Personal genomics is finally here

Want to get your genome sequenced? No problem, all you need is $50,000 .... or you could wait 12 years and, if it follows Moore's law, it should cost under a $1000. Still pretty impressive:

" Illumina, Inc. today announced that it has delivered Hermann Hauser’s genome sequence. Dr. Hauser, Partner, Amadeus Capital Partners Ltd, is the first consumer to purchase Illumina’s individual genome sequencing service working with his physician, Michael Nova, MD, of Pathway Genomics. The genome was completed in Illumina’s CLIA-certified and College of American Pathologists (CAP) accredited laboratory using the Genome Analyzer technology. Over 110 billion base calls were generated, delivering over 30X coverage of the genome. Data analysis showed 300K novel SNPs in the genome that have not been documented elsewhere."

Bayblab Foundation Offers One Billion Dollars for The Cure for Cancer !!!!!!

Attention brilliant young minds of biomedical research, your time has finally come! The BigPharma conspiratists have been permitted to suppress the OneTrueCure for Cancer for long enough. The Bayblab Foundation has decided to finally end the fiasco once and for all. We will be awarding one BILLION CAD to the one to identifty the **ultimate** target for cancer therapy. No magic bullet required (we'll handle that), all you have to do is name the enemy. Should we go straight into the belly of the beast to strike at the tumor cells themselves? They are clearly the agressors, but these genetically labile shape-shifters might be hard to pin down... Should we go after the infrastructure, the tumor's endothelial cells that feed the tumor, or the friendly neighbourhood unknowing accomplices, the stromal fibroblasts? How about the smoke-grenading monocytes laying down the thick cover, or the extracellular matrix protein framework? Or perhaps we shouldn't be destroying bad cells, but strengthening the good guys. Cytotoxic T cells? Natural killers? Antibody-secreting B cells?

What say you Bayblabbers? What do you reason is the best target for cancer therapy and why? Add your answer to the comments below and leave the rest to us...

Hepatitis C: The Curse of the Slave Trade

Ian York at Mystery Rays discusses a recent paper on the geo-molecular origins of Hepatitis C virus. Some interesting findings here, including the notion that Hep C originated in Western Africa and was imported to the Americas through the slave trade that flourished between these regions several hundred years ago. In case we needed more evidence that selling humans is a bad idea...pretty interesting stuff though.

Religion Doesn't Kill People; People Kill People

I recently caught Robert Wright talking to Charlie Rose about his book "The Evolution of God". I thought he had some interesting things to say, though I haven't read the book. You can check it out the interview for yourself here.

His basic point is that religion is not the root of all evil (ie Sept. 11, Iraq war) as the neo-atheist totalitarians Dawkins and Hitchens would have you believe. He argues that religious doctrines evolve to meet the basic biological needs of their followers. He points out the fact that scriptures of all religions are full of obvious contradictions that give them the flexibility to adapt to changing enivronments. When leaders need to rally the troops to "kill the infidels", the appropriate scripture verse is at hand. Likewise when it's time to "love all men as God's creatures" a different verse from those same scriptures provides justification.

If not religion, what is the root of all evil? Wright alludes to what I think is a much more scientific explanation. Human behavioiur is simply driven by competition for finite resources. In this respect, we are no different than any other living organism. When our bellies are full and survival is a given, we all get along. Everyone can be part of the in-group. Philosophers write about the virtues of tolerance. When conditions are not so good and people start to starve, it's another story. Every man for himself. Tribalism rules the day. The all encompassing in-group breaks down and leaders of smaller tribes look for rationale to villify and exterminate the others. In good times or bad, religious scriptures provide group cohesion by justifying whatever behaviours the circumstances demand.

