adaptivecomplexity's column

Phyllis Schlafly's Honorary Doctorate is Shaking the Foundations of Our Commitment to Research

adaptivecomplexity — Sun, 11 May 2008 15:08:02 -0500

As you may have read in the national press, the university where I work, Washington University in St. Louis, is honoring the anti-feminist activist Phyllis Schlafly with an honorary doctorate at the university's commencement this week.

Capitalists, Genetic Tests and Your DNA

adaptivecomplexity — Sun, 11 May 2008 11:43:04 -0500

Everyone knows there is a lot of crazy stuff on the internet, but did you know there is a lot of great writing about genes, genetics, and human diseases? And believe it or not, sometimes these pieces are written by people who know what they're talking about. If you're looking for what's new in human genetics, you've come to the right place.

Welcome to the 31st Gene Genie, a blog carnival dedicated to great blogging about human genes and how they impact our health. This Mother's Day edition includes an in-depth highlight of the growing industry of personalized genetics.

Get your Gene Genie submissions in

adaptivecomplexity — Fri, 09 May 2008 15:45:01 -0500

The next Gene Genie carnival is going to feature a Mother's Day edition right here at Adaptive Complexity.

Get your submissions in now!

What The Platypus Genome Is and Isn't

adaptivecomplexity — Fri, 09 May 2008 14:46:33 -0500

I haven't contributed a single thing to the platypus genome project, but since my desk sits one floor above where people and robots broke the platypus DNA into chunks, cloned those chunks into bacteria, sequenced the pieces of DNA, and used massive amounts of computing power to assemble the stretches of sequence into a complete genomic whole, I'm going to consider myself somewhat of an authority on the subject and tell you what's wrong with other people's ideas about the platypus.

The genome sequence of the platypus was published Thursday in Nature, and from the press headlines, you could be excused for thinking that genomics has in fact confirmed that the platypus is a freak of nature: part bird, part reptile, and part mammal. The animal certainly looks like it - the platypus has the webbed feet and bill of a duck, and venomous spines and rubbery eggs that remind us of reptiles, but it has fur and feeds its young with milk, so it must be a mammal. The confusing press headlines might even lead you to believe that we sequenced the platypus genome just to figure out what this thing is, when the truth is, as we'll see below, that the genome sequence has essentially confirmed what evolutionary biologists have already deduced about the position of the platypus on the tree of life.

Is the platypus part bird, part reptile part mammal, an amalgam of very different groups of animals? Is it a primitive mammal that resembles the early ancestors of all mammals? Can we figure out just what this creature is by gazing at its genome?

Photo Credit: Stefan Kraft, courtesy of the Wikipedia Commons

Intelligent Design: Coming To A State Legislature Near You

adaptivecomplexity — Wed, 07 May 2008 15:28:19 -0500

Would you recognize a legislative push for Creationism if you saw one? After decades of failed legal strategies to overtly ban evolution or make equal time for Creationism in public schools, the latest tack used by the opponents of evolution is to have 'academic freedom' bills that encourage school teachers to include supposed evidence against evolution, or the presentation of 'both sides' of a controversial issue in science class. If you support the integrity of science education, you should oppose bills like this, both because they are redundant when it comes to good science (teachers already can teach both scientific sides of a legitimate scientific debate), and because the Creationist legislators pushing them are up to no good. But are we reaching a point where Creationism is defining itself out of existence? Are they creating a legal loophole too small for their anti-evolutionary propaganda to fit through?

How many genes do you REALLY have?

adaptivecomplexity — Tue, 06 May 2008 16:35:49 -0500

You've probably heard widely varying estimates for the number of protein-coding genes in the human genome. Back before the genome sequence came out, many scientists guessed that the number was around 100,000. When scientists first looked at the newly completed human genome sequence in 2001, they found about 27,000 genes, and ever since then I have seen estimates ranging from 20,000 to 30,000.

What can happen when geneticists play God:

adaptivecomplexity — Tue, 06 May 2008 12:54:17 -0500

Nerdy comics don't get any funnier than xkcd:

Hillary Clinton: 'Elite' Experts are Bad for America

adaptivecomplexity — Mon, 05 May 2008 11:14:31 -0500

Hillary Clinton has gone off the deep end:

This morning, George Stephanopoulos began his televised interview with Senator Hillary Rodham Clinton by asking if she could name a single economist who supported her plan for a gas-tax suspension.

