Information created accidentally, without design

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July 11, 2013

Darwinism, Design inference, News

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Darwinism
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Absolutely no one did this stuff, according to sources, which just shows how silly the idea is that intelligence is needed to create information.

Darwinism can explain it all quite easily. Natural selection acted on random mutation causing certain trees to die. End of story.

Hat tip: The Intelligent Design Facebook group, and especially Timothy Kershner and Junior D. Eskelsen

Comments

ericB I will try to hang in here a bit longer but so much has been written I have rather lost the thread of the debate. I believe the last two comments directed to me were #288 and #289. With respect to #289 you ask why I believe the main reason for referring to DNA as a code is because it sounds more exciting and has associations with unlocking a secret. The answer is – it is just a hunch – I have no insight into biologists motives. #288 you are concerned to differentiate between transcription – which is just copying – and translation which unfortunately you do not go on to define. You then assert that translation is the key thing that makes DNA symbolic. Now I am all for identifying precise differences between the meaning of words and recognise that they mean different thinngs. But I need to understand your specific meanings in this context. Several of your earlier examples of symbols such as reading a paper tape or a punched card are just copying processes. They copy a sequence of bits from one medium to another.I cannot see how they are different in principle from transcribing DNA into mRNA. Translation is normally used in the context of language – translating English into French – where both origin and result have meaning. But I don’t think you can mean that. The question is what is different about the DNA to Protein process that merits the description of translation as opposed to transcription?Mark Frank_{August 10, 2013
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The translation system in cells indicates intelligent design. I would submit that, regardless of how many billions of years one waited, it is not reasonable to expect that unguided chemicals would ever construct a system for translating symbolic information into functional proteins based on stored recipes and a coding convention. [I realize people have thoughts about what happened earlier (e.g. that might not need proteins, for example) and what happened later (e.g. when a functioning cell provides the full benefits of true Darwinian evolution). For the purposes here, attention is focused specifically on the transition from a universe without symbolic translation to construct proteins to the origin of such a system. Whatever happened earlier or later, sooner or later this bridge would have to be crossed on any path proposed to lead to the cells we see now.] One of the key considerations leading to this conclusion is that a translation system depends upon multiple components, all of which are needed in order to function. + Decoding At the end, one needs the machinery to implement and apply the code to decode encoded symbolic information into its functional form. (In the cell, this is now the ribosome and supporting machinery and processes, but the first instance need not be identical to the current version.) Without this component, there is no expression of the functional form of what the symbolic information represents. The system as a whole would be useless as a translation system without this. Natural selection could not select for the advantages of beneficial expressed proteins, if the system cannot yet produce any. A DVD without any player might make a spiffy shiny disk, but it would be useless as a carrier of information. + Translatable Information Bearing Medium There must be a medium that is both suitable for holding encoded information and that is compatible with the mechanism for decoding. Every decoding device imposes limitations and requirements. It would be useless to a DVD player if your video was on a USB thumb drive the DVD player could not accept instead of a suitable disk. In the cells we see, this is covered by DNA and ultimately mRNA. + Meaningful Information Encoded According to the Same Coding Convention One obviously needs to have encoded information to decode. Without that, a decoding mechanism is useless for its translation system purpose. If you had blank DVDs or DVDs with randomly encoded gibberish or even DVDs with great high definition movies in the wrong format, the DVD player would not be able to produce meaningful results, and so would have no evolutionary benefit tied to its hypothetical but non-functioning translation abilities. In the cell, this information holds the recipes for functional proteins following the same encoding convention implemented by the ribosome and associated machinery. + Encoding Mechanisms This is perhaps the least obvious component, since the cell does not contain any ability to create a new store of encoded protein recipes from scratch. Indeed, this absence is part of the motivating reasons for the central dogma of molecular biology. Nevertheless, even if this capability has disappeared from view, there would have to be an origin and a source for the meaningful information encoded according to the same coding convention as is used by the decoding component. (For the moment, I will just note in passing that the idea of starting out with random gibberish and running the system until meaningful recipes are stumbled upon by accident is not a viable proposal.) So there has to be some source capable of encoding, and this source must use the same coding convention as the decoding component. To have a working, beneficial DVD player, there must also be a way to make a usable DVD. + Meaningful Functional Source Material to Represent It would do absolutely no good to have the entire system in place, if there did not also exist in some form or other a beneficial "something" to represent with all this symbolic capability. If you want to see a movie as output, there needs to be a