Thinking For Food

Art imitates life

2006-01-16T01:35:00.000+01:00

Since I can no longer engineer animals in 'real life', I've been devoting some time to one of my hobbies, engineering life 'in silico'... in this case, 3D modelling of animals using the 3D modelling program Povray.

Despite their complexity, organisms are built up from a series of simple rules... and in theory, by applying these rules in a script, we can generate a diverse array of computer images that closely resemble living organisms without having to do a whole lot of fine-tuning and careful editing. This is most easily demonstrated in plants... new cells in plants are generated at the growing tips of roots and branches, and get information on what they should become (leaf, stem, branch point) based on where they are in a hormone gradient generated from the last stem branch point or leaf node. Thus, you can expect a new leaf every X number of inches from the last, and a new stem branching off every Y from the previous branch... and when a new branch point is generated, the new stem (or leaf rib, rootlet) will diverge at a fixed angle from the old one rather than a random angle. This allows a complex branching organism to form from a set of very simple rules governing node spacing and divergence angle - the sort of simple rules that can be easily translated into computer graphics. Indeed, there are quite a few 'plant generators' based on this principle available for 3d graphic imaging... ranging from freeware scripts for Povray to commercial packages such as XFrog. The only difference is the amount of 'polish'... texturing, extra details, etc. which add realism to the image.

Modelling animals is a bit more challenging... unlike plants, animal patterns involve more (and more complex) rules due to their very different method of development and specialized appendages. Yet in principle, with a bit of extra coding it should be possible to create a series of scripts for rapidly generating realistic animals in the same way that plants can be easily generated. In practice, the main limitation isn't the animals structure, but rather the limits of povray itself. Objects in povray are assembled from primitives (balls, tubes, cones, blobs, etc) that don't lend themselves easily to realistic animal structures... at least, not in a way that can be easily put together from scripts (animals in povray generally require quite a bit of tinkering to create a truly organic looking creature, rather than something that appears to be cones and balls stuck together).

My interest is in scripts to model invertebrates... not simply to generate a realistic looking invertebrate, but to quickly generate diverse invertebrates by plugging in a few simple parameters and letting the program use simple rules to do the rest. I've chosen invertebrates for two reasons. Many phyla are clearly externally modular, and much better suited for this approach than vertebrates (which are also modular in places, but internally where it doesn't do me any good). Secondly, everyone is VERY familiar with what a vertebrate should or should not look like, and will quickly note a flaw in leg position, body proportions, etc. Many invertebrates (true worms, insects, etc.) are both extremely diverse in nature and fairly unfamiliar to us.... this allows a greater degree of 'artistic license' in the final product.

I'll talk a bit more about the details in later posts, but just to throw up some examples of Cnidarians I've been working on:

An early test concentrating on ways to generate realistic tentacles.

A much more realistic jellyfish, giving an idea of what I am going for in the final product (the small image doesn't do it justice... click on the image to get the full size picture, in better resolution).

More later.

Respect

2006-01-11T11:49:00.000+01:00

One thing you can't fault the Norwegians for is their sense of community. People in Norway grow up, live, and die in the same towns and neighborhoods. They may leave for a few years, returning with a husband or wife in tow, but they do return. Sure, it makes them xenophobic, insular, a bit conservative, but it also lies at the root of their extensive network of social support and the dedication of their oil wealth to the people, rather than to private profits. Norwegians feel a need to help their neighbors, and by extension their fellow countrymen. Health care in Norway may not be the greatest, but its definately there... from your local doctor to the neighborhood legevakt (walk-in clinic) up to the regional hospital. Crime really is low, and community care is present for the sick, elderly, and those with mental health problems or drug addiction.

In England, the Blair government has been on a seven year spree of dismantling communities in favor of centralization. The police forces are being centralized, the hospitals have been centralized, education has been removed from local control, and large retail corporations have been favoured at the expense of small local business. As communities have broken down and the crime rate jumped, Blairs response has been to boost law enforcement, rather than try to rebuild the institutions that support the community. The result has been new laws, new punishments, and fewer civil liberties. Now we have 'Respect'... Blairs latest response to increased petty crime.... a hodge podge of police quick-fixes (more Asbos, parenting orders, and summary convictions) with a dash of short-term, underfunded programs that will be de-funded and forgotten by the end of the year. No attempt to tackle the root causes of antisocial behavior, and an explicit rejection of poverty (which is increasing in England) as an underlying cause. An outside observer can't help but wonder if this is a 'get-tough-on-crime' attempt to boost popularity, rather than a serious attempt to deal with community problems. Perhaps someone should remind Tony that 'Respect' is something he still has to earn?

DIY data-mining

2006-01-06T10:26:00.000+01:00

Want to do your part for God and Country? Curious if there are subversives in your neighbourhood that need rooting out? In the old days you had to guess who was with us and who was against us, and then go through the annoying leg-work of rooting through garbage for suspicious sales slips, opening peoples mail for subversive literature, or installing wiretaps to monitor their conversations.

No longer. The strategy for the new millenium is to identify subversive ideas and topics, and then prowl databases for information connecting these ideas to individuals. But why let the NSA have all the fun? With a set of simple scripts, Tom at Applefritter describes how you can be a junior G-man and prowl the publically available Amazon wishlist database to find out what people are reading, then use Google maps to track them down. Send your results to the Department of homeland security (202-282-8000 or through their webpage contact), open a brewski, and relax in the knowledge that you have done your part! Hunting the terrorists has never been easier!

From Korea with Stem Cells

2006-01-04T10:06:00.000+01:00

For the past few weeks I've been following the gradual unravelling of that breakthrough stem cell research published last May by a Korean team led by Woo Suk Hwang. For those who don't follow stem cell research (probably most people), Woo Suk Hwang claimed that he had created 11 stem cell lines from patients suffering from various diseases... the first step in being able to use a patients own stem cells as a cure.

No one has been able to repeat their findings, and now allegations have come forward that photos have been reused, data has been fabricated, and DNA tests to match the cells to their donors are being called into question. Hwang admits that mistakes were made in the lab, but claims that his results are still valid, only that there were procedural problems.... the duplicated photos were the result of accidental submission of the wrong photo set, for example, while fungal contamination has conveniently destroyed several of the cell lines.

I can understand the occasional mistake... valuable cell lines do get contaminated and figures can be mislabeled (the most common mistake I have seen is scientists with little statistical background confusing standard error, standard deviation, and 95% confidence level when labeling graphs), but the picture coming out of Hwang's lab is one of extremely poor and confused procedures... and thats putting it in the best light.

I don't like to out-and-out call someone a fraud... its a very serious charge, and not one to be tossed about lightly. Science is a tough field to cheat in, since everyone is trying to replicate everyone elses results. A charitable interpretation is that equivocal results were interpreted as positive results, and that after prematurely announcing their success Hwang and his team cut corners to 'prove' their claim (since I suspect, they had trouble replicating their own results). It is also possible that Hwang honestly feels he was successful and that subordinates supplied him with the data he wanted to see, either out of a desire to please or as a result of pressure to produce a success. For the sake of all those people suffering from congenital illness or spinal cord damage I want to hope that Hwang was genuinely successful but is the victim of a very slopply lab environment... but I'm not holding out much hope.

Hey Tony, George, howyadoing?

2006-01-03T10:19:00.000+01:00

My little break from the internet (a consequence of entrusting my computer system to the tender mercies of the British and Norwegian mail services) has spared me the bulk of the discussion on George 'W for wiretap'Bush and his desire to listen in on the private conversations of ordinary Americans.

However, it has had me wondering if England is any improvement. I've always been under the impression that England has less of a tradition of championing individual liberties.... from what I've seen so far (cameras on every street, plans in the works to track everyones car trips, extrajudicial executions on the London Underground) I'm not confident. Blair seems to be on the same powertrip as 'King' George, tempered only by the fact that the US is a superpower and Englands power has been declining since the second world war.

Happy New Year...

2006-01-03T08:49:00.000+01:00

... in a new country.

Will post more very soon.

What I'm leaving....

2005-12-17T21:09:00.000+01:00

I came across a few winter photos of Norway, while cleaning out my files....

Norway in the evening (about 4 pm).

A sunny day in Norway.

Local wildlife (Willow ptarmigan).

Packing up and tossing out...

2005-12-14T00:47:00.000+01:00

Regular readers... (do I actually have regular readers?) may have noticed the lack of serious blogging... and science blogging... recently. I'm in the process of moving from Norway, which means things are a bit chaotic right now. Hopefully things will 'straighten out' in a week or so.

Many years ago I travelled through the Orkney and Shetland Islands... I bypassed much of Scotland in a desire to go as far north as I could. I remember falling in love with the island culture and its mix of Scottish and Norwegian influences, the history that included everything from the Shetland Bus to stone age Skara Brae, and the many birds and seals that called the islands home. Standing at the northernmost tip of Unst, within sight of Muckle Flugga, I vowed to one day continue on to Norway....

... and now, years later, I'm leaving. Part of me doesn't want to go, and part of me is itching to move on to new horizons. I hope one day to return to these fjords, but I know deep down my track record of return visits is pretty dismal.

Then again, I did return this summer in the Shetlands, so maybe the call of the north will bring me back to Norway.

Until then, god Jul og godt Nyttår!

...and an appendicularian in a pear tree...

