Information created accidentally, without design

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July 11, 2013

Darwinism, Design inference, News

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Darwinism
Design inference
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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

Elizabeth B Liddle @155 wrote:
DNA in any form but a molecule could not do the job. This is not true of, for example, language, which can be not only spoken, but written in countless different media and still convey the same information.
The problem is that your analogy is broken. You are comparing two different issues as if they were the same. As I pointed out earlier, it is true for any of our input devices for symbolic information processing systems that they impose requirements on the media that they will accept and are able to process. Exactly as a ribosome requires mRNA, so also CD drives require CDs, magnetic tape drives require magnetic tapes, paper tape readers require punched paper tape, and so on. This is regardless of the fact that the information contained on any of these mediums could in principle be converted into any other digital medium -- including storage in DNA. Thus, in terms of the requirements for a physically implemented device to "do its job" of translation, the ribosome and other symbolic information input devices are equivalent in this regard. What about the ability of symbolic information (not the device that reads it or the medium it is on, but the symbolic information) to be represented in different forms and carry the same information? Here again the symbolic information in DNA can be converted into many forms, such as into mRNA (a different form that uses uracil rather than thymine) or onto paper or in the form of computer memory and (as Craig Ventor et al demonstrated) back again into an artificially created yet functional DNA genome. Are you really going to deny that Craig Ventor and company did this, or that the symbolic information that they converted back and forth was not equivalent, even though it was held by multiple different mediums? The proof is in the pudding, and the end result was a functional living organism. In short, your analogy was broken only because you did not make an equivalent comparison. When equivalent comparisons are made, the symbolic information in DNA or mRNA fulfills all the requirements for symbolic information and is completely comparable to other examples of symbolic information.ericB_{August 6, 2013
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F/N: Euler's rebuke to the so called "freethinkers." KFkairosfocus_{August 6, 2013
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Mark Frank @156, wrote:
I am not sure what counts as “an assigned or associated meaning”. It is clear enough if there is a convention established either by common usage or by some kind of publication such as a dictionary. But the DNA/Protein link is neither of those. The only thing linking the DNA to the resulting protein is the observed fact that the DNA string causes the protein to appear in a very specific environment. There was no “convention” in any other sense that I am aware of.
I have the impression that you may be getting stuck by thinking in terms of the method by which humans may often establish conventions, rather than thinking about the nature of a coding convention itself. Consider the convention of Morse code, which involves sequences of short signals (or dots) and long signals (or dashes). Notice that these sequences do not carry any inherent meaning in themselves. You could not infer their meaning only by studying the physical and chemical properties of the sequence. Nevertheless, one can translate them (if they carry symbolic meaning) by applying the matching external coding convention. If one can do this and successfully translate the sequence, that shows both the meaning of the sequence and that the sequence was functioning to hold symbolic information. Three dashes do not necessarily represent the letter "S", but by the particular coding convention of the International Morse Code, they do. Likewise, there is no inherent or necessary association between three dots and the letter "O", but by the coding convention of the International Morse code, that association between symbol and meaning applies. Notice that other coding conventions could be used, and in fact the original Morse code (now also known as the American Morse code) was different from the International Morse code. Morse code at Wikipedia The situation in this regard is exactly the same with the coding conventions used for the genetic codes of biological organisms. The mRNA sequence (or the DNA) has no inherent meaning. The very same codon in one organism can mean something else in another organism. This is because some organisms use a different coding convention. There is no universal genetic code. So, in one organism, a certain codon (triplet of bases) might represent the translation instruction to add a particular amino acid. In another organism, that same codon might represent the instruction to add a different amino acid. OR, it might represent the signal to STOP, i.e. marking the end of the sequence for translating into a functional amino acid sequence for a protein. You wondered about "a dictionary" for the convention. In the cell, the coding convention's dictionary or translation look-up table is implemented chemically by the particular set of transfer RNA molecules that it uses to implement its genetic code. As I've mentioned before, there is no inherent or necessary chemical requirement that associates a particular codon/anticodon with a particular amino acid. The codon never even touches the amino acids. The flexibility of being able to have different sets of transfer RNA molecules is what allows there to be alternate genetic codes. You can see plainly that it doesn't have to be one way or the other way. There is no law of chemistry or physics or of cause and effect that requires a particular association between symbol and meaning. Yet at the same time, the associations must not be made randomly. They must be done with complete consistency within an organism, or else the ability to translate the meaning of the symbolic information would be destroyed. That is why it is proper and appropriate to acknowledge this is a coding convention. It is neither a necessary law of nature to make certain associations, nor are the associations formed by random chance. A consistent practice that is not obligatory is a convention. Now, if you like another word that means the same thing, that would make no difference. The reality is these are coding conventions that translate between symbolic information and the associated functional meaning. The severe problem this presents is that chemicals, when left to themselves, have no interest, need, or desire to construct coding conventions for storing and retrieving symbolic information (e.g. recipes to make proteins). You can never reach the construction of such a system through blind chemical processes, no matter how many billions of years you waited.ericB_{August 6, 2013
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There are none so blind as those who refuse to seeAndre_{August 6, 2013
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Andre #165
Mark Frank you can register for free!