I'm not totally sure this is what Wright was getting at, but it's my interpretation. The behaviour of all living organims, humans included, is governed by basic survival, not by cultural cues. Don't buy it? Try witholding a meal or two from your cat...then try it with a human child...and watch peaceful co-existence go out the window. Sure we like to blab a lot about WHY we do certain things. It's the will of God, or whatever. We humans are the blabbiest much of monkeys to ever walk the Earth. Our painfully acute sense of self- and social-awareness demands that we constantly talk about everything we do and why we do it. We are moralizers, justifiers and rationalizers. But being self-aware and telling all about it does not equal self-determination. Ask Hannibal Lecter. The evolutionary chain of causation that determines our behaviour is not altered just because we loud-mouthed humans have the capacity to provide a self-affirming running narrative to anyone who will listen.

Wright's second major point is that religions currently need to and can re-invent themselves to promote harmony in a globalized society. He seems to think the way to get to a more scientifically correct religion is to put purpose back into evolution. That is, evolution unfolded as it did because God rigged up the universe to make it so. He makes this argument in a recent NYT piece. Evolutionary biologist Larry Moran is skeptical (more here); and it's hard not to agree with him. There is no evidence that evolution is directional (what about convergent evolution?). But is there evidence that it isn't ("junk" DNA)? I think this one ends in a draw.

Anyhow regardless of what you think about God, I think it's OK and even desirable for scientists to tolerate religion rather than try to exterminate it from the planet. And shift their attention away from cultural noise and back to the serious biological problems humanity faces. Feeding the world...population control...the end of oil...any takers? I can hear Hitchens already..."Hmmm...that sounds hard...can't we just go back to using big words to make fun of Creationists and blame them for all the problems?"

How to publish a comment

We've all read papers that didn't pass the smell test. I'm willing to bet none of you ever tried to publish a comment in the journal debunking the conclusions of said paper. This PI tried and as you can see, it's nearly impossible to get it published perhaps because it would involve the editors acknowledging that they shouldn't have published the paper in the first place. I highly recommend you read this saga, it is both funny and tragic. Here is how he proposes to fix the system:

1. All data and parameters associated with any open publication should be available to anyone interested in it. The NIH has mandated this for its grant recipients, but sharing data and parameters should also be a required condition for a publication in any journal. Refusing to do so after a paper is published should be considered scientific misconduct.

2. Anyone knowingly publishing a paper that clearly contradicts the work of another group should be required, also as a condition for publication, to discuss the matter with that group well before publication. In the past, this was considered good
scientific etiquette, but gone, apparently, are those days, so a rule is in order.

3. Journal editors should be more aware of referee conflicts of interest. Reviewers should be required to stipulate any conflict of interest in reviewing a paper, even if it’s simply that they don’t like the authors.

4. No journal editor should be allowed to edit a Comment on a paper he allowed to be published. This is an obvious, unacceptable conflict of interest.

5. Comments should not be required to be so short as to prevent them from making sense. I suggest two journal pages, or, better, three. Or how about this radical idea: they should be as long as it takes to make the point.

6. Crazy rules that allow logically offensive situations, like the one that called for rejecting a Comment because the Reply is unpublishable, should be deleted immediately. And Comments and replies need not, and should not, be published together. Indeed, a Comment on a Reply is a good idea, yielding an interesting ongoing dialog that would benefit the community.

7. The reviewers who review a Comment should also review the Reply. They’re the best qualified, as they’re already familiar with the work. This would prevent the insane situation that occurred here, in which the highest quality review of the Comment was simply lost.

8. Reviews should themselves be reviewable. Currently, reviewers can say whatever they like, and there is no check on them. Authors should be allowed to nominate
irresponsible reviewers, such as Reviewer #2 in the above scenario. Confirmed irresponsible reviewers should then be identified and removed from reviewer databases, which would be shared with other journals. Writing an irresponsible review
should be considered a form of scientific misconduct.

9. While removing unethical reviewers would help, improving reviews of ethical ones is also important. Currently there is no compensation of any sort for reviewers and hence no encouragement to do a good job. I believe that reviewers should be paid for their services. People take paid jobs much more seriously than volunteer efforts. Knowing this, social psychologists pay their subjects simply to fill out questionnaires because it yields much higher-quality results. And what could be more important than the accuracy of the archival scientific literature?

