Monday, January 31, 2005
The story continues to grow. Now, the German betting service Oddset is complaining that they had faxed the president of the German League within 48 hours of the main game in question. Why a bookie would complain about a cooked game, don't ask me. Meanwhile, Hoyzer has apparently named 9 players as being paid as well. Cool! German police have already arrested 3 players , including one who made a goal against his own team during an allegedly fixed match. For the moment, it's all in the B-leagues, but even I'm starting to wonder now.
There's also a very serious discussion that some of these microbes might still be viable. People are advised to be really careful when going into graves where smallpox is suspected. The Spanish flu virus of 1918 might still be kicking around somewhere as well.
The authors themselves have been able to confirm that the Justinian Plague (Wiki; see also the comment) in the late Roman empire was due to Y. Pestis (i.e. the Black Death) of the same biovar as the medieval and modern plagues. So it likely originated in China as well. See Plagues and Peoples for more on this.
Sunday, January 30, 2005
Regular computer use for work, but not play, aids student test performance
A new Boston College/UMass study reveals that the more students used computers for school work, the better they performed on a state language/arts test. Conversely, students' recreational use of computers to play games, explore the Internet for fun, or chat with friends at home had a negative effect on their reading scores.
Source: US Department of Education
Saturday, January 29, 2005
The Germans are characteristically mortified. Instead of gleefully turning over rocks, as the NY Post was doing with Kerik, tabloids like Bild are frantically laying bare detail after detail-- how bad is it??-- like a mother dealing with diaper leakage on the subway.
No German source can go two paragraphs without mentioning the World Cup, to be hosted by Germany in summer 2006. Despite the vast indifference of even the rest of Europe, German papers are hanging national prestige on a good games. "We're not Athens" is the mantra. A recent headline trumpeted "500 days away and the stadiums are almost built." ("We're not Athens.") So, in what I can only describe as neurosis, this revelation of corruption keeps getting described as casting a cloud over the World Cup games. ("We are Athens, after all.") In America, the revelation that a 25-year old ref was corrupt would not lead newspapers to worry about the Super Bowl-- especially not a year and a half distant. (I think you would see comparable grousing among American teams and fans though. One coach is blaming his firing on a single questionable game.) In France, he'd probably be "retired" to a government job. In Italy, he'd still be working.
Human nature being what it is, I am sure that venal behavior is just as prevalent here as anywhere else, but I keep getting suprised by the strength of German reactions when it's revealed. There is something about corruption which truly freaks them out. Not only are they angered, but also frightened, as if a corrupt German would bring down the whole house of cards.
UPDATE: Bild's headline today: BUNDESLIGA SCANDAL: THE FIRST ARRESTS.
Friday, January 28, 2005
UPDATE: Much funnier with the sound off.
Wednesday, January 26, 2005
Tuesday, January 25, 2005
Many, and possibly all, adult tissues have a population of special reserve cells, called stem cells , which contribute new cells to the tissue following normal wear-and-tear or injury. For example, stem cells in hair follicles mobilize after a hair is lost to generate melanocytes and other cells. These daughter cells begin building a new hair, and the stem cells become dormant again. This cycle repeats over and over throughout life.
Mice with mutations in the Bcl-2 gene start going grey after just a few weeks of age, and in fact lack all their melanocytes by 6 weeks after birth. The scientists in this paper wondered whether defects in the the stem cell population might be to blame. They used a genetic trick to mark the melanoblasts in Bcl-2 deficient mice, and found that the melanoblasts were dying right at the step in the hair follicle cycle when they should have been returning to dormancy. Mice with a second sort of mutation showed a different type of melanoblast disturbance, but the result was the same: grey hair.
The scientists then looked at old normal mice, which show some greying, and found disrupted melanoblasts in hair follicles from those animals as well. To consider if these changes also occur in humans, they looked at cells which express MITF, a gene they knew from the mouse work to be expressed by melanoblasts. In hair follicles from 70 to 90 year old humans, the MITF-expressing population was absent. Thus, in two different mouse mutations, and in normal greying of two different species, the melanoblast population seems to be the key to color.
