Archive for January 2009

A Pre Snow Shoveling Musical Moment:

January 28, 2009

Because Atrios should not be the only one permitted to post tunes for the (enjoyment of) no apparent porpoise:

Christianity, Red in Tooth and Claw

January 27, 2009

More internet funnies:


You’ll have to zoom to get all the details.

FYI:  This is what the choir is really thinking when they’re hittin’ no.151 for the umpteenth time.  Just in case you were wondering.  (Forwarded to me by a church-singing pro.)

Updike, R.I.P.

January 27, 2009

Just got the word that John Updike is dead.  Too young — 76 isn’t even up to the life expectancy of an American child born these days (though it still puts him just a skosh ahead of the white male number).

Updike was never one of my obligatory reads — I didn’t race to buy each new novel as it came out.  But he was one of the real stalwarts within the American Republic of Letters for the last half century.  He did it all:  short fiction, long, essays, criticism, poetry.  If I sometimes detected circumcision envy in his suburban writing, I loved his touch, his ability to catch emotion in a scene, a scene in a few beautifully carved sentences.  He was a smart writer, and a very funny one when he chose to be.


Image:  Albrecht Durer, “A Young Hare,” 1502

Who Cares About Warrantless Surveillance…

January 26, 2009

When we are so willing to do it to ourselves?   (h/t kos).

Seriously, it’s not just the law that hasn’t caught up with the technological transformation of the last decade or so.  Our own habits assume a level of trust in the cloud that the dataset is too small to justify.  IMHO, as always, and worth precisely what you paid for it.

Image:  Soviet Poster.  The caption reads, “An Easy Talker Is A Great Find For The Enemy!

Live-ish Blogging the MIT Darwin Bicentennial Symposium

January 23, 2009

9:30 ish:  Jonathan King starts us off.  Makes reference to Ken Miller’s visit to MIT last spring, when he told his audience that despite the victory in Dover, the battle is far from over.  That reminded me of something Stephen Jay Gould said after the Arkansas creationism trial in 1981 that in many views marked the legal end to old-style creationism as a potential competitor to evolution in the schools, paving the way for ID revisionism.  Gould said then (I recall, though I can’t track down the cite right now) that the victory in that trial meant that the argument was over.  Miller was right.

9:45 ish.  John Durant, director of the MIT Museum up now, talking about the history of Darwin and Wallace.  First point of emphasis:  the theory of evolution by natural selection owes its origins to natural history over and above all other sources.  We do molecular biology now to penetrate evolution; (which is what this symposium is mostly about), but without close and systematic observation of nature, we got nuthin.

9:46 — John emphasizes that the Darwin that heads out on the Beagle is, in essence, a conventional Victorian naturalist and a creationist (though not a young earth one).  The change on his return:  his observation of deep patterns captured in the range of geological observation and biological specimins.  Connections appear between past and present animals.  John also emphasizes the geographical story that Darwin begins to put together — the evidence for evolution that comes from the distribution of animals in space.  (This will be much discussed at Simple A Beginning on and after Feb. 12 — in part by John, who will be joining that blog effort.)

9:55 ish:  John makes the link between Darwin’s formulation of the problem of the apparent non-fixed nature of species, his reading of Malthus on the war between the tendency of populations to increase and the scarcity of resources, and his working out the idea that under such circumstances, favorable variations would be preserved and those less so would drop away, providing a mechanism for biological change (the exact quote went by to quickly for me to capture).  All this in 1838, at which point Darwin says he now has a theory on which to work.  Whch he does in secret…hence, says John, enter Alfred Russel Wallace.

Wallace, John emphasizes, comes to the idea of natural selection relatively early in his natural history career — but has to collect the evidence to get there.  His ill-luck extends to the loss of four years collecting in a ship wreck after his first voyage, but heads out again to what is now Indonesia (and a bit of Malaysia), and discovers the evidence, especially the biogeography (space, and not just time again…a theme is developing here) that crystallizes Wallace’s thinking.

