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Author Topic:   Information and Biology
Quetzal
Member (Idle past 4038 days)
Posts: 3228
Joined: 01-09-2002


Message 1 of 11 (8911)
04-25-2002 10:16 AM


With the kind acquiesence of Chase, I am reposting my last response to him from our previous discussion. This post contains the majority of HIS previous post, so hopefully we can pick things up where we left off. Anyone has anything to add, feel free to jump in.

quote:
I would say that mutations have to do with 'information' in the sense that they can destroy genetic coding for certain functions (or, in my opinion, the information necessary for certain functions) that will be expressed in the organism's phenotype. A, T, C, and G create a code that gives instructions to build proteins.

Once more you are (mis)using an analogy. “Coding” is a convenient way for humans to visualize the deterministic chemistry involved in DNA replication and transcription, because there are certain semantic similarities between computer coding, for instance, and genetics. There is no more “code”, “information”, or “instruction” involved than there is in 2H2 + O2 --> 2H2O yields water, or any other chemical reaction. All of the terms you are using are abstractions. You cannot state that an abstraction has an intrinsic physical reality.

quote:
As to #2, I think the only difference is that we think of information differently. I would say that nucleotides are a code, and thus information, because they direct the production of proteins and 'decide' what kinds of things are to be produced, depending on the sequence. I note that there is a great difference between complexity and order.

I’m afraid you’re incorrect. The question has absolutely nothing to do with the way we view the subject. It has everything to do with a misunderstanding of basic organic chemistry. A nucleotide is not a “code” (in fact, if you want to use an abstract analogy, a nucleotide would be a “datum” at best). A nucleotide consists of a sugar and either a purine or pyrimidine base. Nothing more. It is not information. DNA does not “decide” anything. Adenine will ALWAYS pair with thymine. Cytosine will ALWAYS pair with guanine. It is a fundamental property of the chemical composition of the molecules and the way molecules combine – there is literally no way they couldn’t (please note the specific chemical bonds below).



The sequence of nucleotides in a functional gene simply dictates which amino acid it synthesizes – again based solely upon the chemical composition and sequence of the nucleotide triplets, again solely because of the rules governing how molecules combine. The entire biochemistry of the cell is wholly dependent on chemical triggers either within the cell or from the rest of the interlocking tissues of the given organism.

As you can see, there is nothing resembling information here. Just chemistry.

quote:
In #3, I would say that I agree for the most part. Overall, natural processes are involved in a species' extinction and in the cause of mutations, etc. However, when a species becomes extinct, all of the diversity contained in that population has now been destroyed. In this sense I would say that 'information' has been destroyed. I find it interesting that species are continually becoming extinct, and all of that variability is being lost. I guess that one of the things I'm driving at in this discussion is that this constant and rapid loss of genetic variability is being observed.

What’s your point? You’re now even further from the “genes-are-information” argument and appear to be claiming “information” is now related to biodiversity. This isn’t even a good analogy – let alone having any basis in observable fact. How on earth would you define the information content of an entire population? You haven’t even shown information exists as anything other than an esoteric abstraction at the organism level (after all, your assertion of an opinion doesn’t make it true). Beyond that, of course extinction causes loss of genetic variability – at least in the sense of diversity loss. Heck, even the loss of a single organism causes it. You can have a butterfly with the most amazing novel genotype in the world, but if a bird eats it before it reproduces, the genotype is lost. Your statement is a non-sequitur.

quote:
I'm not sure that beneficial mutations always cause a phenotypical change. For example, pesticide resistence is certainly beneficial, but has no affect on phenotype, but rather on genotype.

You are incorrect. By definition, the terms “beneficial”, “neutral”, and “deleterious” in reference to mutation can only be attributed by reference to their phenotypical effect. Remember, phenotype = expressed genotype + environment. In the case of a mutation that confers pesticide resistance, it cannot be said to be “beneficial” in an environment that doesn’t contain pesticide. In this case, the mutation is neutral since it has no effect on the organism’s marginal fitness. In fact, it might even be deleterious if the cost of whatever mechanism conferred the resistance makes the organism less competitive with other members of the population who don’t have the mutation.

quote:
I would tend to disagree. The nucleotides in DNA code for different amino acids -- if they were not there, nothing would be created (something would be prevented). Because they are there, and there exists an interpretation system that reads them (through transcription), something is created that wouldn't be otherwise. Life itself would be prevented without this information. I would say that information, or truth, does have an objective reality.

Your statement is a non sequitur. Of COURSE if the triplet sequence was not present there wouldn’t be any product. However, it has nothing to do with whether or not information is an intrinsic property of a gene (which you have not shown). On the contrary, as I showed above it has everything to do with the basic laws governing the interaction of molecules. There is no “interpretation system” at the genetic level – this is a human invention. Chemistry governs DNA -> RNA transcription and RNA -> protein translation. Here’s an expanded view:

Perhaps you could show me with reference to this graphic where your “interpretation system” is located? And show that it isn’t simply related to the chemical properties of the molecules involved?

I’m afraid we are still at square one. You have not shown – merely asserted – that information has some objective reality. (BTW: Where did the “truth” bit come from?)

Looking forward to your reply. Might I suggest you peruse something other than a creationist source? Perhaps something in biology, ecology, or population genetics? You are very adept at synthesizing arguments, and it’s a shame that they’re resting on such erroneous foundations.


Replies to this message:
 Message 2 by Lewissian, posted 04-26-2002 12:23 AM Quetzal has responded

  
Lewissian
Member (Idle past 2892 days)
Posts: 18
From: USA
Joined: 04-21-2002


Message 2 of 11 (8987)
04-26-2002 12:23 AM
Reply to: Message 1 by Quetzal
04-25-2002 10:16 AM


Deleted.

