Tuesday, May 31, 2005

How do I love thee, let me count the waves

Soul-less science uncovers the secret of love. Feh!
May 31, 2005


Instead of a Valentine, maybe you could send an EEG--You are sitting at a picnic table in the shade. You look up. There she is. You look at the blue eyes and womp! That's it. It's love. It's also, apparently brain waves. A bunch of scientists, who apparently have absolutely no soul or romance in them, have proven that love at first sight is a physiological phenomenon. You needed electronics to tell you that? The researchers reported in the Journal of Neurophysiology that brain scan images taken at that blissful, shattering moment when she —or he —arrives actually does weird things to the brain. No shit. In neurological profile it looks like hunger or thirst or the need for a good gin and tonic. As time goes (you must remember this), it settles deeper into the brain, finally arriving in the deepest part of the primitive brain. Or, as the researchers so poetically put it: "Early stage romantic love can induce euphoria, is a cross-cultural phenomenon, and is possibly a developed form of a mammalian drive to pursue preferred mates." I love it when you talk like that. This, the scientists claim, is much different from just good old fashioned lust. How did they know? They looked at 2,500 brain images from 17 college students in the first throes of love. How you can tell a college student in love from one in lust, I have no idea. All seemed the same to me. Oh, and the place in the brain where valentines grow? The right caudate nucleus, which does have a certain ring to it, doesn't it. Like cabernet sauvignon, candles, chocolate, hot tubs, back rubs. Rub my caudate for me won't you dear. The right side please. Ooooh!


Bloody bureaucrats cop a plea, or, when you can’t even trust the Red Cross —After years of chucking and jiving, the Canadian Red Cross finally fessed up to the fact that it let tainted blood get into the blood supply and that people died. In part of a plea bargain that kept them out of criminal court, the Red Cross publicly apologized (on tape, by the way), agreed to a whopping $5,000 fine and to the funding of two endowments for $1.5 million (Canadian). Tens of thousands of people were infected with blood containing hepatitis C, and more than 3,000 people died in what is considered the greatest public health disaster in Canadian history. In January, 1983, the American Red Cross issued a statement to blood donor clinics pointing out specific questions to be asked of donors to help screen out what would later become known as AIDS. This statement was adopted by the Canadian Red Cross but they did not enforce it. Also, in early 1985, HIV testing kits were approved in several countries but again, the Canadian Red Cross did nothing. The delay allowed tainted blood into the system. The organization denied responsibility for years. They are, fortunately, no longer in charge of the blood supply there. You can read their statement here.

Monday, May 30, 2005

Electronics with the blues and other footsteps in the march of science—05.31.05

Annoying blue lights, annoying politicians, annoying fish. Be annoyed.
May 30, 2005
When your appliances get the blues--Few things in the modern world are as ubiquitous as light emitting diodes. My desk looks like a Christmas tree at night when all the other lights are turned off--LEDs on the DSL modem (3), on the Airport base station, the printer, the telephone. They are mostly green, but orange and red are not uncommon in this age of twinkling things. But until very recently, you never saw blue. Now you do, and lots of people don’t like it. LEDs are junction transistors. When electrons move into a hole in the semiconductor, it emits a photon which glows on the surface of the semiconductor. The color of the LED depends on the chemistry of the material, and until recently, the right compound to produce blue was problematic. In 1994, Nichia Chemical in Japan figured out that the right stuff to use was gallium nitride, and suddenly they are in everything, from computers to toaster ovens. One problem, apparently, is that they are much brighter than the normal LED and people find them very distracting. According to Wired, complaints are popping up all over the web in a minor consumer revolt, and manufacturers may have to rethink the old adage, just because you can do something doesn’t mean you should do it.


I don’t much care what you want; I’m running for President—Massachusetts’ odd governor George Romney (odd because he is governor of Massachusetts, not, say Utah) did what he said he would do, he vetoed the bill permitting embryonic stem cell research. He does, unlike the current president, accept the use of left-over embryos from fertility clinics, but wants to ban cloning because it involves the destruction of embryos. "It is wrong to allow science to take an assembly-line approach to the production of human embryos, the creation of which will be rooted in experimentation and destruction," Romney wrote in a letter to lawmakers explaining the veto. It is a gesture as opposed to governance because both houses of the legislature have enough votes to override the veto and surely will do so, and he knows it. But he has been mentioned as a presidential candidate in 2008 and he is playing to the right wing. [And yes, the illustration is an in joke. AMC Gremlin, get it?]

Wait a minute, didn’t I have some Jews behind me?—One of more interesting political alliances of the time is that between observant (mostly Orthodox) Jews, President Bush and the evangelical wing of the Republican party on many social issues. Since Jews are supposed to be all liberals, that intrigues people, but the right wing of the American Jewish population is socially conservative. On the issue of stem cells, however, they are taking a walk. The Union of Orthodox Jewish Congregations of America, the umbrella group for the most conservative (that is a small c), which sides with the Christian right on Terry Schiavo, same sex marriages and federal support for religious activities, has broken ranks, applauding the U.S. House of Representative bill that Bush threatens to veto. The "potential to save and heal human lives is an integral part of valuing human life," it said. "Moreover, the traditional Jewish perspective does not accord an embryo outside of the womb the full status of humanhood and its attendant protections." Liberal Jewish groups, the vast majority in the U.S., agree completely, and that unanimity is rare. Stem cells are a unique issue.


Just when you thought it was safe to go into the water: snake heads—They are ugly. They are totally alien. We can’t get rid of them. No, I don’t mean Republicans, I mean snakehead fish. They even have an ugly name. They popped up last year in the Potomac River, the waterway that separates Maryland from Virginia and runs through the capitol. They are by no means the only aliens in the river (would you believe feral gold fish?), but they do represent a threat, and unfortunately, they are still among us. More than a dozen have already been caught this spring. Of all the alien species in the river, they are the greatest environmental threat. They reproduce like mad and have very healthy appetites, particularly for baby fish of other species, which endangers the fishing industry. Particularly threatened are a species of bass called rockfish when they make it to Chesapeake Bay, a local culinary glory. Snakeheads were imported as food and as an aquarium fish and first showed up in a tributary in 2002. Poison hasn’t worked. Scientists are now trying fish tasers. I don’t suppose speaking harshly to them will help. Maybe if we sent some Congressmen swimming...

Thursday, May 26, 2005

Wingnuts,Sponge Bob and a flying penguin

The March of Science and Medical News investigates the dark side
May 26, 2005


Flying lessons from a penguin--A supporter of the stem cell research bill in the U.S. Senate says there are enough votes to override a presidential veto. Unfortunately, that is probably not true in the House of Representatives. Sen. Arlen Spector (R-Pennsylvania) , now, incidentally, being treated for Hodgkin’s disease, said he did not enjoy being threatened with a veto by the President, so thought it appropriate to shoot back. The bill is supported by almost 60 percent of the American public. Rep. Tom DeLay (R-Texas) said the bill would never become law. DeLay thinks that the procedure of using embryonic cells for research is immoral. Of course, getting advice from DeLay on morality is like getting flying lessons from a penguin. The President restated his objections as well. A move by a key House Republican, David Dreier (R-California) to find a compromise also was shot down by Bush. Meanwhile, a significant number of Republicans are bolting the President’s position.


Nevermind--In a contentious session, the largest union of university teachers in Britain ended its boycott of two Israeli universities, repealing a decision made last month. The 40,000 member Association of University Teachers had voted to boycott both Haifa University and Bar-Ilan because the first had allegedly penalized a professor who disagreed with government policy (never happened) and the latter because it has an affiliation with an Israeli university on the West Bank (happened). The show of hands was decisively for lifting the boycott. Opponents claimed the boycott was counterproductive and a violation of academic freedom. Supporters of the boycott said they would try again.

I’m not making this up—It has nothing to do with science or medicine, but attention must be paid. The wingnuts who have decided to determine the cultural standards of the U.S., have taken after Kraft food company because Kraft was a sponsor of the 2006 Gay Games in Chicago. They also put Sponge Bob Square Pants on their macaroni and cheese boxes and you know what a puss he is. Kraft, in a letter to its employees, told them to fuck off. It’s actually a splendid piece of writing—from a lawyer, yet. You don’t get to see that kind of guts very often.

