Foreword
      Introduction
      Chronology
      Evolution Tribes

1 The Altenberg 16
2 Altenberg! The Woodstock of Evolution?
3 Jerry Fodor and Stan Salthe Open the Evo Box
4 Theory of Form to Center Stage
5 The Two Stus
      Stuart Kauffman – Peace, Love & Complexity
      Stuart Newman – The Chess Master
6 The Two Massimos
      Massimo Pigliucci – Evolution & Flamboyance?
      Massimo Piattelli-Palmarini – Evoluzione senza Adattamento
7 The One and Only Richard Lewontin
8 Knight of the North Star: Antonio Lima-de-Faria, Autoevolution
9 The Wizard of Central Park: Stuart Pivar
10 Richard Dawkins Renounces Darwinism as Religion
11 Rockefeller University Evolution Symposium
12 Mainstream Media Doesn’t Get It – Except Vanity Fair
13 Stuart Newman: Evolution Politics
14 The Astrobiologists
      Bob Hazen: The Trumpeter Of Astrobiology
      Roger Buick & Nasa: Follow The H2O Or Energy Not Selection
      David Deamer: Line Arbitrary Twixt Life & Non-Life
      Ex NASA Astrobiology Institute Chief Bruce Runnegar
      NASA Humanist Chris McKay: Where Darwinism Fails

Appendix — Related Stories
      A Stuart Kauffman: Rethink Evolution, Self-Organization is Real
      B Stuart Newman’s "High Tea"
      C The Enlightening Ramray Bhat
      D Piattelli-Palmarini: Ostracism without Natural Selection
      E Niles Eldredge, Paleontologist
      F Stan Salthe: Neo-Darwinians Risking 'Rigor Mortis'

About the Author

"Well, it’s very unfortunate that you bought into this. There are very few people in evolutionary biology who take Pigliucci seriously, and Fodor, Pivar, et al. are literally unknowns, providing no evidence that they’ve read a single bit of the mainstream evolutionary biology literature. Of the pictures of the Altenberg group, I’m sure that most are unaware of your posting, as I know that several of them are mainstream evolutionary biologists, with no axe to grind with the framework in which most of us are working. We are seeing the field of evolutionary biology being increasingly trivialized and threatened by quacks, and although these folks are by no means creationists, they are every bit as dangerous. All areas of inquiry have limitations, but there is no justification for criticizing a field until one has put in the effort to understand it." – Mike Lynch, Distinguished Professor, Dept. of Biology, Indiana University

March 25, 2008
2:02 pm NZ

IT’S PRIVATE. That is now the word from organizers as to whether or not the public can listen-in to the conversation of 16 scientists meeting to remix the theory of evolution at Altenberg, Austria in July. So while Konrad Lorenz Institute where the symposium will take place may not exactly resemble the sacred pond of Emperor Augustus where priests read the entrails of eels and advised what was to befall Rome – and evolutionary science is nowhere near as primitive – there is still public concern about the emergence of evo high priests, as reflected in a substantial response to my recent series of evolution stories.

      Evolutionary biologist, Massimo Pigliucci, a co-architect of the KLI "major event", emailed me saying "somebody could do a sociological study of science and fringe science just based on the developments from our interview."

      As a rising star on the lecture circuit, Pigliucci knows there is much public interest in a new theory of evolution. Why then must the Altenberg proceedings remain closed?

      Here’s my abstract:

The public says a reformulation of the theory of evolution is bigger than the Altenberg 16 – no matter how brilliant the individuals may be. People think a remix of evolution is high priority and say they have a right to know, since scientists are publicly funded. They want open discussion and say such information should not be locked down for future book and DVD sales. There is too much of that kind of industry already corrupting science.

      Following is feedback on the evo stories – what developmental biologist Stuart Kauffman might consider part of the "ceaseless creativity" of the universe.

      I was happy to see Richard Leakey’s web site pick up the Dawkins story. It was actually Richard Leakey, then director of the Nairobi museum, who secured the plane for my flight into Olduvai to talk with his mother, the late paleoanthropologist Mary Leakey.

      A few of the science sites that picked up the Altenberg story include: Genome Technology Online, Geoscience Research Institute, Nature Publishing Group, and Society of Systematic Biologists.

      The Altenberg articles have been discussed online in at least a half dozen languages: Latvian, Indonesian, Portuguese, Dutch, Italian and Spanish.

      And they’ve been posted to religious sites, such as the Harekrishnas and Church of Jesus Christ of Latter-day Saints.

      Intelligent Designers are apparently some of the most vigorous bloggers on evo, and Paul Nelson’s column on the Altenberg story for Uncommon Descent generated 206 comments.

      Democratic Underground, always a fierce battleground, took up the debate, excerpting natural philosopher and zoologist Stan Salthe’s comments regarding natural selection, i.e., "Summarizing we can see the import of Darwinian theory of evolution is just unexplainable caprice from top to bottom. What evolves is just what happened to happen."

      Michael Purugganan, a professor of genomics and one of the A-16 scientists, emailed from his lab at NYU to say (in jest?), "I’ll have appropriate buttons or pins made that say Altenberg 16 . . . . they will be distributed at the meeting."

      And Yale professor of ecology and evolution Gunter Wagner, another of the A-16 – who I was unable to reach for comment for the original story – wrote "Hey that is great! This is one button I will keep!"

      But there have been grumblings elsewhere in the scientific community about who was left out of the A-16 invite. The name most mentioned as crucial to a successful redo of evolutionary theory and missing from the A-16 list is that of Harvard evolutionary geneticist Richard Lewontin.

      Lewontin told me he would not go, however. "No. No way." Aside from any personal objection to the content of the conference, there may be another reason Lewontin is not attending. According to one admirer, Lewontin doesn’t like to fly.

      One of the other giants I interviewed for the first Altenberg piece – paleontologist Niles Eldredge, originator of the punctuated equilibrium theory with Steve Gould – was apparently also not invited.

      Eldredge told me he only "knows of" Massimo Pigliucci, and actually described himself as "a very conventional evolutionary biologist". "I disappoint people sometimes," he said.

      Evolution’s star public intellectual, Richard Dawkins, might have been too much of an anchor for the A-16 discussions. He wasn’t invited as he hinted during our recent Q&A at Barnes & Noble in Tribeca:

"You’ve been taken in by the rhetoric. . . . You asked the question: Have I been invited? I’m sorry to say I get invited to lots of things and I literally can’t remember whether I was invited to this particular one or not."

But it’s being viewed as a "major event" I told him.

"By whom I wonder?", he jabbed.

      There was a disgruntled posting by "Jim C" from Melbourne on Dawkins.net saying, "We may indeed know more about the nature of DNA and the complex details of its operations, but it is the height of intellectual arrogance to describe the evolutionary theory moving away from a "population genetic-centered view"."

      With noticeable rivalry in the scientific community then, one of the qualifications for the A-16 no doubt must have been congeniality.

      Massimo Pigliucci’s colleague from Stony Brook, evolutionary biologist Doug Futuyma, for instance, is not on the list either.

      University of Toronto biochemist Larry Moran, who runs a popular web site called Sandwalk, which considers itself the rival to SEED blogger PZ Myers’ Pharyngula, asked me: "Why was Doug Futuyma not invited?"

      Niles Eldredge shared the following with me about Futuyma’s treatment of him and Steve Gould in his book:

"I you open Doug Futuyma’s book – the guy at Stony Brook who’s probably one of the most famous evolutionary biologists in the country now if for no other reason than he wrote that widely-read text book – you’re not going to find that Steve Gould and I get a very good shake in that book. And you’re not going to find I don’t think an extended discussion of self-organization, if it’s even mentioned."

