The Book is not the Ink and Hardware is not the Software

r7: If you think you can't explain it, you can maybe quote from Floridi, or anyone else. Take your own responsibilities, instead of just suggesting a bibliography! gpuccio

Perhaps Luciano Floridi can exlain it better than I. Try this: Chapter 6 Biological infromation from Information: a very short introduction, 2010, Oxford University Press. rhampton7

"Therefore the cellular machinery is created by humans." It is a caricature. Nobody says that. The bad thing about this statement of yours is that you know it is not true and yet you say so. Eugene S

r7: You really confound me. Quantum theory, Physical information, and the difference between the MTC and the Philosophy of Semantic information — what you claim must be true is, as of yet, just an metaphysical assertion. What is a metaphysical assertion? I don't understand your point. Let's clarify: I am not saying that information is not physical quantum information, but semantic information. I am just saying a very obvious thing, that physical quantum information certainly exists, and is not semantic information, and that semantic information is another thing, and is always the product of a conscious being. Do you understand? We are talking of two different things. Both certainly exist. There is nothing metaphysical in this concept. Photons may have information or not: it depends on how we define information, and on what we are going to discover in the still rather problematic field of quantum entanglement. But, anyway, even if photons do have information (in the sense of physical information), still that is not semantic information (that is, the explicit product of a cosncious representation). You say: the universe appears to function without self-awareness Maybe. Or maybe not. Very imply, that is not the point we are discussing. We are not discussing the universe. We ar discussing designed things. And we are not discussing whether the universe is designed or not, because, unless I have been distracted, we are not discussing the cosmological argument. And even if we were discussing if the universe is designed or not (which we are not), in any case the universe could well have been designed in its beginning, and then kept going without what you call "self-awareness". Or the universe could just ne self-aware, and you be wrong. The point is, nothing of that is pertinent. We are discussing designed things inside the universe, and designed things inside the universe are the product of conscious representations. We are not discussing the self-awareness of the whole universe, but the awareness of beings inside the universe, manifesting in specific temporal history. We are discussing the design in human artifacts and in biological proteins, that, if I am not wrong, both originated well after the big bang. Furthermore, the existence of a conscious observer outside the universe is a metaphysical claim. Perfectly correct. That's why it is not what we are discussing in ID, in a scientific context. But the existence of a designer of biological information is not, in itself, a metaphysical claim. It could have metaphysical implications (like any scientific view), or just not. But in principle, it is an attempt at explaining what we observe, and therefore a perfectly scientific claim. So to state that 1) a photon emitted from a radioactive decay event must have a higher meaning and/or purpose; and that, 2) (a) supra-universal intelligent agent(s) must therefore exist; is necessarily a metaphysical assertion. IOW: an article of faith. OK. But I have never done any such statement. So, let's recapitulate. What I am stating is: a) that consciousness is a fact, that we perceive directly in ourselves, and infer in others. b) that, being a fact, consciousness must be part of our scientific map of reality, whatever our theories about the ultimate explanations of things. c) that a whole set of observable events, the subjectiive representations of consciousness, cannot in any way be explained by purely objective theoriesn (IOWs, strong AI is false). d) that some fundamental concepts of human cognition (specifically meaning, semantic information and purpose) cannot even be defined without any refernce to subjective representations, that is to conscious agents. e) that design, and the semantic information in it, are always the product of conscious agents. f) that design is onjectively recognizable as such by cosncious agents only if the semantic information in it is complex enough according to Shannon criteria. All of that is empirical reasoning. Nothing of that is in principle metaphysical. I am not saying that cosnciousness is metaphysical. On the other hand, I am cerainly not saying that it is physical. What I am saying is that it exists (which is an empirical fact), and that it cannot be explained by physical theories (which is, IMO, an obvious conclusion, that I have discussed in detailed many times). That can be right or wrong, but nowhere in my reasoning I have used the concept of "metaphysical". Human consciousness may be metaphysical or not (I really don't know, because I have real difficulties in finding a true definition for what is "physical"). But it certainly exists, and it certainly has subjective representations, and it certainly represents meanings and semantic information and purposes. We find nothing like that in the so called "purely onjective physical world" (whatever it is), unless a cosncious designer has outputted semantic information into it. The whole point of ID is that biological information is semantic information, complex enough (by far!) to be recognizable as such, and that therefore the best explanation for it is that it has been designed by one ((or more) conscious intelligent being. gpuccio

I've tried a few searches today and came up empty. I thought it might have been in one of the monkey-typewriter threads, one of which I thought had more than 100 comments, but I can't track it down. I'm not imagining things - really I'm not. As best as I recall, I made the point that a photon contained information about the star that emitted it, temperature, distance, speed, etc. My opponent made the point that these were properties of the star and should not be considered as information. There was a bit more to it than that, but nothing I can quote with certitude. rhampton7

r7, can you provide a link to the conversation you were having, thanks. Upright BiPed

But the concept itself of function can be recognized only by a cosncious observer.

Which goes back to my comment about Quantum theory, Physical information, and the difference between the MTC and the Philosophy of Semantic information -- what you claim must be true is, as of yet, just an metaphysical assertion.

I object to the word “metaphysical”.

So noted, but there is no way around it. There is no empirical method to detect a higher meaning or purpose for the Physical Information of Quantum theory other than a thing's base existence and mechanical function. I had an argument some days ago about photons and if they contained "information" (which I supported). The counter argument - made by an ID proponents - was that a lack of an encoded message meant that the photon did not possess information. Within Quantum theory, however, the photon itself is a singular bit of encoded information regarding the state of the universe at moment C(2) needed to inform moment C(3), and simultaneously a singular bit of a decoded message, the output of the prior moment, C(1), all the while remaining a discrete entity (from the human perspective) the product of the encoded/decoded message. As such, the universe appears to function without self-awareness. Furthermore, the existence of a conscious observer outside the universe is a metaphysical claim. So to state that 1) a photon emitted from a radioactive decay event must have a higher meaning and/or purpose; and that, 2) (a) supra-universal intelligent agent(s) must therefore exist; is necessarily a metaphysical assertion. IOW: an article of faith. rhampton7

r7, Thanks for the link, I had digested that page some time ago. I assume you can see that I am most interested in actual observations. And apparently I have not enticed you to attack my argument directly, so I will leave it at that. cheers... Upright BiPed

Petrushka, GP can choose to answer your silly charge for himself, or not. But I have sense of at least some of the positions he holds on these issues, and you yourself have made comments here and elsewhere that display your position as well. For instance, you say that the action of DNA in decoding information is pure chemistry. And you go on to say that "superimposing a layer of abstraction" is an "equivocation". I would simply remind you that all tranfer of recorded information is physical, so the fact that we can follow a physical pathway for it is hardly a viable argument against its semiotic nature. Also regarding the "layer of abstraction", if you can produce evidence that cytosine-adenine-gaunine is inherently mapped to the binding of glutamine to a polypeptide (in any physical context) as a material property of those three nucleotides (in that specific order), and further if you can produce evidence showing other related phenomena (such as the operational rule of codons being three nucleotides in length) are actually determined by physics - then we'll probably just have to go on the evidence as it is found in nature. I've laid out my argument, and I am fairly sure you have seen it. I would welcome the opportunbity for you to tell me where I have equivocated. Thanks. Upright BiPed

Petrushka, My answer would be that all information, that is instantiated in matter, has ultimately a non material origin, or at least not material in the sense of what we now know /define as the material world. Some day we might find the interface between consciousness and matter and then we will have a clearer view of where information comes from. With our current knowledge of matter and consciousness we can only be amazed by the fact that matter arrange under the influence of intelligence to instantiate information. This is a serious subject of investigation and I have seen great minds engaging with this question. I hold that your materialist notions of information have no empirical support suggesting that information comes from matter arranging itself. mullerpr

r7: You say: "Information need not have a metaphysical “meaning and purpose” beyond its own existence and function" But the concept itself of function can be recognized only by a cosncious observer. I object to the word "metaphysical". I would just say that information, as meaning and function and purpose, exists only in cosnciousness, and is only transmitted by a non conscious vehicle. That the physical vehicle can determine restraints to the transmission of information is certainly true. But that does not change the fact that information is such only in subjective representation. Shannon's work is very deep and pertinent, but it has nothing to do with the meaning, and therefore with semantic information. Indeed, it is not a theory of information, but rather of communication. The ID theory, in all its forms, gives special importance both to the semantic value of information and to its mathemathical complexity. The concept of specification is strictly connected to the meaning of information, to its origin in a conscious purposeful representation. On the other hand, however, the computation of the complexity of the information is done according to the concepts of Shannon. gpuccio

It's true that humans have been "imparting into physical media 'meaning and purpose' for millennia". But note what gpuccio said:

Information is about the meaning conveyed to a conscious observer ny the form imparted to the physical medium

That's why I cited quantum theory and physical information. Information need not have a metaphysical "meaning and purpose" beyond its own existence and function. Furthermore, the "separation between information and its physical medium" isn't an absolute (i.e. quantum theory and physical information). This article on the Semantic Conceptions of Information explains the difference between the mathematical theory of communication (MTC) -- which is inclusive of Shannon's information theory and hence the math that supports the work of Dembksi and Meyer -- and a philosophical understanding of semantic information:

The mathematical theory of communication approaches information as a physical phenomenon. Its central question is whether and how much uninterpreted data can be encoded and transmitted efficiently by means of a given alphabet and through a given channel. MTC is not interested in the meaning, “aboutness”, relevance, reliability, usefulness or interpretation of information, but only in the level of detail and frequency in the uninterpreted data, being these symbols, signals or messages. Philosophical approaches differ from MTC in two main respects. First, they seek to give an account of information as semantic content, investigating questions like “how can something count as information? and why?”, “how can something carry information about something else?”, “how can semantic information be generated and flow?”, “how is information related to error, truth and knowledge?”, “when is information useful?”... Second, philosophical theories of semantic information also seek to connect it to other relevant concepts of information and more complex forms of epistemic, mental and doxastic phenomena.

