Motorsport, Astrophysics and a Nobel Laureate (peripherally)

I'm cheating. This post actually lives over at Occam's Typewriter. So feel free to take a look at it over there, if you like.

Yet even more cross-posty goodness!

If anyone's interested, I've put up a new blog post at Life Science Tools of the Trade. Nothing earth-shattering, just some musings the complexity of high-throughput DNA sequencing data analysis, and the need for clean and clear visualization tools for the end user.

We'll be returning you to the regularly-scheduled wafflings about car racing, as soon as the weather warms up. In the meantime, the Canadian International AutoShow is coming, at the end of February. Stay tuned for the inevitable flood of photos.

Science IS Vital

There is a protest brewing, if I can mix metaphors so early in this post.

Among all the technical widgetry, complex protocols and other knick-knacks that we all use as our daily "Tools of the Trade" (including, I cheerfully admit, the occasional blog-friendly computer), there is one that is the Great Enabler, the Sine Qua Non of experimental research:

Money.

All research scientists spend copious amounts of time applying for it, securing it, agonizing over how best to spend it, and justifying what they did with it. All of us, either directly or through various intermediate agencies, obtain it from taxpayer-funded sources. All of us are dependent on government policies to continue to facilitate this flow of funds, and those policies, in turn, depend on public opinion. Science, politics, money - they're all connected. And in the United Kingdom, that connection is now being rather severely strained.

I am not, I think, the person best equipped to summarize the recent flood of rhetoric resulting from UK politician Vince Cable's remarks about cutting research funding. For one thing, I'm not located in Britain (although I am a British citizen, with a long-expired passport to prove it); for another, it's all been collated for us on the rather informative Science Is Vital website. Let's just say that there are many persuasive arguments why restricting basic research funding in this way is a bad idea: a prominent editor of Nature makes some of them in this slightly whimsical letter, and many more are listed here.

The suggestion that the UK cut science funding dramatically, and focus only on research with immediate commercial applications (at the expense of longer-term projects, and fortuitous discoveries), has galvanized the British scientific community. The result? A call to arms, a petition to sign, currently with over 9,000 signatures, a rally in London on October the 9th at 2:00 PM, and a Parliamentary lobbying session on the 12th. A whole lot of somebodies have been hard at work at this - you can find some of them, and more background information, here. Particularly impressive is the engagement of a number of prominent research institutions and organizations, and some fairly weighty scientific names, including apparently over 25 Fellows of the Royal Society. All of this is supported by a letter-writing campaign, an astonishingly active Twitter feed, and far too many supportive blogposts and news articles for me to even attempt to link them here.

So - if you're in the UK and at all sympathetic, why not start with signing the petition? Don't bother if you're located elsewhere in the world - to maximize impact, it's restricted (by postal code) to domestic signatories only. Fair enough. Then think about writing your MP, attending the rally, and signing up for the lobbying session.

If you're elsewhere, as I am, you could always do your part on Facebook, Twitter, or wherever on the web you hang your virtual hat. Your British colleagues, I am certain, will thank you.

Riffing

A post? Well, kind of. But as a result of a post over at Naturally Selected, by science journalist, editorial-type, erstwhile bemused postdoctoral fellow, former LabRat, and occasional Ricardiblog reader RPG, I came across a rather interesting article about the rate (or guesses at it, anyway), of non-paternity in western society.

You can read my take (i.e., "shameless stealing of RPG's idea and mild analysis thereof") on this at my other blog.

In other news: I am now Twittered. As yet, I have very little concept of why.

Scientia Pro Publica

Just a quick guerilla post to point anyone who might be reading at a worthy initiative - the Scientia Pro Publica blog carnival, which as I understand it is a regular initiative to bring interesting science to the attention of the general public.

I’ll let Stephen Curry, the host of this edition, fill you in on the details. More can be found at this post from his blog, Reciprocal Space, including a link to the submission form. Here’s Stephen…

“…if you’ve read or written a blogpost about science, nature or medicine in the last couple of weeks that you think might enchant or enthrall a public audience, please think about submitting it to the carnival.”

The submission form has more detail on the general idea behind Scientia:

The purpose of this blog carnival is simple: to provide a large public platform that celebrates the best science, nature and medical writing published within the previous month in the blogosphere. This means the host should be able to understand what you’ve written. If the host can’t understand it, neither will the public. Acceptable submissions include “translations” of scientific papers, original essays about a scientific topic or theme, and reviews of books about science. Other submissions may or may not be accepted at the current host’s discretion. Topics range from basic to applied sciences; from physics, chemistry and biology to pharmacology and medicine. Scientia is published on the first and third Monday of each month, and of course, because this is a traveling blog carnival, it is seeking hosts.

