Saccharomyces

Conference time

2006-10-09T10:05:00.000-04:00

Well, I just spent the past 5 days at a conference. I can only say it was amazing - the poster sessions were fantastic, many of the talks were great, and I got to meet a lot of new people, as well as some old acquaintances. Overall it was much calmer for me this time, perhaps because many people have moved on to doing mouse studies. Even though there was only one big yeast talk, there were still plenty of posters, and a lot of discussion between all the grad students and postdocs who are still using yeast to ask their questions.

Everybody gets something different out of conferences like these. One part of what I get is exposure to work that's not at all related to what I'm doing. In general, I'm not going to discuss any work that I saw here. However, one of the presenters did discuss some truly fascinating work that was recently published, "Reversal of Alzheimer's-like pathology and behavior in human APP transgenic mice by mutation of Asp664."

The researchers created mice that lack a caspase cleavage site within the intracellular domain of the APP protein. To quote their abstract, "whereas-amyloid production and plaque formation were unaltered, synapticloss, astrogliosis, dentate gyral atrophy, increased neuronalprecursor proliferation, and behavioral abnormalities were completelyprevented by a mutation at Asp-664." From their paper: "Our data lend support to a recently proposed model of AD, inwhich A binds to and oligomerizes APP, leadingto cleavage at Asp-664 and cytotoxicity."

If they're right, we've just witnessed a radical change in our understanding of how AD causes neuronal death. Pretty cool stuff.

Pithy sayings, part I

2006-10-02T07:21:00.000-04:00

Well, I've been informed that my post the other day was pretty disappointing, so I'm going to try again today. About 10 days ago, I presented at lab meeting. It went fairly well, but there was one long discussion about a particular set of experiments that I could do. To summarize briefly, I showed that under certain conditions, a particular protein can be turned on. For a read out, I used a GFP-tagged reporter protein and took some pretty pictures, and I also did some western blots. The results are completely unambiguous, but one of the postdocs proposed that I do FACS to quantify the changes.

Now it's possible, that FACS is the "right" experiment... although the only reason I even took pictures was because other people tend to like them. Personally, pretty pictures of cells generally don't do much for me, especially when the only message is "the level of this protein increased." Still, in retrospect, maybe FACS is the right way to go in these circumstances... if you haven't done any experiments yet. Thus, my first pithy saying: "The right experiment is the one you've already done."

That sounds terrible, and it doesn't mean that you can or should fit try and fit data into your model inappropriately - lots of time you do have to do a new type of experiment to answer a different question. In this case, FACS would be great if I wanted to know how many cells were expressing the protein, the distribution profile, or to really accurately quantify the level of expression. However, once you've already done two different types of experiment that prove your point, doing it a third way just because you can is pretty much a waste.

How time flies....

2006-09-30T08:25:00.000-04:00

when you're working away. I've been putting in a lot of time preparing for a conference next week, but I emailed off my poster yesterday, so hopefully I can pick it up Monday and I'll be good to go. If not, I guess I'll have other problems. This weekend I'm dragging my butt in both days to finish up some experiments, and I also have to write up my update for my thesis committee by Tuesday. Oh what fun it is to be a busy grad student. Anyway, I'm scheduling my departure for work around the bus, so I have a few minutes this morning.

This sort of continues my whining from my last post, but another grad student in the lab commented yesterday, in response to my complaints about things, that "I never go to beer hour or departmental gatherings", and that if I want things to change, I should "get involved." That kind of pissed me off, and here's why.

First, I always go to beer hour. I went Thursday, for that matter. Now, just because I could only stay for 20 minutes (I had to get back to lab to actually do work) doesn't mean I'm not "involved". And what does that even mean? For that matter, people at beer hour clique up on a lab-by-lab basis anyway. A few people - mainly administrators and those who share a common foreign language - do circulate, but it's pretty limited. Then there were a bunch of new PI's yesterday, and they were all cliqued up with the other PIs. So even if I didn't have work to do, what's the point? I see my lab every day, and I'm going to spend several entire days at a conference with them next week.

Secondly, the person who told me this is part of the departments "trainee" committee, which is made up of students and postdocs, and is supposed to enhance our training experience - ie, dealing with beer hour and retreats. I guess that if one wanted to be involved, one might want to be on this committee. So how does one become a member of this committee? Well, no one knows. It just showed up one day, announced by the head of the department. It may meet every week, or every month - who knows, because it's meetings aren't open to anyone. But there is a suggestion box for them in the hallway, how considerate. Does it have any power? Well, it organized this new retreat, but it apparently has trouble obtaining money for pizza at the seminars/beer hours. Having things organized this way is not conducive to any sort of involvement by others... and then you tell them to "get involved?"

Anyway, here's one example from my department of the new "involved" way to do things. Each year, the grad students get to choose a speaker to invite to give a seminar.
a) Several years ago: the administrators send out an email, inviting all the grad students to help choose a speaker. They bring a couple pizzas, they leave. The 10-15 people who show up talk, draw up a ranked list of names, and give it to the department.
b) This year: a blank sheet of paper was put next to the elevator so people could make nominations. Then people were asked to vote via email on the nominations.

Which way do you think is better to generate involvement?

Programs et al.

2006-09-18T21:56:00.000-04:00

It's been almost two weeks since my last post - my apologies to all. I've been deep in the midst of "the last experiment" for quite some time, and now I'm frantically making figures for lab meeting on Friday, while doing more "last" experiments. A few side projects are rearing up as well, so... quite busy. Still, I should post something, so here are some things I've been thinking about.

I had an interesting conversation about grad programs with a postdoc in my lab. MY program admits 60-80 people per year, but doesn't do interviews - admittance is based only on your application. I figured this was a perk of having a big program (if you only take 5 new students each year, you have to be more selective), but apparently UCSF and UCLA, also really big programs, do require interviews. Which leads to an interesting conclusion - if those people also applied to my program, but were rejected from schools that require interviews, then they'd have to come here - so my program actually selects for people who are a bit socially dysfunctional. It's probably a minor factor, as I doubt my program is the last resort for too many people, but funny.

Now, to retreats - retreat is considered a bad thing in some circles; people who want to retreat are denigrated as "cut and runners" and cowards. So why is it that people want to go on retreats (the relaxing with coworkers kind)? Shouldn't they be called something else? I missed the retreat for my grad program this past weekend, but that's okay - no one with a back like mine should be going on a three hour bus ride and coming back two days later.

That's the thing about retreats I don't get - why do they have to be so far away? My department is having a retreat in a few months, and maybe Newport doesn't seem far away to healthy people who drive all the time - but it's an hour and a half from work by car, and who knows how long by train. Not to mention that it's on a weekend, so how can it be pseudo-mandatory? How does that work for the injured, or the postdoc whose child is due that week, or people who would just rather do something more worthwhile with their time? It's sort of the basic problem with all these social events - they're planned out by extroverts who have lots of energy and time. Me, I woke up pretty early, and despite a rejuventaing breakfast of pumpkin waffles provided by catswym, I was still plenty tired when I staggered back home after a long day of lab - and if I get a day that I don't have to be in lab doing benchwork, why would I want to give that up to haul my butt hours away to hear talks? Plus, no matter how much time I spend in forced social situations, it's not going to change how people relate to me. I'm not going to bond by staying up all night drinking and playing poker, so how is "retreating" to another town going to do anything that having beer hour doesn't do?

They're watching you...

2006-09-07T07:29:00.000-04:00

An article appeared today in the Boston Globe about the operation of a cheap bus line to NYC - $15 one way. As you might expect, such a cheap line cuts corners on maintenance (a bus exploded on the side of a highway a while back) and safety (they speed). They go so fast, they're in trouble with the state and the feds. All in all, not something of interest to many people outside of Boston/NYC, right? However, nestled in amongst the story, we find this:

Using Mass. Pike entry and exit times from the company's electronic toll records, inspectors calculated that seven drivers were driving above the posted speed limit for two-thirds of the time. As a result, regulators fined the bus line almost $13,000 in May for speeding,

That's right, folks - electronic toll records are now being used to fine for speeding. Back when EZpass and the like were originally introduced, we were promised they'd never be used for any kind of fines or criminal investigations. Then we realized that using it to catch murderers wasn't so bad, was it? Or track kidnappers, clearly it's good to use it for that. For examples, see many Law and Order episodes from the late 1990's. And of course defendants could use it to create an alibi. But as far as I know, it's never been used for speeding violations before...

I imagine pretty soon there will be an auto accident, even on the goat-free roads of Massachusetts, and a clever prosecutor will subpoena the electronic toll records of the person who caused the crash. Oh look, they were speeding that night... and they speed on a regular basis. Clearly this driver has a reckless disregard for human life! Lock him up. Or perhaps local governments will realize that fining speeders is a great way to raise revenue - so just fine every registered owner of a car (with an EZpass transponder, of course) when you detect speeding. After all, they have cameras that fine you when you speed in the UK, so what's the difference?

United We Stand

2006-09-05T19:06:00.000-04:00

I noticed a pro-union poster on the T this morning, which reminded me about this post by Young Female Scientist. In it, YFS leads off with the question "What good is a union going to do for me?" I posted a reply, but it hasn't shown up yet, and I think it's an important question - what can a union do for postdocs? Here was my (slightly edited) reply:

"What could the union do for me?" After all, you're correct - mandatory 40-hr weeks or not working on the weekends are pretty useless! So here are things a union could push for:

1) Job security. Postdocs can be fired without cause and without notice, which pushes people to work harder and take less vacation time. In an ideal world, postdocs (after perhaps a 3 month probationary period) would be hired for ~2 year contracts, during which time they could only be fired for cause.
2) Vacations. See above. Everyone needs time to relax and recover, so why don't postdocs get vacation time like everyone else? If you have a good boss, you don't need specified vacation time, but some people probably do.
3) Paid maternity leave.
4) Increased availability of child care.
5) Conferences. One thing I've noticed is that how many conferences you go to vary a lot both by lab and by person. Every postdoc should have a yearly travel budget (probably about $1000-$2000), and perhaps an equipment budget as well. Most good fellowships provide this anyway, but lots of people don't get them.
6) Health care (tho I think we should go for universal health care, so...)
7) Disability/workers comp. Accidents happen. If you're injured at a construction site, no matter who's fault it is, you're entitled to workers compensation payments if you're unable to work anymore. Sure, the system gets abused sometimes, but injuries are a real problem... and accidents are just as likely to happen in a lab, though usually they are less serious. Still,if you get blinded or crippled by a lab accident, wouldn't it be nice to know that you're not going to starve to death as a result?

That's all I got for now. :)

Happy Birthday!

2006-09-04T18:27:00.000-04:00

To Chaucer, who one year ago today moved into both my home and my heart. Awww! Chaucer is seen pictured at left with his new birthday present, which he really loves (catswym picked it out). It also makes a perfect TV watching perch for a kitty!

And for those who just can't get enough of that wonderful pooka, check out Chaucer - The First Year.

Happy birthday, pook.

Thoughts from the Lazy Side

2006-09-03T09:47:00.000-04:00

This weekend, I'm being lazy and not going in to lab. There are justifications for being lazy - it's Labor Day weekend, I have work I could be doing from home, and I don't want to push myself into having more back pain or sleeping problems. Still... I feel bad about being lazy. Guilt stalks me while I doze in bed during the day - surely I should be getting up and doing something? But the last time I listened to those feelings, the gnawing feelings that tell me to go to lab, and do something worthwhile, it was quite a mistake. I pushed myself too hard, and it took me about a week to recover.

But what's the worth of staying home? Maybe I'll get some writing and data analysis done. I have a lab meeting in three weeks, a conference in five weeks, and my thesis committee meeting in six weeks. Or maybe I should be relaxing - after this weekend, I'll have to go in every weekend for at least several weeks. Should I go to work on Monday and get an early start on my westerns? Or take the time to rest up some more? I don't know - I'm torn, riven by feelings that I'm being lazy, but worried that I'm not lazy enough. If I do go in, I'll have to go in for a full day - and can I do that, and still be focused enough to make it worthwhile, on a "holiday"? Will staying home just worry me to death?

Sigh.

In other news, I live pretty far out from the center of town/work - not quite in the suburbs, but reasonably close to the edge. I also live near to a major intermodal transportation hub (MITH), though all the trains pretty much shut down by 12-1am. There's a bit of shopping there, some eateries and bars, a drug store, a dunkin donuts, and super market. Oddly, it's the only 24-hr dunkin donuts I know of, has one of the few 24-hr drug stores, and is now joined by a 24-hr supermarket. I think my MITH is thus probably the most active place in the entire metro area between the hours of 2-5am. Isn't that odd?

Despite their spiffy hours, neither the supermarket or the drug store sells tumeric in pill form. Isn't that odd? They sell all sorts of various and sundries vitamins, oils, and even stuff like St. John's wort that's basically a placebo, but not something that's under active study as an anti-inflammatory and anti-cancer agent. Weird, huh? Anyway, the local nutraceutical store carried it. I'd never been in there before - it's kind of weird and smells funny. Tumeric is sold under the "liver support" section, which is odd - the evidence for any role in helping liver diseases are pretty sketchy at best, while the evidence for things like preventing colon cancer and alzheimers are based in at least some medical data. Anyway, my back has definitely felt better since I've started taking it, though I'm still taking some Aleve as well. Maybe next week I'll try cutting back on the Aleve.

Pedantic people

2006-08-31T07:15:00.000-04:00

pedantic: Characterized by a narrow, often ostentatious concern for book learning and formal rules: a pedantic attention to details.

One of the more annoying yet sometimes enlightening things about blogs is the pedantic attention to details paid by many blog writers and commenters. Sometimes, this attention to detail serves to enlighten everyone. More often though, it really just serves to distract and confuse the initial point. I'm going to provide one example of each kind of behavior that I've seen recently.

Enlightening behavior:
In my last post on Elevators and Polls, I mixed units - I compared the change in potential energy from climbing one floor (300J) to the electric consumption rate of an elevator rising one floor (350W). Commenter Colst caught me out, so bravo to him. To sort of sum up the conclusion, an elevator climbs one floor (10 ft) in 2-3 seconds, using 350W, leading to an energy expenditure of about 1000J. A person climbing expends energy at rate of about 200W. So, if a person takes more than 5 seconds to climb a flight of stairs, the elevator is more efficient. The taller the floors (and the building), the more efficient the elevator will become. That doesn't take into account that fueling a person (growing food, transporting it, eating it) is less efficient than powering an electric motor.

Ridiculous behavior
Over at ScienceBlogs, Carl Zimmer wrote a post attacking an opinion piece about climate change. Quite frankly, I consider it a pretty silly piece, but it's an opinion piece, not a scientific article. However, Zimmer spends him time attacking the piece over a misspelling/"non-word".

Some rare plant and animal species, hyper-adapted to highly specific climate conditions or micobiotic zones, are already unable to cope with the change.

As I commented, people make spelling mistakes all the time. Sometimes the editors don't catch them, and they even get into printed books. Attacking people for spelling mistakes is the not only exhibiting exceedingly pedantic behavior, it's the worst form of attack - one that says an argument is not worth considering because the writer didn't catch a spelling error. While an effective rhetorical device, it's basically saying that "ooo, your spell checker didn't catch a mistake, so you must be a moron."

The entire point of language is to convey an idea - and if, as Zimmer did, you already made the leap from "micobiotic" to the presumably correct word "microbiotic", you should be able to figure out the meaning in this context. To suggest that one would accidentally assume the alternative definition (a collective genome of a set of microorganisms, ie, the human microbiome - the genomes of all our intestinal flora) is ridiculous. In conclusion, if you spend a whole blog post attacking a misspelling in a crappy opinion piece... you just might be pedantic.

Elevators and polls

2006-08-28T07:09:00.000-04:00

At work last week, a sign went up next to the elevator: "Take the stairs... for your health, for the environment." Now, normally, I'm okay with taking the stairs - living on the 5th floor of a dorm with no elevator for four years of college will do that to you. However... this sign was on the 9th floor. Not to mention that science buildings have much bigger floors than college dorms. In college, each floor occupied 10 vertical feet - the building I'm in takes up closer to 15. And for your health? While the postdocs were apparently circulating emails about knees and joints wearing out, I just don't think the human body was designed for climbing that many stairs. Perhaps more critically though, how much energy does an elevator really use? The national park service says "The average office elevator consumes 350 watts of electricity to travel from one floor to the next." The change in potential energy for me to climb 10 feet is about 300 J. An elevator is thus pretty efficient... and probably more efficient than the human body is at converting food energy to power the same journey.

Still, it got me wondering how many stairs are people really willing to walk up? So I looked up what the pre-elevator height of buildings was - turns out it was almost universally five stories, with occasionally one or two extra floors of storage.

Anyway, on to polls... something that made the rounds last week (including on Cosmic Variance) was a poll on belief in evolution (conducted by, or at least published by, Science.)

In surveys conducted in 2005, people in the United States and 32 European countries were asked whether to respond "true," "false" or "not sure" to this statement: "Human beings, as we know them, developed from earlier species of animals."

As pollsters (and those who follow the science of polling) know, you can get most any answer you want out of a poll if you design the question correctly. The most ridiculous part of the whole thing to my mind is this comment, that "individuals who hold a strong belief in a personal God and who pray frequently were significantly less likely to view evolution as probably or definitely true." Well duh! If you get a high positive correlation like this in a poll, you have to wonder if your question was simply polling for religious belief in the first place.

Autopilot

2006-08-22T07:29:00.000-04:00

I'm busy and exhausted - well, not so exhausted right now, because I just had a good sleep, but I'm definitely getting less rest than I need. This was definitely on display yesterday - I had to keep checking and rechecking what I was doing, because my attention kept wandering while I was working. If I'm lucky, I put my western blots in the right antibodies and set up my PCRs correctly.

Which leads me to what I try and teach my undergrads (and myself). Over the years, I've taken home two lessons from watching the tv show ER. The first is the methodology of teaching: "see one, do one, teach one." When I do a protocol with an undergrad, I usually set up enough samples so I can do one and they can do the rest. And, when possible, I have the undergrads teach each other protocols, because I think you really do understand it better once you've taught someone else. Generally, it seems to work out pretty well.

The second thing I learned from ER is: do it the same way every time. There are good science reasons to do this (eliminate variability, etc). However, the reason the tv doctors of County General do it the same way every time is because when you're distracted by something else, or even just plain tired, you won't have to think about what you're doing - you'll do it the right way by reflex.

I haven't had much success training anyone to understand this, but as I discovered while staring off in to space yesterday as my PCR reaction assembled itself, it's true. I'm not 100% sure I did everything the right way- I won't be until I develop my blots and run out my PCRs on a gel. But, if I did, it was all by reflex.

Why can't we bring liquids on a plane?

2006-08-19T08:20:00.000-04:00

Everyone knows about the recent terrorism arrests in Great Britain, which is why we can no longer bring liquids on planes. The inconvenience is often described as a necessary hardship, while others deride the security searches as ineffective - for instance, this week on the Daily Show, Jon Stewart showed a clip from CNN of a reporter successfully hiding a bag of water in his crotch. But is flying without liquids a necessity? Can you even make an explosion by mixing two liquids together?

I had no doubt on this score, until I read this article on "Flying Toilet Terror Labs". The Register is always a bit heavy on the snark but often fairly accurate, and they decided to investigate if the plot was feasible. The Register "asked University of Rhode Island Chemistry Professor Jimmie C. Oxley, who has actual, practical experience with TATP... and she told us that merely dumping the precursors together would create "a violent reaction," but not a detonation." The entire post is worth reading, but here's the basic summary on what the terrorists would need to do after getting their liquids on the plane:

Once the plane is over the ocean, very discreetly bring all of your gear into the toilet. You might need to make several trips to avoid drawing attention. Once your kit is in place, put a beaker containing the peroxide / acetone mixture into the ice water bath (Champagne bucket), and start adding the acid, drop by drop, while stirring constantly. Watch the reaction temperature carefully. The mixture will heat, and if it gets too hot, you'll end up with a weak explosive. In fact, if it gets really hot, you'll get a premature explosion possibly sufficient to kill you, but probably no one else.

After a few hours - assuming, by some miracle, that the fumes haven't overcome you or alerted passengers or the flight crew to your activities - you'll have a quantity of TATP with which to carry out your mission. Now all you need to do is dry it for an hour or two.
The genius of this scheme is that TATP is relatively easy to detonate. But you must make enough of it to crash the plane, and you must make it with care to assure potency. One needs quality stuff to commit "mass murder on an unimaginable scale," as Deputy Police Commissioner Paul Stephenson put it. While it's true that a slapdash concoction will explode, it's unlikely to do more than blow out a few windows.

To summarize the point briefly, even if terrorists did get chemicals onto a plane, it's unlikely that they could manufacture explosives in flight. I'm not a chemist, but I find this article fairly persuasive - one thing I learned while making Ferrocene in chemistry lab is that making compounds of any sort is usually a fairly delicate and time-consuming procedure. I can't say there aren't other binary compounds that would explode when mixed, but the whole thing clearly isn't as easy as the media has presented.

Oh, and sorting out milk and soda from acetone? Several companies make scanners that will do just that, using X-rays or microwaves. Airports just aren't equipped with them due to money issues - it seems that despite knowing about such plots since 1994, it's not really a high priority... perhaps because the bathroom lab idea is so impractical. So, why can't we bring liquids on a plane?

Of carnivals, colds and catfights

2006-08-17T07:16:00.000-04:00

I intended to post several days ago, but work and the general lack of energy caused by back pain have distracted me. Today's post will therefore be a medley of several different topics.

First off, I had intended to submit to a grad student carnival. I've never done that before, both because I don't blog on an existing "topic," and because I thought of carnivals as somewhat stupid. Alas, this time I was the stupid person, because I missed the submission deadline. A lot of other grad student blogs that I thought would have been represented didn't show up either, and many of the posts were kind of old... and about topics that I don't really care about. Plus, how could it miss this incredible lab story that catswym found?

In other news, yesterday at work I sit down for lab meeting, and another grad student walks in. We exchange pleasantness, and she tells me she has a really bad cold... and then she sits down next to me! Then she gets very unpleasant and argumentative when I ask her to sit further away from me. Interestingly, I've told this story to two people - one thought the other grad student was "in the wrong", while one thought I was the one being ridiculous.

Finally... as seen on the Colbert Report, you should all check out Kittenwar, where the cutest kittens battle it out for supremacy.

Undergrads

2006-08-13T08:37:00.000-04:00

I was going to post on an entirely different topic today, but I just saw this truly bizarre post over at Adventures in Ethics and Science. In it, Dr. Freeride explains about a situation that someone asked her for advice about.

You're an undergraduate who has landed an internship in a lab that does research in the field you're hoping to pursue in graduate school. As so often happens in these situations, you're assigned to assist an advanced graduate student who is gearing up to write a dissertation. First assignment: hit the library and write a literature review of the relevant background literature for the research project. You find articles. You read. You summarize and evaluate and analyze, over the course of many pages.