Wednesday, May 25, 2005

A flower of note, a heroic spacecraft and those crafty Canadians

A flower we haven't killed off meets a spacecraft that can't be killed off, and the March of Science and Medical News goes upbeat.
May 25, 2005
And you thought we’d killed off the little darlings--Since we humanoids persist in killing off species, it is always a pleasure to announce one we missed. Last month it was the ivory-billed woodpecker. Now it is the Mt. Diablo buckwheat, a flower everyone was sure was killed off by the developers in Northern California. No one had seen one in 60 years. Known to its friends as Eriogonom truncatum, it was found in a remote section of a Contra Costa County Park east of San Francisco. It looks like baby’s breath. A Berkeley graduate student who is doing a dissertation on integrative biology, Michael Park, found it. One assumes he’ll get the degree.

To boldly go, split infinitives and all—These are the voyages of the starship, well, Voyager, to boldly go where no spacecraft has gone before. The little Voyager 1 spacecraft, which has survived solar wind, more than a half dozen planetary orbits, the asteroid belt and a really bad StarTrek movie, is leaving the solar system after safely transiting the termination shock, the edge. It is now entering the heliosheath, and is heading into interstellar space. The shock comes when the solar winds bump up against gas from deep space. It, and its twin, Voyager 2, have been on their way for 26 years, traveling some 8.7 billion miles and still capable of chirping back data. It was launched to go to Saturn and Jupiter and kept going. Voyager 2 went to Uranus and Neptune. They can keep transmitting to 2020. [I am now thinking of ending a sentence with a preposition and really going over the top. It’s a good thing to end this story with.] WP


If it wasn't so damned cold up there—Health Canada has done something no other country has done, boldly going—ooops. They have published a database of drug reactions. It took a series of stories on the CBC to get them to move but it is there, and you can get it here. In the U.S., the FDA has produced such a list but only on CD-ROM and for a fee. The Canadian list is on the web, free. It will be updated four times a year.

Tuesday, May 24, 2005

House defies Bush and expands stem cell research


The House of Representatives voted to expand federal funding for stem cell research to include cell lines from human embryos under certain conditions. The vote, 238-194, came despite threats by President Bush to veto the bill. Polls indicate it has broad popular support. That support extends to the Senate, including on the subcommittee controlling federal medical research funding. It is likely to pass. Fifty House Republicans bolted the party and joined all but 14 of the Democrats and the lone independent. NYT LAT

And we know where your children go to school

In this brave new electronic world, a new form of extortion has evolved: pay up or we’ll crash your site.
May 24, 2005

Denial of Service!

Let’s say you are running a lucrative web site, popping along raking in the dough when you get an email message. Either you pay $40,000 or we’ll block traffic to your site, the message says. What do you do? In most cases, the answer to this new kind of extortion is to pay the money and move on. This, of course, means that the extortionists will go on to someone else and do the same thing, or they’ll come back to get you again.

A man named Mickey Richardson, who runs one of the off-shore gaming sites, BetCris.com, that operate out of Costa Rica to avoid U.S. gambling laws, got such a message at the end of 2003. “Your site is under attack…. You can send us $40k, by Western Union and your site will be protected not just this weekend but for the next 12 months. If you chose not to pay…you will be under attack each weekend for the next 20 weeks, or until you close your doors.”

And sure enough, his site immediately crashed.

In a chilling story worthy of a novel, a website called CSOonline, which caters to computer network security people, reports what happened next. Click on the headline to read it.

The message come just as BetCris was entering its most profitable time of year with football, basketball and the holidays coming up. If the site came down, the losses would amount to $1.16 per second, $100,000 a day. The method of attack was denial of service attack (DoS) in which hackers flood the site with legitimate messages the servers have to deal with, causing a traffic jam that clogs everything to a halt. Think of the entrances to Fenway Park if 200,000 people tried to get in at one time.

Now having a gambling site in Costa Rica go down is not a major concern to most of us unless we work there or gamble. But as Scott Berinato, who wrote the piece points out, internet extortion is now moving on to more respectable sites, including payment services. It is becoming a major white-collar crime the Mafia never thought of.

In this case, and possibly in many of the others, the extortionists were in Eastern Europe, probably Russia, where the laws are rather flabby.

What did Richardson do? After considerable soul-searching, he hired a 23-year-old computer security whiz and former philosophy major named Barrett Lyon in Sacramento. Lyon once mapped the entire Internet in one day on a bet. Lyon had a plan. The company stalled while he set up a channel with the help of a kindly ISP in Arizona to divert the traffic sent to BetCris, scrub out the hackers’ flood, and then send the legitimate traffic on to Costa Rica. He was acting as a filter. It wasn't easy. Every time Lyon got enough bandwidth to handle the hacking, the hackers increased the deluge. It was like being at the receiving end of a fire hose. A war of attrition erupted that at one point not only threatened to knock BetCris out of business but kill the ISP’s business as well. The hackers used zombies, computers they had already hacked—yours and mine, for instance [well, yours if you use Windows]—to generate the traffic, and at one point were blasting 3 gigs of data at BetCris, hoping to flood Lyon's diversion. They attacked everything from mail to routers to servers. Fix one problem and there would be an explosion someplace else.

What happened? Lyon and Richardson eventually won by overpowering the DoS attack and the hackers moved on to easier marks. In the end, it cost Richardson far more than it would have had he just paid the extortionists. But that's only half the story. Lyon was able to track down the extortionists with the help of Scotland Yard. They are in jail in Russia. He is now in the business of replicating his techniques for others under attack by extortionists and has multiple customers and his own servers and a company called Prolexic Technologies. The war continues.

Great story.

[And thanks, again, to Jonathan Beard, who apparently reads these obscure magazines for fun.]

Meanwhile, CNET reports another embezzlement scheme. Hackers visit your website and if it contains code that takes advantage of a flaw in Microsoft's Internet Explorer [nobody, repeat nobody should be using IE at this stage], it blasts onto your PC [Trojan.Pgcoder] and encrypts your files. A message pops up offering to give you the password to decrypt your files. It is like breaking into your house, changing the combination on the safe and holding the contents for ransom. Naturally, it takes advantage of Microsoft files in Office.

Monday, May 23, 2005

Stem cell research draws money, recruits and lawyers

While California lures scientists with its stem cell research money the process out comes to a halt. May 23, 2005

When voters in California passed a ballot measure authorizing state funding for a stem cell research center in Proposition 71, they were doing two things: one, bypassing the inflexible objections of the reactionary administration in Washington, and two, setting up a center that would draw researchers, private funding and business opportunities to the state. They have only partially succeeded, and there may be some bumpy air ahead even in California.

The lure of the Golden State is being felt up and down the east coast (the scientists haven’t seen the real estate prices yet), reports Nick Wade in the New York Times. The lure is stimulated by telephone calls from recruiters in California, who point out that the state will have $3 billion to spend. Several people may have noted that the experiment last week in South Korea, which seems to have efficiently cloned patient embryos, cost less than $300,000, so we’re talking serious play-around money here.

President Bush has repeatedly said he would veto any move by Congress to loosen the restrictions on federal funding, so if the research is going to get done, the states will have to do it.. The state and private money would have none of those limits and would be beyond his reach.

Other states have tried to get in on the act too, most notably Massachusetts (home of Harvard and M.I.T. et al), but its conservative governor is trying to put restrictions on the research that many feel would spoil the game.

According to Wade, the California recruiters are not having a hard time pulling scientists from the other coast. UCSF, has openings for six to eight biologists who, if they can afford it, get to live in San Francisco. John Gearhart, co-director of stem cell research at Baltimore’s Johns Hopkins, told Wade he was “scared to death” he would lose people to California.

Other states and private organizations are trying to get into the act as well. Three New York City institutions, Memorial Sloan-Kettering Cancer Center, Rockefeller University and the Weill Medical College of Cornell University, received a $50 million grant from the Starr Foundation over three years. The three will collaborate on their research and the grant would make the city another center for stem cell work.