Stem cell disturbances might contribute to other changes which come with age, including heart problems and, of course, cancer . One feature of greying hair which interests me is the apparent "all-or-none" effect of greying. Individual hairs seem to be either fully colored, or fully grey. Does this mean that all the melanoblasts in a given hair follicle stop functioning at once? A second point worth remembering is that grey hair does continue to grow. That is, the other stem cells involved in hair growth (which come from a different developmental source) seem to keep on doing their job after the melanoblasts have given up the ghost.
Monday, January 24, 2005
Based on the LA Times report, it looks like what happened is the contamination came during the expansion of the stem cells, when the stem cells increase in numbers without losing their stem cell properties. During this phase, they do not live well in a petri dish, but need the support of "EMFs" or embryonic mouse fibroblasts, which secrete signals which keep the stem cells undifferentiated. There has been concern that the EMFs might contribute non-human features to the human stem cells. Indeed, the researchers report that the human stem cells incorporate a type of sugar which decorates the surfaces of mouse, but not human cells. Since the sugar is outside the cell's surface, it is "visible" to the immune system and could provoke an immune attack, were these cells to be put in to humans. For the moment, I don't quite understand if there has been a genetic transfer of a mouse glycosylase to the human cells, or if there are just mouse cells mixed in the prep.
Sunday, January 23, 2005
Myself, I am an odd mixture of Luddite and gear-head. You can get me a collapsible wok out of the REI catalogue, and I'm loving it. Just don't ask me to carry a cell phone.
Saturday, January 22, 2005
We had a big scene today, and with my earlier post about cocaine still fresh in my mind, I couldn't help wondering if the game wasn't triggering a related activation of the reward centers of the brain. I think the point of the scientific article was that-- no suprise-- these parts of the brain do function in normal life, and can be more moderately activated by non-cocaine stimuli. (BTW, I now have it on good authority that nursing a baby, although it's relaxing, does not neutralize fatigue. Nor have I noticed any withdrawl symptoms in my wife when the kids stopped nursing and switched over to carrot puree.)
I know exactly where my son gets this tendency. In fact-- no joke now-- Thomas Kuhn once described the scientific personality as an addict to a particular sort of puzzle. When I was a kid, I would play Atari (yes, I'm that old) until my eyes were burning and my joystick wrist ached. And I still get sucked into conquer-the-world games, to the point that the house could probably burn down around me, as long as I was showing the evil Ant People who's the mack. So when my son is basically quivering in a heap on his bedclothes, I know what he's going through- it's withdrawl.
Still, I had to get him off the machine. I wanted to check my site meter.
Friday, January 21, 2005
So: could there be life? It is too cold for a life based on earth-type chemistry. But extremely low temperatures on Titan would mean that information could be stably stored in a whole other kind of molecule, and that the "living" part of life-- metbolism, you name it-- could harvest chemical bonds that are completely unstable in our comfort zone. .. Some interesting speculation here .
UPDATE 22 Jan: The Register does a good job summarizing pretty much the same conference. Does anyone know what the deal is with "primordial argon?"
One of the powerful attractions of cocaine is that the drug activates the reward centers in the brain, giving rise to a sense of elation and reduced fatigue, among lots of other things. These reward centers probably evolved to confer reinforcement for behaviors that are especially important for survival of the species. Cocaine and other drugs hijack this reinforcement property, and the seeking of cocaine becomes the reinforced behavior. Pretty poweful stuff.
Thus it's very interesting to see in Science Now a week or so ago, that nursing rats show the same activation of the reward pathways as virgin rats on cocaine. In fact, mom rats with babies under 8 days' age prefer nursing over a dose of cocaine; and when suckling moms are given cocaine, it actually causes a dip in the electrical activity of the reward center.
I can see where the anti-fatigue effects might come in handy....
Subscription link (Journal of Neuroscience) is here. .
Then, after a minute's pause, he adds a third regret: "The biggest regret is that we didn't stop 9/11. And then in the wake of 9/11, instead of redoubling what is our traditional export of hope and optimism we exported our fear and our anger. And presented a very intense and angry face to the world. I regret that a lot."