Submissions will be published on Monday, March 1, so you’ve got a little time to either write something, or snag a post from the last couple of weeks or so. Of course, since it’s ongoing, you can contribute as often, or as infrequently, as you like.

Go on, you know you want to.

Scholarly Googles, foibles and FAILs

Martin Fenner's recent blog post about ORCID, a way of uniquely identifying research scientists (or, I suppose, in principle, just about anybody) in databases, got me thinking a little about how this might solve some of my own problems. Briefly, as I understand it, ORCID will allow easier identification of published papers in the scientific literature and attribution (correctly, one hopes) to individual authors. It promises to solve a whole host of problems, including differentiating between researchers with identical names (just try looking up papers by "A. Wong", or "J. Smith" - go on, I dare you), or the same person publishing under different names (like a married name, for example).


One example where this might be useful is when granting agencies want to measure the "impact" of the funding dollars they've put into a project. And, in science, the most frequent measure of impact is the publication. Scientist "X" has a grant from the Big Granting Agency, so let's find out how many papers Scientist X has published, count them up, and report that number. Easy, right?


Not necessarily.


Conventional search engines such as PubMed (for the biomedical sciences, which is the area I inhabit) are easy enough to search, but are keyed to a limited number of descriptive terms (keywords, author names, and the like). And PubMed doesn't handle the problems identified above (one name, many people, or one person, multiple names) at all, as far as I can tell. Searching PubMed using "R. Wintle" finds a bunch of publications that I didn't write; by contrast, using "R.F. Wintle" misses one that I did. For people with more common names and/or a lot more publications, sifting through the results for relevant ones becomes a real chore. PubMed, too, only deals with biomedical papers - so if I'd happened to publish some interesting algorithm in a Math journal (oh, go on - it could happen), that would also be missed by both search strategies.


But it gets worse. The issues with PubMed (which is, after all, a curated set of publication data - in other words, it contains only "potentially relevant" information) absolutely pale in comparison with the monster that is Google Scholar. Scholar has a major advantage over PubMed, as it indexes each article's full text, just like Google does with web pages. So, looking for acknowledgments in the text ("thanks to Scientist X for helpful advice", or "experiments were performed in the facilities at Big Shiny Lab") becomes trivial. PubMed can't do this. Not at all.


But - and this is where it becomes tricky - Scholar is not smart enough to do date ranges smaller than a year. So if, for example, one wanted to find all publications acknowledging experiments performed at Big Shiny Lab in the first quarter of 2010 - well, you're out of luck. Or should I say, I'm out of luck. And this, unfortunately, is precisely the kind of data I need to gather. Four times a year, as it turns out, for one funding agency. For others, I'm occasionally obliged to do it based on the fiscal year (April through March), or various types of "government" years (July to June, October to September), which Scholar also can't do. PubMed can deal with monthly date ranges no problem, but not with full-text searches.


See the problem? Presented with the question above, I can search Google Scholar for all of 2010, and then manually go through the resultant mess of hits to (a) find those in the first quarter, rather than the other nine months of the year, (b) eliminate the inevitable duplicates, and (c) trim out the remaining chaff caused by spurious keyword hits. This, as you might imagine, is both time-consuming and irritating. ORCID, truth be told, won't solve this particular problem. Nothing will, unless Google smartens up and puts "proper" date tags on its indexed publications and implements a more sophisticated date-limit on searches (which, by the way, I've asked them to do - go on, you can ask too!).


All this leads me to the inevitable conclusion that there must be a better way. Data-mining from indexed publication records is not an easy task, and people much cleverer than I have spent a lot of time (and money) on it. What I'm looking for, of course, is a push-button solution: show me all the publications, in a certain date range, containing relevant references to the Big Shiny Lab, sorted nicely and with all the redundant hits eliminated. If we (and by "we", I mean "somebody") can search the whole web, harmonize identifiers using something like ORCID, index thousands of scientific journals, and dig through it all with sophisticated keyword strategies, surely a little request like that isn't too much to ask?

OpenLab 2009

An acquaintance (ok, I read his blog, whatever) over at Nature Network just posted a reminder about OpenLab 2009, a worthy initiative to curate and publish (on paper, no less!) the best of science blogging, including prose, poetry, comics and other artwork. So, if you happen to be a scientist, or someone who writes about it, and doesn't already know about it, consider yourself informed.