2005-12-08T13:55:00.000+01:00

In the spirit of the season, I give you the Christmas Oikopleura! No, he's not filled with holiday cheer, rather he's stuffed full of dsRed and nuclear localized GFP protein.... just like I plan to be stuffed full of pepperkake and aquavit over the next few weeks.

(and yes, GFP on a dsRed background should look yellow, but since red and yellow aren't Christmas colors I did a straight image overlay rather than combining the two images.)

The DIY veternarian

2005-12-05T14:10:00.000+01:00

Since I'm on the subject of rodents....

One of the problems of owning exotic animals is that its hard to find a good veternarian. One of the problems of owning pet rats is that they are considered exotic animals. Don't ask me why... you would think an animal as well studied and used in so many research applications as the Norway rat would be a veternarians dream. Unfortunately, its more likely to become a pet owners nightmare.

The problem is that vet schools cover exotic animals as a specialization, and most vets that are going to specialize on exotic animals are going to be focusing on reptiles or birds, not rodents. Couple that with the general idea that 'small' animals are somewhat disposable and the unwillingness of many people to pay a vet bill that may be ten to twenty times what the rat cost in the first place and its not that surprising that most vets have very little experience with rats, whether at vet school or in general practice. As a result, most serious rat owners come to know more about rat medicine than their vets, to the point that some (including myself) have come into the vets office knowing exactly the problem and what treatment to take... the vet is just there to sign the prescription form.

When I first started keeping rats ten years ago, a sick rat meant having to phone several vets to find one willing to treat them, and having to take our chances on the vets experience and competance. Thanks to a proliferation of websites devoted to rat health, contact with serious rat owners (usually breeders), and my own research into the subject I usually have a good idea what is wrong with my pets, and can find recommendations for good rodent veternarians.

Probably the best vet I've dealt with is the teaching hospital at Kansas State University. The staff there have been able to save rats I was sure were past saving, and have always taken their responsibility seriously. Unfortunately the local vet clinic in Bergen hasn't been as impressive... I've had to deal with everything from surgery stitches being chewed out (good rat vets put the stitches internally or use metal stitches that can't be chewed) to being told that my rats distress wasn't sufficiently important to be dealt with (this on a weekend emergency call, with a rat that was had swallowed pen ink and was choking) to having a rat overdosed on anaesthetic. Fortunately the rats in each case have survived (although the last case was pretty touch-and-go), but the effect is to make me feel that if my rat is sick, I'm on my own.

....

The 'inspiration' for this post was my weekend ordeal with one of my rats... she fell sick on Saturday, and with no possibility of taking her to a vet on the weekend all I could do was wait and hope. This morning when I started this post she looked like she might be recovering, and I was just going to discuss some of the health problems rats face.

She died around lunchtime today, before I could get her to the vet.

The effect of ethics

2005-12-05T13:43:00.000+01:00

I dislike animal research.

I fully appreciate the benefits of animal research, would not seek to ban it altogether, and understand that it is a necessary evil of modern society. On the other hand, many of the techniques are cruel and a fair percentage of research using animals isn't necessary. I personally have no desire to cause pain to animals (at least, not those with with backbones... I have fewer qualms when it comes to insects and other invertebrates, although there are certain animals within these groups I would be hesitant to experiment on) and having worked in animal research once, I'm well aware of the pain that can be inflicted even under the best animal welfare regulations.

The ethical stance that I've adopted has real world consequences for me as a biologist, and these are consequences I have accepted. Much of molecular biology, including the best paying jobs, involve research with mammals (mice in particular), and by refusing to work on mice, I have willingly and knowingly cut myself out from a large part of the job market.

I mention this because of the recent action by 4 Illinois pharmacists who refuse to dispense emergency contraception on the grounds that it violates their personal code of ethics. I understand codes of ethics, and I understand how they can place limitations on what a person can do, but I also understand that if you have a limiting code of ethics, you should not pursue a career where you are going to come into ethical conflict with the requirements of your job. If you cannot bring yourself to dispense certain pharmaceuticals (and it need not just be contraception... anti-depressants and vaccines can be just as controversial among certain segments of the population), you shouldn't take a job as a pharmacist.

Deep down, though, I can't help thinking that there is more politics than ethics in the air. The pharmacists in question are supported in their lawsuit against Walgreens by Americans United for Life, a well-heeled advocacy group that champions anti-choice causes. This has all the aroma of a deliberate test case against the recent Illinois law that prevents them from opting out of dispensing contraceptives. If they win their case, I have to wonder about the long term ramifications. Could I then get a high-paying job at a major pharmaceutical company and conveniently 'opt out' of any research that involved animals?

Makes me wonder if I should be supporting them.

Fundamentals

2005-11-30T14:28:00.000+01:00

Buried in the Guardian web site is an announcement about an upcoming speach by Lord May, President of the Royal Society, where he discusses the problems that society faces in the rise of fundamentalism... both religious fundamentalism and its secular twin, ideological fundamentalism.

In his address to the society, titled Threats to Tomorrow's World, Lord May will criticise groups for putting their own traditions, unsupported beliefs and dogmas above scientific evidence. "Fundamentalism doesn't necessarily derive from sacred texts. It's where a belief trumps a fact and refuses to confront the facts.
"All ideas should be open to questioning, and the merit of ideas should be assessed on the strength of evidence that supports them and not on the credentials or affiliations of the individuals proposing them. It is not a recipe for a comfortable life, but it is demonstrably a powerful engine for understanding how the world actually works and for applying this understanding," he will say.

Several instances of ideology triumphing science are singled out by Lord May, including Global Warming, the anti-nuclear power lobby, the Catholic Church stand on condom use, and of course, creationism. In all of these cases, powerful people would prefer to indulge their personal fantasies rather than deal with the cold hard scientific reality that surrounds them. That would be fine if this were just the tin-foil hat crowd, but these powerful people include world leaders, corporate CEOs, and religious figures with audiences in the millions. What hope does civilization have against the vested interests of an elite who refuse to deal with reality?

One feature of the post-war US that has always impressed me is their ability to set up institutions that were independant of the ideological and religious whims of the nations leaders. Institutions such as the FDA, the CDC, the NIH and NAS.... grounded in science and with a mandate to take the best scientific information available and use it to form policy, educate the populace, and steer research.

The past few decades (but particularly the last 5 years) have seen an erosion of these institutions. The FDA has been holding up approval of the Plan B emergency contraceptive not because its dangerous, but because of the personal religious beliefs of certain politicians. The CDC has had to water down information on its website dealing with contraception and sexually transmitted diseases because of pressure from a small but extreme religous minority. The President himself essentially hamstrung stem cell research in the US, and has consistantly ignored scientific consensus on Global Warming, while giving a boost to the supporters of Intelligent Design, a form of warmed over creationism cobbled together to sneak religion into the schools via the back door.

Its ironic that at a moment in history when we have never had so many scientific advances (and the fruits of those advances, whether in vaccines, antibiotics, drought tolerant crops, space travel, or the internet, to name a few) there are so many powerful people who have no tolerance for the scientific method and no grounding in reality. I hope this is just a passing moment in history, and not the beginning of the end of that intellectual experiment that sparked the enlightenment. With over 6 billion people on an environmentally shaky planet, this is not the time to have fantasists at the helm.

Canadian Government Falls!

2005-11-29T03:38:00.000+01:00

Its true, and already rebel forces and Imperial troopers are massing for the coming conflict. No word yet if foreign advisers will be intervening.

Where are these guys when you need them?

Historical perspectives

2005-11-27T17:20:00.000+01:00

The Aftenposten (english edition) recently posted a story on how the Norwegian education minister wants to deemphasize modern history in high-school and focus more on earlier periods:

A key component in the draft national high school curriculum proposes replacing much Norwegian, European, world and modern history with digital presentations of the Viking age, the rise of the Roman Empire and the development of medieval China.
The new program leaves out the world wars, the Russian Revolution, the Cold War, and does not mention the topics of Nazism or Communism.

Its hard to tell from the article why they are doing this, and you have to take the Aftenposten with a grain of salt... their English articles are very tabloid in format and don't have anywhere near the detail of their Norwegian news.

I could be sarcastic and say the reason for this change in the history classes is that Norway doesn't have much history: The popular view is that following the christianization of Norway at the end of the Viking era, Norway went into decline and became a minor province of first the Danes and then the Swedes. Neutral during the first world war, it reappeared on the world stage following the German invasion, where it became a crucial base for German operations in the North Sea. Thus, to the outside world, Norway is Vikings and Quisling, and until the last 30 years not much else. That would be very unfair, however... Norwegian history, while not as colorful as that of Sweden or Denmark, is a big part of the history of whaling, Arctic and Antarctic exploration, the Hanseatic league, the settlement of North America, among other things. Even the Vikings themselves are given short shrift - more than just hairy barbarians, they established continent spanning trade networks that reached to the Byzantine empire and the shores of Newfoundland.

What this news article has reminded me of is just how much history... particularly European history... I was not taught in school, and how much I have learned since coming here. To take just the second world war as an example, depending upon which country I lived in either the English won the war, the Americans won the war (but the English helped), or the English won the war, but the Canadians did all the really dangerous and important work. I was aware that Norway had been invaded, but never new about the role it played in the German plans for the development of atomic weapons (or the important work of the Norwegian resistance in preventing it). Nor was I aware of the complex politics surrounding the German invasion, which saw almost as many Norwegians joining the Wermacht as joined the resistance. How many people outside of Scandinavia know of how the Danish government, while ostensibly cooperating with the Nazis, secretly smuggled their entire Jewish population to the safety of Sweden, or that neutral Sweden became a highway for the movement of German troops who officially were on vacations? In North America, we would believe that nothing much happened in Europe between the Battle of Britain and the landings on Omaha beach when in fact every European country has its own history of dealing with the German and Russian powers (the WWII history of central and eastern Europe is even more complex than that of Scandinavia).

