Adaptive Complexity

Adaptive Complexity is Moving - Update your links

2008-03-22T17:18:00.004-05:00

I'm completely moving this blog over to Scientific Blogging. If you follow this blog via RSS, the new link is: Adaptive Complexity. If you read this through the DNA Network, you'll see the new feed shortly.My Scientifc Blogging column is here.If you're waiting for the long-delayed next installment on the science in Pynchon's Against the Day, it will go up there (soon, I hope).Why am I moving?

Statisticians are verifiably insane

2008-03-07T10:40:00.003-06:00

R is a great free statistical software package. I'm trying to use it frequently enough to get comfortable with the basic commands and data objects, so that I don't have to dig through the help manual every time I want to do some small thing. I'm trying to break my Excel habit - if you want real statistics, you don't use Excel, right?I'm writing my paper, and need to make a simple bar graph. The

Bad Science Journalism: The Myth of the Oppressed Underdog

2008-03-06T21:28:00.002-06:00

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

This is not a real scientific conference

2008-03-06T20:40:00.004-06:00

I'm all for open debate over the genuine science behind global warming - researchers who have research results that don't jive with the IPCC's consensus report should be free to present their stuff at real scientific conferences and not be ostracized just because their results are different.But, as Real Climate points out, the Heartland Institute International Conference on Climate Change didn't

Science Blogging: There are Plenty of Readers Out There

2008-02-27T17:00:00.002-06:00

There is currently a blogging debate going on about the absence of science from science blogs (initiated over at bayblab). Why are the most popular science blogs full of religion, politics, and controversy?Larry at Sandwalk has also weighed in on the issue and notes that his posts devoted to geniune science get only a fraction of the readers that his more controversial posts get. There is no

Plug-And-Play Inside Your Cells: Signals and Side Effects

2008-02-24T16:53:00.002-06:00

My latest column is up on Scientific Blogging:If you've ever had a severe asthma attack or gone into premature labor, there is a good chance you were given the drug terbutaline. Terbutaline can relax your involuntary smooth muscle when it's causing problems: in constricted airways during an asthma attack, or in the uterus during contractions. But if you've taken terbutaline, you've probably also

Making Biology Easy Enough For Engineers

2008-02-20T17:20:00.002-06:00

No, I'm not knocking the intelligence of engineers. But we're still not at the point where, in the words of synthetic biologist Drew Endy:...when I want to go build some new biotechnology, whether it makes a food that I can eat or a bio-fuel that I can use in my vehicle, or I have some disease I want to try and cure, I don't want that project to be a research project. I want it to be an

If Darwin Had A Web Browser, He Would Never Have Written The Origin

2008-02-12T10:28:00.000-06:00

I've got a post on Darwin and the pace of science today up at Scientific Blogging:How can today's wired, multitasking scientist ever compete with the great scientists of the past? One feature of Darwin's work as a scientists was that it proceeded slowly, very, very slowly. He wrote massive groundbreaking books, compiled huge amounts of data on orchids, barnacles, and Galapagos animals, but all

Neil Shubin's Your Inner Fish and More on Darwin Day

2008-02-10T20:08:00.000-06:00

Tuesday, Feb. 12 is the anniversary of Darwin's birthday, and has been dubbed Darwin Day. In celebration of Darwin's scientific achievement, many organizations are holding Darwin Day events.Over at Scientific Blogging, we're celebrating with a feature page chock full of Darwin Day articles, links to Darwin Day blogging around the web, and highlights of events around the country. If you have a

Looking for Darwin Day Writers!!

2008-02-09T11:41:00.000-06:00

Darwin Day is coming up Monday, and I'm sure a lot of you bloggers out there will be writing good stuff. Over at Scientific Blogging, we're organizing a last-minute Darwin Day Carnival. Download the badge here (keep in mind the page is still in the draft stage), put the badge in your post, and we'll provide an intro and link to your post.Scientific Blogging gets almost 600,000 visitors per month

Super Tuesday Links

2008-02-05T21:45:00.000-06:00

I'm trying to find time to write a paper, and thus I've neglected my blog. But here are two interesting links:Super Tuesday and Science Debate 2008: The US National Academies of Sciences have joined in the call for a US Presidential Election Science Debate. The National Academies have offered to co-sponsor this event. If you haven't heard of this movement yet, go check it out.One of the pioneers

Self-Organizing Metabolism and the Origins of Life

2008-01-30T15:47:00.000-06:00

The late Leslie Orgel, a pioneering researcher in pre-biotic evolution, has an interesting essay in the most recent issue of PLoS Biology. A long-running debate in origins-of-life research has been over what came first: genetic material or a self-organizing metabolism.The self-organizing metabolism theory has been most prominently argued by Stuart Kauffman. Orgel doesn't rebut Kauffman's

Sequencing 1000 Human Genomes - How Many Do We Really Need?