If you've written anything excellent since December of 2008, you've got a few days left to submit it... December first is the deadline. Or you could write something new between now and then, presuming you publish just a teeny bit more quickly than I do.

Go on, you know you want to.

Willy Shakespeare's Naughty Bottom Bits

Generally speaking, I don't like to duplicate post content between different blogs that I contribute to, but this was just too good to leave languishing at Life Science Tools of the Trade. So here you go, fortunate readers.

Some of you may know that I spend my days in a research lab (ok, in an office adjacent to a research lab, if you must split hairs) and, as a sideline, yammer on in various science-related discussion groups. Recently, in researching (and I use the term in its modern sense, roughly translating as "looking on the internet for approximately three minutes") in order to find something to contribute to a discussion about inappropriate scientific article titles, I came across this absolute gem of a paper:

All's Well That Ends Well: Shakespeare's treatment of anal fistula, by B.C. Cosman, published (appropriately enough) in the glamourous journal, Diseases of the Colon and Rectum.

I had no idea. With morbid fascination, I read the abstract:

Textual and contextual evidence suggests that the French king's fistula, a central plot device in Shakespeare's play All's Well That Ends Well, is a fistula-in-ano.

Really? I'm fairly certain I've seen this play performed, at least in a television adaptation. It was a long time ago, and certainly long before I began to do research on gastrointestinal disorders, but I would have thought that I would remember references to the French king's backside. And I've already learned something else: I don't think I've ever come across the term 'fistula-in-ano' before.

Reading on:

Anal fistula was known to the lay public in Shakespeare's time.

I suppose that makes sense. I hadn't really thought about it.

In addition, Shakespeare may have known of the anal fistula treatise of John Arderne, an ancestor on Shakespeare's mother's side. Shakespeare's use of anal fistula differs from all previous versions of the story, which first appeared in Boccaccio's Decameron and from its possible historical antecedent, the fistula of Charles V of France.

Ok, now the author's getting serious. Or the article's getting silly. If you've read Bill Bryson's excellent biography of Shakespeare, you'll recall that precious little is actually known about the Bard. I'm willing to give Cosman the benefit of the doubt, and presume that the venerable John Arderne really was a relative. He certainly did write a treatise on the indelicate topic of anal fistulae, which you can even read online. Go on, you know you want to. All the rest of that, about Boccaccio and Charles the Fifth, I really can't be bothered researching.


Onward:

This difference makes sense given the conventions of Elizabethan comedy, which included anal humor.

Again, I hadn't thought about it - but no surprise there, really.

It is also understandable when one looks at what wounds in different locations mean in European legend. In this light, it is not surprising that subsequent expurgations treat Boccaccio's and Shakespeare's fistulas differently, censoring only Shakespeare's.

Well, ok - they removed the reference to the King's bum. I'm not really surprised. Other 'wounds' were much more socially acceptable, I suppose. After all, we're talking about a culture that endorsed public beheadings.

Cosman's abstract ends with this screechingly funny statement:

This reading has implications for the staging of All's Well That Ends Well, and for our view of the place of anal fistulas in cultural history.

Indeed it does. I know that I shall never view the cultural history of anal fistulas in the same way again. Or perhaps at all. And I'm certainly going to be paying closer attention the next time I see All's Well That Ends Well performed. Paying closer attention, but ready to run for the door if the King's nether ailments are about to be revealed in glorious and personal detail.

It's a good thing there are curated literature search engines, like PubMed. Otherwise, how would I ever learn about these things?

Why is science important?

Alom Shaha has an interesting project on the go: a "film and blog project" he calls Why Is Science Important?, which he tells you all about right here. The tagline, encapsulating the idea behind this very nicely, is

"A collection of thoughts from leading scientists, public figures, ...and you."

I've added the emphasis on "and you" to, um, emphasize that anyone can contribute. And I'd encourage anyone who might happen to be reading this blog to give it some thought, if it seems important to you, and send something along. Notable Nature Network blogger and occasional Ricardiblog commenter Richard P. Grant contributed this piece, arguing in his inimitable style that science is "beautiful and essential". And I've put in my own two cents' worth, in this article about how scientific method makes us better able to cope with the barrage of information around us. Unfortunately, it turns out that Jenny Rohn, a much, much better writer than I, made a similar point earlier, in this nicely articulated piece. Ah well.

So - I'd encourage you to peruse Alom's site. It contains contributions from all manner of folks, from a man who's constructing the world's most accurate thermometer, to this very musical physicist, to a 12-year-old student. There are some lovely thoughts buried in there. My favourite so far is astronomer Seth Shostak's quiet understatement:

"Science is, very simply, our future."

