Steve Matheson Archives

Carnival of Evolution 41


CoEButton.jpgThe 41st Edition of the Carnival of Evolution is now up at The Mermaid’s Tale. This month’s carnival is typically diverse in its topics and contributors, and is typically excellent. Watch for cuckoos and other parasites, learn about flapping before wings, explore historical concepts like uniformitarianism, and read about the origins of the human hand. Eyes, nurseryfish, trade-offs, Barbara McClintock. And the suggestion that “evolutionary biology needs better PR.”

Head over to The Mermaid’s Tale and sample the bounty.


The sixth BILL is a visit with two of the biggest names in evolutionary biology, a couple of scientists who have undertaken one of the great long-term studies in recent scientific history. They are Peter and Rosemary Grant, whose work was the subject of the Pulitzer Prize-winning book The Beak of the Finch by Jonathan Weiner.

BILL the sixth is “How and why species multiply”, a tag-team lecture by Peter and Rosemary Grant presented as part of the Darwin’s Legacy course at Stanford University in 2008.

The lectures comprise a wide-ranging, engaging, and accessible introduction to the findings that emerged from the Grants’ three decades of research in the Galapagos archipelago. A book by the same title has just been released by Princeton University Press.

Don’t be put off by the length of the YouTube video; Peter begins his lecture at :14, Rosemary starts at :48 and finishes at 1:14, so the actual lecture is an hour. The remaining time is a panel discussion/Q&A that I haven’t previewed. Rosemary’s excellent lecture can stand alone, so feel free to start at :48 to enjoy a clear and engaging account of the influences of song and size on genetic variation and speciation. She ends with a nice summary of the whole lecture.

As usual, tips and comments are below the fold. Recommendations for future BILLs should be sent to the BILL czar (BILL at pandasthumb dot org) or can be left in the comments.

Carnival of Evolution 40


CoEButton.jpgThe 40th Edition of the magnificent Carnival of Evolution is now up at EvoEcoLab. You’ll find a rich diversity of entries, ranging from antibiotic-resistant ice-age bacteria to penguins in Africa. A book review, a podcast, and Flying Monsters 3D. Letters from Huxley. The cost of lanterns (fireflies are the topic). “Magic traits.” Jawless fish, fish with limbs, malaria. And, of course, sex with Neanderthals.

Carnival admission is free. Rides are safe for people, but may be harmful to ideas. Now run along!

Hitcher-poster180px.jpgGenetic hitchhiking is thought to be an inevitable result of strong positive selection in a population. The basic idea is that if a particular gene is strongly selected for (as opposed to selected against), then the chunk of the genome that carries that gene will become very common in the population. The result is a local loss of genetic diversity: all (or nearly all) of the individuals in the population will have that same chunk of genetic information, whereas before the selection process acted, there might have been a lot of variation in that chunk throughout the population. And this means that areas of the human genome that are less variable between people are suspected sites of recent positive selection. Within that chunk, there are potentially many genes and genetic elements that became more common in the population by virtue of their placement near the gene that was actually selected for. Those other genes are the hitchhikers. And it’s likely that some hitchhikers are bad news - they’re harmful mutations that would normally become rare or extinct in the population, but instead have become common by hitchhiking.

In the last few years, large amounts of genetic information have become available that have enabled biologists to look for evidence of such phenomena in the human genome. Specifically, two major projects have collected genetic data for the purpose of analyzing genetic variation among humans. One project, the International HapMap Project, mapped and quantified sites in the human genome that are known to vary among humans by a single genetic letter. These sites are called single nucleotide polymorphisms, or SNPs (pronounced “snips”). The project has mapped millions of these sites in a group of 270 humans representing various lineages. Another project that has made the news recently is the 1000 Genomes Project, which also seeks to provide a picture of human genetic variation using more people (more than 1000 at present) and slightly different technology. Efforts like these have taken analysis of the human genome to a new level. No longer do we merely wonder what “the” human genome is like - we can begin to learn about how genetic differences give rise to biological differences such as susceptibility to particular diseases.