Most of the foundation money comes from the A.I.G. financial company.

Other organizations also have chipped in research grants, including those centered around diseases some researchers think might eventually be ameliorated by stem cell therapies, such as the Juvenile Diabetes Research Foundation.

But back in California, things are at a standstill. The LA Times reports that six months after Prop 71, the efforts are mired in lawsuits and a move in the California legislature to put restrictions on the research that the proposal was aimed to avoid in the first place.
The California money is 10 times the amount available from the feds, without restrictions so far. It specifically funds somatic cell nuclear transfer, the therapeutic cloning that so upsets the President, especially if it comes from human embryos. Many California schools have also set aside funding to build the kitty.

But a state constitutional amendment is now pending in Sacramento that would give the legislature some say in how the money is used after all, which is forbidden by the proposition.
Opponents to the research also have filed lawsuits challenging the constitutionality of Prop 71, and there are all kinds of conflict-of-interest problems tying things up. The state can’t sell the bonds it needs to raise the money until the legal issues are resolved.

Thursday, May 19, 2005

Koreans clone their patients and all hell is going to break loose--UPDATING REGULARLY

The debate on stem cell research just blew up.
May 20, 2005

Cloned embryo

Now things are going to get interesting, and I am about to use a word I tell all science writing students never to use in a story, “breakthrough.” Fortunately, I can hide it in a quote.

Researchers in South Korea, reporting in Science Magazine, have just turned the debate over stem cell research on its head. They cloned stem cells from injured and sick patients, cells with the exact genetic makeup of the patients. See the word “cloned.” Or, in other words, they produced embryos that are exact genetic clones of the patients from which they extracted the cells. Cell lines usually have been taken from the detritus of fertilization clinics and from aborted fetuses, and we all know how controversial that is. This is a whole different thing. Last year, the group at the Seoul National University derived embryonic stem cells but the technique was very inefficient and generally useless, one cell line in 200 tries. Not all scientists believed them, truth be told. They now report a method that is ten times better, a cell line in fewer than 20 times, and in nine cases with women patients, got one every time they tried. That could mean patients needing stem cell transplants for things like Parkinson’s disease could use clones of themselves, greatly reducing the complexities of rejection and a rebellious immune system. No one has yet expressed any doubts to the veracity of their paper.

The patients ranged in age from 2-56, and interestingly, the younger they were, the easier it was to clone them. The Koreans--a veterinarian, Woo Suk Hwang, and gynecologist Shin Yong Moon--started with oocytes, the cells from which eggs are produced, and replaced their nuclei with nuclei from somatic, or skin cells from different patients. They used a chemical compound to stimulate growth. This was the same technique used to create Dolly, the cloned sheep in 1996. Having no apparent desire to clone a human the way the British cloned Dolly, they only allowed the cloned human embryo to develop for six days, long enough to produce stem cell lines, colonies of cells that will differentiate into all the cells in the body, the universal cell. But that was a cloned human embryo developing in that culture dish. (Technically, they are called blastocysts, hollow balls of cells that divide and develop into embryos.)

Well, you can imagine the fuss this is going to cause. Most researchers, who think stem cells have revolutionary (and so far, unproven) potential for curing diseases such as diabetes, Parkinson’s, and Alzheimer's, as well as spinal cord injuries, are hailing the discovery as “spectacular” and a “breakthrough” [there, I did it. Blame Gerald Schatten of the University of Pittsburgh, quoted in Science.] One cell line was derived from a six-year-old with type 1 diabetes. Another kid has congential hypogammaglobulonemia, a rare genetic mutant disease. It would be possible to see if a therapy can be developed from those cells to treat those disorders. More immediately, it gives scientists a splendid way of studying these disease in the lab.

The Bush administration rules prevent American researchers from using federal funds to create new cell lines and the ones they can use under the rules are too contaminated to be useful. Supporters of the researcher point out that this advance, which one would expect from an American lab, came from South Korea, which has no qualms about funding this work. The researchers had about $200,000 in mostly government money to work with. Some American labs spend that much money coffee in a year.

Folks who oppose the research, or at least object to obtaining the cells from human embryos produced for therapy, already are livid. In order to produce those cell lines, the blastocyst was destroyed and they consider that murder of a human life. What changes the argument, as one MIT professor said, was that the notion this was a clumsy, inefficient way of obtaining these cells, made it possible to talk around the argument. That may have been true on Wednesday, but it is not true today. Now everyone is faced with an astonishingly efficient procedure. The Koreans have made embryo cloning relatively easy, ready for a lab near you.

The Koreans made it clear they have no intention of cloning humans, letting the blastocysts develop further. Reproductive cloning is not our goal," said Woo, the lead researcher. "Reproductive cloning is unsafe and unethical, and so it shouldn't be done in any country." Virtually every scientist in the world agrees with that.

The issue is in front of Congress now, as most members of Congress, like most Americans, favor stem cell research, and there is a brawl about it in Massachusetts. California and several other states, frustrated by the obstruction of the Bush Administration for federal funding, are producing their own funding. Opposition in Congress comes from the right wing of the Republican Party, led by the ethically challenged majority leader, Tom DeLay.

Later Friday, President Bush said he will veto the bill now on its way to passage through Congress in the face of the new process. Every poll shows he is on the losing end of the debate.

The Korean--um, er, breakthrough--could be the tipping point. LAT NYT WP
[illustration swiped from LAT]

We're not in Kansas any more

But if you want a good replay of the Kansas evolution trial, may I suggest this. It was suggested by Panda's Thumb.

The Annals of Junk Science I

When the Redskins play the Cardinals do you get a tie?
May 19, 2005

Take two sports teams or athletes, evenly matched. Who will win? Statistically, the team wearing red. You didn't know that. Researchers in England published just such a finding in Nature, which many reporters found irresistible, but should not have. The two, sports psychologists, did a study during the 2004 Olympics in Athens, using athletes in four sports: boxing, tae kwon do, Greco-Roman wrestling and freestyle wrestling. They assigned half of the athletes red uniforms and half blue. Those wearing red won 55% of the time across all sports. In matches where they were evenly matched, the red uniform wearer beat the blue 60%. [One hopes they did not get a government grant for this]. It apparently works to their satisfaction in team sports as well. Looking at Euro 2004 soccer (football to some of you), teams that had two color uniforms did better when wearing the red suits than they did wearing the alternatives.

Being psychologists, they had an explanation, or at least a wild guess. Red is the color of anger, so maybe the color intimidated opponents. Maybe wearing red increases testosterone production. [I'm not making this up]. It works in the animal kingdom, they reported. When researchers put red color bands on the legs of male birds, the birds got laid more often than they did before the bands. Human military uniforms often have red in them. Maybe, then again, it's just cultural, with red being the color of emperors.

Well, OK, it works for Olympic sports and soccer. Let's do our own research. Baseball. Do teams wearing red do better than teams not wearing red? (Blue is the most common color in Major League uniforms, incidentally). Because of the enormous number of games teams played, I don't have the beginning of enough time to go through them all, so let's leave it to the World Series, the championship.

Wearing red would, on the face of it have nothing to do with success over the years, e.g. the New York Yankees, the best team in history, wears navy blue and white. The Los Angeles (nee Brooklyn) Dodgers wear Dodger Blue, while the Boston Red Sox won their first championship since the early part of the last century, and the Chicago Cubs (blue and red) haven't even done that.

Last year, those Red Sox played the even redder St. Louis Cardinals and the team wearing red won. In 2003, the Miami Marlins beat the Yankees and there was no red in sight. The year before, the black-and-orange San Francisco Giants lost to the Anaheim (nee Los Angeles) Angels, and the Angels indeed wore red and still lost. The year before that, the Arizona Diamond backs (no red) beat the Yankees, which means teams with red in their uniforms weren't helped very much; they all were eliminated. Then there was 2000, when the Yankees beat the red-less New York Mets (ditto), and before that the Braves (a little red) lost to the Yankees (ditto again), and the year before that the Yankees beat the un-red San Diego Padres.

