Friday, July 10, 2015

John Avise doesn't understand the Central Dogma of Molecular Biology

I've just read Conceptual Breakthroughs in Evolutionary Genetics by John Avise. Avise is a Distinguished Professor of Ecology & Evolutionary Biology in the School of Biological Sciences at the University of Califonia at Davis (Davis, California, USA). He has written a number of excellent books including, Inside the Human Genome: A Case for Non-Intelligent Design.

His latest book consists of 70 idiosyncratic "breakthroughs" that have changed the way we think about biology. Each one is introduced with a short paragraph outlining "The Standard Paradigm" followed by another paragraph on "The Conceptual Revolution." There are 70 chapters, one for each "breakthrough," and all of them are two pages in length.

Chapter 42 is entitled: "1970 The Flow of Information."

Here's the "standard paradigm" according to John Avise.
In biochemical genetics, the molecular direction of information flow is invariably from DNA RNA protein. In other words, DNA is first transcribed into RNA, which then may be translated into polypeptides that make up proteins. This view was so ensconced in the field that it had become known as the "central dogma" (Crick, 1970) of molecular biology.
It's true that the Watson version of the Central Dogma was "ensconced" by 1970 and it's true that the incorrect Watson version is still "ensconced" in the textbooks.

It is NOT TRUE that this is the version that Crick described in 1970 or in his 1958 paper [see Basic Concepts: The Central Dogma of Molecular Biology]. Here's how Crick actually described the Central Dogma.
... once (sequential) information has passed into protein it cannot get out again (F.H.C. Crick, 1958)

The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. (F.H.C. Crick, 1970)
The version that John Avise refers to is the incorrect version promoted by Jim Watson.

I understand that many biologists have been taught an incorrect version of the Central Dogma but if you are going to write about it you are wise to read the original papers. In this case, Avise quotes the correct paper but he clearly has not read it.

Now let's look at the "conceptual revolution" according to John Avise.
Researchers showed that biochemical information could also flow from RNA DNA. The key discovery came when Howard Temin and David Baltimore, working independently and on different viral systems, identified an enzyme (reverse transcriptase) that catalyzes the conversion of RNA into DNA, thus enabling the passage of genetic information in a direction contrary to the central dogma.
How do I know that John Avise has not read Crick's 1970 paper? Because here's what Crick says in that paper ...
"The central dogma, enunciated by Crick in 1958 and the keystone of molecular biology ever since, is likely to prove a considerable over-simplification."
This quotation is taken from the beginning of an unsigned article headed "Central dogma reversed", recounting the very important work of Dr Howard Temin and others showing that an RNA tumor virus can use viral RNA as a template for DNA synthesis. This is not the first time that the idea of the central dogma has been misunderstood, in one way or another. In this article I explain why the term was originally introduced, its true meaning, and state why I think that, properly understood, it is still an idea of fundamental importance.
Crick tells us that the discovery of reverse transcriptase did NOT conflict with the central dogma. Thus, John Avise's conceptual revolution never happened. What happened instead, at least for some biologists, is that the discovery of reverse transcriptase taught them that their view of the central dogma was wrong. Most biologists still haven't experienced that particular conceptual revolution.


Crick, F.H.C. (1958) On protein synthesis. Symp. Soc. Exp. Biol. XII:138-163.

Crick, F. (1970) Central Dogma of Molecular Biology. Nature 227, 561-563. [PDF file]

25 comments :

  1. John Avise could not get the premise/definition of the Theory of Intelligent Design right either, and fabricated a whole new one:

    Footprints of nonsentient design inside the human genome
    John C. Avise
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697

    Abstract

    Intelligent design (ID)—the latest incarnation of religious creationism—posits that complex biological features did not accrue gradually via natural evolutionary forces but, instead, were crafted ex nihilo by a cognitive agent.

    http://www.pnas.org/content/107/Supplement_2/8969.abstract


    The real definition/premise is:

    The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

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    1. I say that your definition of ID theory is too vague, and requires elaboration to even understand it, let alone use it. Stephen Meyer has removed that ambiguity by 'explaining' the Cambrian explosion. Didn't Avise make a clear restatement of Stephen Meyer's explanation?. Do you have a statement that better represents Meyer's hypothesis?

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    2. I don't think Meyer actually explained anything. You will search Darwin's Doubt in vain for a clear hypothesis of what actually happened in the Cambrian. All you will find is a list of things that are wrong with evolution.