2008-01-28T22:20:00.000-06:00

A group of the world's leading sequencing centers have announced plans to sequence 1000 human genomes. The cost of the first human genome project was about $3 billion; by comparison, the next 1000 will be a steal at possibly only $50 million dollars (and that's total cost, not per genome). But that's still a lot of money - why are we investing so much in sequencing genomes? It may be a lot up

Richard Feynman on Doubt

2008-01-12T14:34:00.000-06:00

[Fill in she instead of he as appropriate...]"The scientist has a lot of experience with ignorance and doubt and uncertainty, and this experience is of very great importance, I think. When a scientist doesn't know the answer to a problem, he is ignorant. When he has a hunch as to what the result is, he is uncertain. And when he is pretty damn sure of what the result is going to be, he is in some

An "Irrational Attachment to The Theory of Evolution"?

2008-01-12T14:26:00.000-06:00

In Gail Collins' NY Times column today, she says this:Huckabee seems to be a nice guy, but conservatives are afraid he’d break up the old evangelical-plutocrat Republican alliance and most liberals are restrained by their irrational attachment to the theory of evolution.Excuse me? I can't quite tell if Collins is being tongue-in-cheek (I frankly don't read her column enough to get where she's

What Next Generation DNA Sequencing Means For You

2008-01-10T22:24:00.000-06:00

Of all the 'Greatest Scientific Breakthroughs' of 2007 heralded in the pages of various newspapers and magazines this past month, perhaps the most unsung one is the entrance of next-generation DNA sequencing onto the stage of serious research. Prior to this year, the latest sequencing technologies were limited in their usefulness and accessibility due to their cost and a steep technical learning

Real Science vs Intelligent Design

2008-01-10T14:53:00.001-06:00

If Intelligent Design advocates are so insistent that most of the human genome is functional, why aren't they doing any research like this? Eric Lander's group at MIT devised a way to test whether the thousands of non-conserved, putative protein-coding genes are likely to be spurious or true protein-producing genes.From the paper, here is their rationale:The three most widely used human gene

Scientific American and Web 2.0

2008-01-09T21:48:00.000-06:00

What are blogs, wikis, and networking sites doing for science? Scientific American has an upcoming feature article about science and the Web 2.0. And in the spirit of Web 2.0, they're inviting your comments, so go check it out.It's a fascinating topic, and I'll have more to say about it soon.Thanks to Jean-Claude Bradley over at Scientific Blogging for mentioning this.

Nature comments on creationism

2008-01-09T14:23:00.000-06:00

Tomorrow's Nature issue has an editorial (subscription only) praising the latest NAS book on evolution/creationism. The editorial goes on to suggest that: "Between now and the 200th anniversary of Charles Darwin's birth on 12 February 2009, every science academy and society with a stake in the credibility of evolution should summarize evidence for it on their website and take every opportunity to

PNAS Evolution Editorial

2008-01-08T15:36:00.000-06:00

If you can get journal access, check out this editorial by creation/evolution veteran Francisco Ayala in the latest edition of the Proceedings of the National Academy of Sciences

Yes, you do have to be a genius to read this blog...

2008-01-07T14:14:00.000-06:00

Although if the blog is that incomprehensible, I'm not sure what that implies about the writer.

What Genes Did We Lose to Become Human?

2008-01-06T21:32:00.000-06:00

When we think of the genetic changes that to take place during our evolutionary history, we typically think of changes that resulted in a gain of function, like genetic changes that resulted in a larger and more sophisticated brain, improved teeth for our changing prehistoric diet, better bone anatomy for bipedalism, better throat anatomy for speech, and so on. In many cases however, we have lost

A Science Debate in the US Presidential Election?

2008-01-04T16:44:00.000-06:00

It's a long shot, but a worthwhile cause. If you care about science issues in the upcoming US election, consider signing up to support Science Debate 2008.

Check out this book

2008-01-04T16:37:00.000-06:00

The National Academy of Sciences has revised this classic book on Evolution and Creationism. (It's free online.)

How To Grow a New Head: The Amazing Regenerative Powers of Planaria

2008-01-04T16:25:00.000-06:00

Planarians have fascinated centuries of biologists by their amazing powers of regeneration. If you decapitate a planarian, the body can grow a new head, and the head can grow a new body. In fact, if you cut out a very tiny chunk from the side of a planarian, that chunk will be able to regenerate a new, complete organism. How do these strange critters manage this? What genes do they have that we

What's The Matter With Texas? Creationism On Its Way Back

2007-12-21T20:15:00.000-06:00

Is the State of Texas about to offer Master of Science degrees in creationism? The Institute for Creation Research (ICR), an organization that officially believes the earth sprang into existence less than 10,000 years ago, has applied to offer a state-approved Master's program in science education. Last week, an official advisory committee recommended that the State of Texas approve the ICR's

Seeing Human Embryos - Two Different Perspectives

2007-12-11T20:18:00.000-06:00

The NY Times today has a profile on Shinya Yamanaka, the senior author on one of the recent papers reporting the creation of pluripotent stem cells by expressing 4 transcription factor genes in adult fibroblasts. Yamanaka (who "is known on campus for refusing to join colleagues for lunch, choosing to eat by himself so he can keep working" - unfortunate, since informal conversations with

Stem Cell Researchers Respond to Bush's Claim

2007-12-04T10:42:00.000-06:00

The White House has claimed that Bush's firm stance against embryonic stem cell research helped to stimulate the recent breakthroughs in creating pluripotent cells without destroying embryos.In an editorial in the Washington Post, stem cell researchers themselves respond.

