Tuesday, April 29, 2008

Insurance and the Age of Personal Genetics

In the age of the personal genome, companies like 23andMe are springing up, offering personal genetic profiling and ancestry tracing. While there are questions about the accuracy of their claims, the interpretation of the results (are we about to see a boom in genetic counsellors?) and other ethical and privacy considerations, the US Senate has made a pro-active move in passing a bill banning genetic discrimination. In short, the bill prohibits employers or insurers to use personal genetic information in decision making. Ars technica takes a closer look at the insurance angle, explaining why the bill is a good idea. From the article:
Worse yet, the very concept [of insurance based on genetics] threatens to undermine another of the greatest potential benefits of the genome: personalized medicine. The goal of personalized medicine is to tailor treatments to a the unique genetic defects that have helped foster a disease, be it diabetes or cancer. But, if insurers can deny coverage based on those same genetic traits, the patient may never see the treatment.


GSK acquires Sirtris Pharmaceuticals

Pharm giant GlaxoSmithKline acquired Sirtris Pharmaceuticals for the tidy sum of $720 million US last week.

This story is interesting not because of the excitement of corporate deals and stock market fluctuations, but because Sirtris Pharmaceuticals specializes in developing small molecule activators of SirT1. And anything involving SirT1 - my protein of interest - is inherently fascinating.

It's actually more interesting for other reasons. Previously on this blog, I've echoed a sentiment common in the skeptical blogosphere: There's no such thing as alternative medicine. Once a treatment has been shown to work, it becomes part of mainstream medicine. Resveratrol, a polyphenol, is a SirT1 activator. SirT1 (I told you it was interesting) has been shown to be involved in insulin signaling, energy metabolism and lifespan extension in model organisms. Other work has shown resveratrol to have cardioprotective and anti-cancer effects. Resveratrol has long been thought to be a molecule behind the 'drink red wine' wisdom.

This all sounds great. And 'alties' probably feel vindicated: Resveratrol has been on sale in health food and dietary supplement stores for ages. Before many of the studies mentioned above had been done, in fact. But don't go reaching for your wineskin just yet. Studies have also shown that oral resveratrol has poor bioavailability.

That's where Sirtris comes in. They develop compounds that are analogs of resveratrol to improve potency and bioavailability (and patentability), and test those compounds. And Big Pharma (GSK) has taken notice, decided this is viable science, and acquired Sirtris in the hopes of turning these compounds into diabetes, anti-obesity or anti-aging drugs. Like other examples we've discussed this is a case of a natural or alternative medicine becoming mainstream (or, rather, the beginning steps of that process).

The moral of the story isn't that natural products work. In this case it doesn't - all resveratrol supplements will give you is expensive urine. The point is that if the science is there, the medicine will come.

There's still a possibility that these compounds will fail for one reason or another. Perhaps they won't be effective in humans as in rodents. Maybe there will be toxicity issues. If this happens, no doubt that Big Pharma conspiracy theorists will jump up and down saying that GSK made the purchase to squash a promising natural medicine. An almost 1 billion dollar investment seems to be a bit much for such a petty goal. If I was the big, evil corporation, I'd sink that money into the supplement makers and keep it on the shelves. But shrewd companies know that a tested drug has more value than an untested one. The only reason not to get science onside is if you don't think it will support you.


Sunday, April 27, 2008

State-of-the-Art Geeky Coffee

The coffee-maker pictured above is known as a Japanese siphon bar (see the NY Times website to see a slide-show of the thing in action). It is the only one of its kind in the US, imported for a mere $20,000. Eleven dollar globes of the non-espresso coffee product are apparently all the rage on the San Fransisco hipster-blogger-academe coffee-shop scene. The Times recently reported on this new trend in high-end brewed coffee making. The siphon bar is found at the Blue Bottle Coffee Company. Owner James Freeman explains the concept:

“Does coffee brewed from single-origin beans in a siphon or a Clover taste more yummy than, say, Folgers from a percolator? I believe it does. But it would be hubris to suggest that we’re making better coffee than anyone ever has. My feeling is, there are already enough places where you can get a cinnamon latte and a muffin wrapped in plastic. Why would I want to build another one of those?”

Supposedly this thing makes the greatest cup of coffee known to (wo)man. No less than Starbucks has bought the rights to similar technology (the mystical "Clover"). I'll admit, my curiosity has been aroused. But I'm sure as hell not going to pay that kind of cash for a taste (not to mention the plane ticket). So I fired up the YouTube and did a little commercial espionage (see video clip and watch the brewing process in action). Turns out these guys are a bunch of scientist wannabes! I figure it'd be pretty easy to rig one up with a bunsen burner, a couple of flasks, a Buchner funnel and a vacuum line. All easily found within your standard biomedical research lab...except for the Yo-Yo stunt man...


