Monday, October 31, 2005

The New Video

Good friends stayed over this past weekend. The main topics of conversation were blogs, google, science and anxieties over our future careers.

There I found out about Google Video Search. At some point people thought that the internet would replace television, and then more recently this idea has been ridiculed - but something tells me that the death of TV (or at least a great paradigm shift) may actually occur.

Read this interesting article from the Boston Phoenix about the Participatory Culture Foundation.
But as corporations lick their chops at the prospect of digital-video windfalls, Worcester's Participatory Culture Foundation (PCF), a small cadre of young activists and programmers, is heading in the opposite direction. The group has developed an open-source, nonprofit Internet TV platform that looks to draw the average viewer into this brave new world. Called DTV in its current Mac-only beta version (but due to be renamed when it launches for both Mac and Windows in the next few weeks), it's an intuitive, user-friendly way to find free online video, subscribe to daily video feeds, organize your video library, and, importantly, publish your own video content. It's a significant development in online television, and the first major step in the PCF's grand mission to "create an independent, creative, engaging, and meritocratic TV system for millions of people around the world."

Friday, October 28, 2005

Outsourcing Science

More and more this seems to be a reality that the West will have to face. As the number of highly educated individuals in India and China increases and the currents gaps in the cost of living in the West vs. the East are maintained, it will be inevitable that a large amount of commercial (and perhaps academic) science will be outsourced to the East.

And the beginnings of that are almost at hand. From an article in today's NYTimes:

China wants to transform its top universities into the world's best within a decade, and it is spending billions of dollars to woo big-name scholars like Dr. Yao and build first-class research laboratories. The effort is China's latest bid to raise its profile as a great power.

China has already pulled off one of the most remarkable expansions of education in modern times, increasing the number of undergraduates and people who hold doctoral degrees fivefold in 10 years.


The model is simple: recruit top foreign-trained Chinese and Chinese-American specialists, set them up in well-equipped labs, surround them with the brightest students and give them tremendous leeway. In a minority of cases, they receive American-style pay; in others, they are lured by the cost of living, generous housing and the laboratories. How many have come is unclear.

On many occasions (and on this blog and my previous blog) the issue of importing low-wage biological science workers AND outsourcing of science has come up. Now there is a rebirth of academic science in the East. So where will this all end up in 10-20 years? Will this be one of the last generation of graduate students and postdocs who can perform research in the US?

Here are some scenarios:

a) Science will be done in the West, but the pay will be bad. Few Americans enter science, preferring more lucrative jobs (lawyer, stockbroker, florist). The only individuals willing enter biomedical research are imported from other countries. WAIT this is the current situation (and I am imported labour!)

b) Due to the fact that most research grants will continue to come from the NIH, most science will be spearheaded in Western labs, but many smaller sub-projects (constructing genes, purifying proteins) will be sub-contracted to companies in India/China. (Sounds like my entry on kits.) Labs will have a PI (principal investigator) but fewer gradstudents/postdocs. Need a knockout mouse? Call up Beijing.

c) Labs will split into two. An American lab to get grants, and an Asian lab to do most of all the gruntwork. Read about Tian Xu's lab. Just like corporations, labs will go multinational.

d) All basic (i.e. unprofitable) research will be performed in the West, while pharmaceuticals will move the majority of their operations east. Although big pharma would keep outposts here so they could cash in to collaborations with any new hot field.

e) Scientific output from Asian universities increase until it rivals/surpasses Western output. Meanwhile in an anti-evolutionary orgy, American fundies go haywire, chanting "off with their heads" and Science from the US disappears.

f) Nothing much happens. Political instability in China and India cripples government funding towards science. Other impediments include a lack of local biomedical related industries that provide reagents/equipment and other essential tools for science, a cooling down of "globalization" with it's many indirect effects (such as impeding the ability of eastern labs to import equipment from the West). And then there is war, religious strife ...

Note that I'm not saying that these changes are good or bad, but that they may happen and we have to deal with them. OK my head hurts (and my anxiety is high), Friday Happy Hour here I come ...

