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Revisiting the Central Dogma

The Central Dogma has had an enormous impact on the way genetics research has developed over the past 50 years. Basically, the dogma states that DNA genes encode mRNA, and mRNA allows proteins to be constructed, and proteins do all the work needed for cells to function. There is a linear logic here that fits into a view of the genome that is static throughout its life and provides a blueprint for life. This is how Franklin and Vondriska introduce their paper:

“Arguably the greatest postmodern coup for reductionism in biology was the articulation of the central dogma. Not since “humors” were discarded from medical practice and logic and experiment instituted as the cornerstones of physiology (which they remain today) had such a revolutionary idea transformed biology and enabled scientific inquiry. Because of its simplicity, the central dogma has the tantalizing allure of deduction: If one accepts the premises (that DNA encodes mRNA, and mRNA, protein), it seems one cannot deny the conclusions (that genes are the blueprint for life). As a result, the central dogma has guided research into causes of disease and phenotype, as well as constituted the basis for the tools used in the laboratory to interrogate these causes for the past half century.”

In their review of these issues, Franklin and Vondriska present a systems biology perspective which makes it clear that the central dogma is deficient in numerous ways and that our understanding of living things needs extensive revision. This is an imperative drawn from scientific research and should not be regarded as just another ‘point of view’.

“The past decade, however, has witnessed a rapid accumulation of evidence that challenges the linear logic of the central dogma. Four previously unassailable beliefs about the genome – that it is static throughout the life of the organism; that it is invariant between cell type and individual; that changes occurring in somatic cells cannot be inherited (also known as Lamarckian evolution); and that necessary and sufficient information for cellular function is contained in the gene sequence – have all been called into question in the last few years.”

For more, go here.

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22 Responses to Revisiting the Central Dogma

  1. 1
    Kantian Naturalist

    I’m perplexed about something here. Wouldn’t it be bad for design theory if it’s false that “necessary and sufficient information for cellular function is contained in the gene sequence”?

    As I understand it, the basic argument of design theory is that there’s so much functional, complex specified information in the genetic code that an intelligent agent is a more plausible explanation for that information than the laws of physics and chemistry. In light that of that, a more holistic and less “genocentric” view of living systems would undermine a central argument of design theory, no?

  2. Abstract: Systems biology, with its associated technologies of proteomics, genomics, and metabolomics, is driving the evolution of our understanding of cardiovascular physiology. Rather than studying individual molecules or even single reactions, a systems approach allows integration of orthogonal data sets from distinct tiers of biological data, including gene, RNA, protein, metabolite, and other component networks. Together these networks give rise to emergent properties of cellular function, and it is their reprogramming that causes disease. We present 5 observations regarding how systems biology is guiding a revisiting of the central dogma: (1) It deemphasizes the unidirectional flow of information from genes to proteins; (2) it reveals the role of modules of molecules as opposed to individual proteins acting in isolation; (3) it enables discovery of novel emergent properties; (4) it demonstrates the importance of networks in biology; and (5) it adds new dimensionality to the study of biological systems.

    Genomes, Proteomes, and the Central Dogma

  3. KN:

    Wouldn’t it be bad for design theory if it’s false that “necessary and sufficient information for cellular function is contained in the gene sequence”?

    No. There is a larger informational role than just what is in a specific protein coding sequence, and we’ve known this for some time now.

    An interesting exercise, if you choose to do so, is to read the paper and seek out references to the term ‘information.’

    As I understand it, the basic argument of design theory is that there’s so much functional, complex specified information in the genetic code that an intelligent agent is a more plausible explanation for that information than the laws of physics and chemistry.

    I don’t understand why you think this would be a problem. Just because there’s a greater role for information in the cell than just what is encoded in a gene sequence it doesn’t follow that, ID isn’t the best explanation for the information in the gene sequence.

    In light that of that, a more holistic and less “genocentric” view of living systems would undermine a central argument of design theory, no?

