19
Aug
09

The gambit of falsehoods

Recently, Greg Laden put up a list of falsehoods to which I added a few others which needed explaining, among them is my assertion that DNA is not information (or code, or instructions, etc). I intend, hopefully, to support this claim with more fluent logic than done via email.

1: DNA is the double stranded template molecule of material heredity

The “information metaphor falshood” (IMF) is a useful falsehood when used properly, but is overly simplistic. DNA is like instructions in that cells follow predictable patterns due to the pivotal role this molecule plays in the assembly and production of RNAs and proteins. Beyond this, however,  IMF breaks down. The sequence of the DNA molecule does not contain instructions, but rather is a physical structure which responds to interactions with other molecules because of this structure, not because of the sequence. While the sequence partially provides this structure in DNA, this structure is influenced by many factors. For example, histones around which the DNA is coiled play an integral part in what segments are expressed. Sequences of DNA are only partially responsible for the structure of these histones and they are regulated by other external and internal factors aside from other segments of DNA. The IMF is a simplified version of what is actually occurring within the cell and this simplification ignores the three-dimensional and interactive aspects of the molecules within the nucleus. Additionally, IMF assumes that the sequence is the important aspect of DNA ignoring that many sequence changes in DNA do very little to the organism. DNA can be better described for what it is, a molecule which provides the templates for the synthesis of various RNAs under specific conditions. It is not a causative agent or “set of directions” but an interacting part of the cell (albeit an important one) subject to external and internal factors.

2: Information (instructions, code) exist upon the conscious perception of them.

For example, a cookbook written only in English would not be directional or instructional to a person unfamiliar with the language. Just because we are capable of explaining many aspects of DNA as being “instructional” or “coded” does not mean it is actually a code or an IKEA booklet to assemble a chair. Codes and instructions describe, to a conscious and understanding observer, they are not the mold to make the parts and all necessary tools. I’ve often heard that “DNA is analogous to machine code” because both contain sequences which explain precisely how to do a certain task. As I have previously stated, however, DNA does not describe or instruct the cell on what to do, it is the reactive template which responds under certain conditions. Also, while instructions convey meaning and intentionality, DNA provides neither.

3: IMF relies upon known and blatantly false simplification to reach the conclusion

The information metaphor implies that the important aspect of DNA is only the sequence or “content” while ignoring three-dimensional conformations and external influences. Parts of the DNA molecule which have useless sequences, but the lengths are important (separating promoters) as well as regions providing specific binding to histones which allows interaction at other specific points along the molecule are also important.

Finally, “information” implies directionality or intentionality while DNA is not a causative agent nor was it placed, put, or designed by any agent. Instead, it is hereditary material which has been shaped by countless generations with mutation and evolution influencing it. DNA is not a pattern which “represents” or “conveys” anything. It is a template which functions as hereditary material enabling and regulating RNA synthesis.

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21 Responses to “The gambit of falsehoods”


  1. 1 MichelleSedai
    August 19, 2009 at 7:36 pm

    IMF…the international monetary fund?

  2. 2 jaredcormier
    August 19, 2009 at 8:48 pm

    No, that IMF is even more useless than this one…

  3. August 21, 2009 at 12:44 am

    Wow, that totally makes sense to my brain. The “information” metaphor never seemed quite right to me. Thanks for the explaination for non-scientist dummies like me.

  4. 4 jaredcormier
    August 21, 2009 at 2:20 am

    Well, without an intentionality or directionality, nothing is really “information.” Similarly, you can argue for the same reason, it is not a “code.” It is useful to describe this way for simplicity, but it is does not fit with reality. We use the “genetic code” to predict what proteins will result from a given sequence, it’s more of a theory of genetics than an actual code. It is also FAR more complex than many can even begin to contemplate. Examples: selenocysteine, β-alanine, and pyrrolysine. Also, another fun fact: cytosine spontaneously deaminates resulting in uracil, so all these cool little repair mechanisms exist to enforce the fourth commandment of the nucleus [Thou shalt not have uracil in your DNA]. Ironically, just like those commandments of old, all genetic commandments are broken, so they’re more like guidelines, really…
    UGA means stop? Not if there is a special stem-loop structure (called SECIS). UAG means stop, too? Well, there’s another stem-loop override for that one to insert pyrrolysine. AUA means isoleucine, not in mitochondria. Again, you see an example of the STRUCTURE overriding the sequence. Stem-loop forms=keep on synthesizing protein; no stem-loop, then it’s a stop.

