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Thursday, February 28, 2008

Misperceptions meet state of the art in evolution research

The state of the art in the RNA world

As an employee of the National Center for Science Education, Nick Matzke was involved with everything from situations that never made the press to coaching the lawyers in the Dover trial, which gained international attention. One thing that apparently became clear is that, due to the highly technical material and a flood of misinformation on the topic, the public (and even many scientists) simply don't know what the current state of knowledge is when it comes from evolution. As part of an effort to rectify that, the NCSE and the AAAS's Dialog on Science, Ethics, and Religion organized a session on the state of the art in our understanding of evolution, which Matzke moderated.

Four speakers took on topics that appear to be the frequently misunderstood by the public. One of these—the origin of life—isn't directly part of evolutionary theory, but is frequently associated with it by the public. The remaining topics covered major events in the evolutionary history that produced humans, including the origin of bilateral animals during the Cambrian explosion, the origin of tetrapods, and the evolution of human ancestors. Throughout the talks, there were two recurrent themes: we can identify major environmental changes that might have sparked new selective pressures, and many of the major adaptations we view as designed for a specific lifestyle actually originated as an adaptation for something else entirely.

The origin of life

Evolutionary theory, both as proposed by Darwin and elaborated since, deals with the diversification of modern living organisms from a limited number of ancestral living organisms. But the lack of a strong theory for the origin of life is actually treated as an argument against evolution by many of the opponents of teaching the theory. Many of the principles of evolution, including heritable variations and selective pressures, are also applied by origin of life researchers. As such, the two topics appear inextricably linked.

The discussion of life's origins was handled by Andy Ellington of the University of Texas - Austin. He started by noting that simply defining life is as much of a philosophical question as a biological one. He settled on the following: "a self replicating system capable of Darwinian evolution," and focused on getting from naturally forming chemicals to that point. To do so, Ellington developed three different themes.

Chemicals in living organisms can form without life


An RNA ligase ribozyme

The basic idea has been recognized for over a century, but the work of Stanley Miller was cited for triggering the modern era of scientific work on the topic. Since the classic Miller-Urey experiments, science has steadily expanded the range of essential molecules that can be produced under conditions that might reasonably expected to have been present on the early earth.

Ellington emphasized that progress has been slow—we knew how cyanide could react to form the DNA component adenine in the 1960s, but it took over three decades to recognize that a few more reactions converted it to its relative, guanine. And the roadblocks continue to fall. After all attempts to produce sugars created a tar-like sludge, someone eventually found that a small amount of borate could help ethanol form large amounts of ribose, another component of RNA.

The first molecules that could replicate led directly to modern life

With the components of nucleic acids in place, Ellington traced a path through the RNA world to a molecule that could self-replicate. Past attempts to jump to a complex, self-replicating RNA molecule seem to have been on the wrong track. Short palindromic RNA sequences can apparently help catalyze the formation of complementary sequences, meaning what's needed is actually an RNA that can link these short sequences into longer, more complex ones. A number of such sequences, termed RNA ligases, have been identified. Several labs have shown that these ligases can then be improved by an essentially Darwinian process of random mutation followed by selection for increased efficiency.

Modern RNA activities tell us about the RNA world

Ellington's final point was that we can still see remnants of the RNA world in aspects of biology that are common to all life. He noted that many of the cofactors used by modern proteins, including ATP itself, are derivatives of the chemical components of RNA. Researchers have also been able to evolve RNAs that successfully bind these cofactors, which suggests that proteins would only need to have gradually replaced these RNAs. That replacement, Ellington suggested, has never actually been completed: the central core of the ribosome, a complex essential for protein production in all organisms, turns out to be formed from RNA. During questions, he also emphasized that basic cellular metabolism uses some amino acids as intermediates, and suggested that proteins resulted from early RNA "life" simply using what it had lying around, tying in nicely with the theme of preadaptation.

Ars spoke to Dr. Ellington after the talk and asked him about the separate thread of origin of life research that focuses on identifying the energy-harvesting reactions required for the first life. He was very excited about the potential for user-generated genomes to help unify the two fields. The ability to customize a genome would not only help scientists identify the very minimal metabolism necessary for life, but would eventually allow researchers to start replacing proteins with their catalytic RNA equivalents. Ellington suggested that the result—a cell with a hybrid RNA/protein world—would eventually allow us to explore the transition to the first cells.

