Friday, August 26, 2011

Revisiting the Central Dogma in the 21st Century

James A. Shapiro is an interesting character. He claims that he is opposed to both neo-Dawinism and Creationism (upper case "C") and he claims to offer a "Third Way." That "third way" appears to be indistinguishable from Intelligent Design Creationism although Shapiro never admits to being an advocate of intelligent design. Instead, he prefers to let his "science" do the talking and points out that it's science that leads us to the conclusion that life is designed.

Shapiro has published scientific articles with Richard Sternberg who advocates a similar position but who has become one of the poster boys of the Discovery Institute and one of the stars of the movie Expelled: No Intelligence Allowed. Like Sternberg, Shapiro is admired by IDiots [Non-supernatural ID?: University of Chicago microbiologist James Shapiro works with ID guys, dismisses Darwinism, offers third way].

One of the characteristics Shapiro shares with the IDiots is attacking evolution. In this post I want to review a paper he published in 2009 on "Revisiting the Central Dogma in the 21st Century" (Shapiro, 2009).

The correct version of the Central Dogma of Molecular Biology is:
... 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)
In other words, the flow of information is from nucleic acid to protein and never from protein to nucleic acid.

The incorrect version of the Central Dogma of Molecular Biology is what Crick referred to as the "Sequence Hypothesis" and what we now know as a simplified version of the standard pathway for information flow from genes that specify a protein product. The incorrect version is often presented in textbooks as the real Central Dogma although that's slowly changing [The Central Dogma Strawman].

None of this should be a problem for someone who is writing a scholarly article for the scientific literature since we expect such a person to have read the relevant references (Crick, 1958; Crick, 1970). They should get it right. Let's see how Shapiro does when he says ...
The concept was that information basically flows from DNA to RNA to protein, which determines the cellular and organismal phenotype. While it was considered a theoretical possibility that RNA could transfer information to DNA, information transfer from proteins to DNA, RNA, of other proteins was considered outside the dogma and "would shake the whole intellectual basis of molecular biology [Crick, 1970].
That sounds pretty good but the first part is a little troubling. Which version does Shapiro actually believe he's "revisiting"?

For that we have to look to a paper he published last year (Shapiro, 2010) where he says ...
Crick's central dogma of molecular biology:

1. DNA --> 2x DNA
2. DNA --> RNA --> protein --> phenotype
Oh dear, he's got the wrong version. This doesn't look good.

The 2009 paper lists a whole bunch of things wrong with the central dogma but I'll just mention the ones under "Basic Molecular Functions."
The molecular analysis of fundamental biochemical processes in living cells has repeatedly produced surprises about unexpected (or even "forbidden") activities. A short (and partial) list of these activities provides may illustrative complications or contradictions of the central dogma.
  • Reverse transcription ....
  • Posttranscriptional RNA processing ....
  • Catalytic RNA ....
  • Genome-wide (pervasive) transcription ....
  • Posttranslational protein modification ....
  • DNA proofreading and repair ....
None of these things complicate or contradict the correct version of the Central Dogma of Molecular Biology. They don't even conflict with the general flow of information diagram that we see in the textbooks since that diagram is meant to represent a simple version of information flow from DNA to protein. The fact that some species might have a few extra adornments isn't really a problem. Biology is full of exceptions to general rules.

The fact that he mentions reverse transcription is especially revealing since the reason why Francis Crick wrote his 1970 Nature paper was to dispel the notion that reverse transcription had anything to do with the Central Dogma of Molecular Biology. You only need to read the opening paragraph of that 41-year old paper to see how little things have changed.
"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 [1] headed "Central dogma reversed", recounting the very important work of Dr. Howard Temin [2] and others [3] showing that an RNA tumour 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.
Plus ça change (plus c'est la même chose).

So, why do people like Shapiro makes such a big deal of this? It's because claims that the Central Dogma of Molecular Biology have been overthrown1 attract attention and fit into a larger agenda. If your goal is to start a revolution in biology then the first thing you have to do is knock down the existing "dogma." It doesn't seem to matter that you are attacking a strawman. But it's a sign that the rest of your agenda isn't very sound.


1. Such claims are occurring with increasing frequency in the past ten years. It now seems that the central dogma is being falsified about three or four times a year.

Crick, F.H.C. (1958) On protein synthesis. Symp

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

Shapiro, James A. (2009) Revisiting the Central Dogma in the 21st Century. Ann. N.y. Acd. Sci. 1178:6-28. [doi: 10.1111/j.1749-6632.2009.04990.x]

Shapiro, J.A. (2010) Mobile DNA and evolution in the 21st century. Mob DNA. 1:1-14. [doi: 10.1186/1759-8753-1-4]

545 comments:

  1. I'm a little confused. I'm not sure what would be considered a violation of the dogma; would the information have to leave the domain of proteins altogether, or would a self replicating protein molecule count against it?

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  2. Reverse translation would violate it.

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  3. I think that in a strict sense prions violate the central dogma as a genuine protein to protein transfer.
    I've always thought of the dogma as a useless rule of thumb. Note that no one ever thought it worthy of being called The Central Theory

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  4. What would it matter if the Central Dogma was violated anyway? On the one hand, Crick'd be wrong. About the central dogma. So there's that.

    But beyond that, what would it really matter? It wouldn't lend support to ID or anything like that. If anything it'd lend support to Lamarckism and thats about it no?

    I understand that the creationists are saying 'look, the Central Dogma of Biology is wrong, and we hope you take that to me "Darwinism" is wrong and goddless biology is demolished', but it does not follow.

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  5. Moran is such a typical pompous prof. Other profs are fools and knaves. No matter how many degrees they have and how many years they have been at it.
    Only he is pure and knowledgeable.
    No matter how many tricks I have caught him in.

    It is tiresome to see Moran do this shtick.

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  6. Sounds like anonymous hearts Shapiro. You guys should rent a room.

    @Schenck

    It's the Dogma word. Causes a pavlovian response in IDiots. In the world of IDiocy everything is based on authority, dogma and revelation. So if you attack the authority figure you have defeated the idea. Very bronze age. You should see what happens when you try to take a picture of one of them, it's like you're stealing their souls. And there are reliable reports that they can't recognize themselves in a mirror.

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  7. I'm Anonymous and I'm a complete and utter moron! Look at me guys!

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  8. This definitely proves there is more than one individual posting under the "anonymous" moniker.

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  9. Shapiro listed:
    "Reverse transcription ....
    Posttranscriptional RNA processing ....
    Catalytic RNA ....
    Genome-wide (pervasive) transcription ....
    Posttranslational protein modification ....
    DNA proofreading and repair ...."

    Moran replied:
    "The fact that some species might have a few extra adornments isn't really a problem."


    Dr. Moran are you saying the things Shapiro listed are simply "a few extra adornments"?

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  10. @RodW: Even in a strict sense Prions don't violate the Central Dogma, or even the general Information Flow paradigm. Prions are misfolded proteins but their sequence information is the same as the properly folded form. In their misfolded state they act as scaffolds, catalysing the misfolding of other, properly folded, prion proteins.

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  11. Anonymous: He didn't say "simply" extra adornments, he said extra adornments. The two phrases give entirely different implications for those processes.

    The ID folks sure do like to play their silly word games. Besides, none of those violate the Central Dogma anyway...

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  12. So DG, are you agreeing with Moran that the things Shapiro listed are extra adornments?

    Does everybody agree with Moran that the things Shapiro listed are extra adornments?

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  13. Anonymous: I'm saying they aren't challenges to the Central Dogma first and foremost. Everything else is secondary to that point.

    As for whether they are extra? Well, some of them aren't known to be present in all organisms. Some aren't pervasive in the sense that they are limited in scope in the organisms that they are known to exist in, others are basic, pervasive, but well understood aspects of molecular biology, and some are debatable as to whether they are a factual statement.

    The evidence for pervasive (whole genome) transcription/translation for instance is incredibly debatable. I'm of the opinion that newer, better, more sensitive techniques have shown the earlier evidence to be mostly artifactual.

    What exactly does he mean by Post-Transcriptional RNA processing? Does he mean RNA editing? Or any sort of processing, because we've known for a hell of a long time that mRNAs undergo modification. The addition of the 3' cap and poly-A tail in Eukaryotes for instance.

    DNA proofreading and repair is a total non-starter when it comes to the Central Dogma. Its complete nonsense to add it to any list that is meant to "overthrow the paradigm", and should be to anyone who knows even the most basic genetics and molecular biology.

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  14. Those aren't exceptions to the central dogma!

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  15. It looks like DG is agreeing with Moran that the things Shapiro listed are "extra adornments".

    Does everybody think that?

    It seems to me to call that list "extra adornments" is absurd. But then perhaps only DG and Moran think they are "extra adornments" and the rest of us see that list as pretty substantial processes and not what anyone would call "extra adornments".
    But Moran had to say something in response to what Shapiro said, so Moran is stuck saying something absurd. Something to downplay that list of exceptionally significant and substantial things that Shapiro listed.

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  16. Here is a link to the 2009 Shapiro article:
    http://www.agnosticweb.com/download/shapiro_2009.pdf

    Note that Moran did not give us this link. He gave us a link to the abstract - where you have to pay to see the rest. So we could not see the details easily.
    Also the link Moran gave us for Shapiro's 2010 article does not work.
    These are probably quite innocent errors.
    But notice that if anyone else makes an error, Moran goes to great lengths to denigrate the integrity of the person. As if they are hiding something or trying to fool us intentionally.
    This is absolutely part of the Moran shtick and he does it again and again.

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  17. The main problem with Shapiro is that he doesn't accept that molecular mechanisms are taking place without purpose. He doesn't introduce a personal designer but rather refers to "natural genetic engineering" that is somehow guided purposefully by the cell itself. According to a recent review Mobile DNA and evolution in the 21st century (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836002/?tool=pubmed) he beleaves that

    "hereditary variation arises from the non-random action of built-in biochemical systems that mobilize DNA and carry out natural genetic engineering"

    How he came to his ideas is summarized in his freely available paper: Letting Escherichia coli Teach Me About Genome Engineering (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2787414/?tool=pubmed).

    While he obviously doesn't accept the "random variation" part of evolution theory he doesn't seem to deny that selection takes place (he doesn't mention other mechanisms of fixation like drift).

    IMHO Shapiro did some relevant work on mobile elements in bacteria. However, he over-generalizes his findings and ignores other mutation research which has shown that adaptive mutations (earlier even named "directed mutations") are a myth that can be explained by mutator phenotypes under stress conditions. The outcome of the Luria-Delbrück fluctuation test reamins the rule not the exception: Mutations are random.

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  18. Anonymous said:
    Note that Moran did not give us this link. He gave us a link to the abstract - where you have to pay to see the rest.

    This is absolutely ridiculous. It is not un-usual that articles are behind a pay wall. If Dr. Moran has access to the original source why should he assume that a free copy is available somewhere on the web? BTW, it is not even clear if you link to a legal copy.

    The doi-link maybe broken (the visible die is actually right). Still Dr. Moron provided sufficient additional information to get the article.
    Don't you know PubMed or even Google?

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  19. I find it hilarious that Shapiro, who clearly thinks that evolution is an undeniable fact, and is clear that he favours "methodological naturalism", is quoted with approval by the shapeshifters in the Creationist community.

    One cannot completely rule out 'natural genetic engineering' - but I don't see any evidence for it. And like many a 'directed evolution' process, it explains nothing about how evolution may have got to the stage of being directed from one which (we may presume) was undirected. ID-ers throw in the towel and wibble about aliens and ill-defined intelligence.

    But for the methodological naturalist, there must be an evolutionary mechanism that allows such a hypothetical "natural genetic engineering" to evolve in the first place. And one which presumably still operates. By George, I think I've discovered a new evolutionary principle ... oh, hang on ...

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  20. http://en.wikipedia.org/wiki/Adaptive_mutation
    "Cellular processes leading to the mutations are also surprisingly similar between both organisms and include silencing of differentiation, cellular senescence, programmed cell death, and DNA repair on the one hand, and activation of the error-prone replication and transposons on the other. The similarity suggests that the adaptive mutations may be an output of activation in the stressed cell of a special survival strategy for quick adaptation to the stressful environment. This strategy that is also referred as the mutator phenotype is an alternative to other stress-induced strategies, such as senescence and programmed cell death, activated in majority of stressed cells. Continuing stress-induced proliferative and survival signaling may be an important prerequisite for epigenetic reprogramming of some cells to activate the mutator phenotype."

    Excellent example of intelligent strategies that the cell employs.

    If we saw similar types of actions being performed by a person, we would have no doubt that they were intelligent strategies they were employing.

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  21. Here is an analogy.
    Imagine a person in a locked room. He begins to take logical actions to find a way out. He looks for a door, a trap door, a hidden opening, a hammer to break a hole with etc. He steps up his activities. Makes sense.
    But he does not just step up activity in general. He does not start cleaning his fingernails or tapping his left foot or humming a tune or reading a fiction novel etc.
    His increased activity is put into intelligent activity related to the problem at hand.

    Is this not what stressed cells do?

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  22. [...] intelligent activity related to the problem at hand.

    Is this not what stressed cells do?


    Stressed cells respond to stress, just as cells move towards food or away from danger. That's not intelligence; that is signal detection 'hard-wired' to a response. Automation is not intelligence.

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  23. Anonymous writes:

    "It is tiresome to see Moran do this shtick."

    But apparently not so tiresome that Anonymous can't still post 8 times to this one thread in less than 24 hours.

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  24. "Stressed cells respond to stress, just as cells move towards food or away from danger. That's not intelligence; that is signal detection 'hard-wired' to a response. Automation is not intelligence."


    Then it is not random.
    Right?

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  25. Also I've heard that cells can metabolize nutrients effectively. They don't just degrade everything randomly.

    Seems very intelligent to me?

    I've also heard that bacteria with their intelligently designed flagellums can move in particular directions, no? Seems rather.. intelligent.

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  26. I had posted:
    "Then it is not random.
    Right?"
    This was in response to Miller's:
    "Stressed cells respond to stress, just as cells move towards food or away from danger. That's not intelligence; that is signal detection 'hard-wired' to a response. Automation is not intelligence."

