Academic research is pretty much funded by investigators panhandling, using the medium of grant applications. These suck up more than 50% of ones effort in times of poor funding. I’d like to propose a new method of grant applications: the 140 character limit Tweet.
Dear Funding Body, Plz gimme sum munny. My lab iz broke and we need dollahs to buy science. KTHXBAI.
Sometimes I wonder where the breakdown in communication between scientists and journalists lies. In this article about a recent study on a DNA damage checkpoint enzyme, the Beeb describes the study as such:
Research into how the human body repairs damaged DNA has been described as a “major breakthrough”.
The way that cells protect themselves from diseases like cancer has been the focus of a study by scientists at Dundee and Leeds Universities.
The enzyme studied1 indeed has a crucial role in DNA damage repair, a mechanism that prevents the DNA in cells from getting more and more mangled with every replication cycle. But to conflate a study on structural analysis of a bacteriophage2 enzyme with cancer in humans annoys me a little. It’s sexing up the topic beyond its current reach3.
Some of the responsibility for conflation of basic science with translational/clinical applications lies with scientists. We have to justify what we do: to the funding agencies, to our peers, to the editors of journals, and to the public that ultimately funds our research by taxation. So everything we do has to somehow, however tenuously, be tied in to some disease or some way to make human life better4. So every time we publish our findings, we make that link, however thin, to some major health concern: cancer, heart disease, obesity, cancer, diabetes, cancer, auto-immune diseases, cancer, blah blah blah. And the journalists, with their need to write an interesting article, take a lot of our fatuous crap on faith. Don’t ask for solutions. I have none. I am guilty of the same damn crime.
1 Sorry, it’s not open access. You’re unlikely to be able to read the full thing outside of a first world university/college. It’s a bugger isn’t it? Incidentally, does anyone else get annoyed that they don’t link to the studies in PubMed or even list the first author? Then again, if they had, I wouldn’t have seen via PubMed that one of the authors, David Lilley, has published in both Nature AND Science in the space of a week. That’s rare.
2 Bacteriophages are a type of virus that “infect” bacteria. Yep. Even bacteria get viral infections. Isn’t nature amazing?
3 Don’t get me wrong. I think this structural analysis of the protein is a great step forward in understanding how DNA damage repair works. The next step may happen yet. I just don’t think the next immediate step is preventing cancer.
4 Caveat: I refer here to research funded by the Medical Research Council in the UK or the various National Institutes of Health etc in the US. My world is very narrow.
All the elements of a good article: a horror story, some recent headway into the problem and written in plain English, albeit with the occasional technobabble.
Plain english synopsis here.
While we’re blathering about science, the recent award of a Nobel prize to Mario Capecchi, Martin Evans and Oliver Smithies made me remember how much I used to curse their blasted brains during the PhD years. You guys deserve a Nobel prize for making 3 years of my nascent scientific life hell. Then again, without your pioneering work, there’d be no work for the skill-less people in the world like me.
I’ve been thinking about the future1, my place in it, and my place in scientific research. Having bored myself silly with self-centeredness, I looked further afield. Back in July2, Professor Greenfield was deploring the lack of female scientists in the higher echelons of her profession. She makes a few fair points, but, as can only be expected with such a complex problem, has no solutions. I’d only add that many male scientists face the same problems as female scientists3: publish or perish, wave farewell to a life outside the lab, bid your aging reproductive organs good day and goodbye4, watch all peers ascend on the property ladder while you slum it out, suffer from intense self-doubt5, blah, blah, moan, whinge, whine. Oh, we’re back to self-centeredness again. Regardless of the problems and lack of solutions, I got a darn good laugh out of this comment to Prof. Greenfield’s article:
“Maybe women scientists are that much more intelligent so they realise that as a career, scientific research is a joke?” –WinstonTheChair
So true.
1 And no, it’s not orange.
2 When my head was so far down a microscope there was no light input save that of the very expensive laser. And no, it wasn’t orange either.