In fact, you'd have to go back to 1990 to find another team in red winning the Series, fittingly enough, the Cincinnati Reds, over the green and white Oakland Athletics. There were the Cardinals again in 87, but they lost to Minnesota, which wears blue and yellow. In 85, the Cardinals lost to the Kansas City Royals (as in blue) and back in 83, the all-red Philadelphia Phillies lost to the Baltimore Orioles (black and orange). I could go on, but I don't have a government grant.

I did, for many years, subscribe to the theory that no sporting team wearing purple could be worth a damn, but now that I live in Baltimore and the NFL Ravens show up in that atrocious color, I keep my mouth shut.

Wednesday, May 18, 2005

Death in Vermont, death in the jungle, and a vitamin--05.18.05

War comes to the Green Mountains, chimpanzees get revenge, and a vitamin pill for prostate cancer.
May 18, 2005

Moonlight in Vermont, darkness in Baghdad--Guess which state has the highest death rate among soldiers and Marines sent to Iraq and Afghanistan. OK, we gave it away. Vermont. That beautiful, bucolic, and extremely blue Green State. According to a fascinating story in the Valley News, located White River Junction, written by Jodie Tillman, Vermont had a death rate of 5.6 per 1,000 troops, the highest in the country, three times higher than the national average, and four times higher than New Hampshire, across the river. Only the District of Columbia was higher. When measured against state population, it was the winner (or loser) again, 1.64 military deaths per 100,000 people, three times the national average. It was second in injuries, 5.91 per 100,000. Tillman brought in a statistician from nearby Dartmouth, Gregory Leibon to see if there was anything in the data to explain this except for sheer bad luck. Leibon’s conclusion was that there wasn’t a big enough sample to assume it was anything other than ill winds. Research at Berkeley indicates that small states often have higher death rates, but that doesn’t explain how New Hampshire fared. Other researchers have noted that rural states also tend to suffer a higher mortality rate--no one knows why. The story and the analysis are available on Chance, that wonderful statistical site at Dartmouth, full of null hypothesis, confidence levels, equations and all that good stuff. The newspaper did an unusually good job of keeping calm and scientific.

When you eat a chimpanzee, expect revenge--For those of you with not enough to worry about, try this: Researchers have found two new viruses from the same family as HIV in people in central Africa who hunt apes and chimpanzees. The viruses have jumped from the primates to the humans, which, while not unusual, is worrisome because of what the viruses are. The two are retroviruses, dubbed HTLV-3 and HTLV-4. Why would you hunt a chimp? To eat, of course, which may be one of the ways the viruses jumped. The fear, of course, is that once the viruses have made the jump, they may be transmitted to other people. The research was reported in the Proceedings of the National Academy of Sciences by researchers at the Johns Hopkins Bloomberg School of Public Health, led by Nathan Wolfe. Scientists think the original HIV virus used a similar route. HTLV-3 is similar to a simian virus; HTLV-4 is not like any virus identified so far. It is not known if these two viruses are harmful but the researchers said the people involved--who live in the Cameroon--need to be watched. Retroviruses are particularly problematic.

Drinking milk probably wouldn’t help, but keep on trucking--Researchers in Oregon have developed a potent form of good, old vitamin D that seems to extend the life of men dying of metastasized prostate cancer. These are men for whom surgery, radiation and hormone therapy have failed. The scientists at Oregon Health and Sciences University in Portland say that by adding the new form of the vitamin, called DN-101 to standard chemotherapy, they have been able to increase the average life expectancy to two years. Sixteen months was the best you get with the chemotherapy alone, so the pills are adding seven months. That is reputedly the highest survival ever seen in a randomized study. Not only that, some of the data is incomplete because half of the subjects are still alive. There appear to be no serious side effects. As we say in science--often--more work needs to be done, mostly a larger study.

Tuesday, May 17, 2005

Chutpah, the female orgasm, and say, what ever did happened to that drug? 05.17.05

The march of science and medicine marches on.

So how was it for you?--It’s pretty easy to figure out the evolutionary purpose of the male orgasm. That was fun and gee, let’s do it again, an attitude that--among other things--promotes reproduction and literature. For some reason, the female orgasm seems to scientists to be more difficult to explain. Some experts even deny there is such a thing, but whatever. A new book written by a biologist at Indiana University explores the arguments and the various theories why evolution should care if a woman achieves orgasm or not. As reported in the New York Times, Elisabeth A. Lloyd, has a unique theory. She takes on some of the current thinking, such as the orgasm is just a byproduct of the early parallel development of male and female embryos (i.e., the nerves for orgasm are built into the developing embryo to be implanted in the penis and they are still there when the embryo differentiates--just sort of lying around so you might want to put them to some use). That’s the same explanation for nipples on men; they are left-overs from the time before embryos differentiated and serve no useful purpose. But if scientists acknowledge the need for a male orgasm, why do they spend so much time trying to find an evolutionary need for the female variety? Lloyd thinks it’s either because the scientists are invested in believing that women’s sexuality must parallel that of men’s, or just the quiet inevitable feeling that all adaptations had to serve some evolutionary purpose. Nah, says the lady. There is no real reason for a female orgasm. They are just fun. She surmises this because they are not necessary. For one thing, males get to have them every time they want to reproduce (we’re lucky that way); females don’t. It depends. A woman can get pregnant without having one. Ever. In her life. So, women, have fun. Call if you would like help.


Say, whatever happened to that miracle drug?--A while back I mentioned a science writer, David Cleary, who infuriated people at an American Cancer Society meeting by reading back all the “breakthroughs” they had announce five years earlier and wondering whatever happened to those swell advances. Now Derek Lowe, an organic chemist (not the baseball player) who posts on the wonderful blogsite, corante.com, has done Cleary one better. He went back to a Business Week story of May 13, 1991, a cover piece on designer drugs, and asked whatever happened to them. Lowe’s answer: not much. A few are still around but haven’t proven themselves to be the wonders they were touted, and the rest disappeared. Business Week was only one of many places that covered this change in the way drugs were being developed, and almost all of them were just as breathless. The traditional way to find drugs was, everyone admits, logically inefficient. You simply ran through every compound you think could reasonably be expected to work (A to Z) and tried them out. The overwhelming majority didn’t so you moved on and kept going until one of them showed promise. The new rational drug design meant working in the other direction, bottom up, to deliberately and rationally design a drug around what you knew of the disorder. If nothing else, it was supposed to be cheaper. Science writers went to these drug houses and watched dynamite computer generated models showing how the system worked and then, Lowe writes, made the category mistake of forgetting that what they saw wasn’t real. Lowe says nothing has changed. The rational design approach still doesn’t work very well, and most drugs are still developed the old sloppy way. We don’t know enough, Lowe asserts.


I’m not making this up, Chapter III--Quote of the day, courtesy Good Morning Silicon Valley.
We could really speed up the whole process of drug improvement if we did not have all the rules on human experimentation. If companies were allowed to use clinical trials in Third World countries, paying a lot of poor people to take risks that you wouldn't take in a developed country, we could speed up technology quickly. But because of the Holocaust ...

-- -- Francis Fukuyama, a member of the President's Council on Bioethics and director of the Human Biotechnology Governance Project (normally we would add a snarky comment here, but our mouths are still agape).
Mine too.


: [from the Yiddish] def. gall, bordering on effrontery. Syn. Microsoft--This could also be “I’m not making this up, Chapter IV.” Microsoft has announced that it is readying a service that will automatically provide updated anti-virus, anti-spyware, and firewall protection to computers running Windows XP. The service will clean up your disk and back up files. Microsoft realizes that there is a vast industry out there providing anti-virus software to protect PCs and decided that it need a piece of the action, which in Microsoft’s case, means they want to control the business. As David Pogue points out, if Microsoft had designed Windows properly, you wouldn’t need that software and those businesses wouldn’t exist. So they are going to sell you software that you need only because they are incompetent. (Unix, Linux and Mac owners can ratchet up the smug one notch).

