In my last blog, I received repeated accusations of being "anti-evolution" from John Kwok and Keith Roragen. These accusations puzzled me, and I tried to explain why I was puzzled in my online answers to them. But they continued to insist.
My basic argument on the blog (and in my book) was the following: We need to pay far more attention to non-random cell-mediated genome change ("natural genetic engineering") in evolution.
Here's what John Kwok said:
I must concur with Jerry Coyne's assessment of you: "My own theory is that the man simply doesn't understand the kind of population thinking in which 'natural genetic engineering' can result from garden-variety natural selection. (I often find that molecular biologists fail to grasp natural selection, even though it seems conceptually simple.)"
And here's what Keith Roragen said:
Where genome changes come from in the first place is irrelevant. Darwin had no knowledge of genomes. He didn't need it. Darwinism isn't concerned with how genomes change but how those changes propagate through populations and accumulate to form new species. You haven't even come close to explaining that.
Both John and Keith invoked natural selection and population genetics in a way that makes no logical sense. They seemed to believe that incanting "natural selection" would somehow invalidate what I said about the importance of natural genetic engineering. (Readers are invited to dig out the full exchanges and judge for themselves.)
The Jerry Coyne statement that John quoted does not even make sense within the context of the neo-Darwinian Modern Synthesis. Population geneticists recognize the need to use "mutation rates" and recombination events (i.e., genome changes) to generate new allelic variants and combinations as the raw material for selection. There is no way that natural selection can substitute for natural genetic engineering; by definition, it can only work after heritable change has occurred.
Keith simply sticks his head in the sand and introduces stubborn ignorance in place of explanation.
It is difficult to imagine how evolution could occur without genome change according to virtually any theory. Perhaps a purely neo-Lamarckian process, depending exclusively on epigenetic modifications, might conceivably generate heritable (and hence selectable) organism change without alterations to DNA sequences. But I do not think this is what my antagonists had in mind.
The curious responses to my position exposed a fundamental difference in understanding of biological functions between molecular geneticists and these particular proponents of population genetics. Because I can only speak for the molecular side, let me elaborate. I will leave it to John, Keith, and Jerry to explain their assertions.
Molecular geneticists recognize the essential roles of genome structures and multi-molecular networks for cell activities and for morphogenesis.
To a molecular geneticist, evolution is the story of how essential genome structures and networks have changed over the history of life. DNA-based evolution science traces the histories of genome features among distinct life forms.
The basic fact is that natural selection can only pick out the most adaptive existing genome structures once they exist. There is simply no way, even theoretically, that population genetics and natural selection can account for how these structures and networks originated in the first place and then changed over time. That is why John's and Keith's assertions are so perplexing.
Novel genome structures have repeatedly played key roles in evolution of all aspects of biological function:
(Thousands of references [including Scientific American articles] for these and other natural genetic engineering processes in evolutionary history can be accessed through clickable links at shapiro.bsd.uchicago.edu/evolution21.shtml.)
John, Keith, and Jerry have stated that I am mistaken (and dangerously misleading others) by expressing my position that natural genetic engineering is essential to evolution. If they wish to maintain that stance, then I think they need to explain why in detail. Fiat assertions and personal attacks are no substitute for rigorous argument.
2 decades ago I read a book called "Artificial Intelligence", a collection of papers on the subject. The final (?) paper was a speculative comparison of the structure of "silent/junk" DNA with neural networks, noting the apparent layering of structure and function, and drawing attention to the frequency distribution of matching sequences -- almost identical to that found in word frequency plots in a natural language.
I took this thought further, and began to refer to the (highly conserved!) non-coding DNA as the Operator's Manual for activation and alteration of the coding genome. A bit later, I began to refer to this as the inevitable result of "Intelligent Self-Design" and/or random natural selection!