  5. 5 myocalpin
    September 26, 2009 at 8:12 am

    You are right about complexity but way off base with information content. To say the genomes of life do not convey information – in the way of structural codes that integrate chromatin- bound DNA to the nucleoskeleton, regulatory codes that define transcription factor binding sites, protein coding sequence that specify the proteome, and miR codes that are transcribed into small fine tuners of the proteome – is tantamount to saying there is little meaning in what you and I are writing.

  6. 6 jaredcormier
    September 26, 2009 at 9:39 am

    BZZZZZZZZZZZZZZZZZZZZZZTTTTTTTTTTTTTTTTTT!
    Wrong.

    That’s still not “information.” Those are physical conformations in response to biochemical conditions, enzymatic activity, and mechanical action of proteins. It STILL isn’t “information.” It’s still not coding for anything. It is a useful metaphor for explaining this, but it does not represent the reality of the situation.

    Also, you came here via a search for “DNA is quaternary code,” it seems your pre-existing notions that DNA was code interfered with your ability to read my statements and present well structured arguments against it. Congratulations on learning to argue by metaphor, let’s try arguing with reality next.

  7. 7 Gossman
    August 6, 2010 at 1:18 pm

    I realize some do not want to admit DNA is coded because if that fact is a given, then logic would dictate there was a coder because every code or set of instructions encountered was the result of thought. We have never encountered a code or a message that was not the result of thought.

    So, enough of the talk, let’s get to the evidence: The language of DNA is digital, but not binary. Where binary encoding has 0 and 1 to work with (2 – hence the ‘bi’nary), DNA has 4 positions, T, C, G and A. In short, DNA is strikingly similar to byte compiles code. It is in fact stunning. Here’s a decent article on DNA coding through the eyes of a coder:

    http://ds9a.nl/amazing-dna/

    Ps 46:10 Be still and know that I am God.

  8. 8 Gossman
    August 6, 2010 at 1:22 pm

    Small example of stretch of DNA with exons and introns:

    ACTUAL CODEACTUAL CODE
    | | | | | |
    exon 1 acceptor intron 1 branch donor exon 2
    (start of comment) (end of comment)

  9. 9 Gossman
    August 6, 2010 at 1:23 pm

    That post didn’t trasfer so well, lol. Go ahead and check out the link I posted.

  10. 10 jaredcormier
    August 6, 2010 at 4:28 pm

    A quick fisking, I don’t have a whole lot of time:

    I realize some do not want to admit DNA is coded because if that fact is a given, then logic would dictate there was a coder because every code or set of instructions encountered was the result of thought.

    No, it doesn’t; codes can be generated based upon physical interactions. This is precisely how the Genetic Code (which is, as stated, used to predict what protein sequences may result from a given sequence of DNA) developed. It is probably due to RNA precursor codons having similar functions as the amino acids which they stand for, although this is just speculation. The “code/coder” is similar to the “building/builder” fallacy. So please, let’s avoid using it. I see a highly ordered structure of downed trees along the beach, all parallel to each other, does this mean someone put them there? No, it could easily have formed due to tidal action with the trees only washing up as far as the highest tide.

    We have never encountered a code or a message that was not the result of thought

    Really? That’s interesting. Might I recommend Genetic Programming by Koza?

    So, enough of the talk, let’s get to the evidence: The language of DNA is digital, but not binary. Where binary encoding has 0 and 1 to work with (2 – hence the ‘bi’nary)

    Dude, I’m currently working in IT programming computers, I know what binary is.