At least we can forget the refrigerator mom--There are almost as many theories about what causes autism as there are autistics and CDC researchers are adding to the list. A study of 698 Danish children with autism found a disproportionate number of preemies, children with low birth weights and breech births. In other words, difficult deliveries. The children also were more likely to have parents with mental disorders before the children were born. CDC admits this doesn’t prove causation but opens up questions that need to be explored. Perhaps researchers need to look more closely at what goes on during pregnancy. The findings about parents with schizophrenia-type psychosis isn’t new, but the study seems to reinforce that. In the days when people took Bruno Bettelheim seriously, autism was blamed on the mother, who, he asserted, caused the disorder by being indifferent to their children. Fortunately, no one takes him seriously any more.

Monday, May 16, 2005

Panda's Thumb has a question for science writers

Nick Matzke, who runs the blog Panda's Thumb, which has been the best source of coverage of the Kansas evolution trial, wants to know why the media doesn't take on the claims made by Intelligent Design advocates. He thinks the response has been puny. You can read his article here and don't ignore all the comments.

How the inflection point last week will change your life

The daring advances of three companies change the electronics paradigm.
May 16

It's entirely possible that the world of technology changed dramatically last week, and most people didn't notice. One who did was Robert I. Cringely, the technology columnist for pbs.org, who wrote on May 12 that we had just reached an inflection point. The term originated with Andy Grove of Intel who defined it (non-mathematically) as the transition to a new paradigm, like a tipping point to a sociologist.

["Robert I. Cringely" is a pseudonym for a man who has been writing anonymously about technology for more than a decade out of Silicon Valley. I don't know how many people actually know who he is. If I tell you his real name, of course, I'd have to kill you. What you need to know is that he knows his stuff.]

Cringely says this inflection point comes from three companies with a little help from a fourth. They are Microsoft, Google and Apple (with a push from Yahoo). There is some outside evidence I can offer that supports some of it, at least.

First: last week Bill Gates let slip a company secret. He gave some details about the new xBox game system. As everyone knows, Bill Gates doesn't let anything slip. It was deliberate, although we can only guess why he did it. What he said was that the new system would do a lot of things your home computer does now, including play music and movies, surf the web and probably even do Internet telephony--as well as play your basic computer game. What it will be is a limited-use PC, a Microsoft PC. It will be one of the few times Microsoft has gone into competition with its best customers. You can't do your home business on it, but all the peripheral functions we use PCs for will be possible on the xBox by Christmas. Gateway and Dell must be beside themselves.

Second is that remarkable company Google, founded in a dorm by two Stanford graduate students. For sheer technological bravado, they are unequaled and they are about to really do it this time. The new technology is Google Web Accelerator. You may download your very own beta here. Essentially, it lets you browse the web at twice the speed you can now without doing a thing to your computer or your IP connection. Indeed, as Cringely points out, Google is about to become your gateway to the Internet. The technology is something like what engineers to to speed up web browsing using satellite communications: the system anticipates your next page and sends it down compressed before you even ask for it. "This is an absolutely brilliant strategy," Cringely writes, "brilliant both because of the staggering technology effort it represents and brilliant because it promises--as does any inflection point--to change things forever." Only Google he says--and I agree--has the balls to try it.

Even if you are browsing the web on AOL, you will be going through Google to get there. Eventually, you will notice you don't need AOL, or Earthlink, or MSN any more. Perhaps the next step is for Google to sell the machine to get you onto the web. You won't need Microsoft, or Intel, or Dell or HP then either. Maybe they sell you ads. Maybe you get other services that Google will be happy to supply you for a price. They don't even have to charge for the accelerator service. They can afford to give it away.

Third: the world of music and video. Cringely and others points out that Yahoo's new subscription music service (you pay a subscription price to download a certain number of songs whenever you wish) is likely to kill off Napster and Rhapsody and may start undercutting Apple's non-subscription iTunes, which now controls 70% of the market. Yahoo says it will charge $6.99 a month (probably its cost); the other two subscription services are charging $14.99. They are probably toast.

Apple, however, can flip a switch and add a subscription service by Friday. Apple rumor sites are reporting that they are already hiring the engineers to do it, and if the pressure from Yahoo gets too great, they just alter their business plan.

Meanwhile, however, Apple has its own paradigm shift working. They are about to do for movies what they do for music. Buried in the code in Tiger, the new operating system, are supposed to be icons and subroutines that make no sense in the OS-X operating system at the moment but are clearly designed for the day soon when Apple sells you downloaded movies to play on your computer or television set. [Mac OS-X is a shell over Unix. If you can grope your way through Unix you can, I'm told, find them easily]. See an example for yourself in the new iTunes [4.8] that was posted last week. It adds a video button on the bottom left ["show video full screen"] and the iTunes store is already offering music videos. Next comes full-blown movies. Cringely says they even know the specifications for HD display.

The key is the AirPort Express wireless base stations--those cute little white rectangular doohickies with the green light that you use to network your home computers to each other and your stereo. I'm uploading this story on one now. They apparently will come with built-in video capabilities. That's the reason there is no video outlet on the new Mac minis. The AirPort Express WiFi repeater will do all the work. The computer just stores the data.

"So Apple takes over video and movies while Yahoo threatens with a low-priced music subscription service and Google threatens to take control of, well, everything," he writes. "And Microsoft? Microsoft kicks the dog." [I have no idea what that means.]

Go read Cringely to see all the details. And about that Dell stock....

Friday, May 13, 2005

Now they'll pay attention--Sammy has the resistant bug--CORRECTED

Baseball legend Sammy Sosa is out for a month with MRSA.

May 13, 2005


We noted on April 12 [Maybe now that the NFL is involved people will notice] that methicillin-resistant Staphylococcus aureus (MRSA) was popping up in the dressing rooms of sports teams, and while the Canadian media were covering it extensively, the U.S. media still hadn't noticed. Despite the smart-assed headline, that is still true, but maybe now it will change. The Baltimore Orioles’ Hall-of-Famer, Sammy Sosa has it, he has been placed on the disabled list and will be out for a month. Sosa, who is the seventh most prolific home run hitter in the history of baseball, complained of a sore foot and had an abscess lanced and drained twice. It didn’t get better and the doctors reported it was infected with MRSA. Since it has not spread beyond the abscess, he probably won’t suffer a hole in his foot or have nerve damage or chronic pain, which can sometimes happen. (Several deaths have been reported but is not likely for someone with the kind of medical care Sosa is getting). Whatever antibiotics they are using, seems to be working. There also is no sign anyone else in the Orioles locker room has it, so they don’t have to disinfect the place. Technically, he can play next weekend against the Phillies, but doctors said that was very unlikely. Sosa, traded to Baltimore from the Chicago Cubs, is in the twilight of his career, but the O’s, uncharacteristically, are in first place, a game over the world champion Boston Red Sox in the American League East, and he is needed. Sosa is batting .269 (for foreign readers and the baseball illiterate, that means he gets a hit--a good thing--27% of the time he comes to bat). His lifetime average is .277. Doing that 30% of the time you are at bat makes you a star. But he has only hit four home runs this year, and the two times I’ve seen him play, he was more valuable as a fielder, which is atypical. Maybe his foot hurt. Sosa also missed a chance to return to Chicago in triumph as an Oriole, which would have been a major event. The Orioles play the White Sox this weekend, but Sosa is here in Baltimore.

Thursday, May 12, 2005

The march of science, the march of ignorance--who knew? 5.12.05


This is what I get for letting you stick your finger up there?--Back in the item "Blogs and Whales and Idiots, Oh My" [click to the right] I touched the issue of prostate cancer and what a man should do if he has it. The dilemma is viciously simple. If it is the low-grade kind, do you have the surgery, or do you just watch it and wait to see what happens on the theory that you are most likely to die of something else before that cancer kills you? You will be reminded that often low-grade prostate cancer can explode into something far direr—or you may die of heart disease 20 years from now taking the cancer with you. No one had enough data to really say anything definitive. Now they do. A 10-year and apparently well-constructed study out of Sweden published in the New England Journal of Medicine says forthrightly that if you are under the age of 65, having the surgery can save your life. If you are older than that, we still don’t know. The only weakness in the study is the number of subjects, 695. Unfortunately, AP got it only partially right in its widely distributed story, exaggerating the death rate improvement. The research found that the surgery—radical prostatectomy—does indeed reduce the death rate from the cancer (and, oddly, everything else) but it is a small demonstrable reduction. The real news is that the surgery definitely makes a difference in reducing the spread and growth of the tumor, which in the end saves lives. It may just take longer than 10 years to prove the saving. Or, in the words of the researchers: "Radical prostatectomy reduces disease-specific mortality, overall mortality and the risks of metastasis and local progression. The absolute reduction in the risk of death after 10 years is small, but the reductions in the risks of metastasis and local tumor progression are substantial." That makes the decision easier for relatively young men and doesn’t help us old farts a bit.