We Can Reprogram Skin Cells Into Stem Cells - So Do We Still Need Embryos?

2007-11-20T22:56:00.000-06:00

This month we've witnessed the first-time success of two important stem cell research techniques in primate cells. Both techniques were previously developed in mice, but their success in humans and monkeys is important. Stem cells from cloned embryos have been generated from macaque cells. And now this week, two papers (here and here - this last one is a PDF file) have been published that are

Monkey Stem Cells From Cloned Embryos - Humans Are Next...

2007-11-19T21:18:00.000-06:00

Headlines last week reported that researchers successfully produced stem cells from cloned monkey embryos. Using a process that has become almost routine with mice, scientists can now make make primate embryonic stem cells that are genetically identical to a given DNA donor. Once we learn to do this in humans, the possibility of stem cell based treatments for heart disease, neurodegeneration,

Making a Weed that Eats Explosives

2007-11-15T21:28:00.000-06:00

RDX is a common military explosive, and it’s dangerous not just because it explodes - it’s also toxic. Places where RDX is used, produced, or stored often present a serious hazardous waste problem, such at the Massachusetts Military Reservation on Cape Cod, where the local aquifer has been contaminated with RDX. A group of researchers from the University of York in the UK and Canada’s

Intelligent Design's Day in Court on NOVA

2007-11-14T21:58:00.000-06:00

Last night the PBS series NOVA featured a two-hour show on the 2005 Dover, PA Intelligent Design trial. If you missed it, go check out clips and some great evolution resources at the show's website. As a creation/evolution junkie, I had previously read all of the trial transcripts, but reading transcripts was no substitute for seeing and hearing the major participants on camera. And while the big

Do Universities care about more than image?

2007-10-01T20:17:00.000-05:00

"What makes the modern university different from any other corporation?" That's the question asked in the NY Times this week. In light of increasingly unaffordable tuition rates and the profitable but corrupt business of lending huge sums of money to students, do universities deserve their nonprofit status? Is the tight competition for federal grants corrupting the mission of universities?The

Evolution's Balancing Act

2007-09-19T21:58:00.000-05:00

Evolution carries out an incredibly tricky balancing act: the genetic program of a species has to be resistant to small changes, yet also susceptible to the adaptive remodeling of natural selection. The human genome is so robust that over 6 billion variations give rise to viable organisms that have successfully traversed the complex developmental program that produces a live human infant from a

Domesticating Biotechnology in the 21st Century

2007-08-21T21:55:00.000-05:00

Will we domesticate biotechnology in the next 50 years? More than 150 years of spectacular advances in physics, chemistry, and computing have thoroughly transformed the way we live. Yet so far, the big revolutions in molecular biology have had their impact primarily on professional laboratories, not our everyday lives. What do we need to do in order to domesticate biotech?

The Politics of God in the NY Times Magazine

2007-08-19T21:41:00.001-05:00

The NY Times Magazine today has cover piece arguing that while the West may have figured out how to largely separate politics and religion, the rest of the world is unlikely to follow:"Countless millions still pursue the age-old quest to bring the whole of human life under God’s authority, and they have their reasons."If that's really true, we can expect that modern science will be a phenomenon

Ancient Microbes Revived from Antarctic Ice May Be Spreading Their Genes

2007-08-14T22:47:00.000-05:00

After being encased in Antarctic ice for 8 million years, ancient microbes thawed by a team of researchers revved up their metabolic engines again and began making proteins and replicating. These are the oldest organisms ever brought back to life after a deep freeze. The research team, a group primarily from Rutgers, looked at the microbial population in some of the oldest ice known

If you value alternative opinions...

2007-07-11T22:20:00.000-05:00

Don't let Time-Warner and other big media outlets squash smaller, independent media voices that serve up more than just the bland, conformist news and opinion that has led to disaster in the US: Whether you're liberal or conservative, it affects you. Follow the link, sign the petition, and spread the word.I promise to get back to science around here soon - personal things have taken priority

Where is the leadership today?