Saturday, April 26, 2008

Unscientific Art

Found on BoingBoing.
"Science painter Cornelia Hesse-Honegger collects and paints mutant bugs in the vicinity of irradiated wastelands like Chernorbyl, around nuclear plants, and nuclear refining sites."
Here is a link to the title page of this work.
Awesome paintings of messed up bugs. Too bad that's pretty much all it is, and claims that the observed mutant phenotype of the insects has something to do with radiation from nuclear power plants is probably just to attract some attention to the great artwork.
I love entomology and genetics so otherwise this would have been really cool with some statistics and some controls.


Thursday, April 24, 2008

IA updates

Once again informationaddiction.com has some updates. Infrequently updated but always good.


Carnival Call for Submissions

The next edition of the cancer Carnival (#9) is coming up on Friday, May 2nd. Make sure you submit your posts here by May 1st (one week from today). This edition will be hosted by Alexey at Hematopoeisis.


The Joys of Scientific Discovery

Man this little story was just too funny not to make a Ctrl+C, Ctrl+V blog post:

I hope that e-lab notebooks don't catch on, because they lose a lot of character when 'people are watching'. I remember doing in vivo recordings, sometimes for ~20 hours, in grad school. If the neurons were alive, I was recording. Things were pretty automated, so I would pass the time looking at the oscilloscope during stimulation trials while drinking Busch light. After about 10 beers one night, I finally realized what the neurons were doing and got a C/N/S paper out of it. I remember looking at my notes from that fateful night, scribbled with the drunken uncoordination that is only found on pub toilet walls: "THEY'RE FUCKING OSCILLATING!!!!" I wrote this about 10 times as I went back and looked at the sweeps from previous experiments that I had pasted into my notebook. Then, I perfused the animal, drank 2 more beers, had a smoke in our fume hood, and passed out. I was awoken by our TurboTech at 7 am.

I still have the notebook, complete with beer stains and coffee stains (and probably some drool). That's not something I'd be willing to live-blog, or even transfer onto the web, though. It could only be appreciated as a scratch-and-sniff YouTube video; or in my blurred memories of grad school.

This great anecdote courtesy of TreeFish, commenting in response to a post by PhysioProf on the idea of open digital lab books ("Science 2.0 Open Access Lab Notebooks" Is Completely Absurd) over at DrugMonkey.


Wednesday, April 23, 2008

Sugar and spice and everything nice...

...that's what little boys are made of? Nature News is reporting on a paper that suggests that that diet influences the gender of your offspring. In a retrospective study, the authors asked women about their diet in the weeks leading up to pregnancy and analyzed the results. They found that women with a higher caloric intake were more likely to have boys. The researchers think it may have to do with high blood glucose levels. Though a potential mechanism is unclear, they note that many animals give birth to more males when resources are plentiful.


Monday, April 21, 2008

How can chromosome numbers change?

The question:
How did life evolve from one (I suspect) chromosome to... 64 in horses, or whatever organism you want to pick. How is it possible for a sexually reproducing population of organisms to change chromosome numbers over time?
For the answer read this.


Friday, April 18, 2008

Top 5 McGyver moments in the lab

Have you ever had one of those McGyver moments in the lab where you inventively use lab supplies or household objects to make an experiment work? These people brought it one step further:

1- Michelle Kline at the University of California had to improvise a material to build microfluidics chambers when her funding dried out. She turned to Shrinky Dinks, and created a low cost alternative!

2- Ellie Wollman and Fran├žois Jacob had to improvise a way to look at bacterial conjugation and to map the genome simply by measuring the time of transfer. But they needed a way to abruptly stop conjugation, so they use a blender to sever the pili and stop the transfer!

3-Hans Spemman was studying embryology in the 1930's and one of the questions of the time was if every cell has a deterministic fate from the first division on or if they acquire their fate later in embryo development. To divide a cell before it's first division Spemman used a baby hair (since they are sturdy yet very fine) to cleave the cell. In fact just by using this technique and tweezers he was even able to do nuclear transfers and kickstart the study of stem cells. Talk about being ahead of your time.

4-In one the labs I've worked in in the past, we use to cut corners and make our own DNA ladder and our own TAQ polymerase. But Orac takes it further and contemplates how to create your own electrophoresis box. And of course you can make your own DNA columns if you visit the local potery shop, or just reuse your Qiagen columns.

5- Submit your story in the comments, and we'll see if it's McGyver-worthy...


Blogging about Blogging about Blogging

AC recently lamented:

"This blog was more fun when it was about quirky research papers and fart & dick jokes. All this meta 'blogging about blogging' stuff is intellectual masturbation."