Wednesday, October 26, 2005

"The Fashion Journals" or "The Holy Trinity"

Andy (another Rapoport postdoc) and I had a mini debate as to whether Nature, Science and Cell should be referred to as "The Fashion Journals" or "The Holy Trinity". Many institutions of higher learning informally require a tenure-candidate to "get into" one of these publications. In addition many hotshots can get crap into these journals - like trendy bars, once you've made the hotshot list you can come back anytime you want.

Let's evaluate these titles:

"The Fashion Journals" is self explanatory.

But there is more to the "Holy Trinity".
  • Nature being the oldest, would have to be The Father.
  • Since Cell was started by Ben Lewin, a former "Nature" guy who was upset by the other two biggies, and who then "walked the earth" to start his own journal and save science publication, Cell is definitely The Son.
  • That would make Science the Holy Ghost. Since it's a non-profit and the "poorer cousin" of the other two journals, it is fundamentally different thing - just like The Holy Ghost.

  • Not bad. OK so we're not as witty as some ... but we do keep ourselves amused.

    Tuesday, October 25, 2005

    Eye Candy

    Hela cell microinjected with ???

    Monday, October 24, 2005

    Systems Biology DNA Prep???

    Once upon a time, we made the necessary chemicals from scratch to purify DNA from bacterial cultures. These days, for a couple of dollars, you can get all the reagents you need all packaged in a nice box - these things are called commercial "kits".

    You may ask, why do you use these kits - Is it laziness? or consistent results? A combination of these answers I guess. In the end those that never made the reagents from scratch are less likely to understand how the procedure worked, and how to trouble-shoot when the procedure fails. The latest kit (from Qiagen) had this flyer and instruction booklet (pic left). But if you read the flyer closely this is what you'll notice:

    This is clearly a new all time low in kits. A kit for systems biologists?? ... it's as if the kit's label should have read: "Are you a String-Theorist and want to jump into biology? Well we have the kit for you! Use our NEW AND IMPROVED kit and you'll get your DNA faster than ever (and thought-free too). Now even a clueless Physicist can purify DNA without thinking about how this stuff actually works!". The sad thing is that the kit is EXACTLY THE SAME AS THE OLD KIT, except for some blue dye that helps to evaluate if your bacteria have lysed. But Qiagen really wants us to believe that this kit is NEW AND IMPROVED, and so they added this sentence to the cover of their NEW instruction booklet:

    To all those Systems Biologists ... have fun with your blue kits!

    Sunday, October 23, 2005

    My Father's Letters to the Montreal Gazette

    After publishing an article on ID (which unfortunately I do not have) the Montreal Gazette obtained and published the following letter from my father:
    Dear Editor,
    Regarding Janice Keane's letter (Gazette, Oct. 18, "Creation is always a leap of faith") in which she asserts that "it (evolution) still is and remains a theory, rather than a fact", disparages not only evolution but all of science. Newton's law of gravity is a theory, so is Quantum Mechanics and Einstein's famous E=mc2. Yet when it comes to evolution which encompasses well-established principles found in physics, chemistry and biology, people like Janice Keane, who can't accept its implications that life arose on this planet as a random process, resorts to this ultimate dismissive
    that 'it is just a theory', meaning in the sense that it has very little value. Let it be clear and simple: an attack on the theory of evolution, not on its content which is open to debate but on its reason to exist, is an attack on all of science.
    Joseph Palazzo

    Then today the Gazette published a response:

    Joseph Palazzo (Letters, Oct 19) is clearly confused about the difference between theory and fact. If I drop an apple, it will fall to the floor 100 per cent of the time, so gravity is a fact, not a theory. Evolution, however, cannot be proven. So saying that evolution is a theory does not disparage real science.
    Intellectual honesty dictates we recognize that creation and evolution are both theories. I lack the faith to believe that order came out of chaos T the Big Bang theory) or that the complexity of nature is a result of chance development(evolution).
    Rev. Rich Mellette

    My father's new response (just submitted to the Gazette):
    Rev. Rich Mellette's answer (Letters, Oct 23) to my letter (Oct 19) further confuses the issue. Observing an apple falling is a fact, Newton's law of gravity that explains that fact is a theory, not a fact. Nonetheless on that theory -- Newton's law of gravity -- we were able to send a man to the moon and back. That we have such much confidence in that theory might lead us to believe that it is a fact, when in reality it is not.

