Transcription and Translation

Fourty two* and still in need of mentoring?

Thu, 19 Nov 2009 17:54:13 -0500

After a frantic couple of weeks, the lab seems to be finally coming together. This afternoon I sat down and started to peruse the past few issues of Cell Science, Nature, JCB, PLoS etc. and a few of the blogs that I like to check out.

And then I read this strange article in the latest issue of Science: A SMART Plan for New Investigators

The premise is ... that the NIH should not give young investigators a break ... because they are full of crap?!?!!! As a solution the author writes:

Instead of providing special funding directly to new faculty, we should make sure that they receive sufficient mentoring as they work on the projects of more experienced investigators. I propose a new type of grant: the Senior Mentor-initiated Academic Research Training (SMART) award. To obtain this funding, senior faculty must apply to recruit junior faculty or new investigators and groom them for future independent work.

As Physioprof writes:

BRILLIANT!!!!!!!! Let's create yet another way for senior faculty to build empires on the backs of junior faculty, and further delay their genuine independence. Forty-two motherfucking years old as the average age of award of the first R01 is way too young! These whippersnappers need more "mentoring" from senior faculty! And what better way to get it than to work on the senior faculty's own projects!!!!

One reason I chose to move back to Canada is that it is much easier for junior faculty to get funding for their labs up here. Hopefully things will improve for my friends south of the border.

(*for the record I am not 42 years old.)

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Scientific Careers and Job Security

Thu, 19 Nov 2009 17:16:45 -0500

From Study Finds Science Pipeline Strong, But Losing Top Students, Science 30 October 2009: Vol. 326. no. 5953, p. 654

A new study finds little evidence for leaks in the U.S. pipeline for producing native-born scientists except for a steep drop in the percentage of the highest performing students taking science and engineering jobs. The findings suggest that the United States risks losing its economic competitiveness not because of a work force inadequately trained in science, as conventional wisdom holds, but because of a lack of social and economic incentives to pursue careers in science and technology.

Yes that's what I've been ranting about for the past 5 years.

Then towards the end,

Lisa Frehill, executive director of the Commission on Professionals in Science and Technology, thinks the key to keeping talented [science, technology, engineering, or mathematics] majors in science is to emphasize the opportunities that exist to solve society's problems. "Really good people will be less concerned about money if they can do work that is meaningful to them," she says.

No, really good people will stay in science and do work that is meaningful to them if this line of work came with a higher level of job security. The only way to attract more talented students, is to make a scientific career more compatible with living a decent life.

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Olympus BioScapes 2009 Winners

Thu, 19 Nov 2009 09:07:04 -0500

Like Nikon, microscopes manufacturer Olympus has a yearly microscopy photo competition, this years winners are up.

First place: Dr. Jan Michels
Christian-Albrechts-University, Institute of Zoology
Kiel, Germany
Specimen: Daphnia atkinsoni (Water Flea)
Technique: Confocal laser scanning microscopy

For more go to the Olympus BioScapes 2009 Winners Gallery

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Speaking of Talks - Next NERD Club is 11/19/09

Tue, 10 Nov 2009 12:07:36 -0500

When I was a postdoc at Harvard Medical School, I was a founding member of the New England RNA Data Club. We organized a monthly meeting, where RNA researchers from around the New England Area would get together and present data. Over three years, we were lucky enough to hear exciting talks and catalyze many new collaborations between labs at Harvard, MIT, University Massachusetts Medical School Worcester, Boston University, Brandeis and Tufts. We were fortunate enough to get speakers as far away as Yale and Darthmouth.

When I left Harvard to start my own lab in Toronto, I thought that the Club (affectionately dubbed NERD Club) would die and that was the end of that. But fortunately Shenghua "Eddy" Duan, who moved from Craig Mello's lab at UMass Medical School, to join Dana Farber Cancer Institute's Center for Cancer Computational Biology (CCCB) and John Quackenbush's lab at Harvard University has resurected the NERD Club.

They've already met once in my absence, but the second meeting for the 2009-2010 seasson will be taking place on Thursday, Nov 19, 2009 at Harvard Medical School in Cannon Room.