      Maybe Futuyma’s lack of interest in self-organization – a subject which will be explored at the A-16 meeting – kept him off the list.

      That Lewontin, Eldredge, Dawkins and Futuyma will not be a part of the so-called "Extended Evolutionary Synthesis" discussion in Austria does diminish the event. But there’s plenty of fresh talent out there as well. And Massimo Pigliucci and Gerd Mueller have presumably found some.

      Stuart Newman, a professor of cell biology and anatomy at New York Medical College and board member of KLI, is presenting his theory of the origins of form at Altenberg – the current synthesis, remixed 70 years ago, has been without a theory of form. Newman says he doesn’t know half the people who are going to be there and that scientists really need a forum in which to interact with like-minded scientists.

      Newman added, "These groups are kind of carefully chosen so as not to create fights."

      The real disconcerting issue, though, is the public being shut out. The New York Times has now asked to attend after reading my Altenberg story. They too have been turned away. Not the first time the Times has noted my work, incidentally: "New York Times Fesses Up to Another Rip Off".

      Larry Moran at Sandwalk agreed with my suggestion that the conference somehow be made public. Moran linked my posting of the A-16 invite, to which one reader (The Monkeyman) responded:

"It is a shame that this and other conferences that hold interest to many budding scientists who cannot get the money to attend . . . will not be streamed or recorded and put up for download."

      Newman says "private" maybe evokes the wrong kind of image. He says he agrees that a lot of science is publicly funded and he does feel a responsibility to make his research accessible to the public. But he also thinks the event may not be designed for "prime time".

      Says Newman, "If I were to take my undigested ideas and make them accessible to the public, I would lose my reputation very fast because I probably have a lot of stupid ideas also."

      Gunter Wagner commented on Moran’s web site in response to the Altenberg piece, that he didn’t like being lumped together with the likes of philosopher Jerry Fodor and Stuart Pivar.

      Fodor wrote the now infamous "Why Pigs Don’t Have Wings" story in the London Review of Books arguing that the central story of the theory of evolution is wrong in a way that can’t be repaired, which led to a fierce online exchange among leading evolutionary thinkers hosted by Stan Salthe.

      Pivar is the independent scientist whose work has been skewered on the blogosphere for not being a complete theory of evolution.

      But despite the controversy, look for more commentary from Jerry Fodor on evolution without adaptation. He’s taken a year off from teaching as State of New Jersey philosopher at Rutgers University to write a book with Massimo Piattelli-Palmarini, a professor at the University of Arizona, who Fodor says is handling the biology. Fodor also says he has tenure and is not worried about fallout.

      But Salthe also told me he doesn’t like being lumped together with Fodor and Pivar, because he has published papers in the field. On the other hand, this doesn’t seem to make a difference in his attempts to contact A-16’s Gunter Wagner, who Salthe says won’t respond. Salthe says he thinks his view of natural selection makes him "poison".

      Fodor says the careers of most evolutionary scientists are tied up with natural selection.

      Pigliucci defends the natural selection turf. He told me this:

"So to say that natural selection is out of the picture seems to me to discard literally thousands and thousands of empirical papers. And I don’t think anybody can afford to do that, let alone Fodor, who is apparently not familiar with that literature."

      But Salthe says you can’t dismiss the censorship going on in the evo debate. He recently sent me his correspondence with the Neo-Darwinian journal TREE (Trends in Ecology and Evolution) in which he asked them to publish his letter arguing to "save the phenomenon of convergent evolution even if it seems inconvenient" to the Darwinian perspective on organic evolution. Salthe was responding to an article TREE published suggesting the concept of convergent evolution be eliminated based on a totally genetic analysis. TREE refused to publish Salthe’s letter.

      Convergent evolution he says happens when different species become similar without involving "similar genetic representation". Examples of this he notes are old world vultures evolving from hawks and new world vultures evolving from storks. . . .

      PZ Myers/Pharyngula, who Richard Dawkins quoted adoringly at Barnes & Noble last weekend, again trashed Stuart Pivar’s work in his blog after reading the Altenberg 16 story, but liked the fact that I’d interviewed Richard Lewontin.

      Pivar says he did take the advice of NASA mineralogist Robert Hazen and early on approached mainstream evo publishers. He has been repeated rejected he says, but continues to fight on, making the point that he’s the only one with a model.

      Pivar recently offered a research grant to Massimo Pigliucci and his lab to study his Engines of Evolution book, following an exchange of emails with Pigliucci over several months.

      Pigliucci said he considered the gesture "bribery" and refused the offer, adding that he does not share Pivar’s enthusiasm about his theory of form.

      Richard Milner, Steve Gould’s former editor and author of Darwin’s Universe (forthcoming 2009), told me that Darwin, while terrified of controversy himself, was no shrinking violet in sending out his disciples, Thomas Huxley ("Darwin’s bulldog") et al., to proselytize for him. Milner said Darwin kept a list of those he converted to his theory and that Huxley was shut down by the police for holding meetings on Sundays where he’d present his science lectures as sermons, calling them "Lay Sermons".

      I also received an email from a microbiologist named Anders in Denmark, who said Pivar’s concept was not sound science – which I passed on to Pivar to address. Pivar said he emailed Anders, who had not read his book, and told him he was sending a copy to him for review.

      Pivar says he welcomed a recent email with constructive comment from Stuart Newman on the subject of form.

      Newman told me this in a phone conversation about the theory of form he’ll be presenting at the Altenberg meeting:

"The idea is that when multicellularity first emerged [a half billion years ago] the products of a number of genes that existed in single-celled organisms, and had evolved for single cell purposes, began to mobilize physical forces and physical processes that are characteristic of materials at a larger (‘meso’) scale. For instance, single-celled organisms or individual cells can secrete molecules, but it doesn’t really have any consequence for the structure of the organism. But if it’s in a multicellular context, then secreted molecules can form gradients that provide patterns. . . . It’s a simple form of self-organization.

This can help explain the burst of animal evolution that happened in the Cambrian explosion. Consider, in a more complex example, two very distinct physical processes that existed in the single-celled world, the production of secreted molecules and intracellular biochemical oscillations. When they found themselves together in a multicellular-scale structure, their combined effect was to make segmentation all-but-inevitable. In fact, we know that modern-day embryos, including those of humans, still use these ancient "generic" physical processes to form their segmented backbones.

When multicellularity emerged, new physics was brought to bear on the formation of organisms. It’s not that these physical processes didn’t exist before multicellularity. They just didn’t pertain to the development of organisms before. . . .

At the point when the modern animal body plans first emerged [half a billion years ago] just about all of the genes that are used in modern organisms to make embryos were already there. They had evolved in the single-celled world but they weren’t doing embryogenesis. What did it take to get them to do embryogenesis? It took a change in scale. What led that change in scale is that, possibly due to alterations in external conditions, cells became sticky. And once they became sticky, you had multicellular organisms, and mobilization of the self-organizing physical processes of mesoscale materials."

      Newman also said people are working on pre-biotic evolution, but nobody would be presenting a paper on the subject at Altenberg in July.

      Fast forwarding a half billion years, Newman’s got a very interesting article in the March 2008 issue of Capitalism, Nature, Socialism, called "Evolution: The Public’s Problem and the Scientists’" in which he observes that:

"The nearly exclusive focus on genes to account for biological change at the levels of both individual development and large-scale evolution, like the cash nexus of market economies, collapses quality into quantity, life into symbol."

      Speaking of symbols, Ben Stein’s Expelled film people contacted me "to get involved" with the project after reading the Altenberg story. Curiously, they take a pro-war position, and I have not responded to them.

