Pursuing praxis

The musuem and department are celebrating Darwin Day this weekend and early next week. Darwin was born on February 12th (as was Abraham Lincoln). Conveniently, he published Origin of the Species when he was 50, so we get to celebrate nice even numbers of his birthday and the publication of the Origin simultaneously. I am sure this will be ground into your memory come next year, the 200th anniversary of Darwin birth, and the 150th anniversary of the book.

Anyway, someone decided to organize a photo contest for the festivities this year. For once I had something artsy and sciencey and I dreamt up something Darwiny to say about it. Here’s the pic and my blurb about it:

This is a photo of a male mandrill (Mandrillus sphinx) from the San Francisco Zoo, taken in November 2007. Mandrills exhibit strong sexual dimorphism, and the bright facial coloration and larger body size in males is thought to be the result of sexual selection. Darwin originated the concept of sexual selection, and in his 1871 book he uses many examples of sexual dimorphism in primates to build his case.

But when it comes to evolution, many people are still as cognitively trapped as this mandrill is by his cage, comfortable and natural though it might seem. Some people look at primates and think that shared ancestry is a slur on mankind. But no fact changes an ever-present identity, and wonderment is not diluted when extended to facts at all scales of time and space. As Darwin so famously concluded, "There is grandeur in this view of life, . . . ; from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved."

I’m reading biographies of George Gaylord Simpson - his autobiography, Concession to the Improbable: An unconventional autobiography, and Leo LaPorte’s George Gaylord Simpson: Evolutionist and Paleontologist. I don’t know whether I stopped reading La Porte’s book because I wanted to read Simpson in his own words first, or if I just happened to order and receive Simpson’s autobiography ’round about that time.

To cut to the chase - I have no pithy summations, crusading opining or otherwise synthesized thought on the subject yet. I find Simpson fascinating and extremely rewarding to read and read about. In the various mentions of Simpson that I had come across in my previous readings, he was frequently described as irascible, though brilliant, and left at that. I read tonight that Simpson far preferred the written word - on both the giving and receiving ends - to the spoken word, given or received. There is the occasional tetchiness, but it is a tiny minority of the time. That said, I find it funnier when the anecdote is crabby, so there is a selection bias in the quotes copied below. Enjoy.

I was reminded of my short vacation in Egypt, and the few days in Cairo. While I saw less wildlife in the streets than described by Simpson on his (first) round-the-world trip in 1951, I think it’s only apt to cite that long-used, much-discussed maxim (which dates to at least Aristotle’s time): natura non facit saltus [nature makes no leaps]. My experience of streets in Cairo was similar in the feeling, if not in all the particulars. He wrote (pg. 149):

The streets of Cairo are dirty, noisy, and dangerous. As I wrote at the time, "The streets and roads are jammed with pedestrians, camels, donkeys, water buffaloes [Argh! I’m 50 years too late.], bullock-carts and horse-carts, jeeps, Coca Cola trucks, baby carriages, bicycles and motorcycles, crawling infants, dogs, cats, and in short everything imaginable that can move or be dragged with the possible exception of reindeer sledges, and it would not really surprise me to see one of those. There seems to be a slight statistical probability that cars will pass to the right if this is convenient, but otherwise no traffic rules seem to be applied."

For some reason, the following quote (at the very end) is my favorite so far (pg. 157):

It [Life of the Past, a "fairly short and not unduly technical book on general paleontology"] had some good reviews, and one bad one by a British zoologist who objected violently to the illustrations, which I had drawn myself during that winter at [his seasonal home in] Los Pinavetes [New Mexico]. I admit that my drawings are crude and inartistic, but they have a certain amateur freedom that some people find attractive or at least amusing. What did annoy me a bit was that my critic had also illustrated some of his publications and that his drawings were just as crude and inartistic as mine, and moreover that he had the poor taste to die before I could point that out to him. 

Simpson made several expeditions to South America over several decades. At the start of his last field expedition there, the woman in charge of the guesthouse where he and his team stayed for some time went to some length to counter the stereotypes about the town, Cruzeiro do Sul, "effectively the last outpost of civilization in that direction [in Brazil]" (pg. 166). About her he wrote (pg. 167):

A nice woman, talkative and a booster for her home town: "Those people down in Manaus think we are savages up here, nothing but forest and jaguars. Why! Jaguars rarely come into town. This is the healthiest place in Brazil. Almost no tuberculosis and only a few dozen lepers. The malaria is not bad this year. This is real white man’s country. It takes a little planning to get food, is all."

For those of you who don’t know, Simpson spent most of his life married to Anne Roe, a psychologist and for a time also a professor at Harvard (both Simpson and Roe joined Harvard at the same time, and left at the same time, as far as I know). They co-authored a couple of books together, both very good: Quantitative Zoology (1939) and Behavior and Evolution (1958). Simpson recounts the origin of the latter book, and indeed the field of study it spawned (pg. 177):

Another book in the 1950s resulted from a different and delightfully intimate form of collaboration. The idea came to Anne and me sometime in 1953. We remember the incident clearly but are not sure of the date. It was probably a Sunday because she and I were lying late in bed one morning talking about the universe and other things. Psychology is in the main a study of behavior, but up to that time most psychologists took observed behavior as given and paid little or no attention to the fact that it must have originated at some time in the evolutionary history of the species being studied, then usually rats and humans. Such evolutionary concepts as were currently in psychology struck me as generally naive, outdated, or simply wrong. On the other hand, evolutionists were studying mostly morphology, genetics, or to some extent ecology. Some of them did recognize that behavior is also relevant to evolution, but their concepts of behavioral studies in psychology struck Anne as generally naive, outdated, or simply wrong. We decided to something about this, got out of bed, and set about doing so.

[. . .]

That was a seminal work. It strongly influenced the direction of studies both of behavior and of evolution, as attested not only by those who had attended the conferences [organized to promote these kinds of studies] but also many of their colleagues and students. . . .  

The lesson of all this is that an effective method for getting really interdisciplinary studies under way is for students of different disciplines to wake up in bed together.