The key insight is this:

At one extreme of the spectrum, any philosophical theory of semantic-factual information is supposed to be very strongly constrained, perhaps even overdetermined, by MTC, somewhat as mechanical engineering is by Newtonian physics. Weaver's optimistic interpretation of Shannon's work is a typical example. At the other extreme, any philosophical theory of semantic-factual information is supposed to be only weakly constrained, perhaps even completely underdetermined, by MTC, somewhat as tennis is constrained by Newtonian physics, that is in the most uninteresting, inconsequential and hence disregardable sense (see for example Sloman [1978] and Thagard [1990]).

rhampton7

r7: Please, note in the previous definition the two aspects of the word, completely consistent with its true meaning: a) "a message (utterance or expression) or collection of messages that consists of an ordered sequence of symbols". That refers obviously to information coded symbolically in a physical medium. b) "the meaning that can be interpreted from such a message or collection of messages". That refers obviously to the conscious representation and intuition of cognitive meaning that only a cosncious observer can derive form the information coded in the physical medium. In all cases, semantic information is a "message", something that allows the passage of a specific representation from one conscious being (the designer) to another conscious being (the observer/recognizer). That has been true for millennia, and it is still true for all persons of sense. gpuccio

r7: As UB has already pointed out, I was not referring to that kind of use for the word information, which is not pertinent to our discussion. Please, look at the first definition in Wikipedia article about information. I quote it here for you: "Information in its most restricted technical sense is a message (utterance or expression) or collection of messages that consists of an ordered sequence of symbols, or it is the meaning that can be interpreted from such a message or collection of messages." As you can see, this definition, which reflects very well the most common and pertinent use of the word, the semantic use, as again UB has well pointed out, is the only definition pertinent to our discussion. And it is completely connected to cosnciousness, and to the concept of meaning. gpuccio

r7, GP makes the statement that humans have been imparting into physical media "meaning and purpose" for millennia. You suggest that his definitons do not "comport with quantum theory as exemplified by the Black hole information paradox" and you further suggest that "confusion arises from failing to articulate a particular meaning" My comment is that GP's view is well established. Relating my comment to DNA is simply a result of this being an ID blog where these things are often discussed in relation to origins, biology, and other topics under the general heading of ID. Moreover, I was tempting you to assist me by attacking my argument, where I think the definitons of terms and their observable physical properties are well defined. Upright BiPed

I apologize, I have inadvertantly assigned Cabal's statement to Petrushka. My apologies. Upright BiPed

Pet, My comment was specifically relatd to your post. You said "essentially, it is all chemistry, nature at work". I challenge that, and gave a link to contrary evidence. "Shifting definitons" seems to be your counter argument as oppossed to commenting directly on the evidence that refutes the statement you made. Upright BiPed

Speaking of babies, just holding your breath till you turn blue doesn't make your assertions true. You may stamp your feet and have public tantrums, but it doesn't change reality, which existed before your consciousness and will continue to exist after you are gone. Petrushka

There's a name for the shifting of definitions in mid argument. It's equivocation. The cellular machinery is a compiler. Compilers are created by humans Therefore the cellular machinery is created by humans. Petrushka

Upright BiPed, I'm confused as to how your reply relates to gpuccio's comment -- the reason for my reply to gpuccio, et al. rhampton7

Petruska,

Provide an example of information that has no physical instance.

Provide an example recorded information that doesn't use physical representations and protocols. Upright BiPed

r7, The transfer of information from DNA does not involve the Black Hole information paradox, and nor does it require a conscious observer. It is semiotic Upright BiPed

There is nothing that preclude information processing to happen before it instantiate in a physical form.

Provide an example of information that has no physical instance. Petrushka

It finally occurred to me what has been bothering me about this discussion about information. The type of definitions put forth by gpuccio and others does not comport with quantum theory as exemplified by the Black hole information paradox, because it relies on the concept of Physical information (link to wikipedia article with a brief discussion on the various, distinct meanings and uses of information) which has no need for a conscious observer to convey a meaningful instance of information. I think it would be in everyone's best interest to review the article, as it makes clear that confusion arises from failing to articulate a particular meaning. rhampton7

DrRec: "No, it doesn’t, and the paper doesn’t contain the information. The information is represented in the pattern of ink that lies on the papers surface. To create the information you have to add material." ===== All communications/Languages/Codes etc have patterns. All Western European Languages use Roman letter patterns, Ancient Egyptian used hieroglyphic patterns, Eastern Europe uses Cyrillic alphabet patterns, Chinese and Japanese use their own characters as paaterns. But the one thing these patterns have in common is they come from intelligence. Not all patterns in nature have codes or languages. The Grand Canyon is NOT a code or language. Neither are the stars of the Heavens for which Astrologers tried to influence others. The pattern of writing on a paper as we ALL know it comes from minds. DNA by it's very complex and sophisticated communications with it's blueprints, plans, ideas schematics, bytes & bits, etc, etc, etc show us a behavior that infers intelligence. Like it or not, blind undirected forces without purpose loses everytime. Eocene

Cabal, what do you call someone who openly denies observable evidence to the contrary? Upright BiPed

It is interesting to observe how our darwinist friends need to rewrite all concepts about information, software and hardware, concepts that are now clear even to babies! So, now they say that information is not a correct abstract concept because it needs a physical medium to be written down... I suppose we should mention that to Microsoft and a gorup of other people. After all, it's all electromagnetism, nature at work! All this is ridiculous. That is the proof of how far apparently intelligent people must go when they have committed themselves to defending a fundamental original bias in their view of the world. I repeat here: nobody can define concepts such as meaning, purpose or information without any reference to consciousness. These are all concepts derived from conscious representations. The failure of strong AI to derive consciousness and its subjective events from purely objective patterns is also the failure of darwinism to derive information from purely objective explanations. A conscious designer is needed to produce designed things imparting information to matter. And a conscious observer is needed to recognize that information as such. gpuccio

Cabal: essentially, it is all chemistry, nature at work This is one of the most senseless statements I have ever read. I will mark it for future reference, thank you. gpuccio

We can change the state without putting specified information in it. The RAM is still a RAM Information is neither matter nor energy- true matter and energy are mediums for information Joseph

Altering the state of the capicitors does not change the part into something else. Also the information is not the pattern but the recognition- ie mental recognition- of the pattern. Information is neither matter nor energy. Joseph

“OR you can change teh sequence and have the ribosome reject it.”

No idea what you mean here.

The ribosome is a genetic compiler!

The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist.

Think about it- What happens to a newly written or modified computer code that has an error? All new and modified codes have to go through a compiler. A compiler is nothing if not an editorial perfectionist! I bet if we were to watch we would see the compiler doing its thing right up to the point the error occurs and then spits it out much faster than if the code was OK, ie error free. Biologists need to be introduced to and experience computer science. Then this sort of discovery wouldn’t be so “shocking”. Compiler- source code in, object code out. Ribosome- mRNA in (string of nucleotides), polypeptide out (string of amino acids). Joseph

kellyholmes:

It seems you use you blog as a forum to threaten others with violence, abuse them in the most disgusting ways and generally act in quite a different manner to which you comport yourself here.

It seems you have reading issues as I treat people as they treat me and other IDists. IOW kelley it appears that you condone the nastiness of evotards. Joseph

Clive, Is that what happened here: https://uncommondesc.wpengine.com/intelligent-design/a-word-about-our-moderation-policy/comment-page-11/#comment-309228 paragwinn

Compiler- source code in, object code out. Ribosome- mRNA in (string of nucleotides), polypeptide out (string of amino acids).

Water, sugar and yeast in, alcohol out! (Although today I prefer going to the liquor store.) The point is, we may use language to create different views of the same thing but essentially, it is all chemistry, nature at work. Cabal

DrRec: I agree that a change in information is always accompanied by a physical change in the physical medium where information is stored. But that in no way makes the separation between information and its physical medium difficult or ambiguous. Information is about the meaning conveyed to a conscious observer ny the form imparted to the physical medium. It is essentially a consciousness related concept, implying the fundamental consciousness related concepts of meaning and purpose. I don't find at all surprising or confounding that a conscious content can be represented in the form imparted to a physical medium. Humans have been doing that for millennia, through books, works of art, and so on. What has become of human cognition, that now people find so difficult to grasp a concept that has been so constantly in our experience for millennia? gpuccio

Putting information inside a RAM does not change the RAM.

Yes it does. In Dynamic RAM writing data would alter the charge state of capacitors.

Putting information on a piece of paper does not change the molecular structure of the paper.