10. Require scientific ethics courses in grad school. Problems like those that I encountered are a proverbial ticking time bomb for science. What if those opposed to taking action against global warming were to make the claim that science shouldn’t be believed in this matter because its process is so rife with poor ethics that it can’t be trusted?

Bayblab science literacy test

As we're about to reach our 500,000th hit, it's time to pause and look at what we have accomplished so far. So many people have been informed and entertained while looking for animal penis content on Google, so many people have tried to argue with Kamel about the efficacy of herbal supplements, we have offended, maddened, and made you laugh. If you can answer these questions right, you know what we mean:

1) Which group of animals contains many species with bifurcated penises? :

• a) ducks
• b) marsupials
• c) bivalves
• d) spiders

2) Which group is less phylogenetically related to us than to a drosophila?:

• a) Starfish
• b) Salamander
• c) snail
• d) jellyfish

3) Nematodes have how many sexes?:

• a) male and female
• b) male, female and hermaphrodite
  
• c) female only
• d) male and hermaphrodite

4) Regarding the evaporation rate of an ethanol:water solution:

• a) 70% ethanol left out will eventually become pure water
• b) a 95.6% ethanol solution will always remain just as concentrated
• c) 70% ethanol evaporates faster than 50%
• d) all the above are correct

5) What is the proportion of humans who produce methane in farts:

• a) 100%
• b) 30-50%
• c) <10%
• d) 0%

6) Which 4 genes are sufficient to generate an iPS cell:

• a) c-myc, sox4, klf4, oct3/4
• b) c-myc, nanog, lin28, fgf2
• c) sox4, klf4, FoxP3, oct3/4
• d) c-myc, k-ras, P53, Rb

7) which pair of species cannot interbreed:

• a) Zebra and donkey
• b) Plum and apricot
• c) lion and tiger
• d) cat and rabbit

8) Which of these mammals is not venomous:

• a) shrew
• b) platypus
• c) slow loris
• d) solenodon

9) What is the most abundant protein in humans (%weight)?:

• a) histones
• b) ubiquitin
• c) collagen
• d) albumin
  

10) which of these hypotheses has not been proposed on the bayblab:

• a) males can lactate
• b) ingesting semen can prevents preeclampsia
• c) you can catch STDs from blow up dolls
• d) Right-handed people are more likely to be pedophiles
  

Local Science: When Zombies Attack!

A group of mathies from the University of Ottawa and Carleton University have just been published in Infectious Disease Modelling Research Progress. In their paper, they attempt to model a zombie outbreak and it's ramifications. From the abstract:

Zombies are a popular figure in pop culture/entertainment and they are usually portrayed as being brought about through an outbreak or epidemic. Consequently, we model a zombie attack, using biological assumptions based on popular zombie movies. We introduce a basic model for zombie infection, determine equilibria and their stability, and illustrate the outcome with numerical solutions. We then refine the model to introduce a latent period of zombification, whereby humans are infected, but not infectious, before becoming undead. We then modify the model to include the effects of possible quarantine or a cure. Finally, we examine the impact of regular, impulsive reductions in the number of zombies and derive conditions under which eradication can occur. We show that only quick, aggressive attacks can stave off the doomsday scenario: the collapse of society as zombies overtake us all.

They model the spread of infection a number of ways, based on zombie features from classic film (and ignoring nouveau-zombies, such as the fast moving, more aware monsters from 28 Days Later), and playing with variables such as latency of infection and the effects of quarantine or cure development.

Of course a zombie outbreak is far-fetched, and nit-pickers now have another tool in their arsenal when tearing apart the believability of movies ("There's no way that quarantine would be effective!"), but it does demonstrate a neat use of math in modeling disease spread - even fictitious ones. As the authors note in their discussion:

This is, perhaps unsurprisingly, the first mathematical analysis of an outbreak of zombie infection. While the scenarios considered are obviously not realistic, it is nevertheless instructive to develop mathematical models for an unusual outbreak. This demonstrates the flexibility of mathematical modelling and shows how modelling can respond to a wide variety of challenges in ‘biology’.