If anything, students should be taught more history, not less... and covering a broad range of topics rather than just that of ones own country and the "classical" history of Greece and Rome. Local history is fine, but the world is an interconnected place... and only focusing on the local aspects never gives a person an idea of the larger context of events. As a youth I learned about the Vikings discovering North America and their failed attempts at settling here, but as an isolated fact, quickly passed over as we shifted to the later (successful) colonization efforts by the French, Spanish and English. Its only as an adult living in Scandinavia that I have come to see the larger context of trade networks, piracy and raiding, political rivalries and machinations, and changing cultures that resulted in the Viking settlements and their eventual failure. Its that larger context of world events that makes the history of my own country make sense... and turns an item of trivia into an interesting link of a globe-spanning chain of events with repercussions to this day.

Ticket to ride...

2005-11-27T16:55:00.000+01:00

I just realized that its been a while since I've posted anything... not because of thanksgiving (a strictly New World holiday, which I would be celebrating in October anyway) but because I've finally received my settlement papers for England and have to put everything in order for my departure from Norway.

I would have liked to have spent another Christmas in Norway... I'll miss the pinnekjott and the Juløl, the 'old world' feel of christmas here, the sight of snow on Mt. Ulriken on Christmas morn... but reality is an expired work visa in the most expensive country in the world and a need for a change of scenery. With any luck, the snow hitting Scotland will dip southwards a bit, and I can look forward to a white Christmas.

Want to work in Norway? Not Norwegian? Forget it!

2005-11-23T17:25:00.000+01:00

From the Aftenposten english edition:

Norwegian authorities have said the country needs specialists in a variety of fields, and they set a quota of 5,000 work permits that could be granted this year to foreigners with special skills. The result is disappointing. Newspaper Aftenposten reported Tuesday that only 780 have applied for and received work permits in Norway.
Norway's tradition of egalitarianism also makes the country unattractive to foreign workers with years of often expensive education behind them. Most Norwegian employers don't link pay to university degrees, or the length of a worker's education, putting Norway at a competitive disadvantage. Employers in Germany, France and Portugal, for example, are more likely to tie pay levels to education levels.

Well, thats the official line, anyway...

My wife and I used to follow an ex-pat job website for non-Norwegians living in Norway, and just about every week someone would post how they wanted to follow their sweetheart to Norway, this is what they did for a living, and could they find a job here? And the response from the ex-pats, born of hard experience, was NO. It didn't actually matter what you did - if you weren't Norwegian, didn't speak Norwegian fluently, didn't have a Norwegian education, and were seeking a job with a Norwegian company, you had almost no chance of finding work. (If you had skills that a non-Norwegian company would value, your chances were better, but it was highly advised you get a job offer before you came).

Norway is filled with unemployed and underemployed spouses, boyfriends, and girlfriends of Norwegians that have left good jobs in their home countries and cannot find work here. The ugly truth behind this is that deep down Norwegian employers are extremely xenophobic. Unfortunately its an issue that the government can't seem to get their head around. They and the Norwegian industries talk constantly about importing educated talent and the need for it, but when it comes to putting words into action, nothing happens.

Norway is a beautiful country and the people are generally nice, but they haven't really adjusted to the global economy yet (its only the past 30 years that Norway has been a truly first world nation - before the North Sea Oil, Norway was the poorest country in western Europe). They still have a very isolationist attitude when it comes to foreigners. Until they do change their attitudes, the talent they need to compete on the world stage will be heading elsewhere.

In my case, England.

A herd of Zebras

2005-11-21T15:20:00.000+01:00

AIDS "dissidents" are the creationists of the medical world.... in the early 80's when there were a host of competing theories on the cause of AIDS swirling about, they had their place, but now that we have mountains of evidence that a little retrovirus called HIV is the cause of AIDS, you would think they would accept that they were incorrect and focus on the real issue of how to deal with this virus. Instead, unable to convince the scientific and medical community, they started a PR campaign designed to convince credulous politicians and desperate patients that HIV was just an innocent virus in the wrong person at the wrong time, and that the real cause of AIDS was AZT, or 'toxins', or 'lifestyle'....

This would all be well and good if usenet discussions and online blogging were all that mattered, but these people convince patients to forgo treatment, and have even convinced governments to hold off on prescribing anti-HIV drugs! Again, actions driven by ideology with very real and painful consequences for real people.

Orac over at respectiful insolence discusses one example of this, where a child died because her mother was adamant that HIV did not cause AIDS, and where those with ideological axes to grind are fighting to relabel what is very clearly death by HIV infection as something else.

Highly recommended reading.

The Religious Right wants to kill your daughter...

2005-11-20T13:35:00.000+01:00

Nothing pisses me off more than people who let political ideology and religious fundamentalism get in the way of public health. Do you remember last year when some Imams in Nigeria announced a ban on polio vaccines because they believed it was a plot by the Western governments to spread AIDS? ...and that there were serious consequences, including a jump in polio cases in northern Nigeria causing paralysis in children? Remember how many here in the West laughed about it as just another example of Third World crazyness? Would never happen here, right?

In the US, for instance, religious groups are gearing up to oppose vaccination, despite a survey showing 80 per cent of parents favour vaccinating their daughters. "Abstinence is the best way to prevent HPV," says Bridget Maher of the Family Research Council, a leading Christian lobby group that has made much of the fact that, because it can spread by skin contact, condoms are not as effective against HPV as they are against other viruses such as HIV.
Giving the HPV vaccine to young women could be potentially harmful, because they may see it as a licence to engage in premarital sex," Maher claims, though it is arguable how many young women have even heard of the virus.

In other words, Bridget Maher of the Family Research Council wants your daughters to die from a horrible preventable illness so that she won't lose her favourite boogeyman to scare kids into abstenance. Its bad enough she and her friends are determined that your daughters should get pregnant at every available opportunity, whether from a moment of carelessness or from a violent rape.

It is estimated that more than 25,000 women become pregnant in the United States each year as a result of rape, according to statistics given by state lawmakers who have proposed the bill.

In Pennsylvania, hospitals are not required to offer the medication [Plan B]. Some do. Others have policies that allow health-care providers to opt out of providing the medication because of personal religious or moral reasons.

I can sort-of, vaguely, and somewhat unsympathetically understand the Imams response in the face of a spiralling AIDS epidemic and the recent Western hostility towards Moslems, but the American Christian Rights' determination to punish women has gone beyond ignorance and into the realm of criminal perversion. I may not know WWJD, but a part of me keeps feeling that if he could see what some of his followers are doing in his name, he would puke.

Why we lost....

2005-11-17T21:20:00.000+01:00

Not long after reading this post over at Pandagon, I came across this news article:

One Arabic linguist was discharged from the military for violating its "don't ask, don't tell" sexual orientation policy in fiscal year 2004, according to records obtained by an advocacy group. In the first 10 years of "don't ask, don't tell," the military discharged 54 Arabic and nine Farsi speakers for violating the policy, according to the Center for the Study of Sexual Minorities in the Military. In fiscal year 2004, however, there was just one Arabic and no Farsi speakers discharged, the center said Wednesday. That compares to at least three enlisted personnel discharged the previous year.

Apparently its more important to win hearts and minds in Alabama than in Baghdad.

When did ignorance become a virtue?

2005-11-17T11:38:00.000+01:00

The irritating thing about the dustup between Dilberts Scott Adams and Pharyngulas PZ Meyers is the attitude of Scott Adams and some of his fans that being ignorant about something and being too lazy to look stuff up are virtues, while actually investing the effort to educate yourself means that you are biased and 'compromised'.

I ran into this attitude occasionally when I used to teach intro biology back in Kansas... there would invariably be someone in the class who was extremely opinionated (usually on evolution), but didn't know a thing about the subject, were too lazy to learn, and were damn proud of the fact. One young woman in particular stands out in my mind... bottom of the class, spent most of her in-class time surfing the net or chatting with friends, couldn't explain what evolution was if her life depended on it, yet adamant that evolution was wrong. The truly frightening thing? She was planning on becoming a teacher.

I should be too old for this...

2005-11-14T12:11:00.000+01:00

Its been a particularly crappy past three weeks for me... what started as just a bad cold has turned out to be pertussis - and while I'm not burning through a box of tissues a day anymore, I could do without the coughing and that cracked rib I got as a result.

Like most people in the western world, I had always assumed pertussis (better known as whooping cough) was one of those childhood diseases our grandmothers used to worry about, but which had been efficiently dealt with through the miracle of vaccination. Unfortunately, pertussis likes to throw curveballs... over time vaccinated and previously infected people lose their immunity, creating a population of adults that are fully susceptible to the disease. The one saving grace is that usually these later infections are less severe than what is seen in children.

