Sunday, January 28, 2007

Brave Bunny

Sorry, I couldn't resist. This is great...

Friday, January 26, 2007

The African Way

I'm happy to see that the piece I wrote for the Dec / Jan issue of Seed has been posted online. It's about the upcoming African Union Summit, which will focus on the role of science in the continent's development.

In case anyone is interested in reading more, Nature published a feature and an editorial about this topic earlier this week as well.

Thursday, January 25, 2007

Camel fever!

Some of you might have read about the recent launch of the EDGE of Existence program in the UK. Designed to improve upon existing conservation strategies that only focus on the number of surviving individuals in a given species (as indicated by the species’ position on the IUCN's Red List), EDGE—which stands for “evolutionarily distinct & globally endangered”—uses a novel metric, basing the need for conservation action not only on a species' extinction status but also on its level of "evolutionary distinction," the amount of evolutionary history a species represents (determined by an examination of its family tree or phylogeny). The idea is that if an endangered species also happens to be one of the only species of its type left on the planet, a disproportionate amount of unique evolutionary history would be lost with its extinction, and conservation efforts should reflect that.

But what I really want to talk about is one of EDGE's ten focal species this year, the wild Bactrian camel (Camelus bactrianus ferus). These two-humped camels live in the fragile Gobi and Gashun Gobi deserts in northwest China and Southwest Mongolia, and it's estimated that only about 950 remain, making them "more endangered than the giant panda," according to the charity / non-profit organization The Wild Camel Protection Foundation. The foundation, whose patron is Jane Goodall, has recently established a captive wild bactrian camel breeding program in Mongolia to save—and study—these fascinating creatures, for it seems they might be harboring some pretty nifty secrets. First, they have been able to breed normally in an area of Gashun Gobi that has been host to extensive nuclear testing (according to an article first published in the London Independent, China has engineered more than 40 atmospheric explosions in the area in which the camels have lived); they have also evolved the ability to drink salt water slush instead of fresh water, something that domestic Bactrian camels cannot do. And there’s more. According to the foundation,
The immune system of a single humped, dromedary camel is beginning to yield amazing secrets. For example, an increased ability to resist certain types of diseases including diabetes through the consumption of camel milk. As it is possible that the single-humped camels descended from the double-humped camel, scientists have every reason to think that a detailed study of the immune system of the wild Bactrian camel will yield scientific discoveries which will be of benefit to the whole of mankind. For example, how is it that the wild Bactrian camels survived 43 atmospheric nuclear tests and are still breeding naturally without any recognisable deformities? How has the wild Bactrian camel managed to survive on salt water that the domestic Bactrian will not drink?
Getting deeper into the science, here is an excerpt from a 2000 2001 article in The Scientist:
Sabah Jassim, who is originally from Nottingham but now works in the UAE, at the Zayed Complex for Herbal Research and Traditional Medicine, is convinced that camels offer new hope for drug companies looking for treatments for hepatitis C and HIV. "There is something really marvelous in their immunoglobulin," he said. His center has carried out an overview of the existing research into the camel's immune system, going back to 1993, and published in the latest issue of the British Institute of Biology journal, Biologist. "The camel is unique, different from any animal in the world," he explained. "The only animal with anything like it is the shark."
And later on:
The camel's antibodies find it easier to penetrate enzyme—active sites than human antibodies. This, and the relatively small size and weight of the immunoglobulin molecule, offer enormous potential, as it could be used to tackle diseases such as salmonella, TB, hepatitis C, skin disease and HIV, argued Jassim. Camel immunoglobulin could be used to neutralize a viral enzyme, he suggested. And it appears to be able to fight off various pathogens.

Camel antibodies are also being studied by Serge Muyldermans, Senior Scientist at the Flemish Institute for Biotechnology in Brussels. He explained that, because a camel immunoglobulin molecule is much smaller than that of a human, it is able to penetrate the dense layer of protein coat around a virus or parasite more easily. His department has been developing ways of cloning immunoglobulin fragments from immunized camels to produce high yields of recombinant protein. The camel antibodies, he argued, have several advantages over conventional antibody fragments, and could be used as enzyme inhibitors, for diagnostic purposes, or even in treating tumors. "The idea is to link the camel antibody to enzymes which will bind to the tumor," he concluded.