movie that can be encoded as input. If you want functional proteins as output, there needs to be access to information about proper amino acid sequences for functional proteins that can serve as input. Otherwise, GIGO. Garbage In, Garbage Out. If there is no knowledge of what constitutes a sequence for a functional protein, then the result produced at the end of the line would not be a functional protein. + Some Other Way To Make What You Want The System To Produce If we supposed that the first movie to be encoded onto a DVD came from being played on a DVD player, we would clearly be lost in circular thinking, which does not work as an explanation for origins. Likewise, if the only way to produce functional proteins is to get them by translating encoded protein recipes, that reveals an obvious problem for explaining the origin of that encoded information about functional proteins. How can blind Nature make a system for producing proteins, if there has never yet been any functional proteins in the universe? On the other hand, how does blind Nature discover and use functional proteins without having such a system to make them? The core problem is that no single part of this system is useful as a translation system component if you don't have the other parts of the system. There is nowhere for a blind process to start by accident that would be selectable toward building a translation system. The final killer blow is that chemicals don't care about this "problem" at all. Chemicals can fully fulfill all the laws of chemistry and physics using lifeless arrangements of matter and energy. Chemicals are not dissatisfied and have no unmet goals. A rock is "content" to be a rock. Likewise for lifeless tars. The biology of cells needs chemistry, encoded information, and translation, but chemicals do not need encoded information or biology. They aren't trying to become alive and literally could not care less about building an encoded information translation system.ericB_{August 9, 2013
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Upright BiPed, thanks for contributing the extra details @294 regarding translation!ericB_{August 9, 2013
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Hello ericB, I don't have the spare time to participate in this thread, but I have been occasionally skimming it and have enjoyed reading your comments. There is one thing I noticed that really needs to be clarified. The clarification physically demonstrates the argument you've been making. You say:
DNA holds encoded information, but DNA is not the code. The code is implemented by RNA (i.e. the tRNA) in the ribosome
Just to be clear, the code in genetic translation is not established by an RNA. It is established in complete temporal and spatial isolation from the remaining transcription and translation process by the protein aaRS. In other words, it is not the physical structure of tRNA that establishes the code (the tRNA is merely a passive carrier of the code) it is instead the physical structure of the compliment of aaRS. The aaRS charge the tRNA with their correct amino acid prior to the tRNA ever entering the ribosome. They accomplish this by being able to do a unique double-independent recognition (Barbieri) of the tRNA and AAs. This isolation from the translation process instantiates the necessary physicochemical arbitrtariness which is fundamentally required for the system to function. The system would not be able to translates recorded information into a physical effect without it. cheers...Upright BiPed_{August 9, 2013
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Mark Frank:
(Presumably I don’t have to explain that Joe’s “answer” is not an explanation: Because it is a code and that means it is the proper description. )
Presumably Mark can't support anything he sez.Joe_{August 9, 2013
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Short reply to Mark Frank (as I'm past out of time), Personally I would rather that you stay engaged. For example, I am interested in your thoughts about how science can deal with and understand translation systems, if we do not talk in terms of translation and only think about cause and effect. See also my post just made to Elizabeth. I feel that there are some real opportunities of improved communication. Again, I prefer to have you in the conversation. Thank you for your posts.ericB_{August 9, 2013
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Elizabeth B Liddle, I see real progress in communication in your comments @275. Thanks for constructively engaging with these topics. I also see opportunities for correcting what may be misunderstandings.
I don’t think the “sender” is the “programming” in any very sensible sense. ... ... my point is that once you get down to detail, it is extremely difficult to impose a a human-to-human communication system analogy on what goes on in the cell. ... But what is actually going on at organismic and cellular level is way more complicated than that and far too full of feedback loops to be pinned down by a simple Sender – Sign – Receiver model. As I think you agree. ... I am just extremely wary of trying to impose human-to-human communication analogies on a very different information processing system, ...
I'm surprised at this series of comments, since it was only because of your repeated request that I accommodated to fitting what happens in the cell into the simple Sender - Receiver model of human to human communication. If you don't think that fits the situation, why would you want to push the discussion in that direction? If I try to read between the lines, I get the impression that you just might think I am or someone else is actually proposing something like what you are describing and then rejecting, but if so that would be incorrect and a straw man. I hope you are not under that misunderstanding. I am using translation in a sense that applies just as well to the cell as it does to what happens inside computers (e.g. binary code to actions) where there are no human to human conversations taking place. There is no assumption of active/current sentient involvement in recognizing that the cell or the computer has symbolic information that requires translation by a convention.

