23andWe

Wondering how 23andMe plans on making money off of selling SNP chip results, when so little is known about most SNPs? Well, today they unveiled part of their master plan: 23andWe. After getting your results, you can go fill out fun little surveys, all the while helping 23andMe build a massive database of genotype/phenotype information that they can mine for new genetically-influenced traits. Clever.

BuzzYeah has screenshots and more info

Getting genotyped isn’t worth it yet, from a medical standpoint, but if I had 1000 dollars that I didn’t know what to do with, I’d sure do it.

Collins stepping down

Francis Collins is stepping down as the head of the NHGRI. Sure, I don’t agree with his take on religion, but Collins did a damn fine job of heading up the Human Genome Project, and then working his butt off in Washington to secure funding and political support for genomics projects. He’s a major reason that the field has advanced so rapidly in recent years.

In addition to his bureaucratic duties, Collins’ own lab does some pretty nice work related to genetic disease, including the very interesting syndrome known as progeria. He’s also a great communicator, and if you ever get a chance to hear him speak, either on his own research or on genomics as a whole, don’t miss it.

Pre-meds suck

Five reasons to dislike pre-med students. I knew a few who didn’t fit this mold, but a large percentage were exactly this kind of asshole. The major crime, in my opinion, is number one on the article’s list:

They are not motivated by curiosity.
If they ask a question in class, it’s often to find out what will be on an upcoming exam. Some of them volunteer to work in a lab on real research projects, but they don’t give it their all because they have no passion for scientific inquiry — it’s just another line on their résumés.

The biology and chemistry majors in my classes hated many of the pre-meds for exactly this reason.

Picture this: A professor is in front of the class, weaving an elegant story about complex processes working in perfect harmony to sustain homeostasis. She’s just getting to the most fascinating part, and a pre-med’s hand shoots up: “Will we need to know this for the next quiz?”

At this point, the other pre-meds nod in unison, while the science majors do their best to prove that negative thoughts can cause someone to spontaneously combust.

Some of the commentors on that article miss the point completely:

But as to us not caring or being uninterested in learning, I think that is completely false. We may not be interested in learning biochemistry or microbiology because these are courses we are forced to take but will not be needed by most future doctors. We do care about relevant courses that we take in medical school, but any “pre-med” course taken in undergrad is completely useless in our future careers. Would the average biochemistry major be interested in Gross Anatomy if they were forced to take it?

Where do I start…

First of all, if you think that doctors don’t need to know microbiology or biochemistry, I hope that I never end up in your clinic. If you can’t understand pathogenic organisms or the way in which pharmaceuticals affect the body, there’s no way I’m putting my life in your hands.

Secondly, yes, many biochem majors would be interested in gross anatomy. As a biology major, I tried to get into anatomy in college, because I wanted to satisfy my curiosity about how the body works at a deeper level. (The pre-meds were taking up all the open slots, though). A true education demands more than just vocational training. I know this is shocking, but being interested in learning means that you enjoy hearing about things that have nothing to do with your job. I’m a better person today because I dabbled in art, and learned more about world history. Knowing gross anatomy wouldn’t have directly helped my career, but it would have been fascinating.

To the few pre-meds I knew who bucked the stereotype, I’m sincerely sorry. After all, I was able to escape these dipshits after leaving college. You had to spend 4 more years in med school with them.

Dick to the Dawk

Fantastic. If you’re not familiar with the characters, they’re Richard Dawkins, PZ Meyers, Sam Harris, Daniel Dennett, Christopher Hitchens, and Eugenie C. Scott.

Unique Column Count in Open Office

Sandra complained about compatibility issues while teaching an online course, and in response, I and several others recommended using Open Office instead of excel. She responded with a list of reasons why she prefers excel, which included the use of pivot tables to count unique items in a column.

To prove that this is easy to do without using pivot tables in OO Calc, I whipped up a short screencast:

It’s a little small, but you can see the details by viewing it full screen.

I used recordMyDesktop to do the screencast, which makes it dead simple.

