is DNA a code?

37


Discussion by: cynic252

I have been having a running debate with a friend about whether DNA is a code…I believe it isnt but I cont convince of the idea and wondered whether I am wrong.

37 COMMENTS

  1. First define what you mean by the word “Code”

    That is not a challenge. There may well be some definitions of code which will include DNA, and some definitions which will exclude DNA.

    • I can go with the dictionary definition but it doesnt help…The letters agct are a code for the arrangement of adenine guanine cytosine and thyamine in DNA, but the DNA itself isnt a code, I could change agct for symbols and the code still works but you cant change the units in DNA so the dna itself cant be a true code. It is simply a longchain complex molecule that reacts to eventually create proteins. It doesnt actually code for anything it simply reacts…or am I talking rubbish.In reply to #1 by SomersetJohn:

      First define what you mean by the word “Code”

      That is not a challenge. There may well be some definitions of code which will include DNA, and some definitions which will exclude DNA.

    • In reply to #1 by SomersetJohn:

      First define what you mean by the word “Code”

      That is not a challenge. There may well be some definitions of code which will include DNA, and some definitions which will exclude DNA.

      The parallels between DNA and software are fascinating. I wrote a comment that might interest you on a recent article about GMO food:

      http://www.richarddawkins.net/discussions/2013/5/26/genetically-modified-food#comment-box-19

      If by code you mean a way of encoding information that could be used the same way we use binary encoding for computers, then the answer to that is a very strong yes. I saw a fascinating talk at Stanford about fifteen years ago. The researchers had encoded a file (it was a cool trick, they actually stored the PDF format of the paper that wrote up their results using this method) as DNA. Actually I don’t remember if it was DNA, RNA, or what, but I know it was some form of chemical encoding I’m pretty sure it was DNA. And I know that I’ve read in works by Dawkins that he thinks the same that DNA is a method of storing information and whether you store something as variants of ATCG or 1′s and 0′s the same principles about information and communication apply to both.

    • In reply to #2 by SaganTheCat:

      is alphabetti spagetti a work of literature?

      No. And binary code isn’t either. But both DNA and binary code can be used to represent and store Shakespeare or any other work of literature.

      • In reply to #11 by Red Dog:

        In reply to #2 by SaganTheCat:

        is alphabetti spagetti a work of literature?

        No. And binary code isn’t either. But both DNA and binary code can be used to represent and store Shakespeare or any other work of literature.

        as can alphabetti spagetti

  2. From Wikipedia:

    Biological organisms contain genetic material that is used to control their function and development. This is DNA which contains units named genes that can produce proteins through a code (genetic code) in which a series of triplets (codons) of four possible nucleotides are translated into one of twenty possible amino acids. A sequence of codons results in a corresponding sequence of amino acids that form a protein.

    • my point is that dna doesnt produce anything through a code it simply reacts to create a protein…are other molcules a code?In reply to #4 by grumpyoldfart:

      From Wikipedia:

      Biological organisms contain genetic material that is used to control their function and development. This is DNA which contains units named genes that can produce proteins through a code (genetic code) in which a series of triplets (codons) of four possible nucleotides are translat…

      • In reply to #8 by cynic252:

        my point is that dna doesnt produce anything through a code it simply reacts to create a protein…are other molcules a code?In reply to #4 by grumpyoldfart:

        Doesn’t produce anything? Does Jesus tell the embryo how to mature into a human? I don’t see what the point is about the molecule but as I said in an earlier comment if the question is “does DNA store information the same way binary code does?” the answer is yes. And not “maybe yes” but yes, its been done. The guys I saw at Stanford and here is more recent work where they stored some Shakespeare sonnets using DNA:

        Goodbye Silicon, Hello DNA. The Future of Data Storage?

        Read more: http://science.time.com/2013/01/24/goodbye-silicon-hello-dna-the-future-of-data-storage/#ixzz2VH0z6pAk

      • In reply to #9 by cynic252:

        From which perspective is it not a code?In reply to #5 by foryourknowledge:

        its a code and not a code from another perspective…

        Right. I wonder if we can use ‘code’ to describe the chemistry, particle physics involved? Or must we adhere to ‘equations’ and ‘stick diagrams.’ What about the ‘Coded table of elements’? Now I’ve gone too far.

