The present is the past, the past is the present

Ken Ham is preaching about what science is again. He’s accusing the secular activist Zack Kopplin of being “brainwashed” by evolutionist propaganda, and to support this claim, he once again drags out the tired proposition that there are two kinds of science, historical and observational, and that only the observational kind is valid; well, unless the historical version is based on the Bible, which in his dogma is an unassailable compendium of absolutely true facts about the past.

What’s more, Kopplin—like almost all evolutionists—confuses historical science with operational (observational) science. Operational science is indeed observable, testable, falsifiable, and so on—but none of those words describes evolutionary ideas! While biblical creation may not be provable through tests and observation, neither is molecules-to-man evolution (or astronomical evolution). And in fact, the evidence that is available to us concerning our origins makes sense in the biblical creation-based worldview, not the evolutionary one. Of course, secularists mock creationists for separating out historical science and operational science. But they do that because the secularists want the word science to apply to both historical and operational science so that they can brainwash people (like Kopplin) into thinking that to believe in creation is to reject science.

This is utter nonsense. It’s a phony distinction he makes so that he can bray, “Were you there?” at people and pretend that he has refuted anything they might say about the past. It is a set of appalling lies from a know-nothing hidebound fundamentalist who knows nothing about science, and who happily distorts it to contrive support for his ridiculous beliefs.

It is false because of course I can observe the past. The present is the product of the past; if I open my eyes and look around me, I can see the pieces of history everywhere.

I live in the American midwest. I can go into my backyard and see on the surface the world as it is now; fenced and flattened, seeded with short grasses, surrounded by paved roads and houses. But it takes only a little effort to observe the past.

In ditches and pioneer cemeteries and dry unplowable ridges, traces of an older world, the prairie, still persist. I can find clumps of tallgrass, scattered forbs, rivers fringed with cattails, turtles like primeval tanks on the banks, frogs and salamanders lurking in tangled undergrowth, fragmented bits of the pre-European settlement. I can see relics of a changing human presence; there are places where flint arrowheads turn up regularly, and to the south are the native pipestone quarries. I can walk along the increasingly neglected railroads, and trace how they contributed to our presence here; small towns sprinkled along the railroad right-of-way, acting as central depots for tributaries of wagons on dirt roads, hauling corn to the granaries. It’s all here if you just look; it’s not a story told by fiat, poured into books that we accept as gospel. That history lies in scars in the land, observable, testable, falsifiable.

I can dig into the ground with a spade and see the rich dark loam of this country — the product of ten thousand years of prairie grasses building dense root systems, prairie dogs tunneling through it, the bison wallowing and foraging. This isn’t an illusion, it’s the observable result of millennia of prairie ecosystems thriving here, and it’s the source of the agricultural prosperity of the region. I can sieve through the muck that has accumulated in prairie lakes, and find pollen from the exuberant flora that grew here: clover and grasses, wildflowers and the flowering of the wetlands. I can track back and see the eras when the great eastern deciduous forests marched westward, and when they staggered back. It’s all in the record. It all contributed to what we have now.

We can go back and back. We can see the scattered rocky debris left as the glaciers retreated; we can see the vast depressions left by the pressure of ancient lakes; we can see the scouring of the land from their earlier advance. Seeing the landscape with the eyes of a geologist exposes its history. While the glaciers demolished the surface, we can also find places where seismic cataclysms thrust deeper layers to the surface, and there we find that millions of years ago, my home was the bottom of a huge inland sea, that diatoms silted down over long ages, burying the bones of plesiosaurs and nautiloids in chalky deposits.

Again, this is not mere historical assertion (and isn’t it demeaning to treat history as something empty of evidence, too?). Open your eyes! It’s all written in towers of stone and immense fractures in the earth, in microscopic drifts of long dead organisms and the ticking clock of radioactive molecules. We are immersed in the observable evidence of our past. Everything is the way it is because of how it got that way — you cannot blithely separate what is from the process that made it.