Edited by Lewissian, : No reason given.

Edited by Lewissian, : Outdated.


This message is a reply to:
 Message 1 by Quetzal, posted 04-25-2002 10:16 AM Quetzal has responded

Replies to this message:
 Message 3 by Quetzal, posted 04-26-2002 10:39 AM Lewissian has responded

  
Quetzal
Member (Idle past 4038 days)
Posts: 3228
Joined: 01-09-2002


Message 3 of 11 (9002)
04-26-2002 10:39 AM
Reply to: Message 2 by Lewissian
04-26-2002 12:23 AM


Hi Chase. Thanks for your reply. I think I see where you're heading, but feel I need you to clarify a few things before I substantively reply to your last post.

1. What concept or definition of "information" are you using? It appears both from the quotes and your comments that you are mixing several different conceptual frameworks. For example, Wieland is arguing for a semantic definition (purpose or function - which, in the context of biology is basically teleological), the Nature article is using an analogy based on a structural/attributive definition, and Dawkins and Sagan are using an algorithmic description.

2. I'm still not sure what your point is wrt "My point in my paragraph about #3 is that was observe constant extinction, not evolution, basically." Are you arguing against speciation? If so, how do you explain the diversity of life? In addition, please note that one of the most prevalent trends in ecology in nearly every lineage we've investigated is speciation --> adaptation --> relative stasis or drift or subsequent speciation --> extinction. Background extinctions are about as common as sunrise. How does this somehow refute evolution?

e. I agree with you that DNA --> RNA transcription and RNA --> protein translation can be viewed as an "interpretation system". However, this view is a function of the observer, not the nucleotide chain itself. If a DNA or RNA strand is taken as a combination of "signs" forming the object of investigation, the sign (T, A, C, G) is the ultimate carrier of information. But if, on the other hand, the information source which produces the signs is analysed, "information" would consist in the selection of a sign from a pool of signs (the action of the transcriptase), which is basically determined from the particular molecule involved. Please clarify how you are using the term "interpretation system", and how this relates to information.

4. I would appreciate it if you could define what you mean when you refer to "order" and "complexity".

I'm afraid I have to dash off to a meeting followed by a #%$#% reception. I hope to get back to you sometime tomorrow morning, as I have a couple of other questions. Look forward to your response.


This message is a reply to:
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 Message 4 by Lewissian, posted 04-27-2002 7:53 PM Quetzal has responded

  
Lewissian
Member (Idle past 2892 days)
Posts: 18
From: USA
Joined: 04-21-2002


Message 4 of 11 (9069)
04-27-2002 7:53 PM
Reply to: Message 3 by Quetzal
04-26-2002 10:39 AM


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Edited by Lewissian, : No reason given.

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This message is a reply to:
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Replies to this message:
 Message 5 by Quetzal, posted 04-29-2002 5:48 AM Lewissian has responded
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Quetzal
Member (Idle past 4038 days)
Posts: 3228
Joined: 01-09-2002


Message 5 of 11 (9105)
04-29-2002 5:48 AM
Reply to: Message 4 by Lewissian
04-27-2002 7:53 PM


Chase: Sorry about not getting back to you yesterday. Weekends are often family-directed, since I spend so much time either traveling or in the office during the week.

From your replies to my last post, I think we may be getting seriously off on a tangent. I’ll explain what I mean, then afterwards propose a possible solution. Otherwise, I don’t see how we can continue this conversation. Although I personally find the discussion of how information science can be used (or not used) in biology fascinating, your reply shows we don’t share the same degree of understanding of the topic. Permit me to illustrate what I’m talking about. I said:

quote:
1. What concept or definition of "information" are you using? It appears both from the quotes and your comments that you are mixing several different conceptual frameworks. For example, Wieland is arguing for a semantic definition (purpose or function - which, in the context of biology is basically teleological), the Nature article is using an analogy based on a structural/attributive definition, and Dawkins and Sagan are using an algorithmic description.

You replied:

quote:
Tha basic point is that it is information. In this quote from Nature, it does not appear to me that they’re simply using the phrase “genetic information” as an “analogy based on a structural/attributive definition...” They state that “The nucleus of a single cell (left) contains all the genetic information required to make the human body. This genetic information is packaged as chromosomes (right) [emphasis mine].”[1] They are referring directly to genetic information, not using it as an analogy, as you suppose, and are saying that this genetic information, not the analogy of it, it itself “packaged as chromosomes.” Nature also states that “Genes are transcribed as continuous sequences, but only some segments of the resulting messenger RNA molecules contain information that codes for the gene’s protein product. These segments are called exons. The regions between exons are known as introns, and are spliced from the RNA before the product is made [emphasis mine].”[2] Once again, not an analogy. Perhaps if you gave me a quote from Nature stating that they view the genetic information they speak of as an analogy, I would be more inclined to believe this.

This is precisely the definition of an attributive/structural use of information theory to describe genetics. It boils down to a question of how to characterize “information”: is it a process (a la Shannon, Seiffert, etc.) or is information itself a structured object (a la MacKay, Dretske, Nauta, Hyderhoff, etc), or further is “information” a descriptive, illustrative or analytic property (a la Chaitan, Dawkins, Fischer etc) of a system?

