Monday, October 27, 2008

Christopher Hitchens: Defender of Fruitflies

Palin is an easy target for the man who took down Mother Teresa.Update: Dan Warren pointed us to this watercolor by Zina Saunders that sums up Palin's attitude toward fruitfly research.

Update: Jerry Coyne has join the fray.

Friday, October 24, 2008

Rapid Diversification - In Journals

A while back, I was asked to join an editorial board for a new open-access journal called "Theoretical Biology Insights," published by Libertas Academica. I think open access is great, and I am familiar with another LA journal, Evolutionary Bioinformatics, that has published some good things. I responded enthusiastically, and was added to the slate. I haven't yet been involved with the journal in any other way, but it is really just starting out.

Perusing the first two papers of this journal, I couldn't help but notice that one of them seems to be about how the complete state of all human brains might somehow be encoded in the Earth's magnetic field. (image 'borrowed' from here). Now, I may be misinterpreting this paper - in fact, I probably am. But the correct interpretation of this paper has to be equally strange, even if strange in a different way. Here, I must confess that I'm not a (psychologist? physicist? geoneurobiologist?)... well I don't feel really qualified to judge this paper.

The point of this post is mainly to wonder what everyone thinks the role of journals like this one or others from LA will be. There are also the many new OA journals from Bentham Science Publishers (you might have gotten an email or two from them), one of which is about evolution. These may be a different type of thing from the LA journals, but I'm finding it difficult or impossible to really predict where all of this is going.

To me, perhaps the new journal with the best potential is PLoS ONE, which takes papers and then hopes that peer review will be a continuing process; anyone can comment on the papers on the website. However, in my experience (n=1), people don't comment.

I'd love to hear anyone's thoughts on this topic, especially people who have experience with these new journals. Send your electromagnetic waves my way.

Persinger, M. A. 2008. On the possible representation of the electromagnetic equivalents of all human memory within the Earth's magnetic field: implications for theoretical biology. Theoretical Biology Insights 1:3-11.

Thursday, October 23, 2008

The Hassles of High Throughput Sequencing #1

As my lab strives to adopt increasingly high throughput molecular practices, we've hit a few bumps along the way. One involves the first step in the process of obtaining DNA sequence data: extraction. As a molecular biologist, I've grown up in the era of kits: I've always done genomic extractions by pulling a Qiagen/Promega/Viogene kit off the shelf, dropping a chunk of tissue into a tube and following instructions. This simple and convenient approach, however, is challenged by the needs of the very high throughput facility we're working with. They're asking for genomic DNA with a 260/280 ratio (a measure of a sample's quality that reflects the ratio of DNA to undesirable proteins) between 1.8 and 2.0. Essentially, they're asking for genomic DNA that is completely free of protein contaminants. Unfortunately, kits that rely on a silica filters tend to give us ratios in the 1.2-1.3 range. After a week of experimentation, we've been able to get samples with ratios in the 1.6-1.7 range, but only via phenol-chloroform extraction. Although I've spent my career avoiding a method that has always been described as "unpleasant", several gel-based methods make the phenol-chloroform process relatively painless (check out Phase Lock Gel from Eppendorf [apparently discontinued] and MaXtract from Qiagen). I'm sure we're not the first to encounter this problem, but hopefully this post will help others avoid the trouble of extracting dozens of samples only to be told later that the resulting samples weren't good enough!

Saturday, October 18, 2008

R Tip: Labeling Trees w/ Posterior Probability and Bootstrap Support

What's the worst part about making figures for phylogeny papers? When I sat down yesterday to make some new figures I realized that my answer was the same as it was ten years ago: adding support values to each node by hand using programs like Adobe Illustrator. I decided I was never going to go through this archaic error-prone process again. In sharing my solution here, I hope that none of you will either! The text below is an annottated R script that does most of the hard work for you (you'll still have to tweak a few things in Illustrator). Of course, you'll need to get familiar with basic R functions for phylogentics before attempting to use these scripts. The best way to do this is to pick up a copy of Paradis' nice little introductory textabe/half/amzn/bn. Don't be lazy and tell yourself you can label your nodes by hand quicker than you could learn R. This might be true if you only had to label one tree, but what are you going to do for your next paper, or when the reviewers advise you to re-run your analyses? If you know how to use the scripts below you'll just be able to plug any tree in and have your labeled tree almost instantly!