Whooping cough is caused by a nasty little bacterium called Bordetella pertussis, which glues itself to the ciliated cells of your respiratory tract and releases a cocktail of toxins to disable your immune system and damage your respiratory cells. Patients with pertussis go through a two week period of sneezing and runny noses, followed by 4 to 6 weeks of violent coughing. During this period they are highly contagious, but once they recover they can enjoy years of aquired immunity to the disease. B. pertussis evolved from the bacterium Bordetella bronchiseptica, a closely related bacteria that causes a mild but chronic respiratory infection in animals. We can also be infected by B. bronchiseptica, but it doesn’t happen often… B. bronchiseptica isn’t very contagious to begin with, and the immunity most of us have to B. pertussis confers immunity to B. bronchiseptica. In a small number of cases, whooping cough is caused by B. parapertussis… another descendant of B. bronchiseptica. The symptoms are the same (although milder), but significantly immunity to B. pertussis does not make you immune to B. parapertussis.

The evolution of this group of bacteria appears to be tied to the changes in human culture that led us out of the fields and into the cities, and may even be a result of the high density urbanization of the last half millennium. Genetic comparisons among the three bacteria place the divergence of B. pertussis within the past few thousand years, while the first records of the distinctive ‘whoop’ of whooping cough go back only 400 years.

Why is the emergence of whooping cough tied to human cities? The highly infectious nature of B. pertussis means that this disease needs a minimum population size in order to continuously have a supply of new hosts. If the population is too small (e.g., in a medieval town or rural village) the entire population would be infected and subsequently immune in a matter of months. In large cities, however, there are enough hosts present and a constant influx of new hosts (births and immigration) to keep B. pertussis circulating indefinitely. The ancestral bacterium B. bronchiseptica, in contrast, has to survive in animal populations that are at low density, dispersed, and seasonal in reproduction. Instead of trying to infect as many new hosts as possible in a short period of time, it lays low in the hosts nasal passages causing only a mild disease, waiting for the rare opportunities when uninfected hosts are encountered or it can infect its current hosts offspring.

Vaccination for pertussis began in the 1940's and in the western world at least, rapidly transformed whooping cough from a mothers nightmare into one of those 'old tyme' diseases your grandparents would tell you about. In a matter of years, the pool of young children which the pertussis bacterium depended on for its survival virtually disappeared. This could have spelt the end for B. pertussis, save for one factor: unlike many other diseases, immunity to pertussis isn't life-long. Instead, it starts to fade after a few years, and most adults who had been immunized or infected as children become susceptible again to the disease (albeit in a milder form). Adults have always been a reservoir for the disease to hide in when it ran out of children to infect, but the milder symptoms meant that adults were not as good at transmitting the disease. Without children, however, it appears pertussis may not have much of a choice. The last few years have seen a re-emergence in adults and older children and an increase in the severity of the infections. Pertussis, it appears, is evolving to become a significant disease of adults as well.

Something I found out the hard way, three weeks ago.

Eleventh hour of the eleventh day...

2005-11-11T18:14:00.000+01:00

In Flanders Fields

In Flanders fields the poppies blow
Between the crosses, row on row,
That mark our place; and in the sky
The larks, still bravely singing, fly
Scarce heard amid the guns below.

We are the Dead. Short days ago
We lived, felt dawn, saw sunset glow,
Loved and were loved, and now we lie,
In Flanders fields.

Take up our quarrel with the foe:
To you from failing hands we throw
The torch; be yours to hold it high.
If ye break faith with us who die
We shall not sleep, though poppies grow
In Flanders fields.

I've never been very comfortable with the poem 'In Flanders Fields'. In my childhood we would recite it each November 11th, and go over in class the meaning of the verses. Like many war poems from that period, Flanders Fields is both a memorial and an exhortation. It speaks of the dead, touches upon what they have sacrificed, and ultimately urges the living to take up the cause and join the fight. Its final stanza is an exhortation to continue the war, lest the sacrifices of the dead be in vain.

I've come to dislike this poem over the years. As a youth, I had attended remembrance day assemblies at school, where officers who had in their lives never fired a shot in anger would stress that third stanza and speak of the importance of carrying on the good fight and the sacrifices for freedom... odd, considering that the Great War had little or nothing to do with freedom and high ideals, and far more to do with the byzantine diplomacy of the early 20th century.

There have been wars that have been necessary and unavoidable, but far too many have been fought over greed and stupidity... John McCrae's call to 'take up the quarrel with the foe' and 'to you from failing hands we throw the torch' sound similar to the excuses of Vietnam and Iraq, to fight on in a pointless cause so that the dead shall not die in vain. That second stanza, where the dead recount what they have lost: "felt dawn, saw sunset glow, loved and were loved", is too often conveniantly forgotten.

I'll end with the sentiments of another First World War soldier, Wilfred Owen... and a poem that could almost be a reply to John McCrae.

Dulce et Decorum est

Bent double, like old beggars under sacks,
Knock-kneed, coughing like hags, we cursed through sludge,
Till on the haunting flares we turned our backs
And towards our distant rest began to trudge.
Men marched asleep.
Many had lost their boots
But limped on, blood-shod.
All went lame; all blind;
Drunk with fatigue; deaf even to the hoots
Of tired, outstripped Five-Nines that dropped behind.

Gas! Gas! Quick, boys!-An ecstasy of fumbling,
Fitting the clumsy helmets just in time;
But someone still was yelling out and stumbling
And flound'ring like a man in fire or lime...
Dim, through the misty panes and thick green light,
As under a green sea, I saw him drowning.

In all my dreams, before my helpless sight,
He plunges at me, guttering, choking, drowning.

If in some smothering dreams you too could pace
Behind the wagon that we flung him in,
And watch the white eyes writhing in his face,
His hanging face, like a devil's sick of sin;
If you could hear, at every jolt, the blood
Come gargling from the froth-corrupted lungs,
Obscene as cancer, bitter as the cud
Of vile, incurable sores on innocent tongues,-
My friend, you would not tell with such high zest
To children ardent for some desperate glory,
The old Lie: Dulce et decorum est
Pro patria mori.

One way tickets...

2005-11-09T00:29:00.000+01:00

Sometime in the late summer of 1916, in a field in northern France, my grandfathers luck ran out. I don't know how it happened... I suppose no one alive today knows... except that by the standards of the Great War, it was a quiet day on the Line. He was what they call 'trench wastage'... killed not in one of the famous battles but as part of the day-to-day attrition of that horrible war. There are a hundred ways to die on a battlefield - an incoming shell, a stray bullet, a landmine, carbon monoxide from the crude stoves, dysentary from the filthy water, trench fever from the ever-present lice, bottomless wallows of mud that will drown the unwary soldier...

Not much has changed from my grandfathers time.... rich men are quick to send their countries youth to war, and death comes all too easy. In the constant numbers and statistics - 20 dead here, 5 wounded there, only 95 this month, 200 killed or captured - its important to remember the individual stories. To quote Terry Pratchet:

"Sin, young man, is when you treat people as things. Including yourself. That's what sin is."

"It's a lot more complicated than that—"

"No. It ain't. When people say things are a lot more complicated than that, they means they're getting worried that they won't like the truth. People as things, that's where it starts."

Scientific ethics begins with leadership

2005-11-08T18:59:00.000+01:00

After reading a few of the posts at Dr. FreeRides site I've been thinking a bit about the topic of ethics in science. In one of his posts, Dr. FreeRide asks his readers what they would put in a course on ethics... I posted a short comment in response, but the more I've thought about it, the more I've felt that a more detailed answer is deserved.

Ethics courses on scientific misconduct have never impressed me much. After a certain point in life, we either have a well developed idea of what is right or wrong, or we don't. By graduate school its a bit too late to change that... sure, we can instill the fear of God and the Dean by outlining the long list of punishments that will be dealt out to cheaters, but as any school teacher or police officer will tell you, the people most affected by those sort of speeches are the ones least likely to break the rules anyway.

Fortunately, I think that most of those who enter graduate school have a determination to seek the truth... that is the job of a scientist, after all. Unlike most other fields, science is constantly cross-checking itself and publicising for all to see both the results and the methods. This creates an environment where cheating is difficult to sustain... eventually someone will try to repeat what you do, and if they can't replicate the experiment, questions will be raised.

There are a few high flyers who thumb their nose at the system... people like Luke Van Parijs, John Darsee, and Hendrik Schön. These 'scientists' blatantly fake data, draw graphs from scratch, change labels at a whim, and do so for no other apparent reason then self-promotion. They can do quite a bit of damage in their careers, as people waste time using or trying to repeat their results, but on the good side, they are often so obvious that it doesn't take that long until they are discovered.

For some reason, people like these tend to get a lot of attention from scientific ethicists... I guess they have the same sort of attraction that serial killers have to criminal psychologists. Who would you rather profile... Charlie Manson, mass murderer, or Joe Schmoe, robber of liquor stores? Unfortunately, its the Joe Schmoes knocking over corner stores rather than the Mansons of the world that do more damage in the long run. Similarly, I would bet that its the small scale examples of scientific misconduct rather than the high flyers that waste the most time and resources. But are we really dealing with the low level scientific misconduct, or are we acting like 'Officer Friendly', telling the kids at school exactly what happens at a PMITA prison and hoping they will 'just say no'?

Creating data out of whole cloth is difficult, as van Parijs, Darsee, and Schon found out much to their chagrin... on the other hand, massaging data is disturbingly easy. Outlying data points can be dropped. Unsatisfactory experiments can be 'replicated' until desired results are obtained. Graphs can be 'cleaned up' to produce smoother curves. Judgement calls can be made that bias results one way or another. Experiments in molecular biology are rarely 'double blind' (how many researchers ask their lab mate to load their gel for them, just to be safe?), again allowing observer bias. Areas in photographs can be digitally enhanced to turn background into signal (or to remove unwanted signals).

