Showing posts with label DNA. Show all posts
Showing posts with label DNA. Show all posts

16 March 2009

Review of "Prehistory: the making of the human mind" by Colin Renfrew

I just wrote an amazon.com review for a book I finished. Thought I'd post it here too, in slightly revised fashion.

I do recommend this book, but certainly not as highly as I had hoped to. This is partly because it did not meet my expectations. I had very high hopes indeed of uploading a lifetimes worth of synthetic insight into human prehistory from one of the most famous names in the field. That hope was largely disappointed by this book. Perhaps I should have seen it coming, the book is only 240 pages long, certainly not space enough for a detailed treatise on prehistory (for that I have turned to Steven Mithen’s 600 page “After the Ice: A global human history 20,000-5,000 B.C.). Instead, I should have paid more attention to Renfrew’s glinting subtitle “The making of the human mind.” In fact I did see this, and was intrigued, but unfortunately, in the end found Renfrew’s thesis on that subject to be based on a dichotomy that I don’t believe exists.

This book is composed of two parts. The first part is Renfrew’s history of Prehistory, as a field of academic endeavor. This is in itself interesting tale. From a history of science perspective, there is always much to be learned from examination of successive emancipations from past biases and technological boundaries, and how those two factors feedback on each other. However, there is an odd disconnect from that story, it seemed to me, with the second part of the book. Renfrew periodically hypes up the paradigmatic technologies of radioisotopes first, and DNA methods most recently. The big anticlimax to me was that in the second half of the book, the curtain was finally drawn, and the DNA evidence was brought to bear in support of the “out-of-Africa” scenario and damning the longstanding alternative, the “multi-regional hypothesis.” However, Renfrew then dusts his hands, and is finished with DNA, saying that, in so many words, human evolution of any consequence for interpretation of prehistory, ended 60,000 years ago. Thanks DNA for helping us archaeologists put to rest a decades old dispute, and that’s all we need from you, we’ll take it from here again. From this point, Renfrew sets up his two-phase scenario for human prehistory: the "Speciation" phase (which DNA evidence has been and will be informative about), followed by the geologically allusive "Tectonic" phase which has lead to the arts, social, and economic hierarchies. He then erects "The Sapient Paradox" which follows the form of asking how could drastic cultural changes arise in the absence of any evolution in “the” human genotype?

Unfortunately for Renfrew’s entire logical setup, that consequential human evolution ceased 60,000 years ago is certainly not indisputable. He does very little in the way of a convincing argument, and in fact it becomes quite clear that his long and distinguished career in archaeology has not included becoming well versed in human population or evolutionary genetics. His claims that all humanity has one “genotype” is rather naïve. That we are all VERY closely related as members of the species Homo Sapiens is indeed a fact. Depending on exact study and metric, the estimates are 99.1%-99.5% similarity among modern humans. However, chimpanzees are 94-98% similar to us. Even bananas seem to share about half our genes. The question becomes, not how similar is the raw data, but among those small differences, what constitutes consequential difference? For those humans afflicted with cystic fibrosis, and certain other diseases, 99.999999% similarity is still the difference between life and death. One base-pair differences are not always so consequential, more often they are not. Many differences simply influence things like a propensity to grow on average 1cm taller, or to be slightly more susceptible to addictive behavior, or to taste bitterness differently, or to digest lactose past weaning. We are learning that human genetic variation includes millions of sites in the human genome that sum up to only a tiny fraction of the overall genome, yet in concert with each other and the environment, can trigger or suppress expression, and thus have large explanatory value for understanding human phenotypic variation. Such variation is certainly fodder for evolution. Why would natural selection (and sexual and artificial selection for that matter)cease acting on such extant variation? Some readers may not recognize this as such a bold claim, but it is. And of course, extraordinary claims require extraordinary evidence. Unfortunately, the most recent book to come out attempting to do just that, “The 10,000 Year Explosion” is a rather shoddy piece of science writing. In fact, ironically, that book is shamelessly poorly presented and almost infuriatingly flippant at times, while “Prehistory” is rather well executed and erudite, yet nonetheless fatally flawed in its biased assumptions about DNA.

