Tuesday, January 31, 2006

New NIH Grant for Postdocs: K99/R00

The official title is the NIH Pathway to Independence (PI) Award (K99/R00). Note the use of the initials "PI" in the grant title ... very cute. This new grant was announced by the NIH Jan 27th. Here is the link.

Key points (from the NIH website):
The Pathway to Independence Award will provide up to five years of support consisting of two phases. The initial phase will provide 1-2 years of mentored support for highly promising, postdoctoral research scientists. This phase will be followed by up to 3 years of independent support contingent on securing an independent research position. Award recipients will be expected to compete successfully for independent R01 support from the NIH during the career transition award period. The PI Award is limited to postdoctoral trainees who propose research relevant to the mission of one or more of the participating NIH Institutes and Centers http://www.nih.gov/.

It is anticipated that 150 to 200 PI Awards will be issued for this program in the initial year.

Because the nature and scope of the proposed research will vary from application to application, it is anticipated that the size and duration of each award will also vary. The total amount awarded and the number of awards will depend upon the number, quality, duration, and costs of the applications received.

Applications must be submitted on or before the receipt dates described at http://grants.nih.gov/grants/funding/submissionschedule.htm

The average age that an independent investigator get his/her first R01 grant (NIH biomedical research grant) is 42! Translation: junior faculty are having a hard time getting money. This initiative by the NIH will help out young postdocs get funding to help them finnish up their postdoctoral work and to help setup a lab at a period in their life when it's traditionally hard to get an R01. Hmm sounds familiar. Everything you need to know about this funding resource can be found here.

Sunday, January 29, 2006

Want to See a Mad Scientist at a Food Orgy?

Well this is what you might see:

And what is the viscosity of melted chocolate?

If you want to know what was in the big glass with the creamy residue, the remains of soursop vodka.

For more pictures of our massive food experiment visit the SocArt blog. All will be explained ...

Saturday, January 28, 2006


Here is a link to a great debate/lecture between Steven Pinker and Elizabeth Spelke.

(From Gene Expression blog.)

BTW Blogger has been down - this post is via MS Word and a nifty attachment that allows you to post to blogger directly.

Update ... 1/28/06

This past week I heard this great interview on WBUR's On Point, where Norah Vincent discusses how she posed as a man for 18 months to see "the other side". And judging by these pics of Norah as a man (left), she looks the role. Calling the episode an anthropological experiment, she discovers that men and women seem to inhabit separate cultures ... very interesting stuff. Her biggest surprise - she now understands why the two sexes often miscommunicate and misinterpret each other's actions.

Her book Self Made Man, was on the cover of the NYTimes book section from a couple of weeks ago. I'll have to check it out ...

Friday, January 27, 2006

Differentiation within organelles

Non-cell biologists have often viewed the cell as a bag of molecules. Over the years as cell-biology has developed, it became clear that this was a simplistic generalization. Cells are organized by a dynamic cytoskeletal network that can organize the cellular architecture. Cells are also subdivided into membrane bound organelles. The deeper we look into the cell the more we find that each cellular component is subdivided into specialized regions.

Now it would seem that organelles themselves are subdivided. As all good cell biologists know, the endoplasmic reticulum (ER) is a large continuous network of tubes and sheets responsible for synthesizing secreted protiens, metabiolize lipids and store calcium. Part of the ER extends and wrap around the nucleus to form the nuclear membrane. The inner nuclear membrane (INM) and outer nuclear membranes (ONM) are connected by specialized pores (nuclear pore complexes; NPCs) that allow only certain proteins to enter/exit the nucleus. The INM contains a specialized group of proteins that regulate several aspects of nuclear function.

I’ve been reading recent work on a group of proteins called Nesprins that localize exclusively to the ONM. Nesprins are some of the biggest proteins made by the cells. The nesprin proteins are anchored to the outer nuclear membrane by one end of the molecule, called the KASH domain. This domain extends across the the space between the outer and inner membranes (called the perinuclear space) to bind to a group of inner nuclear membrane proteins called SUNs. The other Nesprin end binds to various cytoskeletal elements and probably mediates how the Nucleus gets dragged around the cell. It looks like other proteins have KASH domains as well and may define an entire fauna of proteins that reside on the nuclear surface. So the outer nuclear membrane is further subdivided from the rest of the ER. There is the great spatial complexity that lies within cells, and we’ve only scratched the surface (I know corny pun).

