Conservapedia has posted a new article discussing supposed flaws in Richard Lenski’s paper on historical contingency in E. coli evolution.  Interestingly, the “flaws” are claimed to undermine the conclusion that the evolution of aerobic citrate metabolism was historically contingent.  This is a shift from Conservapedia’s previous tact of disputing the emergence of the Cit+ phenotype altogether.  As you might expect, the new arguments are quite pathetic, and it is clear that whoever wrote the article hasn’t read or understood Lenski’s paper.  So, without further ado, let the fisking begin.

Read the rest of this entry »

It’s almost common knowledge that evolution selects for protein structure.   That is, the 3-D structures of proteins are critical for their function, and mutations that alter structure are fodder for natural selection.  In addition to structure, however, evolution also selects for protein dynamics.  Protein function often depends on specific conformational changes, so mutations that modify motion can impact fitness, even if they don’t change the structure of the protein.  A recent paper published in Biochemistry discusses a new example of evolution acting on protein dynamics:  motion important for protein-protein interactions.

The paper focuses on bacterial two-component signal transduction systems.  Such systems are dependent on transient interactions between two proteins, a sensor kinase and a response regulator.  Bacterial genomes contain many two-component systems, and in order for each system to perform a unique function, the interaction between the two protein components must be highly specific.

Read the rest of this entry »

Today is lab clean-up day for us, and it’s looking like an all-day affair.  So I might not get to post anything until this evening.  If you’re looking for stuff to read, though, I suggest checking out e! Science News, a scientific news aggregator put together by a Canadian grad student. I just learned of it this morning, but so far it looks pretty good.

Ads for scientific products tend to be forgettable, straightforward affairs.  After all, scientists aren’t exactly a huge market, and some of the items advertised run into the $30K or higher range.  From an advertisers prospective, you really just want to present your product and it’s advantages succinctly and be done with it.  Well, Eppendorf, manufacturers of everyone’s favorite 1.5 mL plastic tubes, has thrown that strategy right out the window and produced a music video for their newest product.  It’s some sort of automated pipetting system, and you can see the video here.  Here’s to hoping that this is the start of a new trend in scientific advertising.

ScienceNOW has a brief story about research into tune deafness.  Interestingly, researchers have found that the brains of tune deaf people do detect poorly played tunes and wrong notes, but the individuals are not aware of it:

Can’t stand today’s music? Neither can tune-deaf people. In fact, the disorder makes listening to any music unenjoyable, because the brain can’t organize the sounds into a comprehensible melody. New research indicates that the problem lies somewhere in the conscious mind: The brains of tune-deaf individuals know when a sour note has been played, but the people themselves are unaware of it.

The story provides a link to the Distorted Tunes Test, which you can take and see if you have good pitch or if you’re tune deaf.  It takes a few minutes, but it’s kinda fun.  Apparently I have a good sense of pitch, I scored 23/26.  If you’re interested, take the test here.

Today we hear creationists pleading for science classes to “teach the controversy” over evolution.  By this they mean that science teachers should be free to discuss whether or not evolution is true or supported by the evidence, to teach the “strengths and weaknesses”.  This is unfortunate.  There is simply no such controversy within the scientific community, and wasting class time debating settled science prevents students from studying real and interesting controversies in evolutionary biology.  One such controversy is over the role of historical contingency in evolution.  On one side of this debate are people like the late Stephen Jay Gould who hold that contingency plays a large role in evolution, making the process largely unpredictable.  Gould held that if we could go back in time and replay the “tape of life” from some point in the past, we would arrive at a world wildly different from ours today.  The other side counters that natural selection strongly limits the adaptive possibilities of organisms, that there are many roads to only a few evolutionary destinations.  In contrast to Gould, this side holds that replaying evolution would yield a world highly similar to ours. A new paper in PNAS addresses this debate and suggests that historical contingency is an important feature of evolution.

Read the rest of this entry »

gg at Skulls in the Stars has issued an interesting challenge to science bloggers:  write a blog post about a classic scientific research paper, preferably something pre-WWII.  This is a great idea, and I hope plenty of bloggers take up the challenge.  Reading old papers is great, and I wish that science instructors would utilize them more in their classes.  Not only does it foster an appreciation of the history of science, but it also brings the material to life and makes learning more enjoyable.  Granted, not all old papers are a joy to read, and some are painfully written, but I think they provide the reader with a much deeper understanding of the topic than just learning facts by rote.

Unfortunately, I don’t think I’ll be able to fulfill gg’s challenge to the letter.  My realm of expertise is in biochemistry, biophysics, and molecular biology, and these fields of study only started to take off relatively recently.  Most of the classic papers in these fields come from the 1950s.  Watson and Crick published their paper on the double helical structure of DNA in 1953.  The first protein structure solved by x-ray crystallography was published in 1959. So when I was researching the topic of this blog post, I had a hard time coming up with much before WWII.  Originally I thought I would write about Messelson and Stahl’s 1958 paper on the semiconservative nature of DNA replication.  Their experiment was really quite elegant, and it would be great paper to write about.  But 1958 seemed a bit late, so I searched a bit more and decided on a seminal paper by Oswald T. Avery, Maclyn McCarty, and Colin MacLeod.  Published in 1944, Avery’s paper, Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types, was the first to identify DNA as the molecule that carried genetic information, and became a watershed in the science of genetics.

Read the rest of this entry »

I suppose it’s about time I wrote about some science.  Ideally, I’d like to write about peer-reviewed research once a week, but I don’t know how well that is going to work out.  In this post I’ll be writing about a recent article published in PNAS detailing a method for generating protein structures from NMR chemical shifts alone.  The title of the article is “Consistent Blind Protein Structure Generation from NMR Chemical Shift Data”, and it was a collaborative work between several groups led by some fairly big names in the field, such as Ad Bax and Thomas Szyperski.  I’ll try to keep my summary/discussion free of more technical details, as I’m aware that NMR is a highly technical method that relatively few people are familar with.  Read the rest of this entry »

I was planning on blogging about recent advances in creating high-temperature superconducting materials discussed in an article posted at ScienceNOW, but it looks like Ars Technica beat me to it.  I will, however, discuss the benefits that such materials could have for the field of NMR spectroscopy. Read the rest of this entry »