Of course the real bottom line is when the zombie uprising happens, we're all screwed.

Read the full paper here [pdf].

Science Quiz

Stole a link to a science quiz from Sandwalk, who stole it from The Unexamined Life. Take this science quiz from the Toronto Star, we love this stuff on the bayblab.

Smoke rings

This particular demonstration is a bit outside my field of expertise, however, I think it's pretty clear that the phenomenon is based on magic.
Found on reddit.

Sex, Drugs and Physics

Who said scientists were boring? When particle physicist John Ellis, winner of the Maxwell Medal, Paul Dirac Prize and member of the Royal Society lost a bet over a pint to fellow Canadian Melissa Franklin, first woman to get tenure in physics at Harvard (and on the side DJ) she dared him to include the word "penguin" in his next publication. From the dates, she must have been a grad student at the time. From wikipedia:

"Mary K. [Gaillard], Dimitri [Nanopoulos] and I first got interested in what are now called penguin diagrams while we were studying CP violation in the Standard Model in 1976... The penguin name came in 1977, as follows.

In the spring of 1977, Mike Chanowitz, Mary K and I wrote a paper on GUTs predicting the b quark mass before it was found. When it was found a few weeks later, Mary K, Dimitri, Serge Rudaz and I immediately started working on its phenomenology. That summer, there was a student at CERN, Melissa Franklin who is now an experimentalist at Harvard. One evening, she, I, and Serge went to a pub, and she and I started a game of darts. We made a bet that if I lost I had to put the word penguin into my next paper. She actually left the darts game before the end, and was replaced by Serge, who beat me. Nevertheless, I felt obligated to carry out the conditions of the bet.

For some time, it was not clear to me how to get the word into this b quark paper that we were writing at the time. Then, one evening, after working at CERN, I stopped on my way back to my apartment to visit some friends living in Meyrin where I smoked some illegal substance. Later, when I got back to my apartment and continued working on our paper, I had a sudden flash that the famous diagrams look like penguins. So we put the name into our paper, and the rest, as they say, is history."

Onion Power

The largest onion processor in the US uses archaebacterial fermentors to convert their organic waste into methane for electricity production. Cool. Read all about it.

What products to they make? I want to buy onion and support these guys. Also when will I be able to get an onion powered car?

Tumor Immunology Is A Waste of Time

Ian York recently wrote some interesting stuff about the interesting case of the transmissible tumours that are spreading in Tasmanian devils. The question is how are these tumours transmitted from one host to the next without being rejected by the immune system. He points out some pretty compelling evidence that this is not due to MHC homogeneity amongst the devil population. Therefore, the tumors are persisting despite being MHC mistmatched. In contrast, if you were to transplant normal tissue from one devil to another, it would be rejected by the recipient's immune system. And yet, for these tumors this is not the case. Apparently the same is true of a totally different type of canine transmissible tumor.

We shouldn't find this all that surprising. Tumor cells evolve resistance to almost anything you can throw at them, things that would kill normal cells. Their continued existence demands mechanisms of resistance to death by many diverse types of stimuli. There's only so many ways to kill a cell, so evolved resistance to one stimulus is often cross-protective against many others. The result is that everything down to the most fundamental metabolic processes of the cancer cell are adapted to surviving adversity. In light of this, you would predict T cells would have a hard time killing cancer cells.

Anyhow whatever the mechanism of resistance, all this is enough to convince me that tumor immunologists should give up on trying to make vaccines or other therapeutics that try to cure cancer by targeting "tumor" antigens. If tumors can escape MHC rejection, a natural, more specific and much more robust phenomenon, I find it impossible to believe that effective therapy will ever achieved by artificially stimulating the immune system to attack weak and largely self antigens. I suspect smart immunologists already know this.

