altruistic bacteria putting humans to shame

richard dawkins, in his 1970s must-read the selfish gene, brings up altruism as an apparent paradox, if we take evolution at face-value. of course, he goes on to describe how it is that what we humans naively perceive as 'helping someone in need without expectation of reward', is really a mere behavior instantiated in genes bringing some selective advantage to its beholder.

two cool articles in the last two weeks have addressed this issue in single and multi-cell organisms. first, a group from tubingen, germany showed that a single nucleotide polymorphism changed cheating cells into helper cells. the scientists instantly marketed it in LA, where blondes by the thousands flocked to the product promised to end relational woes. after a quick biology lesson, those still awake left dejected.

second, this week a group from u arizona published an article suggesting how a gene promoting altruism could get into the gene pool initially. since do-gooders don't seem to have much selective advantage, this had been a mystery for a while. in volvox, a self-organizing multi-cellular creature, a gene called RegA shuts down reproductive functions in all but 16 lucky cells in the organism...kind of like our somatic and germ cells. for example, one of your retinal ganglion cells won't be reproducing anytime soon, but it keeps on the lookout for that special someone with whom some of your...other... cells will enjoy the pleasure of reproducing. so, these researchers found that a homologue of RegA found in single-cells is used to shut down extraneous functions when the going gets rough. the story goes that the activity of this gene, which was originally favored for some other function, was exploited for the sake of multicellular reproduction... one of the earliest and most obvious forms of altruism.

of course, the scientists make sweeping claims suggesting that this is how humans do it too. two of my favorite:

"In evolutionary terms, Nedelcu said, there may be no fundamental difference between altruism in Volvox and the generosity that inspires people to give, say, to charity."

and even better:

"Moreover, in tough times, people often come together; so do many bacteria."

now if they'd hurry up and figure out the gene for where i left my keys yesterday...

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a puritan prayer

i was deeply convicted by a prayer of confession dubbed "The Precious Blood", which we read as part of a weekly service at my church recently. some of it is below:

Sin is my malady, my monster, my foe, my viper,
born in my birth,
alive in my life,
strong in my character,
dominating my faculties,
following me as a shadow,
intermingling with my every thought,
the chain that holds me captive in the empire of my soul.

Sinner that I am, why should the sun give me light,
the air supply breath,
the earth bear my tread,
its fruits nourish me,
its creatures subserve my ends?

Yet your compassions yearn over me,
your heart hastens to my rescue,
your love endured my curse,
your mercy bore my deserved stripes.

Let me walk humbly in the lowest depths of humiliation,
bathed in your blood,
tender of conscience,
triumphing gloriously as an heir of salvation.

from The Valley of Vision, put out by Banner of Truth, a publishing company specializing in Puritan literature.

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narnia zone

interesting blogger from new zealand or, as she calls it, narnia zone. this post from march 2006 is an informative round-up of some recent clashes and conversations between science and christianity.

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"evangelicals learn to love big government"

the wall street journal editorial page ran an article on a new breed of evangelicals who seem to embrace big government ideals to accomplish covenantal responsibilities. though it's a bit awkwardly written, the piece raises a good point by quoting a scholar from the Acton Institute:

"You can't be compassionate with other people's money. Even worse, they're not thinking about the consequences of these policies. They're too busy feeling warm and fuzzy and absorbing liberal ideas."

it finishes with a look at the ONE campaign:

Groups representing more than 40 denominations have signed on to the public declaration of the so-called ONE campaign, whose mission is to dedicate 1% of the U.S. budget to foreign aid each year. ONE boasts the support of George Clooney, Naomi Watts and, of course, Bono. It's all very hip, and very vague. "ONE isn't asking for your money," the Web site declares. "We're asking for your voice." Well, actually, ONE is asking for your money, but the checks go to the IRS rather than directly to charity.

i'm as glad as anybody that the evangelical community is trying to seek creative ways to fulfill its perceived responsibility and work for 'common good', whatever that is. but i agree with the columnist that, if it's their responsibility, they should do it... not the government. between friends, i'm a small government guy at heart.

