Sunday, September 30, 2007

Paper recycling

I have recently heard someone say that recycled paper produces just as much environmental issues as virgin paper products. I'm sure that this isn't a surprise but I haven't found much to support that. I did find a relatively decent summary of the environmental impact of recycled paper vs virgin paper. While its clear that recycled paper is still not environmentally neutral it leaves less impact that cutting down more trees. It is however still more expensive. So if more paper is recycled by consumers this brings down the material cost even more for recycled paper making it more competitive.
I did find a wikipedia entry on recycling criticism but the arguments seem pretty weak and not as well referenced.


Shake Hands with the Devil in Theatres

I have to recommend a new film I saw yesterday, "Shake Hands with the Devil". This is an outstanding Canadian film that tells the story of the Rwandan genocide from the point of view of an outstanding Canadian, Lt-General Roméo Dallaire. General Dallaire was in command of a United Nations peacekeeping force in Rwanda, assigned there in 1993 to oversee ceasefire negotiations between the armies of the then-Hutu government and Tutsi exiles. Extremist factions launched the country into chaos and initiated a systematic massacre of civilians in 1994. Abandoned by the UN bureaucracy and helpless to prevent the ensuing genocide that claimed some 1,000,000 civilian lives, Dallaire and a tiny remnant of his original force nonetheless remained in the country to save an estimated 32,000 people. To say he deserves a Nobel peace prize somehow seems a gross understatement. Perhaps we should leave that to Al Gore and global warming for now.

The cast and crew do an excellent job putting Dallaire's story [based on his written account, "Shake Hands With the Devil: The Failure of Humanity in Rwanda"] on screen, with stand-out performances from French-Canadian Roy Dupuis (as Dallaire) and Rwandan actress/writer Odile Katesi Gakire (as Prime Minister Agathe Uwilingiyimana). All scenes were shot in Rwanda on the locations where the actual events took place, providing a haunting sense of reality.

The film offers unique insight into perhaps one of the most terrible events of recent history, but it is not light fare; expect to be moved by heroism as you are simultaneously beaten over the head with human ineptitude and cruelty. Certainly it is the type of film that might cause some to question whether it is really necessary for Western movie-goers to put themselves through such a version (albeit an attenuated one) of the suffering of others. Perhaps it is indeed worthwhile if sharing the burdens of history might somehow offer humanity a degree of vaccination against larger tragedy in the future.

Odile Katesi Gakire suggests that the sharing of these stories also has a subtle, but deeper significance, one that even the pessimist who believes human tragedy unavoidable would not deny:

"It is important to speak of what happened. There are so many histories which we (Rwandans) debate. There are no history classes in school, so it is important to have many points of view so that in the end we can find one common story. We all have a personal history and perhaps in the end we can come out with a national history."

"Shake Hands with The Devil" opened at the 2007 Toronto International Film Festival, and is now playing at the ByTowne Cinema here in Ottawa.


Submit Your Nominees for "The Socrates":
The Bayblab Awards for Scientific Discourse

“Information, usually seen as the precondition of debate, is better understood as its by-product.” - Christopher Lasch

“It is better to debate a question without settling it than to settle a question without debating it.” - Joseph Joubert

In an obvious attempt to capitalize on the popularity of a recent Bayblab post, Seed Magazine has just announced the winners of its second annual writing contest, two short essays on the theme of "What does it mean to be scientifically literate in the 21st Century?"

Both essays are, in my opinion, outstanding and well worth the quick read. [Scientific Literacy and the Habit of Discourse, by Thomas W. Martin and Camelot is Only a Model: Scientific Literacy in the 21st Century, by Steven Saus.]

Both articles rightly point out that the traditions of free expression, diversity of thought, and evidence-based, dispassionate debate are critical for the advancement of science and a healthy society. Besides that, civilized argument is just damn fun; all the fun of a good fist-fight without the blood and bruising. Sadly, the authors are also correct in noting that these triumphs of human achievement are becoming increasingly rare in 21st century culture, as ideology, conformism and rigidity too often dominate our politics, journalism, universities and yes, even our science.

However the art of discourse is far from dead. To celebrate this fact, and to provide examples of how scientific discourse can maintain its relevance in this century, the Bayblab is calling for nominees for "The Bayblab Awards for Scientific Discourse" (aka "The Socrates' "). It's simple, just send in names of a person(s) from any walk of life who you feel have recently exemplified proficiency in the art of scientific discourse (in the comments section of the post below). Here are some ideas for qualities to look out for in potential nominees:

(From Thomas Martin's essay):

- "incessantly try to disprove the ideas generated by other smart people"
- "evidence-based argument"
- "imaginatively create new hypotheses and to dispassionately critique them"
- "criticize each other's ideas firmly yet civilly"
- "commitment to evidence over preconception"
- "create environments in which they [others] can safely have small epiphanies in the light of evidence"
- "changing one's mind in light of the evidence"

(From the Steven Saus essay):

- "Understanding that our scientific knowledge is "only" a model"
- "Critical, independent thought"
- knows that "The edifice of science is not in danger of crumbling; it is under constant renewal."

To get things rolling, I'll throw out a few of my own nominees (by category):

Philosophy - John Ralston Saul:
His Massey Lectures book "The Unconscious Civilization" should be the starting point for any discussion of discourse and democracy in the 21st century. Hailing from Ottawa, home of the Bayblab, this Canadian IS the modern-day Socrates.

Blogging - Prof. Larry Moran, University of Toronto:
Sandwalk, the blog of this Canadian biochemist, is quickly becoming one of my favorites. A master at stimulating and participating in effective discourse, Larry is undoubtedly recruiting converts to the ways of discourse by the minute.

Economics - Prof. John Polanyi, University of Toronto:
Nobel prize-winning chemist Polanyi has used his fame to stimulate discussion of many humanitarian issues over the years, particularly those those arising from the use chemical and nuclear technologies. I was impressed by his knack for dispassionate argument in promoting the SENLIS proposal for the legalization of the Afghani opium industry on a recent CBC radio program.

Politics - Mahmoud Ahmadinejad, President of Iran:
A politician is a politician is a politician, and so despite being my nominee in this category, I must say that Ahmadinejad's skills in the art of discourse are not necessarily in the realm of the other nominees listed above. [But please, judge for yourself by his recent TV interview and Columbia University speech/Q&A]. That said, it is perhaps a testament to the ancient academic traditions of the Persian and Islamic cultures that the Iranian President comes off as a philosopher-king when compared to the cardboard cut-out leaders of the West. So I guess he kind of gets this nomination by default - not so much for being a discourse superstar, but because most other politicians are so very bad at it.

Bayblabbers - Kamel
For a recent political post rich in discourse but devoid of detectable bias. An impressive feat indeed.

So there's my nominees. Feel free to make up your own categories and nominate as many people as you want. Provide as little or as much justification and background as you like. Once we get a bunch, we'll have a vote for the winners. Or maybe just argue about it.