Go and have a look. It's well worth the read.

Arriving

Every now and then, when I despair of finding anything worth reading on the Internet, I come across something like this little gem from Nature Network blogger extraordinaire Richard Grant. Now, he blogs eloquently and wittily on a consistent basis (in at least three places I'm aware of, and probably more besides), but sometimes he outdoes himself.

What grabs me most in his post is his description (in part) of what he likes about a career in science:

"I also love taking people and showing them something new: looking down the microscope and saying will you look at this!... and that enthusiasm for the natural world, that wonder at its beauty and coherence, is what has kept me a scientist."

Sentiments I can relate to, really, even though I spend precious little time these days doing science, and none whatsoever at the laboratory bench. Yes, you can do science in front of a computer, even if you're a biologist. Trust me on this. Even in front of a screen, I still get that "wow" moment from time to time, when something jumps out of the data and says "Hey! Here's something about the way life works that you didn't know before! In fact, here's something that nobody knew before!" Precious moments in between the routine, the reporting, the grant writing, the administration.

Earlier in his post, Richard also muses about why he got into the whole thing in the first place:

"Maybe it was because I couldn’t think of anything anything better to do?"

Which is, I think, meant to be a bit tongue-in-cheek (difficult to believe where Dr. Grant is involved, I know). But I too have often thought that I became a "scientist" because (a) it seemed interesting, and (b) I couldnt' think of anything better to do, either. And yes, it's hauled me around a bit, in and out of industry and to and from humans and their diseases, and nearly-microscopic worms and the secrets of their nervous systems, among other things... but ultimately has gotten me where I am now, through a series of events that make up a story far too tedious to go into in detail (so that'll be next week's blog post, then).

As RPG considers the next phase of his illustrious (or should we say "interesting"?) career, his post makes me think of my own - through this and that, I actually feel as though I've "arrived" somewhere... namely right here, in my current position. That's not to imply that there aren't other places to go. But after this many years, my career seems to be well in order, which is not something I would have said at any time in my life until just about now. Fortunately, Richard has unintentionally managed to remind me of this. So thanks, mate, and good luck with whatever's next.

You are on some road

[This post was written yesterday, on a plane. I've stolen the title from a Susan Musgrave poem.]

And so am I, metaphorically. I’m on the way to San Francisco, a city I’ve only visited once, for dinner. I’ll be delivering a blockbuster (hm, strange, as I typed that my fingers wanted to type something like “bollocks” – I hope that’s not prophetic) lecture tomorrow morning.

But for now, here I am sitting once again in the departure lounge at gate 151 of Lester B. Pearson International, airport code YYZ. Fortunately, the weather is a bit nicer than the last time I was here. Behind me, someone talking on his phone about how he’s off to an Apple conference, how Steve Jobs will be giving the keynote lecture, and how he’s burned a bunch of installation CDs for OS 10.whatever. Perhaps someone should let Mr. Jobs know.

But not me. I’m off to another conference, provocatively entitled “Beyond Genome – Tools to Therapies”, where I will talk about a) the genome, rather than anything that might be “beyond” it, and b) nothing to do with therapies for disease. But it should be fun, and a colleague and collaborator of mine is giving the talk right after mine. Monday morning, 11:15 AM Pacific Time, I will manifestly fail to change the course of scientific research and discovery. But it should be well-received, and I’m looking forward to it.

I don’t do enough of this, lecturing about science, these days. My own personal road has taken me in different directions, but now I find myself back in a research setting and liking it again. I’ve even managed to put the finishing touches on a scientific manuscript that I sent to the editors of the journal in question last week. That will be my first publication since 2006, which those of you in the academic world will recognize as a very low rate. There might be more of this in the future, though, which could be fun. Putting these things together, especially with a veritable host of co-authors, collaborators and hangers-on, can be a bit of an irritating challenge, but the end result, seeing the discoveries in print for the rest of the scientific community to read, is eminently gratifying. It will, ultimately, join my other publications in such esoteric journals as Cytogenetics and Cell Genetics, the European Molecular Biology Organization journal, and Genomics. Don't get all excited, now.

I’d better wrap up – these whimsical posts of mine tend to ramble a bit, and I’ll be boarding soon. In a few hours I’ll be in San Francisco, which is currently a pleasant ten degrees cooler than Toronto.

See you then.

2008 - with 100% more geekiness

Well, the New Year is upon us (hm, I suppose it's landed on most people east of here already), and, recovering from my slice of the Christmas Donut, I have a few seconds to reflect that I come by my science-geekery quite honestly.