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robot-lizard climbs glass

stanford researchers have designed a gecko-like robot whose feet exploit van der waals forces to climb up flat surfaces. check out the video here (24mb video).

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no consciousness sans electrodes

while stanford researcher bill newsome has been talking about this for a while, he recently made public his desire to have electrodes implanted in his own brain. he wants to know the conscious experience of having (read: 'what it's like to have') one's visual decision-making affected by electrical stimulation to area MT, which is involved in motion discrimination.

this is a noble or a selfish act, depending on whom you talk to. but that issue aside, i disagree with his fundamental assertion:
"If we understand the system completely (from input to output) at a cellular level, but still do not know exactly what causes conscious mental phenomena, we will have failed."

sure, it sounds good, but there's an underlying assumption in his claim, namely, that the source of conscious mental phenomena is knowable by scientific means. let's unpack that.

1. "knowable" - whatever the causes of conscious mental phenomena, we can know them. determining what is knowable has a long history (try wikipedia's article on epistemology). many scientists and idealists believe that mental phenomena are identical to physical phenomena (we all know this as the "mind-body problem"). but there are good arguments against this, in my opinion. and, even if you don't buy my opinion, it's undeniably an unsolved issue: i'll give a shiny nickel to the first person who can demonstrate that we humans can, in principle, know all things about mental phenomena.

2. "by scientific means" - whatever the causes of mental phenomena, they can be addressed and answered by the tools of science. this amounts to scientism. simply because science has helped us to answer some questions about how the brain works, we cannot simply assume that it'll help us answer all of them. oh yeah, and all the remaining questions about the mind. don't get me wrong, i'm in neuroscience because i think it can help us answer tons of questions... just maybe not all of them.
note that it's unclear whether bill actually believes this. his interest in doing this experiment suggests that he think that the subjective experience of MT stimulation contains some data that are unmeasurable with traditional scientific tools. or he might just want someone to pay him to shock his own brain.

in the end, what will we learn from bill's experiment? well, to some extent, the experiment has already been done by penfield in the early 20th century and by many current neurosurgeons. today, recording electrodes are implanted in epileptics' brains to determine the initiation zones of focal seizures. but these can be modified to stimulate brains. additionally, neurosurgeons push on random brain parts while awake patients describe their subjective experiences. last, noninvasive, temporary brain lesions are possible with a technique called transcranial magnetic stimulation... so you can shock the right side of your brain and talk about the experience of losing all muscle control on your left side, as you try to pick yourself up off of the floor. two nickels to the sap who wants to do that experiment.

so what'll we learn? well, bill might learn something. but will it count as science? and if doesn't, will it bring us any closer to a fully physicalist understanding of the conscious brain.

in the meantime, it looks like he's still waiting for the right surgeon: "If the risk of serious postsurgical complications was one in one hundred, I wouldn't do it. If it was one in one thousand, I would seriously consider doing it. To my chagrin, most surgeons estimate the risk to be somewhere in between my benchmarks."

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doctor woe

the boston globe just began a new segment on area doctors' experiences on the job. this one, from a psychiatrist whose patient committed suicide two days after discharge, is especially poignant. it brings home the complexity of our minds and impotence of modern medicine:

"Can we really just add up the number of missing serotonin molecules in a person's brain, plug in the number of previous suicide attempts and recent losses, and neatly solve the equation? I doubt it."

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shameless plug

my new, though currently pretty scant, website is now up, graciously hosted by the great lomak, a partner in crime:

www.davematthewslab.com

suggestions welcome...