Refs: Worman, H and Gundersen, G. Here come the SUNs: a nucleocytoskeletal missing link. Trends Cell Biol. 2006 (E-Published)

Update ... some trivia!

So it looks like Nesprins are some of the biggest proteins in the cell. Nesprins are members of the plakin family, all of which are huge. Here is a list of some of the biggest proteins encoded in the human genome (# of amino acids in parenthacies).

Some big proteins:
Giantin (3259)
Titin (33423)

Some plakins:
Nesprin-1 (8797)
Nesprin-2 (6883)
Nesprin-3 (975)
MACF (7412)
Dystonin (5497)
Plectin (4684)

Tuesday, January 24, 2006

Canadian Election Results

Here are the facts and interpretations of last night's elections in Canada.

  • Liberals got the boot. Canadians punished those who have remained in power a bit too long.
  • Conservatives won a minority government. Canadians still don't trust the conservatives enough to give them full control.
  • The NDP (left of the Liberals) does not hold the balance of power. NPD did gain a lot of seats and this is a good sign that the Canadian public has not veered to the right.
  • Conservatives won seats in Quebec. This is the most important event in the elections. The major change in Canadian politics last night was that the Liberals AND the separatists lost votes to the conservatives in my home province. In fact the Liberals had their weakest showing in Quebec in 20 years. Also note that Conservatives won SEPARATIST ridings! Previously the Tories were not seen as viable in Quebec ... if you wanted to boot out Liberals you voted BQ (separatist) ... but after last night this is no longer true. There is a now a viable federalist (i.e. non-separatist) option for French Canadians.

Monday, January 23, 2006

Canadian Elections

Yes it's that time again. Unfortunately I couldn't go back home to vote ... and it looks like the separatists will win my riding (damn).

Having lived in the US for almost 9 years I can probably compare the two systems. Canadian elections are shorter (about 2 months of campaigning). Canadian elections are more unpredictable. Canadian elections cost less and the televised election debates probably play a bigger role. And Canadians vote with a pencil and paper AND still have quicker results and fewer problems than American elections. On this last point, some may say, "the Canadian population is smaller". All I can say is that there are 30 million Canadians (about half the size of France) and that although we're 1/10 the size of the US, each polling station probably has the same number of voters - if they can count paper ballots in Canada, they can do it in the US.

What can I say about what's happening (politically) in the True North Strong and Free? You can probably read up on it. Surprisingly all the major papers here have articles on the Canadian elections.

However if you really want to know what's going on, this video clip (click on "Buckley's Ad") probably sums up the mood in Canada right now.

Sunday, January 22, 2006

Bravo Paul Nurse

I finally got around to reading the much talked about comment by Paul Nurse that appeared in the last issue of Cell. Some background ... Paul Nurse (or should I say Sir Paul Nurse) won the Nobel Prize along with Lee Hartwell and Tim Hunt for the discovery of the cell cycle, arguably one of the biggest discoveries in the past 100 years. He recently moved from London to New York to head Rockefeller University.

Nobel Website Bio.
Rockefeller homepage.

In his commentary, Nurse identifies 3 major problems with academic research in the US today:
  • Academic funding and the pyramid scheme.
  • The attack of science by various religious groups.
  • Recruitment (i.e. the lack of American scientists + the miserable way foreign scientists are treated in the US)

Yes these are all issues that I and others seem to insensately write about on our little blogs. I highly recommend that you read the whole commentary. It's available for free to the general public on Cell's website.

(thanks BC)

Saturday, January 21, 2006

Yet another Interview

I recently had a conversation with my father. He has a degree in Nuclear Physics and was a teacher for over 20 years. Although he is now retired he still keeps up with the latest developments in physics and keeps up a blog on physics called Stings of Ideas. We talked about String Theory, the Big Bang Theory and other things …

Mad Scientist: Could you briefly explain string theory (ST)?