      Sam Smith, the inimitable editor of Undernews, the online publication of Progressive Review, excerpted and linked the Altenberg story with pinups of the various evo thinkers not invited to the A-16 meeting (including the late Andy Warhol), plus that of Massimo Pigliucci. The Undernews comments were growing tense last time I looked.

      Financial guru Catherine Austin Fitts, a former Assistant Secretary of Housing in the Bush I administration, included the A-16 invite story on her Solari.com "Top Picks" list.

      Canada’s Financial Post and National Post linked the Dawkins story.

      New York’s Daily News posted the Altenberg piece. And Fox Television News carried the A-16 story on Sean Hannity’s forum.

      So the public is craving evo enlightenment. But Massimo Pigliucci has said he will keep the lid on the Altenberg proceeding regardless and that he and European co-organizer Gerd Mueller will comment for the group only after returning home.

      "You’re saying that you’re ruling out even a panel in Altenberg at the end of the conference?" – I asked Pigliucci.

      "You mean on the order of: Doctor, how’s the patient doing?" – he responded. "No, the meeting is private."

STUART KAUFFMAN – Peace, Love and Complexity

"I have worked on self organization for years and love it," Stuart Kauffman emailed me from the University of Calgary’s Institute for Biocomplexity and Informatics, which he founded. What’s more Kauffman pinpointed exactly where we are in the quest for that elusive mechanism of evolution during a phone conversation on Valentine’s Day.

      Said Kauffman: "There are people spouting off as if we know the answer. We don’t know the answer."

      Nevertheless, Kauffman has moved on to tackling the "ceaseless creativity" of the universe in his book, Reinventing the Sacred. He described the book to me in an email as "VERY radical scientifically . . . and dangerous culturally," adding "I’m waiting for Jaweh to hit me with a thunderbolt, shades of Thor."

      Following our phone conversation, he sent me a second email clarifying that the book "aims to try to create safe spiritual space across all our traditions". He elaborated:

      "At a time when, with no insult to Catholics, the Pope states that the Church is the only true church, while Jews (like me), Muslims, and the Dali Lama are condemned to Hell, when Left Behind is a video game urging children to kill those who do not embrace Jesus for the Rapture, with Islamic extremists strapping bombs and killing people, we just have to try."

May 5, 2008
1:21 pm NZ

In his new book, Reinventing the Sacred, legendary complexity pioneer Stuart Kauffman continues to challenge the view of most biologists that natural selection is the only source of order. However, Kauffman is more charitable than hundreds of other evolutionary scientists (non-Creationists) who contend that natural selection is politics, not science, and that we are in a quagmire because of staggering commerical investment in a Darwinian industry built on an inadequate theory.

      True to his research roots in self-organization, Kauffman says life is not based on the replication of DNA and RNA. He also questions whether biology can be reduced to physics, writing that lovers walking along the Seine are not just particles in motion.

      He thinks the biosphere constructs itself using sunlight and free energy and that the universe is "ceaselessly creative." And because the future is not really predictable, Kauffman (writing from the Canadian Rockies) recommends we all calm down, remix science with the ancient Greek model of "the good life, well lived," and treat ALL in our global culture as sacred.

      Stuart Kauffman draws on 40 years of work for the book, from his investigation of snowflakes to "coherence-decoherence" of the conscious mind.

      Kauffman tackles evolution of the economy as well. Yes, it’s ceaselessly creative.

      He comes clean in a chapter called "Broken Bones" revealing he has advised the US Joint Chiefs of Staff on asymmetric warfare and terrorism (Kauffman’s been a consultant to Los Alamos too). He notes that "all sought to prevent war," but that "history shows us that war is often excused by a trumped-up atrocity or threatened atrocity."

      I telephoned Stuart Kauffman because I wanted to discuss self-organization, an area he trailblazed in the 1960s at New Mexico’s Santa Fe Institute.

      Kauffman began his career as a medical doctor, has been honored as a MacArthur Fellow, a Marshall Scholar and awarded the Gold Medal of the Academia Lincea Rome. He is a founder of the University of Calgary’s Biocomplexity and Informatics Institute and is currently an adjunct professor in the university’s philosophy department.

      His three previous books are: The Origins of Order, At Home in the Universe: The Search for the Laws of Self-Organization and Complexity, and Investigations.

      Stuart Kauffman spoke passionately about self-organization for much of the 45 minutes of our pre-scheduled talk, taking me on a shamanic flight through his rugged landscapes theory and to the edge of chaos throughout the universe. Then after several pleas (they grew loud) from his handler that my allotted time was up – the vision ended – and Kauffman agreed to move on to his next appointment.

      Excerpts from our interview follow (Appendix A).

STUART NEWMAN – The Chess Master

"He’s a one to watch in the unfolding evolution discourse," I was advised regarding New York Medical College cell biologist Stuart Newman. Many have their money riding on him, so to speak, at Altenberg to provide the convincing theory of form. Coincidentally, Stuart Kauffman was on Newman's PhD committee.

      Stuart Newman is the classic evolutionary scientist, dedicated to his lab and the nurture of his students, like NYMC grad student Ramray Bhat, who has his name on Newman’s Altenberg DPM paper as co-author.

      He’s told me he thinks the public has a right to share in scientific discovery and that he tries to make his papers publicly accessible. "I do care," he said.

      Newman enjoys penning critical professional articles on science and culture as well. And he’s testified before Congress when asked.

      A former student said Newman keeps a Spanish masterpiece on his computer screen for inspiration.

      No one’s said whether Stuart Newman actually plays chess, but he’s a grandmaster at checking the opposition, as the following emails reveal:

" 4/2/2008 Thank you for your kind words about the paper, Suzan. . . . please note, in contrast to other workers in the field – Stuart Kauffman, for instance, but particularly Eric Davidson – we actually de-emphasize the specific role of transcription factors in the generation of form. See the section of the paper that deals with "DTFs."

4/23/2008 I’m disappointed in Dawkins. His response is neither public nor understanding.

5/8/2008 Thanks for this. It sent me to the Sherman paper, which I had not seen. (I have attached it.) I’m not too impressed. The only causal agent is cryptic "programs." It doesn’t explain anything, but exhibits a "generative combinatorics" which is also a feature of our model. I’m also disappointed in Chomsky for endorsing it without probing deeper. It’s not very serious of him.

Piatteli-Palmarini has an instinct for what’s wrong with neo-Darwinism, but he seems to want to fix it with a not-too-coherent eclecticism [See also.. Appendix D]. Eric Davidson’s descriptive biology is very good, but his conceptual framework for evolution is pure neo-Darwinism, and as different as can be from ours. Stuart Pivar is a brilliant eccentric with an aesthetically based Platonistic obsession. His developmental details are almost all incorrect and I don’t think his ideas will contribute at all to an eventual synthesis.

5/11/2008 Thanks for your great efforts to raise the level of discourse (as they say in science studies circles). Of course Chomsky is right about the "Thompson-Turing approach, with its roots in rational morphology." I’m back to being a fan. . . .

5/12/2008 He [Chomsky] thinks Sherman is working in the Thompson-Turing tradition, which is not the case. We are, however. Nonetheless, I would suggest not pressing him on this. He will not be an important participant in this discourse, and there is no need to irritate him, which seems on the verge of happening.

6/17/2008 Interesting article. I agree with L-D-F [Antonio Lima-de-Faria] about Darwinism. But self-assembly is not the answer. Just a temporal version of preformationism: http://en.wikipedia.org/wiki/Preformationism ; i.e., there is nothing new under the sun.

"This order is also patent in the cellular shaping of a living organism. At present it is known that the pattern of an embryo is decided by a large collection of small and large RNAs, i.e., pure atomic processes, which have the ‘road map’ that decides the cellular pathways."