What you write is good. Not only is it praised, but it is incorporated -- in some cases, word for word -- into the chapter the grad student is writing.

Dr. Freeride expounds upon the plagiarism aspects of the situation, but I think the whole situation is bizarre. Over the past few years, I've worked with four undergrads and one high school student. They were all quite bright, although with varying levels of dedication of skill. I think most of them, if asked to do a literature review, could probably come up with something usable. But, why would I use it for anything? Why would I even ask them to do it?

First of all, just as my boss has a more comprehensive knowledge of the literature in my field than I do, I have a better understanding of the literature in my little corner of it than any of my undergrads. That's simply a matter of time - I've been working, reading and thinking on this subject 50+ hours per week for a number of years. By the time I actually write my thesis, I'll probably have written about the subject a dozen times - for posters, papers, thesis committees, and training grant updates. Even if I had my undergrads write something up (and many of the ones I've worked with have or will write an undergrad thesis), I can almost certainly do a better and more comprehensive job in fairly short order.

Secondly though - undergrads don't come to a bio lab in order to do literature research. Sure, they may read some papers for background or protocols, but the point is to get their hands dirty... and free up your hands. Of course, it often doesn't work that way, because undergrads also need a lot of training. Sometimes, it's a net win, especially if you teach them something that has to be done over and over. Sometimes it's helpful because they can do things you can't, because you have a busted back. On the other side, sometimes it's a net loss, because they need tons of help just to pour an agarose gel. Either way - writing a literature review for someone else's thesis? So not a good use of undergrad time, and I can't think of a better way to bore a new student to tears.

In google veritas

2006-08-06T11:00:00.000-04:00

... or, why not to trust blogs.

There's a saying in the open-source software world that "many eyes makes all bugs shallow" - the more people who can inspect the code, the more errors will be found. A similar theory drives wikipedia, where anyone can expand or correct an entry. In the world of scientific publishing, peer review achieves a similar goal of weeding out obvious flaws or errors in a paper prior to publication.

On the other hand, blogs have no peer review, and little capacity for error correction. If someone posts an erroneous technical fact on their blog, the odds of it being caught are low - it has to been seen by someone who notices the error and takes the time to comment. Moreover, many bloggers may not correct the original error, and will instead make a comment or post a separate entry with the correction. Alternatively, a theory or idea in a post may be the subject of vigorous discussion and debate, hidden away in the comments. Both of these scenarios serve to pollute future google searches, and spread erroneous facts or hype theories that are sketchy at best.

I started thinking about this last night after reading two ScienceBlog posts. The first offered a brief review of the different types of RNA. In it, Alex mentions that "miRNAs... are used by RNAi and the RISC machinery to inhibit mRNA transcription." Now, I'm definitely not an RNA scientist - but I did recently read a rather fascinating article, "Relief of microRNA-mediated translational repression in human cells subjected to stress." A small amount of googling confirmed that this the general mechanism by which miRNA works - "the annealing of the miRNA to the mRNA then inhibits protein translation, but sometimes facilitates cleavage of the mRNA." It's a small thing in the big picture - but I'm sure similar mistakes occur every day.

The other post I saw was this one about the role of Toxoplasma in human culture. It's an interesting subject, and discusses a recent PNAS paper. However, at the end of the post, the Razib links to one of his previous posts on "genius germs." In this post, Razib posits that microbes affect human intelligence, and puports to discover "a strong winter-spring birth seasonality effect on "genius," which I take to reflect early infection." He furthermore proposes that improvements in hygiene have led to a decrease in the number of geniuses. Now, there is indeed a well-known correlation between what month you are born in and what diseases you are likely to get... but this theory is pretty out there.

Now, the commenters on this post do a good job of tearing Razib's thesis to shreds. To summarize, the winter-spring difference in diseases is also very likely to reflect different environmental/nutrition conditions. One obvious correlation is that babies born in February/March were raised by mothers who conceived during the preceding summer, and studies have shown increased birthweight for mothers exposed to increased sunlight in first trimester. On average, high birthweight directly correlates with increased IQ. Furthermore, some of the diseases shown (such as schizophrenia) may be related to vitamin D deficiency... which is especially likely to occur during winter months. None of these points say that infection couldn't be playing a role - but there's no evidence.

The part of the commentary I liked best was by Hyperbole, who had this to say about the so-called decline in the birth rate of "geniuses"...

Genius as you define it depends on historical circumstance, whereas bacteria can only affect a person's physical brain, right? Yet your method of identifying geniuses is consulting a book written by an old pompous man who is obsessed with western decline. In that book, a genius is determined by how influential a person has been.

It follows almost necessarily that people earlier in history will have more of a chance to be influential. It takes 4 years of undergrad to reach the pinnacle of mathematics as it stood at the end of the 19th century. It takes highschool to learn it up to the beginning of the 18th century. It takes 9th grade to learn it up to the beginning of the 16th century to the time of the greeks.

It takes 4 years of grad school to be able to meaningfully contribute to mathematics.

How can you compare mathematicians today to those of the past based on your rubric and then use that to claim that there are fewer geniuses now than before? The complexity, depth, and abstraction in mathematics has increased so much that any comparison along those lines is absurd....

I believe that the per capita rate of genius has INCREASED, and you can clearly see it by looking around. I would contend that almost every single fields medal winner ever, is on the level of any of the 8 decile or higher mathematicians. I would contend that Richard Feynmann, Murray Gellman, Stephen Hawking, Paul Dirac, heisenberg, bohr, etc are all up there, and it is a known fact that chess players are getting better and better, younger and younger.

So, I think your theory has a hole in it, since genius has not changed. And you cannot fall back on the "influence" definition of genius, because that clearly is dependent on time period. All you have is a statistical anomaly (maybe, if birthrates by season in those time periods weren't as skewed as we think) that has a dozen or so possible explanations, one of which is really cool and counterintuitive, but which is contradicted by evidence from the 20th century.

A pretty good rebuttal of the idea that infection is necessary to "genius", whatever that is. Yet, if someone interested in the field googles for "birth month infection," they'll find Razib's post... and likely not read the comments. I suppose there's no real solution for this - but when discussing science, bloggers should be careful not to introduce errors, or introduce wacky new theories without appropriate disclaimers.

Leaving the nest

2006-08-04T07:15:00.000-04:00

It was hot yesterday. How hot was it? So hot that some schools had to turn off A/C to various offices so they could divert A/C to the lab areas. Isn't it great to work in a lab? It was even hotter than Chaucer, who is pretty darn hot indeed.

Today's subject is the increasing prevalence of people moving back in with their parents after college... but first, you should all check out the blog of Everything Girl. It's a quite an interesting window into what life is like in a small town... not to mention the challenge of balancing grad school with being a parent.

Enough about that though... let's talk about babies. No, not toddler babies, I'm talking about the young adults discussed in Wednesday's Metro [pdf- page 12 and 14]. For those who don't want to wade through the pdf, page 12 discusses the phenomenon of parents who just can't let go of their children during college.

WestConn student Chris Wallace, 20, whose parents were founding members of the school's parents association, says he learned to navigate school on his own. But when the East Haven resident arrived at school as a freshman, his parents were there beside him. For two years, the Wallaces met jointly with Chris' academic adviser to go over his course load...
For the first time, Wallace chose his own courses for the coming semester. He's enrolled in German, a choice his father questioned, but, "We compromise now."

Now, I'm sure that everyone interacts with their parents in different ways, and certainly parents are almost always going to expect to have input into decisions about what courses to take, and what to major in. But... in large part, being in college is all about learning to be independent. Generally, unless you're living at home, you have to be independent in minor ways - cooking, laundry, etc. On a larger scale though, you have to decide what you want to do with your life - and even if you're lucky enough to have your parents pay for some or all of your education, it's not their life. There shouldn't be a "compromise," because what classes you take is not their choice.

There's another concern about parents who don't want to let go...

Brennan [director of admissions] is concerned children of hyper-involved parents are at a serious disadvantage when they leave the nest. After 18 years with mom and dad hovering inches away, she believes students fail to develop basic safety skills, study and sleeping habits, negotiation skills, sharing skills and self reliance.
"If you have a parent who has done all that, who is going to do that? Nobody," she said.

From personal experience, I can say that's absolutely true. Fortunately, I went to college at a place where I think a lot of students come from "involved" families, where they didn't develop these basic skills, and there was a lot of support. From the first day of orientation, our parents were cut out as much as possible - they were deliberately excluded from campus, and told to come back in two weeks to help us move into our dorms. Our entire freshman year was pass/no record, removing a decent amount of the pressure of adjusting to independent living (and taking really hard classes). Our parents were also never given our grades - it was completely up to me to tell mom and dad how I did.

Moving past college though... the next article, on page 14, is about people who move back in with their parents after college.

Experts call them "boomerang kids" and estimate that between 48 and 66 percent of 2006 college grads are planning to shoot back home this year. But new studies show, boomerang kids aren't just moving back home in higher numbers - they're staying there for a couple of years. Among last year's graduates, four in 10 are still living with their parents.

I certainly think there are a variety of circumstances in which it's normal to move back in with your parents. Health problems, being unable to find a job, or coming straight out of college without money to rent an apartment are all fine reasons. However... once one gets a job that can pay the rent, the normal thing to do is move out.

Now though, we have one 25 year old student living with his parents even though he "makes about $35,000 a year plus commissions." Of course, when he's not out on a "jet boat," I'm sure he's making good progress on "saving up for a place of [his] own." For some reason, I guess his parents, with a "million dollar waterfront home," don't want to help him out with the downpayment. Surprisingly, they prefer that he spend his time mowing the lawn and helping with home improvements, while his sister, a teacher, does laundry and cooking.

Despite the financial arguments, I wouldn't be surprised to learn that those who do live with their parents wind up doing worse overall. When you have such a giant safety net, I bet financial planning skills - as well as all the other things you learn and experience making it on your own- fall by the wayside. Also, I've met a few people around my age who live with their parents, and they all tend to live way out in the suburbs. That really imposes a cost, not only in terms of commute time, but also in limiting one's ability to socialize.

Of course, maybe I'm wrong - maybe the overachieving "Millennials" will do just fine not moving out until they're pretty old. However, if I ever do have kids, they're getting a healthy shove out the door after college - even if a free handyman, chef or maid would be nice to have around.

Inconsiderate morons

2006-08-02T07:20:00.000-04:00

No, no stories from lab today. :) Discretion is sometimes the better part of valor... and I've done my fair share of inconsiderate and/or just plain dumb things in lab. No, today I'd just like to complain about the riders on the shuttle bus I take to work. Pretty much every morning, the bus is standing room only. Yesterday, I'm the last person to get on the bus, and it's pretty much packed. The driver tells me to get behind the yellow line, and then starts the bus.

Of course, the bus isn't really packed... it's just that the people who ride it are too retarded to realize that they need to move in to the center of the bus. So, when I asked the women in front of me to move in, they shrug and say there's no room. Which is not really acceptable, since if I'm not well braced, I'm going to wrench my back. Thus I had to shove between them (earning myself some particularly nasty looks), shove between the next pair of people, and so on, before getting to the center of the bus where there was plenty of room.

Now, the placement of handholds on the shuttle bus kind of sucks. The bar at the top of the bus is placed at exactly the right height for me, and at 5 ft 9, at least half of the people in the city should be shorter than I. Thus, I do have some sympathy for the short people who stand right at the front, where there actually handrails. That said... at least two of the people at the front were guys who were quite a bit taller than me. Not only did they block other people (including myself) from getting past them, but they also were sitting on the low-level handrails, preventing anyone who actually needed them from using them. How rude!

Well, time to once again take the shuttle. It's going to be a bazillion degrees in the northeast today, so stay cool!

More on why we work so hard

2006-08-01T07:10:00.000-04:00

Just a few more thoughts on working so hard.

I used to work a much more business-like schedule back when I was second/third year student - pretty much 9-5, Monday-Friday. I was sort of searching for a project, trying a lot of different things without most of them turning into anything. Eventually, one panned out and I put in a lot more time to get that project in motion. I was able to relax again after that for a little while, but I've been working full-tilt for several months on some new projects. In some respects, I feel guilty about it - I generally like the work, but I think I'm setting a bad example for the younger students, who (IMO) don't need to be putting in super long days at this stage. To each their own, I guess, but I definitely feel a little guilty to be contributing to the culture of overwork.

I realized yesterday that my previous post on why we work could be expanded just a little bit to mention the subject of clothing. One of the wonderful things about science jobs is that, for the most part, there's no dress code. Well, okay, so we're not supposed to wear open-toed sandals in lab - but I only wear sneakers anyway!

Dressing up on the rare occasion isn't that bad. Weddings and funerals... well, you're dressing up to show your support for someone else, so it's ok. But I just couldn't do it on a regular basis, especially when it's at all warm out. Walk around in a suit and tie all day? They may make an anti-perspirant strong enough to keep me from sweating up a storm, but I haven't heard of it. I pity the poor people wearing suits and ties on their way to work today especially - it's supposed to be super hot here.

I also really resent being forced to dress up. Nobody tells you to dress up for a wedding, you just know you should, and there's usually plenty of time to plan ahead. But there are no rules for various conferences, dinners, etc - so I tend to get really mad when someone says "no jeans." Maybe most people have a closet full of slacks and dress shirts, but I don't. If I was that type of person... well, I'd likely be working a different kind of job.

The last time this situation came up, and I thought about getting a pair of khakis, catswym said that at least I could wear the same pants to postdoc interviews. It had honestly never occurred to me that I would dress up for a postdoc interview, which is weird. I mean, I've dressed up for job interviews before. It just feels different - in a job interview right out of college, you're trying to get them to pay you money for a job that probably a lot of other people could do. As a postdoc, it seems different - while you want to get paid, you're really offering your PI your brain, trained hands, and a unique perspective on the world. You shouldn't have to dress to impress... but the world being what it is, maybe you do.

Why we work (so hard, and at all)

2006-07-30T08:40:00.000-04:00

There was a lot of discussion this week on why scientists work so hard - a continuation of discussion that I commented on last week, with respect to mixing academia and family. Some posts on the subject can be found here, here, here, and here. I'd like to offer my own thoughts on both the technical reasons scientists work so hard, and why they do science at all.

Technically speaking, 40 hours a week in lab is definitely enough to do valuable work. I had the privilege of working for a short time with one of the best organized postdocs ever, and she managed to get an incredible amount of work done in 40 hours a week, because she wanted to spend time with her daughters. Now as kstrna points out, people in lab who are there for more time (80 hours a week) spend a lot of time not being productive. Personally, I generally work the entire time I'm in lab - but physically, I'm beat after 9 or 10 hours a day.

Which brings me to my first point about why scientists spend so much time in lab. While some scientists, especially in fields like chemistry and physics, are limited by the equipment they have access to, this is not typically a big problem in molecular biology. Most of the work I do is essentially unlimited by external resources - only by the number of hands you have and the number of hours you can spend in lab control the amount of work you can do. Nitpickers will say that antibodies and primers and media all cost money, and they do - but the most expensive part of many yeast experiments is making a new strain, which really only requires some yeast media, a few primers and Taq.

There is thus a big incentive to fit as many experiments into your schedule as you can handle. Most experiments/tasks require some amount of setup time, followed by waiting - often overnight, but often for two-three days. This means that an additional hour or two in lab usually lets you get a lot of extra things done - in an hour, I can do something to further a western blots, set up a PCR, run an agarose gel, order primers, and still have time to streak out some yeast - all of which will let me get that much more done tomorrow or the day after. Just a little bit of extra time in lab can thus be very productive.

The long lag time in biology experiments also lends itself to long hours- if my cells need to be split today, and I don't split them, I could be set back a week, so I might wind up staying late. If I set something up Wednesday that needs to be dealt with on Saturday, I need to come in on Saturday, or not start my experiment until the next week. That doesn't even count the experiments that need to be tended to every day. Finally, lots of things biologists do require live cultures - so popping into lab on Sunday to start some cultures that can be dealt with Monday is quite common... and pretty soon you're in lab every day.

That concludes my discussion of the technical reasons scientists tend to work hard. Switching tracks slightly, I'd like to discuss why people do science. There's a mistake a lot of people make about scientists, and that's why they choose a career. Despite what a lot of people (especially advocates of a flat tax) think, scientists don't generally choose to become scientists for the money. Despite what Alex says, the money isn't bad - but anyone who just cares about becoming rich will become a lawyer, or get an MBA. So why do people want to do science? I think some people get a thrill out of discovering new things, and learning more about how things (the universe, or a cell) work. Some people like the logical puzzles that are often encountered in research, and enjoy the process of solving them. Some people have personal reasons in their past - a friend or relative who died from a disease. I'm sure everyone has their own set of reasons.

As for my reasons? I enjoy the process of learning new things, working through problems, and I get a thrill out of discovering something that no one else has learned before. Those are my personal reasons to love doing science. In the larger picture though, that's not why the NIH gets so much money. The public funds astronomy and pure physics research far less than it funds the NIH. The reason the NIH is so well-funded is not just to learn about the world- basically we're buying the cure for cancer, and many other diseases, on a layaway plan. Lots of research in basic biology not directly on topic gets funded - for instance research on various model organisms such as yeast - but the goal of all of this research is to get a grasp on how things work in humans... and to learn how to fix us when we break.

Now, we're certainly not there yet - the more we things we know about how biology works, the more basic mechanisms we discover. Still, at some point in the future, maybe in 10 years or a 100 years, or maybe not for a 1000 years, a scientist will be sitting in a conference hall listening to another scientist talk about some new data. That scientist will realize that he or she now finally knows enough about basic biology to stop cancer, cardiovascular disease, or HIV. I don't know how he'll react - I suspect I might cry. This doesn't apply to most researchers outside the biology/chemistry field, of course - but when everything else is said and done, that's why we work.

Academia and a family

2006-07-24T22:20:00.000-04:00

I've been reading a number of posts lately about the conflict between having "a life" and working in academia. Especially in biology, it seems everyone is usually really busy - too busy even to exercise. More interestingly, a number of people on ScienceBlogs have been writing about the conflict between academia and having a family - most specifically from the perspective of women having kids, but somewhat from the male perspective as well. Alex has a summary up with links to the various blogs discussing the subject.

Dr. Freeride has several interesting things to say, and she has what seems to be the prevailing perception among those posting: the idea that in an academic setting, those who choose to have children are seen as less dedicated researchers.

My sense this is even more true for women in fields that are still largely male-dominated; you want people to notice your great research or teaching, not to think to themselves, "See, she's not sufficiently committed to the field, or she wouldn't even be thinking of taking time away from it for something as mundane as childrearing! We were better off before we started wasting our program on these women."

Dr. Freeride also relates the tale of three talented and promising young female faculty members in her department who had children, and who subsequently were denied tenure. In fact, "as far as anyone had been able to ascertain, this university had never granted tenure to a woman who already had children."

Now, I don't think that most people, at least in the biological sciences, view those who choose to start as family as less dedicated researchers. If anything, I think biologists tend to understand the biological facts of life pretty well. There are some perks to having a family while in academia too - while salaries and the availability of child day care can always stand improvement, nothing beats an academic schedule in terms of flexibility. Most universities nowadays stop the tenure clock for a year for women who have a child, and some even offer this flexibility to men as well.

That said, no one in this discussion seems to have stated the obvious - anyone who has a family is at a disadvantage in the race for publications, grants, and tenure. It's really just a question of time and attention - children need to be played with, fed, taken to the doctor. Clothes need to be purchased, schools need to be arranged, and older children may need help with homework. Not to mention of course parent-teacher conferences, school plays, trips to parks, soccer practice, violin lessons and family vacations.

When you have a family, they need to come first - and that means that both men and women parents, particularly of young children, are going to be spending less time in lab. Parents will almost certainly spend additional time thinking about their children, and less time thinking about science. For a variety of reasons, the obligations of family/child care typically fall more heavily on women, and this is something that can and should be corrected. Still, even if parental burdens are more evenly shared, raising children is still a lot of work - and those who don't have to stay up all night taking care of a sick child are probably going to have substantially more energy for lab work in the morning.

Health courts?

2006-07-22T17:48:00.000-04:00

I was reading the Flea recently, and saw that he had linked to a medical malpractice blog. Now, since I'm interested in medicine, and the law in general, I followed along. Most liberal sites that I read tend to be against the reform of medical practice - after all, capping jury awards is most likely to hurt people who have valid cases against their doctors! Medical malpractice rates have also stopped rising in recent years. Still, I was interested to read what a doctor might have to say.

They had quite the number of posts about the idea of "health courts," which are strongly promoted by a group called Common Good. The idea is fairly simple - pull medical malpractice cases out of the traditional jury system, and let them be decided by judges with special health training. Awards would be pre-set based on the severity of the injury, and medical experts in each field would be hired by the court, not by the doctors or the patients. Patients wouldn't have to wait very long to receive compensation either, as trials would be relatively rapid, and lawyers would get paid less.

It sounds like an attractive idea - but the "Common Good" website looked a little too slick to me, so I started thinking. A study reported on last year showed that "85 percent of cases were settled out of court, and plaintiffs lost four-fifths of those that did go to trial." The reasons are relatively obvious - faced with a legitimate injury, it's in the best interest of an insurance company to settle before facing a jury that might award far more money. Those cases that don't settle are thus much more likely to be frivolous. The system is far from perfect, though - while very few uninjured people receive money, the study found that only about "73 percent of plaintiffs whose claims had merit received compensation."

So who is financing the "Common Good" website and legislative agenda? Well, it's a non-profit group, so it's hard to find out exactly where their donations come from. That said, this article states that "The health-court system was the brainchild of corporate attorney Philip K. Howard of the law firm Covington & Burling. Howard says the concept blossomed out of a series of forums held with the Brookings Institution and the American Enterprise Institute, centrist and conservative Washington think tanks, respectively." Of course those on the left call the Brookings Institute " a right-wing, neoliberal, anti-regulation organization." As exhibit B, the Common Good advisory board, while including Bill Bradley, also includes Tom Kean and Newt Gingrich. We report, you decide.

Let first assume that this court system is set up fairly, with reasonable (though not generous) awards to victims of malpractice. So... who benefits? Clearly, those actually injured (perhaps 15-25% of people) who previously would not have received any money, will substantially benefit. However, lets think about those 85% of cases that settle out of court - the insurers are now paying quite a bit of money to keep those cases out of court. Perhaps the injuries are truly horrific and obvious - the surgeon amputated the leg without cancer, and now the patient has no legs. Or perhaps the plaintiff is sympathetic, with numerous children to care for. In these cases, the insurer pays rather than risk the wrath of a jury - and in return, the victim gets an immediate cash payment and no risk of going to trial.