Man from Zohra: Basic idea: everything - quarks, electrons, photons - are made of tiny strings.

MS: Why do many believe that ST is the key to deducing the grand unifying theory?

MfZ: By accident, when it was proposed as a theory for the nuclear force, the graviton appeared in the theory. Up until then gravity was a force outside the scheme that Quantum Mechanics has for all the other forces.

MS: So the elusive graviton can be predicted by ST ...

MfZ: Absolutely, if it were discovered, it would be a great boost to ST.

MS: It is often said that ST can predict 10^500 different types of universes, what strategy do String theorists have to figure out which theory belongs to our present universe?

MfZ: ST relies on mathematics that employs 10 dimensions. The main problem in ST is to go from 10 dimensions ( 9 spatial plus time) to 3 spatial plus time. In other words, we get too much information, and the trick is to try to weed out the useless information. Now what has been identified are Calabi-Yau manifolds which divide higher dimensional space neatly into 4 and six.

MS: So what in our universe is represented by a Calabi-Yau manifold?

MfZ: Nothing that I know, right now it is basically a mathematical structure that theorists are using to break down a 10-D equation into a 4- and 6-space.

MS: So is our universe a Yau-Calabi manifold floating in a 10D reality?

MfZ: Too soon to tell.

MS: What does ST have to say about the cosmological constant?

MfZ: Cosmology theories are separate but ST also might include supersymmetry, which would have a lot to say about the fundamental particles and how the universe was formed in the early stage, but that is another story.

MS: What is supersymmetry and why is it so important for ST?

MfZ: A good definition of supersymmetry can be found here. It is not vital to ST, but a main concern is the Higgs field, in which particles acquire mass. Supersymmetry would be nice if it turned out to be true.

MS: An alternative to the big bang theory has been floating around recently, could you explain what this is all about?

MfZ: The cyclic theory incorporates the big bang theory but it proposes no beginning. The Universe undergoes an endless sequence of cycles in which it contracts in a big crunch and re-emerges in an expanding big bang, with trillions of years of evolution in between.

MS: So the universe is contracting and expanding indefinitely.

MfZ: The seeds for galaxy formation were created by instabilities arising as the Universe was collapsing towards a big crunch, prior to our big bang.

MS: How do they explain that the expansion in our universe is accelerating? Shouldn't it be slowing down?

MfZ: In the initial phase, think of a spring compressed and released, it would accelerate then slow down. If the spring is attached to a wall, it will then reverse direction. The universe is believed to behave in that fashion.

MS: But if gravity acted as the accelerating force during the big crunch, shouldn't it be the deaccelerating force during the expansion?

MfZ: Dark energy would fueling our expansion. Eventually, we will slow down as gravity caught up. For the next trillion years or more, the Universe undergoes a period of slow cosmic acceleration (as detected in recent observations), which ultimately empties the Universe of all of the entropy and black holes produced in the preceding cycle and triggers the events that lead to contraction and a big crunch. Note that dark energy is not simply added on -- it plays an essential role.

MS: So what is this dark energy?

MfZ: If I knew, I would win the nobel price.

MS: Do they have any idea at how far out the universe will expand before the forces of gravity start to over come the dark energy and start contracting the universe?

MfZ: No, this is beyond our measuring capacity. According to the latest theory, the universe would be expanding for trillions of years, who knows how far it will reach is anyone's guess.

MS: One last question ... what will be the next big idea in cosmology? (if you were to guess)

MfZ: That a trick question?

MS: No - it's the big guess question. BGQ

MfZ: Maybe our latest probe to Pluto might tell us we are wrong on gravity???

MS: Wow.

MS: Ok thanks for the interview.

MfZ: Bye.

Friday, January 20, 2006

Lots of work = few posts

Tending a blog can be a bit like having a pet. Fun to play with, and when you're busy easy to ignore (and let die).

OK so the word of the day is ... antediluvian. It refers to the period before the biblical flood. It can also refer to an oldfashion or antiquated person ... a remnant from a long ago era.