2007-07-09T20:47:00.000-05:00

Damn, times have sure changed. In 1944, FDR could get up before Congress and say this:"We cannot be content, no matter how high that general standard of living may be, if some fraction of our people—whether it be one-third or one-fifth or one-tenth- is ill-fed, ill-clothed, ill housed, and insecure..."We have come to a clear realization of the fact that true individual freedom cannot exist

More Confusion about Junk DNA and Regulatory Sequences

2007-07-09T13:18:00.000-05:00

Back in June, John Greally, a biologist at Albert Einstein, wrote a frustrating Nature commentary on the ENCODE project in which he repeatedly and wrongly suggested that before ENOCODE, biologists were only paying attention to regulatory sequences:"We usually think of the functional sequences in the genome solely in terms of genes, the sequences transcribed to messenger RNA to generate proteins."

Mammas, Don't Let Your Babies Grow Up to Be Postdocs

2007-07-07T20:28:00.000-05:00

In most careers, when you do a good job, you get rewarded - a promotion, a bonus, a raise, whatever. These things are the incentives that make you strive to do your best.In science, as a postdoc, you get penalized for your success.I did something postdocs are supposed to do - get money by writing a research proposal that you submit to a funding agency. The process is competitive and

A Plug for Scientific Blogging

2007-07-06T13:11:00.000-05:00

And I mean sepcifically, the site Scientific Blogging, not jut blogging in general. Scientific Blogging features science news and blogs by working scientists (including yours truly). The bloggers cover every thing from math and physics to psychology, and range from lowly grad students and postdocs, like myself, to real science professors, as well as some science-trained bloggers working outside

Junk DNA in the Opossum Genome

2007-07-05T21:54:00.000-05:00

Vertebrate genomes are full of junk. Despite the occasional confusing magazine article, the spurious claims by creationists, or obfuscatory statements by some scientists, we know that our genomes are stuffed full of DNA sequence that serves no functional role for the organism. The vast bulk of this junk sequence consists of molecular parasites, called transposable elements, whose only 'function'

Untangling the Logic of Gene Circuits

2007-06-25T22:03:00.001-05:00

How does a cell process information? Unlike computers, with CPUs to carry out calculations, and animals, which have brains that process sensory information, cells have no centralized device for processing the many internal and external signals with which they are constantly bombarded. And yet they somehow manage just fine. The single-celled brewers's yeast, for example, can know what kind of

Our Genomes, ENCODE, and Intelligent Design

2007-06-20T16:58:00.000-05:00

What has the ENOCODE project done, and how do their results change our understanding of the human genome? In the last post I put this project into perspective by briefly outlining some past concepts of the gene and highlighting some of the ENCODE findings. Now it's time to take a closer look at the results of the ENCODE project and their significance for our understanding of the human genome.

Time to Rethink the Gene?

2007-06-17T21:05:00.000-05:00

After the tremendous discoveries in basic biology of the last 100 years, you might think that we would understand by now what a gene is. But the big news in genome biology this week is the publication of the results of the ENCODE project, a large scale experimental (as opposed to purely computational) survey of the human genome. The leaders of the ENCODE project suggest that we need to, yet

A Two-Minute Education in Molecular Biology

2007-06-17T13:24:00.001-05:00

Most readers of science blogs already have at least some basic knowledge of molecular biology, but in my experience there are many people interested in science, including academics in non-science fields, lawyers, and older physicians, who aren't famliar with the basics. Such people might have a hard time figuring out where to start learning among all of the many technical terms and techniques.If

Al Gore's Plea for Reason

2007-06-16T21:17:00.000-05:00

This blog is not meant to be a political blog, although it inevitably becomes one when those who reject evolution fall predominantly into one US political party. For the most part though, I prefer to get readers from any part of the political spectrum excited about fascinating developments in biology.But in this post I'm going to favorably review a book that some readers will have (mistakenly)

Non-coding DNA, Junk and Creationism

2007-06-13T21:09:00.000-05:00

Larry over at Sandwalk straightens out a very confused writer at Wired. (Also check out the links in Larry's post to other responses). Larry does a great job going over the article in detail, but I can't resist commenting on a piece that is so badly off track.Catherine Shaffer, who claims to be very knowledgeable about genomics has written an extremely confused article about the non-debate over

Genome-wide Association Studies - Are the Long-Promised Benefits of the Human Genome Project on the Horizon?

2007-06-13T17:16:00.000-05:00

Genome-wide association studies (GWAs) have received a lot of media attention in the last several months as various research groups have released over a half-dozen such studies, all focused on some of the most widespread Western diseases, including heart disease, type II diabetes, and breast cancer. (See here, here, and here for some examples.) These studies have the potential to substantially

Science in Against the Day: Vectors and Quaternions

2007-06-10T16:15:00.000-05:00

Here at last is the long-delayed next installment of my ongoing primer on the science in Thomas Pynchon's novel Against the Day. The draft of part 1 can be found here. Illness and major deadlnes put me back by months. I hope to have more installments out soon.Anyway, here is part 2: Quaternions and Vectors in Against the Day:Science and Against the DayPart 2: Vectors and QuaternionsI. The need

Sean Carroll's Smackdown of Michael Behe

2007-06-08T21:40:00.000-05:00

This week's issue of Science has a book review (subscription required unfortunately) of Michael's Behe's latest effort to defend Intelligent Design Creationism. Michael Behe's latest book, The Edge of Evolution, contains Behe's latest incarnation of his idea of irreducible complexity. A few years ago he put forward this latest argument in a paper in Protein Science (a journal which one of my

Thoughts from our appallingly ignorant national leadership...