I didn't notice - thanks! I have done it now and the story substantiates what I said. It is the scatter plot that is symbolic not the DNA!Mark Frank_{August 6, 2013
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“Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.” (Hubert P. Yockey, Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005)
BTW codes use symbols...Joe_{August 6, 2013
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Mark: DNA/RNA sequences could be used to hold information. Joe: In living organisms they are.
That is exactly the issue we are debating.
Who doubts that? IOW why would anyone debate that other than ignorance or an agenda?
As far as I know, biologists and information scientists do not say that nucleotide strings hold symbolic information.
So you rely on ignorance then. The following site talks about the genetic code and symbols: the genetic codeJoe_{August 6, 2013
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MF "This goes back to your example of someone deliberately using DNA to store a recipe for making a protein. It is the external fact of the intention to communicate that makes it symbolic information." What for the cell have the DNA if it is not to "comunicate" to the "doughter cells" how to build proteins?Chesterton_{August 6, 2013
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EL "What we are saying is that it is not symbolic Of course it is information." It is simbolic. You can use the same code to make a computer read the DNA, a machine sintetize proteins and we and you can use it to talk. Also you can use it to modify proteins using aminoacy tRNA modified in the lab.Chesterton_{August 6, 2013
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Lizzie:
What we are saying is that it is not symbolic.
It is wrt protein synthesis. And nothing you can say will ever change that fact.Joe_{August 6, 2013
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Alan Fox:
DNA’s relationship to protein is so obviously physico-chemical, it is hard to comprehend the suggestion of symbolism.
Unfortunately for Alan he cannot provide any evidence that supports his claim wrt the DNA to protein relationship. If Alan Lizzie or mark had any evidence to support their position they would present it. Yet they have either failed or flat out refused to do so. I am sure all of that is not lost on any onlookers.Joe_{August 6, 2013
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F/N: It should be noted that I have designed and built digital, info processing systems, and when we get down to hardware in action working on machine code, "all" that one sees is physico-electronic transitions, based on materials and structures and cause-effect bonds in accord with physical and chemical laws etc, but the arrangement of all of that is riddled with functionally specific complex info and related organisation that carries out algorithmic step by step goal-oriented processes. What is going on here is refusal to see a machine level molecular nanotech info system for what it is, a sure sign that the evidence is strongly against the deniers. Euler's rebuke to the free thinkers so called is looking ever more dead on target. But then, what do we expect from people who refuse to acknowledge the patent reality that error exists is undeniably true, or fought long and hard before grudgingly acknowledging that one cannot be mistaken that one is aware, and still fight tooth and nail to resist the implications of a red ball sitting on a table and the implications of being able to ask why there is that ball there. This is ever more plainly a priori -- and demonstrably self refuting and amoral -- materialist ideology speaking through dismissive and distractive talking points that we are dealing with, not reasonableness and docility before evident truth. KFkairosfocus_{August 6, 2013
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Mark Frank you can register for free!Andre_{August 6, 2013
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EL and MF: Please don't try the deny and evade game, just as was doe with slander against me at your blog EL. If you do not intend to communicate denial of info -- and functional, coded info is inextricably entangled with meaningfulness -- in DNA, functionally specific complex coded and control info, I think you need to revise your talking points drastically:
MF: I am not sure what counts as “an assigned or associated meaning”. It is clear enough if there is a convention established either by common usage or by some kind of publication such as a dictionary. But the DNA/Protein link is neither of those. The only thing linking the DNA to the resulting protein is the observed fact that the DNA string causes the protein to appear in a very specific environment. There was no “convention” in any other sense that I am aware of.
