental requirements of recorded information between a sender and a receiver) from a source of nothing more than chance contingency and physical law. LIDDLE: Cool. I like that. BIPED: And therefore, to be an actual falsification of ID, your simulation would be required to demonstrate that indeed symbols and their discrete protocols came into physical existence by nothing more than chance and physical law. LIDDLE: Right. BIPED: The question immediately becomes “how would we know?” How is the presence of symbols and their discrete protocols observed in order to be able to demonstrate they exist? For this, I suggest we can use life itself as a model, since that is the subject on the table. We could also easily consider any number of human inventions where information (symbols and protocols) are used in an “autonomous” (non-conscious) system. LIDDLE: OK. BIPED: For instance, in a computer (where information is processed) we physically instantiate into the system the protocols that are to be used in decoding the symbols. The same can be said of any number of similar systems. Within these systems (highlighting the very nature of information) we can change the protocols and symbols and the information can (and will) continue to flow. Within the cell, the discrete protocols for decoding the symbols in DNA are physically instantiated in the tRNA and its coworkers. (This of course makes complete sense in a self-replicating system, and leads us to the observed paradox where you need to decode the information in DNA to in order to build the system capable of decoding the information in DNA). LIDDLE: Nicely put. And my intention is to show that it is not a paradox – that a beginning consisting of a unfeasibly improbable assemblage of molecules, brought together by no more than Chance (stochastic processes) and Necessity (physical and chemical properties) can bootstrap itself into a cycle of coding:building:coding:building: etc. BIPED: Given this is the way in which we find symbols and protocols physically instantiated in living systems (allowing for the exchange of information), it would be reasonable to expect to see these same dynamics at work in your simulation. LIDDLE: Yes, I agree. Cool! BIPED: I hope that helps you “get to the heart of what [I] think evolutionary processes can’t do”. LIDDLE: Yes, I think so. That is enormously helpful and just what I was looking for.
Yes, except that I need to know a little more about what you would regard as the minimum for the “symbolic” requirement. This is not part Dembski’s definition, and, as I think I said, when I made the claim, I was thinking in those terms. I’m not saying the symbolic layer is impossible for me, just that it adds a further requirement, and I need to have a clear metric.
- – - – - – - – - – - – - – - With these agreements in hand, it seems that the primary question now on the table is getting your simulation to ascend to the appropriate structure required for the transfer of information. After all, not just any structure will do. Here I am not speaking to the initial conditions of your simulation, but only the end result. Whatever the initial conditions of the simulation I will leave to your expertise, with the only caveat being that the simulation operates in good faith with the claim that chance and natural law are the only causal forces allowed to impact the output (the simulated environment).
Yes, and I will (indeed have) given my operational definitions of those, for your approval. As to that structure, I think it is important to take a full accounting of what is observed in nature. Again, I am not speaking here of your initial conditions (or whatever reaction pathways your simulation may take in the process of leading up to the rise of information) but only speaking of the structure of the final condition once attained. In that regard it seems that we should highlight two or three observations (some we’ve already discussed). The first of those is the presence of certain discrete objects. Here I am, of course, talking about the discrete representations and protocols. Both of these objects should be fully observed as such in your simulation, and I think we’ve discussed them well enough to understand what they are. If there is any ambiguity remaining, then we can certainly discuss them further. Probably worth doing. I’ll describe what I hope will be the end product of my simulation, and check that, if I succeed, that that end product will satisfy your criteria.
The second structural item has to do with a necessity that the output of information transfer must be dynamic, based upon the input of that information. If the output is not dynamically driven by the representations being given at the input, then the input cannot be seen as informative to the output.
I’d like that unpacked with some ferinstances if possible :)
Thirdly, to facilitate this dynamic property, there must be a necessary break in the causal chain. This break is exemplified within the cell by the simple fact that proteins are not created from nucleotides. In other words, if you plucked the ribosome from the cell’s protein synthesis machinery, and put yourself in its place, in one direction you would see sequences of nucleotides coming in for translation, and in the other direction you would see sequenced amino acids floating off into the distance to be folded into proteins. One of these marks the input of information (representations instantiated in matter) and the other is the output (a process being dynamically altered by the input). But these are two entirely separate causal chains (if I may use that word).
Ah. A problem. No, I cannot incorporate a “necessary break in the causal chain”! To insist I do so is to make the criteria for my success the refutation of my claim! By claiming that “Chance and Necessity” can produce information, including symbolic information, I am, of course, saying that there is a direct causal chain between the starting conditions and the final conditions – between the input and the input. If, to quote the old cartoon, I have a “break in the causal chain” I am essentially saying “a miracle occurs here” which is precisely what I am claiming to demonstrate need not occur! This is why I think that if we were ever to get to the stage where it was clear to both of us what my claim is and what your counter-claim is, my demonstration would be unnecessary – either it would be clear that I had made a logical error or that you had. So, let’s persevere. I sort of hope I’m wrong, because the project would be cool, and I might do it anyway :)
The first causal chain is the sequence of representations, which I say is the product of design, and you contend is the result of chance/necessity. It is made up of nucleic acids. The second causal chain is the bonding within the resulting polypeptide. It is made up of amino acids. The amino acids and the nucleic acids do not interact. They are connected at this dynamic break only by the protocol itself, which I say is the product of design, and you say is the result of chance/necessity. Regardless of who is correct, this dynamic break in the causal chain must be represented in the simulation.
My challenge to you is to rewrite this paragraph in such a way that it is clear to me that it is not circular. I am not saying that it is – there may be something important that I am missing. But to me, you seem to be saying that my simulation must involve a pairing of symbol with meaning (cf DNA sequence with amino acid) that does not arise from either Chance or Necessity, which seems to me to be the same as saying, “that is not causal”. That I must Design It In from the start. But obviously I can’t do that, because the whole point of my simulation is that all I’m allowed to input is Chance and Necessity, or my claim will fail. So as it stands right now, if I succeed in setting up a simulation, where the starting conditions are simply a set of physical/chemical laws (Necessity) and random kinetic energy (Chance), and I end up with a mapping of virtual DNA and virtual Amino Acid, you will reject my achievement because there is no “break in the causal chain”. But if I make a break (by Designing In a mapping) then obviously you will reject it also, because I have failed to demonstrate that I can do this solely by Chance and Necessity. Where am I misunderstanding you? Or have you made an error?
Lastly, there is the structural entailment of information always necessarily being ‘about’ something. Therefore, the output (being driven by the input) must serve some identifiable necessary function within the system. In a living system, one of those necessary functions of information is to create the protocol required to make the system work. Given that your simulation is designed to demonstrate the origin of information, it is at least reasonable to think this will be a function of the information within the simulation as well. By doing so, this entailment will be satisfied.
That’s fine. My sim wouldn’t work if there were no functional parts within the system. As you recognise. If I’m going to demonstrate the spontaneous emergence of a self-replicator from non-self-replicating starting conditions (and that was my original intention) then by definition I’m going to need functional parts. It was my original anticipation that this would, by definition, fulfil my claim (that not only could information be generated by self-replicators-with-variance, but that the original self-replicators could emerge from a non-self-replicating “soup”). Getting some kind of symbolic layer in there will be trickier (an equivalent to tRNA), although not, IMO, impossible, though I’d rather do it as a separate sim. But it will be impossible if that bit has to involve a “break in the causal chain”! I willingly concede that only a Designer can produce a function that can only be produced by a Designer :)
So, in order to fully demonstrate the rise of information, this is the structure your simulation must ultimately assume. And as you will note, none of these have anything whatsoever to do with measuring or quantifying information (either by ‘this person’s metric’ or ‘that person’s theory’). The question is simply “Is information present?” To answer that question, these are the observable entailments that would indicate that it is.
Well, it looks we have at least one major wrinkle to sort out first. And even if we do, I’m not sure I can demonstrate that Chance and Necessity can produce information by your definition (though I would certainly claim that it can produce information as defined by Dembski, the complex specified kind). I can see how it could (as long as we iron out that wrinkle) I’m just not sure I can simulate it. Still, if I bring off the first part, maybe someone else can take on the second. Elizabeth Liddle

Nullasalus:
I mean, I know you disagree about evidence, but the burden of proof is usually to those making the claim for the existence of something, rather than on those who do not accept the claim.
No, the burden of proof is ‘usually to those’ making a claim, period. ‘There is no God’ is a claim. ‘Naturalism is true’ is a claim. ‘Theism is false’ is a claim.
Oh, indeed. I would agree. But most atheists do not claim "there is no god" nor that "naturalism is true" nor that "theism is false", merely that there is no good reason to assume these statements are untrue.
And just who has what ‘burden of proof’ isn’t made clear to begin with. The Maverick Philosopher had a good mini-series on this. But you are right, “atheism” is not verified. It’s very hard to verify a null. So? “Gosh, it’s hard to verify the atheism!” So… What, then we just treat atheism with kid gloves then? There’s no good evidence for the position, there’s no proof of it, but that’s okay, let’s go easy on them?
No, not at all. You can go as hard on them as you like. But if you want to rebut the position that there is no good reason to posit God, then you need to provide a good reason.
No. I would think that ‘it’s very hard to verify this position’ would, at the very least, suggest someone should be hesitant before committing to it.
Sure. Elizabeth Liddle

Mung:
Hi Elizabeth, According to latest theory, what is a representation? What part does representation play in information processing? Have you heard of David Marr? c.f. http://mitpress.mit.edu/catalo.....8;tid=3958
Yes indeed. But do you know about the concept of active vision? http://ukcatalogue.oup.com/product/9780198524793.do It's even better :) Elizabeth Liddle

Also had omitted to bookmark this thread. Have it bookmarked now. Elizabeth Liddle

Upright Biped:
Dr Liddle, I see that you have made a response at 46. I will catch up and read it later.
Thanks for your responses, which I have just located. Will have to respond later. Elizabeth Liddle