I have always been sympathetic to Colin Powell and Richard Armitage, as the moderates in a hard-right administration. In particular I was grateful for Powell going in front of the U.N. in the run-up to the war in Iraq, even knowing that the outcome was foregone. After a while I started to question their sanity, though; and their continual losses in the bureaucratic tussles with Defense have now left State on the brink of irrelevance. (I seriously doubt Condoleeza Rice will be able to reverse this. )
But Armitage's valedictory regret has real poignance for me. We, as a nation, have let a couple of hate-filled terrorists push us off of our biggest asset in the world-- our Will Rogers friendliness, optimism, and yes, hope. The tumult of the last few years has resulted in U.S. foreign policy decisions which Europe would never agree to-- and no one should pretend otherwise. But the tone-deafness of this administration, and its open disdain for the opposition from other liberal democracies, has exacerbated this policy gap, made its own efforts that much harder, and, yes, needlessly put U.S. military lives at risk. National prestige comes from self confident presentation, not from hectoring and displays of anger.
Mr. Bush was re-elected with a mandate that includes keeping our nation secure. Let's hope together for a decent result in Iraq, and an decision by Mr. Bush to project his famed personal warmth and optimism out onto the international stage.
Nothing is so strong as gentleness. Nothing is so gentle as real strength.
St. Francis de Sales
UPDATE: Greg at Belgravia Dispatch is very impressed with Condoleeza Rice, both her testimony and personnel decisions. Not to put words in his mouth, but maybe she could rescue State AND change the international tone. I'd be glad of that. Also see Greg on Barak Obama.
Thursday, January 20, 2005
Ok, so I looked at their dating methods and it looks just beautiful. Of the 900 K basepairs they focused on a smaller piece which overlaps with a known gene. This is necessary and pretty standard practice. The killer, for me, is a "sliding window" analysis in which the molecular clock method is separately calculated for each 5 K window of this smaller piece. Remarkably, the inverted sequences throughout the window always fall pretty much halfway between modern H. Sapiens and modern chimpanzees-- exactly what you'd expect for indeed a very ancient divergence.
So, how did Europeans get it? The two possibilities were that either it was always there in the European peoples (for 3 million years!) and recently became more common; or that some very divergent hominid contributed DNA to much more recently to the European lineage. This isn't just a question of, ahem, close contact. This means successful interbreeding. Just astonishing.
Wednesday, January 19, 2005
Tuesday, January 18, 2005
Wired mag has an article about an Australian initiative called BIOS to free up some patented genetic information for widespread dissemination, subject to patents structured like those in open-source software efforts.
The main target of this effort is the interface between agriculture and biotech. Many patent-owning ag companies are not interested in small market agricultural applications, because development costs would be too high relative to the potential payoff. (Wired cites the example of Kenyan sweet-potato farmers, who would benefit from GM yams but probably not enough to lure a major patent holder). Nevertheless, these companies would not like to surrender their intellectual property to just anyone, in case another, bigger ticket, application, emerges later. A similar situation occurs in the pharmaceutical industry. In general, my end (academic) of the molecular biology world is already geared toward dissemination of these kinds of building blocks. For example, journals like Nature stipulate that authors who publish with them make tools like plasmids and sequences available to essentially anyone who asks. The NIH grant system makes similar conditions with the US public's money. Even with these conditions, though, the fruits of publicly funded work often end up effectively in private hands, so the situation which BIOS is trying to address is real. (Follow this link to a Nature editorial on the topic. )
I am very sympathetic to the aims of this movement, both as a share-the-wealth liberal, and on an intuitive level that science at its best is a community effort. However, my strong impression from both the Wired article and the BIOS web pages is that the intent is a "taking," in the legal sense of a condemnation of property from a private owner for public purposes. Is BIOS aiming to reverse or erode existing patents? If I am wrong, and this approach applies only to new ideas, then it will still take some effort to reach critical mass, i.e. for an application assembled from "freeware" to reach the agricultural end users. Rather, I would guess the existing information divide will instead be eroded the old-fashioned way, via intellectual piracy. Digitized data, in particular, are prone to leakage.