Consider: if purely by chance a bit of junk DNA should have the fortuitous effect of trimming the "tree" of possible mutations in conjunction with some environmental signal, it would convey immense survival advantages to that genetic line. Accumulation of such "rules" would accelerate, and swiftly dominate selection processes. Layers, as in neural network "supervisory" layering, comprising meta-rules for lower layers, would arise and be swiftly refined and strongly conserved, also.
IOW, "intelligence pays" when it comes to evolution's mechanics, and would be an inevitable development. I also think that the communal gene-swapping pools of bacteria constitute a similar "Intelligent Self-Design" network.
I think we are in agreement in principle but perhaps not in detail.
The agreed principle, I believe, is that cells and organisms possessing an orderly process of genome variation when it is needed will have greater success in overcoming selective challenges as they occur. This is what I have been calling natural genetic engineering, and empirical evidence for it is extensive. Note that orderly does not mean deterministic or prescient but simply tending to make useful changes at appropriate times.
Where we may disagree, I believe, is in how natural genetic engineering is regulated. I think we have clues in the complex multimolecular networks cells are known to use for sensing, signaling and making decisions about what they do with their genomes. But we still need more empirical and theoretical research before we can comprehend how these networks operate. The same is true, as far as I know, of neural networks.
Have I understood your point correctly?
1) Much of the "silent 95" is conserved. This makes it de facto important, used and useful
2) Its implicit structure resembles neural web organization, as noted.
There are no "coincidences" at this level.
At the organism level, optimization of use of genetic resources is much enhanced by this kind of organization. At the species level, it permits development and dispersal of tactical and strategic improvements.
Intelligent is as intelligent does. Neuron-based intelligence is just one variety.
As for John's "natural selection" terminology below, it seems to me that the ability to trim and limit susceptibility to "random mutation" (leaving some parts of the genome more vulnerable "on purpose") is a huge multiplier of evolutionary effectiveness. There are trade-offs, as it precludes major changes that would be desirable, perhaps, such as adopting the octopus' retina by a mammal, but it makes substantial change workable with limited populations. It reminds me of the punk eek hypothesis in that respect.
Too much randomity is bad, as it demands impossible numbers. Not enough leaves you trapped in narrow channels.
Moreover, Shapiro needs to explain why he thinks it is time for a "paradigm shift" in modern evolutionary theory, especially - as his colleague University of Toronto biochemist Larry Moran has noted - since we've known about mobile elements for decades and yet there wasn't any need to discard Natural Selection and random genetic drift to account for them. Nor does Shapiro's emphasis on "natural genetic engineering" address such fascinating issues as speciation and punctuated equilibrium. (I believe such a "paradigm shift" is needed, but one based on the principles stated by Stephen Jay Gould and Massimo Pigliucci, among others, not Shapiro's.)
John Kwok is making a statement that it is the duty of science to "Trash creationism" and that you are negligent in that duty. Care to comment?
........."trashing creationism". (Which, I might add, not only myself, but Scott Hatfield, Allen MacNeill, Massimo Pigliucci and many other scientists and science-literate members of the public regard as something that is unfortunately necessary; a duty that has eluded you given your support of your Huffington Post creationist fans as well as those at the Discovery Institute, the notorious "think tank" of Intelligent Design creationism.) - John Kwok
.
"Nor should anyone consider Mazur as credible when she refers to Coyne's lecture as one that began with 'trashing creationism'."
My critique was aimed more at Shapiro's willingness to be interviewed by someone like Mazur, especially when she isn't viewed as a credible science journalist by yours truly, Scott Hatfield, and others who shall remain nameless.
It seems that Shapiro is simply making explict something that science has always done in practice but not realised in theory and that is that wholes and parts are impossible to really understand without reference to one another.
What science does is it takes nature apart reassembles it and makes it revolve around us. The idea that science can reduce us to bits and pieces and disassemble our sense of human purpose into fundamental particles of matter is rightly resisted by religion but for the wrong reasons.