I will stop here with the quotes tonight. As you can see, I can’t even copy other people’s words briefly.  

In unrelated and present news: This rockin’ coffee shop I’m in at an ungodly-early hour of the morning usually plays straight up classical music, unless it’s closing time, and then they blast Brazilian mariachi music or something equally intrusive. It took me a minute to recognize the music just now - and it was the theme music to Jurassic Park by John Williams. (If you like his music, he took a lot of cues from Dvorak. Check out Dvorak’s 9th Symphony, "From the New World." Really.) (PS: as a favor to those who don’t know the missing accents on Dvorak’s name and what they mean: it’s pronounced like Duh-VORE-zhock, where that "zh" is like a cross between "sh" "z" and "j" sounds. It’s Czech.)

Wow. It’s been a long time; I’d forgotten how awesome that music is, and it still evokes the giddy awe (and visuals) of the scientists arriving at the island of dinosaurs, "pristine" jungle amid state-of-the-art technology. That was a great movie. Great music, great graphics, decent book, cool dinos, scary dinos, scientist-heroes, a man in black, the lawyer gets eaten while sitting on a toilet, and you’ll never look at rings in a glass of water quite the same again. Plus the follow-up book was kinda heavy on theoretical math (for a high schooler, that is). I’m kind of a wuss when it comes to suspence and scariness, but if I had to pick, getting hunted by Deinonychus in a stainless steel kitchen, or having a piece of plexi-glass between you and the business end of a T. rex is the way to go. 

Who’s Deinonychus, you say? Deinonychus is "Velociraptor" in Jurassic Park. They combined the real  Deinonychus’s scary body and wicked-cool claws with the spiffy name of Velociraptor for the movie. I mean, it’s Hollywood’s schtick to rewrite the facts of nature and science for box-office sales. Real Velociraptors were, if I remember correctly, about knee- or hip-height, and had fingers about as long as their forearms, with smaller claws, and were more snatchers than eviscerators. The morphology of their wrists, as well as the proportions of their forelimbs, are "adaptations" previously thought to only be part of the package-deal for flight in birds. Turns out the proportions of the forelimbs and shape of some of these wrist bones (and probably other stuff) is needed for both flight and snatch-n-run predation. The rest of their bodies was very obviously unrelated to flight; they were made for dog-eat-dog (Deinonychus-eat-Deinonychus?) life on the ground. So you get this piece-mealing of very purposeful traits "leading up to" or even concurrent with the emergence of powered flight capability in birds, and in close-but-separate branches of the family tree, rather than a clean, exclusivist monopoly of useful-for-flight morphologies marching towards the acquisition of avian flight. Being bird-like in some very key morphologies was not the sole province of birds. [Note to self: double-check this with labmates for any slight errors]. [Self: See Sarah’s comment below.]

Of course, as I recall it, the over-riding message of Jurassic Park was "Don’t mess with nature," which I disagree with. You gotta mess with nature in light of nature, and not dictate your terms to it; but messing with nature is critically important in general. As Sir Francis Bacon emphasized, "Nature, to be commanded, must be obeyed." It’s the purpose of that bubble-shaped boney structure sitting atop your vertebral column, the latter which also broadly supports a body that is the bipedal, terrestrial version of sushi. I like "Man tames Nature" themes, not "Nature tames Man" themes.

Still, fabulous music. Makes my cd-buying sense start to itch. Really badly. Argh!

And where the devil is the soundtrack to any of the Pirates of the Caribbean movies? That too is half the appeal of the movie (the other three-quarters being an amalgamation of ships, bad hats, heavy eyeliner, and subtle, witty retorts). 

[June 30: Methinks I spelled Caribbean wrong? Surely not Pirates. In any case, my labmate helped me fix this hole in my music library. And I’ll be watching Pirates 3 tonight. I’m looking forward to Pirates 5 and 9 and 24 and however many they make.] 

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From Sarah:

Sorry to go all dino weenie on you(and even worse, I\’m about to correct your theropod comment, and even even worse, I\’m talking about dromaeosaurs), but velociraptors were very similar to the JP evil beasties in most aspects but size. And Deinonychus was, alas, also too small to be the nasty raptors in Jurassic Park. Deinonychus was about 4 feet tall at the most.

However, there was a dromaeosaur about that size, Utahraptor. It was named in 1993 and was about 6 feet tall. It\’s also one of the three dinosaurs that appear in every day\’s installment of Dinosaur Comics at http://www.qwantz.com

Some good reconstructions:
http://en.wikipedia.org/wiki/Image:Velociraptor_skeletal_by_Scott_Hartman.jpg

http://en.wikipedia.org/wiki/Image:Deinonychus-scale.png

http://www.marshalls-art.com/images/ipaleo/paleopg25/utahraptor_final300web.jpg

http://www.qwantz.com/archive/001019.html

I subscribe to an email list that is currently re-hashing hilarious student responses:

A student identified the tail of the shark [the caudal fin] as "the cuddle fin."  (It probably co-evolved with internal fertilization, right?)

Oh man, I love science humor.  

Lesee, where was I….

Oh yes. We’ve said buh-bye to Stanford and Davis, Silicon Valley is either soggy or has moved to high ground (not without considerable cost), SF is now two islands instead of one, Berkeley’s enjoying fresh fish n’ chips… what about the precious salt-marshes, and the 12,000 breeding pairs of god-knows-what birds (let’s call’m schmatzels; I never had a Polish grandmother)? And the three recently-identified sub-species, upstream on the Sacramento River, that (now that we know about them) are also threatened?

Now, let’s take an historical perspective on marshes too. A marsh, being a combination of certain kinds of plants, and a certain depth of water, is highly subject to changes in water level. Too much water, the plants drown, and you’re left with more bay/lake/river/ocean/whatever, and the critters using the marsh are SOL (for that marsh). The SF bay is a fairly recent phenomenon (c. 8000 years it started trickling in), so all the marshes here (or that were here in the 1800s) are a pretty darn recent phenomenon. And given that most established species last on the order of 100,000- 1-million years, 1) 8000 years is a drop in the bucket even for species, and 2) it’s reasonable to infer that most organisms have ways of moving (individually, and between generations) and repopulating (even if a region of critters gets wiped out). That is, a lineage of organisms *not* capable of withstanding and/or accomodating (over the long haul) significant change would be highly unlikely to get beyond the toddler phase of specieshood.