    No. ;)

    It’s as if you are arguing that because a computer is designed a program running on the computer is somehow less in need of an intelligent cause.

  4. As I understand it, the basic argument of design theory is that there’s so much functional, complex specified information in the genetic code that an intelligent agent is a more plausible explanation for that information than the laws of physics and chemistry.

    First we’ll need an example of the ‘laws of physics and chemistry’ producing the necessary material conditions required for recorded information. Only then can we assess what is more plausible. As it stands right now, those material conditions are only produced by living things (massive pre-existing organization) and hence, there is only one viable explanation on the table.

  5. KN:

    Gene-coding sequences are just one example of complex specified information found in living systems. Sometimes people focus on gene-coding sequences because they are easy to understand, easy to specify, and give the lie to the materialist creation myth. However, there is much more information in an organism than just its gene-coding sequences.

    The Central Dogma is not really a helpful way to look at what is going on. I, for one, will be happy to see it go the way of the dustbin . . .

  6. I’m with KN honestly. Obviously the central dogma is simplistic. But it’s not wrong. ID people should not be attacking it as if it was. Those attacks undermine our position, and they aren’t accurate regardless.

  7. The current paradigm is as if there were a running computer program and the only way to change the program was to make random changes to some bit location in random access memory and hope it led to an improvement in the running of the program without crashing it.

    I fail to see how changing that could possibly harm ID.

    In order to ‘program’ the cell, the cell must be programmable. The program(s) must be stored, and one would think, modifiable. This means that something other than random changes to the DNA itself needs to be in play.

  8. This means that something other than random changes to the DNA itself needs to be in play.

    Of course. What’s in play is non-random changes to the DNA. Intelligently designed changes to the DNA.

    What’s your point?

  9. To take Upright’s comment “First we’ll need an example of the ‘laws of physics and chemistry’ producing the necessary material conditions required for recorded information.” one step further…

    It is impossible, in principle, in the same way it’s impossible for a circle to be not a circle, a square, for instance, for the laws of physics and chemistry to produce any conditions for information. Information requires language which means symbols and (arbitrary) rules for the arrangement of those symbols in order to encode information into matter/energy. Since the laws of physics and chemistry are only about sub-atomic particles in energy fields they have NOTHING to say about why a particular sequence of DNA “means” human being and another sequence means “spider” and another sequence means nothing at all. They will never have anything to say about information. Ever. Language is the link between the world of mind/information and the physical world. Physics explains the one but has NOTHING to say of the other.

  10. Dr. Tyler, of related note, Koonin recently pointed out this ‘direct violation’ of the central dogma:

    Does the central dogma still stand? – Koonin EV. – 23 August 2012
    Excerpt: Thus, there is non-negligible flow of information from proteins to the genome in modern cells, in a direct violation of the Central Dogma of molecular biology. The prion-mediated heredity that violates the Central Dogma appears to be a specific, most radical manifestation of the widespread assimilation of protein (epigenetic) variation into genetic variation. The epigenetic variation precedes and facilitates genetic adaptation through a general ‘look-ahead effect’ of phenotypic mutations.,,,
    http://www.ncbi.nlm.nih.gov/pubmed/22913395

    If that wasn’t bad enough for the reductive materialism of noo-Darwinism, these following studies showed that epigenetic influences on genes can even originate from ‘mental states’:

    Anxiety May Shorten Your Cell Life – July 12, 2012
    Excerpt: These studies had the advantage of large data sets involving thousands of participants.
    If the correlations remain robust in similar studies, it would indicate that mental states and lifestyle choices can produce epigenetic effects on our genes.
    http://crev.info/2012/07/anxie.....cell-life/