I can see it in me, too — biology is just as much a product of the changing past as is geology and ecology. I can look in the mirror and see my mother’s eyes and my father’s chin; I can observe myself and see my father’s sense of humor and my mother’s bookishness. I remember my grandparents and my great-grandparents, and looking back at me are a collection of familial traits, all shuffled and juggled and reconstituted in me.

Beyond those superficial impressions, I can have my genome analyzed and find my particular pattern of genes shared in distant places in the world. I know that my family came from Northern Europe, that in turn they migrated out of central Asia, that before that they were living in the Middle East, and long before that, a hundred thousand years ago, they were an adventurous (or desperate) tribe of people moving northward through East Africa. This is not a mere story, a fairy tale invented by ignorant scribes — my ancestors left a trail of alleles as they wandered over three continents, a trail we can follow even now.

“Were you there?” Yes. Yes, I am here, imbedded in this grand stream of history, aware of my place in it, seeing with open eyes the evidence that surrounds me. And I pity those unable to see the grand arena they are a small part of, who want to deny that history is observable.

New bloggers for Science!

As is my custom, my upper level courses have an expectation that students will do this blogging thing. They’re just now getting set up so there isn’t a lot of content yet, but here’s the current list of student web pages. Cruise on by and talk to them!

Methinks it is like a sauropsid

Eugene McCarthy, the author of that crackpot stabilization theory, has discovered my review and is now making a noise on twitter. He’s gone from thanking me profusely for mentioning him, to whining that I stole his figures, to complaining that I don’t understand his theory at all, all in the last 24 hours.

But here’s the fun part. Recall that one of his bizarre claims is that whales did not evolve from terrestrial artiodactyls, but from mosasaurs, mesozoic marine reptiles, instead. But the anatomy shows that mosasaurs are derived squamates, reptiles, with a completely different skeletal organization than a mammal. This has attracted the attention of Darren Naish and Tom Holtz, fully qualified comparative anatomists and paleontologists, who actually know a great deal about the structure of these animals, and are giving him a spectacular ass-whooping. Browse it on Twitter.

The basis of his claim is that mosasaur teeth “look like” sperm whale teeth. That’s not a good criterion, and it’s not true; as has been pointed out to him, basal mosasaurs are pleurodont (that is, the teeth are fused to the inner side of the jaw bone), not socketed as are sperm whale teeth. He’s also now claiming that mosasaurs swam by vertical motions of their tails, like whales…but he’s citing articles with poor comprehension. The cited articles show evidence that mosasaurs propelled themselves with axial motions of the tail, which is a far more general statement; they moved by sweeping their tails like oars, but it says nothing about vertical vs. horizontal undulations.

So I went back to McCarthy’s book to see how he backed up this ridiculous claim. He doesn’t. He cites Pieter Camper, an 18th century anatomist, as proposing the idea that whales are related to mosasaurs. His critics are citing contemporary and detailed papers. This, however, is really the totality of McCarthy’s argument:

The varanid theory was based on Adriaan Gilles’ assertion that certain skeletal characters found in mosasaurs are not found in modern whales. However, a glance at figures 9.4 and 9.5, will convince most readers that mosasaurs have much in common with early whales. Certainly, they have far more in common with whales than does the late Cretaceous terrestrial insectivore traditional theory posits as the common ancestor of whales and all other placental mammals (it should be emphasized that all of the various forms classified as mosasaurs, too, are of late Cretaceous age). They are also far more similar to whales than is Pakicetus. One would not expect the ancient ancestors of whales to have every characteristic of modern whales. Their dissimilarity with respect to a few minor bony traits should not be allowed to obscure the well established fact that mosasaurs were huge, whalelike, air-breathing animals with whalelike teeth and that they had the same sort of prey as modern whales.

The referenced figures are grainy, low resolution images that do not do an adequate job of displaying the structures. The “dissimilarity with respect to a few minor bony traits” is trivialized; these are actually substantial differences in the arrangement and number of bones in the skull, where the mosasaur displays a fairly standard reptilian pattern and the whales show a mammalian pattern. They only look alike if you don’t look at all closely. How can you say that the jaw joint or the auditory complex of a whale look anything like that of a reptile? Only by not looking.

