Thursday, June 26, 2008

I won't surrender my idealism

There's a thought provoking discussion going on among some of the heavier weight science bloggers which has so many subthreads running through it that it's hard to summarize. So it's prolly best to go check out the posts over at DrugMonkey (here) and YoungFemaleScientist (here)

It's a back and forth that goes back a number of posts, with a lot of commenting. Essentially I think it boils down to this: YFS is a postdoc who thinks the system of science is in many ways fundamentally unfair, and as such needs changing. Physioprof and DrugMonkey are faculty members who aim to describe the system as it is, to help postdocs succeed in that system (which they readily grant it flawed, yet over which they feel they have limited ability to change).

Overall both make good points, but I take issue with some of the things that PhysioProf says in his latest post.

The money quote:

"In a winner-take-all system like this, there will always be people who do not succeed through no fault of their own. People who are smart, talented, dedicated, hard-working, articulate, persuasive, and who do all the right things sometimes still fail. This is the nature of a winner-take-all system: there is an intrinsic randomness that influences to some extent who succeeds and who fails. It is the same in professional sports, law, medicine, performing arts, entertainment, comedy, business, entrepreneurialism, journalism, engineering, and most other professional career enterprises.

Many of us may not like this situation, but this is how things currently work. Academic science is not a fucking Care Bears tea party, and wishing that it were is not going to make it so."

I have two big issues with this. First, there's no consideration for how well the current system of science might work to improve, or hinder, the quality of the end product: knowledge. Might it be that the system as is exists produces worse science than a different system? The fact that the essential randomness of the system might lead people to lose faith in the justice of the entire process. And when they do that, they start behaving badly. Dr. Free-Ride has it right, so check out her post.

If it is the case that the system is worse than it was (or might be), don't you have some obligation to change it? DrugMonkey does say in the comments that his blogging is one way of changing things, and that he also does his best to nudge things towards a better course in his real life working as a scientist. That's good, but it leaves me to wonder why the vitriol towards YFS, who is doing the SAME thing, in her way.

Secondly, I hate the way that PhysioProf impugns people who might want to change the system with the dismissive reference to a "CareBear tea party." I read it as saying to anyone who is an idealist about science qua science, or who feels that some current practices pervert what we see as a noble a pursuit worth dedicating one's life to, is hopeless naive. To that I say, fine, and can I get another helping of naivete?

Because I won't surrender my idealism for the project of Science. If that means I "fail" in the end, well, I will have my head held high when that time comes. I would rather live with the failure than to abandon my principles.

Tuesday, June 24, 2008

The Messy Phase of a Scientific Problem

-juniorprof started an interesting discussion about whether to be a producer or consumer of the literature. I started to write a comment in response, but it sorta ballooned up, went off on a bit of a tangent, and so I moved it here. Be sure to check out his post there (and his blog in general, it's a good one).

Overall, I find the message behind the dictum of the famous neuroscientist that juniorprof relates, which is to "be a producer not a consumer [of the scientific literature]" to be kinda ambiguous; of course all scientists need to have some engagement with the body of work they're involved in, and of course it can be easy for some folks to be too wrapped up in the literature to the detriment of their own creativity and experimental production. As juniorprof added in the comments, with which I agree, it's best to start a new project by going through the literature, and then after that to let your experiments guide you.

As part of his post juniorprof also warned against getting too wrapped up into the minutiae of details that can at times overcome a particular subfield (the state of which can be diagnosed by the presence of negative results against this or that hypothesis). I like that too in principle, but I can think of a couple examples where it took the field several years and a lot of negative experiments to converge on a better understanding of a process, and in so doing helped to reveal a more broadly interesting and relevant results.

Cases in point are the signalling mechanism that causes M current inhibition by receptor activation, and whether long-term potentiation (LTP) occurs as a result of changes in pre- or postsynaptic properties. It took a long time before it became generally agreed that PIP2 depletion inhibits M channels, or that postsynaptic glutamate receptor insertion underlies many forms of LTP, and I can think of lots of experiments with negative results done to assess the multiple alternatives. Sure, in isolation any one of those results isn't terribly informative, unlike a good positive result would have been; yet in the aggregate they reflect the shared knowledge of the field which had to be accounted for in the final scheme. And I would argue that only the existence of these negative results enabled the final positive result. (Still though, if you do have a negative result, stick it somewhere where you also have some amount of positive results and appreciable march towards the final answer. And by the gods do NOT highlight the negative result in the title. GAH!).