Hi Elizabeth, According to latest theory, what is a representation? What part does representation play in information processing? Have you heard of David Marr? c.f. http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid=3958 Mung

Mung at 55: It’s a Southwest influence.
lol. I actually read about that when looking it up. Mung

If the sim is supposed to model an organic environment, then a proper energy variable must incorporated. If the necessary high energy value is set, then so should proper decay rates. junkdnaforlife

Mung at 55: It’s a Southwest influence. Mung at 57: Thanks, and correct. Hence - the observed break in the causal chain; the point of transfer where information is introduced and the output is constrained. Dr Liddle says from natural law she can recreate that point, and that those observations (which allowed us to discover it in the first place} will be there to verify her success. I say its very existence is a physical artifact of design. Information injected into the causal chain (natural law) in order to cause something to happen. In time we may see who is right, but I find it interesting; she states that ID proponents have failed to make their case, yet she has had to assume the responsibility of designing a simulation in order to refute the very thing she says doesn’t exist. In light of this fact, it seems like she might back off that claim, but that’s not in the cards. Upright BiPed

Wow, sorry.
In my original plan, I was not going to attempt …
When recorded information is transferred from a medium it goes through protocol to its effect. See my comment #50
This is what I meant when I said DNA is not “inert” – its state at the beginning and end of the process is unchanged, but it undergoes a state change during the process.
We can talk about the backbone of DNA if you wish; it’s an extremely rare object that allows any of the four nucleotides to occupy any position along its length without influencing their order. But as interesting as it is, the sequence of nucleotides seems more interesting, given that it is where the information is. And that sequence doesn’t change as an observable effect of being unzipped for transcription. Upright BiPed

Dr Liddle, Below is my response to your post at 46. I hesitate to post it yet, given that I don’t want to cover up your response to my post at 50. - - - - - - - - - - -
My own view – or perhaps “hunch”- is that the reason that IDsts regard evolutionary scientists as missing a Glaringly Obvious Fact (and therefore assume at best stupidity and/or ignorance, and at worst deliberate dishonesty) while conversely evolutionary scientists regard IDists as Completely Missing The Point (and therefore assume ditto) is not because they disagree on some level at which the disagreement can be resolved in favour of one or other to the satisfaction of both, but because they have very different “problem statements”.
I’m not interested in political statements at this juncture. If your point is that people who are competing with ideas argue about them, then thanks for pointing that out, but it’s irrelevant to the content of the conversation we were having.
Unfortunately, the converse is probably true as well – that we don’t manage to agree on the problem statement, or, worse (for me!) we appear to agree with it, and I produce a demonstration that I think supports my view, and then we find that actually we didn’t actually agree in the first place!
You have my apologies if you cannot tell it, but I am trying to be clear and descriptive of the observations. When I say something and you reply “Yes!” or “Right!” or “Cool, I like it” then I assume you understand what I am saying. If you make that same reply several times in a row to several interrelated comments, then I assume you understand a whole class of interrelated comments. Beyond that, I have asked you for a reasonable preliminary overview of how you plan to integrate the observations we’ve agreed upon into your simulation. I think it’s reasonable to expect at some point that overview might include such words are “representation” and “protocol” and the like – given that is what the conversation is about. Conversely, it would seem odd to acknowledge the observations of a phenomenon on the front side, then to attempt a simulation of that phenomenon without addressing those observations.
For that we needed an operational definition of both “information” and “Darwinian processes”. For the latter, I have operationalized “Darwinian processes “ as comprising of no more than Chance and Necessity. I haven’t done this formally, but I’ll do so now: “Chance” processes will be generated by a random number generator with a flat distribution, and will govern the movement of elements in my model, in a manner analogous to Brownian Motion. “Necessity” processes will govern the conditions under which the basic elements of my model bind and/or repel each other. These will be laid out at the start, and will not be changed during the running of the model – the “chemistry” of the system.
No problem.
Meyer’s account of Shannon information is … … So it seems that Shannon information supplies us with… …and is what Dembski calls… … Dembski, talks about … … But Meyer talks about…
Again, these things may be interesting on their own merit, but they have nothing to do with the conversation we have been having. These concepts were not required by Nirenberg, and they aren’t a requirement for us.
Two things were missing …
I have not seen this exchange between you and KF - but to my understanding of them, I agree with both points. To my mind, they speak to the same structural problem. If such a structure somehow existed in the genome, we would have never discovered the genetic code. There would have been no observations in which to discern it as we did. At the same time, we are not looking for a new way in which information can exist; we are looking for it as it does exist.
In my original plan, I was not going to attempt …
When recorded information is transferred from a medium it goes through protocol to its effect. See my comment #50
This is what I meant when I said DNA is not “inert” – its state at the beginning and end of the process is unchanged, but it undergoes a state change during the process.
We can talk about the backbone of DNA if you wish; it’s an extremely rare object that allows any of the four nucleotides to occupy any position along its length without influencing their order. But as interesting as it is, the sequence of nucleotides seems more interesting, given that it is where the information is. And that sequence doesn’t change as an observable effect of being unzipped for transcription.
Upright BiPed

Hi faded_Glory, Stonehenge, the Sphinx and Easter Island (specifically, the Easter Island statues) are not a product of wind, water and other forces of nature. That was the point. Like the cell, they were clearly fabricated. That the cell is capable of biological reproduction simply makes it much more difficult to fabricate than Stonehenge. It is certainly not your knowledge of prehistoric people that leads you to conclude that Stonehenge, the Sphinx and the Easter Island statues could not possibly have made themselves because it is plainly obvious that they were made. No, your knowledge of prehistoric people kicks in AFTER you've reached that conclusion. I'm not entirely convinced that our knowledge of "prehistoric people" can provide satisfactory explanations for these three things anyway but that's another subject. So, whatever it is that leads you to a certainty of Intelligent Design in these three things it is not the absence of biological reproduction nor is it your knowledge of prehistoric people. That which is plainly obvious about ID in these three things is even more plainly obvious about ID in the cell. Now then faded_Glory, we have already considered "the probability that [the cell] originated through (bio)chemical means given the known laws and mechanisms of biochemistry" and can correctly dismiss any possibility that the cell originated in such a manner. The more we learn about the cell, the more improbable naturalistic explanations become. For the sake of this discussion, it is totally irrelevant to ask of the cell, Stonehenge, the Sphinx or the Easter Island statues: were they man-made or God-made? We simply need to know that they were actually made: and eliminate the possibility that they could ever make themselves. Chris Doyle

Chris Doyle, Some comments to your last post here: - Biology concerns itself with entities that reproduce. Clearly the examples you mention are not the product of biological reproduction but are either fabricated, or result from the activities of wind, water and other forces of nature. - This leads to the suggestion that Bayesian hypothesis testing would be far more useful when investigating these provenance questions than Fisherian testing. Given that we know of the existence of prehistoric people, and given what we know of how forces of nature can shape rocks, the probability of the things you mentioned being man-made will vastly outweigh the probability that they were formed by forces of nature (let alone by reproduction!). When it comes to the cell, we need to consider the probability that it originated through (bio)chemical means given the known laws and mechanisms of biochemistry, versus the probability that it was created by God given the existence of God. To compare these probabilities using Bayesian methods we need to know the probability of God. To you that would be 1, to an atheist that would be 0. This is why they end up with a different conclusion from you, yet their conclusion is very logical and reasonable given their assumptions. - If you assume that the probability of God is 1, have you ever considered whether it is more likely that God made Stonehenge, the Sphinx and the Easter Island statues, than that people made them? If not, why not? And yes, I do think that this is not an unreasonable question to ask a theist. fG faded_Glory

Morning Lizzie, There is a big problem with this statement that you made: “A-theism is surely the default in the absense of evidence for a theos? I mean, I know you disagree about evidence, but the burden of proof is usually to those making the claim for the existence of something, rather than on those who do not accept the claim.” I think identifying this problem gets us closer to the question that we need to answer: if the basis for the atheistic worldview is neither rational, nor empirical, then what is it? You get way ahead of yourself Lizzie when you get preoccupied with questions about HOW Intelligent Design was implemented and by WHO. Front-loading, tinkering, aliens, the Creator: all interesting technical details but utterly irrelevant until you admit that Intelligent Design is the best, and only, scientific explanation for existence. After all, we are in complete agreement that everywhere we look and anything we look at is giving us the overwhelming impression of design. The only disagreement lies in the fact that atheists and evolutionists claim that this appearance of design is not real, it is only an illusion. Yet, atheists only ever employ this rather absurd line of argument when it comes to one thing: the Creator. In all other walks of life, they wouldn’t entertain it for a minute. Take three examples: 1. Stonehenge 2. The Sphinx 3. Easter Island Atheists never, ever say that the null hypothesis is that these things just made themselves. Atheists never say that the default position is that these things were put together by Chance and Necessity and that the burden of proof is on those who claim that these things required Intelligent Design. Atheists never say that people who reject purely naturalistic explanations for these things are Completely Missing The Point. Atheists would be the first to agree that the burden of proof lies COMPLETELY with anyone who claimed that Stonehenge built itself, that the Sphinx carved itself and that the Easter Island statues buried themselves. Atheists would have no doubt that anyone who advanced such absurd claims would have entirely irrational and non-empirical reasons for rejecting that which is plainly obvious. And yet, it is far more probable that Stonehenge made itself than that the cell made itself. It is much more obvious that the cell requires Intelligent Design than Stonehenge. There is no logic, no reason and no evidence to support the belief that Stonehenge made itself and that is even more true of the cell. It seems that atheists only ever reject arguments for Intelligent Design if there is a possibility that the Intelligent Designer might be the Creator (a point previously hammered home by Cannuckian Yankee). So it all comes back to, what is really going on with atheists? Why do they ignore science whenever science points to the Creator? Something emotional or cultural perhaps? If we can identify the true (no doubt, very personal) motivation behind atheism, we need not concern ourselves with trying to define our disagreement in the most acceptable terms: or even quibbling over the meaning of the term “information”. Chris Doyle