In this new court system, the maximum possible awards are likely to be quite low - a recent attempt tried to cap malpractice awards at 200k, which isn't going to do very much for our now-legless cancer patient. An insurer isn't going to offer millions to settle this case when the risk of losing a "trial" is so low. The insurer will simply offer the maximum award - and for less clear-cut cases, risk going to court.

Overall, the insurance industry will probably be heading to court more often, and paying out far less - though in the best case, it may be spread out a little more. Somehow, I doubt those savings are going to be passed on to the consumer. If we want cheaper health insurance, we need to start paying for preventive care. An ounce of prevention is worth a pound of cure... and a metric ton of lawsuits after the fact.

On the scientific method (and government)

2006-07-18T09:16:00.000-04:00

Long time without blogging - unfortunately, sitting is rather painful, and thus I generally haven't been blogging. To quote my doc, "Prolonged sitting is notorious for causing discomfort in people in your shoes." Right now I'm standing, so my post may be more direct and to the point than usual. Fear not though - a laptop is on the way, for plenty of future bed-blogging.

Anyway, to my post - I read something from Dr. Freeride this morning about how to teach/communicate scientific principles to non-scientists. She uses the example of changing pans (as well as other conditions such as ingredients and temperature) while baking.

My best suggestion for how to get this kind of basic grasp of science (at least for those who no longer have easy access to science classes and science teachers) is to try thinking like a scientist in real life... Let's say you bake. Take your favorite brownie recipe and try baking it in pans of different size and shape. Hold everything else constant and observe the differences....
There are a bunch of nice lessons you get from this kind of experiment. Controlling different parameters takes time, as well as careful measurement. Some of the characteristics we might observe are more objective, others are more subjective. Predictions generally get easier the longer we work with a system.

It's hard to say anything bad about this in theory, but in practice I have a few problems with it. First, at this point in my life, I consider the scientific method rather intuitive... but is it? Over four years of college, I took numerous courses in which I was taught how to figure out how to solve a problem instead of simply regurgitating answers. A lot of these classes were really hard... at least until I started to figure things out. Given how much effort goes into training most people in the scientific method (years of college + grad school) I'm not sure that the scientific method is really that intuitive. Certainly, a lot of undergrads (and grad students, and postdocs, for that matter) I've worked with over the years don't really understand the importance of running all the appropriate controls.

Secondly, while scientist may theoretically change only one variable at a time... that's often not the time-efficient approach. Just as an example, sure, if your PCR doesn't work, you could simply lower the annealing temperature a few degrees and see if it works now. Or... you could use Pfu instead of Taq, use the gradient function on your PCR machine to try three different annealing temperatures at once, and try several dilutions of your template. Sure, now you're running nine PCR reactions at once, but since the PCR is going to take three hours to run, you've come out ahead. Now, technically, one might say that the "experiment" I just described is just problem solving (or engineering) rather than science, but the principle is the same for quite a lot of biology - set up your experiments to ask the maximum possible number of questions at the same time, even if it takes more work upfront.

Finally, I noticed Ed Brayton is back complaining about anti-gambling laws again. Now he's up in arms about the arrest of a Carruthers (there's an English name), a UK citizen who runs a vast online-gambling empire... the gentleman in question was arrested while switching flights at a US airport. To quote Ed, "they're already engaging in vast overreach by arresting foreign citizens for doing something perfectly legal in their countries." Now, there may be perfect valid reasons to allow (or not) online gambling - personally I'm against it. Still, it's a long established principle of the law that doing business in a state or country renders one subject to the jurisdiction of the courts of that state or country... and it seems that, at the absolute minimum, everyone involved failed to pay taxes. Whoops.

Did grad school make me crazy?

2006-07-08T15:07:00.000-04:00

Or, was I crazy to go to grad school? That is the question... and I'm fairly certain that, if I was crazy to start with, grad school has made me crazier. catswym has a really good post up about "grad school depression" - also known as what happens once you realize that "they really are out to get you."

I don't think that "they" are really out to get grad students- certainly those in charge want students and postdocs to have a good experience, learn a lot, and talk favorably about their program to incoming students. I think the problem is time and experience. Administrators, even those with previous lab experience, have the time to take care of students - but they don't really understand the "care and feeding" of grad students, or what we need to be happy and productive. The faculty, on the other hand, have the experience - but every moment they spend doing that could be spent doing research, writing grants, etc. Grad students have the same problem - complaining about things really only distracts from doing work (and graduating), so most minor annoyances have to go uncorrected. As the most obvious example, what's the point in trying to improve how courses are taught when you don't have to take them again? Still, it would take a lot of time, effort and thinking to improve how courses are taught - so that doesn't bother me too much. I'm much more bothered by the little things - the shuttle buses that don't run on schedule, equipment that isn't repaired, and most of all, the food situation.

The cafeteria here has terrible hours - no real food is available after 2, and it's quite expensive. The coffee supply is erratic at best, and most people consider it pretty terrible. It's also never available after 7pm or on weekends - times when the faculty may largely be away, but the laps are hopping. Going outside for food and coffee is an option before 6pm or so, when most of the local places shut down - but that adds about 15 minutes or more to a coffee run. That adds up pretty quickly. Coffee and food of some type should be available 24 hours a day - and in an ideal world, it should be free for students, postdocs, and faculty. The most productive scientist is a well-caffeinated scientist.

I'm mad as hell...

2006-07-05T21:38:00.000-04:00

and I'll take my coffee with milk and sugar, please.

What you are about to read is the true story of a grad student in search of coffee. Names haven't been changed, because those standing between a grad student and his coffee are never innocent.

So, I have a meeting at 11 am. Planning ahead, I walk downstairs to get a coffee from the cafeteria at 10:50. For background, recently the cafeteria has been rearranged slightly, so that "breakfast" is served from the "coffee shop," as opposed to the main cafeteria. A big sign displaying the hours that each will be open is out in front - it's a brand new sign, with hours effective this week. To summarize the sign in terms I was interested in, coffee will be available from 7am - 7pm. That's actually the normal hours of operations - just moved around slightly.

I walk into the coffee shop, to discover the manager (of the whole cafeteria/catering services) and the cashier.
Manager: "Sorry, we're closed."
Me: "Okaaaay... you're not open?"
Manager: "No, we close for an hour at 10:30. You can come back at 11:30."

At this point, I must have had quite the dumbfounded look on my face, as I contemplate the impossibility of getting coffee in time for the meeting.
Me: "You're the manager?" (Just checking before I accidentally lit off at a poor cashier.)
Manager: "Yes."
Me: "You know, this is what really pisses me off. You've got a big sign out front, saying what your hours of operations are. First Monday afternoon, you're supposed to be open to 7, and you close at 2 or 3. Now today, your sign says that you'll be open, so I plan to come down and get a coffee. Tell me, exactly where am I supposed to get a coffee in the next five minutes?"
Manager: "I'm look into Monday, but I'm sorry, our sign says we close at 10:30."
Me: "Oh really? "
Manager: <> "Oh..... I'll go get you a coffee."

Shortly after, I received a free (and spit-free) coffee. What was truly ridiculous was that they had a whole pot of hot coffee sitting there the entire time - they just didn't want to serve it to me!

Happy 4th of July...

2006-07-04T12:17:00.000-04:00

From the most independent species of all, Felis catus.

Holiday for the man

2006-07-02T10:43:00.000-04:00

Well, I'm in lab again on a weekend, but this weekend is special... it's the Fourth of July on Tuesday. I will grant you that most people aren't coming into lab this weekend - some people are taking trips, others are off watching the World Cup (or recovering from doing so yesterday). Still, if there's an area in Boston that literally "never sleeps", the Longwood Medical Area is probably it. In the surrounding four hospitals, hundreds of nurses and doctors are taking care of hundreds of patients, because illness doesn't take a holiday weekend. Of course, that doesn't count the scattered grad students and postdocs tending their experiments.

Still, it got me thinking - who gets a holiday anyway? The people at CVS who filled my prescription for erythromycin (guess who got conjunctivitis?) are still working. The security guards in my building are still here. The bus and subway drivers don't get today off either, though their will likely be reduced service on the fourth. Restaurants and food delivery services are still mostly working. Cops and firefighters will probably be working overtime. The military, especially overseas, still has duties to perform. Electricity, water, and phone service are still being provided to our homes. Many supermarkets are open to provide the busy party host with the essential charcoal and meat.

So who really benefits from a "holiday" weekend? Lots of people do benefit... not so much in retail or essential services, but those who work in manufacturing and industry will likely get the day off. Still, that's a shrinking portion of the American work force. Some construction workers benefit as well - though many others are working this weekend. Trash workers get the day off - but they have to make it up later in the week.

In actuality, I think the largest beneficiaries of a holiday are those who need a holiday the least - those who work in offices, especially the financial sector, banks, billing offices, and call centers. People, in other words, who probably do the least physically strenuous labor, and who could probably arrange to simply take the day off if they wanted to. In return for this communal day off, they inconvenience and inspire bitterness in lots of other people who do have to work. The holidays are also a bad time to become ill - fewer doctors are around, and lots of people will likely flood the emergency room with injuries (from fireworks, sports, hiking, etc) or food poisoning.

Don't get me wrong - if anything, I think the typical worker needs to take more time off, not less. Still, where is the need to take it at the same time as every other white collar worker in the country?

The progress of technology

2006-06-24T14:28:00.000-04:00

At work on the weekend, and with a little bit of downtime... so plenty of time to comment yet again on the Daily Transcript. Alex has a post up on "Does technology make you happy?" The answer to that is, in my opinion, quite obviously no - things in general don't provide happiness. You'll never hear a song on the radio about how happy someone is now that they have an ipod, but there have been thousands of songs written about how happy people in love are. Moving on though...

Alex says "What ended up happening is that instead of getting you job done sooner, MORE IS EXPECTED OF YOU." Well, duh. From the standpoint of the biologist, cloning used to take months - now, you can do it in days (if you're lucky). Sequencing used to be terribly expensive and time consuming - now you just send it to someone who sends it back to you for about $10 bucks. The same is true for almost any technique you can name - nowadays, it's easier and faster. Thus, the amount of scientific information in a paper is now much more than it was 20 years ago, even though it took an equal amount of work. That's not his real problem, though...

"How could you ever tell your boss, I had a tough day, it's hard work doing X, Y and Z? Now with your laptop, your microarrays and all other technological gadgets your expected to perform X, Y, Z ... the rest of the alphabet AND a couple of greek letters. Anything less and you're not performing your duties (or as a scientist, you'll get scooped)."

Well, if your boss insists on bothering you at home all day, you have a number of choices, starting with not answering email at home. Scientists generally don't work all the time - just like anyone else, we need downtime. If you're scared to take time off, or tell your boss that you're overworked, you're in a bad situation. Moreover, if you're really going to get scooped if you work less than 12 hours a day, maybe you should just work on a new project. Part of not getting scooped is just staying out of the way of the factory labs where 10 postdocs are all working on your project. They're just going to win, and if you insist on stepping out in front of a mac truck, the truck's not the one getting hurt.

Finally, I liked this line: "Why aren't we living in the Star Trek Universe where there's no money and everyone plays in their own holodeck?"

There are plenty of reasons for this, including social and political ones, but let's focus on the technological ones. Frankly, we're just not up to Star-Trek snuff. Someday, we'll have solved all the biological problems. We'll have sequenced every major organism, we'll be able to predict the function of a protein from it's structure, and we'll have extremely complex models to predict what a cell will do when we apply an external stimuli. We'll have drugs or genetic therapy for every disease, and we'll be able to tailor therapies based on an individuals genetic code. Cancer will be easily controlled, and we'll all live long and healthy lives. I think that day will be here sooner than we think - but you know what? We're not there yet. Get back to the bench, slackers.

Postdoc myths

2006-06-23T06:52:00.000-04:00

Alex over at the Daily Transcript is once again whining about the terrible plight of postdocs again. Now, as I previously wrote, postdocs actually do quite well in terms of salary. Still, since the plight of the postdoc is a common myth, I'll do my best to debunk it here.

First, Alex links to a recent Cell commentary on NIH funding and how grants are reviewed. He provides a graph which shows declining grant funding rate -fair enough. The graph is deceptively scary, in that it seems to show that no new investigators received R01 grants in 2005. Ack! Don't be that scared, though - the actual NIH presentation the graph comes from (powerpoint) simply lacks those types of statistics for 2005.

Alex then proceeds to make a number of suggestions to deal with "an oversupply of postdocs", including increased funding and more money for junior faculty, which are fine ideas. Then he once again complains about postdoc pay. Now look, postdocs obviously make quite a bit less than people could make going into industry or consulting - but that's because it's necessary for an academic career, and provides freedom that working in a company doesn't. Obviously, the pay level is set at a rate where lots of people want to do academic postdocs - and if you don't, there are plenty of other career options.

The coup de grace is this paragraph:

"Encourage lifelong postdocs. Why don't we have this? ... Because the NIH and the system refuses to pay postdocs a living wage... In addition increasing postdoc pay and job security, will encourage females to stay in academia. Many females are jumping ship, because postdoc-hood is incompatible with family life and pregnancy."

Now, I have no problem with encouraging lifelong postdocs, but let's analyze the rest of this statement:

The NIH salary scale is a living wage. A family of two postdocs who've been working for 3 years each is making 80k. Is that a lot in the grand scheme of things? No. It is, however, twice the average US household income (~43k).
More money and more job security will encourage anyone, male or female, to stay in academia.
Being a postdoc is not incompatible with family life and pregnancy- or at least, not any more incompatible with family life than being a young faculty member. I think the primary issue is not money (see above - a postdoc family makes more money than about half the families in the country), it's time. Any job that "demands" 80 hours/week is going to be hard, whether that's a postdoc position or being a young faculty member. Still, that can be managed as well - one very successful postdoc in my lab worked a strict 9-5 schedule, while her husband stayed home with their two kids. Numerous postdocs in my department have been (and are) pregnant, and while I'm sure it's not wonderful, they've managed to keep working away in lab until quite close to the due date. It seems to me that the biggest challenge facing postdoc families today is the lack of affordable, onsite child care.

I think it's great that people want to improve the postdoc experience, and provide more career paths for those who don't want to manage a lab. That said, the NIH funds an enormous amount of research - asking for more money to appear is, IMO, pretty greedy, especially when we could be making better use of the money we have. There should be institution-wide registries of equipment on the web, so (for example) that you don't have trouble finding a plate reader if another lab nearby has one tucked away. Perhaps there should even be a computerized system for tracking and sharing reagents - why buy more drug when another lab has some they don't use any more in the back of their -80? More money isn't a bad thing - but we can use what we have now more efficiently.

More on breastfeeding

2006-06-21T07:24:00.000-04:00

To followup on my previous post: Dr. Free-ride continues to misunderstand the point of the campaign to encourage breastfeeding. The entire point of the campaign is not to ban the use of formula (which has many legitimate purposes), but simply to encourage breastfeeding. I think Corpus Callosum puts it very well indeed:

A public health campaign is NOT about what benefits a given individual. That is a question that only the individual can decide. I am not disputing anyone's right and responsibility to make an independent choice. But that is not the point at all, when it comes to public health. The point of public health is to improve the average health of the population.

Similarly, society in general asks women not to drink alcohol while pregnant. One commenter in my previous thread wondered about the actual risks, given that people have been drinking for a long time, and many women do drink occasionally during pregnancy. One study looking at these issues found that consuming five or more drinks per week tripled the risk of stillbirth. Of course, maybe one drink a day counts as "heavy" drinking.

Yeast Tips, Vol. III: Don't be cheap

2006-06-20T07:30:00.000-04:00

Everyone's heard the old saying that you have to spend money to make money. Well, everyone except Bill Gates (Oh, I didn't get rich by writing a lot of checks!) and the people running the cafeteria where I work. You see, when running a business such as a cafeteria or restaurant, one generally orders slightly more food than one needs, and winds up throwing some out when it goes bad. The marginal cost of the wasted food is low, while not having the ability to prepare food for a customer carries a high opportunity cost. However, the cafeteria where I work is deathly afraid of wasting any food... and is thus frequently out of perishable items. Today, they were out of bread, and thus were unable to sell me a sandwich.

So, how does this story relate to yeast tips? Well, it's a classic case of being penny-wise (no wasted food!) but pound foolish (no food to sell). Yeast research is full of opportunities to make similar mistakes, because yeast work is carried out on an open bench. So, here's my yeast specific advice:

Always filter your media. I autoclave the components separately, which is definitely cheaper - but when you mix five amino acid solutions, YEP, and glucose, there's a pretty high chance that one of those will be contaminated with a single spore of something. Especially the amino acids, which are shared, and get opened 50-100 times before they get used up. A filter unit may cost 10 bucks... but you can ruin a weeks worth of experiments using contaminated media.
Use 0.22 uM filters. Those .45uM filters are a bit cheaper, but they're worse than useless, in that both spores and bacteria can go through them.
Toss tips that aren't sterile. If a box of tips has been uncovered on your bench for a while, don't use it for anything sterile - save it for PCRs and gel loading, or give it to someone doing protein work. What, you filtered all that nice media and now you're going to foul up your cultures with a dirty tip?
Minimize air flow. Air flow is the enemy, even when it's generated by PCR machines.

My non-yeast specific advice comes from something my old boss once said: "Your time is the most valuable reagent." Everything depends on how much money your lab has, of course - I wouldn't try and save 5 minutes by pouring my own agarose gels, because it's easy and those are expensive. On the other hand, buying precast SDS-PAGE gels is, IMO, the best use of money ever. I'll be a happy grad student if I never have to deal with that toxic gel sludge leaking over my bench again.

Death by caffeine

2006-06-18T12:40:00.000-04:00

Once, over ten years ago, I drank approximately 18 cups of coffee in roughly two hours. It wasn't exactly intentional (long story), but there you go. That doesn't even cover the time I drank several liters of Jolt back in college, but apparently 12oz of Jolt = 1 Coffee, for caffeine purposes. Today, my caffeine habits are much more normal - on average, only one or two cups of coffee per day, in the liver-protecting range.

So how toxic is caffeine? I've looked up studies on this from time to time, and my interest were rekindled today when I read a post about energy drinks. Shelley Batts had this to say about caffeine:

FYI, the LD50 for caffeine (this means the amount of caffeine it requires to kill 50% of an animal test group) is about 10g (or 10,000 mg). You'd have to drink 125 Red Bulls to get that much caffeine.

First of all, the toxicity of most drugs depends on body weight, and caffeine is no exception. According to this site the LD50 in rats is 192 mg/kg. Directly extrapolating from rats, Shelley is thus assuming that the average person weighs only 114 lbs. To her credit, though, many people appear quite confused about the toxicity of caffeine. That site I just mentioned says that the LD50 in humans is 1-4 grams (clearly too low), while the Caffeine FAQ agrees with Shelley that "The LD_50 of caffeine (that is the lethal dosage reported to kill 50% of the population) is estimated at 10 grams for oral administration." A higher estimate is reported by this vetinary site, which says that "With adults (humans) caffeine deaths start at 18-50g." So who's right?

For obvious reasons, no one has really done a good death-response curve for caffeine intake in humans. A few years ago, I discovered TOXNET, which is a service of the National Library of Medicine. First off, numerous cases of death from caffeine are reported in the literature. For the most part, these cases (where dose intake is known and reported) seem to average around 20 grams, mostly from suicide attempts (although accidental deaths from a lower quantity of caffeine have been observed). As this abstract points out, "Death due to caffeine overdose is rare, due in part to its marked gastric irritation resulting in spontaneous emesis." This report states that out of some 7,655 exposures recorded by a poison control center in Texas, there were only two deaths. Sadly, I don't have access to this journal... and we don't know how much help those other 7000 individuals required to survive (or even how much they took). One more point about caffeine - high levels of caffeine can leave you with permanent neurological damage, or put you into a coma, even without killing you.

So, obviously, too much caffeine is bad for you. However, just one more benefit of caffeine I came across while reading about caffeine: it may help ward off suicidal depression. One study found a strong inverse correlation between drinking two-three cups of coffee each day and committing suicide.

Onto the pharmaceutical industry: this morning I saw a post knocking the pharmaceutical industry, stating that instead of finding new drugs in the rain forest, " it is far more likely that the final aim of field pharmacology is eliminating potential sources of loss rather than improving the lot of patients." Dr. X may be a researcher/corporate type, but I've been there and done some of that myself, and at least two of his statements are way off base.

"Remedies of natural origin are very hard to patent; for this reason, drugs of natural origin are generally replaced with synthetic or semi-synthetic derivates. For example: heroin is a semi-synthetic derivate of morphine created by Bayer"

While it's true that heroin is a chemical derivative of morphine, it was synthesized with a noble purpose - to make a less addictive and toxic version of morphine (source: Aspirin). It didn't exactly work out that way... but since they successfully made aspirin the same week, it turned out pretty well anyway. Speaking of which, aspirin itself is a "synthetically produced compound derived from the naturally occurring salicin, found in the bark of the Willow tree." Of course, salicin wasn't really all that popular, since it kind of burns a hole in your stomach. It took years of work before Bayer came up with modern-day aspirin, which in comparison doesn't hurt the stomach too badly. That's generally the real reason drugs of natural origin are only used as a starting point - to improve their target specificity, reduce side effects, and improve their pharmacokinetics.

"Most natural drugs are so chemically complex that a synthesis is either impossible or antieconomical."

Which is why it's better to harvest them directly, if possible. On the other hand, how many willow trees would need to be cut down each year to satisfy our insatiable demand for aspirin? Or, for that matter, the anti-cancer drug Taxol? The compound was discovered in the bark of the slow-growing yew tree, and "the treatment of just one patient requires the cutting down and processing of six 100-year old trees." Fortunately, chemistry came to the rescue of the Pacific Yew Tree (not to mention many cancer patients).

Ok, that is definitely enough blogging for a Sunday. :)

Finding time to post

2006-06-16T06:57:00.000-04:00

After a pretty good start (while I was laid up at home for 5 weeks with a herniated disk/recovering from surgery), my posting schedule became pretty erratic. Why? Well, I was busy. Sometimes, even finding ten minutes in the middle of the day to blog is quite a challenge.... there is literally always something else I could be doing that's more productive- looking at cells, ordering primers, responding to emails, pouring plates, planning out cloning strategies, you name it. This week has been pretty good, but some weeks I've only managed one post.

So, why bring this up? Well, I noticed that over at ScienceBlogs, the question this week is: "How is it that all the PIs (Tara, PZ, Orac et al.), various grad students, post-docs, etc. find time to fulfill their primary objectives (day jobs) and blog so prolifically?"

Those who have time to kill can browse through the different answers (many say "insanity"), but there's really a more common thread: they're not in lab. One of the few PhD students is apparently at home writing a thesis, while most of the others are either not scientists or are PIs. Alex (a postdoc) is an exception, and he's been posting more erratically of late due to time constraints. I'm sure there are one or two other grad students who post there, but I think it's a trend that the more bench work you do, the less time you have to post.