Comes to the core idea no later than 1855, writes the famous Linnean paper in 1858, with the marvellous analogy to the “centrifugal governor of the steam engine.”

10:05:  John tells the story of the simultaeneous publication of Darwin and Wallace’s papers at the Linnean Society in 1858, after the shocking receipt by Darwin of Wallace’s writing in the post.  That shock propels the writing of the actually quite brief Origin of Species, instead of what John calls the looming doorstop of what Darwin actually intended to produce.  See this post and the link to John Wilkins on Wallace for a little more detail.

1006: A little of Huxley bashing by self professed Huxley fan John Durant, in dismissing Huxley’s claim that the theory was sufficiently obvious that he should have thought of it, the “duh!” reaction.

10:15:  Lot of Wallace love in the brief Q & A.   Of which I heartily approve.

Now up:  Hazel Sive on “Evolution of the Vertebrate Brain”

10:20  Her interest is in understanding brain structure through evolutionary conservation.

“Fruit Flies have a perfectly fine brain.”  — now there’s a quote to be going on with.  In fact she’s drawing attn. to the vertebrate brain’s structure as a tube, in contrast to the invertebrate brain structrure.  It’s more fun in isolation.

Sive takes us through a brief tour of brain birth defects as a wake-up call to the significance of specific structure.  Then she gets to the first punch line:  “Vertebrate brain structure is highly conserved.  Slides range from zebrafish to human.

Sive’s lab uses inter alia the zebrafish as a model organism for all this; check out the link for more.

This is good public communication.  For example, Sive’s discussion of the Snakehead (snk) mutant begins with her statement that they had found a mutant that appeared to have no brain.  The discussion of the experiments that followed was clear, worked into pretty fine grained detail by smooth steps, but allowes an audience that includes a high school class from a nearby suburb right into the sequence of steps and thought about how this lab works out the relationship between brain structure and development and the insights to be gained from such thinking about brain defects.  Nice stuff.

In Q & A, starts to talk about the genetics of the ion pumps implicated in the snk mutant.

Also, question comes whether if there are problems with brain tube folding, does that correlate with heart tube folding issues, and the answer is that there are correlations and/or shared folding programs going on.

10:45.  In discussion of another experiment — on epithelial relaxation — Sive gives a hint of how cool (read technically sophisticated) the experiments in this work have to be. Imagine, she asks us, micro-dissection of brains in .2 mm long organisms.

10:50.   Last thought on distinction between model and tool.  The zebrafish is a tool — allows lab to do assays on ideas and molecules that may be relevant to humans.  E.g. — studying autism and schizophrenia associated genes in fish, even though there is no thought that the fish will exhibit the behavior associated with those genes in humans.

11:08  Susan Lindquist is up now.  Her questions:  How do organisms stay the same?   How do they change?  No heavy lifting before lunch, eh?

She is in fact going to confine herself to a narrower route into the large issues.  She’s starting us off with two beautiful flowers:  Mimulus lewisii and Mimulus cardinalis.

They raise the question of how such different fertilization mechanisms that the two plants employ could evolve when the intermediate steps are not fertile?

First step:  protein folding is the key, but it has to happen in “a ridiculous environment” — inside a cell crowded with other proteins.  Think about what proteins have to do int hat environment:  it “is not like Fred Astaire and Ginger Rogers.”  Rather, more like the  stateroom scene in the Marx Brothers Night at the Opera.  (Not making this up folks — this is again, some fine fun science communication.)

11:18  Now we are getting down to specifics.  We are going to look at Heat Shock Protein 90 (Hsp90) which maintains phenotypes — keeping things the same — and facilitates evolution.

She takes us through the steps through which Hsp90 inhibitors enable different protein folding events to take place.  She emphasizes that this is an oversimplified account, but that at least the basic  picture Hsp90 can in fact aid a mutant protein forms to fold appropriately — thus providing a crucial molecular-level mechanism to permit the fine grained work of evolution to take place.