The real question for scientific ethics isn't what makes a van Parijs or a Schon do what they do, but why an ordinary researcher working on an ordinary project feels it is acceptable to alter the data in order to produce better results. This is where we step away from the black and white examples taught in ethics class into the muddy world of real lab-bench science. There are going to be some researchers who are going to alter data.... even if only slightly or in the grey area of judgement calls... for no better reason than the advancement of careers. But there are also researchers, particularly at the bottom ranks (grad students, post docs) who are going to see data massaging as a matter of self-preservation in the 'will I still have a job tomorrow' sense of the word.

The field of science creates a uniquely perverse working environment in which low level researchers, particularly grad students, are completely dependant upon their immediate supervisors and often have no recourse should unusual or extreme demands be placed on them. This is particularly true for foreign researchers, who face the additional demands of restrictive immigration laws, who are unable to claim unemployment benefits, and who often have to support family members who are unable to work. At one university I attended, it was said (only half-jokingly) that you could tell the personality and quality of a supervisor by the nationality of his graduate students... native citizens, after all, had the freedom to leave an undesirable supervisor.

More than most fields, science should be tolerant of failure... failure eliminates fruitless lines of enquiry allowing us to focus our research, while the freedom to fail encourages the sort of risk-taking and experimentation that leads to great breakthroughs. Realistically, however, failure means that grants are not renewed, contracts are ended, and degrees go ungranted. Fourty years ago, a freshly graduated PhD. could look forward to his own laboratory and research program in a university. Now, you generally need several low paying post-docs before you have even a chance at a permanent position... and if those degrees and post-docs aren't at the right universities, and don't produce enough papers, you may as well quit while your still young enough to retrain.

It doesn't take a series of post-docs at Harvard to see that this creates an unhealthy environment that would promote low level cheating... the sort that doesn't try to stand out, but which may mean the difference between an unproductive year and a mid-level publication. How much falsification actually takes place, I don't know, but I've seen some numbers floating around for biomedical science that suggest the amount is low, but not insignificant. (I suspect that more cheating occurs in biomedical science than other fields, simply because results are often fuzzier... small differences in blood serum components, or qualitative patient assessments of well-being. Its hard for an astronomer to fake the existance of a new star or a taxonomist to fake a new species, although in the latter case I have seen some really bad judgement calls that created new species where none really existed).

So what does this have to do with teaching ethics? Whether a person crosses the line from ethical scientist to fraudulant science depends on whether they feel the benefits of cheating balance out their own internal moral compass. Undue pressure to produce positive results, confirm a supervisors hypothesis, or support a funding agencies preferred conclusion acts like a massive thumb on the ethical scale, pushing the researcher across that line. Ethics courses that I have run across only deal with one side of the scales... the moral compass. They rarely deal with the larger picture of the work environment, and how to cope with the pressures to alter results that a researcher may face. Instead, the ethicist comes off as 'Officer Friendly' - strictly crime and punishment.

In addition to the basics of right and wrong, young researchers need to know how to deal with the pressure to produce in order to avoid the temptation to cheat - this includes learning about university expectations for supervisors, grievance procedures, university standards for handling corporate funding of research, and even transferring academic skills from the university environment into the general workforce ('leaving academia'). It also means that universities have to have expectations of supervisor mentorship, effective ombudsmen to aid grad students and post docs, clearly stated guidelines for accepting outside funding, and a view of the world that goes beyond the ivory tower. It also means that ethics classes have to be for professors, not just students. Good ethical behavior is learned not from lectures but from observation of those in leadership positions. Its one thing for a supervisor to tell a student that pruning data is wrong. Its another to have a supervisor suggest that an unfavorable experiment be rerun until a desired result is obtained.

I hope that the level of fabrication is low (after all, I depend on other peoples results for my own research), but I'm not naive, and I've seen and heard some things that have made me wonder. It would be good to see some solid data on why researchers fabricate their results, although that may be hard to obtain. I suspect most small scale cheating that is discovered is quietly buried... after all, more than one reputation is on the line. Ultimately, a response to the problem that deals with only one side of the problem will be ineffective. We have seen how well the law-and-order approach has worked on the War against Drugs, War against Poverty, and War against Terror.... without a two pronged approach that not only deals with the symptoms but also the underlying problems all of these 'wars' have stagnated. The last thing we need is a similarly effective War against Fabrication. Its not like Nancy Reagan needs the work.

Weapons of Mass Destruction found in Iraq

2005-11-08T12:12:00.000+01:00

..except, it was us that was using them. In a report in the Independent, US forces are accused of using white phosphorus shells as a weapon.

Powerful new evidence emerged yesterday that the United States dropped massive quantities of white phosphorus on the Iraqi city of Fallujah during the attack on the city in November 2004, killing insurgents and civilians with the appalling burns that are the signature of this weapon.

But now new information has surfaced, including hideous photographs and videos and interviews with American soldiers who took part in the Fallujah attack, which provides graphic proof that phosphorus shells were widely deployed in the city as a weapon.

Is there any low the Bush administration won't sink to? Torture, abductions, secret trials, chemical weapons... I don't recognize the U.S.A. anymore.

Tangled Bank 40

2005-11-03T00:05:00.000+01:00

Tangled Bank #40 is up... with lots of interesting articles. Give it a look.

We salute our tentacled overlords!

2005-11-02T22:38:00.000+01:00

Off to Miskatonicon for the weekend, to enjoy some affordable beer, Swedish hospitality, and gibbering horrors. I'll post a bit about it when I get back, as well as the much anticipated 'what is an Oikopleura and why are they more fun than sea monkeys' article.

Until then, have a good weekend, and to my Swedish readers (I know there is at least one), hope to see you there!

For a laugh, check out Howard Hallis's classic tract: Who Will Be Eaten First?

Absinthe

2005-10-30T22:32:00.000+01:00

An interesting application of chemistry:

Breaux has made understanding the drink his life's work. He has pored over hundred-year-old texts, few of them in English. He has corresponded with other amateur liquor historians. The more he's learned, the more he's felt compelled to use his knowledge of chemistry to crack the absinthe code, figure out exactly what's in it, puncture the myths surrounding it - and maybe even drink a glass or two.

I've tried the so-called absinthe available from the Czech republic... it really is just green vodka with anise. It doesn't go milky when you add water, and it isn't an appealing taste. I'm curious to try a bottle of the Nouvelle-Orleans, but with a price-tag of 55 pounds a bottle, its a bit on the expensive side. Then again, a bottle of marginal whisky costs about 300 kroner (about 30 pounds) at the vinmonopolet, so maybe its not that bad a deal.

Oikopleura

2005-10-30T18:24:00.000+01:00

I just realized that two weeks on, I still haven't said anything about oikopleura besides a general description of urochordates. I'll post something soon, but just to keep people interested, here is a picture of one of the little fellows:

If your wondering about why he looks so funny, its because he's glowing green (unfortunately, the camera was black-and-white only).

And no, they don't normally glow green. Thats where I come in.

Visitors....

2005-10-30T15:46:00.000+01:00

I've been stuck at home sick for the last few days, which for me usually means a combination of frustration and boredom, interrupted by bad 50's sci-fi movies (today: Invaders from Mars, original and remake) and flipping through blogs. One of the nice utilities of the site meter is that it takes note of where a person came from when they arrived at my site. A lot of the new visits are thanks to a I and the Bird... I'm not really a bird person, preferring invertebrates, but maybe this might motivate me to post a few of my pics of the Norwegian and Shetland birdlife. We don't get a huge number of bird species up here, but up in the mountains I've seen a few ptarmigan, while the Shetland islands are a good place for gannets, skua, and guillemots.

Some of the referring links don't make much sense... blogspot has a feature that lets you jump randomly to another blog, and I think thats where a few of the hits are coming from. One odd one comes from what I'm guessing is a right wing site that quoted my commentary on Arctic penguins. I'm thinking they missed the point (I don't think they read the original Guardian news story) since their take on it is that global warming is already here, so there is no point trying to do anything about it.... lets just keep partying. I hope for their sake they don't live in a coastal area and that they don't care much for seafood.

I'm going to give a tip of the hat to one reader I came across, at The House and Other Arctic Musings. The Canadian arctic is the one part of that country I never had a chance to visit and I've always wished I had. In my university days, I knew people who did research up in the Arctic, from Tuktoyaktuk to the Queen Elizabeth Islands... including one fellow who worked on the overwintering of the Arctic Woolly Bear caterpillar. Apparently the subject of exactly how many years these caterpillars overwintered was quite contentious, and I remember one very angry blow-up at a conference between the 14-year side and the 8-year side of the question. I guess if you spend that many years watching a caterpillar grow, you take the subject very very seriously.

Random 10

2005-10-28T21:18:00.000+02:00

To Die For, "Crimson Twins"
Cradle of Filth, "The Mordant Liquor of Tear"
54-40, "Easy to Love"
Cradle of Filth, "Mother of Abominations"
Rolling Stones, "Paint it Black"
Silke Bischoff, "Love Never Dies"
Cradle of Filth, "Thank God for the Sufferin"
Deathstars, "Synthetic Generation"
MC Hawking, "Gin and Juice"
Mindrot, "Burden"

Its been one of those days....

