Sunday, October 17, 2010

Formulary of Ten

Here's a quick question: if you had to trim the formulary of a hospital down to just 10 adult meds, what would they be? I'm sure a careful and informed individual could make a comprehensive choice based on "Quality of Life Year" information and some epidemiology of the area. Here's what I am thinking:

1) Morphine
2) Aspirin
3) One or two antibiotics (Guess who doesn't remember micro enough to know which ones? I am guessing Cipro/levo and Vancomycin)
5) Insulin
6) Beta-blocker
7) A statin
8) Doxorubicin (What my boss called: the one chemo you'd bring to a desert island)
9) Warfarin
10) Lidocain

Thoughts? It might be a little over-covered for heart disease and under-covered for diabetes. Also, is it even worth it to have a chemo agent, from a utilitarian perspective? I know that's heretical from someone who is interested in cancer research, but how much life are you really adding with one therapy alone?

Also: does Morphine/lidocain deserve a place? Pain management is important, and I didn't want to leave it out. But when there are other diseases being left uncovered, should this be a top priority?

Anyone care to offer an opinion? It's an interesting way of thinking about priorities in U.S. medicine, and pondering how much we take for granted. What medicines are those that we can't make due without?

Thursday, October 14, 2010

Peer Review

If you've spent some time in graduate school you might have learned a thing or two about the open secret about peer review: it's not entirely done by peers and it's not always that thorough of a review.

Like it or not, grad students often find these reviews on their desk. I've heard of PIs leaving the job to grad students alone, though this does not occur in my lab. It's understandable, though, that this might happen. PIs have huge demands on their time. As invaluable as their opinions are, there is no way some PIs can field every manuscript. Apparently they have their own concerns about peer review (some of which apparently involves colorful dinos)

But what of the reviews performed by graduate students? There are two ways of looking at the duty of peer review.

Looked at one way, a peer review is a learning opportunity. Often the material details development on the edge of some field that contacts at least tangentially upon the student's research. It's a chance to see another lab's raw, early draft manuscript, and learn what merits publication in high level journals and what does not. It is a learning experience, and a chance to contribute to the body of science as a whole.

But let's just step out of the shiny world of gumdrops and candy canes for a moment. Peer review can be an inane chore. While students provide some value added to the journal and the author of the manuscript, it's harder to see where the review process benefits their progression in the ladder. Their role in the review is, effectively, anonymous, and comes with no honor, distinctions, gold stars, pats on the head, brownie points or first author publications.

Stated simply, there is no clear match between incentives and the quality of the peer review. Mistakes are often buried somewhere deep in the unending, jargon-filled paragraphs of the methods section. Whether a grad student takes the effort to check these methods, line by line, comes down to a question of how many hours (if any) of sleep they might prefer to have that evening.

Where's the incentive to dig in? Some grad students seem to possess a deep personal drive to throw other scientists under the bus, but it's probably a minority at most institutions. We can't rely on pure sadism to drive the scientific engine. There must be a way to reward careful and well considered reviews, particularly where they find obscure errors and tenuous methods.

I don't claim to know what the reward should be or how it could be structured. I've considered the possibility that confidential peer review is a mistake, and that publications should instead be edited by the journal seeking to publish. If Nature wants the value added of an expert opinion in the field, let them pay for it! Certainly they demand payment for their subscriptions, so why should their product be provided for free?

At risk of shifting to a seemingly radical alternative, perhaps open access and open comment system is the way to go. Take all comers that pass a basic editorial spot check, and allow insightful, observational comments to come from the community. Those comments can then be tied to the reputation of those who make them. Great insights can be noticed, and unnecessary bickering (I'm looking at you, reviewer #3), can be ignored. Online systems for grading and sorting comments based on reputation systems exist in many forms. Perhaps its time to turn them loose on science.

Concurrently, give labs the hard task of determining their own publication threshold. Perhaps more self review will go on in-house if authors know that they can publish whatever they please, and that they'd better get it right the first time. Perhaps some systems could allow papers to have a 'versioning' system, wherein they could be updated (to a point) to reflect public comment.