On the flip side, a number of my favorite bloggers have apparently been far too busy recently to post much, including YFS (a postdoc) and Naked Under My Lab Coat (a grad student). Perhaps not coincidently, they actually do lab work. :)

Breastfeeding

2006-06-15T07:51:00.000-04:00

There's a post over on Adventures in Ethics and Science about the government's new breastfeeding initiative. To summarize for Tivo users such as myself, they've been running some ads:

A two-year national breast-feeding awareness campaign that culminated this spring ran television announcements showing a pregnant woman clutching her belly as she was thrown off a mechanical bull during ladies' night at a bar, and compared the behavior to failing to breast-feed.
"You wouldn't take risks before your baby's born," the advertisement says. "Why start after?"

Dr. Freeride engages in quite a bit of debate about the appropriateness of this campaign, and what obligations this knowledge imposes upon society - and asks, "does a new mother have an obligation to breast-feed her baby?" She concludes that

Breast-feeding has a lot going for it. Breast-milk is essentially free, and even the cost of bottles and a good breast-pump ends up being a lot less than the cost of formula during the first year of a child's life. But there are other costs to consider here -- not just the economic impact of the mother being part of or staying out of the workforce, but also the emotional impact for mother, as well as child. Being with the source of the breast-milk 24/7 might be suboptimal if she's isolated and unhappy.

Sharing scientific information is a good thing. It lets people make better informed choices. But using knowledge to get paternalistic and shame people -- especially when it's selective shaming (e.g., of mothers who might use formula but not of employers who could be providing more reasonable conditions for lactating employees) -- strikes me as a bad thing.

All of her points are well made - especially that employers (and society at large) should make many more accommodations for public breast feeding and pumping rooms. Still, I don't reach her conclusion.

If formula feeding really does lead to health risks, and even to lower intelligence, how is this campaign a bad thing? For very similar health reasons, society generally views pregnant women smoking or drinking as a bad thing- does Dr. Freeride view this as also overly paternalistic? After all, various kinds of warning labels (ie, this one or this Canadian one) advise against the use of these products by pregnant women. While formula has many legitimate uses, it should, in general, be viewed negatively - and the government should be applauded for not caving to the demands of the formula industry.

Getting into grad school

2006-06-13T15:09:00.000-04:00

Two posts in one day is pretty high for me, but just this once... unlike Alex at the Daily Transcript, I have a bit of extra time these days. Speaking of which, I've long thought that the most useful invention for biology would be a fast-time box. Put your plates in the box, set the dial, and presto! Your plates have grown for two days. Of course, then bio students wouldn't really have any time to blog.

But I mostly wanted to comment on this series of posts on getting into grad school (part one, part two). The advice in part one is pretty sensible - you should have research experience, letters of recommendations, and you should really apply to schools based on labs (or their strength in a particular area), not their rankings. Generally speaking though, you shouldn't email the professors before you're invited to interview - it won't hurt, but it probably won't help.

Which brings me to the first point - my grad school experience was slightly atypical, as I was accepted prior to an interview. Generally though, if you're invited to interview, you're basically in. While I think you really should know what's going on in science news, I've never had anyone interview me and ask "why do you want to do research?"

Part two I have a few more problems with.
-"Don't be afraid to get out if it isn't working." The problem here is that things never work, at least not at first. You're learning the lab, and getting your hands, and juggling classes with research. Things don't really settle down until your third year - and everyone I've met knows that the third year in a bio phd really sucks. If people left just because things aren't working, then everyone would leave.

-"Share most of your ideas, but keep a few to yourself." This is good advice when you've got a project that's rolling along... but during the admissions process? Please. Chances are pretty good that, if an undergrad can think of an idea, it's sufficiently obvious that it has already occurred to the students and scientists who are working on the project full time. Furthermore, most scientists are pretty stubborn - they may acknowledge that your idea might be valid, but unless it plugs in very neatly with their current work, it's unlikely they'd pursue it. Finally, you're not going to have time to really jump into any project for at least a year, as you deal with classes and rotations. Just speak your mind.

-"Know who won the Nobels that year, in your field." Yawn. It's not like it could hurt.

-"Email the students in the program, and in the lab." Well, it's one thing if you know then personally... but if not, how do you evaluate what they tell you, good or bad? And are the people who don't respond down on the program, or are they just too busy to respond?

-"Find out where/what students from that program are doing now." I'd be pretty surprised if everyone coming out of a program wound up in academia, or big pharma, or wherever. Either way, just because people going through the program often make one choice, it doesn't mean you have to make the same one... let alone change how much your degree is worth.

Ok, that pretty much wraps up my commentary for today. Now back to doing some science, instead of blogging about how to start doing it.

Health and nutrition

2006-06-13T11:31:00.000-04:00

Today in the Boston Metro I saw a nice blurb about what they called "every man's dream to hear that beer and pizza can prevent cancer." The Metro is generally pretty bad about posting articles on the web, but here's the summary from Forbes. Of course, it involves drinking 17 beers a day, but what do you expect, nothing comes free.

Except maybe drinking coffee. CBS says that "Coffee may contain an ingredient that protects the liver against alcoholic cirrhosis." According to the study leader, "For every daily cup of coffee that participants reported drinking, they were 22 percent less likely to have been diagnosed with alcoholic cirrhosis during the study." Now that's pretty awesome! Unfortunately, tea drinkers probably don't get this beneficial effect.

It's interesting that nutritionists are pretty much the most cautious people in the world about making dietary recommendations. However, vitamin D is making a comeback. It seems most people believe that the current vitamin D recommendations should be substantially raised, because more appears to have lots of beneficial systemic effects, including lowering the risk of cancer. Various groups are meeting to determine if the government will officially up the recommended dose.

So... more vitamin D plus more coffee = lower risk of cancer and cirrhosis. I'll drink to that.

Home, and blogger is back

2006-06-09T09:42:00.000-04:00

Well, I'm sitting at home, waiting for the RCN guy to come fix the cable modem/internet access. How can I still post, you ask? Well, the internet connection only fails when it's raining. Of course, even though it was supposed to be quite rainy today, it's not raining right now... and might not until after the RCN guy has left. So, I'm re-writing a paper, and blogging a little.

I don't have much for you all, but I will give you this, the world's most misleading article title: Influence of sex on in-hospital outcomes and long-term survival after contemporary percutaneous coronary intervention. What they meant was influence of gender, but I guess they thought they'd get more readers this way.

Oh, and this is cool too: bacteria that eat plastic. Really, I think in the long run this can only be a good thing - there's way too much plastic and polymers running around in the environment.

Finally, here's a cute cat to brighten your day.

Conference blogging

2006-06-06T11:06:00.000-04:00

I haven't been blogging much lately, because I was busy attending the 2006 conference of the American Aging Association. It was quite enjoyable and informative, even though I had to miss the last day in order to attend the Harvard/Paul F. Glenn symposium on aging (which was also excellent). All in all, they were both great - though I seem to be coming down with a cold now. If it's not one thing, it's another, but I hope to blog much more over the coming weeks.

What has TV come to?

2006-05-30T07:12:00.000-04:00

I'm not opposed to reality TV. I watch Survivor, Big Brother, and Amazing Race each year. A couple years ago, catsywm and I watched "Test the Nation," a televised IQ test... from the people who brought you the Simpsons. Back in college, my friends and I gathered around to watch Dick Clark's "Battle of the Child Geniuses", also from the Fox network.

But a show based around the spelling bee? I watched "Spellbound." It was pretty good. But that was a story of many children, over a year, and all packaged up and delivered in a compelling 90-minute story. It's very different from ABC's current plan : televise the spelling bee finale live. They have filler material ready to go, but the basic problem is they have no way of predicting how long it will be.

The problem for television is that, like any live sports event, there is no way to predict the ending. After the spellers are winnowed down to the last 10 or 15 Thursday (with ESPN on hand beginning at noon Eastern time), bee officials will stop the daytime event and delay what ABC is calling "the title rounds" until 8 p.m. Once the lights dim and the cameras zoom, anything could happen. A lot of kids could fade early. Or two could keep battling off words such as "logorrhea" (excessive wordiness) and "smaragdine" (the color of emeralds) until long past the network's planned 10 p.m. signoff.

Even if things go as planned, and everything wraps up in just under two hours... is this truly exciting enough for live TV? Maybe it would be... if the final contestants had to correctly spell words while immersed in a gigantic bubble of water.

Weekend Whimsy - Long Weekend Edition

2006-05-28T10:13:00.000-04:00

Theoretically, this is Memorial Day weekend - a three day weekend during which we remember those in the US military who died for their country. Of course, what better way to remember them than by taking long trips, breaking out the white clothing, and watching X-men III [mild spoilers]? Eh, don't mind me, I'm just bitter from tooling away in lab all weekend. Today though, I go forth to do battle with a ferocious enemy - Drosophila Melanogaster. I discovered one in lab yesterday - and unless stomped out quickly, they will soon feast upon my poor defenseless yeast. In truth that's not a problem - the problem is, bacteria and spores of other fungi travel on the legs of fruit flies, and they leave contamination everywhere.

Enough of my complaints, though - this is kind of an interesting idea, one's website as a graph. I saw this off of Stranger Fruit, and it's interesting to compare how different it is from one of the SB blogs.

Moving on from pretty pictures, though, I notice that the "question of the week" on SB is "Since they're funded by taxpayer dollars (through the NIH, NSF, and so on), should scientists have to justify their research agendas to the public, rather than just grant-making bodies?" Perhaps surprisingly, the SB crew chooses to answer "No." (PZ, KV)

I'll be a little bit contrary, and say that, and it should be obvious, not only should scientists have to justify their agenda to the public, but that they already do. It's not usually direct... but if research sounds too ridiculous, it gets publicized, and perhaps defunded. If research is controversial, the politicians may decide not to fund it (ie, stem cell research), and the scientists may choose to try and make their case directly to the public (ie, the California stem cell initiative). Advocates for various diseases, such as AIDS and different types of cancers, have brought their complaints with low levels of funding to Congress, who responded by earmarking specific blocks of money to research in those areas.

PZ says:

They don't have to justify, but they should explain. It might be a useful condition of a grant to require that the recipient give an open lecture summarizing in terms a non-specialist can understand the results of their work, at the end of the grant period.

I don't agree - why wait till the end of a grant period? Most NIH-funded researchers are familiar with CRISP, a grant database - you can enter the name of a PI, for instance, and pull up their current list of grants. Why, however, are the grant proposals and updates not available to the general public? Not only would that promote more openness in science, it would help prevent redundancy - few things are more wasteful than multiple groups working on the same project and all but one getting scooped. Unlike publication, it wouldn't require you to share reagents. However, making grant proposals and updates available online would help keep everyone in the loop on preliminary and ongoing projects, and because grants are on the line, PI's will probably not be tempted to hold back interesting data.

Friday... fires?

2006-05-26T07:01:00.000-04:00

A house down the street caught on fire sometime last night, and it took an hour or so until the fire trucks went away. If there's one thing I don't need before a long day in lab, it's being woken up at 4am. Ah, the suburban life.

Speaking of which, a funny story in today Boston Globe: a parking ticket-writer who got a ticket. You probably don't see how that's funny yet:
A city parking-ticket writer... last week discovered a ticket on her car, a citation for parking in a resident-parking zone without a sticker. The officer marched into work the next day, ticket in hand, and told her boss that she, in fact, had a resident sticker and wanted the ticket cleared.
Her supervisor went outside to have a look. Sure enough, there was the sticker, properly mounted in the right rear window of the officer's car. But it didn't look right. It was severely faded, and when the supervisor ran the sticker's serial number through city computers, it drew up someone else's name. A disciplinary hearing was called.
Have I mentioned how I think gambling is one of the most ridiculous wastes of money ever? Especially when playing online, where one doesn't even get free drinks? Anyway, I'm not saying Ed Brayton has a gambling problem... but he's been playing poker both day and night. If you're his friend, may I recommend 1-800-Gambler? Still, to give credit where credit is due, this is an awesome post about the ACLU.
I'm both sad and happy that the Scientific Activist is moving to ScienceBlogs. I'm happy that the site, which is a good resource for a quick read, is getting more real scientists. On the other hand, as YFS says, "First off, you should know what Seed offers to pay: zero." Seed pretty much has the perfect business model - writers who create content, which Seed can then resell at essentially zero marginal cost. In this age of the internet, there shouldn't be any inherent need for readers (or writers) to gather at any one site - and as the number of writers increases, the RSS feed will become increasingly useless.
Randomly, I came across this blog: Sexy Science - a look into the hottest science currently going on today and the hot scientists behind that work. Pretty wacky idea.

100 years from now

2006-05-23T07:29:00.000-04:00

One hundred years ago (well, maybe 50), people thought that by now we would live on the moon, and in domes under the sea. Hypersonic planes would rocket us across the sky as our rocket ships plowed across the stars, and solar power and clean nuclear fission/fusion would power our factories. For better our worse, our technology didn't go down that path - rocket planes and domes under the sea simply cost too much power and effort, while improving computer technology and biological science has been far cheaper. (Even if emergency responders may soon have the ability to leap tall buildings in a single bound!)

Given the past performance of futurists, last week's question at ScienceBlogs was particularly wacky: "Will the human race be around in 100 years?"

I'm not a Science Blogger, and even if I was, I don't have anything in particular to add to the answers of Orac ("Yes, but sadly I won't") or Tara ("Short answer: yeah"). I do wonder though about the answers of some people, such as Greta Munger:

"in 1,000 years, we may have discovered the secret of aging, and it might be possible for people to live infinitely long lives. Would such a creature be human? Isn't mortality part of what makes us who we are?"

Yes, mortality is part of what makes us human: but anti-aging cure or not, mortality will always be with us. There will always be traffic accidents and natural disasters, and eventually, we will all be caught in one. In the 1970's, Genron calculated the average lifespan in the absence of death from aging as about 700 years. That's obviously enough to cause major changes in society - but not matter how subtle the medical care, we are all mortal.

Anyway, it looks like the "question of the week" over at SB will continue along it's oh-so-insightful track.

Congratulations!

2006-05-22T15:12:00.000-04:00

Congratulations to Joolya and Springy, on the occasion of their marriage. They deserve massive props for being engaged only one week - and thus not having much time to fret and worry about dresses, bachelor parties, or choosing the right wine. It definitely sounds like one of the lowest-stress weddings ever!

Education schmeducation

2006-05-22T07:55:00.000-04:00

Again, a long time between posts - sorry everyone. Work has been virtually all-consuming, and today is a brief respite before it's time to start a new round of experiments. However, you didn't visit this site just to hear me whine about work, so...

Various bloggers on various sites have been thinking about how to improve science education. Mike the Mad Biologist started the latest round of this discussion, with a remarkably sensible idea:

To get the ball rolling, I'll throw out my wacky idea: I think the problem is that we do a very poor job of teaching the basics. By basics, I mean arithmetic and basic scientific facts. Without that foundation, it is very difficult to get to the next level.

Of course, this is pretty obvious, right? Evolgen picked up on this idea, (Mike discusses it here) and says:

I haven't always felt this way, but the spectacle of college students having to think about 8x7, or being unable to add 1/2 and 1/3 in their head, is pretty persuasive evidence that the constructivists have the wrong emphasis. To have any hope of being successful in higher levels of mathematics, it is essential first to be comfortable with arithmetic... On top of that, there is a limit to how much abstraction young children can handle. A typical bright eight-year old can learn his multiplication tables without too much difficulty, but abstract set theory is probably beyond him.

I think the most interesting part of this discussion is that this is a) a new idea or b) likely to lead to any striking advancements whatsoever. While the National Reading Panel debates how to teach reading, more students are being left behind.

I read somewhere (I can't find the source) that only 6% of those who enter the Chicago public schools will graduate with a 4 year college degree. I find that somewhat unbelievable - but on the other hand, the four year college graduation rate is only about 50%. That's pretty unbelievable, especially given how much college costs. Nationally, only 26% of those over 25 have a college degree - so roughly 1/2 of Americans have tried college, and only half of those manage to finish it.

Now, I'm not one of those who believes college is for everyone - I think we need more vocational and trade schools, and learning a trade via an apprenticeship is underrated as a training tool - it worked for society for thousands of years, why abandon it? However, thinking about this lead me to some interesting thoughts.

What would society be like if everyone in this country did go to, and finish, college? What would that do to the job market? Would there be a vast economic expansion, or would the unemployment rate skyrocket as the new college graduates shunned jobs in the service and retail industries, and "white collar" jobs were in extremely short supply? Interesting tidbit - the national unemployment rate goes up and down between 5% and 10% with the strength of the economy, but that's mainly on the backs of those who have only graduated from high school. Unemployment rates for college graduates have generally held very steady between 2-3%. Of course, given how the "new thing" for today's youth to do after college is to move back in with your parents (perhaps becoming a yoga instructor), I don't know if those statistics really reflect the number of college graduates with jobs.

As an aside: From the article,
Their 27-year-old son's decision to come back took them by surprise. Tom Jr. went away to college and had lived on his own since. He works as a medical sales representative. Even though he was sharing a place, his monthly expenses in the pricey Boston market topped $1,500 a month. When he got engaged, he asked to move home to save money for a diamond ring and a house.
Here's a hint (at least for those in the Boston area)- if you're sharing a place and still paying $1500/month, you're paying too much money! Or you're really loaded, in which case you could have a really nice one bedroom for the same amount of money. Too bad Tom Jr.'s college didn't force them to take some sort of financial planning course on living within your means.

Another idea that occurred to me - many people talk about college loans and the crushing debt burden many students are under. What if the government wrote off student loans for anyone who successfully completed college? That would force up graduation rates almost immediately - although I don't know how much the students would benefit from being forced to do something they don't want to do. Still, if the horse is held near water long enough, he might decide to drink some.

How important is science?

2006-05-15T06:57:00.000-04:00

The Scientific Activist has a post up discussing the burning question of: is science overrated? It's based on a post from PZ Myers on roughly the same idea. The basic topic was the relative value of the humanities vs the sciences, but there's not much to say there- or at least, I agree that the study of arts, literature, and history has value.

However, there are a couple of points of science-career FUD that they both regurgitate, and I feel it's worth my time to rebut them. First off, according to PZ Myers,

more students are going through the science mill than can ever acquire jobs doing science. If every PI is taking on one new graduate student and one new postdoc every year over a career spanning 30-40 years- well, that's a situation that is rather ruthlessly Malthusian.

Of course it would be... if that's what happened. As a practical matter, many people drop out of academia following grad school - they've discovered it's not for them. They don't perish, they simply move onto jobs in industry, consulting, teaching... and generally, we're better off for having educated them. Many (about 50%) of postdocs are from other countries, and return there after their studies. The remainder of the trainees may want to stay in academia - but again, even if they fail, there are plenty of positions in industry, consulting and teaching to ensure that no one is going to starve.

it is definitely not a practical career, either - the excessively long training period and relatively low salaries mean that, in a purely economic sense, it would be more profitable to plunge into a blue-collar job straight out of high school.

That's just pure nonsense. The US Census in 1999 compiled a list of education levels vs projected lifetime earnings. On average, someone with a doctoral degree will, over the course of 40 years, earn almost 3x more than someone who went to work as a high school graduate. That doesn't mean that you wouldn't be even better off with an MBA - but this ranks up there with the "Five Reasons to Skip College."

Finally, PZ Myers (who is responding to someone else's post) takes issue with the phrase "Science has not been cultivated in this country out of a love of learning."

Science is a field whose practitioners, like those in English literature or American history or philosophy, pursued it because of a love of knowledge. They work to understand, not because they're out to blow up the world. To even suggest that science isn't done out of a love of learning is offensive and ignorant.

That, of course, is not what the poster said. The government doesn't fund science out of a love of learning. Just like the Apollo program and the space race, the government funds science because a) it doesn't want our country to be out-competed by other nations, and b) for the economic, social, and technological applications it provides. Individuals choose to become scientists because of a love of learning - but that's separate from the reasons the country chooses to fund us. The public certainly wants to know more about biology - but the reason the NIH got over $28 billion last year is because we want the cure for cancer (among other things).

Two types of scientists

2006-05-11T07:00:00.000-04:00

In the spirit of Alex's post on "The three types of experiment" (which I previously discussed), I'd like to propose that there are also two types of scientists. As with the classes of experiments, these are also broad, and perhaps a bit simplistic - but nonetheless, I think they're somewhat useful in thinking about one's own work.

The theorist: The theorist is perfectly capable of performing experiments, but will quickly use these experiments to generate an overarching hypothesis. The primary strength of the theorist is the unifying theory behind their experimental work - and most of the big names in science seem to have this type of theory. The theorist will concentrate primarily on generating new data that supports their existing theories. The biggest weakness of the theorist is a tendency to discard and/or ignore data that contradicts their central hypothesis.
The experimentalist: Unlike the theorist, the experimentalist is much slower to generate new theories. Indeed, almost every theory has holes, and the primary strength of the experimentalist is the ability to find and exploit these holes to prove existing theories wrong or incomplete. The greatest weakness of the experimentalist is the inability to come up with a comprehensive theory that encompasses all of the existing data.

Perhaps obviously, I think I lean towards the experimentalist side - I also often let myself get carried away with preliminary experiments that may have alternative explanations, and I tend not to put enough importance on understanding the mechanisms behind the various results I get. I guess everybody has their strengths and weaknesses.

Well, except Ed Brayton. He felt the need to respond to my previous post, though he didn't have much interesting to say. He did feel the need to point out that he gets more visitors each day then I do:

His total hits since he started his blog are less than what this blog averages in half a day. Keep on chugging along, little engine that could. One day you'll say something intelligent and people might start paying attention.

Actually, Ed gets about 120x more visitors than I do (interestingly, a brief sampling shows at least 20% of these come via the ScienceBlogs homepage.) Of course, the Drudge Report had almost 4000x (no, that's not a typo) more visitors yesterday than Ed... so by Ed's logic, I guess he has even more intelligent commentary than either Ed or I.

Ed also had this little gem: "I'm not against the government mandating that evolution be taught as a theory in schools at all." I wonder what happened to the relentless anti-creationism crusader?

Watching the writers

2006-05-10T07:38:00.000-04:00

Everyone's gotten a nasty rash or a bugbite from time to time... you just need to leave it alone, but you just can't stop scratching it. Apparently, my itchy rashes are Tim Lambert and Ed Brayton over at ScienceBlogs. Yes, the ones I've been whining about for months. Anyway, they're back and being silly once again.

We'll start with Tim Lambert, who responded to a question on which "invention from the last hundred years" would you remove with this reply: "Easy. Cold fusion." Just to rub it in, he then stated in the comments that "Well, the scientific consensus is that there is no such thing."