Creeping nightmare... of Lewy bodies!

2005-10-27T16:44:00.000+02:00

This is truly scary... apparently a new line of thought holds that Parkinsons disease is just the final stages of a progressive brain degeneration that works its way up the brain stem, disrupting functions as it goes. The problem is, since these disruptions cause only minor behavioral and sensory changes, the only way to know for sure that your on the road to Parkinsons is to have your brain sliced up in a hunt for Lewy bodies... clumps of the protein -synuclein in the brain. Not really a practical test, although I'm sure its great fun at your autopsy to see what diseases you were in line for if you hadn't had those three bottles of Norwegian moonshine at the Christmas party.

The worrysome bit is that the 'early' symptoms caused by this gradual brain degeneration include muscle movement during REM sleep. Normally, when you sleep a part of your brain called the pons shuts off all of your muscles except for those of the eyes... people who have damage to the pons 'act out' their dreams, flailing arms and legs around as they run and jump in their dreamworld. Up from the pons is the substantia nigra, the part of the brain that gets damaged in Parkinsons disease and causes loss of muscle control. What they think happens is that first the Lewy bodies show up in the lower brainstem, work their way up through the pons, and then expand into the rest of the brain, including the substantia nigra. Only when it hits the substantia nigra are the symptoms strong enough to get attention, however... by which time Lewy bodies are all over the place.

So now I have to worry about whether I move in my sleep... am I just rolling over, or is this the first sign of a downward spiral? It could be worse though...

Sleep neurologist Brad Boeve recalls one couple who described a particularly horrendous night-time event. While they slept in their bed, the husband suddenly grabbed his wife's head, shook it around roughly, then slammed it down hard and threw up his arms. Far from being intentional, this distressing episode was the result of a disorder that sees sleeping people physically act out their dreams. In this instance, when the husband woke up he revealed that he had been playing rugby in his dream, had scored a try and then raised his arms in victory.

That fellow may not live long enough to get Parkinsons, if his wife has anything to say about it.

2000

2005-10-26T16:30:00.000+02:00

Its strange to think how two and a half years ago I sat eating lunch in a Kansas sportsbar, watching the first rockets strikes hit Baghdad on the big screen TV and listening to people cheering each explosion, as though celebrating a touchdown by the home team.

I thought then that no good could come of this war, but I don't feel any satisfaction in being proven right.

This Saturday Staff Sgt. George T. Alexander Jr. became the 2000th US casualty of the war. Our allies together have lost over 200 men, and countless tens of thousands of Iraqis have been killed in this disaster. I'd like to think that with Bush's poll numbers crashing we have reached a turning point, but Bush is not a man given to admitting wrong. I can't help thinking there will be far more than 2000 US dead by the time this is all over.

For sale: One childs mind

2005-10-26T09:57:00.000+02:00

This is a worrying development:

Private education companies and Christian groups are lining up to enter the education market created by yesterday's pivotal reforms of the state school system.

The moves follow publication of the education white paper unveiling plans to turn all primary and secondary schools into "self governing independent state schools". Every school will be encouraged to acquire a trust, made up of business charities, faith groups, universities or parent and community organisations. The trusts will be able to appoint the governing body, own their own assets, set their own admissions policies as well as control teachers' pay and conditions.

This sounds like a perfect setup for corporate and religious groups to influence (= muck about with) the curriculum. I know the British education system has its problems, but this reeks of some ideological quick fix. Coupled with the rise in American-style fundamentalism and creationism in England, I'm wondering if Blair is taking a page from the Republican playbook and starting to pander openly to the religious right.

Go West, Young Blackcap!

2005-10-25T13:34:00.000+02:00

Considering that I will soon be 'migrating' to England this winter, it seems fitting to mention another group of migrants who are willing to pass up the warmth and culture of the Spanish Mediterranean for milky tea, warm beer, and Fray Bentos meat pies.

Every year, Blackcaps (Sylvia atricapilla) migrate from their summer breeding grounds in Central Europe to wintering grounds in southern Spain and Portugal. Over the past 40 years, a subpopulation of these birds has decided to go west instead, wintering in the much less pleasant British Isles. Since migration routes are genetically determined, this is a fairly radical change of direction which has raised numerous questions. Scientists want to know both why some of the birds are heading westwards (there must be some selective benefit, or this trait would die out of the population) and how can two genetically different populations maintain their distinctiveness if they breed in the same location?

The problem scientists encounter in studying this question is how to determine which birds came from where. These birds are too small for radio collars, and there are too many for mark and recapture studies. The genetic differences between the England winterers and the Spain winterers is probably extremely tiny, since the genetic change that led some to migrate west only turned up 40 years ago. This prevents any simple DNA tests to determine where the birds came from.

In a recent Science paper, Bearhop et al. make use of an original method to figure out where they birds come from... they measure the stable hydrogen isotope ratios in the birds tissues. The amount of deuterium (hydrogen with a neutron attached) to regular hydrogen (no neutron) in a bird is determined by the rainfall in the birds environment. Since England and Spain have very different rainfall profiles, Bearhop et al. were able to take small samples from birds as they arrived in Central Europe to breed and use the ratios to figure out whether the birds were Spanish or English.

What they found was that British birds arrived in Central Europe earlier than Spanish birds. When these birds went looking for partners, all they would find would be other Brits. By the time the Spanish birds arrived most of the English birds were already partnered up and the Spanish birds would naturally have Spanish partners.

The mechanism for this difference in arrival times is a very simple one... the birds use day length to tell them when to head for the breeding grounds. At northern lattitudes, the critical day length is reached earlier than at the more southerly lattitudes, causing the British birds to pack off to Europe 10 days earlier. The end result is two populations of birds breeding in the same location at more-or-less the same time but only breeding with their fellow countrymen despite the presence of other potential partners (a process called assortative mating).

So why go to England anyway? One obvious advantage is that by returning to Central Europe earlier, the British birds get first claim on breeding territories. Other possible advantages are the shorter distance that British birds have to fly, while the increase in backyard bird feeders in England may be aiding Blackcaps through the winter.

It will be interesting to know what happens to this population in the long run.... are we watching speciation in action, with the Blackcaps splitting into a British species and a Spanish species? Or are we seeing a selective sweep.... the eventual replacement of Spanish migrating Blackcaps with English migrating Blackcaps?

This will be one bird I'll be keeping my eye on when I have my own 'winter migration'.

Shake hands with the Devil

2005-10-23T22:23:00.000+02:00

In 1994, the world stood by and watched while all hell was let loose in a small African country called Rwanda. When a rocket destroyed the airplane of Rwandas President Habyarimana, the brutul Interahamwe militia backed by the the Rwandan military unleashed their guns and machetes on the Tutsi population... killing men, women, children, stranger and neighbor alike.

In the middle of that barbaric massacre, desperately trying to bring order and save lives, stood Lt. General Romeo Dallaire and a small force of 300 Tunisian, Ghanian, and Bangladeshi soldiers. Overwhelmed, outnumbered and abandoned by the UN, they fought on to save as many lives as they could. Their actions are credited with saving the lives of 20,000 Tutsis and Hutu moderates... a feat in itself, although but a shadow of the 800,000 people murdered during those 100 days.

Shake Hands with the Devil documents Gen. Dallaires return to Rwanda 10 years later. One of the most powerful movies I've seen in a long time, this movie relives through the generals memories the bloody events that engulfed Rwanda, and how the country is still coming to terms with the genocide. As Romeo describes the events of those horrible days, we are taken from the bustling streets of Kigali in the present day to those same streets 10 years ago... piled with corpses and patrolled by the machete-weilding death squads. We see a man still racked with guilt for a massacre he could do nothing to prevent, despite heroic efforts against impossible odds.

The movie pulls no punches. We see the grandstanding Belgian senator Alain Destexhe accuse Dallaire of complicity in the death of 10 Belgian soldiers, saying in effect that the general should have risked his entire force to save 10 European whites, nevermind the 800,000 black Africans dying all around them. We hear how the the Catholic Church stood by as Hutu extremists used the pulpit to spread hate against the Tutsis. We learn of how the French government aided and armed the Rwandan military and the Interahamwe militia (to this day, leaders of the Interahamwe live in luxury in France). Ultimately, we see a country descending into flames and the outside world at best, turning away... at worst, feeding the fire.

And in the middle of it all, one man trying to do what was right.

Conservatives eat their young...

2005-10-23T16:33:00.000+02:00

...at least, that was my first impression when I read this:

While the recent nomination of Hariet Miers for the Supreme Court by George W. Bush may have revealed more than a few cracks in the usually lockstepped Conservative Movement in America, Daniel Borchers has been calling out "fake Conservativism"
...
Borchers' organization, Citizens for Principled Conservatism (CPC) is currently in-production of a documentary named The Truth About Ann which aims squarely at political and religious hypocrisy of Rightwing commentator and author, Ann Coulter.

I don't have a lot of regard for the Christian Right, and none at all for Ann Coulter, but I've lived in the midwest long enough to know that somewhere obscured by the self-serving pundits, hate-spewing preachers, and their extremist supporters there are decent conservative Christians who do not stand with the hate and the hypocracy that has engulfed the conservative side of politics.

There is much more at bradblog... its worth a look to see how Ann Coulter is beginning to alienate her base. Hopefully, obscurity beckons.

