Damned Heretics

Condemned by the established, but very often right

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Qualified outsiders and maverick insiders are often right about the need to replace received wisdom in science and society, as the history of the Nobel prize shows. This blog exists to back the best of them in their uphill assault on the massively entrenched edifice of resistance to and prejudice against reviewing, let alone revising, ruling ideas. In support of such qualified dissenters and courageous heretics we search for scientific paradigms and other established beliefs which may be maintained only by the power and politics of the status quo, comparing them with academic research and the published experimental and investigative record.

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It is really important to underscore that everything we’re talking about tonight could be utter nonsense. – Brian Greene (NYU panel on Hidden Dimensions June 5 2010, World Science Festival)

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Darwin plus

Times essay salutes need for Darwin 2.0 at last

Douglas Erwin’s decency misleads him somewhat

Paradigm change not joyful to some, Doug

darwin.jpegAnyone who has heard top creationist intellectuals in action knows they are as clever as any Jesuit in pointing to holes in our understanding of evolution and how it works, holes in which they find God hiding, but which others expect to be filled with science anon.

As the fine exhibition on Darwin at the American Museum of Natural History last year showed, this cleverness has led to a certain panic among evolutionists, who too often have pretended that the gaps don’t exist, and that mutation plus the Darwinian struggle explains all, as in the “modern synthesis”.

The exhibition studiously avoided all mention of the creationist argument, treating it as beneath contempt, which it probably is, logically speaking. But as we have noted in previous posts, much has been learned in the past decade which is filling in the gaps in our understanding of how new species pop up, which is the fundamental puzzle the modern synthesis doesn’t solve.

This morning the New York Times Science section is devoted to a nice set of pieces entirely devoted to “Evolution” and saluting these advances, and the changes in the paradigm they herald. “This special issue of the Science Times is an attempt to help make sense of evolution, as a living, changing science” says the introduction.

The key essay on the paradigm issue is Darwin Still Rules, but some Biologists Dream of a Paradigm Shift by Douglas H. Erwin, a senior scientist at the Smithsonian’s National Museum of Natural History and a research professor at the Santa Fe Institute, home of the farthest out, beyond the edge scientific and other thinkers in the nation, and possibly on the planet.

Douglas Erwin is Senior Scientist and Curator in the Department of Paleobiology at the Smithsonian Institution’s National Museum of Natural History and a part-time research professor at the Santa Fe Institute. He began studying the end-Permian mass extinction in the early 1980s and has traveled many times to China, South Africa, and Europe seeking its causes and examining its consequences. His work on the end-Permian event stems from an interest in evolutionary innovations; extinction events are classically seen as generators of evolutionary novelty. Erwin studies patterns and time frames of biotic recovery, focusing particularly on gastropods of the Permian and Triassic. Erwin takes a broad look at the evidence and controversies concerning the end-Permian event in his book Extinction: How Life on Earth Nearly Ended 250 Million Years Ago (Princeton University Press, 2006).

dougerwin.jpgParadigm shift coming…sometime

“Is Darwin due for an upgrade?” Erwin asks and the answer he gives in a tactfully fudged manner aiming not to offend anybody is “yes”. But it is hard to nail down exactly why. He focuses on the new findings in evolutionary developmental biology, or “evo-devo”, which have shown how much goes on in the embryo where little changes can alter the shape of the resulting life form wholesale.

The developmental mechanisms involved can be experimented with, Erwin notes, with “exciting” results involving wingspots on butterflies and the gut of sea urchins and starfish, showing which genes are the essential core genes or kernel which cannot be modified without stopping the embryo’s development completely.

The Achilles’ heel of the modern synthesis, as noted by the philosopher Ron Amundson, is that it deals primarily with the transmission of genes from one generation to the next, but not how genes produce bodies. The recent discoveries in the new field of evolutionary developmental biology, or evo-devo, that the gene Pax-6 controls the formation of eyes in mice and humans, Nkx2.5 heart formation, and a suite of other genes the formation of the nervous system, has provided a means to investigate the genetic and developmental mechanisms influencing how the form of organisms has evolved, not just their genes. Perhaps the most exciting area in evolution is in exploring how rewiring the circuitry of genes produces different arthropod appendages, or wingspots on butterflies.