Upright BiPed @50. Well stated. One thing that must be present are potentialities. Necessity is the enemy of such. Another thing that must be present is communication. Chance [aka noise] is the enemy of such. Would you agree? Mung

I'm a lawyer, doncha know. I noes all them latin phrases. Mung

mia? Mung

mia culpa. Upright BiPed

Upright BiPed, Null, I think you might have mis-posted from another thread. No, I was addressing comments made in this thread. I'm just coming in late. nullasalus

Dr Liddle, I see that you have made a response at 46. I will catch up and read it later. -cheerz Upright BiPed

Null, I think you might have mis-posted from another thread. Upright BiPed

Dr Liddle, From my previous post to you, I have assumed that we came to some valuable agreements, based upon your responses. For instance we agreed that the presence of information has specific requirements. To my mind, these requirements are the primary agreement needed in demonstrating that information did in fact arise from your simulation. Those requirements consist of the presence of discrete representations, as well as the discrete protocols needed to decode them. I make the above assumption from the following exchange:
BIPED: In retrospect, when I stated that recorded information requires symbols in order to exist, it would have been more correct to say that recorded information requires both symbols and the discrete protocols that actualize them. Without symbols, recorded information cannot exist, and without protocols it cannot be transferred. Yet, we know in the cell that information both exists and is transferred. LIDDLE: Yes. And I like that you refer to “the cell” and not simply “the DNA”. BIPED: This goes to the very heart of the claim that ID makes regarding the necessity of a living agent in the causal chain leading to the origin of biological information. LIDDLE: Let me be clear here: by “living agent”, are you referring to the postulated Intelligent Designer[s]? Or am I misunderstanding you? BIPED: ID views these symbols and their discrete protocols as formal, abstract, and with their origins associated only with the living kingdom (never with the remaining inanimate world). Their very presence reflects a break in the causal chain, where on one side is pure physicality (chance contingency + physical law) and on the other side is formalism (choice contingency + physical law). Your simulation should be an attempt to cause the rise of symbols and their discrete protocols (two of the fundamental requirements of recorded information between a sender and a receiver) from a source of nothing more than chance contingency and physical law. LIDDLE: Cool. I like that. BIPED: And therefore, to be an actual falsification of ID, your simulation would be required to demonstrate that indeed symbols and their discrete protocols came into physical existence by nothing more than chance and physical law. LIDDLE: Right. BIPED: The question immediately becomes “how would we know?” How is the presence of symbols and their discrete protocols observed in order to be able to demonstrate they exist? For this, I suggest we can use life itself as a model, since that is the subject on the table. We could also easily consider any number of human inventions where information (symbols and protocols) are used in an “autonomous” (non-conscious) system. LIDDLE: OK. BIPED: For instance, in a computer (where information is processed) we physically instantiate into the system the protocols that are to be used in decoding the symbols. The same can be said of any number of similar systems. Within these systems (highlighting the very nature of information) we can change the protocols and symbols and the information can (and will) continue to flow. Within the cell, the discrete protocols for decoding the symbols in DNA are physically instantiated in the tRNA and its coworkers. (This of course makes complete sense in a self-replicating system, and leads us to the observed paradox where you need to decode the information in DNA to in order to build the system capable of decoding the information in DNA). LIDDLE: Nicely put. And my intention is to show that it is not a paradox – that a beginning consisting of a unfeasibly improbable assemblage of molecules, brought together by no more than Chance (stochastic processes) and Necessity (physical and chemical properties) can bootstrap itself into a cycle of coding:building:coding:building: etc. BIPED: Given this is the way in which we find symbols and protocols physically instantiated in living systems (allowing for the exchange of information), it would be reasonable to expect to see these same dynamics at work in your simulation. LIDDLE: Yes, I agree. Cool! BIPED: I hope that helps you “get to the heart of what [I] think evolutionary processes can’t do”. LIDDLE: Yes, I think so. That is enormously helpful and just what I was looking for.
- - - - - - - - - - - - - - - With these agreements in hand, it seems that the primary question now on the table is getting your simulation to ascend to the appropriate structure required for the transfer of information. After all, not just any structure will do. Here I am not speaking to the initial conditions of your simulation, but only the end result. Whatever the initial conditions of the simulation I will leave to your expertise, with the only caveat being that the simulation operates in good faith with the claim that chance and natural law are the only causal forces allowed to impact the output (the simulated environment). As to that structure, I think it is important to take a full accounting of what is observed in nature. Again, I am not speaking here of your initial conditions (or whatever reaction pathways your simulation may take in the process of leading up to the rise of information) but only speaking of the structure of the final condition once attained. In that regard it seems that we should highlight two or three observations (some we’ve already discussed). The first of those is the presence of certain discrete objects. Here I am, of course, talking about the discrete representations and protocols. Both of these objects should be fully observed as such in your simulation, and I think we’ve discussed them well enough to understand what they are. If there is any ambiguity remaining, then we can certainly discuss them further. The second structural item has to do with a necessity that the output of information transfer must be dynamic, based upon the input of that information. If the output is not dynamically driven by the representations being given at the input, then the input cannot be seen as informative to the output. Thirdly, to facilitate this dynamic property, there must be a necessary break in the causal chain. This break is exemplified within the cell by the simple fact that proteins are not created from nucleotides. In other words, if you plucked the ribosome from the cell’s protein synthesis machinery, and put yourself in its place, in one direction you would see sequences of nucleotides coming in for translation, and in the other direction you would see sequenced amino acids floating off into the distance to be folded into proteins. One of these marks the input of information (representations instantiated in matter) and the other is the output (a process being dynamically altered by the input). But these are two entirely separate causal chains (if I may use that word). The first causal chain is the sequence of representations, which I say is the product of design, and you contend is the result of chance/necessity. It is made up of nucleic acids. The second causal chain is the bonding within the resulting polypeptide. It is made up of amino acids. The amino acids and the nucleic acids do not interact. They are connected at this dynamic break only by the protocol itself, which I say is the product of design, and you say is the result of chance/necessity. Regardless of who is correct, this dynamic break in the causal chain must be represented in the simulation. Lastly, there is the structural entailment of information always necessarily being ‘about’ something. Therefore, the output (being driven by the input) must serve some identifiable necessary function within the system. In a living system, one of those necessary functions of information is to create the protocol required to make the system work. Given that your simulation is designed to demonstrate the origin of information, it is at least reasonable to think this will be a function of the information within the simulation as well. By doing so, this entailment will be satisfied. So, in order to fully demonstrate the rise of information, this is the structure your simulation must ultimately assume. And as you will note, none of these have anything whatsoever to do with measuring or quantifying information (either by ‘this person’s metric’ or ‘that person’s theory’). The question is simply “Is information present?” To answer that question, these are the observable entailments that would indicate that it is. Upright BiPed

I mean, I know you disagree about evidence, but the burden of proof is usually to those making the claim for the existence of something, rather than on those who do not accept the claim. No, the burden of proof is 'usually to those' making a claim, period. 'There is no God' is a claim. 'Naturalism is true' is a claim. 'Theism is false' is a claim. And just who has what 'burden of proof' isn't made clear to begin with. The Maverick Philosopher had a good mini-series on this. But you are right, “atheism” is not verified. It’s very hard to verify a null. So? "Gosh, it's hard to verify the atheism!" So... What, then we just treat atheism with kid gloves then? There's no good evidence for the position, there's no proof of it, but that's okay, let's go easy on them? No. I would think that 'it's very hard to verify this position' would, at the very least, suggest someone should be hesitant before committing to it. In fact, I'm tempted to think the old chestnut of 'extraordinary claims require extraordinary evidence' may pop in here. Atheism, the claim that there is no God or gods, is an extraordinary claim. Where's the extraordinary evidence? If 'It's tough to get the evidence!' flies as a defense here, it flies everywhere. A-theism is surely the default in the absense of evidence for a theos? And what's the default in the absence of evidence for naturalism, or atheism? No, just what 'the default' should be is itself the stuff of debate. But atheism is by no means the default view. Though I offer this much up: Can one reasonably infer just how much confidence a person has in their position by how strenuously they insist that they are under no or minimal obligation to defend and argue for their position? I would think the fact that so many atheists squirm at the very prospect of having to actually present and defend their idea, or shoulder any burden of proof, says quite a lot. nullasalus

Might I offer a suggestion? Begin with something both can agree upon as being clearly representative of the thing in question, whether that be a system within the cell (DNA - Ribosome - Protein) or something artificial, or whatever. Then let Elizabeth attempt to come up with a minimalist version of it that she thinks can be reached by Chance+Necessity sans intentional Design. Just an idea. Mung

oops sorry, forgot to explain the above: it's my belated response to a post by Upright BiPed on a thread whose title I have forgotten! Elizabeth Liddle