Is A Biochemistry Major Too Hard?

adaptivecomplexity — Fri, 02 May 2008 21:38:11 -0500

I missed this interesting discussion at Larry Moran's Sandwalk: Are biochemistry programs too hard compared to other biology majors? Larry says his biochemistry program is losing students to other biology majors that don't require as much physics and chemis

Anticipation for Carl Zimmer's New Book on E. coli

adaptivecomplexity — Fri, 02 May 2008 20:23:21 -0500

Science writer Carl Zimmer is building anticipation for his new book, Microcosm: E. coli and The New Science of Life. His latest hype-building piece is up at Wired. It's short and worth checking out.

Confusion over Cloning

adaptivecomplexity — Fri, 02 May 2008 13:24:36 -0500

Ethical debates over cloning are confusing enough, but even without the ethics issues the terminology of cloning is extremely confusing. Scientists bat around the word in many different contexts, often with subtly different meanings; if you don't know the biological background, it's easy to become disoriented.

A gene controlling brain size and schizophrenia?

adaptivecomplexity — Fri, 02 May 2008 08:58:44 -0500

When it comes to manipulating your body with drugs, you have no better friend than your G-protein coupled receptors. G-protein coupled receptors (ok, you can call them GPCRs) are proteins embedded within the membrane that makes up the outer border of our cells, and their exposed cell-surface position makes them great targets for drugs. If you've ever taken Claritin, Zantac, beta blockers like Lopressor, oxytocin, epinephrine, Zyprexa, antihistamines, some anti-HIV drugs, opioids, cannabis, or merely consumed a caffeinated beverage, then you've medicinally manipulated some of your GCPRs. Nearly 1,000 of our 24,000 genes encode GCPRs, which testifies to the major role this class of proteins plays in our physiology.

Given the importance of these receptors, it is not surprising that an interesting new study is describing a GPCR which may play a role in brain size, memory, and social interaction, and mutations in this GPCR could play an important role in schizophrenia.

Getting Rejected!

adaptivecomplexity — Mon, 28 Apr 2008 22:51:50 -0500

Interested in being a scientist? Then you had better get used to rejection and failure, because the truth is that most of your experiments will fail, most of your original ideas will be wrong, and most of your grant proposals and papers will be rejected on the first submission (especially if you submit to competitive journals).

The Benefits of Our 100 Million-Year Relationship With Herpesviruses

adaptivecomplexity — Fri, 25 Apr 2008 07:51:56 -0500

We go back a long way with herpesviruses. Our evolutionary line has been living with these genomic parasites for more than 100 million years, and today herpesviruses infect nearly all humans, as well as all other mammals, birds and reptiles that scientists have checked. We aren't born with these viruses, but most of us acquire multiple infections of various types of herpesviruses during childhood.

Unlike our relationship with many other, more notorious viruses, we've learned to peacefully coexist with herpesviruses for the most part. They set up shop in our cells, they use our molecular machinery to replicate themselves, and they take advantage of the influx of energy we provide from our diet. Sometimes the relationship goes sour, with the unfortunate results ranging from chickenpox to mononucleosis, genital herpes, and Burkitt's lymphoma, but by and large, most humans, and mammals in general, are never seriously harmed by these house guests. But do we get anything out of this relationship? Remarkably, recent research suggests that this 100 million-year coexistence may have been good for us too, helping our immune system to ward off even more serious pathogens.

Photo Credit: US Centers for Disease Control, courtesy of the Wikipedia Commons

Taxes and Science Don't Mix

adaptivecomplexity — Mon, 14 Apr 2008 00:47:53 -0500

There is no better way to fall into an IRS black hole than to try to become a scientist. I'm a postdoctoral fellow - which means that I have my PhD, but no permanent job; I'm spending a few years doing research in a lab run by a more senior scientist.