Eric H. Davidson, a colleague of mine at CalTech, has dissected the network of interactions between the genes that build the gut of sea urchins and starfish during development. When he compares these gene networks, there is a core of about five genes whose interactions are essential to forming the gut, and which have been preserved for some 500 million years.

One advantage developmental biologists have over paleontologists is that they can experiment on the development of these animals. Most of the genes in this network can be removed, and the developing embryo finds a way to compensate. But these five core genes, which form what Davidson calls a kernel, cannot be modified: change any one of them and no embryo forms at all.

Unfortunately he stops short of clearly explaining how this line of research will produce additional evolutionary mechanisms to add to Darwin and mutation. If anything he emphasizes how the mechanisms being elucidated in the embryo’s developmental process lead to restrictions on the path along which the organism can evolve. “Once the kernel formed it locked development onto a certain path.”

What creationists keep pointing out is the lack of adequate (to them) explanation of how complex systems such as eyes arise from random mutation and survival competition, and what Erwin describes doesn’t answer this question, though he hints that it will.

What we need we daresay is something more along the lines of Lynn Margulis’ conception of simpler elements merging to form more complex species. She is surely right on the micro level in saying that microorganisms evolved through symbiotic merging, and that one way to view a human being is a vast agglomeration of cellular life forms.

But do larger forms merge in some way to form new species? Presumably not, but something has to account for the abrupt transition between species observed in the fossil record, and the modern synthesis doesn’t do it.

Transitions between species documented by the fossil record seemed to be abrupt, perhaps too abrupt to be explained by the modern synthesis. If this were generally true, it could render irrelevant much of natural selection occurring within species, because just as mutations are produced randomly with respect to the needs of a species, with selection shaping these into new adaptations, new species might evolve randomly with species selection shaping them into evolutionary trends. This challenge was greeted with less than fulsome praise by evolutionary biologists studying changes within species. The resulting hubbub has yet to fully die down. But the newer work cuts closer to the core of the modern synthesis, and is potentially more revolutionary, because it addresses the fundamental question of how really new things happen in the history of life. What brought about the origin of animals, or the invasion of land?

Erwin’s essay doesn’t seem to suggest anything very specific as an additional mechanism, except a sort of modern mix of Lamarck and Gaia whereby species might change their environment and this might feed back into their own adaptation.

But just as the erosive power of a river changes the future options for the course of the river, so evolution itself changes future evolutionary possibilities. This can happen in simple ways, as termites construct their own environment by building termite mounds. These mounds may last for dozens or hundreds of years and provide a sort of ecological inheritance for generations of termites.

The first cyanobacteria turned carbon dioxide into oxygen and set off a revolution that completely changed the chemistry of the oceans and atmosphere. Most species modify their environment and this often changes how selection affects them: they construct, at least in part, their own environment. As evolutionary biologists we have little understanding of what these processes mean for evolution.

All in all, the essay hints at expected change without really showing much movement in the paradigm to date. But even that simple acknowledgment of the need for the paradigm to evolve is refreshing after the peculiar silence on the topic at the American Museum of Natural History in New York.

Does all this add up to a new modern synthesis? There is certainly no consensus among evolutionary biologists, but development, ecology, genetics and paleontology all provide new perspectives on how evolution operates, and how we should study it. None of these concerns provide a scintilla of hope for creationists, as scientific investigations are already providing new insights into these issues. The foundations for a paradigm shift may be in place, but it may be some time before we see whether a truly novel perspective develops or these tensions are accommodated within an expanded modern synthesis.

The political innocence of good scientists

darwinbeagle.jpegOne thing we did conclude as soon as we started reading the Erwin rumination was that among real scientists who are genuinely more interested in reality that what works career-wise, there is still a certain naivete as to what is happening in some realms of research where scientific activity is being warped by vast sums of money, where paradigms with no proven merit whatsoever may be sustained and promoted far beyond their due date of replacement by forces of human nature far beyond science

Here is how Erwin views the possibility of a paradigm shift – with excitement, joy and anticipation.

There is nothing scientists enjoy more than the prospect of a good paradigm shift.