In the end, I do think that much of the remainder of Renfrew’s book shows great synthetic understanding from the mind of a great scholar, and much worthwhile insight surely exists. I certainly don’t hold that Renfrew’s invocation of such concepts as “Institutional Facts” and the idea of increasing material engagement in prehistory do not offer some explanatory power toward understanding human prehistory. I would suffer from the same error Renfrew makes in dismissing a whole category of potentially useful analytical approaches to say so. However, I have to admit that I don't have a great deal of enthusiasm for “cognitive archaeology” and the book in general. If the entire premise is based on a false dichotomy, I’m not sure I have the wherewithal to parse out the truly explanatory bits from those that are intricate heuristic explanations that will soon be more elegantly explicable in light of the very methods he first touts when they fit his pre-conceptions and then arbitrarily dismisses when they don't: those methods using the inherent record of prehistory inside us: DNA.

28 March 2008

Nanook of the south...

A record was broken today that I think will get some national and international attention. OK, what is one of the most important issues facing modern civilization? Global Warming/Climate Change. And, what is one of icons of this issue? The Polar Bear. So, what happened today? A Polar Bear wandered into Fort Yukon, an Athabaskan village in Interior Alaska that's 250 miles from the coast. That's as far inland as a polar bear has ever been documented in the state. That's very interesting. What happened to it? Well, a local gunned it down with an assault rifle. Unfortunately, that act is going to get a lot of attention and hubub, and while that may not have been what I'd personally like to have seen happen, I think it may distract from the far more interesting thing. What the heck was a "marine mammal" doing in the middle of the state?

Last fall, while way up on the Dalton Highway for a caribou hunt, a friend, who had recently moved to Interior from Southeast, asked a reasonable question. "Do polar bears ever come this far south?" With the kind of foolishly assured bravado that even 10 years of science training still hasn't purged me of (but should), I said "Nah... Prudhoe and Deadhorse area, sure, but not this far down into the foothills of the Brooks range..." Never say never. We were in the Happy Valley Area, a good 80 miles from the oil complexes on the coast where I assumed polar bears were invisibly tethered to there sea-ice habitat. A few short weeks later I found myself in a discussion with a hunter. Now I can't remember how it came up, but he volunteered that yea, actually about 5 years ago he and his partners came across a polar bear feeding off a caribou carcass just off the Haul Road, literally, in the Toolik Lake area, a good 125 miles south of the coast. Wow, OK, I guess I was wrong, oops, my bad. But was such southern meandering common then? No, not at all. Apparently, until today, that instance was the farthest inland documented polar bear in Alaska. That 2002 lost bear was a bit luckier than today's, as assault rifles are rather uncommon weapons in the Dalton Highway hunting corridor... it's surmised, I think, that the bear mosied on back to the ocean...

OK, so let's be blunt. Are there links between Global Warming and a polar bear in Fort Yukon? Well on a number of grounds I object to the question being raised at all... but let me be circuitous in giving an answer to my own blunt question. First, not all the results are in. Apparently there's a minsicule chance the bear is a polar/grizzly hybrid. A hunter in April 2006 shot a polar bear with odd brownish spots... hmm... couple tests later... and the DNA don't lie, momma and papa, well, shouldn't have got along as well as they apparently did... But in fact, hybrids do occur (and in fact are reportedly fertile) and perhaps have enough anatomical, physiological, and behavioral traits that could sometimes allow them to do well in grizzly country... i.e. terra firma. This fact, hybridization potential brings up two related issues, or rather two related views... one view back on polar bear history, one forward on polar bear future. Basically this is a fascinating evolutionary tale with some policy implications I think.