    DNA has 4 positions, T, C, G and A. In short, DNA is strikingly similar to byte compiles code.

    Wait, what?

    It is in fact stunning. Here’s a decent article on DNA coding through the eyes of a coder:

    Through the eyes of a coder; how much of a background does this guy have in genetics? Right, very little. Describing it as “code” is a very useful tool for education, but it’s not reality; sorry. He even makes a disclaimer that he is not a molecular geneticist. Read thoroughly and not just pick out the parts you want to read.

    Ps 46:10 Be still and know that I am God

    Wow, that’s so cool, but your idea of god is dead, and Craig Venter demonstrated that he is, in fact, god.
    By the way, have you read that book cover to cover and actually understood most of the fictional shit in it?

  11. 11 PG
    December 22, 2010 at 10:07 pm

    Interesting opinion Jared, but its not consistant with the scientific convention….

    “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)

    DNA is infact a literal code!

  12. 12 jaredcormier
    December 23, 2010 at 1:13 am

    And yet, none of these really mean the same thing as they do in information theory, I wonder how Dr. Yockey plans to explain that.

    Proofreading, for example, isn’t the same as “finding mistakes” but is instead “removal of non-complimentary bases.” It is defined as 3′-5′ exonuclease activity which removes mismatched base pairs on the daughter strand. This is more akin to removing artifacts on a copy than a person proofreading a paper.

    Transcription and translation are particularly misleading in that transcription (in information theory) involves a one to one copy of information whereas in genetics, transcription involves the selective production of an mRNA sequence which actively participates in its own production. That last part is the most important.

    Dr. Yockey and many others have misapplied information theory by not taking into account new developments in our understanding of genetics and the fact that these are legacy terms which remain in place due to established meaning within the scientific community.

    I could go on, and if you really are interested in discussing this, feel free to drop me an e-mail.

  13. 13 Anonymous
    December 23, 2010 at 7:42 pm

    jaredcormier says: December 23, 2010 at 1:13 am
    “Dr. Yockey and many others have misapplied information theory…”

    PG says:

    Jared, Do you have any Peer reviewed papers to substantiate your position that DNA is not a literal code and that Dr. Yockey and many others has misapplied information thory?

  14. 14 jaredcormier
    December 23, 2010 at 10:55 pm

    Actually, the question here is can you provide PEER REVIEWED research which supports Dr. Yockey’s claims in this particular sentence. Dr. Yockey’s work you cited is a non peer reviewed book. He uses CE Shannon’s work and assumes this is sufficient evidence, which it only demonstrates that the same words are used, not that the processes are identical and not metaphorical, etc. It would be akin to saying “book” in the phrases “a book” (as in the text) is the same as “to book” (as in to arrest and formally charge of a crime) mean the same thing because they have the same ultimate origins.

    Also, out of curiosity, have you read this book, or are you pulling quote mines from page 6? I might reread it, to see if it actually supports those claims, but I wrote in the margin “unsupported by citation.” I might upload a picture of that page later…

    If you want Shannon’s paper, so you can actually read it, it is here:
    http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.161.4366&rep=rep1&type=pdf

    Read it, notice it never mentions biology at all. Dr. Yockey assumes their meanings come from information theory without citing any biology works which cite Shannon’s text or any information theory works which describe how it can be applied to molecular genetics. In fact, the names were chosen because they were most easily described as such. Information theory is useful in communication, but as soon as intentionality is added to an object without the capacity for such intentions, it becomes the ultimate example of pareidolia.

  15. 15 PG
    December 24, 2010 at 1:29 am

    Jared,

    As I stated prior, the current scientific convention is that DNA is a literal code with a 4-letter alphabet, not a figurative one. Thus the term “genetic code” is considered a proper scientific term. Books and papers discussing linguistics and universal grammars in DNA are exhaustive.

