Deficiencies in modern evolutionary theory

This is a post originally made on the old Pharyngula website; I’ll be reposting some of these now and then to bring them aboard the new site.

There are a number of reasons why the current theory of evolution should be regarded as incomplete. The central one is that while “nothing in biology makes sense except in the light of evolution”, some important disciplines within biology, development and physiology, have only been weakly integrated into the theory.

Raff (1996) in his book The Shape of Life(amzn/b&n/abe/pwll) gives some of the historical reasons for the divorce of evolution and development. One is that embryologists were badly burned in the late 19th century by Haeckel, who led them along the long and unproductive detour of the false biogenetic “law”. That was a negative reaction; there was also a positive stimulus, the incentive of Roux’s new Entwicklungsmechanik, a model of experimental study of development that focused exclusively on immediate and proximate causes and effects. Embryology had a Golden Age of experimentation that discouraged any speculation about ultimate causes that just happened to coincide with the time that the Neo-Darwinian Synthesis was being formulated. Another unfortunate instance of focusing at cross-purposes was that the Neo-Darwinian Synthesis was fueled by the incorporation of genetics into evolutionary biology…and at the time, developmental biologists had only the vaguest ideas about how the phenomena they were studying were connected to the genome. It was going to be another 50 years before developmental biology fully embraced genetics.

The evolutionary biologists dismissed the embryologists as irrelevant to the field; furthermore, one of the rare embryologists who tried to address evolutionary concerns, Richard Goldschmidt, was derided as little more than a crackpot. It’s an attitude that persists today. Of course, the problem is mutual: Raff mentions how often he sees talks in developmental genetics that end with a single slide to discuss evolutionary implications, which usually consist of nothing but a sequence comparison between a couple of species. Evolution is richer than that, just as development is much more complex and sophisticated than the irrelevant pigeonhole into which it is squeezed.

In her book, Developmental Plasticity and Evolution(amzn/b&n/abe/pwll), West-Eberhard (2003) titles her first chapter “Gaps and Inconsistencies in Modern Evolutionary Thought”. It summarizes the case she makes in the rest of her 700 page book in 20 pages; I’ll summarize her summary here, and do it even less justice.

She lists 6 general problems in evolutionary biology that could be corrected with a better assimilation of modern developmental biology.

