archive for the biology category

for those in the area, james watson, of double helix fame, just finished a “public conversation” at the salk, and will be speaking at d.g. wills books in la jolla tonight at 7. according to the link, he may discuss his plans of “making all girls pretty.”

watson recently published Avoid Boring People: Lessons from a Life in Science (available for pre-order on amazon). if you think of attending tonight, remember the title’s deliciously double entendre! (photo credit: max gerber, la jolla village news)

credit: blog carnival

welcome to the twenty-eighth edition of encephalon, a circus of recent highlights from the neuroscience blogentsia. this time around, we had many reviews of some interesting original research, along with posts on everything from aesthetics to eulogies. enjoy!

neo-neuro fields

one of the beauties of neuroscience is its universality: at some level, everything involves the brain. too often, though, people affix “neuro-” to the front of their favorite subject, then claim victory over a paradigm-shifting new discipline. two blogs dealt with this issue recently: neuroaesthetics led to some deep insights, whereas “neuro-leadership” just fell flat. both posts were entertaining and insightful.

over at the third culture, jon follows up his two part series on neuroaesthetics with a post on art, context, and the brain. he asks with subtlety, “if we are to believe that there is some way to understand reactions to art by understanding the brain (or to understand the brain by understanding art), how are we to incorporate context-specific reactions?” jon takes on the question with a review of some neuroeconomics and an apropos reference to ucsd neuro-rocker ramachandran.

meanwhile, the trusted advisor asks “is neuroleadership more than reinventing wheels?” he decides that neuroscience hasn’t contributed novel insights to business management, despite the claims of people like the prolific jeffrey schwartz. i couldn’t agree more: projects such as “neuroleadership theory” only detract from more legitimate descriptive science aimed at understanding the brain more than making a buck.

credit: david linden

and now for some reviews…
biology and neuroscience

  • yeastbeast of ouroboros reviews a recent science article reinvestigating the role of a receptor gene previously shown important to insulin signaling. among the findings was that mutant mice lacking the gene had much smaller brains, leading to some sweet speculations.
  • at neurophilosophy, mo writes of two recent studies that challenge some long-held dogmas in neuroscience. first, and perhaps more important, researchers in roger traub’s lab discovered gap junctions in hippocampal cells, with obvious implications for epilepsy. second, he writes about a two-neuron digestive system circuit that transmits signals in two modes, the faster one using action potentials and the slower (on order of minutes) using a ceramide-activated second messenger system. as always, he provides great historical context.
  • medopedia briefly reviews two papers, one on brains and one on hearts. the first connects glutamate receptor mGluR1 in its role in memory and addiction, as described by johns hopkins researcher david linden, who stopped by recently to talk about two photon imaging of cerebellum. the second looks at regenerating cardiac cells. medopedia speculates on melding the two studies to rewire brains, an idea that already has a lot of steam in neurodevelopmental labs, such as anirvan ghosh’s here at ucsd.
  • brain in a vat reviews a paper on integrator neurons. the duke researchers report neuronal subpopulations in lateral intraparietal area (a part of the parietal lobe) that use spike rate to encode the number of dots in the monkey’s visual field. nice!
  • psychology and neuroscience