FYI, MF, there is a specific code, one identified and tabulated decades ago. That constitutes meaning. Next it is not just an environment that is at work, but an info processing system that uses molecular nanotech. There is transcription, editing, transmission, translation and expression as the end product of a highly complex process, leading to proteins that function on folding etc. MF, you used to work for IBM, so you must know better than you have spoken. EL, I am through with your evasion, denial and distortion games, given your track record as a harbourer and denier of vicious slander. Good day, KFkairosfocus_{August 6, 2013
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Its sadly telling that KF does not consider himself bound by the same standards he demands from his perceived opponents. DNA's relationship to protein is so obviously physico-chemical, it is hard to comprehend the suggestion of symbolism.Alan Fox_{August 6, 2013
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Andre #161 I cannot access even the abstract of the first paper but the title suggests it is about how a scatter plot can symbolise DNA patterns i.e. the symbols are the scatter plot not the DNA. The second paper is utterly bizarre but in any case is irrelevant as to whether DNA contains information about proteins. It is exploring the hypothesis that something used DNA to communicate that it was intelligent. I think it is absolutely nutty but even it is true it is independent of the ability of DNA to produce proteins.Mark Frank_{August 6, 2013
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Dr Liddle and Mark Frank
What we are saying is that it is not symbolic
Really? http://www.genomeweb.com/sequencing/symbolic-scatter-plot-helps-visualize-patterns-within-dna-sequence I wonder..... Does the one below not count because perhaps those kooks from Kazakhstan are religious fundamentalists? http://www.sciencedirect.com/science/article/pii/S0019103513000791Andre_{August 6, 2013
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KF - I only echo both of Lizzie's comments. The Wikipedia article does not conflict with anything we have been trying to say and there is no gambit - it is genuine attempt to explain my/our point of view. It takes quite a lot of time and thought to express things as precisely and concisely as possible. I may well do it badly, but it is a bit galling to have it all dismissed as a gambit on the basis of a quote that is irrelevant.Mark Frank_{August 6, 2013
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Seriously, KF, if you would for one moment consider that perhaps we are not using a "gambit" at all - but trying to explain in all seriousness why we think the way we do, it would probably aid communication!Elizabeth B Liddle_{August 6, 2013
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KF: nobody is saying "DNA is not info". What we are saying is that it is not symbolic Of course it is information.Elizabeth B Liddle_{August 6, 2013
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F/N: I am not surprised to see the DNA is not info gambit at this stage, but MF, if he were willing to examine even Wikipedia, would find the following regarding the genetic code in the article of that name:
The genetic code is the set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins by living cells. Biological decoding is accomplished by the ribosome, which links amino acids in an order specified by mRNA, using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries. The code defines how sequences of these nucleotide triplets, called codons, specify which amino acid will be added next during protein synthesis. With some exceptions,[1] a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. Because the vast majority of genes are encoded with exactly the same code (see the RNA codon table), this particular code is often referred to as the canonical or standard genetic code, or simply the genetic code, though in fact some variant codes have evolved. For example, protein synthesis in human mitochondria relies on a genetic code that differs from the standard genetic code. Not all genetic information is stored using the genetic code. All DNA contains regulatory sequences, intergenic segments, chromosomal structural areas, and other non-coding DNA that can contribute greatly to phenotype. Those elements operate under sets of rules that are distinct from the codon-to-amino acid paradigm underlying the genetic code.