2007-05-31T15:14:00.000-05:00

Blogging around here really will resume soon, as soon as my talk is over after tomorrow. Right now I don't have time to comment on two appalling expressions of ignorance, one on evolution by Republican Senator and Presidential candidate, Sam Brownback, and the other on global warming by NASA administrator Michael Griffin; I'll just direct readers to some other good blog responses.For a critique

My dirty secret...

2007-05-25T21:14:00.000-05:00

It's been a little busy around the lab and home, but more science is coming up soon: The new technique of ChIP-seq, the opossum genome, book reviews of Uncertainty and I am a Strange Loop, and hopefully this weekend a piece on quaternions and vectors in Pynchon's Against the Day.And now for my confession:OK, I watched the American Idol finale. In fact, I've watched much of the

It's not just the pet food...

2007-05-20T14:02:00.000-05:00

Why is the US so driven by greed? Somehow we care so much about corporate profits that we can't even effectively make sure that our food is safe. This story in Sunday's Washington Post (free registration required) details the tainted food (human food - not just pet food) shipments from China that the underfunded and understaffed FDA is trying to keep out of the US food supply. The foods that

Studying General Principles of Biological Systems - How flies make sense of smell

2007-05-16T22:58:00.000-05:00

About two months ago I was in Steamboat Springs, Colorado, attending the Keystone Symposium on Systems Biology and Regulatory Networks. I went hoping to hear about forward-looking research that deals with some of the most fundamental outstanding questions in biology - fundamental in the sense of being relevant not just to a particular cell type or organism, but to most cells, developmental

A Bad Mix: Psychiatric Drugs, Money, and Children

2007-05-10T11:09:00.000-05:00

I gripe about the poverty of postdoctoral scientists, but I'd rather be poor and keep my professional integrity than be lavishly paid by drug makers and lose my conscience. The NY Times has a story about psychiatrists who receive payments from drug makers, and who also just happen to have a tendency to frequently prescribe 'atypical drugs' for children. (Atypical here means prescribed for an

Darwin Among Republican Presidential Contenders

2007-05-05T13:26:00.000-05:00

One third of the Republican presidential candidates, when asked in their recent debate whether they believed evolution, admitted that they don't buy it. The blogosphere has already said much about this, and today the NY Times picks up the story.The NY Times includes this appalling quote by Larry Arnhart, a poli sci professor at Northern Illinois University:"The intellectual vitality of

Will the real systems biologist please stand up?

2007-05-04T21:37:00.000-05:00

According to the NIH, you can't be a systems biologist and an experimental geneticist at the same time. The NIH has issued a call for applications to:"use systems biology approaches to investigate the mechanisms that underlie genetic determination of complex phenotypes. These projects will combine computational modeling approaches and experimental validation of predictive models."This is

Douglas Hofstadter is a Strange Loop

2007-05-01T21:40:00.000-05:00

If you liked Godel, Escher, Bach, you'll be happy to see that Douglas Hofstadter has a new book out - I Am a Strange Loop. This new book, according to Hofstadter, gets to back to the heart of the subject that Hofstadter dealt with in GEB, much more so than his other books. I never read any of his other books after GEB - I loved GEB, but somehow the other books just didn't catch my interest. I

Are boring science classes the reason we aren't training enough American scientists?

2007-04-28T11:55:00.000-05:00

Tom Friedman, in his Friday's NY Times column (subscription required) comments on Walter Isaacson's new biography of Einstein and asks:"If Einstein were alive today and learned science the boring way it is taught in so many U.S. schools, wouldn’t he have ended up at a Wall Street hedge fund rather than developing theories of relativity for a Nobel Prize?"While our schools can

The Rhesus Macaque Genome - Can it help us learn about ourselves?

2007-04-24T22:56:00.000-05:00

Just recently Science published the paper describing the latest primate genome - the rhesus macaque genome. (Check out Science's macaque website for some good (and free) articles on the subject.) Sequencing a large genome like this one is resource intensive (unlike microbial genomes, which are now easily and routinely sequenced), so why did scientists sequence yet another primate genome? In

Fattening up our nation with farm subsidies...

