Balancing Act

I constantly hear that the lack of women in Science, Technology, Engineering, and Math (STEM) is a huge problem that we must work to overcome. To a large degree, I support this view, but I always wonder if these rabid proponents think that it works both ways. Should we also be trying to increase the number of males in traditionally female-dominated professions, like Nursing?

Look at the facts: Nurses are in high demand and well-compensated, with median salaries around 45k, and specialists making much more than that. The lack of males in the field can, in large part, be attributed to societal pressures that say what jobs a man can and cannot do. This closely mirrors the situation with females in STEM fields. So where are the male-only recruiting scholarships in Nursing? Shouldn’t we be trying to break gender barriers in both directions?

I’m sure that this post is going to get me labeled misogynistic by some people, but I’m genuinely curious to hear responses.

Esoteric Jokes

A mosquito did cry out in pain,
“A scientist’s rotting my brain!”
The cause of his sorrow
was para-dichloro
diphenyl-trichloroethane

When Curtis Cooper and Steven Boone discovered the 44th Mersenne prime, Bruce Schneier had to change the combination on his luggage.

Man goes into a bar: Can I have a pint of adenosine triphosphate please?
Barman: Certainly sir, that’ll be 80p

Jean-Paul Sartre is sitting at a cafe, revising his draft of Being and Nothingness. The waitress comes out and asks him if he would like to order. “Yes madame, I would like a cup of coffee, please, with no cream.” The waitress hurries back inside, and just as quickly comes back out and says to Sartre “I’m so very sorry monsueir, but we seem to be out of cream. Would you like it with no milk instead?”

via this AskMe thread

Why Fund Basic Research?

The true power of things like abstract math and experimental science is not that it enables to invent things which we have conceived of but do not have, it is that it enables us to conceive of entirely new things which previously did not even exist in imagination.

Read the whole thing by 0xFCAF on Metafilter

Tips for New Grad Students

A fantastic list of Tips for new graduate students. If you’re a first year or thinking about grad school, memorize the contents of that post.

Cost of Sequencing

Over at Discovering Biology in a Digital World, Sandra Porter asks: Why is sequencing a human genome so expensive?. I chimed in in the comments talking about why Jim Watson’s genome was so much less expensive than the other current genome assemblies.

The other two, of course, are the Human Genome Project’s reference sequence, and J. Craig Venter’s genome, which was released just the other day. Did I mention that it was released in PLoS One, so it’s open access? Yay!

Auto-correct This

Keeping the bashing-on-excel theme going, here’s an old paper from BMC Bioinformatics: Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics

First of all, they got a paper out of stating the obvious? That’s it. I’m going to stop blogging and submit these posts to journals low on the prestige scale.

Second of all, duuuuuh. Auto-correct makes dumb assumptions about dates and numbers, so ‘RP11 | 12E3′ gets changed to ‘RP11 | 12000′. (12E3 = 12e3 = 12×10^3 = 12,000) Awesome, huh?

Another reason why you should stay the hell away from Excel.

Long Day

Some days it feels like all I do is convert files from one ill-defined data format to another.

And for those thinking about storing their massive dataset in Excel, let me give you some advice: Don’t.

If you don’t know why this is a bad thing, find yourself a bioinformatician and ask. Be sure to observe the look of horror on their face when you show them your workbook with 16 different sheets, all cross-referenced and full of arcane formulas that you’ll never be able to decipher. For bonus points, store multiple types of data in the same text field and don’t bother using a consistent format. (It’s okay because, I know that FM85436 is the same thing as 98TBE3)

Sigh. . .

More depressing news

From the latest issue of Nature:

NSF data show that the number of students in US graduate programmes in the biological sciences has increased steadily since 1966. In 2005, around 7,000 graduates earned a doctorate. But the number of biomedical PhDs with academic tenure has remained steady since 1981, at just over 20,000. During that period the percentage of US biomedical PhDs with tenure or tenure-track jobs dropped from nearly 45% to just below 30%.

That means 7,000 new graduates are fighting each year for one of the 20,000 total professorial positions available in academia. When you consider that a tenured prof may stick around until they’re 65 or longer, the situation looks grim.

Another scary stat:

And the average age of scientists earning their first R01 grant — the NIH’s bread-and-butter grant to an independent researcher — has risen from 34 in 1970 to 42 now.

This means that new researchers are being given fewer opportunities to get established. Without an NIH grant to your name, it’s damn near impossible to get tenure at a A-level research institution.

If there’s any good news to come out of this report, it’s this line:

The percentage of biomedical PhDs going into industry has tripled, from 10% to 30%, since the 1970s, the NSF reports.