Upright BiPed:
I think we may be talking past each other here. I was indicating that the ribosome does not change its state as you had suggested in your previous post. Instead, it assembles polypeptides based upon the informational sequence given to it by mRNA. It does so by bringing the mRNA sequence together with the charged tRNA, which has an amino acid bound on one end of the molecule and an anti-codon discretely positioned on the other (isolated from the amino acid). In response to this you return to say that you’ll make sure the “original informational sequence” is left unchanged (except for any random variation that may impact it). (?!?!) What “original informational sequence” are you referring to? For there to be an informational sequence, it would require that arbitrary symbols and discrete protocols already be established – the rise of which is the very thing that you wish to demonstrate.
Well, this is exactly why I wanted to thorough thrash out the "problem statement" before we proceed. My own view - or perhaps "hunch"- is that the reason that IDsts regard evolutionary scientists as missing a Glaringly Obvious Fact (and therefore assume at best stupidity and/or ignorance, and at worst deliberate dishonesty) while conversely evolutionary scientists regard IDists as Completely Missing The Point (and therefore assume ditto) is not because they disagree on some level at which the disagreement can be resolved in favour of one or other to the satisfaction of both, but because they have very different "problem statements". And it may well be that if we can agree on the problem statement, the answer to which of us is right will become obvious to both of us, without need for further demonstration or argument. But I’m looking forward to my project, so I hope there will still be case to be made! Unfortunately, the converse is probably true as well - that we don't manage to agree on the problem statement, or, worse (for me!) we appear to agree with it, and I produce a demonstration that I think supports my view, and then we find that actually we didn't actually agree in the first place! So while this is time-consuming, I don't think it is time-wasting, and while it may seem as though I being evasive, I'm not. One of the reasons I've enjoyed being here, and am grateful for the opportunity, is that I think that during at least some conversations, we have made some progress in drilling down to that place where the fundamental disagreement lies. But I don't think we are quite there! I hope when we get there, there will be an interesting problem to solve, but it may be that at that point, it simply makes a noise like a hoop and rolls away. Which, actually would also be cool, come to think of it :) So, preliminaries over.... Let’s regroup: My original claim was that I could demonstrate that Darwinian processes could generate information “from the start”. For that we needed an operational definition of both “information” and “Darwinian processes”. For the latter, I have operationalized “Darwinian processes “ as comprising of no more than Chance and Necessity. I haven’t done this formally, but I’ll do so now: “Chance” processes will be generated by a random number generator with a flat distribution, and will govern the movement of elements in my model, in a manner analogous to Brownian Motion. “Necessity” processes will govern the conditions under which the basic elements of my model bind and/or repel each other. These will be laid out at the start, and will not be changed during the running of the model – the “chemistry” of the system. I should note at this point that I will be doing some heavy “designing” of the “Necessity” laws, but that they will not include designing an unfaithfully self-replicating self-replicator. It will not, in other words, be a genetic algorithm, at least in the beginning (I’m hoping one will emerge). If so, Darwinian processes will take over, which I will operationally define as self-replication with heritable variance in probability of successful reproduction in the current environment. So that leaves “information” to operationalize. Meyer’s account of Shannon information is as a reduction of uncertainty, regardless of whether the message has meaning. He gives as an example:
Consider two sequences of characters: “Four score and seven years ago” “nen ytawoi jll sn mekhdx nnx” Both of these sequences have an equal number of characters. Since both are composed of the same 26 letter English alphabet, the amount of uncertainty eliminated by each letter (or space) is identical. The probability of producing each of these sequences at random is identical. Therefore, both sequences have an equal amount of information as measured by Shannon’s theory. But one of these sequences communicates something, while the other does not. Why?
So it seems that Shannon information supplies us with some aspect of what we want to measure, and is what Dembski calls Complexity. But it is missing something that we want to include in there, which we might refer to as “meaning”. The following has been redrafted, in light of our recent conversation You have talked about meaning in terms of “symbols” which we defined as something like the mapping of protocols (which I take to mean “stuff to be done”) on to some intermediate carrier-of-meaning from some source. Dembski, talks about “specification” in terms of compressibility (“ease of description”) which is interesting because on the whole it is negatively correlated with Shannon information content. But Meyer talks about specification in terms of “producing a specific effect”, which may be closer to your definition. Now, it seems to me that any self-replicating entity is a “sender” of information to its copy, in this sense. Encoded within the parent entity is the information required to specify the protocols that will build its daughter entity. However, when, early on, I presented what I called my “Duplo Chemistry” – in which fairly well specified information (enough to ensure that a fairly faithful copy of the original was built) that was also moderately complex (it was an essentially random sequence of units), this was rejected (by kairosfocus anyway) as not being adequate. Two things were missing (at least from the prototype): one was that the sequence did nothing except specify its copy; it did not enable something to happen that would make the sequence’s survival more likely; secondly the coding was a direct template with no equivalent of tRNA – no equivalent of a unit that translates from a sequence with no direct function in maintaining the system to a building block that does. In my original plan, I was not going to attempt that last thing. I was going to attempt to devise a simulation that started with no more than a Physics-And-Chemistry (Necessity) on the one hand, and stochastic energy, in the form of Brownian motion (Chance), but from which self-replicators emerged and evolved. However, I can see that there is some point to building in this “symbolic” layer, and I’m trying to think of a way of implementing this! I can see how it might be done, but it will certainly make the job a little harder (and was not, in fact, part of my original claim, as I was thinking in terms of Dembski’s notion of “specificity” rather than Meyer’s and yours). But are we getting closer to something that might satisfy you if I achieved it? PS: We can probably agree that when DNA (which is one of the main information sources that is transmitted from cell to cell) is transcribed, the portion that has been signalled to be transcribed is temporarily "unzipped" by helicase i.e. its state is temporarily altered, its hydrogen bonds being broken, so that it becomes two single strands instead of one, exposing the bases so that they bond with their complementary RNA bases, ie. the separate DNA strands form a template, or jig, on which the RNA is assembled; eventually the complete RNA strand is released and the DNA strand reforms into its starting configuration. This is what I meant when I said DNA is not "inert" - its state at the beginning and end of the process is unchanged, but it undergoes a state change during the process. Elizabeth Liddle

Dr Liddle:
It concerned the principle of information being created by “Chance and Necessity”. To discuss that we need an operational definition of “information” (also, incidentally, of Chance and Necessity) . . . . What I cannot do is “show the rise of information proceessing [where did "processing" come in?] by means of chance and law” without an agreed operational definition of those terms. I’ve been trying, with the help of Mung and kairosfocus, to drill down to an operational definition of those terms.
First of all, operational definitions are themselves a suspect matter, given the fate of logical positivism and its verifiability principle. In effect the principle failed its own test and self destructed in a spectacular own-goal. Also, we have given enough to work on over and over again. Okay, one more time. Definitions, IMHO, start with concepts, often identified on recognising a pattern in key example[s] and close enough family resemblance. That is why I have consistently provided the pattern of given examples: 1] Mechanical necessity issuing in lawlike regularity: --> e.g. a heavy dropped object falling under g, reflecting . . . --> the dynamics of gravitation as a capital example in point where F = dP/dt = m*d2x/dt2, more familiarly F = m*A, where m is constant. --> Classically, ideally reducible to a Diff eqn, initial conditions, parameters, playout as one solves the eqn, plugging in parameters, initial conditions etc. --> hence, Laplace's handy little demon. --> this sort of reduction is a classic paradigm for physics, the hardest of the hard sciences. 2] Chance, issuing in stochastic distributions of outcomes on distributions reflective of random variable models: --> if the dropped heavy object above is a die, the story does not stop with falling and with maybe air resistance slowing down a bit towards a terminal velocity. When it hits, it has edges and corners plus energy. --> it will tumble and settle essentially at random to values from the set {1, 2, . . . 6}, on a near flat random pattern on average if the die is fair. --> This traces to clashing uncorrelated streams of cause-effect, so that under similar initial conditions, outcomes radically diverge across a distribution, statistically distributed contingency producing patterns similar to mathematical random variable distributions. --> Quite common in thermodynamics settings,such as the random motion of molecules, the driving force of diffusion, brownian motion, etc etc. --> under quantum circumstances, similar random distributions occur. --> relevant to something like dna strings, if a binary output device has a random distribution [Zener noise or sky noise flattened by a PRBS generator will work . . . but a pseudo random source by itself is not good enough], it can be used to generate ascii text strings at random, which can be tested for production of intelligible text. --> So far, and as repeatedly cited, a 24 symbol ascii text string has been produced, from 1 in 10^50 possibilities:
The infinite monkey theorem states that a monkey hitting keys at random on a typewriter keyboard for an infinite amount of time will almost surely type a given text, such as the complete works of William Shakespeare. In this context, "almost surely" is a mathematical term with a precise meaning, and the "monkey" is not an actual monkey, but a metaphor for an abstract device that produces a random sequence of letters ad infinitum . . . . The theorem concerns a thought experiment which cannot be fully carried out in practice, since it is predicted to require prohibitive amounts of time and resources. Nonetheless, it has inspired efforts in finite random text generation. One computer program run by Dan Oliver of Scottsdale, Arizona, according to an article in The New Yorker, came up with a result on August 4, 2004: After the group had worked for 42,162,500,000 billion billion monkey-years, one of the "monkeys" typed, “VALENTINE. Cease toIdor:eFLP0FRjWK78aXzVOwm)-‘;8.t" The first 19 letters of this sequence can be found in "The Two Gentlemen of Verona". Other teams have reproduced 18 characters from "Timon of Athens", 17 from "Troilus and Cressida", and 16 from "Richard II".[21] A website entitled The Monkey Shakespeare Simulator, launched on July 1, 2003, contained a Java applet that simulates a large population of monkeys typing randomly, with the stated intention of seeing how long it takes the virtual monkeys to produce a complete Shakespearean play from beginning to end. For example, it produced this partial line from Henry IV, Part 2, reporting that it took "2,737,850 million billion billion billion monkey-years" to reach 24 matching characters: RUMOUR. Open your ears; 9r"5j5&?OWTY Z0d...
--> to rise above modelling micro evo, models of the claimed power of evolution will need to show how a functional entity that metabolises and self replicates can credibly arise within cosmos scope resources from a plausible prebiotic soup of chemicals interacting under known chemical and physical mechanisms, including the relevant codes, and algorithms --> Similarly, they will need to show how a one celled ancestral organism could so transform itself by chance driven processes and blind mechanical necessity that it can give rise to embryologically feasible complex body plans within the resources of a solar system, or if a cosmos is assumed, it needs to show how many solar systems of suitable type would arise to provide a scope of resources. 3] Intelligence, issuing in purposeful, functionally specific, complex organisation of parts in a whole in the face of highly contingent possibilities --> text in this post is an example 4] Information: --> Wiki's definition as rearranged in the UD glossary:
“ . . that which would be communicated by a message if it were sent from a sender to a receiver capable of understanding the message . . . . In terms of data, it can be defined as a collection of facts [i.e. as represented or sensed in some format] from which conclusions may be drawn [and on which decisions and actions may be taken].”
--> Information can be observed from coded patterns of glyphs organised on meaningful rules such as in the text of this post --> Symbol distributions can be used in a metric, I = - log P --> functional specificity can be identified from vulnerability to perturbation or conformity to tight vocabulary and rules of meaning constraints etc --> complexity can be identified from a threshold that makes chance based random search on a gamut of available resources an ineffective strategy to get to tight zones of interest. In short if a monkey type test will overwhelmingly be likely to fail we are in the zone of relevant complexity. --> Putting together and using the log reduced Dembski chi metric: Chi_500 = I*S - 500, bits beyond the solar system threshold +++++++++++++ The challenge under these circumstances is to generate a system with sufficient capacity to do something analogous to metabolism, building structures under instruction, on taking in energy and simple parts as components, while being able to replicate itself under the same conditions. Components must be able to be joined together in several ways each, and must be able to decouple within reasonable energy resources in the system, even from the "right" combination -- cf here death and decay etc. Or simply lego bricks. Once a simple system self assembles on chance plus necessity, it may hill climb as it leased on chance variation and differential success at replication. Only, the hill climbing has to be innate to the system, either coded in spontaneously, or emerging as a natural property. For a simple test, the usual random number generators commonly available will be acceptable, but the real run for serious results should use a genuine random number source. That would I think be a rough first pass test. Others may want to refine or correct. GEM of TKI kairosfocus