The taxonomists’ revenge: Cute and new and broiled for dinner—It’s always fun when biologists find a new species and even more fun when they discover a new family. Just think, we haven’t eradicated it yet. Meet the kha-nyou, trust me, you’ve never met before. According to John Noble Wilford in the New York Times, the cute little fella is found in the forests and limestone outcrops in Laos. It is not a rat or a squirrel and does have some resemblance to a chinchilla or guinea pig, but it is of its own family entirely. The announcement came from the Wildlife Conservation Society and is to be published in a scintillating journal called Systematics and Biodiversity [which, if it has a webpage, Google can’t find it]. Wilford writes that the last time a new family was discovered might have been 30 years ago. And where did they find this little beastie? In a market. The locals serve it for dinner.


Don't forget his father ran American Motors--Mitt Romney, the governor of Massachusetts, is something of the odd-man out. He is a Republican in a heavily Democratic state. He is a Mormon in a state that is predominantly Roman Catholic. He is a conservative in the bluest of all blue states. Back in February, we reported that his opposition to stem cell research was a major issue in Massachusetts [see "State vs. State, State vs. Church, State vs. Scientists"]. The issue is back again. Romney has now proposed more limits on the research, asking the legislature to amend a bill permitting the research far more restrictive. He has said he will veto it if he does not get his way. He wants to change the definition of when life begins and exclude the kind of research he opposes. Specifically, he wants to ban the creation of embryos for research, an idea the legislature has already rejected. He admits he won’t get much more traction this time, but he has added proposed amendments that still put limits on the research. The legislature has defined the beginning of life as when an embryo is implanted in the uterus, which would permit creation of embryos in the test tube, just a ball of cells 14 days old or less, which is exactly what Harvard intends to produce. Romney wants the definition changed to the moment of fertilization. Interestingly, the Catholic Church agrees with that position but most people, including Catholics, don't, and support the research. The scientific community in the state, one of the world's biggest and best, opposes his moves as well and they have substantial clout. Supporters of the research have enough votes to override his veto. And the business community is watching while California and other states move ahead in what could be a most lucrative field. Why is he still pushing? Two reasons: one, he undoubtedly sincerely believes all this; and two, he is probably going to run for President in 2008. Well, they can’t call him a "Massachusetts liberal."


Hey, they just asked God’s scientific opinion—Anyone puzzled by the refusal of the Food and Drug Administration to approve Plan B, the emergency contraceptive, might have an answer. [See "If Plan A fails and they won't let you have Plan B..." below] According to the Washington Post, “an outspoken evangelical conservative doctor on the panel” reported in a videotaped sermon, he was asked by the FDA commissioner to comment on the 23-4 decision by the scientific panel to permit sale of the pills. Dr. W. David Hager was asked to write a minority report on why they should not be sold. He did and they aren’t. He said he didn’t write the report from an evangelical perspective, mind you, but a scientific one. He said the panel had too little information on the effects on girls under the age of 16, a position few others hold. "I argued from a scientific perspective, and God took that information, and He used it through his minority report to influence the decision. Once again, what Satan meant for evil, God turned into good." Satan, however, seems to be winning elsewhere. The pills are available all over the world to prevent unwanted pregnancies and to reduce abortions. Don't ask me to explain. I'm apparently not plugged in to the right channels.

There is more to the good Dr. Hager. See Wonkette (the funny and totally salacious blog--this time, however, written by a substitute since she's off writing a novel or something).

Those people just don’t know their place—The British have a long history of silent social anti-Semitism. They actually don’t kill anyone—or at least haven’t for several hundred years—but the prejudice is under the surface and never quite goes away. On April 22, the British Association of University Teachers (AUT) voted to boycott two Israeli universities, the University of Haifa and Bar-Ilan. They claimed that Haifa disciplined a professor who disagreed with government policies on the occupation of Gaza and the West Bank (untrue) and that Bar-Ilan had an affiliation with a small college in a West Bank settlement (true). This isn’t unique. One British researcher fired two Israeli scientists from a journal she published a while back. I am not one to accuse people who oppose or criticize Israel of being anti-Semitic since I do it myself regularly. I also oppose the settlements and the occupation. But this is much too stupid to be anything else. It comes as Israel is pulling out of Gaza at great expense in resources and with the threat of internal disruption—perhaps even the risk of civil war—and while a truce with the Palestinian authority has ended the intifada. Picking on Haifa University is particularly weird. The city of Haifa is the most integrated city in Israel, and the university’s student body is about a quarter Arab. As to the college in the West Bank, I have two words “so bloody what!” Fortunately, the Israelis are fighting back in the p.r. war, and there has been enough outrage in the British press and academe to force the AUT to revisit its decision in two weeks time. On Friday, the Jerusalem Post reported that three British Universities--Sussex, Warwick and--drum roll--Oxford, told the AUT to shove it.

Wednesday, May 11, 2005

The bucktoothed Pharoah, Republican stem cells and something simply unspeakable--05.11.05

How'd you get so funky?--He had buckteeth, a face that was unusually elongated, pronounced lips and perhaps a receding chin. We don’t know about his complexion. But CT scans of the mummy of the 19-year-old King Tutankhamen show a lad who was not especially handsome. But, as they used to say in burlesque, it’s good to be king and presumably his love life was not affected. Using the CT scans, three teams of scientists and artists reconstructed what he probably looked like—and the mask that covered his mummified face, wasn’t too far off. Buckteeth appear to be a family trait. He had a small cleft in the roof of his mouth, but nothing that interfered with speech. He was about 5-6 and slim. He had great teeth except for an impacted wisdom tooth that must have hurt like hell. The researchers made 1,700 three-dimensional images, more detailed than ever before. Fortunately, the face was the best preserved. The teams—one each in France, Egypt and the U.S.—agreed on most of the details; the Egyptians gave him a stronger chin than did the other two. The French and Egyptians knew which mummy it was while the Americans did not, so the reconstruction would appear to have merit. What killed him? No clue. He had a hole in his skull but that was likely put there long after he died by someone trying to pry the mask off the face. He may have died of infection from a broken leg. The Egyptian antiquities ministry released the pictures, and as John Wilford points out in the New York Times, probably motivated by a tour of artifacts associated with Tut that just happens to open in June in Los Angeles and then goes to Ft. Lauderdale, Florida, Chicago and Philadelphia

I want three Anne Coulters and a Randall Terry to go--While conservatives love to call us liberals out of touch with America, evidence constantly emerges they got it backwards. Take stem cell research, something of a campaign issue last year. While whopping majorities of Republicans, approve of President Bush’s actions in general (90 percent, believe it or not), they part ways on a number of issues, including stem cell research. The Washington Post reported that a poll of Republicans for Republicans showed that 57 percent of those surveyed favor embryonic stem cell research while only 40 percent opposed it. Fifty-four percent said it was a medical issue, not an abortion issue. Embryonic stem cell research has been a controversial issue for several years. Supporters say it holds the potential to find treatment or even cures for a variety of diseases, including Alzheimer’s and Parkinson’s. But abortion opponents argue it involves the taking of a nascent human life. Even most Republicans, apparently, don’t agree. Delaware Republican Mike Castle, a supporter of the research, has introduced legislation allowing federal funding for the research on lines created after Aug. 9, 2001, when President Bush banned the creation of further lines, as long as they used the same ethical standards. Since Congresspersons read polls, attention may be paid.