I have the impression you are referring to comments I made in my recent interview with Suzan Mazur on Counterpunch (http://www.counterpunch.org/2012/05/07/the-evolution-paradigm-shift/). Is that correct?
"I am reminded of the keynote speaker of the Rockefeller University Evolution symposium — University of Chicago biologist Jerry Coyne — who stood before an audience of distinguished scientists in the spring of 2008 to do damage control, first trashing Creationism and then declaring that he could cite 300 examples of natural selection but didn’t have enough time to do so. The speech was arranged by the National Center for Science Education — an appendage of the American Association for the Advancement of Science."
I attended that symposium (and met Mazur), and I know that Jerry Coyne's "speech" (lecture) was not paid for by NCSE.
I am generally coming from a view of science propounded by Jacob Bronowski many years ago. He emphasises the relation between science and human values.
There is science and there is scientism that stems from mistaking the way that science presents its ideas with scientific method itself. The way that science presents its ideas can encourage the idea that the truths of science are a kind of mathematical certainty etc. A kind of superhuman truth the ordinary human world becomes a kind of illusory realm where scientific facts trump human values every time. Bronowski shows where this leads in episode 11 of his TV series the ascent of man.
The philosopher Wittgenstein also set himself against scientism where science lays claim to be the only truth. He failed to see I think the distinction that Bronowski made between science and scientism which sent him off on a bit of a mystical tangent.
Reductionism is an ideology. All ideologies have a grain of truth to them or no one would believe in them reductionism has been enormously fruitful but it and its view of the world as a humpty-dumpty-verse have had their day.
I must confess that I had no idea, based on your posts that you harboured such relativistic thoughts. Bronowski proposed the idea that science enabled us to act without fear. As with many of his formulations this sounds like a simple idea. It's only when you start to think about what it might be like to act in a world full of fear that you start to see the point of what it is he is getting at. In this respect both scientism and religion can be held to account.
I think there is a phrase that deals with your last point. In philosophy there is the idea of an ad hominem argument. It is widely agreed to be fallacy. Obviously one has to discriminate but I have the feeling that the is something here that needs to be said.
By the way I don't think that scientism is a disease of scientists. It is more a problem with the way that it is perceived in wider society. If someone says ' it is a scientific fact' you are supposed to fall to your knees. I personally only kneel before my own conscience, and even then only sometimes.
My original post asked for an explanation of Jerry Coyne's statement cited repeatedly by John: "My own theory is that the man simply doesn't understand the kind of population thinking in which 'natural genetic engineering' can result from garden-variety natural selection. (I often find that molecular biologists fail to grasp natural selection, even though it seems conceptually simple.)"
There is still no answer from anyone on how "garden-variety natural selection" can account for the appearance of DNA structures underlying many evolutionary innovations. As I said, I am still waiting for this explanation.
In discussing the active 19th Century history of evolutionary science, I cited Wainwright's web site for documentation of pre-1859 thinking on the subject. Wainwright's bias against both Darwin and Wallace as originators of evolutionary ideas is explicit. John cited a BCSE link as evidence that Wainwright is an ID advocate, but clicking on the link turned up a different evaluation: Wainwright is not a Creationist, is a religious agnostic, but is open to considering intelligent design ideas.
The major issue of how creative a force natural selection can be when it only acts after hereditary variation has been generated remains largely ignored in the recent back-and-forth. My position is that the production of hereditary variation in the form of genome changes is the real creative force in evolution. It would be good to hear reasoned arguments addressing that position, pro or con.
"It has been suggested that replacement of cellular proteins by viral ones also occurred in early evolution of the DNA replication apparatus and/or that some DNA replication proteins originated directly in the virosphere and were later on transferred to cellular organisms. According to these new hypotheses, viruses played a critical role in major evolutionary transitions, such as the invention of DNA and DNA replication mechanisms, the formation of the three domains of life, or else, the origin of the eukaryotic nucleus."
