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:
What I do not agree with is that such a system cannot arise from a simpler information processing system as a consequence of Darwinian evolution, nor that the the simplest possible Darwinian-capable information processing system is too complex to have occurred as a result of physical and chemical reactions, which also involve information (patterns of things that cause specific effects).
Whetever Lizzie. What you do NOT have is any evidence to support that scenario. Science works via positive evidence and your scenario doesn't have any. That means it isn't science. Nice job.Joe_{August 8, 2013
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EL "What I do not agree with is that such a system cannot arise from a simpler information processing system as a consequence of Darwinian evolution, nor that the the simplest possible Darwinian-capable information processing system is too complex to have occurred as a result of physical and chemical reactions, which also involve information (patterns of things that cause specific effects)." Like disprove the existence of God it is impossible to disprove that that happened. Could you demostrate that a code can appeare by darwinian evolution?Chesterton_{August 8, 2013
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ericB I think the same comment applies your responses to Lizzie and myself. I am all for detail and not being vague. I think we all quite understand at a similar level of detail how DNA/RNA is transcribed into proteins. 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)? You write:
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. I think it is less common to call the bases symbols and when it happens I would say it is poor choice – possibly arising from a muddle with the letters G, C A, and T which are symbols. 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? You have offered a couple of items as reasons for talking of symbols but they appear to apply equally to the moon/tidal creatures example.
There is no chemical necessity to those associations, and in fact we know different associations are used by some organisms.
There is every necessity if you place the DNA in a specific environment. In the same sense there is no physical or chemical necessity to the association between the Moon’s orbit and tidal creatures. You cannot tell simply by inspecting the moon and its orbit where and when on earth the creatures will be active. You need to consider the moon in a specific environment i.e. the earth and the details of its surface. If it were orbiting another planet it would have a quite different effect.
The codons represent amino acids, even though they are not amino acids and have no inherent or intrinsic relationship to any amino acid.
The orbit of the moon is not the activity of the creatures and has no inherent or intrinsic relationship to any activity of the creatures.Mark Frank_{August 8, 2013
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Elizabeth is right, of course, to say that Shannon information is an inadequate model to account for the DNA code having specific effects. On the other hand, it is a useful handle for deciding in what sense DNA is information at all. As Yockey says, DNA ticks all the boxes for an arbitrary semantic code, if an optimised one, (as do the others codes in life). But semantic codes also all conform to the constraints of Shannon information, such as entropy, channel width and so on, whereas purely chemical reactions do not - so those who say that "smoke" is information about there being a fire are using information in a non-Shannon, non-semantic way. DNA conforms to Shannon information in every respect, which is why Yockey has every right to say it is, at least, Shannon information. Then again, semantic information conforms to Kolmogorov complexity, whereas most natural self-organising structures like crystals do not. It has proven hard to get a handle on the concept of the "functional meaning" for semantic information in human communication as well as in DNA - but however much one disputes Dembski or Abel or Durston, the fact remains that the degree of theoretical intractability remains exactly the same for Shakespeare as for the genome: it has not proved possible to describe DNA's "function" any more easily in maths than it has to differentiate a useful computer program from a poor one. Which is suggestive of their being the same category of information. So DNA "quacks" like a semantic code, obeys Shannon's law, has Kolmorgorov complexity, and resembles the "mreaningfulness" of human semantic information. The only point at which "analogy" can legitimately be introduced in in the causation. Human information is produced deliberately, and has not proved possible to assemble by random variation and environmental selection, whereas DNA ('tis said) assembles by random variation and natural selection, and cannot have been assembled by mind. (Computer sims of life, of course, are useless in establishing that analogy in causing DNA only to appear to be "information", because they rely on representing life by semantic information in the computer program.) So what we observe, in effect, is conceptually-identical systems produced from completely different causal categories. Which is, I think, unusual in nature.Jon Garvey_{August 8, 2013
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Elizabeth B Liddle @240:
Now, would someone like to take a look at the information transfer cascade in my DAT example?
and @155:
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? ...