I'm not sure what intellectual masturbation is exactly, but if it's anything like the real thing... Anyhow, nobody likes an unhappy Coward so here are some Bayblab blasts from the past:

For those looking for some new material, here are some quick hits:

And now back to your regularly scheduled programming


Wednesday, April 16, 2008

Arguing From "Authority" Instead of Evidence

DrugMonkey has written up a great post on the problem of relying on "authority" or credentials in scientific discourse:

"In science, the distinction arises when one wishes to short-circuit the process by which the expert demonstrates her expertise by providing the interpretive narrative and rationale by which she has arrived at her conclusions. Once one moves on to the "just trust me on this" or "well, my professional experience and judgment lets me know that ...." argument, it becomes an appeal to "authority" for authority's sake, as opposed to an appeal to the experienced individual's actual related expertise."

One would think this would be self-evident, especially to bloggers professing to be scientists of great "authority". However it was none other than Greg Laden who kicked off the whole discussion with commentary following Kamel's recent post on anonymous blogging. Laden seemed to be arguing that anonymous blogging is a bad thing because one is unable to assess the credentials of the speaker, and therefore unable to determine the validity of their arguments.

I've said most of what I have to say on this topic in the comments to Kamel's post and over at DrugMonkey's place. Here I'll summarize by saying I tend to think that the validity of an argument has to do with evidence and reasoning, and not how many degrees or prizes the speaker has won. An accurate statistic quoted by an anonymous blogger for example, is no less accurate because the identity of the person citing it is unknown. Likewise, it is no more likely that HIV is not the cause of AIDS just because Kary Mullis won a Nobel prize for the invention of PCR.

But that's just my opinion.

UPDATE - Greg Laden has now posted a clarification of his position on anonymous/pseudononymous blogging at his place. Go there to read his opinion for yourself.


Random Genetic Drift

The anti-evolution film Expelled: No Intelligence Allowed is being released on Friday and the US National Centre for Science Education site Expelled Exposed has gone live. The site is a point-by-point examination and de-bunking of the claims made in the film. The site hit Digg and is currently working out the high traffic issues, but some of the comments at Digg were interesting.

I am not an evolutionary biologist, but the comments seemed off. Most of the pro-science commenters there equate evolution with Darwinism - that is, speciation by mutation and natural selection. Natural selection is one evolutionary mechanism - indeed, the one people are most familiar with - but it is not the only one. Larry Moran at Sandwalk kicked off a bit of a discussion of this when he asked his readers to define evolution, and many different ideas were kicked around. Larry also has a nice explanation of one of those mechanisms, random genetic drift, in a piece at talkorigins.org. From the article:
"If a population is finite in size (as all populations are) and if a given pair of parents have only a small number of offspring, then even in the absence of all selective forces, the frequency of a gene will not be exactly reproduced in the next generation because of sampling error. If in a population of 1000 individuals the frequency of "a" is 0.5 in one generation, then it may by chance be 0.493 or 0.505 in the next generation because of the chance production of a few more or less progeny of each genotype. In the second generation, there is another sampling error based on the new gene frequency, so the frequency of "a" may go from 0.505 to 0.510 or back to 0.498. This process of random fluctuation continues generation after generation, with no force pushing the frequency back to its initial state because the population has no "genetic memory" of its state many generations ago. Each generation is an independent event. The final result of this random change in allele frequency is that the population eventually drifts to p=1 or p=0. After this point, no further change is possible; the population has become homozygous. A different population, isolated from the first, also undergoes this random genetic drift, but it may become homozygous for allele "A", whereas the first population has become homozygous for allele "a". As time goes on, isolated populations diverge from each other, each losing heterozygosity. The variation originally present within populations now appears as variation between populations." (Suzuki, D.T., Griffiths, A.J.F., Miller, J.H. and Lewontin, R.C. in An Introduction to Genetic Analysis 4th ed. W.H. Freeman 1989 p.704)
(A quote of a quote? How meta.) I think some of the numbers were miscopied from Suzuki et al. so I've changed them here, but it isn't the actual numbers that are important so much as the concept. Read the full article, it's quite informative and covers a variety of examples of genetic drift.


Tuesday, April 15, 2008

Magnetotactic Bacteria

Recently heard about this strange class of microbes, magnetotactic bacteria, which produce and contain magnetosomes. These are iron complexed with protein and are arranged intracellularly as a chain. The iron is in the form of magnetite, the same form present in naturally occurring lodestone. Magnetite, as you might have guessed, is magnetic. The magnetosomes in the magnetotactic bacteria facilitates magnetotaxis ie. their movement based upon the magnetic field of their environment. And this, it is thought, is the purpose of these structures in the magnetotactic bacteria. These bacteria are very senstive to the redox potential of their environment and use the magnetic field of the earth in order to find "down" to a less oxygen rich environment. Thus bacteria in the northern hemisphere have their magnetosomes arranged in such a way as to get them to swim to magnetic north, which is slightly down in the northern hemisphere, away from oxygen. The opposite it was thought was true in the southern hemisphere. I ran into a great science article that sheds some doubt as to this purpose of magnetosomes. Apparently this group found "south-seeking" magnetotactic bacteria in the northern hemisphere.
I'm just guessing here but when I first heard about these bacteria I thought that the magnetic field they produced might have been useful for biofilms or to arrange themselves in some bacterial community. But that's a nature paper for someone else.
Magnetosomes are pretty interesting themselves and have some biotechnology applications.
What is actually pretty spooky is that not only do migrating birds and salmon have magentosomes, but so does the human brain.