Saturday, September 29, 2007

Marky Mark & QuickClot

I just saw the movie "Shooter". It's OK for a no brainer. I noticed, as it was probably product placement, that our hero, played by Mark Wahlberg, uses a package labelled QuikClot to stop the bleeding of a serious gunshot wound. I checked it out and it is a real product and apparently it works. Check out a pretty graphic demonstration of QuikClot on a pig.
The disappointing thing is that it's not very hightech. I thought it would contain some recombinant clotting factor or something but instead it works by concentrating clotting factors already in the blood by sequestering water. This does eliminate the problem of immune reaction and probably makes it have better shelf life, but it's just not as cool.
I read some medic blogs that suggested the stuff really isn't that good and causes quite an exothermic reaction when placed on an open wound. And there are similar products out there. The manufacturers website suggests that it is used in Iraq by the U.S. military.


Friday, September 28, 2007

Chasing Immortality

Nature is featuring a collection of open access articles on the topic of ageing. Some very interesting science from the lab to be sure. That said, it is somewhat disappointing that the research they (the world's greatest scientific journal in the universe) chose to feature is somewhat skewed toward an obsession with the quest for magic pills and miraculous cures, without any attention to the question of whether it is desirable or even advisable to set out on such a journey in first place.

Certainly, the human struggle to accept the inevitability of death is nothing new. The many religious sects who have successfully convinced a great number of otherwise sane people to commit insane and suicidal acts over the years have clearly understood the susceptibility of the human mind to the promise of immortality. Will molecular biology and stem cells finally lead us to the holy grail?

At this point, it would seem pertinent to ask, what is ageing, really? A plague or biological destiny? A burden or a blessing on society? I guess we're left to discuss these types of questions amongst ourselves. If Nature's editorial selection is to serve as a barometer, science would seem not to have any insight to offer.

Perhaps we can at least find wisdom in the words of ageing evolutionary biologist Richard Dawkins, who said "you never really quite die; as long as there is some of your genetic material left behind in this world". Surely this is a feat of biology that no pharmacologist will ever equal.


Wednesday, September 26, 2007

Electoral Reform: Referendum 2007

The bayblab has been getting a bit political lately, and who am I to buck a trend? Just to stay somewhat relevant, let me wrap it in Bayman's anti-denialist post. In it, among other things, he calls out simply parrotting "common wisdom" or appeals to authority in favour of actual examination of evidence before committing to an opinion on a given theory. This isn't just true for ideas like man-made global warming or the stem cell hypothesis. Here, in Ontario, Canada, we're about to have a referendum on electoral reform - whether we should stick with our current first-past-the-post (FPTP) system or switch to a mixed-member proportional (MMP) system.

Almost everyone I know seems to have a strong opinion on the upcoming reform question (and by strong here, I really mean a decisive opinion - more than just 'whatever' or 'I haven't fully considered it yet'). This in itself is interesting since Angus Reid polls indicate that 38% of Ontario voters are undecided in the matter. More interesting is that not all can explain *why* they have that opinion and fewer still are aware of any of the downsides or counter-arguments to their choice. Since I believe in an informed voting public, I thought I'd go over some of the pros and cons of each system. In the interest of full disclosure: I support the MMP system, but I'll try to be unbiased. To see the question as it will appear on the ballot and to learn the details of the two systems, visit the Ontario Referendum website.

First Past the Post
The main argument in favour of FPTP is its simplicity. One person, one vote. The straighforward nature is less confusing and less likely to keep voters at home because of voting complexity. Let's not forget the Florida debacle in the 2000 US election due to voting complexity (though that was a question of confusing ballots, not a confusing system, but it's an example of what can happen with confused voters). Being simple, a FPTP election is easier and cheaper to administer and quicker to tabulate. First past the post tends to produce more majority governments and therefore more stable governments, reducing the need for frequent elections when confidence motions fail and parliaments held hostage by small parties owning the balance of power.

On the other hand, many people feel disillusioned with the FPTP system because if your vote isn't cast for the winner in your riding, it is essentially wasted (with the exception of additional funding that goes to parties based on votes). Not only does this leave a large chunk of the population feeling unrepresented, but it can also lead to 'tactical' or compromise voting which is best summarized not as a vote *for* a representative or party but a vote against an undesireable based on perceived outcomes. This has the added effect of giving power to the media since, by and large, they provide the public knowledge of who is polling well and who isn't. Finally, first past the post leads to disproportionate representation. A party that gains 30% of the popular vote can win over 50% of parliamentary seats. One of the most striking examples of this problem is the 1926 Canadian federal election results for Manitoba where the Conservatives earned over 40% of the vote but failed to win a single one of Manitoba's 17 seats.

Mixed Member Proportional
MMP attempts to eliminate the above disparity between votes and seats by allocating a set of 'list seats' that are awarded based on the percentage of votes received on a second ballot. This second ballot also provides a disconnect between local representation and overall party values. Under this system, the electorate are now able to vote for a local member of parliament who they feel will be the best advocate for the riding as well as the party they feel will provide the best overall leadership and best represents their views as opposed to choosing between one and the other (should such a difference exist). Finally, MMP gives a voice to supporters of minor parties that might not otherwise win a seat. This is accomplished in two ways: First, having separate local and party votes enables voters to cast a ballot for a minority party without feeling that the vote is 'wasted'. Second, minority parties are more likely to win a seat and have a voice in parliament without having to beat out major parties in individual ridings. The threshold for representation in the proposed Ontario form of MMP is 3% of the vote. No minor party met that criteria in the last provincial election (the Greens were close with 2.7%), but if this system had been in place in the last federal election, the Green Party would have won around 14 seats (with 4.5% of the vote), instead of the 0 they actually had.

Despite the perception, there are a few arguments against MMP other than far flung "what-if?" result scenarios or election manipulation with decoy lists. A choice for MMP in Ontario leads to bigger (and more expensive) government with less representation. Currently the number of ridings is 107, which will be reduced to 90 local representatives. That means not only fewer people taking care of the local needs of their constituents, but depending on the way the riding borders are redrawn it could lead to poorer representation in other ways (for example, if rural ridings are merged with each other or with more heavily populated urban areas that would dominate results they lose a voice). The 'proportional' part of MMP comes from 39 seats (increasing the total number of seats to 129) that are filled with party members who are not directly elected by the public. Under this system, for those 39 seats, parties are elected but list members are selected meaning that 30% of parliament is chosen by politicians and accountable only to party leaders.

There are obviously more arguments for and against each system, and rebuttals to them all. There are also many other voting systems out there, despite the fact we'll only see our current one and the form of MMP recommended by the Ontario Citizens Assembly. In the end, all one can do is make an informed choice.


Mahmoud Ahmadinejad Talks to Charlie Rose

Charlie Rose shows why he's one of the few credible journalists left in America by sitting down for a discussion with Iranian President Mahmoud Ahmadinejad, a man most mainstream media don't want you to hear from.


Monday, September 24, 2007

Whatever Happened to Peace?