#Fist we need to open some necessary libraries
#The getAllSubTrees function below is a necessary subfunction that atomizes a tree into each individual subclade and was provided compliments of Luke Harmon.
getAllSubtrees<-function(phy, minSize=2) {
for(i in 1:phy$Nnode) {
l<-node.leaves(phy, ntip+i)
bt<-match(phy$tip.label, l)
if(sum( {
} else st<-drop.tip(phy, phy$tip.label[])
if(length(st$tip.label)>=minSize) {

#The plotBayesBoot function below plots both posterior probability and bootstrap values on each node of the consensus tree obtained from your Bayesian analysis. Bootstrap values will appear in bold text immediately below and to the left of the node they support, whereas Bayesian posterior probabilies will appear in regular face above and to the left of the node.

plotBayesBoot <- function(bayesTree,bootTree) {
#The commands below compare all the subclades in the Bayes tree to all the subclades in the bootstrap tree, and vice versa, and identifies all those clades that are identical.
for(i in 1:Nnode(bayesTree)) {
for(j in 1:Nnode(bootTree)) {
match(bayesSub[[i]]$tip.label[order(bayesSub[[i]]$tip.label)], bootSub[[j]]$tip.label[order(bootSub[[j]]$tip.label)])->shared
match(bootSub[[j]]$tip.label[order(bootSub[[j]]$tip.label)], bayesSub[[i]]$tip.label[order(bayesSub[[i]]$tip.label)])->shared2
if(sum(,shared2)))==0) {
plot(bayesTree, cex=1, lwd=0.5) #Plots your Bayesian consensus tree
nodelabels(bayesTree$node.label, adj=c(1.2, -0.3), frame="n", cex=1, font=1) #Adds posterior probability values to the tree. Change the 'cex' value to make the fond smaller or larger. A value of 1 will give you a readable result in the R quartz window, but a value closer to 0.25 might be better for publication)
nodelabels(bootList, adj=c(1.4, 1.3), frame="n", cex=1, font=2) #Adds bootstrap values.

#Now you're ready to read your trees in and make your figure!"yourBayesTree.con")->bayesTree #Reads in the .con file that results from analyses in MrBayes.
bayesTree[[1]]->bayesTree #Extracts one of the two trees in the .con file."yourBootTree.nex")->bootTree #Reads in the consensus tree from a bootstrap analysis in PAUP.
plotBayesBoot(bayesTree, bootTree)

Friday, October 17, 2008

Nothing To Do With Phylogenetics...

but it's Friday, and this is my new car.

Penalized Likelihood for Trees

The parsimony versus likelihood debate seems to have cooled off considerably in recent years. Still, we don't know how complex of a model is appropriate for building trees from DNA sequence data. This is expressed, for example, by the question of how many separate partitions should be used for a particular data set. Basically, we create models with widely varying numbers of parameters, and it is not always obvious when to stop doing this to avoid overparameterization.

One solution to this problem is a method called penalized likelihood. In PL, parameters are allowed to vary in the model, but there is a penalty for dramatic changes in parameter values. For example, one might want to vary the rate of evolution across a phylogenetic tree, but give a penalty when parameter values change a lot between adjacent branches. This is the basic idea of PL in the r8s program.

Kim and Sanderson have now implemented this approach as a way to build phylogenetic trees. This could be very useful; as the authors mention, various other phylogenetic reconstruction methods can be viewed as special cases of penalized likelihood, which can thus cover ground in the spaces between existing methods. This seems promising to me, I'm excited to try it on my own data.

The picture, brought to my attention by Brian O'Meara, is from Sanderson's lab page. I think I need that for my own lab.

Thursday, October 16, 2008

The $3-million "Overhead" Projector

While occupants of the White House clearly have indirect effects on nearly every aspect of our lives, at least two phrases or topics mentioned in last night's presidential debate directly concern science. 