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. 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). 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. The message is carried by the messenger RNA, hence its name. The recipient is the ribosome that receives the mRNA. Notice that the DNA is not "causing" anything to happen. It is not the active agent. It is an information store and is passive in this whole affair. 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. 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.
... And which of the information-transfers involved is, in your view “symbolic”, and why?
As I've consistently maintained, the hallmark for recognizing the presence of symbolic information is the need for translation by a coding convention. 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. 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.ericB_{August 8, 2013
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Re: Elizabeth B Liddle @258, the significant problem with defining the protein coding information as
a pattern in which the arrangement causes specific effects.
or
patterns of things that cause specific effects
is that it is a retreat into vagueness -- a vagueness that is so broadly inclusive that it includes much that is irrelevant. All matter has arrangements that cause specific effects. Talking merely in terms of cause and effect is unhelpfully vague, as it avoids addressing the reality. What is fundamental and essential to biology -- and distinct from anything else we find anywhere in nature in the entire universe (excluding designed artifacts) -- is that biology depends upon the use of codes and translation. We know of no other instance of undirected nature that has this property. If we cannot talk clearly about what is unique and essential to biology, how could we begin to truly understand it? Whether we say "symbol" or not, there is indisputably and observably a translation to an amino acid sequence from a sequence that is not an amino acid sequence. There is no chemical necessity to those associations, and in fact we know different associations are used by some organisms. It is an association by a coding convention. The codons represent amino acids, even though they are not amino acids and have no inherent or intrinsic relationship to any amino acid. If we could not talk clearly about codes and translation from information to the associated meaning it represents, we would be unable to meaningfully deal with the reality. How could we begin to explain something, if we fail to even describe it accurately?ericB_{August 8, 2013
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Re: Mark Frank @257, I use those terms because they do indeed describe the details of what happens -- a translation from nucleotides functioning as a symbol sequence to the associated meaningful amino acid sequence via the particular conventions of an implemented code. This recognition of translation via a simple but real code is foundational biology, going back to the sequence hypothesis correctly posed by Francis Crick. Consider the consequences if biology had stopped at the vague statement, "All that we know for certain is that the same DNA string can result is different proteins depending on the context." In order for biology to advance, it has been necessary for biologists to be able to describe in meaningful and clear terms exactly what is happening inside the cell, without apology and without averting the eyes. Consider Hubert P. Yockey (my emphasis added):
It is important to understand that we are not reasoning by analogy. The sequence hypothesis applies directly to the protein and the genetic text as well as to written language and therefore the treatment is mathematically identical. - Hubert P. Yockey, “Self Organization, Origin-of-life Scenarios and Information Theory,” Journal of Theoretical Biology, Vol. 91 (1981):16
and
5. The ‘‘order’’ and ‘‘complexity’’ of DNA and protein sequences The question of whether ‘‘complexity’’ increases along a phylogenetic chain can be addressed only when the well-established de?nition and quantitative measure of ‘‘complexity’’ such as that given by Chaitin and Kolmogorov [14,16,17] is adopted in molecular biology. ... A sequence of symbols is highly ‘‘complex’’ when it has little or no redundance or ‘‘order’’ and cannot be calculated by an algorithm of finite length. ... 6. Conclusion The segregated, linear and digital character of the genome has allowed us to apply information theory and other mathematical theorems about sequences or strings of symbols to make a quantitative rather than an anecdotal and ad hoc discussion of significant problems in molecular biology. This procedure has led us to avoid a number of illusions common in the literature. The application of these mathematical procedures will play a role in molecular biology analogous to that of thermodynamics in chemistry. Information theory, evolution and the origin of life, Hubert P. Yockey, Information Sciences 141 (2002) 219–225
It would never serve science to retreat into a vague, black box description that cannot address what is happening in detail. So, 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. It is because that is the true reality that needs to be understood clearly, if one is to have any hope of coming to an understanding of how it came to be so.ericB_{August 8, 2013