So there seem to be opportunities elsewhere, as the biological revolution takes off and more industries begin doing their own research. As someone tentatively chasing the dream of a tenure-track position, though, it’s a little scary. Languishing in post-doc after post-doc doesn’t sound like much fun. I figure I have two things going for me, though. I don’t mind teaching, and bioinformatics is often fairly low-budget research. That opens up opportunities at smaller, liberal-arts type schools that many researchers won’t consider.

Hat tip: PZ Meyers (who seems to have hit all the same points I did). The comment thread over there is also worth reading.

The Strength and Weakness of Bioinformatics

In the “old days”, you would devote yourself to the study of a single system - a process, an organism or even a gene. You’d publish 20-30 papers entitled “Gene A in organism B encodes protein X involved with process Y” and eventually, be in the running for tenure. Bioinformatics means that we don’t have to work that way anymore. I can look at archaea one day, humans the next. I can apply whatever computational methods I see fit and am able to learn to any dataset that takes my fancy. In short, I don’t fit well into academia at all :)

–Neil Saunders

Link

Yeah, that sums up the situation pretty well.

The Trouble with Wikis

There’s been the usual buzz this year about replacing your notebook with a wiki for taking notes in class. Frankly, the buzz is bullshit. Wikis will never catch on as notebook replacements for a couple of reasons:

1) Mathematical symbols are a pain in the ass to represent in wikis. By the time you get the appropriate symbols and formatting in, you’re three equations behind the professor.

2) Assuming you don’t have a fancy-pants tablet PC, there’s no way to copy diagrams off of the board. I suppose you could use a digicam or something if you were really dedicated, but syncing all the pictures up with the appropriate pages of the wiki would be a pain.

3) Formatting is a pain in the ass to do in a wiki. When I’m taking notes, and there’s a REALLY important point, I might write it larger, underline it three times, or put a big star next to it. How do I do that quickly in a wiki? How do I connect concepts with an arrow, or write notes in the margins?

In my experience, wikis and other electronic note-taking tools have far too many disadvantages to make them viable alternatives to paper and a pencil. Sure, having a searchable archive of all my collegiate notes sounds great in principle, but ask yourself: How often do students really reference their notes from years ago, or even from the previous semester? (hint: it’s pretty close to never)

Wikis are great for doing some things, but note taking is not one of them.

Big Fish in a Little Pond

In Never trust a hypothesis?, Suicyte pens a good write up of the current state of big biology and small biology:

Imagine an old fashioned biologist, throwing out his hypothesis-driven fishing line into the pond of science, hoping that a particular fish will be attracted by the highly specific bait. Then imagine a group of contemporary way cool high-throughput researchers (those guys always come in large groups), trawling the same pond with their fishing net, catching literally thousands of fishes in the same time.

He goes on to talk about ways to think about the reliability of information gained in both types of studies. It’s a good read, but I have just one one minor complaint, which I commented on and will repost here:

Good write-up of the current situation in biology.

My only complaint is that I think your fisherman analogy sets big science and little science up as adversarial, where I see it as more of a synergistic relationship.

Big biology (high-throughput screens, genome-wide association studies, etc) is there to narrow down the list of potential targets to a manageable size. This knowledge allows your lone fisherman to test 2 or 3 likely hypotheses, rather than facing overwheming numbers of gene or proteins in a list.

I understand that the two approaches are competing for grant dollars right now, but I don’t think it’s a situation that will last much longer. Sequencing genomes is getting ridiculously cheap, and I expect that we’ll see similar advances in high-throughput proteomics over the next 20 years of so.

As the high-throughput technologies mature, they’ll require less R&D funding, and the small science labs will be able to pick up that money and go back to what they do best - proving hypotheses. The difference is, at that point, they’ll be doing it with vastly more information at their disposal. I see it as a win-win situation.

Star Light, Star Bright

Light pollution map of the Houston Area. So much for seeing the Perseid meteor shower tomorrow night.

The stars are one of the few things I miss about Kirksville.

Science is a bitch

Doing research in graduate school is a fairly bipolar experience. Some days, everything just seems to go wrong, and you feel like you should just drop out and join the circus. Other times, you finish a project and think, “Damn Straight - I am a fucking scientist!”

Today was a day when I hit both extremes within the span of 24 hours. In honor of that, here are links representative of the highs and lows of science:

The Good: Science. It works, bitches. (backstory)

The Bad: Study Finds Jack Shit.

And just for the hell of it, the ugly.

QOTD

“A knowledge of the true age of the earth and of the fossil record makes it impossible for any balanced intellect to believe in the literal truth of every part of the Bible in the way that fundamentalists do. And if some of the Bible is manifestly wrong, why should any of the rest of it be accepted automatically?”