  3. Found this quote:

    The genetic code is not a binary code as in computers, nor an eight-level code as in some telephone systems, but a quaternary code with four symbols. The machine code of the genes is uncannily computerlike.

    Richard Dawkins
    — River Out of Eden: A Darwinian View of Life, p. 17, 1995

    Note found it here: http://strangewondrous.net/browse/subject/d/dna So not absolutely certain its accurate but although its a long time since I read River Out of Eden I remember Dawkins saying things like this in it and other books.

    • In reply to #14 by Peter Grant:

      The only sense in which it is not a code is that that there is no coder, other than natural selection.

      Careful….I feel a “great encoder in the sky” argument may come up!

  4. DNA fits the definition of a sequence of program instructions, in that DNA is information instructing how to build life.

    As a SoftWare (SW) engineer, code is just a name for what I write as instructions on how to process information or even what to tell a robot how to do things in response to its environment or its motivation. So code can be whats in your brain as well as in your DNA.

    What is important to realize is code represents the blurry line where information is understandable by interpreters. Another way to put this is code is one level (a lower level) of abstraction. In SW, abstraction levels are required for SW developers to be able to grasp complexity with our small brains. Yes I could look at microcode or assembly and its all there, but not in my lifetime would I understand the whole from its parts. Same with DNA. What is the next level of abstraction up from DNA? Proteins? From Proteins? When does it stop being code? Animal behavior is certainly complex. Animal populations more so. An ecology?

    I write SW to be understandable (interpreted, compiled, run) by both my fellow developers and the compiler and the hardware it runs on. I use the term “Future proof”, for SW this means it will run everywhere, not need maintaining etc. Sort of a SW survival manual.

    DNA is evolved emergent complexity and has but one interpreter. As scientists write more DNA, they will make it easier to read I hope. I comment my code, maybe there are comments in DNA?

    • In reply to #16 by OriginalGunner:

      DNA is evolved emergent complexity and has but one interpreter. As scientists write more DNA, they will make it easier to read I hope. I comment my code, maybe there are comments in DNA?

      If we found comments in DNA I might rethink this God question. Come to think of it whenever I inherited someone else’s code I would always consider it a minor miracle if there were useful comments so there are even more similarities between the two ;-)

  5. I’m fascinated by DNA. I never had the chance to learn about this at school, so all I know is what I’ve picked up as I go along (any school knowledge would be far out of date, anyway). Forgive my ignorance if this is well-known, but could somone explain in simple terms so I can understand how such a complex molecule evolved from nothing to what it is today and, presumably, has been in all living things since life first appeared on earth? I could Google it, but often the articles are not explained in sufficiently simple terms.

    Thanks.

    • In reply to #19 by Lonevoice:

      I’m fascinated by DNA. I never had the chance to learn about this at school, so all I know is what I’ve picked up as I go along (any school knowledge would be far out of date, anyway). Forgive my ignorance if this is well-known, but could somone explain in simple terms so I can understand how such…

      If someone can answer that question simply I would love to see it as well but its not a simple question. The simplest answer is we don’t know. What you are referring to is called Abiogenesis, the question of how the first organic molecule came into existence from basic chemicals. Its still very much an open question. Others maybe can give a more complete answer but I wouldn’t want to say more. The wikipedia article on the topic looked pretty good:

      http://en.wikipedia.org/wiki/Abiogenesis

    • In reply to #19 by Lonevoice:

      I’m fascinated by DNA. I never had the chance to learn about this at school, so all I know is what I’ve picked up as I go along (any school knowledge would be far out of date, anyway). Forgive my ignorance if this is well-known, but could somone explain in simple terms so I can understand how such…

      There seems to be something approaching a concensus that DNA came late on the scene (it’s just too complex too have been there at there at the start). It seems very possible that RNA had done a similar job before, but whether there had been an even simpler replicating agent beforehand is difficult to fathom – the life forms would have been small and soft and haven’t been preserved.

    • In reply to #24 by P0L:

      DNA is code-like, because it can be looked at as such by our human eyes. But strictly speaking, no it is not an actual code. Code infers intent. Sometimes in instances like this it is helpful to refer to a common source of reference to clear things up. Here from http://www.merriam-webster.com/dictio

      First of all I don’t agree that using a dictionary definition is the definitive answer in cases like this. When someone asks “is DNA code” a quite reasonable interpretation of that question is “does DNA represent information the way binary code does?” Its possible for us to all accept that as our frame for discussion even if that isn’t how the word is normally used in every day discussion. That happens all the time in science, we give precise definitions for terms that are only somewhat related to their use in normal life. “Spin” and “Inflation” in physics are examples.

      And the answer to “does DNA represent information the way binary code does?” is an unqualified yes. I keep harping on this because its rare that we get a definitive answer to questions on this site but I think this is such a case. The answer isn’t “yes there are many similarities” the answer is just yes. DNA has been used to store computer files.

      But even going by your dictionary definition I think it still holds. One of the definitions in the link you gave was:

      a system of signals or symbols for communication

      That doesn’t imply a creator or even an intelligent agent doing the communication. In information theory and Telecommunications we talk about systems communicating all the time and those systems don’t have to have any intelligent agents in them, they can be computer systems for medical records or shop floor control. Or they can be purely natural systems, people talk about Black Holes using Information Theory.

  6. It is not a code in the sense of “encryption”. It does nothing to hide or scramble its meaning.

    A DNA strand is formed of guanine, adenine, thymine, and cytosine molecules. G-A-T-C is a 4-letter code. Each letter stands for one type of link molecule.

    That is certainly a code by the Oxford dictionary. It has an fixed collection of symbols that have meaning.

    If you group these by 3s, there are 64 possible combinations. This forms a higher level code there each triple is usually associated with the assembly of a particular amino acid, Some codes generated the same amino acid, e.g. GTC and GTA generate valine. Some codes are “stop” markers to create longer sequences, e.g. TAG.

    The system seems much better suited to storing arbitrary digital data than a microrobot to construct a lifeform, but it apparently pulls it off.

  7. What is it bioinformatics? The IT of biological data? Some of the obscure tenets and terminology of SW development are cruft and DRY (Don’t Repeat Yourself), “maintenance disaster” I mentioned “future proof” below. Software also propagates (or deploys) and we speak of field sightings (bugs that show up after we ship). Cruft in current usage is code that no one knows why it is there and are too afraid to delete. So large SW systems accumulate cruft and eventually become non-viable as all SW code must evolve (or not make money/survive). DNA has lots of cruft, but is it a hindrance? What is the percent energy spent of a organism to carry around code for useless proteins? I recall Craig Venter did experiments as to what is the minimal DNA required for a viable organism in a highly controlled environment. SW bloats when it tries to adapt to everything (like MS word), then becomes unusable as I can no longer figure out how to format a simple paragraph. Kind of implies a limit to the organizational ability of large SW systems, is there a limit to DNA complexity that codes for ultimate survivability? DRY (corollary “do not reinvent the wheel”) is a tenet in that SW systems always need to do the same basic functions. We use standard libraries of common functions and spend time searching for code that does what we want. If I see a DRY violation I fix it. Common high levels of abstraction are the same across species, but looking at the intersection of all DNA functions of all current organisms, how many different ways to encode the same function have evolved? Is one function more efficient than another? This is again a SW problem. If I did a code review of DNA it would be a maintenance disaster ;)

  8. DNA is a code, like a product number is a code. For example, my modem is a Motorola SBG900MZUCSPK. SBG900MZUCSPK is the code for my modem. DNA codes indirectly for amino acids, (via RNA).

    Chains of DNA codons, code for chains of amino acids, making proteins. The electrochemical properties of the amino acids lead to the active properties of the proteins. In many cases they curl up into complex shapes.

    So DNA codes for amino acids, just like SBG900MZUCSPK codes for a particular Motorola modem. Presumably inside the modem are a lot of parts, each with their own part numbers or codes. So there’s a lot more product codes in the world than there are DNA codons for amino acids. There are only 20 amino acids to be coded for.

    DNA does not, for example, code for something like a heart, or a wing etc.

  9. I would say that DNA is a code, in the same sense that we speak of the ASCII code. DNA is a 3 digit base 4 code, whereas ASCII is a 7 digit base 2 code (with extended codes using the 8th bit and now pairs of bytes for more universality).

    For a long time I couldn’t see how such a complex code could have evolved. But recently, I read Life Ascending by Nick Lane and his chapter on DNA finally brought some light to this enigma.

    It seems that the 3 letters are not equally important. The first letter of the triplet is associated the steps to turning simple precursors into amino acids. The second letter appears to determine solubility, and the third letter seems to be somewhat extra in that given the first 2 letters, the same amino acid will result regardless of the third letter in many cases. Thus one can see how the code might have been a doublet in early times. Going back even further, it might be that a singlet could have also been used with the solubility coding done some other way.

    It is also interesting to note that in the mitochondria, there are some slight coding differences. Whether this occurred before or after these formally free living bacteria set up shop in a larger bacteria is an interesting question. If I were to guess, I’d think they changed after by some mutation.

  10. Go right back to post one. Coding implies language. Language (at least according to the dictionary definition) is information encoded by one mind for decoding by another.

    However information is present within all nature and although minds are necessary to perceive it and attach meaning there is no requirement for a mind to create it.

    Take chemistry for example, the number of protons and electrons dictate what an atom is. If they change then so does the atom, to a different element. So each atom contains information about what kind of element it is.
    Molecules contain a number of atoms packed in at different densities – more information.
    DNA is a complex arrangement of molecules – more information but no more need for a mind to specify it.
    So the word coding is at best misleading. I think we should stop at information.

  11. My understanding is this: DNA is a complex structure comprising, essentially, defined sequences of related amino acid pairings which serve to act as templates for the timely and accurate production of protein products via the orchestrated process of transcription.

    This seems to be its sole functional context, and seems to be irrelevant to any concept regarding an overall ‘code’, as some seem to think exists somewhere within it’s organisation. Especially as, given an article I read recently, a “gene” (a term I don’t like) might be split between more than one chromosomal structure, I can’t quite see how a dominant code concept directing anything above this works in this context.

  12. I’m going to say minds did create DNA as a mind creates behavior and is the biggest baddest driver of evolution. The “arms war” as scientists call it. Lots wrong with this line of thinking, like when did life acquire a mind.

  13. It’s not necessarily a code, depends what he means by code.

    He wants to use semantics to try and later assert that a code has to be made by an intelligence. The only code there is, is the order that the base-pairs are in. This is strictly chemicals. There is no interwoven code or divinely inspired intelligence.

    They oftentimes try to assert it is a “computer code” in a sad attempt to later assert that “information” can only be created by intelligence. There are a few problems with this.

    • Firstly, they can never define what they mean by “information”. They often will compare it to a book or a computer. There are false equivocations. DNA is strictly just chemical reactions.
    • Secondly, the only “information” there is, in DNA, is in the base pairs, it’s a log2(4) system with the four nucleotides: adenine(A), guanine(G), thymine(T) and cytosine(C). So each base pair can express 4 nucleotides in any number of arrangements. When you chain
      these base pairs together, you get a strand of DNA. The “information” that we prescribe to DNA is simply our reduction of uncertainty in how this system of chemical reactions takes place and what affects it and how. Keep pressing the point that DNA is ONLY chemicals, chemicals undergoing specific chemical reactions based on the fundamental laws of chemistry. There is nothing divine about it.
  14. If by ‘DNA is a code’ you mean ‘DNA contains hidden information’ then you are sadly deluded. DNA is just what it seems to be, a load of sequences of amino acid pairings organised to facilitate protein manufacture. I wish people would stop elevating it to a primary cause, because it is merely a part of the way in which things are put into effect.

Leave a Reply