Here's the email that Eddy sent out last week:

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I'll be giving a talk on Thursday

Tue, 10 Nov 2009 11:43:12 -0500

Seminar Series of the CIHR Training Grant in Protein Folding

Dr. Alexander Palazzo
Department of Biochemistry
University of Toronto

Specialized Nuclear Export of mRNA Encoding Secreted and Mitochondrial Proteins

Thursday, November 12, 2008 - 12:15pm
Medical Sciences Building, Rm. 4279
University of Toronto

I'll see you there

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Shinya Yamanaka - The George Clooney of Science?

Sun, 01 Nov 2009 10:35:23 -0500

The value of having large public award ceremonies for scientists, is that it gives their work some exposure to the public.

Take for instance Shinya Yamanaka. His discovery of iPS cells in 2006 was one of the most important discoveries this past decade. It not only taught us how to generate stem cells from any normal adult cell, but it also gave us a window into celluar programming. It is now clear that going from stem cell to normal differentiated cell is not an irreversable process. According to Google Scholar this paper has been cited 1400 times!!!!

This past week Shinya was one of the recipients of the Gairdner Foundation Award. As part of the ceremonies, he gave a couple of lectures at the University of Toronto. The awards were covered by several local papers, and as a result some basic science can reach the public. Does the average Joe appreciated it? You betcha. Here'san example. Friday morning as I stood in line to get the H1N1 vaccine (for myself, my wife and my 8 month year old son) I spotted an article in the Toronto Star - an interview with Shinya Yamanaka - and pointed it out to all the folks nearby. Many of them read the article and were impressed by his remarkable finding. They asked me to tell them more. "Has anyone else been able to do this?", "Can this technology be used to make eggs and sperm from adult cells?", "are people working on therapies?", "are there any problems with these cells?". Write it, and they will read!

Here are some of the local articles on Yamanaka & the Gairdners:
Toronto Star: Superstars of science converge on Toronto
Toronto Star: Stem cell breakthrough 'too simple' - Interview with Shinya Yamanaka
Globe and Mail: Canadian Gairdner prize a marker for future Nobels (This article features Liz Blackburn who just won a Nobel for her work on Telomeres)
Toronto Star: The chance to pick some brains of note
Globe and Mail: 'When we began, we were almost pariahs' - Interview with Dave Sackett, who studies evidence-based medicine, a topic that is of extreme relevance for the healthcare debate in the US.

On Yamanaka's collaboration with several U of Toronto Scientists:
Toronto Star: Ontario takes big step in cutting-edge stem-cell research
Globe and Mail: Ontario targets $25-million for stem-cell research
Canadian Press: Toronto researchers to co-lead international cancer stem cell projects

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Map That Campus XLIX

Fri, 30 Oct 2009 12:51:41 -0500

It's that time again. Here's this week's mystery campus:

And the hint: Where cellular alchemy began.

If you know the answer, or just want to take a cheap shot at Willie the Wildcat and his posse, leave it in the comment section.

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Gairdner Talks Begin

Wed, 28 Oct 2009 11:17:49 -0500

Well this week the University of Toronto hosts the 50th anniversary of the Gairdner Foundation.

If the Nobels are the Oscars of science, and the Lasker Awards the Golden Globes, this event is akin to the 50th anniversary of some big Hollywood studio. There are talks by many of today's hottest science rock stars and many smaller celebrations, which include lunches cocktail parties etc.

This morning we heard from Shinya Yamanaka, probably the hottest rock star scientist of our generation. If you've been asleep for the past few years, Yamanaka's lab discovered how to generate iPS cells from skin cells. This result launched a tsunami of research. And after listening to his talk and those of Gordon Keller and Andras Nagy, the revolution is well on its way. In fact we heard today that Kyoto University, where Yamanaka works will be launching a whole new institute for the study of iPS cell and iPS cell therapeutics in February.

For more on the impressive lineup of talks - see the Gairdner Foundation Schedule.