No, it doesn't, and the paper doesn't contain the information. The information is represented in the pattern of ink that lies on the papers surface. To create the information you have to add material. DrBot

kellyhomes,

Previously Clive has banned people here for things they have said on other sites, unrelated to this one. I guess double standards are only OK if they help your supporters…

Only if they were outed as a sock puppet on another site and banned previously. Clive Hayden

Petrushka, Your certainty about the relationship between energy and information processing is only founded in a presupposition of materialism and completely ignore the points made by Deutsch in his talk. If you can show insight into Deutsch's position on materialism highlighted in his talk then you will have to admit that there are no known physical barrier for information processing. There is nothing that preclude information processing to happen before it instantiate in a physical form. This non-material aspect seems to be required to instantiate things like creativity, love etc. How stupid does Reductionism look when it tries to explain the artifacts of intelligence... Another thought... How about the modern notions of information escaping from black holes? mullerpr

Alternatively it wasn't so much an insight as a bit of a muddle :) Referring to "information" as an agent is fraught with problems. Elizabeth Liddle

Physical things that "process information" are changing their physical state while doing so. Every instance of information is also an instance of a physical entity. Talk about defying entropy. Try processing information without expending energy. Petrushka

I tried, but it is clear that you are sufficiently obtuse not to grasp the insight that was presented to you. All the best... mullerpr

My point here, from post 1, is that the hardware/software analogy is tortuous, and leads to misunderstandings. Your link doesn't do much to suggest otherwise, or convince me the physical state of a processor is unchanged as information is passed to it, as JoeG suggests. DrREC

DrREC, It might stand you in good stead to consider the insight of David Deutsch presented in this post. Information is not defined by physics, it is as far as we know simply instantiated in physical things. The greatest wonder of it is that it can change the state of physical things profoundly. Going against this observed reality has no support in nature or consciousness. mullerpr

Could you give an example of where “software is loaded” in biology? As per comment 10. If software and hardware exist in biology then can you give a couple of examples of what specific biological structures represent hardware and software? Also how much ram does the hardware have? What programming language is the software in?

I think that is what the biologist and "allied sciences" researcher within the ID "movement" is attempting to discern at present, is it not? Specifically, things like "How much RAM does the hardware have?" or even more fundamentally "Does it (system) have RAM at all or is it all ROM?".

One of the features of language is that it can be translated into other languages.

I assume you mean "programming" languages? If so, then the "feature" you call out only exists because each "high level" language serves as an abstraction from the hardware's logic circuits. Logic circuits which are designed to produce certain "states" (i.e. on or off) given external stimulation (current of a particular voltage). Interestingly enough, the arrangement of the logic gates in a CPU's arithmetic logic unit (ALU) has a significant impact on the performance (usually measured in time) of the CPU at performing addition, subtraction, and basic logic operations such as AND/OR. Similarly, in the "genome" world, the arrangement of proteins in a DNA have a significant impact on the processing of that DNA does it not? Perhaps, as in the case of ALU design, there are "optimizations" of the arrangements that exist to achieve a desired outcome more quickly or efficiently? The CPU (general purpose processors) translation of the results of the execution of logic gates (i.e. voltage manipulations of transistors)in a particular arrangement into "0" and "1" produces machine code (0s and 1s in a particular sequence). My understanding of cellular hardware is that its execution of DNA (i.e. transcription, loosely) produces RNA which is proteins in an ordered sequence is it not?

Would you be able to translate some of the “biological software” into, say, Pascal? Or Forth? Or Python?

The languages (Pascal, Forth, and Python) you mentioned are all fairly abstracted from the hardware. They are high level languages in that respect. I speculate that the "language" represented by DNA is more akin to a machine language. I think once we understand the base "logic" (i.e. AND, OR, XOR, etc...) of the machine language being used then we can begin creating abstractions from the hardware. I think, in the biology world, we are still trying to decipher what logic is being applied and how the hardware creates an environment for the execution of that logic. Perhaps when we understand "enough", we can talk about creating language abstractions. There are researchers that are attempting to utilize the biological hardware to solve problems using our developed logic (AND, OR, aritmetic, etc...). Specifically, with respect to using DNA to input the "problem" and having cell systems "solve" for that problem. See this reference: Computing with DNA However, note that this would be co-opting the biological hardware and its native machine language to solve some of our logic problems. Though, this sort of research does bode well for identifying the sorts of "logic" capable of the biologic hardware.

If not, is “software” really the right name for it? Presuming that you can actually come up with some examples of “biological software” in the first place, of course.

I think it depends. If by "software" you really mean an application program, most (if not all) software is "written" in a high level language. It is always executed in machine language. Language with facilities specific to that platform (i.e. Complex Instruction Set Computer [CISC], Reduced Instruction Set Computer [RISC], and Exclusively Parallel Instruction set Computers [EPIC]). If you are referring to the DNA then I would probably say the metaphor to use is a machine language. If you are referring to the functionality provided for by the cellular and organ systems, then I would say the metaphor to use most likely would be assembly language (a singular abstraction). If you are referring to the complex functionality that occurs in both conscious and unconscious thought, then most definitely you could use software as a metaphor. ciphertext

You can't load software onto a molecule? Maybe, if you're just talking about one molecule. But I hope you're not suggesting that you can't load software onto a sequence of molecules? How do you think software is represented in a physical medium -- surely through an arrangement of particles, whether on a hard disk, magnetic disk, DNA or otherwise. Eric Anderson

"Putting information inside a RAM does not change the RAM. " Of course it does! Digital information isn't magical, or disembodied from the physical. For example, the capacitors of an integrated circuit represent bits 0 or 1 based on the state of their charge-charged or discharged. That is a physical change. DrREC

Unfortunately your "evidence" and "reasoning" leave much to be desired. Putting information inside a RAM does not change the RAM. Putting information on a piece of paper does not change the molecular structure of the paper. Joseph

It's true that sometimes I simply state what I think to be true, Joseph. But I will always cite evidence or provide reasoning if asked, and have done so, repeatedly, in this case. However, thank you for addressing my question:

How do you program a molecule without altering it? Well again information is neither matter nor energy, so why would putting it on/ in a molecule change it?

But I find your answer very odd! How would you put information on/in a molecule without changing it? Can you give me an example? Elizabeth Liddle

Elizabeth- you always baldly assert and that is why I always respond with TINAE. If you can't grasp that then you have a problem. How do you program a molecule without altering it? Well again information is neither matter nor energy, so why would putting it on/ in a molecule change it? Joseph

Dr REC:

Joe, you know changing the DNA or mRNA sequence changes the protein.

Not necessarily.

Are DNA or mRNA elements that code and bind other proteins for regulation hardware of software?

Hardware “programmers program disks without altering the disk- the prom is still a prom.”

And nothing on the disk changes when they do that?

It is still a disc- it's chemical and physical properties are the same. But sure once programmed it is a programmed disc with little deformaties that denote the program. Joseph

I asserted nothing, Joseph. I asked you tell me something. Asking someone to tell you something is the opposite of asserting something. Let me repeat my request: Tell me how you “program” a molecule, without altering the molecule. And if you do alter the molecule, tell me in what sense that not a hardware change. Thanks. Elizabeth Liddle

Question 1. Correct! Information exchange is successful only if you have a priori defined common: 1. alphabet. 2. language. 3. semantics.

I did not say that, Eocene. I was answering your question about about "text". I did not generalise to "information". whether it generalises depends on your definition.

Question 2. While these may be of help, they are not critical for inferring design.

Your question was not "was it designed"? It was "can you tell that it was written by a human"? The information I gave is absolutely critical for inferring human authorship. These are not mere nitpicks, Eocene - this kind of equivocation lies at the heart of the ID fallacy (my view is that the ID inference is a fallacy). You might, or might not be able to infer "design" even if the think clearly pre-dated human culture. However, we know there is another alternative to "design" for such patterns, and that is self-replication with heritable variance in reproductive success. So, provided the scroll seemed to have no self-reproductive capacity, I'd infer that it was the artefact of something that did. Otherwise, my inference would not be justified.

Question 3. “It depends…” I define information in the sense of Shannon.

Please give the definition itself. Thanks.

Question 4. The answer is, “No known examples today”. The difference is outlined here.

That answer makes no sense to me. I asked what you mean by "self-organising". Substituting:

Can you give at least one provable example of genuine no known examples today (not to be confused with self-ordering)? Life does not count as such an example simply because we want to prove or disprove the ability of living systems to no known examples today. So again, the question is whether you can give at least one example of no known examples today in the true sense in non-living matter.

:D Please give me your definition of "self-organisation". The paper you cite is useless. Abel goes on and on about how other people are using "sloppy definitions" and how important it is to have a rigorous one - and then does not give one! Just keeps going on about how Chaos doesn't count and "self-ordering" doesn't count, and about his "Cybernetic Cut". No-where is there even an attempt at an operational definition of self-organization. And to answer your question, obviously, we need one. Can you give me yours? Elizabeth Liddle

I started this thread by stating what a disaster this analogy is for the discussion. Thanks to Joe for demonstrating this. Joe, you know changing the DNA or mRNA sequence changes the protein. Are DNA or mRNA elements that code and bind other proteins for regulation hardware of software? What about a RNA virus, or catalytic RNA. "programmers program disks without altering the disk- the prom is still a prom." And nothing on the disk changes when they do that? DrREC

The finetuning is still obvious. Its precision is O(nanometer). Eugene S

Eric, Absolutely! The question is how it was possible that the same physical properties of matter lead to such a difference in behaviour within and without the cell: complexity of organisation vs chaos or order without complexity. Eugene S

The ribosome is a genetic compiler!

The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist.

Think about it- What happens to a newly written or modified computer code that has an error? All new and modified codes have to go through a compiler. A compiler is nothing if not an editorial perfectionist! I bet if we were to watch we would see the compiler doing its thing right up to the point the error occurs and then spits it out much faster than if the code was OK, ie error free. Biologists need to be introduced to and experience computer science. Then this sort of discovery wouldn’t be so “shocking”. Compiler- source code in, object code out. Ribosome- mRNA in (string of nucleotides), polypeptide out (string of amino acids). Joseph

Why don't YOU use "I'm going to baldly assert now" And geez Elizabeth programmers program disks without altering the disk- the prom is still a prom. When you download software does the hardware change? Joseph

"And why do you think all those things are required for first life?" Strange indeed. When one wants to prove something, the burden of the proof is usually on his/her shoulders. It is not enough just to say it may not have been required. I can substantiate this requirement by looking at the cell today. How can you substantiate your claim? For a cell to function as a whole (at the very least, metabolism and replication) a lot is required by definition. Eugene S

Why don't you use an acronym, Joseph? TINAE. Tell me how you "program" a molecule, without altering the molecule. And if you do alter the molecule, tell me in what sense that not a hardware change. Elizabeth Liddle

Cell software is whatever is responsible for reading codons in and processing them (the "what" part). Each codon encodes a set of actions. By virtue of this it complies with a certain software interface. Hardware is whatever stores the codons (the genes) and makes sure the information is physically transmitted between senders and receivers (the "how" part). Eugene S

There isn't any evidence that the hardware is the software. The molecule is programmed- the program is the software. Joseph

Kelly:

How does ID explain the origin of the “information” you mention? If it’s not a property of the matter in which it is encoded then how *did* it get encoded into matter in the first place?

By design- just as programmers encode information onto a disc or into a prom

When/where/how/how many times etc?

That is what science is for. Geez your position doesn't have any answers and it has all the resources... Joseph

How about this java like snippet... Sequence mySequence = getSequence(DNA); Codon currentCodon = mySequence.getCodon(0); If (!firstCodon.equals(AUG)) { System.exit(-1); } Iterator it = mySequence.iterator(); while ( it.hasNext() ) { currentCodon = it.nextCodon(); process(currentCodon); } Eugene S

1.1.1.2 Elizabeth, Thanks. Question 1. Correct! Information exchange is successful only if you have a priori defined common: 1. alphabet. 2. language. 3. semantics. You are right, jibberish is defined only with respect to those three above, i.e. whenever something does not comply with the three above, it is jibberish. However, there may be defined common alphabet, language and semantics that what was jiberrish before, becomes a meaningful piece of information. There is no evidence of those three emerging at the same time with participants involved in information exchange. Information exchange rules may well become more elaborate on the go, but to kick off information exchange in the first place you need those three above well defined a priori. In practice this is defined by intelligent agents. There are no known cases of this being defined spontaneously. So by far the best explanation for information exchange if we see one is intelligent design. Question 2. While these may be of help, they are not critical for inferring design. Question 3. "It depends..." I define information in the sense of Shannon. Question 4. The answer is, "No known examples today". The difference is outlined here. Eugene S

kellyhomes: What's the problem with you? The sequence of nucleotides coding for a protein is obviously software. The nucleotides themselves, the physical gene itself, are obviously hardware. What's the problem? gpuccio

But the real problem is how do blind undirected purposeless forces accidently screw with chemcial toxic waste cocktails create even one intelligent code.

Well, yes, sort of, but lets remove the loaded terms however. Chemicals can only be "toxic" in the presence of something they are "toxic" to. So before you have something that can be poisoned, you don't have a poison. You might want to phrase that as "chemicals that are toxic to modern life forms". As for "waste" - again you viewing pre-biotic conditions from a post-biotic perspective - "waste", like "noise" and "weeds" is only meaningful relative to some thing someone wants. "Waste" is what is rejected by some process. Without some process to do the rejecting, you don't have "waste", and even when you do, it's a relative term! A wildebeest's "waste" is a dung beetle's dinner. And we've already got "undirected" in there, so we don't need "purposeless" or "accidentally", and "screw" is a bit emotive. Also "blind" and "undirected" essentially mean the same thing, so let's stick with "undirected": So let's edit: "But the real problem is how do undirected purposeless forces acting on a cocktail of organic molecules create even one intelligent code." And the hypothesis put forward by Szostak is that lipid vesicles, which form spontaneously within certain "cocktails" are permeable to organic monomers but not to polymers. As monomers enter the vesicle, those that form polymers are then trapped within it. Some of these polymers become self-replicators (we know of some self-replicating polymers but what these were is still up for grabs). The vesicles tend to grow, by "eating" other vesicles (this is the part the Szostak lab has been working on), so that they tend to grow into tubular structures that then tend to break up, simply owing to mechanical forces. If those vesicles contain self-replicating polymers, the "daughter" vesicles will "inherit" the sequence of polymer contained in the "parent". So we have the first information transfer - from "parent" to "daughter" vesicle. But so far the information isn't doing anything, so we might no even want to call it information. However, if certainly polymer sequences enhanced the chances that a vesicle would eat rather than be eaten, and divide successfully, clearly vesicles containing those polymers would start to dominate the vesicle population. And now we have evolution, and real information transfer, because the sequence of polymer actually contains "information", passed from parent to daughter, about how to enhance the chances of reproduction. It's not very intelligent code yet, but it's got something, and, more importantly, it's got something that can be built on. Elizabeth Liddle

Indeed, such language and degraded experessions are yet another part of your articles of faith and worldview as you see it.

Goodness me, Eocene! That's another allegation (slander IMO) that you need to support! And the standard of argumentation you seem to be rising to this morning is no higher than that of a playground! "well, you guys do it too, and anyway you smell". Since when did two wrongs make a right? And since when were "such language and degraded experessions" part of an atheist "articles of faith"? Atheists are people who don't find the evidence for God or gods convincing. Some think the evidence actually supports the position that they don't exist. Period. Now please stop tarring good people with a tarbrush of your own manufacture. Sure some atheists are rude. So are many theists. tbh you are being pretty rude right now! Elizabeth Liddle

kellyhomes: "And by not condemning but instead condoning Joe’s behavior those expressions are now part of your articles of faith too." ===== And what part of the "While I don't agree with the JoeG approach" didn't you actually get ??? Next time get a clue. On another note, the post you replied to him and refering to didn't actually have any of those JoeG-isms as you suggest. Rather you brought up the language issues which he and your side are prone to do on his own separate blog as even he readily admits, yet it had ZERO to do with any of the topic here or anything he actually said here. So apparently besides the "Burden Shift" tactics you are prone to use here, you also find "deflecting off topic" as another one of those adaptive traits when your answer Tank is running on empty. Maybe you should take off your own double standards glasses and view the real world. Eocene

1. Can you tell the difference between jibberish and a text that has a meaning, e.g. this post?

No. I can say for sure that a text is meaningful; I cannot say for sure that it is not meaningful.

2. When you see an ancient Egyptian or Chinese scroll can you tell that it was written by a human even though you may not know the language? To answer this question do you need to know how and on which medium it was written?

Yes, but I cannot tell whether it is jibberish or not. And while I would not need to know the medium in which it was written, I would need to know that it was written by in a medium that humans can use. That of course includes scrolls. I'd also need to know something about its provenance - how old is it? Were humans alive at the time it seems to have been made? Do we know that humans alive at that time had a written culture?

3. Do you agree that different parts of a biological cell pass information between them?

Depends how you are defining information. But in according to the Merriam Webster definition: "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", yes. The arrangement of nucleotides in DNA produce specific effects, for example the synthesis of specific proteins under specific conditions. Information could also be said to be passed from parent to progeny - information that produces the "specific effect" of causing the development of a phenotype with certain attributes, including attributes that will tend to enhance its chances of survival when compared with an ancestor in which those attributes were not present. This last kind of information - information regarding how to construct a phenotype well-adapted to its habitat - comes from the process of "natural selection" i.e. the differential reproduction of genotypic variants.

4. Can you give at least one provable example of genuine self-organisation (not to be confused with self-ordering)? Life does not count as such an example simply because we want to prove or disprove the ability of living systems to self-organise. So again, the question is whether you can give at least one example of self-organisation in the true sense in non-living matter.

Could you explain what you mean by self-organisation, and how it differs from what you call self-ordering? I asked you this on another thread, but can't remember where, so forgive me if you have already answered it. Elizabeth Liddle

Kellyhomes, Just some further ideas in addition to Question 2. To infer whether the script on the scroll has an intelligent cause, do you need to know who it was written by? In conversations like this one, do we always need to know the country of domicile, year of birth or the genuine full name of participants to conclude that they are humans, not malicious software? Eugene S

Kellyhomes, 1. Can you tell the difference between jibberish and a text that has a meaning, e.g. this post? 2. When you see an ancient Egyptian or Chinese scroll can you tell that it was written by a human even though you may not know the language? To answer this question do you need to know how and on which medium it was written? 3. Do you agree that different parts of a biological cell pass information between them? 4. Can you give at least one provable example of genuine self-organisation (not to be confused with self-ordering)? Life does not count as such an example simply because we want to prove or disprove the ability of living systems to self-organise. So again, the question is whether you can give at least one example of self-organisation in the true sense in non-living matter. Thanks. Eugene S

Yes, Craig Venter's , Gerald Joyce's and Nodel Laureate Jack Szostak's manipulating tinkering intelligences have all been well documented. Eocene

InVivo,

The plain existence of the cell as an exquisite assembly of hardware and software makes an even stronger argument that it was DESIGNED.

Here is a picture of a cell. http://www.mcb.ucdavis.edu/images/advising/cbi/cell-biology.jpg What is hardware? What is software? If you can't say, don't you need to reassess your "argument"? kellyhomes

KellyHomes: "Barry, How does ID explain the origin of the “information” you mention? If it’s not a property of the matter in which it is encoded then how *did* it get encoded into matter in the first place?" ===== Classic 'burden shift'! You can point to almost any OOL experiment done by an evolutionist to illustrate just how intelligence works and manipluates material componants. The problem is not how does intelligence create codes and encode material, we already know and relate to that in real life. But the real problem is how do blind undirected purposeless forces accidently screw with chemcial toxic waste cocktails create even one intelligent code. If the Miller/Urey experiments created intelligent codes as opposed to nothing more than rearranged material substrate, we wouldn't be having this conversation. Eocene

Indeed. It seems that many ID supporters have already made their mind up before they even know about ID and just see ID as validating those prior beliefs with "science" without looking much further into it then the surface claims (buy my book!). And when people move from the designer of life (which, after all, could be aliens) to "the world is designed" and "the cosmos is designed" then it's obvious that no alien could have designed the cosmos it itself lives in and that those people are really talking about god. A poor scientific facade indeed. It also illustrates the inability to actually rule things out of ID and why ID cannot ever be science in it's current form. For example, if the designer is what we understand as "material" it could not have designed the universe itself. That might have been a different designer. But ID cannot, will not, determine if there was more then one or a single designer. It cannot say if the designer is material or other. It cannot say if the designer acts constantly or just once or somewhere in between. What use is ID if it can't answer any questions at all? And if ID is about studying the design, Joseph, then what has ID discovered so far? Can ID tell me a single thing about anything that is currently unexplained? What is the origin of "biological information" Was it "designed"? Lol. kellyhomes

Kariosfocus,

Software is where EXPLICIT, prescriptive, functional info gets loaded into a digital system.

Could you give an example of where "software is loaded" in biology? As per comment 10. If software and hardware exist in biology then can you give a couple of examples of what specific biological structures represent hardware and software? Also how much ram does the hardware have? What programming language is the software in? One of the features of language is that it can be translated into other languages. Would you be able to translate some of the "biological software" into, say, Pascal? Or Forth? Or Python? If not, is "software" really the right name for it? Presuming that you can actually come up with some examples of "biological software" in the first place, of course. kellyhomes

Yes, it seems that designers are inclined to see design. Not surprising, perhaps. Elizabeth Liddle

Well, there are lots potential homologs with computers, but few are a perfect fit, and a cell is very different to a computer in many respects, no least being the fact that it self-replicates! One of the thing that bugs me a bit is the insistence on calling DNA "digital". It is only "digital" at the level of an entire population over time, in which some "digits" are shuffled and produce different phenotypes, which I think is a stretch. Much more interesting is switching at the level of the gene - discrete sequences of DNA can be switched on or off, depending on a cascade of on-off signals from elsewhere. But then we are not just talking about the cell being computer-like but the whole organism, and the "programming" of the cells happens during development, from the toti-potential early cells to the highly differentiated cells we end up with. Elizabeth Liddle

InVivo

As a person with a math and engineering education, I could not reach but a single firm conclusion: that our world is a DESIGNED world, that the LIVING WORLD is a DESIGNED world.

Funny how the vast majority of people who actually study *biology*, the field you are making claims against, disagree with you. Perhaps you should study some and then perhaps reassess? kellyhomes

We have full DNA sequences for many organisms now. Could you point to one such and show me where the "software" is encoded? Could you point to one such and show me where the "hardware" is encoded? If those two things do not make up 100% of the DNA for an organism how does ID explain the remainder? kellyhomes

Barry, How does ID explain the origin of the "information" you mention? If it's not a property of the matter in which it is encoded then how *did* it get encoded into matter in the first place? When/where/how/how many times etc? Can you tell me *anything* about that at all? kellyhomes

Eocene, I thought your side took the moral high ground? Instead we get X does it so it's OK if Joe does it too? Really? Previously Clive has banned people here for things they have said on other sites, unrelated to this one. I guess double standards are only OK if they help your supporters...

Indeed, such language and degraded experessions are yet another part of your articles of faith and worldview as you see it.

And by not condemning but instead condoning Joe's behavior those expressions are now part of your articles of faith too. kellyhomes

And yet that is what every intelligently directing manipulative mind of an Evolutionist has done when they rig an experiment for using a biased personal goal directed purposed outcome.

Please support this allegation. Elizabeth Liddle

And yet that is what every intelligently directing manipulative mind of an Evolutionist has done when they rig an experiment for using a biased personal goal directed purposed outcome. Gerald Joyce actually used previously and specifically intelligently designed replicating molecules working with a chemical catalyst in his experiment which out of necessity used a goal directing computer program to force and select the fittest molecules according to criteria of what Gerald Joyce's intelligent mind wanted/intended. The big problem comes later when Gerald Joyce later proceeded to fabricate a mythical RNA-World story of evolving molecules out competing other molecules for food, having offspring or babies, etc, etc, etc and all the while sneaking in the concept of self-awareness in this phony fabled RNA-World experiment. People just aren't that dumb anymore to believe in such myths, especially since lying and denying are neccesary to pimp this worldview of "No Intelligence Allowed". Eocene

I am a software engineer with tens of years of experience of implementing software systems.

I'm a hardware engineer, I frequently work with software engineers and unfortunately many of them, whilst being great coders, don't really get engineering. DrBot

I love the self-righteous indignation here. While I don't agree with the JoeG approach, your side uses such approaches X 10,000 if you were to ever visit any of the more popular Atheist combat forums where members are given a free hand at any manner of filth, vulgarities and insults. Indeed, such language and degraded experessions are yet another part of your articles of faith and worldview as you see it. Eocene

DrRec: "I hadn’t brought up religion. I don’t know Szostak’s beliefs. But apparently you are threatened by this research." ===== Yet the continued Faith statements of these experiments do point to a different type of religious worldview. Clearly faith, which is the belief in something not observed, but hoped for at a future time is exactly what this discussion is about. Nobody is arguing here against the actual processes involved in the carrying out of experiments. What they point out is that whether it's Craig Venter, Gerald Joyce(and his magic intelligently designed molecules) or a Nodel Laureate Jack Szostak, all of them using their collective intelligent minds formulate biased opinions, presuppositions, purposely intended goals of what they personally have reasoned with their own intelligence of just how life should have come about. Yet they clearly do meditate on the architectural plans and contemplative mechanical procedures of just how to construct just such nano-machine componants from materials they themselves have chosen and selected for. Doing so under environmental conditions their own religious predjudice has selected for and then further proceeding to pimp to what they consider a public who they consider complete imbeciles who need their superior guidance to understand anything. Then they take liberties in the explanation of their intelligently rigged experiment to fabricate a story line of a mythological prebiotic world where no intelligence existed and try and force feed this down others throats, all the while disconnecting their own intelligence from the explanation. Yet they(Evolutionists) apparently need constant reminding of their own religious FAITH = "NO INTELLIGENCE ALLOWED". Even hardware has instructions for it's manufacture, but it's those instructions that comes first and this is all they have ever proven when they continually manipulate, rig and guide every experiment with their own goal driven intelligent minds. It's the lying part in discounting or disconnecting their own intelligence as having nothing to do with these experiments that others don't like. Most people are not simple minded ignoramuses. Try as you might to distance yourself from faith and required intelligence is an impossible goal here. You continually prove what you aim to refute. Clearly you are wanting others not of your FAITH to believe in your own chosen FAITH(No Intelligence Allowed) and that just isn't going to happen very easily when you support the hijacking of I.D. concepts in experimentation and then proceed to lable it blind undirected forces and deny it's anything of the sort. This isn't about the Great Shamman storytelling time around a Kampfire and most modern people today aren't ignorant guillible tribesman who will in fear obediently hang on your every word as some supposed mystic truth. ----- DrRec: "I understand your reaction better now. I also don’t think anything I say, or the progress of the field will impress you much." ===== Yes, ultimately I'd say it safe to say your continued prosyletizing probably won't move others to apostacize from their own previously held religious beliefs and convert to your brand of faith based beliefs espoused by your Church. The main difference here between the two sides is that the I.D. crowd will admit they have an element of faith they work with. Your side by necessity latches onto faith and allows it to influence everything they do and say and then turns completely right around and denies it is anything of the sort at the same time. It's almost like your side in it's attempt at research is in effect employing the old joke line: "Look Up. Look down. Look all around. See my thumb, gee your dumb." Eocene