PIC of the week

Anyone care to guess what this is?

Edit: This is actually SPACE DNA. Famous lab guru and saxophonist, Kenny G, used it as a background at lab meeting. The picture was taken a little over a year ago, and shows the double helix nebula, near the center of our galaxy. Watson and Crick might as well have been peering at the heavens to come up with their model. Upon seeing the picture I wondered what kinds of processes could give rise to such a structure. There has to be a force driving a rotation and another driving the elongation that combined create a torsion of the gas in the nebula:

"We know the galactic center has a strong magnetic field that is highly ordered and that the magnetic field lines are oriented perpendicular to the plane of the galaxy," Morris said. "If you take these magnetic field lines and twist them at their base, that sends what is called a torsional wave up the magnetic field lines."

Follow the link to read a more detailed explanation.


Monday, April 14, 2008

AACR mini-carnival

The American Association for Cancer Research (AACR) annual meeting is going on right now in sunny San Diego. I'm not there, but a few stories from the conference are hitting the news.

A group from Texas is reporting a possible predictive test for lung cancer from oral swabs. The test looks at p16 and FHIT, two genes with known cancer links. These genes are deactivated in a large percentage of smokers with a 95% correlation between mouth and lung samples. The authors hope cheek swabs can be used as a less invasive monitor of pre-cancerous genetic changes in tobacco related cancers.

Other researchers at the conference are reporting data from cancer vaccine trials. The vaccine, E75, was shown to reduce mortality among patients with HER2/neu-positive breast cancer. In a small clinical trial, breast cancer patients receiving the vaccine had lower recurrence and up to 100% decrease in mortality compared to controls after 30 months (depending on the HER2 levels of the tumour). The vaccine is about to start phase III trials.

Finally, a group from Duke presented data that showed that, in mice, prostate cancer was worsened by exercise. In this study, prostate cancer implants grew faster on mice provided an exercise wheel compared to mice without a wheel. The authors believe it may be because of increased blood flow to the tumour and hope to apply this knowledge to improve drug delivery and treatment. They also stress that the risks of heart disease, diabetes and obesity far outweigh those of prostate cancer, so don't trade in your treadmill just yet.

One of our friends colleagues is at the AACR meeting, so hopefully we'll have more details and more interesting news pieces to report. If you're a blogger and at the conference, submit your posts to the Cancer Research Blog Carnival.


Sunday, April 13, 2008

Scientific Apathy at Seminars and Lab Meetings

Some great discussion going on regarding Speaking Up in Seminars and Grad Student Solidarity, courtesy of PhysioProf (@Drugmonkey) and A Lady Scientist. Lady Scientist's first remark was interesting:

"Students don't tend to ask questions at these Journal Clubs. In fact, I think that the prevailing sentiment is that we're supposed to go easy on the students, because if we were up there wouldn't we want the same consideration? So, easy questions (eg. Can you define that negative control?) are ok, but the hard ones (eg. Those controls are very off. Can you still interpret the data?) are not."

As was the response from PhysioProf:

"The issue under discussion is whether there should be a principle of "solidarity" among trainees--grad students and post-docs--in public venues such as seminars and journal clubs, pursuant to which trainees do not challenge one another publicly, so as not to show each other up, or embarrass one another. The answer is a resounding, "Fuck no!"...

This kind of attitude is completely insane. The entire essence of science--what defines it as a profession--is that scientists ask all questions that present themselves, either of themselves or of others...

I gave a research seminar at another institution this week during which the audience absolutely hammered me with really good perceptive critical questions. I fucking loved it. It meant they were interested and engaged. What could be more boring than standing in front of a room blathering on in the face of polite indifference

When you fail to ask a question, or raise a criticism, based on some misguided sense of "loyalty" or "solidarity", you are actively harming the scientist you think you are protecting. Because someone somewhere will eventually ask the question--a paper reviewer, a grant reviewer, a thesis committee member, a job search committee member, a job seminar audience member--and the sooner the issue gets raised, the sooner the scientist can address it."

These are just excerpts but there's lots more interesting discussion over at their sites and in the comments.

I don't have much to add (I think PhysioProf is bang on, but I'm sure many students share Lady scientist's concerns) but I can certainly relate to the observations - Audience Apathy at lab meetings, journal clubs and seminars has long perplexed me. Even harder to understand is Speaker Apathy. Why do so many students and post-docs (sometimes even the ones giving the talk) bother to show up to group exchanges week after week if not to participate and interact?