  • cognitive daily reviews a new paper on multitasking and stress. in the study, average performance of human subjects on two different tasks was not different between high- and low-stress situations. however, the researchers pursue a subtler point, arguing from reaction times that the high-stress group uses the same strategy for both tasks, whereas the low-stress group uses different strategies. in my opinion, making conclusions from reaction times is always a tricky business, but historically it has provided some useful insights into brain processing.
  • jeremy, of psyblog fame, discusses a study showing that couples tend to look more similar as they grow older. the researchers speculate that, because married folks empathize with one another, they mutually mimic facial expressions, leading to similar-looking faces. however, happiness–and thus, perhaps, the degree to which couples empathize with one another–didn’t correlate significantly with apparent similarity. good find!
  • brain in a vat reports that a new anti-smoking pill may treat alcohol dependence. rats trained to self-administer ethanol reduced their consumption when treated with the active ingredient in a popular smoke-stick-stopping drug. the ingredient, varenicline, works as a competitive antagonist on nicotinic acetylcholine receptors. it may point to a shared mechanism mediating addiction of both flavors.
  • credit: mindhacks
  • in a related post at mindhacks, contributor vaughan bell discusses addiction as more than a mere “brain disease”. he puts the neuroscience of addiction into the larger context of psychology and sociology. he also quotes the delightful theodore dalrymple, who warns against the excesses of medicalization in substance abuse. importantly, vaughan points out that diagnosing a “brain disease” can reduce the stigma that comes with being different.
  • sudip at brain blogger writes a meditation for troubled minds, a review of a metastudy on meditation. apparently, mindfulness meditation has a checkered record in ameliorating stress.
  • the neurocritic reviews an fmri study suggesting that ten year olds better able to resist peer pressure also have better executive control in prefrontal cortex and a higher correlation between prefrontal and posterior brain activity during certain activities.
  • reviews of books and lives

  • providentia gives us worm running, a reflection on the life of the late iconoclastic researcher and joker james mcconnell. you may remember him from a famous research project called memory transfer through cannibalism in planaria, in which worms learned a task faster after eating compatriots who had already learned the task. the underlying theory of memory rna never caught on, much to the chagrin of the food industry (how much would you pay for nobel laureate soup?).
  • alvaro at sharpbrains records an interview with yaakov stern, a columbia doc who studies alzheimer’s. he has tried to tackle a central paradox in the disease: pathology without presentation. it’s like DC, only weirder.
  • thinking meat’s mary gives a nice review of two new books on neuroplasticity, one on personal accounts of the phenomenon (norman doidge) and one on the plasticity research in animal models, including young and adult humans (sharon bergley).
  • and in other news…

    at sharpbrains, andreas describes how dancing is mental exercise. he created a video on the neural substrates of dance, and goes on to cite a study in the new england journal of medicine showing that dancing, more than any other physical activity studied, is correlated with less presentation of dementia later in life. sudip at brain blogger provided a brief discussion of a recent science article on the role of nmda receptors in dentate cells of the hippocampus. the exciting work was done in the lab of susumu tonegawa, a ucsd grad and nobel laureate. brain in a vat gave a shout-out to america’s nerdiest videos, a.k.a. the journal of visualized experiments. to be sure, it looks less like a journal and more like a youtube with citations. but it seems like a useful, if small, repository for teaching biological methods.

    phew! that’s all folks. the next stop is at memoirs of a postgrad in mid-august. as always, submit here. happy posting!

    this morning i had a banana topped with peanut butter… so you can imagine my surprise when these two videos (viewed over at richarddawkins.net) demonstrated that the proof of creationism had been sitting right there under my nose!

    one piece of advice. stop reading and position a cup below your chin: your brain will likely implode and ooze down through your nostrils midway through the video.



    (note bene: if you don’t like science, you may still like this post) last year, i first learned of electric fields around fresh wounds from the great harvey karten, whose narrative method of teaching neuroanatomy is always iconoclastic and never predictable. during a four-person seminar on, well, something less interesting, he launched into a discussion of electric fish. this thing has an organ that constantly generates an electric field so that its electrosensitive cells can determine when an object is near its body. here’s a bbc bit on it, from which i ganked the graphic.

    anyway, sharks are extremely sensitive to electric fields too*. They exploit electric fields for finding mates, negotiating underwater crags, and killing prey… which is where this story gets crazy.

    i just came across a nature paper not only claiming that these fields exist in every species tested to date, but also demonstrating that they recruit the machinery necessary for wound healing by turning on genes responsible for migration. in other words, if you get a cut, there’s an instant battery created around your skin. most biologists wouldn’t dream that endogenous electrical signals could be exploited for cell movement, except in the nervous system.

    it’s amazing that, everywhere we turn our collective microscope lens, a new and mind-blowing mechanism rears its sometimes gorgeous head.