We Can Design Cars, But Why Can't We Design Cells?

adaptivecomplexity — Tue, 08 Apr 2008 22:09:23 -0500

Let's suppose that, knowing nothing about cars, you wanted to learn how they worked. You happen to have a friend who is an auto mechanic, so you ask him to explain cars to you: How do they start? How does burning gasoline make the engine go? How does the force generated by the engine get transferred to the wheels? Imagine that in answer to your questions, your mechanic friend brings you to an auto parts shop and begins to take parts off the shelf, explaining to you what each one is. By the end of the little lesson, your friend had shown you every piece that goes in your car and explained its function. Do you now know how a car works?

Well, no. Even if you could recite what each part does, you probably still have a poor understanding of how the parts work together to make a vehicle go. Let's take a more extreme scenario: you are teaching a class full of aspiring automobile engineers, and you want to teach them how to design cars. Would you teach them by just going through all the car parts one by one? Maybe you could even bring it all together at the end of the class and show them some diagrams of the parts put together: the chassis, the electrical system, the drive train. But even with the diagrams, these would-be engineers still won't be able to show up for work at Mercedes and design the next state-of-the-art engine. Parts lists and diagrams aren't enough; as any engineer can tell you, you need to get quantitative, you need to understand math and physics, and you need to be able to build model engines on computers, models which you can then test in silico without actually trying to physically build every new idea for an engine.

In many ways, molecular biologists are like that class of auto engineers.

Waning Science Journalism and Web 2.0

adaptivecomplexity — Mon, 31 Mar 2008 16:26:36 -0500

What ecological niche does a site like this occupy in the world of science journalism?

It turns out that beer drinking isn't bad for science after all

adaptivecomplexity — Mon, 24 Mar 2008 11:23:10 -0500

A recent Czech study about a supposed inverse correlation between beer-drinking and scientific output (the more beer you drink, the less productive you are - read the NY Times report) has been the butt of jokes around the scientific blogosph

Are Beards Bad for Labwork? Then Why Do So Many Scientists Wear Them?

adaptivecomplexity — Sun, 23 Mar 2008 22:10:56 -0500

This piece is slightly old, but it's amusing: over at Inkling Magazine, they're examining why beards may not be the best thing for a job that requires sterile conditions.

Expelled Movie Promoters Expel Critics - Except Richard Dawkins

adaptivecomplexity — Fri, 21 Mar 2008 10:46:30 -0500

The promoters of Ben Stein's anti-evolutionist movie Expelled have been holding screenings around the country to drum up enthusiasm for the movie.

Good science writers talk about good science writing at AAAS

adaptivecomplexity — Wed, 19 Mar 2008 21:15:42 -0500

While I recently slammed bad science writing, I do enjoy good science writing and recognize that there are many good science journalists out there.

Would you know a genetically engineered microbe if you saw one?

adaptivecomplexity — Wed, 19 Mar 2008 11:35:47 -0500

If you had a sample of bacteria taken from an environmentally sensitive area, or from a patient with a severe infection, would you be able to tell if any of these bacteria had been genetically engineered?

Using Our Genomes To Reconstruct Human Geography

adaptivecomplexity — Tue, 18 Mar 2008 14:09:01 -0500

If you had one hundred unlabeled DNA samples, taken from people all around the world, could you use that DNA to determine where the original donors came from?

With major improvements in genotyping technology, geneticists are now getting better and better at this game, and a recent paper in Science reports the largest study to date of human genetic diversity: 650,000 genetic differences scrutinized in nearly 1000 different individuals from 51 different populations.

Studies like this one lay important groundwork to help us understand how human genomes differ around the world, how differences in our genes and environments together make us healthy or sick, and how very ancient migrations led to the structure of today's human populations around the globe.

The ever-inspiring Richard Feynman tells us how to evaluate science

adaptivecomplexity — Sat, 15 Mar 2008 21:42:10 -0500

In the popular science arena, we occasionally (and in the case of evolution vs creationism, frequently) debate just how likely it is that those who aren't trained scientists can competently evaluate an area of professional science. I love Richard Feynman's somewhat idealistic answer, given in his 1966 talk to the National Teachers Association:

This is why politicians aren't in charge of study sections

adaptivecomplexity — Wed, 12 Mar 2008 20:12:26 -0500

This is why politicians shouldn't choose what science projects get funded: John McCain puts his science ignorance on display by knocking a population genetic study on bears he knows nothing about. All he knows is that it was bears, DNA, and 3 million dollars.