Christopher Hitchens predicts that Al Gore is about to get the Nobel peace prize for his recent efforts in promoting global-warming denial denialism. Hitch further calls on big Al to take advantage of the status the award would bring and take a run at the Democratic ticket. Good for Al Gore, probably good for America and by proxy the rest of the world, and good for mother Earth.

Kind of ironic though, that with at least two ongoing wars to get worked up about, the closest thing to peace advocacy we can find worthy of rewarding is environmentalism. Maybe they should change the name from "Nobel peace prize" to "Nobel warm-and-fuzzy" prize. At this rate, I predict we're headed for a future Earth teeming with bountiful life, a balanced carbon cycle, an intact ozone layer, completely "natural" temperature cycles, shelled-out terrain, bombed-out buildings, spent ammo and no human beings.

Clearly this is not the 60s. I guess these days we're lucky if pop culture awareness is focused on even one real issue at a time.


Scientists, Arm Yourselves Against DNA Denialism!

These days it seems that anyone who questions a widely held scientific belief is a delusional "denialist". Are you considering suggesting the hypothesis that global climate change is driven primarily by cosmic radiation rather than human activity? Don't bother. Everyone knows global-warming deniers are in cahoots with big oil. Pondering whether public health and education measures might be more effective than anti-retroviral drugs in combating AIDS in South Africa, or asking exactly how HIV infection eliminates CD4 T cells? Shut the !@#$% and get back on the band-wagon already you HIV-AIDS denialist! You've obviously been brainwashed by the LSD you got from some burnt-out, pot-smoking scientist from California, like Peter Duesberg or Kary Mullis. Have you ever dared to question the prevailing deterministic model of stem cell division? Stem cell denialist! Every day you spread doubt is another day a person with ageing cells will have to go without replacements. Or worst of all, has it occurred to you that all available molecular phylogenetics data does not fit into the "universal tree of life"? Ha! Did God tell you that on a mountaintop, you evolution-denying, modern-day Moses? I hope you burn in hell!

With all the rampant denialism going on out there, we smarty-pants scientists need to prepare for the next outbreak. The question is, which form of denialism will be the next to hit? I think it only makes sense that those conniving little bastards will go after the very foundations of modern genetics and molecular biology - the "theory" that the genes encoding our biological traits are contained in cellular deoxyribonucleic acid (aka "DNA").

So how to prepare? I propose a new tactic. No more bloody and violent exchanges of capital letters and exclamation marks on the battle fields of the blogosphere. Enough with the "YOU ARE A DENIALIST BECAUSE YOU ARE DUMB AND IRRATIONAL AND WILL NEVER ACCEPT REALITY!". No more "it's in a peer-reviewed journal and has been regurgitated by a lot of other peer-reviewed journals so it must be true". No more "this is not even really a debate amongst REAL scientists, so I don't have to bother to explain it to you". No more "I did a PubMed search on your hypothesis, no hits came up, so you're wrong!!!". No more "I hold a BSc, an MSc and a PhD from Oxford, Cambridge and Hogwarts, whilst you barely satisfied the conditions of your community college, ergo I am clearly in the right and you, sadly, are mistaken".

Yes, I would like to propose a radical new approach in the war on denialism. I call it "explaining science". This means doing nothing except explaining experiments and their results. (aka "the evidence"). When people are unconvinced or do not immediately understand, we rephrase and try again. And again. And again. They still don't get it? Maybe we draw a picture. A cartoon. Maybe an animation. Maybe a bulleted list. Maybe use statistics, a pie-chart or a bar graph. Make a video, a hologram or a video-game. Do an interpretative dance. Whatever it takes. Just don't call them denialists, or you'll remind them they're supposed to be denying something (shhhhhhh). And maybe, in the end, we will convert the denial-lovers to science-lovers. Or perhaps some will resist and forever remain beyond our reach. Maybe the disease of denialism is incurable or even genetically encoded in an unlucky few defectives. But I'll be damned if we don't die trying!

So, to prepare for the eminent strike against DNA, all we have to do is remember how we know that DNA is the genetic material. Keeping the experimental evidence at our fingertips, we will be well-armed to defend science from the denialists. What? Can't remember why? Don't worry, me neither. Hey I'm just a graduate student in biochemistry after all. Luckily, Larry Moran, a real scientist who's old enough to still remember the evidence and knows how to blog, points to the experiment in question (that's why they call him 'Professor'). It was Canadian Oswald Avery's 1944 paper which showed that DNA, but not RNA, carbohydrate or protein could transfer the genetically transmitted trait of virulence from bacterium to another. You can read commentary in science blogger John Dennehy's "Citation Classic of the Week". Even better, check out this awesome Cold Spring Harbor animation describing the experiment. No denialist can withstand the power of animations!

So, fellow scientists, be vigilant for the emergence of the DNA denialists when they strike. Know the enemy, but more importantly, know the evidence!

(PS- This was a humor piece, whether you find it funny or not. Except the part about the Avery paper. So don't be sending me any hate-mail.)


Sunday, September 23, 2007

I Knew Jesus Was Cool!

Jesus takes down two bouncers on his way into the bar, drinks a bottle of JDs and picks up two women in less than 60 seconds, showing obvious signs of superior Darwinian fitness. Naturally, God gets jealous.


Neutrophil moving to the site of infection

Another cool video. This one combines video microscopy (looks like in vivo) and cgi. Very cool.


Lights Out For Merck's HIV Vaccine Program?

Perhaps underscoring ARW's suggestion re the need to explore alternative approaches to dealing with infectious disease, Merck have ended their phase II HIV vaccine trial due to lack of efficacy. This spells the end for their Adenovirus-based vector, the fruits of 20 years of R & D work. At least for the time being, they apparently have no specific plans to continue their HIV vaccine program.

Maybe a vector that induces a more vigorous immune response, such as VSV or vaccinia, will be more successful...and maybe Merck or competitors will be shopping around for new vector platforms in the near future...


Friday, September 21, 2007


So in an effort to generate some discussion of a topic I've been interested in for a while but am too busy right now (writing grant applications) to get into details... I'll throw this out there and see what happens.

Commensal microbes are generally overlooked but likely have a greater influence on our biology than the pathogenic microbes that get all the attention (and research bucks!).

- role of commensal gut flora in obesity
- commensal viruses such as Torque Teno and the dozens (hundreds?) of papillomaviruses that can be isolated from everyone's skin... no warts, no pathology
- recent recognition that an ongoing herpes virus infection significantly impacts on the ability of mice to fight bacterial infections... raises worrying proposition that studying the immune system of "pathogen-free" mice may be as misleading as studying muscle function in a quadroplegic...
- should we devote more funding to these microbes? with limited funds should we tackle the problems (HIV, TB, malaria) or should we (also) study commensal microbes which have (likely) figured out our immune system and could probably teach us a thing or two... thi is actualy the topic I've assigned in the undergrad virology course I teach...

So... very little content... just the nidus of a (hopefully) fruitful discussion/discourse...