This could not be more wrong.

6/4/2008 Hi Suzan, I just should tell you that every time you mention Stuart Pivar in one of your articles it cuts your credibility among actual scientists to a small percent of what it would otherwise be. Though mentioning my work in the same context does not do me much harm, since it leads to dismissal of your views, it does me no good either."

      Newman also told me that he objected to the title "The New Charles Darwin," but not to "The New Master of Evolution", adding, "Let’s hope it’s true." Eight minutes later he followed up saying: "I meant the theory part, of course, not the master part."

April 8, 2008
11:37 am NZ

"A molecule of water does not form itself into waves and vortices. However, a mass consisting of trillions of water molecules does. You don’t need new substances. It’s just a matter of changing the scale and bringing new physical processes into play.

So if you have cells with genes that evolved for single-cell functions, and you put the cells together into clusters, then those clusters of cells have physical properties – including self-organizing properties – that individual cells never had. And then those cell clusters can make 40 or 50 different kinds of forms very rapidly by virtue of the physics mobilized by the existing gene products in the changed scale. They don’t need a lot of genetic changes to go from one form to another. And the forms produced in this way can become locked in later by natural selection." –Stuart Newman

      On his recent PBS television show One On One, John McLaughlin quizzed two religion authors about whether the idea of the Virgin birth in the oral accounts of the Bible had a reference in biology, with someone mentioning parthenogenesis – asexual reproduction. But could those early storytellers have actually been feeling their way around the idea of orthogenesis, i.e., spontaneous birth, where life has the innate ability to move linearly?

      The idea of orthogenesis was particularly popular with 19th century scientists, such as Ernst Haeckel and Jean-Baptiste Lamarck. Darwinian politics, however, coupled with fossil evidence showing non-linear patterns, led to an abandonment of the theory.

      But orthogenesis has recently regained credibility and the puzzle’s possibly solved as to why that fossil trail is actually linear. Paleontologists Niles Eldredge and Steve Gould suggested in their pivotal paper on punctuated equilibrium, for instance, that there was a deficiency of transitional forms.

      Further scientific investigation has revealed why, and now our nearly 150-year old evolutionary synthesis – which has never had a coherent theory of form – is about to get one.

      It was thrilling and somewhat humbling to read cell biologist Stuart Newman’s hypothesis of the evolutionary triumph of life as it self-organized half a billion years ago, using what he calls toolkit genes from single-celled highly plastic organisms to make a balletic leap into multicellularity at the time of the Cambrian explosion when virtually all of today’s modern animal forms (35 phyla) first appeared, as evidenced in the fossil rock.

      These toolkit genes, some of which act to mobilize basic physical forces and processes, thereby becoming what Newman calls DPMs (dynamical patterning modules) – along with others, the DTFs (developmental transcription factors) – performed an almost hallucinatory dance on the page as I read through his paper about a pattern language calling up certain physical processes to enable multicellular animals, i.e., metazoa about a millimeter in size to body-build – cavities, layers of tissue, segments, extremities, primitive hearts and even eyes.

      And while the DPMs got the DTFs to arrange the matter of cell types and region functions – Newman says it was the DPMs that really provided most of the pizzazz.

      Interestingly, Newman says this part of evolutionary history turns the Darwinian theory upside down in the sense that natural selection is not central.

      Stuart A. Newman is currently Professor of Cell Biology and Anatomy at New York Medical College in Valhalla, New York where he teaches and directs a lab.

      He has collaborated with University of Vienna theoretical biologist Gerd Mueller, University of Missouri biological physicist Gabor Forgacs as well as Ramray Bhat, on aspects of his DPM hypothesis. He has also co-authored the textbook Biological Physics of the Developing Embryo (Cambridge University Press) with Gabor Forgacs, and with Gerd Mueller co-edited Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology (MIT Press), a volume about the origination of body form during Ediacaran and early Cambrian periods, also contributing a few chapters to it.

      Newman’s A.B. degree is from Columbia University and his PhD in chemical physics from the University of Chicago where he also did post doctoral studies in theoretical biology, as well as at the School of Biological Sciences, University of Sussex. Newman’s been a visiting professor at Pasteur Institute, Paris; Commissariat a l’Energie Atomique-Saclay and the Indian Institute of Science, Bangalore.

      But Stuart Newman’s also a public intellectual. Through the years he has commented on social and cultural issues affecting science. He chose not to stand on the sidelines regarding the ethical issues surrounding human genetic and bioengineering, for instance.

      In 1997 along with Jeremy Rifkin, then president of the Foundation on Economic Trends, Newman attempted to patent a part human, part animal chimera to highlight the dangers of the commercialization and industrialization of organisms, which he fears will ultimately include humans.

      In 2002 he testified before the US Senate saying:

"Since my student days I have also been concerned with the uses to which scientific research is put. Having become convinced that scientists, who are beneficiaries of public resources [Newman has been the recipient of NSF and NIH grants for 30 years], have a deep responsibility to anticipate what lies down the road in their own fields and to serve as a resource for the public on the complex issues around applications of scientific research, I joined with other scientists, social scientists, women’s rights advocates and environmentalists, to found the Council for Responsible Genetics in the late 1970s."

      Newman has also weighed-in on politics’ impact on science in Capitalism and Socialism, noting how political interference can indeed warp research and deprive society of its benefits. Newman wrote recently in "Evolution: The Publics’ Problem and the Scientists" appearing in Capitalism, Nature, Socialism:

"The Soviet doctrine of Lysenkoism represented by ideological distortion of evolutionary biology that may be thought of as generic to top-down socialism . . . the genetic determinist ideology that it both rejected and gave life to . . . comports well with the worldview of advanced capitalism."

      But getting back to Stuart Newman’s theory of evolution – what exactly did the DPMs (dynamical patterning modules) – I count eleven – look like singly? And moving in combination?

      It seems that if these DPMs were physical-genetic modules, as Newman says in the paper, there ought to be a way to visualize them.

      Did some appear as kind of wobbly electric neon discharges? And others maybe resemble the old Camel smoke ring that once wafted through Times Square?

      Newman does provide a schematic drawing at the end of the paper showing the effects of various DPMs acting singly and in combination. And there is a table listing the DPMs with the molecule each is linked to, its physical principles and its role in evolution-development.

      He also says what DPMs were made of. They were gene products (proteins) but also networks of physical processes that shaped and patterned organisms using adhesion, polarization, viscoelasticity, etc. DPM elements also combined with one another to make oscillations and segmentation, as well as morphogens from secreted multicellular molecules.

      The morphogens then traveled through the organism to create organismal forms. Newman says the survival of cell types later became a matter for selection.

      There were also certain signaling pathways, like the Notch pathway, he says, that factored in. Notch was established several billion years ago before multicellularity occurred, as was the Wnt pathway, for example. Wnt in conjunction with the Frizzled family receptors of signals made cells polarize.

      Newman explains how spots and patterns were generated by morphogens. Lateral-acting inhibitors and reaction-diffusion systems came into play. He says skeletal elements, bones, feathers and hair were created this way.

      He also indicates that while some DTFs (developmental transcription factors) did exist in single-celled organisms for the purpose of cell contractility and light sensitivity, other DTFs – those participating in segmentation and tissue identity – did not exist in single-celled organisms. And he notes that combinations of DPMs and DTFs enabled segmentation, skeletogenesis, eyes to form and heart-like structures to develop.

      Stuart Newman concludes that it was the multicellular state that led to the appearance of developmental mechanisms, and that transcription factors in regulating cell fates did not play a starring role in the pattern language at the time of the Cambrian explosion.