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who's god? who's godel?

a new study from researchers at harvard and u chicago asks the question "how do children learn about science and god?" (link to press release).

while the researchers find things like 'children add interpretation to learned items', the most interesting conclusion (to me, at least) was that children are more confident about the scientific information they learn than the religious information. from the press release:

"We don't have a firm view on why it is they're a bit more confident on the scientific information," says Dr. Harris, "but one possible plausible reason is that when we talk about things like germs or body organs, we talk in a very matter-of-fact fashion. We don't say, "I believe in germs," we simply take it for granted that they exist." In talking about religion and other spiritual matters, however, adults tend to assert the existence of God more strenuously, possibly raising doubts in children's minds as to the existence of an unseen deity.

a few points of interest:

1) i wonder whether harris meant "tenuously" rather than "strenuously". it's remarkable enough that children can learn a particular item of knowledge. but here, they're also learning meta-knowledge, that is, to what extent an item of knowledge represents the actual world. but harris's suggestion about "strenuous assertion" would require the sociological acuity of a nathaniel hawthorne...at childhood! her claim amounts to the following:
a) the kid encounters an item of knowledge.
b) the kid remembers it.
c) the kid evaluates the fervor with which the teaching adult spoke and makes the following judgment:
c1) if spoken stolidly, believe it.
c2) if spoken without confidence, don't believe it. (this is not explicit from their research)
c3) if "strenuously asserted," question it. the adult is probably insisting on it because it ain't true.

it's hard to construct an environmental or even a common social situation in which encountering and recognizing such a form of subtle reverse psychology directly from the teacher would be evolutionarily advantageous. indeed, it seems that this assertion (kids question things that adults insist on) requires some hoop-jumping in order to be reconciled with another evolutionary argument, the common claim of religion-as-human-construct. in particular, how can humans be inclined both to doubt what they're told about religion, and to accept what they're told about religion? (well, there are at least a few creative ways to claim that both are simultaneously true, but i'll curb the urge to write them... i'd be interested if anyone wants to post their favorite way)

enough ranting on what was probably a misnomer.

2) this study is potentially century-dependent: conducting this research 200 years ago would have flipped the results, i bet. for example, asking a kid in 1800 questions about electricity and about the Christian God, he'd have much more to say--and i'd imagine more confidence in saying it--regarding God. obviously, electricity was a fledgling science (heck, they were thinking of current as a fluid rather than a field and of magnetism as about as valuable as a piece of bread toasted to look like the virgin mary... how times have changed). so you could say that this poor kid would at least be more confident of something like simple mechanics in physics (newton's stuff, remember?), which he might know something about if he went to a good school like boston latin. ah, i'd reply, if he went there, he could tell you about mechanics in latin or greek, since the culture then held the serious study of religion (and the language learning it entails) in such high regard.

so what? well, the assumption (or well-reasoned observation, depending on to whom you talk) is that we believe these "scientific" things more because they're more believable. but, most of us couldn't say, let alone reproduce, thomson's experiment demonstrating the existence of the electron back in 1897. sure, we'd say "but i know the electron exists because it's making my computer run right now!" but how different is that reasoning from the faithful christian who might say "i know god exists because he's saving me right now!"

the culturally convoluted and logically incoherent claims about epistemology in the domains of "science" and "religion" are fodder for many years of research...

(note: the limited access original article is here)

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chinese spy worked with US's lockhead for 10+ years

we all know china has a spy program. and if we're honest with ourselves, we'd realize that spies are likely in our scientific ranks. still, this story on reuters (about a chinese who tried stealing american arms secrets from inside for about a decade) comes as a jolt to me.

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neural computation

the annual joint symposium on neural computation is being held this weekend at the salk institute. it includes a poster from yours truly:

A Tunable Silicon Hodgkin-Huxley Neuron
Jonathan D. Driscoll, Stephen D. Larson, James B. Aimone, David W. Matthews, Gert Cauwenberghs

unfortunately, the ucsd neurosciences retreat outside of LA is also scheduled for this weekend.

...oh the humanity!!!

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some clever (and crazy) inventions

new scientist columnist barry fox scours US patent offices for new, kooky inventions. the one for this week is particularly exciting: the human cannonball launcher. i was disappointed that one of my recent ideas had already been patented: the snore-sizzler, which forces contraction of relaxed soft tissue in the breathing column by electrical pulses generated when the sleeper snores. it's probably for the best, though; the lawsuits would have been a pain.