Gotta Have My Orange Juice

Richard Fenyman, world-class physicist:

Feynman remade quantum electrodynamics–the theory of the interaction between light and matter–and thus altered the way science understands the nature of waves and particles. He was co-awarded the Nobel Prize for Physics in 1965 for this work, which tied together in an experimentally perfect package all the varied phenomena at work in light, radio, electricity, and magnetism

Richard Fenyman, world-class orange-juice lover:

Science Debate 2008

No time to write this subject the entry it deserves, but I’ve been meaning to mention Science Debate 2008. We’re trying to get the presidential candidates to debate on issues of science and technology prior to the election (I signed on as a supporter). It’s a great idea with a lot of strong backers.

The pragmatist in me believes that it doesn’t have much of a shot, though. I mean, what campaign is going to let its candidate make an ass of themselves while trying to answer 6th-grade science questions?

That’s science for ya

Last week, I was working on a new script, and needed some answers to questions about microarrays that I thought were pretty straightforward. A week later, I’m still digging through papers on microarray normalization, and discovering that things aren’t quite so simple as they seemed.

It’s nearly enough to make me wish I had never asked.

Great Moments in Science

Or in this case, mathematics. The question is simple: If you walk up to a bus stop and there is no bus waiting for you, is it quicker to start walking, or to wait for the next bus to come along? After modeling the system, it turns out that in most cases, waiting is the best strategy. The edge cases which break down are when the buses are very widely spaced or when the distance to be traveled is very short.

Link: Walk versus Wait: The Lazy Mathematician Wins

Bug links

The 5 Most Horrifying Bugs in the World is an amusing round up of some scary-ass bugs:

They embed one video of a botfly being removed, but I remembered seeing this one, which gives a much better view of the removal process. They also somehow missed the grandaddy of all botfly stories. Needless to say, neither of those links are for the squeamish.

Turtles all the way down

Today I had to look up the origin of the phrase “Turtles all the way down. It’s rather amusing:

A well-known scientist (some say it was Bertrand Russell) once gave a public lecture on astronomy. He described how the earth orbits around the sun and how the sun, in turn, orbits around the center of a vast collection of stars called our galaxy. At the end of the lecture, a little old lady at the back of the room got up and said: “What you have told us is rubbish. The world is really a flat plate supported on the back of a giant tortoise.” The scientist gave a superior smile before replying, “What is the tortoise standing on?” “You’re very clever, young man, very clever,” said the old lady. “But it’s turtles all the way down!”

This is the Bees’ Knees

Okay, lame title, but it’s a great example of how exotic species can sometimes be at a disadvantage. (as opposed to cases like the cane toad in Australia)

The Saunders principle

The Saunders principle reads thusly:

The first step in any collaboration is to reformat the data sent by your collaborators.

What’s he mean by that?

Here are the sequences that you asked for. They are in fasta format, except that I’ve marked the acetylation sites with a “*” and after that, a score in square brackets.

Gee thanks - oh, it’s a Word file too, better and better.

90% of labs I’ve come across would benefit from someone with bioinformatics skills, and maybe 10% of them have that role filled. I see labs with the results of 1000 experiments, each saved in a separate excel file, with different column orders in each file. Then they want to mine the data and can’t figure out why it should be so hard. I see labs who are still running hundreds of blast searches by hand, one at a time, through a GUI web interface. I see labs with 5 years worth of data stored on an ancient computer with NO BACKUPS.

Do you see why I cringe?

Until biologists get serious about their data, and become willing to devote resources to IT infrastructure and hiring knowledgable bioinformaticists, the field is going to continue to be a giant mess. You can only ignore things like good software design and standard file formats for so long before these things begin to hinder your ability to produce quality research.

Two preeminent aging experts are on opposing sides of a bet that someone living today will be alive in 2150.. Another fantastic science article by Carl Zimmer.

Who Knew?

In 1921, Thomas Midgley, Jr. discovered that leaded gasoline made engines knock less. A decade later, he developed dichlorodifluoromethane, or Freon, which was widely used as a refrigerant until the 1990s.

Well, it turns out that burning leaded gasoline releases massive amounts of toxic lead into the air, and that CFCs were largely responsible for the loss of the ozone layer. Thus, it’s entirely possible that this man’s work did more to endanger public health than anyone else in history.