    Upgrade Your Brain
    Excerpt: The Research; In his book The Genie in Your Genes (Elite Books, 2009), researcher Dawson Church, PhD, explains the relationship between thought and belief patterns and the expression of healing- or disease-related genes. “Your body reads your mind,” Church says. “Science is discovering that while we may have a fixed set of genes in our chromosomes, which of those genes is active has a great deal to do with our subjective experiences, and how we process them.”
    One recent study conducted at Ohio University demonstrates vividly the effect of mental stress on healing. Researchers gave married couples small suction blisters on their skin, after which they were instructed to discuss either a neutral topic or a topic of dispute for half an hour. Researchers then monitored the production of three wound-repair proteins in the subjects’ bodies for the next several weeks, and found that the blisters healed 40 percent slower in those who’d had especially sarcastic, argumentative conversations than those who’d had neutral ones.
    http://experiencelife.com/arti.....our-brain/

    Genie In Your Genes – Book
    Book review: First of all, if you are a newcomer to Dawson Church’s writing, you need to know that his facts are unimpeachable – they were stringently peer-reviewed before publication. What is more, when Church makes categorical statements, he provides research to corroborate them.
    http://www.amazon.com/gp/produ.....1600700225

    Genie In Your Genes – video
    http://www.genieinyourgenes.com/ggtrailer.html
    main website
    excerpt: There are over 100 genes in your body that are activated by your thoughts, feelings and experiences
    http://www.genieinyourgenes.com/

  11. tragic mishap:

    Obviously the central dogma is simplistic. But it’s not wrong.

    It is not just that the Central Dogma is simplistic description of a correct concept. It was built upon the following (now known to be false) ideas: (i) essentially all biological information worth talking about is in DNA, (ii) the building of proteins is the ultimate act of the organism (after that, nearly everything just happens by biochemistry), (iii) tweaking a genetic sequence for proteins is what ultimately drives biological change, (iv) DNA is what it is (outside of mutational events during replication) and is not influenced by the organism or the cell over time; etc. The Central Dogma has also been one of the primary contributors to the idea of pervasive junk DNA — the thought initially being that anything that didn’t translate into proteins was junk.

    It is not just an oversimplification. It represents a flawed paradigm that has, frankly, kept people from seeing the broader picture for a long time. Thank goodness the picture is starting to change.

    Now, on the other hand, there is some truth in the Central Dogma. For example, if we want to redefine the Central Dogma to just be the raw fact that some genetic sequences eventually get translated into proteins, fine. But then it is less of a “Central Dogma” of biology and more of a “Basic Statement of Protein Production” or something.

    As the central cornerstone of biology, as first intended, the Central Dogma fails. As a more precise statement of one specific activity in the cell, it is true; but is then more appropriately regarded as sitting alongside thousands of other critical activities in the cell, no more “central” than the others.

  12. Anecdote: Three years ago I began playing classical guitar, and the technique involves plucking with the nails. Mine would grow to a good playing length, then invariably crack or split. The problem was exacerbated because in my trade I work with my hands. After struggling for the better part of a year, I began coating them with clear nail polish. This allowed them to stand up to playing. But lo and behold, over the last six months or so I have quit using the polish, and have not broken a nail once. Somehow or other, they have toughened up. I am unsure if this would involve what’s being discussed, but some kind of feedback mechanism is in play that is a whole lot less direct than, for instance, exercising a muscle. What I am sure of is that I look a lot less weird than I did with shiny nails on my right hand… :D

  13. (i) essentially all biological information worth talking about is in DNA

    It still is. Just because much of it is not directly protein coding doesn’t mean it’s not in the DNA and not important. All of this information is in DNA and in some way shape or form is still involved in making proteins through splicing and gene regulatory networks, to name a few.

    (ii) the building of proteins is the ultimate act of the organism (after that, nearly everything just happens by biochemistry),

    Um, what? Are you aware of something in an organism that is not “biochemistry”? Do tell.

    (iii) tweaking a genetic sequence for proteins is what ultimately drives biological change,

    Since I’m a creationists I don’t require change in the protein coding genes to occur for biological diversity to be created. But for anyone who still believes in the evolutionary timeline, i.e. common descent etc., this sort of change is still required, Darwinian or not. Besides, there are a great deal of undesirable changes in protein coding sequences that do drive biological change, it’s just in the wrong direction.