I'll clone my heart in San Francisco--
While the Feds dithered, the good folks of California, of course, voted to spend state funds on stem cell research and this week the announcement came that the headquarters of California’s efforts would be San Francisco. With UC San Francisco (mostly a medical school and hospital) in town, Stanford and Silicon Valley down the road and Berkeley over the bridge, it seemed logical. The City By the Bay beat out San Diego (boring but at least near a UC campus and the Salk establishment) and Sacramento (boooring, and near almost nothing). Except for the housing prices, it is more likely to draw top-notch scientists to that area than say, the central valley. It’s also good news for the area, where the Dot.com boom decimated the workforce. Californians authorized $3 billion worth of state bonds to fund the research and the offices of the new center, the California Institute for Regenerative Medicine, already has a home just the UCSF mission Bay campus, and more importantly, the ball park.


A kiss is just a kiss, a sigh is just sigh--And finally, in the category of animal husbandry... And I’m not making this up. A blog called News Hounds (“We watch FOX so you don’t have to”), posted part of a conversation between Alan Colmes and Neal Horsley, an anti-abortion “extremist,” on Fox Radio. Colmes asked him to explain a statement that he once admitted to bestiality sex. The entry goes like this:
At first, Horsley laughed and said, "Just because it's printed in the media, people jump to believe it."
"Is it true?" Colmes asked.
"Hey, Alan, if you want to accuse me of having sex when I was a fool, I did everything that crossed my mind that looked like I..."
AC: "You had sex with animals?"
NH: "Absolutely. I was a fool. When you grow up on a farm in Georgia, your first girlfriend is a mule."
AC: "I'm not so sure that that is so."
NH: "You didn't grow up on a farm in Georgia, did you?"
AC: "Are you suggesting that everybody who grows up on a farm in Georgia has a mule as a girlfriend?"
NH: It has historically been the case. You people are so far removed from the reality... Welcome to domestic life on the farm..."
I didn't know that.

Tuesday, May 10, 2005

The patron saint of nerds, confidential sources and forget the statistics--UPDATED 5.12.05

It was not a swell week for writing about science and scientists
May 10, 2005

Well, if you write 200 stories a year you have to take some shortcuts--The most scandal in journalism, as we reported earlier, had to do with the freelance work of Michelle Delio, a prolific and presumably profitable writer in New York and her work for Technology Review, the magazine associated with M.I.T. One website bills her as the "patron saint of nerds." Tech Review retracted two of her stories when the editors could not confirm her sources. Now Wired News, which has published 700 (!) of her stories under the name Michelle Delio and (presumably, her maiden name--or is it the reverse?) Michelle Finley since 2000, went back to look at their stories. They hired Adam Penenberg, the editor who uncovered the Andrew Glass scandal at New Republic, to do the review. Penenberg and his graduate students reviewed 160 articles, mostly from 2004. Penenberg told Wired News he could not fined sources in 24 of the stories, 40 people. Delio, who blames her trouble on sloppy organization, told Penenberg and Wired News that she stands by her reporting and points out that most of her sources were located by the students. (Isn’t that nice? Most). The sources affected content in varying degrees, Wired News said. In many cases, the quotes from the unconfirmed sources were not crucial to the stories, merely supported contentions contained elsewhere. In four of the stories, however, Penenberg said that they arguably played a more prominent role. The Penenberg report can be found here [PDF]. The web story included a list of the stories, reporting that it is not retracting any of them but is appending a note describing the problem and editing appropriately, which seems a reasonable approach. According to the AP, Wired News publishes stories from Wired Magazine but is an independent operation, separately owned. Penenberg is a Wired News columnist who teaches at NYU. Here's an interview. Ms. Delio, 37, is apparently going to be an unemployed freelance.

There appears to be an epidemic going on. The Sacramento Bee just fired a columnist for faking sources. [I must be doing something wrong. I've been a journalist for more than 35 years and it never occurred to me--with one exception. In the early days of my stint at the Philadelphia Inquirer, I was asked to do a man-in-the-street interview, which I hold to be the lowest form of journalism, a useless way to fill space and a diversion from real reporting. It's a sign of a bored or lazy editor. A columnist friend with a similar assignment (I don't remember the story that stimulated the idiotic request) suggested we do what he always does in a case like that: head over to the neighboring Press Bar and interview anyone we could find at the bar. Since most of the people at the bar were other Inquirer reporters, we took down the quotes and made up the names. I had a guilty conscience and never did it again, but any editor who asks for man-in-the-street interviews deserves what he gets. Never mind.]

There are lies, damned lies but I don't have time for statistics--But over at the Washington Post, the newspaper has begun (or at least, I never noticed it before) an irregular series on how the media handles or mishandles health stories. In this case, the stories being scrutinized were generated by a report in JAMA last year suggesting that aspirin might lower the chances of a woman getting breast cancer. The research was widely reported, including in the Post and all the television networks. Women who took aspirin regularly had a “20 percent lower risk” compared to nonusers, the stories said. (I'll bet that line came from a press release). The inability of the media--many science writers included (and most of all, their editors)--to deal with statistics in medical research is widely known, and this was no exception, although that the reporters were not totally at fault. The three authors of the Post stories, clinicians at the Department of Veterans Affairs, said the stories misled readers about the size and certainty of the benefits. Key questions weren’t asked, such as how big the benefit was and whether the benefits outweighed the side affects of taking aspirin. Most of all: Does taking aspirin really prevent breast cancer or is there something else at work, such as something about women who take the pills versus those who don’t? The Post points out that the JAMA article didn’t answer those questions either, a failure of the JAMA editors. Still, the statistics were mishandled.
The 20 percent reduction in risk certainly sounds impressive. But to really understand what this statistic means, you need to ask, "20 percent lower than what?" In other words, you need to know the chance of breast cancer for people who do not use aspirin. Unfortunately, this information did not appear in any of the media reports. While it might be tempting to fault journalists for sloppy, incomplete reporting, it is hard to blame them when the information was missing from the journal article itself.

In the study, Columbia University researchers asked approximately 3,000 women with and without breast cancer about their use of aspirin in the past. The typical woman in this study was between the ages of 55 and 64. According to the National Cancer Institute, about 20 out of 1,000 women in this age group will develop breast cancer in the next five years. Therefore, the "20 percent lower chance" would translate into a change in risk from 20 per 1,000 women to 16 per 1,000 -- or four fewer breast cancers per 1,000 women over five years.

For people who prefer to look at percentages, this translates as meaning that 2 percent develop breast cancer without aspirin, while 1.6 percent develop it with aspirin, for an absolute risk reduction of 0.4 percent over five years.

Another way to present these results would be to say that a woman's chance of being free from breast cancer over the next five years was 98.4 percent if she used aspirin and 98 percent if she did not. Seeing the actual risks leaves a very different impression than a statement like "aspirin lowers breast cancer risk by 20 percent."

In an ideal world, the reporters would have jumped on the phone and chased the answers to those questions, but this isn’t an ideal world and reporters always face the problem of confronting editors with the news that a story that is getting played all over the world is less than it appears. You don’t get points in the newsroom that way. The Post article is terrific. Bravo.

If only Robert Novak was a science writer (only kidding, only kidding!)--Meanwhile, the battle over protecting confidential sources, is spilling out all over Washington. Five reporters found in contempt for refusing to name their sources in the Wen Ho Lee affair, should not have to reveal those sources, their lawyers claimed in hearings at the U.S. Court of Appeals for the District of Columbia. It was up to Lee’s lawyer to work harder at finding them without the reporters’ help. Lee's lawyers blamed “officially authorized” leaks for the series of stories, most famously in the New York Times, that alleged that Lee, a scientist at Los Alamos, was guilty of espionage. It turns out he wasn’t, the case collapsed in great embarrassment for the government and insufficient embarrassment for the media that reported those leaks. Lee is suing. Lawyers for the journalists say Lee’s lawyers had an obligation to exhaust every other avenue to finding those sources before going after the reporters. His lawyers said they ran into a brick wall of obstruction by the FBI and the Justice Department, which were busy covering their collective asses, and the only thing left to do was to go after the reporters. One doesn’t know who to root for in this case.