    _____________________
    *nerdalert: in fact, for the afficianado, their sensory cells, called the ampullae of Lorenzini, might be the most sensitive in the animal kingdom. see here. however, this site’s claim of sensitivity to 1 nanovolt/cm2 is a bit dubious, since e-fields are measured in one spatial dimension. hat tip to jd.

    in case you’ve been in hydrogenation-induced coma over the last few weeks, nyc passed a measure on tuesday that prohibits restaurants from using trans fat. this is disturbingly hilarious on several fronts.

    1. the LBJ-style uber-maternalization of government. of course trans fats are bad for you, but so are skittles, butter, and cake. historically, government was around for building roads and establishing security. now, it’s here for welfare, education, healthcare, building self-esteem, and establishing insecurity. i once read a delightfully non-pc book by a blissfully out-of-touch southern preacher detailing how the rise of feminism was the cause of all sorts of social evils, including this shift in politics from the safekeeping of the state to that of the individual. if you’re interested, ask me for the title; in public, i’d never admit to believing a word of it.
    2. super-confused social liberals’ and conservatives’ heads are exploding. clove-smoking, tree-hugging vegetarians want freedom to choose their own food… they’ve been shouting ‘1984′ the whole week. on the other hand, though, they want to help obese people live more wisely, establish the “positive freedom” of good health, and end socioeconomic exploitation by mcfood. meanwhile, bowtie-wearing, hair-parting stiffs love enacting laws to enforce their conception of what’s right, but they don’t want to let down a great corporate lobby or give up that delicious mcchicken sandwich. here’s an all-too-graphic visual aid to help you remember this point:
      head exploding
    3. the government is, almost literally, spoon-feeding us. reality has become a parody of itself. i’ll leave you the pleasure of coming up with other examples.

    the one good reason for outlawing trans fat is that state-funded healthcare costs associated with it are exhorbitant (more on healthcare costs in a future post). but other arguments are weak. for example, some people claim that the public didn’t elect to have trans fats in their foods, so they shouldn’t have a say in phasing them out. um, i’m no economist, but i’d say the public demand for crisco since 1911 is a pretty good indicator of its popularity. if consumers are the end-users, they can decide, just as they do with cigarettes. in fact, public information campaigns and heavy taxes on fast food might be a better alternative. as another example, some say there’s a precendent for this measure in laws against drugs and alcohol. but this is a slippery slope argument; it could take us all the way to outlawing too little sleep because it makes you fat.

    a lot of the arguments against the law are obvious, but a few warrant mention. first, it’s legally dubious that a city could outlaw something the fda has approved. second, to get the same taste in food, restaurants might use excessively high amounts of saturated fat, which aren’t much healthier (in fact, they’re one of the reasons for the success of the hydrogenated stuff to begin with). third, it could hurt, or even phase out, smaller restaurants more than the chains that are really to blame. fourth, it doesn’t outlaw all the trans fat sitting on grocery shelves: it’s still accessible.

    eh, at least we don’t have to worry about the denizens of houston, winner of america’s fattest city four of the last five years. they’d never let legislation like this slip by. i mean, even new jerseyites, not exactly known for their fitness, didn’t let it slide: “elected officials in Chicago and New Jersey met with resistance — and even ridicule — when they proposed similar measures. Democratic state Sen. Ellen Karcher, who proposed the New Jersey measure in October, received such a wave of angry calls and letters that she temporarily closed her office.” (la times)

    the onion reports that kansas has outlawed evolution. from the article:

    From now on, the streets, forests, plains, and rivers of Kansas will be safe from the godless practice of evolution, and species will be able to procreate without deviating from God’s intended design…This is about protecting the integrity of all creation.

    and again

    “Barn swallows that develop lighter, more streamlined builds to enable faster migration, for example, could live out the rest of their brief lives in prison,” said Indiana University chemist and pro-intelligent-design author Robert Hellenbaum, who helped compose the language of the law. “And butterflies who mimic the wing patterns and colors of other butterflies for an adaptive advantage, well, their days of flouting God’s will are over.”