The fact that camel antibodies are so light, proposed Jassim, makes them ideal for new clinical compounds. The antibodies have a molecular weight of 100 KDa, much lower than human antibodies, at 150 KDa, while the recombinant version weighs just 15 KDa. "I think pharmaceutical companies are not really aware of this," he said. But he thinks that camel antibodies are set to become big business in the future.
But that article was written back in 2001, so the obvious question is, what have these scientists learned since then? Sadly, I can't find a website for Jassim, and a PubMed search suggests he's published no camel-related papers since then. A look on Muyldermans' website reveals that although he is ostensibly still studying camel antibodies, he hasn't published any related studies since 2003, when he published in Nature that a particular camel antibody fragment inhibits the aggregation of a protein variant of human lysozyme that is involved in the production of amyloid fibrils—the signature of diseases like Alzheimer's and Parkinson's. The paper says that "the binding of the antibody fragment achieves its effect by restoring the structural cooperativity characteristic of the wild-type protein...Reducing the ability of an amyloidogenic protein to form partly unfolded species can be an effective method of preventing its aggregation, suggesting approaches to the rational design of therapeutic agents directed against protein deposition diseases."

Sounds exciting, and I'll look forward to hearing more about the medicinal potential of Bactrian camel immune proteins, but I'm not holding my breath either. These substances have barely been studied in the lab, let alone developed into potential therapeutics, where they'd have to undergo further scrutiny in animal and clinical trials. You can’t predict much from research at this stage, but it's certainly fascinating to follow, so I'll continue to do so.

Assuming these camels don't go extinct, of course.

Tuesday, January 23, 2007

Science, schmience, says the Huffington Post

I've been setting up my new Google Reader account (I know, I'm probably the last blogger on earth to set up an aggregator) and I was hoping to add Michael Shermer's blog from the Huffington Post to my list. But in trying to do so yesterday afternoon, I discovered that the Post doesn't allow you to choose specific bloggers for your feed; I was, however, happy to see that I could at least choose among a number of topics.

I browsed through these topics—which included "Paris Hilton," "Tom Cruise" and "Yellow Cake"— searching, of course, for "science." Alas, the list jumped from "Samuel Alito" to "scientology." isn't a worthy topic, but scientology is??

The evolution of cancer

In a 1976 article in Science, Peter C. Nowell pronounced that "more research should be directed toward understanding and controlling the evolutionary process in tumors." In the thirty years since, what have we learned? Enter Carl Zimmer, who has written a fascinating article on this very topic in January's issue of Scientific American (He also blogged about it, and there is a podcast of a related interview with him here). Zimmer begins by explaining, in a rather novel way, why cancer is so "successful":
Cancer, in other words, re-creates within our own bodies the evolutionary process that enables animals to adapt to their environment. At the level of organisms, natural selection operates when genetic mutations cause some organisms to have more reproductive success than others; the mutations get “selected” in the sense that they persist and become more common in future generations. In cancer, cells play the role of organisms. Cancer- causing changes to DNA cause some cells to reproduce more effectively than ordinary ones. And even within a single tumor, more adapted cells may outcompete less successful ones. “It’s like Darwinian evolution, except that it happens within one organ,” explains Natalia Komarova of the University of California, Irvine.
Then he introduces some potential reasons why the genes that predispose us to cancer might be propagating in the gene pool. The fact that cancer is so commonand that our defenses against it fall shortsuggests that perhaps there are evolutionary reasons for it, Zimmer says. (He does rightly point out, however, that natural selection doesn't care what happens to us when we're old. It favors only for those genes that affect our ability to reproduce.)

First, Zimmer describes a potential link between genes that help protect us against cancer (aptly named tumor-suppressor genes) and aging. Research suggests that, though they are at a heightened risk for cancer, mice lacking a tumor suppressor gene called p16-Ink4a do not age as quickly as mice containing normal copies of the gene:
But losing the p16 gene had an upside. When the mice got old, their cells still behaved as if they were young. In one experiment, the scientists studied older mice, some of which had working p16 genes and some of which did not. They destroyed insulin-producing cells in the pancreases of the animals. The normal rodents could no longer produce insulin and developed fatal diabetes. But the ones without the p16 protein developed only mild diabetes and survived. The progenitors of their insulinproducing cells could still multiply quickly, and they repopulated the pancreas with new cells. The scientists found similar results when they examined cells in the blood and brains of the mice: p16 protected them against cancer but also made them old.
Could a missing (or non-expressing) tumor expressor gene, though bad for us in the cancer sense, actually have the hidden benefit of slowing down the aging process? Who knowsmice aren't the perfect models for humans, but it's a possibility. But that's just the start. Another gene that is highly associated with cancersome cancer cells can't live without its expressionproduces a protein called fatty acid synthase, which (again, as its name suggests) synthesizes certain fatty acids. The gene, scientists have found, has undergone big changes since humans first evolved from mammalian ancestors, and while no one can be certain yet why, there is some evidence that the protein helped us evolve bigger and better brains. In other words, then, a gene that potentially increases cancer risk could have been what essentially made us human in the first place.

And there's more. Sperm that divide more quickly (a natural advantage) may be expressing genes that increase cancer risk; and genes that help fetuses grow in the womb could inadvertantly help cancer cells:
Genes that allow cells to build a better placenta, Crespi and Summers argue, can get hijacked by cancer cells—turned on when they would normally be silent. The ability to stimulate new blood vessel formation and aggressive growth serves a tumor just as it does a placenta. “It’s something naturally liable to be co-opted by cancer cell lineages,” Summers says. “It sets up the opportunity for mutations to create tools for cancer cells to use to take over the body.”
Yet even though activation of these usually quiet genes may make cancers more potent, natural selection may still have favored them because they helped fetuses grow. “You may get selection for a gene variant that helps the fetus get a little more from mom,” Crespi says. “But then, when that kid is 60, it might increase the odds of cancer by a few percent. It’s still going to be selected for because of the strong positive early effects.”
Through these examples, Zimmer suggests that looking at cancer through the lens of evolutionary biology may provide some novel insights. As behavioral ecologist Bernard Crespi says in the article, whereas other science tends to focus on the "how" of cancer, evolutionary biology instead investigates the "why." And that question may have some pretty fascinatingnot to mention useful!answers.

Monday, January 22, 2007

10 myths deflated

Livescience has a list up of the top 10 scientific myths of all time, with explanations for why they are mythical. I'm surprised that some of them actually made the list—do people really think that there is no gravity in space, or that chicken soup cures a cold? Either way, it's a fun read.

One of them on there—that yawning is contagious—surprised me, because I'd always believed it. Turns out that it could, in fact, be true.

And no matter what they say, I'll still use the five-second rule. Especially if it involves crumb coffee cake.

Sunday, January 21, 2007

Time does science (hopefully not for the last time)

When I received the latest issue of Time a few days ago, I was excited to see that the cover story was "The Brain: A User's Guide." (I also got a little sad, because I recently heard from someone who works there that the magazine's ongoing restructuring may mean that there are fewer science cover stories, despite the fact that they sell amazingly well.)

I haven't read all of the articles yet, but here were the highlights from what I've read so far.

There is an article about brain rewiring that is actually an excerpt from Sharon Begley's new book The Mind and the Brain. Among other things, it reports on research that challenges the long-held hypothesis that a person's "happiness set point" is (as implied by the phrase) basically unmovable. A person's happiness, it was thought, returns to approximately the same level even after great tragedy or joy. But recently, Richard Davidson from the University of Wisconsin-Madison (with the help of the Dalai Lama) recruited Buddhist Monkswho had spent more than 10,000 hours of their lives meditatingfor tests in which they were asked to meditate under fMRI scans. The scans showed "dramatic changes in the parts of the brain associated with happiness" as compared to a group of students who had recently undergone a crash course in meditation. Begley writes,

But perhaps the most striking difference was in an area in the left prefrontal cortexthe site of activity that marks happiness. While the monks were generating feelings of compassion, activity in the left prefrontal swamped activity in the right prefrontal (associated with negative moods) to a degree never before seen from purely mental activity. By contrast, the undergraduate controls showed no such differences between the left and right prefrontal cortex. This suggests, says Davidson, that the positive state is a skill that can be trained.

For the monks as well as the patients with depression or OCD, the conscious act of thinking about their thoughts in a particular way rearranged the brain. The discovery of neuroplasticity, in particular the power of the mind to change the brain, is still too new for scientists, let alone the rest of us, to grasp its full meaning. But even as it offers new therapies for illnesses of the mind, it promises something more fundamental: a new understanding of what it means to be human.