    Now Creationism can be construed as a theory but not as a scientific theory. The danger of this misconception as led as in the case of the Kansas State Board of Education to force science teachers to give equal time in their biology classroom to Creationism. But Creationism, and its hybrid Intelligent Design, have failed on all counts on the Popper's fallibility test and have been rejected as a scientific theory by the science community. In a democratic society, the religious beliefs of any person are nobody else's business. The creationists are free to believe whatever religious tenets they like. And Creationism can be taught as a course in the religious studies or the humanities, but it has no place in a science class.

    Joseph Palazzo

    So why is the Gazette taking ID so seriously? Well that's easy, this newspaper is owned by Conrad Black, a newspaper tycoon and staunch conservative. Unfortunately, the Gazette (an awful paper I must add) is the only English language newspaper that delivers in the Montreal area (I'm not sure if the National Post delivers in the Montreal Area, but that paper is even more Right-wing and it's also a Conrad Black production). So as a result ID gets air time in Montreal. This is a great example of how a media monopoly can adversely affect the public debate of important issues.

    Saturday, October 22, 2005

    Nice Profile of Tian Xu in Today's NY Times

    Well after complaining that Scientists are rarely featured in the American press, I found a profile of Tian Xu from Yale's Genetics Department in today's NY Times. To visit his lab's website click here.

    {update 10/2/05}

    Sorry I usually take out some excerpts from NY Times articles, as they are only freely accessible for about a week. Foretunately there are other bloggers who DO copy whole articles, such as Dr Xu's Profile. For a discussion related to Tian Xu's lab see my post (9/28) on outsourcing science.

    Friday, October 21, 2005

    Happy Hour Follies

    There has been an ongoing "friendly rivalry" between our lab and the neighboring lab. When ever it's one lab's turn to host the weekly happy hour, it usually advertises it in a way that ridicules the other lab.

    This week it was our neighbor's turn. However instead of mocking us their poster's title was: Want Avian Flu? followed by a picture of a virus, followed by a + sign, followed by a picture of a chicken followed by "= chicken wings".


    We then decided to post this poster next to their poster ...

    From: John XXX
    Sent: Thursday 10/20/2005 8:11 PM
    To: XXX Lab
    Subject: Happy Hour
    >>> John,
    >>> We have a problem, one day left, no theme for
    >>> happy hour, we're screwed.
    >> Dear Lab,
    >> Don't bother me with this crap. By the way I need a place with window
    >> seats to eat dinner on Friday. Someone make reservations.
    > Dear John,
    > The situation is critical, people are going to starve, and we need an idea
    > quick. You're not coming to happy hour?

    Dear Lab,

    Happy hour? A Harvard big-shot PI like me has better things to do on a Friday night. Chicken wings are cheap these days - build your happy hour with that - think of a good reason why we should eat chicken wings - and please MAKE YOUR POSTER APPEALING! Why aren't our posters ever as good as those from the Rapoport lab???

    You're doing a heck of a job. Don't bother me about this again,

    Thursday, October 20, 2005

    Random Thoughs on Big Polymers

    Yesterday I attended an interesting talk by Xuetong Shen from University of Texas (Smithvile, TX) about how actin, a cytoskeletal protein normally found in the cytoplasm, was a component of several chromatin remodeling complexes. For non biologists, chromatin is the DNA/protein complex that makes up our chromosomes and is found in the nucleus. DNA is wrapped around a proteinacious complex, called the nucleosome. For more on this topic click here.

    Why is actin in the nucleus and why hasn’t anyone ever seen it before? (Alright some have claimed to have done so.) Perhaps actin polymerizes in short sequences and acts as a mini track thus providing a surface to push nucleosomes along the length of a DNA strand? These remodeling complexes also help fix DNA double strand brake – perhaps short actin polymers act like “splints”?