Friday, April 11, 2008

The coolest/grossest thing I've seen (today)

The birthing process of the Surinam toad:Yes, those are babies bursting from its back.

(HT: Zooillogix)


Answers and Winners of the Bayblab's Animal Evolution Challenge!

Ok people, as promised it’s time for the answers to the Bayblab’s recent evolution challenge! The task was to determine whether certain organisms were more, less or equally related to us humans than the model organism Drosophila melanogaster. Thanks to everyone who gave the challenge a shot, to Nimravid and Larry Moran for sending over participants from their blogs (both worth checking out). As many of you noticed, this seemingly simple task is a lot more difficult than it seems on first glance (and second, third and fourth glances). That was the point. I certainly would have flunked the challenge had I not myself devised it whilst staring at a phylogenetic tree. (Even with the tree I find it difficult). I was interested to see how others would fare.

I chose the comparison to Drosophila for two reasons. First it is an intensely-studied model organism. This means that Drosophila geneticists are constantly trying to convince us that their flies are virtually identical to humans (due to evolutionary conservation of molecular pathways and so forth) and therefore highly relevant to biomedical research. Second, many of the obvious physical characteristics of arthropods like Drosophila confound their true evolutionary relationship to humans and vertebrates in general. Until recently, I had a vague notion in my head that flies belonged to some sort of phylogenetic group of things with limbs, bodies, heads and eyes. It was just that flies don’t have backbones, and we do. I remember being shocked a couple years ago when a visiting speaker declared that sea urchins were a better model for studying development because they were so much more related to us than D. melanogaster. Turns out she was right. According to phylogeny, it would seem that many of the macroscopic similarities between humans and flies are examples of parallel or convergent evolution.

So this brings me to the main point of the challenge and the key to solving most of the questions. Drosophila melanogaster and Homo sapiens belong to phyla from opposite sides of two major branches of the animal tree, the deuterostomes and the protostomes. These lines split off from a common bilateran ancestor around 670 million years ago. The main features that distinguish these groups of phyla are embryological, like which hole becomes the anus and so forth.

At any rate, D. melanogaster belongs to the arthropoda (insects), which share a common protostomian ancestor with a diverse crowd of phyla that includes the molluscs (ie clams, snails, squid, octopuses) the nematodes (roundworms) and annelids (earthworms, leeches). On our side (the deuterostomes) we have the chordates (includes all animals with notochords like the tunicates and the lancelet, as well as all vertebrates) as well as the echinoderms (includes the sea urchin, starfishes and sea cucumbers).

So with this in mind most of the questions can be answered. Deuterostome species share a more recent common ancestor with each other than they do with the protostomes, so we are more similar to each other than to D. Melanogaster (a protostome). Falling in to this category are 1) starfishes, 2) the spotted salamander 7) the tunicate, Botrylloides violaceus, 8) the lancelet and 10) the yellowfin tuna. On the other hand, sharing a more recent common ancestor with the arthropods, other members of the protostomians are likely to be (roughly) equally similar to us as D. melanogaster is. So equally similar are 4) the common snail and 9) the roundworm C. elegans.

So this leaves: 3) the Palau stinging jellyfish, 5) Trichoplax adhaerens and 6) the cloud sponge, Aphrocallistes vastus. Both we and our protostomian cousins parted ways with these guys before the proto/deuterostome split. So both we humans and Drosphila share a common triploblastic bilateran ancestor that they do not. The major phylum falling into this category is the Cnidaria (jellyfish, corals, anemones). Our ancestry with the Porifera (sponges) and Placozoans (ie the peculiar Trichoplax adhaerens) appears to be an even more ancient one. So, the remaining species 3), 5), 6) are less related to us humans than D. melanogaster is.So, to summarize, the correct answers are as follows:

1) more related to humans D. melanogaster (starfish)

2) more related (salamander)

3) less related (jellyfish)

4) equally related (snail)

5) less related (Trichoplax adherens)

6) less related (sponge)

7) more related (tunicate)

8) more related (lancelet)

9) equally related (roundworm, C. elegans)

10) more related (yellowfin tuna)

11) equally related (squid)

And the winner is…

A three way tie! Between Adrian Thysse FCD, michaelf and windy. Congratulations guys! You got all 11 questions correct. Very impressive. (You must be geniuses, evolutionary biologists, or both). You get to split the karma!

And the runnner up is...Rebecca! Rebecca got only one wrong (#11) and was the fastest to buzz in. Fast and accurate. Very nice. Congratulations to you as well!