And in fact, the long-term pattern of ecosystems is one of colonization, expansion and adjustment, stabilization, destabilization (several reasons), collapse/transformation, repeat. And most lineages of organisms suffer regional extinction one or more times, only to recolonize from populations elsewhere and do it all again. In fact, regional death and re-colonization can be part of the meta-strategy/niche of the group. Hard to tell. More research is needed (way way way more research) before we determine that holding things still as best as possible is the best feasible short-term solution to a long-term problem. It makes a lot of effectively arbitrary assumptions about the biological world, many of which are suspect if not false on their face. That’s what scientists *aren’t* supposed to do.

So the SF Bay marshes are an historically recent phenomenon, and only about 5% of marshes (from the 1800s) remain. Understandably this crimps the style of a lot of marsh-using critters, and it’s therefore expected that there are fewer critters than there used to be. A lot fewer. Only 12,000 breeding pairs of schmatzels or whatever. But, it’s not like these marshes were always there, and in terms of biotic and abiotic history, they represent an unprecedented regional surplus of opportunity for marsh-dwelling critters. So really, maybe we’re looking at the whole "low numbers" problem the wrong way. Maybe we’re coming off a local maximum of bird population numbers, and effectively returning to the norm of the last 40,000 years or so.

Well, the bird aspect of this story was the topic of a seminar attended by our hero in the not-so-distant past. The historical aspect of this story, extending beyond 250 years ago, was part of what our hero discussed in seminar yesterday, and a perspective he conveyed to the ornithologist at the end of that talk. The ornithologist, visibly agitated by that challenge to the welfare of local schmatzels, eventually burst out with, "Won’t you leave!!" Our hero pressed his point, and the angry ornithologist spouted forth with, "I don’t give a shit about the last 4.5 billion years, and I don’t give a shit about the next 4.5 billion years!!" A little more discussion, and our hero got the A.O. to admit that he didn’t care about anything after his own death. Being a conservation biologist in addition to an A.O., this is eyebrow-raising to say the least. Then our hero learned that not only was the A.O. not a graduate student (as he had assumed), but he was the chair of the department!

God save the schmatzels. With folks like this making policy recommendations, He’s the only one who can.  

But, then again, seeing’s that schmatzels have gotten along without the aid of god for… well if you trace it back, you’ve got 3.5 billion years of life continuity, without His divine non-existent help. Not only can the schmatzel take care of itself jim-dandy-thank-you, a few informed scientists and rational policy makers can make sure both humans and schmatzels are here well into the next centi-millenium.

 
Next time: "Hitting bottom, or, Why the Bay might not be totally fucked: A perspective from benthic foraminifera, Pleistocene to Present."

I’ll be here all week. Don’t forget to tip your waitresses. 

Fortuitously (given yesterday’s rant on rhinos), and hilariously, the following anecdote came up in a seminar today:

The speaker, (micropaleontologist and world expert on shelly protists, foraminifera, a deep thinker on deep time, and funny as hell to boot), recounted how he was attending a conservation biology seminar, where the speaker was talking about endangered birds requiring marsh habitat in the bay area if they are to survive. Something about only 12,000 breeding pairs of X species locally.

Back up a sec, and let’s talk about the "recent" history of the SF Bay area. Recent in geological terms means the last 125,000 years. Or even 8000 years, since that’s when the first humans (probably…) arrived, and started leaving giant mounds of clam shells around the bay area. Around 125K years ago, the earth was doing it’s glacial cycling, where you have a little ice age followed by warming, and it does this like 5 times or something, over 10s of thousands of years. And in fact the ocean levels were a bit lower than they are today, when this was happening. Then about 40,000 years ago (or was it 11000? nuts…) we had a glacial maximum, and everything was #@*$ing cold. Like, the line practically bored through the bottom of the graph. That cold. (haha).

Now, to step this out for the kiddies, that means there was a lot of ice. And ice is made of water. And that’s a lot of water. And that water has to come from somewhere. That water comes mostly from the oceans, since most of the water on earth is in the oceans. And when you freeze up a bunch of water at the poles, that means there’s less left for everywhere else. This means that ocean levels fall - quite a lot, actually. In the SF Bay area, they were about 360 FEET lower than they are now. That is, if you stood on the easy bay mountains and looked out where the Golden Gate Bridge is across the bay - you just MIGHT be able to see the water on a clear day. And this was normal, for a long time.

But, the good news is (well, not good - it’s just news, cuz it’s just the facts) since that glacial maximum is in the past - everything’s been warming up since then. And the interesting facts are these: Unlike the previous lukewarm-cool cycles that were happening 125K years ago, it’s been an almost continuous increase in ocean levels since that maximum cold. None of that up-down cycling bit, although there have been greater and lesser plateaus. And, some 8000 years ago, there was really just this piddly little body of water that was where the bay is now. Just pathetic. And it’s been slowly increasing ever since. By about 2000 years ago, we crossed the previous high water mark (of 100K years ago, give or take). In comparison to the last 125K years, sea levels are the highest they’ve ever been - but just a little bit (probably within 10 meters). This is also at the tail end of a very long upswing in sea levels. (I should probably point out the obvious and say that sea levels and global temperatures are positively correlated). And it is true that the slope of the graph is a bit steeper over the last little bit (500 years? 1000 years? Bit hard to tell on a graph covering that amount of time), than say 5-10,000 years ago.