Update:

The afternoon session was entitled The Cell: An Endless Frontier Elizabeth Blackburn in her talk commented that she actually study the end of chromosomes. Bob Horvitz took that idea one step further and commented that he studied the end of cells. We got talking after the presentations and noticed that Vic Ambros talked about the end of mRNAs and Avarm Hersko talked about the end of proteins.

As all good biochemists would tell you, the end is just as important as the beginning.

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It's been a while

Tue, 27 Oct 2009 18:05:45 -0500

Today I used a pipette for the first time in three and a half months.

What a strange feeling it is to work in one's own lab.

While I've been submitting papers and grants, my technician has been busy preparing solutions, ordering equipment and even performing a few "experiments" (if you can call transforming bacteria tan experiment). It's almost as if we've been supplying the ship, one that's getting ready to sail off into the unknown. I was looking after the financing, while my technician stocked up the ship with supplies. We've even managed to recruit a couple of undergrads who are in the lab performing independent research projects. I even managed to bring in some Port - after all you can't run a ship without some fine spirits.

We may find new land, or we may fall off the edge of the earth.

Having no microscopes yet we are constructing new genes and purifying proteins expressed in bacteria. But that's good enough for me. So here I am finally working away in my own space, on work that is 100% mine, and I don't even know where we keep the ampicillin. With my those first few microlitres, the HMS Palazzo-Laboratory officially sets sail.

Now where's the champagne?

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Nikon's Small World Competition Winners

Wed, 21 Oct 2009 15:30:08 -0500

Go and check 'em out.

4th place - James E. Hayden, Anglerfish ovary (4X)

For more visit http://www.nikonsmallworld.com/

This year's event even got covered in the New York Times.

And if you want to enter into next year's competition the deadline for entries: April 30, 2010. Get clicking.

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Discussion with a Cancer Surgeon

Mon, 19 Oct 2009 19:40:48 -0500

This weekend, I had the opportunity to sit down with a friend, a cancer surgeon who works at a major teaching hospital in the US. He, his wife and two kids were up visiting us for the weekend.

Over coffee, I was asking him about the state of cancer therapeutics. Although he himself does not administer drugs or design treatments, he is part of a larger team which includes molecular oncologists that perform this task. What I heard was quite surprising.

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Link love - RNA Nobels Edition

Sun, 18 Oct 2009 08:32:14 -0500

Well this year was a big year again for RNA at the Nobels. Both prizes were essentially given to RNA dependent processes. In the case of Telomerase, an RNA molecule, Telomerase RNA (hTR or TERC), acts as the template strand to help Telomerase Reverse Transcriptase (TERT) elongate the end of the telomere. Here's a great vid explaining the whole process:

In the case of the Ribosome - well it is only the granddaddy of all ribozymes. To illustrate this point, here's a great video from the Steitz Lab with an incredible soundtrack:

(HT: Sunil)

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Map that Campus XLVIII

Fri, 16 Oct 2009 08:35:14 -0500

Last week was way too easy. Let's see how fast this one will go.

Here is this week's mystery campus:

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All Your Ribosomes Belong to Us

Thu, 15 Oct 2009 20:16:39 -0500

So more than a week has gone by and there has been little press about the science Nobels. And I must say that this year's Medicine and Chemistry prizes are some of the most important in quite a while. But even between the two, the Chemistry is especially important.

Why? I'm not sure. Maybe they were overshadowed by Obama's award??? Or maybe science journalists are sleeping on the job.

I can hear them now "Ribosomes ... boring."

Nothing could be further from the truth.

Ribosomes are arguably the most important biological molecule that we know of. I don't have much time to write long essays on the subject so I'll just throw some ideas at you.

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Quote of the Day

Mon, 12 Oct 2009 09:45:43 -0500

Unraveling the ribosome is one of science's Holy Grails. Were God a molecule, he or she would be a ribosome, a veritable galaxy of atoms whose job is to translate genetic code into the stuff of life--protein.

- Brian Maffly, reporter for the Slt Lake Tribune in a recent article, Ramakrishnan: Nobel-winning work started in Utah

(and yes the article features a good friend of mine who worked in Venki's lab)

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