Anyway these are the correct answers as I (a lowly “biomedical researcher”) understand phylogeny based mainly on my interpretation of Mayr (What Evolution Is, Mayr 2001). The most recent molecular data as discussed a current Nature paper, (HT windy and Nimravid) seems to support them. (A beautiful animal phylogenetic tree from that paper is available here. Great poster for your wall!) Nonetheless, if anyone has a grievance and wants to make their case, bring it!

Stay tuned, as I’ll be adding a breakdown of the “class’s” answers. This should be interesting. Also, I hope to discuss what this all means with respect to the relative value of Drosophila as a model system for human biology in a future post. Are there organisms we're not paying much attention to that would be better? If you have comments on this topic they would be interesting to hear so feel free to kick it off below.

PS – If you want to look at the answers from commenters on the original post, you’ll have to click on the post title to see them all. Or click here. Seems our comment script is bugging out and spitting out incomplete comment listings in the main page.


Thursday, April 10, 2008


Measles seems to be popping up everywhere these days. In February, 3 children in San Diego were diagnosed with the virus, the first reported outbreak since 1991. This initial outbreak spread to another, followed by another 6 and a quarantine. In March, health authorities in Seattle warned travellers of possible exposure. This past week, a measles warning was made for guests at a wedding in Rockland County, NY and, in a separate case, Nassau County, NY. In Milwaukee, four cases have been recently identified, 3 of them in children under 2 years of age. Twelve other children have been quarantined. In Canada, health officials in Guelph have issued a measles warning after an individual who was diagnosed may have exposed others. And in Toronto, 5 cases have been confirmed in the past 4 weeks.

Measles is a highly contagious virus. Symptoms include fever, cough, runny nose, conjuntivitis and a potentially itchy rash. Complications are common and include pneumonia, encephalitis and corneal scarring. In developed countries, the fatality rate is about 1:1000 in otherwise healthy people.

If only there was some sort of shot to prevent infection.


Scientists on drugs

Nature published today the results from a poll about cognitive-enhancing drug use amongst scientists. The results are shocking. 20% of responders have admitted to using drugs for non-medical reasons in order to boost concentration and work. Top amongst these are Ritalin and beta-blockers. I knew kids nowadays used Ritalin to study for tests but I had no idea PI used it too. The scientists who didn't get prescriptions, got their drugs on the internet not surprisingly. I guess coffee is just not enough when it comes to grant deadlines. Is this a reasonable use of drugs? Should we be scared of this. I know I could use beta-blockers when giving talks to large audiences, and I wonder how many do...


Tuesday, April 08, 2008

Malignancy from organ transplants?

I've always wondered about this: Is it possible to get cancer from a donated organ? In theory the organs are inspected and come from healthy donors, but microscopic lesions would be undetectable. Furthermore, the recipients are on immune suppressants, making the cancer even more likely to develop. In fact it's a common occurrence in recipients to develop de-novo tumours after transplantation, but it's usually from their own tissue and a direct result from the drugs. For example, melanomas are 1.6-2.5 times more likely in the transplant population. Well a story this week explains how a 15y old boy who was mis-diagnosed with meningitis but who in fact had lymphoma, ended up causing the death of 2 of the four recipients of his tainted organs. The other two had the organs removed and are undergoing chemo. I wonder if they have improved chances of survival once they are off the immunosuppressants since the cancers are mismatched or whether the match required for transplantation is close enough for the tumour to behave like a de-novo host tumour... The Lancet has a great review on how to threat both types of malignancies:

"Transmission of an undetected tumour in the donor is rare (incidence 0·02%).77 The question of whether a tumour in the recipient has arisen de novo or by transmittance from the donor can be answered by doing a biopsy of the tumour and cross karyotyping the recipient and donor tissue to establish tumour origin. [...] The overall mortality from donor-related malignancies is calculated at 38%, with that of transmitted tumours at 46% and derived de-novo tumours at 33%. Cadaveric-donor-related tumour mortality is 0·007% (8 of 108 062 recipients).77"


Monday, April 07, 2008

Test Your Evolutionary Knowledge

Time for a fun game here at the Bayblab to give you a break from the usual highly demanding intellectual content! The topic is evolution and the subject is the fruit fly Drosophila melanogaster. As you should know D. melanogaster has long been used as a model organism in biology and has been particularly instrumental in most of the important advances in genetics over the past century. It is now being extensively used by researchers to understand human diseases such as cancer and Parkinson's.

So today's game is simple enough. I'll list off a bunch of organisms, and you say whether each is more, less or equally related (biologically) to us human beings than the fruit fly pomace fly?, D. melanogaster. So, for example, if the organism were the chimpanzee, the answer would be "more", as we clearly have more in common with chimps than fruit flies.