UPDATE: In a follow-up post, York points out an important difference between transmitted and spontaneous tumors I hadn't fully considered. That is, the transmitted tumors have a much longer evolutionary history that spans multiple host generations, whereas a spontaneous tumor's evolution follows a blind alley that ends when the host dies. Therefore there has perhaps been greater opportunity for immune evading characteristics to emerge in what may be a more genetically diverse population of transmitted tumors. If this were true, the kinds of non-transmitted tumors we'd like to vaccinate against in humans wouldn't necessarily be as difficult to get the body to reject. At any rate, York remains optimistic re tumor immunology and promises to elaborate so stay tuned...

A Good Idea

"The LHB Program has two goals. First, it will provide PhD students with a working knowledge of the fundamentals of human biology and disease, primarily through a series of courses, to enrich their basic science training and broaden their research interests. Second, it will demystify the culture and practice of medicine, facilitating future collaborations with clinicians and physician-scientists, through activities designed to bring students into a hospital environment into direct contact with physicians, patients, medical students, and physician-scientists."

The Leder Human Biology and Translational Medicine Program is available to Harvard PhD students in the biomedical sciences. Do any Canadian institutions offer the kind of training described by LHB's second goal? It is more important than the first and should be the top priority for institutions purporting to train biomedical PhDs.

Carbonsink Concrete

One of the origonal posts on the bayblab, when it was just a babylab, was about concrete. Recently a company out of the UK has made cement that absorbs more CO2 than it produces in it's production. Essentially turning concrete into a carbon sink!
It is kind of scary to mess with such a fundamental material of man that has been slowly evolving since Roman times. Also if it costs significantly more I'm sure it will go nowhere, however the idea of a material as prevalent as cement being a carbon sink is inspiring.

A Quote for the Day

Maxwell wasn't thinking of radio, radar, and television when he first scratched out the fundamental equations of electromagnetism; Newton wasn't dreaming of space flight or communications satellites when he first understood the motion of the Moon; Roentgen wasn't contemplating medical diagnosis when he investigated a penetrating radiation so mysterious he called it "X-rays"; Curie wasn't thinking of cancer therapy when she painstakingly extracted minute amounts of radium from tons of pitchblende; Fleming wasn't planning on saving the lives of millions with antibiotics when he noticed a circle free of bacteria around a growth of mold; Watson and Crick weren't imagining the cure of genetic diseases when they puzzled over the X-ray diffractometry of DNA; Rowland and Molina weren't planning to implicate CFCs in ozone depletion when they began studying the role of halogens in stratospheric photochemistry.

These discoveries and a multitude of others that grace and characterize our time, to some of which our very lives are beholden, were made ultimately by scientists given the opportunity to explore what in their opinion were basic questions in nature.

Cutting off fundamental, curiosity-driven science is like eating the seed corn. We may have a little more to eat next winter, but what will we plant so we and our children will have enough to get through the winters to come?

-- Carl Sagan, The Demon-Haunted World: Science as a Candle in the Dark

The Crow and the Pitcher

Thousands of years ago, Aesop wrote a fable about a crow who used stones to raise the water in a pitcher so he could have a drink.

The latest issue of Current Biology documents this behaviour in a member of the crow family, the rook.
The authors next plan to use General Relativity/time dilation to determine who actually crossed the finish line first: the tortoise or the hare.

The crows are a resourceful family of birds. They have been shown to employ teamwork, use tools and solve multi-step problems. (Follow links for video) So much for birdbrains.

Cancer Research Blog Carnival #24

Welcome to the 24th edition of the Cancer Research Blog Carnival - your monthly roundup of writing from the cancer blogosphere. This month, the CRBC turns 2 years old (on August 24th, to be precise), so a special thanks to AC for starting the whole thing, Ben who designed our awesome logo, Walter for setting up new subscription options and general support and of course all the hosts and writers who have got us this far. Of course to keep going for another year, or 2, or 4 we still need your help - the carnival is always looking for new hosts, so drop us an email, or a comment here, to sign up and keep sending us your submissions here.