    So no disrespect to your lack of credentials, but The book Information Theory, Evolution and the Origin of Life is written by Hubert Yockey, the foremost living specialist in Bioinformatics. The publisher is Cambridge University press. Yockey rigorously demonstrates that the coding process in DNA is identical to the coding process and mathematical definitions used in Electrical Engineering. This is not subjective, it is not debatable or even controversial. It is a brute fact:

    “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)

    If you disagree, then you you will need more than your personal opinions or reasonings, you will need to provide scientific publications that substantiates your position that DNA is not a code.

    Now about “pareidolia”

    There are scientific journals such as The Journal of Bioinformatics and Computational Biology published by World Scientific. If you are correct then your accusing them of having an overactive imagination and that they are dillusional because according to you, DNA only appears to process and store information in the same way like clouds look like sheep. You should write to their journal objecting to their very existance as a publication. Im sure they would be interested in your opinions.

  16. 16 jaredcormier
    December 24, 2010 at 4:11 am

    Are you really going to make me open up this damn book again? You stated that “current scientific convention is that DNA is a literal code”–except that it isn’t; it is a common misunderstanding by those unfamiliar with the intricacies of genetics. Here we go, introduction, page x, Yockey demonstrates his complete lack of understanding of modern genetics with the following statement “I show in this book that only because the genetic message is segregated, linear, and digital can it be transmitted from the origin of life to all present organisms and will be transmitted to all future life.” Look, I didn’t have to go far, now why is this wrong?
    The genetic sequence is not linear, it forms complex loops interacting with itself and other molecules in three dimensions, (four if you wish to include time) influencing expression of genes. While the individual genes are segregated, very few traits are ever absolutely controlled by one gene. The “one gene one trait” hypothesis was shot to hell decades ago with the exception of those biochemically tested traits (e.g. sickle cell). Specific genetic combinations can have the same effects such as in Ehlers-Danlos. One gene may result in many polypeptides (discovered way back in the 70’s, hell, that’s before I was even born). A coded sequence, by its very nature, cannot produce multiple results when “decoded” under identical conditions; DNA can.

    1) If you want to cite peer reviewed research, that’s fine, but don’t pull from a book and claim it’s peer reviewed. It is disingenuous to anyone unfamiliar with his works.
    2) I’ve offered numerous examples of how a genetic sequence does not behave like a code. These are from peer reviewed sources, if you want me to track them down, I can.
    3) The descriptions used by Yockey (in his book) to support that DNA is a code are generalized, vague, and wrong. He does no such thing in his peer reviewed papers, although he does in his books. Which leads me to my anger over “Science by Press Release.” He explicitly (in at least 3 papers) describes the code as the way in which DNA is converted into proteins, not the sequence itself. He proposed a model based upon encoding/decoding principles in information theory. It was partially right.

    Are you really that dense, or are you clinging to your misunderstanding (of genetics, bioinformatics, computational biology, etc.) because of your religious views? Do you think because Dr. Yockey was wrong about his description of the genetic sequence that it changes his observations? No. The groundwork of information theory to help build models of population genetics was very useful. Population genetics (and bioinformatics, for that matter) has pretty much outgrown this little room you are trying to keep it contained in, it’s not even in the same city, anymore. It was useful as an early model, but those models didn’t quite work, we discovered why, fixed the models, and moved on.

    Now, have you actually read Yockey’s book? Do you understand the difference between peer-reviewed and a book? Do you know that most of the examples he uses to support his ideas are completely bogus given new insights into how cells actually function? I’m also not breaking from convention, I’m explaining it, as it was originally proposed and is currently understood: the “genetic code” is the way we can predict a peptide sequence from an open reading frame. That IS the convention of the usage of that term. It is not the sequence, it is not always accurate (thank you alternative splicing, self-splicing introns, codon bias, ancestral tRNA mutations…), but it is the convention of genetics.

    The pareidolia note was to wishful thinkers such as yourself.