Well... that's misleading, at best. Tabletop fusion is apparently real, and cold, although it will probably be useful mainly as a neutron source. Sonoluminescent fusion is roiled in controversy, but the "consensus is that bubble fusion is theoretically possible." As for the type of experiment done by Pons and Fleischmann, well, as reported back in 1998 , many countries (including our own) fund quite a bit of cold fusion work on the QT. It's not due solely to the potential payoff - it's because a lot of people believe very strongly that it's real. Most others, even the skeptics who believe that fusion is not what researchers are observing, will admit that there's something funny happening in those electrodes.

Which brings us around to Ed Brayton, who pontificates on local laws in a recent post.

The first is from Arkansas, where a bill has just passed both houses of the legislature that would ban smoking in any car if there's a child in the car... Anyone wanna start a pool on how long before it becomes a crime to take a child to McDonald's? Isn't this exactly what we want, the government telling us how to raise our children?

Actually, that doesn't sound like a bad idea - maybe it should be a crime to take kids to McDonald's. We don't let children buy alcohol - and long term, fast food might overall be even worse. More to the original point though - in terms of risk to a child's health, being trapped in a car with a smoking parent might be just as risky to the child as not placing an infant in a child car seat. Maybe Brayton's against that too.

After all, he's also against regulating gambling...

The second report is from the state of Washington, which just made online gambling a felony punishable by up to 10 years in prison... Not a single state congressman voted against the bill... If the legislature doesn't understand that adults have the right to gamble with their money if they see fit, throw the bums out.

Of course, they don't have that right - indeed, every legal gaming establishment in every state is regulated by the local government. This is for a variety of reasons - to get a piece of the action, to ensure reasonable odds, and to keep criminal influence out. This is all aside from the problem of addiction (especially when gambling in private), which obviously has implications for society. Thus, the state has a vested interest in regulating gambling. If you live in Washington and disagree, try to amend your state constitution to allow online gambling - and see how far you get.

Actually, this all explains a lot. It's not that Ed Brayton is against the government mandating that evolution be taught as a theory in local schools for scientific reasons - it's that Ed Brayton is against government mandates. Sigh. For those interested in reading an awesome book which illustrates exactly how well a libertarian society might work, I recommend Jennifer Government by Max Barry:

Welcome to paradise! The world is run by American corporations (except for a few deluded holdouts like the French); taxes are illegal; employees take the last names of the companies they work for; the Police and the NRA are publicly-traded security firms; and the U.S. government only investigates crimes it can bill for.

Work work work

2006-05-06T17:52:00.000-04:00

Apologies to all of you, my loyal readers - this last week has been extremely hectic, and something had to give. Well, my social life also had to give, but so did my blogging! Things will continue to be hectic for the next several weeks, but hopefully not quite as badly. So, onto some ranting...

First, some thoughts from lab life. Back in March (wow, how time flies when you're blogging) I posted about my desire for a database of negative results. I no longer believe this is such a good idea. Seriously, the flaw in this in that you need to know the experiment was actually done correctly - and you can't really trust things other people have done if they get a negative result. Only if each experiment in the database was also coupled to a positive control would this type of database be somewhat useful.

The only good stuff to rant about this week that I've read (admittedly, not so much) is over at ScienceBlogs. Alex comments about his issues with journals, and complains about the short Science/Nature format, as well as supplemental figures and protocols. To his complaints, I say this:
1) Short is better. Who wants to read a 15+ page Molecular Cell paper, anyway? Nobody, that's who. Short and snappy will inspire people to read the paper, and not just the abstract.
2) Supplementary data rocks. If the author/journal is smart, it will also be deposited in PubMed... and if the internet ceases to exist, we're all in pretty big trouble anyway.
3) Protocols (printed) are dead or dying. Protocols on websites and the internet in general are alive. Use them!

And, in the spirit of keeping this entry short and snappy, I bid you all a good weekend!

Weekend Whimsy - Gah Edition

2006-04-29T14:18:00.000-04:00

Because some things just make you want to go "Gah!"

First, via Left I on the News, comes the story of the person with the longest commute in America, David Givens. Mr. Given drives 186 miles each way to his job. The trip requires 3 1/2 hours.
The Boston MBTA is trying to raise bus and subway fares - and "simplify" them...
Some of the fare exceptions are so old and entrenched, such as the free outbound rides on the Green Line surface stations, that current T officials can't fully explain their history.
Hmm, do you think that maybe it has something to do with the Green Line riders paying double on the way in? Or perhaps that it lets people get on and off the trains much more quickly? And, if you're really interested in simplifying things, why would you charge sharply higher fares for people who buy single rides?
Forbes has an article on the Five Reasons to Skip College. One of these reasons is that you could simply invest the 160k you would presumably spend. I'm with Tara Smith, who says: "where are all those people who had $160,000 up front to invest as an 18 year old?"
Finally, Mojo Blog has a post on How to spot a terrorist. Some of the characteristics of terrorists according to the state of Texas:
Focused and committed
Team-oriented and disciplined
Familiar with their physical environments
Employ a variety of vehicles and communicate by cell phone, email, or text messaging
Try not to draw attention to themselves
Look like students, tourists, or businesspersons
Travel in a mixed group of men, women, and children
Avoid confrontations with law enforcement
Use disguises or undergo cosmetic surgery

Yup, that's some real useful advice there, Texas, top quality. Gah!

friday science roundup

2006-04-28T13:56:00.000-04:00

i'm no physicist, and certainly no cosmologist, but apparently the big bang theory is not so quantum physics friendly. one way to get around that is to posit that instead of the "big bang", we may have had the "big bounce", or loop quantum theory as they prefer to call it, from a previously contracting universe. a study published in physics rev. let. says they have theory that supports this bounce regime.

It's nice to see a main-stream news outlet that many folks respect tell parents they should actually allow their children to be exposed to dirt and germs at a young age in order to build up their immune system.
The prevalence of allergies has increased substantially in the past 15 years, according to the National Institute of Allergy and Infectious Diseases, and some experts believe that too much cleanliness might be a contributing factor.
count me among them.

male birth control "pill" is reversible within 3-4 months so men needn't worry about long term infertility. the "pill" in this case is actually a small insert and shot given every three-four months which doesn't seem too inconvenient to me.

apparently, vit C and E given to expectant mothers provides no benefit to the baby (in terms of birthweight) or mother (in terms of pre-eclampsia) and may even be harmful to the mother.
Vitamin C and E supplements during pregnancy in normal-risk nulliparous women did not reduce their risk of pre-eclampsia, or the risk of low birthweight or death in their infants
and later,
Women in the vitamin group had an increased risk of being hospitalized antenatally for hypertension and having to take antihypertensive medication. In addition, a subgroup of women in the vitamin group had a higher frequency of abnormal liver-function tests, although tests were done only on women with clinical indications.
i'm not sure why they specficially chose C and E (although those are two powerful anti-oxidants), but apparently, as long as you are getting adequate amounts in your diet, extra is not going to help.

Fraud, lies, and the police

2006-04-27T07:01:00.000-04:00

I saw something about this in the Metro the other day, but it had slipped my mind: the story of young Harvard "author" Kaavya Viswanathan. Her just-released book, some sort of typical coming-of-age stuff, became controversial when is was disclosed that she "unconsciously and accidentally duplicated numerous passages" from books by Megan McCafferty. Plagiarism aside, the whole story seemed unbelievable to me - how does a 19 year old have a book? Or a two-book contract worth 500k? The Metro article talked about how good her writing was, but it still seemed sketchy to me.

Turns out that it was sketchy. As discussed by Dr. Freeride, it seems that the book was produced with the aid of a "book packager." I had never heard of such a thing, but...

Book packagers, it seems, have stables of hungry young (and swift) writers who will do that pesky writing involved in turning out a novel (or many novels in a commercially popular series) for a paycheck but no author's credit. Viswanathan gets her name on Opal Mehta, but she doesn't have to sweat over actually writing it all. Indeed, under the terms of the arrangement, it's unclear that the public would ever get to know how much of the resulting novel was written by the author of record and how much was written by those anonymous wordsmiths.

The book packager does co-own the book's copyright, which is presumably how this arrangement came to life. The Harvard Independent explains more about the seamy underside of the literary world:

Many of the middle grade and young adult series you see on your library and bookstore shelves are written by various writers hired to create a specific volume of the series. The book packager...offers a flat fee, a deadline (usually six weeks from the day the contract is signed in the case of the Sweet Valley Twins), and an outline of what has to happen in the story. For 17th Street Productions, once you sign the contract, the editor sends you a two-to-three page outline that relates the plot of the story and which characters are involved. The writer then creates a more in-depth chapter outline and returns it to the editor, who may require some changes, after which the writer completes the first draft.

The real question is: will Viswanathan be asked to leave Harvard? Or will she go on and eventually get her MBA?

In other news, I saw this over on Decision of the Day:

The facts of this Seventh Circuit qualified immunity decision are a must-read for anyone who needs some convincing about whether our criminal justice system sends innocent people to prison. After serving 27 years of a 200-400 year sentence for a crime he did not commit, Michael Evans was released based on DNA evidence that cleared him. Evans sued the Chicago police and various individuals for railroading him.

Now, in his lawsuit against the police, he discovered this about the one eyewitness to his crime:

Evans got a new perspective on her motivations back in 1976. She explained that after weeks of insisting to the police that she did not know the assailants' names, the police again brought her to the station, held her there from morning until late evening locked in a roach-infested interrogation room with no bathroom, and made veiled threats about their ability to make people talk. She also revealed that the police were the first ones to bring up Evans's name, asking Januszewski whether he could have been among the men she saw. None of this was known to Evans at the time of his trials.

The police lawyers first argued that Evans, due to his conviction, was estopped from making this claim. The appeals court says this argument is "absurd." The police also argued that Evans, even though he didn't know about this misconduct until now, waived his rights by not pursing this claim back in the 1970's. The appeals court wasn't buying it, to say the least:

The defendants' [the police] remaining argument, that Evans waived his claim against them by not pursuing it back in the 1970s, is too ridiculous to merit comment.

Some people always complain about supposedly frivolous lawsuits, and keep trying to impose limits on medical malpractice claims. How about some sanctions on completely frivolous defenses by law enforcement officers, instead?

Organelles

2006-04-25T06:53:00.000-04:00

Gah, so much work... so little time for posting.

However, I did see this post yesterday on the Daily Transcript. Alex had this to say:

Non-cell biologists have often viewed the cell as a bag of molecules. Over the years as cell-biology has developed, it became clear that this was a simplistic generalization. Cells are organized by a dynamic cytoskeletal network that can organize the cellular architecture. Cells are also subdivided into membrane bound organelles. The deeper we look into the cell the more we find that each cellular component is subdivided into specialized regions.

A typical cell biologist view. Now, I grant you that organelles do exist... but the idea that everything within a cell is neatly compartmentalized is a myth. It's a useful model - just like we tell even college students that there are only twenty amino acids, talking about the real complexity of the cell to college students is probably something to be avoided. We want to believe that everything has it's place - thus, we have things like the Yeast GFP Fusion Localization Database, which attempts to localize every yeast protein.

Of course, it's not that simple. The cell is basically a big gooey mess - the protein concentration of even a bacterial cell is about 135mg/mL. Proteins relocalize all the time in response to environmental cues. Moreover, things leak between compartments with some regularity. Just because a protein is predominately cytoplasmic doesn't mean it only has a role in the cytoplasm - it could easily be performing a vital role in the nucleus at the same time.

Weekend Whimsy

2006-04-21T13:20:00.000-04:00

It's been a long week, so why don't we go straight to weekend whimsy?

This was sent to me by a friend a while back: Angry Alien Productions, home of "the 30-Second Bunnies Theatre Library... in which a troupe of bunnies parodies a collection of movies
by re-enacting them in 30 seconds, more or less."

I haven't watched all of them yet, but Highlander and Star Wars are both excellent.

Genetic engineering

2006-04-20T07:49:00.000-04:00

I'm a strong proponent of genetic engineering. Drugs are fine way to treat various kinds of diseases, but they're messy - they typically have all sorts of side effects, both because they are generally systemic and because they tend to react with many different targets. They also generally can't restore the function of a broken protein - and protein based drugs generally require injections and expensive manufacturing. Eventually, the real cure for all sorts of inherited diseases, will have to come from genetic engineering.

I was thus horrified to read about the new Pope delivering a statement that attacks genetic engineering:

The Pope will deliver a blistering attack on the "satanic" mores of modern society today, warning against an "inane apologia of evil" that is in danger of destroying humanity...
Particular condemnation is reserved for scientific advances in the field of genetic manipulation. Warning against the move to "modify the very grammar of life as planned and willed by God", the Pope will lead prayers against "insane, risky and dangerous" ventures in attempting "to take God's place without being God".

Genetic engineering is hard enough to do when the Pope isn't attacking you! The genome is, perhaps not surprisingly, rather resilient to intervention. The FDA says that over 400 clinical trials of gene therapy have been performed, with little result - but we're learning.

Not all the news about gene therapy is bad... Ashanthi DeSilva, the girl who received the first credible gene therapy, continues to do well a decade later. She suffered a type of inherited immune disorder called Severe Combined Immune Deficiency, or SCID (pronounced skid), that left her susceptible to every passing microorganism... NIH researchers inserted a normal copy of the broken gene into some of her white blood cells, healing them, helping them function normally to restore her immune system.

In April, French scientists reported convincing evidence that they successfully treated a different form of SCID (X-linked severe combined immune deficiency, the type suffered by the boy in the bubble) with gene therapy. Four of the first five babies treated by Alain Fischer, M.D., of the Necker children's hospital in Paris have had "a complete or near complete recovery" of their immune systems after the treatment.
Meanwhile, researchers at Children's Hospital of Philadelphia, Stanford University and Avigen, Inc., a biotech company in Alameda, Calif., have reported promising results in hemophilia B patients. The team packaged a gene for Factor IX, a blood clotting protein, in a defective adeno-associated virus (AAV). They then used the AAV to insert the gene into patients who suffered abnormal blood clotting because they lack Factor IX. Normally, these hemophilia patients needed to inject Factor IX to prevent uncontrolled bleeding. In June, the researchers reported treating six patients with the Factor IX gene therapy. Even though the dose of the gene therapy was so low that no one expected it to help, it reduced the number of injections of Factor IX that these patients used on an ad hoc basis.

That doesn't mean it isn't dangerous - first of all to the patients! Jesse Gelsinger died in a trial of viral delivery vectors, and at least two of the French children later came down with leukemia. So, like everything else in life and in medicine, there's a tradeoff... but one of the children (at least) was later cured of the leukemia.

What makes it even more frustrating is that previously the Church gave germ line genetic engineering (a far scarier idea) some qualified support:

Germ line genetic engineering with a therapeutic goal in man would in itself be acceptable were it not for the fact that is it is hard to imagine how this could be achieved without disproportionate risks... A possible alternative would be the use of gene therapy in the stem cells that produce a man's sperm, whereby he can beget healthy offspring with his own seed by means of the conjugal act.

In any case, with or without the support of religious leaders, genetic engineering marches on- this time, a trial of a potential treatment for muscular dystrophy. Apparently the Church believes that we don't have the "full right of disposal over [our] own biological nature." It remains to be seen if that's true or not - but it doesn't take away from our responsibility to relieve suffering, if we can.

Ah, Congress

2006-04-19T10:16:00.000-04:00

No, this isn't a complaint about Congress - quite the reverse. One of the postdocs in my lab was having quite the problem with the INS - seems they wouldn't even answer the phone for him, and most of the automated phone trees lead to dead ends. So, he called his congressional representative - in the case, Michael Capuano. Two days later, the piece of paper he needs is now on its way. Hurray!

In other news, Alex over at ScienceBlogs sums up recent discussion on the biologist vs physicist debate with The Biologists Strike Back. He doesn't do a good job discussing the point I made - despite the quantity of biologists with good math skills, at the upper end, there are a lot more physicists who are really good at math. Razib now concedes the point that the GRE is a bad metric to use, though he still hasn't talked about how he used the wrong scoring threshold in an attempt to prove his point.

Random stories

2006-04-18T06:52:00.000-04:00

Yesterday was Patriot's Day (and more importantly from a traffic perspective, Marathon Day) here in Boston, so I took a posting holiday. Pretty busy this week, so I'm just going to mention a few interesting posts.

Over on Aetiology, there's a cool post on the genetics of obesity. Some researchers looked for single nucleotide polymorphisms linked to a high BMI, and they found one:
the SNP is about 10,000 base pairs upstream of another gene involved in fat metabolism, INSIG2 (insulin-induced gene 2), which encodes for a protein that inhibits the synthesis of fatty acid and cholesterol. This gene has already been implicated as a genetic factor in obesity in a previous study in humans, as well as a study using a mouse model, so it's likely that this SNP may be just a genetic marker for polymorphism in the INSIG2 or other genes in the region.
There were a couple of interesting posts last week over at YFS on the subject of being a scientist. One of the comments linked to this speech on You and Your Research, and it's a pretty interesting speech. One part that caught my eye was this:
If you do not work on an important problem, it's unlikely you'll do important work. It's perfectly obvious... The three outstanding problems in physics, in a certain sense, were never worked on while I was at Bell Labs... We didn't work on (1) time travel, (2) teleportation, and (3) antigravity. They are not important problems because we do not have an attack. It's not the consequence that makes a problem important, it is that you have a reasonable attack... The average scientist, so far as I can make out, spends almost all his time working on problems which he believes will not be important and he also doesn't believe that they will lead to important problems.

Finally, I noticed that my previous post is now linked to by an internal, password-protected forum over at Science Blogs. To those reading/discussing it (which, from IP addresses seems likely to include Dr. Smith, Dr. Lynch, and Dr. Myers) - internal forums of this type are contrary to the whole idea of blogging. If there's something to discuss, why not just comment or post on your own blog about it?

Controls and Physicists

2006-04-15T08:25:00.000-04:00

Two (ok, three) different posts over at Science Blogs caught my eye this morning. So, even though you were probably all expecting weekend whimsy today, we're taking a break.

The first was a post from Alex about the significance of negative data. It's a followup to his post about the three types of experiments, which I previously discussed. Alex points out the importance of controls:

Now to get back to the three types of experiments ... Many inexperienced researchers fail to perform control experiments and this often transforms explanatory science from type A into type B experiments (or into type C experiments). It is important to recognize that if you aren't performing exploratory experiments you should try to perform enough controls so that any particular result that you get from your experiment is informative. You should also perform controls when you undertake exploratory science, but it's hard to control for everything.

As a geneticist, I have something to say about controls - the most important thing to do before actually doing a screen (which is almost always a lot of work) is to test both positive and negative controls in your system before you actually do the screen. If your positive control doesn't work (or your negative control does), you need to rethink your screen. Of course, you'll still pull out false positives for whatever phenotype you're looking for - that's inevitable, but that's why secondary screens were invented. :)

Moving on, let's talk about physicists vs biologists. Over at Gene Expression, Razib first tries to apply a "cognitive smackdown" to physicists, and then attempts to move on to why physicists can't talk about biology. Basically, we have another continuation of the argument that people outside the field of biology can't possible be qualified to talk about evolution.

He first demonstrates that, on average, physicists score higher on the GRE in verbal, math, and writing than biologists:

Verbal Mean:
Biological Sciences - 491
Physics & Astronomy - 534

Quantitative Mean:
Biological Sciences - 632
Physics & Astronomy - 738

Writing:
Biological Sciences - 4.4
Physics & Astronomy - 4.5

Pretty impressive - the biggest shocker for me was that physicists write so well. Razib tries to make a leap - saying that "there are so many biologists out there today that there may simply be more high IQ biologists running around than high IQ physicists in absolute numbers." If, as Razib does, one sets a score threshold of 700 for math, there turn out to be more than twice as many biologists.

Of course, as one of his commenters points out,

It looks like there's an ~.5 SD spread between the two groups.... Quant thresholds of 700 just aren't high enough. It's rather easy to list a dozen physicists who simply seem to have been smarter than any biologist, and the best biologists are shockingly frequently from physics.

So, I took a look at the source cited by Razib - which also offers data on the top score for the writing and math sections, 800. 0.2% of both biologists and physicists scored 800 in the verbal section, so there's no real difference there - and in raw numbers, there are a lot more biologists. However, in the math section, while 4.9% of biologists scored 800, 26.4% of physicists scored 800 - in raw numbers, the number of physicists and biologists who achieved the top score are almost identical. On a slightly harder test, it is almost guaranteed that there would be more physicists with the top score than biologists. Just more proof that while statistics don't lie...

Anyway, Razib goes on to say:

just because most physicists do have a non-trivial potential in applying their skills in the biological sciences, that does not mean that they can pass judgment with any level of credibility from a position outside of that system science. There are many details specific to each domain of knowledge which are implicitly assumed, and so there are many technical issues and nuances which must be internalized in the biological sciences... But, a physicist has to immerse himself in the literature and internalize some of the implicit assumptions of biology, and so, become a biologist, to make credible comment.

Of course, when a mathematician does immerse himself in the biology literature and makes a statement Razib doesn't like, that isn't good enough for Razib. Interesting, isn't it?

ETA: To those visiting from the ScienceBlogs internal forum, please see my next post.

Jealous docs (and taxes)

2006-04-14T06:25:00.000-04:00

Ah, tax season. Most people like tax time at least a little, because they get a refund from the government. Alas, many grad students have to pay estimated taxes four times a year, including on April 15th, which usually more that offsets any small refund. Before I muse about taxes, though, a story about jealous doctors.

My neurosurgeon rocks. He routinely makes the list of "top doctors", both in Boston and nationally. He's smart, has great bedside manner, and admits when he doesn't know things - I was extremely lucky to be referred to him. So when I told him I was going to see an orthopedic colleague of his about how I was walking now, his response was "Yea, he's great! He'll be able to tell you what to do."

I guess there's a rivalry between neurosurgeons and orthopedic surgeons for herniated disk patients. It is apparently one-sided, like between the Yankees and the Red Sox. The orthopedist was full of snide remarks, like "Ohhhhh.... you went to a neurosurgeon." The best comment, though, was in reference to how well my first surgery went in relation to my second surgery: "I guess even [my neurodoc] can't get a miraculous result twice in a row." WTF? Who says that to a patient?

So, to summarize, my experience (which extends to a few other orthopedists) says this: if you have a herniated disk, go see a neurosurgeon. Heck, the problem (and pain) is that your nerve is injured. The trick during surgery is to keep the nerve healthy and not injure it further. Why wouldn't you go see someone who specializes in operating around nerves?

Onto taxes, though - every now and then, I hear grad students complaining about taxes, and sometimes claiming that grad students don't have to pay them. Firstly, grad students do have to pay taxes. To quote the IRS :

A stipend is defined as a fixed sum of money paid periodically for services or to defray expenses. The fact that remuneration is termed a "fee" or "stipend" rather than salary or wages is immaterial. Wages are generally subject to employment taxes

Now, why are grad students taxed? Really, it's for the same reason federal employees are taxed- because otherwise how do you compare salaries with others, who are taxed? I get emails every so often about trying to exempt graduate students stipends from taxes. It's really a pretty worthless idea - the moment such a thing was done, our stipends would all be slashed by 10-20% as the schools and the NIH saw the opportunity to save money. I wish people would put their energy into more useful quests - for instance, why aren't students eligible for the Saver's Tax Credit, which encourages low-income workers to save for retirement?

Health Care FUD

2006-04-13T07:00:00.000-04:00

The governor of Massachusetts yesterday signed into law a "universal" health care bill. Health care, especially that which requires hospitalization, is of course extremely expensive, and high health insurance costs bankrupt over a million American each year. About 75% of these people had health insurance, so insurance is not a panacea - but this bill is a step in the right direction.

The finances on this plan were delicately balanced. The state would have lost money from the federal government if it didn't manage to expand insurance coverage, and the state has a "Free Care" pool that covers the uninsured anyway, so some of this simply involves the diversion of existing funds. No sooner than the ink was dry on the bill though, than people started worrying about the cost:

A legislative staff analysis estimates that the groundbreaking healthcare plan would start losing money in two to three years, which could put pressure on lawmakers to spend more tax money, increase the fee on businesses or scale back the coverage of the sweeping bill. The analysis projects that the plan will be about $160 million short of its estimated cost of $1.56 billion in the fiscal year that starts July 1, 2008.

In truth, this has nothing to do with the health care insurance bill. Health care costs rise, and with or without insurance, the state would face a choice between providing care for the uninsured by raising taxes and fees, or cutting services. There's no reason to blame this (or even associate this) with the insurance bill. If anything, requiring those who can afford it to purchase insurance will cost the state less than simply providing care out of pocket.

So why the fuss? Well, certain people are scared. People like the editors of the Wall Street Journal, who say the plan ''is a recipe for higher taxes and more government intervention down the road." Even Romney, the governor, is a little bit scared - why else would he veto the $295 per worker Fare Share fee that is a vital part of the plan? It's pretty much a useless political gesture, as the legislature will override him. Moreover, it's an essential part of the plan, providing an incentive for companies to keep from dumping their health insurance costs onto their workers and the state.

Even with the FUD and the political battles, it's a good day for Massachusetts. Hopefully, it will soon be a good day for the rest of the nation.

Vendor reps

2006-04-12T07:36:00.000-04:00

I'm all excited about actually doing science this morning, so my post will be brief. Yesterday, Becky from IDT came to the lab and fed us pizza. IDT sells oligos (short pieces of single-stranded DNA), and are in a pretty highly competitive business, which is probably why they're my favorite company. They treat their customers really well - I've gotten lots of Tshirts (as seen on the left), a couple pizza meals, and various other assorted fun things from them, simply because we're such good customers. Their oligos are pretty good too.

If I'm going to praise one company, it's only fair to bash on some others. Qiagen, which sells kits to prepare DNA, is technically in a competitive market, but they're the equivalent of Microsoft; everyone uses their stuff even though it might be inferior and/or cost more. Getting stuff from those guys is difficult, but not impossible. All you really have to do is pull out an Invitrogen kit (ideally from another lab or stockroom) and start talking about how you're thinking of switching. Even so, they generally don't bring pizza.

Then there's my least favorite company of all, Denville. Don't buy from Denville! Even though their stuff costs a little less than good old VWR, you're definitely not getting the same quality product. Their reps can also be more than a little aggressive, and unable to take a hint. So, don't buy Denville!

Tuesday Roundup

2006-04-11T07:07:00.000-04:00

Fascinating, if true: the Boston Globe reports on a battery built by viruses.
A study on the project appeared in the April 7 issue of the journal Science....Tiny ''nanowires," one ten-thousandth the width of a human hair, run the polymer's surface and act as electrodes, the MIT study says. Each wire is a byproduct of benign viruses that have been genetically altered to string metal molecules along the polymer as they replicate. By manipulating a few genes inside viruses, the MIT team is able to coax the organisms into collecting molecules of cobalt oxide and gold.

Science

The NYTimes has an article on research into regeneration. Do we still have the latent ability to regenerate body parts (aside from the liver)?
Mark Keating, who studies regeneration in zebra fish, identified a gene that is essential for initiating blastema formation when the fish's fin is cut. Both this gene, called fgf20, and another he has found, hsp60, also exist in people, suggesting the genetic basis for regeneration may still be in place even though the body can no longer evoke it.
Yes, women can actually smell fear. A NY Times article (link not working) has this to say:
Women can unconsciously detect the smell of fear, new research suggests, and the smell improves their performance on mental tasks. Scientists collected sweat from seven volunteers -four men and three women- who watched horror movies while holding gauze pads in their armpits. Then, their sweat was collected while they watched videos with neutral emotional content. Sixty-eight women next performed a word-association task while smelling the pads... Without sacrificing speed, the women smelling the fear pads were more accurate than those in the other two groups when processing meaningful related words.

Chemosignals of Fear Enhance Cognitive Performance in Humans

Pathogen resistance as the origin of kin altruism

Science Education

2006-04-10T07:12:00.000-04:00

A great deal of effort goes into thinking about how to fix science education (and, I think, education in general). Dr. Freeride had quite the post on this last week, and (no surprise) US science education compares unfavorably to those in other countries such as Japan and Australia. The proposed solution is to involve scientists more closely in the teaching process.

Maybe it's time to re-examine what we require of people looking to be science teachers. Maybe we need to find an alternative route to credential those with serious scientific training who want to be science teachers.

Now, I don't think that this is necessarily a bad idea - I think it would be great if kids in high school got more exposure to "real" science, and getting teachers with more background in the science would be good as well. But is this the real problem? For starters, how are people supposed to proceed in science if they can't read?

In the United States alone, one in seven people (i.e., over 40 million people) can barely read a job offer or utility bill... the US Department of Education found that fourteen percent of American adults scored... below basic level in prose literacy.

Science is fun. People (kids especially) often find at least parts of science really cool. However, if they don't know how to read, they're never going to become scientists.

I also have been reading a lot of angst about postdocs and faculty jobs recently, both at YFS and The Daily Transcript. Over at the Daily Transcript, Alex had this to say:

this is a horrible time to be in academics. Low pay, high debts from years of schooling, and no time to have a family. Gone are the days when you can clone a gene and then get a faculty position out of grad school. But I guess our role today is to be kamikazes for the good of the nation, and if we don't like the situation it's because we're a bunch of whiney lazy GenXers.

Please. The pay has always been low, but postdoc salaries used to be much, much lower. What is low, anyway? Yes, you could have made a lot more going into industry. On the other hand, the NIH starting postdoc salary for 2005 was $35,568. Thus, any household with two postdocs is probably making at least $70,000. For comparison, the median household income in the US is about $43,000. So, a household of two postdocs is quite well off... not only is it enough to make you comfortably upper middle class, but you can even start a family.

Moreover, another commenter agreed that "the old-timers whine and yet - their PhD Dissertations are sometimes at the level of seniors honors research today." Gee-whiz, you mean it's easier to clone a gene nowadays? For those that are curious, PCR was only invented in 1985. I sometimes wonder how those old-timers managed at all.

Weekend Whimsy

2006-04-08T17:23:00.000-04:00

It's Saturday, and even though grad students everywhere (including myself) still have to go into lab, it's time once again for weekend whimsy!

Our first item of whimsy comes via Naked Under My Lab Coat, which points out this, um, great article, Sex Advice from ... Scientists. I don't know who these people they interviewed are, but their advisors clearly aren't working them hard enough.
I've been saving this post for a rainy day: Asparagus, Stinky Pee, and Scientific Curiosity. Asparagus can make the urine of most people smell. However, due to genetic variability, it's not true for everyone... and there's also a partially overlapping set of people who can't smell the effects of asparagus on urine. A pretty interesting read.
Last but not least, what weekend wouldn't be complete without another ridiculous post from Ed Brayton? This time he's taking on Cynthia McKinney, the representative who was grabbed while going into the House and hit a police officer. Apparently he's never heard of racism... or this thing called the U.S. Constitution, which specifies that members of Congress
be privileged from Arrest during their Attendance at the Session of their respective Houses, and in going to and returning from the same.

Still, at least he can provide us with amusement. That's all for this edition of Weekend Whimsy!

ETA: This is a little serious for weekend whimsy, but since Brayton takes issue with my comment... a commenter on Brayton's blog has this to say: "The constitutional issue is a non-starter. SCOUTS has already ruled that immunity doesn't apply to criminal issues."

Actually, the issue isn't that clear cut. For example, many police departments have rules mandating that "Members of Congress may not be detained for the issuance of a citation while they are in transit to or from the Congress of the United States." As for the civil vs. criminal issue, let's read what CSPAN wrote on the issue in 2000:

The Supreme Court ruled in 1908 that immunity pursuant to the arrest clause was applicable only to civil cases, and offered Members no protection against arrest on criminal charges. The courts have been otherwise liberal in their rulings pertaining to this matter... Freedom from "arrest" has been interpreted to mean also from detention or delay during an attempt at civil law enforcement. One jurist wrote that a Member of Congress should be given the maximum leeway in protection from routine law enforcement efforts because "a Member has superior duties to perform in another place." The argument went on to cite that when a Member is detained, the people he/she represents lose their voice in debate and in votes cast.

An ID check is, obviously, a "routine law enforcement effort," and in this case involved both detention and delay.

Oh, and what does Congress think? Well, the 107th Congress House Rules Manual has, among other things, this to say:

The Constitution of the United States limits the broad Parliamentary privilege to the time of attendance on sessions of Congress, and of going to and returning therefrom. In a case wherein a Member was imprisoned during a recess of Congress, he remained in confinement until the House, on assembling, liberated him.

Indeed, members of the House may not even be subpoenaed to testify in a trial about someone else:

The House has decided that the summons of a court to Members to attend and testify constituted a breach of privilege, and directed them to disregard the mandate (III, 2661); but in other cases wherein Members informed the House that they had been summoned before the District Court of the United States for the District of Columbia or other courts, the House authorized them to respond... The House, however, has declined to make a general rule permitting Members to waive their privilege, preferring that the Member in each case should apply for permission (III, 2660).

This little discussion of congressional law isn't so whimsical, but learning something new is always fun.

Friday Book Report

2006-04-07T07:47:00.000-04:00

I recently finished Polaris, a relatively new book (or at least a new paperback) by Jack McDevitt. He's a relatively good science fiction author, who tends to approach things as mysteries: why did this ancient civilization disappear, or why did these people die? Polaris is a locked-room mystery: the ship was found adrift in space with no one on board and apparently no way off.

Polaris was a luxury liner of sorts, and included six VIPs on board. As the protagonist explores the mystery of the ship, she explores the life of each of the people on board in some depth, searching for clues. One of these people was an anti-aging researcher, believed to finally be on the edge of a breakthrough. There are a couple quotes in the book that struck me, and I thought I'd share them.

People should only die when they fall off of bridges. Or swim with the sharks. No one's lights should go out because a clock hidden in his cells has struck midnight.

If we can stop the automatic funeral, kill it dead in its tracks, if we can stop the slow degradation that leads eventually to the grave, we will have the given the human race a gift beyond measure.

Wait for the first effects of winter to settle in your joints. Feel the first flutter of your heart, the numbness of your fingertips, the growing chill deep in your stomach as the horseman gallops closer. And he is coming. At a gallop, as you'll learn. Youth is an illusion.

Perhaps a little melodramatic, but after all, McDevitt is a writer. For the latest on aging research, check out the Anti-Aging Medicine and Science Blog, which I found only recently. There's an interesting post on someone who's building new bladders for patients from their own bladder-wall and smooth muscle cells.

More on the grandmother hypothesis

2006-04-06T07:03:00.000-04:00

Yesterday was a very busy day, because as I was walking back to lab after getting some coffee and a bagel, I heard some people in the elevator talking about a seminar by Cynthia Kenyon. Kenyon is one of the original generation of researchers who studied the genetics of aging, and discovered that the daf-2 mutation in C. elegans extended lifespan. daf-2 was later identified as an insulin receptor, thus launching the idea that lifespan could be extended by manipulation of the insulin signaling pathway. Continuation of this work recently led to the discovery of Klotho, an anti-aging hormone. So I dropped my work and my lunch, and hurried to the talk. The room was packed, but it was worth it - she's a great speaker.

At the end of the seminar, she stopped talking about worms and started talking about aging in people. As I've previously mentioned, humans live longer than would be expected - other primates die soon after their reproductive years, while humans have an extended post-reproductive lifespan.

The lack of an obvious evolutionary advantage to post-reproductive survival has led to the grandmother hypothesis: namely, that the existence of grandmothers, who can care for infants and provide wisdom and knowledge, conveys a survival benefit to a family or tribe that has a few elder members.

Kenyon mentioned this idea briefly, and then went on to claim that the validity of the grandmother hypothesis was demonstrated during the 2004 tsunami. Apparently, the survival of families that contained an older member was dramatically higher than those families that did not. Elderly people remembered previous tsunamis, and were able to get their families to safety. As Kenyon put it, "having an older member provided an enormous survival advantage."

I haven't found a study that talks about this, though one news article does talk about an island where it may have played a role.

On the island of Simeulue, reached by an aid flight late last week, they remember a tsunami of 1907... Locals never forgot the disaster and it helped them to survive when they felt the quake on Boxing Day.... "It became part of the folklore that as soon as we feel a quake we must run to high land."

If the survival benefit is true, it would certainly be dramatic evidence in favor of the grandmother hypothesis.

Universal Health Care

2006-04-05T07:21:00.000-04:00

On Monday, I posted about the costs of my surgery, and how I couldn't make a better argument for universal health insurance. Universal coverage is back in the news again, though, as my own Commonwealth of Massachusetts moves towards mandating universal health insurance. As Left I on the News points out, the bill works by requiring "all Massachusetts residents to obtain health coverage by July 1, 2007."

Now, that blog takes a pretty pessimistic view of this health care bill, viewing it providing nothing "other than subsidies to private insurance companies." I think that's unduly pessimistic. Even though other countries provide medical care, someone still has to pay for the doctors, medicines, and hospitals. In Massachusetts, anyone who doesn't have health insurance and "can afford it" will have to pay an additional tax - so basically, for the first time, health care will be explicitly covered via taxation, very much like the European model.

Now, there is an important difference here, in that it's still only insurance: every thing isn't free, and there will still presumably be high deductibles and other limits. On the other hand, even the Swedish system has a deductible (though at about 120 US dollars, it's pretty low).

I'd also like to answer a few questions from a commenter on my previous post, who apparently doesn't know too much about how health care works.

"Is MGH, Inc. making a fortune? Are its executives?" MGH is part of Partner's Health Care, which is a non-profit. Some parts of Partner's make a profit, others do not.
"If not, why would universal health care cost any less?" MGH and others charge patients without insurance substantially more than those who have insurance. Part of this is due to negotiated rates, but part of it is practical - MGH provides a lot of free care to those who can't afford it. In part, MGH makes up on this by soaking those who can afford to pay their rates, but don't have insurance - especially wealthy foreigners. For every patient who pays the full cash rate, MGH can afford to treat one or two other patients with similar symptoms for free. The big downside to this is that people who aren't wealthy but do have to pay, or who hit the limits of their insurance coverage, get hit with hefty medical bills. That's why medical bills and illness are the leading cause of bankruptcy.

This system is really only a step towards providing universal coverage, but I think it's important step to take. One problem though is the lack of an incentives for preventative care. An ounce of prevention is still worth a pound of cure, and children and their parents still have to go through all sorts of paperwork to receive free child care. Why doesn't the state simply cover every child, and increase taxes accordingly? Health insurance rates for family plans would probably even fall substantially as a result. We provide kids with free schooling, regardless of need, until at least age 18 -so why not free health care as well?

One more word about health care. Mojo Blog has a post about health savings accounts, in which they quote an administration official as saying:

Health care is expensive because the vast majority of Americans consume it as if it were free. Health insurance policies with low deductibles insulate people from the cost of the medical care they use — so much so that they often do not even ask for prices.

This is completely wrong. Actually, people don't use health care enough due to the expense. If you don't have a doctor because you can't afford one, and your child develops green poop, are you really not going to the emergency room? Of course, once you do that and you get a $900 bill, you're not going back unless you're at death's door.

Again, what we need is more medical care - where everyone can afford yearly checkups, and can catch things at an early stage. As a good example of this, Medicare pays for colorectal cancer screening - it's pretty expensive, but extremely cheap compared to treating cancer.

And of course, if you're in trouble, of course you're not going to care about the cost. Generally, the most expensive medical care is the urgently required kind. It's not like a new car or a big screen TV - there's no flexibility here. Even if the surgery will leave you in debt for the next twenty years, are you really going to stop the doctors from rolling you into the OR and saving your life?

Yeast Tips, Vol. II

2006-04-04T07:50:00.000-04:00

Alex over at The Daily Transcript has this post on the three different types of experiments that are referred to frequently in labs that he's been in.

Type A Experiment: every possible result is informative.
Type B Experiment: some possible results are informative, other results are uninformative.
Type C Experiment: every possible result is uninformative.

Now, I've heard of "the three experiments" as well, though it's been years since I've thought about it. Most of the commenters at Alex's site focus on the need to maximize the amount of type A experiments, but in my opinion, that's really hard. Even picking type B experiments can be difficult; once experimental variability is taken into account, it's often not possible to figure out ahead of time which experiments are type B and which are type C.

On to my yeast advice - a population of yeast has inherent variability. Even a clonal population of yeast will exhibit some variability. Colonies will grow at different rates, some colonies will suffer mitochondrial damage and grow up as petites, and viability assays in particular exhibit random fluctuations due to chance, as well as to tiny pipetting and plating differences. So, my rule of thumb for yeast work at the moment is: if your experiment only results in a 10% change in phenotype, it's time to give up and move on. I mean, yeast work isn't biochemistry!

The sort of inherent variability of yeast experiments leads to my second rule - do it in triplicate. There's a limited number of plates and cultures anyone can handle at one time, so this leads to an inevitable decrease in the numbers of strains or conditions you can look at, but it's worth it. Either it works, in which case you've got error bars and you're good to go, or you'll prove to yourself that it's not going to work. Error bars (and/or P-values) are critical if you're taking numeric data out of a yeast experiment. If you don't do things in triplicate, you're likely to get excited by data that won't turn out to be reproducible.

Previously: Yeast Tips, Vol I

The cost of surgery

2006-04-03T07:19:00.000-04:00

One month ago today, I was released from the hospital after surgery (an open semihemilaminectomy for a herniated disk at L4-L5). I was waiting with some anticipation for the bill. This is the first major medical procedure I've received the bill for, and am I ever grateful for insurance. So what does a laminectomy cost? This data is for Massachusetts General Hospital, March 2006.

Inital consultation with neurosurgeon: $310
Pre-surgical office visit: $169
Pre-surgical lab tests: $95
X-ray: $26
One neurosurgeon, for about 2 hours: $6,200
One anesthesiologist (priceless): $2,530
One night in a semi-private room: $1,925
Everything else, including fees to the hospital for the OR: $22,535.67
Post-surgical followup visit: $169

And the total is: $33,959.67... which doesn't include the visit to the orthopedist who diagnosed me, or the MRI needed to confirm the diagnosis. That's for a relatively short surgery (about 2 hours), with no complications and only one night in the hospital. I can't make a better argument for universal health care.

Identity and the internet

2006-04-02T09:58:00.000-04:00

I don't usually post on Sundays, but something interesting came up last night. John Lynch responded to my criticism of his previous blog entry. He didn't have anything shocking to say- although he states that I believe Hart to be "qualified to make comments on evolution sensu stricto." That's of course not true - I don't know Hart, I only know that he claims to have studied the field at some length (despite being a mathematician). As I commented to Lynch:

I don't claim that Hart is qualified to comment on evolution - I do, however, note that he claims to be (and gives reasons why). If we take his comments at face value, he seems to have put a decent amount of study into the question. You, however, saw fit to dismiss his criticisms out of hand due to his CV.

Something else caught my attention, though - the inability of Lynch to accept "dlamming" as a name. He tries to make it seem like I'm really sketchy by putting my name in quotes:

someone by the moniker of 'dlamming'... 'dlamming' makes a number of claims

Now, calling myself dlamming isn't exactly an attempt at disguise - it's fairly obviously the concatenation of an initial and a last name. It's also a fairly unique username, and a google search gives over 500 hits, including my web page. So, for the record, let me paraphrase Orac:

dlamming's "real" identity is an open secret, but he nonetheless keeps using the dlamming pseudonym because (1) he doesn't want his blog to be the first thing that comes up when people Google his name; (2) he has a long history on the Internet under this particular pseudonym; and (3) he likes it.

Weekend Whimsy - Dragon Edition

2006-04-01T10:25:00.000-05:00

I'm not a big fan of April Fool's Day, especially on the internet. While Google's jokes are usually pretty good, all other news items need to be taken with a big grain of salt. Some websites such as slashdot become completely unreadable.

On the other hand, sometimes people put enough work into their pranks that they are truly awesome. So, in honor of scientists with too much time on their hands, I give you The pyrophysiology and sexuality of dragons, published in 2002 in the journal, Respiratory physiology & neurobiology. In it, the authors examine "the means whereby dragons produce fire and steam", and answer the burning question of "how, since dragons are invariably male, the species can be propagated." The answer is both disturbing and misogynistic, but what else do you expect from S.T. Georgy?

Of course, you might not be into scientific reading on the weekend. In that case, I recommend checking out Cute Overload. There's even a picture of ponies.

Coffee time

2006-03-31T06:49:00.000-05:00

No one knows exactly when and where humans first discovered the uses of the coffee plant, though legend generally attributes it to an Arabian goat herder named Kaldi. However,

"Recent botanical evidence indicates that Coffea arabica originated on the plateaus of central Ethiopia and some how must have been brought to Yemen where it was cultivated since the 6th century." -- coffee research

Since that time, coffee spread across the Middle East, and eventually to Europe. Legend has it that many thought coffee should be banned by the Church, but "to their surprise, the pope, already a coffee drinker, blessed coffee declaring it a truly Christian beverage." Since then, coffee has become the world's most popular beverage, with over 400 billion cups consumed each year. Coffee is also the "second most traded commodity in the world, trailing only petroleum." And as everyone knows, coffee is the lifeblood of scientific research.

Despite the pope's blessing, some people have continued to study if coffee is bad for you. A variety of studies have generally been inconclusive, but some studies have suggested a link between coffee drinking and heart attacks. Now, Gene Expression points out a new paper suggesting that the risks of heavy coffee drinking are genetically determined.