Now, this raises a few very practical points, the insanity about global warming not withstanding. Because earth temperatures have been warming (period) over the long haul, and because the rate of increase is slightly steeper more recently, we might reasonably expect temperatures to increase slightly over the next 50 years. And, reasonable projections indicate a rise in bay water levels of maybe 3 feet. 50 years and 3 feet are chump change for paleontologists, but even paleontologists are land-owners and (usually) law-abiding, tax-paying citizens, and have some investment in the 100 years of their existence on this hunk o’ rock. So, applying our knowledge of historical patterns, and looking at a detailed topographic map of the bay area water levels, present areas of settlement, industrialization, and major economic import (including the marshes - I haven’t forgetten about the story), the following is indicated:

Some of the most important companies of Silicon Valley, which evidently have arrayed themselves along the western shoreline of the bay, including Sun Microsystems and others I recognized by can’t now recall (BIG names), fall within this 3 foot span. Yessiree, it’s true. 3 feet of water - for any reason, and "NASA, we have a problem." Gone, guys. Unless these companies pick up shop and move, they’re toast. Of course, they won’t go without a fight, but even dikes (or is it dykes? I can’t remember) and levees and seawalls are short-term fixes for a major problem - a gagillion cubic tons of water pressing in from the bay, non-stop. Better to re-locate uphill than fight such a brainless behemoth. Hopefully that’s what they will do - becuase unless it’s a tsunami or something, 3 feet doesn’t happen overnight. Still, this is a major, major economic drain for a very, very important sector of the global economy. I expect stocks to rise in the dredging industry, however. 

But wait, it gets better. Our valiant speaker informed us that, without a doubt, 3 feet of water will wipe Stanford off the map. Simultaneously, the island of SF will be cut in half with a straight of water running NW-SE through Colma. Next goes UC Davis, which sits well upstream on the Sacramento (I think) River, but will nonetheless be subject to the effects of higher water levels, and will get swamped. The hikes uphill on the Berkeley campus do indeed have a long-term benefit beyond my heart, quads and ass: Berkeley will remain untouched. In fact, there’s this nice little restaurant about five blocks down from the western-most border of campus that, with a slight shift in its business strategy, is exellently located to exploit the "fresh fish n’ chips" corner of the market. New student hangout?? We’ll see…

More later… must run. The fate of the marshes and the character of a prominent conservationist remain to be seen…. 

I should have started the previous post on adaptation with this (also excerpted from my letters to a coordinator on this book project I’m helping out with).

Adaptation is, for evolutionary biologists, a complex word. In the general sense, which I understand is what you’re going for here [for third graders], it’s an observation that organisms are, by and large, pretty good at doing what they do for a living. They’re a good match for their way of life. Bats are adapted for flying. Horses are adapted for eating grass. Bats don’t eat grass, and horses don’t fly. Etc. In second sense, an adpatation is a structure or function of an organism that does a particular thing. The conspicuous examples are bird wings, long jackrabbit ears, spinnerets on spiders, giant fangs on carnivores, bright coloring in birds, rodent incisors, etc.  In a third sense, adaptation is a process (in evolution) of producing those finely-tuned structures and functions.

HB wrote: "Small gradual changes can accumulate over huge periods of time (an idea Darwin got from Lyell’s Principles of Geography* and from observations he made on his journeys, particularly in South America)"

An interesting side-note on Darwin’s usage of the word "gradual": while in South America, there was an earthquake, and upon surveying a section of rock that had dropped many feet (I can’t recall the exact distance), exposing new strata, Darwin referred to this change in his notebook as "gradual", in the sense that a graduated cylinder is graduated - by steps. What Darwin comfortably folded under the term "gradual" is rather different from what we mean today.

Although Darwin convinced many people of the idea of evolution with his Origin, the mechanism of natural selection, which he labored so long and hard to explicate, did not have an immediate or lasting hold among biologists. By the turn of the century, natural selection was perhaps the least favored mechanism for evolution. Above it was saltation (often favored by those with an embryological bent), orthogenetics (often associated with paleontologists), the neo-Lamarkians, and combinations of these.

(Saltation is the idea that discontinuous change is an important source of novelty and variation. Orthogenetics was based on observations of long-term, apparently directional trends in both the fossil record and living organisms, and concluded that organisms are more or less pushed in a similar direction evolutionarily, and you see more and more exaggeration of distinctive traits until it becomes too much and the critter goes belly-up. The giant Irish elk (which was neither Irish nor an elk, and died out about 10,000 years ago), is frequently cited as an example of this. Neo-Lamarckianism centers on the inheritance of acquired traits - that, for example, if you work out regularly and cultivate giant pecs, your offspring will have larger (though perhaps not immediately as large) pecs as well.)

Thanks to the huge advances in genetics, by the 1930s evolutionary biologists finally had a way to track heritable changes. Combined with a R. A. Fisher’s mathematical prowess, natural selection could be demonstrated, tested, and simulated. Darwin’s mechanism was back. As the evidence and rigor increased, the competing (though not always contradictory) lines of thought and evidence were first set aside, then criticized, then denounced, then stigmatized and banned from the profession. While much dirty bathwater was tossed out, a few babies went with it.

The view that evolution is gradual, in the sense that it is *only* slow, seamless, and practically imperceptible was a view held (more or less willingly) by mid-20th century evolutionary biologists. Interest in step-wise changes,  was derided as distinctly un-Darwinian, unevolutionary, and unscientific, and specifically directed at the saltationists. "Hopeful monsters"[2] was apparently the catch-phrase for discontinuous change, the signal for rolling your eyes as proof that you were part of the in-crowd that knew better.

It wasn’t until the 1970s that the notion of apparently discontinuous change became a viable research question again. In paleontology, the application of a population genetics model of speciation to observations from the fossil record resulted in the now-famous concept of punctuated equilibria. And, even more important in my view, a few years later there was a merging of embryology, classical and molecular genetics, evolutionary biology and paleontology into what is now called evolutionary developmental biology - "evo-devo," though it didn’t really take off until the 1990s. Now we are tracking the origin, control and deployment of changes in general (including step-wise ones) at multiple levels of biological organization - from genes, proteins, cells and gross morphology, to making predictions about ancestors, and testing them with old and new fossil finds.

The linking of the concept of natural selection with smooth, seamless, imperceptible change is not a logical necessity, but simply a question of scale and frequency - within and among lineages - and this is an active area of research.