[ericB:] Where translation by conventions is present, symbolic information is being processed, whether by sentient agents or by unthinking systems such as computers or cells. No translation = not symbolic.
OK, but that just moves the definitional burden to “translation”. I’m not nit-picking here – I am perfectly in agreement with you that information-processing takes place – if anything, I am making a more thoroughgoing analysis of the information transfer that takes place in living systems than you are – not restricting it to the DNA-RNA-protein system.
I think there is a misunderstanding here. I did not say that "information transfer" was restricted "to the DNA-RNA-protein system". I was answering the question you asked, which was stated as follows.
And which of the information-transfers involved is, in your view “symbolic”, and why?
Only "the DNA-RNA-protein system" is symbolic because only it requires translation. Both your question and my answer allow that there can be many other "information-transfers" that are not symbolic.

[ericB:] As I’ve consistently maintained, the hallmark for recognizing the presence of symbolic information is the need for translation by a coding convention.
Well, I’ll accept your use of the word. We just have to be careful not to import the baggage that may come with it. But to me “convention” means “agreed by a community of users”. I don’t think anything was “agreed” among cells to “use” a certain set of “symbols”, nor that there must have been a single designer who arbitrarily decided on a sest to use. That is would be assuming one’s conclusion. ...
That is one sense of "convention" -- a sense that focuses on the process by which a convention may have come into existence. But it is not the only sense for "convention". The more relevant meaning here is to focus on the nature of a convention itself (regardless of how it came to be). It is not inherently required (i.e. not a law in the natural sense). Yet it is regular and consistent, not capricious or random or haphazard (i.e. not a variable association determined by chance of the moment). If you like a different word that captures these ideas as well or better, alternatives could be considered. Regarding the concern about connotations and the illegitimacy of begging the question, if you check out my response to Mark Frank @251, you will see that I've already expressed the same thoughts. We don't want to mix in inappropriate connotations and then base conclusions directly upon those implicit assumptions in a question begging fashion.
I am just extremely wary of trying to impose human-to-human communication analogies on a very different information processing system, and then drawing conclusions about where an intelligent agent might feature in the system. I do not think that there are intelligent agents in the cell sending signals to each other, and I don’t think IDers do either, on the whole.
;-) I'm glad you concede that IDers "on the whole" don't propose that there are tiny "intelligent agents in the cell sending signals to each other". That's a relief ;) Again, about the concern of unwarranted conclusions depending only on connotations about words, I would invite you to please call me out whenever you sense that I might be making such a unwarranted, question begging inference. I welcome your correction. (out of time for now)ericB_{August 9, 2013
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ericB I don't know about you but having enjoyed our debate and learned from it, I am now finding it a bit repetitive and barren. I don't want to be accused of opting out but would you be put out if I dropped it? MarkMark Frank_{August 9, 2013
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Mark Frank, I have a more fundamental question for you, regarding your answer @265 to my earlier question.

[ericB:] I would ask you again to consider why it is that those advancing the science of biology, who are trying to be clear and descriptive, find themselves needing to talk in terms of symbols, codes, and translation.
To support this you quote from the rather controversial Hubert Yockey but clearly it is very common to refer to DNA as a code. I believe the main reason for this is because it sounds more exciting and has associations with unlocking a secret.
[In passing a correction: DNA holds encoded information, but DNA is not the code. The code is implemented by RNA (i.e. the tRNA) in the ribosome.] Why do you hold onto this belief that "the main reason for this is because it sounds more exciting and has associations with unlocking a secret"? A. Is it because you actually have any evidence supporting this fact, such as drawing upon material written by biologists that introduced this terminology? If so, please share this evidence. or B. Do you hold onto this belief without any direct evidence of that kind? If B, is it because you really don't want it to be true that biologists use the word "code" in a meaningful and warranted way because there is an actual code and actual translation happening in the ribosome? For comparison and contrast, consider that programmers use the word "code" regarding the binary code in a computer (note I am being specific in stating binary code). Would you likewise hold onto the belief (despite having no evidence to support it) that "the main reason for this is because it sounds more exciting and has associations with unlocking a secret."? Computers work by cause and effect. Binary code is involved in cause and effect. Its effects are connected to a specific context. Is binary code translated into operations? Is it truly a code? Or are these only euphemisms that programmers adopt because they like the excitement of the inappropriate connotations?ericB_{August 9, 2013
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Mark Frank @270 wrote (my emphasis added):
But you would understand in great detail how those reactions happened. I admit you would not know to what end and that is precisely the point – we have no reason to suspect there is an end for the DNA/Protein transcription. If the chemistry underdetermines DNA/Protein transcription then let us know what it is that is not determined.