Coffee is a major source of caffeine, which is metabolized by the polymorphic cytochrome P450 1A2 (CYP1A2) enzyme. Individuals who are homozygous for the CYP1A2*1A allele are "rapid" caffeine metabolizers, whereas carriers of the variant CYP1A2*1F are "slow" caffeine metabolizers....Intake of coffee was associated with an increased risk of nonfatal MI only among individuals with slow caffeine metabolism, suggesting that caffeine plays a role in this association.

Since there are no tests to determine which allele you have, the authors of the study suggest limiting yourself to "no more than four cups a day."

Ok, so where do you go for your coffee? Here in the northeast United States, there are two main options: Dunkin Donuts and Starbucks. Starbucks is more expensive, has (IMO) crappier coffee, and suffers from a distinct lack of bagels and donuts. So obviously Dunks is the place to go, right?

Well, imagine my disappointment when I read this blog entry about Dunkin Donuts yesterday. Flea, a pediatrician who frequents Dunks, had this to say:

Most of the moms in my practice pour coffee for Dunkin' Donuts. It's not a great job, but it's one of the only jobs they can get. There are several reasons for this, but the essential reason is that DD's doesn't ask them about their immigration status.... Why? Because DD's dirty little secret is that they cannot stay in business without illegal aliens. Conservative protestations to the contrary are simply not credible. Consider the testimony of Ana (not her real name), a new mom I saw in my office yesterday.
"I've worked in Dunkin' Donuts for five years. In that time I worked with at most 20 Americans. They were basically very stupid high school students who after one week would still ask me how to make a coffee. They did not stay very long. And a Brazilian can pour four coffees in the time it takes an American to pour one."

Now, Dunks is a franchise system, so the actions of the location near Dr. Flea may be quite different than the Dunks near you. He also doesn't mention how the workers are treated. It's something to think about the next time you get some coffee - are the workers who are toasting your bagel and pouring your coffee being taken advantage of, just because they want a better life and opportunity for their children?

Thursday in the news

2006-03-30T13:14:00.000-05:00

Quite a few interesting items in the news today...

catswym points out this item on IQ and brain development. Basically, it seems that the brains of smart kids seem to develop more slowly:
The brain's outer mantle, or cortex, gets thicker and then thins during childhood and the teen years. The study found that in kids with superior intelligence, the cortex reaches its thickest stage a few years later than in other children.... One analysis found the cortex in kids with the highest IQs -- 121 to 149 -- didn't reach maximum thickness until age 11. Children who were just slightly less bright reached that point at age 9, and those with average intelligence at around 6.
Don't know what your IQ is? You can always wait for the next airing of Test the Nation.
There's an article on Seed about the new Thank You For Smoking movie. The writers at Seed take issue with "the outrageous claim that smoking might help alleviate Parkinson's disease." Of course, as previously mentioned here, smoking is correlated with a decreased risk of Parkinson's. When a movie actually gets some science right, it's good to applaud them.
A Chance to Cut is a Chance to Cure has this year's entry for grossest pictures. Hernias are pretty scary stuff.

Admitting problems

2006-03-30T06:28:00.000-05:00

Spring has now definitely arrived, and along with winter, college admission season is also drawing to a close. Now, students across the country have offers in hand, and they'll have to decide where they want to go. Of course, as Uncertain Politics discusses, just deciding who to admit is traditionally a hard problem. The students most desired by any school are likely to receive offers elsewhere; and while it's beneficial to admit the maximum number of students your school can handle, going over that number is a big problem. Ensuring racial, ethnic, and now gender diversity adds to the difficulty of this problem.

Today, two-thirds of colleges and universities report that they get more female than male applicants, and more than 56 percent of undergraduates nationwide are women. Demographers predict that by 2009, only 42 percent of all baccalaureate degrees awarded in the United States will be given to men.

As a society, I think we tend to overvalue college degrees; many jobs, including some highly technical ones, really shouldn't require a college degree. The article goes on to discuss the validity of affirmative action for white men, so that less qualified men are accepted in order to maintain the gender balance of a college. Of course, this is essentially a zero-sum game; there are really only so many college students to go around, so even if a few schools practice this kind of affirmative action, most schools in the future will have far more women than men.

Graduate school admissions are a different problem entirely, and I found these two posts on how to get into grad school and choosing a grad school. There's some good points there, but I have my own comments on getting into grad school.

Biology grad schools do look at grades, but if you majored in something like nuclear engineering, your grades don't reflect too much on your biology skills. The general consensus when I was applying seemed to be that the GRE Subject test was more important for me, and also more important for anyone who had been out of school more than a couple years.

In my opinion, bio grad schools mainly look for one thing - research experience. For most people, it takes probably about a year of lab experience before things start to work and you get "the hands." The hands can also be lost in as little as 6 months, so recent research experience is best. Anyone who has decent grades can be trained in lab work, but it takes time and money - so they'd rather take people who already have basic lab skills. Just as important, you also have some idea of what you're getting into, since the reality of lab work is quite different from the theory.

One other comment - just because you want to work with a professor, even if you get along with them, it doesn't mean that the lab environment there will be right for you. Some labs are quiet, some are loud, and in some everyone can quote the latest episode of the Simpsons. Finding a lab that fits you is maybe even more important than finding an advisor you get along with.

Sleepy Wednesday

2006-03-29T07:10:00.000-05:00

Wikipedia defines sleep as "the regular state of natural rest observed in all mammals, birds and fish." Others define sleep as "a natural and periodic state of rest during which consciousness of the world is suspended." However you define it, most people I know are usually pretty tired due to a lack of sleep. Many people have sleep problems of one kind or another.

How much sleep do we really need? A few years ago an article came out demonstrating that those people who got about 7 hours of sleep per night actually lived longer than those who got 8-9 hours per night. New research shows that even less sleep is required.

A six-year study Kripke headed up of more than a million adults ages 30 to 102 showed that people who get only 6 to 7 hours a night have a lower death rate than those who get 8 hours of sleep... The Cancer Prevention Study II even showed that people with serious insomnia or who only get 3.5 hours of sleep per night, live longer than people who get more than 7.5 hours.

Even though you may not be happy about it, 3-4 hours of sleep each night is better for you than getting 8 hours per night. Given this result, it's odd that about 25% of Americans now use sleeping pills. Says the article, "The risk from taking sleeping pills 30 times or more a month was not much less than the risk of smoking a pack of cigarettes a day."

Next up, I'm a bit of a morning person- I have been since my senior year of college. On my own, I generally wake up by 7 am, and get pretty sleepy by 10 or 11 pm. Most people I know get up at least an hour later, which lets me get a slightly early start on the day. So what would life be like if your body forced you to wake up by 4 am every day? That's the case for one family in North Carolina, where two of the four people have Advanced Sleep Phase Syndrome. People with this syndrome generally wake up between 1 and 3 am, and fall asleep between 6 and 8pm. And you thought I went to bed early!

Once you've headed off to bed, if you're a postmenopausal woman, you may suffer from hot flashes. Estrogen is one possible solution, but it can't be used by women who've had breast cancer, and it has a variety of other side effects. The NY Times has an article on gabapentin, which seems to treat hot flashes with a minimum of side effects and drug interactions.

Finally, have you got something on your mind? You might have trouble sleeping. Livescience reports on a study of how many people find something morally wrong. It includes:

Drinking alcohol excessively: 61 percent
Having an abortion: 52 percent
Smoking marijuana: 50 percent
Homosexual behavior: 50 percent
Telling a lie to spare feelings: 43 percent
Sex between unmarried adults: 35 percent
Gambling: 35 percent
Overeating: 32 percent

So, the lesson here is: don't drink to excess. If you do, you might wake up in the middle of the night worrying about it... and even if you don't, drinking increases the likelihood of sleep apnea. People with sleep apnea don't sleep as deeply as normal, and don't dream as much.

Of course, as seen at left, grad students and postdocs need to get sleep whenever and wherever they can.

Praying for an open mind

2006-03-28T07:20:00.000-05:00

Last Friday, the Washington Post published an article on the effectiveness of prayer for healing. It's not surprising that this was done; scientists and doctors have studied the effect of prayer on individuals for years, and as one researcher said, "It's one of the most prevalent forms of healing. Open-minded scientists have a responsibility to look into this." Indeed, over the years, it's been shown that

the devout tend to be healthier. But the reasons remain far from clear. Healthy people may be more likely to join churches. The pious may lead more wholesome lifestyles. Churches, synagogues and mosques may help people take better care of themselves. The quiet meditation and incantations of praying, or the comfort of being prayed for, appears to lower blood pressure, reduce stress hormones, slow the heart rate and have other potentially beneficial effects.

Sounds pretty good, right? For similar reasons, doctors even recommend meditation as a complementary therapy for those undergoing cancer treatment. Now, given the success of these types of studies, it's not surprising that one might also study intercessory prayer (which involves other people praying for a sick person). The government, along with some other groups, has spent some $2.2 million over the last five years studying this effect, with mixed results to date.

Now, this isn't a lot of money, basically enough to run one research team for a few years, but PZ Myers is outraged. Indeed, he goes so far as to say that he rejects prayer research out of hand... and even offers some specific criticisms.

He says that "It has failed multiple prior tests." Well, there certainly is such a thing as beating a dead horse, but the article actually also mentions studies where prayer may have worked.
He says "There is a lack of mechanism... even if a statistical correlation popped out of the results, there is no prospect for deeper understanding. It lacks predictive utility." That's just silly. Something can be useful to people even without a known mechanism, and deeper understanding of physical mechanisms can really only come once you have a reproducible effect to study.
One of the anti-prayer researchers complains about the study design, saying that "In science, you have to predict in advance what effect you may have." Well... that's true, and it's not true. In a preliminary study, predicting a beneficial effect, without specifying exactly what you're looking for, is perfectly fine. Once you find a possible effect, you then need to do a new study to see if it's real. Some of the researchers mentioned in the article have done that, and are, for example, specifically measuring the growth of collagen.

In any case, whether it works or not, the government really isn't spending a lot of money on this. And, quite frankly, I think it's important that we continue to try and research things that are a little outside the mainstream. One example of this was the NASA Breakthrough Propulsion Physics project, which for six years funded quite a bit of thought and research on the subject of antigravity and faster-than-light travel. Now of course we don't have FTL travel yet... but as I previously noted, the Europeans may be on the trail of antigravity after all.

So hopefully PZ Myers will keep an open mind, and behave more like a scientist:

[They] would not try to stop an attempt... They would wait with intellectual interest to see how it turned out. They might believe or disbelieve or suspend judgment. But they would not oppose; they would be delighted if [he] succeeded. The joy of intellectual discovery - the mark of a true scientist. --Robert Heinlein

Evolutionary math

2006-03-27T07:02:00.000-05:00

Mathematics isn't biology, and with a few exceptions, mathematicians aren't biologists. On the other hand, math is very important to some areas of biology, including those dealing with evolution. For example, population genetics can be defined as

a family of mathematical structures the aim of which, as Richard Lewontin (1974, p.12) puts it, is the "study of the origin and dynamics of genetic variation within populations". --hpb

Math enables scientists to calculate when man diverged from primates, and to figure out when and where the mitochondrial eve, "the most recent common matrilineal ancestor of all living humans," lived. Mathematics combined with computer science has allowed evolutionary biologists to create in silicio simulations of gene flow within a population, and even force the evolution of computer circuits.

So one might think that a mathematics professor and computer programmer who's "read countless texts on geology, biology (and cosmology) in a multitude of sub-disciplines, " might be qualified to discuss evolution. You might think that... until you learn that he disagrees with you.

Yes, the DI has added another 100 or so names to their list of scientists who doubt evolution., including an assistant math professor, Dr. William Hart. Much like Ed Brayton did, two bloggers have gone on the attack, including Razib and John Lynch, an evolutionary biologist, who tears into Hart as someone without "any relevant training and experience in the life sciences." Of course, if they had read his letter, they would also have seen this:

As a mathematician and experienced computer programmer, I find it disconcerting that genetic and other evolutionary algorithms are pointed to as evidence that evolution works. The fundamentally flawed principles that these "experiments" are based upon and the derisible simplicity of the systems "evolved" both have more to say about the failure of evolution to produce meaningful innovations than it does about the robustness of the theory of evolution.

Now, I'm no expert on genetic and evolutionary algorithms, so I can't say how valid Hart's specific critique may or may not be. However, Hart seems to have relevant experience and expertise in regards to (at least) this one area... while Dr. Lynch seems to mainly study the morphology of bones.

In the end, this is just another example of the hypocrisy practiced by Ed Brayton. If you express doubt about evolution and you're not a biologist, you clearly don't know what you're talking about. Even if you're a physician or chemist who's studied biology for years, sitting through tons of organic chemistry and pre-med classes, it doesn't matter, because you're not a biologist. And of course, if you are a biologist and you expresses doubt about the theory of evolution, well then, your opinion doesn't matter because you're not an evolutionary biologist.

On the other hand, if you support evolutionary theory, you can tell everyone else they don't know what they're talking about... even if they're a mathematician, the subject is evolutionary algorithms, and your own area of study is the "temporal bone morphology of great apes and humans."

Weekend whimsy

2006-03-25T10:29:00.000-05:00

Sometimes it's hard to separate the whimsical from the weird, but I saw this over at Pharyngula: a sculptor made a statue of B ritney Spears giving birth.

"Monument to Pro-Life: The Birth of Sean Preston," believed Pro-Life's first monument to the "act of giving birth," is purportedly an idealized depiction of Britney in delivery. Natural aspects of Spears' pregnancy, like lactiferous breasts and protruding naval, compliment a posterior view that depicts widened hips for birthing and reveals the crowning of baby Sean's head.

The monument also acknowledges the pop-diva's pin-up past by showing Spears seductively posed on all fours atop a bearskin rug with back arched, pelvis thrust upward, as she clutches the bear's ears with "water-retentive" hands.

Of course, I doubt that anyone would think twice about this statue if it wasn't one of Britney Spears... but I do find it weird that the bearskin rug is "traditional." At least sculpting a bearskin rug doesn't harm any bears.

In less weird news, and for hours (or seconds) of whimsical weekend fun, I give you Homer's Beer Run! Catch all you can... unless it's on fire. You just can't get enough of that wonderful Duff!

Friday Round Up

2006-03-24T13:00:00.000-05:00

It's Friday again, so time for a quick science roundup to start the weekend off right!

First off, we have breaking news from Europe: Scientists there have successfully made a gravitomagnetic field by rapidly spinning a superconductor. To quote a slashdot commenter, it's not a gravitational field
but a "gravitomagnetic one", which is a field that moving objects with "gravitational charge" (i.e., anything that produces gravitational force) make. it acts to repel or attract other gravitational charges. Still a huge discovery if true, could lead to inventions like (non-electromagnetic) "artificial gravity" or "force fields" or "levitation fields"
Nanotech finally shows some therapeutic utility in biology, with the advent of nanoknitting. Injected nanofibers were able to stimulate the repair of damaged optic nerves in 3/4 of hamsters. Human trials are of course far, far in the future.
Hot or cold comets? Comets are supposed to be the remnants of the solar system, and formed far out in the depths of space, where it is very cold. However, particles that NASA retrieved from a comet "include an exotic titanium-vanadium-nitrogen blend that forms in temperatures higher than 2,012 degrees Fahrenheit." Models of how the solar system formed will have to be reexamined, providing employment for many NASA scientists.
A story I've been meaning to get to for a few days: hot peppers may be good for prostate cancer. "Capsaicin, which makes peppers hot, can cause prostate cancer cells to kill themselves" via apoptosis. More reason to eat spicy foods.
Finally, via The Scientific Activist, genetic engineering can be used to make tiny structures, including smiley faces. Something to brighten anyone's day.

classifications B

2006-03-23T13:31:00.000-05:00

so, i'll pipe in again here.

altho, i rather enjoyed the description of geneticists the biochemist description was QUITE lacking.

as another biochemist points out here.

"Palazzo has omitted perhaps the most important machine for the biochemist: the spectrophotometer...and not just the kind molecular biologists try to avoid using except to measure cell ODs. A real biochemist's spectrophotometer has a stopped-flow attachment. If you ask a real biochemist to show you pretty data, they don't show you bands...they show you a table of numbers with headings like K_m, k_cat, and V/K. In fact, they hesitate to show you primary data at all. They might show you the fitting program they still have running on an aging computer, written in FORTRAN."

i completely agree with not showing people your gels. unless you're a nucleic acid biochemist, maybe. or a molecular biologist.

altho, i still take issue with the "stopped-flow" sentence.

who needs stopped flow when you have lasers and are using single molecules?

Classifications

2006-03-23T11:47:00.000-05:00

A number of bloggers are apparently talking about the taxonomy of scientists. Some of it's clever, some fairly dull, but of course I was most interested in the description and classification of the biological sciences. I guess I'm closest to being a geneticist:

Geneticist:
Geneticists make mutants - that's it. You might think that this sounds boring, but you have to see it from their perspective. They're like the druids, or the freemasons ... in others words some club. Well really 3 or 4 clubs: fly geneticists, worm geneticists, yeast geneticists, and others. Incidentally this last group is the weirdest - they chant incantations such as "the awesome power of yeast genetics". And that's not to say that the others aren't weird. For example, fly geneticists torture the rest of the biological establishment by giving crazy names to their mutant flies (for example Sunday driver - whose neurons have aberrant vesicular traffic). The key to being a successful geneticist is to set up a good "genetic screen". If you ever meet geneticists, ask them about their screen; it'll make them happy. Using their powers, geneticists have probably had the most insightful discoveries of all the disciplines described here. Geneticists kill whole organisms, not only to find out what gene they've "knocked-out", but to see how their poor mutant creations look. Scary.

Some of this is true - although for a geneticist, I haven't conducted very many screens... and it's fair to say that those I had conducted are fairly biased. I am, however, a fan of the awesome power of yeast genetics. Unfortunately for the yeast, there are a variety of techniques under development to enable targeted knockouts in human cell culture - and if it ever becomes really easy, the awesome power of yeast genetics may fall out of favor.

In my opinion, the true beauty of yeast is that it's a simple system - there are many fewer genes than in human cells, there are expression profiles for almost every gene under many different conditions, and the pathways seems to be much more straightforward. Not to mention that growing yeast will always be faster than growing cells in a tissue culture dish. :)

Holding it all together

2006-03-22T10:33:00.000-05:00

Surgeons may believe that a chance to cut is a chance to cure, but once all the cutting is done, the wound site needs to be closed. The first time I had back surgery, in 2000, my wound was closed conventionally, with dissolvable stitches. This time, I had the pleasure of being sealed up with Dermabond, which is basically a coat of Krazy Glue. Aside from being purple, what's the difference?

The difference between the Krazy Glue and [Dermabond] is that Krazy Glue is Methyl Cyanoacrylate, and [Dermabond is] 2-Octyl Cyanoacrylate. What's the difference? The Methyl Cryanoacrylate (Krazy Glue) makes a stronger bond, bonds immediate and is almost impossible to remove. --http://www.unhinderedliving.com/tears.html

Overall, it's pretty good stuff, and also enables you to take a shower 48 hours after surgery, while also acting as a barrier against infection. It is however a little disconcerting, because (at least in a mirror,) it looks like a giant bruise. It's supposed to come off within 10-12 days, but that doesn't seem to happen unless you're washing it every day.

Speaking of gluing people up, I was reading this article about QuikClot. It's a mineral powder that absorbs water at the site of a wound, causing clotting to occur much more rapidly than normal. It's pretty cool stuff, and is being used by the military and police departments. So why doesn't everyone use it?

"The safety problem in the way of QuikClot's wider use arises because of the large amount of heat the material releases when it absorbs water, sometimes enough to cause second-degree burns."

Whoops. So basically, the material also cauterizes the wound site, just like Sayid did to Charlie in Season One of Lost.

The Future

2006-03-21T13:55:00.000-05:00

I don't normally think too much about the future. While I do plan out the course of experiments, I don't usually worry too much about where I'll do my postdoc, or what kind of career I want going forward. Other people, though, think a lot about the future.

Some of the predictions I think most likely:

There will be more change in the next 50 years of science than in the last 400 years.
This will be a century of biology. It is the domain with the most scientists, the most new results, the most economic value, the most ethical importance, and the most to learn.

I agree generally speaking, but I question if the results of science will profoundly influence culture. It's hard to say, of course... but biology, generally speaking, doesn't seem as likely to change culture as computers and instant communication has. Then again, I'm not a futurist.

One of the predictions I hope becomes true:

Compiled Negative Results — Negative results are saved, shared, compiled and analyzed, instead of being dumped. Positive results may increase their credibility when linked to negative results.

I'm a big fan of negative results, having gotten oodles of them. I believe they should be shared as widely as possible. :)

The fight against bacteria

2006-03-20T07:34:00.000-05:00

As many people are aware, bacteria are increasingly becoming resistant to antibiotics. Some of this is due to improper use; antibiotics really shouldn't be used prophylactically in farm animals, and sick patients need to complete a full course of antibiotics, or the bacteria will rebound and become resistant. Some antibiotic resistance is probably unavoidable, a inevitable consequence of placing a great selection pressure on bacteria. One solution is to continue to make new classes of antibiotics, specifically tailored to beat resistance. My own former company, Enanta, is pursuing this route, and currently has a new antibiotic in phase 2 trials.

As an alternative, Mike the Mad Biologist tells us about phage therapy. Phage therapy relies on targeting bacteria with their natural enemy, bacteriophages, viruses that only target bacteria. Phage therapy was worked on extensively before the discovery of antibiotics, and continued to be used and improved upon in Eastern Europe and the Soviet Union. Phage therapy needs to be precisely targeted, as most phages only attack one species of bacteria, which is probably why it had a spotty record in the pre-antibiotic era. Furthermore, just as with antibiotics, bacteria can also become resistant to phages.

Finally, there's a solution that doesn't really involve drugs: crowd out bad bacteria with good bacteria. Instead of feeding the animals antibiotics throughout their life, baby chickens can be fed good bacteria, which colonizes the digestive tract and keeps salmonella from gaining a foothold. In the end, in addition to using less antibiotics, this should reduce the amount of food poisoning in humans. Of course, the best way to avoid salmonella poisoning is to become a vegetarian.

Friday thoughts

2006-03-17T15:43:00.000-05:00

Isn't he adorable?

In the news, Stephen Colbert mentioned the Ambien story last night. In true Stephen style, I'm forced to assume he stole the story from me. Stephen, you're on notice! Actually, he showed a CNN clip of the story, in which it appears that they actually filmed people in the act of sleep-eating. I still think it's incredible, though I learned today that one of my friends sleep-ate as a child. Wow.

DarkSyde decided to take up front-page space at DKos with these thoughts about alien life. If you're going to talk about alien life, why do you have to focus on sci-fi novels, and discredit them by adding crappy illustrations? Aliens might not look like us, or even want to interact with us, we get it. DarkSyde's had some good posts, but his science posts (ie, The Imaginary Conception) are starting to lose me.