Lastly, let me indulge in some elitism. Although molecular biology techniques are astonishingly portable, it is not in the same league as the internet miracle. You can't do much without ultrapure water, for example, or precise thermostats. The community which would make something out of increased dissemination of these data and tools must be an order of magnitude smaller than what is found in the internet world. Don't expect any pajamahadeen knocking off any agribusiness Dan Rathers any time soon.
Monday, January 17, 2005
To say more, I will need to see the original article, and I will describe why a bit below. But first, why Icelanders? The company which published this study, DeCode, is bio-prospecting for human genes which might contribute to diseases. The idea (NatGen, subscription link) is that Icelanders are unusually genetically homogeneous. They have lived isolated from other populations for a very long time, and in addition passed through two "bottlenecks," or catastrophic eras (including the Black Death), when very few Icelanders were left to repopulate the island. (See this history of Iceland.)What this genetic homogeneity does is reduce the prevalence of small genetic differences, especially in families, which are seen in more heterogeneous populations. This means that if a genetic disease runs in a given Icelandic family, researchers don't have to sort through such a long pile of differences (of which most will be unrelated to the disease) between family members who do and don't have the disorder. Moreover, Iceland, like other Scandinavian nations, keeps extremely detailed medical databases of all its nationals, stretching back for years and years. This is also a help for gene prospectors to locate new instances of a disease.
Ok, so Icelanders, as a nation, have very similar genomes, and 20% of them share with Europeans an inversion on chromosome 17. Those lucky 20% are overrepresented among very old people and among people with big families. So far, so good. But I would like to see the original article to judge the demographic association of the polymorphism with family size, and the connection between family size and fertility. Europeans generally do not breed to their physical limits, so this connection sounds a bit sketchy as presented. I also, without more information, have trouble with a second claim in the Times, that this inversion has been isolated from its normal cognate for 3 million years. The scientists likely used a molecular clock method (a way of comparing related sequences to see how long ago they diverged), that I would need to see, in order to arrive at this figure. This date seems improbably old, as it predates the emergence of the Hominid lineage (see Wiki on hominid evolution). A beneficial mutation, if present from very ancient times (and if relevant for natural selection) should be seen in humans all over the world, but this inversion is not. The Times offers an alternate explanation, that there has been genetic interchange between the Homo Sapiens group fated to populate Europe and non-human cousins (possibly Homo Erectus- see Carl Zimmer at the Loom for the story-behind-the-story of lice ). But let's be clear here. To pick up a stretch of DNA that divergent, some ancestor of Europeans (i.e. a pretty recent homo sapiens) had to be having sex with chimps.
My guess is that their molecular clock is wrong, possibly because the inversion accumulates mutations faster than expected, and that this genetic novelty came into the picture much more recently. UPDATE: The deCODE site (see below) says that actually the inversion has been subject to low internal mutation.
All in all, I can't argue with the demographics-- in fact, I'm inclined to believe them-- but I see some red flags in the biology. Please, anybody comment who's interested!
UPDATE:deCODE has a different article in the December Nature Genetics. This looks fantastic!
The deCODE web page says the inversion story will appear in the February issue.
Sunday, January 16, 2005
"Zoka is pretty much their office," said Reid Hickman, a Zoka barista. "It's a pretty good deal. They hang out here all day and they often get lunch and dinner here. They take good care of us."
Ah, these kids. When I was taking CompSci, we all lived on Coke and Snickers.
Friday, January 14, 2005
Here are some links:
Timeline of splashdown at European Space Agency
Cassini-Huygens page at JPL/NASA including animation scenarios for landing on wet stuff or solids
A great site by Susan A. Kitchens, who's posting at 2:16AM: 20/20 Hindsight She says that earth scopes have picked up the carrier, so the probe has at least "woken up" properly.
I may do a Technorati later to see what's up.
UPDATE: Technorati is going nuts! There are 1800 recent weblog posts on this topic. The parachute on Huygens deployed (hurray, no Beagle ) and the probe has powered up.