Every little bit does count in biology and evolution - and sometimes a little bit of change (at the genetic level) turns out to be a whole lot of change (at the developmental level). And a whole lot of change in development, can be one of the "little bits" of accumulated change leading to speciation. Or not. A lot of things don’t play out. There are far better odds in Vegas.

*Corrected: Charles Lyell, Principles of Geology, 1830

 
[1] Cool examples of step-wise changes in development (not evolution): the bithorax mutant in the fruit fly has two thoraxes, with a pair of wings each, instead of the normal single pair of large wings.  In the antennapedia mutant, the fly grows mutant legs where antenna should have been. Or you can grow an extra set of fly eyes instead of antennae, albeit rather smaller than normal. Or you can turn fly mouthparts into legs with the proboscipedia mutation. Or eye tissue (lenses and all) on a fly leg by tweaking the activity of the eyeless gene. [The associated news article on eye evolution is an indication of what evo-devo is about; very, very cool stuff.] I’d dig up non-fly examples, but it’s late.

[2] "Hopeful monster" was a one-time, unfortunate phrase used by Richard Goldschmidt, a displaced German Jew interested in butterflies, development, and evolution. Metamorphosis is a kind of double-development for a single individual, where a larval butterfly becomes a fully functional caterpillar, then at metamorphosis, basically dissolves its first body and builds a second from a collection of cells set aside in the first round of development. A highly reasonable 1940s view of this situation is that an individual houses the ability to produce two radically different bodies. He also knew that if you tinker with development a little bit, you can get big, big change. Should even a minor beneficial variant of this sort arise in nature, it would still be a very significant departure from the norm. And given that even closely related species differ in important ways, he reasoned this might be a way to eventually bridge the gap to speciation. This put him in both the orthogeneticist camp (since development is a highly directional and programmed process) and the saltationist camp (evolution can happen in steps or jumps) at precisely the wrong time, and he and his "hopeful monsters" became the whipping boy of the Modern Synthesis.

PS:  I’m planning a follow-up post on the role of gradualism in Darwin’s formulation of natural selection, and in current understanding of rates and frequencies of processes in evolution, in terms of the law of cause and effect.

Update 10/9/06: I realized I should have first presented some distinctions that have to be made in understanding the word adaptation. Posted here.

I’m helping out with a book project on adaptation and variation for 3rd graders, through the Lawrence Hall of Science . I wrote this to explain the difference between "adaptation" as the public understands the term, and "adpatation" as evolutionary biologists mean the term, for one of the book developers. Maybe you’ll find it helpful too.

—

Adaptation, in the technical sense, directly implies that a trait evolved for the purpose it is used for today (for extinct animals, you pick a reference critter or group, and whatever they used that trait for). So this means a researcher must establish that a trait does what we think it does - that the organism actually uses it for that. As you might imagine, this is especially difficult in extinct organisms, though sometimes there are obvious or clever ways of weeding out possibilities and putting together a reasonable hypothesis. Then we have to show that the historical origin of that trait was FOR that purpose. This is very, very hard. Plus, if a structure arises in the context of one function, then gets co-opted into use in a second function, that structure is no longer called an adaptation in the context of that second function; we call it an exaptation, and the process of co-opting is also called exaptation. (Bird wings and feathers are a good example of this). For the cases where we haven’t established the function and original context of a trait (which turns out to be most of the time, since there’s so much to do) the trait is just called an aptation (or trait, or character, etc.) A neutral, assumption-free term.

On top of that, it’s entirely possible that a structure arises for no purpose - it’s piggy-backing on the development and selection of another trait. Then, this piggy-backed trait (Stephen  Jay Gould coined the term "spandrel" for this), can get exapted for new functions. All these things get lumped under the general banner "adaptation" among the public, which is only somewhat necessary in my book, since more precise and equally understandable words (like trait, character, evolved, changed, etc) are available.

Furthermore, much of the evolutionary concepts people have today are derived from the way they were used in the ’50s and ’60s. Then, the word adaptation was used by scientists much as it is used by the public today - any and all structures and functions were called adaptations, and they were assumed to be helpful to the organism, and odds were those adaptations evolved for the purposes we see today - thus, by a process of adaptation. Everything was amazingly "fit" for its niche. But this is all assumption; not much testing accompanied these nifty stories of adaptation and evolution. It wasn’t the most rigorous of science at the time. (You see some of the same vocabulary trends in scientists who don’t work in evolution directly, but want to invoke it in their own work - cell biologists talking about receptors and proteins "evolving for" the studied function, and "being adapted for" the present context, without any historical evidence provided; this reveals assumptions of the researchers, which really ought to be tested, or labeled as hypotheses for future testing). It turns out many critters have traits simply because their ancestors did. They may not use those traits at all, they may use them for something new (by exaptation), or they may be a burden to the organism, but one it hasn’t managed to shed, evolutionarily, for one reason or another.

So to (mis)-quote me as saying "I want to know how this adaptation helped the first animals that had them" implies that I assume horns had a function in the beginning, that this function was helpful, and that it was the same function we see today (and there are many functions). All of this remains to be seen. And, given the spotty fossil record of bovids, we may never know the answer. So I steer away from the word ‘adaptation’ in my work.

But I think we can find a balance between jargon and general concepts. It shouldn’t be hard to find the sweet spot between (modern) scientific accuracy and concept-formation in 8 year olds. I think it will prevent future confusion and apparent contradiction, and help educate a generation in 21st century science, instead of 1960s science. In fact, I think a general presentation of changes in structure and function/purpose over time should include mention of the possibility of something having no apparent purpose(1), or not being perfect at what it does(2), or being an actual burden to an organism(3). Including this aspect in a discussion of adaptation (in the general sense) paves the way for more advanced understanding of evolutionary processes and biological complexity in the future. (Because the Perfect Structure Perfect Fit paradigm really isn’t very advanced; it’s an initial impression noted since Aristotle). The whole idea of "tinkering" - of just-good-enough evolutionary solutions using materials presented by (geneological) history is really quite fascinating, and I think it’s an idea kids can grasp based on their own experiences trying to make stuff but lacking the perfect materials.