The oldest known fossil of a polar bear is only 100,000 years. I say only, even though that's a long time. I mean, start counting to 100,000 and tell me how far you get. That's a lot of years. But in evolutionary and geologic time, not so much. To put it in perspective, the dozen or so bear species on earth today shared a common ancestor that branched off from other carnivores 38 million years ago or so... by that clock, the polar is a brand new bear. But it might not even REALLY be a new bear. The folks at Alaska Department of Fish and Game who are going to verify whether or not this is a hybrid bear, are likely going to look at it's teeth, particularly the molars, and in a couple days there'll probably be some DNA results. A close look at that DNA, whether mom and pop were the same species or not, holds a fascinating tale. Recently, researchers, in comparing DNA from polar bears to that of brown/grizzly bears from various populations, uncovered a really fascinating story. Some brown bears are more closely related to all polar bears than they are to other brown bears. Think about it. Get it? By a lot of scientists' definition, polar bears can't even be considered their own species. They're just a really unique sub-species of brown bear. In fact, just 10,000 - 20,000 years ago, from the fossil evidence, those teeth that are today diagnostic, weren't all that distinctive... that's how rapidly the polar bear has adapted to it's sea-ice habitat and specialized diet... it's a very different way of life, and selection has resulted in some very fast evolution to form earth's largest living carnivore and current icon of change in the north. In a way, it's rather fitting. Change, at this moment in time, is happening at potentially unprecedented rates in the North. And, low and behold, our chosen icon is this crazy species who itself shape-shifted in the blink of a geologic eye into our beloved Nanook...

OK, finally... looking forward and the policy implications... Clearly, no matter how quickly the polar bear evolved, or how genetically distinct it is, there is nothing else like it. I say it is worth treasuring and fighting to save at whatever the cost. If we can't muster the will to care unconditionally about the polar bear, do we have any hope for caring at all, for saving anything? I can certainly see a couple of the above mentioned facts, wielded in the wrong hands, being used in a case against the polar bear. I'm going to play devil's advocate, and leave the last word with the devil. There are certainly rebuttals, and rebuffs to those rebuts, but I'll leave it open... "If it's not even really a real species, why should it be considered for listing as a Threatened Species?" (I actually don't know about this, perhaps sub-species can be...). And, relevant to today's event... "If a polar bear can make it down into Interior Alaska and remain healthy [untill gunned down with an AR-15], doesn't that show potential that they could adapt well to a world without summer sea ice? I mean, they evolved so quickly in the past, perhaps they'll just adapt to the new regime... " What do you think?

20 March 2008

"I could care less..."

So, though it's been a couple weeks, I should probably not be blogging at this precise moment. I've got some rather pressing things to do, namely I need to put together a talk for a branch meeting this Saturday (American Society for Microbiolgy, AK Branch). It'll be a rather small affair, one invited speaker, a famous microbiologist I've not hear of, and well, a bunch of locals. Despite that dis, I really like this meeting. This year, basically I will have 20 minutes to convince - mostly people from my lab- that I've made progress in the last 6 months. I guess I'm as curious as they are really...

In any case, no, I don't want to work on that right now... what I want to do is tell sundry things to the whole world (or those handful of individuals that will read this in no particular hurry relative to my urge to write it). Aside: The etymology of "Blog" is pretty well established, being a very recently born word... it's a portmanteau of weblog. But I'd argue it's also onomonopoetic. I don't know if anyone has yet to argue that blog is onomonopoetic. I don't want to know, so I won't Google it. I would like to think this afternoon that I'm the first person to be struck that Blog has connotations similar to burp, or belch, barf, other b- words. Like... like.. the sound that verbal diarreah makes when it can't be held back from the keyboard. We all have to blog at times, just let's try not to do it in public or more than we abosolutely have to.

So, despite that introduction, I'd like to announce that I have nothing particularly well thought out or formulated for you today. Don't get your hopes up (ever...), it's just that my fingers get to itching, and I feel like I may suffer consequences if I don't write together the loose threads of thought that seem like they might be braided into something emergent. (I'm seriously swapping/mixing metaphors here, sorry... am I braiding or barfing? not sure)... In any case, today's meandering musings will be on: science training, scientific success, apathy, causation vs. correlation, and beer. Or maybe something else. Oh, and the Gray Lady, the New York Times . She'll make a couple cameos. She's always invited... poor Gray Lady, she probably get's blogged on more than almost anyone else...