Next step:  fungal drug resistance.  Resistance is as ever a great way to enter into the fact of evolution.  She says, “mutations simultaneously solve and create problems” — which is true both in the formulation of drug resistance and in evolution more generally.

Lindquist then returns to a diagram she’s put up before which looks at cellular circuitry ; it’s a crowded, unreadable diagram, which is the point for Lindquist:  Hsp90 is all over the connections between events in the circuit, mediating the commands expressed in the genome as they unfold in the cell.  That leads to another point:  the diagram captures the idea I was trying to express in this post: that the “environment” of genes begins right at any given gene’s door.

Further to that point:  Lindquist describes forcing evolution in an Hsp90 – involved trait in flies by both genetic techniques — selective breeding — and by selection pressures induced by external, chemical stresses.  Mutations accumulate (genes) and manifest themselves in living organisms in response to stress (environment)…which is, among much else, one way to get rapid evolution of a trait within a population.

To hand the stage back to Lindquist:  she talks of the “translation” of genetic traits into phenotypes, what critturs (and plants and fungi) actually experience.

Conclusion:  getting to an understanding of a “plausible mechanism for understanding rapid evoluiton.”  That is:  environmental stress affecting the machinery of protein folding allows hidden variation to manifest itself in biologically (and evolutionarily) significant ways.

11:53  Russell Fernald on the “Evolution of Eyes, What do we know and how do we know it.”

Starts us off with the basic structure of the human eye: cornia, iris, lens, photorecepters, and pigment (for directional information).

Basic story:  each structure has evolved independently; the one common element:  photoreception, turning photons into electrons.

The key reminder:  light is the primary selection pressure on the eye. Depending on what function you are interested in, eyes respond to specific properties of light.   E.g. scallops have eyes sensitive to light intensity; jumping spiders have several eyes tuned to different functions:  the jumping eyes are sensitive to parallax; others look for mates and so on.  Subtext:  nature, and natural selection, produce so many really cool surprises.

Taking a different tack:  mimicry in animals turns on properties of potential predators’ eyes.  Same thematic point above:  natural selection has produced an extraordinary range of adaptations…and with the subtext:  ID cannot in any satisfying way account for this.

12:05.  Moving to history of eye evolution studies.  Lovely story of how eye research turns on the carniverousness of the US, choosing to raise cows and eat them yielded buckets full of large eyes available for biochemical studies.  Eat steak and advance science!

More seriously, Fernald traces the competing hypotheses of many origins to eyes vs. a single origin, coming to rest on the multiple origins for eyes, coopting properties for different solutions.

12:20 Next, Fernald goes through the sequence of molecular studies to find the genetic origins of eyes — which have been shown to be diverse.  When organisms need eyes, or when eyes need a lens protein, e.g., they grab one that possesses the basic properties needed across a wide range of possibities.  Result:  lenses (among much else in the eye, can be shown to have evolved many times independently.

The cool thing here from a science communication perspective is the way Fernald is building an incredibly powerful picture of the detailed facts and processes of evolution, and, barring his opening remarks (and, I’m going to hazard a guess, his conclusions) he has no need to mention the obvious:  who needs a Designer when you have such a compelling picture of evolution as handyman, grabbing the nearest available tool to do the job.

The story continues with the account of the photoreceptor cascade, in which we learn recent work has undone the older picture of distinct invertebrate and vertebrate cascades; now we find that each division of animals have organisms within them that employ both (or at least bits of both) forms, heedless of what the textbooks told them what to do.

The surprising twist to this already surprising story:  different eye types collaborate, rather than compete within organisms to deliver information to the eye….

Moving towards the conclusion, Fernald now looks at the question of how eyes could evolve — how fast, how valuable at different stages or pathways to the analysis of information of light, and the answer in model runs is not that long:  half a million years from flat sheet of photosensitive cells to a vertebrate eye — with lots of functionality available along the way.

12:30 The same subtext as above emerges:  the growing knowledge of the multiple pathways and crossovers between pathways to make eyes creates a picture that satisfies the evolutionary picture and dashes any of the foolishness from ID types trying to resurrect the Victorian criticism of Darwin based on the seeming impossibility of the evolution of a complex eye from simpler origins.