2007-04-22T21:47:00.000-05:00

By the end of this week, this blog should be back in full swing - I've got a post on Vectors, Quaternions and Thomas Pynchon's Against the Day coming up, a review of David Lindley's new book Uncertainty, and a discussion of why the newly sequenced macaque genome, published in Science, is going to help us learn great things.In the meantime, here's a thought provoking, if somewhat obvious, article

David Brooks and the Age of Darwin

2007-04-15T18:09:00.000-05:00

NY Times columnist David Brooks has written about our society's new grand, all-encompassing narrative - evolutionary theory (Times select - subscription required).His point is basically this:"And it occurred to me that while we postmoderns say we detest all-explaining narratives, in fact a newish grand narrative has crept upon us willy-nilly and is now all around. Once the Bible shaped all

Apologies for the extended absence

2007-04-02T15:50:00.000-05:00

I apologize for being absent the entire month of March - some sort of respiratory infection has now dragged on for two months, culminating in middle of the night trip to the ER Friday for what was probably a bad reaction to some cold medication. It's been impossible to keep up with this blog. I also recently got back from a very interesting systems biology conference in Colorado, which I hope to

Where you go to college matters...

2007-02-26T20:38:00.000-06:00

Barry Leiba (a fellow Indy Science Blogger) has an interesting discussion on whether it matters where you go to college. If you are a good student, does the success of your future career really depend on where you go?Barry makes some good points about this issue from the persepctive of someone working as a computer scientist for a tech company. I think much of what he says applies to academia

A Genome-wide Association Study to Find Genes Linked to Diabetes

2007-02-26T20:15:00.000-06:00

I meant to get this post about an important new paper up 10 days ago, but illness intervened. The paper I discuss has now been published in the latest print issue of Nature.Genome-wide association studies are hot right now, and Nature has recently published a large study that identifies new genes possibly linked to type II diabetes. For those of you not familiar with such studies, here is a

President's Day Miscellany

2007-02-19T13:13:00.000-06:00

Extended, rampant illness at home has adversely affected lab work and blog posting, including a forthcoming post on a recent genome-wide association study identifying some new genes possibly linked to diabetes.However, here are a few links to a couple of stories about about our culture's baffling, hyper-squeamish approach to sex:Cosmic Variance's take on a children's book that for an absurd

Should a mainstream university grant a doctorate to a Young Earth Creationist?

2007-02-12T21:54:00.000-06:00

That is the question people are asking in this NY Times piece about a recent geosciences PhD graduate from the University of Rhode Island - a well-regarded school in this field. Marcus Ross is a Young Earth Creationist who submitted his dissertation in paleontology in December and is now teaching at Jerry Falwell's Liberty University. So is it bad thing that the U of RI granted this guy a

A New Book by David Lindley on Quantum Mechanics

2007-02-12T10:42:00.000-06:00

The NY Times has a review of a new book, Uncertainty by David Lindley, author of Boltzmann's Atom, a superb book on the late 19th century debate over atoms and the development of statistical mechanics. This latest book is about one of the most fascinating periods in the history of science - the development of quantum mechanics and its aftermath, especially the debates among Einstein, Bohr, and

The Latest IPCC Report on Climate Change

2007-02-07T11:30:00.000-06:00

The Intergovernmental Panel on Climate Change has released its latest report, which of course has been all over the headlines. This report, already obsolete since it couldn't include the most recently published research, states more strongly than ever that humans have clearly contributed to global warming. We're reaching the point where professional scientists who continue to deny this are at

Making Simple Model Systems to Study the Design Principles of Biological Networks

2007-02-05T22:33:00.000-06:00

The speaker at our departmental seminar last week, Wenying Shou, discussed a system of cooperating yeast strains she has constructed, forthcoming in PNAS (link to abstract, full article requires subscription). She created two yeast strains which absolutely depend on each other for survival. Yeast are normally free-living single celled organisms. But Shou knocked out a gene required to make

Apologies to any Pynchon readers for the delay...

2007-01-31T11:28:00.000-06:00

I have to apologize for the fact that I haven't posted any new Pynchon material recently. I still am working on the essay/science primer for Against the Day, however the task has turned out to be more formidable than I first anticipated. The problem is this: there is so much material that could be included in a primer on vectors, quaternions, space-time, etc., much more than I have the time or,

Introducing Indy Science Blogs Part 2

2007-01-22T20:27:00.000-06:00

I didn't get a chance earlier to introduce all of the fascinating blogs on the newly launched Indy Science blogs. So here are the rest of the introductions:If you like robots, astronomy and rocketry, check out Ed at Robot Guy.Barry Leiba is a researcher at IBM, and he writes about life, politics, and technology issues at Staring at Emtpy Pages.Emily DeVoto is an epidemiologist who writes about

John Tierney's Science Blog at the NY Times

2007-01-21T20:40:00.000-06:00

John Tierney, a conservative/libertarian/who knows? columnist at the NY Times has started a science blog. I'm usually not very optimistic about pundits commenting on science - the results are rarely good, with one of the worst cases being Gregg Easterbrook. The pundits usually have a muddled grasp of the technical issues and view scientific debate through a deep partisan tint.However, the NY

Is Systems Biology Teaching Us Anything New?