I suspect that it may have just been a careless error on your part, not a real failure of understanding, to use the word "transcription". Nevertheless, in answer to some of the questions you have asked me in other posts, it is instructive to reflect on the following fact. There is no such thing as "DNA/Protein transcription". You absolutely cannot create proteins merely by any process of transcribing DNA. Transcription -- across writing -- only describes a copying process, such as in the case of making mRNA from DNA, which does allow moving the sequence into a different medium. By itself, transcription does not involve any translation, which as I've pointed out is the crucial distinction with regard to symbolic information. No Translation = Not Symbolic Notice that even though the genome is widely transcribed into RNA (it is functional, not merely junk), nevertheless only a small part of it is encoded with protein coding information that is later translated. There are ways that we can consider the rest of the genome in terms of information, and it does indeed have functional value. However, without translation, that is not "symbolic information". You have asked @265:
The question I have is what does it add to describe that process as the translation of symbols which represent the proteins using a code over and above just describing the process (in detail)? ... I am reversing the question and asking you what you think the value is of describing the process in terms of symbols, codes and translation as opposed to just describing the process in detail in terms of chemistry? Compare it to another complicated causal chain such as the position of the moon in its orbit and the resulting effect on when and where on the earth’s surface tidal creatures will be active. I don’t think you would describe the position of the moon as being a symbol of the creature’s activity or the process as being one of translating the position of the moon into creature’s activity. What is the relevant difference to the DNA to protein process?
The difference is translation. Consider that we have before us this incredibly amazing fact. In all the universe, we never see translation taking place except 1. in the ribosomes of cells as an essential part of their operation, and 2. in the artifacts and activities of intelligent agents. Now surely, on any view of reality, this is an amazing fact that cries out for explanation. If science is going to address it at all, it must be able to at least talk about it. Now consider how your own statements are answering your own question. So long as you continue to talk and think in terms of complex cause and effect chains, you have been unable to see any significant difference of kind. That is why you ask questions about what is the difference, and what is the value of adding this terminology. The inability to see any difference comes directly from relying on terms and thinking that do not identify anything that is different between the cases at hand. As long as you only talk and think about what they have in common, of course you will not be able to see and meaningfully consider how they are profoundly different. Systems that include translation follow cause and effect. Systems that do not include translation follow cause and effect. Talking and thinking only about cause and effect makes one blind to the difference between these profoundly different categories.ericB_{August 9, 2013
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Re: DNA in computing. Last night, when I opened my recently received copy of the monthly journal of the ACM (Association for Computing Machinery), it happened that the first page I opened to contained this very timely news article. A New Approach to Information Storage By Samuel Greengard Communications of the ACM, Vol. 56 No. 8, Pages 13-15 Excerpts:
When George Church, a geneticist at Harvard Medical School, decided to produce 70 billion copies of his book, Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves, he skipped printing presses, Kindles, and hard drives. The professor of genetics instead turned to a most unlikely medium: DNA, the same long molecule that serves as the building block for life on Earth. "It has worked remarkably well as a storage medium for 3.5 billion years," he says. ... Welcome to the emerging world of data storage. While hard drive and solid-state drive manufacturers are attempting to increase storage densities and push the limits on speed and performance, a handful of researchers around the world are hard at work on the next generation of systems and devices that would crash standard thinking about storage. Some, like Church and the European Bioinformatics Institute (EBI), are focusing on DNA. ... For perspective, all the data humans produce in a year could fit into about four grams of DNA. "There is an opportunity to create storage systems that are a million to a billion times more compact than existing technology and provide a level of longevity that is unheard of today," Church points out. The DNA of Storage The need for more efficient data storage methods is rooted in today's radically changing world. According to IBM, humans collectively produce about 2.5 exabytes of data each day; market research firm IDC says roughly three zettabytes of data exist in the digital world. Remarkably, 90% of the data in the world has been created over the last two years alone, say researchers at IBM. ... Storage: The Next Generation In the end, it is not so much a question of if next-generation storage technologies will go mainstream, but when.