Fernald excavates this subtext  by giving Charles the last-ish word:

To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree. Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real.

Fernald ties this together thusly:  eyes are made of multiple parts, each with a discoverabe history; phototransduction oldest, and with the fewest solutions (2) known so far to have survived; Optics are really important; and the history of the eye involved repeated evolutionary invention.

To bring this back to John Durant’s talk at the beginning of this session:  the theory of evolution depends incredibly strongly on natural history.  That was true for Darwin; Fernald’s talk reveals how much that is still true.  The observational focus of natural history has become more subtle — but the discovery of varieties of different eyes and all the details of the molecular natural history of the different paths to photodetection are driving an every richer understanding of the way natural selection actually works day by day in the real world.  Good times!

Images:  John Gould “Rhea Darwinii, from The Zoology of the Beagle. Janet Browne writes of the close call this Rhea had:  Darwin shot and mostly ate his only specimen before realizing that what he had was not a juvenile example of another, larger Rhea, but a new species.

Punch Almanack, 1883, “Man is but a Worm” published 1881.

Gaetan Lee, “Human Brain in a Vat,” 2007.

Leonardo da Vinci, Mona Lisa, (detail).

Yes I Can…

January 20, 2009

Post this once more:  Bruce singing us into the possibility of a different world:

Read it and weep…

January 20, 2009

I did, listening to the 44th President of the United States, Barack Hussein Obama, deliver this text.

Have I Got A Good Job Or What?

January 19, 2009

Via Michael Drake over at Strange Doctrines, the link to a WSJ article and study on the best and worst jobs in America.

Clearly, the math folks have the last laugh:  rated number one, they get the money, the working conditions and no stress:

She [Jennifer Courter] telecommutes from her home and rarely works overtime or feels stressed out. “Problem-solving involves a lot of thinking,” says Ms. Courter. “I find that calming.”

Astute readers might be guessing some of the ways this study may be less useful to folks thinking about switching careers than one might hope…but this kind of silliness is typical post holiday, pre-spring recreation in the news business.

(The worst, jobs, by the way, are what you would expect: low paid, physically demanding and dangerous.  The three at the bottom of the 200 entry list are taxi driver, dairy farmer, and, dead last, lumberjack.  Break into song here if you must.)

And anyway, finding out about a list like this leads directly to the inevitable question:  how does your own daily grind rate?

For me, it depends on how I think of myself.  If I call myself a historian — and why not, with two books of history of science/culture out and one more coming this June — then I’m in clover, baby.  Historians, whose capsule job description reads, “analyzes and records historical information from a specific era or according to a particular area of expertise,”rank seventh on the list of desirable jobs, one ahead of sociologists (hah! take that, sister-in-law!)

That it is one behind computer systems analyst takes me down a peg, I guess, and my biologist friends will condescend from their perch at number four. (Though this description seems a little limiting:  “Studies the relationship of plants and animals to their environment.”)

Still, in my guise as historian, I hold bragging rights over eleventh ranked economists (so, Brad DeLong.  You might be a sought after authority, a player in national policy making and an utterly dauntingly prolific blogger, but I like my job better…or something); philosophers at number twelve, (Hilary Putnam respectfully disagrees, and provides a quite telling data point to the contrary); and at thirteen, physicists, (so Sean Carroll, are you just going to sit their and take it?)

All well and good, until I decide to think of myself as an author, dragging in at 93.


(And as a lagniappe — what do you make of the fact that clergy come in at 70, one behind federal judges at 69?  Hanging out their between God and man carries some stress, I guess.)

Much nonesense.  Fun on a holiday morning.  Now for the French Freedom Toast.*

*Just a little trip down memory lane here to remind us of how wonderful it is to trade idiocy for at least the possibility of engaged intelligence, starting tomorrow at noon.

Image:  Paul Signac, “Le Démolisseur,” 1897-1899.