2007-01-21T16:26:00.000-06:00

What I find most exciting about basic molecular biology today is the prospect of building a quantitative understanding of how a cell works. Many other scientists are excited about this as well, leading to the current popularity of what's being called 'systems biology.' The idea is that maybe we can understand the design principles behind a cellular process - how the behavior of a cell emerges

Introducing Indy Science Blogs

2007-01-21T12:05:00.000-06:00

This blog is part of the newly launched Indy Science Blogs - a group of science bloggers that coalesced in the wake of a mass rejection email from Science Blogs. Science Blogs didn't have the courtesy to blind cc the addresses of all the recipients, exposing our email addresses to dozens of strangers. Some of us strangers got together and formed the brand new Indy Science Blogs.There are some

The Science of Light, Space-Time, and Vectors in Thomas Pynchon's Against the Day

2007-01-15T22:14:00.000-06:00

OK, Pynchon fans, this is the first draft of my first installment on the science in Against the Day. I have to preface this with two cautionary notes:1. This is an early and still very rough draft.2. There are many more connections to be drawn with the book. I'm on my second reading, taking notes as I go, so by the time I finish I'll be able to flesh this out much more.This essay will come in 4

How the microorganisms in your gut can make you fat...

2007-01-11T15:10:00.000-06:00

Blogging around here has been slow lately - now that the crazy holiday season is over, I'm immersed in an essay I'm writing on the remarkable use of science in Thomas Pynchon's latest novel Against the Day. I think what Pynchon did in this novel has been severely underappreciated in the reviews that have been published, because you have to have enough awareness of the science to pick up on

Carl Zimmer on the Two (Biology) Cultures

2007-01-07T13:20:00.000-06:00

C.P. Snow lamented the divide between the Two Cultures - the Humanities and the Sciences, since he felt that they each had so much to offer the other. There is a similar divide in biology - two cultures, representing those biolgists whose work is rooted in natural history, and those whose work is rooted in molecular biology. Biologists who attach cameras to deep-diving sperm whales, who trudge

More in the NY Times on women in science

2006-12-31T17:44:00.000-06:00

The NY Times is reporting on a conference at Rice University about women and science. (Free registration required.)I've probably already said more than I should have about this subject, but there is stuff in this article that I can't let pass without comment.I do agree that:- Women make great scientists. We should have more of them.- Women have faced severe discrimination on the road to a

Are some gene names too demeaning?

2006-12-31T17:40:00.000-06:00

Recently, science journals have reported on criticism of whimsical gene names - critics say that names like sonic hedgehog and lunatic fringe are offensive to people (or parents of children) who have a disease caused by an altered variant of one of these genes. This is also occasionally being picked up by the larger media - I heard a brief reference to this debate on NPR the other day. In the

A Scientist's take on Thomas Pynchon's Against the Day

2006-12-09T15:33:00.001-06:00

Thomas Pynchon is an author that scientists should love. No other first-rate novelist has engaged more deeply with the actual content of our civilization's scientific discoveries, especially math and physics. His latest book, Against The Day, is no exception, and in fact incorporates even more scientific content than the rocketry-obsessed Gravity's Rainbow. This is because Against the Day spans

Going though the NIH review process

2006-12-07T22:46:00.000-06:00

One of the most critical things a postdoc in science has to do is get independent funding. Even if your mentor is rich, proving that you can put together a research proposal and successfully obtain funding is a critical career step.I submitted four funding applications this year, my first year as a postdoc. It's a long, slow process - each funding application has different length and content

Molecular biologists don't understand molecular biology, but Creationist engineers do?

2006-12-06T11:59:00.000-06:00

Via Pharyngula I heard about these thoughts by a Creationist engineer musing on the contents of a molecular biology textbook (the link is to All-Too-Common Dissent, a pro science blog written by a scientist, where you can find the link to the original Creationist post):"My hypothesis is that the field of molecular biology is simply not understood by the majority of biologists and thus pretty

Best Science Books

2006-12-03T14:36:00.000-06:00

Once more, it's the most commercial time of the year, and every one is coming out with their Holiday Book recommendations. While the NY Times and the Washington Post put out the most well known best books list (and I'm peeved, but not surprised, that Thomas Pynchon and Richard Powers didn't make these top 10 lists), Discover Magazine has put out a list of the best 25 science books of all

Sequencing technology and the Neanderthal Genome

2006-11-30T21:57:00.000-06:00

You've probably read about the two recent papers in Science and Nature reporting the sequencing of portions of the Neanderthal Genome. (Subscription required for full text of the Nature and Science papers. Check out Google for the many news stories on this.) This is exciting work, but I'm not really going to comment about the signficance of the results - I think it's worth understanding how new

Where did all these scientists come from?

2006-11-21T15:43:00.000-06:00

It's no secret that it's now more difficult than ever to get funded by the NIH, in spite of the fact that Congress doubled the NIH budget between 1998 and 2003. Researchers have been frustrated and wondering, over coffee and in print, where all the money has gone.NIH director Elias Zerhouni explains what's going on in the November 17th issue of Science. Grant applications have nearly doubled

How should we teach our kids math?