Now, without further ado, here is the latest Cancer Carnival:

First up, we have a new blog, Blue Genes, that offers their first part of a series on understanding cancer.

What is cancer? Everyone knows that it is a terrifying disease and has some ideas about a mass of cells that grow uncontrollably but I get the feeling that many people don’t quite understand how it actually happens.

They promise to continue the series in the futures with posts on cancer treatment, different cancer types, and other cancer topics. Blue Genes is written by a pair of young scientists and is worth keeping an eye on.

Next up, we have a pair of posts from The Spittoon, the blog of genetic testing company 23andMe. From the SNPwatch files, these posts highlight research identifying new genetic variants associated with cancer. First off is a discussion of CDKN2A and CDKN2B variants associated with certain brain and skin cancers.

Five reports, published online this week in the journal Nature Genetics, show that variants near the CDKN2A and CDKN2B genes increase the risk of certain types of tumors. Previous research has implicated these “tumor suppressor” genes in both skin and brain cancer. Mutations in CDKN2A are found in about 2% of all people with melanoma, and outright deletion of CDKN2A and CDKN2B is seen in approximately half of all brain tumors.

The second new SNP is associated with follicular lymphoma.

In a study by Skibola et al., scientists analyzed the genomes of 4,805 people of European descent from the United States, Germany and Canada to search for genetic associations with four different subtypes of lymphoma. The results, published online this week in the journal Nature Genetics, newly linked one SNP to an elevated risk for developing FL in European populations.

A submission from Healthcare Hacks is next, which discusses triple-negative breast cancer

Negative--that's good, right? Unfortunately, this is one of those times that negative results aren't so positive. This form of breast cancer is named "triple-negative" because the tumor lacks the three receptors for the hormones estrogen, progesterone or Her-2/neu.

The post offers some facts about triple-negative breast cancer before briefly discussing some new therapies in the pipeline that offer hope to patients, as well as support resources for people diagnosed with this cancer.

Suture for a Living talks about a topic we've discussed a bit in the past: overdiagnosis of breast cancer, in this case putting some actual numbers to the problem.

Are breast cancers over-diagnosed? If so, how often? Those are the questions looked at by the systematic review of incidence reported data/articles done by Karsten Juhl Jørgensen & colleagues. Their results are published online in the June 9th issue of the British Medical Journal. Their review shows an estimated 52% over-diagnosis of breast cancer.

Click through for more stats and analysis.

Elsewhere in the blogosphere, Alexey at Hematopoiesis provides a nice review of ways the immune system can be harnessed to kill cancer stem cells, as well as progress made to date. Orac at Respectful Insolence has a really interesting piece on the problems recruiting patients to clinical trials and what it means for cancer research. And Science and Reason discusses a new targeted therapy for leukemia stem cells.

That's it for the 24th Cancer Research Blog Carnival. For older editions, visit the Carnival Homepage. Don't forget, the CRBC has subscription options; you can follow by email or RSS feed. An aggregated feed of credible, rotating health and medicine blog carnivals is also available.

Late breaking abstract!

The anthropological implications of proper habiliment usage on micturition

The evolution of the erect posture in the genus Homo has created physical constraints on urination, particularly in males. It has also been observed by multiple groups that the act of wearing garment can impede the urinatory process by increasing the latency between the initiation of the behavior and the opening of the urethral sphyncter. In the general population of males there exist variation in the exit strategy employed for the exposure of the phallus through the underclothes. To model the population variation of these behaviours, a questionnaire was designed and given to 41 subject over the course of 7 days. Results indicate that most subjects (70%) choose to expose their penes by going over the elastic band while a minority (29%) use the undergarment flap. These results raise questions about the validity and usefullness of the undergarnment flap given the low propencity of usage. Futhermore it was serendipitously discovered that analogous female garment lack such vestigial features. A correlation was observed between individuals of french background and users of the undergarment flap (16% were French). While correlation does not imply causation, we wish to bring forward the hypothesis that urination behaviour may be ethno-culturally determined. Further studies will be needed to determine how urination behaviour varies geographically.