"The sequence of protein or RNA produced by DNA is a direct consequence of the order of the chemical bases on the DNA." Yes, but the sequence of the DNA bases is not determined by the property of the matter (i.e., the nucleotides). Information is not the same as the medium in which it is encoded. Eric Anderson

DrREC, I didn’t brought up religion explicitly myself – but to sympathize with Bornagain77's opinion. I am not shy though to bring it in our discussion. Let me help you with explaining my thinking. I am fascinated by science. Although a software engineer, I started paying attention for the last 10 years to biology, molecular biology, genetics, origin of life, etc. I keep an open eye to the research and current understanding of particles physics, astronomy and astrophysics, cosmology, history, geology. I think that being a software engineer gave me some understanding how working systems can be designed, assembled, constructed. That gave me also a basis to evaluate and compare the complexity and intricacy of some sorts of human artifacts (computers, computer-based systems) and the living world creatures – that I sometimes, through a crude and unfair simplification – tend to see as machines. I am very interested in the Origin of Life research and I did some reading in this area. I am following the news in this domain. I have some “preconceived ideas” related to this research. But those ideas were though “conceived” and structured after educating myself in systems theory, a little in the molecular biology, the main themes of OOL research and my general world view – which in itself - I like to believe has a rational and defensible origination. The simple story is that the biology, micro-biology research of the last 50 years are continuously unveiling levels of complexity over levels of complexity. As a person with a math and engineering education, I could not reach but a single firm conclusion: that our world is a DESIGNED world, that the LIVING WORLD is a DESIGNED world. We, normal human beings are looking for models, heroes and persons to admire and idolize. Is only rational for a human being like me to remain in awe to the Universe around us, to the Galaxies, our Living Planet, our animal, plants and human beings that populate this world. It is also human to recognize the single Person that deserve to be admired, revered and adored: is the Designer of this wonderful world, our Most Excellent God, our Most Excellent Engineer. I try to show to you that by a honest, rational approach, a human being can arrive to the idea of God – the Supreme Creator and Designer. I happen to be lucky to be born in a Christian family and to get a personal acquaintance with this God – and He fully deserve our worship! For me real science is just revealing new aspects, details and layers of the magnificent Creation, uncovering things left there by the Creator to direct our attention to Him and His Omniscience and His Omnipotence and His Benevolence. InVivoVeritas

I would suggest from a slightly different perspective the following: 1. The cell can be seen as a harmonious, intricate, coordinated composition of “hardware” and “software” elements. The plain existence of the cell as an exquisite assembly of hardware and software makes an even stronger argument that it was DESIGNED. 2. The hardware parts are constructed from atoms, cells, molecules, proteins, enzymes, cell organelles, nucleus, protoplasm, membrane - listing them in an increasing level of composition and organization. These hardware parts and their structured sets are used both as information storage, information communication and information processing support. They exist and manifest also as the material results of the cell processes: DNA replication, protein construction, cell development, cell division, etc. 3. The software in the cell may be presumed to drive many complex cellular processes: DNA replication, transportation, communication, cell division, immune reactions, chemical recycling, etc. It is not clear how much we understand the “languages” in which the cell software is expressed. 4. The miraculous thing is that the cell marvelous design is the basis of single-cell organism autonomy as well as one basic foundation for the autonomy of multi-cellular organisms. 5. The autonomy of the living world means a LOT: that the members of the living world can take care pretty much of themselves: they can feed themselves, arrange for intake of energy, can move to better places when needed, can sense and react to danger, can reproduce themselves, can exhibit tremendous flexibility, versatility and adaptability to external conditions. 6. There is no equivalent human-designed artifact that even come close in terms of the exquisite design and autonomy to the members of the living world. This clearly tells that the hypotheses that the Life originated through natural processes is totally unfounded in reason. InVivoVeritas

No. Membranes themselves are selectively permeable. This is easily demonstrated in the lab. No parts list. No memory. Just the properties of the membrane. Don't even need pores. DrREC

Thanks to BA77 and InVivoVeritas for answering a nagging question. I was wondering where this visceral reaction against origin of life research comes from. Other posters described it as "irrational" and "Wasted money. Wasted time. Wasted science." You called a Nobel laureate "extremely naive and uneducated." But now I get it: "a man would deny the source of all life, God, all the while severely deceiving himself and others that he can create ‘simple’ life without any need for God whatsoever???? " I hadn't brought up religion. I don't know Szostak's beliefs. But apparently you are threatened by this research. I understand your reaction better now. I also don't think anything I say, or the progress of the field will impress you much. DrREC

DrREC, In your reply you mention: "Nutrients and wastes can selectively pass, without a ‘parts registry’-…..” Which is a contradictory statement in itself. If the nutrients pass “selectively” as you say, isn’t that logically equivalent to saying that only a “selected list of nutrients” are passing through the pores? And that “selected list of nutrients” is reasonably called a “nutrient registry” in an informational lingo that hints also to the fact that there is some kind of Memory So, to make the absurdity of your statement more clear, let’s reformulate it: “Nutrients can selectively pass without practically conforming with a selection list of nutrients” Now if, for example, the membrane has two type of pores: P1 - having a triangle shape of size S1, the other P2 having a pentagon shape of size S2 and there are only two “good” nutrients that can “pass” through these pores because nutrient N1 has a triangular cross-section of a S1 size and the other nutrient N2 has a pentagonal cross-section of the S2 size, this, logically is still equivalent with a “nutrient registry” located at the membrane level. The big questions here are: 1. How come that the cell developed a triangle-shaped pore P1 that matches perfectly the shape and size of the good nutrient N1? And the same for pore P2 matching nutrient N2? 2. How come that the nutrient N1 passed by the pores of type P1 is also a “good” nutrient for the cell, i.e. it happen to feed the metabolism of the cell? 3. Was any “coordination” or intelligence manifested in the nature of N1, its size and shape and the “construction” of the pores of type P1? It is very hard to accept that so numerous MATCHES, COINCIDENCES that can be observed in the structure, composition of a cell in cell bodies and their coordinated functionality is the result of random processes and random occurrences. InVivoVeritas

I think Dr. Liddle has a point if she means the hardware and the firmware are essentially the same thing, just as it is for computers. Although software can be built atop, the founding layer of instructions is simply the byproduct of electricity passing through the chip's physical architecture. Thus if you want to change the instructions at the lowest level, you must do so by creating a new chip with a different architecture (excluding field-programmable gate arrays). Deciding which functions of the cell are analogous to firmware or software is another matter. rhampton7

InVivo, I,m sorry, perhaps I wasn't clear, I was directly addressing DrREC, and was not addressing you save only to compliment you for your post! bornagain77

bornagain77 I am sorry that you misinterpreted my blog entry. I really wrote that entry just to start illustrating the arrogance of scientists believing the materialist Creation Myth. I guess my point was not clearly made! However, I was preparing to reply to DrREC on the same line with your line: I might be arrogant to qualify Nobel laureate Dr. Jack W. Szostak as ‘uneducated’ (and maybe my choice of words was bad) but isn’t he much more arrogant to – as you say – “deny the source of all life, God” ? InVivoVeritas

InVivo, though the information processing is missing, here is a video that goes well with your rough sketch:

Cell Membrane - video http://www.metacafe.com/watch/895198/

As well, seeing that Szostak's very own work testifies against him ever finding functional proteins, It is safe to assume that he is operating on imagination instead of any rational evaluation of evidence that life could have arisen materialistically;

Szostak on Abiogenesis: Just Add Water - Cornelius Hunter - Aug. 2009 Excerpt: "While Szostak and Ricardo may sound scientific with their summary of the abiogenesis research, the article is firmly planted in the non scientific evolution genre where evolution is dogmatically mandated to be a fact. Consequently, the bar is lowered dramatically as the silliest of stories pass as legitimate science." http://darwins-god.blogspot.com/2009/08/szostak-on-abiogenesis-just-add-water.html

Even the low end estimate, for functional proteins given by evolutionists (1 in 10^12 Szostak)), is very rare:

Fancy footwork in the sequence space shuffle - 2006 "Estimates for the density of functional proteins in sequence space range anywhere from 1 in 10^12 to 1 in 10^77. No matter how you slice it, proteins are rare. Useful ones are even more rare." http://www.nature.com/nbt/journal/v24/n3/full/nbt0306-328.html

It is very interesting to note that the 1 in 10^12 (trillion) estimate for functional proteins (Szostak), though still very rare and of insurmountable difficulty for a materialist to use in any evolutionary scenario, was arrived at by calling a binding/sticking of ANY random protein to the 'universal' ATP energy molecule, a functional protein. It is severely misleading of Szostak to say 'sticky' proteins are functional to put it very mildly.