Look, any number of researchers have used “information” as a conceptual framework for understanding DNA/RNA and the chemical processes that govern life, just like the authors of the Nature article. Heck, I use it myself. Molecular biologists are always talking about "codes", "cybernetics", and "information". For example, in the follow-up to their famous paper describing the structure of DNA, Watson and Crick said:

quote:
The phosphate-sugar backbone of our model is completely regular, but any sequence of the pairs of bases can fit into the structure. It follows that in a long molecule many different permutations are possible, and it therefore seems likely that the precise sequence of the bases is the code which carries the genetical information[1]

Abstracted as a language or a code, genetic "information" can exist in its own abstract domain, available for theoretical analysis on its own terms, and dissociated from the dull considerations of mere "context" – energy budgets, coenzymes, histones, methylation patterns, etc. But in fact, this context in which DNA exists – the nucleus of a cell – is itself filled with implicit information and information-bearers. Considering genetic information apart from its context, and expecting to be able to do anything with it, is roughly comparable to imagining that a dictionary would be all you would need for a useful translation of “Lord of the Rings” into Xhosa. This is the fundamental fallacy of creationists arguing “information” – Wieland, Dembski, etc, all demand that an undefined “information” be accepted as an intrinsic, fundamental property of DNA. It isn’t.

To translate anything into a culture unlike ours, for instance, you have to add what would be understood here (knowledge). In a place where there aren’t any elevators you would have to add information about elevators. To translate the DNA into a human-readable form, you have to add information about the context in which the DNA is to be read. You have to make explicit information that is implicit in the construction and chemistry of the cell from which the DNA came.

Let me give you a simple example, using your “interpretation system”. Even to simply use an information concept to describe protein synthesis, you have to “add information” to the system. First you have to transcribe the DNA onto an mRNA template. You need to make sure there are enough bases of the right kind in the right order, and you need an enzyme (RNA polymerase), along with an assortment of eight or ten different "general transcription factors", molecules whose jobs vary from marking the start point of the transcription to providing the energy the polymerase needs to do its job. Since you’ve changed the basic DNA “recipe” by including all these other molecules, you’ve already added more “information” to the system.

The next step is to edit the mRNA template. As you noted, DNA consists of protein-encoding parts called "exons" interspersed with parts whose function (if any) is still a bit mysterious: "introns". There are enzymes – spliceosomes – whose job is to remove the introns, and splice the exons together. Now the edited mRNA must be applied to some ribosomes, supplied with amino acids, dozens more enzymes, and a supply of tRNA to translate the base code of the mRNA into the protein's peptide chain, a linked train of amino acids. More information added to the system.

Each step of the way, the recipe for the new protein becomes a little more intricate and a little more complicated. And each step adds more “information” – information that cannot be understood or even described hors context. We know more or less how it all works, but somehow the detail – the translation into a language we understand – remains elusive. Cells contain a complex and sophisticated mixture of molecular and chemical components that allow DNA to replicate, produce proteins, etc, as well as all the myriad systems for creating and maintaining those components. This is the “information” content of the cell – it isn’t just a DNA strand that needs to be taken into consideration.

Let me take just one further example of why I have a problem with creationist arguments inre information. Above I talked about how spliceosomes edit out the introns from the exons during translation. Even this description isn’t entirely accurate. It turns out that splicesomes play a sophisticated role in constructing proteins out of assembled pieces, regardless of the order in which they appeared in the DNA sequence. With the help of these enzymes, one stetch of DNA can be responsible for hundreds of different proteins. A recent study for example, showed that a single gene may be responsible for the synthesis of 500 proteins! The hairs on chick cochlear cells, which are independently “tuned” by separate proteins to be sensitive to different frequencies, are generated by recombination of the cSLO gene. This recombination apparently occurs during the time between the deletion of the intron and the lining up of the exons. The problem is that it isn't really clear what controls how the recombination is done, nor is it clear how it is decided which cell gets which recombination. Random?[2] How in the world do you think you can measure the “information” content of this system?

Something very similar happens with our immune system, which needs variety to work. We need lots of different kinds of antibodies to throw at whatever antigens appear in our blood. Antibody variety is created by enzymes in bone marrow which constantly reorder the genes in a certain stretches of immune-system DNA to create a huge number of possible antibodies. Lymphocytes armed with these new proteins go out and attack intruders. The successful ones reproduce, which is how immune responses become sensitized over time. How this happens is another form of “information” – necessary to the functioning of the system.

Spliceosomes, mutases, homeobox genes, etc are only the tip of the iceberg as far as cellular “information” goes. Transposable DNA elements, functional overlap, horizontal gene transfer, multiple genetic codes all render any argument based on some kind of physical “information” irrevocably meaningless.

quote:

Four decades of dissecting genome function at the molecular level have brought many insights that were not anticipated in 1953. Two of the most far reaching are:

1. Many different genetic codes exist in addition to the triplet code for amino acids. These codes affect many diverse aspects of genome function, such as replication, transcription, recombination, DNA packaging and chromatin organization, imprinting, RNA and protein processing, and chromosome localization, pairing, and movement.

2. There do not exist fundamental genomic units larger than the individual codons in the various functional codes.[3]


In spite of creationist misunderstanding of Dawkins, Sagan, Shannon, etc, and in spite of the usefulness of information science to the understanding of genetics, it is useless to talk about the "letters" of DNA making up "words", or whatever other quibbles creationists keep coming up with, since many of the "words" overlap, or are interpreted in different ways by different mechanisms, or they appear in different places. Under these circumstances, words such as “information”, "code", "coding region", “interpretation system” and even "gene" don’t indicate specific functional units of DNA, but rather overlapping and shifting assemblies of base pairs. That is, they’re purely conceptual entities, abstractions that help us organize our thoughts about genetics, but without corresponding directly to any underlying physical reality. They are, fundamentally, metaphors.