His other argument is that it would take fewer evolutionary changes to transform a mosasaur into a whale, than a shrew into a whale. This is nonsense. Turning a reptile into a mammal requires a major reorganization of the bones of the skull, and further, requires that those shifts exactly mimic the pattern found in other mammals. There is no reasonable way to accomplish that. Again, the basis of his entire argument is a complete ignorance about the anatomy!

This is the well-supported pattern of whale evolution. Notice: no mosasaurs.

whale_evo

Jenna Cavelle wants to correct ‘Chinatown’

If you’ve heard any history of the California desert at all, you’ve likely heard of the Owens Valley Water War.

Here’s the canonical version of that War: The Owens Valley is watered by runoff from the immense snowfall from the Sierra Nevada to its west, much of which runs into the Owens River when it melts. The Owens Valley is an endorrheic basin: it has no outflow. The Owens River never reaches the ocean. Instead, it flows into Owens Lake, in the valley’s lowest point at its south end.

Late in the 19th Century a thriving network of agricultural communities was developing due to the river’s water, growing a vibrant local economy along with their crops. Enter the Los Angeles Department of Water and Power, led by engineer William Mulholland. DWP quietly bought up water rights throughout the Owens Valley in a series of deceptive land deals, then built a 223-mile aqueduct to bring Owens River water to Los Angeles. The aqueduct was finished in 1913 — 100 years ago this November — and farms started going out of business in the decade after. Owens Valley farmers dynamited parts of the aqueduct in 1924, but the rebellion was short-lived. Owens Lake, which had been a rich habitat for waterfowl, dried up and is now the single largest point source of particulate matter pollution in the U.S.

As canonical histories go, it’s pretty accurate. Or at least more accurate than the version a lot of people have in their heads due to the film Chinatown, which was based on the Owens Valley story. But it’s a woefully incomplete history nonetheless. The history of the Owens Valley didn’t start in the late 19th Century. Before the first European settlers arrived there were people living in the Owens Valley for thousands of years. The Owens Valley Paiute took advantage of the relatively well-watered landscape by gathering seeds, hunting the Valley’s abundant game, and — though this hardly ever gets mentioned in any of the formal histories — diverting the water of the Owens River and its tributaries to irrigate their crops.

Journalist Jenna Cavelle wants to correct the canonical history to include the Owens Valley Paiute, who are still very much alive and shaping the valley:

This film documents the history of Paiute Native Americans who constructed 60 miles of intricate irrigation systems in Owens Valley for millennia long before LA secured its largest source of water through modern engineering a century ago. After the Indian War of 1863, surviving Paiute returned to the Valley from the Eastern Sierra and White Mountains to find their ancient waterworks taken over by white settlers. Today, over 150-years later, the Paiute continue to fight to save their waterworks, which are remnant in the Owens Valley landscape, along with water rights the city of LA never granted. PAYA (“water” in Paiute) stands to recover both Paiute history and water rights by increasing awareness through the powerful medium of documentary film.

She’s working to put together a set of resources, centering around a documentary film, before the last remaining Paiute elders who have some tenuous personal knowledge of their ancestors’ irrigation systems aren’t around to document anymore.  Here’s Cavelle’s Kickstarter trailer:

She’s halfway to her goal with half her fundraising period left. This project combines history, the California desert environment, and social justice, so you won’t be surprised that I really want to see it happen. I’m scratching together a few bucks to throw Cavelle’s way: maybe you’ll want to as well.

Should we resurrect the Neandertals?

I was reading an interview with George Church, who was discussing that very same question, and somehow I had to rethink some things.

There was the question of technical feasibility, and Church thinks it’s going to be entirely possible in the near future.

The first thing you have to do is to sequence the Neanderthal genome, and that has actually been done. The next step would be to chop this genome up into, say, 10,000 chunks and then synthesize these. Finally, you would introduce these chunks into a human stem cell. If we do that often enough, then we would generate a stem cell line that would get closer and closer to the corresponding sequence of the Neanderthal. We developed the semi-automated procedure required to do that in my lab. Finally, we assemble all the chunks in a human stem cell, which would enable you to finally create a Neanderthal clone.