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madness mechanism

a paper in this week's pnas describes a possible mechanism for why fluoxetine (of prozac fame) effectively combats depression. in particular, the dudes find neurogenesis among a certain class of progenitor cells, as opposed to dentate gyral cells, using a mouse reporter strain. see nice lay coverage in new scientist.

i usually steer clear of hype-generating, easily-accepted-by-major-journals, stem cell papers since they're often just observational, but SSRIs are of personal interest...

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more lasers...now they're faster than the speed of light!

it looks like lasers are faster than...themselves. a sweet experiment at u rochester shows light exiting an optical fiber at virtually the same moment it enters. see the site for a brief explanation, or the article (in science) for the whole shebang ("observation of backward pulse propagation through a medium with a negative group velocity").

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hot stuff...coming through

a new laser shot through sapphire, heating it faster than any previously recorded explosion. in a brilliant display of comic prowess, nature reports: "The experiment was a blast, say physicists who reckon their laser can drive temperature increases of a billion billion (10¹⁸) degrees per second, although they could only keep it going for a couple of hundred femtoseconds (with a femtosecond being 10^-15 s)." (the picture is of two incisions left by the laser)

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more science fraud

a chinese computer scientist, who supposedly designed China's first dsp chip, apparently faked all the research, stealing the plans from a foreign company. nyt asks: "Could Mr. Chen's downfall, they ask, represent an example of how even smart and successful people in China are being forced to cut corners to meet the nation's hyper-ambitious goals?"

The article included this ominous quote: "Professor Chen is really unlucky," said a male student named Wu, who asked not to be further identified for fear of recriminations. "He lied and was caught. I think there are other people faking their research, but they haven't been caught yet. He's probably not the worst."

I'm glad nyt steered clear of challenging the peer-review process on this one. research fraud is of primary importance, and it's understandable that the larger community has begun to question science's system of checks. but it's dangerous and irresponsible to reject the peer-review process as flawed when it's not only worked quite well in general, but also has no viable alternative.

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book-scanning vs book-burning... you decide

the ny times just ran a nice article on google's book scanning project, couching it in the age-old dream of assembling all knowledge in one space: "Since [the library at Alexandria in 300 BC], the constant expansion of information has overwhelmed our capacity to contain it [...] until now."

the amount of info to scan is staggering: "From the days of Sumerian clay tablets till now, humans have 'published' at least 32 million books, 750 million articles and essays, 25 million songs, 500 million images, 500,000 movies, 3 million videos, TV shows and short films and 100 billion public Web pages." this would fit on 50 petabytes (the value of peta--which i previously thought to be ~zero
...just kidding, don't hatemail me--is 10^15).

google's goal for the project: "make it easier for people to find relevant books – specifically books they wouldn't find any other way such as those that are out of print – while carefully respecting authors' and publishers' copyrights." (obviously, they've had to deal with some po'd publishers already)

of course, i think most of us derive some simple, irreplaceable pleasure from reclining with a tangible book whose pages come from chopped-down trees. i doubt we have anything to fear. but even if we do face a future of exclusively digital print, at least it'll protect against the crazies at landover baptist. {note added later: to those concerned, the landover site is a parody on fundamentalist religion, specifically fundamentalist christianity. i don't share the views or the sentiment of its message. to the extent that its designers think it legitimately undermines thoughtful christianity or offers any serious response to spiritual conviction, i'd recommend they grow up. it's just a funny, stupid website.}

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Baldwin gene expression

...and the Onion parodies Allen's achievement. hilarious.

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gene expression in the brain

the Allen Institute in Seattle has re-released a database of gene expression data for some 20,000 genes throughout the mouse brain. the information was collected by an automated process of tissue sectioning (coronal and saggital planes) and in situ hybridization. previously, there were some concerns about the quality of the data, but at least some of these concerns have been addressed. some related links, courtesy of futurefeeder, a sweet site: [High-Resolution Brain Atlas][Blue Brain : The First Complete Virtual Brain][Cartography of the Digital World][Brain Cells on Demand][Scan my Brain & Tell me What I See][Adult Brain Cell Growth][Non-Invasive Brain-Computer Interface]

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