How Proteins Evolved - Cornelius Hunter - December 2010 Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function. http://darwins-god.blogspot.com/2010/12/how-proteins-evolved.html

The entire episode of Szostak’s failed attempt to establish the legitimacy of the 1 in 10^12 functional protein number from a randomly generated library of proteins can be read here:: https://uncommondesc.wpengine.com/intelligent-design/proteins-fold-as-darwin-crumbles/comment-page-2/#comment-358394 This following paper was the paper that put the final nail in the coffin for Szostak's work:

A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells Excerpt: "Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division." http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0007385

Further notes:

On The Origin Of Life And God - Henry F. Schaefer, III PhD. - video http://www.metacafe.com/watch/4018204 "The Origin-of-Life Prize" ® (hereafter called "the Prize") will be awarded for proposing a highly plausible mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life. http://www.us.net/life/index.htm

Music and verse:

John 14:6 Jesus answered, "I am the way and the truth and the life. No one comes to the Father except through me. Steven Curtis Chapman - God is God (Original Version) - http://www.youtube.com/watch?v=qz94NQ5HRyk

bornagain77

InVivo, very good for off the top of your head? DrREC and you don't find it the least bit arrogant that a man would deny the source of all life, God, all the while severely deceiving himself and others that he can create 'simple' life without any need for God whatsoever???? Perhaps we should back up a little and take things one step at a time since you seem to think the job for God is up for grabs,, shall we??? Can you please cite just one experiment where a single photon was created from absolutely nothing???

One day a group of scientists got together and decided that man had come a long way and no longer needed God. So they picked one scientist to go and tell Him that they were done with Him. The scientist walked up to God and said, "God, we've decided that we no longer need you. We're to the point that we can clone people and do many miraculous things, so why don't you just go on and get lost." God listened very patiently and kindly to the man and after the scientist was done talking, God said, "Very well, how about this, let's say we have a man making contest." To which the scientist replied, "OK, great!" But God added, "Now, we're going to do this just like I did back in the old days with Adam." The scientist said, "Sure, no problem" and bent down and grabbed himself a handful of dirt. God just looked at him and said, "No, no, no. You go get your own dirt!" http://www.getyourowndirt.com/

bornagain77

Maybe instead of picking one line from an interview, and concluding someone is "extremely naive and ‘uneducated," you could read his publications, summarize them, and critique his research or the state of the field. DrREC

"In conclusion, Mr. Jack W. Szostak – the Nobel laureate – seems to be extremely naive and ‘uneducated’ about the complexity of the task he started on about 25 years ago: to figure out the origin of life." That is Dr. Jack W. Szostak, and man what arrogance! Just so you know, Szostak has multiple publications experimentally probing the permeability of model membranes. Nutrients and wastes can selectively pass, without a 'parts registry'-which isn't really how most pores operate (although there are some specific transporters). Other suggestions-such as motility, chemotaxis, advanced cell signaling, and a circadian clock aren't even found in all modern life! DrREC

Yes, kf, but what some of us are saying is that that's where the analogy simply breaks down. You can't "load software" into a molecule the way you might "load software" into a digital computer. The molecule is what it is. Elizabeth Liddle

Here is the Quote from the Jack W. Szostak interview: "We think that a primitive cell has to have two parts. First, it has to have a cell membrane that can be a boundary between itself and the rest of the earth. And then there has to be some genetic material, which has to perform some function that’s useful for the cell and get replicated to be inherited. The part we’ve come to understand reasonably well is the membrane part. The genetic material is the harder problem; the chemistry is just more complicated. The puzzle has been understanding how a molecule like RNA can get replicated before there were enzymes and all this fancy biological stuff, protein machinery, that we have now in our cells." I am a software engineer with tens of years of experience of implementing software systems. A sane software engineer when given a new project, it has a well defined approach for taking the project from a starting idea to the final, working product. One of the first steps of this professional approach is to write a "Requirement Specification" to clearly, neatly and accurately specify each and every demand that need to be fulfilled by the final product. I thought that it would be very instructive to only START sketching such a "Minimum Requirements Specification for a Most-Primitive Life Form" and after a first sketch to compare notes with Mr. Jack W. Szostak statements in his interview. Below you can find the first iteration of such requirement specification, and detailed (somewhat, but not too much) only for the first of the eight major requirements. Please do not forget, that this is the first write up, produced with not too much thought - where I am sure I may have missed many other major requirements. Some conventions: - we will call this "most primitive" form of life a "cell" - for convenience - we will call the needed boundary of this 'cell' a 'membrane' Here is the Initial Requirement List: 1. The cell must have a physical boundary around its volume to clearly delimit the inside of the cell from outside of the cell. Let's call this boundary "membrane" List of minimum requirements for the membrane of the cell 1.1. Must provide reliable isolation of the cell content from the outside world 1.2. Must be "permeable" to specific materials or sources of energy that "feeds" the cell 1.3. Must have 'substance recognition' capabilities in order to allow or prohibit admission inside the cell of the good respective bad 'materials' (sensory capability). 1.4. Must have 'open gate through membrane' and 'close gate through membrane' reactions and mechanisms to open 'pores' (openings) in the membrane when good versus bad 'materials' are recognized outside or inside the membrane (reactive capability). 1.5. INFORMATIONAL SUPPORT PERSPECTIVE: 1.5.1. The membrane must exhibit a capacity to store and process information locally about the nature/identity of the good materials as well as about bad materials. Logically that is equivalent with a 'registry' of good/bad materials. 1.5.2. Pattern recognition: the membrane must have pattern recognition informational capabilities to accurately recognize any 'material' (or 'material pattern') that is available in its own 'registry' memory and to send appropriate signals to the control agents in the membrane when such materials are detected in its external or internal environment. 1.5.3. The membrane must have a set of control mechanisms on how to react to an 'inventory' of stored information of good and bad materials, in particular on what membrane 'pores' to open or to close when particular materials are identified. 1.5.4. Most probable the membrane should have ability to 'communicate' information/signals to the inside the cell when material 'signatures' are detected. (information communication and signaling) 2. The cell must have mechanisms to feed itself from outside world with specific substances that provide food/sources of energy for the (metabolism) processes that animate the cell. 3. The cell must have mechanisms to replicate itself into one or more similar descendent cells that exhibit the same behaviors and capabilities as the mother cell. 4. The cell should/may have mobility in order to leave a world environment that it detects as unfavorable and move toward other areas of the environment that are more favorable to its continued existence and proliferation. 5. The cell should/may have mechanism to 'sense' its environment and to 'react' accordingly. To 'recognize' 'favorable' conditions/elements in its environment as well as 'recognize' unfavorable conditions/elements in its environment. 6. The cell must have ability to transform the raw materials/energy received from environment through its membrane and transform them into different type of materials that are proper for its own internal 'construction' projects. 7. The cell should/may have capability of identifying 'refuse' materials resulting from its material transformation and conversion processes and forcing these 'refuse' out of the cell through the membrane to outside world. 8. The cell should/may have time measuring / time signaling capabilities in order to control its own material input, material transformation, material output and cell replication processes on specific timelines and coordinated schedules. I develop to the next level of detail only the 'membrane requirements' for this 'most primitive' form of life. I guess that some serious thought on these major requirements will distil into somewhat unexpected - but logically defensible - lower level requirements that involve information processing, material transportation, information communication inside the cells - that, together will construct an objective picture of the REAL COMPLEXITY that would be required for such a MOST PRIMITIVE FORM OF LIFE. What is not immediately apparent for anyone is that the living world and all its members manifest - it's true, in a varied degree - the "autonomy" characteristic which is another name for ‘viability’ ‘survivability’. This autonomy capability is extremely complex, demanding and multi-faceted and is also "extremely expensive" to "implement" by a designer, by evolution or by any entity. Let's do not forget that humankind in its most advanced state of technological progress, was not ever capable of dreaming to construct any artifact to an approaching level of autonomy - as it is routinely end richly encountered among the members of the living world. In conclusion, Mr. Jack W. Szostak - the Nobel laureate - seems to be extremely naive and 'uneducated' about the complexity of the task he started on about 25 years ago: to figure out the origin of life. InVivoVeritas

“Software” = “Information.” Equating the two seems like a stretch. But the point of the original post, and my objection was the use of hardware vs. software in the analogy. If we describe hardware as the physical medium of a computer, and software as what runs on it, how does this relate to early life? Is a self-replicating set of polymers hardware or software? It just isn't a meaningful analogy, and calling out EL for pointing that out isn't meaningful either. "information is not a property of the matter in which it is encoded." The sequence of protein or RNA produced by DNA is a direct consequence of the order of the chemical bases on the DNA. DrREC

Barry, you misundertood me. Joseph said: "Yup, perhaps 1/2 way there pertaining to the hardware (big maybe) but pertaining to the software scientists haven’t even started." My response, that the hardware is the software in a cell assumed that Joseph was not simply talking about the lipid vesicle membrane by "hardware". That isn't "hardware" by any analogy with a computer - that's just the case. The "hardware", therefore, has to be the polymers enclosed in the vesicle. But there is no additional "software" that has to be installed on that "hardware" The molecule is both software and hardware. Elizabeth Liddle

Joseph, I went to your blog and after reading the post you had linked to I started to look around. It seems you use you blog as a forum to threaten others with violence, abuse them in the most disgusting ways and generally act in quite a different manner to which you comport yourself here. Why is that Joe? Why? kellyhomes

Jack Szostak says: “And then there has to be some genetic material, which has to perform some function that’s useful for the cell and get replicated to be inherited” What, exactly, is the property of the genetic material that is so important? It’s the stuff that gets “replicated and inherited.” And why is it important that there be something that gets “replicated and inherited”? Szostak again: “You want something that can grow and divide and, most importantly, exhibit Darwinian evolution.” The sine qua non of Darwinian evolution: Information! We are not talking about something that is “analogous” to information. We are talking about information. “Software” = “Information.” And no matter how you slice it, information is not a property of the matter in which it is encoded. Barry Arrington