A compilation for future use, and public reference

Transcript of the ID trial Kitzmiller v. Dover Area School District
     - Of particular interest, and public value, here is the examination of Kevin Padian on day 9. It’s long, and there are typos, and he was using a slide presentation, but for a mostly plain-speaking presentation of what modern evolutionary biology has to say on a lot of "hot" topics is presented. Transitional forms abound, even when the fossil record sucks.

     - I should also say that I think KP misstated a couple things, in terms of the science content, but that they are not essential for the concepts presented. I also diverge from KP, the NCSE, and many/most other scientists in thinking that consensus of a group (of experts, in this case) does not by itself validate an idea (though it can be a gambler’s rule of thumb), I think that truth and certainty are contextual and therefore possible to science (and elsewhere in life), and other important points. The value of his testimony (which I view as considerable) is as a resource of facts, which is the place to start in all this. That "Tasmanian  Wolf" marsupials share more physical similarities (by the dozens) with other marsupials than with regular dogs and wolves is a numerical fact. That the main textbook of ID has morphed, by known and observable steps, from a special creation textbook to an intelligent design textbook is a fact.  And on and on. If you seek to begin at the beginning in the matter, this is a good place to start.
     
     -The public’s (even the educated public’s) understanding of what is meant, understood, entailed by, and in support of evolution as a phenomenon and process is … beyond paltry. This is for several reasons, I think. First, and most importantly, schools and teachers have been either prohibited from teaching evolution, told what limited portions they may teach (many of which are inaccurate and/or outdated by at least half a century), intimidated into discussing evolution as little as possible, and/or forced to include ‘alternative viewpoints’ that unnecessarily confuse students about the nature of the questions, the methods of investigation, and the state of knowledge. There is so, so much more to it than "random mutation" (a terrible term, by the way, and hugely misunderstood) and natural selection. More later on this.

     - Secondly, evolution as a concept, and as a science, is far removed from the perceptual level. It subsumes spans of time, and stretches of space, and numbers of organisms that far exceed what your eyes or your mind can hold at any instant. We organize all this raw data by forming concepts, by carefully building a chain of progressively more abstract concepts in your mind, that subsume more and more. That doesn’t mean the more abstract concepts are less right, it just means it’s more difficult to form them quickly and accurately (thus: take your time), and it’s farther removed from immediate observation.

     - In this sense evolution is closer conceptually with particle physics and astronomy, in terms of the amount of mental effort required to hold all the relevant concepts in your mind, understand their relationships, and how those concepts trace back to reality. Jumping straight to the concepts, without building the chain, practically guarantees a broken chain (which may or may not concern someone). This is largely how modern education proceeds, unfortunately. You’re told about subatomic particles, or processes best characterized in terms of millions of years (in the case of evolution) or even billions of years (in the cases of astronomy, I presume). Then you memorize information about them, crunch through the formulas and work the practice problems. But where those concepts came from, and how they trace to reality in person, personally, by your own observation is usually left aside, or only given short treatment. Then you stare at reality and try to see how it all hangs together. Most people try to  stitch stuff together in their minds, as best they can, if they’re interested in how whole fields relate. (A lot of people don’t really care, which is of less concern to me.) This is what educators should be helping students do, not what they leave them to do solo. The guideposts for stitching ideas together are not something you’re born with. The odds of doing it correctly, off the cuff, picking up tips and ideas here and there from whatever cultural or intellectual soup you live in, are quite low, if you look at it probabilistically. Again, this is the role for educators, and exceedingly good ones at that. I don’t know anyone at my school who teaches in this manner. That’s the kind of bar, standard, I’m talking about.

I’m soap-boxing again. Back to the task.

Here’s a good article, though with a very delimited focus (unlike my endless tangents and addendums and clarifications).

The Bait and Switch of Intelligent Design. - why ID is irreducibly about supernaturalism and faith.

Arguing for an accurate understanding of ID. A pro-ID article. Interestingly, Dembski is quoted as saying that ID isn’t an anti-evolution statement/position/method/whatever. Bet you didn’t know that. Which begs the question - what is it? Ah, it’s a method - an epistemology, as I said before. There’s a whole post coming on that one. 

     - Check out the irregularities in argumentation - in both the article itself, and in the authors the article quotes. The primary point of argumentation is never stated, and it’s this: can science ever scientifically identify the existence of something not amenable to science? That is, the article vehemently points out that ID has nothing to say about the nature or identity of the designer (apart from the fact that it is supernatural, it is undesigned itself, and it is not amenable to scientific study - that sounds like a ‘nature’ and an ‘identity’ to me; a proper name is not the be-all and end-all of identity).

     - Even given this self-contradictory point, the argument fails - because the question of ID’s scientific status does not center on the alleged identity of the designer, but the existence of the designer at all. Not what it is, but that it is. That point alone is not a possible conclusion of science. Science, honestly conceived, cannot conclude that something is beyond science, that is, beyond nature. It’s a contradiction and violation of the rules (epistemology and metaphysics) of a scientific worldview. (Another post on that later). A phenomenon may be beyond our technological or instrumental capabilities - temporarily or permanently - but that doesn’t render it unnatural or supernatural, much less intelligent (and intelligence requires consciousness, so the designer must also be conscious). The phenomenon itself would just be naturally intractable given our capabilities. (And the odds of this ever happening are remote, in my view, and certainly don’t crop up surrounding the concept of evolution. The odds are better for sub-particle matter, if such thing exists, in the far-distant future.)

My mom sent me a newspaper clipping a while back about Jonathan Wells - an intelligent design proponent with a new book out - and asked me if I’d heard of him, and what I thought. Well:

Yes, I know of Jonathan Wells. My advisor has written at least one review article on the man. I’ve read a couple of his scientific papers, in preparation for the Dover Trial last fall. Wells is full of bunk. His legit science papers in no way admit of intelligent design, much less supporting it in opposition to evolutionary viewpoints. Naturalistic explanations far and away account for what he’s shown; in fact, his paper on the microstructure and function of microtubules and centrioles in cells, is utterly indistiguishable from something another scientist, accepting evolution, would write.