Yeast, Sex, and You

adaptivecomplexity — Wed, 12 Mar 2008 07:00:00 -0500

Wild sex is a staple of nature films, but there is one sex scene David Attenborough has never narrated: the mating ritual of yeast. That's right: yeast. Sex isn't just limited to lions, birds of paradise, and aphids; single-celled fungi do it too. Although most people don't like to hear the words 'fungus' and 'sex' used in the same sentence, yeast mating is a remarkable phenomenon and worth a closer look.

You can see this amazing scene, played out billions of times every day in wine vats and under oak trees, captured on film. As is the case with most wild mating rituals, filming yeast sex requires great patience - yeast are slow to commit and even when they do, they don't rush things. The beginning of foreplay itself takes several hours, as you can see below:

Bad Science Journalism and the Myth of the Oppressed Underdog

adaptivecomplexity — Sun, 09 Mar 2008 11:43:29 -0500

There is a particular narrative about science that science journalists love to write about, and Americans love to hear. I call it the 'oppressed underdog' narrative, and it would be great except for the fact that it's usually wrong.

The narrative goes like this:

1. The famous, brilliant scientist So-and-so hypothesized that X was true.

2. X, forever after, became dogma among scientists, simply by virtue of the brilliance and fame of Dr. So-and-so.

3. This dogmatic assent continues unchallenged until an intrepid, underdog scientist comes forward with a dramatic new theory, completely overturning X, in spite of sustained, hostile opposition by the dogmatic scientific establishment.

We love stories like this; in our culture we love the underdog, who sticks to his or her guns, in spite of heavy opposition. In this narrative, we have heroes, villains, and a famous, brilliant scientist proven wrong.

Mind-Bending Science in Thomas Pynchon's Mind-Bending Novel Against the Day: Part II - The Quaternion Wars

adaptivecomplexity — Fri, 07 Mar 2008 19:47:30 -0600

Interested in the strange, turn-of-the-century science and math in Thomas Pynchon's novel Against The Day? In part 2 of my primer on Pynchon's science read about the obscure conflict among mathematicians over quaternions, before modern vector analysis largely won the day. (If you missed part 1, read it here).

Science and Against The Day Part 2: Vectors and Quaternions

I. The need for algebra in more than one dimension

In Against the Day, Pynchon frequently refers to a relatively obscure conflict in the mathematics and physics community that took place in the early 1890's between advocates of quaternions and proponents of the newer vector analysis. This conflict is tied in to major themes in the book, such as the tensions between the old and the emerging world that culminated in the conflict of World War I, and the ability to perceive and describe the world in more than the three dimensions of Euclidean space. Quaternions, like the luminiferous aether discussed in Part 1 of this essay, became superfluous and obsolete, mostly unnecessary in the efforts of physicists to describe the natural world after the advent of modern vector algebra and calculus.

The Panda's Thumb has the latest deconstruction of Intelligent Design Insanity

adaptivecomplexity — Mon, 03 Mar 2008 11:29:50 -0600

Biologist Ian Musgrave take ID promoter Jonathan Wells to task for trying to argue that a recent paper on the detailed mutations that take place in bacterial evolution of antibiotic resistance has nothing to do with - you guessed it, evolution!

Mind-Bending Science in Thomas Pynchon's Mind-Bending Novel Against The Day: Part I

adaptivecomplexity — Fri, 29 Feb 2008 11:49:52 -0600

Do you like Thomas Pynchon, but are you stumped by the crazy turn-of-the-century science in his latest novel, Against The Day? You're not alone! I've put together a little guide for the perplexed, a three-part primer on special relativity, vector analysis and quaternions, and Riemann surfaces, just for Pynchon readers.

OK, it's not just for Pynchon readers - I think this science is fun even if you haven't read Pynchon. So check out part one, about how Michelson and Morley realized that something wasn't quite right with the 19th century understanding of space and time: