Doctor Who

No, not that Doctor Who. (Although, it's worth flagging up the Official BBC Doctor Who website for anyone remotely interested in science fiction.)

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Is there a Doctor in the (JoVE blog) house?

There is now !!!



Trusty Coturnix was the first to flag up Doctor Kushnir's announcement on her excellent blog Lab Life.

Welcome back to the World Anna, pardon my ScRussian, Dr Kushnir....

From her very detailed account:-

"They then went around the table asking me questions they had prepared having read my thesis. And you know what? They actually read it! all 230 pages of it. I was shocked. I honestly didn’t expect them to read the whole thing."

I liked that Para a lot.

Since this blogger is more than remotely interested in virology etc., in due course, will Dr Kushnir be making her thesis freely available online? (Assuming that Dr Kushnir's liver recovers from a well earned pounding)

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Finally, FOOD. (there is a liver connection)

Enjoy this classic sketch from BBC's Scott Mills.

Software for Scientists

Here is the crazy thing about software designed for scientists – most of the time, it’s not scientists that design it. How can a computer architect or programmer truly understand the needs and requirements of a profession that is not their own? They kind of, well, can’t. They do the best they can, they hire scientific consultants (ahem, if you are reading this, please consider hiring me), so on and so forth, and yet occasionally, they still fall short.

Take for example, PubMed. I wrote a post on another blog about my hatred… ok, I am slowly learning to moderate my language… my dislike, let’s say, of PubMed. I, someone who is pretty freakin' far from computer illiterate, find it difficult to use. I think it is counter-intuitive and counter productive. The response to that post has been nothing short of atomic. My rant somehow wound up on a medical librarian listserv and they came out in force defending NCBI and PubMed, listing pages and pages of helpful and warm instructions and hints on how to make it do what I need it to do, pages of suggestions, with offers of hands-on assistance and training, which have all been wonderful. Occasionally though, they were biting and harsh, saying that if I only knew what I was doing (and only if I weren't so ignorant... yup, ignorant), PubMed would seem to me the greatest thing ever.

But here’s the thing. Besides the fact that I hope never in my lifetime to be called ignorant again, in their generous offers of help and advice (which I very VERY much appreciate and cannot give thanks enough everyone's support and attention), they proved my point. I am a research scientist by long, hard training. I am a fairly web-savvy research scientist, and still, I have trouble with PubMed.

The search engine is not made for medical librarians. It’s not made for computer programmers. It’s made for scientists, to be used by scientists, needed most by scientists. It should be easy for scientists, goofy, only moderately-computer literate scientists, to use. It should be intuitive (read: Google), it should not have a ginormous page of inscrutable instructions, it should not require the hour-long training sessions, kindly offered at most medical libraries. It should be plug and chug.

It isn’t. Neither is the statistical software I (try to) use, nor are the scary molecule modeling modules I had to use my first year of grad school. Although that may have more to do with my general ineptitude with chemistry than anything else. So here is my question – how do we make all these, dare I say, web2.0 technologies not only user friendly, but scientist friendly?

We, as scientists, are not like most computer users. We have gobs of education in fields that often do not intersect with computer things. We can have more degrees than we have socks, and still not be able to find the paper we need on a medical literature search engine. How do we fix this, and why is it happening?

I think I am now starting to understand yet another barrier of scientists to web2.0. Until the technologies are easily accessible and usable, no one, myself included, is going to use them.

Bah humbug, whatever that means.

Signing off,

Your loyal cranky scientist blogger.

Cellular Visions: The Inner Life of a Cell

The blogosphere is awash at the moment about PZ Myers being expelled from the film Expelled.

A short video was uploaded yesterday where PZ and Richard Dawkings discuss what actually happened as well as discussing the film itself.



One of the issues discussed was that the film contained some really well put together computer animation about the inner life of a cell. PZ noted that this was probably footage made last year at Harvard. It emerges from the discussion that the makers of Expelled removed and over-dubbed the original commentary most probably without permission. Copyright infringement? You betcha.

Anyhows, I went to Dawkins site (very cool) and from the comments on this thread, found two versions of the video.