Reading Thomas Freidman's OpEd in the paper today makes me wonder whether the we are living in a period just before "the flood" ...

From his article:
Friends, we are in the midst of an energy crisis - but this is not your grandfather's energy crisis. No, this is something so much bigger, for four reasons.

First, we are in a war against a radical, violent stream of Islam that is fueled and funded by our own energy purchases. We are financing both sides in the war on terrorism: the U.S. Army with our tax dollars, and Islamist charities, madrasas and terrorist organizations through our oil purchases.

Second, the world has gotten flat, and three billion new players from India, China and the former Soviet Union just walked onto the field with their version of the American dream: a house, a car, a toaster and a refrigerator. If we don't quickly move to renewable alternatives to fossil fuels, we will warm up, smoke up and choke up this planet far faster than at any time in the history of the world. Katrina will look like a day at the beach.

Third, because of the above, green energy-saving technologies and designs - for cars, planes, homes, appliances or office buildings - will be one of the biggest industries of the 21st century. Tell your kids. China is already rushing down this path because it can't breathe and can't grow if it doesn't reduce its energy consumption. Will we dominate the green industry, or will we all be driving cars from China, Japan and Europe?

Finally, if we continue to depend on oil, we are going to undermine the whole democratic trend that was unleashed by the fall of the Berlin Wall. Because oil will remain at $60 a barrel and will fuel the worst regimes in the world - like Iran - to do the worst things for the world. Indeed, this $60-a-barrel boom in the hands of criminal regimes, and just plain criminals, will, if sustained, pose a bigger threat to democracies than communism or Islamism. It will be a black tide that turns back the democratic wave everywhere, including in Iraq.

Wednesday, January 18, 2006

Julia, Queen of EMBO Covers

Every year, Julia from our lab submits photo art to EMBO (European Molecular Biology Organization) Journal's cover art contest. Last year they chose this great fall image for their November 16th issue.

And this year they chose another one of her photos. It's on the cover of their current issue.

I was going to post something on the contest (it ended Jan 11th), but I guess I didn't get around to it. Maybe next year ...

Tuesday, January 17, 2006

What's your h-index?

About a month ago I had a conversation with my thesis advisor about the h-index. It is a new method, proposed by Jorge E. Hirsch of UCSD to quantitatively measure a scientist’s influence. His proposal was published in PNAS and Nature had a little report on it. Here's a publically available link to the paper (for those who don't have institutional access to PNAS).

The Abstract from the original PNAS paper:
I propose the index h, defined as the number of papers with citation number is [equal or greater than] h, as a useful index to characterize the scientific output of a researcher.

And here is the rationale from the paper:
Why would you try to quantitatively measure a scientist’s influence? For the few scientists who earn a Nobel prize, the impact and relevance of their research is unquestionable. Among the rest of us, how does one quantify the cumulative impact and relevance of an individual's scientific research output? In a world of limited resources, such quantification (even if potentially distasteful) is often needed for evaluation and comparison purposes (e.g., for university faculty recruitment and advancement, award of grants, etc.).
So what is my h-index? To find out log into Thomson Scientific's ISI Web of knowledge, find all your papers and sort them based on citations. Scroll down the list until your paper rank is equal or greater than the citations for that paper. In my puny grad-student/postdoc career, I’ve only published 9 peer-reviewed papers. What follows is a bar graph of the number of times each paper was cited (citation number), and the paper rank where rank=citations, is paper #8.

Benefits of the h-index:
- It is quantitative.
- It takes into account not just the number of publications or how well a couple of publications are cited, but the QUANTITY of well cited publications.
- Older, well established professors will have accumulated many citations for initial work that is still relevant. Thus h-index goes up with time.
- As you increase your h-index number, it becomes harder to increase it further. Take my h-index: all i need to get to h-index=9 is to publish another paper and hope that it gets cited at least 9 times (and that my current #8 gets cited an extra time). So right now my h-index will roughly grow with the number of publications. Eventually as my h-index grows (to say 50), each new paper has to be cited at least as many times (in this example, 51 citations) to boost my h-index.