"Intensive" use of statins may reverse plaque build-up in the arteries of people who've lived the American lifestyle. Pretty cool.

Could Crohn's disease be caused by bacteria? Tara Smith points to recent evidence that it is. Apparently 95% of patients with Crohn's treated with specific antibiotics by an Australian doctor have improved. The conventional wisdom is that Crohn's is an autoimmune disease that causes inflammation. The evidence isn't clear; a specific bacteria can induce Crohn's disease in mice but not other animal models, and some antibiotics suppress inflammation.

That's it for today. Have a happy St. Patrick's day!

That tricky brain

2006-03-15T08:33:00.000-05:00

I suppose many people have by now seen the NY Times article about the side effects of Ambien. It's incredible - Ambien, which is supposed to just be a sleeping pill, causes sleep-eating in a number of people, some of whom even cook while sleeping. One person even managed to get to the refrigerator each night while in a full body cast!

Less dramatically, I came across this article in Nature: Empathic neural responses are modulated by the perceived fairness of others. Functional MRI was used to play an economic game, in which some of the players were fair and others were unfair, and pain was applied to one of the players. Interestingly, men and women both showed empathy (as measured by brain activity) towards fair players who received pain, but only women were empathetic towards unfair players. The authors "conclude that in men (at least) empathic responses are shaped by valuation of other people's social behavior, such that they empathize with fair opponents while favoring the physical punishment of unfair opponents." There's unfortunately no way of telling from this experiment if the differences are due to nature or nurture.

Pregnancy and epigenetics

2006-03-14T10:54:00.000-05:00

The NY Times has an interesting story today about the struggle for resources between a mother and child. I can't do it justice here, but basically, epigenetic silencing of genes by the mother seeks to limit the amount of resources devoted to a developing embryo. However, epigenetic silencing by the father does the reverse, and seeks to increase the amount of resources devoted to the offspring. Overall, quite a fascinating story.

Money and medicine

2006-03-13T11:51:00.000-05:00

The ability of money to corrupt the practice of medicine isn't exactly breaking news. Pharmaceutical company representatives treat doctors who prescribe their drugs quite well, supplying them with free drug samples and informational seminars in tropical locations. Researchers with conflicts of interest have increasingly become an area of concern.

Even so, this story took me by surprise. To summarize briefly, a cardiology practice lied to a patient about the availability of a heart surgeon in another group. The patient was thus steered to a surgeon within the cardiology practice. Unfortunately for the patient, complications ensued. In the end, the cardiology practice will have to pay $5 million in damages for defrauding the patient.

Something to think about the next time you get referred to a surgeon.

Reading Incomprehsension

2006-03-13T08:15:00.000-05:00

A few weeks ago, I had the dubious pleasure of arguing with Ed Brayton, a "freelance writer and businessman." Our discussion was based on a NY Times article, "Few Biologists but Many Evangelicals Sign Anti-Evolution Petition". Brayton stated that "lots" of engineers had signed this petition, and that only "very few" biologists had done so. Since the article text makes it clear that this is not true (the petition was signed by 128 biologists and 75 chemists), I began to suspect that Brayton had at best only skimmed the article.

However, a new post by Brayton makes it clear that he actually has a problem with basic reading comprehension. As reported by the Boston Globe, "Catholic Charities of Boston announced yesterday that the agency will end its adoption work, deciding to abandon its founding mission, rather than comply with state law requiring that gays be allowed to adopt children." The board of Catholic Charities had voted unanimously to continue gay adoptions, but top church officials overruled them, saying that it was banned under church doctrine. It's a very sad story, especially for the children in foster care.

Back to Brayton, who posted that "Interestingly, the group decided not to ask for a religious exemption, which they can do under Massachusetts law." Of course, the Boston Globe article points out that:

Two leaders of the group asked the governor for an exemption, who replied that he didn't have the authority to do so;
The governor is planning to introduce legislation "to exempt religious organizations that provide adoption services from the state's antidiscrimination laws."
The legislation is considered unlikely to pass.

To summarize, not only did the group ask, but there is no such exemption under current Massachusetts law. This isn't a small point, either - a good chunk of the article deals with it, which is why I was surprised when I happened upon Brayton's post. I don't think Brayton made this mistake intentionally, but I'm surprised and dismayed that he appears to be unable to fully read an article.

Those dangerous law-abiding fools!

2006-03-10T16:10:00.000-05:00

I missed this story of reckless college students while I was out, but I noticed it today over at A Chance to Cut is a Chance to Cure : College students driving the speed limit. Apparently, these brave and foolish students decided to drive four cars at 55 mph on a highway near Atlanta, blocking all four lanes of the highway. As someone who drives quite rarely, the idea that everyone usually speeds has always bothered me.

The drivers behind then students were, as you might imagine, rather irate, and some behaved rather recklessly. The video, called Meditation on the Speed Limit, is pretty awesome, although I don't know if it deserves to win a film contest.

Something interesting to consider - if an accident had occurred, what crimes would the college students driving been charged with?

Back from surgery

2006-03-09T11:30:00.000-05:00

As previously mentioned, I had back surgery last week. Back surgery is fairly strenuous, and even though I only stayed in the hospital one night, I wasn't in shape for blogging until now. Even so, I will probably keep my entries fairly short - following back surgery, sitting is encouraged, but only in 15-30 minute intervals.

For those who are curious, I guess it went fairly well - I was out of the hospital quickly, and the surgery appears to have successfully resolved my leg pain. Unfortunately, I had some side effects - part of my foot is numb, and I have a pretty substantial foot drop. Now that my nerve is no longer compressed these may improve, but only time will tell.

I'll have more tomorrow, but for today, here are a few interesting items:

The Best: Accidental Discoveries (via Keat's Telescope)
Keat's Telescope also has a discussion on the evolution of alcohol production by yeast
Record Hot Gas: 3.6 Billion degrees Fahrenheit

RNA world, stuff.

2006-03-03T14:56:00.000-05:00

anyone who studies biology will know that current evolutionary theory proposes an "RNA world". "RNA world" describes a time when RNA would have served as genetic material (the way DNA does now) and as the primary catalysts (the way proteins do now).

RNA, however, is tricky stuff. It isn't very stable in water, and takes some energy to form (among other problems it has). So this leaves biochemists wondering how it got it's start--where was RNA first formed in any reasonable quantity? The suggestions up till now have been primarily warm places due to the need for energy in the formation of the molecules.

But Hauke Trinks thought about the problem a little differently. He thought sea ice might be the answer here. So he went up, WAY north and did some research to better understand the properties of sea ice.

Sea ice is quite different from freshwater ice, he explains.It's made of salt-free ice crystals enveloped by membrane-like layers of water, highly concentrated brine, carbon dioxide bubbles and salt crystals. The network of countless channels and compartments could provide surfaces on which RNA molecules could assemble and grow.

Back in the lab, Christof Biebricher "created artificial sea ice in a freezer, turning the freezer off and on every few hours to simulate the temperature fluctuations of the Arctic. He added a group of nucleotides, and waited."

Over a year later, they got their results.
They found long chains of RNA (over 400 nucleotides), mostly in the correct chemical composition.

This is especially auspicious result given the relative abundance of ice on other planets and the hope that they may contain life, also.

It doesn't answer many questions (where did the nucleotides come from? they seemed to have an RNA template around. etc); and it raises new ones (the earth wasn't presumed to cool for a long while so how far back would this push the start of evolution?).

But it is always very cool to see science looking at problems from different angles.

(BTW, i apologize in advance if you do not have access to the nature link, but i couldn't seem to find a news brief from any other source, at least not in english.)

Off to surgery!

2006-03-01T09:56:00.000-05:00

I hope all of you who've stopped by over the last few weeks have enjoyed reading Saccharomyces. Unfortunately, I am undergoing a discectomy to resolve problems with my back (specifically, a disk herniation at the L4-L5 level). While this type of procedure generally requires only one night in the hospital, it's likely that I won't be in any condition to blog for several days thereafter. My regular posts will resume later next week. In my absence, catswym may post a few thoughts of her own, so be sure to continue to stop by!

Recent news items

2006-03-01T09:41:00.000-05:00

I don't have time to go into these stories in depth, but here are some interesting stories I've seen recently.

Are hard workers more likely to get Parkinson's disease? It's possibly that a hard-working, risk-adverse personality correlates with Parkinson's.
How much oil does Saudi Arabia supply? Everyone knows that Saudi Arabia supplies a lot of the world's oil. However, Juan Cole makes the interesting point that many countries (like the United States) count towards that oil production total, but use that oil for domestic consumption.
the Saudi production is 11 percent of the world total, but it is far more than that of the amount of petroleum available for anyone else to buy.
If we ever do get off of oil and move towards a hydrogen economy, it could be powered by mutant algae.
Finally, a terrible story in which a cardiology group lied to a patient about the availability of his surgeon, because they wanted him to be operated on by someone within the group. On the bright side, he won $5 million dollars in compensation for the injuries he suffered as a result.

Virus linked to prostate cancer

2006-02-28T10:07:00.000-05:00

Prostate cancer is an interesting disease. The primary risk factor (other than being male) is age, and the average age of detection is about 70. Only about 10% of men die from prostate cancer, but many men die with prostate cancer: autopsies show that 80% of 80-year old men may have prostate cancer. Generally though, men diagnosed with prostate cancer need to be treated; on average, 60% of untreated men will die from their cancer.

To date, the cause of prostate cancer is unknown, although it has been linked to genetic factors, as well as to eating a western diet. Now, there's evidence linking prostate cancer to a virus. Research presented at a conference last week has located a virus in tissue samples from almost half of the men who had a genetic factor previously linked to prostate cancer. Perhaps not surprisingly, this defect is believed to impair the ability of the prostate to fight off a viral infection.

The technology used to find the virus is really cool - the ViroChip. The chip contains the sequences of all known plant and animal viruses, and thus enables samples to be rapidly screened for the presence of a virus. The ViroChip was also used to characterize SARS, and won its inventor a MacArthur fellowship in 2004. The discovery of a link between viruses and prostate cancer is exciting enough, but once the ViroChip technology is applied to other diseases, I suspect we're going to find many more cancers and diseases linked to viruses.

My evolved thoughts

2006-02-28T09:40:00.000-05:00

Well, after a number of back-and-forth comments, Ed Brayton finally said "I don't believe that educated people in general have a good idea what evolution is about." If that's not elitist, I don't know what is, so I think I've proved my point.

What this all boils down to is that Ed Brayton, as well as many commenters, think evolution is hard. It's not particularly hard - and it's certainly not so difficult that any doctors or chemists are going to have trouble with it. In many ways, it's similar to talking about physics - very, very few biologists are going to be able to do any of the math associated with general relativity, but the concept can be explained even to members of the general public in a few chapters of A Brief History of Time. Few doctors and chemists are probably able to walk straight into a lab and do PCR, or head out to a dig and excavate a fossil, but they're still capable of understanding evolution - and I think most do.

The hostility that this view has generated surprised me. While many commenters disagreed with me politely, some did not. According to various commenters, I am "incredibly dense", I have "no idea what scientists do", and it was implied that I am "unskilled and unaware of it." Most amusingly, I am apparently a "schmuck with delusions of grandeur yammering on his own ignorance, with no idea on what makes up science, how to do it or how one makes a contribution to science."

If the commenters feel so strongly that they're right, they should always trust the experts. The next time an engineer wants to put a perfectly safe nuclear power plant in your town, or your mechanic says you need a new transmission, please just step back and let the experts handle it.

Alternatively, if the commenters want to conduct an experiment to prove that doctors and chemists don't know squat about evolution, they should go out and conduct an experiment. Go forth, and ask a variety of people (chemists, doctors, biologists - heck, ask the people off the DI list) to describe evolution to you. Don't ask if they believe in evolution - just ask them to explain it to you. Write down or record the whole exchange. Always ask the same questions, and don't forget to get some evolutionary biologists to comment too - we'll need a positive control. Post the responses below, and we'll see who's right. Now that's the scientific method.

ETA: Wow, Brayton dropped the f-word on me.

Evolution and the scientific community

2006-02-27T14:03:00.000-05:00

Last Tuesday I posted "A little bit of hypocrisy," my take on the growing controversy about the list of 500 scientists who don't believe in Darwinian evolution. In short, I didn't like the approach taken by Ed Brayton, who dismissed the list on the basis that there were very few biologists. In fact, he went so far as to say that

How many biologists, geneticists or anthropologists are on that list? Very few. Lots of engineers of various types, a few chemists, but if you narrowed it down to those in actual relevant fields the number would be much smaller.

I called this position the absolute worst form of elitism. Now, Ed Brayton has a new post up, in which he admits he might be elitist, but he thinks that's ok. He repeats his previous argument, and says that "The DI's list of "dissenting" scientists is a very simple appeal to authority, but if one is going to make such an appeal the authority should at least be legitimate."

I've already replied on his blog, but lets think about the DI list:

Brayton misleads his readers as to how many biologists have signed the petition. The NY Times reports that of the 514 signers, there were 128 biologists, 76 chemists, 75 engineers, 63 physicists, 26 biochemists, and 24 professors of medicine. More biologists/biochemists signed the list than chemists and engineers put together. According to Ed Brayton and the NY Times, 128 biologists is "very few".
Ed Brayton says that "I'm certainly not going to put my name on any list to suggest that I have any legitimate authority in the field." Yet, he concludes that the non-biologists on the DI list, who are risking their professional reputation by signing, haven't put any thought into evolution at all.
Ed Brayton and the NY Times have pointed out that of the biologists, "few conduct research that would directly address the question of what shaped the history of life." It should be apparent that academic evolutionary biologists are a self-selected group who choose to study evolution, and who receive grants to do. Very few of these people are likely to have doubts about the validity of Darwinian evolution, and even fewer would be willing to admit it to their peers, let alone the public.

I think Ed Brayton, and anyone who supports the theory of evolution, should consider these three points. No matter how much Ed Brayton wishes it wasn't true, the DI list demonstrates there are a number of people within the scientific community who doubt the theory of evolution.

ETA: Brayton has posted a reply to this post, but has unfortunately chosen to attack this author instead of addressing the three points here. However, he does believe that there are people within the scientific community who doubt evolution; I may have misunderstood his views on this point. Interestingly, many commenters on his blog (and this one) still do not agree with this.

ETA: I've summed up my thoughts on this mini-controversy here: My evolved thoughts.

Patently obvious

2006-02-27T07:48:00.000-05:00

You've probably seen TV ads for Paxil, a drug for the treatment of "social anxiety disorder." It's also indicated for the treatment of depression, generalized anxiety disorder, panic disorder, obsessive compulsive disorder, and post-traumatic stress disorder. That's a pretty comprehensive list, so if you're wondering which of these problems you have, the manufacturer offers some online tests (GAD, SAD, PD, PTSD).

How can one drug treat so many problems? Well, Paxil (paroxetine) is a selective serotonin reuptake inhibitor, and thus increases the amounts of serotonin in your brain. In some people, Paxil can even be used to treat headaches, the side effects of diabetes, and bipolar disorder. With such great properties, it's no surprise that it made GlaxoSmithKline (GSK) $2.2 billion in 2002.

It also should come as no surprise that GSK patented Paxil in 1986, and filed an additional patent two years later. The second patent contained such novel ideas as drying paroxetine and "compressing the mixture into tablets." When Apotex, a Canadian generic drug company, filed with the FDA for approval to make paroxetine in 1998, GSK sued to stop them. Apotex finally began to sell paroxetine in 2003, after it was determined that GSK never held a valid patent. How much money did GSK make from the delay? It's impossible to tell exactly, but sales of Paxil fell 39% from 2003 to 2004.

The court battle continued even after generic Paxil hit the market, and finally wound down either in 2005 or 2006 - Decision of the Day seems to think 2006, but this decision is dated 2005[pdf]. GSK lost, Apotex won, and GSK's second patent on paroxetine was also ruled invalid. The decision on the second patent is quite interesting to read.

GSK's later patent was a "product-by-process" patent. "A product-by-process claim is one in which the product is defined at least in part in terms of the method or process by which it is made." These types of claims were at one time quite useful, because it allowed chemicals or medicines to be patented even if an inventor didn't know the chemical formula or structure of the medicine. A patent could still be filed, so long as the steps to create the compound were disclosed. As the judges in this case point out, "Today, however, product-by-process claims are used by inventors even if the invention could have been described independent of the process."

The key misunderstanding of GSK in this case was that product-by-process claims protect only the product, and if the product has previously been made and/or patented, it cannot be protected.

[Even] though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process.

Is there a good side to this story? GSK successfully made billions of dollars from a drug that was in reality first patented in the 1970's. Even now, they're taking in plenty of money from a new "extended release" form of Paxil, and they successfully delayed the introduction of generic Paxil by at least five years. There's no refund to the consumer here - those who bought Paxil at monopoly-inflated prices are out of luck. On the other hand, Apotex finally won. The only good news here is that once again, Canada has brought lower drug prices to America. Thank you, Canada.

Weekend whimsy

2006-02-25T14:05:00.000-05:00

Courtesy of Discovering Biology in a digital world, check out the wonders of Plants in Motion.The videos of the Venus flytrap are cool enough, but I especially like those of the "sensitive plant," Mimosa. The time-lapsed videos of plant growth and germination are also really cool.

And in the lighter side of news, apparently H&R Block messed up their own tax return. They understated their earnings by approximately $32 million - a "bookkeeping error". Oops.

Aging and the grandmother hypothesis

2006-02-24T09:25:00.000-05:00

The average human lifespan in western countries is about 77-81 years, but human lifespan is anomalously long. In contrast to most other species, including other primates, humans normally survive well past our reproductive years. The lack of an obvious evolutionary advantage to post-reproductive survival has led to the grandmother hypothesis: namely, that the existence of grandmothers, who can care for infants and provide wisdom and knowledge, conveys a survival benefit to a family or tribe that has a few elder members. Kim Lewis provides an excellent introduction to this theory in his paper, Human longevity: an evolutionary approach.

A new paper tests one aspect of the idea behind the grandmother hypothesis. As Keat's Telescope explains, different populations of guppies have different lifespans due to the environments in which they have been raised. The authors wished to see if the long-lived guppies were simply fertile for longer, or if the longer lifespan also lengthened the post-reproductive phase. The long-lived guppies did not have an extended post-reproductive lifespan, showing that there is not a grandmother effect in guppies. Since guppies do not care for their young, this was the predicted result.

The paper is a good source on other studies that have attempted to examine the survival advantages of post-reproductive survival. In some studies, reproductive success seems to be linked to post-reproductive survival.

Salmon are a particularly dramatic example of the evolution of resource allocation to reproduction, somatic maintenance, and post-reproductive lifespan because they stop feeding as they migrate from the ocean into their natal streams... In the population that Hendry et al. studied, there is variation in when females arrive at the breeding ground. Early-arriving females have an advantage in attaining the best breeding sites, but they must also live long enough to protect their nests... There is thus positive selection for post-reproductive survival in early-arriving females. These females do indeed live longer after laying their eggs than late-arriving females... but do so at the expense of reduced fecundity.

The salmon make a trade-off - they live longer, but lay fewer eggs while hoping that those eggs will have a better chance at survival. How about in humans? Lahdenpera et al. explains that "the post-reproductive lifespan of menopausal woman is strongly associated with their children's reproductive success." The children of post-reproductive mothers "enhance the lifetime reproductive success of their offspring by allowing them to breed earlier, more frequently and more successfully."

While the grandmother hypothesis remains to be proven, the guppy researchers also made a more fundamental discovery about fish biology: fish experience reproductive senescence. Just one more similarity between the aging process of Saccharomyces cerevisiae and fish.

Decline of the life aquatic

2006-02-23T07:53:00.000-05:00

Human activity has threatened life in the ocean since at least the early 1800's, when whale oil soared in price as whales became scarce. The decline of fisheries around the world isn't exactly breaking news either, and has been recognized as a serious problem since at least the 1950's. Fortunately, some whale populations have at least stabilized, thanks to the Endangered Species Act, and the attention brought to the problem by the popular album, "Songs of the Humpback Whale." Fans of Billy Joel got to hear about the plight of the fisherman (and the decline in the fish population) in 1989:

I've got bills to pay and children who need clothes
I know there's fish out there but where God only knows
They say these waters aren't what they used to be
But I've got people back on land who count on me

Despite the small steps we've taken to protect fish and whale populations, the impact of human activity upon the sea continues to increase. Drowning polar bears have been in the news recently; it seems that melting polar ice caused by global warming forces the bears to swim huge distances in search of food, and not all of them are able to make it. A new study has discovered that sharks inhabit only the top 30% of the ocean, implying that they are less resilient to human activity (primarily fishing) than previously thought.

Finally, if you thought that cats were a danger only to the proverbial goldfish in a bowl, think again: catswym points out that sea otters are being killed by toxoplasma, a cat parasite we've previously discussed. The otters are probably being infected by eggs found in cat feces, which in the case of outdoor and feral cats is deposited outside and eventually washes into the ocean. Toxoplasma infection "is a major cause of mortality in sea otters living off the Californian coast: Toxoplasma caused 17% of deaths in sea otters examined from 1998 to 2001."

There aren't any easy answers or quick solutions here (though you should keep your cat indoors and away from infected birds and rats). Unless we start treating the oceans and oceanic life a lot better, we're just going to keep losing more and more species to the side effects of human activity.

When I was your age

2006-02-22T14:02:00.000-05:00

When I was young, I could read and watch TV at the same time. Now that I'm in my late twenties, I can't do that anymore. The Boston Globe has this short piece on how our brains age. It seems that "older adults often struggle to focus on a task and are more easily distracted," and these findings correlate with the amount of activity in specific areas of the brain. Researchers have found that MRI scans of middle-aged adults show decreased activity in certain areas of their brains. As they age, these areas progressively slow down, becoming more and more like those of adults over the age of 65. Thus, "brain changes may actually begin in middle-age, long before the appearance of any outward signs of cognitive problems."

I don't want to drive any more book sales to Michael Crichton, but this might explain an observation made in Sphere, in which one of the characters deplores that he is now forty and hasn't accomplished anything.

Biologists can sometimes do important work late in life. Darwin was fifty when he published the Origin of the Species. And chemists sometimes do good work when they're older. But in physics, if you haven't done it by thirty-five, the chances are, you never will.

I might be done with my postdoc by then, so I guess it's fortunate I'm not a physicist.

Inital consultation with neurosurgeon:	$310
Pre-surgical office visit:	$169
Pre-surgical lab tests:	$95
X-ray:	$26
One neurosurgeon, for about 2 hours:	$6,200
One anesthesiologist (priceless):	$2,530
One night in a semi-private room:	$1,925
Everything else, including fees to the hospital for the OR:	$22,535.67
Post-surgical followup visit:	$169