None so blind as those who, after repeated opportunities to get it right, still refuse to see. But, the very fierceness of the refusal to look at standard, well grounded facts of life, tells us volumes about the type of ideology we are dealing with and, inadvertently, about just how strong the inference is from code and code processing info systems to design. $0.02 KFkairosfocus_{August 6, 2013
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Eric You can of course define symbolic information any way you wish and DNA may well conform to one of those definitions. All I can do is point out a couple of problems in your definition. This paragraph seems to be the key one.
The core idea of a symbol is that, in addition to and distinct from its own inherent properties, it also has an assigned or associated meaning such that it represents something other than itself. That assigned or associated meaning is extrinsic to the thing itself. It is not inherent, since the association is by an external convention, not by its inherent properties.
I am not sure what counts as “an assigned or associated meaning”. It is clear enough if there is a convention established either by common usage or by some kind of publication such as a dictionary. But the DNA/Protein link is neither of those. The only thing linking the DNA to the resulting protein is the observed fact that the DNA string causes the protein to appear in a very specific environment. There was no “convention” in any other sense that I am aware of. (I can also think of an associated meaning without a convention arising from knowing human intentions – but that is an aside) The phrase “in addition to and distinct from its own inherent properties” also needs clarifying. Whenever there is a causal chain then the effect will be distinct from the cause. Suppose a thunderstorm causes a flash of lightening which causes my internet connection to go down which causes this comment to be delayed. This delay is quite distinct from the properties of a thunderstorm. Is this all you mean? Mark Frank_{August 6, 2013
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Hi, Eric. What I meant by "the thing itself" is not the thing that the DNA specify, but is the physical means by which it does so. DNA in any form but a molecule could not do the job. This is not true of, for example, language, which can be not only spoken, but written in countless different media and still convey the same information. That is why I say there is a key difference between symbolic and non-symbolic information (I do not of course deny that DNA contains information). A DNA sequence does not "represent" a protein. It is, rather, a segment of a polymeric molecule which, in an environment that contains certain other polymeric molecules, results in a specific protein. It is, in other words, a physical object that is a necessary, but not sufficient, for that protein to be formed. No alternative representation can be substituted. On the other hand, you may be reading this post on a touch screen or a CRT, or listening to it with automated text-to-voice software - the medium makes no difference to your ability to receive the information. That is because I am using symbols, I am not making physical objects that will be inserted into your brain in order to reconfigure it in a manner that results in your understanding my post. This is why, if we are using data-transmission metaphors, that IMO it is important to keep track of who is the sender and who is the receiver and what is the message. In this post, it is perfectly clear that I am using the written English symbol system to send a message - this post - to you. In a cell, what is happening? Who is the sender? What is the message? Who is receiving it? I completely agree that information is being transferred, but I think it is salutary to analyse the transmission pathway. Take a protein like like the dopamine transporter, DAT. What is sending what information to what when DAT is expressed? And which of the information-transfers involved is, in your view "symbolic", and why? I suggest none are. Rather it is a highly complex cascade of physico-chemical interactions. Which doesn't make the system any less marvellous of course. Nor the resulting expression of our thoughts any less symbolic :)Elizabeth B Liddle_{August 5, 2013
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Re: the definition of symbolic information, Elizabeth B Liddle @116 showed an understanding of the relevant distinction in concepts, but there was a problem with the application.

[ericB:] Suppose we have begun to use DNA to hold information for our computational needs. Would you grant that in that case the DNA is a medium for holding symbolic information?
[EL:] Yes.
[ericB:] If yes, suppose that one of the pieces of information we store in that DNA is the recipe for a protein sequence. Would that still be symbolic information? Or would it cease to be so?
[EL:] Yes, unless of course you were using it in situ in the cell. Then it wouldn’t be a symbol, it would be the Thing Itself.