I don't claim that pay-to-review or open-comment systems solve the problems inherent in the current publication regime, but I think they deserve consideration. Let us at least recognize that good work deserves good incentives, and that the adding motivation to peer-review can only improve our scientific rigor.

Grad Year 1, Tiny Learnings

Tiny learnings from grad year 1, stated briefly, for my own purposes. Trite? Maybe. Suck it up.

Mentorship is everywhere, always take the opportunity to meet people doing different things in different labs. The guy down the hall may solve the problem that's been killing you all month. That actually happened to me today, and it was great.

Look out for #1, a little bit. Cognizant of the goal being science, remember that not everyone has your interests at heart. Example: you are very cheap labor for your PI and he/she isn't itching to see you leave. This cuts both ways, remember that you might not be respecting someone else's need to look out for #1. Example: Your PI has duties besides being on-call for you 24/7.
Related Fact: When your PI says it's easy, it's probably hard. If he says it's doable, it'll probably consume all of your attention for as long as you want to work on it. Remember that you are missing years of experience on the person you're talking to.

Write up your research goals early and often, and set some timelines. I almost never make my own deadlines, and almost always find new other goals that I forgot. But you can get a long way by taking a step back and seeing the big picture in which you are swimming, rather than that one method that hasn't been working for a month. Stupid library preps...

All that is gold does not glitter, and all that glitters is not gold. Corollary: Not all new technology is what it claims to be. Stronger claim: It never is. Stay frosty.

When you are on a roll, rock it. There is no more scant resource then genuine excitement. Push it.

Tons of papers are wrong. Downright wrong. Sometimes scandalously wrong. It's embarrassing, and some of it represents systemic problems with peer review and that whole mess. You can moan about it for a long time (I did). Not sure if that's worth the bellyache, but I'll keep you posted.

Don't make second-hand goals that stake your success on the assessment of the Nature/Science/NEJM intelligentsia, or the ivy pillars of the academe.  Those gals and guys have their own little world, and it should come as no small surprise that the people in that club house aren't always all that fun to play with anyway.

Say something, or suck it up. I love to whine. It's a problem that I have. I'm still waiting for an example of when it has helped me. If you have problems with something that's going on in the lab, nip it in the bud and have a conversation. You might learn something, you might stop the problem, or you might at least feel better for having it off your chest. Otherwise suck it up.

The goal is knowledge. The goal is not a first author publication. Find the pleasure in solving the puzzles and exploring the science; it is its own joy. The other rewards may find their way to you somehow or another. Remember what you are building, and why you are building it. Remember your ideal.

Saturday, August 21, 2010

Words that I am getting sick of

This is a silly thing to write about, but the are some phrases I am getting tired of. Very tired.

  • X abrogates the activity of Y signaling - Seriously? Abrogates? Again? Biologists bring this one out at every opportunity, probably because they think it makes them look scholarly.
  • X is essential to our understanding of Y - It's usually not. It might help, but it's not essential.
  • Almost infinite - This one goes without saying. It's a lot, I get it. No need to go overboard
  • On the ground - You don't see this in science, but it's everywhere in the news. Mix it up, people.
That's all for now. Next time I see "abrogates" a paper is getting thrown across the room.

Tuesday, May 18, 2010

The Enzyme is NOT the Protein

In my previous post I emphasized that the map is not the territory. I took String Theory off the shelf, dusted it off a little, and then mercilessly beat it up for no good reason. That was all well and good, but I want to address a point about biology that I think we sometimes loose site of.

The enzyme is not the protein. More precisely, the enzymatic activity is not the protein. Really said most completely, the function is not the protein.

Really, I am attacking a map. It's a map many have seen. It looks something like this. Or even like this.

As biologists, we often want to identify a protein's function. We're sort of obsessed with it, I guess. If a protein is necessary to survive, presumably it does something in the cell that allows life to happen. Maybe it helps break down bad stuff, or build up good stuff. Maybe it replicates DNA. Maybe it guards against invaders somehow. Perhaps it's a messenger of some kind, 'transducing' signals through the cytoplasmic ether.