–Francis Crick

QOTD

“Society bends over backward to be accommodating to religious sensibilities but not to other kinds of sensibilities. If I say something offensive to religious people, I’ll be universally censured, including by many atheists. But if I say something insulting about Democrats or Republicans or the Green Party, one is allowed to get away with that. Hiding behind the smoke screen of untouchability is something religions have been allowed to get away with for too long.”

–Richard Dawkins

I know the type

A shepherd is tending his sheep, and a man comes by and says, “If I guess the correct number of your sheep, can I have one?”

The shepherd says, “Sure - please try.”

The man looks at the flock and says “Eighty-three.”

The shepherd is completely amazed that he got the right number. The man picks up a sheep and starts to walk away.

The shepherd says, “Wait! If I guess your profession, can I have my sheep back?” The man says, “Sure.”

The shepherd says, “You must be a mathematical biologist.”

The man says, “How did you know?”

“Because you picked up my dog.”

(via the always excellent Carl Zimmer)

Cancer Genome Mapping

Our lab got some good press today, as one of our cancer genome mapping grants was officially announced. The goal is to use next-generation sequencing methods to quickly and cheaply identify structural variation in cancer genomes. This isn’t my primary project, but as always, the whole lab will be providing some peripheral support of the project.

Story in the Houston Chronicle and on the BCM webpage.

Dunning-Kruger effect

Simply put, the Dunning-Kruger effect is that dumb people tend to think they’re much smarter than they actually are.

Across 4 studies, the authors found that participants scoring in the bottom quartile on tests of humor, grammar, and logic grossly overestimated their test performance and ability. Although test scores put them in the 12th percentile, they estimated themselves to be in the 62nd

Also notable is that truly competent people tend to underestimate how smart they are.

See also:
Grad school makes you dumber
Lake Wobegone Effect

Is a PhD for you?

I ran across a great response to this question today:

Is it worth it for me to get a PhD if I don’t intend to hold a job that would require one and my only reason for wanting one is so I know lots of stuff?

Some excerpts from the best response (a few comments down):

Absolutely not. I don’t know what you plan to get a PhD in, but at least for my program you don’t burn 7 years of your life doing extremely difficult and complicated work for long hours with little pay if you are not planning to use it.

In the end a PhD is only school for a year or two. After that it is a job. A difficult, time-consuming, high-pressure job with little pay and a time limit.

There’s more:

It is not a place to be unless you are absolutely, 100% sure it is what you need for the life you want to live. It is not something that a sane person does for fun, and certainly not what someone does for no reason.

I enjoy it, I really do. But I know it is what I need to live the life I want, the life I have wanted since before I can even remember. And I am sacrificing a huge amount to do it. I do not know a single PhD student who is not certain that this is what they need for the career they have chosen. Those that were not certain are no longer in the program. And there are plenty who have developed doubts since entering.

He’s on a roll:

If your goal is to have fun it is even worse. You will be sacrificing a lot of potential pay you could be earning while working a normal job. When you get out you will have to compete with younger people who are more up-to-date on the latest material (since you would have spent the last several years focusing on an extremely narrow and probably esoteric topic to the exclusion of all else). It has serious costs that will hurt you unless you specifically plan your career path to take advantage of it.

These are the kinds of facts that everyone should know before they enter a serious PhD program. It’s not extended college, it’s not a lot of fun some days, and it certainly doesn’t make financial sense.

That said, most days I wouldn’t want to be doing anything else with my life.

Secularism and Stem-cells

John Wilkins writes a post about religion and society clashing down under:
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Clerical Catholic Imam, George Pell, has done it again. Proven why secularism is a necessity, that is.

He has threatened politicians who are Catholics with exclusion from communion, which is not quite excommunication but nevertheless still pretty drastic, if they vote in favour of a secular law permitting stem cell research.

He goes on to say:

Look, I don’t give a shit if Catholics think stem cell research is genocide and leads to dancing. They have no right to impose that view on the rest of the community that think it is just a procedure that offers some benefits in medical knowledge, and so far as most of us can tell, has no downsides to anyone.

I replied thusly:

While I’m an atheist and certainly support stem cell research, I can’t fault the Catholics here. From their perspective, this is a form of murder. Is that a ridiculous position? Absolutely. But given that they’ve taken that position, they believe that they have a moral obligation to try to prevent the murder. (Say what you want about the Catholics, but at least they’re consistent)

As long as they don’t use force or violence to achieve their goal, I don’t give a shit how they campaign for it. In fact, I’m glad they’re denying communion to supporters of stem-cell research. What they’re doing here is undermining their own institution. When they start denying communion to formerly wheelchair bound patients, or to the blind who have regained sight, the PR will be atrocious. Some of those people who are at odds with their pastors on this issue will be driven away from the church and towards a more secular lifestyle.

In general, when a religion stakes out ridiculous positions like this, the reality-based movement wins. In my book, that’s a good thing.