  1. The problem of unimodal adaptation. You can see this in any textbook of population genetics: the effect of selection is to impose a gradual shift in the mode of a pattern of continuous variation. Stabilizing selection chops off both tails of the distribution, directional selection works against one or the other tail, and disruptive selection favors the extremes. This is a useful, productive simplification, but it ignores too much. Organisms are capable of changing their specializations either physiologically, in the form of different behaviors, morphologies, or functional states, developmentally in the form of changing life histories, or behaviorally. Evolution is too often a “theory of adults”, and rather unrealistically inflexible adults at that.
  2. Cohesiveness. There is a long-standing bias in the evolutionary view of development, that of development imposing constraints on the organism. We can see that in the early favor of ideas like canalization, and the later vision of the gene pool as being cohesive and coadapted, which limits the magnitude of change that can be permitted. It’s a view of development as an exclusively conservative force. This is not how modern developmental biologists view the process. The emerging picture is one of flexibility, plasticity, and modularity, where development is an innovative force. Change in developmental genes isn’t destructive—one of the properties of developmental systems is that they readily accommodate novelty.
  3. Proximate and ultimate causation. One of the radical secrets of Darwin’s success was the abstraction of the process away from a remote and unaccessible ultimate teleological cause and to a more approachable set of proximate causes. This has been a good strategy for science in general, and has long been one of the mantras of evolutionary biology. Organisms are selected in the here and now, and not for some advantage many generations down the line. Evolutionary biology seems to have a blind spot, though. The most proximate features that affect the fitness of an organism are a) behavioral, b) physiological, and c) developmental. These are the causes upon which selection can act, yet the focus in evolutionary biology has been on an abstraction at least once removed, genetics.
  4. Continuous vs. discrete change. This is an old problem, and one that had to be resolved in a somewhat unsatisfactory manner in order for Mendelian genetics (an inherently discrete process) to be incorporated into neo-Darwinian thought (where gradualism was all). Many traits can be dealt with effectively by quantitative genetics, and are expressed in a graded form within populations, and these are typically the subject of study by population geneticists. We often see studies of graded phenotypes where we blithely accept that these are driven by underlying sets of graded distributions of genes, such as the studies of Darwin’s finches by the Grants, yet those genes are unidentified. Conversely, the characters that taxonomists use to distinguish species are usually qualitatively distinct are at least abruptly discontinuous. There is a gap in our thinking about these things, a gap that really requires developmental biology. Wouldn’t it be useful to know the molecular mechanisms that regulate beak size in Darwin’s finches?
  5. Problematic metaphors. One painful thing for developmental biologists reading the literature of evolutionary biology is the way development is often reduced to a metaphor, and usually it is a metaphor that minimizes the role of development. West-Eberhard discusses the familiar model of the “epigenetic landscape” by Waddington, which portrays development as a set of grooves worn in a flat table, with the organism as a billiard ball rolling down the deepest series. This is a model that completely obliterates the dynamism inherent in development. Even worse, because it is the current metaphor that seems to have utterly conquered the imaginations of most molecular biologists, is the notion of the “genetic program”. Again, this cripples our view of development by removing the dynamic and replacing it with instructions that are fixed in the genome. This is bad developmental biology, and as we get a clearer picture of the actual contents of the genome, it is becoming obviously bad molecular biology as well.
  6. The genotype-phenotype problem. Listen to how evolutionary explanations are given: they are almost always expressed in the language of genes. Genes, however, are a distant secondary or tertiary cause of evolutionary solutions. Fitness is a collective product of success at different stages of development, of different physiological adaptations, and of extremely labile interactions with the environment. Additionally, a gene alone is rarely traceable as the source of an adaptive state; epigenetic interactions are paramount. We are rarely going to be able to find that a specific allele has a discrete adaptive value. It’s always going to be an allele in a particular genetic background in a particular environment with a particular pattern of expression at particular stages of the life history.

One unfortunate problem with discussing these issues in venues frequented by lay people is, you guessed it, creationism. Any criticism of a theory is seized upon as evidence that the theory is wrong, rather than as a sign of a healthy, growing theory. The Neo-Darwinian Synthesis is not wrong, but neither is it dogma. It was set up roughly 70 years ago with the knowledge that was available at the time, and it is not at all surprising that the explosion of new knowledge, especially in molecular biology, genetics, and developmental biology, means that there are radically different new ideas clamoring to be accommodated in the old framework. The theory is going to change. This isn’t cause for creationists to rejoice, though, because the way it is changing is to become stronger.

MLK on fighting the fight

Hey, Norbizness is supposed to be a funny guy. So what’s he doing posting an excellent excerpt from a Martin Luther King letter?

I must confess that over the past few years I have been gravely disappointed with the white moderate. I have almost reached the regrettable conclusion that the Negro’s great stumbling block in his stride toward freedom is not the White Citizen’s Councilor or the Ku Klux Klanner, but the white moderate, who is more devoted to “order” than to justice; who prefers a negative peace which is the absence of tension to a positive peace which is the presence of justice; who constantly says: “I agree with you in the goal you seek, but I cannot agree with your methods of direct action”; who paternalistically believes he can set the timetable for another man’s freedom; who lives by a mythical concept of time and who constantly advises the Negro to wait for a “more convenient season.” Shallow understanding from people of good will is more frustrating than absolute misunderstanding from people of ill will. Lukewarm acceptance is much more bewildering than outright rejection.

If only he were alive today, I’d have to politely toss that one back in his face and remind him of what freethinkers think of the progressive Christian community. Confrontation and forthright expression is always going to be preferable to meek appeasement by a minority to an oblivious majority.