    Clearly what Miller is describing is not "random".
    If Miller is correct, then evolution theory based on random mutations is incorrect.

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  27. http://en.wikipedia.org/wiki/Adaptive_mutation
    "The similarity suggests that the adaptive mutations may be an output of activation in the stressed cell of a special survival strategy for quick adaptation to the stressful environment. This strategy that is also referred as the mutator phenotype"

    In order that there be no misunderstanding, we are talking about "adaptive mutations'.
    The adaptive mutations according to Miller are examples of "signal detection 'hard-wired' to a response."

    As I have said - if that is the case, then evolution theory based on random mutations is incorrect.

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  28. Evolutionary theory is not based entirely on random mutations as you doubtless know, tiresome, disingenuous troll.

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  29. When people ramp up the insults like jaxkayaker, you know that I have hit a nerve.

    If Miller is correct (and I think he is) then the changes that occur in adaptive mutation are not random.
    That is the issue.

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  30. Miller posted:
    "Stressed cells respond to stress, just as cells move towards food or away from danger. That's not intelligence; that is signal detection 'hard-wired' to a response."

    Miller posted this in the context of the discussion of adaptive mutation. As if the changes in adaptive mutation were an example of "signal detection 'hard-wired' to a response."

    I did not correct him at the time but the changes we see in adaptive mutation are not an example of signal detection 'hard-wired' to a response.

    Think about the example I gave of the person in the locked room. His actions are not hard wired to a response.
    That is not the correct picture.
    His actions are a form of intelligent, directed, creative trial and error.

    That is a better model for what we see in adaptive mutation.

    It is not random, but neither is it "hard wired".

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  31. Schenck said...

    "What would it matter if the Central Dogma was violated anyway?"

    Very good question. As "The Principle of Recursive Genome Function" quotes Crick on this very issue:

    Crick FHC. Central dogma of molecular biology. Nature. 1970;227:561-563.

    "If it were shown that information could flow from proteins to nucleic acids, he said, then such a finding would “shake the whole intellectual basis of molecular biology”"


    Indeed, Crick was dead wrong with his Dogma, but right on target when he realized that once it is proven wrong, it is a game changer. Now we know that proteins (e.g. methyl transferase) are capable of changing sequence information of DNA (e.g. the retrieval of DNA sequence information due to methylation). Why is it a game-changer? Because the DNA>RNA>PROTEIN obsolete model is an "open loop", while the PROTEIN>DNA hitherto missing link makes genome function recursive. Abstract concepts may be somewhat hard to understand, but when algorithms of recursion, e.g. fractal iteration are no longer blocked by dogmatic minds, software-enabling algorithms make genome analytics an entirely new science, technology and business. Moreover, the obsolete "open loop" model implies the philosophy that "Your Genome is your Destiny" - while The Principle of Recursive Genome Function forever alters the gloomy philosophy; proteins altering DNA sequence (retrieval) information mean that "Your Genome is NOT your Destiny".

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  32. "Now we know that proteins (e.g. methyl transferase) are capable of changing sequence information of DNA (e.g. the retrieval of DNA sequence information due to methylation)."

    Methylation of DNA bases does not change the sequence of DNA bases. Crick said that the central dogma (poor word choice on his part) forbade transfer of sequential information (i.e. residue to residue, in some ratio, not necessarily 1:1). Methylation doesn't do that.

    "When people ramp up the insults like jaxkayaker, you know that I have hit a nerve."

    You have a very low bar for what is considered an insult.

    "If Miller is correct (and I think he is) then the changes that occur in adaptive mutation are not random.
    That is the issue."

    Oh, the old moving the goalposts trick. The appearance of new mutations occurs randomly, as far as we can tell. The change in frequency of occurrence of a mutation in the gene pool of a population may be random in some cases (e.g. drift, mutation) and nonrandom in other cases (e.g. selection). As I already said, evolutionary theory doesn't rely wholly on randomness, and your assertions to the contrary are a strawman.

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  33. "The appearance of new mutations occurs randomly, as far as we can tell."
    As far as you can tell. For you that is a matter of fundamental faith.

    There is a better model for what we see in adaptive mutation.

    It is not random, but neither is it "hard wired".

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  34. ""The appearance of new mutations occurs randomly, as far as we can tell."
    As far as you can tell. For you that is a matter of fundamental faith."

    No, it's based on evidence from observation and experimentation. You make a claim for an intelligent designer for which no evidence exists. You claim a designer exists, but provide no evidence to back up said claim. Adherents of intelligent design "theory" repeat the same claims over and over which are either outright false and have been disproven or for which no evidence exists. That is what makes them (e.g. you) tiresome and disingenuous.

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  35. One of the Anonymi said that natural genetic engineering is not random, and Shapiro also says that it is nonrandom, but as far as I can tell, Shapiro may just mean that it is not uniformly or randomly activated, but activated in response to stress. It is still random with respect to outcomes. It could be modelled within the standard evolutionary framework as a larger-than-normal, time-varying mutation rate (with alleles as the unit of analysis, and with the meaning of "mutation" expanded to mean not just point mutations but any kinds of reorganization of the allele's sequence). This does not seem terribly controversial, and has no relevance to the argument over Intelligent design (as the genetic engineering mechanisms themselves can be products of evolution).

    In fact, an increase in the effective mutation rate weakens the "argument" for design, which is often based on the idea that mutations (especially beneficial ones) are too rare to explain the observed diversity of life.

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  36. I should say that I still have not been able to see Shapiro's book, so maybe he does say that the genetic engineering is "directed".

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  37. Dear Anonymous, please learn what "random mutation" means before attacking established ideas, otherwise you just make yourself look like a fool.

    If "Adaptive evolution" was able to predict a novel future need and make specific mutations in order to adapt to that need, that really would be non-random mutation. All the evidence strongly indicates that the mutation rate increases in such a stress response but the mutations themselves are still random. (Note that "random" and "uniform" are not the same thing and we can still have "hotspots" in a random system. The important aspect is that the system does not choose which spot (hot or otherwise) to mutate.) Most of the cells with the "adaptive evolution" mutator phenotype actually get riddled with bad mutations and die. This is not an "intelligent" response.

    There are indeed examples of non-random genetic change in response to recurring situations. We call these "genetic switches" and they usually involve recombination, similar to that promoted by the transposable elements that Shapiro works on. Indeed, such non-random switches may have evolved from a random "mutator" response, and we can model this.

    None of this is new nor does it violate any of the underlying basics of evolution. Truth in science is not found by word-play and debate, it is found by evidence and experimentation. If you try to re-define "random", "mutation" or the importance of either to evolution, you do nothing but highlight your own ignorance, I'm afraid. If you don't understand these things, please ask - there are many here who would happily explain them to you.

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  38. Shapiro/Anonymous aside, Prof Moran makes a very important point about the teaching of the Central Dogma. I know that I am not clear in making the distinction when I teach protein evolution to undergraduates, and I am not sure whether the lecturers actually covering transcription and translation are, either. Although not excusing the erection of straw men for destruction (or the confusion of random and uniform), I think we all have to accept a bit of the responsibility for the confusion over the term. It is not hard to see why Creationists and others might give evolution a hard time if they see "The Central Dogma" still being supported by scientists when what they think (and some textbooks (eek!) say) is the central dogma is so clearly wrong, and has been for years.

    So, thank you Larry for drawing attention to this Central Dogma definition violation; I, for one, am inspired to be a bit more careful in future as a result.

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  39. @Anon

    His actions are a form of intelligent, directed, creative trial and error.

    That is a better model for what we see in adaptive mutation.

    It is not random, but neither is it "hard wired".


    You seem to confuse the multiple meanings of words like "adapt" and "random".

    Scientists have a choice when they require a word for a phenomenon. They can either use an existing one, thereby adding a definition to a word which already may have more than one. Or they can create a new word, thereby alienating the non-specialist in a welter of geschtumpengibberinity. It can be confusing, but it helps to understand the source of that confusion, rather than exploit it.

    Individual organisms adapt Sense 1. This boils down to environmental cues being picked up by the products of one or more genes, and a response of one or more genes or gene products ensues. It is nonrandom in the sense that the input signal does not just produce any old response. But it's hardly intelligent.

    Populations adapt Sense 2. This means that selection eliminates some variants and concentrates others, and the population is enriched in the qualities that better fit the circumstances. This is a random process even when biased, in the sense that it is stochastic - probabilistic. Intelligent? Well, it kind of is, in a strictly non-cognitive sense. But that's the very process you are saying can't do what intelligent design can.

    The origin of variants in Adaptation Sense 2 is mutation, however caused. These are random (nondirectional wrt the future), random (probabilistic) and nonrandom (not all equally probable), all at once.

    Now, when we say that a stress-linked mutator gene causes an elevated mutation rate, this is an Adaptation Sense 1 (debatably). Stress is detected by gene products, and the 'response' (which may be a by-product of some other response) is an elevated mutation rate. But the mutations produced are the same mixture of good and bad as those from any other cause.

    The mutations feed into the process of Adaptation Sense 2 - Natural Selection, with unavoidable Drift. Successful organismal adaptive responses - signal-response couplings - arise from this process of population adaptation - Adaptation Sense 2 produces Adaptable organisms Sense 1; they don't produce themselves.

    There is also scope for non-stress-linked mutator genes - they are not associated with any cellular signal-response mechanism, but simply find themselves attached to fitter phenotypes in certain evolutionary scenarios, and spread by that means.

    To summarise, genetically-initiated increase in mutation rate is a nonrandom (directional) response resulting in an elevated rate of random, nonrandom but random (stochastic, nonequiprobable but undirected) mutations that feed into the random (stochastic) process of population sampling that contains both Drift (random) and Selective (nonrandom) elements.

    You're welcome.

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  40. cabbagesofdoom, please learn what "trial and error" means, otherwise you just make yourself look like a fool.

    If you don't understand this, please ask - I am here and would happily explain it to you.

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  41. Allan Miller.
    You seem to be confused about the meaning of a phrase like "intelligent, directed, creative trial and error."

    I am happy to help you.
    You're welcome.

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  42. Hello Lou Jost.
    It will be helpful if you realize that the "natural genetic engineering" that Shapiro is documenting, and publishing about, relates to adaptation and not the origin of new species.

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  43. Anonymous writes:

    Here is an analogy.

    Imagine a person in a locked room. He begins to take logical actions to find a way out. He looks for a door, a trap door, a hidden opening, a hammer to break a hole with etc. He steps up his activities.

    Makes sense.

    But he does not just step up activity in general. He does not start cleaning his fingernails or tapping his left foot or humming a tune or reading a fiction novel etc.

    His increased activity is put into intelligent activity related to the problem at hand.

    Is this not what stressed cells do?

    No, it is not what they do. What they do is exactly what you described as an example that would contradict what you are saying: They "just step up activity" (mutation) "in general." The activity (mutation) is *not* related to the problem at hand.

    Shapiro implies differently, but even the people who did the research from which Shapiro draws his arguments no longer agree with him here. They saw too many research results to the contrary. Lenski's experiments are one example. Know about those?

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  44. jaxkayaker quotes me...
    "Now we know that proteins (e.g. methyl transferase) are capable of changing sequence information of DNA (e.g. the retrieval of DNA sequence information due to methylation)."

    jaxkayaker said...

    Methylation of DNA bases does not change the sequence of DNA bases.

    ---

    One can clearly change sequence information without changing the sequence. (Methylation does change the accessible sequence information). My thesis is based on the clarification that a "formation of A,C,T,G bases" (a "sequence") should not remain confused with the "sequence information", for the simple reason that neither Schrödinger (1944) nor Crick (1953) defined how a DNA sequence codes (the hitherto also undefined elsewhere but in FractoGene) biological information; an algorithm of governing physiological growth (such that we'll also understand pathology, such as uncontrolled growth, like cancer). Indeed, that is the most cardinal question left for for postmodern genomics. Just as Crick was very improper with his use of the Latin word "Dogma" (he failed school because of Latin) is is also almost unthinkable that he meant "sequence information" according to Shannon's definition of 1 bit information (as the half of the inverse of a probability of 1/2). In another comment elsewhere in this blog I recalled the simple metaphor that making the directory of a computer OS unreadable renders every single bit of the memory of the computer devoid of information for the OS user - though the "sequence" of zero and one bits on e.g. the hard disk remain there.

    I don't think anyone has a problem here with the fact that methylation (and chromatin modulation) can render a formation of bases (a sequence) unreadable. The Principle of Recursive Genome Function (popularized in YouTube, see particularly at min. 30:00)shows how fractal iterative recursion from PROTEINS to DNA relies on rendering the perused auxiliary (formerly "Junk") DNA sequences unreadable upon perusal. Recursion (the algorithm of "growth") must be bounded - this is how aberrant methylation and chromatin modulation (e.g. if already perused instructions are not cancelled) result in runaway, uncontrolled DNA>RNA>PROTEIN>DNA>RNA>PROTEIN... growth processes (often collectively called "cancer"). Our role here is not to chew on mistaken Dogmas in 1956 (or 1972) or lack of proper definitions at a time when genome informatics (just after the seminal but not elaborated essay by Schrödinger in 1944), especially not by simply (blindly) borrow crucial definitions in an utterly confusing manner from other disciplines (e.g. from Claude Shannon in 1948, "A Mathematical Theory of Communication".) Our role was defined by Crick (1970) when he (correctly) anticipated a time when "the intellectual foundations would be shaken", or by Collins (2007, upon concluding ENCODE; "the community of scientists will have to re-think long-held beliefs"). I am simply following up on their advice and quoting McCulloch when biology had to struggle with embracing the concept abstract to them, though very familiar in control theory as "feedback" (Cybernetics, coined by Wiener), "Don't bite my finger - look where I am pointing".

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  45. @Anon: Yes, please explain what you think "trial and error" means, how it is "intelligent", and how you think bacteria are doing so? You do realise, I hope, that a mutator phenotype is an impairment of the usual DNA repair mechanisms? The bacteria are not actively mutating themselves, they are just less able to repair the damage that is happening anyway and so more mutations result. "Error" in this case of "trial and error" is usually death for the individual concerned - not very intelligent, just random variation, filtered through selection. It only works because the population is big.

    You still don't seem to understand the random thing, even though at least two of us here have explained it. Which bit is the sticking point for you?