The full article is here.ericB_{August 9, 2013
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Mark Au contraire I think the macaques make a good point, because in their case using the language of meaning (and even of codes, to a limited extent) explains purposeful behaviour that is not dictated by human intentions. In that physiological, ie physical, processes underlie animal behaviour then trivially one can explain it chemically, whilst explaining nothing useful at the higher level. The language of function, even of purpose, is necessary to explain what behaviour facial expressions call out (using Margaret Mead's term)in monkeys. Is the same true in genetics? Given that the strong appearance of design is admitted by everyone from Dawkins up, "we have no reason to suspect there is an end..." is simply untrue. We have plenty of reason from the highly organised outcomes. The question is only whether we might have reason to suspect our impression to be wrong. But as the cases of macaques and computers show, finding there is a complete chain of physical cause and effect is insufficient support for that suspicion.Jon Garvey_{August 8, 2013
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Jon #273 I think you are rather confusing things by introducing the macaques. If I could demonstrate that the behaviour of macaques had the same relationship to their internal chemistry as the execution of a computer program has to the electronic states changes in a computer then I think most people would say I had demonstrated reductionism of behaviour to chemistry. Indeed a computer programme is often the metaphor opponents use to characterise reductionism: "you are just reducing mental events to a computer programme". The fact is that the behaviour of a programme running on a computer is completely determined by the electronic events happening inside it. The work of animal behaviourists with macaques is not fluff, whether you can reduce their behaviour to chemistry or not, because even if you knew the chemistry it would be hopelessly hard work to try explain it all in those terms. Similarly using the language of codes and representation is helpful for extracting key characteristics of that electronic behaviour so you need to be concerned about details of the hardware. But that language, while extremely useful, is losing detail not adding it. You only get to add something if you start to consider what the bits mean and that requires knowledge of human intentions.Mark Frank_{August 8, 2013
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Of related note: Anthropic Principle - God Created The Universe - Michael Strauss PhD. - video http://www.metacafe.com/watch/4323661 This preceding video, at the 6:49 mark, has a very interesting quote: "So what are the theological implications of all this? Well Barrow and Tipler wrote this book, The Anthropic Cosmological Principle, and they saw the design of the universe. But they're atheists basically, there's no God. And they go through some long arguments to describe why humans are the only intelligent life in the universe. That's what they believe. So they got a problem. If the universe is clearly the product of design, but humans are the only intelligent life in the universe, who creates the universe? So you know what Barrow and Tipler's solution is? It makes perfect sense. Humans evolve to a point some day where they reach back in time and create the universe for themselves. (Audience laughs) Hey these guys are respected scientists. So what brings them to that conclusion? It is because the evidence for design is so overwhelming that if you don't have God you have humans creating the universe back in time for themselves." - Michael Strauss PhD. - Particle Physicsbornagain77_{August 8, 2013
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Elizabeth B Liddle """Which isn’t even non-Christian. John tells us that Jesus quoted the psalmist who said “ye are Gods”, with approval."""