Up Yours Scotiabank!

Today I went to Scotiabank, where I have held an account for the past 20 years or so, to cash stipend/scholarship cheques issued to me from a relatively reputable establishment, the LARGE university at which I study, and another from the Government of Canada. Rather than depositing at the ABM, I went in to see the teller, in the hopes that my money would immediately become available for me to pay on a bill that was due.

The teller quickly informed me that I wouldn't be able to get at my money for 7 days...unless I "negotiated" with my home branch. Yeah that's what I what I want to spend my day doing. Instead of, you know, working. Or, she asked, "is there anyone who would know you at this branch"? Hmmm...that depends...have they been monitoring my internet banking activities, or spying on the ABM machines? Like I have time to build a rapport with my local banker. Like they have time to care who the !@#$ I am. Has anyone told the people working in banks that we live in a "digital" age? Anytime I mention internet banking to a bank teller they look at me like I'm talking about flying dragons or Atlantis or some shit.

Whatever happened to good old-fashioned photo ID? I've got so many ID cards stuffed in my wallet I can barely walk straight, and yet I need some banker to vouch for me just to deposit a cheque? WTF??

Actually, the Canadian Bank Act states that banks must cash cheques on the spot with two pieces of photo ID, even if the cashee doesn't have an account at their bank. The catch is that the cheques have to be for less than $1,500 each. So, a stranger with no account could go into a bank and show 2 pieces of ID, getting cash for 10 cheques worth $1,500 each. But, you can't put a single cheque worth more than $1,500 directly into your own bank account. Clearly these regulations need to be updated. A 7 day hold in the age of electronic commerce is just ridiculous, and so is keeping track of your customers by personal rapport.

Oh, and since my cheques were for less than $1,500 each, I could have asked for cash instead and then deposited it back into my account. Instead, I'm waiting 7 days while the bank sits on its thumbs before I can access my money to pay my bills. All this "service" in return for all the "service charges" I'm nice enough to pay them for the privilege of lending them my money. What a bunch of bums.


The Memo Behind PRISM: A Battle Plan for Attacks on Open Access Publishing and Intelligent Discourse in General

Eric Dezenhall is a PR consultant who has distinguished himself by advising such wonderfully truth-fearing organizations as the Regan government, Exxon and Enron. Lately he's been working for the Association of American Publishers (which includes publishers such as Elsevier, Wiley and the American Chemical Society) in support of their efforts to impede technological and societal progress by attacking the open access publishing movement. Leading to the joke that is the infamous lobby group PRISM.

Now you can read all about the tactics he has recommended in this leaked memo (reprinted in text form below). Dezenhall concedes that reality is poised against the AAPs positions, therefore obscuring and confusing the truth with "high-concept rhetoric" is what is needed:

"Proposed Coalition Strategies and Tactics


The Coalition faces the daunting task of trying to win support for an issue in which publishers are not sympathetic — continuing to charge fees for access to scientific journals. It’s hard to fight an adversary that manages to be both elusive and in possession of a better message: Free information. There is no magical sound bite that will cure this issue, however, at the present time, there is little to no “pushback” from the publishing industry. To inject the industry’s position into the debate, we recommend bypassing mass “consumer” audiences in favor of reaching a more elite group of decision makers employing strategies that emphasize “high-concept” rhetoric and in-the-trenches political-style communications.


  • There are no clear villains.
    • Government is looking to give taxpayers free access to the research that they fund and publishers are trying to protect their business and the integrity of the research they publish.
  • The free internet movement is strong and getting stronger
    • With the growing availability of free information on the Internet, the public feels that this is one more thing that should be accessible to all people at no charge.
  • The public access issue is dry, bloodless, complex and, to most, uninteresting


  • The publishing industry provides genuine value-added in its production of scientific journals
    • Publishers invest considerable resources through the peer review process to ensure that only the best articles are published in their journals.
  • There is an epidemic of bad information on the internet and elite media know it
    • With the number of surveys and studies available on the Internet, it is difficult to separate genuine science from junk science. Peer reviewed journals are the only reliable source for sound science.


  • Supplement the Coalition’s lobbying efforts with communications “air cover”
  • Simplify the Coalition’s arguments into easily digestible concepts (e.g., censorship)
  • Mobilize a discretionary campaign-style team to inform key intellectuals about the risks associated with supporting the public access movement
  • Communicate directly on some issues, but seek the support of third-party support on others (e.g., dangers of censorship, threats to free enterprise)

Target Audiences

  • Members of Congress
  • Targeted regulators
  • Key media
  • Think tank community
  • The larger publishing community, librarians, researchers and scientists to reach more potential allies


1. Form a Single-Issue Coalition

A coalition of concerned publishers must be formed as the industry’s collective point-group on the public access issue. A spokesperson must be selected and media-trained and a clearinghouse for information must be established. A website should be strongly considered.

2. Rhetorical Campaign Points

  • Develop simple messages (e.g., Public access equals government censorship; Scientific journals preserve the quality/pedigree of science; government seeking to nationalize science and be a publisher) for use by Coalition members
  • Develop analogies that put the public access issue in a context whereby target audiences will understand its pitfalls and perilous implications not to mention the hypocrisy of science leaders getting salaries and honoraria but declaring the publishing industry’s need for capital as being somehow immoral
    • Paint a picture of what the world would look like without peer reviewed articles.
    • In theory this may provide free taxpayer access to research that they fund, but they will pay eventually with substandard articles and their money being used to develop and maintain an electronic article depot rather than to fund new research.

3. Opposition Analysis

Inventory the Coalition’s adversaries, their arguments and weaknesses prior to launching communications.

4. Enlist Think Tank Support

Seek studies, white papers and public commentary from think tanks that may quantify the risks, the societal price tag of public access. Groups that may be considered include the American Enterprise Institute, Brookings, Cato, Competitive Enterprise Institute and National Consumers League.

5. Media Briefings and Placement

Conduct a fresh round of media briefings with high-end editorial, health and science writers and reporters. Conduct op-ed article placement.

6. Targeted Advertising

To trade journals and Beltway publications (e.g., The Hill, Roll Call) emphasizing key rhetorical points.

Estimated Budget

$300,000 - $500,000 for a six month program."

Feel free to point out the many flaws in his arguments in comments below.

Credit to Palazzo for pointing to this info, Blake Stacey for converting the memo to text format (which I have copied and pasted here) and Jim Giles for posting the leaked memo on his blog.


Ontario Election Debates

The first leader's debate for the upcoming Ontario election went down yesterday.

- Watch the big three party leaders go at it here if you missed it.

- Also, you can get Green party leader Frank de Jong's debate responses here. He had to record his responses while watching the debate on TV all by himself since the Greens aren't big and powerful enough to get invited to the prom (ie debate).

Hopefully, if the citizen committee's recommendations on electoral reform are passed (referendum to occur on the upcoming ballot) the Greens will win a more representative share of seats and get to be heard alongside the cool kids in future electoral campaigns. Despite their traditionally poor electoral success, they represent unheard, but I think fairly common Canadian values.