"The origin of viruses and their possible roles in major evolutionary transitions."
Forterre P.
It would seem reasonable that the insertion of 'functioning' genome sequences 'purified' by natural selection would provide material more suitable for the elocutionary process that would random 'errors' filtered by natural selection.
I am excited for you. There is an excellent write up on you at evolutionnews.org.
".......He continues to win our admiration, while evoking some poignancy as well."
"In one post that got a fair amount of attention he had some sensible things to say to fellow evolutionists. Rather than hide behind "absolutist statements like 'all the facts are on my side,'" as his University of Chicago colleague Jerry Coyne does, Shapiro advocates "active engagement" with Darwin critics. Enter into the controversy over evolution, he says, rather than pretend it doesn't exist. "
http://www.evolutionnews.org/2012/05/more_reasons_to059221.html
What your detractors dont seem to grasp is that eventually the millions of people who would otherwise reject evolution, will read your book and accept the empirical evidence of "natural genetic engineering".
Your detractors meanwhile, will pretend as always that there is no issues in evolution and and continue try to shove it down our throats. The definition of insanity is doing the same thing over and over but expecting different results!
Regardless, ultimately in science the empirical evidence prevails!,
.
That's a good thing and speaks volumes!
I am especially concerned with Shapiro's substantial misreading of Darwin's life and work, having claimed that Darwin didn't conceive of Natural Selection until Darwin had received Wallace's essay in early 1858,demonstrating that Wallace had conceived of it independently of Darwin.
However, it can be shown via Darwin's own notebooks that he was thinking seriously of Natural Selection by 1840, having been influenced by his reading of Malthus:
http://www.amnh.org/exhibitions/darwin/idea/theory.php
And by the late summer of 1842, he had stumbled upon and coined the term "Natural Selection":
http://www.amnh.org/exhibitions/darwin/idea/adding.php
Unfortunately this is just one of many examples where I agree with Coyne that Shapiro may be "dangerously misleading" Huffington Post readers into thinking that there is something seriously wrong with both modern evolutionary biology and current evolutionary theory. (As an aside, I think current evolutionary theory will be eventually replaced, but not along the lines which Shapiro believes.)
Therefore I don't regard Wainwright as a credible source"
Wow, just wow! If we replace the words "Intelligent Design apologist" with say black, woman, gay, then it becomes very obvious as to the non-science issues challenging Shapiro!
http://www.ncse.com/evolution
http://www.ncse.com/religion
Not only is Wainwright an Intelligent Design apologist, he is also a terrible historian of science since his allegations with regards to Darwin's work were repudiated years ago. State of the art thought with regards to Darwin's impact on science can be found here:
http://www.amnh.org/exhibitions/darwin
Can you give us an example of a statement by Wainwright that has been refuted?
http://darwin-online.org.uk/content/frameset?itemID=F1556&viewtype=text&pageseq=1
Here's also a revealing quote from someone who has posted succinct informationn on those who had conceived of evolution before Darwin:
"Although Charles Darwin was not the first person to consider that life on this planet evolved, it is important to keep in mind that he was the first to come up with a viable working mechanism on how it happened."
You can look at that quote and other related information here:
http://www.aboutdarwin.com/literature/Pre_Dar.html
Speaking of looking up information, I hope you've begun studying the contents of:
http://www.ncse.com/evolution
http://www.ncse.com/religion
First I want to thank you for the references you have provided. All of us, without exception, benefit by by examining the way others understand scientific principles, especially when they see things differently than we do. However, your failure to provide examples of Wainwright's statements which have been 'refuted' brings into serious question your statement "his allegations with regards to Darwin's work were repudiated years ago".
Indeed, we can conclude, contrary to your assertions, that Wainwrights historical analysis of the development of evolutionary science is accurate any worthy of our attention. This is to be expected, as Prof. Shapiro's credentials and record of scientific publications attest to his knowing what he is talking about when he cites Wainwrights material as accurately describing the development of evolutionary thought.
Erasmus Darwin, Geoffroy Ste. Hillaire, Jean-Baptiste Lamarck, William Lawrence, Robt Grant, Robert A. Chambers, Richard Owen and William Lawrence.
Moreover, the idea of natural selection was articulated before Darwin and Wallace by at least three scientists: William Charles Wells, Patrick Matthew, and Edward Blyth.
There is an interesting web site that presents all the significant propositions from Origin of Species published prior to 1859 (http://wainwrightscience.blogspot.com/).
In other words, as many people pointed out at the time, there was nothing truly novel in Origin of Species, and Darwin neglected to properly acknowledge his precursors, including his own grandfather. The impact Origin had was due more to the social standing and scientific prestige of its author than to the originality of its contents.
Although Wallace was more modest, Darwin did claim to have solved the problem of origin of species. We know his explanation had to be at best only partial because of his ignorance of heredity. The Modern Synthesis tried to correct that in the first half of the 20th Century, but that attempt was also doomed because of the ignorance of how hereditary variation operated. Today, we are making progress now that we know about natural genetic engineering as the source of much (but probably not all) heritable change. At each stage, conceptual reformulation has been necessary to incorporate new knowledge. I hope we can agree upon that.
http://www.bcseweb.org.uk/index.php/Main/MiltonWainwright
Therefore I don't regard Wainwright as a credible source.
Yet again name-calling rather than substance. If Wainwright's evidence is flawed, explain.
Dr Milton Wainwright is a senior lecturer in molecular biology at the University of Sheffield. Contrary to some claims by creationists and IDers, Wainwright is neither an ardent IDer nor a creationist. He has, though, made it clear in public that scientists should be open to the concept of Intelligent Design. Wainwright has also said that he is, from a religious viewpoint, agnostic.
He does, however, appear to be open to Intelligent Design and, indeed, has not made up his mind about it. Some may take the view that he is now, post-Dover, openly sitting on the fence about it.
His academic position is confirmed at http://www.shef.ac.uk/mbb/staff/wainwright
This letter from Milton to the Times http://www.timesonline.co.uk/article/0,,59-1625988,00.html demonstrates that he is no creationist.
This letter to the Independent confirms that he is an agnostic: http://comment.independent.co.uk/letters/article327971.ece
"James Shapiro is "dangerously misleading others" when those who support his views here are Intelligent Design creationists Lee Bowman, Perry Marshall, Peter Rivera and THEMAYAN, and other creationists like Wendell Read. Several of us, including Scott Hatfield, myself and Allen MacNeill find this association both problematic and worrisome"
I know the man is not an ID'er or a creationist. I heard him speak on this issue in a lecture and he made this clear. This goes back to the point that I made earlier, that if in someway an IDer agrees, then the information no matter how relevant becomes spoiled goods, and the originator of the data becomes a persona non grata. In my opinion, this kind of "a friend of my enemy is no friend of mine" attitude does not belong in science. Politics yes. Science no. I think this also says volumes about the kind of mindset that seems so pervasive today concerning this subject. By the way, I also agree with many things that Darwinist have said including Darwin himself. I spoke earlier of his great work showing how finch beaks could vary through the process of natural selection.
I continue to notice how you are more prone to insult or question the intelligence (and to be more concerned with the perceived motives) of others than to respond to any points in a logical fashion. My motive is to search for truth and accuracy in science even if it's politically incorrect.
With respect to punctuated equilibrium, the historical record is this. Eldredge originally came up with a version of it during the course of his Ph. D. dissertation research on the Devonian trilobite Phacops, realizing that he could apply Ernst Mayr's theory of allopatric speciation. He and Gould collaborated on that seminal 1972 paper, and in the process of writing it, Gould coined the term "punctuated equilibrium". Later they developed the theory further by suggesting that it contradicted substantial portions of the Modern Synthesis Theory. (I've only accused you correctly of misquoting Gould, period.)