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  46. Latest Anonymous: Adaptation to a changing environment is one of the mechanisms for generating new species. Adaptation (plus genetic drift) is why we don't look like our chimp-like ancestors, and why we are not considered conspecific with them.

    If undirected natural genetic engineering makes this happen faster than traditional point-mutation, it further weakens the probability arguments used by IDers.

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  47. cabbagesofdoom, you still don't seem to understand the trial and error thing, even though I have explained it. What is the sticking point for you?

    ReplyDelete
  48. Lou Jost, adaptation to a changing environment is not one of the mechanisms for generating new species.

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  49. Anonymous, of course it is. A lineage that adapts to a changing environment will often change over time until it would no longer be considered conspecific with its ancestor. When humans and chimps diverged, the lineage that turned into us did not start out looking like us. Our morphology adapted to bipedalism, running, hunting, etc. We are no longer the same species as our older ancestors. The same thing is apparent in other lineages.

    If you think this is not so, please explain.

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  50. Lou Jost, you might find this helpful:
    http://www.allbusiness.com/science-technology/life-forms-mammals-primates/14093863-1.html

    We can discuss if you wish.

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  51. Not to point out the obvious, but since impairment of cellular processes is expected in response to environmental stress how can this even be used as evidence of cellular 'intelligence' unless the mutations were being selectively directed at a particular gene locus? An idea for which there is little empirical support.

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  52. Boojum, when you say there is little empirical support, that implies that you are aware of some empirical support.
    Could you give us link(s) for that empirical support material please?

    ReplyDelete
  53. I think it was entertained as a possibility by John Cairns back in 1988 however it was quickly ruled out as he expanded on his original results.

    ReplyDelete
  54. So the big question is, do the various commenters here have more patience than the anonymous troll has stupid ?

    I think we know what the answer to that is.

    Speaking of conspiracy theories, I visited the Pellionisz web site after demangling the link. I'm not competent to comment on the science aspect but I get the sense that what we are seeing here is someone on the fringes of current thinking in genomic science.

    I appreciate the fact that Pellionisz sequestered himself away for 15 years before gifting the world with his paradigm shattering discoveries, but I wonder if he should have waited another 15 years or so.

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  55. Anonymous, that was an interesting article, but it has nothing to do with my point. The article discusses the causes of lineage divergence. My comment and example referred to changes in a single lineage over time, without divergence. Most species transform themselves over time by adaptation and drift, so that they are not conspecific with their own distant ancestors. Human evolution provides a good example. If you disgree, please argue against this point.

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  56. Lou Jost, the article describes Pagel's work that shows that species do not appear as a result of adaptations.
    "To Pagel, the implications for speciation are clear: "It isn't the accumulation of events that causes a speciation, it's single, rare events falling out of the sky, so to speak. Speciation becomes an arbitrary, happy accident when one of these events happens to you."

    ReplyDelete
  57. Also
    http://www.allbusiness.com/science-technology/life-forms-mammals-primates/14093863-1.html
    "The key point emerging from the statistical evidence, Pagel stresses, is that the trigger for speciation must be some single, sharp kick of fate that is, in an evolutionary sense, unpredictable. "We're not saying that natural selection is wrong, that Darwin got it wrong," Pagel adds. Once one species has split into two, natural selection will presumably adapt each to the particular conditions it experiences. The point is that this adaptation follows as a consequence of speciation, rather than contributing as a cause."

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  58. Pagel was talking only about lineage divergences ("speciation events" when a lineage divides into two). You are avoiding my point, which is that a single lineage (even if it never diverges) changes over time due to adaptation and drift, so that after enough time passes, it is not conspecific with its ancestor. I have repeated this three or four times for you, but you still have not addressed it, except to say that I am wrong. If you have reasons for your opinion, give them.

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  59. Lou Jost, I know this topic exceptionally well and it is an interesting one.
    In your vision of adaptation does the lineage evolve into a different species?
    If so, what Pagel is saying is completely relevant.
    He is talking about your single lineage scenario.

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  60. He is talking about lineage divergence--his closing example of the two kinds of monkeys that live sympatrically is an example of lineage divergence. He does not discuss the difference between one of those monkeys today and the ancestor of that monkey several million years ago.

    Do you claim that my example of human evolution is not a case of adaptation? Or do you think that we are conspecific with our ancestors of 5-7 millions of years ago?

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  61. Lou Jost, let's see if we can come to an understanding on this fascinating topic.
    In your vision of the single lineage I assume you are visualizing a particular species evolving over time into a different species.
    Is that what you are talking about?
    I think that is what you are talking about and I have no problem with that.
    In that case there is a speciation event. There is a new species. Do we understand that the same?

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  62. I agree speciation is a fascinating topic; I work on it a lot. Yes, your paraphrasing of my point is right, though with one correction---there is no identifiable speciation event, but rather a continuum. The initial form and the final form are too different to be conspecific, but there is not a precise moment when one form changes to another, as most evolution is gradual.

    So you agree that this kind of speciation often involves adaptation?

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  63. In order to save time, I can say with certainty that you are talking about a situation where one species evolves into another.
    I say that with certainty because you have said they are NOT "conspecific".
    http://en.wikipedia.org/wiki/Conspecificity
    "Two or more individual organisms, populations, or taxa are conspecific if they belong to the same species."

    So you are talking about a situation in a single lineage of one species evolving into a different species.

    Pagel is talking about any speciation event. In the example of the monkeys at the end he does not say "sympatric" or "single lineage" as you have done.
    What he does say clearly is:
    "The point is that this adaptation follows as a consequence of speciation, rather than contributing as a cause."

    He is clearly saying that adaptations are not the cause of any speciation events.

    As the article clearly says:
    "To Pagel, the implications for speciation are clear: "It isn't the accumulation of events that causes a speciation, it's single, rare events falling out of the sky, so to speak. Speciation becomes an arbitrary, happy accident when one of these events happens to you."
    __________________
    The whole article supports that and his DNA supports that.

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  64. We have to realize that Pagel's DNA analysis leads to a quite new and different view of "evolution".
    As he says this is "a disquieting one for evolutionary biologists".
    New species do not appear as the effect of a series of adaptations.
    His data show that the "trigger for speciation must be some single, sharp kick of fate".
    "The notion that the formation of a new species has little to do with adaptation sits uncomfortably with fundamental ideas about evolution."

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  65. Anonymous: You say "I can say with certainty that you are talking about a situation where one species evolves into another." Of course!! I directly said that.

    Pagels is talking only about speciation events as splitting of lineages. The temporal distribution of those splits is the statistical evidence he analyzed. Nothing is said about the kind of speciation I described, which does not require lineage divergence.

    Please answer my question--do you think that the changes in our own lineage (adaptation to bipedalism, etc) are accidents and not adaptations? I don't deny that some changes over time are due to drift, but others clearly involve adaptation.


    I am pointing out that another kind of speciation is

    But you are misreading Pagel's article

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  66. Notice the timing of the posts. I posted mine just as you were posting yours.

    If you wish to think that I am misreading Pagel's article there is not much more to say.
    I would suggest however that you are making your assertions simply because you do not like the conclusions that Pagel comes to.

    In answer to your question, I would say that the changes in our own lineage (adaptation to bipedalism, etc) are the effect of the intelligence of NATURE.
    What I am saying is completely consistent with (and supported by) Shapiro's work and Pagel's work.

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  67. No, I really don't have any problem with Pagels' conclusion (though I don't think it is completely demonstrated).

    But you really have misread Pagel's article. If you think I am wrong about that, you should be able to show me where he deals with single-lineage changes. But the data he is working with are the timings of lineage divergences. Therefore his conclusions are about the causes of these lineage divergences. He never talks about what happens within a single, non-diverging lineage. If you think I am wrong about that, show me.

    I do not know what you are talking about when you say our adaptations to bipedalism are due to "the intelligence of nature". I also cannot imagine why you would say something like that, when there are obvious known mechanisms that allow us to explain these adaptations.

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  68. Allan Miller.
    You seem to be confused about the meaning of a phrase like "intelligent, directed, creative trial and error."

    I am happy to help you.
    You're welcome.


    Confused? Well, I am confused as to why you think those terms - other than "trial and error", which is what all evolution boils down to - remotely relevant to a process of mutagenesis. But no, don't bother; I'll stay confused, ta.

    Show me you now understand the proper usage of "random" - the head of a long list of terms you abuse - and I might submit to some semantic education from you. Till then, toodles!

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  69. @Anon, "cabbagesofdoom, you still don't seem to understand the trial and error thing, even though I have explained it. What is the sticking point for you?"

    Ah, the old ignore-all-the-questions-and-parrot-back-fragments trick. You are managing to slide further down in my estimations, which is a big achievement, given your initial position following your opening post.

    I understand trial-and-error very well. It the refuge to which one goes for a solution when intelligence has failed to identify a solution. It is the path that "blind" evolution takes because it has neither intelligence nor foresight guiding it. Error in this case is death. A lot of death. It makes perfect sense for evolution to use trial-and-error through Natural Selection - indeed, it is currently impossible to formulate a scenario that fits the observed data in which it doesn't happen. (There's a challenged for you if you are bored.) It is not the work of an Intelligent Designer unless they are (a) of very limited intelligence, and/or (b) incredibly cruel.

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  70. @Anonymous. I don't have time to read the article yet but if your quote is reflective, I don't need to, so I will just address that.

    - "To Pagel, the implications for speciation are clear: "It isn't the accumulation of events that causes a speciation, it's single, rare events falling out of the sky, so to speak. Speciation becomes an arbitrary, happy accident when one of these events happens to you."

    This is, quite simply, hogwash. Apart from very rare situations (e.g. Polyploidy), speciation is not a sudden event at all. It happens VERY slowly, with a very long period of potential hybridisation. The species concept itself is not truly a biological reality, it is an artefact of human classification. It is possible when all the intermediate individuals have disappeared (e.g. LONG separation) but there is (most of the time) no literal transition from one species to another.

    Take lions and tigers. When did they become separate species? They can still hybridise and may even be able to have fertile offspring. (Interbreeding doesn't happen enough to be sure.) Look up Ring Species. Look up sperm competition in abalone - it is often selection on sexual characters that finally prevents hybridisation but only once it is disadvantageous to hybridise. In other scenarios, "hybrid vigour" can even slow down the speciation process - indeed, current evidence suggests that hybridisation and hybrid vigour may have played an important role in the spread of modern humans out of Africa. (I don't have the link handy for that someone, perhaps someone else can oblige?)

    Just because one person has a crazy idea and you like it, I'm afraid that doesn't make it true. It also has to match reality. The quote you quoted quite simply does not. (Unless it is talking about a very limited and specific subset of speciation that does not come remotely close to being universal.)

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  71. @Anonymous. Just had a quick skim of the article. It is indeed interesting but I don't think it's that revolutionary. It just means that speciation does not happen at a constant rate - it is not driven by neutral divergence through drift.

    It is well established that selection and adaptation do not tick along at a constant rate. Rare, sudden events - generally outside the organism - generate adaptive sweeps. (Think ice ages and the like.) The fact is, you generally need a new niche to open up in order to promote divergence and diversity. This happens erratically, such as populating a new island, or a natural disaster wiping out existing populations/species. We see this in the fossil record too - look up Punctuated Equilibria. These ideas are old and entirely consistent with standard evolutionary observations and theories.

    Sadly, I think this is another case of someone trying to stir up revolution and controversy from an interesting but wholly explicable result. I will read the original paper when I get the chance, though. And if you can point me in the direction of something that explicitly states why the results are inconsistent with temporal variation in selective pressures, I will take your conjecture more seriously. If not, I think it's time to stop flogging this particular horse, for it appears to be dead.

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  72. PS. Also, don't confuse the rate of individual speciation events with the frequency/rate of multiple speciation events. The article is only about the latter - the expected/observed interval between speciation. (The article is massively over-hyping the impact of this work. It incorrectly implies that separation equals speciation thus speciation comes first. This is not true. If the barrier is removed before adaptation and divergence have occurred, the two populations will interbreed and remain a single species. Reading more of the article, it looks like irresponsible science journalism rather than a dodgy original paper but I still need to read the original.)

    ReplyDelete
  73. Boojum writes:

    I think it [directed mutation] was entertained as a possibility by John Cairns back in 1988 however it was quickly ruled out as he expanded on his original results.

    Yep, leaving Shapiro as pretty much the only "jockey" of any academic repute flogging this particular dead horse.

    Anonymous is a bit (OK, more than a bit) behind the times, and is unfamiliar with the past couple of decades of research work that have shown elevated levels of mutation in response to stress are *not* directed toward particular loci/results. For instance, he's plainly unfamiliar with Lenski's results (which are quite famous, so there's no real excuse for Anonymous' unfamiliarity), which really prove beyond serious doubt that there is no increased efficiency of mutation in response to stress, such as would result from directed mutation, intelligent direction, or both.

    ReplyDelete
  74. A good example of a 'mutator phenotype' is provided by cancer - gross elevation of mutations is diagnostic of a number of cancers. Whether that elevated rate is a cause or effect of the cancer is perhaps unclear - but if Nature is intelligently directing elevated mutation levels here, I wish He/She would f*** off!

    These are somatic cells, of course; the kind of 'directed evolution' that might lead to those Creationist favourites Human Intelligence or Bipedalism for example would first have to target the right gene in the germ line (and DNA polymerase or DSB repair haven't got a damned clue what their target actually does when expressed, any more than a computer disk copy process has any way of 'knowing' whether a particular file is a virus or a picture of a horse) and then make sure that this was the progenitor of the gamete that, out of the billions that eventually get squirted out, actually hit the syngamy jackpot. And somehow survived and prospered against the rub of the selective green, as it was escorted across the Maladaptive Slough to the sunlit uplands of eventual adaptive advantage.

    ReplyDelete
  75. Anonymous, like I said, I don't have a problem with Pagel's statistical conclusion. Lineage splitting will often be the result of rare long-distance dispersal events, like a South American finch reaching the Galapagos. If these dispersal events were not rare, there would be interchange of genes, and speciation would be unlikely.