And we begin to look for evidence of positive selection in the human genome.

Read a primer on hitchhiking, then read the rest of the story about harmful mutations in the human genome, at Quintessence of Dust.


The fifth BILL is a lively and entertaining look into modern research in evolutionary biology, presented by Hopi Hoekstra of Harvard University. Professor Hoekstra’s lab explores evolutionary mechanisms at multiple levels, moving seamlessly between the field (more precisely, the beach) and the lab.

BILL the fifth is “What Darwin Did and Didn’t Know: the Ultimate and Proximate Causes of Evolutionary Change”, a lecture by Hopi Hoekstra presented at the Darwin/Chicago 2009 conference. It’s a .mov file, which you watch streaming or download.

Hoekstra’s lecture is a superb and approachable introduction to the key questions in evolutionary genetics, and contains some fascinating surprises. Her lab website is a treat, too, with great images and access to numerous publications, including review articles.

As usual, tips and comments are below the fold. Recommendations for future BILLs should be sent to the BILL czar (BILL at pandasthumb dot org) or can be left in the comments.


The fourth BILL is a tour de force of scientific explanation, presented by a well-known scholar described by a colleague (who introduces him in the video) as “the principal guru to go to on evolutionary genetics in the world.”

BILL the fourth is “Why Evolution Is True”, a lecture by Jerry Coyne presented at the 2009 Atheist Alliance International convention. Coyne is the author of the excellent book and blog by the same name.

It was one of several very good lectures at that convention, some of which would make excellent future BILLs. Coyne’s lecture is a perfect BILL: illuminating and lively, basic enough for laypersons but stimulating for all.

As usual, tips and comments are below the fold. Recommendations for future BILLs should be sent to the BILL czar (BILL at pandasthumb dot org) or can be left in the comments.

Carnival of Evolution 39


CoEButton.jpgThe 39th Edition of the Carnival of Evolution awaits your arrival at The End Of The Pier Show.

This lovingly prepared version includes nematodes, spider mites, mimiviruses and some information about an odd genus called Homo. Don’t miss great entries from the BEACON Center for the Study of Evolution in Action.

It’s a very nice edition of an excellent carnival. Click on over.

If you decided not to enjoy the Ramachandran lecture when you saw that it was in a format that reminded you of Windows 3.1, I have good news. The post has been updated with links to the new Reith Lectures site at the BBC, and now you can listen to the lecture in your browser or download it as a podcast.

It’s great stuff, so don’t miss it. Oh, and send me nominations for future BILLs. The email address is BILL at pandasthumb dot org.

Party on!

Bill&Ted2Crop.jpgUPDATE: Links are now changed to take you to the newer BBC site, on which you can listen to the lecture without the hassle of getting RealPlayer. And you can download the lecture as a podcast if you prefer.

The third BILL is a brilliant foray into neuroscience, focused on consciousness and the human brain.

BILL the third is “Synapses and the Self,” by Vilayanur S. Ramachandran. Ramachandran is the author of Phantoms in the Brain (1999) and most recently of The Tell-Tale Brain: A Neuroscientist’s Quest for What Makes Us Human, published this year.

This lecture is audio only, accompanied by a transcript. It was the second in Ramachandran’s five-lecture series “The Emerging Mind,” which was the 2003 installment in the fantastic Reith Lectures. All five lectures are riveting; this one includes some thoughts on human evolution and might thereby ensnare many Panda’s Thumb regulars. If you can’t get enough of Ramachandran after this introduction, you’ll find videos of other lectures and a NOVA appearance on the ‘tubes. And he blogs a bit; the most recent entries discuss his remembrances of Francis Crick.

I encourage you to listen without referring to the transcript; he’s very clear and fun to listen to.

Bill&Ted2Crop.jpgThe second BILL is an entertaining and accessible introduction to evolution, with a focus on Mr. Darwin himself.