So, my title... So, today I sub tought a science course lab for a friend who is out of town. It was a computer lab, and I arrived early to set up the projector. Two students, who having never seen me before, were having no reason not to speak candidly. "What the hell are we doing in lab today?" asks one to the other a few yard away from me (diligently futzing with the projector setup, which I thought might have been a good clue). "I have no idea... I could care less." Right... Actually, I think it might be telling (about me) that the first thing that entered my own private thought baloon was: "Could NOT. You could NOT care less!" A reaction of secondary intensity was the more obvious mild annoyance at the blase attitude. It turned out later these were a couple rather sharp students... but that's immaterial... I've been through enough educational institutions to know that blase is cool someplaces (Turlock High School, I was VERY cool...) and the antithesis of cool elsewhere (At Berkeley, I was, well, sort of cool... I think, but don't quote me on that)... In any case... the first thing I did in lab was have everyone discuss a recent article in the NYT by Amy Harmon. She covers a lot of DNA and genome issues. You can email her at dna@nytimes.com. 'Nuff said. Nick Wade is good too. Read his book: Before the Dawn. Um... OK. So the article we read (http://www.nytimes.com/2008/03/04/health/research/04geno.html)
deals with the story of the first millionaire to pay a commericial outfit to sequence his genome. He forked over $350,000. If you'll allow me to do some math that I believe is original to me and not something Ms. Harmon figured... we have the following:

Equation 1.

three hundred fifty thousand [dollars] divided by six billion [approximate base pairs in a diploid human genome] times 100 [pennies in a dollar]

I kid you not: if you copy and paste the above into Google (sans brackets and included text), it will duly crunch those words and spit out: 0.00583333333. That's right. Folks, by my calculation this guy bought his own "book of life" for 0.005 cents per letter. So, is that a "good deal"? It's a ridiculous question of course. Amy Harmon reports the conceit of comparing the total price tag to a new Bently. Old Jim Watson is then quoted as saying to him it's a toss up between a Bently and one's genome sequence. He of course had his genome sequence a bit back now, for the price tag of $1.5 million... not out of his own pocket though. Jim think's the Bently is a "nice car," but hey, he's already got his genome sequenced... he's looking forward to the day of the "Chevrolet genome." And that's of course the point of the article... the price is dropping... someday... soon... we, me and you, will have the option, or doctor's recommendation...we'd better figure out whether we could care more or less, 'cause soon we'll have to start making some decisions... In fact, there's a whole slate of things to talk about regarding that, but I have two very discrete things I meant to be on track for with this post. First, I wanted to use a slightly different conceit than the luxury car metaphor... how about the more apt metaphor of a book. I'd argue that the story contained in a human genome is the single most interesting story that the universe has ever produced. Woaa, that sounds pretty bold now that I'm looking at it... I'm wanting to hedge now- my natural instinct is to say incredibly declarative brazen things and immediately hedge- but no. I do think this. The human "book of life" says more of interest than any other single record that has ever existed. I believe that. So how does the price compare... Well using the following Google Search

"average book new york times bestseller 'number of words'"

The hit that I liked occured midway down the first page and stated:

"Most nonfiction books average about 50,000 to 80,000 words."

OK, rigorous research done. Let's say 60,000. I'm going to say that $30 is average for hardcover. Please, don't argue... you'll see why...

So, Google, tell me... 30 [dollars] divided by sixty thousand [words] times 100 [pennies per dollar] = [drumroll] 0.05 cents. (finishing touch to the fuzzy math is that the average word has 10 letters, I have no reason other than my own desire to believe that is true... but hey.)

Wow. So I'd say the current rate of a genome is about the same as a new hardcover book on a per letter basis. Or within an order of magnitude one way or another. So, I think IT IS a good deal... And only getting better as the paradigms shift... So, can I ask you "Could you care less?" I know I could. A lot.

Ian

P.S. I just blew an hour on this digital back of the envelope blog and it's math. I'll try to stay away from even my brand of fuzzy math in the future... But, having worn myself out, I'm going to save my musings on the relationship between scientific success and beer and the Times article that goes with that for another day soon. I'll keep you posted. Hey, but I'll put up a couple quotations to end this particularly bloggy blog entry...


"Education is a progressive discovery of our own ignorance."
- Will Durant

... a lot of quotations say about the same thing, to varying degrees of pith, but they're all true...


"Against logic there is no armor like ignorance."
- Laurence J. Peter

... yep... but wearing armor couldn't be bliss... that crap looks uncomfy at best...


"Reminds me of my safari in Africa. Somebody forgot the corkscrew and for several days we had to live on nothing but food and water."
- WC Fields

... this will segue nicely into my next post on scientists and beer and causation vs. correlation...