- Self citations. Although this could easily be eliminated.
- Papers which are wrong. This is not so bad. If you are influential, by definition, people will have to confront and address your "bad data" and explain why it is wrong.
- Cross field comparison. Currently biologists have much higher h-indexes than physicists, simply because there are more scientists who study biology (and thus more individuals who can cite you). Even within biology, it looks like researchers studying signal transduction and oncogenes get a boost to their h-index.

Some h-indexes for notable biologists:

Francis Crick: 53
James Watson: 43
Sydney Brenner: 92
George Palade: 105
Keith Porter: 70

Some people in our vicinity ...

Marc Kirschner: 90
Tim Mitchison: 59
Tom Rapoport: 60
John Blenis: 64
Joan Brugge: 67
Tom Maniatis: 115
Lew Cantley: 97
Steve Harrison: 74
Jack Szostak: 63

other big guys ...

Gunter Blobel: 120
James Rothman: 92
Randy Schekman: 76
Ian Mattaj: 65
Rudolf Jaenisch: 96
Elaine Fuchs: 93
Richard Hynes: 94
Michael Sheetz: 65
Ron Vale: 56
Bert Vogelstein: 143
Bob Weinberg: 113
Susan Lindquist: 74
Harold Varmus: 103
Michael Bishop: 112
Phil Sharp: 115
Joan Steitz: 91
Tom Steitz: 85
Thomas Cech: 82
Alexander Varshavsky: 62
Eric Kandel: 117
Richard Axel: 80
Paul Nurse: 90
Lee Hartwell: 61

One problem with these lists ... we did the searches on ISI, but could not account for papers where the middle initial was omited so the true values for some researchers may be slightly higher ...

OK I've wasted enough time. I'll end with this quote from Hirsch's PNAS paper:
In summary, I have proposed an easily computable index, h, which gives an estimate of the importance, significance, and broad impact of a scientist's cumulative research contributions. I suggest that this index may provide a useful yardstick with which to compare, in an unbiased way, different individuals competing for the same resource when an important evaluation criterion is scientific achievement.

But of course this is all bxxl sxxt ...

{Update 1/28/06}

Acme Scientist informs me that Michael Behe's h-index is 15 ... interesting. Someone should compile the h-index of all these so-called experts ...

Sunday, January 15, 2006

Another Victory for Idiocy

I just read a disturbing OpEd in the NY Times by Robert L.Park form the University of Maryland. It tells how the Bush administration killed the Deep Space Climate Observatory (aka Triana), a satelite wich would monitor Earth's energy balance ... and thus inform us on the rate of global warming. This is another example of government squashing good science in the name of big oil interest. From the article:

Development began in November 1998 and it was ready for launching three years later. The cost was only about $100 million. For comparison, that is only one-thousandth the cost of the International Space Station, which serves no useful purpose.

Before Triana could be launched, however, there was a presidential election. Many of the industries favored by the new Bush White House were not anxious to have the cause of global warming pinned down. The launching was put on hold.

The disdain of the Bush White House for Triana goes much deeper than just a desire to avoid the truth about global warming. Triana began life in early 1998 as a brainchild of Al Gore, who was then the vice president. Mr. Gore, the story goes, woke up one morning wondering if it would be possible to beam a continuous image of the full Earth back from space to inspire people with the need to care for our planet. The 1972 portrait of the full Earth, taken from the Moon, had inspired millions with the fragile beauty of our blue planet. Why not beam the image live into classrooms, allowing students to view weather systems marching around the globe?

Scientists had dreamed of such an observatory for years. They hoped Mr. Gore's influence would make it happen. Mr. Gore's support would end up destroying it. Those who hated him, hated Triana. His dream of inspiring environmentalists and schoolchildren served only to trivialize the project. It was ridiculed as "Gore's screen saver."

Triana is terminated, but global warming is not. Someday, there will have to be an observatory at L1. Perhaps the most important lesson from our exploration of the solar system is that the most terrible place on Earth is a Garden of Eden compared to the best place anywhere else. We must find out how to keep it that way.

For more on Robert Park click here. Triana's NASA webpage used to be here.