The term "God" is used frequently in the Bible. I believe there is however good reason to recognize distinction in this regard. Take the difference between God and gods; and the god of this World; compared to the actual true creator God of Abraham. In the setting of this topic the overall narrative of the Bible seems unambiguous in its affirmation of a one and true creator God.DinoV_{August 8, 2013
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Liz: Elohim is translated "angels" elsewhere and has multiple meanings. In the context of Psalm 82, it is clearly speaking about magistrates and rulers with authority who "will die like mere mortals," and "fall like every other ruler." Jesus' point was to show his accusers' hypocrisy in their charge of blasphemy, not to approve the notion that we are all gods.Phinehas_{August 8, 2013
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I realise you have other things on your mind right now, KF, and I do hope all is going well. When you have time and mind to spare, perhaps you could say more clearly what you think it is I trying to "avoid acknowledging". Because my guess is that I'm probably not! But for now you have nothing but my very best wishes. LizzieElizabeth B Liddle_{August 8, 2013
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EL: There is a two-year track record. KFkairosfocus_{August 8, 2013
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No, that's OK, "atheist" is probably the simplest description. But yes, I do think that "nature takes on the creative qualities of a metaphysical “god” in an impersonal sort of manner" - and indeed, in a personal manner in the form of people :) Which isn't even non-Christian. John tells us that Jesus quoted the psalmist who said "ye are Gods", with approval. Cheers LizzieElizabeth B Liddle_{August 8, 2013
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Ok Liz, I was just curious about your thoughts on consciousness and now I understand you would hold to non-reductive physicalism, generally speaking. I was under the impression that you were an atheist, I apologize If I misrepresented you. If you believe that nature takes on the creative qualities of a metaphysical "god" in an impersonal sort of manner, you wouldn't be the first person on earth to have held to this view of reality. Thanks for the clarification.DinoV_{August 8, 2013
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I guess my view is nearest to that of Douglas Hofstadter. I think mind emerges from matter, rather than being separate from it. I think that "conscious" makes more sense as a verb (being conscious of something) than as a noun "consciousness", and I think it consciousness falls on a continuum from not being conscious of very much (a moth; an early embryo) to being conscious of a great deal (a human child or adult). I don't think consciousness can be "reduced" to matter - I think it is the property of a system, not shared by its constituent parts. I also think that consciousness of one's own consciousness - specifically of one's own existence as a conscious volitional agent is an intrinsically reflexive phenomenon arising from the reentrant loops that are part of our brain-body architecture. That's as succinct as I can make it in the context of an internet post :) But when you describe me as having an "atheistic worldview" - I'm not sure what you imply by that. I was a theist for most of my life. I still have a basically theistic "worldview". I just don't think that mind is separable from matter, so I don't believe in a creator mind that gave rise to matter. If that makes me an atheist, I'm an atheist. I think "pantheist" is probably a better term. I still have a referent for the signifier "God", and just as I still have a referent for the signifier "morally responsible person".Elizabeth B Liddle_{August 8, 2013
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Liz - a bit off topic and it is not my intention to shift it, but I was curious; In the context of your experience and atheistic worldview, what philosophy of mind paradigm do you believe best explains consciousness?DinoV_{August 8, 2013
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Eric:
I would first qualify that what we see happening in the cell is more like a programmed information processing system than just sending a letter, so “sender” “receiver” does not quite capture the situation. But, we can work with that for the moment.
Yes, I agree, but like you I am happy to work with it.
In passing, in a meta sense, one could consider the “sender” to be the who or what that programmed the system. The protein coding information had to come from somewhere and the cell itself does not have the ability to create and populate its own protein coding information store from scratch (cf. the central dogma of molecular biology).
Well, all dogmas are likely to be false, but I agree that the general direction of information flow is from DNA to RNA to protein. That may not always have been the case, however, and it is a very small part of the cascade, particularly in multicellular organisms. And we also have to consider the information transfer that takes place during cell division(when information from the parent cell is duplicated), and the information transfer that takes place when a cell in a multicellular organisms does its job in the organism (for example when genes are expressed in neurons during thought, for instance), and during development (determining what genes will be expressed in the daughter cells).
Leaving that to the side, within the cell the “sender” would refer to the control programming (including epigenetic factors) that determines what genes will be expressed and (in eukaryotes) which alternative splicing of that gene will be used to construct the mRNA. It would also include the mechanisms for transporting the mRNA to a ribosome — the literal act of sending.
This seems a rather crude way of looking at it. I don't think the "sender" is the "programming" in any very sensible sense. It seems to me better to think in terms of signal cascades, which are two-way (in fact multi-way - full of feedback loops). In a multicellular organisms when for example the organism gets a "message" from the environment - radiant heat, for example, or sound, or pressure, or smell, or light - genes are expressed and cells send signals to other cells, which return more information. In other words, signals are bouncing around inside and between the organism and the environment in multicellular organisms all the time, from conception to death. What the "programming" does is to allow this signalling to take place.
The message is carried by the messenger RNA, hence its name.
Sure. But DNA is also carries information from cell to cell. And that information includes its the epigenetic settings.
The recipient is the ribosome that receives the mRNA.
Well, sure, but it in turn becomes a sender. It is also itself a "message" sent from the DNA sequence that codes for it.
Notice that the DNA is not “causing” anything to happen. It is not the active agent.
It both causes and is caused by things. It contains information in the sense that its sequence, to requote Merriam Webster "produce[s] specific effects". A stone can "cause" me to trip without being an "active agent". Not only that, but your post can cause me to respond to you, even though it is not an "active agent".
It is an information store and is passive in this whole affair.