Ellington's summary of the state of the art is that "we'll never know exactly what happened, but we're getting a really good idea of what is possible."

The Cambrian explodes and fish get limbs

The Cambrian explosion


A Halwaxiid, poised to explode into
three branches of animal life

Douglas Erwin of the Smithsonian then made the jump to the origin of modern animal life during the Cambrian explosion—as he put it, "3 billion years of boredom later..." Erwin presented the Cambrian explosion as a matter of three big ideas as well: biological challenges, ecological opportunities, and developmental potential. The biological challenges of the era are pretty obvious: in his view, the global glaciations that left glacial sediments in the tropics and are likely to have shut down or severely limited the global carbon cycle.

These changes, however, were accompanied by two events that, in Erwin's view, were essential enablers of a broad radiation of species. Both had the common feature of allowing many organisms access to a resource that was essentially unlimited, and thus free from competition. The first of these was oxygen, which reached unusually high levels in the Cambrian atmosphere. Results published while this article was in preparation reveal that the radiation of animal life closely tracked oxygenation of the ancient ocean. The second was nutrient-rich sediments. Tracks from the first burrowing animals appear in sediments just prior to the Cambrian, and Erwin argues that these animals kept resources in the sediments circulating within the biological community long after they would have otherwise settled out and been buried.


This Cambrian jellyfish probably shared many genes with the first bilateral animals

Erwin also described animal life that was poised to explode. The prior era was filled with the Ediacaran Fauna, which he described as, "no eyes, no appendages, lots of fronds, and maybe some guts." But that era also generated fossil embryos that suggest that bilateral animals predated the Cambrian. More telling, however, has been the findings of modern genomics and evo-devo. Genomic studies reveal that many of the genes involved in producing complex animals predate animals themselves, and some of the key regulators of bilateral animal development exist in Cnidarians, which don't share that body plan. Other work has revealed that genetic networks of regulatory genes that are used in appendage and body plan specification probably predate the origins of either limbs or a body plan.

In short, the genetic tools were in place were in place for millions of years before the Cambrian, but it took the Cambrian's unique combination of environmental challenges and opportunities to force organisms to deploy them in new adaptive combinations.

Vanishing gaps in the vertebrate invasion of land

A key event in the origin of modern humans occurred in swamps nearly 400 million years ago. Prior to that time, vertebrates made do with fins and life in the water. Ted Daeschler of the Academy of Natural Sciences in Philadelphia reviewed our latest understanding of how those fish wound up on land, with limbs to propel them.


Which is a fish, which is a tetrapod? Trick question—they're all tetrapods.

Daeschler pointed out that a few decades ago, we had two species that don't even appear on the diagram here, Eusthenopteron and Icthyostega, and a big gap in between them. Although scientists always want to know more, the gap wasn't a huge problem for them, as they could recognize subtle features of skeletons that the lobe-finned fish shared with the earliest tetrapods. But it was a problem in terms of public relations, as the public had a hard time tracking these subtleties, allowing opponents of evolution to focus on the gap and declare it unbridgeable.

In the 1980s and 90s, other species, such as Pandericthys and Acanthostega, began to fill this gap. Daeschler indicated that a clear pattern emerged, one that linked the appearance of these species with a specific environment and one that represented a new ecological opportunity. All of the fossils were found on a band that, given the then-current arrangement of the continents, was equatorial. The specific environment, however, was one that hadn't existed previously: broad, alluvial valleys and flood plains that were transformed in the wake of the origin of trees. The recognition that this environment spurred tetrapod evolution has led directly to the discovery of Gogonasus and, perhaps the most famous transitional species ever, Tiktaalik.

In this environment, many of the features of the transitional species were preadaptive. Lobed fins aided maneuvering in a complex environment in the same way that limbs later did, in water or out. Muscle attachment sites in the bones of the fins worked equally well when used in legs. For paleontologists, the discoveries that filled the gaps revealed that this major transition occurred through a series of forms that were mosaic, with features added to the tetrapod repertoire in an order that's essentially random. Tiktaalik has a broad, fish-like snout, but the far end of its skull has been reordered to allow the first flexible neck seen in a tetrapod.