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    3. The problem with IDiots like Gaulin is they don't understand what "best explained" means. Their non-theory doesn't explain anything about the design process (and no, GG. your stupid cockroach simulator is not the answer). It has zero predictive power and essentially is all about the "not an undirected process" part. A (failed) negative argument is not an explanation, let alone the best one.
      "Best explained" in a scientific theory is redundant anyway. It's already implicit in the scientific framework that the theory that provides the best explanation is the accepted one.
      We all know they will never have a proper theory because that would imply figuring out the designer itself, but of course it's a well known fact that he works in mysterious ways.
      But crooks like Meyer, Luskin & Co. don't really target scientists or educated people. They target the simpletons that will believe any crap thrown at them disguised in science to keep them from quitting religion and make a living out of these gullible minions.
      Gaulin must be so mad at the DI for ignoring him completely. They don't want to share the income with you, deal with it GG

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    4. @John Hashman

      You are right. Intelligent Design Creationism explains nothing. It is essentially a series of attacks on evolution, assuming a false dichotomy. The proponents of Intelligent Design Creationism can't even agree on some basic facts.

      For example, Stephen Meyer seems to accept the basic idea of common descent and the fact that Cambrian fossils are more than 500 million years old and look nothing like modern species. Here's his explanation (p 412) ...

      Unlike the theistic evolution of Francis Collins, however, the theory of intelligent design does not seek to confine the activity of such an agency to the beginning of the universe, conveying the impression of a decidedly remote and impersonal deistic entity. Nor does the theory of intelligent design merely assert the existence of a creative intelligence behind life. It identifies and detects activity of the designer of life, and does so at different points in the history of life, including the explosive show of creativity on display in the Cambrian event. The ability to detect design makes belief in an intelligent designer (or a creator, or God) not only a tenet of faith, but something to which the evidence of nature now bears witness. In short, it brings science and faith into real harmony.

      Now, I've looked really hard at the latest reconstructions of Hallucigenia and I really don't see the evidence of design, let alone intelligent design. I'm guessing that Stephen Meyer sees it differently but forgot to explain why god made such a strange animal. .

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    5. The problem with IDiots like Gaulin is they don't understand what "best explained" means.

      Apparently, with enough mental masturbation even the phrase "best explained" becomes incomprehensible.

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    6. Larry says: Intelligent Design Creationism explains nothing.

      Then what does "Evolutionary Creationism (EC) viewpoint on origins." explain?

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    7. Gee Gee, nice projection, as usual.

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    8. Then what does "Evolutionary Creationism (EC) viewpoint on origins." explain?

      The same as Evolutionary Alienfartism, that posits evolution is true but there's a mutation only when an alien farts, and life was created when an alien took a big dump long ago

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    9. It's all about critical thinking—something that seems to be in short supply these days.

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    10. @Gary Gaulin

      There are many naturalistic explanations of the Cambrian explosion. They all conform to the available evidence including the molecular evidence that shows a common origin for all those fauna. None of the explanations are so convincing that scientists universally accept them but they are, at least, plausible.

      Now, put on your critical thinking cap and give me an explanation that's consistent with all the data but requires gods. Tell me which species were "designed" and when, and why you think your explanation is more reasonable than the scientific ones.

      I bet you can't do that. You have nothing worth saying beyond "gods did it."

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    11. Larry,

      Stephen Meyer seems to accept the basic idea of common descent and the fact that Cambrian fossils are more than 500 million years old and look nothing like modern species.

      He clearly accepts the age of the Cambrian, but I don't know that he accepts common descent at all. There's a whole chapter in Darwin's Doubt that attempts to cast doubt on phylogenetic analysis. And if you assemble all his little hints, his hypothesis about the explosion appears to be that all the phyla, at least, appeared instantly and without ancestors. He has elsewhere denied that there is any good evidence that humans are related to chimpanzees.

      All told, the best guess is that he's an old-earth, progressive creationist. Granted, due to his skill in concealing his ideas, this is at best tentative.

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    12. Well Larry, seeing that you asked I went over the grammar and composition for that section of the theory, at:
      https://sites.google.com/site/theoryofid/home/TheoryOfIntelligentDesign.pdf

      Cambrian Explosion

      Fossil and phylogenetic evidence shows that soon after our planet formed a solid crust molecular level intelligence was already thriving, over 3,000 million years ago. There is next expected to have been a proliferation of cellular level intelligence including plants and eukaryotic cells (single cell animals) which have a nucleus and specialized organelles. Then next, roughly 600 million years ago, there was the well documented “Cambrian Explosion” where a large biodiversity of multicellular intelligence (animals with brain made of neurons) rapidly proliferated. Relatively complex eyes suddenly appeared and are still here in much the same form as in the beginning.