As for my two cents, I could get behind any party that isn't proposing further cultural segregation of children by funding more religion-specific public schools. This is the ass-backward proposal of the Conservatives, whereas the Liberals and NDP are against this type of move. The Greens in my opinion the most progressive of all parties on the issue, calling for end to all public funding of religion-based schooling (meaning the elimination of the existing Ontario Roman Catholic school board).

In this day and age it's kind of frustrating to see that attention is directed at this issue instead of many other important ones (ie modernizing public transit to move Ontario cities away from our ridiculous reliance on cars). However I think the issue will linger as long as we in Ontario continue to hypocritically fund Roman Catholic education, a policy that really just does not belong in our secular and integrative multi-cultural society.


Tuesday, September 18, 2007

Fishy post

I'm big on fish science I guess as I have done a few bayblab posts on fish before. Here's a couple of 'good news' fish science stories:
1. Apparently Ontario has done a large study showing that mercury is eliminated from an aquatic ecosystem relatively quickly.
2. It is possible to derive trout from salmon. Apparently this could be used in various conservation approaches. The method involves injecting trout spermatogonia into salmon embryos. Some of the adult salmon then produce trout gametes.


Monday, September 17, 2007

Neutrophil Eating a Bacterium

Resistance is futile...

Kudos to Palazzo for finding this kick-ass video...

Oh yeah, apparently Dave Rogers made this video "over 50 years ago".


Open Access Workshop

There's been a lot of talk on the Bayblab about open access publishing, with our own Bayman making waves in the open publishing community. For those in the Ottawa area who want to learn more about open access publishing, and what it means for you, the University of Ottawa is hosting an open access workshop. The details:
Date: Wednesday 10 October 2007
Place: Room 140, Residential Complex, 90 University
Time: Seminar, 15:00-17:30 -- Refreshments, 17:30-18:30
RSVP to by Wednesday 4 October 2007

Among the speakers is Michael Geist, Canada Research Chair in Internet and E-Commerce Law. The event seems worth checking out.


Sunday, September 16, 2007

Number 1 or Number 2?

We've all heard of the Richter scale, used to measure earthquake intensity. Fewer may be familiar with the Beaufort Scale of wind force. In 1982, the 14th edition of the Merck Manual introduced a scale to measure a different kind of wind: flatulence. The Merck Flatulence Scale describes 4 familiar categories of fart, including the famous "silent but deadly" (aka 'slider' or crowded elevator type). I couldn't find the scale in my 17th edition of the book, but it's still found on the Merck website. If that wasn't scatalogical enough, there's also the Bristol Stool Scale, used to categorize the more solid (but not always!) releases from your backside. Now next time you go for a number 2 you'll know if it's a true 2.


Saturday, September 15, 2007

Cancer Research Blog Carnival #2

The second edition of the cancer research carnival is happening on Ben's Blog on Oct 5th. A carnival is basically a collection of links and a review on a particular topic. The intent is to bring together information on cancer and encourage an exchange of ideas between bloggers and readers. You can check here for our last edition. If you wish to submit a post simply fill out this form or paste the link to your story on the comments of Ben's blog by October 1st!


Friday, September 14, 2007

Questioning the Church of Cellular Determinism: The Trials and Tribulations of a Stem-Cell Denier

Sean Morrison, author of a recent Nature paper disproving the dogma of asymmetric hematopoietic stem cell chromosomes segregation, now discusses the challenges of challenging a prevailing theory in the peer-reviewed literature:

"One reviewer moved to reject the paper because of its foundation on negative results, he recalls."

"Morrison and colleagues grew individual HSCs on plates, stopping cultures after one or two divisions and probing all the colonies to see whether there were any in which all the newly synthesized chromosomes moved together into new daughter cells. None turned up, but the reviewers pushed Morrison to look for smaller and smaller subsets."

"He says the work was held to a higher standard than usual. "Papers that present evidence in favour of an idea don't show that most stem cells do something, only that some stem cells do something."

Of course as we already know, this scientific Cinderella story has a happy ending. Morrison and his group jumped through all of the reviewers' hoops, the paper was strengthened, and published in the world's greatest scientific journal in the history of the universe. Not to mention a great blow struck on behalf of stem cell atheists everywhere.


Wednesday, September 12, 2007

Tangled bank #88

Just ran into a great blog carnival at the behavioral ecology blog. Check it out, it's got some really good posts. Also our friend Kevin Z gave it a thumbs up in the comments. We gotta get more into the blog carnival business. A bunch of blog carnivals are posted at the tangled bank.



So apparently vegans bring their activism and animal restriction all the way to the bedroom. No get your mind out of the gutter, I'm not talking about bestiality (or lack thereof). However they have to be choosy when it comes to lubricants. Rather I'm talking about a new form of protest:

"They are mainly women, well educated and politically active, but are squeamish about having sexual contact with meat eaters. [...] Another vegan woman was so repulsed by the practice that she wouldn’t even let a carnivore get to first base: “I couldn’t think of kissing lips that allow dead animal pieces to pass between them.”"

Talk about restricting your dating pool... However I'm sure you could exchange fruits for sexual favors. It also begs the question, can vegan women swallow?


Forbidden fruits

I think Chimps are awesome. They keep reminding us that we're not so different. I also like the way they organize their society, especially the bonobo. You can see in them some inkling of culture, society, morality and altruism. Proof that you don't need religion to have those. Sometimes chimps can also be violent, selfish and cruel. Proof that religion hasn't invented those either. I must confess that I've never read the bible growing up, I didn't need to, popular culture already shoves those stories down your throat. So when I finally got my hands on one, I skipped straight to the end, and read about the apocalypse which at least had some entertainment value. Genesis particularly seemed awfully simplistic and a thinly veiled metaphor about why Adam shouldn't have banged Eve. How did Adam convince her? Well maybe by giving her an apple... at least that's what the chimps would do according to PLOS one:

"The sharing of wild plant foods is infrequent in chimpanzees, but in chimpanzee communities that engage in hunting, meat is frequently used as a ‘social tool’ for nurturing alliances and social bonds. Here we report the only recorded example of regular sharing of plant foods by unrelated, non-provisioned wild chimpanzees, and the contexts in which these sharing behaviours occur. From direct observations, adult chimpanzees at Bossou (Republic of Guinea, West Africa) very rarely transferred wild plant foods. In contrast, they shared cultivated plant foods much more frequently (58 out of 59 food sharing events). Sharing primarily consists of adult males allowing reproductively cycling females to take food that they possess. We propose that hypotheses focussing on ‘food-for-sex and -grooming’ and ‘showing-off’ strategies plausibly account for observed sharing behaviours. A changing human-dominated landscape presents chimpanzees with fresh challenges, and our observations suggest that crop-raiding provides adult male chimpanzees at Bossou with highly desirable food commodities that may be traded for other currencies."