    (iv) DNA is what it is (outside of mutational events during replication) and is not influenced by the organism or the cell over time; etc.

    I don’t understand. It’s as if you believed that DNA was some sort of book and not a computer program. The central dogma never implied that DNA had no ability to respond to environmental feedback. I never took it that way. In fact, this ability to respond to feedback is encoded in the DNA itself. It’s not evidence against the central dogma to say that part of the coding in DNA, perhaps a very large part, deals with adjusting to feedback. You are agitating against all sorts of things, but none of them cuts against the central dogma.

    The Central Dogma has also been one of the primary contributors to the idea of pervasive junk DNA — the thought initially being that anything that didn’t translate into proteins was junk.

    Um, I think you are mistaking the central dogma for Darwinian evolutionary theory, a mistake a lot of people around here are in the habit of making apparently.

  14. tragic mishap”

    (i) First, the Central Dogma was all about protein-coding sequences. So, yes, the fact that there are other — extremely important — aspects of DNA that are not involved in protein coding shows that the Central Dogma was grossly inadequate in its view.

    Second, we do not know that all the relevant information is in DNA. Life cannot arise just from DNA sitting in a pool of chemicals. You must have existing structural arrangements in place — other parts of the cell, other functional machines — in order to have a living cell. Those other parts constitute information (their location, function, and in some cases, instructional elements within them). It may be the case that DNA contains the protein-coding sequences to build the proteins that make up all of these other cellular components, but DNA has nothing to say about what happens with a protein once it gets built. There is a whole additional layer of computation going on. So it is not at all clear that DNA contains all the information needed for an organism.

    (ii) You are misunderstanding my comment. Once a protein is made, then what? The Central Dogma just stops there (well, actually it includes the trite phrase: “proteins build us”.) But proteins don’t just build us through chemical interactions. That is my point. The literature is full of references to proteins being screened, tagged, shepherded to locations, incorporated into structures, etc. This doesn’t just happen naturally through chemical affinities. These are computational and programmed operations that occur completely outside of and above and beyond the simple chemical affinities.

    (iii) I don’t know that we disagree here. My point is that although tweaking protein sequences may drive some change, but it is certainly not the ultimate source of organismal origin and diversification. This would be like suggesting that I can create a completely different and more powerful computer by tweaking some of the characters in my hard drive’s database. Much more is needed. Higher protocols to find, read, interpret, translate, utilize, build, etc. Protein sequences simply don’t exist at that level of operation.

    (iv) There is growing evidence that outside influences (other things within the cell, perhaps environmental stimuli) can actually cause portions of DNA to be rewritten, at least in small part. The Central Dogma explicitly rejects the ability of information to flow in this direction. Of course people think the organisms can respond to its environment. That’s not what we’re discussing. I’m talking about a possible flow of information into DNA itself, which was explicitly rejected by the Central Dogma.

    Finally, the Central Dogma (with its coding-for-proteins-is-all-that-matters attitude) is very much responsible for the idea that much of DNA was junk. It is the precise fact that much of DNA didn’t code for proteins that led to the idea that it was junk in the first place.

    —–

    I think there is much we can agree on, but I’m not sure why you think we should defend an out-of-date idea based on several (now known) misconceptions that — at best — was wildly oversimplified and incomplete, and — at worst — downright wrong on many levels.

  15. It may be the case that DNA contains the protein-coding sequences to build the proteins that make up all of these other cellular components, but DNA has nothing to say about what happens with a protein once it gets built. There is a whole additional layer of computation going on. So it is not at all clear that DNA contains all the information needed for an organism.

    Or which protein will be created, or when. Somehow the cell seems to know it is time to build more of a given protein and acts to bring that about.