Also, the final papers which cemented the current understandings of these processes were published by people who were actively researching these questions throughout the messy period when lots of negative results and back and forth papers were being produced. So, I find it unlikely that any single researcher could sit out the ugly phase, work on something else, and then "swoop back" in and make a strong positive situation). Instead, I think that only by those people actively involved and invested in the line of inquiry were likely to have the ability to make the final connections and apply them to their question.

Now, I'll grant first that spending time on expts in the "dirty" phase isn't glamorous, and might be a hard sell to funding and promotion folks. I'm more thinking about how this process plays out for science per se (naive and unwise, I understand). Secondly, you have to make sure your initial process has some level of importance before you decide to commit to it. In this way it helped that M current (as an example of ion channel modulation more generally) and changes in synaptic strength such as LTP were intrinsically important questions. These two also had the lucky effect that their answers became important in and of themselves, as examples of PIP2 modulation of ion channels and activity dependent insertion of ion channels, respectively. Maybe it's not lucky though, since you should probably assume that a question which takes that long to settle is likely to generate an answer that is pretty novel when all is said and done.

So where does that leave us? Hmm, my main dictum is, "Do good science".

Thursday, June 19, 2008

Well, at least it wasn't a terribly offbase decision...

You Should Get a PhD in Science (like chemistry, math, or engineering)

You're both smart and innovative when it comes to ideas.

Maybe you'll find a cure for cancer - or develop the latest underground drug.

Ok then, so I chose correctly, and I certainly did enjoy getting the Ph.D. (as well as generally enjoying my time now). Though it might also explain why the whole current situation in science feels so...psychically disturbing at times.

Friday, June 13, 2008

Do citations in supplementary data not count in ISI?

I came across something troubling today in the supplementary information that accompanied a paper I was going over. Now I have a lot of misgivings about the whole concept of supplementary data, yet I hadn't realized this one until now.

That is, in the Thomson ISI database, citations made in supplementary data are not counted in the "Times Cited" count. That's worrying to me, because one of the most prevalent ways for people who are not experts in a given field (or subfield, or subsubfield...) to assess the influence of a scientist or paper is to use the number of citations the paper garners. For example, these citation counts are used to create the impact factor to rank journals (and at times erroneously to rank individual papers), and the Hirsch, or h-, index used to evaluate scientist output.

Meaning, if these citations are not included in ISI, then for all intents and purposes they do not exist.

So now, not only can supplementary info be used as a dumping ground for your inconclusive or crappy data, but you can also stick references to your competitors in there and shaft them their citations.

But hey, at least you've got your plausible deniability!

Anyone else troubled by this? Anyone else have opinions on supplementary data?

Thursday, June 12, 2008

Some open access goodness from the Clapham lab

Recently, my colleagues in the lab have published open access papers describing their work on various TRP channels.

One, headed up by Sebastian Brauchi (a former postdoc in the lab, who now has his own lab in Chile) and Grigory Krapivinsky, describes the role of TRPM7 on cholinergic vesicle fusion. It was published as open access in PNAS. Download it here.

The second describes work by Stephanie Stotz and colleagues on the sensory transduction mechanisms elicted by the chemical citral (a component of lemongrass). They found multiple effects of citral on a number of TRP channels expressed in sensory neurons, and published their work in PLoSOne. Get it here.

Yay for open access! Actually though, my advisor David always self-archives all of his publications, and they're available at the lab website here.

Wait! You're a postdoc, blogging under your own name? Are you insane?

Heh, I know, it does seem a little kooky at times.

Am I worried that my current advisor, or future colleagues (wherever they may be) will look askance at the idea of spending time blogging? I'd be lying if I said I was completely at ease with it, but I always come back to convincing myself of the personal utility of blogging. What do I mean by that?