This I find fascinating. I have never doubted that meditation had positive health effects, but this research implies that meditationor, more broadly, the practice of particular thought patternscan rewire the brain.

Begley's article also mentions another interesting finding. Not only does the repeated use of certain musclessay, by practicing a certain passage on the piano each daycause the brain to "devote more cortical real estate to it," even just imagining the practicing elicits the effect:

"Mental practice resulted in a similar reorganization" of the brain, Pascual-Leone later wrote. If his results hold for other forms of movement (and there is no reason to think they don't), then mentally practicing a golf swing or a forward pass or a swimming turn could lead to mastery with less physical practice. Even more profound, the discovery showed that mental training had the power to change the physical structure of the brain.
Steven Pinker has an interesting article about the nature of consciousness, in which he describes the so-called "Easy Problem," the difference between conscious and unsconscious thoughts, and the "Hard Problem," or why there is first-person, subjective experienceand why it's so difficult to solve this problem. (I recall being in elementary school and asking my parents how I could be sure that the "green" I saw was the same color that my classmates saw when they saw green. This article gets at just that.) There's also an interesting (and mildly amusing) sidebar by Daniel Dennett that begins, "Suppose Steve Pinker contracts a terrible progressive brain disease..."

article by Michael Brunton argues that we may have been giving babies too much credit. Challenging research from the '80s that suggested babies have a certain amount of "built-in knowledge" about the workings of the world, new research suggests that "a baby's fascination with physically impossible events merely reflects a response to stimuli that are novel."

And our memories are heavily driven by emotion, writes senior staff writer Michael Lemonick in his piece, "The Flavor of Memories." He points out something I never knew: the reason that memories grow more inaccurate over time has to do with the fact that when we remember old events, we are not calling up the original memory but the last time we thought about it:
Each time we retrieve and re-store a memory, it can be subtly altered by all sorts of factors. What goes back into our brains is like the new version of a text document, overwriting the old.
And last but certainly not least, there was a very interesting essay by Harvard psychologists Daniel Gilbert and Randy Buckner. When people are not performing specific mental tasks that require them to be "in the moment"like following instructions, or answering the telephonewhat are their brains doing? Traveling through time, apparently, either re-living past events or imagining the future. Gilbert and Buckner offer some potential reasons for this:
Why did evolution design our brains to go wandering in time? Perhaps it's because an experience is a terrible thing to waste. Moving around in the world exposes organisms to danger, so as a rule they should have as few experiences as possible and learn as much from each as they can. Although some of life's lessons are learned in the moment ("Don't touch a hot stove"), others become apparent only after the fact ("Now I see why she was upset. I should have said something about her new dress"). Time travel allows us to pay for an experience once and then have it again and again at no additional charge, learning new lessons with each repetition. When we are busy having experiencesherding children, signing checks, battling traffic--the dark network is silent, but as soon as those experiences are over, the network is awakened, and we begin moving across the landscape of our history to see what we can learnfor free.
Certainly some fascinating pieces herethere are more I haven't read yet, tooand most appear to be available for free online, at least for now.

Thursday, January 18, 2007

When the clock strikes midnight...

Those great thinkers mentioned in my last post have garnered more support for their pessimism. The Bulletin of the Atomic Scientists, a non-profit organization dedicated to global security analysis, has moved its famed Doomsday Clock forward by two minutes for two reasons: the spread of nuclear weapons and climate change. Now it sits just five minutes shy of midnight, the marker for the "end of humanity." You can read more about the Clock and its history here at Nature.

Monday, January 15, 2007

Where are all the optimists?

Each year,, John Brockman’s well-known “Third Culture” website devoted to discussions of scientific and philosophical ideas, poses a question to a chosen number of big thinkers in science, technology, journalism and philosophy. This year, Edge asked its 160 respondents, “What are you optimistic about, and why?” Edge explains,
As an activity, as a state of mind, science is fundamentally optimistic. Science figures out how things work and thus can make them work better. Much of the news is either good news or news that can be made good, thanks to ever deepening knowledge and ever more efficient and powerful tools and techniques. Science, on its frontiers, poses more and ever better questions, ever better put.
Here's what's interesting. Having read all 160 answers, I noticed that a shocking 21 of the respondents, in describing what they are optimistic about, delineate some very strong caveats. Some go as far as to say that they believe we’re all doomed but that they are "optimistic that they will be wrong" (given that these are some of the world's best thinkers, I don't feel especially comforted). Perhaps considering one side of the coin makes one automatically think about the other; I don’t know. But one thing's for sure: these 21 didn’t seem optimistic about much.

