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.

Sewage by any other name would smell just as putrid

William Dembski doesn’t think the way you or I do. When we encounter a problem in biological science, we try to think of experiments and observations that would help us resolve the question: Dembski thinks of public relations and commercial opportunities. Thoughts from Kansas catches him admitting that ID has experienced a setback, and what does he think of? Broadcasting infomercials, and a commercial venture to sell ID-themed toys. (Those are Josh’s comments in brackets below.)

For some time now I’ve been wanting to complement Darwinalia, Inc. [apparently to be stupid plush toys or something] with an ID-based success and motivation course (complete with infomercials). I had been thinking about something like “Designed for Success” or “Designed to Flourish.” But the more I thought about it, especially with intelligent design taking the hits it has lately [my emphasis], it’s time simply to co-opt the language of evolution and interpret it in an ID-friendly way (in this vein, recall my post about intelligent evolution on this blog some months back—go here). Yes, ID is itself evolving! I was able to procure www.evolveyourself.net (.com and .org were unfortunately taken) and expect to start another corporation once Darwinalia, Inc. is fully up and running.

And of course, one step is rebranding. Creationism got renamed to “Intelligent Design” to smuggle it into the schools, (and we now know how well that worked) so now Dembski is thinking about renaming it again.

I therefore offer the following proposal if ID gets outlawed from our public schools: retitle it Intelligent Evolution (IE). … [H]ey, it would still be evolution, and evolution can be taught in schools. In fact, I think I’ll title my next book Intelligent Evolution: The Mindful Deviation of Evolutionary Pathways. Perhaps this book has already been written.

“Intelligent Evolution”? Dembski really doesn’t get it, does he? The game should be about finding evidence and backing up your claims, not rummaging around to find the catchiest slogan.

I do think we need to keep those words of Dembski’s around for the next trial, though. Whatever label the Discovery Institute comes up with, we now have the admission of one of their foremost proponents that he’s consciously trying to merely retitle creationism. Again.