UPDATE: Susan is tele-live-blogging (?) the press conference here in Germany. A huge success!
9:40 PM. German TV is showing an image with methane? rivers and drainage basins. The probe reported winds of 500 km/hr (about 310 mph)
Thursday, January 13, 2005
The Register thinks that if Apple is nimble enough, they could seal up the portable music player market pretty well. This would give them Wintel-like leverage in the download market. The Mac mini is supposed to be bought as a boutique computer, but to be in the house the next time a virus takes out the main, windows based pc. And like the boyfriend's best friend, Mac will be there when the breakup happens to steal you away.
What I don't know is if Apple can stay fast enough, even with Ipod. Even cell phones are going to play mp3s, and I'm not so sure that there are enough people like me who would buy something just for music. And I wouldn't write Microsoft out of the picture yet.
UPDATE: Apparently the flash-Ipod shuffle is doing pretty well.
These finds may provoke re-thinking of the idea that mammals were being kept exclusively to the margins by dinosaurs during the Cretaceous era; indeed, in the fossil bed where the finds were made, the R. giganticus fossil is the bigger than most of the dinosaur fossils. In this local context, then, it's the mammals who were top dog.
The Yixian formation in northeast China continues to yield spectacular fossil finds, upending all sorts of ideas about the folkways of the Cretaceous era. For an idea of the detail of preservation in these fossil beds, check out this Pharyngula post from a while back. Phenomenal!
QUICK UPDATE: The BBC has a good summary, and linkouts to other media.
Wednesday, January 12, 2005
Roaches (inside the blast) and humans (outside) are all fine. Of course, these are New Jersey roaches.
UPDATES: HBO should start a sequel to the Sopranos, entitled "the Ultrasonics," featuring the real Jersey tough guys. Bad-a-bing!
And of course, we should remember the semiretirement of Dave Barry whose last column appeared a week or so ago. Bryan Curtis is way too nice to Dave, who was genius funny, but who definitely had a formula and milked it. (If he wrote one more beer=sustenance joke I was going to smack him.) It was the right time for Dave to bow out and recharge. Still, I wonder what he could have done with the cockroach story.
Tuesday, January 11, 2005
Philipkoski and the Science authors point out a wrinkle in the natural biology of this microbe: it is pretty heavily specialized for metabolizing compounds which have only existed in significant amounts for about fifty years. Thus, the polluted environment might have in effect created a brand-new ecological niche, which then, via natural selection, stabilized a very recent genomic transfer of the right metabolic capabilities. A peek at at the genome of D. ethenogenes supports this idea: the genome is full of what appear to be fairly recent modifications, including gene duplications and large inserted elements (IEs). Some of the IEs contain chlorine-reducing genes, including the one which confers the ability of this microbe to remove the final chlorine from pollutants. All these genomic changes may have damaged other capabilities of the ancestral microbe, and present-day D. ethenogens survives in the wild via symbiosis with other microbes. It's probably successful mainly because there's very little competition for this niche. An interesting question, given how fast this microbe arose, is whether a second, independent microbe is out there exploiting the same niche elsewhere.
I think these observations can be very good news for the prospect of cleaning up chlorinated compounds from the environment. The genome of this microbe was essentially cobbled together on the quick by natural selection. This gives hope that scientists could do the same artificially, creating new microbes to clean up sites where D. ethenogenes has trouble growing, or even to help detoxify other classes of chlorinated compounds. The Institute for Genomic Research, the main authors of this work, have also looked at other bugs which which can tackle other kinds of pollutants.
The second notion which struck me upon reading this article is that there seems to be literally nowhere on Earth where there is liquid water and not life. E.O. Wilson tackled this idea in some detail in The Future of Life . For me, this suggests that life on Mars, which would require a combination of capabilities not found in Earth microbes , is still a distinct possibility. Microbes continue to be discovered on earth in "improbable" settings. As a recent example, the same issue of Science has a second article discussing sea-floor microbes which grow in the presence of incredibly high levels of magnesium. Michael Faraday's remark that "nothing is too wonderful to be true" seems tailor made for the microbial world.