My suggestion is that you either 1) drop the information argument as spurious, or 2) choose and defend a specific definition of “information” in relation to your original argument concerning “no new information” and “mutations cause loss of information” (my recommendation would be to research and use Shannon Communications Theory - that's the one most creationist writers seem to be fixated on. You'll find lots of info on creationist websites and articles relating to their misuse and misunderstanding of Shannon). Alternatively, you can pick some other aspect (I especially like the extinction and biodiversity bit) or assertion that you’ve made to defend. I honestly don’t think you have either sufficient knowledge of genetics or information theory to go much further along this road. However, I’m willing to continue IF you can define your terms. Which, of course, was my original question.

Just to show that I can cite references, too:

[1.] Watson, James D., & Crick, Francis H.C. 1953. “Genetical Implications of the Structure of Deoxyribonucleic Acid” Nature, #171(30 May), 964-967.

[2.] Black, Douglas L. 1998. “Splicing in the inner ear: a familiar tune, but what are the instruments?” Neuron, #20 (February), 165-168

[3.] Shapiro, James A. 1999. “Genome system architecture and natural genetic engineering in evolution” quoted from ppg 23-35 of: Caporale, L.H. (ed), “Molecular Strategies in Biological Evolution” Annals of the New York Academy of Sciences, vol. 870


This message is a reply to:
 Message 4 by Lewissian, posted 04-27-2002 7:53 PM Lewissian has responded

Replies to this message:
 Message 6 by Lewissian, posted 05-05-2002 5:27 PM Quetzal has responded

  
Lewissian
Member (Idle past 2892 days)
Posts: 18
From: USA
Joined: 04-21-2002


Message 6 of 11 (9244)
05-05-2002 5:27 PM
Reply to: Message 5 by Quetzal
04-29-2002 5:48 AM


Deleted.

Edited by Lewissian, : No reason given.

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Edited by Lewissian, : Outdated.


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Quetzal
Member (Idle past 4038 days)
Posts: 3228
Joined: 01-09-2002


Message 7 of 11 (9254)
05-06-2002 3:37 AM
Reply to: Message 6 by Lewissian
05-05-2002 5:27 PM


While I compose an answer to your most recent post, I want to take this opportunity to clear the air.
quote:
Thanks for insulting my intellect time and again, Quetzal.

And

quote:
I site them only because it gives more credibly to what I write, seeing that most people don’t trust or respect me, let alone think that I know much--being in 8th grade.

I don't know what chip you have on your shoulder, and I don't particularly care. I also don't care one one iota what grade you're in. I stated on the previous thread, and will now state here once and for all (and for the last time), that you present excellent well-researched arguments. That they are wrong doesn't detract from the quality. I also stand by my statement that your knowledge of information science and biology is somewhat superficial. Again, this doesn't detract from the quality of both your research and your posts; merely your understanding. Which, of course, is the basis for this discussion.

You will be hard-pressed to discern any ad hominem or personal attacks on you in anything I have written. If I felt that you were somehow inferior in intellect or any other capacity, I would simply refrain from responding to you. Disagreeing with you does NOT constitute ad hominem. On the other hand, you have based your premises on typical creationist writings and arguments - note that I am not saying you are a "typical" creationist; far from it - and typical creationist misunderstandings of both genetics and information science. This being the case, the observation that these writings are in general erroneous contained in my last post is valid.

Take it as you will. This will be my last word on the subject. I'll respond to the remainder of your post as I have the opportunity.


This message is a reply to:
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Dr_Tazimus_maximus
Member (Idle past 1383 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 8 of 11 (9258)
05-06-2002 9:56 AM
Reply to: Message 6 by Lewissian
05-05-2002 5:27 PM


quote:
Originally posted by ChaseNelson:
Information is information--look up the definition in any dictionary. It can take on several forms--one form as the thoughts form in my brain, another as I type them, and yet another as I print them out on paper.

Actually I rather doubt that you will find a formalized and applicable (to biology that is) definition of information in a dictionary. And that is what you are apparently being asked for.

quote:
Describe how all of the precise conditions required by proteins and DNA were met in the past and somehow allowed the evolution of DNA by random processes, 3) Explain how genetic information arose in the past (i.e., how mutations can add information to the genome)

First the precise conditions for the initial generation of DNA and proteins are not germane to evolution and also not to the evolution of information within living organisms. As to the increase in information that deals with populations as well as the organism (populations evolve, not individuals). Work by Sitiram, Rao and Witten (references are at home, I will try to add them later but they are in the J. of Theoretical Biology) demonstrates info increase at the gene level. The key thing that has neither been proven nor disproven by anyone is increase in information in the evolutionary sense. One of your citations is by Lee Spetner, in his one refereed paper on the subject (also in the J. of Theoretical Biology) he admitted that he was unable to address this point due to current limitations in information theory as well as in problems with the complexity of the system.

I have one additional comment, concerning the statements by Meyers that you cited. First, there are statistical correlations between groupings of amino acids and their associated tRNA's and the sequences that they bind to (ie the codons). Second, Meyers treatment of the DNA/Protein coding question is inappropriate in that he is treating it as an isolated system. To say that there is no STRICTLY chemical basis for the sequencing of any strand of DNA is accurate, as far as it goes. It completely leaves out the question concerning other physical effects as well as the system effects. For example, RNA has been demonstrated to polymerize and propagate on clay, mineral or silicate matrixes. The propogation of these sequences is actually a kinetic event where certian free forming sequences propogate faster than others. This "information" is passed down to the daughter strands. An interesting aside is that it is in the realm of kinetics that the left vs right hand issue appears to be solved, namely homogeneous strands propogate faster than heterogeneous strands, probably due to the increased stability of stacking within the homogeneous strands. Also, changes to a pre-existing code (ie mutations) result in a chemical change (ie the mutated protein). That protein may be better, worse or just different from the original protein. Couple that with gene or full or partial chromosomal duplication, an event which has been shown to occur, and you get a variety of information changes that account for the raw material which plays a role in evolution. To the best of my knowledge there is no real analogy in any other system described by info theory.