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MF: You are manifesting exactly what EB is warning against. DNA is a passive info storage entity in the process, a memory bank. It is unzipped, transcribed, edited. I leave off maintenance. mRNA, already in a different code due to U not T, is transferred to ribosome, and threaded. It is a control tape for an NC machine (and that is not mere analogy, cf images and vid here noting the way paper tape readers worked), using prong height patterns to convey info. tRNAs serve as AA taxicabs and position-arm devices with universal CCA coupler tool tips. That means there is no deterministic setting of a given AA to a given codon-anticodon pair. Loading enzymes match config of tRNA and load per a code. That is an implicit dictionary. And of course there are natural and now artificial variants. The many to one variable pattern from codon triplet to AA added to protein string also bespeaks the same. I think you need to think again. KF PS: to get that link, I copied that for a comment then edited out: "#comment-467195" to get desired function. I trust that helps yo0u see the significance of editing.kairosfocus_{August 8, 2013
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F/N: I think I can safely say scoliosis (rapid onset) and surgery. Thots and prayers appreciated. KFkairosfocus_{August 8, 2013
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I am talking about information defined according to Merriam Webster' 2b 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
which is also a definition that Upright Biped has used. To be even more succinct: a pattern in which the arrangement causes specific effects. This is not the same as "Shannon information" because to quantify Shannon entropy you do not specify the arrangement - it merely gives you an estimate of the information-carrying capacity of the channel. The vast majority of possible arrangements in a wide-capacity capacity channel will not cause "specific effects". Clearly, the arrangement of nucleotides in DNA or RNA, or indeed the arrangments of amino acids in a peptide or protein, cause "specific effects" in a cell. What effects they cause is also a function of patterns of input of smaller molecules and ions. In other words, in living things, including multicellular organisms, what happens ("specific effects") is a result of a complex cascade of information - patterns of events. They are therefore complex information processing systems. If that is what Upright Biped is saying, I agree with him. What I do not agree with is that such a system cannot arise from a simpler information processing system as a consequence of Darwinian evolution, nor that the the simplest possible Darwinian-capable information processing system is too complex to have occurred as a result of physical and chemical reactions, which also involve information (patterns of things that cause specific effects).Elizabeth B Liddle_{August 8, 2013
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ericB #251 I think there is a danger of repeating the debate on symbolic with terms like "real code" and "represents". To try to avoid that can you explain what is going on besides DNA creating proteins in specific environments with slightly different proteins in different environments?Mark Frank_{August 7, 2013
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Elizabeth Liddle:
Clearly Mark and I are using different definitions of “symbol” from the rest of UDers.
Over at Elizabeth's blog, Neil Rickert posts:
I take the “information” of “information processing” to be Shannon information. I take Shannon information to be a sequence of symbols (such as bits). Categorization is how we get symbols in the first place. So categorization is prior to information processing.
Anyone familiar with Elizabeth's history here at UD will recall her reliance on "Shannon Information." So under what definition of "symbol" is Shannon Information not "symbolic"? Does Elizabeth even have a coherent position capable of explication?Mung_{August 7, 2013
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ericB:
We can say more than that. We can legitimately say that the genetic code is a real code
Absolutely. This has been demonstrated here at UD in the past. The objectors prefer to ignore THE FACTS and insist that all we have here is an analogy. Unacceptable.Mung_{August 7, 2013
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Elizabeth Liddle:
Nobody is disputing that DNA is part of an information storage-and transfer system, nor that it is part of a complex information processing system.
And the components of an information processing system are? If you cannot say, then you cannot know. So, for the record, you now agree with Upright BiPed?Mung_{August 7, 2013
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Elizabeth Liddle:
Clearly Mark and I are using different definitions of “symbol” from the rest of UDers. I suggest we move on.
I suggest that you learn to communicate clearly and effectively and without equivocation. The effort can do wonders for addle-headedness. How do you propose to even begin to defend the thesis that a codon is not symbolic? Are you going to claim that codons are meaningless information?Mung_{August 7, 2013
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Alan Fox:
Firstly, you don’t have a method of calculating CSI. You don’t have an agreed concept of CSI and its variants.