      He says he’s not comfortable with the title "The New Charles Darwin", though. Well, how about "The New Master of Evolution"?

      Additional resources follow (Appendix B: "Stuart Newman’s "High Tea"" Appendix C: "The Enlightening Ramray Bhat").

(continuing… )

Appendix A:

STUART KAUFFMAN: RETHINK EVOLUTION,
SELF-ORGANIZATION IS REAL

May 5, 2008
1:21 pm NZ

Suzan Mazur: You were one of the pioneers of self-organization. I’ve looked at your new book, Reinventing the Sacred. You’re thinking in a much bigger way.

Stuart Kauffman: It has to do with getting older. You don’t write a book called Reinventing the Sacred when you’re 30. . . .

Suzan Mazur: Are there alternatives to natural selection?

Stuart Kauffman: I think self-organization is part of an alternative to natural selection. Let me try to frame it for you. In fact, it’s a huge debate. The truth is that we don’t know how to think about it.

Suzan Mazur: You said in your forward to Investigations: “Self organization mingles with natural selection in barely understood ways to yield the magnificence of our teeming biosphere. We must, therefore, expand evolutionary theory.”

Stuart Kauffman: I’m still there. . . . Investigations is the weirdest book I’ve ever written and it is the prelude to Reinventing the Sacred. I’ve gone through a trajectory in my life. I started with pure self-organization and I originally thought 40 years ago – let’s see how far we can get without any selection at all. . . . Just think about a snowflake.

Suzan Mazur: You’ve said: “The snowflake’s delicate six-fold symmetry tells us that order can arise without the benefit of natural selection.” So it can arise without natural selection, but it’s not living.

Stuart Kauffman: But it’s not living. Right. There are all sorts of signatures of self-organization. I’ll give you one that very few would doubt. I don’t spend time talking about it in any of my books. But here it is.

If you take lipids like cholesterol and you put them in water, they fall into a structure – a liposome, which is called a bilipid membrane, that forms a hollow vesicle. . . . Now if you look at the structure of this bilipid membrane, it’s virtually identical to the bilipid membrane in your cells. So this is a self-organized property of lipids.

That’s physics and chemistry. . . . And evolution has made use of it to make lipid membranes that balance cells. So that’s a snowflake. It’s hard to look at that and doubt it. Nothing mysterious or mystical. . . .

Suzan Mazur: No genes in the mix.

Stuart Kauffman: Genes by themselves are utterly dead. They’re just DNA molecules. It takes a whole cell in the case of a fertilized egg to grow into an adult. So there’s a lot of physics and chemistry. . . .

And somehow the right answer is that this is a whole integrated system in which matter, energy, information, whatever that means – it turns out to be a very slippery concept – and the control of process is all organized in some way.

The philosopher Immanuel Kant talked about this – the self-propagating organization of process. . . .

Suzan Mazur: You say in Reinventing the Sacred: “I have always believed that that basis of life is deeper and that it rests on catalysis. The speeding up of chemical reactions by enzymes.”

Stuart Kauffman: And then I have a chapter called “The Cycle of Work”.

Suzan Mazur: You say: “My second intuition is that it’s based on some form of collective autocatalysis.”

Stuart Kauffman: Right. So remember Charles Darwin starts with life. He doesn’t get you to life. . .

Suzan Mazur: Are you saying form came first and genes later?

Stuart Kauffman: You mean in the origin of life.

Suzan Mazur: Yes.

Stuart Kauffman: I’ll tell you what I think. Current cells use DNA, RNA and proteins. It’s really unlikely that the earliest life on Earth used anything as complicated as contemporary DNA, RNA and protein, because the machinery by which our DNA gets translated into proteins is incredibly complicated and it includes the fact that the genes code for that protein that carries out the translation for those proteins. They’re called amino acid synthesizers. So life couldn’t have started out that complex.

Assuming life started on Earth – it had to start somehow else and evolve into current life. People are working on the origin of life, including me, including my idea on collective autocatalysis. It is a debate about self-organization. But it’s before there is life.

There’s a guy named Reza Ghadiri. And Reza has made a collectively autocatalytic system of proteins where protein 1 catalyzes the formation of protein 2 out of protein 2 parts and protein 2 catalyzes the formation of protein 1 out of protein 1 parts.

There’s no molecule in Ghadiri’s system. This system catalyzes its own formation. The set as a whole is collectively autocatalytic. It achieves catalytic closure. That’s a done deal experimentally. Molecular application’s in the bag. Ghadiri at Scripps Research Institute has done it.

Now before he did that he also made a protein that catalyzed its own formation. So that’s both logically possible and that’s in the bag experimentally too.

Next thing to tell you is that a cell really is a collectively autocatalytic whole. There is no molecule in the cell that catalyzes its own formation. The cell as a whole builds itself. . .

Suzan Mazur: Originally genes were or were not part of the story?

Stuart Kauffman: Nobody knows.

Suzan Mazur: Your sense is that it was more of a mechanical and chemical process first.

Stuart Kauffman: My sense is that it was a catalytic process. Collectively autocatalytic. I have a whole theory about it – chapter 5 in the new book. But that’s just a theory.

What Reza’s done is fact. Whether the theory turns out to be correct, we don’t know. It’s a beautiful theory.

Suzan Mazur: But in the beginning when you had this simple cell there were no genes.

Stuart Kauffman: It depends what you mean by genes. If you mean by a gene a sequence of nucleotides that codes for a protein, I think it’s extremely unlikely that at the start of life – if life started on Earth or wherever it started – that you started with genes that coded for proteins. That’s just utterly remote.

But it may have been that the earliest catalysts were polynucleotides rather than proteins or something else. In that sense of gene – yes. But they wouldn’t have coded for proteins. It’s just remote.

So what we’re talking about is how do you get life in the first place?

Suzan Mazur: Where do the work cycles fit in?

Stuart Kauffman: Think about choo-choo trains. A train uses heat. It turns it into mechanical work train pistons. That’s a work cycle. It uses the transfer of heat from a hot to a cold place. And it manages to get the pistons to go around.

It’s been around since 1830. A guy named Sadi Carnot worked out the principles of a thermodynamic work cycle.

I think that an essential part of life is that it does work cycles. It’s not enough that life is markedly reproducing. . . Every free living cell, in fact, all the cells in your body do work cycles – chemical work cycles and mechano-chemical work cycles. And that’s missing from what most people think about life. . . Buried in this are the roles of self-organization and natural selection.

Selection couldn’t have played a role before there were organisms. You couldn’t have had natural selection because there were no organisms. It’s a different debate whether some other form of selection for chemical stability might have played a role.

There are some physicists who are asking questions like: Is natural selection an expression of some more general process? Like entropy production. And it’s all up in the air. But at least people are thinking about it. Meanwhile, we’ve got self-organization.

Suzan Mazur: Are evolution and development the same thing?

Stuart Kauffman: Sure.

Suzan Mazur: You mention Nobel laureate Murray Gell-Mann in your book. I know you were colleagues at the Santa Fe Institute. Do you think similarly about self-organization?

Stuart Kauffman: Probably not. . . . Murray is a profound reductionist. He’s been a major voice in the Santa Fe Institute and is a superb scientist. I’m not a reductionist. Reductionism meaning everything is due to the physical laws down there.

What’s happening is that the physics community is dividing now. . . .

But let me tell you where I started 40 years ago. And where it is now. I literally started on this when I was 24 and I’m 68. . . That was about 1964.

You know that cells get to be different from one another – cell differentiation. You make liver cells and kidney cells and spleen cells. And the question at the time was: So how do cells get to be different?

We thought – different cells get different genes from the fertilized egg. That turned out to be false. Just wrong. All the cells in your body have the same genes.