    However, in almost every case where dispersal has led to a new species, that species shows adaptation to its new environment. Pagel's article says nothing about what happens to a single lineage over time, but it is clear that most lineages adapt to their environment. They can do this either by accumulating favorable point mutations or by rearrangements of the genome through "natural genetic engineering", if you like. There is no evidence that these are goal-oriented. They are just ways of generating variation, on which natural selection (or drift) acts.

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  76. The reason I said this topic is fascinating, is because the root of the issue goes deep.
    The root of the problem is the misconceived idea that lineages split into two species.
    That idea is never analyzed or questioned. Upon analysis it shows itself to be misguided.
    The best way to understand that is to have someone give a purported example. We can then analyze it.
    I don't mean a hypothetical one. I mean an actual one.

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  77. The starting question is - do people visualize lineage divergence as the appearance of two new species or the appearance of one new species and the continuation of the original species?

    ReplyDelete
  78. Anonymous writes:

    The root of the problem is the misconceived idea that lineages split into two species.

    That idea is never analyzed or questioned. Upon analysis it shows itself to be misguided.

    Yet another self-contradiction. You wasted ~100 comments on a risible "theory" about where dogs and cats came from. Now you say lineages never split. If that were true, none of your notions about what happened to dog and cat lineages could have occurred.

    I don't know whether you don't know enough to realize the fact of the contradiction; realize it but think we won't; or know we will realize it, and don't care as long as you gain what passes for human interaction through comments on this website.

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  79. Anonymous: "The reason I said this topic is fascinating, is because the root of the issue goes deep.
    The root of the problem is the misconceived idea that lineages split into two species."

    This is only misconceived if you add the word "only": "lineages split into only two species." Even this is a "problem", why? One-to-many speciation events are not precluded by evolutionary theory and I suspect they happen, particularly upon colonisation of a new island etc.

    "That idea is never analyzed or questioned."

    Well, what idea? That lineages split into multiple species? This is now an iron-clad observation, analysed but not "questioned" in the same way that we do not "question" whether the Earth is flat. The one-to-two or one-to-many question is analysed and questioned regularly. The "Tree of Life" Hypothesis itself is routinely examined.

    "The best way to understand that is to have someone give a purported example."

    OK. Let's look at primates. Show me any evidence to begin with that humans, chimps and gorillas did not split from a single ancestral lineage. Critique, if you like, the extensive molecular evidence that indicates quite strongly that humans and chimps share a more recent common ancestor than either do with gorillas. Or, is your point that the human-chimp ancestor split into human ancestor, chimp ancestor and other (now extinct) lineages at the same time? If so, I don't get the "problem". Might have happened. Totally consistent with the evidence and evolutionary theory.

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  80. Anonymous: "The starting question is - do people visualize lineage divergence as the appearance of two new species or the appearance of one new species and the continuation of the original species?"

    This question is semantic and essentially meaningless. What does a "new" species even mean? In this context - evolutionary history of a lineage - is an arbitrary division made by taxonomists. You might as well ask when a "short" child grows into a "tall" child, or when a "young" man becomes an "old" man. It is a continuum with man-made divisions, placed for a purpose but only meaningful within the realm of that purpose.

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  81. cabbagesofdoom's posts are beginning to show the problems inherent in this topic.

    I am still hoping that someone will give an actual example including actual taxa.
    That will be very helpful.

    ReplyDelete
  82. The starting question is - do people visualize lineage divergence as the appearance of two new species or the appearance of one new species and the continuation of the original species?

    ReplyDelete
  83. "cabbagesofdoom's posts are beginning to show the problems inherent in this topic."

    Or, more accurately, the lack of problems other than those you are trying to invent through willful, or accidental, failure to understand fundamental biological concepts. Have fun playing your word games but don't be surprised if no one takes you seriously!

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  84. Anonymous, take the Galapagos finches, descended from a mainland Latin American finch. The mainland lineage split at the moment that the first finches made it to the Galapagos. If this was a very rare event, gene flow between mainland and island stopped at that moment. Molecular clocks would reveal that date (roughly). But initially, the finches of mainland and island would be morphologically identical. Over time, they would diverge enough to be considered separate species, and eventually they would not be able to interbreed. Because the island is quite different from the mainland, the island form would initially do most of the changing and adapting, as it is the form exposed to new selective forces. These forces and their genetic and morphological consequences have been studied in detail by the Grants, who have shown that the process continues even today.

    The mainland finch probably hasn't changed its niche. The mainland environment has changed over time, particularly during glacial times, so we can expect that even the mainland form may have diverged significantly from the form that existed back when the Galapagos were colonized by them. Drift may also cause them to diverge from their ancestral form. So if we compared today's finch with finches from that time, we might see enough differentiation to consider them as different species. But there could just as well be no important changes in the mainland finch over this timeframe, so in that case the lineage divergence only led to one new species (or actually a whole bunch of species, as the Galapagos finches radiated onto different islands).

    So the answer to your question is "it depends". And it is not really a fundamental question.

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  85. cabbagesofdoom seems to want to give up on analyzing this topic.
    Anyone else?
    It really is quite interesting.

    Do people visualize lineage divergence as the appearance of two new species or the appearance of one new species and the continuation of the original species?

    and

    I am still hoping that someone will give an actual example including actual taxa.
    That will be very helpful.

    ReplyDelete
  86. Lou Jost posted:
    "But initially, the finches of mainland and island would be morphologically identical. Over time, they would diverge enough to be considered separate species, and eventually they would not be able to interbreed."

    Now we are making progress.
    So the initial split into two groups is not a speciation event. Right?

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  87. The reason I say that the initial split into two groups is not a speciation event is because you have acknowledged that the two groups are
    morphologically identical.

    ReplyDelete
  88. As a sidenote:
    Later on, I want to analyze the idea of what constitutes a "species" but we can take that up later.

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  89. The reason I say that the initial split into two groups is not a speciation event is because you have acknowledged that the two groups are
    morphologically identical.

    To continue:
    If the island group evolves into a new species, it must be a single lineage type of evolution based on adaptation.
    Right?

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  90. Anonymous said...on Monday, August 29, 2011 11:13:00 AM

    I am still hoping that someone will give an actual example including actual taxa.
    That will be very helpful.


    Why don't you give yourself any examples? That will be very helpful, because it would show whether Anonymous has any grasp of biology whatsoever.

    I'll give Anonymous species' names only. If Anoonymous cannot find what these cases are about, fine, Anonymous does not know its way in biology.
    Buteo galapagoensis
    Buteo swainsoni
    Felis silvestris

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  91. The island group evolving into a new species is no different than your standard single lineage evolution scenario.

    The total scenario of some birds making their way to the island and others remaining on the mainland - adds no different process than the single lineage scenario we are familiar with.
    There is only one process of speciation.
    All speciation is through single lineage adaptation.
    When the whole thing is analyzed that is what we see.

    And if the mainland group evolves into a different species, that is again a single lineage evolution scenario based on adaptation.

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  92. "Do people visualize lineage divergence as the appearance of two new species or the appearance of one new species and the continuation of the original species?"

    Apparently, anonymous has never heard of cladogenesis and anagenesis. I recommend taking some biology courses which include evolutionary theory so that your knowledge is based on a bit more than one author pushing his particular point of view as the one true truth.

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  93. To continue.
    We have seen that there is only one speciation process and it is based on adaptation.

    Here are some variations on the theme.
    The island example is labelled "allopatric" speciation. As we have seen it adds NO new speciation process.

    The other possibilities are labelled "peripatric", "parapatric" and "sympatric" speciation.

    They add NO new speciation processes either.

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  94. I purposefully avoided the words "anagenesis" and "cladogenesis" since just adding new words does not always help.
    I have described the situations.
    Do you follow this so far?

    ReplyDelete
  95. cabbagesofdoom writes:

    Critique, if you like, the extensive molecular evidence that indicates quite strongly that humans and chimps share a more recent common ancestor than either do with gorillas.

    Ecch, don't bother. When genetic identities such as GULOP were raised, Anonymous refused to concede animals with the GULOP pseudogene obtained from dietary sources the nutrients that would have been provided via the action of the GULO gene.

    Or, to put it more simply, Anonymous refused to concede that the fact humans, gorillas and chimps are here today proves our ancestors didn't all die of starvation.

    Not much you can do with that sort of weapons-grade willful(?) ignorance.

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  96. "cabbagesofdoom seems to want to give up on analyzing this topic ... I am still hoping that someone will give an actual example including actual taxa."

    Oh, Anonymous, you do make me laugh! Yes, I give up. You can choose whether I have been over-awed by (a) your vast intellect, or (b) your expectation that someone will continue to engage with you when you ignore everything they say!

    I can see why you choose to remain Anonymous. You wouldn't want anyone building a shrine to you.

    For the sake of the original topic, though, if you are going to ramble on and on about some half-baked notion of speciation, could you please: (1) collect your thoughts into something coherent, (2) post them up somewhere else, and (3) direct us there to continue the "analysis". Prof Moran made a serious point in the original post and it is rather rude to hijack it with this drivel/startling insight.

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  97. As people know, Jud's posts are confused. I ignore them.
    But he does use one underhanded technique that does need to be exposed.
    He refers to other discussions and talks as if I have been shown to be wrong (or wrong headed). That is simply his spin on it.
    In fact the previous discussions did nothing of the kind. It is Jud's after-the-event spin.
    But this is not worth arguing about. I am just exposing it.

    I really do not intend to be sidetracked by this.

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  98. We have seen that there is only one speciation process and it is based on adaptation.
    Here are some variations on the theme.
    The island example is labelled "allopatric" speciation. As we have seen it adds NO new speciation process.
    The other possibilities are labelled "peripatric", "parapatric" and "sympatric" speciation.
    They add NO new speciation processes either.


    Does anyone disagree with this analysis so far?

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  99. "He refers to other discussions and talks as if I have been shown to be wrong (or wrong headed)."

    Perhaps if you stopped posting as "Anonymous", such confusions wouldn't happen? (It was obviously another Anonymous that keep getting called out for being wrong!)

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  100. @Jud: "Not much you can do with that sort of weapons-grade willful(?) ignorance."

    You can laugh, make a cup of tea, and then sit back to enjoy the Masterclass of Crazy. I'm only one Creationist cliche short of "Bingo!".

    ReplyDelete
  101. I have posted:
    We have seen that there is only one speciation process and it is based on adaptation.
    Here are some variations on the theme.
    The island example is labelled "allopatric" speciation. As we have seen it adds NO new speciation process.
    The other possibilities are labelled "peripatric", "parapatric" and "sympatric" speciation.
    They add NO new speciation processes either.

    Does anyone disagree with this analysis so far?

    As often happens, some people simply ignore the content of the discussion and wander off into insult and personal attack.
    Lou Jost was good enough to begin this analysis by presenting the mainland/island bird scenario.
    Perhaps we will have to wait for Lou Jost to return in order to have any further serious discussion of the line of analysis I have presented.

    ReplyDelete
  102. @Anonymous: OK, I can play for a little while. I disagree with your "analysis", so far. You have not described a "speciation process" nor even what you mean by "speciation".

    The general working definition of species is that two different species cannot interbreed and produce fertile offspring. As I have already said, and you have already ignored, this definition is arbitrary and artificial and phenomena like Ring Species do not fit this general mold, largely because they are in the process of speciating (or not - we don't know yet -) but have not yet completed that process.

    However, if we assume that you are talking about traditional non-interbreeding species then, no. This does not have to happen through adaptation. Reproductive incompatibility can occur through neutral evolution and genetic drift. (Do you know of these?)

    So, please back-track and:
    1. Define what you mean by speciation in this context.
    2. Be more explicit about what you mean by a "speciation process".

    While you are at it:

    3. Explain how geographical isolation (allopatric speciation) does not bring something different to the table compared to sympatric speciation. It does: speciation cannot occur by drift without a barrier to gene flow but can when there is such a barrier.

    If you can deign to grace us with an answer to all three of these, I will continue to play.

    ReplyDelete
  103. "This does not have to happen through adaptation. Reproductive incompatibility can occur through neutral evolution and genetic drift."

    When I said "adaptation" that was short form for the set of single lineage processes (such as neutral evolution and genetic drift).
    These are all processes within a single lineage. Correct?

    The point I am making is that there is not an additional process called "lineage divergence".
    There is just the single lineage process based on adaptations (drift ETC).

    ReplyDelete
  104. What the heck, I'll play along. Anon, the event that starts the speciation process is the initial colonization of the Galapagos. This is the date that will be identified by a molecular clock (and the one that will appear in calibrated phylogenetic trees). But immediately after that event, the Galapagos bird and the mainland bird are still the same species. Reproductive isolation (by distance in this case) is what allows the two lineages to go off in different directions and eventually evolve into distinct species. The lineages may diverge because of adaptation, or may diverge due to drift. Most often, both processes operate. Sometimes neither happen.

    While the instant that begins the speciation process can be identified, as mentioned above there is no exact moment when we can say that the two forms are now different species. There will be a large gray area. Eventually, though, once the forms become so different that they cannot interbreed even if juxtaposed, we can quite safely and unambiguously call them different species.

    ReplyDelete
  105. Anonymous said: "When I said "adaptation" that was short form for the set of single lineage processes (such as neutral evolution and genetic drift).
    These are all processes within a single lineage. Correct?"


    Then you should be more explicit, because Adaptation is a specific subset of evolutionary processes, referring only to the fixation of mutations through Natural Selection.


    "The point I am making is that there is not an additional process called "lineage divergence".
    There is just the single lineage process based on adaptations (drift ETC)."


    What do you even mean by this? As someone who works in molecular evolution this just reads as gobbledygook. It makes no sense. Perhaps you should clarify what you mean by a lineage. Even within evolutionary biology the term lineage can be fuzzy and mean different things in different contexts. When we talk about the divergence of lineages in evolutionary biology we generally are talking about the divergence of sub-populations (that were once part of a large single population) into distinct lineages/species.

    The only meta processes (on top of the molecular processes driving the genetic differentiation between populations) I can think about that people tend to talk about in terms of speciation are the ecological/geological processes that contribute.

    ReplyDelete
  106. This is where we started. Lou Jost posted:
    "But you really have misread Pagel's article. If you think I am wrong about that, you should be able to show me where he deals with single-lineage changes. But the data he is working with are the timings of lineage divergences. Therefore his conclusions are about the causes of these lineage divergences. He never talks about what happens within a single, non-diverging lineage.If you think I am wrong about that, show me."