BILL the second is “Endless Forms Most Beautiful,” by Sean Carroll. (Not the cosmologist or the biologist formerly in Joe Thornton’s lab and currently at Harvard, but the evo-devo thinker who is Vice President for Science Education at the Howard Hughes Medical Institute [HHMI].) Carroll’s talk is the first in a four-part series on evolution, the 2005 Holiday Lectures sponsored by HHMI. The Holiday Lectures are probably an exaptation of The Royal Institution Christmas Lectures that gave us our inaugural BILL.

Here are some things to look for and think about:

  • An extensive historical account of Darwin’s thought, including some questions about the reactions of his family.
  • An emphasis on the fossil record.
  • A very interesting choice of an experimental study to illustrate natural selection: coat color in pocket mice. Why interesting? It’s the work of Hopi Hoekstra, coauthor of a harsh critique of evo-devo that started a quaint little scientific dustup. (The article and dustup were a couple years after the lecture. More at Pharyngula.)
  • Some simple math to show the reasonableness of evolutionary change over actual time scales.
  • Good questions from the audience, about how the mutations got there in the first place and whether the changes are a “coincidence.” In the cartoon version of evolution that is often employed by critics of the theory, a new protein (B) can arise from an ancestral version (A) by stepwise evolution only if each of the intermediates between A and B are functional in some way (or at least not harmful). This sounds reasonable enough, and it’s a good starting point for basic evolutionary reasoning.

But that simple version can lead one to believe that only those mutations that help a protein, or leave it mostly the same, can be proposed as intermediates in some postulated evolutionary trajectory. There are several reasons why that is a misleading simplification - there are in fact many ways in which a mutant gene or protein that seems to be partially disabled might nevertheless persist in a population or lineage. Here are two possibilities:

1. The partially disabled protein might be beneficial precisely because it’s partially disabled. In other words, sometimes it can be valuable to turn down a protein’s function.

2. The effects of the disabling mutations might be masked, partially or completely, by other mutations in the protein or its functional partners. In other words, some mutations can be crippling in one setting but not in another.

In work just published by Joe Thornton’s lab at the University of Oregon, reconstruction of the likely evolutionary trajectory of a protein family (i.e., the steps that were probably followed during an evolutionary change) points to both of those explanations, and illustrates the increasing power of experimental analyses in molecular evolution.“The Selfish Gene.” “Selfish DNA.” Oh, how such phrases can get people bent out of shape.  Stephen Jay Gould hated such talk (see a little book called The Panda’s Thumb), and Richard Dawkins devoted more time to answering critics of his use of the term ‘selfish’ than should have been necessary. Dawkins’ thesis was pretty straightforward, and he provided real examples of “selfish” behavior of genes in both The Selfish Gene and its superior sequel, The Extended Phenotype. But there have always been critics who can’t abide the notion of a gene behaving badly.

Leaving aside silly bickering about the attribution of selfishness or moral competence to little pieces of DNA, let’s consider what we might mean if we tried to imagine a really selfish piece of DNA. I mean a completely self-centered, utterly narcissistic little piece of DNA, one that not only seeks its own interest but does so with rampant disregard for other pieces of DNA and even for the organism in which it travels. Can we imagine, for example, a piece of DNA that deliberately harms its host in order to propagate itself?

It is of course a cliche to state that eukaryotic cells (i.e., cells that are not bacteria) are complex. In the case of an animal, tens of thousands of proteins engage in fantastically elaborate interactions that somehow coax a single cell into generating a unique and magnificent organism. These interactions are often protrayed as exquisitely precise, using metaphorical images such as ‘lock-and-key’ and employing diagrams that resemble subway maps.

Many of these interacting proteins are enzymes that modify other proteins, and many of those enzymes are of a particular type called kinases. Kinases do just one thing: they attach phosphate groups to other molecules. This kind of modification is centrally important in cell biology, and one way to tell is to look at how many kinases there are: the human genome contains about 500 kinase genes.

