Tuesday, January 11, 2011

Another move

In case you missed it over at LabSpaces, I've moved the blog. Again. You'll find me at http://scientopia.org/blogs/blather/. See you there.

Thursday, August 05, 2010

Right, I'm off then.

Okay, so you probably realized from my last post that the blog is moving. I'm off to LabSpaces.net. This is a homegrown science news site run by Brian Krueger. Brian invited me to set up shop over there. He already has an impressive (and young) group of bloggers - go check them out. My new home is here. I'll continue to blather on incessantly about the things that interest me, while simultaneously raising the average age of the bloggers at LabSpaces.

Later today I'll be changing the RSS feed on this site to point over to the new blog. This site will remain and I'll pop over to check on things every now and then. But all new posts will be at my new home.

See you on the other side!

And Blogger, thanks for all the fish.

Wednesday, August 04, 2010

Wanted: good moving company.

Must be good at moving glass without breaking it. Especially glass filled with a variety of beverages. Mostly beer.

Tuesday, August 03, 2010

A successful brainwashing

I have had an exceedingly bright undergrad working in my lab over the summer. This week is her last before heading off to her home institution. Today she told me she didn't want to leave. She wants to stay and try to figure out what the enigmatic protein she's been working with really does.

Yes!!!!!!!!!! (Odyssey pumps fist in air)

Of course, she'll head back to her home at the end of the week. Maybe she'll come back next summer...

Demise of The Academic Jungle

GMP has taken down her blog, The Academic Jungle. In her final post she asserted that academic/science blogging (as she sees it) has little or no significance. That the disappearance of such blogging won't make any difference.*

Perhaps that's true for her, but not for me.

I am continually learning a lot from other blogs. Reading about the trials, tribulations and triumphs of tenure-track faculty as chronicled at Prof-like Substance, Professor In Training, Blue Labcoats, ChemBiLOLogy and The Prodigal Academic has no doubt had a positive effect upon my interactions with junior faculty at my institution. I've learned much about women in science from some of the same blogs, plus Isis and Zuska. Drugmonkey and Comrade PhysioProf have dispensed invaluable advice on obtaining funding, particularly from the NIH. And Janet Stemwedel's Adventures in Ethics and Science blog is always food for thought.

In addition, the interactions I have had with people in the comments sections of this and numerous other blogs have in general been a blast.

My own blog has allowed me to share frustrations and triumphs, dispense advice unasked, and generally blather and pontificate. Maybe not useful for others, but certainly cathartic for me.

Blogging and reading academic/science blogs have significance for me.

* Hopefully I'm not getting her comments wrong or out of context. Since her blog no longer exists I'm having to go by memory - I read the post last night.

Monday, August 02, 2010

What? But... Hang on a sec...

I go away on vacation (hmmmmm, vacation.... sun, beer, sand, beer, waves, beer, seafood, beer and beer...) and all hell breaks loose.

Well, maybe not hell. But a whole new blog collective just... appeared. Scientopia. And many of my favorite science bloggy types have moved there. I was going to list them but Bora over at A Blog Around the Clock has already done so here.

Tres cool.

Tuesday, July 20, 2010

Disordered ramblings

Of late I've become interested in so-called intrinsically disordered proteins (IDP's).* These are proteins that contain one or more "significant" regions of sequence that are unstructured. "Significant" can range from perhaps ten or so residues, up to the entire protein. There are experimental data suggesting that the disordered regions in some of these are vital for function. It is generally thought that disordered regions important for function might undergo a folding reaction when bound by another protein, or a nucleic acid, or even a small molecule.

I'm interested in IDP's** because two of my favorite proteins have disordered domains that are essential for function and that do undergo the kind of folding upon binding mentioned above. This makes these proteins more interesting to me intellectually (not that they would be boring without disorder), but can also make them significantly more difficult to study than your garden variety well-folded, globular protein.

The IDP field is populated by large numbers of bioinformaticists (spawning my last post). There are also experimentalists and computational biologists (of the molecular simulation kind), but much of the initial driving force in creating this as a field appears to have come from the bioinformaticists. A small group of them.

Who are seriously over hyping the field.***

The hype being based largely on predictions of disorder. Predictions. Not much data. A prediction is just a pointer to something that might (or might not) be interesting. It's pretty much meaningless without experimental verification.

This is a problem. Yes, we all need to sell ourselves and our research. We all need to convince others that what we do is important and should receive gobs of funding $$$'s. But what you're selling has to have some connection to reality. A track record. Data.

Right now the IDP field has all the appearances of an infomercial for some kitchen gadget that is promised to mix, knead, puree, blend, chop, slice, dice, julienne, fry, roast, bake, boil, steam, load the dishwasher, sweep the floors, put the children to bed, and polish your shoes. Only believable in the wee hours of the morning after a long evening consuming copious quantities of the alcoholic beverage of your choice.

For now I'm keeping my credit card in my pocket.

* There are many, many recent reviews on the subject. This one is okay (and free).

** I seriously dislike the name "intrinsically disordered protein." For a start, the majority of the IDP's that have been identified are mostly well-structured and only have a fraction of their sequences disordered. I saw someone use the term "intrinsically disordered region." That's an improvement.

*** Case in point: the many, many reviews. Many, many of which were authored/co-authored by this guy. Dude, enough already. Go spend some time in the lab generating new data.

Monday, July 19, 2010

Data mining talks

As a molecular biophysicist I often hear talks (and see posters) given by bioinformaticists.* I am struck by how these are almost uniformly abysmal. I'm not necessarily referring to the data, but rather the presentation as a whole. This has reached the point where I don't think I can bring myself to sit through another bioinformatics talk (or poster presentation) for at least the next three months.

Why has the quality of the now dozens of such talks I've suffered through been so low?

In the majority of cases I posit it's a combination, in varying degrees, of a lack of imagination and a disconnection from the underlying biology. Too many of these presenters regale their audiences with interminable laundry lists of how property X is over-represented in sequences of class A, and under-represented in sequences of class B. Ummmm... So what? Why should I care? Often such presenters either don't know or are too lazy to spend the time connecting their data with known biology. As an example, I recently sat through a talk where the speaker made a big deal about the prevalence of glutamine-rich sequences in proteins involved in transcription. Not once did he refer to the fairly substantial body of experimental data on these very same sequences. In fact, when asked, he couldn't offer up any explanation for this observation.** Major fail.

I can't explain why this happens. Obviously it shouldn't. Perhaps it's a function of the relatively immature nature of bioinformatics as a field. It's still at a stage where method development trumps method application. Application of the intelligent kind.

I remember when macromolecular crystallography talks suffered from similar issues. They would often be these long detailed descriptions of the structure(s) just solved by the crystallographer. No connection to the biology, just the details of the structure. Listen, I don't give a rat's arse that there's a type VIIb turn between helices 7 and 8. What I want to know is what the structure tells us about the biology. Nowadays most crystallographers do make the connections. One can't get a grant for simply solving structures any more.***

I've heard through the grapevine that getting a grant to do bioinformatics has become increasingly difficult. More so than would be expected from the downturn in science funding. Perhaps we'll see the field forced to mature more rapidly and presentations improve.

* By "bioinformatics" I mean the data-mining thing. A colleague once defined it thusly: "Bioinformatics is the mining of biological databases for profit (not necessarily of the monetary kind)." This is distinct from computational biology which, at least at the molecular level, tends to employ an energy function of sorts.

** Glutamine-rich regions can be involved in DNA binding - the glutamine side chain is quite good at making hydrogen bonds with nucleic acids.

*** Not when I'm reviewing the grant. :-)