    (tip to jd for the link)

    first, there was the wheel. then, maps of the human genome and single base pair changes. now, u toronto scientists report a killer result in genomics this week. copy number variations (chunks of repeated base pairs) were found on 12% of the genome, suggesting much greater diversity among humans than was ever appreciated previously.

    a friend just showed me this new animation exploring the vibrant biological milieu. it’s kind of gratuitous, and the music is wretched, but it does a nice job with DNA transcription, cytoskeletal reorganization, and stylized myosin trafficking (here’s one that takes fewer liberties). unfortunately, the animation doesn’t really capture the feverish pace or elegant complexity of these biochemical interactions…to get an intution for that, it’s better to watch a philip glass serial film. still, it’s a fun cartoon.

    for my money, i’d stick with that hilarious 1970’s version of DNA transcription filmed by a bunch of bored, artistically-stifled grad students given afternoon access to a football field. if anybody can find a clip of that, pass it along.

    (picture courtesy cgl.ucsf.edu)

    just found out about the very small release of mike judge’s new film idiocracy and read a nice review at slate. apparently, it’s everything you’d expect from the creator of beavis and butthead in the time of george w bush: a humor that laments incompetence and laziness. i’m in no rush to see it, thanks to a few other reviews, one of which sums it up best: the movie is “so puerile and gross that[,] though the movie wants to say something about the dumbing down of America, it winds up not so much commentary as part of the problem.” there’s also a conspiracy theory saying that the distributor (FOX) intentionally squelched the film

    what was supposed to be a week away from blogging turned into a healthy month; i’ll be making up lost time in the next few days.

    first up, e.o. wilson’s new book The Creation: A Meeting of Science and Religion came out this past month and was just reviewed in the magazine
    first things by particle physicist
    stephen barr. he compliments wilson’s engaging prose on the intricacies of nature and the debt we owe it, but ultimately recognizes wilson’s insistence on naturalism for what it is–idolatry. wilson’s commitment to the “ancient, autonomous creative force” of nature has been unabashedly prevalent in all of his books on religion and science, including one i reviewed (consilience: the unity of knowledge) for the journal revisions: a journal of christian perspective (see pdf or html).

    while he emphasizes that we should take care of the environment, he accuses Christians of being anti-green because of their belief in an afterlife. this misrepresentation of the christian camp has continued for far too long, despite pleas and arguments to the contrary (briefly, one quick-and-dirty argument for pro-green christianity is that God has created this world for His glory and has created us to be stewards of it… so, we should be).

    one nice point that barr brings up is wilson’s poor understanding of Christianity: “he plays with the word creation, even choosing it as the title of his book, while evincing no grasp of whati it means. in its traditional and profounder meaning, creation is that timeless act whereby God holds all things in existence. it is not an alternative to natural theories of origin or natural explanations of change […] did this insect evolve or is it created by God? to ask that is as silly as to ask whether polonius died because hamlet stabbed him or because shakespeare wrote the play that way.”

    a new study from ucsc shows that a gene active during cortical development in humans is a lot different from its counterparts in other mammals. HAR1F, active in Cajal-Retzius cells during development and possibly interacting with the protein reelin (involved with cortical layering), was recently identified in a non-coding region of human DNA: it had changed forms 18 times compared with its analogue in chimps. meanwhile, it (and a second, related HAR gene) are virtually identical in non-human mammals. the hunt for what makes our brains so special is taken up with equal fervor in computational biology and theology, and, as always, the findings in one don’t by necessity negate the claims of the other…

    see the original article, or nature’s reader-friendly intro, or the BBC coverage.

    nature this week covered a new book by geneticist and public christian francis collins, best known for heading up the human genome project. the article’s pretty drab, but i’m anxious to check out a copy of the book. i also enjoyed reading vehement atheist PZ Myers’ blog response to the article (in which he’s quoted) along with other comically atheistic musings on his site.

    the summary: collins writes book about how faith and science are compatible. typical atheists like dawkins bash it. but because collins disses creationism and ID, he gets praise from some unlikely people, like the head of an anti-ID lobbying group.

    judging from the article, the book seems to push for greater dialogue about faith and science and for greater lay appreciation of the fact that they are not mutually exclusive (the article cites that 40% of scientists in america are also christians). a call to the discussion table by a scientific figurehead is certaintly welcome. but i’m anxious to see if the book lays out some suggestions for the exchanges once we’re seated. the critical thing missing in many of today’s “debates” about religion and science (including the ones that go on daily in labs) is nuts-and-bolts philosophy. to be sure, most scientists are at home in the land of logic, but don’t have time and/or desire to read nuanced tomes on epistemology. still, as long as someone knows the arguments–and the onus of responsibility, i think, sits on the christians’ shoulders here–the claims and conclusions of christianity and secularism can lead to fruitful debate… and, in many cases, a reconsideration of whether naturalism is an air-tight worldview.