  16. As I have said before when this comes up, show me the money. If you have a concrete location for information other than DNA, let’s see it. You talked about evidence for DNA being rewritten. Well, how does that work? I’d be willing to bet that goes back to DNA as well. You can write a program that writes other programs in response to various stimuli.

    All those codes, tags, spliceosome, etc. ultimately come from DNA and you know it. I have worked in a RNA lab. Have you? RNA deteriorates even more quickly than proteins do. That’s why DNA functions as the information carrier. It’s stable. You can’t just say this information “must” be there and not tell me a location.

    No of course DNA cannot build a cell by itself. But neither can a computer build a fully-automated factory. Once the factory is built however a computer can run the thing by itself. It cannot significantly change the original design, though the original design may contain various contingencies for slight modification. Your problem is probably that you are not a creationist, and so you are trying to find a way that body plans can be adjusted more than we have any evidence to believe that they can.

  17. Saying that the central dogma only concerned protein coding regions is a dodge. It’s only a slight modification to say that much, even most of this information only goes to the level of RNA.

  18. tm:

    RNA deteriorates even more quickly than proteins do. That’s why DNA functions as the information carrier. It’s stable.

    I know. Isn’t it a great design? Use RNA as a short term information carrier and use DNA for long term information storage. RNA also acts as an information carrier, so it’s not restricted to DNA. And RNA isn’t restricted to some static location within the cell.

    You can’t just say this information “must” be there and not tell me a location.

    Sure we can. The cell is a dynamic system. Information doesn’t just remain statically in a specific location. There’s no reason at all to think information is restricted to DNA and many good reasons to think it’s not.

    In what sense is the information about when to create more of a given protein stored in the DNA?

    In what sense is the information about how much to create of a given protein stored in the DNA?

  19. I never said information was restricted to DNA. Don’t put words in my mouth. I said it comes from DNA. Show me some evidence of RNA that isn’t translated from DNA. Until then you have no evidence that RNA is an information carrier independent from DNA.

    In what sense is the information about when to create more of a given protein stored in the DNA?

    In the same sense that a computer program is written so that the letter “w” appears on the screen when the key “w” is pressed on the keyboard. Not before, not after, but precisely when a given input occurs the program is written to specify a given output.

    In what sense is the information about how much to create of a given protein stored in the DNA?

    That’s what all these complicated gene regulatory networks do. A simple example would be an enzyme whose regulatory network is controlled by the level of the enzyme’s substrate in the cell. The classic example is the lac operon:

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

  20. tragic mishap:

    I never said information was restricted to DNA. Don’t put words in my mouth.

    1. You are asserting that all information in the cell comes from information stored in DNA.

    2. You are asserting that all changes to information in the cell comes from changes to DNA via direct manipulation of the DNA by the designer.

    3. You are excluding that the designer might change the information in DNA by changing information in the cell that is not in the DNA in such a way that the effect is to change the information stored in the DNA.

    #3 follows from your stance on #1.

    tm:

    In the same sense that a computer program is written so that the letter “w” appears on the screen when the key “w” is pressed on the keyboard.

    Those functions are typically handle by the operating system, yes another source of information separate and distinct from any specific program.

    Would you care to re-think your analogy?

  21. Those three are actually all correct representations of what I’m saying, yes. I’m willing to change my mind if presented with evidence. I don’t have any particular reason to believe them except there’s no evidence otherwise.

    As for my analogy, you’ve got to be joking. Your interpretation of that analogy fails unless you can provide evidence that it translates to the cellular environment.

  22. Q: “How does the cell know how to build all of these machines, fuel them, orchestrate them?”

    A: “It uses the same thing a computer uses, Information. Some of that information – not all of it – is stored on the DNA.”

    Borrowed from:

    Intelligent Design Uncensored
    William Dembski and Jonathan Wells

    Agreed, that’s not evidence. But it shows I’m not off making up my own little world of ID (or maybe I am). ;)

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