Too bad you wasted your time in searching for me online. (I can assure you that Scott Hatfield, Todd Stark and Allen MacNeill, among others, would strongly disagree with whatever nonsense about me that's been posted.) You could have used your time far more wisely by reading Ken Miller's website, AMNH Darwin exhibition website, NCSE's website, and Carl Zimmer's website. Obviously your priorities are misplaced by not looking at them.
You could start here at the American Museum of Natural History's "Darwin" exhibition website:
http://www.amnh.org/exhibitions/Darwin
and then, once you've studied that, I would recommend looking at the sections on "evolution" and religion here:
http://www.ncse.com/evolution
http://www.ncse.com/religion
and finally you should study the content posted here:
http://evolution.berkeley.edu/evolibrary/home.php”
You should also look at Ken Miller's web page:
http://www.millerandlevine.com/km
And lastly, at Carl Zimmer's:
http://www.carlzimmer.com
I strongly advise you to look at all of these since you've displayed consistently, a profound ignorance of science and the scientific method, as your HuffPo comments on the "fine tuning" of the universe, the "errors of Darwinism", probability and statistics and paleobiology demonstrate. Trying to smear me isn't going to work since you are simply displaying your profound ignorance of science, scientific methodology, and the history of science.
Shapiro however provides a different perspective with his concept of natural genetic engineering. He has shown that cells are capable of modifying their genomes in response to environmental challenges. In other words, the cells themselves in this respect are agents of change. Perhaps evolution is mainly driven by genome changes engineered by the cells themselves. If so we would have teleology in evolutionary mechanisms, not driven by an external (supernatural) agent but in a completely 'natural' way, engineered by the cells themselves.
This of course raises an obvious question: How are cells able to do any natural genetic engineering at all? Our current inability to answer this question is a reason to try to find the answer rather than assert that it does not happen. Current data show it does happen.
http://www.amnh.org/exhibitions/Darwin
and then, once you've studied that, I would recommend looking at the sections on "evolution" and the religion here:
http://www.ncse.com/evolution
http://www.ncse.com/religion
and finally you should study the content posted here:
http://evolution.berkeley.edu/evolibrary/home.php
Permit me to disagree. To a considerable degree, we know down to the level of specific chemical bonds HOW cells carry out natural genetic engineering. References on this are in my book and online at http://shapiro.bsd.uchicago.edu/ExtraRefs.MolecularMechanismsNaturalGeneticEngineering.shtml.
Where we remain ignorant is in understanding how the products of natural genetic engineering succeed in encoding novel functional systems with probabilities high enough to help generate the diversity of life we know to have existed on earth.
I started by asking how the abundant evidence for natural genetic engineering at key stages in evolution could be explained as the result of natural selection, which can only act upon pre-existing variation. That question remains unanswered, and I think the reason is that no satisfactory answer can be given.
Arguing over who believes in what philosophy, who are the most "eminent" evolutionists, and who is the most credible science journalist are diversions from the main question: How do we account for functional innovations in the course of evolution? That's where the science is.
As for making ad hominem attacks and neglecting the science, just take a look at what you just wrote. Let's try to elevate the tone and deal with the issues.
"That question remains unanswered, and I think the reason is that no satisfactory answer can be given"
My own personal take on it is, why is that? Its interesting that people like Carl Sagan or Michio Kaku could speak of type 2 and 3 civilizations. Francis Crick didn't get much flack from anybody for proposing Directed-Pan Spermia. We have the SETTI project with billions spent of the last forty years, and no one is going on with a hunt, claiming that science should not dabble in the supernatural. Because everyone knows little Green or Gray men are real, but fairies and leprechauns are fake. Yet when when we just speak of the possibility of teleological origin, just the implications alone are enough to get you tard and feathered in halls of academia. Just maybe, like the 18th century scholarly sceptic who thought that the concept of a telephone was supernatural and therefore outside of the realm of science, was as ignorant then as we are today. I.e. maybe we dont understand the natural world as much as we think we do and therefore refer to what we dont understand as supernatural.
