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Author Topic:   Dr. Schwartz' "MIssing Links"
Percy
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Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 31 of 86 (403988)
06-06-2007 9:00 AM


Schwartz is just an anthropologist venturing outside his field. Based upon the Science Daily article, he has a fundamental misunderstanding of the simple rate of copying errors during cell division or gamete formation. This quote from the article clearly brings out this misunderstanding:
Science Daily writes:
This regular cellular maintenance is what Schwartz points to regarding his refutation of constant cellular change. "The biology of the cell seems to run contrary to the model people have in their heads," says Schwartz, and he contends that if our molecules were constantly changing, it would threaten proper survival, and strange animals would be rapidly emerging all over the world.
But our "molecules" (he means DNA, I assume) *are* constantly changing. Copying errors are unavoidable - cell division resulting in a perfect copy probably almost never happens, and this is true of both normal cells and gametes. He proposes nothing new when he mentions stress, as it is already well-established that environmental stress increases mutation rates, though the processes are not well understood at this time, and since he's an anthropologist and not a molecular biologist he's an unlikely candidate for groundbreaking work in this area.
But none of this calls the molecular clock into question. The title of Schwartz's article is "Do Molecular Clocks Run at All? A Critique of Molecular Systematics." The answer is that of course they run, only perfect copying could stop them, and perfect copying almost never happens.
The article itself appeared in the February 9th issue of Biological Theory. Subbie had a link to the article that didn't work for me, this one seems to work:
The article's authors are Jeffrey H. Schwartz, Departments of Anthropology and History and Philosophy of Science, University of Pittsburgh, and Bruno Maresca, Department of Pharmaceutical Sciences, University of Salerno.
In other words, this article on molecular clocks is by an anthropologist/historian/philosopher and a pharmacist. I think it's nonsense. The abstract says nothing about molecular clocks, even though the phrase "molecular clocks" appears in the article's title, so apparently he's confusing chemical measures of relatedness with molecular clocks. Here are the first two paragraphs of the article, just to give people a clear idea of the nonsense:
Jeffrey H. Schwartz writes:
Claims that humans and chimpanzees are essentially identical molecularly, and therefore the most closely related largebodied hominoids (humans/hominids and great apes), are now commonplace. Indeed, in a science in which philosophers (Popper 1962, 1968, 1976; Wiley 1975; Patterson 1978) have long argued that nothing can be proven, only falsified, this hypothesis is so entrenched that any explanation of inconsistency in the data is accepted without question. Witness, for example, the recent scenario that for some millions of years after their lineages split, hominids and chimpanzees continually interbred and produced reproductively viable hybrids (Patterson et al. 2006).
For historians and philosophers of science the questions that arise are how belief in the infallibility of molecular data for reconstructing evolutionary relationships emerged, and how this belief became so central, especially to paleoanthropology, which as a paleontological enterprise can only rely on morphology. Part of the answer comes from the history of human paleontology itself.
Just as we have no idea what was going on in genius Fred Hoyle's mind when he ventured outside his own field of physics to make boldly wrong declarations about biology, we can have no idea why Jeffrey H. Schwartz is doing the same in molecular biology.
The Biological Theory journal that printed this nonsense is associated with the Konrad Lorenz Institute for Evolution and Cognition Research. Going to their website, their About KLI and Research webpages seem comprised of the stuff of fringe (read questionable) science and is pervaded by relativism. Alan Sokal, where are you, we need you!
--Percy

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 32 of 86 (404000)
06-06-2007 9:47 AM
Reply to: Message 31 by Percy
06-06-2007 9:00 AM


Schwartz is just an anthropologist venturing outside his field.
I've tried to find a reference to his degree and school without luck. This was my first impression, but I'm hesitant to pronounce such without actual evidence.
The article itself appeared in the February 9th issue of Biological Theory. Subbie had a link to the article that didn't work for me, this one seems to work:
I agree with your view, thanks for the link (I'm sure we'll see more on this from the creos & IDos).
Still I am interested to see what he has to say. If nothing else this may form a basis for a discussion on molecular basis for PunkEek and more review on stress relations to mutations.
Thanks.
ps - we could invite him to this thread, and that may answer the questions we have eh?
Edited by RAZD, : ps

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molbiogirl
Member (Idle past 2641 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 33 of 86 (404129)
06-06-2007 6:47 PM


It's official!
I've just invited Dr. Schwartz to visit us.