    Genomics luminary weighs in on US faith debate
    Erika Check
    Top geneticist asks the God question.

    Is it really possible to combine dedication to science with belief in God? In a new book, prominent US scientist Francis Collins sets out his case for combining a strong religious faith with a zeal for the scientific method. But his views have already sparked debate, with critics suggesting that more talk of religion is the last thing that science needs.

    Collins, who directs the National Human Genome Research Institute in Bethesda, Maryland, and headed the Human Genome Project, has never hidden the fact that he is a devout Christian. But he has never spoken quite so publicly about his faith. He says he felt compelled to write his book because the popular debate on faith and science has become dominated by extreme voices, leaving many feeling that there is no way to reconcile religious and scientific views of the world. “Our society is not well served by portraying a future which is either entirely secular or entirely religious in a fundamentalist way,” he says.

    Collins also hopes the book, The Language of God (Free Press, 2006), will provoke thought in academia, where, he says, the subject of faith isn’t exactly popular. “In most academic circles, a discussion of spiritual matters tends to clear the room fairly quickly.”

    Discussion, Collins suggests, might rectify the misconception that most scientists are atheists. Surveys find that about 40% of US scientists believe in God, but Collins says that is not reflected in science’s public face. That hurts science, he argues, because it drives away curious people who might also be religious believers.

    Collins takes a strong stand against some religious beliefs, such as creationism and ‘intelligent design’. He considers both to be views that restrict faith to covering gaps in scientific knowledge, leaving it in a tenuous position.

    Instead, Collins embraces a theology sometimes called theistic evolution, or BioLogos. This embraces the idea that human evolution occurred through natural selection according to God’s plan, and that God instilled humanity with certain characteristics, including a ‘moral law’, that can’t be explained by science.

    “The moral law is a signpost to a God who cares about us as individuals,” Collins says. “God used a mechanism of evolution to create human beings with whom he could have that kind of fellowship.”

    Many scientists disagree strongly with such arguments. Some suggest that science is on the defensive today — not just in the United States — and that society needs exactly the opposite of what Collins suggests: less talk about faith and more about reason. Religious concerns are largely behind the US law restricting federal funding of stem-cell research, for example. And many feel threatened by the influence of intelligent design in science education.

    In the United States, “the default position right now is to assume that religion is perfectly OK”, says Paul Myers, a biologist at the University of Minnesota in Morris and author of the popular science blog Pharyngula. “Collins is taking that default position, and while a large majority of scientists will shrug their shoulders, a few voices will be shouting out, saying ‘wait a minute, this is nonsense’.”

    “I cannot see how this could be good for science — supernaturalism is fundamentally anti-scientific,” says Richard Dawkins, a biologist from the University of Oxford, UK. “Scientists work hard at trying to understand. Supernaturalism is an evasion of this responsibility. It’s a shrug of the shoulders.”

    Dawkins acknowledges that, particularly in the United States, there might be tactical reasons for trying to get on with religious people. “That is a perfectly reasonable political stance, but it has nothing to do with truth.”

    Others welcome Collins’s book, however. “I think it’s helpful when scientists of Francis’s prominence speak out on the compatibility of faith and science,” says Eugenie Scott, executive director of the National Center for Science Education, a group based in Oakland, California, that lobbies against creationism.

    Scott agrees with Collins that so far the harshest voices have achieved most prominence, and that this situation doesn’t help either side. “Creationists love quoting Dawkins and Daniel Dennett,” she says. “But those individuals don’t represent the fairly sizeable proportion of non-theists who are not out to destroy religion.”

    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…