------------------
"Chance favors the prepared mind." L. Pasteur
Taz


This message is a reply to:
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Quetzal
Member (Idle past 4038 days)
Posts: 3228
Joined: 01-09-2002


Message 9 of 11 (9261)
05-06-2002 10:55 AM
Reply to: Message 6 by Lewissian
05-05-2002 5:27 PM


Chase, I appreciate all your efforts to provide citations and all the hard work that you expended. However, you have fundamentally missed the entire point. “Information” in the context of molecular biology is not “information” under any definition you can extract from Webster’s Dictionary. I doubt you will find any molecular biologist, geneticist or evolutionary biologist who cannot differentiate between the use of information theory as a analytical tool – and an extremely good one, to boot – and some intrinsic, physical property of a cell.

Dr. Ridley, the “renowned evolutionist” who wrote the “famous” book “Genome: The Autobiography of a Species in 23 Chapters, and whom you seem to feel is using information in this sense, recognizes the analytical or metaphorical basis of his book. See this interview for example. A short extract:

quote:
Matt Ridley: Well, I think, in a funny way, the genome is a book. I mean, that's one of the great discoveries, is that there is an instruction manual-- a recipe, if you like-- written inside ourselves. It's 800 times as long as the Bible, but it's very small, because we've got 100 trillion copies of it. And it's broken up into 23 chapters-- 23 individual pairs of chromosomes, we call them. And so that's what I did with my book, was split it into 23 chapters and try to tell one story from each chromosome. The stories are the genes, if you like. There's 80,000 of them on these various chapters.

Genome was written to provide the non-scientist with an understanding of genetics. To do so, Dr. Ridley used a common analogy to get his point across – one which an intelligent layman can understand. (BTW: Be careful about the adjectives you use – the words I placed in quotes above smack of some kind of appeal to authority. Also, there have been numerous biologists who’ve taken Ridley to task for that book. Jerry Coyne is one. See ”Not an Inkling”. This is not an attempt to discredit Dr. Ridley – he’s a very good author, and Genome is a very good text on the human genome and the value of the Genome Project. Just a suggestion that you watch the adjectives when discussing science.)

Even the creationist Dr. Spetner states this (from your last post)

quote:

Dr. Lee Spetner describes the metaphors as such: “The bases play the role of the letters of the DNA alphabet, and the genes play the role of the DNA words. In the protein alphabet, the amino acids play the role of the letters, while the proteins themselves play the role of the words. Three DNA letters translate into one protein letter, and one DNA word encodes one protein word. The stop codes in the DNA translate into the spaces between the protein words.”[3] It’s simple—metaphorical language is almost required to explain which DNA is, because it is information as we know it, only there aren’t four letters floating around, but four bases which play the role of letters. Obviously there’s something going on--the RNA bases, DNA, etc, carry out specific commands to the cell determining what it will do. (emphasis added)

I agree with this statement (never thought I’d agree with Spetner!).

You demanded I provide you with my definition of “information”. I generally follow the concensus of molecular biologists that use information theory in their work, specifically Shannon-Weaver Information. Here’s one example of how Shannon Theory can be an extremely useful tool in genetics: The Information Content of Binding Sites on Nucleotide Sequences. Here’s another paper from Tom Schneider: Sequence Logos, Machine/Channel Capacity, Maxwell’s Demon, and Molecular Computers which provides a good overview of information theory as it relates to molecular biology. These are legitimate uses of information theory. I do not now nor have I ever had a problem with the use of information theory as a tool in molecular biology. You have NOT shown, merely continuously asserted, that information in any form is an intrinsic property. Nor have you shown, in any of the articles you’ve cited, that the authors (i.e., non-creationist authors) are using the term in that sense.

I am not making any kind of “radical” or controversial stance here. Just one example is Lily Kay’s seminal “Who Wrote the Book of Life: A History of the Genetic Code”. I also recommend a search for books and articles by R.C. Lewontin, Stephen Gould, etc.
"Code," and "information" are metaphors, terms used by science and technology and given special content for special purposes. Saying that DNA contains information about amino acid sequences is simply to say that a knowledge of the DNA sequence is sufficient to provide knowledge of the amino acid sequence. DNA is not self-replicating any more than a letter put into a photocopier is self-replicating. DNA sequence does not specify protein, but only the amino acid sequence. The protein is one of a number of minimum free-energy foldings of the same amino acid chain, and the mechanisms and chemistry of the cell together with the translation process influences which of these foldings occurs – as I noted in my post about spliceosomes, which you seem to have either ignored or misunderstood. Finally, organisms are not determined by their DNA but by an interaction of genes and the environment.

quote:

So the sequence ACGT become TGCA in the copy, which transcribes back to ACGT in the copy of the copy [speaking of transcription and translation]. This enables DNA to replicate indefinitely, yet still contain the same information [which is the fallacy in your argument that through trancription and splicing, information is added]