I agree entirely: no problem. It would be very hard and expensive to do right now, but not impossible. Biotechnology is advancing at such a rapid rate, though, that in 5 years it will be difficult but within the range of what a few well-funded labs could do, in ten years it will look like a straightforward, simple exercise, and in 20 years high school kids will be doing it in their garage.

The technology is not the issue, and it isn’t even a particularly interesting technological problem. The issue is one of ethics. Church takes a reasonable tack on that one: he punts.

I tend to decide on what is desirable based on societal consensus. My role is to determine what’s technologically feasible. All I can do is reduce the risk and increase the benefits.

Fair enough. We will face clear social dictates as the tech becomes more and more readily doable, and that’s ultimately going to determine whether the experiment is done or not.

But I started to think about reasons for and against, and I must confess something terrible: my first thought was that it shouldn’t be done, and to come up with arguments against it. I know, that’s weird…my mad scientist gland must be on the fritz. But my primary concern was that this is science that could create a human being, a human being with significant genetic differences from other human beings, and that should be accompanied by heavy responsibilities — a lifetime of responsibilities. It’s easy to look at it as an exercise in gene-juggling, but this is an experiment you don’t get to dump into the biological waste receptacle when the molecular biology is all done — it has an outcome that is conscious and communicating, damn it. It’s an experiment that at its end makes someone in the lab a parent, with all the obligations associated with that. And that’s a tremendous burden. There’s the cost, the time, the emotional investment…not stuff we usually take into account in the lab.

So I tried to think about what we’d have to do to morally justify Neandertal cloning. As Church also mentions, we couldn’t just do one, we’d have to create a cohort so that these people wouldn’t be alone. The budget would have to include a substantial trust fund for each — you can’t just create a person and then kick them out into the street to fend for themselves.There would have to be adults dedicated to providing for the emotional needs of these children…

Wait a minute. That’s where my brain froze up for a moment. If a scientist is expected to feel that kind of moral responsibility for his children, what about other people? We live in a culture where teenagers carry out a similar experiment every day, with no thought at all except personal need and gratification, and are then compelled to carry the experiment to term and produce a baby they are ill-equipped to care for, because their parents insist that that is what good Christians must do. Single mothers are treated like scum, and on average have the lowest income of any group — they are expected to raise children in poverty. We let children starve to death in this country all the time. Even when they’re fed, we feel no obligation to provide them with a good education — we’re in the process of dismantling the public school system and letting future generations fester in ignorance. There is a societal consensus right now, and it’s nowhere near as demanding as I expected!

And with that, my mad scientist gland was unshackled and grew two sizes larger. We can do the experiment! We should just go ahead and do the molecular biology, produce human stem cells with Neandertal sequences inserted (ooh, even partial sequences — that would be exciting!) and get them implanted and born, do a few preliminary experiments on their behavior, and then wrap them up in a blanket, put ’em in a basket, and have a grad student drop them off at the nearest orphanage. Especially if it’s a Catholic orphanage. Easy! There don’t seem to be any societal constraints against doing that with Homo sapiens sapiens infants, which we supposedly value most highly, so there shouldn’t be any ethical concerns at all in doing it with the mutant lab-born spawn of a test tube and a sequencer.

My mistake was in holding scientists to a higher ethical standard. If all we’ve got to do is match societal norms, we’re suddenly open to doing all kinds of ghastly horrible things to children.

Of course, this grand plan would be short-circuited if society did start expressing higher concerns for children and demanded better of parents. I’m thinking as a developmental biologist, I should start voting Republican, simply to keep the raw material of our work sufficiently devalued and cheap.

Hah! I must be smarter than Stephen Darksyde!

Two years ago, I took a walk and felt a very mild twinge…and chose to go straight to the local clinic to have it checked out. You don’t fool around with a family history of heart disease! As it turns out, I didn’t have a heart attack, but was at risk and did get some preventative cardiac work done.

Now compare this with Darksyde: he felt chest pains, found that they eased with antacids and prilosec, and figured it was just heartburn, and so skipped going in to the doctor. Wrong move! It turns out he actually had a heart attack (a fact that gives Christians and libertarians cause for glee, apparently).