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 34 of 86 (404147)
06-06-2007 8:23 PM
Reply to: Message 33 by molbiogirl
06-06-2007 6:47 PM


Re: It's official!
Cool.
And welcome to the fray molbiogirl.

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molbiogirl
Member (Idle past 2641 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 35 of 86 (404150)
06-06-2007 8:37 PM
Reply to: Message 34 by RAZD
06-06-2007 8:23 PM


Mercy bow coo, RAZD.

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crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 36 of 86 (404405)
06-08-2007 5:06 PM
Reply to: Message 17 by Modulous
06-05-2007 4:35 AM


Ok, I admit error. I assumed he was being misquoted because I made the charitable assumption that he wasn't an idiot.
I stand corrected.

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Modulous
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Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 37 of 86 (404407)
06-08-2007 5:13 PM
Reply to: Message 36 by crashfrog
06-08-2007 5:06 PM


No need to admit error - I already did that

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jhs
Junior Member (Idle past 6135 days)
Posts: 2
Joined: 06-10-2007


Message 38 of 86 (404912)
06-10-2007 2:21 PM
Reply to: Message 33 by molbiogirl
06-06-2007 6:47 PM


Re: It's official!
I have found your discussion of my recent articles with Bruno Maresca - "Sudden origins..." and "Do molecular clocks run at all?" - interesting. Since comments seem to derive primarily from press releases and secondary citations thereof, I shall try to clarify a few things. First, I am an evolutionary biologist who happens to teach in an anthropology dept. My courses are often cross-listed with Biology and Geology as well as History and Philosophy of Science. My first published volume was Models and Methodologies in Evolutionary Theory (1979), co-edited with H. Rollins (who did his PhD in geology with Eldredge and Gould). Maresca is a leader in the field of cell membrane physiology and stress proteins, who happens to teach in the school of pharmacy at the University of Salerno.
Cells' molecular (DNA etc) are not constantly changing in any significant way. Mutation rate (a combination of UV-induced change and transcription error) is extremely low, c. 10 (superscript -8 to -9) - and mutation can affect any cell, not just gamets. We point out that in order to provide the potential for change - e.g. by allowing different signalling pathways - there has to be a mechanism for increasing the effective mutation rate. We suggest that spikes in stress that exceed an organism's capacity to produce sufficient stress proteins to maintain DNA homeostasis represent a possible mechanism. However, as has been known since the early 1900s (see Bateson) and was fundamental to the statistical formulations of the mathematical population genetics (Haldane, Wright, Fisher), most "mutations" (however defined) emerge in the recessive or unexpressed state. As such they spread silently through a population until heterozygotic saturation is achieved, when homozygotes for the "mutation" will begin to emerge. Of course, different individuals will have different stress responses. But while the "environment" may provide the provocation for potential change (unless, as if most likely the case, the result is cell/organism death), the expressed novelty will have nothing to do with the "environment" in which its bearers find themselves. This is not the model of punctuated equilibria, as either first formulated by Eldredge or later co-opted by Gould, since the original model was strictly selectionist. Our model is not (or was it when I began formulating it in Sudden Origins). As for criticizing Darwinian emphases on constant and gradual change, while the quote from Darwin indicates that he recognized that there could be stasis, it is obvious from the total corpus of his writing that he believed this to be a minor case. If one reads the fundamental monographs underlying the evolutionary synthesis by Fisher, Morgan, and then Dobzhansky (2nd ed) and Mayr, gradualism is the major tempo, with accumulated small change the scenario. It is this version of neo-Darwinism informed the hardcore sociobiologists and their scions the evolutionary psychologists. The history of evolutionary biology gives the needed perspective here, as it also does to appreciating that the extrapolation from bacterial genetics/genomics of the 1960s to multicellular organisms, while seemingly valid at the time, is now known to be totally inappropriate, even though it continues to inform the use of molecular clocks. With regard to those of you who are interested in the increasingly influential field of evolutionary developmental biology (perhaps some of you may know it as "evo-devo"), I direct you to publications by Gerd Mller (director of the KLI), Stuart Newman, Massimo Pigluicci, Gnter Wagner et al, who are among the leaders in what is clearly an intellectual shift from Darwinism - which we know is not a viable model for the origin/emergence of novelty.