Anomalocaris

2005-10-21T22:36:00.000+02:00

Pharyngula has a slightly different take on the same article.... focusing more on the tagmosis side of things (appendage homology based on which segment they emerge from). Tagmosis is a bit of a nightmare though... the farther back from the head you go, the more the appendages diverge into different specializations among different arthropod lineages, and the less sure you are about homology. Molecular work on developmental genes is going a long way towards sorting this out (thats how we know that the chelicerae in spiders is innervated from the deutocerebrum rather than the tritocerebrum), but for me its less interesting to argue over whether a pincer in one lineage is homologous to a paddle in another than to examine how both derived from an ancestral precursor.

That said, the more I think about linking the chelifores of sea spiders to the 'great appendages' of Anomalocaris, the more uneasy I get that we are leaping well ahead of the data. The big problem with the Cambrian lagerstatten is that they are snapshots in time... you don't get much in front of them and even less behind as they formed under fairly rare conditions. Anomalocaris appears then disappears, and its next to impossible to link it to any previous ancestor or descendant species. Although a few interesting lagerstatten fossils have shown internal anatomy, thats pretty rare, and usually confined to digestive systems. We don't have any idea how the neuroanatomy of Anomalocaris is arranged, and barring some miracle we find them swimming about a deep sea trench, we never will. The problem we have with Anomalocaris (and with other Cambrian arthropod-like fossils) is the same problem we have with contemporary arthropods... uncertainty about which segment is truly homologous with which, and (until recently) only the appendages to give a clue as to identity. What work like that of Maxmen et al. have done is show that appendage identity is really not that reliable a marker for segment homology. Unfortunately, studies such as hers are impossible on 500 million year old fossils.

Comments back up again

2005-10-21T22:16:00.000+02:00

Looks like haloscan was having a bad day.

Comments look down

2005-10-21T18:59:00.000+02:00

Wonderful... haloscan doesn't appear to be working this morning.

Getting a head in the world...

2005-10-20T11:39:00.000+02:00

The power of segmentation has always fascinated me. Starting with some generic animal where every segment is identical, you can evolve a myriad assortment of specializations: segments with legs, with wings, with cutting jaws, with specialized hairs for digging, with paddles for swimming, flaps for moving water through a burrow, tentacles for filter feeding.... the possibilities are tremendous. The diversity that can emerge from a simple body plan through specialization of segments can be seen all around us - from centipedes and spiders to giant Atlas moths, dragonflies, lobsters and barnacles.

One of the side effects of segmentation in arthropods is their decentralized nervous system. Each segment has its own mini-brain – a cluster of neurons organized into a mass called a ganglion – that takes care of local tasks such as moving that segments appendages and collecting information from that segments sensory neurons. The arthropods actual brain is more of a coordinator… it tells the segment what to do, but leaves it up to that segment to handle how to do it. That’s why when you remove the head of a cockroach, the body can scuttle away in one direction while the head flops about in the other.

Interestingly, the brain of arthropods started out as a set of segmental ganglia like those found in other segments. While most segmental ganglia specialized to coordinate movement, the ganglia of the first three segments of the ancestral arthropod developed around collecting and processing sensory information, and coordinating activity for the other body segments. Even though arthropods no longer have obvious head segmentation, we can see remnants of this ancestral segmentation by looking at what appendages are directly controlled by the brain.

The arthropod brain consists of three parts – the protocerebrum at the front, deutocerebrum in the middle, and the tritocerebrum at the rear. In insects, the deutocerebrum supplies nerves to the antenna while the tritocerebrum sends nerves into the labrum (a plate in front of the mouth that helps hold food in during chewing). In crustaceans, the deutocerebrum and tritocerebrum feed nerves into the primary and secondary antenna respectively. In spiders, it is the deutocerebrum that handles the head appendages (in this case, the chelicerae – the ‘fangs’ of the spider).

The big question has always been where did the protocerebrum come from? Unlike the other brain segments, there are no appendages associated with the protocerebrum – instead, it sends nerves into the eyes. This has led some people to think that the protocerebrum is a special structure originating from a hypothetical anterior region called an acron that never had appendages.

However, a recent paper in Nature describes how an obscure group of arthropods known as sea spiders or pycnogonids uses its protocerebrum to control its feeding arms (known as chelifores). These animals start out almost as little body-less heads… they have only a set of chelifores and two pairs of legs, innervated by the proto, deuto, and tritocerebral ganglion respectively. As they get older, they metamorphose into a creature that resembles a very thin spider, with 4 to 6 pairs of true legs. The head retains the chelifores and the larval legs are modified into feeding appendages (palps).

a, The three appendages of the protonymphon larva (shown) correspond to the cephalic appendages of the adult pycnogonid. b, The adult male cares for embryos until hatching (Nymphon rubrum).

Neuroanatomy of sea spiders implies an appendicular origin of the protocerebral segment
Amy Maxmen, William E. Browne, Mark Q. Martindale and Gonzalo Giribet
Nature 437, 1144-1148 (20 October 2005)

While insights into the brains of arthropods are interesting in their own right, whats fascinating about these findings is that we may be getting a glimpse into the ancestral arthropod ground plan. An accumulating body of evidence suggests that sea spiders represent the earliest branch of the arthropod lineage, before it diverged into insects, spiders, and crustaceans. While sea spiders are clearly specialized and have a fossil record that only goes back to the Devonian, the presence of appendages at the very anterior of the animal is tantalizingly similar to structures found on several Cambrian fossil animals such as Anomalocaris.

Its possible that the ancestral arthropods started life much as sea spiders do – as a body-less ‘head’ with a pair of anterior feeding appendages and two pairs of legs, and that as they grew they added additional leg bearing segments. Over the course of evolution, the legs (both the original two pairs and those occurring on later segments) specialized, with the anterior legs becoming additional feeding appendages and the posterior legs devoted entirely to walking. Finally, a point was reached where the appendages of the first segment were no longer needed and they were lost in the ancestor to most modern arthropods… except for the sea spiders, which had already diverged. During the course of these events, the original three ganglia expanded their function form simply moving the appendages to coordinating the sensory input and behavior of the entire animal.

Of course, this last bit is speculation… the Cambrian fossils have left no trace of their nervous systems and little is known about the larval stages of most Cambrian animals…. but if correct, it would go a long way to explaining how simple segmentation led to the most diverse group of animals on this planet.

Back away slowly....

2005-10-20T00:32:00.000+02:00

From Krauthammer at the Washington Post:

Beyond the brilliance lies the sheer terror. We have brought back to life an agent of near-biblical destruction. It killed more people in six months than were killed in the four years of World War I. It killed more humans than any other disease of similar duration in the history of the world...

...resurrection of the virus and publication of its structure open the gates of hell. Anybody, bad guys included, can now create it....

Why try to steal loose nukes in Russia? A nuke can only destroy a city. The flu virus, properly evolved, is potentially a destroyer of civilizations.

We might have just given it to our enemies.

Ooookaaaayyyy..... Someone needs a dose of reality. This is the sort of bad writing on science that is fueling the current panic over Avian flu. Sure, there are dangers involved in influenza research, particularly with the recreation of the 1918 Spanish Flu strain, and yes Avian Flu has the potential (albiet small) to adapt to human-to-human transmission and become a major threat. However, the last thing we need is crazy doomsday scenarios being touted as established fact and an already jittery public whipped up into a frenzy.

To begin with, we have had the ability to recreate influenza strains for some time now... almost a decade in fact. Since the influenza genome consists of 8 small stretches of RNA, its not hard to translate the RNA into a more stable DNA molecule and 'store' each stretch as a plasmid... a circular loop of DNA with extra sequences that allow it to grow and be maintained within bacteria. If you want to reconstitute your flu, all you need to do is put all 8 stretches of RNA into a cell (well, its not THAT easy, but definately not new technology). The real innovation in the recreation of the Spanish Flu was recovering the original RNA from samples preserved or frozen for almost 90 years.

That said, we are a far cry from Osama bin Laden cooking up fresh flu in some cave in Pakistan. You need a fair amount of specialized equipment and know how to do this... not easily accessable to terrorists. Sure, the sequence is published online, but despite what Krauthammer thinks, companies that make DNA do not just sell it to anyone who asks. Trying to remake Spanish Flu by stitching together several thousand tiny bits of DNA is going to require an incredible amount of patience and will definately catch the attention of the authorities.

What frustrates me is Krauthammers conflation of Spanish Flu and Avian Flu... these are two very different flu strains, and the fact both originated in birds is meaningless. What is important is that Avian Flu is a new virus with a high mortality rate, but a very low level of transmission in humans. Its not adapted to us, and with as a high a mortality rate as it has, its unlikely it will get the chance. Spanish Flu, on the other hand, is a product of the unique environment of the first world war. Unlike Avian Flu, it actually got worse as time went on.... adapting to an environment of crowded conditions and poor health, where a highly virulent pathology meant greater success at spreading, rather than being trapped in a dying, isolated host.

Or is it?

2005-10-19T20:06:00.000+02:00

If there is one hope for the Antarctic organisms threatened by rising ocean tempertures, its phenotypic plasticity.... the ability to be flexible in response to environmental change.

When we usually think of populations of organisms responding to a change in the environment (rising temperatures, new or better predators, new diseases) we often think in terms of genetic changes. In most populations of animals, there is usually genetic variation for any given trait (phenotype)... for example, some animals will be genetically programmed to have taller necks, or more body fat (better able to withstand lower temperatures), or brighter coloration. If the environment changes, some genetic variants within the population will be favored and produce more offspring, while others will die out or fail to reproduce. The end result is that when the population is viewed as a whole, both the the trait in question and the underlying genetics can be seen to change over time... natural selection and evolution at work.