Here is the shorter version with fab music:-




And here is a link to the original longer version with commentary.

Here's a link to some background on the making of the animation.

"The Inner Life of a Cell, an eight-minute animation created in NewTek LightWave 3D and Adobe After Effects for Harvard biology students, won’t draw the kind of box office crowds that more ferocious˜and furrier˜digital creations did last Christmas. But it will share a place along side them in SIGGRAPH's Electronic Theatre show, which will run for three days during the 33rd annual exhibition and conference in Boston next month. Created by XVIVO, a scientific animation company near Hartford, CT, the animation illustrates unseen molecular mechanisms and the ones they trigger, specifically how white blood cells sense and respond to their surroundings and external stimuli."

I certainly agree with Dawkins in that this is a seriously impressive piece of work....

(HT to "sent2null" for locating the video)

+++UPDATE+++ Thanks to a comment from Bob O'Hara, see yesterday's update from PZ.

+++UPDATE 2+++

'Inner Life' and all of its yellow permutations are out of EXPELLED.

More under the fold.

JoVE on the box

JoVE.com: Posting scientific experiments online



AFTER CLICKING PLAY, CLICK ON THE BOTTOM R/H/S BUTTON TO WATCH IN FULL SCREEN

March 12th 2008

"(NECN) - Dr Moshe Pritsker, co-founder and CEO of JoVE.com, joins NECN's Chet Curtis on Business Day.

Biomedical research might go a lot faster and yield more results if scientists could cut down on time wasted reproducing experiments.

JoVE, The Journal of Visualized Experiments, is bringing scientific publishing into the 21st century, allowing researchers to post their experiments online.

It is like a YouTube for scientists, and it could mean faster discovery of life-saving technologies, and greater access for Third World countries."





Whilst JoVE has been featured before in the press, blogosphere and on radio, this was the first (hopefully not last) coverage on TV.

As such, this was certainly worth mentioning on the official JoVE blog.

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JoVE website
JoVE blog
JoVE wiki

Thinking outside the box...

...but still inside the cubicle.



After getting stuck with my earlier optical tweezer studies, I was seriously concerned about spending the rest of my time in Singapore bent over an optical table and minutely adjusting the same set of mirrors and lenses. However, then I switched projects to explore the Tethered Particle Motion technique. Although this was supposed to be a more difficult project, I soon found an amazing "lazy" protocol on-line and was getting results within a couple weeks.

However, I had recently reached another seemingly impassible barrier. This time I was worried about spending my last couple months on the island alternating between filling flow channels with with micropipettes and spending hours staring at Excel spreadsheets on my laptop. I felt terrible that I may leave NUS with such a limited perspective of what the other lab members did, let alone the rest of the Physics Department. I asked myself Why am I here? and seriously considered dropping everything to work in cafe.

I opted for a less drastic approach, but hopefully one that is just as significant. I had great conversations with my advisor about my goals for my remaining time in his group. I mentioned that the other researchers could do ten times as many experiments as me, but my strengths from high school science fairs and my Stanford experience centered around my communication skills. He admitted that most of the people in his group were great at reading papers and taking massive amounts of data, but did not have much experience in making a coherent story out of their results.

As a result, this weekend I will be giving a workshop about presentation skills at the bi-monthly group meeting. I will also be helping the others with creating effective presentations and writing clear scientific papers. I am excited to see where this could eventually lead, since I have plenty of other ideas related to the non-technical aspects of Lab Life. I occasionally daydream about traveling the world as the scientific equivalent of Gordon Ramsey on Kitchen Nightmares (but with a vocabulary better-suited to the academic environment).

As an aside, I wish my cubicle looked like the one in the photo (see Lifehacker for more). Perhaps that will be my next project.

Going Incognito

We have quite a discussion going on my previous post! Anonymous, whoever you are, you have some very interesting things to say. Thank you. The following thoughts and musings were inspired by your comments:

Scientists, at least the ones I have met, are brimming with opinions. Most of the time, I don’t have to ask for those opinions - I am presented with them, over and over again. Sometimes loudly. Scientists ask questions at seminars all the time. Sometimes they really go on. Really. If questioning, giving opinions, and discussing are a part of every day science, why are online discussions of articles/manuscripts so slow to catch on?

