NYT Admits Neo-Darwinism Faces a "Paradigm Shift" Over "Failure" to Explain Body Plans

Full Title:A Lapse in Watchfulness: New York Times Admits Neo-Darwinism Faces a "Paradigm Shift" Over "Failure" to Explain Body Plans

Despite keeping a watchful eye out for inklings of heresy on Darwinian evolution, the New York Times occasionally lets its guard down. Such a lapse was the only way to explain the recent review of Harvard computer scientist Leslie Valiant's book Probably Approximately Correct in which Berkeley mathematician Edward Frenkel was allowed to acknowledge a "gaping gap" in "Darwin's theory."

Now a colleague has pointed out to me a 2007 article in the Times that I hadn't previously seen. The author is Smithsonian paleobiologist Douglas H. Erwin, author of the 2013 book The Cambrian Explosion, and the article's title is "Darwin Still Rules, but Some Biologists Dream of a Paradigm Shift." Erwin opens by asking, "Is Darwin due for an upgrade?" and notes "There are growing calls among some evolutionary biologists for just such a revision, although they differ about what form this might take." He then explains what's at the heart of the modern neo-Darwinian synthesis of evolution:

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.

(Douglas H. Erwin, "Darwin Still Rules, but Some Biologists Dream of a Paradigm Shift," New York Times (June 26, 2007).)

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.

What's that? "Every element" of the neo-Darwinian paradigm "has been attacked"? He's not talking about the "creationists" that the New York Times loves to abuse, but, clearly, scientists who are decidedly in the mainstream. Erwin explains that cracks in the modern synthesis began to appear when it was discovered that:

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?

This, of course, is very similar to the story told by Stephen Meyer in Darwin's Doubt. Meyer notes that even in Darwin's time, scientists recognized that the appearance of animal body plans in the Cambrian seemed "too abrupt" (as Erwin puts it) to be explained by an unguided evolutionary model. This problem persists to the present, Meyer explains, as modern neo-Darwinian theory also lacks an explanation for how new complex features like animal body plans arise. Questions about the "origin of animals" remain unresolved.

Another fundamental problem Meyer recognizes with the neo-Darwinian synthesis is that it doesn't deal with the realities of how organismal body plans are built in the first place. Erwin acknowledges the same:

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.

This is, of course, one of Meyer's main points: the modern synthesis is fundamentally incapable of explaining the origin of body plans. Now that we're beginning to understand the biological mechanisms at the heart of generating body plans, can those developmental processes evolve in an unguided fashion? Erwin thinks they can:

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.

This paragraph raises another point made by Meyer: our experiments on gene regulatory networks show that if you modify genes at the core, they don't operate. This is essentially a form of irreducible complexity in animal development--a major problem for Darwinian explanations.

The rejoinder from evolutionary biologists is that perhaps in the past developmental gene regulatory networks were very different from the ones we observe today. Maybe these irreducibly complex systems could then evolve quite easily. Erwin writes, "There is no reason to think that there was anything unusual about how this kernel first evolved some 500 million years ago." Likewise, in reviewing Darwin's Doubt in the journal Science, UC Berkeley paleontologist Charles Marshall wrote that "today's GRNs have been overlain with half a billion years of evolutionary innovation (which accounts for their resistance to modification), whereas GRNs at the time of the emergence of the phyla were not so encumbered." So even though all the available experimental data on organisms today suggests that the kernels at the core of developmental gene regulatory networks are irreducibly complex, and not amenable to evolution by natural selection, evolutionary biologists assume that these kernels could and did evolve 500 million years ago. Erwin wants us to think nothing unusual is necessary. No explanatory details are called for. The reality is that if unguided evolution is correct, everything unusual is necessary.

In response to Marshall, Steve Meyer points out that evolutionary biologists are contradicting the principle of uniformitarianism. Rather than studying present-day forces (e.g., mechanisms of animal development) and applying them to explain the historical record, they assume that animals in the past developed in a manner entirely unlike anything in our present-day experience. The present is no longer the key to the past. Uniformitarianism has been abandoned in favor of, well, imagining whatever you theory requires, the facts notwithstanding. Writing at ENV ("When Theory Trumps Observation: Responding to Charles Marshall's Review of Darwin's Doubt"), Meyer elaborates:

By ignoring this evidence, Marshall and other defenders of evolutionary theory reverse the epistemological priority of the historical scientific method as pioneered by Charles Lyell, Charles Darwin and others. Rather than treating our present experimentally based knowledge as the key to evaluating the plausibility of theories about the past, Marshall uses an evolutionary assumption about what must have happened in the past (transmutation) to justify disregarding experimental observations of what does, and does not, occur in biological systems. The requirements of evolutionary doctrine thus trump our observations about how nature and living organisms actually behave. What we know best from observation takes a back seat to prior beliefs about how life must have arisen.