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Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(1)
Message 39 of 86 (404923)
06-10-2007 4:27 PM
Reply to: Message 38 by jhs
06-10-2007 2:21 PM


Re: It's official!
I think the Lawrence Krauss response to Stuart Hameroff's presentation on another topic at the Beyond Belief 2006 conference is the one that is most appropriate here: "I think everything you say is nonsense. And maybe I'm being too polite."
If you stick around we can get into the details, but I'm sure you're already well aware of the reasons why you had to publish this in an obscure journal from a research organization whose focus isn't even on molecular biology.
But this other comment you made has aroused my curiosity:
My first published volume was Models and Methodologies in Evolutionary Theory (1979), co-edited with H. Rollins (who did his PhD in geology with Eldredge and Gould).
I assume you mean he was in the same program at Columbia at roughly the same time as Eldredge and Gould? Anyway, I hope your mention of these names is not meant to imply that they agree with you that Darwinism (by which you mean the ideas of Darwin as distinct from the modern synthesis, or are you referring to the modern synthetic theory of evolution?) "is not a viable model for the origin/emergence of novelty."
--Percy

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jhs
Junior Member (Idle past 6135 days)
Posts: 2
Joined: 06-10-2007


Message 40 of 86 (404926)
06-10-2007 5:05 PM
Reply to: Message 39 by Percy
06-10-2007 4:27 PM


Re: It's official!
The preface to Eldredge's "Time Frames" acknowledges Rollins at one of the two individual who in graduate school influenced him.

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crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 41 of 86 (405436)
06-12-2007 9:59 PM
Reply to: Message 38 by jhs
06-10-2007 2:21 PM


Re: It's official!
Mutation rate (a combination of UV-induced change and transcription error) is extremely low, c. 10 (superscript -8 to -9) - and mutation can affect any cell, not just gamets.
I didn't understand this in your paper, and I don't understand it now. When you say the "mutation rate" is "10^-8 or -9", 10^9 what? Mutations? Over what period of time, per what reference frame?
Page and Holmes' "Molecular Evolution: A Phylogenetic Approach" - a standard text in the field - says "Mutation rates are notoriously difficult to measure directly," so I wonder from what basis you're claiming this measurement. Furthermore, it cites a figure of 10^-9 synonymous substitutions (aka "neutral mutations") per base per year as a general figure for eukaryotes.
Is that the measurement you're referring to? With a human genome consisting of over 3 billion base pairs in every cell, that's between 1-4 synonymous substitutions per cell per year, which would add up to a considerable number of mutations by the time an organism is able to reproduce, even discounting somatic cell mutations. While it's been abundantly clear for a very long time now that mutation is not the primary motivator of morphological variation among individuals, it seems premature at this point to assert that mutations are so rare that they have no place in explanations of the origins of biological novelty, as you seem to be doing.

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MartinV 
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Posts: 502
From: Slovakia, Bratislava
Joined: 08-28-2006


Message 42 of 86 (405540)
06-13-2007 2:11 PM
Reply to: Message 38 by jhs
06-10-2007 2:21 PM


Re: It's official!
As for criticizing Darwinian emphases on constant and gradual change, while the quote from Darwin indicates that he recognized that there could be stasis, it is obvious from the total corpus of his writing that he believed this to be a minor case.
And yet according view of evolutionary biologist Jaroslav Flegr from Charles University Prague stasis is the basic evolutionary phenomenon. He wrote an intresting book "Frozen Evolution or, that’s not the way it is, Mr. Darwin". He is also author of monography "Evolutionary biology".
quote:
What is the actual basis for my heresy? While Darwin’s original theory assumed that the species that are encountered in nature are evolutionarily plastic and more or less willing to respond to the selection pressure of the environment - i.e. usefully adapt to its changes, the new theory 1.4 assumes to the contrary that the vast majority of species does nothing of the sort and, in fact, cannot do so. These are species that I will call evolutionarily frozen in this book. These species respond to changes in their environment like rubber - initially they give in to the environmental pressure and change somewhat, however, the more their traits differ from the original state, the greater resistance they exert against the pressure until, at a certain point, they cease to react to even the greatest pressure. While, in a Darwinistic world, all the species gladly develop and continuously change in response to ever newer demands from a changing environment, in a world with frozen plasticity, species remain more or less unaltered and mostly only sadly wait until the changes in their environment accumulate to such a degree that they will have no other alternative than to simply pass into extinction.
The quotation and the content of the "Frozen evolution" in english is at:
Frozen Evolution. Or, that’s not the way it is, Mr. Darwin. A Farewell to Selfish Gene. | Introduction to Frozen plasticity theory by Jaroslav Flegr.
Edited by MartinV, : No reason given.