So here you go, chimp males exchange fruits for sex, and they are willing to take great risks in order to get the fruits. Shows you things haven't changed much since our last common ancestor...


Avoid boring people

James Watson just came out with a new memoir entitled "Avoid boring people: lessons from a life in science". I have just been itching for a good biography of a scientist, I need the inspiration right now. So I might just pick this one up. From this excerpt, it sounds like it is a goldmine of scientist gossip, and the content and writing style remind me of Joel's writing on the bayblab (I wish we could get more of it). It also seems sprinkled with opinions about science such as this funny quote:

"Only belatedly did Harvard try to enter the Genome Age by committing itself, as the 21st century began, to becoming strong in systems biology, a discipline so sprawling and unwieldy as to merit comparison to Enron in its limitless expansions before the collapse into nothingness."

Way to undermine an entire field! Actually I partially agree, system biology to me seems like the marriage of high-throughput molecular techniques to physiology. It reminds me of an incident at a cocktail party, where I managed to get the president of Genome Canada to admit that genomics wasn't a field at all, but a tool that is applied to cell biology, or genetics.... Genomics in itself isn't hypothesis driven.

Anyways the reason I need inspiration is that doing a PhD sucks the dreams out of you. I think this is a common phenomenon in anyone who is knee deep in a PhD. At first it's the honeymoon, chances are if you are committing to a PhD it's because you love science. And when you start out there is so much to learn, so many possibilities that it fills your head with dreams about discoveries, publications, fame. And little by little those dreams get crushed. First you find out that your smarts wont save you this time around. No, smarts have little to do with it. What you need is 50% intense hard work, and 50% sheer luck. The hard work, especially at the beginning tends to be in vain. Experiments don't work out, or worse, results are negative. Here you have a choice: keep hammering at it or find a new path. The former may get you stuck, while the latter leaves you unfocused. And there is nothing worst than doing experiments in order to find what question you should be asking. Then there is the stress. The stress that you won't be able to graduate, the stress that your paper will never get published, and the stress that at the end you won't be able to compete with the elite who have top tier publication and ivy league backgrounds. But ultimately you stick to it, because you'd rather be doing science than anything else and you hope the 50% luck will kick in at some point. Ah, the life of a grad student!


Tuesday, September 11, 2007

Bayman is A God:

A recent bayblab discussion on the topic of open publishing apparently caught the attention of our friends over at the Nature Publishing Group. First, Hilary from Nature Precedings jumped in with excellent commentary and discussion on this post. Now, in a post on NPG's blog Nascent (Nature's blog on web technology and science), Timo Hannay firsts blasts PRISM (as did we) and then goes on to cite one of my more provocative comments on the topic and has this to say about it:

"Some people are just too quick to assume base motives, and employ words like "boycott" as if they were punctuation marks. Also, let's be honest, sometimes open access publishers have stoked these flames to their own PR ends. For me, this cynical and wrongheaded mindset reached its apotheosis (so far) in a comment on this blog post, which suggested that — wait for it — scientists should boycott NPG for having set up the free preprint server and document-sharing site, Nature Precedings:
'[G]ood call on Nature preceedings being designed to fail - I totally agree, had the same thought. I think it's Nature's effort to sandbag open publishing. Scientists and open publishing supporters should be crying bloody murder on this. I suggest a boycott of Nature preceedings. Hell maybe even the rest of Nature journals...'

Yeah, right, that would be good for open access..."

My gut reaction was that I just got bitch-slapped by someone at Nature, but I wasn't totally sure because so many big words were used (damn those writers and their big dictionaries). Naturally I immediately the hell out of his post to figure out what he was saying:

a·poth·e·o·sis [uh-poth-ee-oh-sis, ap-uh-thee-uh-sis] Pronunciation Key - Show IPA Pronunciation –noun, plural -ses [-seez, -seez] Pronunciation Key - Show IPA Pronunciation.
1.the elevation or exaltation of a person to the rank of a god.
2.the ideal example; epitome; quintessence: This poem is the apotheosis of lyric expression.

Hmmm. Elevation to the rank of a god. Ok, I can take that. Now let's look at the context, I seem to remember something from high school about meaning and context. Hmmm...

"cynical and wrongheaded mindset reached its apotheosis"

So, I'm the god of cynical wrongheadedness. Ok maybe not the best god if one had one's choice, but still, a god's a god.

Seriously though, I thank Timo for taking the time to clarify his position and respond to our provocations. Whether or not one believes the the NPG is seriously dedicated to open publishing as a corporate entity, he and others (see Hilary from NPG Precedings' comments on this post) demonstrate that some individuals within the organization are very dedicated to modernizing scientific publishing. His post and is worth reading. Hopefully I will muster up a more challenging response to his arguments in the future...


The good the bad and the ugly: medical science in Japan

Have you ever wondered how science is done in Japan, no?, well too bad, here is a random assortment of observations I've made so far:

- Work ethics are really important here, and researchers really go the extra mile to get things done, even if it means having less time for fun or being with the family.

- After work casual beer amongst student is relatively rare, instead, when people go out drinking they get shit-faced. PIs are no exception, and they tend to buy the drinks of the students.

- Grooming in the lab is ok here. People actually brush their teeth in TC or shave in the lab. I'm not even joking.

- Keeping food in the lab, or lab stuff in the lunch room is common. In fact in my shared office there is a freezer with enzymes and rice balls.

- Japanese are much better at reading English than speaking it.

- There is no law on animal research ethics, what you can or cannot do is up to the individual researcher or its institution. Yikes, I've seen some scary stuff.

- Many researchers are reluctant to go to meetings abroad because they fear speaking English in public.

- Patient consent for research is really easy to get, people here really trust their doctors.

- Science agency funding is a nightmare here. Different ministries may fund different types of projects, depending on your research institution's affiliation. For example your grant for cancer research might be coming from an entirely different ministry depending on whether you are in a regional hospital (science and tech) or a university hospital (education).

- Medical education here is sink or swim. It's easier to get into some universities, but depending on your university, license exam success rate may be as low as 30%.

- Team work is difficult because of both professional hierarchy and conflict avoidance. This got me really frustrated at first. Japanese tend to avoid conflict at all cost, so they will not share information with you if it may displease you. If an experiment doesn't work, they will act like it never happened. For example a particular experiment failed and I was trying to ask my boss why, but he kept changing the subject, or telling me we'll have a meeting later. The reason was a mistake made by one of his students. I now understand how to get such information, you have to read between the lines, or ask people lower in the ladder. I think high-placed people can't admit mistakes. Also, you don't ask things straight to the people at the top, you ask the person directly above you, and it gets transmitted up the ladder and then back down the ladder for your answer.


Monday, September 10, 2007

When is the best time to pickup?

Well according to this graph, girls should have the best chances to pickup guys in their early 30's while for guys it's all gravy all the way up to the 50's. This is supposedly based on US census information, except it doesn't add up... How can there be so much more single girls then guys? I mean, I understand the lines should taper off at different rates because of life expectancy. But I don't see why the area under the curve should be so different.. unless man are marrying each other?