Actually, it doesn’t mean I’m smarter than he is — you know he’s learned a lesson with this event. The real difference between us is that I have very good health insurance and can afford not to hesitate when symptoms strike…while he is less well insured and is more likely to be reluctant at the expense. And that difference can cost someone their life.

There are two lessons here. One is that it is a wasteful injustice that we don’t have reasonable universal health coverage. The other is that you shouldn’t try to second-guess chest pains and other symptoms, you middle-aged and older people!

What I taught today: a little old-school history of embryology

This is an abbreviated summary of my class lecture in developmental biology today. This was the first day of class, so part of the hour was spent on introducing ourselves and going over the syllabus, but then I gave a lightning fast overview of the history of developmental biology.

Classical embryology began with Aristotle, whose work was surprisingly good: he approached the problem of development with relatively few preconceptions and fairly accurately summarized what was going on in the development of the chick. Most of this old school embryology is descriptive and was really a narrow subset of anatomy, but there were a few major conceptual issues that concerned the old investigators, in particular the question of preformation (the plan of the embryo is laid out in the egg) vs. epigenesis (the plan of the embryo emerges progressively). Aristotle, by the way, was on the right side of this debate, favoring epigenesis.

In the 19th century, development was seen as a progressive process that paralleled the hierarchical organization of nature — that is, developmental biology, what there was of it, was coupled to the great ladder of being. This is not an evolutionary idea, but reflects the view that there was a coherent pattern of greater and lesser development that was part of a coherent divine plan for life on earth. The German ‘Natural Philosophers’ pursued this line of reasoning, often to degrees that now look ridiculous in hindsight. In contrast, there were developmental biologists like Karl Ernst von Baer who wanted nothing to do with a cosmic teleology but instead preferred to emphasize observation and data, and simple minimal hypotheses.

In the late 19th century, developmental biology split into two directions. One was a dead end; Ernst Haeckel basically lifted the explanatory framework of the natural philosophers, replaced divinity with evolution, and tried to present development as a parallel process to evolution. Von Baer had already demolished this approach, and despite a few decades of popularity Haeckelian recapitulation died as a credible framework for studying evolution in the early years of the 20th century. The other direction developmental biology took was Wilhelm Roux’s Entwicklungsmechanik, or experimental embryology. This was an approach that largely eschewed larger theoretical frameworks, and focused almost exclusively on observation and experimental manipulation of embryos. It was a successful discipline, but also divorced mainstream developmental biology from the evolutionary biology that was increasingly influential.

As examples of Entwicklungsmechanik, I discussed Roux’s own experiments in which he killed one cell in a two-cell embryo and saw partial embryos result, an observation that fit with a preformationist model, but more specifically a mosaic pattern of development, in which patterns of development were encoded into the cytoplasm or cortex of the egg. Those experiments were seriously flawed, however, because the dead cell was left attached to the embryo, and could have deleteriously affected development. The experiments of Hans Driesch were cleaner; he dissociated embryos at the four cell stage, cultured each blastomere independently, and discovered that each isolated cell developed fully into a complete, miniature larva.

Driesch, unfortunately, interpreted these results to imply that there was an entelechy, or guiding intelligence outside the embryo, and that the only conceivable explanation was the existence of purpose behind embryology. This was also a dead end; the modern explanation for the phenomena is that they regulated, that is, that cells determine their fate by interacting with one another, rather than some kind of cosmic plan. And that’s really going to be a major focus of this course: how do cells communicate with one another, how are genes regulated to set up coherent and consistent patterns of gene expression that produce the organized cell types we find in an adult multicellular plant or animal?

That set up the next lecture. Entwicklungsmechanik, while representing a solid and productive research program, quickly reached its limits, because what we really needed to examine were those patterns of gene expression rather than trying to infer them from observations of morphology. The big breakthrough was the melding of developmental biology and molecular biology — most of the modern developmental biology literature focuses on examining interactions between genes. So on Wednesday we’ll get another fast overview of the molecular genetics research program, and a bit of evo-devo.

Slide thumbnails (PDF)