Now, kinases tend to be pretty picky about who they stick phosphate onto, and this specificity is known to involve the business end of the kinase, called the active site. The active site is (generally) the part of the kinase that physically interacts with the target and transfers the phosphate. You might think that this interaction, between kinase and target, through the active site, would be by far the most important factor in determining the specificity of kinase function. But that’s probably not the case.

Carnival of Evolution 38


CoEButton.jpgThe 38th Edition of the Carnival of Evolution is now open for business at Sandwalk.

It is massive and magnificent. Bats, bears, bugs. “The science of sexism” and “How to save your marriage.” Using deleterious mutations to cross fitness valleys. Cryptozoology. And, of course, a nice list of recommended iPhone apps.

Get comfortable and enjoy this epic edition of the carnival.

Design and falsifiability


Last month I had an interesting conversation with Casey Luskin of the Discovery Institute (DI), at Evolution News and Views (ENV), a DI blog/site that recently opened some articles to comments. The topic of the original post was common ancestry in humans and other primates, but Casey and I discussed various aspects of design thought.

One subject that came up was the falsifiability of design. I maintain that design arguments, whenever they also postulate the existence of an omnipotent deity (or any super-powerful being, for that matter), are inherently unfalsifiable. And I want some feedback on my argument.

Bill&Ted2Crop.jpgThe inaugural BILL, BILL the First, primordial BILL, the founder, the prototype, the archetype, the Platonic BILL form. It has to be something special.

The inaugural BILL is “The Ultraviolet Garden,” one episode from a 1991 lecture series by Richard Dawkins. The series of five lectures was called “Growing Up in the Universe” and was the 1991 edition of The Royal Institution Christmas Lectures. That series is meant to be enjoyed by children and adults alike, and “The Ultraviolet Garden” accomplishes this quite well.

TED.jpgThey have TED. We have BILL.Bill&Ted2Crop.jpg

We here at Panda’s Thumb are pleased to announce the establishment of a new video lecture series: Brilliantly Illuminating and Lively Lectures, or BILLs.

Once every two weeks, a new BILL will be posted along with commentary by a PT crew member. Topics can vary widely, with the only criteria being brilliance, illumination, liveliness, and/or financial contributions from members like you. Feel free to nominate lectures for inclusion in this prestigious series by leaving a comment here or by emailing the director of the BILL series at BILL at pandasthumb dot org.

Our first two BILLs are already selected, and the inaugural BILL will be posted on Wednesday 27 July.

TED is cool. But BILL is more excellent. Party on, dudes!

Carnival of Evolution 37

CoEButton.jpgThe 37th Edition of the Carnival of Evolution is on display at a very interesting blog called The Lessons of Evolution run by William, who describes himself thus: “I’m thirteen years old and I hope to become an evolutionary biologist but I have diverse interests.” William’s edition of the carnival includes posts on zombies, the Tree of Life, epistasis, Darwin’s library, and digital organisms. He even includes a link to a post that was rejected (selected for extinction).

It’s July. Go enjoy a carnival run by a teenager. Free admission!

Carnival of Evolution 36


CoEButton.jpgThe 36th Edition of the Carnival of Evolution is in progress at Greg Laden’s Blog. The theme: “If you love evolution, tweet about it.” Guppies. Sharks. Crayfish. Bacteria. Blind fish. Hyenas. Cows. And more. Visit, and tweet generously.

ResearchBlogging.orgA few months ago, we were looking at the concept of a fitness landscape and how new technologies are creating opportunities for biologists to look in detail at relationships between genetics and fitness. The first post discussed the concepts of a fitness landscapes and adaptive walks, with some focus on the limitations of the metaphor. The second post summarized some recent work on bacterial fitness and mutation rates, with the concept of a fitness landscape as a theme, and the third post reviewed another recent paper, one that described techniques for studying fitness landscapes in detail by linking protein function (which can be screened and/or selected) and genetic information. Here we’ll look at yet another approach to the problem, in which the subject of the analysis is not an organism (as in the first paper) or a protein (as in the second paper) but an RNA molecule.

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