Everyone, including Creationists, can play. But no cheating please! That means no Google, Wikipedia or textbooks, etc. We just want to get an idea of what the average, highly intelligent Bayblab reader thinks. There's no penalty for wrong answers, but cheaters' comments will be deleted, they will be banned from the Bayblab for life, banished to PZ Myer's dungeon and forced to read Greg Laden's blog for the rest of their days. And Larry Moran will call you mean names. The winner will become very famous and enjoy 100 years of good blogging karma. The correct answers will be posted in a few days. Good luck!

Here we go:

1) The Starfishes (Asteroidea)

2) The Spotted Salamander

3) Palau stingless jellyfish

4) The Common Snail

5) Trichoplax adhaerens

6) Cloud Sponge, Aphrocallistes vastus

7) The Tunicate, Botrylloides violaceus

8) The Lancelet or Amphoxius

9) The roundworm, Caenorhabditis elegans.

10) Yellowfin Tuna (Thunnus Albacore)

11) Market Squid


April is National Poetry Month

Well, maybe not in our nation, but it is in the USA. I'm not going to drop any rhymes on you, but I will direct you to The Digital Cuttlefish who elevates science blogging to an art form. Whether it's growing hearts in a jar, the latest PZ Myers story or anonymity in blogging the cuttlefish delivers and always in verse.


Pseudonyms and Blogging

A few days ago, the following comment was left on a post I wrote about StemEnhance (yes, people are still commenting on that one):
It's easy to be a holy man on a mountain top, and it's even easier to be critical hiding behind the anonymity of the internet. I'll have more faith in your opinion when you stop hiding behind Bayman, The Doc and Kamel. At least Anonymous Coward had the integrity to advertise himself honestly.
Arguments about pseudonymity/anonymity are as old as the internet and often boil down to accusations of cowardice or questioning credibility. Ironically, they often come from likewise pseudonymed writers or people who think revealing an untraceable first and last name (or in the case of the above commenter, first initial) amounts to any difference from a fake name.

First of all, using a pseudonym is not the same as being anonymous. Dr. Crazy at Reassigned Time has a nice discussion of this. A pseudonym is an alternate, online identity. How 'alternate' is entirely up to the user. For me, Kamel the Bayblabber isn't really that different from Kamel in RealLife(tm). I suspect someone like PhysioProf holds the same opinions on and off the blogosphere (including, unsurprisingly, an opinion on anonymous blogging), but the language used to express them differs (I don't know PhysioProf though, so I could be completely wrong). Others are probably even more radically different online than off. Anonymous is different. Anonymous is no identity.

I don't have any problem with either approach. I've always considered that the nice thing about anonymous argument is that the argument can stand on its own merit and not get bogged down in who's saying it. It doesn't matter if I'm a corporate shill, a doctor, a professor, or just a grad student with a computer and an opinion as long as the arguments make sense. In fact, as someone who blogs with a pseudonym, I may even have to work harder to establish credibility rather than relying on credentials.

There are any number of reasons why one would choose not to reveal their identities on their blog or in comments, many of which are legitimate. Some bloggers, like FemaleScienceProfessor, do it for safety. There are hateful people who will threaten or attack you for your argument or even for who you are. She writes:
Every week I reject (delete) a number of obscene and/or threatening comments that are sent to me via this blog. [...] Do I only get these comments because I am anonymous? I don't believe that. And why would I want these sick people to know exactly who I am, where I live, where my daughter goes to school?
It may not be misogynists you're trying to avoid, but racists, people who don't like your political views, who don't like it if you do animal research, etc.

Some people use a pseudonym for privacy reasons. Some people are very protective of their personal information and don't want it readily available for anyone who wants it, or don't want their email flooded or phone calls about things they write. Others do it for security. Perhaps a science grad student doesn't want political views to hurt future job prospects, or a tenure track prof has similar worries. Maybe, if you blog about personal experiences, you want to protect the identities of other players involved. The reasons to take on a pseudonym are personal, and I don't think need to be justified to anybody else.

There is a downside. Some people will just focus on the anonymity of a blogger rather than engage the actual arguments being made. Like the comment I mentioned at the outset, it can be a distraction. Or it could cost you some respect, or you might not get taken seriously at all.

A recent article in the Chronicle's Careers section doesn't address blogging directly, but tries to take take on anonymity in writing but with no real point. Using 3 recent examples of pseudonymous writers from the same publication, the author - rather than focusing on the problems of blogging with a pseudonym (the article, after all, is titled 'The Dangers of Anonymity') - chooses to attack possible justifications for taking on a fake name instead. In this medium, no justification is required. Nevertheless, the 3 writers he called out responded with their reasons anyway.

What do people think? Do you pay more attention if you know the name of the writer? Do bloggers need to justify their pseudonymity?


Friday, April 04, 2008

Cancer Carnival #8 is UP!

The 8th Edition of the Cancer Research Blog Carnival has gone live at The Skeptical Alchemist. Your host, Steppen Wolf, has done a great job so check it out. The next edition will be hosted by Hematopoiesis on May 4th. Get your submissions in here.