"No transcription, and no translation of the mRNA codons in the ribosome to make proteins in a step by step AA sequence." We're discussing origin of life scenarios. You've given me a litany of the stuff of a modern cell: Transcription (DNA) and translation, mRNA, codons, ribosomes, and proteins. I'm betting Jack Szostak thinks those came later. DrREC

"1- There aren’t any self-replicating RNAs." I'd disagree with that, and I think you're trivializing the research. It doesn't really matter to the discussion here. 2- That ain’t proto-life Not alone, but an important proof of principle. "3- In order to repair something you have to know A) it is broken and B) how to fix it" "you have to know" is really inserting agency in there, isn't it. Enzymes like Photolyase can physically recognize change to the DNA structure that mispairing, or DNA adducts cause. It is a physical recognition, independent of what the DNA codes for. These are enzymatically reversed. They can also be removed, and the strand repaired, using the DNA bases on the other strand as template. 4- Without that you don’t have first life Who says first life had to be accurate/repairing? DrREC

Software is where EXPLICIT, prescriptive, functional info gets loaded into a digital system. if you want to deny the reality of that FSCI, then it make sense to pretend that there is no software in DNA, just chemicals in a strange polymer. No transcription, and no translation of the mRNA codons in the ribosome to make proteins in a step by step AA sequence. And most of all no von Neumann self replicator in the living cell. NOT!!!! kairosfocus

"Because life replicating is about informational coded instructions for replication, " And is that hardware or software, in the hypothetical case of a closed catalytic pool of RNAs that can catalyse themselves and other reactions? Is each RNA the hardware or software? "Well it’s your religious belief, not mine. It’s not up to someone else to prove your religious worldview to you. That burden is your responsibility." I'm finding it harder to have a discussion here without having some odd rambling about my religious worldview tacked on. Seems like a default, when you have nothing better to say. I'll ask the question again: "In the combustion of hydrocarbon by oxygen to produce carbon dioxide, water, heat and light, what is the hardware and software? Silly, isn’t it?" DrREC

DrRec: "Analogies are only useful to a certain point. In this case, dwelling on the “software” versus “hardware” of early life obfuscates rather than clarifies." ==== Obfuscates ??? Hardly. The Software question is the number one important point of discussion that should always be dealt with first and foremost, but we all know why it's one of those subjects that needs muddling in any discussion. If the Miller/Urey experiment had created informational codes, then that would have certainly provided all the proof your Church needs for an arguement. ----- DrRec: "What meaning does hardware or software have to self-replicating RNAs, or a pool of molecules that collectively has catalytic and self-replicating properties?" ==== Because life replicating is about informational coded instructions for replication, not some stupid blind luck of lightning from a Volcano striking a toxic waste chemical cocktail pond found in some mythology. ---- DrRec: In the combustion of hydrocarbon by oxygen to produce carbon dioxide, water, heat and light, what is the hardware and software? Silly, isn’t it? ==== Well it's your religious belief, not mine. It's not up to someone else to prove your religious worldview to you. That burden is your responsibility. Eocene

Joe, nitpicking doesn't help here. A. change to the sequence can result in a change to the instructions "With large proteins that require chaperones you can change the sequence and still get the same result." Ok, not all mutations disable function, and chaperones help. "OR you can change teh sequence and have the ribosome reject it." No idea what you mean here. No idea what you mean here. DrREC

Dr REC:

Both sides are always templates for DNA replication, and either side can template mRNA.

When I wrote it I was stuill thinking "sense/ antisense"- well that is what I was taught too. But yes now we know both sides can code for RNAs Joseph

With large proteins that require chaperones you can change the sequence and still get the same result. OR you can change teh sequence and have the ribosome reject it. Joseph

"So this is how I envision DNA- both sides of the ladder carry redundant information. One side does the work, that is transfers programming data to other molecules it contacts (mRNA for example) and the other side is a template for DNA replication" Both sides are always templates for DNA replication, and either side can template mRNA. "These instructions are not the sequence, rather they are embedded on the sequence" Is physically a distinction without a difference. Change the sequence, and the "instructions" change. DrREC

1- There aren't any self-replicating RNAs. The best we have so far is two RNAs one for the template and one that can catalyze one bond between two other RNA sequences that form on the template. 2- That ain't proto-life 3- In order to repair something you have to know A) it is broken and B) how to fix it 4- Without that you don't have first life Joseph

"What self-replicating RNAs?" Those proposed by RNA-world advocates, and to some extent, selected for in laboratories. "or a pool of molecules that collectively has catalytic and self-replicating properties?" "Why does that require software?" So proto-life could be software free? Interesting? "OTOH transcription, translation, proof-reading, error-correction, editing and splicing require software OR agency involvement…" Again, the software analogy isn't helpful. DNA repair enzymes operate by shape-physically recognizing and correcting mismatches and bulges. That is software? And why do you think all those things are required for first life? DrREC

DrREC:

What meaning does hardware or software have to self-replicating RNAs,

What self-replicating RNAs?

or a pool of molecules that collectively has catalytic and self-replicating properties?

Why does that require software? OTOH transcription, translation, proof-reading, error-correction, editing and splicing require software OR agency involvement...

Joseph

As I said on my blog almost three years ago: Up to now biological information has always been related to the DNA sequence (sequence related). IOW the information depended on the sequence. I do not believe this is a tenable position. I say that because in biology we observe that DNA just doesn't replicate itself, it does so with the help of other molecules in the cell. Those molecules are constructed by the information stored in the DNA. That's right- stored in- as in the data that is stored in a computer's hard drive, ROM and RAM. And this is my point- that DNA, RNA and other cellular components are actually data carriers just like the computer components I just mentioned. IOW the sequence is not the information. The sequence is important to carry out the instructions, that is the information embedded in the DNA (and perhaps other cellular components). As I said in an earlier entry- Just for a eukaryotic cell to make an amino acid (polypeptide) chain- Transcription and Translation: You start with a tightly wound piece of DNA. Enzymes called RNA polymerases, along with transcrition factors, begin the process by unwinding a portion of DNA near the start of a gene, which is specified by sequences called promoters. Now there are two strands exposed. One strand is the coding strand- it has the correct sequence information for the product- and the other strand is the non-coding strand. That strand contains the complimentary layout. At this point decisions have to be made. Where to start, where to stop and although it may seem counterintuitive the mRNA goes to the non-coding strand in order to reconstruct the proper codon sequence (nucleotide triplets which code for an amino acid) for the protein to be formed. Both sides of the parent DNA are exposed yet the mRNA "knows" to only form on one. This process is unidirectional (5’-3’). There is only one start codon which also codes for an amino acid (met) and therefore all amino acid sequences start with methionine. The stop codons don’t code for an amino acid. Transcription actually starts before the “start” codon and continues past the stop codon. Before the mRNA leaves the nucleus any/ all introns are cut out and the remaining exons spliced together. A chemical cap is added to the 5’ end, the non-coding stuff at the end is cut off by a special enzyme (endonuclease) and a string of A’s is added in its place. You now have a processed mRNA. So now we have this piece of processed mRNA which leaves the nucleus and has to rendezvous with a ribosome-the protein factory within the cell. A ribosome consists of over 50 proteins and 3-4 different kinds of rRNA (ribosomal), plus free-floating tRNA (transfer). Each tRNA has a 3 nucleotide sequence- the anti-codon to the mRNA’s codon plus it carries the appropriate amino acid molecule for its anti-codon. To attach the appropriate amino acid to the correct anti-codon an enzyme called amino-acid synthetase is used.

There, large workbenches made of both protein and nucleic acid grab the mRNA so the correct amino acids can be brought up to the mRNA. Each amino acid is escorted by a module called tRNA or transfer RNA. It is important to note that the escort molecules have three bases prominently exposed on their backsides and that these molecules also use the base U instead of T. The kind of amino acid is determined precisely by the tRNA escort’s anticodon, or triplet set of bases on the escort’s backside.-pg 23

And then the chain starts forming until the stop codon terminates the process. Next is the folding process. That is what allows the protein to be useful- its spatial configuration. That is just the basics of what one is introduced to when reading biology textbooks. And it doesn't include the proof-reading and error correction that accompanies the process. So this is how I envision DNA- both sides of the ladder carry redundant information. One side does the work, that is transfers programming data to other molecules it contacts (mRNA for example) and the other side is a template for DNA replication. Once DNA replication is complete the program is transferred to the newly constructed side via the hydrogen bonds that connect the two sides. When other molecules are made- mRNA for example- they are given their instructions via the same hydrogen bonds. That information consists of editing instructions, as well as configuraion/ assembly instructions and destination instructions. These instructions are not the sequence, rather they are embedded on the sequence, just as computer data is embedded on the disk. ----------------------------------------------------------- Joseph

Analogies are only useful to a certain point. In this case, dwelling on the "software" versus "hardware" of early life obfuscates rather than clarifies. What meaning does hardware or software have to self-replicating RNAs, or a pool of molecules that collectively has catalytic and self-replicating properties? In the combustion of hydrocarbon by oxygen to produce carbon dioxide, water, heat and light, what is the hardware and software? Silly, isn't it? DrREC