Saturday, January 14, 2006

Podcasts Podcasts Podcasts

Over the holidays we got an iPod.

My wife (a non-scientist) has used it to listen science podcasts.

Science Podcasts? It would seem that any large institution/media outlet/media program that specializes in Science news/reporting has a podcast. Science based media is ahead of the curve on this technology. Here is a short list of science podcasts.

Nature (hey Science, wake up! Although Science Magazine also has the occasional podcast.)
The Naked Scientist (BBC)
Science Fridays (NPR)
Quirks and Quarks (CBC)
The New Scientist
The Scientist
Seed Magazine
This Week in Science (UCDavis)

Thursday, January 12, 2006

Authorship Disclosure

Due to the whole stem cell scandal, both Science and Nature are considering changes in the mechanisms of publishing scientific results . One "reform" is authorship disclosure. From an article in yesterday's NY Times:

One change Science is considering is to require a statement from each author describing his or her contribution to an article. These statements would be published, probably online, Dr. Kennedy [editor of Science] said.

And it's about time. This idea that the actual contributions of authors be disclosed has been bouncing around for a while. There are too many authors whose sole contribution was the donation of an antibody, DNA plasmid, or other PREVIOUSLY published reagent.

Ben Lewin, the former publisher of Cell had this to say:
If this proposal took hold, it wouldn't be a bad thing since you would have a better sense of people's contributions.
For more on the stem cell affair, link to the latest articles in Science and Nature ... and a nice time line of all the events.

[Update 1/14/06]

There is nice discussion on ethical behavior in the scientific community on the Scientific American (SciAm) blog. (Thanks Gaw3)

Wednesday, January 11, 2006

Likelihood Statistics

I was just reading this great post from Mike the Mad Biologist (I know ... a much more original name than my nom de plume).

In this entry, he discusses Falsification (as in the theory of scientific theories espoused by Karl Popper) and likelihood Statistics (a much more realistic description of how science works).

From his post:
The difference between the two approaches is that falsification tests data against an a priori model, while likelihood uses the data to build the most likely model given the existing data. The strength of likelihood is that it does not assume how the world works. It also allows you to judge the relative likelihood of different models (or processes). The disadvantage is a garbage-in garbage-out problem: 92% of the time, an unbiased coin would yield an observed ratio that is not 50:50.
It's worth reading the whole entry - and if the detailed discussion frightens you, Mike also incorporated cuddly pictures of baby pandas and puppies.

Monday, January 09, 2006

Occupational Names for Scientists

Not much happening - reading quite a bit of papers. As I was perusing the literature on nuclear export, I came across a paper by a researcher named Cumming. This reminded me of a passage in Jared Diamond's The Third Chimpanzee about scientists whose surnames reflect their area of expertise (I'll post it when I have the time). Off the top of my head, here is a list of researchers whose name say quite a bit about what they study:

Polymeropoulos Mihael is one of the world's leaders in analyzing the genome, in particular to sequence, map and analyze many mRNAs (or ESTs - expressed sequence tags).

Here's a good question for you ... who identified the taste receptor that recognizes sugars? Charles S. Zuker of course!

Then there is the famous (now retired) ornithologist Mitchell Byrd.

I guess I should have been an archaeologist ...

Saturday, January 07, 2006

Interview with a Crazy Scientist

I interviewed a former colleague of mine, the crazy scientist. We discussed the next big thing in cell biology, his outlook for 2006 and his prospects at finding a job as a PI (principal investigator i.e. professor) ...

Mad Scientist says: How long after a vacation does it take before you are able to perform experiments?

Crazy Scientist says: Well, that is a very interesting question. When I leave, I plan ahead so that I can start an experiment as soon as I get back. The problem is that normally those experiments don't work because I end up making stupid mistakes. So in the end, only after 3-4 days, or a stupid mistake, am I able to run a decent experiment.

MS: It takes me about a week. As hard as I try it would seem that the forces of Nature are against me.

CS: For example I arrived Wednesday evening from Europe with a 5 hr jet-lag. Thursday morning I was running gels to test some serum I received during the holidays. Tuesday I realized I screwed up the experiment. Friday I had the result.