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 43 of 86 (405541)
06-13-2007 2:42 PM
Reply to: Message 38 by jhs
06-10-2007 2:21 PM


Dr. Schwartz
jhs, Dr. Schwartz, welcome to the fray.
My dad taught biology at the U of Mich for many years before moving to Harvard, and he brought us up on evolution. I have studied some biology in university but not majored in it. We often talk about evolution these days, since my interest in the creation v evolution debate and his retirement. He knew Gould and Mayer and met Fischer. One of his biggest complaints about molecular biology is the seeming mental fixation on gradualism, which he says is not part of classical biology. I have to agree with him, particularly on the issue of "genetic clocks" because the assumption of a steady rate of mutation is at odds with the evidence, particularly when other selection systems can be in play (such as sexual selection).
Cells' molecular (DNA etc) are not constantly changing in any significant way. Mutation rate (a combination of UV-induced change and transcription error) is extremely low, c. 10 (superscript -8 to -9) - and mutation can affect any cell, not just gamets.
We suggest that spikes in stress that exceed an organism's capacity to produce sufficient stress proteins to maintain DNA homeostasis represent a possible mechanism.
The way I see this is that you have an organism under survival stress situation (environment or climate change) and this causes higher mutation rates. We've seen similar in bacteria, so this is no big surprise (a cell is a cell).
But I don't see how this challenges the concept of evolution - the change in hereditary traits in populations over time - other than to provide a mechanism for increase mutations in stress situations and which are then still selected by their fitness to the changed condition. If anything this is a genetic mechanism for the change part of punk-eek, thus making between the two a more robust cause and effect situation for sudden change in the geological record.
Certainly it does not challenge the theory of common descent or the increase in diversity accumulating over time between species that have separated into daughter, granddaughter, etcetera species.
Yes it will make the job of the paleontologist harder to try to find examples of such quickened change in the fossil record, and exciting at the same time to see if one can be found. It will make the job of the geneticist more interesting to have to look at rates of change and possible changes to genetic clocks.
But it won't change cladistics significantly, whether by morphology or genetics (or both), and it won't change places where we know gradual change has occurred (see The Foram Fossils: A Classic Tale of Transition), so overall it does not disrupt modern evolutionary biology much that I can see. Not any more than Punk eek did.
Perhaps you can explain why you think it is so revolutionary?
Enjoy.
ps - I'm reading your book "Sudden Change" but have not got beyond the beginning yet. My first impression is that it is weighed down by listing virtually every saltationist from Cuvier on, and it's relevance to the modern synthesis of evolution. You seem to draw a line between gradualistic darwinism and modern synthesis evolution, when one has grown out of the other with increased information.
Edited by RAZD, : .
Edited by RAZD, : name
Edited by RAZD, : .

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Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 44 of 86 (405544)
06-13-2007 3:16 PM
Reply to: Message 38 by jhs
06-10-2007 2:21 PM