    But another strange fact popped into my head – a fact we use to think about when I was in the cytoskeletal field ... DNA, membranes and the cytoskeletons are the 3 biggest continuous portions of the cell, and all three of these are highly negatively charged. There is something to that … but I’m not sure what …

    Wednesday, October 19, 2005

    David Suzuki - Canadian Icon

    If you grew up in Canada at any period between 1970 to 1990, seared on some corner of your brain is a photo of the geneticist, environmentalist and TV personality David Suzuki. He is so loved and well known, he was recently nominated for "The Greatest Canadian".

    Growing up I remember watching his show "The Nature of Things", a program that aired on CBC. Similar in format and content to PBS' Nova, the Nature of Things was a great show and I suspect had a greater viewership (as a % of the population) than Nova ever had. Well in yesterday's NY Times Science section there is a great profile of Dr Suzuki - although contrary to certain statements in the article, I think that many Scientists from the True North Strong & Free have great respect for his tireless work of educating the population. Perhaps if the US had more personalities who were Scientists, instead of having these ID debates, we could foccus the public's attention to other issues ... like global warming.

    Tuesday, October 18, 2005

    Marc Kirschner Interview on NPR

    Today, Marc Kirschner, head of the Systems Biology here at Harvard Medical school was interviewed on NPR's On Point program. There Prof Kirschner talked about his new book, The Plausibility of Life, evolution and what is the fabric of what he use to call evolvability. Click here to listen.

    All I can say - great interview. Prof Kirschner made a couple of points that most other Scientists in the spot light fail to mention. He clearly states that there is Science and there is faith and the two should never be mixed up. He also states that Science should never be used to explain things that we do not understand, and that it is a great disservice to Science to claim that we have "all the answers".

    He also talks about the great mystery of developmental biology - that actually there is not much difference at the genetic and cellular level between us and all other animals. To make an eye is not hard - most eyeless creatures have most of the building blocks (i.e. genes) to do it. It's actually easy to come up with intermediate eyes (and many of these intermediates exist in nature). And it's easy to see how the body can foster any change when things like eyes evolve. The body of multicelllular organisms is full of buffers and self organizing systems that permit these evolutionary changes, and the core components (genes) are almost universal and interchangeable. Infact the greatest mysteries in Biology escape the general public and the ID guys' imagination - how do these self-organizing principles work and how does a cell "work" (included in this second question is how do cells communicate). In the realm of evolution the biggest questions are how did life originate, how did the first (bacterial or prokaryotic) cell come about, and how did the first eukaryotic cell come about. Excluding consciousness and the mind, you can boil down 99% of the mysteries of "life" down to the cellular level. The rest (how to make limbs, eyes and) is infact trivial in comparison.

    Sunday, October 16, 2005

    Happy World Day of Bread

    Yes it's true, today is World Bread Day.

    And why is the Mad Scientist so enthralled by another gimmicky "World ... blah blah blah ... Day"?

    Well I was reading my good friend's blog (Tales of a Tall Medstudent) where he was describing how he was attempting to bake his own bread and succeeding. Now it turns out that I've gone down that path too. I wrote back to him:
    Confession - I bake my own bread too (did I ever give some to you?) It all started with crappy bread-machine bread. I loved the freshness but could not stand the crappyness - and the crust was the worst part. One day I marched down to the library and discovered "The Bread Bible" - great book BTW - and now for almost 8 months I've been baking bread - about 1-2 times a week.
    Once you start baking, it's hard to stop. It's hard to explain. Part of it is the side of me that likes to tinker around and try stuff (I've been experimenting with every loaf). Another part must be a subconscious urge to create.

    Another comment to the Tall Med Student's blog was from Floyd, who has a great blog on bread baking (on the Fresh Loaf site). That's where I read about World Day of Bread. Just like academic journals, there's a blog for every topic. Anyway ... Floyd exclaims on his blog:

    "Hello, my name is Floyd, and I am a bread-aholic."

    I went crazy this weekend. Kaiser rolls, a french bread, oatmeal raisin cookies, pumpkin bread, ciabatta, a raspberry cheese braid, honey wheat bread. Not to mention that I made a batch of apple butter, specifically for eating on home baked bread.

    Next weekend, I've gotta stop. Maybe one or two batches but that is it.