Let’s all pretend New Orleans will be OK!

Chris Clarke sees that we’re Abandoning NOLA in Orion:

“[W]hile encouraging city residents to return home and declaring for the media audience that “we will do whatever it takes” to save the city, the President… formally refused the one thing New Orleans simply cannot live without: A restored network of barrier islands and coastal wetlands.”

Leiter reports on the human catastrophe and the same shortsightedness:

The Army Corps of Engineers is still not doing anything on stopping the loss of the coastal littoral. Before Katrina, Louisiana lost some 40 miles of coastline over the last three decades. Congress has only appropriated $200 million for a coastal restoration study when $14 billion is required for coastal restoration and another $25 billion is needed for Category 5 hurricane levee preparation.

It’s all a hollow shell. The Bush administration throws a pittance at a problem, enough to put up a façade of actually caring, while letting the infrastructure rot and the underlying problems grow. They’re all bluster, and why should they care? They’ll reap their profits now, and let future generations pay for it.

Open Thread

This is the place to bring up any old thing that strikes your fancy. I’m also asking some of the commenters from The Panda’s Thumb to bring their gripes about the ludicrous management of Uncommon Descent, that bastion of Intelligent Design close-mindedness, over here, just because the outrage is spilling over into far too many irrelevant threads.

But don’t let that stop you from mentioning anything else of far more interest than Dembskian dogmatism…

Textbook vs. Frontier

The Hwang Woo Suk stem cell research scandal has triggered quite a bit of concerned introspection in the scientific community. Orac has some useful comments on a good article in the NY Times that makes the distinction between “frontier science” and “textbook science”, where much of the current stem cell research is clearly on the frontier.

Much of science at the very frontiers turns out not to be correct. However, the way it is all too often reported in the press is that it is correct. We in science understand the difference between textbook science and the sort of frontier science that makes it into journals like Science. Indeed, we often lament that the very highest tier journals, such as Nature, Science, and Cell, tend to be too enamored of publishing what seems to be “sexy science,” exciting or counterintuitive results that really grab the attention of scientists–in other words “cutting edge” or frontier science. Such journals seem to pride themselves on publishing primarily such work, while more solid, less “sexy” results seem to end up in second-tier journals, which is why they are so widely read and cited.

I would add another factor, though: Hwang Woo Suk’s results were not at all unexpected, did not contradict any accepted scientific concepts, and were dramatic because they represented a methodological breakthrough. In a way, it was almost a “safe” category in which to cheat: lots of people are trying to transform adult cell nuclei into totipotent stem cells, it looks like a problem that’s just going to require a lot of trial-and-error hammering to resolve, and what Dr Hwang did was steal priority on a result he could anticipate would be “replicated” (or more accurately, done for the first time) in short order. This is one of the hardest categories of science to police, I would think. It’s frontier science all right, but it’s only one step beyond the textbook.

Orac’s comments about those sexy hot scientific results that get into the top-ranked journals also applies to weblogs. I’m guilty of the same thing: the articles I tend to summarize here are the ones that push at the edges of what we know, rather than the ones that consolidate what we already knew, which actually represent the majority of what I read. The solid stuff that is packed with gobs of detailed data on expression patterns of a single gene, for instance, is hard to make exciting to a general audience—when the conclusion of a long paper is that Hox1 represses transcription of Pax1/9 in the endoderm, it takes an awful lot of background exposition to try and make that interesting.

For the creationists out there, by the way, most of evolutionary biology is solidly in the “textbook science” category, which is one of the reasons biologists are so baffled about why the general public embraces criticisms of it.