Phenotypic plasticity is the ability to alter ones traits (neck size, fat layer, coloration, etc.) without undergoing a genetic change. The plant or animal may sprout spines in response to predators, change color to better blend in to the background, or produce more offspring when food is abundant.... without changes in the underlying genes. Whats interesting is that this ability to respond to the environment is genetic. When environmental conditions change rapidly, an organism that can alter its traits will do better than one that takes a gamble on its genes and either lives or dies as a result.

I mentioned in my last post how global warming is like a giant man-made experiment in adaptation... well, one of the ways plants and animals are adapting to the rapid changes in climate is to evolve the ability to adapt. In this weeks Science there is an article on how climate change is causing Great Tits (Parus major) to become more flexible as to when they lay their eggs. Great Tits, like most passerine birds, feed their young on caterpillars. In order to ensure their young will have an ample food supply, they try to time the laying of their eggs so that when the eggs hatch, the number of caterpillars available to feed them will be at its peak. Because the growth rate of caterpillars is directly affected by the climate, if the birds want to get the most caterpillars for their chicks they have to breed earlier in warm years than they do in cold years. With recent changes in climate, the Great Tits have been getting more and more out of sync with the caterpillars they depend on, as the caterpillars now peak two weeks earlier, around when the Tits are laying their eggs - not when they are hatching.

What Nussey et al. have found in their review of 30 years of Dutch bird data is the emergence of a sub-population of Great Tits that has become much more flexible in its response to rising temperature and caterpillar emergence. While the Great Tit population as a whole is in decline, these adaptable birds are managing to hold their own and produce more offspring than their less adaptable peers. Its still early in this 'grand experiment', but the outcome looks like these birds that have evolved flexibility will take over and replace their more 'conservative' bretheren. The next big question is whether these birds can evolve enough flexibility to survive as the pace of climate change increases.

Last chance to see.... penguins?

2005-10-19T17:34:00.000+02:00

Depressing news from the Antarctic... ocean temperatures are rising much faster than expected, with potentially devastating effects on the marine wildlife.

Animals that live on the seabed around the Antarctic Peninsula, where summertime water temperatures currently peak at about 0.5C, are sensitive to small shifts in temperature. In water just two degrees warmer, molluscs become unable to bury themselves in seabed sediment, limpets cannot turn over and scallops lose the ability to swim. These changes would make them more susceptible to predators, disrupting the food chain and quickly endangering larger animals and birds. "If the warming goes on at the same rate for 50 years or 100 years then lots of populations of animals I work on, and maybe entire species, would be at risk," Professor Peck said.

This doesn't really surprise me.... the arctic and antarctic regions of this planet have been seeing some of the strongest effects of global warming, with average air temperatures rising and glaciers showing signficant melt. It only makes sense that the warming would affect the ocean water itself. Unfortunately, these effects are not going to limit themselves to just the polar extremes.... its tempting for some to think that we are just going to lose a few obscure animals in a place that no one ever visits, so who is going to care? However, the Antarctic and Arctic oceans are important food resources for birds and mammals (particularly whales) that migrate there to feed before returning to more temperate water. Extinctions at the extremes of the globe will have effects that reach far into our own familiar territory.

The worst part is that there isn't much we can do about it now... we've passed a point of no return in global warming. Not much to do now but enjoy the worlds largest experiment in organismal adaptability.

Journalism and Science

2005-10-19T03:00:00.000+02:00

Once upon a time I thought of being a science journalist instead of a scientist.... this blog is in some ways an attempt to try and write about science for a general audience. I've always felt that it is important for scientists to convey to the 'ordinary Joe' what it is they do, not the least because the 'ordinary Joes' of the world pay our salaries.

So why did I major in Biology instead of Journalism? Well, for a start, attitudes like this one:

A problem exists within the high-school education system: It doesn't prepare students for their careers. When I decided in high school that my major was going to be journalism, I took the only class offered by my school in hopes of learning the journalistic writing style. I didn't learn anything from that class. My teacher was not a journalism teacher; she was an English teacher. We spent every class silent reading instead of learning about the inverted pyramid.

The school system needs a reality check; most students aren't going to be mathematicians, historians, or chemists. So why do we have to take these classes

This from a journalism major. Worse, this was printed in a school paper, with the approval of various collegues and editors... also (I would guess) journalism majors and professors.

PZ Meyers and SuperDoomedPlanet have already had a take on it, so I'm not going to say more about our budding young journalist from Iowa. Her attitude doesn't surprise me though... I've written for several university papers, and one thing that has struck me is how journalists are encouraged to be empty vessels that merely regurgitate whatever is fed to them. This makes the average journalist fresh from J-school a terrible science reporter, since they lack any background at all to understand what scientists are telling them, never mind to evaluate what they are saying. What I've always found ironic is that the one area of journalism where this emty-vessel attitude is not encouraged is sports journalism. Would a newspaper hire a sports journalist who thought Knute Rockne was the British ski jumping champion? Why then do they discourage thinking skills in other forms of journalists?

Journalism shouldn't be a major at all, but rather a set of courses that focus on the specialized style of writing and information gathering journalists need, taught alongside a major in some other field... science, english, psychology, philosophy... something that broadens the future journalists horizons so that they can understand, evaluate, and ultimately select the information given to them for inclusion into their articles. Journalists need to be intelligent, well rounded individuals. Not empty echo chambers like our aspiring journalism major from Iowa.

Adding a site counter

2005-10-19T00:55:00.000+02:00

Perverse curiosity if anyone is actually reading any of this...

Urochordates

2005-10-19T00:43:00.000+02:00

Well, now that the introduction is out of the way, time to bring out the first (of I hope, many) creatures I'll be highlighting on this blog. And what better organism to start with than the one dear to my heart, Oikopleura dioica? But first, I need to throw in a bit of general background on the larger group of organisms to which Oikopleura belongs.... the urochordates.

So what is a urochordate? Probably the most familiar member of this group is the sea squirt... a marine animal that sits attached to rocks, spending its life sucking in water through one hole, filtering out the food with a big bag of mucus, and then sending the waste water out another hole. Sea squirts lead a sedentary existance, quietly filtering away until old age or predators get them. However, for a very brief period in their life sea squirts can be very active. Newly hatched sea squirts come out of the egg looking like little tadpoles... a lump of a body with a tail attached to the rear. They swim about for several hours looking for a solid surface to land on, then glue their heads to ground, absorb their tails, and metamorphosize into a sac-like creature with an intake and an outflow hole.

Its that tail that makes sea squirt larva so interesting... it has several features that indicate urochordates branched off early from the same evolutionary line that led to us. Running down the center of a sea squirts tail is a rod-like structure known as a notochord, which gives support to the tail and helps provide something for the muscles to act upon. Running the length of the tail just above the notochord is the dorsal nerve cord, transmitting signals from the sea squirts brain to the tail muscles.

If this sounds a bit familiar, its because we have a similar system in our bodies... a dorsal set of vertebrae to which our skeleton and muscles are attached and a dorsal nerve cord running above the main axis of the vertebral column (although also surrounded and protected by vertebrae). Early in our development, we also have a notochord, but as we grow it becomes replaced by our bony vertebrae. The reason for this replacement is obvious... what can provide structural support for a 2mm long aquatic larva would barely hold together a 6 foot tall terrestrial biped. In fact, only two other groups retain their notochords... the lancelet fishes (not an actual fish, but similar in appearance) and the hagfish. In all other chordates, the notochord is replaced by either bone or cartilage.

Although all urochrodates have a notochord, a dorsal nerve chord, and thrive by filter feeding plankton through a mucus bag, not all have become sedentary animals like the sea squirts. Oikopleura belongs to a group of urochordates called the Appendicularians.... these fellows hatch out of the egg looking like sea squirt tadpoles, but instead of attaching to a rock and losing their tails, they keep their tails into adulthood. Whats unusual about the Appendicularians is that to help themselves get food out of the surrounding water, they build for themselves houses of protein and cellulose that contain an elaborate system of filters to concentrate the food, remove stuff they can't eat, and bring the rest into their mouths. The beating motion of their tails powers this massive food concentrator, drawing in the food laden water to the filters.

I'll have more to say about the Appendicularia in my next post... hopefully with some pictures included.

Year 0

2005-10-18T19:59:00.000+02:00

Welcome to yet another blog cluttering the pages of the internet.... though hopefully this will be a blog with a difference.

The aim of this blog is to talk about my favorite subject, the biology of obscure organisms.... all of those little creatures that rate only a paragraph or two in the back pages of dusty tomes, or which occupy a single slide on the neglected shelves of museum collections. You might remember them from some college lecture... mentioned briefly then forgotten. Something jelly-like, or with legs sprouting in all directions, or tendrils creeping through some other creatures body. The strange plants and animals that made you sit up in biology class and think 'that is really weird'.....

Of course, I'll be posting on other subjects as well.... mostly science related with a few scattered rants, though I want to avoid this becoming a political blog. Hopefully every week or two I'll be able to profile an obscure organism... something newly discovered, or more likely, almost forgotten.

2005-10-18T18:18:00.000+02:00

Haloscan commenting and trackback have been added to this blog.