A non sequitur, you say? Well, yes, but I have to exercise some sort of literary device in order to get me to the rather irrelevant observation that, upon visiting my parents this holiday season, I came across the following reprints from Scientific American, perched on their rather elegant bureau. Four articles, provocatively entitled:

1) Checks on Population Growth: 1850-1950,
2) The Tool-Sharing Behavior of Protohuman Hominids,
3) THE BLACK DEATH, [yes, the all caps are left sic]
and
4) The Ancestry of Corn.

Can you believe they read this stuff, for fun? And the source of these articles, of course, was my brother. There, the whole family's involved in one convoluted mess of scientific trivia, from the prehistoric through the medieval to the (almost) modern.

The sad bit is, I'm kind of interested in numbers 3 and 4 myself, and Mrs. Ricardipus would definitely read number 2. Sigh.

Now, off to read a much more sensible article that I have on hand, entitled Large-Scale Pyrosequencing of Synthetic DNA: a Comparison With Results From Sanger Dideoxy Sequencing. None of that dorky stuff from the parents' bureau here, oh no.

Happy New Year, everyone.

It's called a knowledge management system, allegedly

There is a pile on my desk at work, a nice, neat pile of papers that I have decided I need to read. Some are reports, some are guidelines, some are entire journals or trade rags, but most are reprints from genetics journals that are more-or-less relevant to what I do all day.

Once in a while, I will take one or more of these and put them in my briefcase for reading on the bus to and from home (or work, depending how you look at it). When they've been read, they get filed appropriately, given to someone else who might be interested, or recycled. Sometimes, they don't get read right away and become ratty and dog-eared. Occasionally, they get put back in the pile. Even more occasionally, they sit around in the briefcase for so long that they're just not relevant any more, and then I can happily toss them in the blue box. Which doesn't help me to learn anything, but certainly contributes to decreasing the amount of paper I'm carrying around. Ignore it until it goes away - the quintessentially Canadian solution.

The pile of papers, as you may guess, expands continuously. It never gets smaller, except by one or two papers every now and then, and tends to experience a net gain of two or three every week. It's been there for months, growing deeper and deeper as time goes by.

When I'm feeling like the office needs tidying, the pile gets straightened up, moved to a more aesthetically pleasing location, and then goes on existing just like it did before. Sometimes when I do this, it winks at me, as if to say "I'm still here, and you know it. Thanks for the new spot in the sun." It makes sense that it's developing sentience - after all, as each week passes, the amount of knowledge contained in the pile increases. In another year or two, it'll be humming to itself and reading Wikipedia when I'm off doing something else. Give it a few millennia, and it'll pretty much be running the joint.

So there you have it. Me and my pile of papers, sharing an office and slowly evolving towards achieving the sum total of all human knowledge. Or at least those specific bits that might be useful for someone like me. I suppose I could make a concerted effort to read everything and make the pile disappear, but I know it would be a losing battle, and I haven't the heart anyway. I kind of like it when it winks at me.

A minor rant

Despite all my complaints about being too busy, it seems that I just keep taking on other projects. You know, projects that get done in my "spare time". Remember that? Thought not.

Anyway, the latest requires digging through a large amount of scientific literature looking for articles on a certain topic, then summarizing the findings in an easily-digestible format. No problem. It's a lot of reading (a couple of hundred articles, of an average of about eight pages each), but I take a 45-minute bus ride to and from work every day, so that makes over seven hours a week I can dedicate to reading this stuff. Easy.

However (and here comes the rant-y part)... although I can easily look up scientific articles on the mighty PubMed database, which life scientists of all stripes use all the time, and I can stay on top of new ones that might not have made their way into PubMed yet via RSS (and I thank Black Knight for hooking me up there), I still have to go to the journal sites (or in some cases, repositories of multiple journals) and download the individual articles. Which would be fine, if all journals had one of these: You see? If you know the volume and page number, you just type 'em in, and bingo! you have the article you want all tied up in a shiny PDF wrapper just a-waiting for you to read it.

The alternative, unfortunately, is that most journals just have an ugly front page with a huge list of back issues, which you have to browse through to find the article you want. This gets to be a problem when the issue you want is several years old and sitting on the fourth or fifth screen of available issues. I can't even begin to imagine how much time I've wasted used up simply navigating around these things.

So - a plea to all scientific journals, everywhere. Take a leaf out of Science's book, and put a little search box on the front page. Please. It will make my life easier.

And you thought that I only complain about trivial things.