MS: At least the rabbit was working hard while you were away. How do you think this year (2006) will go for you?

CS: Very exciting. Since I'm in the job market, I am very excited to know where I will get the next interview, will I like the place, when will I move, etc.

MS: I'm glad that you are optimistic.

CS: Also, I am finishing up some exp for the next paper .

MS: So it sounds like 2006 will be a good year for you. Speaking of the new year, what do you predict will be the biggest discovery (in 2006) in Cell Biology?

CS: Uhm, that's easy. RNA transport from the nucleus (just kidding...)

MS: Wow I chose the right field!

CS: Ok, now for the right answer. I think a lot will be discovered about local regulation of cellular functions by small hairpin RNAs (shRNA), also known as micro RNAs (miRNA). These activate the turnover of mRNAs. Right now this field is very hot, but the field is limited to the role of shRNAs in development. There is some cell biology being done, but some questions such as whether degradation of mRNAs within a region of the cell can allow for local regulation of protein turnover are not yet addressed. This local protein control may contribute to generating different cell shapes and other morphological aspects. This will be very cool.

(Post interview note: for more on shRNAs and miRNAs, click here.)

MS: So RNA is the place to be!

CS: It is a good place, however, remember that all starts in the nucleus, and that big ball is very fascinating ... and what do you think?

MS: I think that we've seen the genome, we've seen the transcriptome, the kinome, the proteome ... now it's time for the glycosylome! (as in glycosylation ... or the compiling of how sugars are added to proteins, and the different functions of each type of sugar modification)

CS: What about the phosphorylome? Can you imaging knocking-out one kinase at a time a measure phosphorylation of 100-1000 proteins?

MS: I think that too many people study phosphorylation. Two groups (one in our department) are doing that just that (the phosphorylome). The one in our department did mass spec and pulled out every phosphopeptide enriched in mitosis. There is also the ubiquitinome - but it's an oversaturated field as well.

CS: Good. They'll hopefully repeat it for each knock-down kinase.

MS: Maybe they can hire you! I think that if those systems biologists can get their act together, maybe getting some insights into how signaling "modules" work could be big in 2006. Speaking of jobs - what is the thing you look for when interviewing for positions?

CS: Critical mass. How smart and how interesting is the work of my future colleagues. That is the key thing.

MS: So interaction is the most important feature - is it better in large institutions, or smaller ones?

CS: You can find good group of people in small institutions and you can be completely alone in large ones. My experience with Columbia (a huge institution) is that you end up talking with the same 4-6 labs. So I think we cannot make a rule for that. The next important factor is the working conditions (space, core facilities, startup package, funding). The perfect situation is a big institution with a good core of 4-6 groups.

MS: I see - do you feel that as a scientist with a background in "live cell imaging" you have an advantage over other scientists (in that you have more to offer in your interactions with colleagues)?

CS: Not necessarily. I think every scientist have their "background" and their specific "advantage to offer". My background is not better than someone that has a protein-interaction background.

MS: But getting back to biggest areas in 2006 - more and more people are adapting their assays to microscopy - such as single molecule enzymology ... you do have some technical expertise that is not that widely spread.

CS: I guess depending on your question, some backgrounds are more suitable than others depending on the colleagues you find yourself with. Again interaction plays a very important role. (I have to go soon, one more question)

MS: What is the next big thing in cytoskeletal research? (I had to ask a big question since it's my last one)

CS: I think it will be the connection between actin and microtubules, and how this is involved in regulation of both cytoskeletons and their function. Some call it cytoskeletal cross-talk.

MS: I guess you're in the right field! It's funny, because this question has been studied for years, and we've made lots of progress, but it is one of the trickiest questions in all of Cell Biology.

CS: I guess so!

MS: Thanks for chatting. Have a good weekend.

CS: Thanks, you too.

Thursday, January 05, 2006

Positive Entry

OK I promised people that I would write a positive entry today, so here goes ...