Paradigm shifts are the stuff of scientific revolutions. They change how we view the world, the sorts of questions that scientists consider worth asking, and even how we do science. The discovery of DNA marked one such shift, the theory of plate tectonics another.

Many scientists suffer from a kind of split personality. We believe that this is the most exciting time to be working while yearning for the excitement of a revolution. What ambitious scientist would not want to be part of a paradigm shift? Not surprisingly, this yearning occasionally manifests itself in proclamations that a revolution is at hand.

This is how good scientists think and feel. How telling that there is no sign whatsoever of these attitudes in HIV∫AIDS.

If anything, the exact opposite prevails. Top scientists in HIV∫AIDS seem to view the prospect of paradigm change with the same distaste they might feel at discovering a dead rat amid the bounteous feast they are dining on royally at the top table.

The New York Times
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June 26, 2007
Essay
Darwin Still Rules, but Some Biologists Dream of a Paradigm Shift
By DOUGLAS H. ERWIN

Is Darwin due for an upgrade? There are growing calls among some evolutionary biologists for just such a revision, although they differ about what form this might take. But those calls could also be exaggerated. There is nothing scientists enjoy more than the prospect of a good paradigm shift.

Paradigm shifts are the stuff of scientific revolutions. They change how we view the world, the sorts of questions that scientists consider worth asking, and even how we do science. The discovery of DNA marked one such shift, the theory of plate tectonics another.

Many scientists suffer from a kind of split personality. We believe that this is the most exciting time to be working while yearning for the excitement of a revolution. What ambitious scientist would not want to be part of a paradigm shift? Not surprisingly, this yearning occasionally manifests itself in proclamations that a revolution is at hand.

To understand the current tumult it helps to understand how our evolutionary framework developed. It was constructed from the 1930s to 1950s by early geneticists, paleontologists and others, who disagreed about the efficacy of natural selection in driving evolutionary change (Darwin’s big idea) and about the nature of the underlying genetic variation upon which natural selection could act. What they came to agree on was called the modern synthesis, and it established an intellectual zeitgeist that continues today, and has been continually adapted, in the best evolutionary fashion, to encompass new discoveries.

That synthesis holds that mutations to DNA create new variants of existing genes within a species. Natural selection, driven by competition for resources, allows the best-adapted individuals to produce the most surviving offspring. So adaptive variants of genes become more common. Although selection is often seen, even by biologists who should know better, as primarily negative, removing poorly adapted individuals, Charles Darwin understood that it was a powerful creative tool.

It is the primary agent in shaping new adaptations. Computer simulations have shown how selection can produce a complex eye from a simple eyespot in just a few hundred thousand years.

In the past few years every element of this paradigm has been attacked. Concerns about the sources of evolutionary innovation and discoveries about how DNA evolves have led some to propose that mutations, not selection, drive much of evolution, or at least the main episodes of innovation, like the origin of major animal groups, including vertebrates.

Comparative studies of development have illuminated how genes operate, and evolve, and this places less emphasis on the gradual accumulation of small genetic changes emphasized by the modern synthesis. Work in ecology has emphasized the role organisms play in building their own environments, and studies of the fossil record raise questions about the role of competition. The last major challenge to the modern synthesis came in the 1970s and 1980s as my paleontological colleagues, including the late Stephen Jay Gould, argued for a hierarchical view of evolution, with selection occurring at many levels, including between species.

Transitions between species documented by the fossil record seemed to be abrupt, perhaps too abrupt to be explained by the modern synthesis. If this were generally true, it could render irrelevant much of natural selection occurring within species, because just as mutations are produced randomly with respect to the needs of a species, with selection shaping these into new adaptations, new species might evolve randomly with species selection shaping them into evolutionary trends. This challenge was greeted with less than fulsome praise by evolutionary biologists studying changes within species. The resulting hubbub has yet to fully die down. But the newer work cuts closer to the core of the modern synthesis, and is potentially more revolutionary, because it addresses the fundamental question of how really new things happen in the history of life. What brought about the origin of animals, or the invasion of land?