We're helped along by the fact that a lot of genes really do seem to have a particular task to which they are assigned. Hexokinase has a very specific enzymatic reaction that it appears to be dedicated to catalyzing. It lives for the service of catalysis. Our very understanding of genes is driven largely by the observation of mendelian inheritance of genes that break these rigidly defined and clearly necessary functions. Animals with defects in these sorts of genes often suffer most obviously from some metabolic dysfunction, and we assign the gene to the metabolic disfunction.

Now that we have moved past simple metabolism to much more murky phenotypes, we seem to still be tied to the idea of proteins as acting to fulfill a certain function. It's as though they are machines designed to act as some cog that a watchmaker planned to use. Some examples: p53 protects against tumors. It's a tumor suppressor. Hif is a hypoxia sensor. VEGF is an angiogenesis factor.

Why can't these proteins have hobbies? Let's remember that evolution pressures a cell to survive, not to be elegant. In as much as survival is elegant, I guess that gets the cell there. But in the end the thing we're talking about is the most complicated gamish of protein you could think of, and it will do just about anything to get by. Whose to say that VEGF, in its off hours, doesn't swing by the glycolytic cycle for a little regulatory interlude. Perhaps Hif, during lunch hours, cruises by the spliceosome for a little slice and dice. Even the 'housekeeping gene' and paragon enzyme GAPDH appears to spend lazy sundays in the nucleus, a horrifying prediction for the one protein one function minded.

Let us remember that's what really happens in the cell is a very very complicated mess of reactions. Once a day in some cell in the human body I'd guess that every possible protein interaction pairing can and does occur. There's no reason that the cell hasn't evolved to use some of those strange pairings to give it a little more juice towards the end of its endless quest for self replication.


Which is all just to say that a protein doesn't need an easy to pin down function to be very important for the cell. Nor does a transcript with a well defined function necessarily not have other very important roles.


Here is the question we should be most concerned with. In all the cartographic glory of drawing out these maps, have we missed something essential? I've argued above that we've probably missed the fact that some proteins act in different places, and again missed that some places might occasionally be occupied by different proteins. I would argue that this is more than a frivolous attack, it explains why our experiments are so difficult to replicate and real advances are only rarely driven by deduction alone. We've only just scratched the surface of the combinatorial possibilities.

Monday, May 17, 2010

The Map is NOT the Territory

I know very little about Alfred Korzybski, and even less about general semantics for which he is famous. I do, however, know his most famous quote: "The map is not the territory". So it is with complete academic ignorance that I co-opt the term for use in the world of biology. You've been warned.

Here's the idea, as I conceive it. You have a map. You have a model. You have a theory. Your theory is awesome, beautiful, exciting and entrancing. Let's say it's string-theory. Let's say it's relativity. Let's say it's evolution. Whatever.

This thing you have, this idea, it's a map. It's a guide to something. It's a flat piece of paper that represents and distills something about reality. It is not its own reality. It is not its own truth. It's serenity is not the same as the actual cold hard truth of the thing that it describes.

In the case of a map, like the kind you hang on your wall, this is obvious. No one is lining up troops to defend the borders on the map in the atlas on your coffee table. They are lining up to defend the real borders of the real states on the real rivers of the real earth.

But in the ivory tower there is a proneness to confusion. String theory, perhaps the best example I can think of, is lauded for its elegance and seeming brilliance. Few people could imagine an explanation for the complexity of quantum physics and relativity in a set of dimensions coiled down so small that they cannot be perceived at our scale of life. It is an impressive theory.

Where is the territory to go with it? String theory has yet to make a single testable prediction. Its details are so arcane that those who study it seem to inevitably be lost in its folded dimensions, content to treat the theory a platonic ideal to which the universe we live in might aspire to reach.



The map exists in service of those who live in the territory. Our theories exist in service of our abilities to make predictions and interact with our world. We draw Australia into our map because it helps us to make predictions about the consequences of certain actions (e.g. hey, I wonder what will happen if I sail South from Indonesia).

In Biology we are plagued by pseudo-predictive models. We spend a lot of time flailing around trying to come up with "mechanism" to explain our observations. We often find that we can come up with two or three. Sometimes we bother to test the predictions that our hypothetical mechanism would imply. Too much of the time the data show muddled and confusing support. We often pick and choose the experiments we want to perform that seem to bolster our point, and dig in for the academic fight over the arcana we've brought into the world.