Want to see a crazy scientist? Here's many pictures of a former colleague of mine, taken by his wife Claudi (who is also a scientist). For more amazing and fun filled photos, visit her blog aroundaboutme ... and they say scientists aren't fun. Whoo-hoo!

Want to read more on RNA? Visit Bartholomew Cubbins' blog (Bartholomew Cubbins on RNA) ... the blog in his words:
Ribonucleic Acid - it's not just for transferring genetic information between DNA and proteins anymore. This blog will discuss current gossip, news, and major papers within the field. The level of discussion will be quite detailed, yet I hope that non-scientists who are interested in RNA will be able to follow.

And to all the nay-sayers that may dismiss a blog on RNA, this is what BC has to say:
It is my hope that there are legions of non-scientist men and women out there frothing at the mouth to learn more about RNA. And I'm not talking about the RNA drops therapy variety (I'd link to it but I just ran out of Purell).

Wednesday, January 04, 2006

The Final FY 2006 Appropriations Bills for Federal R&D

From a statement released by the AAAS:

On December 30, nearly three months into the fiscal year, President Bush signed the last two FY 2006 appropriations bills into law, bringing the FY 2006 appropriations process to a close. AAAS estimates that the federal R&D portfolio totals $134.8 billion in 2006, a $2.2 billion or 1.7 percent increase. But 97 percent of the increase goes to just two areas: defense weapons development and human space exploration technologies. Funding for all other federal R&D programs collectively will barely increase, and will fall nearly 2 percent after adjusting for inflation.


Many flagship federal science agencies have disappointing budgets in 2006: the National Institutes of Health (NIH) budget falls for the first time in 36 years; the National Science Foundation (NSF) wins a small increase but has less in real terms for its research portfolio than in any of the last three years; the Department of Energy (DOE) Office of Science budget declines, and despite big increases in development funding the Department of Defense (DOD)’s basic research funding declines.


...the bill also contained a 1 percent across-the-board cut for all discretionary programs, even those whose budgets had already been signed into law earlier. Even before the across-the-board cut appeared, the President and Congress had agreed to cut overall domestic discretionary spending by nearly 1 percent, but now it appears that domestic spending will fall almost 2 percent in 2006.

And now time for some data. Funding of several federal R&D agencies over the past 10 years (adjusted for inflation):

R&D (deffence and basic research) funding as a percent of GDP:

The future of funding for federal R&D programs? Here's the last paragraph of the report:

Although many lawmakers of both parties have called on the U.S. to dramatically boost its investments in basic research in order to ensure U.S. innovative capacity and therefore future economic competitiveness, these proposals have run into a brick wall of tight budgets. Looking back on 2005, there finally appeared to be bipartisan and widespread recognition that the U.S. leadership in science and technology, innovation, and technology-based competitiveness were under threat from emerging economic competitors, especially India and China, but instead of boosting R&D investments policymakers cut them to meet restrictive budget targets. And things could get worse before they get better: the Bush Administration’s FY 2007 budget proposal, due in February, is primed to continue the same combination of tax cuts, declining discretionary spending, and modest entitlements reforms that have characterized past budgets, resulting in what is likely to be another year on the downward slope for most parts of the federal R&D portfolio.

Tuesday, January 03, 2006


A new year, full of hope ... and anxiety.

During our trip to Seattle, anxiety was a common topic discussed.

Now back home I just read in the NY Times an obituary of Dr George Gerbner. From the article:

He founded the Cultural Indicators Research Project in 1968 to track changes in television content and how those changes affect viewers' perceptions of the world. Its database has information on more than 3,000 television programs and 35,000 characters.

Mr. Gerbner said people no longer learned their cultural identity from their family, schools, churches and communities but instead from "a handful of conglomerates who have something to sell."

He coined the phrase "mean world syndrome," a phenomenon in which people who watch large amounts of television are more likely to believe that the world is an unforgiving and frightening place.

"Fearful people are more dependent, more easily manipulated and controlled, more susceptible to deceptively simple, strong, tough measures and hard-line postures," he testified before a Congressional subcommittee on communications in 1981. "They may accept and even welcome repression if it promises to relieve their insecurities. That is the deeper problem of violence-laden television."