Depends what you mean by "passive". But I agree that for some meanings of "passive" it's "passive". I don't think it's a particularly important point. It's still causal in the sense that if it was otherwise, other results would be produced.
The agent that does “its work” to make proteins is the ribosome, which uses the information encoded into the mRNA as data, specifically as a recipe that it can translate into an amino acid sequence.
Why not the mRNA, or the tRNA, or the RNA polymerase? They all play roles in the information processing, and they all contain information, according to that Merriam-Webster definition. And the DNA contains the sequence that gives rise to all these RNA molecules. Without the DNA there would be no ribosome.
This is why it is improper to attribute the processing input requirements and limitations of the ribosome translation unit as though these were properties of the information in DNA, or to infer any conclusion about the nature of information. All devices that do work, including ribosomes, impose requirements on their inputs. That doesn’t define the nature of symbolic information.
Not sure what you mean, but my point is that once you get down to detail, it is extremely difficult to impose a a human-to-human communication system analogy on what goes on in the cell. There is plenty of information processing going on, but to try to express it in Saussurian terms seems to me doomed to failure - and to be misleading. The only half-way decent version of the analogy that I can see is that information from the environment is transferred to the gene pool of a population as a record of what sequences result in most effective replication in that environment. But what is actually going on at organismic and cellular level is way more complicated than that and far too full of feedback loops to be pinned down by a simple Sender - Sign - Receiver model. As I think you agree.
As I’ve consistently maintained, the hallmark for recognizing the presence of symbolic information is the need for translation by a coding convention.
Well, I'll accept your use of the word. We just have to be careful not to import the baggage that may come with it. But to me "convention" means "agreed by a community of users". I don't think anything was "agreed" among cells to "use" a certain set of "symbols", nor that there must have been a single designer who arbitrarily decided on a sest to use. That is would be assuming one's conclusion. tRNA is coded by DNA, and organisms with DNA that happened to code for a set of tRNA molecules that gave reasonably faithful results would tend to reproduce more reliably, so we need not necessarily invoke "convention" to account for an arbitrary set of "symbols".
Both symbolic information processing operations and operations that do not involve any symbolic information operate by cause and effect. The concept of cause and effect provides no discrimination whatsoever between these distinct categories.
I don't understand this, and this may because of the "baggage" I refer to. Or it may be because I am not on board with your idea that DNA is not "causal". I think that is an unduly restrictive view of "cause". DNA stores information (we agree) as defined as a pattern that produces specific effects. In that sense it is causal.
Where translation by conventions is present, symbolic information is being processed, whether by sentient agents or by unthinking systems such as computers or cells. No translation = not symbolic.
OK, but that just moves the definitional burden to "translation". I'm not nit-picking here - I am perfectly in agreement with you that information-processing takes place - if anything, I am making a more thoroughgoing analysis of the information transfer that takes place in living systems than you are - not restricting it to the DNA-RNA-protein system. I am just extremely wary of trying to impose human-to-human communication analogies on a very different information processing system, and then drawing conclusions about where an intelligent agent might feature in the system. I do not think that there are intelligent agents in the cell sending signals to each other, and I don't think IDers do either, on the whole. So it's important, I think, not to jump to the conclusion that because information transfer occurs in living systems, that therefore an intelligent agent must be sending the information. The information is not being sent by intelligent agents; it may, nonetheless, be true (although I don't think the inference is warranted) that an intelligent agent designed the system. A robot is an information processing system, designed by people. But that robot is not processing information sent to it by its designers, necessarily. The two levels of analysis are very different.Elizabeth B Liddle_{August 8, 2013
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We need to ask ourselves what is so telling about the obvious info processing system in the cell that builds proteins (and similar systems) that makes the likes of MF and EL so desperate to avoid acknowledging the obvious. And if that is what hey are reduced to doing, that is telling indeed.
What is it that you think I am trying to "avoid acknowledging", Kairosfocus? The only thing I am disputing is that the system can be reasonably called "symbolic". But it's not something I'm going to go to the stake over. It is what it is. What you call it is essentially up to you.Elizabeth B Liddle_{August 8, 2013
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...we have no reason to suspect there is an end for the DNA/Protein transcription.