But Elizabeth Liddle did? Or was her entire exercise a fraud? Creating CSI with NS Yes, folks, EL claimed to generate CSI and also claimed to be able to calculate it. Where was AF in that thread? Didn't he tell her she was on a fool's errand?Mung_{August 7, 2013
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Regarding anthropomorphism, Mark Frank @239 wrote:
However, I do disagree with this statement which has more implications:
That meaning is assigned according to the convention of a particular code
“Assigned” gives the impression that someone thought up a convention and then decided to use different variants in different situations. As I have stressed “convention” implies one or more parties agreeing on something. ... It is interesting but we should be wary of anthropomorphising it in an attempt to explain it or make it more dramatic.
I agree that it is good to be careful about connotations and inadvertently adding unwarranted assumptions. In all my references to "conventions", "codes", "symbols", "symbolic", etc., I am always using these in a denotative sense that describes their function in a "complex information processing system", as Elizabeth said @240. I don't intend by any of these terms to merely and directly assume that the convention was made by sentient agents, and so on. Without begging the question, one of the possibilities to be considered is whether it makes more sense to attribute such a "complex information processing system" to an origin from undirected chemical processes or to an origin from intelligent agency. I do, of course, think all considerations point soundly and conclusively to the latter conclusion. I would maintain that it is not possible for chemical processes to develop this type of complex system for manipulating symbolic information that is stored and translated according to an extrinsic code. This would not happen regardless of the time allowed. However, I do not merely suppose that by assuming an anthropomorphic connotation to these terms, and I would not consider that a legitimate way to draw conclusions. At the same time, I would say there is an equivalent danger on the flip side. It would be easy for those who do not welcome an intelligent source for life to choose to avoid acknowledging the appropriateness of terms that correctly imply a real difficulty for their position. Word connotations can be used to tilt perspective in an unwarranted manner in either direction. For example, I would disagree with this characterization.
All that we know for certain is that the same DNA string can result is different proteins depending on the context.
We can say more than that. We can legitimately say that the genetic code is a real code (which is what makes it possible for your observation to be true), even without supposing it was made by intelligent agents. Even if chemicals made it, it is still a real code -- not an analogy to a code, but a genuine code. We can also say that each codon "... represents, [or] stands for ... an ... action, or material entity" [such as STOP making the protein, or add the associated amino acid (a material entity) to the growing polypeptide chain]. This, of course, is wording adjusted and borrowed from the definition of symbol, as provided by kairosfocus @249. This is similar to "Something that represents something else by association ... or convention, ..." provided by CentralScrutinizer @186. Even if you preferred to avoid the term "symbol", what matters is that you do not deny the reality described by these definitions. So long as we agree to affirm the reality, that particular term is not strictly necessary. The meaning of the term is an essential part of the reality of the situation to be studied and explained. Therefore, its reality must not be denied.ericB_{August 7, 2013
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kairosfocus @231, I don't know the particulars about the situation. Nevertheless, I join with what others have expressed. May it go well with you and with your son!ericB_{August 7, 2013
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F/N: On "symbol," wiki: >> A symbol is an object that represents, stands for, or suggests an idea, belief, action, or material entity. Symbols take the form of words, sounds, gestures, or visual images and are used to convey ideas and beliefs. For example, a red octagon may be a symbol for "STOP". On a map, a picture of a tent might represent a campsite. Numerals are symbols for numbers. Personal names are symbols representing individuals. A red rose symbolizes love and compassion. >> In this generally accepted sense, AUG is a symbol for start and load Methionine in an AA string. Since the tRNA -- cf the video in the post I made -- is coupled to the AA with a CCA universal coupler end, the specific AA for each tRNA is programmed. And obviously, with the anticodon at the other end of the folded tRNA, there is no necessary connexion between a given anticodon and a given AA. Indeed in several cases in the code(s) there are different anticodons that target the same AA. There are also three stops, and advantage has been taken to reprogram so that different AA's are loaded. None of this should have to be belaboured, but this is all to revealingly familiar. KFkairosfocus_{August 7, 2013
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AF: It's a little late to try a take-back, given your tactics that are even manifested in the catchphrase you propose relative to quite evident facts on the table. We will take due note, and respond accordingly to the tactics we are so plainly seeing. KFkairosfocus_{August 7, 2013
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MRI scankairosfocus_{August 7, 2013
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Ribosomes are ubitiquitous and vary across archaea, bacteria and eukaryotes. Shades of evolution there too.Alan Fox_{August 7, 2013
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BTW Alan, ribosomes are not generic- there are differences.Joe_{August 7, 2013
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Elizabeth:
Clearly Mark and I are using different definitions of “symbol” from the rest of UDers.