2006-11-15T21:35:00.000-06:00

The NY Times is reporting on the lagging math skills of US kids and efforts to change, yet again, how we teach math. I'm sympathetic to the desire to teach math in a way that doesn't turn people off. Too many people (including some people who grow up to be biologists) go through their education feeling very, very insecure about their ability to do and understand math.What's tough about this

The problem with computational biology papers

2006-11-12T23:00:00.000-06:00

OK, my title is too general - it should be, "The problem with some computational biology papers that deal with certain research questions." There is a type of trendy science that frequently crops up in many journals (including good ones like Nature and Science. It basically goes like this (for a prime example, look here):1. A computational biology lab sees one or more genomic-scale datasets

A Republican War on Science? Nature's editors cop out

2006-11-01T21:14:00.000-06:00

The Oct 19th issue of Nature contains a feature section on science and the upcoming US Conrgessional elections. In one of the editorials, (subscription required) Nature's editors criticize the phrase "Republican war on science": "Slogans such as the 'Republican war on science', meant to sum up a host of perceived abuses, do not do justice to the complex relationship between science and each of

Classic papers in quantitative biology

2006-10-28T14:46:00.000-05:00

The hot trend in biology education right now is to train undergrads, grad students, and postdocs in not only biology, but also in enough math, computer science, and physics so that they can function successfully in the highly interdisciplinary research fields that are starting play a more important role in current research. Most major research universities are spending serious time and money

Comparing Genomes on a Chip

2006-10-26T22:20:00.000-05:00

Last week at our lab meeting I had a chance to hear a presentation by Doug Berg, a microbiologist here at Washington University. Berg's work is a great combination of new technology, genomics and evolution, and it happens to also have potential medical relevance. He's studying the evolution of drug resistance in Helicobacter pylori, a ususally benign bacterium that is responsible for stomach

NY Times feature on science fraud

2006-10-26T22:11:00.000-05:00

The NY Times has a feature article about the first case of scientific fraud with NIH money that resulted in a jail sentence for the scientist involved. A young technician in the lab of Eric Poehlman risked his reputation and future career to expose years of fraudulent research in the Poehlman lab. The grad students and postdocs in the lab were willing to look the other way for years, even though

Can you learn lab skills with a keyboard and mouse, instead of pipettes and test tubes?

2006-10-20T10:58:00.001-05:00

Today's NY Times features an article about a conflict among educators over online lab courses. Universities are debating whether to accept virtual lab courses as a substitute for real Freshman science labs, especially when it comes to AP credit. Online schools allow students to do virtual pig dissections, virtual DNA gels, and virtual chemistry experiments, and defenders of the vitrual lab

Reasons to oppose stem cell research? Debunking the opposition to Missouri's Amendment 2

2006-10-15T14:13:00.000-05:00

Around my neighborhood here in St. Louis you can find a lot of lawn signs dealing with "Amendment 2" - a stem cell research and therapies amendment which will be on the ballot next month.As a general principle, I think the public (the taxpayers funding scientific research in the US) should be involved discussing what kind of science should be done in our society. Mind you, they shouldn't be

Nobel week kicks off with a well-deserved award for RNAi

2006-10-03T11:35:00.000-05:00

It's Nobel week, and I'm enough of a nerd to anxiously look forward to this week every year. Yesterday the Nobel committee annouced that the Medicine/Physiology prize is going to Andrew Fire and Craig Mello. Fire is currently at Stanford, and Mello is at U. Mass in Worcester.It's great to see the prize go to scientists who are under 50, recognizing work that was done less than a decade ago. When

Tierney weighs in on the Gender Bias Panel

2006-09-26T10:48:00.000-05:00

In my last post I discussed the recent National Academies panel on gender bias. In today's NY Times, John Tierney weighs in on the issue. (This one is 'Times Select' - subscription required.)I'm usually at ideological odds with Tierney, but not quite so much this time. He comes up with a great Onion title for the panel's work: "This is the kind of science you expect to find in The Onion: 'Academy

The long road to a career in academic biology...

2006-09-25T10:13:00.000-05:00

What's a postdoc? 90% of the time, that's the next question I'm asked after people ask me what I do for a living. Or worse, people who know I spent 5 and a half years in grad school will say "wow, I can't believe you're still a student!" It's clear that most people outside the scientific community don't know what postdocs are - Students? Interns? Trainees?People should know what postdocs are -

National Academy panel tries to tell us how to keep more women in science:

2006-09-18T21:46:00.000-05:00

The NY Times has published an article titled Institutions Hinder Female Academics, Panel Says. (You can check out the full report and the panel's press release.) The panel in question was convened by the National Academy of Sciences to look at how women are faring in academic science and technology careers. Unfortunately, I think this whole issue is tainted by ideology, resulting in often