Yes we do, but it is possible to deny it even in the case of the computer software - if, for example you're an eliminative materialist. "Chemistry->genetics->mind->computer software (->blog posts about it, come to that)". Sticking to undoubtedly natural systems, though, we have no reason to limit genetic activity to the chemical realm any more or any less than we do to limit the behavioural characteristics of macaque monkeys to chemistry - they are after all the end result of those genetic changes. But in the case of monkey social and physical activity too if you studied the chemistry "...you would understand in great detail how those reactions happened" so the monkeys would have been fully explained, but only to an reductionist who considered all that zoologists and animal behaviourists find useful to be fluff. I'm actually quite saddened to see that there are still people who embody the old nineteenth century hyper-reductionist stereotype, "There, it's nothing but a bag of chemicals reacting." If it were, it would interest only chemists. But it interests information scientists like Hubert Yockey too - whose contribution to the understanding of DNA goes back to the dawn of its discovery, but whose insights, though they were clear to Watson and Crick, seem to have gone over some people's heads even 60 years later.Jon Garvey_{August 8, 2013
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PS: We need to ask ourselves what is so telling about the obvious info processing system in the cell that builds proteins (and similar systems) that makes the likes of MF and EL so desperate to avoid acknowledging the obvious. And if that is what hey are reduced to doing, that is telling indeed. (And I have again outlined what we are dealing with above, cf also here -- especially note the video.)kairosfocus_{August 8, 2013
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Folks, See what I mean about needing familiarity with machine level processing in info systems? Device physics (or chemistry) is an enabling phenomenon. Structures apply that phenomenon to signal processing. Systems then use the structures based on the underlying processes to achieve information level results. MF is doing the equivalent of suggesting that once we understand in some way semiconductor physics and the phenomena of junctions and such like, we can then describe what is going on in a CPU and do so without residue. That is why one studies devices (and underlying phenomena), signals, structures and systems without making the blunder of imagining that more information functional levels are not adding tot he understanding. FYI, MF, Electronics is not simply Quantum physics. Devices, circuits and networks are not systems, and hardware is not software. On the soft side, machine, assembly and higher level code are not equivalent either. We all should know and readily recognise this. We should know that when we see object code working at machine level and executing algorithms [step by step, goal directed finite sequences of steps], that is what we are seeing. That is why when I see the sort of line of objections that is cropping up yet again in this thread, all it tells me is that we are seeing little more than refusal to recognise the compellingly obvious. Sad, but on track record, not unexpected. And utterly telling. KFkairosfocus_{August 8, 2013
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#269 Jon
One could describe the running of a computer program in terms of physics, and extremely tedious it would be, ending up by telling you that this electronic change happened in slightly different ways a few billion times, and here’s a printout of the pattern (which reproduces what you can read in the program only at much greater length). And you’re no closer understanding how, or to what end, those reactions happened.
But you would understand in great detail how those reactions happened. I admit you would not know to what end and that is precisely the point - we have no reason to suspect there is an end for the DNA/Protein transcription. If the chemistry underdetermines DNA/Protein transcription then let us know what it is that is not determined. (Presumably I don't have to explain that Joe's "answer" is not an explanation:
Because it is a code and that means it is the proper description.
)Mark Frank_{August 8, 2013
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It cannot be described in terms of chemistry.
Or to be more precise, it is completely underdetermined by chemistry, which is evident to anybody not being willfully obtuse. One could describe the running of a computer program in terms of physics, and extremely tedious it would be, ending up by telling you that this electronic change happened in slightly different ways a few billion times, and here's a printout of the pattern (which reproduces what you can read in the program only at much greater length). And you're no closer understanding how, or to what end, those reactions happened. Describing genetic events chemically will leave you with no idea that there are, and must be, error correction mechanisms, that there are levels of organisation of information processing (because there can't be if there's no information involved), opr, of course, that there is any actual organisation involved, chemistry not being a subject involving organisms.Jon Garvey_{August 8, 2013
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Mark:
The question I have is what does it add to describe that process as the translation of symbols which represent the proteins using a code over and above just describing the process (in detail)?
Because it is a code and that means it is the proper description.
To support this you quote from the rather controversial Hubert Yockey but clearly it is very common to refer to DNA as a code.
In what way is Yockery controversial? Is it because he contradicts what you are saying? LoL!
I am reversing the question and asking you what you think the value is of describing the process in terms of symbols, codes and translation as opposed to just describing the process in detail in terms of chemistry?
It cannot be described in terms of chemistry. If it could be then scientists would. IOW Mark appears to be totally clueless wrt transcription and translation.Joe_{August 8, 2013
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