Meyer has thus exposed Marshall's implicit rejection of the principle of uniformitarianism. But other evolutionary biologists come closer to admitting the same of themselves. Erwin himself writes in his New York Times piece:

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.

Erwin explains that this principle no longer works to explain the origin of animals:

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.

OK, so perhaps when writing for the masses who read the New York Times Erwin doesn't have the courage to explicitly say that uniformitarianism has betrayed evolutionary thinking. He just artfully dances around the notion. But in another 2011 paper in Developmental Biology titled "Evolutionary Uniformitaranism," he makes this much more explicit:

Evolution has been implicitly viewed as a uniformitarian process where the rates may vary but the underlying processes, including the types of variation, are essentially invariant through time. Recent studies demonstrate that this uniformitarian assumption is false, suggesting that the types of variation may vary through time.

The ubiquity of morphological discontinuities between clades of organisms has troubled evolutionary biologists since Cuvier and Darwin and remains one of most important questions in evolutionary biology. Why is it that the distribution of morphologies is clumpy at virtually all scales? Although both Darwin and the proponents of the Modern Synthesis expected an 'insensible' gradation of form from one species to the next, this is only sometimes found among extant species (for example, among cryptic species) and is rare in the fossil record. Gradations in form are even less common at higher levels of the Linnean taxonomic hierarchy.

Couched in technical language is a frank admission from Erwin: the history of life shows abrupt jumps in form that are not bridged by gradual "gradation of form from one species to the next." In other words, it's the opposite of what an evolutionary view might expect. Erwin even admits the first appearance of body plans is "abrupt":

The pattern of first appearances confirms earlier suggestions for an abrupt, asymmetric pattern of morphological innovation during the early Cambrian.

Erwin closes his New York Times piece with the obligatory disclaimer that even though neo-Darwinism faces challenges, "None of these concerns provide a scintilla of hope for creationists, as scientific investigations are already providing new insights into these issues." So he does get around to abusing the all-purpose bogeymen, "creationists," after all.

But given that evolutionary biologists cannot explain how animal body plans arose unless they reject what scientific experiments have taught us about how organisms develop, there are many reasons to anticipate that the "paradigm shift" in neo-Darwinism is just the beginning. When it comes to unguided materialist models of evolution, natural selection is, thus far, the best game in town, and anything biologists try to replace it with is bound to have inferior explanatory power. The rejection of natural selection is the beginning of a process that will ultimately lead to the acceptance of a different kind of paradigm altogether. Namely intelligent design.

Currently evolution is a hand-wavy soft science. A paleontologist expounding ostensibly authoritatively on gene regulatory networks is a perfect example.

In the next 20 years it may become much more hard as genomes are sequenced and associated chromosomal organizations are determined in large numbers of wide ranging organisms.

This will provide the basis for a “new synthesis” and will probably bring about big surprises.

Weren’t the “bursts of change” among the first failures of Darwinian predictions? In response ideas such as punctuated equilibrium were developed.

That’s my impression.

To requote Erwin, who is a proponent of biological evolution:

Erwin finds these discontinuities as troubling.

What has been part of evolutionary thinking for decades is to casually dismiss these concerns since they don't have a reasonable answer for the morphological discontinuities or the lack of fossil records.

Let me propose a different thing
Is there natural logic?..
Can or do natural laws interact in a logical fashion with each other?
Can they interact with each other to a point that they behave in a fashion that seem intelligent and directed?..not unlike a computer program?
If so what is intelligence?

In response ideas such as punctuated equilibrium were developed.

You knoiw you have arrived at the pinnacle of your field when you propose a scientific theory that actually predicts you wont find any evidence to support it.

Is there natural logic?..

There exists Natural Law and there exists the Laws of Logic. They are two different invariant abstract entities.

Can or do natural laws interact in a logical fashion with each other?

Natural Law , like physical laws, are descriptive. They do not interact.

Intelligence could roughly be defined as a quality or characteristic of mind characterized by a panoply of features such as thought, perception, sentience, and many other invariant, abstract (non-physical) entities.

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