My fallacy? Too funny. That’s your misunderstanding of what I wrote. In order to measure the Shannon information content of the process of transcription/translation, as I noted in my previous post, you cannot simply take the DNA strand or the readable portion of the strand out of context. The DNA exon doesn’t even constitute the entire information content of the process. If it did, information would axiomatically be “lost” during the process through Shannon entropy. Since DNA does get replicated – usually pretty well, in fact - obviously something else is going on. In this case, the other elements in the cell (from various types of RNA to enzymes to RNA polymerase to the various transcription factors) constitute additional information needed for transcription/translation. If you want, you can add all this “information” content to the system before replication, transcription/translation starts – I don’t have a problem with that since the in reality the maximum information potential of the system doesn’t change. However, doing so has significant (negative) implications for your argument that mutations don’t add information. Under Shannon, ANY change to the system by definition “adds” information. In addition, this leaves open the possibility of adding information by increasing the string length – through gene duplication, insertion of new bases, cross-over, etc. As far as I can see, information theory poses no problems for any aspect of the ToE, except as misused by creationists.

quote:

There is a codon that specifies where the mRNA is to begin transcription: “The primary ‘start’ codon on an mRNA molecule is AUG, which codes for the amino acid methionine. Therefore, each mRNA transcript begins with the AUG codon, and the resulting peptide begins with methionine.”[2] There are also different codons which code for “stop.” Even if mRNA begins trancription on a ‘randomly chosen’ spot on DNA, even between individual bases, the tRNA and ribosomes only begin on the codon AUG. Therefore, the process is by no means random and has a definitite starting point (the codon AUG) and definitite stopping points (the codons UAA, UAG, and UGA).

Thank you. I am well aware of the process. Just note my first post on this thread. Also, I have never – not once – indicated anywhere that the transcription starting point is “random”. I think you’re confusing me with someone else.

However, since you brought it up, further to my last post, since, as you mentioned, there are sequences that designate what is an exon in the gene that cellular machinery must recognize, mutation can cause the machinery to "read" the DNA in different ways or alter the mRNA transcript. For example, mutation might cause the machinery to read an intron (non-coding DNA) as an exon. The intron, when incorporated into the final protein, can alter the protein structure and either hinder, help, or even create a new function for that protein. Further, the machinery might skip an exon that was previously read before the mutation, or alter the transcriptional rates of exon and intron reading - all these would alter the final product of the protein in a major way – and hence change the information content!

quote:

From reading your response to my posts, one would think that the dummy Chase Nelson holds to the idea that there are literally four different letters floating around in everyone’s DNA!

Really? Where did I say anything remotely resembling this? Better knock that chip off your shoulder or I WILL start thinking of you as immature.

quote:

Explain why Dawkins would say that one cell in the human body is equal to dozens of Encyclopedia Britannicas. He doesn’t mean that there’s literally 30 Britannicas floating around in every cell--he means that there exists an amount of information in every cell equivalent to 30 Encylopedia Britannicas.

Here, read this article, The Information Challenge. I don’t intend to cut and paste all of Dawkins’s reply to your argument. Feel free to discuss the difference in your interpretation after you’ve read it. Also, another good read would be Chapter 6, “Genetic Book of the Dead” from Dawkins’s “Unweaving the Rainbow” for a clearer understanding of how he uses information. The article also provides a nice counterpoint to Bradley and Thaxton, Spetner and Meyer. When you’re finished, we can discuss whether you still think Dawkins and I are speaking a different language.

quote:

I’ve noticed throughout this discussion that you’ve succeeded in avoiding the majority of my posts, especially my point about specified complexity.

Not at all. In fact, the only person who’s been avoiding the substance of remarks is you. I haven't broached specified complexity because you haven't bothered to define it. However, specified complexity it is.

Specified complexity is a veeery slippery concept. The “father” of specified complexity, William Dembski, in “The Design Inference” defines specified complexity as events that both match some predefined meaningful pattern (that's the 'specification') and also are highly improbable under the appropriate "chance hypothesis," i.e. the probability distribution that we'd expect given only unguided natural laws with no intelligent interference (this improbability is what he calls “complexity”). In other words, anything that exhibits specified complexity has been designed.

Rather than addressing the specific cut-and-pastes you quoted, I’ll focus on some of the very real problems with SCI. In the first place, the entire concept of “appropriate chance hypothesis” is problematic without knowing the causal history of the phenomenon or event or structure in question. Otherwise, there is no empirical method of determining whether the properties were unlikely to occur under a given chance hypothesis. This leaves the entire idea basically up to the observer. Worse, according to Dembski, “apparent” specified complexity can in fact arise by non-intelligent means, but this isn’t truly specified complexity because specified complexity can only come from intelligent means. His intention was simply to be able to look at an end product, without reference to how it came about, to determine design or not. Unfortunately, it seems you need to refer to how it came about just to determine if it really is specified complexity. Basically, we have here an assertion without evidence: specified complexity can only come from intelligent design, because any specified complexity known not to have an intelligent origin is not really specified complexity. This of course also means again that any thing examined where the origin of it is not known defaults to "intelligently designed".

quote:
Specificity is required. How can you explain active sites in the light of random processes? How did this irregular, unpredictable, highly specified, complex information in the DNA come about (let alone the ability of mRNA to transport it, the ability of tRNA to interpret it, the ability of ribosomes to carry out its commands, and the languages used by DNA and RNA to give the commands and understand them (which it does--how else would the cell be able to distinguish AUG from UAA?)). Bases are not associated chemically in the order that they’re read in transcription (only one side of the backbone is read). Proteins need to have a specific order of amino acids in order to have their correct functions. Therefore, random assembling of A-T and C-G bases doesn’t cut the cake. The light shining through the computer screen has no affect on the information present in my writing

Start here: Self-Organization of Template-Replicating Polymers and the Spontaneous Rise of Genetic Information, then read Evolution of Biological Complexity, and finally Evolution of Biological Information. I’m sure you can dig up more references if you’re so inclined.

quote:
Considering the above information, I suggest the following: 1) Define what you mean by information--something I have repeatedly done and you have yet to do, 2) Describe how all of the precise conditions required by proteins and DNA were met in the past and somehow allowed the evolution of DNA by random processes, 3) Explain how genetic information arose in the past (i.e., how mutations can add information to the genome), and 4) Quit the semantics, and stop arguing ad hominem against me and repeatedly against creationist who, you claim, 'misrepresent' or don't understand the evolutionists' or your position(s).