John,
How do you ignore a monolith or central dogma? I.e. something thats been shoved down your throat since grammar school. As for your other point, I might actually agree with you on your statement above. However, my point is that a theory which is so outdated, in cohesive, weak and inadequate in light of 21 century data, and yet which can still be regarded as the "most comprehensive scientific statement" …..says it all. I know many will disagree, and that's fine, but if you don't have a sound theory, then all your left with is a handful of educated guesses. The amount of failed predictions relating to the modern synthesis are numerous. Again all I ask is, Will the Real Theory of Evolution Please Stand Up?
In the late 19th Century, physics was in a far worse state than biology is today. Having realized that Classical Mechanics was failing to explain the wave-like behavior of light, physicists didn't throw their hands up in the air and opt to quit, realizing that all they had "left with a handful of educated guesses" as well as substantial data pointing to grave issues with Classical Mechanics. They continued to do science, accumulating data that would later be a much better fit with the theories proposed by Einstein and Planck. For you to imply that current biological science is worthless because of the "falied predictions" of the Modern Synthesis, really demonstrates that you, despite your claims to the contrary, really don't understand science well. Henceforth, read Carl Zimmer, not Suzan Mazur, please.
"However, I agree with Allen MacNeill that we will need an 'Extended Synthesis' of the kind proposed by Stephen Jay Gould and Massimo Pigliucci."
If the Modern Synthesis is so unsuccessful, then explain why paleobiology has flourished, in part, by applying population ecology theories to analyze and interpret diversification patterns in the Phanerozoic Eon (last half biillion years of Planet Earth's history)? Or the rise of molecular systematics as a powerful tool in understanding the "tree of life"?
If anyone is being dogmatic, THEMAYAN, it is you by making false and misleading statements and relying upon the words of mediocre science journalist Suzan Mazur. You would be better served reading Natalie Angier, Cornelia Dean, Faye Flam, and especially, Carl Zimmer's extensive popular science writings pertaining to biology, and especially, biological evolution.
This type of reasoning has always puzzled me, and I only spoke of Mazur to accentuate a point, and the point is, that there are many dissenters out there who feel the modern synthesis is outdated, including atheist and agnostics alike who have no religious bone to pick.
I promise this will be the last mention of Suzan Mazur alias the Messenger of Doom, so let me just summarize by saying that your statement kind of reminds me of Massimo Pigliucci who actually wrote Mazur and commented on what a good article she had written. At least until IDers ran with the story, and then once again it became contaminated and she instantly became a persona non grata. This kind of religious like fervor in itself reminds me of the fifties when anyone who dare question the government was accused of being a communist. Only now, its creationism that puts you on the sh#% list. The real kicker is, that I neither said a word about creationism or ID.
The "contamination" you describe --- "if our enemies like it, it must be evil" is exhibit "A" of good old fashioned prejudice. And as Ron my father-in-law likes to say, "You can't reason with prejudice."
The only way to fight the religious fervor of the Darwinian old guard is not not give in to their bullying and intimidation. Otherwise you imply that their prejudice is acceptable and normal.
If we consider Shapiro's experiance here at Huff Post, Its becoming readily apparent that this treatment extends to any scientist who doubts some evolutionary mechanisms and proposes theories that threaten their philosophical view of life!
Don't cry for me, Rivera. The attacks just present an opportunity to restate the new data and repeat the arguments for a necessary rethink of evolutionary theory.
You ask "5) Explain why Natural Selection shouldn't be viewed as an Evolutionary Law in much the same way that Van Valen and Rosenzweig's concept of the Red Queen is."
I don't believe in immutable Laws of Nature. All scientific explanations are human creations and subject to change as we learn more about the natural world. If Newton couldn't get it right in a fundamentally unchangeable way, what hope is there for the rest of us?