He and Michael Behe and Dembski like to make an "argument from complexity." Basically they haven’t got past the 3rd grader’s observation of "Wow, the world is complicated! How do things do what they do?" But instead of listening to their 3rd grade science teachers, or picking up Dad’s "The Way Things Work" book, Wells and Behe and Dembski then suspend any inquiry and conclude that it "must" have been intelligently designed.

Really, the Argument from Complexity is an Argument from Wowness. And if the Argument from Wowness is to stand as a conclusion (rather than as the motivation for inquiry), it presupposes a view that humans are either incapable or not allowed to mentally dig beyond the Wow Observation using the same mental tools as before. The supposed intractability of such Wow Observations ("It’s just too complex!!") implies that we’re either supposed to be omniscient, or that we’re intractably retarded. And it conveniently ignores how many Wow Observations preceded this moment in history, resolutions of which enabled the culture, technology and standard of living we currently enjoy - one that is unprecedented in the history of the known universe. Chew on that one for a minute.

ID is not just an alternative viewpoint, or an a-scientific position, it’s an anti-scientific concept, because if it’s accepted as a valid way of investigating the world… all investigation stops! You don’t get past the point of wonder. Nobody - not Aristotle or Newton or Darwin or the Wright Brothers or Louis Pasteur or anybody - could have done what they did with such an approach. Put away your calculators and test tubes, lock the lab door behind you and go to church. That’s all you can do. There’s nothing deep or hard or new that can be done with such an approach to thinking.

Now try to imagine a world without the achievements of the giants on whose shoulders we stand. Now think of all the existing scientists - the highest percentage and the greatest raw number to date, and with more funding and knowledge and opportunity than ever before - but each requiring a very specific mental protocol for successfully engaging with reality at the boundaries of knowledge. What if you effectively deleted all these people, or tried to commandeer their work, replacing thinkers with saintly nuns or day laborers? That is what is at stake. Nothing less.

ID proponents claim that ID is compatible with science, but basically they’ve just worked hard to explain away all the methods and knowledge that already exist. Apart from their explanations being logically, scientifically and philosophically wrong (and they’re very good at selling these invalid arguments, preying upon subtle and common errors in thinking and language), this sort of approach doesn’t let you do anything truly new. You’re also not allowed to significantly revise anything. You just have to do more of the same. Describe a new species of mold or look a little closer at the process of cell division - but not too closely. And god help you if you are intrigued and baffled and amazed by the stuff you study - the moments when science is pure adrenaline, and nothing can keep from diving in and figuring it out - cuz that’s the point at which ID people say you can’t do your work any more. Science stalls, knowledge stops, thinking vanishes.

And it’s those moments of heady discovery, as a student or researcher, that are the irreducible reward of the scientist - of any thinker, in fact. It’s the thing you can’t take away, or ignore, or mask. The free and capable exercise of one’s mind, and the positive internal feedback of sheer happiness when you’ve done it well - that is the motor of knowledge-expansion. And without it, the downstream applications and technologies will slow down, stagnate and dry up if we stifle any thinker’s mind. As with anything - just give it time.

It is essential to think of all the times you’ve cracked open a problem, when the "irreducible complexity" of the initial task starts to give (because it does, time and time again). Only by daring to assail the confounding, petulantly resistant problems can a thinker - the scientist within all of us - reach into the black box of reality, and pull out handfuls of treasure. And, as a principle of a free market, enterprising individuals pick up this new knowledge, and make novel applications and products, improving our capabilities and standards of living, and changing humanity’s worldview time and time again. Science - that is, principled and uncompromising application of reason - as a method of thinking, is responsible for getting us out of the jungle, and getting us out of the Dark Ages and into the Information Age. That is the single largest, and irrefutable, testament to the singular importance - and efficacy - of a free mind.

And there it is: the secret ingredient of civilization. Free use of your mind, with reality being the ultimate judge, is the foundation for knowledge production and, through industry, for economics. And through economics, for politics. (Economics and politics being the principles underlying acceptable human interaction, whether in monetary or interpersonal relations). Stifle one, you stifle them all. Throttle back the human mind - and what have you got? … Nothing that’s essentially human. Just as a dog wouldn’t be what we understand a dog to be, if it didn’t have its jaws and teeth and bark, or a horse wouldn’t be a horse if it didn’t have long legs, hooves, and succeed in killing grass - a human isn’t what a human should be if he can’t use his mind freely. Not all dogs win fights, not all horses are the fastest, and not all humans are always right in their judgement - but it’s the use of these capabilities that has to be uninhibited, for everyone, in every line of inquiry. Then, as a lovely side-consequence of people freely thinking and acting to the best of their abilities, in the heat of the crucible of reality, the best of the best rise to the top, and take us all with them.

I know I sound like I’m ranting and pushing things to their extreme, but that’s the best way to expose crappy ideas: put them through their paces, and see who comes out in the long run. ID is not about evolution. It’s not even about biology. It’s about how to think, and that applies to all branches of science, all areas of intellectual activity, all human action. Just as a cancer, with enough time, will pervade the entire body, so an invalid method of thinking in biology is not ultimately confinable to biology, and it spreads to all science, all thinking. This is especially true in a society like ours, that looks strongly to precedent - in its laws, culture, norms, and values. Compromise a principle once, and you have to work ten times as hard to get that little bit back - if you can at all.

ID is nothing less than a veiled advocacy for a return to the Dark Ages. And while I can have sympathy for the Average Joes of the populace getting hoodwinked by ID, who have only mediocre levels of science education or intellectual agility, I haven’t the slightest shred of patience or the remotest hint of respect for Wells and Behe and Dembski - at least 4 PhDs among them - who have been twisting creationism into palatable versions for the scientific community, while preying upon the sympathies, feelings, and ignorance of a majority of the population. They’ve slipped cyanide into the potatoes we live on. And few people will call them on precisely what they’re doing. We hear platitudes that, in effect, potatoes are outside the province of nutrition, or that just a little cyanide isn’t bad for you, or that it’s a novel and under-appreciated approach to human health, one that is wrongfully marginalized by the elitist, institutionalized, narrow-minded potato industry.