Midgely died in the 1940’s, which meant that he never had to live with the soul-crushing guilt of what his inventions had wrought.

Collins on Watson

Jim Watson Is At It Again

I don’t often find it necessary to put this disclaimer here, but let me reiterate that my views are mine alone and are not necessarily the views held by Baylor College of Medicine, the HGSC, or members of my lab. That clear? Okay, let’s dive into this mess

Let me start by saying that I respect the scientific contributions of Jim Watson. He and Francis Crick discovered the structure of DNA, which was one of the first steps that led us into the current era of genomics. I haven’t criticized him in the past because I also work in genomics, and as a junior scientist, I need to be careful about offending people who I may need a job from one day.

After his most recent comments, though, I’ve had it. Here’s what he had to say to the Sunday Times:

Dr Watson told The Sunday Times that he was “inherently gloomy about the prospect of Africa” because “all our social policies are based on the fact that their intelligence is the same as ours – whereas all the testing says not really”.

Wow, that’s going to piss some people off. But, wait! There’s more:

He said there was a natural desire that all human beings should be equal but “people who have to deal with black employees find this not true”.

These kinds of statements aren’t exactly new behavior for Watson either. During his talk at BCM a few months ago, he said some mildly offensive things about the Irish. He’s said some pretty controversial things about women and homosexuals too. And none of this even begins to delve into the complete disdain he’s shown for Rosalind Franklin. Not only does he refuse to acknowledge her full contribution to solving the structure of DNA, he ’s taken to calling her autistic. Seriously, Dr. Watson. She’s been dead for almost 50 years. Let this one go.

Whether he gets slack because he’s old or because he’s a Nobel prize winner doesn’t matter in my book. One seminal discovery doesn’t excuse your behavior for the rest of your life (and neither does being old and set in your ways).

There are plenty of other great minds in genetics that deserve to be giving lectures. Perhaps it’s time to start calling on them to serve as figureheads instead.

Update: edited slightly to remove some language that was perhaps overly harsh. It’s also worth noting that a London museum canceled his lecture after the uproar.

‘Tis Better to Give

Both my birthday and the holiday season are coming up soon, so I’ve updated my wishlist. (link in the sidebar). In addition to asking for books and video games this year, I thought I’d try something a little different. I’m asking you to help some underprivileged kids learn science.

Donors Choose is a site where teachers in low-income areas and underfunded schools submit proposals for what they’d like to do in their classroom. Today, I set up a challenge, and picked a few science-related projects that I liked.

Now I’m asking you to help by donating to one of these projects. I set a goal of 200 dollars, which is pretty modest. So skip your grande lattes for a week, click on the link below and donate 10 or 15 bucks to a pretty darn good cause. It’s heartbreaking to see how little most of these classrooms are asking for, and easy to see how many children’s lives can be affected by such a small amount of money.

And in case you needed more reason to donate, here’s my blurb from the challenge page:

In an era of increasing politicization and misrepresentation of science, it’s more important than ever to teach children about how the scientific method works. Science teachers are on the front lines of this culture war, and it’s important that they have the resources that they need.

Solutions like this are no substitute for adequate school funding, but we can’t wait around for that kind of education reform. Doing so would mean losing a whole generation of scientists. The potential to change the world is in these children’s minds. Let’s give these kids and their teachers the support that they deserve.

Limericks for Nerds

The Omnificent English Dictionary In Limerick Form (OEDILF) has some pretty amusing definitions of words. Here are a few from biology:

The agarose polymer may
Come in handy to scan DNA.
It’s great at perusing
Large molecules, using
Electrophoresis, I’d say.

Biosystematics suggest
How each creature relates to the rest.
Biochemical data
Yield tree-like schemata,
With taxonomic relations assessed.

There’s a form of molecular keno
In the global genetic casino,
Where each bet that we rode on
(A triplet, or codon)
Is cashed for an acid (amino).

These remind me of high school chemistry class, when I wrote one of my lab reports entirely in limerick form. My teacher was not amused, but I thought it made the cookie-cutter lab considerably more interesting.

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.