Original Thread Mung

Perhaps start here:
Dr Liddle, I have looked over your post at 17, but to be completely honest with you, I don’t see the dire connection between these questions and the conversation we have been having. Perhaps these questions are arising in your mind as a result of reading “Sig in the Cell” – which is all fine and good – but they don’t seem to directly bear on the topics we had been discussing. Perhaps you can set me straight on the implications of these questions to the larger set of topics in our previous posts. To help make the connection, I will post the bulk of your last substantial post from the previous conversation.
Upright BiPed Hope that helps. Mung

Upright BiPed:
Offended? Yeah, I know the feeling. I am more than happy to call off the dogs Dr Liddle.
No problem :) Just let's try to communicate OK?
Just don’t try to abandon the previous conversation so that we can spend the next eternity arguing over Dembski and Meyers. And, do you think I care in the least that you think an material intelligence of some disembodied sort exist in the whatever whatever. I don’t. I want you to show the unguided rise of a discrete representation and the protocol to decode it within a system.
Well, I didn't claim to be able to demonstrate that (not least because I don't know what it means). But, sure, I'm happy to continue where we left off. Will this thread do? Seems a bit of a hijack. But first, remind me of the claim (in my words) you want me to defend. I know you've done it before, so your search skills are better than mine. Elizabeth Liddle

Upright BiPed:
LIddle:
You claim that compressibility, probability and complexity have nothing to do with the conversation I was having with you. Well it may well be true that they did not come up, but to claim that they have “nothing to do with it” seems to me to be utterly astonishing!
Knock yourself out, Liz. Tie them to the previous conversation at the point of the previous conversation, and I’ll recant. Otherwise, I will note that you said NOTHING in your last post that had anything to do with the previous conversation.
I'm not asking you to "recant", UBP, I'm pointing out their relevance to any demonstration of information generation by Chance and Necessity!
So what kind of information could this be? Well, the owner of this blog, a man at the forefront of the ID movement, defines that information in terms of complexity, compressibility and probability.
We weren’t talking about “kinds” of information, Liz, we were talking about the phenomena of information ITSELF, how it exists, and how it is tranferred. This doesn’t have a damn thing to do with Dr Dembski, Liz.
Oh. Well, I misunderstood.
Not one thing.
So how can those concepts have “nothing to do” with those topics?
You already participated in that conversation, Liz. You already know how.
No, I don't. OK, then, back to the drawing board: How are you defining information here? Because without a definition of information, we can't discuss how it comes into existence or is transferred, can we? Elizabeth Liddle

back later.... Upright BiPed

A long long time ago I said I was going to leave that up to you two to work out. I was just an interested bystander. I did however wonder at why you at first chose Shannon information and then discarded it. Mung

Elizabeth Liddle:
but the answer I was preparing for you was based on my reading of the Signature in the Cell, which I believe you recommended...
iirc, it was Chris Doyle who suggested you read SitC. [sorry, it's the lawyer in me] Or is it Friday, "just the facts maam."
I’ve been trying, with the help of Mung and kairosfocus, to drill down to an operational definition of those terms. Don't drag me into this, lol! A long long time ago I said I was going to leave that up to you two to work out. I was just an interested bystander. I did however wonder at why you at first chose Shannon information and then discard it. Shannon information requires symbols and protocols, I believe. Am I wrong? diagram
Mung

Offended? Yeah, I know the feeling. I am more than happy to call off the dogs Dr Liddle. Just don't try to abandon the previous conversation so that we can spend the next eternity arguing over Dembski and Meyers. And, do you think I care in the least that you think an material intelligence of some disembodied sort exist in the whatever whatever. I don't. I want you to show the unguided rise of a discrete representation and the protocol to decode it within a system. Upright BiPed

Mung:
Elizabeth. Your claim, as I understood it, was that you could provide a demonstration by which it would be shown that a system of information and information processing could arise by some combination of chance and necessity sans intelligence.
sans intentional Design. Not sans intelligence.
You cannot. You will not.
I cannot, indeed, without an agreed operational definition of the terms.
The attempt to now shift the burden of proof is intellectually dishonest.
I am not attempting to shift the burden of proof.
I have no doubt that we can provide the relevant quotes and links to the originals should it be necessary.
Feel free, but I'm not sure it will help. I'd rather the original thread was re-opened and we can read the conversation in context.
If you don’t care for the way I characterized your claim, how would you state it?
Much as you did, or there are alternative formulations of it. I'm not sure which version of it is the urtext. But as my first attempts got befouled on definitions of information, it's important to get that properly operationalised first. It seems very clear to me that there isn't even a shared understanding on this site as to how information, in an ID context should be defined conceptually, even, and until we do that, we can't operationalize it. I'm not going to spend time programming a demonstration without a clear agreed metric for whether or not I have succeeded. Elizabeth Liddle

LIddle:
You claim that compressibility, probability and complexity have nothing to do with the conversation I was having with you. Well it may well be true that they did not come up, but to claim that they have “nothing to do with it” seems to me to be utterly astonishing!
Knock yourself out, Liz. Tie them to the previous conversation at the point of the previous conversation, and I'll recant. Otherwise, I will note that you said NOTHING in your last post that had anything to do with the previous conversation.
So what kind of information could this be? Well, the owner of this blog, a man at the forefront of the ID movement, defines that information in terms of complexity, compressibility and probability.
We weren't talking about "kinds" of information, Liz, we were talking about the phenomena of information ITSELF, how it exists, and how it is tranferred. This doesn't have a damn thing to do with Dr Dembski, Liz. Not one thing.
So how can those concepts have “nothing to do” with those topics?
You already participated in that conversation, Liz. You already know how. Upright BiPed

Upright BiPed
Because the previous conversation had absolutely nothing whatsoever to do with those topics. You had stated that you could demonstrate the rise of information processing by nothing more than chance and law. And I was describing the particulars of that phenomenon in order that –if– your simulation were successful, then it might be regarded as a true falsification of one of ID’s central tenets. That conversation was centered on the actual physical observations of information instantiated in matter – that of symbolic representations, the protocols necessary to decode those representations, and so on.
Well, that is exactly what was at issue, if you remember - how to devise an operational definition of information that would allow an independent observer to test whether I had fulfilled my claim. We had not got there.
But clearly that conversation came to a point that no longer suited you. After initially making some headway, you began to go off into delirium about how the chemicals involved would change states, and what not. I then reminded you that the ribosome does not change states as an observed effect of information processing. Neither does the discrete sequence. When Yockey said that there is nothing in the physico-chemical world that even looks like reactions being governed by sequences, he was correct. We were not talking about changing states, Liz, we were talking about something entirely different in nature – the processing of sequenced representations and their protocols.
My claim did not concern the ribosome. It concerned the principle of information being created by "Chance and Necessity". To discuss that we need an operational definition of "information" (also, incidentally, of Chance and Necessity).
And that is precisely were the train left the track. The stipulations involved in actually showing the rise of information were just simply too much to overcome, and you reacted to it in order to defend yourself from being shown incapable of defeating the very ID tenet you sought to demonstrate.
Well, no.
Anyone who cares to read the dialogue can easily see that. Your responses became more off base, and then simply slowed to nothing more than a drip. You even mentioned to other people that you would ‘soon’ have a response. You’ve been stalling ever since. And please save me the dung about losing track of ‘this’ and not enough time for ‘that’. I have seen you make literally dozens upon dozens of posts on this forum in the past three weeks.
Yes indeed, Upright BiPed, but the answer I was preparing for you was based on my reading of the Signature in the Cell, which I believe you recommended, and by the time I had my response drafted, the thread was closed to comments. I am happy to post it in some other thread. In the mean time I summed it up in a recent post (again, I can't remember which thread).
The reason you stopped the previous conversation is because you had nothing to say in front of the evidence as we find it. I even went to the trouble to post our last substantive exchange in order to get the conversation back on track. But now, unfortunately, you want to double down with topics irrelevant to the issues at hand. The grass is certainly greener over there (away from the evidence), but you discredit yourself as a price to pay.
I have to say, I find this a little offensive, Upright BiPed. One of the reasons I struggled with my response (still unposted) to you, was not because I "had nothing to say in front of the evidence as we find it" but because I was trying to find some common ground so that we could at least agree on some common definitions and a problem statement. That was why I found Meyer useful. If I have discredited myself in your eyes, I guess I have to live with that, but I can only say that you have completely misread me.
You cannot show the rise of information processing by means of chance and law, and despite your protest, you haven’t the gut to admit it. (Such an admission can not be integrated with your position, so guess what that means?)
No. What I cannot do is "show the rise of information proceessing [where did "processing" come in?] by means of chance and law" without an agreed operational definition of those terms. I've been trying, with the help of Mung and kairosfocus, to drill down to an operational definition of those terms. They remain somewhat problematic, IMO.
All your considerate politeness aside, to stand there and say you won’t hear of any charges of ‘intellectual dishonesty’ is no less expected than was the necessary change in topics of conversation.
I should hope it was not unexpected, Upright BiPed. When you accuse an honest person of dishonesty, expect to hear the charges denied. Elizabeth Liddle