    What I have shown is that there is a fundamental misconception underlying this.
    There is ONLY single line lineage.
    There is no other speciation process.
    If Pagel is talking about speciation (and he is) then his data is only about single lineage evolution - because there is ONLY single lineage evolution.

    There is not some other second speciation process. Lou Jost was talking as if there were two different processes.
    There aren't. There is just one.

    ReplyDelete
  107. Anon, the divergence of two lineages (populations) is an objective fact. As soon as two formerly-united populations are no longer interbreeding, their genetic codes at neutral loci will begin to diverge. This will happen even if there is no adaptation.

    "Adaptation" as used in biology does not generally include drift, as has been pointed out.

    ReplyDelete
  108. Anon--I posted my last answer while you were writing yours....will answer your new one shortly...

    ReplyDelete
  109. Pagel is talking about the timing of events such as the initial colonization of the Galapagos. As even you agree, that event did not immediately result in two distinct species, it set up the conditions under which adaptation and drift can lead to new species. I think Pagel's conclusions are only about the causes of these initial events, not about the processes that lead to later divergence.

    ReplyDelete
  110. "Pagel is talking about the timing of events such as the initial colonization of the Galapagos. As even you agree, that event did not immediately result in two distinct species, it set up the conditions under which adaptation and drift can lead to new species. I think Pagel's conclusions are only about the causes of these initial events, not about the processes that lead to later divergence."

    Pagel's data is just data about speciation. It is not based on any presumed timing of physical divergence events.
    You are the one who is focusing on physical diversions.
    Pagel's data is not based on that.

    His study is about speciation. And I have shown that speciation is only a single line process.

    And his study goes even further and shows that adaptation does not even explain speciation.

    Please take a moment to try and understand what I am getting at.

    ReplyDelete
  111. The reason it is difficult for people to grasp what I am saying is that I am presenting a completely new way of understanding "evolution".
    And Pagel's study which is based on actual real DNA evidence forces us to a completely different way of understanding "evolution".

    To understand this, you have to go right back to your fundamental assumptions and analyze them.

    ReplyDelete
  112. Anonymous writes:

    He refers to other discussions and talks as if I have been shown to be wrong (or wrong headed). That is simply his spin on it.
    In fact the previous discussions did nothing of the kind. It is Jud's after-the-event spin.


    Well, let's see. You've contradicted yourself several times, so one or both of your ideas must be wrong.

    For example, in your comments about the origin of dogs and cats, you theorized that various different orders and suborders were ancestral to families within a single order. In other words, you hypothesized that divergent groups became more closely related over time, which (as I noted in that thread) was the same as saying my children are more closely related to their cousins than I am to my siblings. It's of course fundamental that inheritance works the other way - diverges rather than converges over time - so yes, we can definitively say you've been shown to be wrong, and that can't be put down to my own "spin." Or do you contend that you are more closely related to your cousins than you are to your brothers and sisters?

    Then you said in this thread:

    The root of the problem is the misconceived idea that lineages split into two species. That idea is never analyzed or questioned. Upon analysis it shows itself to be misguided.

    This contradicts what you said all through the cats-and-dogs discussion, where you talked about various animals being ancestral to various other animals. This can't happen without various species turning into other species. So you've contradicted yourself, but in an absolute tour-de-force you've managed to be utterly wrong about both of your contradictory ideas - (1) Groups of living things become more closely related over time, and (2) lineages never split into two species.

    Again, clearly and definitively wrong, not just my say-so. Or do you contend saying some groups of animals are ancestral to others is *consistent* with lineages never splitting into two species?

    And then there is my old favorite, the refusal to acknowledge that animals with the GULOP pseudogene obtained vitamin C through their diets. You refused to acknowledge this because it would have meant conceding a common genetic ancestry in humans and apes.

    You argued against common ancestry in two ways: (1) You said GULOP in apes and humans was the result of convergent evolution. Note this contradicts your statement in this thread that lineages do not split into different species. (2) You refused to acknowledge that the current existence of apes and humans proves our ancestors must have been able to obtain vitamin C from their diets. Again, definitively wrong, not just my "spin." Or do you refuse to concede your existence is conclusive proof your parents didn't starve to death before you were born?

    ReplyDelete
  113. Tell me then, exactly what is Pagel's data? What was he analyzing? What units did it have?

    And do you deny that the chimp-like ancestors of humans adapted to their new niche through natural selection? If so, why?

    ReplyDelete
  114. And do you deny that Galapagos finches adapt to their environment? Even though you can actually see it happening now?

    ReplyDelete
  115. Hi Lou Jost.
    Take a look at:
    http://www.allbusiness.com/science-technology/life-forms-mammals-primates/14093863-1.html

    ReplyDelete
  116. "When I said "adaptation" that was short form for the set of single lineage processes (such as neutral evolution and genetic drift)."

    - Say "single lineage processes" then. Confusing adaptation and neutral processing is just confusing.

    "The reason it is difficult for people to grasp what I am saying is that I am presenting a completely new way of understanding "evolution"."

    - No. The reason it is difficult for people to grasp what you are saying is because you are misusing terms and failing to define what you actually mean. Then, when challenged, you just ignore the wisdom of people who clearly know a lot more about this.

    "And Pagel's study which is based on actual real DNA evidence forces us to a completely different way of understanding "evolution"."

    - No, it doesn't. Not even slightly.

    "What I have shown is that there is a fundamental misconception underlying this."

    - You have shown nothing, I'm afraid, except ignorance and bad manners. You have stated stuff, been corrected and then re-stated the same wrong stuff.

    "There is ONLY single line lineage.
    There is no other speciation process."

    - This, as DG said, "just reads as gobbledygook".

    By definition, a single lineage cannot diverge, for what is it diverging from? You need at least two lineages to have divergence. Lineages only exist in hindsight, when looking at history. For contemporary matters, as pointed out, you are talking about populations.

    Sorry, shouldn't be replying - you've not answered my three questions yet.

    ReplyDelete
  117. "And do you deny that Galapagos finches adapt to their environment? Even though you can actually see it happening now?"

    I have no argument with that. Adaptation is a single lineage process.
    Single lineage process was your helpful term.

    ReplyDelete
  118. "Hi Lou Jost.
    Take a look at:
    http://www.allbusiness.com/science-technology/life-forms-mammals-primates/14093863-1.html"

    - This is not the original data. It is a bad summary of the work and its implications. Stop being lazy and define your terms, your hypothesis, the analyses performed, what they show, and why. I have read this article and I am familiar with the data (being a molecular evolutionary biologist) and I can say without fear of contradiction (that is subsequently shown to be correct) that this is not a challenge to existing evolutionary ideas. If this is all you have, we should all stop now. Is this all you have?

    ReplyDelete
  119. cabbagesofdoom* if you wish to stop now, that is your choice.


    *Before you go, I do want to say that your name "cabbagesofdoom" is very cool.

    ReplyDelete
  120. Anonymous said... on Monday, August 29, 2011 12:27:00 PM

    We have seen that there is only one speciation process and it is based on adaptation.
    Here are some variations on the theme.
    The island example is labelled "allopatric" speciation. As we have seen it adds NO new speciation process.
    The other possibilities are labelled "peripatric", "parapatric" and "sympatric" speciation.
    They add NO new speciation processes either.


    Does anyone disagree with this analysis so far?


    Well, as there is no analysis in what Anonymous asserts, 'this analysis' cannot be agreed or disagreed on.

    ReplyDelete
  121. cabbagesofdoom said...
    Sorry, shouldn't be replying - you've not answered my three questions yet.

    Anonymous never answers questions, never explains, and never has the pluck to engage in any real argument.

    ReplyDelete
  122. Anonymous said...Monday, August 29, 2011 12:25:00 PM
    He (Jud) refers to other discussions and talks as if I have been shown to be wrong (or wrong headed). That is simply his spin on it.
    In fact the previous discussions did nothing of the kind.


    That is the uttermost thick statement by Anonymous given the wild ignorance Anonymous displayed about the fossil carnivores. Misreading Wikipedia was all Anonymous attempted.
    Anonumous wrong? Utterly wrong. Incorrigibly wrong. Never wanted to admit he/she/it hadn't a clue. All Anonymous can do is make wild assertions: he/she/it does not know what evidence is.

    ReplyDelete
  123. Anon, you already had given me that link. I was specifically asking what was the raw data Pagel analyzed? If you read the article at the link, you will note that he is analyzing the branch lengths of phylogenetic trees. In the case of Galapagos finches, the datum is the date of first colonization. We all agreed that at this date, both island and mainland forms were the same species. So Pagel's data is not speciation time. His analysis only applies to the dates at which isolation begins. This means his conclusions also only apply to those dates. His conclusion is that these kinds of events (eg the initial colonization of the Galapagos) were very rare. Big deal. And as you agreed that adaptation occurs in lineages and, along with drift, actually produces the morphological changes that turn one species into another, I really do not see your point about the importance of this.

    ReplyDelete
  124. Let's take one of the variations.

    Say there is a large group of creatures on a large plain.
    And let us say that a sympatric speciation process occurs.
    So within the plain, a subgroup evolves into a new species. (The remainder of the original group continues to survive.)
    The evolution of the subgroup is what we have been calling a single lineage speciation process.

    Pagel would count this as a speciation event. Where previously there was one species we now have two.

    Pagel's analysis of the data does not care how a new species came to be. Just that it did.

    And his analysis shows that:
    "It isn't the accumulation of events that causes a speciation, it's single, rare events falling out of the sky, so to speak."
    and
    "The key point emerging from the statistical evidence, Pagel stresses, is that the trigger for speciation must be some single, sharp kick of fate that is, in an evolutionary sense, unpredictable."
    and
    "The point is that this adaptation follows as a consequence of speciation, rather than contributing as a cause."

    So the sympatric speciation mentioned above, was not the result of adaptation, drift etc.

    This is a pretty significant finding.

    ReplyDelete
  125. Lou Jost posted:
    "So Pagel's data is not speciation time. His analysis only applies to the dates at which isolation begins."

    How in the world would the dates at which isolation begins be available? He could not possibly have that data. (The groups are still morphologically identical, as you pointed out).
    What he is actually analyzing is actual speciation data.

    http://www.allbusiness.com/science-technology/life-forms-mammals-primates/14093863-1.html
    "The team gleaned more than 130 DNA-based evolutionary trees from the published literature, ranging widely across plants, animals and fungi. After winnowing the list to exclude those of questionable accuracy, they ended up with a list of 101 trees, including various cats, bumblebees, hawks, roses and the like.

    Working with each tree separately, they measured the length between each successive speciation event, essentially chopping the tree into its component twigs at every fork. Then they counted up the number of twigs of each length, and looked to see what pattern this made. If speciation results from natural selection via many small changes, you would expect the branch lengths to fit a bell-shaped curve. This would take the form of either a normal curve if the incremental changes sum up to push the new species over some threshold of incompatibility, or the related lognormal curve if the changes multiply together, compounding one another to reach the threshold more quickly.

    To their surprise, neither of these curves fitted the data."

    ReplyDelete
  126. "The key point emerging from the statistical evidence, Pagel stresses, is that the trigger for speciation must be some single, sharp kick of fate that is, in an evolutionary sense, unpredictable."
    and
    "The point is that this adaptation follows as a consequence of speciation, rather than contributing as a cause."

    So the sympatric speciation mentioned above, was not the result of adaptation, drift etc.

    This is a pretty significant finding. "


    You are confusing the original cause of speciation (the "trigger for speciation") with the process. Please re-read my previous response to your posting of this article. Pagel's data simply shows that speciation does not occur at a constant, predicable rate. It says nothing about the nature of individual speciation events, just their temporal separation in evolutionary history. It is mildly interesting but not that new or significant, I'm afraid. We know that the environment (including other species in the ecological network) are not static in time, so we have no reason to expect that adaptation or speciation would occur at a constant rate. Quite the opposite, in fact. Far from surprising, I would have found it very surprising if Pagel did not find this result (or something qualitatively similar).

    It's all hype, I'm afraid. Sorry.

    ReplyDelete
  127. *Before you go, I do want to say that your name "cabbagesofdoom" is very cool.

    Well, you have a pretty snappy name as well.

    ReplyDelete
  128. For those who are not familiar with it, take note that cabbagesofdoom's post takes a very common form of response.

    The initial response to new significnt data is to argue that it is not so.
    Then when you have to accept the data, the next step is to downplay it and often to go even further and say it is what would have been predicted.

    I have seen this pattern many times. Elsewhere I even documented it precisely. (There is even a step after this one.)

    It seems valid but it is not.

    ReplyDelete
  129. http://www.allbusiness.com/science-technology/life-forms-mammals-primates/14093863-1.html
    "If speciation results from natural selection via many small changes, you would expect the branch lengths to fit a bell-shaped curve."
    "To their surprise, neither of these curves fitted the data."

    The issue is not the trigger.
    As the study shows:
    "The point is that this adaptation follows as a consequence of speciation, rather than contributing as a cause."

    ReplyDelete
  130. Pagel even gives it to you on a silver platter, and you don't understand:

    "... the trigger for speciation must be some single, sharp kick of fate that is, in an evolutionary sense, unpredictable..."

    He is talking about the isolating event, the initial colonization of the Galapagos in our example. And those are the events whose statistical distribution he is analzying.

    You ask how he can possibly know those dates. Well, that is what a calibrated phylogenetic tree is for. That is what Pagel analyzed. That is what molecular clocks let us figure out (with some significant uncertainty, of course). That is why, in my Galapagos example, I told you (several times) that the molecular clock was set to zero when the colonization happened, but that at this time the island and mainland forms were the same species.

    No biologist would expect to see speciation in your plains animal example, so it is hard to understand why you think it is a big deal for Pagel to say that such a scenario is unlikely.

    I have to do some work, no more responses for a while....

    ReplyDelete
  131. "For those who are not familiar with it, take note that cabbagesofdoom's post takes a very common form of response.