Suzan Mazur: Right.

Stuart Kauffman: Now it’s essential to know that different cells in your body make different proteins. Red blood cells make hemoglobin. That’s because different genes are active. Where active means making more protein.

Two guys who got the Nobel prize for this, Francois Jacob and Jacques Monod, in 1961 showed in bacteria that genes could turn one another on and off. This is absolutely essential now. One gene can make a protein that binds to a little DNA region near another gene and turn the other gene on or turn it off.

Suzan Mazur: Right.

Stuart Kauffman: So there’s a sense – leaving out the rest of the physics and chemistry of the cell, which we cannot do, but just for the moment – then you could imagine genes turning one another on and off. Jacob and Minod published a document in which they said imagine you’ve got two genes.

You and I are the two genes. And we’re both spontaneously active, if nothing happens to us. But Stu makes the Stu protein which goes over and binds next to the Suzan gene and shuts Suzan off. And vice versa. Suzan makes a protein that shuts Stu off.

So it’s a tiny circuit, a genetic circuit. You can think of it like an electrical circuit. Then that circuit – and I think you can see this immediately – has two alternative steady states. Suzan on. Stu off. And Stu on. Suzan off. Can you see it?

Suzan Mazur: I think so.

Stuart Kauffman: So what they said was – look the same genome is giving rise to two patterns of gene activity. Suzan on. Stu off. And the other way around.

Suzan Mazur: Right.

Stuart Kauffman: This could be what controls cell differentiation. And they revolutionized the whole field of developmental biology with that paper.

I came along about a year later. And what I said was – we used to think 100,000 genes. We now know it’s about 25,000 or 30,000 genes. And I thought, well, there’s some sort of regulatory circuitry among these 25,000 or 30,000 genes. And there is. Forty-four years later we know something about it.

Imagine you’ve got 30,000 genes and somehow they’re turning one another on and off in some complicated way. Okay. What I did – this is Stu’s early foray into self-organization. . .

Suzan Mazur: So how many of the 25,000 or 30,000 are doing the turning on and off?

Stuart Kauffman: Nobody knew 40 years ago. . . Here’s what we know now. In the human, there are approximately 2,000 genes that seem to play the role of turning one another on and off and the rest of the genes on and off. . . . They’re called transcription factors. And they’re also regulating the other genes.

Hemoglobin is probably not regulating anything. It’s regulated, but not regulating.

Suzan Mazur: Right.

Stuart Kauffman: So here’s what I did. This is an essential core of current biology.

Suzan Mazur: The endogenous variables. . . .

Stuart Kauffman: Right. You also have all the proteins. . . . Let’s suppose that there are 25,000 genes. And 2,000 of them are playing the role of regulating one another and regulating the other 22,500. Just imagine that genes can only be on or off. That’s false. That’s an idealization. Then how many possible patterns of gene activity are there?

Well there’s 25,000 genes. So each could be on or off. So there’s 2x2x2 25,000 times. Well that’s 2 to the 25,000th. Right?

Suzan Mazur: Right.

Stuart Kauffman: Which is something like 10 to the 7,000th. Okay? There’s only 10 to the 80th particles in the whole universe. Are you stunned?

Suzan Mazur: It’s getting pretty staggering. . .

Stuart Kauffman: So, 25,000 is plenty if you start thinking about all the possible combinations of their activities. It’s super- hyper-astronomical.

Suzan Mazur: Right.

Stuart Kauffman: The next idea you need is somehow this network among the genes is controlling their activities. We don’t know what this network is. My colleagues and I have just published a paper in which we think we maybe know. We have the first sketch of what this regulatory network looks like. . . .

Anyway here’s what I did when I was young. I asked the following radical question. . . I said does this regulatory network have to be really really special and tuned by natural selection to give rise to normal development? Or could it be spontaneously self-organized so that there’s a huge set of possible networks and they’re sort of all good enough? In other words, is it a spontaneous self-organized property of complex networks that they just do the right thing?. . .

So I was saying ignore selection. Let’s just ask whether or not there’s a self-organized property and complex network of genes.

And what I showed in my mid 20s – I was 27 when I published it for the first time – was that my intuition was right. There really are. And so I modeled genes like they were lightbulbs, which they’re not. And I made random lightbulb networks.

They’re called Boolean networks because of a guy named George Boole. We now know a vast amount about the behavior of really complicated Boolean networks. Even random Boolean networks. So I’m just going to tell you a couple of things.

Suzan Mazur: Okay.

Stuart Kauffman: You know how I had you and me turning one another on and off and we had two steady states.

Suzan Mazur: Yes.

Stuart Kauffman: So the fancy word for those two steady states is attractor. That’s the mathematical word. And you can think of it like a mountain region with a bunch of lakes in it. And each lake is like an attractor. And you know how streams flow into a lake. So in the space of all the possible pattern of gene activity, most of them constitute streams that flow into the attractor lakes. So the hypothesis I’ve had for 45 years, partially taken from Jacob and Monod, is that cell types – livers, kidneys, etc. – are these attractors.

Suzan Mazur: I see.

Stuart Kauffman: So one lake is a liver. Another lake is a kidney. Another lake is. . . You with me?

Suzan Mazur: Yes.

Stuart Kauffman: So we’ve got evidence that that hypothesis is true. Cell types look like they’re attractors. Now, if that’s true, cells getting to be different from one another happens in basically one of two ways.

You hop out of one lake into a mountain pass and flow down a creek into another lake. And then there’s a fancier way in which you wiggle the mountains and change where the lakes are. That’s called a bifurcation.

So this is sort of the two ways that it can happen. And we’ve got evidence for both. So we’re beginning to understand that the cell and the organism is a very complicated set of processes activating and inhibiting one another. It’s really much broader than genes.

Suzan Mazur: And form arises?

Stuart Kauffman: To say we know nothing about how form arises is wrong. There’s been 70 years of superb developmental biology. . . .

Suzan Mazur: Can you, for instance, do plastic surgery embryonically where the correction will take – say to an arm? . . .

Stuart Kauffman: You mean could you conceivably take a thalidomide baby and do surgery and make it grow a normal arm?

Suzan Mazur: Yes.

Stuart Kauffman: Conceivably.

Suzan Mazur: You can?

Stuart Kauffman: No. Nobody’s ever done it. But it doesn’t seem impossible. And this has to do with what I’m working on right now. A lot of people are working on controlling and steering cell fates. That’s exactly what I’m doing right now. I’m trying to get cancer cells to differentiate into normal cells. I’m trying to get a new way to treat cancer. . . .

But to get back to self-organization, I showed two main things. Years ago I showed lakes of the kind you would need to explain cell types as lakes as attractors. And we know that cell types are actually attractors. It’s early evidence. I think that it’s very likely that it’s true. . . .

Now I’m going to tell you something that’s just stunning. All of this work that has been done on random Boolean knots – it turns out that they can behave in three broad ways: ordered, chaotic, and there’s a phase transition between the ordered regime and the chaotic regime where cells are poised at the “edge of chaos.”

That’s a phrase we came up with at Santa Fe Institute. A whole bunch of us – Chris Langdon, Norman Packard and I are the three main people who focused on all of this.

I have ever since 1987 believed that cells are poised on the edge of chaos. You’ll find it in my first two books.

The easiest book of mine to read, by the way, is my second book: At Home in the Universe, which a lot of people have read. Al Gore read it. I wrote it with Gore in mind. . . .

So there’s this poised edge of chaos state between order and chaos. Here’s what we’re beginning to know now, 20 years later. There’s evidence that cells are at the edge of chaos. The mathematical term is critical. Ordered, chaotic and critical. Edge of chaos will do.