Boy, is a thread on dung heaps ever appropriate here. Mung

Upright BiPed, you can be as frank as you like, but I do not accept your charges. You claim that compressibility, probability and complexity have nothing to do with the conversation I was having with you. Well it may well be true that they did not come up, but to claim that they have "nothing to do with it" seems to me to be utterly astonishing! My claim, to quote your quotation of my words, was:
my position is that IDists have failed to demonstrate that what they consider the signature of intentional design is not also the signature of Darwinian evolutionary processes.
And by that I meant (as became clear in our conversation) that the kind of information IDists claim cannot be generated except by Design could in fact be generated by evolutionary processes. So what kind of information could this be? Well, the owner of this blog, a man at the forefront of the ID movement, defines that information in terms of complexity, compressibility and probability. So how can those concepts have "nothing to do" with those topics? It seems to me they are absolutely fundamental, and, because they are, I continued to explore them in your absence with Mung, kairosfocus and others, and also continued to read Meyer's book, who also references them frequently. I'll deal with the rest of your post in a moment. Elizabeth Liddle

Upright BiPed:
You had stated that you could demonstrate the rise of information processing by nothing more than chance and law. And I was describing the particulars of that phenomenon in order that –if– your simulation were successful, then it might be regarded as a true falsification of one of ID’s central tenets. Yes. We were told that we could expect a falsification of a major tenet of intelligent design. We're waiting. Lacking one, we're awaiting the retraction of your claim that you could/would provide one. That would be the honest thing to do.
Mung

"I’d be even more interested in a short summary of the rebuttal. Here ya go: EL: I can show the rise of information processing by nothing more than chance and physical law, falsifying a major claim of ID. UB: You'll need to show the rise of discrete representations and protocols, since that is how information is instantiated in matter and tranferred. So get after it! EL: Err...I think that intelligence is deeply nested in the universe of contingencies for outcomes of compressibility, and specified foresight, and repetitive stuff. Upright BiPed

Elizabeth. Your claim, as I understood it, was that you could provide a demonstration by which it would be shown that a system of information and information processing could arise by some combination of chance and necessity sans intelligence. You cannot. You will not. The attempt to now shift the burden of proof is intellectually dishonest. I have no doubt that we can provide the relevant quotes and links to the originals should it be necessary. If you don't care for the way I characterized your claim, how would you state it? Mung

Dr Liddle, Allow me to be frank. The entirety of your last post was one long line of moribund cow squeeze. You have now accomplished the ideologically-necessary turn that all ID critics are forced to take when the discussion is allowed to become too honest, and too real. In your response above you mention: Complexity? Probability? Compressibility? Let me ask you a question. You mention (and I agree) that at one point in the discussion we were making progress on the issues. So, take a guess as to how many times the concepts of “complexity”, “probability”, and “compressibility” came up in that conversation? Exactly, none. Not even once. Why? Because the previous conversation had absolutely nothing whatsoever to do with those topics. You had stated that you could demonstrate the rise of information processing by nothing more than chance and law. And I was describing the particulars of that phenomenon in order that –if– your simulation were successful, then it might be regarded as a true falsification of one of ID’s central tenets. That conversation was centered on the actual physical observations of information instantiated in matter – that of symbolic representations, the protocols necessary to decode those representations, and so on. But clearly that conversation came to a point that no longer suited you. After initially making some headway, you began to go off into delirium about how the chemicals involved would change states, and what not. I then reminded you that the ribosome does not change states as an observed effect of information processing. Neither does the discrete sequence. When Yockey said that there is nothing in the physico-chemical world that even looks like reactions being governed by sequences, he was correct. We were not talking about changing states, Liz, we were talking about something entirely different in nature – the processing of sequenced representations and their protocols. And that is precisely were the train left the track. The stipulations involved in actually showing the rise of information were just simply too much to overcome, and you reacted to it in order to defend yourself from being shown incapable of defeating the very ID tenet you sought to demonstrate. Anyone who cares to read the dialogue can easily see that. Your responses became more off base, and then simply slowed to nothing more than a drip. You even mentioned to other people that you would 'soon' have a response. You’ve been stalling ever since. And please save me the dung about losing track of ‘this’ and not enough time for ‘that’. I have seen you make literally dozens upon dozens of posts on this forum in the past three weeks. The reason you stopped the previous conversation is because you had nothing to say in front of the evidence as we find it. I even went to the trouble to post our last substantive exchange in order to get the conversation back on track. But now, unfortunately, you want to double down with topics irrelevant to the issues at hand. The grass is certainly greener over there (away from the evidence), but you discredit yourself as a price to pay. You cannot show the rise of information processing by means of chance and law, and despite your protest, you haven’t the gut to admit it. (Such an admission can not be integrated with your position, so guess what that means?) All your considerate politeness aside, to stand there and say you won’t hear of any charges of ‘intellectual dishonesty’ is no less expected than was the necessary change in topics of conversation. Upright BiPed

Upright BiPed
Dr Liddle, You made a claim against ID, and then had that claim shown to be false. That was a process you yourself participated in. You are now avoiding a simple recognition that your claim has been addressed.
Please show me where my claim was shown to be false.
That is intellectually dishonest.
It would be if it were true. I will happily confess to missing posts, missing the point, ignorance, and even obtuseness. But I am not going to accept the charge of intellectual dishonesty. If you think my claim was rebutted, I'm interested to know where. I'd be even more interested in a short summary of the rebuttal. Thanks. Lizzie Elizabeth Liddle

Upright Biped
Dr Liddle, it is now a recorded fact on this forum (over the course of three or four threads) that you have not only been given some central claims made by ID proponents, but have also been given the reasoning as to why ID proponents claim that these observations are artifcts of design and cannot be assigned to purely material processes.
And I have posted my counter-arguments.
It is a conversation that documents an increasing reluctance on your part to engage. Im happy to cut and past the converastion and its timestamps if need be.
That would actually be very helpful. I am certainly not reluctant to engage, although I do find the format of this blog somewhat difficult to navigate and keep track of (and I still have a drafted reply to you on a thread now closed to comments!) So I'm sure there have been some excellent points left unaddressed, and some counter-rebuttals uncounter-counter-rebutted. I do only get time in teaspoonfuls, and conversations have a natural tendency to, er, speciate from a common ancestor :)
It has come time for you to recant this statement: …”my position is that IDists have failed to demonstrate that what they consider the signature of intentional design is not also the signature of Darwinian evolutionary processes.”
No, I certainly will not recant it :) There's been an ongoing conversation about the nature of that signature, and a great deal of disagreement. However, on at least one thread we seemed to be coming towards some kind of limited consensus that the kind of information that people consider the signature of design is that that falls outside the generally negative correlation line between complexity (as measured as something like low probability in bits) and compressibility (the measure of which I don't think we have yet, but is essentially to do with "ease of description"). I will try to get back to those conversations (though they tend to slip off the front page, and move to new threads), but to do justice to them requires more time than I tend to have at any given slot. However, I will try to give you the substance of my argument as briefly as possible: I agree that there is a class (or region) of patterns that are part of a very large set (i.e. are highly complex) but that are also more "specified" (easy to describe, structured) than most patterns of that degree of complexity. And that if patterns of this type are observed (a living thing being an example) that we can reasonably infer that they are not the result of combinations of repetitive processes governed by simple natural laws and stochastic events orthogonal to those laws. I also agree that such patterns are likely to be the result of deeply nested contingencies, and would also suggest that they include feedback contingencies. And I would call these deeply nested contingent feedback process minimally "intelligent", involving as they do, decision trees, i.e. nodes at which outcomes depend on incoming information And it is those that I think are indicated by the "specified complexity" signature, and while I would regard them as a subset of intelligent processes, I don't regard them as very intelligent because on the whole they are immediately reactive, and do not embody much in the way of "foresight". Elizabeth Liddle

Dr Liddle, You made a claim against ID, and then had that claim shown to be false. That was a process you yourself participated in. You are now avoiding a simple recognition that your claim has been addressed. That is intellectually dishonest. Upright BiPed