Well, I plan on focusing primarily on blogging about science related topics, whether it be my own research, commenting on other research in my fields, and in thinking about issues related to science at large. This won't be a blog where I discuss my personal life, or complain about coworkers or things like that. There are definitely places for those kinds of blogs, but this isn't one of them. There won't be a hard firewall between the personal and professional, but there won't be LOLcat links (beyond that one, promise).

Instead, I see this as a way to more fully explore and think about issues that are already kicking around in my head. Stuff that my brain is chewing over, and will not let go. So while it may seem that this blog is going to take up a lot of time (and it may) but it might just let me offload some of that congitive processing time, refine its use, and free up resources for more obviously pertinent tasks. And this is one reason why I decided to do my blogging under my real name. That will force me to think a little more about my writing. Also, I didn't want to worry about my anonymous blog becoming 'outed' at some point, and risk hurting people I had written about. Better to prevent that temptation from doing that in the first place (but I certainly don't fault anyone for being anonymous. Sometimes a little spleen needs to be vented, and somethings in science are all messed up, and talking about that helps us all. A great example is YoungFemaleScientist).

And there will prolly be more indirect, and more distant in time, benefits of the blogging, related to becoming part of the broader science blogging community. That community is just a tip of the iceberg in the burgeoning Science2.0 movement (though I hesistate to call it a 'movement', that implies too much of a top down approach - it's more organic and distributed). I've got another post in the brain to discuss some aspects of Science2.0, but it seems obvious, and I'm convinced, that the increases in communication and interaction enabled by the spectrum of Web2.0 technologies can only help improve science and will improve the research and recognition of those involved. If I can get some 'early adopter' advantage, well, at this point I'll take whatever I can get! See, there is a selfish benefit to it all, which is a good way to motivate people to do things that also benefit the group at large.

Thursday, June 5, 2008

The Very First Post

Well, everything has a beginning, and so it is with this blog. Today, appropriately enough on Harvard's commencement day, I begin my foray into blogging. It's been some time coming, and I've wrestled with whether I should even get into this in the first place, and if I did take the plunge, what I hoped to accomplish.

Having no particularly clear answers to those questions, I just decided to take the plunge, and let the blog evolve towards whatever state the forces involved dictate. Consider it a beta version if you wish.

Of course I do have things I want to talk about, thoughts to share, and conversations I hope to start. Many of them will likely involve neuroscience, my academic field, which at least in terms of cellular neurophysiology seems poorly represented in blogspace (I couldn't use the term blogosphere here; to me that connotes some cloud of more politically interested blogs, carrying on discussions between themselves. I have no interest in becoming a part of that). I think it's clear that blogs will emerge as an important medium to enhance communication among scientists, and that's something of which I want to be a part. As a place for less formal communication about science, blogs appear ideally suited; I just wish there were more researchers doing it.

Beyond that, I've always taken a keen interest in "Science" and the big issues that surround it: the ethics of science, the practice of science, and how we can organize science to produce the best ultimate outcome, which in my view is the production of information that informs and improves humanity. I don't claim to be anything more than an interested layperson in these areas, but I can bring a "view from the trenches."

Lastly, why "The Junction Potential" for a blog title? There are a couple of reasons. First, it's an electrophysiology thing. As every young electrophysiologist learns, there is a junction potential between your pipette solution and the external solution, arising from the different ion mobilities. This affects the actual voltage you're applying to the cell membrane, and needs to be correctly measured or calculated, and then offset. In terms of electrophysiology, the junction potential isn't always paid a lot of attention, nor it is usually a big deal if you don't account for it initially (you can always correct it after the fact). That's a perfect analogy for this blog I'd wager.

The second reason is perhaps more profound. I have become convinced recently that many aspects of Web2.0, be they social networking/bookmarking tools, folksonomies, wikis, and blogs, will profoundly change the practice of science (this is by no means an original conclusion of course). They have the potential to drastically increase the junctions scientists make with their subjects and with their colleagues (yes, I know, groan). Besides, I needed to call it something.