Journey to the other side

Lya Kahlo carried out an
informal atheistical survey of Christian forums—she visited 35 online religious forums as an openly atheist but friendly visitor, to sample their attitudes. The results aren’t pretty. Her summary:

The entire experience can be summed up fairly easily. Generally speaking, they know next to nothing about atheists, they are extremely emotionally attached to their deities, and they are just people looking for truth as we are. The animosity that sparks between atheists and theists seems to stem from the two camps speaking two different languages – atheists speak in terms of empirical evidence and logic; theists speak in terms of faith, emotion, and the unknown. An atheist expects proof before acceptance, a theists sees acceptance as proof.

Do I see it as a waste of time? On some of the boards (*cough*HolyCultureRadio*cough*) it was a waste of time. On boards frequented by a large teenage population or a way-out-there new-agey element, it was a waste of time. But this is not the case overall—surprisingly some of the more useful conversations happened on some fairly conservative forums.

Lastly, I think there are some allies to be made out there in the fight against an impending American Theocracy (okay, that’s a little dramatic), women’s rights and anti-war activism. There are plenty of good, decent xtians out there. However, we are never going to understand each other. We speak different languages.

I don’t doubt that the majority of Christians have good intentions. That language barrier, though…that’s a killer, especially since there’s little mutual interest in learning to speak each other’s language.

In which I dwell on the flaws in King Kong

In Peter Jackson’s Return of the King, there was a spectacular scene in which the elf Legolas single-handedly takes out a giant war elephant, first dispatching the entire crew riding its back, then firing a couple of arrows into its skull. Finally, with cool aplomb, he slides down the dying beast’s trunk, looking like a skateboarder doing a simple skid. He isn’t just a superlative shot with a bow, he has a semi-automatic bow and arrow and can take out entire platoons and mega-monsters without breaking a sweat.

I hate that scene.

It represents the worst of fanboy juvenilia—the hero inflated to god-like status, his actions no longer tethered by mere physics but become an exercise in supernatural wish fulfillment. It’s how comic book series die; not by closure of a good story, but by the steady pumping up of the central character until it becomes so central to the meaning of the entire universe that the only conflict is between the demiurge’s desires and the believability of the story’s reality. It’s damned boring stuff.

Peter Jackson showed some painful signs of susceptibility to that fanboy disease in the Lord of the Rings, and now having seen King Kong, I can say that he almost ruins the whole movie with ridiculous excess. Almost. There’s a great movie in the beginning and end of the story, and a ridiculous Dungeons & Dragons monster hunt with an indulgent Dungeon Master in the middle. The ending was so good I walked out of the theater feeling terrific about the whole show, but after thinking about it, there was an awful lot of crap going down through most of the movie.

A good science fiction story usually postulates one important novelty, and explores how that difference from the real world ramifies and causes complex consequences. There’s a wonderful, simple story in King Kong: that amazing giant ape, the interactions between him and a girl, and the disastrous collision with civilization. It’s Tarzan rewritten as a tragedy. That part is beautifully done in the movie, and Kong is a sympathetic and heroic figure, while Anne Darrow is empathy personified. That story works well.

Unfortunately, in the middle, Jackson translates a childhood fondness for the original King Kong into a kiddie cartoon. The whole Skull Island scenario is a botch.

He had to bring in the whole old bone-in-the-nose naked racism of the original; he did a great job of reveling in the wholly cruel and brutal savagery of a strangely prolific people somehow living on the rocky barren edge of an island full of monsters, in a stony city whose most common architectural features are the bones and corpses of its inhabitants. It made no sense, and was a distraction from the Kong story.

These entirely unsympathetic people are terrifying and murderous, and have the useful property of vanishing completely when the good guys fire a few guns. They are a caricature and a plot device, easily plucked off the game board whenever their presence might hamper the introduction of a new monster. They are also too easily dismissed. There is an entire city of these people, the small team of good guys have walked right into their midst, and have been completely surprised…they should have been dead. But no, the deus ex machine gun, which appears several times on Skull Island, makes the awkwardness of a massacre vanish.