What definition of symbol are you using?Joe_{August 7, 2013
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I had no idea there were so many variants on the standard genetic code. So I was wrong in thinking there was only one known “machine” for transcribing DNA into proteins.
The "machine" that translates mRNA into proteins is the ribosome and all living cells have them. The variations in the genetic code are small but highly significant. Most variations occur in prokaryotes and mitochondrial DNA that hints at an evolutionary element to the genetic code.Alan Fox_{August 7, 2013
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To clarify my remark Karthago (sic) delenda est, I was suggesting I should end all my comments with "and has anybody got a hypothesis of "Intelligent Design" yet?" after the habit of Cato appending Karthago delenda est to all his Senate speeches. BTW it translates as "Carthage must be destroyed" and is often a text book example of the use of the gerundive. I was not intending to imply any parallel between the fate of Carthage and that of ID.Alan Fox_{August 7, 2013
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I could go on and on, but I have much more important, closer to home medical issues today, a big day for my son.
I echo Lizzie's sentiment. Best wishes for the best possible outcome, G.Alan Fox_{August 7, 2013
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Clearly Mark and I are using different definitions of "symbol" from the rest of UDers. I suggest we move on. Nobody is disputing that DNA is part of an information storage-and transfer system, nor that it is part of a complex information processing system. Now, would someone like to take a look at the information transfer cascade in my DAT example?Elizabeth B Liddle_{August 7, 2013
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ericB I have moment to look at this again. First - thank you for your comment #238. I had no idea there were so many variants on the standard genetic code. So I was wrong in thinking there was only one known "machine" for transcribing DNA into proteins. As I have stressed many times above, it seems not to be very interesting to debate the correct meaning of "symbolic". However, I do disagree with this statement which has more implications:
That meaning is assigned according to the convention of a particular code
"Assigned" gives the impression that someone thought up a convention and then decided to use different variants in different situations. As I have stressed "convention" implies one or more parties agreeing on something. All that we know for certain is that the same DNA string can result is different proteins depending on the context. It is interesting but we should be wary of anthropomorphising it in an attempt to explain it or make it more dramatic.Mark Frank_{August 7, 2013
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Mung's STOP example @219 is instructive and revealing.
T – is a symbol that we happen to use, by convention, for thymidine. A – is a symbol that we happen to use, by convention, for adenosine. G – is a symbol that we happen to use, by convention, for guanosine. Put them together and what do they spell? TAG! or STOP!
Even among the nuclear genetic codes, TAG does not always represent a STOP code. In the Ciliate, Dasycladacean and Hexamita Nuclear Code and in the Blepharisma Nuclear Code TAG is used to represent an amino acid (specifically (Gln/Q) Glutamine), not a STOP code. While the standard code also uses TAA and TGA as STOP codes... the Euplotid Nuclear Code uses TGA for an amino acid (specifically (Cys/C) Cysteine), and the Ciliate, Dasycladacean and Hexamita Nuclear Code uses TAA for an amino acid (specifically (Gln/Q) Glutamine). So we see, even from Mung's example of STOP codes, that different genetic codes follow different coding conventions for STOP. In short, there is no inherent meaning of STOP for a sequence of nucleotides. It cannot be deduced from the properties of nucleotides. That meaning is assigned according to the convention of a particular code. It is extrinsic, not intrinsic. In other words, these codons are functioning as symbols that represent certain assigned meanings according to a convention. That is exactly what it means for a sequence to be functioning as a carrier of symbolic information.ericB_{August 7, 2013
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