    The initial response to new significnt data is to argue that it is not so.
    Then when you have to accept the data, the next step is to downplay it and often to go even further and say it is what would have been predicted. "

    Don't give me that one, sunshine. I have never changed my stance on this issue. I have provided explanations and reasons for all my arguments. There is only one of us who is playing games here. I'm not the one who is so insecure in my position that I won't even reveal my identity. If you disagree with what I have said, then feel free to present a counter-argument. Please indicate which bits of my statement are not true. Quoting someone else who says "this is surprising" is not the same as demonstrating that it is surprising. In this entire comment thread, you have as yet failed to present a single coherent argument in support of your position!

    ReplyDelete
  132. @Anon.

    You are Paul Crowley and I claim my 5 pounds. Or you're Rumpelstilskin; I don't actually care.

    I predict your next step to be a dissection of how bipedalism could not have evolved naturally because speciation was somehow prohibited between proto-chimps and proto-humans because the latter should have been competed off the planet by the former.

    As to your confusion re: 'single-line speciation', consider this: there is one process of flow involved in the movement of water downhill: gravity. But if a barrier pushes some of the flow one way and some the other, do we still only have single-line flow, completely overlooking the role of the barrier? The internal mechanism of speciation is the mutation-amplification process of selection/drift, operating separately on each side of the barrier. Yes, it is one process. But it is happening in two places independently.

    ReplyDelete
  133. "He is talking about the isolating event, the initial colonization of the Galapagos in our example. And those are the events whose statistical distribution he is analzying."


    He is talking about the fact that adaptations do not cause speciation. (They do not "contribute as a cause".)
    Could he have said that more clearly?
    I have quoted the relevant passages multiple times. For example:
    "The point is that this adaptation follows as a consequence of speciation, rather than contributing as a cause."

    As a side question.
    Are you thinking that the physical separation model (eg. the mainland/island example) is the vastly most common form of speciation?
    Do most new species arise from that type of situation?
    I have never seen that idea anywhere, so I am wondering if that is your thinking?

    ReplyDelete
  134. In spite of Dr. Moran alerting us to the very real problem about revealing personal info, as we saw in the Rhett S. Daniels case, Allan Miller cannot help himself.
    He just has to speculate (incorrectly) about my personal identity and try to post about it.
    That is loathsome.
    If Moran were consistent he would ban Allan Miller or at least publicly admonish him.
    This is a serious issue that people think is a game till it happens to them.

    ReplyDelete
  135. Lest I am accused of reactionary games to this "new" data again, please read this blog post I just found from 2009.

    Favourite quote, because I know Anonymous loves to run with quotes:

    "Although, this ‘rediscovery’ of what’s been known for about the last 30-years may not seem too earthshaking, I’m confident that (with Nature’s help of course) creationists around the world will be harvesting quotes from the article and its associated news release."

    For those interested in the truth of the matter, the original article is simply the final nail in the coffin of the lesser known part of the "Red Queen Hypothesis", which did predict a constant rate of speciation. When? In 1973.

    I am genuinely surprised that anyone still subscribed to this hypothesis, far less that disproving it would be worthy of a Nature article. I have been an evolutionary biologist in an academic environment for over fifteen years and I have never come across the idea that speciation happens at a constant rate. It's never really come up, it is true, but still. The Red Queen Hypothesis is generally discussed in terms of an evolutionary arms-race, which is totally independent of speciation.

    Anyone else come across the speciation aspect of The Red Queen before? Maybe I'm just too young!

    ReplyDelete
  136. Anonymous writes:

    What I have shown is that there is a fundamental misconception underlying this.

    There is ONLY single line lineage.

    There is no other speciation process.


    If Pagel is talking about speciation (and he is) then his data is only about single lineage evolution - because there is ONLY single lineage evolution.

    There is not some other second speciation process. Lou Jost was talking as if there were two different processes.

    There aren't. There is just one.

    Nope. You really seem to have a fundamental reading comprehension problem. From the article from which you're supposedly getting all this:

    This would take the form of either a normal curve if the incremental changes sum up to push the new species over some threshold of incompatibility, or the related lognormal curve if the changes multiply together, compounding one another to reach the threshold more quickly.

    * * *

    The lognormal was best in only 8 per cent of cases

    So a little under 10% of the time by Pagel's reckoning, "the changes multiply together, compounding one another to reach the threshold more quickly." That's not a sudden speciation event, it's speciation via adaptation.

    These bursts of speciation suggest that organisms need not wait for some rare event to push them into speciating, but instead can be pulled there by natural selection. "I would take it that there is quite a bit more pull than push," says Leigh Van Valen at the University of Chicago.

    But is there? In his analysis, Pagel specifically looked for the signature of this kind of evolutionary exuberance. Bursts of speciation would manifest as trees with lots of branching at irregular intervals; in other words, a highly variable rate of change over time, giving rise to a subtly different curve. "It was the model that, going in, I thought would explain far and away the most trees," says Pagel.

    He was wrong. "When it works, it works remarkably well," he says. "But it only works in about 6 per cent of cases. It doesn't seem to be a general way that groups of species fill out their niches."

    Again, speciation via adaptation rather than a sudden triggering event.

    So what we have - even in this reporter's summary of one scientist's contention regarding a single research project using a single hand selected data set - is the information that there are at least a couple of different ways speciation is triggered.

    And by the way - if you'd ever bother to read this blog, you'd find Dr. Moran has already posted at length on these supposed earthshaking thoughts about speciation triggers. So it doesn't shake Dr. Moran's world, or the world of the folks who read this blog - even if it turns out to be wholly true, which would be quite something for one research project using this particular method of inquiry. More usually, these "earthshaking" results are modified by later research until some reasonable scientific consensus is arrived at.

    ReplyDelete
  137. He just has to speculate (incorrectly) about my personal identity and try to post about it.

    This is a serious issue that people think is a game till it happens to them.

    True enough. I did this to you a couple of times here, and I apologize.

    ReplyDelete
  138. cabbagesofdoom quotes from a "naturalist" blogger.
    As if that is equivalent of Pagel's study.
    This is the kind of absurd thing people here do.
    And yet you think I should take you seriously.

    ReplyDelete
  139. http://www.nature.com/nature/journal/v463/n7279/full/nature08630.html
    "By comparison, 78% of the trees fit the simplest model in which new species emerge from single events, each rare but individually sufficient to cause speciation. This model predicts a constant rate of speciation, and provides a new interpretation of the Red Queen: the metaphor of species losing a race against a deteriorating environment is replaced by a view linking speciation to rare stochastic events that cause reproductive isolation."

    This is consistent with the model that I have proposed.
    Speciation is directed by the intelligence of NATURE.
    As the article says:
    "It isn't the accumulation of events that causes a speciation, it's single, rare events falling out of the sky, so to speak."

    ReplyDelete
  140. As a side question.
    Do people think that the physical separation model (eg. the mainland/island example) is the vastly most common form of speciation?
    Do most new species arise from that type of situation?
    I have never seen that idea anywhere, so I am wondering if that is your thinking?

    ReplyDelete
  141. Anon, I can't stress enough that Pagel looked only at the distributions of branch lengths of calibrated phylogenetic trees, as estimated by molecular clocks. That is what his study is about. As I said multiple times, the dates of those divergences are the dates of the isolating event, not the dates of speciation. Remember that we all agree that once there is an isolating event (trigger event), adapation and drift cause forms to become more different from each other, until eventually they are no longer the same species.

    Now you quote the article:
    "The point is that this adaptation follows as a consequence of speciation, rather than contributing as a cause."

    This sentence is not expressed correctly. We agreed that speciation doesn't happen at the point where lineages divide (the date that Pagel used in his analysis, the date of colonization of the Galapagos by the finch), but long afterwards. The sentence would reflect what Pagel actually studied if it said
    "The point is that this adaptation follows as a consequence of lineage divergence (or trigger event, or isolating event), rather than contributing as a cause."

    As a general rule, most biologists would agree that this is probably the most common way for new species to arise. That also gives the answer to your side question. Sympatric speciation is generally thought to be quite rare.

    ReplyDelete
  142. Lou Jost just summed it up pretty much perfectly. Again, it can't be stressed enough that the divergence points (internal nodes) in calibrated molecular clock phylogenetic trees are equivalent to the point at which the populations diverged which we use as a proxy for the speciation point (since it is effectively the point at which significant gene flow stopped).

    None of what has been quoted from that paper is even remotely controversial in terms of speciation dynamics. Most biologists would agree that Allopatric and Peripatric are probably the two most common forms of speciation, followed by Parapatric, and then Sympatric.

    We should also keep in mind that all of these "rules" and most examples are drawn almost exclusively from the literature on animals.

    ReplyDelete
  143. First we had cabbagesofdoom giving the standard "nothing new here, go about your business".
    Now we have DG giving the same standard line.
    "None of what has been quoted from that paper is even remotely controversial in terms of speciation dynamics."

    Go back to sleep everyone. Nothing to see here.
    People can buy that line if they wish. It actually means nothing.

    ReplyDelete
  144. People are overlooking the most significant "trigger" of all.
    A substantial genetic saltation change.
    The Pagel analysis is perfectly consistent with that form of speciation.

    ReplyDelete
  145. Anonymous: It isn't something new to anyone who works in evolutionary biology. Punctuated Equilibria was proposed in 1972, and owes a lot to Mayr's work from 1954.

    There may still be debate about whether speciation is gradual or punctate, but a paper looking at population divergence estimates on calibrated phylogenetic trees in animals and showing a punctate distribution for those divergent events isn't revolutionary or earth shattering to evolutionary biology.

    We've been debating gradual versus punctate for at least 40 years...

    ReplyDelete
  146. Lou Jost posted:
    "Sympatric speciation is generally thought to be quite rare."

    That opinion is not due to evidence. It is simply an opinion based on the already assumed idea of how speciation takes place.

    ReplyDelete
  147. What evolutionists do is work out a story for every new finding.
    That is all we are seeing with the tap dancing of the folks here.
    You guys are so used to it that you don't even see it any more.

    If you were able to step outside of the little box you have placed yourself in, you would see it.
    But as it is, you are able to say the most absurd things, have others agree with you and go on as if nothing were odd.

    If Pagel's study had shown exactly the opposite of what it did show, you would have an equally good story for that. Is there anyone honest enough to admit that?

    You are able to overlook that what Pagel has found is actually astonishing.

    ReplyDelete
  148. Saltation/Saltationism is a word that unfortunately has a hell of a lot of negative baggage with it. But its not an entirely bogus idea. The thing is there are a lot of different things that can happen that result in speciation, the fixation of a relatively major (in terms of impact) evolutionary change, which many would describe as a saltation event, could be one of this. Hybridization that results in speciation, as has been documented in plants and at least once recently in animals (in rats), could maybe be described this way as well.

    But the work cited is only as consistent with this explanation as it is with many others, such as speciation via reproductive isolation.

    Again, remember that calibrated molecular clock phylogenies only give you an estimate of the time at which populations ceased significant gene flow between them.

    ReplyDelete
  149. Anonymous said: "You are able to overlook that what Pagel has found is actually astonishing. "

    I would hazard to say that I have looked at far more phylogenetic trees than you have. Both species trees and gene trees. I would have found it surprising if most species trees were consistent with a regular smooth pattern of speciation for animals. It just wouldn't make sense to me.

    I'm more likely to find Pagel's interpretations astonishing (and perhaps wrong) than the findings themselves in this case.

    ReplyDelete
  150. And again, I think most of the confusion about this comes from the rather poorly written peice linked, not Pagel's actual work.

    There are probably many evolutionary biologists who do find these ideas controversial or shocking, but personally I think most of them are dinosaurs stuck in wrong and outdated modes of thinking about evolution.

    These would be the same types that Dr Moran lambasts regularly on this blog for being Adaptationists. So it is hardly surprising that many knowledgeable commentators in this thread, don't find it shocking because we have always been pluralists when it comes to evolutionary theory.

    That accidents and historical contingency are important in driving evolutionary change isn't controversial to me.

    ReplyDelete
  151. "But its not an entirely bogus idea."

    You have no evidence that it is bogus at all. You can admit it.

    And in fact, it is a more parsimonious explanation of Pagel's results than the contorted stories you folks are coming up with.

    ReplyDelete
  152. DG posted:
    "That accidents and historical contingency are important in driving evolutionary change isn't controversial to me."

    DG you are still looking in the wrong direction. This is not a question of accidents and historical contingency.

    That is just your spin on it based on your biased assumptions.

    ReplyDelete
  153. @Anon
    Why do you even insist on having these arguments, as far as I can tell your only objective to ignore and denigrate those that reply to you. Your certainly not convincing anyone of the merits of your argument and if you were honest (or intelligent as seems more likely) you'd have to admit that Lou Jost's point were quite correct. The paper uses cessation of gene flow as a proxy for speciation, while Lou was discussing a scenario in which a speciation event occured without any cessation in gene flow. The paper you were citing as evidence cannot detect the presence of his scenario irrespective of whether it occurred or not. For this reason it cannot be used as evidence of absence. The fact that you have not grasp this extremely simple point after fifty replies, speaks more about your reasoning abilities then it does about the tiptoeing of evolutionists.

    ReplyDelete
  154. Pagel produces an analysis that is actually astonishing.
    You simply shoehorn it into your pre-existing fixed ideas.
    The only way you can make sense of it is to actually believe that mountain ranges are popping up* all over the world all the time creating all the artificial speciation opportunities.
    Even a moments thought should make you realize that that is not nearly common enough to explain the vast number of speciation events that have taken place all over the world.


    *I am using that often purported mountain popping phenomena as a placeholder for the set of such types of purported species splitting phenomena.

    ReplyDelete
  155. If Pagel's study had shown exactly the opposite of what it did show, you would have an equally good story for that. Is there anyone honest enough to admit that?

    ReplyDelete
  156. Anon, you said biologists have no evidence for their opinion about sympatric speciation. Biologists do have reasons to think that sympatric speciation is less common than other scenarios. These include mathematical reasons (based on population genetic models), biogeographical reasons, and others.

    The difficulty of sympatric speciation is that unless gene flow is very low, or unless divergent natural selection is very strong, random effects will wipe out any incipient divergence between two sympatric groups.

    To discuss this in detail, we would have to get into some math. My own work is on the mathematics of genetic divergence, and I'd be happy to discuss it, except that I don't think you are really interested in details like this.