History Matters (and so does the environoment) — Steven Pinker/Personal Genomics dept.

January 18, 2009

Steven Pinker has made something of a splash with his account of confronting his personal genome, published in the NY Times magazine last week.  The article is interesting, though Pinker’s hint of nervousness about just how much he wants to know of himself genetically gives it a slightly odd list to port.

There was also a problem, IMHO (humble, and without professional expertise, too) with the presentation of the article.  Though Pinker was careful to undermine from time to time what he recognized as one of the fascinations of personal genomics — that “the human mind is prone to essentialism — the intuition that living things house some hidden substance that gives them their form and determines their powers” — the piece still teetered on a kind of 1980s “We’ve discovered the gene for X!” hoopla.

Much of that impression was conveyed by the photos that accompanied the print version of the article, with headshots of Pinker captioned with the trait identified within his genome.  Partly, though, it derived from Pinker’s own ambivalence, as he acknowledged the pitfalls of essentialism in a genome in which so much of the information is not devoted to protein coding, and yet wrote sentences like this:

For some conditions, like Huntington’s disease, genetic determinism is simply correct: everyone with the defective gene who lives long enough will develop the condition.

This is true, of course, and yet…the genetic signature of Huntington’s disease involves the number of repeats of a short section of the genetic code, just three bases or genetic “letters,” associated with the Huntingtin gene.  There is a number of repeats below which someone is not at risk for the disease — less than 27 copies — and a number above which disease essentially always occurs — 39 repeats and up.  In the middle, the issue is more ambiguous, and a repeat total in that range may result in late onset of the disease, or even a progression to overt symptoms that is so slow that the affected individual dies of some unrelated cause before the production of the damaging form of the Huntingtin protein actually does enough harm to notice.

What governs the number of repeats is unclear; it is not, seemingly a matter of pure  inheritance.  Masha Gessen in her excellent Blood Matters tells the story of two brothers at risk for the Huntington gene.  One develops symptoms early, gets tested, and receives confirmation that he possesses the gene with sufficient repeats to account for his relatively early onset of the disease.  The other brother, who presumably inherited the same gene from the same parent, possesses an intermediate number, and may or may not end up with symptomatic Huntington’s at some later point in his life.

What does this all mean?  That even in cases where the overwhelming effect of heritable genes is obvious, where possession of a given form of genetic information directly correlates with a particular observable trait, there are processes involved in the replication and inheritance of that information that produce variation.

I am no biologist, so I’ll defer here to John Maynard Smith, with whom I had the good fortune to have a conversation the one time we met, a few years before he died.  He emphasized what I don’t think has seeped deeply enough into the popular understanding of modern genomics.  In his phrase, (from memory), the environment for a gene begins at the chromosome.

That is, the genes that actually code for a protein do not do their work or move from generation to generation in a vacuum.  Rather they exist in a physical environment that begins with its most immediate context — the DNA that exists surrounding coding regions — and the extends outward through the structure of DNA and other organic material that makes up the chromosome; the nucleus of a cell; the cell as a whole and so on and on and on. Things happen at each level of organization and between them that can affect what happens when the rubber hits the road and a protein gets made.

All of which to say is that even though Pinker certainly did not claim that genes are destiny in any crude way, his article still falls into a tradition that I do not think has fully caught up with the richness and the complexity of modern genetics and cell and organismic biology.

That said, the other matter that made my antennae twitch in Pinker’s article came in this paragraph:

Though the 20th century saw horrific genocides inspired by Nazi pseudoscience about genetics and race, it also saw horrific genocides inspired by Marxist pseudoscience about the malleability of human nature. The real threat to humanity comes from totalizing ideologies and the denial of human rights, rather than a curiosity about nature and nurture.

I agree with the last sentence (though I’d hardly say that it covered the sum of threats to humankind), but the claim that the genocides perpetrated by Marxist regimes are an example of blank-slate ideology gone very wrong is problematical on two levels.