    And for some strange reason I perfectly understand. And I think to myself this whole baking thing is like some strange cult of underground bakers. Reminds me of the whole MAKE phenomenon (listen to this episode of NPR's Weekday about MAKE Magazine). There is an urge for people to reconect with "everyday things", take them apart, put them back together and figure out how to do it yourself. Call it MacGuyverism.

    To all those mad bread bakers out there ... have fun.

    Saturday, October 15, 2005

    RNA World - Search for the self copying molecule (RNA)

    Well we're almost there!

    Here is some rainy day (Saturday) reading for you. David Bartel (of RNAi fame) has an interesting article in a recent issue of the journal RNA on RNA-ligase ribozymes (link). Have fun.

    Friday, October 14, 2005

    Marijuana makes your brain grow!

    It seems like every couple of months there is a new study that reports the medical wonders of Marijuana. From the latest Nature News:
    The researchers injected rats with HU210, a synthetic drug that is about
    one-hundred times as powerful as THC, the high-inducing compound naturally found in marijuana. They then used a chemical tracer to watch new cells growing in the hippocampus. They found that HU210 seemed to induce new brain cell growth, just as some antidepressant drugs do, they report in the Journal of Clinical Investigation.

    Cannabinoids to make your neurons grow, to treat atherosclerosis ... what's next?

    Thursday, October 13, 2005

    Scientific Establishment to the US: Shape Up!

    In today's NYTimes:

    A panel of experts convened by the National Academies, the nation's leading science advisory group, called yesterday for an urgent and wide-ranging effort to strengthen scientific competitiveness.

    The 20-member panel, reporting at the request of a bipartisan group in Congress, said that without such an effort the United States "could soon loose its privileged position." It cited many examples of emerging scientific and industrial power abroad and listed 20 steps the United States should take to maintain its global lead.

    "Decisive action is needed now," the report warned, adding that the nation's old advantages "are eroding at a time when many other nations are gathering strength."

    As I've said before - in the realm of science education, the US has to shape up!

    We need more and BETTER science and math teachers in the high schools if we want to increase science literacy. But that's not all, the US has to support basic research (something that's been going downhill recently).

    Some recommendations (as stated in the NYTimes article):

    ¶An Advanced Research Projects Agency modeled after the military's should be established in the Energy Department to sponsor novel research to meet the nation's long-term energy challenges.

    ¶The nation's most outstanding early-career researchers should annually receive 200 new research grants - worth $500,000 each, and payable over five years.

    ¶International students in the United States who receive doctorates in science, technology, engineering or math should get automatic one-year visa extensions that allow them to seek employment here. If these students get job offers and pass a security screening test, they should automatically get work permits and expedited residence status. If they cannot get a job, their visas should expire.

    ¶The Research and Experimentation Tax Credit, scheduled to expire in December, should be made permanent and expanded. It goes to companies that increase their spending on research and development above a certain level.

    To encourage private investment in innovation, the panel said, the credit should increase from 20 percent to 40 percent of qualifying investments.

    Follow this link to read the original press release from the National Academies.

    Wednesday, October 12, 2005

    Systems Biology - Some Insights

    Yesterday, I saw a Systems Biology talk by Peter Sorger, and well there was some hocus pocus, but some insight. Professor Sorger is part of the new Cell Decision Processes Center at MIT, a fancy name for the new Systems Biology Center there.

    Sorger’s strategy is to study intracellular signaling cascades with a mix in silico models with cell based experiments. The former involves identifying all the signaling components and their various states and assigning differential equations to describe how a molecule changes from one state to the next or how one molecule alters a second molecule.

    Molecule changing state: A1 =(v)=> A2
    Molecules interacting: A + B =(v)=> AB
    Molecule changing state (catalyzed by a second molecule): A1 =(v[B])=> A2

    The in vivo experiments involve the activation of cellular signals by adding various extracellular factors and/or removing signaling components (or reducing their levels) using RNAi. These cells are then analyzed by measuring various factors such as the “activation” state of a key downstream signaling molecule. Using the in vivo data points, Sorger’s group has been able to “teach” their model. After tweeking the model they attempted to generate in silico based predictions and gained some insight into how the system is rigged – and you know what? their model produced some interesting ideas.

    They first studied the programmed cell-death pathway (apoptosis; read the history of this field from The immediate problem with such a decision, is that the cell must either choose to die or not – you do not want a half-dead cell. By adding signaling factors that activate the death pathway and then measuring a key downstream component (caspase activity) on a cell to cell level, Sorgers group found that when the decision is made, cell death is always fast. As they reduced the level of extracellular signal, cells took longer to make the decision to go from low caspase activity to high caspase activity, but once the decision was made the kinetics of caspase activation was always the same. Thus the way this system was set up, was using a “light-switch” mechanism. Levels of signal influenced how long it took to flip the switch, but once it was flipped the pathway acted just the same. The insight is that the model predicted a "switch" and pointed that switch-components were set up in several feedback mechanisms. These switch-components at first glance seem to act redundantly - there are many loops, and several interchangegable components took part in each step of the loop. Remove components and the pathway could be activated but the switch was now not as rapid and became sensitive to the levels of other “switch factors”. You still got cell-death but the switch mechanism was altered. So the intact system is ROBUST and INSENSITIVE to the fluctuations of other components – in other words the feed back loops buffer slight changes to generate a bistable equilibrium. So molecular components of the death pathway should not be seen as “pro-death” or “anti-death” but compoenents of the switch.

    I sense a paradigm shift here.

    Classical biochemistry/cell biology involves determining the molecular components involved in a process. Molecule X repairs DNA damage, molecule Y helps cells to stop dividing when there is DNA damage, and molecule Z relieves the inhibition allowing cells to finally divide. The moto of our field for the last 30 years has been, “find the molecules”. But X, Y and Z are interlocking components – and a better way of looking at these is part of a module that has certain properties (it can act as a switch ...) So to understand X, Y and Z you need to understand the module. So maybe a better moto would be “understand the module”.

    Some problems:

    These modules act independently between cells, so by studying whole populations we may miss how the module works IN THE CONTEXT OF A SINGLE CELL. To better understand this we need to have biochemical assays at the single cell level, and preferably we would want temporal information too. So you need to look at how the molecular state evolves in a single cell over time.

    There are (often too) many parameters. Sorger’s group simplified their model by excluding how the molecules are made and destroyed – with each level of complexity you get more equations, more variables and then many potential models fit the data. What Sorger’s model was good for was to indicate which molecules fit together in a module. The system was insensitive to the levels of some molecules while extremely sensitive to the levels of other molecules. Thus certain molecules were purely functioning to "make things work" and their concentrations mattered little, while other molecules acted to probe the biochemical state of the cell and their levels had great influence over how cellular decisions were being made. The key then is to figure out in which of these two groups any particular molecule falls into.

    Lots of voodoo. The models are so complex that we need new ways to present how they work. It was very hard to evaluate his approach because a lot of these in silico findings ... you just have to accept what he says ... and it isn’t apparent what are the caveats (and other problems) are. This is highlighted by the fact that crucial factors (such as protein/molecular synthesis and decay) were not taken into account.

    The final judge of good science is (IMHO) is the insights generated by the work. On that account, Systems Biology (despite what I've written in the past) may be good for biology after all.

    Tuesday, October 11, 2005

    Game Theory Wins Nobel

    So the latest Nobel for Economics was awarded to Robert J. Aumann, and Thomas C. Schelling for the development of Game Theory. Interestingly Game Theory has not only affected economics, politics (especially with regards to nuclear proliferation) but also Evolution. Gene Selection employed ideas from Game Theory to predict how genes could spread in a population by promoting altruism. Genes that promote certain "rules of behavior" that reward other individuals that play by the rules (and thus share the gene in question) while punishing those that cheat (and hence do not share this gene) can become stable in a population. Such a behavioral strategy is called (in Game Theory and Evolution Biology) an Evolutionary Stable Strategy (or ESS). One famous example is the Tit-for-Tat behavior (read this great site for more on Tit-for-tat). One offspring of gene selection is Sociobiology, which in my view has been unfairly attacked for political reasons - if you can get a hold of the last issue of Seed Magazine, it has an excellent article on the history of Sociobiology.