Is attaching one’s name to a comment for all eternity an obstacle to online scientific discussions (or for commenting on the online manuscrips/articles)? As far as I am aware, no anonymous comments are allowed on either PLoS ONE or Nature Precedings. You have to have an account with a reasonably realistic name and affiliation in order to comment on the articles on these sites (note that this is not the case for JoVE – anonymous comments are permitted). The permanence of a comment and the ease with which it can be traced back to the commenter can be rather intimidating.

The fears are understandable. Say you have a negative comment or criticism of the work. I, for one, would be a lot less likely to leave that comment for fear that I will be 1) proven wrong, and/or 2) placed on a scientific black list that will affect my future chances at grants or manuscript publications. As huge as science is, the fields within it are remarkably small, incestuous, and often competitive. Everyone knows everyone else. Open criticism, on record, is scary.

But what if your comment is simply a question, clarification, or an idea for future research? Is anonymity as much an issue then? Or is it just a pain to have to register an account? Is the solution to the low commenting problem as simple as streamlining or minimizing the registration process?

Naturally, disallowing anonymous comments has clear benefits – screening out rude or inappropriate comments, ensuring that people consider what they write before they write it - but are these benefits negated by the number of scientists that are deterred from commenting? Certainly there are ways to filter out the crazies without mandating every one put their name on their comments? Slashdot is a great example, one that relies on huge traffic for efficacy, but still, it is a functioning viable model of community comment moderation.

I can keep bringing up pros and cons till I (and you) turn purple, so I will stop here. Back to my original question. Why do people not comment? What has to change in order for commenting on online work to be as easy and natural as asking questions at a seminar?

Pharma's Double Dose of Depression

It's sure been an "interesting" time of late for major Pharma.

This Paper by Kirsch et al in PLoS Medicine on 26th February resulted in a phenomenal amount of media and also blogosphere coverage. Re. the latter, see the likes of here, here here and here.

From what I've seen, most of the blogosphere coverage was very good and well balanced. On the other hand, many mainstream media outlets were less accurate. Indeed, McDawg contacted Prof Kirsch directly who wrote back and said (personal communication) " You are absolutely right in saying that the press has misrepresented the study in a number of ways."

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Just over a week later, today, the UK's Medicines and Healthcare products Regulatory Agency (MHRA) publicly release eight documents under the Freedom on Information Act following a four year investigation into GlaxoSmithKline (GSK) and its antidepressant drug, Seroxat.




What's the story here?

McDawg became aware of this investigation shortly and unrelated, after they had this letter published in PLoS Clinical Trials, originally, in Dec 2006.

BBC's Panorama programme ran with a fascinating documentary about GSK/Seroxat entitled "Secrets of the Drug Trials" on 29th January 2007. See this BBC news item.

Essentially, "Panorama reveals that GlaxoSmithKline (GSK) attempted to show that Seroxat worked for depressed children despite failed clinical trials."

Here's todays related news item from the BBC.

This letter dated today from the CEO of the MHRA to GSK makes interesting reading.

From the investigation, "Together with this report, the MHRA is releasing documents relating to the matters set out in the report. Legal constraints make it impossible to disclose any information or evidence gathered during the course of the investigation itself except to the extent
that it is already in the public domain."

Now, as one would expect, GSK have issued a statement which can be found here.

"This press release is intended for business journalists and analysts/investors. Please note that this release may not have been issued in every market in which GSK operates." So from the onset of this release, GSK are being "selective". Open and transparent?

Andrew McCulloch, chief executive of the Mental Health Foundation said it was "totally unacceptable" to hear that young people may have taken their own lives due to a lack of transparency by a pharmaceutical company.

+++UPDATE, A PHARMA DIPS A TOE (or was it a TOAD) INTO THE BLOGOSPHERE+++ PODCAST

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"Search for the truth is the noblest occupation of man; its publication is a duty".
Madame de Stael (1766 - 1817)