Funding HQPeeps: "Fellowships" vs. The Grant

Some wacko/Nobelist (Roald Hoffman) is suggesting that American labs should be banned from funding graduate students through the PI's operating grant. Apparently, this is how the vast majority of students are funded in the States and I'm pretty sure the same is true in Canada (ie their salaries are paid through the lab's grants as opposed to an independent fellowship awarded directly to the student.) This idea has some appeal:

"The real power of an individual fellowship is that it empowers a young scientist to act in a more independent manner, on something creative and for which they have a passion," says Thomas Cech... "And that's what science is really about." Under the current system, he says, "a graduate student is told, ‘Do experiment 2a because it's in our grant.’ That turns the student into a pair of hands. So I think a shift to fellowships would be an excellent idea."

I like what Cech is saying here. The same thought occurred to me, except I was looking at POST-DOC, rather than graduate student funding. At least here in Canada, even post-docs, who are supposed to be even further along in developing their independence, are unable to get truly independent funding at all, even through external fellowships. So even if all HQPs, grad students and post-docs alike were funded through external fellowships, Cech's vision still wouldn't be assured.

The problem is that although the would-be post-doc can apply for "independent" funding directly to agencies he/she cannot do so without a PI co-applicant. So before applying for funding, would-be post-doc must meet with PI and discolses his/her interests and ideas, gain a conditional position in PI's lab, identify a putative project that fits into PI's interests and grant funding, write up a proposed project in collaboration with PI and likely write a grant proposal or two for PI pertaining to said project. So much for independence.

On the other hand, true independent funding would consist of the following: Would-be post-doc or graduate student concieves of an interesting problem and possible approaches. Writes up proposal and submits along with CV etc to funding agency. Funding agency awards fellowships to promising candidates. Awardees contacts existant labs..."I have funding to carry out the following research project. Are you interesting in hosting?"

This scheme is ultimately the most liberating for the trainee. The only real potential flaw I can see is that in theory, trainees could be granted salaries to conduct a proposed project for which the proper infrastructure does not already exist. However this could be easily overcome by properly evaluating the feasabilities of proposals.

Anyhow there's some interesting argument presented in the Science article on which is better, grant-based or independent fellowship-based funding of students. I'm not sure if either is better, actually both setups can probably work. However it's clear that the current grant-based trainee-funding regime empowers PIs at the expense of grad students and post-docs. It gives them access to a much larger putative work force, allows them to hire whoever they want and as many students/post-docs as their grant funding allows (as opposed to who and how many they can properly train). At the same time it generally tends to screw over the individual trainee by dimishing their intellectual autonomy, decreasing the availability of scientific mentorship, creating a crowded and more cut-throat and overall shittier research environment, and flooding the job market with an excess of jobless PhDs. Conversely, independent funding schemes would tend take power away from PIs and put it back in the hands of trainees to pursue their own ideas in an environment that favors quality of work over quantity. Anyone see this happening anytime soon?

Of course there are exceptions. For example, grad students who get funded through PI grants can possibly focus more directly on their research because they don't have to waste as much time filing fellowship applications or engage in meaningless CV-building arts and crafts. So long s long as they're happy with what PI decides they're working on and what training PI decides to offer, it's a sweet deal.

Overall my opinion would probably be that we don't necessarily need more independent funding for nascent grad students...what the hell do they know anyways? But truly independent fellowships for post-docs would be a great option.

Any other perspectives?

About F-ing Time

Someone in the scientific publishing biz is thinking, there might be a better way to format articles, one that isn't based around the printing press, but the so-called "Information Superhighway". Check out the samples here and here. Imagine the possibilities!!!! Could this be the end to the time-honored tradition of re-formatting scientific data into a useless and archaic format when it comes time to publish?