Elizabeth appropriately alludes to the relevant distinction, i.e. that symbolic information represents something other than itself in contrast to a sequence that is only "the Thing Itself." Every object -- even a symbol -- is always itself, but symbolic information is additionally a coded way of representing Something Else (other than itself). The problem is that no DNA sequence -- even one carrying symbolic information representing the recipe for a protein's amino acid sequence -- ever becomes an amino acid sequence itself. There are two possibilities: + All DNA sequences are (at least) themselves, i.e. a sequence of DNA nucleotides. + In addition, some may also symbolically represent Something Else according to an external coding convention (e.g. the amino acid sequence for a functional protein). Whether the translation of the symbolic information is performed in the cell by the ribosome or in the computer by an algorithm applying the same coding convention as the ribosome, the translation to the amino acid sequence for a functional protein would give identical sequence results. We could even engineer an artificial process for constructing the amino acid sequence physically based on the computer's translation of the identical symbolic information. Thus, the location of the DNA sequence is irrelevant to this distinction between those sequences that do and those that do not hold symbolic information. Those with symbolic information can be translated to yield the functional meaning of that symbolic information by applying the appropriate coding convention.ericB_{August 5, 2013
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Mark Frank @145 wrote (re: the definition for symbolic information):
Sorry about that. I am confused as to what is the definition you have provided – no doubt me being careless. Can you repeat it?
Here are the essential ideas that make up the concept of symbolic information. Every object has its own intrinsic properties (e.g. of physics, chemistry, etc.) that can be studied directly. These properties are inherent in the thing itself. The core idea of a symbol is that, in addition to and distinct from its own inherent properties, it also has an assigned or associated meaning such that it represents something other than itself. That assigned or associated meaning is extrinsic to the thing itself. It is not inherent, since the association is by an external convention, not by its inherent properties. Therefore, it is necessarily true that one can never determine the symbolic meaning of something (or even whether it has a symbolic meaning) by studying the thing itself. When we consider a sequence of objects, the sequence likewise has intrinsic properties that can be revealed through study of the sequence itself. In addition, the sequence may serve as a medium for holding symbolic information. In that case, the sequence also has an assigned meaning according to the convention of some external language or code. Since the convention is external, not a property of the sequence itself, the assigned or associated meaning (if any) cannot be determined by studying the sequence itself. The hallmark of symbolic information is the process of translation whereby the convention of the language or code is applied to convert between the symbolic sequence form and its meaning, i.e. the functional form. (This could be either encoding, going from functional to symbolic, or decoding, going from symbolic to functional.) Notice that it is not required that a conscious agent is the recipient of or observer of the process of translation. For example, we routinely make automated computing systems that manipulate symbolic information without human supervision or direct human involvement. Protein coding DNA and mRNA fully satisfy the requirements of symbolic information bearing sequences. They hold the recipes for protein amino acid sequences in a symbolic form. This is clearly symbolic information since it cannot be accessed apart from applying the correct coding convention for that organism. When the process of translation produces the functional protein, we observe the proof that the input sequence carried symbolic information.ericB_{August 5, 2013
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UB #150
DNA is not part of a semiotic system merely in theory; it is a demonstrated empirical reality. The demonstrated fact is that the cell processes information under the same steep physical requirements as found in an ant producing a pheromone, or a bee communicating the direction of food to the other bees, or a human writing “apple” on a piece of paper – and these material conditions are singularly unique among all physical conditions.
Let’s get precise here. I keep on writing just “information” when I mean “symbolic information” so it is my fault. Some systems that process information are semiotic - use signs or symbols - others do not. Your examples include a mixture. The ant does not uses a symbol and is not semiotic The human writing “apple” is semiotic. The bee is somewhat debatable although I would say not. Do you want to claim DNA transfers information, which I would accept, or that it is semiotic, which I would not? What are these steep physical requirements and are they requirements of semiotic systems or any old information processing system?
Also, re: your position that in order to know that information exists we must first know the intention of the human sending it. Obviously this is unusably anthropocentric. We know any instance of recorded information exactly the same way as any other instance of recorded information – and that is by the functional effect it has within the animate natural world. When we see ants attacking their enemies in unison, we ask the question of how the ant coordinate their attack and we naturally look to the presence of information. When we see a bat honing in on its prey in the darkness, we do not look to gravity and thermodynamics, we look to complete systems capable of offering a valid explanation, and again, we look to the presence of information. The translation of information harnesses the laws of physics to produce material effect not reducible to those laws, but reducible only to the local organic systems that transcribe and translate that information. Human intention has nothing to do with it except where humans are concerned – a mere drop in the bucket to the total volume of information transfer taking place in nature.