    For more on all these related topics I highly recommend Richard Dawkin's landmark book, The Selfish Gene.

    Sunday, October 09, 2005


    Last night we saw Downfall, which portrays Hitler's last few days before the end of WW2.

    As the director, Oliver Hirschbiegel, explained "The fascinating thing is that [Hitler and the Nazis] were human, not monsters with claws and fangs." Indeed Bruno Ganz (one of my favorite actors - see Wings of Desire), was excellent in portraying the dictator. The danger in a role such as this, as he puts it, is to portray Hitler as a caricature.

    Why is it dangerous to portray Hitler as not being human? Because the ideology that precipitated WW2, and the horrors of WW2 was caused by humans. By calling Hitler a monster and separate from humanity, we implicitly say, we would never cause that because we're no monster. We run the danger of not learning how Germany fell under the spell of a dangerous and crazy ideology, because we're no monster. So when Politicians are compared to Hitler, this is not simply an insult ... we should take pause that such comparisons are worthwhile and instructive. Or are we trapped in the ideology that we could never cause such atrocities ... I only wish that this were true.

    Friday, October 07, 2005

    Time Wasting

    So it's Friday, you've had a long week - you need to take a websurfing-enhanced brake. Where to go?

    Here are a couple of (Scientific leaning) time-wasting websites:

    • Meaning of Life TV. Several interviews of prominent thinkers (including Daniel Dennet and John Maynard Smith, who have done much to shape our knowledge of evolution). Unfortunately the interviews are conducted by Robert Wright who can get a little nutty (certain individuals have referred to him as a mysterian).
    • Evolve TV. A new website (a la ".tv" variety) - so far there are only two interviews, the last having Pharyngula's Paul Myers as a guest. Hopefully more good stuff to come.
    • And if all that wasn't enough you can read a profile of my current mentor Tom Rapoport in the latest issue of PNAS. His family's story is actually quite interesting and was the subject of a documentary aired on German TV (if you can read German click here). This film focused on Tom's parents who were quite important researchers but who were chased around the world - first out of Austria by the Nazis, then out of the US by Sen. McCarthy, then out of Austria by the CIA. They finally set up shop in East Berlin, where Tom grew up. Eventualy Tom climbed the ranks to become a Professor himself. When the Berlin Wall fell Tom could not renew his position (probably due to politics) and so fled to Harvard Medical School where he now resides.
    • Tired of the Nobels? Well if you missed it you can watch last night's Ig Nobel Ceremony. For a taste, here is the winner for the Medicine prize:

    MEDICINE: Gregg A. Miller of Oak Grove, Missouri, for inventing Neuticles -- artificial replacement testicles for dogs, which are available in three sizes, and three degrees of firmness.

    REFERENCES: US Patent #5868140, and the book Going Going NUTS!, by Gregg A. Miller, PublishAmerica, 2004, ISBN 1413753167.

    Wednesday, October 05, 2005

    News Coverage of the Nobel Prizes

    The idea behind the Nobel and other prizes, is to increase awareness of scientific endeavors.
    Unfortunately the local media is doing a horrible job of covering the awards.

    Let's look at Monday's Medicine award. Marshall and Warren's "story" includes a great narrative where they battled Dogma and eventually resorted to SELF EXPERIMENTATION inorder to prove their hypothesis. Their findings affected many people and led to a straight and simple cure (antibiotics) for many stomach problems such as ulcers. Despite this here's how the local newspapers reported this story:

    Boston Globe
    Where: pA11 (no mention on the front page)
    How long: A couple of Columns
    Grade: B-

    NY Times
    Where: A sentence on the cover, article on D5 (the Science Section)
    How long: Half a page
    Grade: B

    Boston Metro
    Where: No article!
    How long: No article!
    Grade: F

    Yesterday's Nobel in Physics was a bit better, although the news (as I heard it on NPR) seemed to emphasize "GPS" and "lasers", instead of the true nature of the work ... the quantum mechanical description of light and it's application in measuring sub-atomic distances. The coverage in this mornings papers was better. The Boston Metro had a cover story (and I suspect the Boston Globe as well) but this was due to the fact that Roy Glauber (who first used quantum mechanics to calculate how light interacts with matter) was from Harvard. The NY Times had an article on page A22 that did a good job of explaining the nature and importance of the work.