Chris:
But then atheists start putting speech marks around the word ‘intelligent’ and then start looking for ways to explain away this plainly obvious evidence for Design as something that is merely an illusion, concluding that there is no Intelligent Designer(s) because chance and necessity (ie. Evolution) is capable of explaining the things you describe in your comment. Atheists even claim that their worldview is all perfectly rational and empirically verified! But that claim does not stand up to any kind of scrutiny whatsoever. That is because there is in fact nothing, not a single thing that is rational or empirically verified about the atheist worldview. So, whatever the basis for maintaining the atheistic worldview, it is neither rational nor empirical.
The reason I put scare-quotes round "intelligent" when describing, say, evolutionary processes, is, firstly, that most people don't use the word to describe evolutionary processes, and secondly, because "intentional" is, in most usages, integral to the concept. And I don't think most of the systems I mentioned are have the capacity for intention. But you are right, "atheism" is not verified. It's very hard to verify a null. A-theism is surely the default in the absense of evidence for a theos? I mean, I know you disagree about evidence, but the burden of proof is usually to those making the claim for the existence of something, rather than on those who do not accept the claim.
If it is not rational or empirical, then what is it exactly? Cultural or emotional maybe? I suggest that we need to get to the bottom of this because both parties agree that existence is absolutely amazing. But only one party has logic, reason and evidence on their side: and it’s not the atheists.
Well, obviously I disagree :) But that's the problem, isn't it? Both sides think the logic, reason, and evidence is on their own side. So simply saying so doesn't really get us anywhere!
I know that sounds a bit strong, Lizzie but that is my honest opinion. If atheism had anything rational, empirical or otherwise persuasive about it, I would have mentioned it above. And it leaves me wondering: why on Earth does Lizzie, an exceptionally intelligent, courteous and reasonable person, believe that the “great many intelligent systems” in our universe all somehow made themselves
Because (leaving aside the question as to why there is something rather than nothing, which is a rather different question to questions regarding what that something is like) I think it is a property of the universe we are in that self-organising systems tend to form. It's chaotic, in the technical sense, and what we now know about chaos is that it isn't chaotic! That it is both unpredictable and highly structured. And that what is required for chaotic structures to form is feed-back loops, in which our universe is abundant. So, if you were trying to persuade me that only an amazing God could have not only spoken the stuff of the world into existence, but also set it about with feedback loops so that it would self-organise into complex and beautiful structures, and that those structures would, eventually, include creatures capable of awe, and also of goodness, then I might buy it :) My only problem then would be the identification of that God with moral good. However, if you are trying to tell me that the the stuff of the universe can't self-organise, but has to be constantly poked and tinkered with to produce the occasional biosphere, then, no, I'm not convinced. It think the truth is far more amazing than that. Elizabeth Liddle

(23), "It has come time for you to recant this statement: …”my position is that IDists have failed to demonstrate that what they consider the signature of intentional design is not also the signature of Darwinian evolutionary processes.”" I don't know why she would. You've still failed to demonstrate it. What do you think your single best piece of evidence is? Grunty

Upright: "Show a little leg." Yah, that's what we meant. Mfrank in nylons. allanius

Dr Liddle, it is now a recorded fact on this forum (over the course of three or four threads) that you have not only been given some central claims made by ID proponents, but have also been given the reasoning as to why ID proponents claim that these observations are artifcts of design and cannot be assigned to purely material processes. It is a conversation that documents an increasing reluctance on your part to engage. Im happy to cut and past the converastion and its timestamps if need be. It has come time for you to recant this statement: ..."my position is that IDists have failed to demonstrate that what they consider the signature of intentional design is not also the signature of Darwinian evolutionary processes." Upright BiPed

Well I guess I have my answer. The answer is dishonest. Empiricism among materialists amounts to no more than showing a little leg. /yawn Upright BiPed

(20), "Atheists even claim that their worldview is all perfectly rational and empirically verified!" Wrong. As an atheist, I can tell you that my atheism is not empirically verified, it's a position based on the fact that we have no objective evidence for the existence of gods. So in that regard it is a rational decision, but one that is not so much empirically verified as justified on the basis that those who claim gods exist have failed to empirically verify their claim. Now, if there was overwhelming valid, objective evidence for such a god, then I would of course make the rational decision to cease being an atheist. But at present, there isn't. Grunty

Good Afternoon Lizzie, I hope that visiting universities with your son is going well enough. I made it relatively easy for my parents by insisting on only applying for one university (albeit one that was 400 miles away from home)! Just picking up on your comment: “I think the universe includes a great many “intelligent” systems, by which I mean systems that incorporate what look like highly ingenious feedback mechanisms to maintain themselves in existence, and that these are often nested – our cells are “intelligent” homeostatic systems nested within homeo-static tissues and organs and organisms; organisms themselves may be “intelligent” homeostatic systems in the sense we more normally use the word. And populations are “intelligent” systems at yet another level of analysis.” Remove the speech marks from the word ‘intelligent’ and we’re all singing from the same hymn sheet here. In other words, everywhere we look, anything we look at, is literally screaming at us “THIS IS ABSOLUTELY AMAZING!”. Naturally, this is all to be expected if you are a Believer (Christian, Jew, Muslim, etc). It is also most satisfactorily explained by Intelligent Design theory. In fact, the belief in Creation or the scientific fact of ID is so sure and convincing to the majority of people alive (or who have ever lived) precisely because of the way everything in existence is screaming at us “THIS IS ABSOLUTELY AMAZING”. In other words, the evidence for Design is plainly obvious precisely because of the things you describe in your comment. But then atheists start putting speech marks around the word ‘intelligent’ and then start looking for ways to explain away this plainly obvious evidence for Design as something that is merely an illusion, concluding that there is no Intelligent Designer(s) because chance and necessity (ie. Evolution) is capable of explaining the things you describe in your comment. Atheists even claim that their worldview is all perfectly rational and empirically verified! But that claim does not stand up to any kind of scrutiny whatsoever. That is because there is in fact nothing, not a single thing that is rational or empirically verified about the atheist worldview. So, whatever the basis for maintaining the atheistic worldview, it is neither rational nor empirical. If it is not rational or empirical, then what is it exactly? Cultural or emotional maybe? I suggest that we need to get to the bottom of this because both parties agree that existence is absolutely amazing. But only one party has logic, reason and evidence on their side: and it’s not the atheists. I know that sounds a bit strong, Lizzie but that is my honest opinion. If atheism had anything rational, empirical or otherwise persuasive about it, I would have mentioned it above. And it leaves me wondering: why on Earth does Lizzie, an exceptionally intelligent, courteous and reasonable person, believe that the “great many intelligent systems” in our universe all somehow made themselves (when it is plainly obvious that they didn’t!)? Chris Doyle

Dr Liddle: Both proposals are a reconstruction of the remote, unobserved past. Direct empirical tests leading to falsification are impossible. However, we do know something about thermodynamics, chemical kinetics and the subject of the source of functionally specific complex organisation and associated information. Which account for the origin of a case of FRSCO/I, in the context of a machine involved in a self-replicating system using the von Neumann principles, is better warranted? ANS: Absent a priori imposition of materialism, we know the only credible source of codes, algorithms, language, complex funcitonal organisaiton per a wiring plan, etc. We also know that such configs are maximally isolated in the space of all possible configs and that without these subsystems in place and properly working no self replication will be possible, and indeed as this is the protein factory, no anabolic metabolism too. So, the answer is obvious: design is best explanation absent censorship, and is testable on demonstrating the opposite empirically. So -- with apologies to the Elizabethans -- go thee and build thy self-assembling FSCO/I system with self replication and metabolism, without intelligent direction. But, build thou not a simulation merely, but an on the ground kinematic system. At a simpler level, if you can demonstrate that FSCO/I emerges spontaneously from chance based random walks across config space [no oracles, please, and no preloading of targetting information please], hill climbing only after function requiring a complexity of at least 500 - 1,000 bits has been achieved, that would be credible evidence against the inference to design on FSCO/I. A monkeys at the keyboards program, with filtering against say the Gutenberg database of online texts, would do. 73 or for preference 143 ascii characters worth of functional text in coherent language. As has been said from the outset. GEM of TKI kairosfocus

kairos; I found this video you may be interested in: The Stages of Mitosis - molecular animation http://www.youtube.com/watch?v=VGV3fv-uZYI ,,,the site has several more animations that you may find helpful for your work; =============== also of interest: Human Anatomy - Impressive Transparent Visualization http://www.vimeo.com/26011909 bornagain77

So faced with two stories about the origin of the ribosome: A: That it was designed by a designer or designers unknown B: That it evolved by means of the following selectable precursors... Which would you say was the more "empirically testable"? Elizabeth Liddle

Dr Liddle: Morning. Perhaps you should redirect that to Mr Lewontin in his infamous 1997 NYRB article:
Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism.
Looks to me that Just-So stores in origins science are after the fact, ad hoc patches over the facts [look at what happened with discovering cells and soft, stretchy tissue in T Rex dinosaur remains to see what I am questioning . . . ], tend to lack observational warrant per actual evidence, and tend to reflect an a priori commitment to materialism. A proper explanatory hypothesis, by contrast is empirically grounded, seeks to move towards the truth without a priori censorship on what is possible, and is set in the context of not explaining away so that it can be called on with equal virtuosity to "explain" any and all possible facts because it locks one into an a priori circle. At minimum, it should be empirically testable and its core research programme should be subject to the possibility of real refutation, i.e. the armoured belt of auxiliary hypotheses should not be getting into the habit of patching any and all possible leaks. Put more directly science in a metaphysical circle is out. As, Newton implied. GEM of TKI kairosfocus