Again there seems to be some confusion between symbolic/semiotic information and any old information. To know about the information conveyed by symbols we definitely have to know the intention of the agent creating the symbols. In theory this could be the intention of any animal but I think humans are probably the only ones capable of it. There are some debatable cases with apes. On the other hand I agree that a wide range of living creatures and indeed non-living systems are capable of transferring information in the generic sense. The light transmitted from a star conveys information about the gasses in that star. However, the light is not symbolic information about the gasses in that star.Mark Frank_{August 5, 2013
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Dr Liddle, your comments are duly noted. Where they are not incoherent, they are trivial.Upright BiPed_{August 5, 2013
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Mark,
I don’t dispute that DNA could in theory be used as a semiotic system and therefore meets the operational requirements.
Information processing systems have been characterized in this thread using language that does nothing to illuminate the operation of the systems in question. And from those characterizations, statements have been made that do not reflect the actual operation of those systems. DNA is not part of a semiotic system merely in theory; it is a demonstrated empirical reality. The demonstrated fact is that the cell processes information under the same steep physical requirements as found in an ant producing a pheromone, or a bee communicating the direction of food to the other bees, or a human writing “apple” on a piece of paper – and these material conditions are singularly unique among all physical conditions. This reality makes some people uncomfortable because of the potential implications it raises on the origin of such systems. But at last checking, the political and social discomfort of human beings did not alter reality in the natural world, it only impeded the recognition of that reality. Also, re: your position that in order to know that information exists we must first know the intention of the human sending it. Obviously this is unusably anthropocentric. We know any instance of recorded information exactly the same way as any other instance of recorded information – and that is by the functional effect it has within the animate natural world. When we see ants attacking their enemies in unison, we ask the question of how the ant coordinate their attack and we naturally look to the presence of information. When we see a bat honing in on its prey in the darkness, we do not look to gravity and thermodynamics, we look to complete systems capable of offering a valid explanation, and again, we look to the presence of information. The translation of information harnesses the laws of physics to produce material effect not reducible to those laws, but reducible only to the local organic systems that transcribe and translate that information. Human intention has nothing to do with it except where humans are concerned - a mere drop in the bucket to the total volume of information transfer taking place in nature.Upright BiPed_{August 5, 2013
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Joe #148
Mark: DNA/RNA sequences could be used to hold information. Joe: In living organisms they are.
That is exactly the issue we are debating.
Mark: As far as I know there is no evidence that they are. Joe: Biologists and information scientists say that they are.
I am sorry. I should have used the phrase “symbolic information” throughout. The word “information” is far too ambiguous. This particular discussion is specific to symbolic information. As far as I know, biologists and information scientists do not say that nucleotide strings hold symbolic information. If they do then I would like to understand what they mean by symbolic information and how they know nucleotide strings hold it.
Mark: Similarly you cannot tell whether a nucleotide sequence holds information by examining the sequence and the cell mechanism you need to know of an intention behind it. Joe: Umm we observe the nucleotide sequence doing something and try to figure out what it is doing and why. IOW you have it backwards.
I am having difficulty understanding this. We normally observe the protein doing something, not the nucleotide. Is that what you meant? But it is a big jump from observing that to deducing or assuming an intention behind it. Again that is what we are debating. Mark Frank_{August 5, 2013
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DNA/RNA sequences could be used to hold information.
In living organisms they are.
As far as I know there is no evidence that they are.
Biologists and information scientists say that they are.
Similarly you cannot tell whether a nucleotide sequence holds information by examining the sequence and the cell mechanism you need to know of an intention behind it.
Umm we observe the nucleotide sequence doing something and try to figure out what it is doing and why. IOW you have it backwards.Joe_{August 5, 2013
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