    Let's see if in tomorrow's papers, the Chemistry prize gets as much attention.

    Tuesday, October 04, 2005

    More Data on Religion and Behavior

    I have been known in the past to be fascinated with how religious faith correlates with "immoral" behavior such as high divorce rates. In the US religious fanaticism has been coopted by the far right to distract the public while it defunds public institutions.

    Now I don't know if you've read this article in the London Times about how religion correlates with all sorts of societal problems such as high infant mortality, STD and crime, but I wanted to check it out and downloaded the original paper from the Journal of Religion and Society ... here's some data from that study:

    - If you exclude the US, crime does not correlate with belief in God ... infact there is NO CORRELATION. The US does have more crime and a high percentage of believers, but it's an outlier.
    - No correlation between the belief in God and many societal indicators such as suicide, life expectancy, and (excluding the US) STDs. The story with STDs is like crime, the US is an outlier, having both high rates of belief and high rates of STDs.
    - The authors did find a good correlation between the belief in God and infant mortality, abortion rate, and teenage pregnancy (see figures from the paper below).

    A = Australia
    C = Canada
    D = Denmark
    E = Great Britain
    F = France
    G = Germany
    H = Holland
    I = Ireland
    J = Japan
    L = Switzerland
    N = Norway
    P = Portugal
    R = Austria
    S = Spain
    T = Italy
    U = United States
    W = Sweden
    Z = New Zealand

    So religious belief does not prevent you from committing a crime, committing suicide or dying early. It does make your teenage daughter more likely to get pregnant. In addition the more religious a society is, the more likely that a childbearing woman gets an abortion. And if the child is not aborted, it has an increased chance of dieing before the age of five. Perhaps increased religiosity results in a lack of education, especially for women? Or perhaps religion tends to antagonize woman's rights?

    Monday, October 03, 2005

    Goodbye Kass

    Just got back from the conference. There (over a lot of wine) I had an extremely interesting conversation with Elizabeth Blackburn, of UCSF about the role of scientists in the political process. Spurred on by a belief that people in the scientific community should be involved so that they "get the science right" she joined the President's Bioethics council. But many in the pannel seemed to have their mind made up before any discussion started, and many others were not used to rigorous scientific debates, taking the criticisms personaly. Sounds familiar? If you can't get the facts straight, and don't attemp to learn from your peers what is the point of discussing the ethical consequences? As I've stated before, it's tough being in the scientific community - the best scientists are those that understand the nature of lively scientific debate. Unforetunately certain public pundits (i.e. ideologues) maskerading as intelectuals don't understand this and comfort eachother's egos by claiming that the criticisms are unfair. What they don't get is that criticism is of vital importance, and that it's only through a critical inspection of your assumptions/ideas/models that scientific advance is made. Eventually Dr Blackburn was not asked to return and this upset many in the scientific community, but by excluding her and thus debate, the Pannel made itself less relevant.

    If you haven't heard Leon Kass is steping down as head of the council. I hope that this will precipitate a change in the chemistry of this vital council - but as I've said in the past I'm not hopeful.

    Sunday, October 02, 2005

    Cephalopod Movies

    Wow what a weekend. I'll write a bit about it tomorrow.

    But last week, spurred on by the news of the first filming of a live giant squid (18 meters long!) I went hunting for the elusive video across the www ... but no luck. Well at least I can point you to the article where this observation was published.

    But wait ... here are other cephalopod videos:
    - An octopus eating a shark!
    - Cuttlefish videos from Richard Ross who's trying to raise and breed these fantastic creatures, to read more on his valiant attempts read this article.
    - One thing that those cephalopods can do well is camouflage. Watch this incredible video of a camouflage octopus on marine biologist Roger Hanlon's webpage. Then watch these movies of octopuses disguised as corrals and rocks, walking around the ocean floor. And here is a previous post on cuttlefish research.