Senator McCain repeated his charge that Senator Obama engaged in wasteful pork barrell politics when he sponsored a request for three million dollars for "an overhead projector at a planetarium in Chicago, Illinois." This is deeply misleading. The projector in question is Zeiss Mark VI (similar to photo shown at above-left). As PolitiFact put it:
McCain refers to the item as an "overhead projector," conjuring images of those little projectors on carts in public school libraries all over America, but calling this piece of equipment an overhead projector is like calling the space shuttle a bottle rocket. 
In addition, the Adler Planetarium has published this press release to explain its involvement in this funding request. The Planetarium uses the projector to show the position and glow of thousands of stars in the sky to its visitors, including joint programs with the Chicago Public Schools. In other words, the funding for what is perhaps the most inspiring human experience, that of considering the imponderable size of the universe, was turned into a political weapon. Boo.

Disclosure: I will openly admit that my lip quivered with delight when Senator Obama mentioned "basic science research." I bet he meant population genetic and phylogenetically-informed analyses of plant mating system evolution.

Monday, October 13, 2008

New Journal - Mitochondrial DNA

There's a new journal by Informa Press called "Mitochondrial DNA". From the announcement by the editor-in-chief, Rob Desalle, the list of topics that this journal hopes to cover is as follows:
* mapping, sequencing, and analysis of mitochondrial DNA and RNA
* descriptive studies of DNA sequences from whole mitochondrial genomes
* population genetics, medical genetics, phylogenetics and human evolution that use mitochondrial DNA as a source of evidence for studies
* population genetics and systematics theory that specifically address the use of mitochondrial DNA sequences
* utility of mitochondrial DNA information in medical studies and in human evolutionary biology
* DNA barcoding studies using both empirical approaches and theory-based critiques
Plus, timely reviews on subjects relevant to mitochondrial genomics, genetics and medicine and a regular feature each issue called “mito-communications” that highlight and summarize published research or conference summaries that are relevant to the subject of mitochondrial genomics and genetics.

To access journal information and to submit a manuscript please go to the following URLs.


Friday, October 10, 2008

Why Do People Believe Weird Things?

I'm not really sure if this is a recent phenomenon or not, but there is a super-abundance of people out there who believe in "weird things" - or, things that are directly contradicted by scientific information. Painting with a broad brush, I would include things like creationism, but also anti-vaccination, psychic detectives, Sept. 11 conspiracy theories, alien abductions, etc. I'm sure you can think of your own examples (it's worth clicking on that one). One interesting thing about these types of beliefs is that they cut across the "divide" between conservatives and liberals; there are examples on both sides of the aisle. Given this, I've been thinking about what people with beliefs like this have in common. It seems to me that some of these ways of thinking might be on the rise across all of our society, and could potentially explain the rise of such distinctly different phenomena as the Discovery Institute and the crusade against vaccinating children.

I think that many people who believe things like this share the following beliefs:

1. Anecdotal information, especially when it's personal, is more convincing than statistical analyses. For example, there are a few strange artifacts that some creationists believe are fatal to the theory of evolution; similarly, there are some emotional case-stories about kids with autism that can sway people to forgo shots.

Why is this misleading? Because human brains are trained to see patterns where there is none, anecdotal information can be misleading. Broad statistical methods are designed explicitly to address these sorts of issues.

2. It is possible that powerful groups in society are secretly operating vast conspiracies against the people. Creationists believe that biologists are actively collaborating to prevent their false believe in evolution from being exposed; anti-vaccine advocates believe that the entire medical (or, perhaps, pharmaceutical) industry is conspiring against them.

Why is this misleading? Although our government is not exactly "open source," it is impossible to coordinate conspiracies as vast as the ones required to support some of these theories. In particular, science is very competitive, and scientists are skeptical of other scientists' work. I can't even imagine how someone would get all of us to agree to mislead about data. Also, bureaucracies are incompetent.

3. Sharing radical ideas provides a deep connection with people, even over the internet. I am sometimes struck by the reasonably cohesive nature of these sets of people. The best example of this is moderated internet forums or blogs where large sets of people, all in agreement with each other, can discuss the issues without dissent. If you are a creationist, you might feel an instant connection when, say, you sit near another creationist on an airplane. By contrast, it is entirely unremarkable to meet someone else who accepts the evolutionary worldview.

Why is this misleading? This is a trickier one, because it has more to do with human society than any particular worldview. However, I can speak from personal experience. Some people think that people's political views are a good predictor of whether or not they will make good friends; I have found this not to be the case. Hanging out with people who disagree with you can be much more interesting, and I think personalities cannot be pigeonholed like that.