Fact or Fiction: Full moon baby boom

Compulsive gamblers will tell you that to win a baby pool, always pick the date of the full moon closest to the actual due date. It's common knowledge that more babies are born on the full moon, right? Even nurses and doctors in labour and delivery will tell you that. So is there any truth to this ancient belief, or is it just a medical myth? A quick pubmed search reveals the answer: there is no correlation between lunar phase and birthrate. This evidence was been reported in 1979 in the New England Journal of Medicine, prior to that (1975) in the Canadian Medical Association Journal [pdf], and time and time and time again since.

There are two questions that immediately arise. The first is why is this belief still held, including by many well educated people, in the face of a large body of evidence to the contrary? (and supplementary to that, why are studies to that end still being done?) Obviously cultural reinforcement plays a large role - the myth continues to be repeated as fact. The second is where did the belief come from in the first place? Is it some leftover animal instinct where it was easier to deliver and/or protect newborns by the light of the full moon? Is it some cultural remnant from days when we worshipped celestial events like full moons and solar eclipses; some long, lost supersition? Is it simple recall or confirmation bias among mothers and hospital staff?

As for other common lunar beliefs, such as increased psychiatric disturbance or more full moon emergency room visits, again the literature doesn't support those beliefs (with the exception of a single study that showed clustering of seizures around the full moon). The Skeptic's Dictionary has a summary of full moon myths and some debunking. The bottom line is that the full moon has little effect on birth rates, hospital emergencies, stock market prices and (despite the root of the word) lunacy. Unless, of course, you're a werewolf.


Sunday, September 09, 2007

HIV cure Quack?

Call me a cynic but when I saw this press release stating that the CEO of a pharmaceutical company was donating an HIV drug to the public I smelled something fishy. It's not that I don't think that deep down a person would not give up fame and fortune for the benefit of the rest of humanity, I would like to believe that most of us could do that, it's just that public companies are legally required to act in their shareholders best interest. In fact a CEO could go to prison for doing something like that. But more importantly no one would develop and test and produce a drug if there wasn't a profit to be made. I have yet to see a government doing the research and doing the clinical trials and producing a drug to give out for free to its own citizen, let alone a company.
Even if the company couldn't afford to continue research on a compound they would probably try to sell it to someone. yet this is their mission:

" Because we believe human life to be more valuable than a profit margin, our goal is to aid in curing the world of HIV with our new medication that will be developed and distributed at generic prices from their inception."

Sounds to good to be true. So I went to check out the data, it's not published in any peer-reviewed journal but the initial screen that they paid the nih to do seems promising, albeit very preliminary. The compound seems to help block virus entry into the cell.

Yet here is what Dr. Hershline had to say about his drug: "I think we have to talk in terms of a cure for HIV. I want to cure HIV and that is why my foundation is called"
"This gift is intended to extend technology that no one else posses on this planet."

I noticed that Dr. Hershline is taking donations to help support his foundation. What are they doing with the money? Well the associated blog was a first hint:

"The CureHIV blog is intended to be an open forum for helping those being irresponsible by their use of addictive drugs and alcohol, to those wanting to help CureHIV spread the good news of the potential cure for HIV, to those who just want a better world.


Oh I see it's drugs and alcohol that is to blame and abstinence that is the cure. That doesn't sound like a drug developer, more like right-wing propaganda. Lets imagine a completely unrelated situation, If you wanted to raise funds for a cause wouldn't it look good if you made it appear as though you gave away a potential cure, even if that drug is completely worthless. I mean theoretically, wouldn't that be a good strategy?

I mean you could build stuff like a holistic creative recovery center:
"The mission of HCRC is to bring healthy natural food and activity, self-introspection and self-expression and the knowledge that the highest euphoria is experienced through a drug free mind-body experience. "

"My deepest concern is the spread of HIV through sexual intercourse in the young adults of America while under the influence of cocaine and alcohol . Dr. Hershline"

I mean I don't doubt this guy has his heart in the right place, and I don't know if he personally profits from this, but it just sounds fishy... Yet I hope to hear about this compound again, maybe in a peer-reviewed journal sometime soon. Until then call me a skeptic.


Friday, September 07, 2007

What Type of Pawn are You? Chess and Success in Research

"Pawn" is often taken to mean "one who is easily manipulated" or "one who is sacrificed for a larger purpose."

Combining three of my favorite topics (science, philosophy and healthy irreverence) into a single post, Alex Palazzo over at the daily transcript compares graduate students and post-docs to chess pawns in a discussion with a labmate (over beers of course). To give you the gist:

German Nihilist Postdoc: You know what we are?
Me (Palazzo): No, what?
GNP: Leibeigenschaft.
Me: What's that?
GNP: A serf, you know like in the middle ages.
Me: You mean XXX is our lord and we follow his commands?
GNP: Yup. Or a pawn, yes that is what we are.

So does chess strategy offer any insights as to how to succeed in the "competitive" world of research as a graduate student/post-doc? Let's see what wisdom Google has to offer:

"The Pawn's only movement is forward, except for capturing."
Chess Basics

"a player may end up with two pawns on the same file, called doubled pawns. Doubled pawns are substantially weaker than pawns which are side by side, because they can't defend each other, and the front pawn blocks the advance of the back one."

"pawns gain strength as they advance because they pose the threat of queening...however, an overadvanced pawn is then often a liability."

"A passed considered more valuable - especially if it is protected with other pawns."
Chess/Strategy (Wikibooks)

"A pawn which has no friendly pawns in adjacent files is an isolated pawn. The square in front of an isolated pawn may become an enduring weakness. Any piece placed directly in front not only blocks the advance of that pawn, but can't be driven away by other pawns."

"1. Connecting Pawns = good 2. Isolated Pawns = bad 3. Doubled Pawns = even worse"
Devilant's Kung Fu Chess Strategy Guide

Hmmmm...Well, I'll just leave the chess stuff at that. Anyway, all this brings me to my actual point. One comment of his in particular -
"If we are not protected or backed up by the other pawns",

reminded me of a post topic I've been wishing to explore. Actually I haven't had time to come up with anything interesting yet, but here are the questions I'd like to look at before I forget:

  • How do perceptions of "success" and how to go about getting it vary amongst grad students/post-docs (GS/PDs) ?
  • How do these perceptions guide them to develop different strategies to attain that "success"?
  • What is the impact (if any) of the execution of each possible strategy on:
  1. The GS/PDs own stress levels and overall health.
  2. How s/he interacts with labmates (particularly one's peers, ie other GS/PDs).
  3. Lab-wide social dynamics amongst peers.
  4. The stress levels and overall health of their peers (GS/PDs).
  5. The general lab culture, environment and morale etc.
  6. Scientific "productivity".
Ha! Now that I write that out it's no wonder I haven't had time to think about it. Actually it's not really a topic I've been interested in thinking about at all in the past, until I became aware of how radically perceptions of the obstacles to, and conditions for, research "success" seem to vary amongst students/PDs.