First, it is simply wrong.  For example Stalin’s war on the Kulaks — well-off peasants/farmers — treated Kulak resistance to collectivization as a symptom of an inherant, non-malleable quality, the class identity of the offending farmers. Similarly, Mao’s campaign against landlords (and others) immediately after the 1949 victory of the Chinese Communists, identified class and or occupation as a kind of original sin from which there could be no return.  The same basic notion underlines the horrors inflicted on class or educational level by other regimes.

Of course, in China and the Soviet Union, exterminations justified by the identification of a human stain that needed to be eradicated to open the possibility of forging a new Communist humanity had roots that have nothing to do with a real commitment to either essentialism or a blank slate view of humanity — though at different stages of the process, both ideas were invoked.  Rather they were all about power and resistance.

But at the same time, any finer grained look at what happened in the state-massacres of the 20th century does not support the simple-minded notion that as much or more harm was done to human beings through a commitment to a false perfectability of humankind as as was done through a commitment to a false notion of ineradicable genetic defects in particular groups.  Essentialism was an integral part of both Nazi and Communist murders.

And that leads to my second objection to what I see as Pinker’s false equivalence of two evils.  It isn’t just that he admits no complexity to the history; it is that the moral argument he seems to be making is itself highly suspect.

The real question Pinker avoids here isn’t whether evil comes to the world down multiple avenues.  It is whether or not evil flows from a given cause, and if so, what can be done about it.

That dictators have used many justifications to treat other human beings as things rather than moral ends in themselves does not let you — or Pinker — off the hook on the specific issue of the misapplication of genetic ideas to divide humanity into those worth keeping and those it is permissable to destroy.

It is therefore also true that the pursuit of genetic knowledge, of that part of the human condition that is genuinely in ourselves, and not in our circumstances, needs to be concerned about the moral and ethical hazards raised by the research.

Of course, the field(s) are in fact acutely aware of this, as is Pinker himself, no doubt.  But that he dredged up the old shibboleth that the Commies did it as his first response to the anticipated objection against the spectre of genetic determinsm betrays to me a kind of weariness with the argument.

I can understand that too — plenty of heat and not much light has been poured on this argument often enough.  But it is still a bit of rhetorical sleight of hand, and it’s been popping up a bit in defenses of the new genomics.  And that can’t be a good thing.

Update:  I omitted thanks due to Abel Pharmboy and Janet Stemwedel, each of whom looked over sections of the post above to help preserve me from my own ignorance.  Any errors that remain are, of course, all mine.

Image:  Giotto, “The Massacre of the Innocents,” 1304-306

Quick Question: David Brooks — willed stupidity or mere useful idiocy?…part one

January 16, 2009

Just a quick post before heading out to contemplate much more interesting minds than that of Mr. Brooks at Science Online ’09, but reading today’s column, a number of howlers stood out.  I’ll try to get to the meat of them in posts between conference sessions tomorrow, but to begin at the beginning — check this out:

Once there was just Newtonian physics and the world seemed neat and mechanical. Then quantum physics came along and revealed that deep down things are much weirder than they seem.

Reading Brooks say anything about science produces the sensation of watching a kid play with a whole box of kitchen matches.  Nothing good can come of this.

Between Newton and the quantum revolution you had this and this and this, just for starters.

I admit that this has nothing to do with the main argument of his piece, which possesses its own follies to be ridiculed in due course.  And maybe it’s pedantry to demand a bit of rigor in all those intellectual glittery bits Brooks wants to toss off so casually so that we may bow down (and suspend our critical judgment) before his transcendent wisdom on all other matters.

But I’ve found it a pretty good guide that if someone b.s.’s you on the small stuff, he or she is probably not what you would call reliable on anything of more import.  Brooks doesn’t disappoint in the rest of the piece — but that exegesis is for another post.  Here just ponder his latest monument to what very clever people worked very hard to understand over a span of centuries.

Image:  nonexistent due to painfully slow internet connection at the hotel within which I type this. Sorry.  To be adjusted if the wireless at the meeting site can take the strain.