1. I have done so. You HAVE NOT. You have merely cut-and-pasted a plethora of different articles – many of which use different types and definitions of information. If you want to continue with Shannon, which is what is used extensively in molecular biology, then we will do so. However, be aware that so conceding the definition to me means your argument concerning the physicality of information is baseless, since Shannon is a measurement system – an analytical tool – as I’ve been maintaining all along.

2. See the above referenced articles.

3. See the above referenced articles.

4. Watch your tongue. I have not used ad hominem arguments on you, although keep up comments like this one and I will resort to them, just to show you what it really feels like. The semantic argument stands as unresolved until you either define information as I have done, OR concede this particular field to me.

quote:

Besides this, proteins may only contain peptide bonds, but non-peptide bonds are equally likely to occur in nature.[14,15] Also, proteins may only contain L-amino acids (left-handed amino acids), while D-amino acids (right-handed amino acids) are equally abundant and redily react with L-amino acids.[16] If proteins come in contact with air, they oxidize.[17] The process of photodissociation assures us that there would be a significant amount of oxygen present on Earth at any point in time,[18] and geological evidence such as red beds[19] and pitholiths[20] affirm this. (Since you’re obviosuly extremely superior compared to me in intelligence as you pointed out in your previous post, (Quetzal: This statement is an out-and-out lie. I strongly suggest you refrain from imputing statements to me that I haven’t made.) I’m assuming you know what these things are. If not, however, check the references.) The sequence specificity discussed above is also required (at least 1/2 are active sites). “His [Robert Sauer of MIT] results have shown that, even taking the possibility of variance into account, the probability of achieving a functional sequence of amino acids in several functioning proteins at random is still ‘vanishingly small’, roughly 1 chance in 10^65...”[21]

I deliberately did NOT respond to this paragraph for the very simple reason that it is a transparent attempt to change the subject. I recommend you return to your original assertions concerning mutation, biodiversity, mass extinction, or other topics. I will not be pulled off on a tangent into an Origin of Life argument. You have enough problems.


This message is a reply to:
 Message 6 by Lewissian, posted 05-05-2002 5:27 PM Lewissian has not yet responded

  
derwood
Member (Idle past 42 days)
Posts: 1457
Joined: 12-27-2001


Message 10 of 11 (9265)
05-06-2002 11:57 AM


Hi Chase,

I lived in Grand Rapids for several years - went to Grand Valley for my undergrad work. Is the "Something Better News" still churned out?

I just had a few comments on your posts.

You quote anti-evolution philosopher Meyer:

quote:

Stephen C. Meyer:

quote:----------------------------------------------------------------
They [Watson and Crick] discovered that the specificity of amino acids in proteins derives from a prior specificity within the DNA molecule--from information on the DNA molecule stored as millions of specifically arranged chemicals called nucleotides or bases along the spine of the DNA’s helical strands...
----------------------------------------------------------------------

This is not merely a chemical process, as the bases are not bonded in the order that they are read. The RNA reads from up to down (if you were looking on a diagram of DNA). Say there is CGATTGCGCAT, etc. These bases are not bonded--they have no association with each other directly whatsoever.


Your last sentence above is absolutely incorrect. The nucleotides in a strand of DNA most certainly are bonded to one another via the 'spine' as Meyer says in your next quote (more later). If they were not, there would not BE a strand of DNA. It would not be called a moleculae, it would be a collection of free nucleotides, and they would encode nothing.

quote:

However, the mRNA reads them this way:

Stephen C. Meyer:

quote:
----------------------------------------------------------------------
There are bonds fixing individual (nucleotide) bases to the sugar-phosphate backbones on each side of the molecule. Yet notice that there are no chemical bonds between the bases that run along the spine of the helix. Yet it is precisely along this axis of the molecule that the genetic instructions in DNA are encoded[7]...
In short, differing chemical affinities do not explain the multiplicity of amino acid sequences that exist in naturally occurring proteins or the sequential ordering of any single protein. In the case of DNA this point can be made more dramatically... There are bonds, for example, between the sugar and the phosphate molecules that form the two twsiting backbones of the DNA molecule. There are bonds fixing individual nucleotide bases to the sugar-phosphate backbones on each side of the molecule. There are also hydrogen bonds stretching horizontally across the molecule between nucleotide bases making so-called complementary pairs... Most importantly, however, notice that there are no chemical bonds between the nucleotide bases that run along the spine of the helix. Yet it is precisely along this axis of the molecule that the genetic instructions in DNA are encoded. In other words, the chemical constituents that are responsible for the message text in DNA do not interact chemically in any specific way.[8]
----------------------------------------------------------------------

Therefore, the information encoded or instructions given in DNA is not merely a chemical process.


This sort of confusion follows from an attempt to find 'meaning' where there is none. I like to refer to these 'specificity' arguemtns as classic cart-before-the-horse exercises. We take extant protein X. We see that it is encoded by gene Y. We see that proetin X is useful, maybe even necessary to us (and perhaps many other organisms). We then conclude that this particular protein - extant protein X - is a necessary requirement for us to live, and so must have been in its present conformation/sequence/etc. from the beginning. Thus, it was specified from the get-go - impossible for protein X, encoded by gene Y, to have arisen via 'chance' because, afterall, we NEED protein X in itgs extant form and therefore gene Y must have been placed as-is in the genome.