Re: It's official!
I see you've picked up a concurring response. If descent with modification and natural selection are insufficient for the production of novelty, then how do you explain novelty? Flegr explains it like this in his paper Where is Modern Evolutionary Biology Heading - The Theory of Frozen Plasticity and Biological Psychiatry:
Flegr writes:
The theory of frozen plasticity, published in 1998, shows that sexually reproducing species can respond evolutionarily to selection pressures (they are evolutionarily plastic) only when the members of the particular species are generically uniform, i.e., after splitting of and subsequent rapid multiplication of part of the population of the original species. Following a short period of time, estimated on the basis of paleontological data to correspond to 1-2% of the duration of the species, genetic polymorphism accumulates in the gene pool and thus, in each generation, the new mutations are in the presence of different alleles - the species ceases to behave in an evolutionarily plastic manner and begins to be evolutionarily elastic. It then exists in this state until such time as such changes accumulate in the environment that the evolutionarily frozen species becomes extinct.
After all Flegr's popular press criticism of evolution, his "novel" idea comes down to nothing more than that only small isolated populations can evolve significantly in response to environmental stress. He ties this in to "biological psychiatry", I suppose because he was unable to publish his ideas on evolution in any respectable biology journal, so like you he sought other outlets, in this case an obscure psychiatry journal where his evolutionary ideas wouldn't receive review by actual peers competent to comment. Just add a few gratuitous references to psychiatry and voil, the paper is published!
I'd say his ideas about the insufficiency of mainstream ideas of evolution seem as unfounded as your own. When one flies with the loons I guess one has to expect cuckoos joining the flock, too.
So how are things in Pittsburgh? I haven't been back in a long while, but back in the 70's I attended grad school just up Forbes Avenue from you at Carnegie Mellon.
--Percy

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Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 45 of 86 (405557)
06-13-2007 4:43 PM
Reply to: Message 38 by jhs
06-10-2007 2:21 PM


Re predicting gaps vs. expecting gaps
quote:
If one reads the fundamental monographs underlying the evolutionary synthesis by Fisher, Morgan, and then Dobzhansky (2nd ed) and Mayr, gradualism is the major tempo, with accumulated small change the scenario. It is this version of neo-Darwinism informed the hardcore sociobiologists and their scions the evolutionary psychologists. The history of evolutionary biology gives the needed perspective here
I am not quite sure that this is not simply self serving.
I understand your linking of what you claim is readable as "the major tempo" 'informing' sociobiology and I understand how ****if***** your target of criticism was that change in biological study and reserach since the 60s you THEN say,
quote:
appreciating that the extrapolation from bacterial genetics/genomics of the 1960s to multicellular organisms, while seemingly valid at the time, is now known to be totally inappropriate, even though it continues to inform the use of molecular clocks.
but there are miles of interpretation of the history of biology between
"as it also does" and " to be a minor case. If one reads the fundamental monographs underlying the evolutionary synthesis "
My grandfather taught evolutionary biology at SUNY Fredonia during the these time periods and passed onto me the "sense" of gradualism INDEPENDENT of sociobiology. That doctrine was only of major psychological importance during my education AFTER I got to Cornell and saw the links between the Neurobiology and Behavior Dept. and the Psychology Dept. even though others under the same influence were in the Dept of Evolution, Ecology and Systematics. Gradualism probably comes more properly from somewhere during WWI, historically, if not earlier, I would guess( I also can imagine it later but not from the 60s only on). It was needed for eugencis it seems again.
As for the whole idea of molecular clocks...
Well, I took a course called "Molecular Evolution" at Cornell in the 80s wherein that, was the subject. I did well, an A-, but I did not enjoy the experience as I was called on to subvert my organismic sense of morphological change to purely defined entities. Just as I reacted to Gould's ideas during High School as proposing a "second" evolutionary theory (than Mayrs') when/as the first one did just as well, I had felt that this notion simply introduced a supplement that depended on atomic knowledge even if this was not supported by whole organisms.
I do not have a good molecular sense of the need for and "increased mutation rate". Could you explain atomically why this is a desired outcome.
There is quite a bit of difference between expecting and being able to predict a morphological gap in anatomy and another one to simply NOT expect any continuity at all ( I even suggested to Henry Morris that if creationists could predict the morphological disjunctions creationists might be able to do for science what evolutionists had not done. Creationists DO seemed to have missed this opportunity but I may be misreading what Wise is doing).
It seems to me that the "silent spreading" indeed has many consequences for predicting gaps which nontheless appear in whole organism shapes (changing D'Arcy Thompsonian reference frames) regardless of the specific hypothesis for the change, and your very particular attachment to a specific group of proteins.
Do you think I am mistaken in so thinking ??
Edited by Brad McFall, : clarity of thought
Edited by Brad McFall, : title simely removed

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