So maybe we can do this one in true web 2.0 style instead and everyone else can offer the opinions and answers. Anyone??

In the mean time, check out the post and comments and have a laugh.

(PS - While one might indeed find similarities between lab oligarchies and chess, I personally find GO a lot more appealing...). Maybe that's because I'm a pawn. Power to the peasants!


Acupuncture and back pain

Many health websites actively promote acupuncture for back pain. I've always considered acupuncture with a doubtful eye, mostly because it is based on unfounded anatomical features, and involves an energy which by its own definition is undetectable by empirical science. One skeptic put it as such:

"The meridians of acupuncture are no more real than the meridians of geography. If someone were to get a spade and tried to dig up the Greenwich meridian, he might end up in a lunatic asylum. Perhaps the same fate should await those doctors who believe in [acupuncture] meridians."

Yet there are meta-analyzes and even a lancet publication showing that acupuncture does have a modest significant effect over sham needles (but is not superior to standard treatment). This raises questions has to why an effect was observed. One possibility is bias, since the trials are not double-blind, the acupuncture practitioner knows when he is putting the needles in the supposedly real points or when he only inserts them superficially on random places. As such the patient may be consciously or subconsciously influenced to agree with the practitioner's own beliefs, even if he/she is well intentioned. Another possibility is that there is indeed a real effect. For example, inserting the needles in deeper may have elicited more pain signal and allowed the release of more endorphins than the superficial sham needles. I think the only way to truly test if acupuncture works would be to compare the same needles, inserted the same way in a double blinded manner. Someone who was trained on how to insert the needles but not "where" would be given two "maps" and not told which is which. Of course if that would fail to work the alternative medicine practitioners would probably say that it is an unfair comparison and that only they have the holistic energy channeling knowledge. But it would sure satisfy me.

Placebo is most potent in terms of reducing pain, which suffers a large influence from the state of mind. Another hallmark of placebo is that it tends to be most effective acutely and tends to diminish with time, and with repeated treatment. acupuncture seems to satisfy both these conditions.

Anyways all this was to introduce the Traditional Chinese Medicine Act, 2006, which allows tradional chinese healers to be called Doctors and allows them to communicate a diagnosis to a patient based on traditional practices in Ontario. I really do wish western evidence-based medicine and alternative medicine would be treated equally, that is that both would have to prove efficacy and safety in controlled trials. Soon we'll be in the same situation than the UK which has multi-million dollar homeopathetic state-funded hospitals, complete with ambulances.


Thursday, September 06, 2007

God is not great

That is the title of Christopher Hitchen's new book. While I can't say that I admire Hitchens as much as Dawkins, in fact he is a bit obnoxious, I do enjoy seeing him debate. On a recent tour for his book, he's decided to do his debates in the bible belt, taking the enemies of reason head-on.

In Dawkins' review of his book, here is what he had to say about Hitchen's debating skills:
"I hadn’t met Hitchens before, but I got an idea of what to expect when Grayling emailed me to discuss tactics. After proposing a couple of lines for himself and me, he concluded, “. . . and Hitch will spray AK47 ammo at the enemy in characteristic style”.
Grayling’s engaging caricature misses Hitchens’s ability to temper his pugnacity with old-fashioned courtesy. And “spray” suggests a scattershot fusillade, which underestimates the deadly accuracy of his marksmanship. If you are a religious apologist invited to debate with Christopher Hitchens, decline."

I think Hitchen's should come debate with John Torry, before the conservatives start including ID in out science books.


Sequence of an epidemic

454 has potentially uncovered the cause of colony collapse disorder (CCD) that has been plaguing North American honeybee colonies for a couple of years. 454 has sequencing technology that allowed them to simply sequence collapsed colonies and non-collapsed and compare.
However, one sequence appears particularly significant: that of the Israeli Acute paralysis Paralysis Virus (IAPV), which was only detected in the collapsed colonies.
Hopefully this awesome display of the power of sequencing will help 454 overcome it's embarrassing contamination in their work with the Neanderthal genome.


Wednesday, September 05, 2007

conservation != importance

A paper in PLOS has shown that ultraconserved elements, these stretches on hundreds of base pairs that are perfectly conserved between mice, rats and humans, can be deleted without any ill effect on the mice. evolution works in mysterious ways...
"It is widely believed that the most evolutionarily conserved DNA sequences in the human genome have been preserved because of their functional importance and that their removal would thus have a devastating effect on the organism. To ascertain this we removed from the mouse genome four ultraconserved elements—sequences of 200 base pairs or longer that are 100% identical among human, mouse, and rat. To our surprise, we found that the mice lacking these elements are viable, fertile, and show no apparent abnormalities. This completely unexpected finding indicates that extreme levels of DNA sequence conservation are not necessarily indicative of an indispensable functional nature."


Science Horoscopes: Are You a) A Morning Graduate Student, b) an Evening Graduate Student or c) All of the Above?

"I know a lot of morning people and I know a lot of night people but I have yet to meet a late afternoon person". ----- Douglas Coupland, Starbucks The Way I See It #277.

Nowhere are variations in individual work routines more apparent than in an independent and liberal work environment such as the research lab I work in. It is easy to observe, for example, subpopulations of obligate morning-workers and obligate evening workers, as well as the facultative morning/evening workers. Then there are the really crazy (but increasingly rare) individuals who just never go home.

But what underlying differences cause different people to gravitate towards different work schedules? Are certain work schedules more productive than others?

I recently came across a paper that found some interesting correlations between student work schedules and tendencies in two areas of personality that are highly relevant to scientific research: 1) How students internalize information about their environment and 2) how they communicate with others.

Basically, morning-types tend to be conformists:

"Specifically, morning-types gather their knowledge from the tangible and concrete, trusting direct experience and observable phenomena (realistic/sensing), prefer to process knowledge using analysis and logic (thought-guided), and transform new knowledge according to what is known (conservation-seeking). Their behaviour style was upstanding and self-controlled; they relate to authority in a respectful and cooperative manner and tend to behave in a formal and proper manner in social situations (dutiful/conforming). Finally, morning-types care about giving a positive impression"

Whereas evening-types tend to be innovators:

"the thinking style of evening-types was based on the symbolical and unknown data more than on concrete and observable ones (imaginative/intuiting), they tend to be creative and to take risks, ready to transform and recast whatever they come upon (innovation-seeking). As for behaving style, evening-types tend to act out in an independent and nonconforming manner and resist following traditional standards (unconventional/dissenting)."

It's interesting to speculate as to the underlying biological basis for these differences (ie circadian rhythms, etc.). But to me the real take-home message from this work is that different people probably perform to the best of their abilities on different working schedules. Thus the most productive research environment is likely to be one that respects the individual's freedom to work on one's own schedules. On an individual level, this study might also suggest that different research tasks (ie repetitive labor vs. idea brainstorming) are best performed on different schedules.