3 I should know; I live with one.
4 Granted, this is more a problem for XX than XY. But without XX, XY in a partnership with a scientist XX can’t do much about it.
5 Believe me, even the most arrogant of scientists has moments of self-doubt. There is perhaps, though, a reciprocal relationship between success in science and self-doubt.
Win what? Well, nothing more than a few months of hard work, hopefully followed by a nice wee paper…
We’re in the mood for science on akatsuki talks rot. Perhaps this has come about since I’ve acknowledged that I will always be a mediocre blogger, but I could become a better science communicator if I practice writing about things I work on more. And all that stuff about the bloody Viagra-jet lag story (and the media coverage of it) made me realise there is a middle-ground for scientists in the know to discuss hot topics without resorting to the extremes of technobabble (which we’re used to applying in our daily work) nor the overly condensed data-free reportage by the media.1
I’ve toyed with the thought of using this blog to practice writing mini-reviews of interesting published scientific studies, but have been to lazy to date. This may continue, or it may not. But given that nobody actually reads this crap, it doesn’t matter. (Hi P! You still reading this surreptitiously? I have a site counter, you know…)
At any rate, since my laptops have a tendency to die after a few years, and I’m not very good at backing up non-essential data, here follows an email I spent a good 15-20 minutes on this evening to a colleague. I think I was being Ms Good Postdoc, but I often fear that I don’t give good advice. Time will tell.
The premise: a friend of a colleague needed a starting point for a promoter assay s/he is planning.
My reply to the request, slightly edited:
Hi [colleague],
There are several approaches to finding the promoter of a gene. The
first would be to do a quick literature search to see if anyone has
already determined the components of that gene’s promoter.If not, the second approach would be to retrieve the gene information
from a genomic database (like Ensembl or the UCSC genome browser). These two sites are
particularly useful because they allow very quick and easy comparisons
across species (e.g. human/mouse/rat/fish). Such comparisons often show
what sequence is most conserved: usually the exons and any regulatory
elements that are essential (like promoter elements). This only works
some of the time and will only highlight very conserved regions. There
will be species-specific differences in promoter sequence.The third, slightly more laborious approach, is to take several
kilobases of sequence upstream of the first known exon and perform a
promoter prediction. This has become relatively easy on the internet. A
quick Google search found these possibilities.Of course, the difficulty is in choosing one. I cannot recommend one
over the other because I haven’t tested them myself. There is one
particular site I know of that is quite easy to use: Promoter 2 prediction. It looks for known promoter motifs based on already studied PolII promoters.After that, your friend will have to make the decision of how much of
the promoter to clone, and how many different construct lengths he/she
wants to try. I guess it will also depend on the restriction sites
available in the sequence and how big the sequence is.As for getting the DNA, it can either be cloned by PCR if it’s very
small (around 10kb), or it can be “cut” out of a BAC (bacterial
artificial chromosome) or PAC or cosmid (large-capacity plasmid) that
already contains the genomic region (can be bought from places like the
BAC/PAC resource or Invitrogen or Roswell depending on species). The restriction digest method is preferred because it will have no additional errors, and it is also easier to change the length of the promoter region by choosing different restriction enzymes. Some people even use the entire BAC and make small deletions to eliminate predicted regulatory elements.I hope this is will be helpful in getting your friend started. The real
difficulty will be making the construct and testing it; I wish your
friend the very best of luck with this!
After sending it, I read what I wrote2 and thought: goddamit, it’s all too simplistic. They probably already know all this crap and were probably looking for something concrete. Like a real protocol. Unfortunately, for this and quite a lot of the other molecular biology I do, I do it on the hoof. At some point in the last 10 years, I followed somebody else’s protocol (usually the postgrad/postdoc/technician I was asking advice from at the time). Then found alternatives, some of which I now use routinely, some of which I was too lazy to follow-up. Then I switched specialities. Twice. Now, I am used as a mol bio repository by my (ex-)lab. They sometimes even think of me as an expert. But a real expert wouldn’t feel so fraudulent in giving advice, would she? Self-doubt creeps in… Oh what if I’ve screwed up somebody’s project giving bad advice?