Monday, January 10, 2005
The Whale and The Antibody addresses one such challenge to the idea of natural selection, namely, where are all the missing links? If apes and humans share common descent, why aren't there apemanzees (or hurillas?) This problem becomes acute when you consider animals like whales, who, when first investigated, seemed literally related to nothing else on earth. On the face of it, it would be easier to explain such a phenomenon using instantaneous creation, or at a minimum, a blind watchmaker. Carl had a whole book showing that, in fact, the fossil record is full of transitional forms between the bearlike ur-ancestors of the whale lineage, and increasingly aquatic and successful intermediates.
Carl uses this analogy to tackle a similar paradox occuring on a different level of life. The immune system of gnathosomes (fish, mammals, etc.)involves a very complicated set of cells, organs, and signals, which do not occur at all in lampreys. This seems to be a case of de novo creation of a new capability within a set of species. Recent work, however, makes clear that each of the components of the gnathosome immune system do in fact exist in lampreys-- just not in assembled, coordinate form. So not only for species, but also for capabilities, natural selection seems to be the absolute rule by which life rolls on.
I've seen this type of anecdote most thoroughly examined in Daniel Dennett's book Darwin's Dangerous Idea . Possibly no scientific notion has been as rigorously tested, by so skeptical a cohort of opponents, as Darwin and natural selection. It's just hard to believe that Darwin's simple rule can explain all the vast complexity of life! But time after time, tests of these principles, when designed to be falsifiable, confirm Darwin's ideas, past even his relatively modest assertions.
There's lots more like this on Carl's site!
Saturday, January 08, 2005
How big my daughter looked!-- freckled, with sloping daughter's shoulders, standing at the height of health beside the shrunken stoic shape from whom she was descended, And for me (the father) it was as if, in one of those swift thrilling crossovers the good jitterbuggers could do, they had switched positions from the distant moment when my toddling infant daughter had fallen against a hot wooden stove in Vermont and her grandmother, so calm the cigarette never left her mouth, applied ice and butter and soothing words to the scorched arm that must have felt, to the astonished, shrieking child, seized by Death itself
Updike perfectly captures the mysterious, capsizing power children have over one's assumptions. Kids keep growing up, faster than you'd like. They race through their stages before you can mentally adjust to their last achievement. It keeps you breathless. Sad, happy and in awe. And like a photographic negative of Shakespeare's "Sweets and Beauties" sonnet, a droplet of death is right in there with that torrent of life.
I got some very good news in December, then good news again, and yet a third piece of good news this week. We are certain about heading home now; we still need to figure out a lot, but it's done. And I feel that same strange admixture of emotions, normally provoked by my kids, but now just coming with glimpses of our life in Munich. Only this time I'm the one whose changes are upending the established order. My consciousness is repeatedly astonished to remember that these are the days, the final days before... other days.
--Winter blue skies and bike trails. Grumpy, aged dayhikers, miles from anywhere and nevertheless in a rush.
--A German yogurt, blueberry, the most intense 35 cents I'll ever spend.
--The continual three-way fluster of cashier and customers, as each paid-out customer gets bombarded with the next guy's stuff, time after time.
--Tegernseer beer, pure Bavarian Helles, from a lake that will break your heart, and a sledding slope that will break
--The mystifying and immediate feeling when you cross between France and Germany. Even the air is different. How do they do that?
Happy new year, everyone.
Thursday, January 06, 2005
I am so proud of the outpouring of help, from all over the world, to help those in the affected regions. I have seen a little bit of score-keeping among blogs about what nation gives which help. Let's just get it done. As the Times illustrates, time is of the essence.
People should read these stories and think ahead to the spread of antibiotic-resistant bacteria, which already cause problems in hospitals and among people with weakened immune systems. In the bad old days-- and possibly in the future-- any kind of break in the skin, if contaminated, could become life-threatening. Just off the top of my head, I think it was Grover Cleveland's son who ended up dying because of a tennis blister.
Wednesday, January 05, 2005
But I think Wardrobe Malfunction still has some zip!! Sorry, couldn't resist a pun.