Inocculations against these predators of poor thinking are, however, in short supply. Because ID proponents prey on people’s thinking skills, the only way to really get rid of the problem - to remove the fuel instead of putting out countless fires - is to supercharge people’s ability to wade through complicated arguments. That is, the ability to accurately identify and evaluate ideas, and see past all the frills and facades that obscure the heart of an idea, and see what makes it tick, and to judge it appropriately. I’m just learning how to do it myself. I’ve been evaluating ideas for a long time, but it’s almost always been by non-essential points - just whatever I could get a handle on, mentally, sometimes better and more right, sometimes decidedly less so. And even if I was right, I wasn’t sure how to go about proving that it was right. Vehement argumentation is no substitute for watertight logic based on reality. That much I knew, but I didn’t know how to do it.

Now, the antidote to this is not dogmatism. That’s just an even more extreme form of un-thinking. What this problem requires is unabridged thinking - showing people how to think accurately, usefully, and cumulatively about the world. The thing is, they often already do it. It doesn’t require omniscience, but the kind of mental growth and progression that comes with experience, and honest  reflection on that experience. Most people do this intuitively, but because they don’t have a name for it, they can’t call it up in their defense when someone attacks the base of knowledge. And most people don’t recognize the attack as one of terrorism against the mind, but instead see it as an isolated incident by well-meaning, if pitifully confused, people - that is, if they don’t already buy the terrorists’ arguments and fund them on the side.

Thinking well is no small task - for an individual, or for a society. I know first-hand the challenge of re-learning how to think at the age of 25, and the mind-warps and growing-pains - and the thrill, pride, and leaps forward in ability and success - that go with it. I have no illusions about how tall the order is - for me to complete, or for other people. Or how long it will take.

All this is, in fact, the task of philosophy. At the end of the day, ID is an assault on epistemology, not evolution. Evolution is the convenient voodoo doll through which ID is trying to kill the human mind. Which is one of the many reasons I am an Objectivist - it’s the one group of people I’ve found that recognize this problem for exactly what it is, and know how to solve it. But they know you can’t solve it for another person. You can’t think for another person. Don’t tell people how to think - why would they listen now? - show them. Show them how to do it, and why it works, and why it’s this method of thinking that underlies human growth, potential, achievement, security and happiness.

But, at the end of the day, each person has to choose for himself - more or less knowledgably, it’s still a choice, though not equal in strength or in responsibility. And that’s why I hold the most knowledgeable people - the Wells and Behes and Dembskis of the world - explicitly culpable. They hurt people in the long (and not-so-long) run, and they have the ability and experience to know better. So, whether they think of it directly or not, by their actions they are harming people, and in the uninhibited exercise of my judgement, I will freely and knowledgably denounce them to the ends of the earth, in defense of my own mind and the world in which I live.

Close! Very close to what I’m after. However, I was told by my recommender that it’s written from a Modern Synthesis pan-adaptationist perspective, which kinda sucks, but hey, it’s a start. At least someone is thinking similarly.

William S. Cooper. 2003. The Evolution of Reason: Logic as a Branch of Biology. Cambridge Studies in Philosophy and Biology. Michael Ruse, series editor. Cambridge University Press.

Description:

The formal systems of logic have ordinarily been regarded as independent of biology, but recent developments in evolutionary theory suggest that biology and logic may be intimately interrelated. In this book, William Cooper outlines a theory of rationality in which logical law emerges as an intrinsic aspect of evolutionary biology. This biological perspective on logic, though at present unorthodox, could change traditional ideas about the reasoning process. Cooper examines the connections between logic and evolutionary biology and illustrates how logical rules are derived directly from evolutionary principles, and therefore have no independent status of their own. Laws of decision theory, utility theory, induction, and deduction are reinterpreted as natural consequences of evolutionary processes. Cooper’s connection of logical law to evolutionary theory ultimately results in a unified foundation for an evolutionary science of reason. It will be of interest to professionals and students of philosophy of science, logic, evolutionary theory, and cognitive science.

The review on Amazon is also helpful.  

Previous related posts:

People are Logical
Reflecting Myself (see comments) 

Today begins five days of rubbing heads with people who hopefully think like I do - or at least, they think about the things I think about. My first strictly academic philosophy conference. And a whole session on (what I consider to be) one of the great outstanding questions for both philosophers of biology and biologists - particularly paleobiologist: the (disputed) existence of levels of selection, which employs concepts, definitions, and assumptions about evolutionary trees and the nature of species. Very, very cool. Answering this question is on my 10-year to-do list.

I’m going to cave in to both my list-making compulsion and my desire for pithy efficiency:

Here are some really cool posts I’ve read elsewhere, but don’t want to clutter up my blog by posting fully. Check ‘em out. They range from interesting to cool to fucking awesome.

Living the life of a space-explorer: Antarctic perspectives from a Navy HELO pilot - I am Jack’s inflamed sense of jealousy.

Visions of myself in 40 years

A complex method by which to "Oooh pretty colors!" - go ahead, click it. And click it again. No one will see.

Nikola Tesla quotes Part I

Nikola Tesla quotes Part II 

A sketch of Tesla

On the levels of selection debate (I don’t expect everyone’s mouth to water on this topic the way mine does):

From hpb.etc blog

From Gene Expression blog

Intros to Phenomenology (I’m interested in Phenomenology because of a few perplexing conversations, which made me realize it’s one of those variants of philosophy that’s easily glazed over and branded as "deep but incomprehensible, and therefore probably right" and/or science-friendly, which as far as I can tell, it is not. It’s (yet another) primacy-of-consciousness worldview, despite protestations to the contrary, trying to remove the humanity from a human process.)

For the free-time poor

For the free-time rich