Transcription and Translation

My Year in a Picture

Mon, 28 Dec 2009 15:18:36 -0500

For those interested in the organization of trust in the scientific establishment

Tue, 15 Dec 2009 07:21:53 -0500

Two great interviews with Steven Shapin and Simon Schaffer, two philosophers of science.

CBC Ideas - Interview with Simon Schaffer on Leviathan and the Air Pump

CBC Ideas - Interview with Steven Shapin on how science and truth are derived from social interactions within the scientific community

If you like these interviews, visit CBC Ideas - How to think about science although I must say that some shows are better than others.

Also for anyone who is interested in the history and philosophy of science and is ready to go beyond Kuhn and Popper, I highly recommend Leviathan and the Air Pump. It gives a great overview of how Boyle and the Royal Society laid the ground work for experimentalism and it provides a great case study of how scientific theories are generated by social interactions.

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Trust & Influence - The Real Human Currency

Sun, 13 Dec 2009 09:49:58 -0500

There's a battle going on out there. A battle for trust. Do you get the H1N1 vaccine? Is global warming true? Will you go to hell? Is the free market the best way to run an economy?

How to answer these questions? The conventional wisdom is that all members of our society should get informed. Many here at ScienceBlogs would like to convince you that the problem is anti-intellectualism. These evolution-disbelieving folk have been called deniers and the anti-science movement has been rebranded as denialism. But I think that this view of the world is not really representative of what is really happening. According to this line of thought the problem lies within the public indifference, or worse hostility, to the latest scientific advances. But is this what is going on? Reading "denialist" blogs, they use what they claim as "science" to counter claims of global warming. ID folk point to some hidden (i.e. non-existent) controversy within the life sciences to argue against evolution. The remedy to all this "denialism", we are told, is that each member of the community should get acquainted with mainstream scientific arguments and some of the data, and *poof* they will thus accept the basic theories that most scientists subscribe to. But to have everyone go over the raw data to the point that they can give you a good unassailable argument for evolution or global warming or the big bang is absurd. Very few people are experts in all of these areas. I'm sure that if you walked up to the average liberal, they would not be able to give a water-tight argument about how evolution explains the world we live in. Acceptance of evolution, contrary to conventional wisdom, has very little to do with the knowledge of the primary data. So how can the average citizen make up their mind? How do they navigate the world with all these competing theories?

Trust.

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Slicing a famous brain, streamed live on the web

Fri, 04 Dec 2009 06:55:00 -0500

I'm siting at my breakfast table when I read this in the NY Times science section:

Dissection Begins on Famous Brain
The man who could not remember has left scientists a gift that will provide insights for generations to come: his brain, now being dissected and digitally mapped in exquisite detail.

The man, Henry Molaison -- known during his lifetime only as H.M., to protect his privacy -- lost the ability to form new memories after a brain operation in 1953, and over the next half century he became the most studied patient in brain science.

This dissection is being documented LIVE ON THE WEB. So here I am, watching a streaming video, dirrectly from "The Brain Observatory" of an embeded brain being shaved.

3:30 am: The brain marathon continues. The current crew of Paul Maechler, Natasha Thomas, and Dr. Annese are approaching the posterior end of the thalamus. The lesion persists in the left parahippocampal gyrus. The distance from the first tissue section is the bottom left green number on the console (plus 40,500 cut yesterday) in microns. (1 micron=0.001mm)

Click here to see for yourself.

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NIH Grants by Age

Thu, 03 Dec 2009 08:28:33 -0500

The graph is from Are there too many PhDs? at Mendeley Blog

In the U.S., we are constantly hearing about how the country is falling behind in science. We need more scientists to fill all of those jobs we want to create. And the cure to that is to fund more PhD programs! Yet, when you ask graduate students and postdoctoral scholars what their individual experiences are, a science career is a very tough road with low pay and few career prospects. It's such a tough path that an entire PhD comic strip was born to alleviate the situation with laughter. Why then, is there such a disconnect?

HT: Razib @ Gene Expression.

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A small sense of accomplishment

Mon, 30 Nov 2009 17:28:35 -0500

Last week was demo week here at the Palazzo lab. Both Zeiss and Nikon dropped off their latest equipment and we had the chance to image some RNA. In addition we finally completed some badly needed lab renovations and as a result had an operation tissue culture area. I went ahead and transfected COS7 cells with a plasmid that we just received from Open Biosystems that contains a gene of interest (a membrane bound protein whose RNA did not contain an SSCR, for those keeping track) and tried out a new FISH probe. Of course we were missing forceps and those great porcelain coverslip racks from Coorstek and I had to steal cells from our neighbouring lab (thanks Angus) but over the weekend I did some great imaging of the newly expressed mRNA.

The result:

Oh yeah! It was the first time I was on the 'scope since early summer, and
I have to say that It felt good to be "doing science" again.

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Map that Campus L

Tue, 24 Nov 2009 08:13:35 -0500

This week we have a special edition of Map that Campus.

A few weeks ago I I wrote about my new voyage on the HMS Palazzo Lab. Well the resident of this campus had some advice on this topic:

In a moral point of view, the effect ought to be, to teach him good-humoured patience, freedom from selfishness, the habit of acting for himself, and of making the best of every occurrence. In short, he ought to partake of the characteristic qualities of most sailors. Travelling ought also to teach him distrust; but at the same time he will discover, how many truly kind-hearted people there are, with whom he never before had, or ever again will have any further communication, who yet are ready to offer him the most disinterested assistance.

Leave all your answers, thoughts, quotes and eulogies in the comments.

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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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