    ReplyDelete
  157. Lou Jost I have a question for you.
    If Pagel's study had shown exactly the opposite of what it did show, you would have an equally good story for that. Are you anyone honest enough to admit that?

    ReplyDelete
  158. This is a good post from DG:
    "Saltation/Saltationism is a word that unfortunately has a hell of a lot of negative baggage with it. But its not an entirely bogus idea. The thing is there are a lot of different things that can happen that result in speciation, the fixation of a relatively major (in terms of impact) evolutionary change, which many would describe as a saltation event, could be one of this. Hybridization that results in speciation, as has been documented in plants and at least once recently in animals (in rats), could maybe be described this way as well.
    But the work cited is only as consistent with this explanation as it is with many others, such as speciation via reproductive isolation."

    I agree that Pagel's study is "consistent with this [saltation] explanation".
    That is what I have been saying.

    But the "reproductive isolation" explanation does not pass the smell test.

    ReplyDelete
  159. [Allan Miller] just has to speculate (incorrectly) about my personal identity and try to post about it.
    That is loathsome.
    If Moran were consistent he would ban Allan Miller or at least publicly admonish him.
    This is a serious issue that people think is a game till it happens to them.


    I apologise if I caused offence. As someone who chooses his own name, not even an anonymous pseudonym, I don't share your touchiness about revealing identity, and hence am not as sensitive as I might be. If such (jocular) speculation is a bannable offence, so be it - but if a further consequence were the disabling of Anonymous posting, I would at least be better able to follow the discussion as a lurker. Calling yourself "Intel1234" would in no way compromise your anonymity, but but assist the ability of your readers to distinguish your arguments from those you may or may not wish to be associated with.

    Incidentally, why are we deep into speciation on a comment section about the Central Dogma? The Internet is full of discussion forums for this kind of debate.

    ReplyDelete
  160. Anonymous said...onMonday, August 29, 2011 4:49:00 PM
    cabbagesofdoom quotes from a "naturalist" blogger.
    As if that is equivalent of Pagel's study.
    This is the kind of absurd thing people here do.
    And yet you think I should take you seriously.


    Since Anonymous admits here that he does not take anyone who argues with him seriously, why is Anonymous here at all?

    ReplyDelete
  161. "Speciation is directed by the intelligence of NATURE."

    Riiiiiiight. And speciation is an intelligent response, why? What's wrong with adaptation and/or migration? Speciation is directly linked to its counter-point, which is extinction. Extinction does not seem very intelligent to me.

    Congratulations on finally painting your colours explicitly on your mast and highlighting why you are listening to no one. If only your stamina was matched by comprehension.

    BTW, the answers to all the questions you keep parroting are already in the comments in this thread - just re-read them.

    On the subject of extinction, though, Anonymous, perhaps you would care to explain how they accounted for potential differential extinction rates in that paper? When you are looking at relationships between extant organisms, you are not looking at all speciation events. Or is extinction another blind "assumption" of ours, with only hundreds of years of data and evidence to support it.

    ReplyDelete
  162. Anonymous said...onMonday, August 29, 2011 5:01:00 PM

    This is consistent with the model that I have proposed.
    Speciation is directed by the intelligence of NATURE.


    Anonymous has not proposed any model of speciation.
    Anonymous has never explained who Nature is.
    Anonymous has not explained where or when intelligence comes in.
    Anonymous has not told how speciation is directed by the intelligence of NATURE.

    Come on, Anonymous, tell how your model works!

    ReplyDelete
  163. Alan Miller: "Incidentally, why are we deep into speciation on a comment section about the Central Dogma?"

    Sorry. We made the mistake of humouring Anonymous to see if his/her arguments would actually go anywhere. (Or, indeed, whether (s)he had any arguments at all.) Not entirely sure how it went from Central Dogma to Red Queen speciation.

    ReplyDelete
  164. heleen said...
    "cabbagesofdoom said...
    Sorry, shouldn't be replying - you've not answered my three questions yet.

    Anonymous never answers questions, never explains, and never has the pluck to engage in any real argument."

    CODA.

    ReplyDelete
  165. @Anonymous. A couple of direct quotes from the actual Pagel paper for you:

    [In their model] "... there are many potential causes of speciation, including environmental and behavioural changes, purely physical factors such as the uplifting of a mountain range that divides two populations, or genetic and genomic changes."

    and

    "Factors apart from biotic interactions that can cause speciation include polyploidy, altered sex determination mechanisms, chromosomal rearrangements, accumulation of genetic incompatibilities, sensory drive, hybridization and the many physical factors included in the metaphor of mountain range uplift."

    Compare and contrast with what (a) you, and (b) everyone else has been saying about speciation. Are even Pagel and coauthors wrong?

    And here are the references they cite for this extensive list (numbered from source):

    21. Soltis, D. E., Soltis, P. S. & Tate, J. A. Advances in the study of polyploidy since plant speciation. New Phytol. 161, 173–191 (2003).

    22. Mitsainas, G. P., Rovatsos, M. T. H., Rizou, E. I. & Giagia-Athanasopoulou, E. Sex chromosome variability outlines the pathway to the chromosomal evolution in
    Microtus thomasi (Rodentia, Arvicolinae). Biol. J. Linn. Soc. 96, 685–695 (2009).

    23. Navarro, A. & Barton, N. H. Chromosomal speciation and molecular divergence — accelerated evolution in rearranged chromosomes. Science 300, 321–324 (2003).

    24. Orr, H. A. & Turelli, M. The evolution of postzygotic isolation: accumulating Dobzhansky-Muller incompatibilities. Evolution 55, 1085–1094 (2001).

    25. Seehausen, O. et al. Speciation through sensory drive in cichlid fish. Nature 455, 620–626 (2008).

    26. Mallet, J. Hybrid speciation. Nature 446, 279–283 (2007).

    Go away and do some reading. If you still think you have something, post it in the appropriate place.

    ReplyDelete
  166. Alan Miller: "Incidentally, why are we deep into speciation on a comment section about the Central Dogma?"

    Sorry. We made the mistake of humouring Anonymous to see if his/her arguments would actually go anywhere...


    No, it's cool - I too have become so engaged. And I'm very interested in speciation. I think the error we all make is that, from whatever position of clarity we may think we have achieved through study and cogitation, we feel that all we have to do is explain rationally why one position is sound and another not, the scales will simply fall from our opponent's eyes. We are deluded!

    On speciation ... One plausible model rarely mentioned is that of local extinction. It only requires a species to range wide enough, then excision of the bridging individuals that allow gene flow right across the range, to create the right circumstances for divergence. No mountain range required, but equally little chance of determining this as a cause after the event.

    ReplyDelete
  167. For those of you watching this car crash that actually care about the science... there does seem to be a bit of a flaw in the conclusions of the paper.

    They introduce the model being tested by saying: "Van Valen suggested that extinction occurs when species lose a battle against a biotic environment that is constantly changing. Subsequent work showed that this model predicts not only a constant rate of extinction, but also a constant rate of speciation and evolution in a homogeneous group." [My emphasis.]

    In terms of the data, they analyse: "The length of each internal branch in a phylogeny records the expected amount of genetic divergence per site inferred to have occurred between two adjacent nodes of the tree, corresponding to events of inferred speciation minus any species missing from the tree owing to extinction or sampling." [My emphasis.]

    Regarding results: "Missing species and extinctions could influence our results if not randomly distributed in the tree, but neither of these would bias the results towards the exponential model (Supplementary Information)." [My emphasis.]

    However, in the Supplementary Information, the only modelling of extinction/sampling considers that "that extinctions and missed samples are distributed geometrically". This is not enough to declare with confidence that non-random extinction could not produce an exponential pattern.

    Unless I am missing something - and someone please tell me if I am - the results do not say anything about the speciation process alone but, rather, are looking at the combined results of biases in (a) speciation, (b) extinction, and (c) taxonomic sampling. It is true that the Van Valen hypothesis being tested featured both constant speciation and extinction rates based on accumulated changes, and so this model is still rejected. Beyond that, however, any conclusions about speciation alone are largely conjecture.

    Personally, I favour a model of adaptive radiations and multiple extinctions, which I think their data (and conclusions) are quite consistent with, but we still need to be careful about saying too much based on just these data.

    Finally, let us be clear what the the conclusions of the paper are. The best model tested is actually one of a constant rate of speciation-extinction but a rate that is determined by a constant probability of single speciation-extinction events, rather than than the accumulation of lots of changes.

    What does this mean? Adaptation is not happening? No. It just means that the probability of a given speciation is independent of the time since the last speciation. Multiple changes accumulating (by selection or drift) are neither necessary not sufficient to generate a speciation event. Instead, some other factor, e.g. a niche opening up, must be involved.

    This is not surprising. What is surprising to me is that these external factors appear to have a fixed probability within a taxonomic group, according to their models tested. I find this somewhat unlikely and wonder whether there is an underlying bias that they haven't considered, such as a non-geometric non-random pattern of extinction, or non-random deviations from their molecular clock assumption, that artefactually produces an exponential distribution of branch lengths. (Note that the fixed rate is probably different in different taxonomic groups but everything is relative to genetic change, not time.)

    ReplyDelete
  168. Anonymous writes:

    Pagel produces an analysis that is actually astonishing.

    It certainly would be to someone of your (lack of) background. As I and others have noted previously in the comments, you can look back at any number of Dr. Moran's own posts on this blog going back years, and find discussions quite similar to what Pagel and the commenters here have been saying.

    Thus when you say we should admit surprise, all you reveal (as usual) is your own utter lack of knowledge, both about the subject in general and about this very blog.

    ReplyDelete
  169. If Pagel's study had shown exactly the opposite of what it did show, you would have an equally good story for that. Is anyone honest enough to admit that?

    Is anyone going to answer this question?

    ReplyDelete
  170. Another thing to remember about that paper, is that they were looking at single molecular phylogenies, not species phylogenies. This can potentially add a lot of unknown variation on to the branch lengths. It is not clear whether they use multiple sequences for each taxa to get a better estimate of the relative speciation pattern but the implication is that they are dealing with single trees based on single sequences. I am not sure what affect, if any, this added error would have on their findings but they do not seem to discuss it at all.

    Unfortunately, although the Supplementary Material provides a long list of the source publications, there is no explicit listing of the sequences, or even species, used for their phylogeny construction. This is a shame as it also means that we cannot be sure over what evolutionary scale this pattern is observed.

    "Datasets varied from 9-229 taxa (mean = 42.9), with forty-seven sampling species from within a genus, forty-one within a family and thirteen within an order." This also implies that a lot of the results are based on quite small numbers of branches.

    I still think this paper is very interesting - and Mark Pagel is certainly a big hitter - but I think it is a long way from conclusively demonstrating a universal principle of speciation. More research needed! (Yay!)

    ReplyDelete
  171. "If Pagel's study had shown exactly the opposite of what it did show, you would have an equally good story for that. Is anyone honest enough to admit that?"

    In general terms, it is answered many times above. We have outlined what we expect.

    In specific terms, it makes no sense as a question. What would "exactly the opposite" look like? They were comparing five models.

    If you simply mean that the "normal distribution" of branch lengths was prevalent, then that would obviously support Van Valen's original hypothesis. The one being tested, remember? As indicated, this would be very surprising and, no, I don't think we would have as "good" a story for it because, also as indicated, it would contradict our current understanding of speciation.

    Now, please, go away and do some reading on speciation. (Or just pick one of those two activities.)

    ReplyDelete
  172. Does everybody agree that if the results were exactly opposite that they would not have an equally good story to give?

    Anyone honest here?

    ReplyDelete
  173. Anonymous writes:

    If Pagel's study had shown exactly the opposite of what it did show, you would have an equally good story for that. Is anyone honest enough to admit that?

    Still haven't bothered to read anything else on the topic, even on this blog, have you?

    If you do bother, you'll then come to the (astonishing!) realization of what the rest of us already know: Dr. Moran and the people in the field who are more or less regular commenters here would have been fairly surprised if Pagel's result had been the opposite. The people who would have said the opposite result was just as they expected would be evolutionary biologists sometimes referred to as "adaptationists," people such as Richard Dawkins and Jerry Coyne.

    Of course this doesn't fit with your biased and uninformed viewpoint of evolutionary theory as some sort of monolithic dogma that brooks no dissent. It's anything but. There are lively arguments going on about many topics in evolutionary theory. You don't see them for two reasons: (1) You don't want to; and (2) The price of admission is taking the time and trouble to learn the science behind the discussions, and you're far too poor in that coin.

    ReplyDelete
  174. If Pagel's study had produced the opposite results (which by the way they expected) the people here would sanctimoniously present a story about why that was not controversial and even to be predicted.
    I realize that nobody here will admit that. If they did admit it, it would mean that the whole game was exposed.
    People here think that I must take their story seriously.
    And if the results were the opposite, they would have produced a different story - and expected me to take THAT story seriously.

    Why not just admit it? Why all the hiding and tap dancing?
    The tip off is the increase in insults. How you are "playing along". How all this is "humorous".
    I am very familiar with talk like that. It is a smokescreen to hide something you do not want to admit.
    The only ones you are fooling are yourselves.

    ReplyDelete
  175. @cabbagesofdoom

    What is surprising to me is that these external factors appear to have a fixed probability within a taxonomic group [...perhaps] non-random deviations from their molecular clock assumption

    I have the expectation that mutation rates vary between taxonomic groups. Nothing concrete; just a hunch. We know that DNA polymerases tend to have a fairly predictable error rate, but the role of recombinational mutagenesis and transposon-mediated mutagenesis and germ-line weeding-out of errors by cross-reference introduces a dose of stochasticity that may still provide some degree of clustering within, but divergence between, groups.

    Population size is another factor that may come into play. Taxa that tend to have small or wildly fluctuating populations could give different clock rates for non-neutral alleles from those with large or static pools.

    The research (or the reporting of it) seems to attack a strawman, though. We are told that the orthodoxy is that adaptation is the key driver of speciation. I would hope that the orthodoxy would favour mutation, however concentrated. Random mutation and a population sampling process (ie birth and death) are all that is required to drive divergence. Some alleles will be fixed at the mutation rate (the neutral ones) and some at a rate dependent upon s - but it's all just divergent substitution of mutations, rendered unpatterened by internal (mutation rate, gamete compatibility) and external (mechanical, geometric and ecological) variation in actual histories.