1 I’m in no way implying real media gets it wrong (although some, like the gawd-awful Daily Mail, get it wrong and deliberately so!); just that they make the assumption that folk just want the headlines. Which may be true. But not this particular folk or her ilk.
2 And after writing this post, I read it and thought: WTH? Why can’t you stay on topic? I give up. It’s time for dinner.
While I’m in a mini talk-about-science mode, have a look at the female hammerhead who didn’t need a male (Is anyone else bothered by the way these news articles never provide a link to the scientific article being quoted? I’ve had a cursory look at Biology Letters and can’t find it. This bugs me because I can’t accept it on the word of a journalist; I need to see the data. And I’ll forget by tomorrow to have a look for the published article again.)
Parthenogenesis, the somewhat sci-fi process of asexual reproduction, even in vertebrates doesn’t particularly surprise me2. What does surprise me is that they didn’t ask DTB for a quote3…
1 Or is it the other way round?
2 But it makes me think again of why we (as in the generic we) evolved to require sexual reproduction, why parthogenesis doesn’t happen more often, and what have those “Red Queen” proponents been up?
3 For P’s benefit…
BBC picks up on the hot jet-lag study of the day: Sildenafil accelerates reentrainment of circadian rhythms after advancing light schedules, PNAS U S A, 2007.
Some initial thoughts:
Maybe more on this later. While the world gets excited by yet another use of the blue pill, I still have to ask people for money to fund my somewhat less titillating work. Hmm… Maybe I can incorporate this into my grant application. But somehow, I think jumping on the bandwagon will not go down so well. If only I could think of a clever selling ploy to convince reviewers of the importance of my work4.
1 This is just one of many examples; I’m too lazy to dig them all up right now.
2 For interesting, read: involving sex, drugs and rock and roll. Titillation galore!
3 Well, the thought struck me when I read a colleague’s paper on our common model and he mentioned how Viagra worked via the same pathway as the molecule we work on. But I didn’t act on it because… I am not as inspired as these clever folk down South.
4 It’s perhaps not commonly known (or rather, I didn’t know this when I was a lot younger and a lot more naive) that scientists also have to be good salespersons. It’s obvious once you get to the post-graduate level (or before if you’re somewhat less cossetted), but the more I get into this, the more I wonder about whether the amount of bullshitting that is done is actually detrimental to the science (even though it is currently the default; no bullshit, no funding). But this mini-rant deserves a full post at some point. Not now. Not until I’ve finished prostituting my work.
Can anyone tell me what the hell an akatsuki enzyme is and why it keeps popping up in my keyword search1? Is this predicting the day that I discover a new enzyme and egotistically name it after myself? Or is it some crappy New Age bullshit treatment2? You will be sorely disappointed if you’re here for that. If anything, I should be joining Ben Goldacre in rubbishing these pseudo-science pieces of crap that purport to make people’s lives better when all they do is make them poorer.
1 Statwhore admission: once in a while, I look to see if anyone from an interesting country has stumbled onto my insignificant spot on the www. And I was slightly surprised to find a Kiribati ISP in the collection this week. Hello. I hope I wasn’t overly offensive with that silly off-the-cuff remark about coconut oil. And how are the Atollettes?
2 For the record, I enjoy the occasional reflexology massage. I don’t buy into any of the claims of direct linkage of my big toe to my brain, ok? It’s just a damn foot massage. It feels nice when you’ve spent the whole day standing while doing experiments to go home and massage your foot. Or hire someone to do it for you. There are no other significant health benefits.
So, the kryptonite story is old hat now. But the article made me wonder why the makers of Superman Returns used “sodium lithium boron silicate hydroxide” as the chemical formula for kryptonite when we already have an element named krypton (Kr), which they could easily have faked a compound name with. They missed a trick there. (Unless there’s some kosher DC Comic reason for it.)