In sum, we look at the extant and conclude - without evidence or a knowledge of the history of the molecule of the lineage(s) in which we find it - that it must have been always so, and that therefpore it must have been 'designed' because of the extant specificity and such...

By the way - does Meyer explain how nucleotides are placed in their specific order?

You then quote creationist extraordinaire Jerry Bergman:

quote:

Jerry Bergman:

quote:
----------------------------------------------------------------------
The correct amino acid sequence is ordinarily critical for most of the protein chain, but proteins with a few incorrectly placed amino acids can sometimes still function, although often not as well. Conversely, many single changes can be critical or lethal. An example is sickle cell anemia in which there is one single incorrect amino acid out of 300. The replacement of glutamine with valine produces red blood cells that tend to deform (called sickle cells) in certain environments. In the homozygous sickle cell condition the blood functions poorly under certain circumstances, causing anemia, severe pain, and even strokes in children. Many other mutations prevent the production of functional enzymes. The consequent lack of a necessary component in the cell causes dysfunction or disease.[10]


The use of hemoglobin to prop up his claim is disingenuous, in my opinion.
Indeed, there are examples of "necessary" proteins - cytochrome C for example - that are found in nearly all forms of multicellular life and yet can function while being as much as 50% different in amino acid sequence in different lineages. Does Jerry mention this fact? Or just the one fact that he can use to support his implications?

I am sure that Holland has a strong anti-evolution public sentiment. Shame that it does not also have a strong critical-thinking one...


    
Peter
Member (Idle past 2089 days)
Posts: 2160
From: Cambridgeshire, UK.
Joined: 02-05-2002


Message 11 of 11 (9624)
05-14-2002 9:15 AM
Reply to: Message 4 by Lewissian
04-27-2002 7:53 PM


[b] [QUOTE]
Tha basic point is that it is information. In this quote from Nature, it does not appear to me that they’re simply using the phrase “genetic information” as an “analogy based on a structural/attributive definition...” They state that “The nucleus of a single cell (left)
contains all the genetic information required to make the human body. This genetic information is packaged as chromosomes (right) [emphasis mine].”[1] They are referring directly to genetic information, not using it as an analogy, as you suppose, and are saying that this genetic information, not the analogy of it, it itself “packaged as chromosomes.” Nature also states that “Genes are transcribed as continuous sequences, but only some segments of the resulting messenger RNA molecules contain information that codes for the gene’s protein product. These segments are called exons. The regions between exons are known as introns, and are spliced from the RNA before the product is made [emphasis mine].”[2] Once again, not an analogy. Perhaps if you gave me a quote from Nature stating that they view the genetic information they speak of as an analogy, I would be more inclined to believe this.
[/b][/QUOTE]

It is VERY important to distinguish between a lay use of the term
'information' and the term 'information' as used in information
science.

The above is lay use, and 'infomation' above should be replaced
by 'data'.

[b] [QUOTE]
Dawkins and Sagan both appear to be talking about information, in the sense of meaning and specificity, andnot using an “algorithmic description,” as you say. For example, Dawkins (in The Blind Watchmaker) uses a computer to see if he can generate the sentence METHINKS IT IS LIKE A WEASEL by chance. (Of course the major flaw in his experiment is that he has a pre-set ‘target sequence’, which nature would not have: “Despite superficially impressive results, these ‘simulations’ conceal an abvious flaw: molecules in situ do not have a target sequence in mind, nor will they confer any selective advantage on a cell and thus differentially reproduce until they combine in a functionally advantageous arrangement.”[3]).

Notice that Dawkins’ sentence makes sense. It is not FHAMEBDD HD BC QBXY D YSULFD, but METHINKS IT IS LIKE A WEASEL. It makes sense. In like respect, the order of nucleotides make sense to DNA, mRNA, tRNA, and ribosomes, etc. A sequence like AHBHAHBHAHBHAHBH is ordered, but has no information or meaning. It is simply ordered, like a crystal’s structure. However, the sentence HELP ME PLEASE! has information content because it has specified complexity. It is not ordered in a pattern, but carries meaning. Say the sentence HELP ME PLEASE! is what we want. On our first try with Dawkins’ computer program, we get HWNTYXLISQNXVRT.
[/b][/QUOTE]

'HELP ME PLEASE!' does NOT have an objective information content.

If you place this sequence of letters in front of an individual
with NO knowlegde of western european languages it is meaningless.

'Information' is OBTAINED from data by an interpretive act.

We consider genetic data to contain information because we observe
a relationship between DNA sequences and functions within the
organism.

It is the OBSERVATION OF A RELATIONSHIP which is information, not
the DNA (which is just data).

quote:

We do not conclude then that information can arise by chance, because this sentence has absolutely no meaning!

In evolution we are NOT dealing with random chance.

Basically the situation is that some sequences which are formed
are unviable in a particular environment (or at all). Those
sequences are NOT carried forward to the next generation, because
the organism within which they reside is NOT viable under the
current environmental conditions.

Only viable sequences are carried forward to the next generation.

I once wrote a computer program which generated decimal digit
sequences, and had only a few simple rules::

1. A sequence can repicate after it has existed for 3 time periods
2. Sequences containing even digits 'die' immediately
3. Replication can contain errors

Not suprisingly only sequences containing all odd digits proliferate.

The analogy here concerns viability.

Viability is related to the environment.

Biological information can only be connected to the relationship
between the organism and the environment within which it finds
itself.


This message is a reply to:
 Message 4 by Lewissian, posted 04-27-2002 7:53 PM Lewissian has not yet responded

    
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