Monday, May 09, 2005

There will be a slight adjustment in reality, folks

Just when you thought the constants in physics were constant....
May 9. 2005


Getting particle physics into a newspaper ain’t easy, but sometimes it can be done. The remarkable Keay Davidson of the San Francisco Chronicle managed it today with an intriguing story about how the laws of physics may change over time. Or, they may not. Davidson writes that one of the fundamental values in physics, the “fine structure constant,” (alpha) which measures how subatomic particles interact with light and each other, may change very so slightly over the life of the universe. It turns out that some observations of very old quasars (like 12 billion years), have different dark lines in their spectra than what you would get from laboratory instruments. That would imply a change that is not supposed to happen. What the physicists are actually fighting about, however, is a bit more arcane: whose measurements are more accurate. Measurements came from the Keck telescope in Hawaii and from a natural uranium deposit in Gabon. The doubters to the theory--perhaps most physicists--are unimpressed by the measurements of the proponents which are detecting the changes. And even the proponents are a bit shy about making major assertions because of the implications. Laws of nature aren’t supposed to change. Does it matter? Well, actually, probably. One never knows. The fun part of theoretical physics is that one can’t predict what a discovery or theory will lead to. Think Einstein and television. If nothing else, it’s nice to shake up one’s view of reality. It’s also good to see serious science in a newspaper. It probably means no runaway bride, no more vitamins curing cancer in mice, or Paris Hilton was taking a day off. Oh, and remember how in "A Hitchhiker's Guide to the Galaxy" it was revealed that the meaning of life was 42. Wrong. It's 1/137.

Sunday, May 08, 2005

The wonderful thing about Tigers; is Tigers are wonderful things--UPDATED 5.17.05

Apple's new operating system works without being bouncy, trouncy, flouncy, or pouncy
May 8, 2005

In an item below, I reported on Apple’s release of its newest operating system, OS-X 4.0, code-named Tiger. It arrived and is installed in two of the four computers in our house, including the one I’m writing this on. (It hasn’t made it to the other two Macs because Apple, in its infinite wisdom, sent it out on DVDs, and those two computer can’t read DVDs. I have to get CDs from Apple. Jeez!). I thought, for those interested, a quick review of how it works, and if you are a Mac user, whether you should spend the bucks to upgrade. The short answer to the last question is: yes.

(I promise not to get too carried away with this stuff; this isn’t a Mac fan site. The fact remains, a disproportionate number of writers and creative people use Macs--much higher than the general population--so this shouldn’t be a complete waste.)

Like all new operating system releases from Apple, this one isn’t perfect, and the Apple rumor websites--the guys Apple is busy suing--report that the first upgrade is due in a couple of weeks. (UPDATE: They did, on May 16.) So far, however, it works just fine for most people and I’ve had no trouble. The worst bugs are in corporate networking, which doesn’t matter to most Mac users and is the kind of thing IT people expect anyhow. Apple should have that fixed shortly. Other problems seem to center around third-party software, also normal. That will go away when those third parties upgrade their programs for Tiger. For a list, see Macintouch here. One of those incompatibilities appears to be Entourage, which Microsoft said was upgraded for Tiger. Remember that one or or two reports doesn't a real problem make.

Looks-- it doesn’t look materially different from Panther or Jaguar, the same bright candy drop design. The Apple aesthetic still pertains. (Even though Microsoft puts out some excellent Mac software--Entourage is splendid--there is something about that company that doesn’t understand aesthetics. You can spot a Microsoft Mac program in a flash because it simply isn’t as pretty. Silly, but true). However, if you look carefully at the new Mail and Safari (the web browser), you can see some changes coming--somewhat less colorful, more subdued. I’m not pleased.

Spotlight--the feature that has received the most publicity and deservedly so. It appears as a icon in the upper right corner, on the bar, as a spyglass in blue. If you click on it, or COMMAND-SPACE, a window opens. You can hunt for any item anywhere on your computer no matter when or how it got there or what program it used. Just type in the words and it starts before you even finish typing. If I search for, say, “cancer,” I get an instant list of everything on my hard disk with the word cancer in it, including mail, documents, PDF files, pictures with the word in the captions--anything. You have to index the computer the first time you open it (which could take time, depending on how much you have on the disk and how big it is), and then never again. It keeps everything in memory and the response is scarily quick. While Windows has some third-party software that does some thing like this, they apparently aren’t close in speed or thoroughness, and it won’t have a match until Longhorn in 2006. I have used it often and smile every time the little sucker opens up.

Dashboard--is cute, replacing many of the functions of Sherlock. It sits on the dock. It comes with a dictionary (which I just used to look up “scarily”), a flight tracker, calculator, Yellow Pages (we looked up pizza last night and got the telephone number of our usual pizza place--the computer knew we lived in Baltimore), local weather, etc. The little subprograms are called “widgets” and the community is already producing and posting new widgets by the hour, including one that gives local traffic.

Automater--is a way of automating procedures on the computer, like uploading photos, etc., without messing with programming codes, something like macros. Haven’t tried it yet.

Safari--is the web browser that blew Microsoft Explorer out of the Mac business. The main improvement is RSS, which, after a few days of figuring out, now works splendidly. If a website has RSS syndication (this one does), a blue rectangle with the words RSS appears on the Go window. You click on that and a new window opens with all the items at that site. You just click on "add bookmark" and tell it where you want the bookmark and from then on Safari monitors what's posted on that site. I have more than two dozen now posted and am trying to figure out how to organize them. You also have the option of using an aggregator function so you get all the RSS items from all the sites on one window. It's good enough for me to kill NetNewsWire, my old RSS reader. This version seems faster, it is still far more secure than Explorerw and still has problems with a few websites, including the one I use to upload to this blog, for which I still need to use Mozilla.

There are other additions, things I rarely or never use (I don’t teleconference, for instance) but as I work with them, I’ll report back. I don’t want to bore all you Windows users out there, or take your attention away from that spyware and virus stuff.

Friday, May 06, 2005

When is a "theory" not a theory?--UPDATED 05.13.05

When a non-scientist with an agenda uses the word. Or when a non-scientist who slept through biology classes uses it. It's very popular in Kansas these days.

The word "theory" means something different to a scientist than it does to a non-scientist, especially a fundamentalist Christian, apparently. Theory does not mean "guess" or "estimate" or "extrapolation." It describes the result of a scientific process; it is not itself a process. The best explanation is this one, presented in blog called Balloon-Juice (out of Texas, believe it or not) run by John Cole. You can read the whole entry here.
A scientific theory or law represents an hypothesis, or a group of related hypotheses, which has been confirmed through repeated experimental tests. Theories in physics are often formulated in terms of a few concepts and equations, which are identified with "laws of nature," suggesting their universal applicability. Accepted scientific theories and laws become part of our understanding of the universe and the basis for exploring less well-understood areas of knowledge. Theories are not easily discarded; new discoveries are first assumed to fit into the existing theoretical framework. It is only when, after repeated experimental tests, the new phenomenon cannot be accommodated that scientists seriously question the theory and attempt to modify it. The validity that we attach to scientific theories as representing realities of the physical world is to be contrasted with the facile invalidation implied by the expression, "It's only a theory." For example, it is unlikely that a person will step off a tall building on the assumption that they will not fall, because "Gravity is only a theory."
Note the part about "confirmed by repeated experimental tests." The best source for information on the Kansas trial is Panda's Thumb posted by Tom Matzke. And, the Moonies are involved. Also try Red State Rabble. It has an audio link. The wrap-up is from the Kansas City Star.

The hearings did not go well, and my belief that the science community was wrong to boycott it, was misguided. They were right. Now the infighting in the ID crowd has begun, and as usual Panda's Thumb is your best source.

William Saletan, in Slate, writes a defense of Intelligent Design, claiming that it shows that the anti-evolutionists have evolved from those opposing the teaching of evolution, to those saying, well, maybe there was a Creator who pushed this along. Saletan's problem, however, is that a lot of people believe that (maybe even me), but that, as one rabbi said, is religion not science and doesn't belong in a science classroom.

And if you really want to throw up: here.