In addition, as I explained in the earlier blogs that so distressed Jerry Coyne, I think the importance of natural selection has been greatly exaggerated. Moreover, many neo-Darwinists (like Jerry) invoke natural selection as a Deus ex Macchina to solve problems they really are not in a position to clarify.
I'm confused. Which "Law of Gravity" are you indicating? Newton's expired early in the 20th Century, and people are working hard to replace Einstein's with a quantum version.
Could it be that you are confusing observation (attraction between massive bodies) and a human abstraction (gravity) that changes with the progress of science?
among the Galapagos finches and so forth, but what he nor anyone else could do (aside from educated guessing) is tell us how finches got here in the first place. Maybe your right. Maybe NS should be regarded as a law. l'll leave that to others to decide and only go one to say, that it's not NS that is in dispute, but the role that NS plays in the larger scheme of things.
I find it interesting that you contend that the name we dare not mention knows little of biology when in fact, with the exception of evolutionary biologist, most biologist can do their work and do it very well without ever hearing or even knowing about the neo Darwinian synthesis. Evo devo is a specialized field and its not surprising that many evo devo are also some of the biggest critics of the neo Darwinism/the modern synthesis.
I.e. many biologist who are actually in the field of evolutionary development biology are the ones who are trying to reformulate or extend the current theory.
You go on to say "I don't think she really understands anything about modern biology, only to discern controversy and scientific disputes that are somewhat divorced from reality"
I think to contend that there are no scientific disputes as you put it, is in itself "divorced from reality"
Darwin gave us demonstrable proof that biological evolution does exist and is still occurring. Darwin gave us a mechanism, Natural Selection, that could explain at least some of biological evolution, which he realized operated via heredity. (Though he did not know anything about heredity; that would come later via genetics and population genetics.) Darwin conceived of Natural Selection from his reading of Malthus - so too Wallace - and was also inspired by Adam Smith's writing on economics (which inspired Darwin to conceive of his "economy of nature"). Darwin used artificial selection of domesticated plants and animals as an analogy to Natural Selection (which gave his version of it more scientific credence than Wallace's, since Wallace had no opportunity to do anything more but a "thought experiment" based on his knowledge of tropical biodiversity and his reading of Malthus).
Darwin was both a great field naturalist and a fine experimental scientist. Among his other achievments was his theory on the formation of atolls; sunken volcanic islands ringed by coral reefs, which is still seen as scientifically accurate by geologists, more than a century and a half after he proposed it.
Much of science depends on inference ("educated guessing") and it would be best to say that I accept Natural Selection as an evolutionary mechanism as inferred by the data that has been collected for decades, including those of Darwin's Finches which have been studied for decades on the Galapagos Islands by the husband and wife team of evolutionary ecologists Peter and Rosemary Grant.
As for Suzan Mazur, I have met her and have discussed in person and via e-mail, evolutionary biology. Her understanding of it pales in comparison to other science writers whose work I am familiar with (including several I have met) such as Natalie Angier, Cornelia Dean, Faye Flam and especially, Carl Zimmer.
You ask "4) Explain how much you understand my point about the relevance of historical contingency."
I do not know a lot about historical contingency. SJ Gould was big on emphasizing this. But a respected evolutionist like Simon Conway Morris argues that evolutionary convergences are so common that there may not be as much contingency as Gould would like to believe.
I do know, and did mention in my book, that previous adaptations (such as a bilateral body plan) constrain the nature of future changes that will integrate successfully into the organismal phenotype. If this is what you mean about contingency, I agree. But that is very different from what Gould meant.
As for myself, I realize now that I should have said "historical constraint" in lieu of "historical contingency", which is a point I have emphasized repeatedly in replies to your creationist fans. (Speaking of which, I think you need to emphasize the first sentence of your second paragraph merely as edification to those I am referrring to.)