The really surprising thing, to me, is that I understand why these ways of viewing the world are appealing. As a parent, I rely to a great extent on anecdotal information about how to handle certain situations with the boys. I think the current administration is operating, for the most part, under a cloud of secrecy. And I like radical ideas, and feel bonded to others who can think "outside the box." But together, these things are a potent cocktail for misunderstanding.

To me, this is relevant to my teaching. Perhaps science classes can help students reconcile their framework for the world with scientific information, so that they aren't taken advantage of by these sorts of, to me, counterproductive movements. There are strong arguments against all three of these viewpoints when it comes to complex issues; anecdotal information is deceptive, bureaucratic organizations are too incompetent to really succeed in fooling everyone, and radical ideas don't really lead to lasting relationships. Perhaps we should think about how to get this sort of information across.

One reason why I wanted to post this is that I think the common way of interpreting creationists as "nutcases" or "religious fanatics" is not really a proper explanation (the cartoon here illustrates this way of thinking). In fact, the belief that people who disagree with you are less intelligent and morally inferior in some way is a common thread that is lurking behind many issues in society today - in fact, perhaps both Bush and Bin Laden share that way of thinking. But that seems like another post. Here, my goal is to point out that there are real reasons why people hold the beliefs that they do. If you want to really affect these people - or even coexist with them - then you have to get to the core of the issue.

Wednesday, October 8, 2008

Two more malaria parasite genomes

In this week's Nature, the complete genome sequences of two additional species of malaria parasites, Plasmodium vivax and Plasmodium knowlesi are reported. These two species both are capable of infecting humans - in fact, P. vivax is probably the most common malaria parasite in people, though does not share the high mortality rate of its cousin, Plasmodium falciparum, whose genome was published in 2002. P. knowlesi has recently gained more interest in the biomedical community as this parasite that was thought to use macaques as its hosts was found to infect humans at a much higher rate than ever thought. These two genomes will mark a significant stride forward toward being able to do real comparative biology of these parasites and to use key differences in the life cycle and other biological factors toward perhaps finding new drug and/or vaccine therapies. The P. knowlesi genome was completed largely by a team from Sanger and congrats to my my friend, Jane Carlton, formerly of TIGR and now on the faculty of the NYU School of Medicine and her team for their huge accomplishment on the P. vivax genome (and thanks for the acknowledgment in the paper -- I did the phylogeny for Jane that's in the supplemental methods.)

Friday, October 3, 2008

Evolutionary Applications: A New Journal Worth a Look

There is a new journal, Evolutionary Applications, that everyone should check out. I know there's a glut of journals out there, so sometimes new ones can get lost in the shuffle. But I think the first three issues of this journal (available online free in 2008) speak for themselves. First of all, there are papers from many outstanding scientists that have already been published. Second, I think this journal covers a subject that is of critical importance. Evolutionary applications in medicine, for example, will likely form a cornerstone of many advances in health care over the coming years. Showing that our work has practical importance to society may also help in the discussion about the role of evolution in education. So, check it out!

Thursday, October 2, 2008

What Do Sarah Palin & Ricky Gervais Have in Common?

Shortly after Sarah Palin delivered her rousing speech at the Republican National Convention, I received a gloating e-mail from my Republican father about his party's "home run." Although I responded with concern that her religious zealotry committed her to the denial of established scientific facts, he suggested that this concern was premature. It was true that she advocated creationism in previous campaigns, but I had to admit the possibility that that she had changed her mind since. I decided to withhold further slander until she made her latest views clear. Well, here they are.

Her "teach the controversy" perspective suggests that, at best, she views the first few pages of the Old Testament as an equally meaningful perspective on life as decades of intense study by thousands of other evolutionary biologists. We all know, however, that her true ignorance runs much deeper: "teach the controversy" is merely cover for those who view evolution as a hoax and Genesis' account as literal truth. Now that her zealotry has been confirmed, I hope she'll consider following Ricky Gervais example by expressing her views more directly.

PS - It gets better! The LA Times ran a story a few days ago which quotes Palin saying "dinosaurs and humans walked the Earth at the same time." Note to Gwen Ifill: Please ask the candidates about dinosaurs at the debate tonight. Don't give Palin a chance to spin her "teach the controversy" BS by asking a general question about evolution, just come right out and ask about the dinosaurs!