  17. 17 jaredcormier
    December 24, 2010 at 4:21 am

    By the way, failure to logically support your argument again will result in me deleting your comments. Argument from authority doesn’t work, and I won’t be playing the logical fallacy game, nor have a pissing contest with someone pulling quote mines. You must show how he demonstrated that “DNA is a code.” He didn’t, you didn’t, let’s move on.

  18. 18 PG
    December 24, 2010 at 12:25 pm

    Jared,

    I can offer peer reviewed papers that supports Yockey’s work, but first I need clarification.

    Lets start with your comment: “He proposed a model based upon encoding/decoding principles in information theory. It was partially right.”

    Did he get the part right that Code is defined as communication between an encoder (a “writer” or “speaker”) and a decoder (a “reader” or “listener”) using agreed upon symbols?

    Did he get the part right that DNA transcription is an encoding / decoding mechanism because the sequence of base pairs is encoded into messenger RNA which is decoded into proteins?

    Did he get the part right that this code has much in common as the human language and computer language?

  19. 19 PG
    December 24, 2010 at 1:40 pm

    After re-reading your post, perhaps I should get even further clarification from you. Do you disagree that information is existant and being transfrered?

  20. 20 jaredcormier
    December 24, 2010 at 3:06 pm

    No, neither of those parts were correct, but they were useful. The model he proposed further clarified the “Central Dogma” in mathematical terms, and the parts which are incorrect are the parts where he equates the Central Dogma to an information system. The part where he actually did something useful is treating DNA sequence as any other nonrandom sequence allows us to perform complex statistical analysis of the sequences, the sequences were termed “information” even though they are only tautologically such by the definition used in genetics. Information, as described in genetics, is the ordered sequence of nucleobases in a nucleic acid chain. As such, information is explicitly being transferred, but to confuse this definition with any other definition of “information” is blatantly incorrect.

    DNA transcription utilizes a “template” molecule; does this mean the molecule which is being made is identical? No, it is all metaphor because we had no words to describe them in our everyday language. This is the same problem introductory chemistry students have when discussing electrons; they think “particle=ping-pong ball” and they are wrong. If you think “DNA sequence=DNA code” you are similarly wrong, and if you think “DNA sequence=meaningful data” you are wronger than wrong.

  21. 21 jaredcormier
    March 1, 2011 at 11:12 am

    Here are my conclusions:
    1) You are a creationist cdesign proponentsists design proponent that doesn’t understand even the basics about genetics. You (or someone else, which you then decided to use) quote-mined Dr. Yockey’s work on information theory (probably never actually read the book) and present this as “evidence” when it only establishes why it is useful to treat DNA as a code (he claims it is actually a code, but never demonstrates this throughout his entire book, I know, I read it, I don’t think you did) for purposes of computational biology and claim it supports your position. This is a common tactic by creationists and the anti-science crowds of various types (anti-vax, HIV denial, aspiring amateur conservative climatologists, etc.), and for purposes of civility, I didn’t just block you, but tried to explain why you were incorrect. I realize now that this was a bad move and it will not happen again.
    2) Discussing with you is much like having a discussion with a brick wall, pointless, futile, and ultimately unsatisfying. You’ve presented me nothing new to convince me of your position, when your initial argument failed, you tried another, when this also failed, you began to repeat them, they failed once already, perhaps find something new?
    3) I did learn one thing recently though, and it wasn’t from you, but an acquaintance that runs a bioinformatics and immunology research lab in Florida: computational biologists are often glorified statisticians with little or no understanding of the interactions of DNA inside of a cell, instead viewing DNA as a linear bit of string that is “read” from start to finish rather than as it actually exists. This makes sense for them, but not for someone interested in specifics about the in vivo interactions of genes within a cell. This may be part of the reason computational biologists and information theorists make good targets for creationist quote-mining; DNA in their world is linear.
    4) Attempting to be a condescending asshole to someone with more credentials in the area of discussion than you do is something only a lawyer, creationist, or Christian could do, I think it is due to a broken irony-meter.
    5) Useless comments are now being deleted.


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