So two main papers have been published. One came out just a couple of weeks ago and I’m one of the authors on it. . . . It is the first direct evidence that maybe cells are at the edge of chaos. There’s really dramatic evidence. It’s gorgeous. But it’s only one example.

Suzan Mazur: Can we draw conclusions?

Stuart Kauffman: No. But could you say – neat, let’s explore it further? Yes.

Suzan Mazur: If it’s right?

Stuart Kauffman: I suspect, I hypothesize that we may have found something general about life anywhere in the universe. That cells or whatever the analog of cells are anywhere are going to have to be at the edge of chaos because they could do all sorts of neat things.

They can coordinate the most complicated behavior. They can propagate information most efficiently. There are all sorts of neat reasons why it’s incredibly advantageous to be at the edge of chaos.

Notice that I just used the word advantageous. Now you start hearing natural selection creep in. So it turns out that to be at the edge of chaos, networks have to be pretty special. They can’t just be any old network. They have to be tuned to be at the edge of chaos.

And what could possibly be doing that tuning? Well, natural selection, because it’s highly advantageous. So here is a marriage of self-organization and selection. Both are necessary.

In other words, the self-organization part is that large classes of networks have a property that they’re either ordered, chaotic or edge of chaos – critical. . . . So self-organization affords the capacity to be critical and then selection gets it and maintains it. And maybe it’s so general that it’s a law for any biosphere.

Suzan Mazur: So natural selection exists throughout the universe?

Stuart Kauffman: Well, yes, wherever there’s life. But notice that there’s self-organization too. . .

There are people who are spouting off as if we know the answer. We don’t know the answer.

Suzan Mazur: So you’re saying we should enjoy life.

Stuart Kauffman: Well, we should enjoy life. But we have to rethink evolutionary theory. It’s not just natural selection. Self-organization is real.

…appendix ends…

Appendix B

STUART NEWMAN’S “HIGH TEA”
Before Genetic Programs There Were DPMs

March 31, 2008
9:14 am NZ

While some scientists prefer shaping their opinions about evolution based on audience reaction while on book tour – others are actually looking for answers in the lab. Stuart Newman, Professor of Cell Biology and Anatomy at New York Medical College, is the real deal.

Newman will be presenting his full theory about “dynamic patterning modules” (DPMs) and “form” in evolution at a symposium in Altenberg, Austria this July at Konrad Lorenz Institute. The conference – first highlighted in my story “Altenberg! The Woodstock of Evolution?”, carried by Scoop Media – is designed to discuss a remix of the existing theory of evolution.

Charles Darwin’s theory was last updated 70 years ago. “Extended Evolutionary Synthesis” is the working title of the new one.

In a phone interview, Stuart Newman told me that some of his work on the theory of form – which the current evolutionary formula lacks – was done in collaboration with Gerd Mueller, a theoretical biologist at the University of Vienna. Mueller is also Chairman, KLI and one of the organizers of the Altenberg symposium.

Newman has co-authored the textbook Biological Physics of the Developing Embryo (Cambridge Univ. Press) with Gabor Forgacs, a biological physicist at the University of Missouri, and co-edited the volume Origination of Organismal Form (MIT Press) with Gerd Mueller, also contributing a few chapters to it.

On Tuesday, March 25, Newman spoke at the University of Notre Dame’s Interdisciplinary Center for the Study of Biocomplexity. Newman states that “in contrast to the Neo-Darwinian principle . . . phenotypic disparity early in evolution occurred in advance of, rather than closely tracked, genotypic change.”

Here’s the abstract from Newman’s Notre Dame “high tea”:

“The shapes and forms of multicellular organisms arise by generation of new cell states and types and changes in the numbers and rearrangements of the various kinds of cells. This talk will consider the role played by a core set of “dynamic patterning modules” (DPMs) in the origination, development and evolution of complex organisms. DPMs consist of the gene products of what is known as the “developmental-genetic toolkit,” but considered in subsets, as dynamical networks embodying physical processes characteristic of chemically and mechanically excitable meso- to macroscopic systems like cell aggregates: cohesion, viscoelasticity, diffusion, and spatio-temporal heterogeneity based on lateral inhibition, and multistable and oscillatory dynamics.

I will focus on the emergence of the multicellular animals (metazoa), and show how the toolkit gene products and pathways that pre-existed this form of life acquired novel morphogenetic functions simply by virtue of the change in scale and context inherent to multicellularity. We show that DPMs, acting singly and in combination with each other, constitute a “pattern language” capable of generating all metazoan body plans and organ forms.

This concept implies that the multicellular organisms of the late Precambrian – early Cambrian were phenotypically highly plastic, fluently exploring morphospace in a fashion decoupled from both genotypic change and adaptation. The stable developmental trajectories and morphological phenotypes of modern animals, then, are considered to be products of stabilizing selection. This perspective provides a solution to the apparent “molecular homology-analogy paradox,” whereby divergent modern animal types utilize the same molecular toolkit during development by proposing, in contrast to the Neo-Darwinian principle, that phenotypic disparity early in evolution occurred in advance of, rather than closely tracked, genotypic change.”

…appendix ends…

Appendix C

THE ENLIGHTENING RAMRAY BHAT: ORIGIN OF BODY PLANS

April 15, 2008
12:32 pm NZ

"Our theory does not stand against natural selection in its entirety – it relegates it to a less important role,” says Ramray Bhat, cell biologist Stuart Newman’s co-author of the just published paper in Physical Biology: “Dynamical patterning modules: physico-genetic determinants of morphological development”. Nevertheless, neo-Darwinians – to whom natural selection is central to evolution – have tended to bury their heads in the sand when presented with a theory for form, which the neo-Darwinian model lacks. Why spoil next year’s commercial celebration of the 150th anniversary of Charles Darwin’s Origin of Species for a really coherent new theory?

I asked Ramray Bhat, now a graduate student at New York Medical College, if he’d answer a few questions about his paper and tell me about his journey from Calcutta to Valhalla and a collaboration with Stuart Newman. Our conversation follows.

Suzan Mazur: Are you and your distinguished co-author Stuart Newman saying that you have the first really coherent theory of evolution with regard to how virtually all of today’s animal forms self-organized – 35 phyla – roughly a half billion years ago?

Ramray Bhat: I would rather put it as follows – we have the first really coherent framework to explain the origination and evolution of body plans and organ forms within a short evolutionary period, known as the Cambrian explosion.

Within this framework we also explore the relationships between gene products mediating the physics of biological matter (which we denote as DPMs) and transcription factors (DTFs), which carry out effects of the former within cells and tissues and hardwire DPMs’ molecular players within regulatory networks. This framework also solves the Molecular Homology-Analogy paradox – why same/similar sets of genes are employed to build functionally or structurally similar organ forms in widely divergent organisms.

All of these are inconsistent with and cannot be explained by the classical neo-Darwinian model. We accomodate the role of natural selection in our framework mainly to lock the already-emerged but immensely plastic forms into place, and to render them robust.

Suzan Mazur: How do you define self-organization?

Ramray Bhat: By self-organization we mean the generic property of biological matter to attain a certain complexity in size, shape and pattern without depending on a blueprint or a recipe that is coded within its genome, or for that matter any other “ome”. Rather this property comes from the physics and chemistry that make up biological matter.

Suzan Mazur: You state that you take a physicalist perspective. And you identify a “pattern language” that shaped multicellular life as it emerged from the single-cell state at the time of the Cambrian explosion. You call this language DPMs – dynamical patterning modules. The concept of DPMs is the main thrust of your paper just published online in Physical Biology, correct?