      JoeMeertTimeline.jpg
      Chart supplied by Professor Joseph Meert

      Since the Intelligence Design Lab models the mechanism that is expected to produce these three exponential biological diversification rates we can use it to demonstrate the mechanism that caused the most recent, the Cambrian Explosion. In the run shown below a two lobe compound eye critter is kept busy chasing a feeder for one million memory (write/read) cycles. The green foraging success line shows how well (on average) it is foraging on its own, keeping its stomach full. When using the model for the Cambrian Explosion the foraging success relates to the survival rate of species, which would rapidly decline during mass extinction events then quickly recover. The blue line shows average confidence level, their brain's proficiency at acquiring useful knowledge. The black line shows total memory locations used, which relates to the overall brain capacity of animals. Taken together these show the variables associated with a learning rate which takes into account how much can be learned during its lifetime, and on average how much of that knowledge is actually useful to their overall confidence (well being) and survival success.

      https://sites.google.com/site/intelligenceprograms/Home/TypicalRunChart.png

      The lines seen here are representative of the development of multicellular level intelligence during the predicted period of time known as the Cambrian Explosion. There are also two earlier predicted events of the same magnitude (for molecular and cellular level intelligence), where due to not leaving behind much fossil evidence are harder to detect but none the less await future paleontological discovery.

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    13. @Gary Gaulin

      Oops! My apologies. This is the first time I've looked at your website.

      I won't be bothering you again. Keep taking your meds.

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    14. Larry

      I think you may have meant "start taking your meds" haven't you?

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    15. Larry says: Oops! My apologies. This is the first time I've looked at your website.

      At least you have the honesty to admit that after all these years you did not even look at what you claim to be an expert in.

      Your critical thinking score is now zero.

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  2. If the contenders in this fight can get so much wrong about these matters then creationists must be excused for making mistakes when dealing with these issues.
    why does the guy think paradigms are being broken if they are not? Why such wrong perception? it suggest these things are not settled or proven. Room for insight and so a option for creationist insight.

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  3. Anyway, what's so weird about Hallucigenia? It's just another armored lobopod.

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    1. Giving it an eccentric Latin name was a good PR move. It attracts people's attention more effectively than its anatomy.

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  4. This is the 1st time I've really understood the nature of Crick's thinking on the Central Dogma. Thank you, Professor Moran.

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  5. Mung on July 12, 2015 at 3:47 am said:
    Actually, don’t we now know that the central dogma is in fact false?

    Here:

    http://theskepticalzone.com/wp/?p=28378#comments

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  6. Hi Larry

    Not to be nit-picky, but if I understand correctly, to my reading your problem with Avise is that he cites Crick’s own later citation of an earlier paper by Crick. The earlier 1958 paper by Crick did in fact posit the naïve version of the Central Dogma that clearly required correction as correctly explained by Crick in his later 1970 paper.

    In other words, Avise was correct to include Crick’s narrative in Avise’s book on shifting paradigms in Biology.

    My problem with all this is that the French Chauvinism claims credit for the Central Dogma and they may have a point. Unless I am missing something, the earlier Jacob-Monod hypothesis is in fact an earlier incarnation of the Central Dogma.

    http://www.bookrags.com/research/jacob-monod-hypothesis-wob/#gsc.tab=0

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    1. Dear nit-picky,

      You clearly have not read the 1970 paper. Allow me to quote from it to show that Crick's first version of the Central Dogma was exactly the same as the one he emphasized in 1970.

      At this stage I must make four points about the formulation of the central dogma whihc have occasionally produced misunderstandings.....

      4. It is not the same, as is commonly assumed, as the sequence hypothesis, which was clearly distinguished from it in the same article [Crick, 1958]. In particular, the sequence hypothesis was a positive statement, saying that the (overall) transfer nucleic acid --> protein did exist, whereas the central dogma was a negative statement, saying that transfers from protein did not exist.


      I don't see how you can possibly think that Avise got the concept right if he quotes Crick. Avise was right to say that many people misunderstood the Central Dogma and they should have corrected their misunderstanding by reading Crick's 1970 paper. Realizing that you were too stupid to understand a key concept in the field is not my idea of a shifting paradigm. Is it yours?

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    2. thank you for correcting me

      I still remain unclear whether Jacob and Monod can claim precedence with their Jacob-Monod Hypothesis

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