Here is an excerpt from the most decidedly negative of the answers, provided by Nobel Laureate cosmologist George Smoot of the Lawrence Berkeley National Laboratory. He opens with this:
A careful assessment and years of experience that show that the long-term future is most bleak: Entropy will continue to increase, and a heat death (actually a misnomer as it means the degredation of usable energy in a dull cooling worthless background of chaos) is the very likely fate of the world. This is the fate that awaits us, if we manage to work our way past the energy crisis that looms as the Sun runs out of fuel and in its death throws expands as red giant star likely to engulf us after boiling away the seas before it collapses back to a slowly cooling cinder eventually to leave the solar system in cold darkness.
A few paragraphs later, it only gets better (worse?):
One cannot live by the Hippocratic dictum "Do no harm". But the best one can hope for is the weak mantra "Do minimal damage". I was often bothered by this inevitable conclusion and tried to see that if one could write a great work of literature, make art, or most optimally a great science discovery could one objectively leave the world better than one found it? Each time I worked out an example, the impact was negligible however great it was found by human culture compared to the damage done by mere existence. The only discovery that would make a difference called for repealing or avoiding the laws of probability or making a whole new universe. Both of these are quite extreme. Perhaps the discovery of extra dimensions would allow some leeway in what otherwise seems an inescapable doom after a long period of unrighteous degradation of the universe. We face a continuous downward spiral of no return. This is not a moral or ethical statement only an engineering evaluation though it is some indication of original sin. So even living one's life as a vegetarian that only eats fruit dropped into one's hand by a willing plant is only going so far as to be very kind and considerate to other beings that are also worsening the universe for the sake of a little more order in their own self.
There’s plenty more where that came from. So: is it unrealistic to be optimistic these days? Are we really heading towards an imminent apocalypse (with two books, here and here, supporting this idea)? Or are brilliant intellectuals just more likely to be pessimists? I certainly don't have the answers, but if you're looking for some interesting ones, you can find them on Edge...

You might, however, want a stiff drink first.

Wednesday, January 10, 2007

Slackerpedia Galactica!

At this past week's annual American Astronomical Society meeting, a new astronomy-themed wikipedia was unveiled. Called Slackerpedia Galactica, the wiki is designed to be both informative as well as "loaded with humor, jokes, cheesieness and the absurd." Users can add info to the many existing entries (this one is my favorite) or create new ones; they can also join the Slacker Union to help realize the following four goals:

- To give creative names to each of the Twin Planemos

- To decide on a better third definition of a planet

- To come up with a catchy theme song and a secret handshake

- To find an asterism that resembles the Flying Spaghetti Monster, so that the SU can start to define its own constellations.

Sorry, I think I can only help with the third one, guys...

Tuesday, January 02, 2007

Snow for sale!

I was highly amused to read on about one Colorado woman's snow sale on Ebayyep, that's right, she's selling the snow that fell on her property thanks to the recent blizzards.

Apparently she didn't originally expect to find any buyers
she posted just for a laughbut as of the time of this blog post, she had received 72 bids on her most recent sale (her Ebay post reads, "1 more time! End of 2006 snow! We're overstocked! All of it must go!," so I'm guessing there have been other successful sales), and the current price was $39.89. Her caveats: absolutely no refunds, and quantities vary. The best part, however, is the shipping details:
Just to be clear...we can ship your snow 1 of 3 ways. 1) For the shipping stated in the auction we'll put snow in a leakproof container (jar or zip lock bag) and ship it in a box. Yes, it will melt. You'll have to refreeze it and shave it to return it to it's natural state. 2) To keep it frozen we need to use dry ice and a foam cooler and ship it overnight fedx. Probably a gallon zip lock bag of snow. That will be a lot more, but you'll get snow. 3) You can come get it...
I particularly love the last option (she also mentions earlier in the post that people who might like to avoid paying shipping charges should feel free to come to her home with a dump truck and shovel). To find people willing to pay you to shovel snow from your driveway? Brilliant.