The Achilles’ heel of the modern synthesis, as noted by the philosopher Ron Amundson, is that it deals primarily with the transmission of genes from one generation to the next, but not how genes produce bodies. The recent discoveries in the new field of evolutionary developmental biology, or evo-devo, that the gene Pax-6 controls the formation of eyes in mice and humans, Nkx2.5 heart formation, and a suite of other genes the formation of the nervous system, has provided a means to investigate the genetic and developmental mechanisms influencing how the form of organisms has evolved, not just their genes. Perhaps the most exciting area in evolution is in exploring how rewiring the circuitry of genes produces different arthropod appendages, or wingspots on butterflies.

Eric H. Davidson, a colleague of mine at CalTech, has dissected the network of interactions between the genes that build the gut of sea urchins and starfish during development. When he compares these gene networks, there is a core of about five genes whose interactions are essential to forming the gut, and which have been preserved for some 500 million years.

One advantage developmental biologists have over paleontologists is that they can experiment on the development of these animals. Most of the genes in this network can be removed, and the developing embryo finds a way to compensate. But these five core genes, which form what Davidson calls a kernel, cannot be modified: change any one of them and no embryo forms at all. There is no reason to think that there was anything unusual about how this kernel first evolved some 500 million years ago (before sea urchins and starfish split into different groups), but once the kernel formed it locked development onto a certain path. These events, small and large, limit the range of possibilities on which natural selection can act. These questions about mechanism were not even being asked under the modern synthesis.

The failure to consider how biodiversity grows reflects an even more troubling flaw in the modern synthesis: it lacks any real sense of history. This may sound odd, as evolution is about history. A geologist would describe evolutionary theory as uniformitarian: “The present is the key to the past.” This is the principle we use that by understanding how processes operate today we can understand past events. Evolutionary theory assumes that the processes we can study among fruit flies disporting themselves in a laboratory capture the broad sweep of evolutionary change.

But just as the erosive power of a river changes the future options for the course of the river, so evolution itself changes future evolutionary possibilities. This can happen in simple ways, as termites construct their own environment by building termite mounds. These mounds may last for dozens or hundreds of years and provide a sort of ecological inheritance for generations of termites.

The first cyanobacteria turned carbon dioxide into oxygen and set off a revolution that completely changed the chemistry of the oceans and atmosphere. Most species modify their environment and this often changes how selection affects them: they construct, at least in part, their own environment. As evolutionary biologists we have little understanding of what these processes mean for evolution.

Does all this add up to a new modern synthesis? There is certainly no consensus among evolutionary biologists, but development, ecology, genetics and paleontology all provide new perspectives on how evolution operates, and how we should study it. None of these concerns provide a scintilla of hope for creationists, as scientific investigations are already providing new insights into these issues. The foundations for a paradigm shift may be in place, but it may be some time before we see whether a truly novel perspective develops or these tensions are accommodated within an expanded modern synthesis.

Douglas H. Erwin is a senior scientist at the National Museum of Natural History at the Smithsonian Institution and a research professor at the Santa Fe Institute.

2 Responses to “Darwin plus”

  1. martinkessler Says:

    The interesting thing about evolution science is that it may appear to be “less rigorous” than “AIDS” science, because Christopher Hitchens had a chapter ( Chapter 6 Arguments from Design) on Creationism vs Darwinian Evolution in his book: “God Is Not Great”. Either Mr. Hitchens was being disingenuous or diplomatic in claiming ignorance of “AIDS” science. I think he wanted to avoid controversy on that subject – strange for a person who may already have a fatwah on him.
    In Hitchens’ chapter 4 “A Note on Health, to Which Religion Can Be Hazardous”), he devoted several pages to condoms and their prevention of the infection of HIV. I guess he didn’t want to contradict himself – a criticism of his aimed a most of the Holy Texts. Had Hitchens changed HIV to STD’s I wouldn’t have had a problem with his rants.

  2. Nick Naylor Says:

    Nice, very good TS, raising the evolution controversy; indeed related – but I would say in unexpected ways – to matters debated in the other threads.

    Did you know that in Europe there is a non-Darwinian, non-Creationist school of evolution – so called process models?

    Can “purpose” and “design” be superficial organizing principles “emergent” from random phenomena?

    Rather than Hitchens, I would recommend Richard Lewontin’s essays, obtainable at the New York Review of Books website, for sharp insights into problems with the neo-Darwinian consensus.

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