Gil: Thanks for your reply! You say:
Elizabeth Liddle: Lovely story, Gil,… Sorry, but my story is the opposite of lovely. Nadas miraculously survived Nazi torture (they pulled his fingernails out with pliers and subjected him to much worse torture I won’t describe) and murder in the death camp.
Poorly chosen word on my part. I meant, moving, touching. Apologies.
Group-think is the antithesis of lovely when the group has the power to impose its views through intimidation.
I couldn't agree more.
Intimidation is the heritage of Darwinism in academia. That was the ultimate point of my post. If you are not aware of this, you need to educate yourself.
I'm aware of all kinds of biases in science. However, the good thing about science is that IMO it is ultimately self-correctly. For somewhat unlovely reasons - in science success does not come with supporting the consensus but with changing it. So there is huge incentive to falsify the status quo. Yes, sometimes good ideas struggle for recognition, but in some ways that is as it should be - extraordinary claims require extraordinary evidence. But when you can support an extroardinary claim with extraordinary evidence, then your success in science is assured as it is not with a merely ordinary claim supported by ordinary evidence, though you may get a longer publication list that way. But Impact Factors count :)
Just as an experiment, try telling those with whom you associate in the Darwinian evolutionary community (you’ll need to feign sincerity with your best acting skills!) that you have rethought evolutionary biology, and have come to the conclusion that intelligent-design advocates are really on to something, and that you think Darwinian theory is in need of a major revolution of thought concerning real design as opposed to apparent design in biology.
Well, Gil, unfortunately I don't lie :) However, that doesn't matter, because I have frequently advanced the argument of "Intelligent Design" in the sense that I actually disagree with those who dismiss the idea that there are patterns that are a signature of a set of processes that include intelligence That occasionally raises an eyebrow or two, and often some interest. However, my position is that the common denominator of that set of processes is not "intentional intelligence" as I would put it, but processes that involve deeply nested contingencies and feedback loops. These processes are found, paradigmatically, in human brains, but also, I would argue, in evolutionary systems. In other words, that "intelligent systems" are worth investigating as systems, not just in AI, but in systems like habitats and biospheres. But of course there's nothing novel about that.
Try that experiment and get back to us with the reaction of your peers.
If I could do it honestly, I'd do it in a heartbeat :) But then I wouldn't be able to do it successfully if I couldn't do it honestly, so if you want me to try, you'll have to first persuade me of the argument :) It hasn't happened yet :)
P.S.: Elizabeth, I for one, and I’m sure the rest of us at UD, really appreciate your contributions here. It keeps things lively, and it is evident that you are a very thoughtful, intelligent, articulate, good and sincere person. We just think that you are wrong, and you think that we are wrong. The truth is not in the middle, however. Either design exists in the cosmos and living systems, or it does not.
Thanks for the welcome, Gil :) I appreciate it. I agree that the truth is not "in the middle". However, I do think that the truth lies in an understanding of what constitutes a "design" system, whether in a brain or outside it. Also in a clear understanding of what constitutes "intention". I think the universe includes a great many "intelligent" systems, by which I mean systems that incorporate what look like highly ingenious feedback mechanisms to maintain themselves in existence, and that these are often nested - our cells are "intelligent" homeostatic systems nested within homeo-static tissues and organs and organisms; organisms themselves may be "intelligent" homeostatic systems in the sense we more normally use the word. And populations are "intelligent" systems at yet another level of analysis. However, only, to our knowledge, at the level of the organism, and even then, only in some organisms, does that intelligence reach much beyond the immediate to weigh up future benefits against present benefits, thus forming what we call "intentions". But I think that viewed in that nested way, the whole thing hangs together very nicely IMO. It's not a conventional view, although not that original a one neither. And perhaps I could express it by saying that I think that it is vital to understand biology at the systems level, and to recognise that at the systems level, we see what is reasonably well described as "intelligence". Denying that is foolish IMO. But so, IMO, is stopping there, and inferring some external designer! And this is why I keep saying that the objection to materialist that it is "reductionist" is to make the same mistake as materialists sometimes make when they say it is! Materialism need not, and should not, IMO, be "reductionist". Systems have properties that their subsystems and sub-sub systems do not, therefore systems cannot be "reduced" to a list of subsystems. And highly complex systems that result in the utilisation of energy to maintain patterns in existence over time cannot be "reduced" to chemistry, or atoms, or hadrons and leptons. They have to be understood at the level of the system, and some of those systems have properties that we recognise as at least a kind of "intelligence". And some of those systems are people who have the Thing Itself :) Oops, short post turned into a long one. Be back soon! Cheers Lizzie Elizabeth Liddle

How do you distinguish between a hypothesis and a "just-so story", jstanley? Elizabeth Liddle

There are specific ~~hypotheses~~ just-so stories concerning the evolution of the ribosome, for instance, also for the origins of the first protocells.
FIFY. :) jstanley01

Elizabeth Liddle: Lovely story, Gil,... Sorry, but my story is the opposite of lovely. Nadas miraculously survived Nazi torture (they pulled his fingernails out with pliers and subjected him to much worse torture I won't describe) and murder in the death camp. Group-think is the antithesis of lovely when the group has the power to impose its views through intimidation. Intimidation is the heritage of Darwinism in academia. That was the ultimate point of my post. If you are not aware of this, you need to educate yourself. Just as an experiment, try telling those with whom you associate in the Darwinian evolutionary community (you'll need to feign sincerity with your best acting skills!) that you have rethought evolutionary biology, and have come to the conclusion that intelligent-design advocates are really on to something, and that you think Darwinian theory is in need of a major revolution of thought concerning real design as opposed to apparent design in biology. Try that experiment and get back to us with the reaction of your peers. P.S.: Elizabeth, I for one, and I'm sure the rest of us at UD, really appreciate your contributions here. It keeps things lively, and it is evident that you are a very thoughtful, intelligent, articulate, good and sincere person. We just think that you are wrong, and you think that we are wrong. The truth is not in the middle, however. Either design exists in the cosmos and living systems, or it does not. GilDodgen

My, my, Elizabeth. I thought you weren't a reductionist. Yet the first refuge you take in response to Upright BiPed's question is, well here's a part, and there's a part ,and every where there's a part part.... And voila! Explained. Mung

EL, "But the fact is that many smart people disagree for good reasons." Would those reasons be supported by any direct experimental evidence showing that material processes are even capable of creating the specific properties and dynamics (those you and I have have discussed) observed regarding the rise of information, and the exchange of information? This is a central question Dr Liddle, I do hope you'll answer it appropriately. "Appropriately" in this instance would be the answer "YES" if there are any experiments that demonstrate to some degree that chemistry can (upon its own physical forces) result in the rise of representations and the protocols that actualize them --or-- the answer "NO" if there are no such experiments available to cite. Are there any such experiments available to cite, Dr Liddle? If there are, then you answer is "YES", but if there are not, then your answer (by any rational implementation of intellectual honesty) must be "NO" Upright BiPed

Liz: "They may be wrong, and may, ultimately, be impossible to verify," Slick. junkdnaforlife

It depends what, specifically, you are talking about, Upright Biped, and at what level of theory. There are specific hypotheses concerning the evolution of the ribosome, for instance, also for the origins of the first protocells. Also for tRNA. They may be wrong, and may, ultimately, be impossible to verify, because the relevant data is unobtainable. But that isn't the same as saying that no materialist explanation is possible, or even plausible. I do realise that many people here, yourself included, consider that there is something fundamentally implausible about information being created by material mechanisms. But the fact is that many smart people disagree for good reasons. Again, they may be wrong, but to assume that they are obviously wrong is to seriously misunderstand the counter-arguments to your position. Is my point! Elizabeth Liddle

It’s possible the theories are wrong (some of them almost certainly are) but people don’t support them because they are scared of looking stupid, or being fired, but because they are smart, well-informed people, and they think it makes sense, and that the counter-arguments don’t.
Interesting comments Dr Liddle. Tell me, what exactly is the materialist' theory for the rise of the discrete representations and protocols that make the transfer of biological information possible? Given the gravity of the role that biological information plays, surely this is one area where we would not want to assume too much, no? Upright BiPed

um underestimate. oops. Elizabeth Liddle

Lovely story, Gil, but completely irrelevant to Darwin. And depending on what the "random cacophony" really was, possibly even irrelevant to the music. I know it's a tempting fable, the Emperor's New Clothes - the idea that a widely accepted idea is only accepted because people are too scared to admit they don't believe it - but it is simply not applicable to evolutionary theories about biology. It's possible the theories are wrong (some of them almost certainly are) but people don't support them because they are scared of looking stupid, or being fired, but because they are smart, well-informed people, and they think it makes sense, and that the counter-arguments don't. I am in that camp. Don't underestimage it :) Elizabeth Liddle

Gil, this is an excellent post. Any naturalistic account of life is just ridiculous. Another great analogy is the fairy tale of the Emperor's New Clothes. In a decade or two, if it takes that long, it will be impossible to find anyone who will admit to ever believing such utter nonsense. How clueless must one be to believe that biological information can be generated by the laws of physics? Pretty clueless... tgpeeler

Berceuse, It's all part of the group-think package in academia. Diversity is great, as long as everyone thinks alike. The other factor is fear of chastisement by one's peers. If you think that atonal music, atheism and Darwinism are bunk, you dare not speak out, and must applaud along with the crowd. GilDodgen

I could be way off the mark, but it seems to me that the ones who champion modern atonal music as not only high art but superior to euphonic music are typically the same individuals who have an atheistic/materialistic view of the world. I wonder why that is. Berceuse

This is another good example of speaking truth ot ones opinion of the truth in a free nation. Ignoring all pressures to be silent. May i do so too. I'm glad this , Jewish I presume, man escaped the Nazi's. yet that doesn't mean that if the Nazi's had not turned against the Jews they still would of been on the allies side. In fact as in WW1 they would of been loyal German or austrian etc citizens and trying to kill us. The priority is always ones own people and friends. Then the rest of mankind. This man got Americas good things and did all right for most of his life. Many Americans, and Canadians, lost people in the war and didn't get the good things and even suffered from the foreign competition. Is this man any different then the rest of them and merely a victim? I understand the Jews over there were the backbone of the soviet union and very powerful in pre-WW11 Europe. they were a important part of the foundations that led to the native uprisings and the lack of Christian resistance. As in origin subjects let investigation be done first before conclusions about what the truth is. I'm speaking truth as I see it here. Weigh the evidence of good and evil and right and wrong. As in origin subjects time changes conclusions about interpretations. The author makes a good example for resisting error and evil. Evil is simple to figure out but error requires more reflection after investigation. Robert Byers

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