    ReplyDelete
  176. Anonymous said... on Tuesday, August 30, 2011 8:12:00 AM

    Anyone honest here?

    Almost all people are honest here. Almost all people here have some understanding of the subject of speciation.

    There is a notable exception, it would seem.

    ReplyDelete
  177. Anonymous said...on Tuesday, August 30, 2011 7:41:00 AM

    If Pagel's study had shown exactly the opposite of what it did show, you would have an equally good story for that. Is anyone honest enough to admit that?

    Is anyone going to answer this question?


    And after this question had been answered, Anonymous refuses to accept the answer.

    As usual.
    Anonymous never listens to an argument.

    ReplyDelete
  178. Does everybody agree that if the results were exactly opposite that they would not have an equally good story to give?

    Anyone honest here?


    If circumstances were different from what they are, would we find that as easy to explain? No, absolutely not. The same applies to the famed rabbits in the Cambrian.

    I would be astonished if speciation was a regular, predictable event, because it depends so critically on 'random' factors such as mutation, drift, movement of individuals, the whims of females, what other species and the planet, climate etc are doing ... if you think we are getting confirmation bias here, show us a different paper that shakes us out of the current paradigm.

    I can assure you that, if that was what the data showed, subject to the usual caveat about extraordinary claims, then I would accept it at face value. Then, my immediate question would be: "mechanism, please".

    Still, since we have no phenomenon requiring a revision of paradigms, the situation is entirely hypothetical.

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  179. "Multiple changes accumulating (by selection or drift) are neither necessary not sufficient to generate a speciation event. Instead, some other factor, e.g. a niche opening up, must be involved."

    Yes - some other factor must be involved. That factor is the intelligence of Nature.

    ReplyDelete
  180. "Multiple changes accumulating (by selection or drift) are neither necessary not sufficient to generate a speciation event. Instead, some other factor, e.g. a niche opening up, must be involved."

    Yes - some other factor must be involved. That factor is the intelligence of Nature.


    That factor is a barrier to free gene flow, howsoever caused.

    Random movement of water molecules is neither necessary nor sufficient to generate a differential in surface level. Instead, some other factor, e.g. a dam, must be involved.

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  181. Allan: "We are told that the orthodoxy is that adaptation is the key driver of speciation. I would hope that the orthodoxy would favour mutation, however concentrated. Random mutation and a population sampling process (ie birth and death) are all that is required to drive divergence."

    Actually, I think the adaptation thing is a bit of a red herring. If you look at the data presented in the paper, there are really assessing five competing models in which they vary: (a) the number of "events" needed for speciation; (b) the relative rates (and constancy of those rates) of those events.

    The work says absolutely nothing about the nature of those events. They could be adaptations, neutral mutations, abiotic events, anything.

    The "Red Queen" hypothesis tested is that speciation does not happen consistently following the accumulation of lots of changes. This itself is built on a model of adapting to a changing environment (running to stay where you are) but it would work equally well if the mutations were all neutral, as long as they accumulated at a steadyish rate and approximately the same number of mutations were needed each time to result in speciation. (Like you say, a bit of a straw man.)

    The alternative model that fits the data better is that single event is enough to cause speciation and that the probability of this event is constant through time. As this single event could be anything, I do not find the first bit surprising. The "constant through time" bit is surprising to me and makes me wonder whether (a) this is just constancy within a clade (there was no attempt to compare trees as far as I could see); (b) whether the apparent constancy is just an artefact of the limited number (and nature) of models tested. I don't think they could mathematically test a truly random variable-rates model, as they would always over-fit parameters and converge on the real data, so they didn't bother. (Unless I am missing something.)

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  182. "And if the results were the opposite, they would have produced a different story - and expected me to take THAT story seriously."

    Oh, no! Anonymous has discovered the big secret of science. We change our theories to fit the data, not the other way round. Quick, somebody stop him/her before they alert the authorities.
    [Face-palm].

    ReplyDelete
  183. If only you would change your theories to fit the data.
    What you actually do is shoehorn the data into your theory.

    No matter what evidence is obtained you never conclude that you are seeing the effect of intelligence.
    The intelligence of Nature.

    ReplyDelete
  184. Anon, I did not tell you any nice stories based on Pagel. I just gave my Galapagos example as a nice clean well-studied case that was also historically important, whose anatomy we could discuss with confidence.

    For someone who is sensitive about insults, you sure send out a lot of them.

    I will answer your question though, about what I would have thought if Pagel's results had been different. I have different levels of confidence for different kinds of evidence. When thinking about speciation, I put most weight on observable biogeographical patterns. Next, down from there, I put a lot of weight on the statistical behavior of simple population genetic models. I would weigh any new evidence, such as Pagel's, against all that. As there is really quite a lot of evidence of various kinds about speciation, I would not blindly dump all the other evidence based on just one assumption-laden study. If, however, multiple lines of evidence began to converge on the results of that study, I would change my opinion.

    By the way, the following comment of yours is a sign that you have no real understanding of Pagel's result, or of any context for it (it is as if Pagel is the only thing you ever read), and without context, your fixation on any single study is a dangerous thing:

    "How in the world would the dates at which isolation begins be available? He could not possibly have that data."

    If you don't even know how phylogenetic trees are constructed, you shouldn't be so quick to tell us what this study of phylogenetic trees means.

    Alan Miller, you mentioned that there are forums devoted to speciation discussions. Can you recommend a good one? Thanks,

    Lou

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  185. "If only you would change your theories to fit the data.
    What you actually do is shoehorn the data into your theory.

    No matter what evidence is obtained you never conclude that you are seeing the effect of intelligence.
    The intelligence of Nature."

    OK, Anonymous, come clean. You don't have to reveal your identity but you are just someone parodying an IDiot, right? You don't really believe what you have just written. Right? (You might need help.)

    ReplyDelete
  186. Lou Jost, what you are not taking into consideration is that there is not nearly evidence enough for all the "physical reproduction isolation" that would be required for those trees to be correct. (The trees, if and when they are correct, have a different explantion - namely the intelligence of Nature.)

    For example, there were not enough new mountains popping up, or rivers splitting species etc to account for the vast amount of speciation that took place throughout the millennia all over the world.

    That is the issue.
    I would be very interested in any link that anyone might give that addresses that issue.

    ReplyDelete
  187. Anonymous said...

    .. you never conclude that you are seeing the effect of intelligence.
    The intelligence of Nature.


    Anonymous still has not explained who Nature is, or what the intelligence of Nature is, or how one would go about testing the intelligence of Nature, or why any data would support the intelligence of Nature. Anonymous hs to explain how the conclusion about the intelligence of Nature follows from any data, with a mechanistic actual biology.

    No matter what evidence is obtained...
    However, Anonymous has never shown any evidence he/she/it can distinguish between evidence and assertions.

    ReplyDelete
  188. I have shown the evidence. It is the same evidence that is already well known. DNA transposons for example.

    It may be that people think I need to give other evidence. I use the same valid observations that you use.
    It is the interpretations that differ.
    You have no actual explanation*. I have proposed an explanation.

    My explanation is not as large as the Gaia hypothesis but it is of that kind.


    *Your "explanations" are all simply describing how things happen. Not why. In fact you think it is a badge of honor that you do not even try to explain why things happen.

    ReplyDelete
  189. @anus In fact you think it is a badge of honor that you do not even try to explain why things happen.

    Science is limited by it's unwillingness to make things up.

    ReplyDelete
  190. Anonymous writes:

    Yes - some other factor must be involved. That factor is the intelligence of Nature.

    Yeah, what a great "explanation." Now please explain the Lenski experiment, in which E. coli subjected to environmental stress in the form of restriction of their original food source took over 30,000 generations to evolve the capability of using an alternate food source. Why is Nature so "unintelligent" in this instance?

    And of course we're still enjoying your "explanation" of cancer as the equivalent of a criminal intelligence. Why don't you start posting that brilliant idea on some oncology blogs and see what the reaction from all those stuffy, hidebound cancer researchers is?

    ReplyDelete
  191. "In fact you think it is a badge of honor that you do not even try to explain why things happen."

    Things happen because (a) they can and (b) the conditions for them to happen are met. There does not need to be a deeper "why" than that. Go post comments on a philosophy blog if you want to discuss unnecessary hypotheses with no additional explanatory power.

    If you think Intelligence is needed here, are you also a believer in "Intelligent Falling"?

    ReplyDelete
  192. @cabbagesofdoom

    Actually, I think the adaptation thing is a bit of a red herring.

    Yep, teach me to go to the primary sources rather than the summary on allbusiness.com!

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  193. Anonymous, there are and have been lots of different kinds of barriers to migration. Maybe you haven't thought about past climate change and the way this would periodically isolate populations on high mountains, and later rejoin those populations as they lowered in elevation when temperatures cooled. Maybe you haven't thought about how the sudden appearance of a grassland due to drier climate can isolate forest organisms on either side of the grassland. Maybe you haven't thought about glaciers isolating pockets of slightly higher ground, long enough for those isolated populations to diverge from each other.

    And maybe you haven't thought about what happens when isolated populations, that now cannot interbreed, rejoin and mix together. With my mountain example, with two peaks, next time the climate warms, you will have TWO species stuck on each mountaintop instead of just one. If they stay isolated long enough to evolve reproductive barriers, the next cool spell will see them mixed together in the lowlands, and next time there is a warm spell, you will have FOUR species stuck on each mountaintop. After the next cycle, you will have 8 species. In general you would have k^x species produced by k mountain peaks after x cycles. That is a lot of species!!!! Starting with one species and ten peaks, after four cycles you would have 10000 species. Is that enough for you???

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  194. @Lou Jost,

    re: discussion boards, I'm afraid I can't recommend a decent active forum at the moment. For the good of my other pursuits, I'm best off not getting sucked in to 'em! As I'm sure you're aware, sensible discussions can get hijacked, and so you either get moderation (stifling) or a free-for-all (pros and cons).

    I sometimes go to www.rationalskepticism.org which arose from the ashes of the Richard Dawkins.net forum - with the attractor of his name on the door, it was pretty good, though it has gone rather quiet since the separation, and some very good threads were lost with the deletion of the RDF board (along, fortunately, with some pretty embarrassing guff from me! See Anonymous, people can change their minds!).

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  195. Lou Jost posted:
    "And maybe you haven't thought about what happens when isolated populations, that now cannot interbreed, rejoin and mix together. With my mountain example, with two peaks, next time the climate warms, you will have TWO species stuck on each mountaintop instead of just one. If they stay isolated long enough to evolve reproductive barriers, the next cool spell will see them mixed together in the lowlands, and next time there is a warm spell, you will have FOUR species stuck on each mountaintop. After the next cycle, you will have 8 species. In general you would have k^x species produced by k mountain peaks after x cycles. That is a lot of species!!!! Starting with one species and ten peaks, after four cycles you would have 10000 species. Is that enough for you???"

    Let's imagine they are goats, so we can talk about this.
    After all of this will we have more species of goats? Let us say that we do. (We would not but let me be generous) Will we have a new species - for example horses develop from this?

    You may recall that much earlier I said that there is more to this that I will talk about later - that has to do with the definition of a species?
    Well later has come.
    Does the physical reproduction isolation bring about the evolution of horses (for example)?

    Your mountain tops does not explain the appearance of horses, or bears or llamas etc.

    You have a problem to begin with, that these physical barriers are not common enough, but the huge problem is that the physical barrier "explanation" does not explain the appearance of a true new type of creature such as horses etc.

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  196. Anonymous said:
    .. you never conclude that you are seeing the effect of intelligence.
    The intelligence of Nature.


    Anonymous still has not explained who Nature is, or what the intelligence of Nature is, or how one would go about testing the intelligence of Nature, or why any data would support the intelligence of Nature. Anonymous hs to explain how the conclusion about the intelligence of Nature follows from any data, with a mechanistic actual biology.

    No matter what evidence is obtained...
    However, Anonymous has never shown any evidence he/she/it can distinguish between evidence and assertions.

    DNA transposons? Oh No: just empty assertions by Anonymous about what DNA transposons might do, misreading Shapiro.

    It may be that people think I need to give other evidence.

    Any real evidence will do.

    I have proposed an explanation.

    The Intelligence of Nature? That is not an explanation. It is three words. Nothing more, no content.

    *Your "explanations" are all simply describing how things happen. Not why.
    'We' explain how the world works: starting point of all good understanding.

    Why things happen?
    'Why' as in: by what mechanism, by what development, to what function, with what history? That is how 'we' explain why things happen.

    Anything else wanted? Don't bother with science, go to a metaphysics course, or to a blog on spiritual elevation. Non-scientific is LOTS more fun on the 'intelligence of Nature' side.

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  197. I see that heleen is still being rude and referring to me as "it".
    I overlooked that but will stop discussion with him/her.

    Just as I try to not respond to vulgarities.

    If people have something worth saying they can say it in a decent way.

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  198. And I know the next post coming is that I cannot tell people how they may post. And of course that is true. I am just telling you how I will act.

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  199. Allan, thanks for the tip to RDF but I was actually hoping for a more technical forum for people working in population genetics and evolution, a place where detailed, quantitative scientific discussion could occur. Anyone know any place like that? Thanks in advance.
    Lou

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  200. Come on, Anon, show some honesty. You said mountains weren't common enough to explain observed diversity. I gave you a simple model to show that they are, if the isolation lasts long enough to result in reproductive incompatibilities. Just one little mountain chain with ten peaks, through four cycles, could generate vast amounts of diversity (though I have ignored extinction, which would reduce the total of ten thousand species to something less, but still a lot).

    If your real beef is that isolation cannot produce new species over time, then you are ignoring vast amounts of biogeographical evidence, not to mention your own discussions here agreeing that over time, a lineage can change by adaptation and drift into a species different from its ancestor.

    You say that goats won't develop into horses on my mountaintops. Hate to tell you, but goats and horses had a common ancestor, so yes, given enough time, that common ancestor could evolve into things as different as goats and horses on different isolated mountaintops. And if history is any guide, today's goats (or horses) could evolve into very different creatures given some tens of millions of years. If you don't believe the evidence for common ancestry of mammals, then indeed you are lost and need to do some reading. I hope that is not your position.

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