In the end, the mechanism doesn't mater. The elegance of our theory doesn't matter. We can fight over the lines on the map until Armageddon, but what matters is whether we've done something positive in the real world. This should be completely obvious, but I am shocked at how quickly I am loosing touch with that simple fact. Keep your wits about you, and tuck Korzybski's saying in the back of your mind.

Sunday, April 18, 2010

Evolution and Financial Markets

I am way out of my league writing this post, but life is short and its fun to get ideas out there.

I was listening to one of those iTunesU podcasts about behavioral economics and I was moved to throw the following hypothesis out into the intrawebular ether. It's an explanatory hypothesis, and I can't figure out any useful predictions that it might make, but when has that ever stopped anyone before?

The idea is this: The boom and bust cycle of the markets is driven by an ingrained human tendency to barrel forward full bore when we and those around us have resources, and hoard resources when we and those around us have little. The key here is the social nature of the tendency, we don't just pay attention to our own resources, but also of the perception of the total resources available in the environment.

Furthermore, this tendency might be the result of evolutionary pressure. When the environment is perceived as resource rich, the most evolutionarily favorable strategy is to voraciously consume those resources rapidly. This has two benefits. First, it makes those resources available to an individual for making offspring. Second, it removes those resources from the pool, keeping them away from equally hungry competitors.

Biology has shown time and time again that this approach has consequences. In almost every species studied that I know of, permitting organisms to eat as much as they want shortens their lifespans and decreases their overall health. These animals are willing to make a sacrifice to be able to consume as much as possible and have the best chance of leaving the population with abundant offspring.

However this technique only works so long as the resources are present. When hard times come, animals convert to a different strategy, sometimes a radically different strategy. In C. elegans, for example, a relative starvation causes the worm to choose a completely different life cycle. The worm forms a 'Dauer' instead of an adult. This smaller form lives many fold longer, and waits until better times to spring into its adult form. When resources are scarce, survival beats out consumption.

And of course, humans are no exception. In good times, when resources are abundant, we are prone to consume those resources. Moreover, we are prone to turn into the voracious creature of our evolutionary history, making sacrifices for our future financial health to ensure we are not left behind in the rush. When time are hard, however, we throw a bit of a switch. We act much more cautiously, recognizing that surviving through to the next boom is our top priority. We are much more cautious with our investments, and put in the due diligence that was starkly absent in the good times.

I know I haven't really identified anything new here, but it was an idea that had never occurred to me. What does all this mean? My one conclusion would be that any large financial system, inasmuch as it tends to aggregate human perception, will be prone to the boom and bust. The deep psychological root of the human tendency (this is something that goes all the way down to worms, after all) means that it will happen again, and it there is probably little that we can do to stop it.

The Open Revolution

Read this: http://www.nytimes.com/2010/04/18/education/edlife/18open-t.html

The question raised most loudly, I think, is how educational institutions and the educational process should change in a world where educational materials are much much more freely available. Like everything else in the internet age, there are two fundamental things missing. The first of these is human contact. You know, the kind you get from actually sitting in the room with a group of fellow students working on the same thing. The second is a filter. How on earth do you find the good and reputable information in the vast sea of the internet. Who compiles a menu of course offerings that pull together the richest and most savory elements. After all, you could try reading wikipedia from a to z, but I don't know that would really be an education.

Finding a way to incorporate contact and filters into university education are challenges, but they are challenges that learners can solve independently. There's always meetup.com for finding a learning group, and online aggregate ratings can steer towards the good courses (if imperfectly). But there is one problem that fundamentally cannot be solved by a single person working to elevate their education on an individual level.

This problem is certification. Once you complete a course at a traditional university it gives you credit towards something called a degree. This degree is backed by the institution, and comes with a reputation that acts as a signal to people in the marketplace. As odd and unsavory as it may sound, the degree 'brands' you, and gives you the benefits (and sometimes detriments) that brand confers. There is nothing I can think of that allows an independent learner to acquire such a certifying brand. Institutions that acknowledge and certify learned skills are desperately needed if the open courseware revolution is going to take another leap forward.