Ramray Bhat: Correct. While the paper published in Physical Biology has been written with emphasis on the physics and physical phenomena that DPMs embody, our contribution to the International Journal of Developmental Biology explores in some depth the relationship of DPMs with DTFs.

We also believe that the forms preceding the Cambrian explosion need not have been necessarily single-celled. They might have been transiently and variably multicellular sheets. Diverse three-dimensional “plastic” (i.e., polymorphic) body plans came about within a short evolutionary period as a consequence of the DPMs acting singly or in combination with each other.

Suzan Mazur: You identify nine DPMs but say there are possibly more, as well as illustrate their effects. Are you saying in your paper that DPMs still exist? That while DPMs explored the formation of internal body cavities, segmentation, appendages, primitive hearts and eyes in highly plastic ancient multicellular organisms, DPMs continue to have a role in modern-day organisms – though only to a degree?

Ramray Bhat: Of course, DPMs continue to have a prominent role in the development of extant multicellular organisms. My experimental research involves trying to tease out the DPMs involved in patterning the skeleton of limbs. However, the DPMs can no longer explore as many new possibilities in terms of organ forms or body plans as they did in the ancient past; that is because their effects are now hardwired to the genome through millions of years of stabilizing evolution. The result of stable body plans and organ forms has come with a trade-off: the ability of the DPMs to freely explore what we call morphospace is severely constrained.

Suzan Mazur: Why did you decide not to present a model for DPMs?

Ramray Bhat: Our first task was to build a theoretical framework within which to resolve issues that loom large in the field of evo-devo, such as the Cambrian explosion and the Molecular Homology-Analogy paradox. This framework was built by assimilating previous research in this area by Prof Newman and his colleagues. Having put forward the same in the form of these two papers, we would embark on our next step shortly – to devise a computational model of the action of the DPMs.

Suzan Mazur: What do DPMs look like?

Ramray Bhat: DPMs per se are not readily visualizable like, say, proteins or genes, which are particular kinds of molecules. Each DPM consists of gene products and the physics they mobilize. For example, the DPM we annotate as ADH consists of cadherins and lectins and their associated physical property of adhesion. These DPMs were present in unicellular organisms but assumed their physical role (relevant to rapid and exhaustive exploration of multicellular form), only in the context of multicellularity. The effects of DPMs are easy to visualize, however, and we have done so in a series of “before” and “after” figures in our Physical Biology paper.

Suzan Mazur: You identify DTFs – developmental transcriptional factors – as coming into play as stabilizers but only after considerable body-building took place in the multicellular organisms at the time of the Cambrian explosion. Could you say a bit more about the role of DTFs?

Ramray Bhat: Developmental biologists have observed a small set of genes, coordinating organismal development, to be highly conserved across the multicellular kingdom. They call these genes the Developmental Genetic Toolkit. The genes whose products constitute DPMs (along with the physical phenomena they mediate individually, and in combination) are components of this toolkit.

There is another class of molecular players which also figure in the Toolkit but are not tied to any physics per se. They act in consequence to the action of DPMs to switch on and off certain genes and thus mediate cell-specific or tissue-specific effects of the DPMs. Since the DTFs are as ancient as the DPM Toolkit components, they had roles in the unicellular world in mediating transcriptional responses to internal and external signals.

Since embryonic regions and organs did not come into existence before multicellularity, the association of the DTFs with the DPMs as well as with their own biological effects can be regarded more as “frozen accidents”. They may also have been the reason for a somewhat constrained genotype-phenotype relationship in extant organisms as they hardwire the DPMs by participating with them im regulatory networks.

Suzan Mazur: As a graduate student, does your experimental work in Stuart Newman’s laboratory have anything to do with the DPM theory you have put forward in the two papers?

Ramray Bhat: An underlying theme in Prof Newman’s lab has been to not only study the molecular players involved in developmental phenomena and to tease out their dynamics, but also to understand the physics that goes along with their role. I investigate the pattern formation of limb skeletons – the underlying principles of which are ubiquitous in the vertebrate kingdom. A lot of the molecules and the dynamics involved in this process such as cadherins, galectins, morphogens and the Notch pathway molecules are components of the very DPMs we have described in the paper. Using a cell-culture model, I am trying to pin down a core network of molecules patterning the process of cartilage formation in chicken limb buds.

Suzan Mazur: Do you expect resistance to your theory in light of all the celebration surrounding the 150th anniversary next year of Darwin’s publication of the Origin of Species?

Ramray Bhat: Science takes place through a continual process of dialectics. We expect resistance and debate from the scientific community regarding these new ideas, as it is only through this that a collective understanding of the origination and evolution of organismal form can be bettered. Our theory does not stand against natural selection in its entirety – it relegates it to a less important role – one of fine-tuning and building upon the body plans and organ forms, brought by actions and interactions of DPMs.

Suzan Mazur: How did you find your way from Calcutta to Valhalla and into Stuart Newman’s lab and collaboration on a paper he has said reflects a synthesis of 20 years of his work?

Ramray Bhat: I developed an interest in evolution while in high school and studied organismal development and embryology during my first year in medicine at the University of Calcutta Medical College. This interest grew into a passion and alongside the drudgery of my medical curriculum I was largely teaching myself evo-devo through the works of Stephen Gould, Stuart Kauffman, Mary Jane West-Eberhard and Wallace Arthur.

During this period, I was immensely encouraged to learn more and guided to a great extent by prominent scientists in India such as Prof Vidyanand Nanjundiah, Prof Partha Majumder and Prof Amitabh Joshi. It is through them that I came to know about the contributions in this field by Prof Newman.

Prof Newman’s theoretical-cum-experimental approach to research on limb skeletal pattern formation, his formidable contribution to the growth of the evo-devo field, as well as his attention to the socio-cultural and philosophical aspects of biological research motivated me to apply to New York Medical College.

The inspiration to co-write this paper largely came about through continuous discussion with Prof Newman as well as a long-held desire to resolve the above-mentioned evo-devo issues, which had been needling me ever since I started reading about evolution.

Suzan Mazur: How long have you been working with Stuart Newman?

Ramray Bhat: I have been working under him as a graduate student for the past two and a half years.

Suzan Mazur: How would you describe your collaboration with Stuart Newman?

Ramray Bhat: I would qualify my experience under him as more of an education than collaboration. Not only has my experimental research in his lab been stimulating, our daily, and sometimes into the night discussions on my research as well as biological theory and philosophy, which I feel is integral to an ideal scientific education, will go a long way in forging a meaningful and productive career, for me, in natural sciences.

Suzan Mazur: When will you complete your PhD, and will you stay in the US or return to India following your studies?

Ramray Bhat: I expect to complete my PhD within the next two years. I haven’t really thought about a next step, as I want to concentrate on the present, which is actually a fantastic period of my scientific life. However, I feel strongly about imbibing all that I can from this scientific environment and country and returning to India where I can contribute in a meaningful way to Indian science, research and education.

…appendix ends…

ABOUT THE AUTHOR

Suzan Mazur’s interest in evolution began with a flight from Nairobi into Olduvai Gorge to interview the late paleoanthropologist Mary Leakey. Because of ideological struggles, the Kenyan-Tanzanian border was closed, and Leakey was the only reason authorities in Dar es Salaam agreed to give landing clearance. The meeting followed discovery by Leakey and her team of the 3.6 million-year-old hominid footprints at Laetoli. Suzan Mazur’s reports have since appeared in the Financial Times, The Economist, Forbes, Newsday, Philadelphia Inquirer, Archaeology, Connoisseur, Omni and others, as well as on PBS, CBC and MBC. She has been a guest on McLaughlin, Charlie Rose and various Fox Television News programs.

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