“They should be dead” is a thought that ran through my mind several times. When they encounter the dinosaurs (which I thought were great, if unrealistic—they had the look of old-time Charles Knight illustrations, and their movements were beautifully slithery), they first get involved in an absurd stampede in a narrow defile. Everyone should have been dead, but instead credibility is strained overmuch with people darting in and out between legs and dancing along the edges of crumbling cliffs and bouncing off of and between and out from under tons of rubbery flesh.

There is a scene with giant bugs and some very cool sluglike beasties that were a cross between a giant leech and a chaetognath (heads full of spines, everting probosces, etc.—I want to go on record for having said “These guys have a lot of potential to be great horror movie stars” way back when. Peter, have your lawyer call my lawyer, we’ll talk). Once again, with a whole island full of giant hungry invertebrates, everyone should have been dead. But no, some survive, conveniently. (By the way, normal-sized fanged and envenomed invertebrates would have been just as lethal and scary, and far less prone to being trivially blown away with a gun.)

Once we were at the scene with the T. rex trapeze artists, my suspension of disbelief was gone completely. Laws of physics don’t matter anymore, all that mattered was how many giant flesh eaters could be squeezed onto the screen at once, and how many incredible positions and actions the CGI could render. Everyone should have been dead—people, flying and bouncing dinosaurs, gnawed-upon giant ape. Anne Darrow’s neck should have been snapped over and over again as she was tossed about like a rag doll.

The entire Skull Island sequence was like an overdone Warner Bros. cartoon, with cartoon physics, irrelevant consequences, and random rescues. It got in the way of the story. I think Jackson got so carried away with the horror monster special effects that he probably threw away most of the human parts of the tale, too…for instance, whatever happened with that subthread of James, the kid with the troubled past who was reading Heart of Darkness? Dropped and chopped to make room for more pointless creature wrestling, no doubt.

You know, Jackson could have simplified this part of the story. Forget the ghastly primitive natives; have the island contain only abandoned ruins. Drop the stupid battles between the people and dinosaurs and giant slugs; keep a few of the fights between Kong and T. rex (but having him fight 3 at a time was a bit much), since that’s part of the character’s development as an embattled loner. The capture of Kong was well done, I thought, as were the scenes with Anne and Kong, but everything with the crew and Wandering Monsters was a waste of screen time. Except, maybe, for hardcore geek fanboys.

Still, though, the last act of the movie was magnificent. It switched focus to Kong and the girl, where all the talent was any way, and although we all knew exactly what was going to happen, it was still wrenchingly done. Kong’s final torture was heartbreaking (Passion of the Ape, anyone?). The big gorilla’s character as a tragic figure was vivid, and saved the whole movie from being little more than a gussied up Friday night Sci-Fi Channel creature feature. It’s just too bad Jackson didn’t think on a slightly smaller scale for the rest.

(crossposted to The American Street)

Orsten fossils

Bredocaris admirabilis

Ooooh, there’s a gorgeous gallery of Orsten fossils online. These are some very pretty SEMs of tiny Cambrian animals, preserved in a kind of rock called Orsten, or stinkstone (apparently, the high sulfur content of the rock makes it smell awful). What are Orsten fossils?

Orsten fossils in the strict sense are spectacular minute secondarily phosphatised (apatitic) fossils, among them many Crustacea of different evolutionary levels, but also other arthropods and nemathelminths. The largest fragments we have do not exceed two mm. Orsten-type fossils, on the other hand, have the great advantage in being three-dimensionally preserved with all surface structures in place and thus easier to interpret than any other fossil material. Orsten fossils are preserved virtually as if they were just critical-point dried extant organisms. Details observable range down to less than 1 µm, and include pores, sensilla and minute secondary bristles on filter setae and denticles. Orsten fossils also give an insight of meiofaunal benthic life at small scale, including preservation larval stages, and hence a life zone inhabited by the earliest metazoan elements of the food chain.

It’s a good browse over there. I think it’s useful to remember that the majority of the fauna of the world both extant and half a billion years ago is and was tiny and unfamiliar.