Two messages were clear from Daeschler's summary. The first is that there's so much left to discover; we don't know which gap will wind up filled next, just that gaps continue to be filled with rich information. He'll continue chasing road crews as they dig through Pennsylvania for as long as they'll let him. The second message is that it's time to let go of the false distinctions that are left over from Linnean times and only serve to confuse the public. In Daeschler's view, all of these animals, on both sides of the former gaps, are tetrapods. Some have limbs, some have fins, but they're clearly all part of a boundary- and gap-less transition.

Modern human origins and learning

The origins of modern humans

The final scientific speaker in the session was John Relethford, an anthropologist in the SUNY system. He had so many big messages that he settled on a top-ten list to present them. The first item was simply that humans have evolved, period. The evidence is so overwhelming that Relethford feels that any remaining argument is simply between two religious perspectives on that fact; science has moved on. Item two was to emphasize that we did not evolve from modern apes. Ape is both a generic and a species term, and biologists need to be careful to use it correctly, because we're confusing the public by being sloppy.


Meet a few of our many relatives

His third message was that scientists study human origins—the plural part is important. The toolkit that we regard as human, including upright walking, tool use, brain size, etc. all arose at different times, some separated by millions of years. A correlate of this was point four: "humanity's birth was feet first," as he put it. Upright walking may date back over six million years, and was definitely present four million years ago. At the time, there were no tools and our ancestors had ape-like teeth and cranial capacity. Relethford suggested we're still not sure what walking adapted us for, but it clearly kept us going for millions of years before we realized it liberated our forelimbs to manipulate sophisticated tools.


Big brains took their time

That delay might have been due to point five, the fact that cranial capacity increased very slowly and gradually over the course of human evolution. This illustrated Relethford's idea six: there's no free lunch. Any adaptation has a cost, and the advantages of expanding brain size were constantly balanced against the selective cost of a big brain's increased energy use and heat output. There was also more than one way to achieve these balances as, for much of their history, our ancestors were not alone. There were many overlapping homo and australopithecus species in the past, as Relethford noted in point seven, and the question of what constitutes a species is often contentious when it comes to our ancestors.

Relethford's final points backed out to the big picture of science and humanity in general. Eighth on his list was the contention that we should always expect the unexpected, as new discoveries represent the strength of science, not its weakness. He suggested that if people didn't like the excited confusion caused by H. florensis, then they probably shouldn't be paying paleontologists. He also voiced disdain for those who speculate that some form of alien intervention was necessary to produce sophisticated humans or the great works of prehistory. "Our ancestors were not dummies," he stated as point nine, suggesting that this type of thinking was little more than a generation gap taken to an extreme.

His final point was that the full package of modern human traits took millions of years to evolve, so questions as to where we're headed are somewhat irrelevant. In the time span we should be concerned with, Relethford suggested, all the relevant evolution will be cultural.

The state of the art meets the public

With the state of the art established, the final speaker, Martin Storksdieck of the Institute for Learning Innovation looked at how to get that information to a public has such a hard time accepting what science is discovering. He argued that, while most of the attention has focused on childhood education, we really should be going after the parents. Everyone is a lifelong learner, Storksdieck said, but once people leave school, that learning becomes a voluntary matter that's largely driven by individual taste.

Storksdieck discussed a number of key aspects of this voluntary learning. He argued that a surprising amount of it is faith-based; adults don't have the time or need to learn large frameworks like evolution, so they're often willing to accept or reject information based reasons beyond its consistency with scientific understanding. As an example, he noted his own understanding of chemistry was weak, so he'd simply have to accept what Andy Ellington told him about the RNA world. The result is that what's accepted or not becomes largely a matter of social influences.

Here, Storksdieck offered two specific suggestions. The first is to get people in positions of leadership involved, as people pay attention to them, regardless of their grip on the facts. His example was Thabo Mbeki of South Africa, who set the country's battle against AIDS back significantly simply by expressing doubt in our scientific and medical understanding of the conditions. His other suggestion was that we should, as he put it, keep preaching to the choir. Enthused learners are the best communicators of information, and arming them with more of what we know is the best way to get that information before the public.

The series of talks was possibly the best overview of the state of knowledge in any field that I have ever seen, and the enthusiasm of the researchers and their excitement about the topics was palpable. I expect that, if the public saw more presentations like this, which revealed not only the full depth of our understanding, but also the enthusiasm, humor, and humanity of the people that have generated that understanding, then the teaching of evolution would generate only a small fraction of the resistance that it currently does.

Original here

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