As always, hats off to Ben for designing the logo.


Wednesday, April 02, 2008

Publish and/or Perish: When to Submit that Manuscript?

During my early days in grad school, I couldn't imagine a time when writing and publishing a paper describing my own research wouldn't be just the greatest damn thing to ever happen. But this was before I knew how demanding the process would be. While I have found it to be extremely rewarding in certain ways, I find it also consumes a lot of time and energy that can never be fully recovered. Here's an interesting couple of quotes I came across on making the decision of when to publish:

"In deciding when to publish, you will have to balance several considerations, but try to resist the temptation to rush into print, if you have a choice. Remember, the quality of your publications is what matters most in the long run. A paper that is incomplete or carelessly put together is less likely to be accepted for publication and will be an inefficient use of your time. Even worse, incorrect results will damage your reputation."

"Writing up an incomplete or flawed story is not time-effective, since writing a good or bad paper generally takes the same amount of time."
—Tom Misteli, National Cancer Institute

Quoted from: Making the Right Moves: A Practical Guide to Scientific Management for Postdocs and New Faculty

Of course, waiting until you have the "perfect" paper in hand before submitting is a luxury most of us can't afford, especially grad students in the twilight of that PhD. We need the recognition a paper offers to get funded, finish our degrees and move on to the next career stage. More established scientists, like Nobel winners, NationalHeroes and tenured profs can afford to be as patient as they want. But even for us lowly and desperate students, it's valuable to realize that to "publish or perish" is not always the best path to pursue. Getting a paper to your name is nice, but it comes at a steep cost. You'll only have so many papers in you, so use them wisely!


Quote of the day from Judah Folkman

A pediatric surgeon in Boston just finished
a difficult operation. To relax, he went to the Charles River and sat
down on a bench. Suddenly, he heard cries of ‘Help! Help!’ and saw
a person drowning. The surgeon jumped into the river and pulled
the person to safety. He lay exhausted on the banks of the river and
again heard, ‘Help! Help! ’ He glanced at the river and saw another
person drowning. Despite his exhaustion, he jumped into the river
and pulled the second drowning person to safety. Now, he was truly
exhausted and lay on the ground huffing and puffing and again
heard, ‘Help! Help! ’ He raised his head to look toward the river
and saw a third person drowning, but he also noticed two basic
researchers walking by the river. The surgeon shouted, ‘Colleagues,
you must help! This is the third drowning person in the river in one
afternoon! ’ The researchers looked at the river and then at the
surgeon and said, ‘Three people drowning in one afternoon? This
is very interesting! We’ll walk upstream to see who’s throwing
them in!’.’’


Tuesday, April 01, 2008

Learn Immunology Fast. Now!!!

For those of us who find immunology confusing but can never quite seem to avoid it, Realscientist Ian York's got a great and quick primer on cytotoxic T cells and the strengths and weaknesses of the assays used to detect them. So do check it out - What’s in a name? (Are cytotoxic T lymphocytes cytotoxic?) - and if you end up craving more there's plenty of great immuno-virology stuff over there to keep you going for a while.


The Bayblab joins Scienceblogs TM

The bayblab is pleased to announce that after some lengthy negotiations we have agreed to be amalgamated with ScienceBlogs. This was not an easy decision. We had some concerns that we wouldn't be able to retain our freedom to write tongue-in-cheek posts about how stem cells don't exist, penises and fart jokes, or poke fun at PZ Myers to drive traffic. However Seed media has informed us that according to our traffic statistics we could earn up to $1000 a year, and we feel that the amount of beer this will buy us should be sufficient to cover the pain. In the deal we negotiated we will have to blog only about things that other science bloggers are currently discussing and allowed to give only slightly divergent opinions on such things as "framing". As part of the deal the bayblab bloggers will have to reveal their identity and will be audited weekly by the blogging ethics committee lead by Greg Laden. At least one member of scienceblog welcomed the news, Physioprof commented that: "I hope these wackadoodle douchesquirting blogger douchehounds continue to douchewrite more dumbfuck antics about douchegrads in science".


Dawkins calls it quits

In an unprecedented move, the famous author and atheist Richard Dawkins says he will quit his quest to expose religion as a delusion. In a public statement Dawkins explains he is tired of repeating the same arguments over and over, and suffered a mental breakdown during a recent debate in Texas. "I can't help feeling that my position, though logically sound, leaves believers feeling pretty unsatisfied, and that although atheism might have been the only logically tenable life philosophy for me, I no longer think one needs to accuse religion of being the root of all evil to be an intellectually fulfilled atheist." said the famous evolution scientist. Although Dawkins maintains that evolution remains the only satisfactory explanation for the diversity of life on earth he concedes he might have been belligerent and overly pugnacious in previous encounters and feels he now lacks the will and energy to inform all these people about their own stupidity.