April 2013 Archives

More on home schooling materials and evolution


A few weeks ago I wrote on the desire of (some) evangelical home-schooling parents to have honest materials for science education. Now Christianity Today has picked up that story, adding at least one new wrinkle: it claims that at least some of the parents who want such materials are young-earthers who want their children exposed to different perspectives. Interviewees from both BioLogos and the American Scientific Affiliation make that claim.

Iguana iguana


Photograph by Daniel Sprockett.

Photography contest, Honorable Mention.


Iguana iguana – “dominant green iguana, high up in the treetops. He is orange because it was mating season while we were in Costa Rica, and he had been protecting his harem from invading males all morning.”

Musings from the mind of a mouse


Casey Luskin is such a great gift to the scientific community. The public spokesman for the Discovery Institute has a law degree and a Masters degree (in Science! Earth Science, that is) and thinks he is qualified to analyze papers in genetics and molecular biology, fields in which he hasn't the slightest smattering of background, and he keeps falling flat on his face. It's hilarious! The Discovery Institute is so hard up for competent talent, though, that they keep letting him make a spectacle of his ignorance.

I really, really hope Luskin lives a long time and keeps his job as a frontman for Intelligent Design creationism. He just makes me so happy.

His latest tirade is inspired by the New York Times, which ran an article on highlights from the coelacanth genome. Luskin doesn't think very deeply, so he keeps making these arguments that he thinks are terribly damaging to evolution because he doesn't comprehend the significance of what he's saying. For instance, he sneers at the fact that we keep finding conserved elements in the genome, because as we all know, there are lots of conserved elements.

Today we’re going to talk about snail sex.

There was recently a hubbub about an National Science Foundation (NSF) funding a grant to study snail sex to Maurine Neiman, John Logsdon, and Jeffrey Boore. Because, y’know, snails are so slimy, and sex is gross, so that makes snail sex… icky, and what is it good for?!?

E.O. Wilson wrote an essay entitled, “Great Scientist ≠ Good at Math”. If you haven’t read it, here is my summary of E.O. Wilson’s statement:

I didn’t learn much math, and I am a successful scientist because I think critically and found collaborators who were good at math. If you think critically, and find collaborators who are good at mathematics and statistics, you can be a successful scientist without personally knowing much math. 

The name of my blog is mathbionerd. I loved math in high school (thanks Mr. Boerner), and majored in Mathematics in college at Creighton University. I did a summer research experience at the University of Nebraska, Lincoln in the Mathematics department. And, for graduate school, I applied to both Mathematics programs and Bioinformatics programs, ultimately choosing the latter, but volunteering to be a teaching assistant for Calculus. I currently study biological questions and large datasets using computer programs and statistical models. So, uh, yes, I think math is important.


A lot of my friends have been passing around this recent comic from the Oatmeal. First, take a few minutes to go read it, laugh, and be in awe of the amazing mantis shrimp:

READ THIS — > http://theoatmeal.com/comics/mantis_shrimp

The cartoon, the information, the presentation, are all excellent! After the awesomeness of the mantis shrimp wore off, I started thinking about how the Oatmeal, especially with this piece, is an excellent example of how to communicate science to the public.

Bombings and biased samples


Jerry Coyne, over at Why Evolution is True, has a post up entitled “Islam apparently behind Boston bombing.” He writes,

Narcissus sp.


Narcissus sp. – daffodil. Slightly off task, but this daffodil was one of many passed out at a ceremony during which the Polish government awarded my friend Walter Plywaski, a Holocaust survivor, the Knight’s Cross of Merit, “in recognition of outstanding services to the Polish-American community in disseminating historical awareness on Polish and Jewish fates in the occupied Poland.” The 6 sepals represent the star of David.

The first one, “Survival of the Fittest” is the one that is most annoying to me. Why? Because it is often used as a synonym for evolution, but evolution is about so much more!

The coelacanth genome has been sequenced, which is good news all around…except that I found a few of the comments in the article announcing it disconcerting. They keep calling it a "living fossil" — and you know what I think of that term — and they keep referring to it as evolving slowly

The slowly evolving coelacanth

The morphological resemblance of the modern coelacanth to its fossil ancestors has resulted in it being nicknamed 'the living fossil'. This invites the question of whether the genome of the coelacanth is as slowly evolving as its outward appearance suggests. Earlier work showed that a few gene families, such as Hox and protocadherins, have comparatively slower protein-coding evolution in coelacanth than in other vertebrate lineages.

Honestly, that's just weird. How can you say its outward appearance suggests it is slowly evolving? The two modern species are remnants of a diverse group — it looks different than forms found in the fossil record.

By Steven Mahone

David Klinghoffer has exploited the recent national tragedies to insult people he calls “Darwinists,” a term that he incorrectly conflates with callousness, indifference, and atheism. My colleague Steven Mahone was unimpressed by Klinghoffer’s post, penned the following reply, and graciously agreed to share it with our readers.

Update, April 24: Mr Mahone seems to have gotten Mr. Klinghoffer’s attention.

David Klinghoffer of the Discovery Institute is despondent over the recent string of tragic events that have befallen our nation. This despondency is understandable – especially since every mentally healthy person I’ve come across either in person or on social media shares essentially the same sorrow and anguish for those who were affected. Which is why I’m confused as to the intent of Klinghoffer’s recent online article, If Darwinists [sic] won the debate, what would they say to impart comfort, meaning to those in grief? In that article, Klinghoffer seems to imply that it would be a difficult task indeed for anyone who’s not inclined to pre-order the latest “game changing” polemics from his colleagues Berlinski, Meyer, or Luskin, to offer genuine consolation or even a sincere word of encouragement to anyone who is in need. Klinghoffer is convinced that while those cold, heartless, and impersonal men and women of material science might be able to cure the disease, afterwards you’d better not expect anything more than a firm handshake.

How useful are words?


On something as simple as posting about a conference for bringing together Mathematicians and Biologists there are commenters questioning the utility of Mathematics.

To me, questioning the utility of Mathematics to Science (and to Biology in particular) is like asking why words are useful to communication.

AIG live chat on “When was the Ice Age in Biblical History?”


This ought to be good. In a comment, diogeneslamp0 alerts us to a live chat on that topic scheduled for tomorrow (Tuesday) on the Facebook page of AIG’s Answers Magazine. Diogeneslamp0 notes

On the topic of how kangaroos got to Australia after Noah’s Flood: at 2pm tomorrow, April 16 Answers in Genesis will hold a live chat at Facebook about AIG’s marvelous Super-fast Ice-Age Timeline and Map (which has the Ice Age lasting from about ~2220 to ~2115 BC, and all recorded human civilization post-2100 BC). I predict that any pointed questions they receive will be deleted quickly and permanently, so if you want some entertainment you will have to monitor it live. You may want to copy and archive any choice questions they receive before they’re deleted.

I presume that AIG’s “2:00 pm” is Eastern Daylight Time (=1800 GMT). Diogeneslamp0 has some representative questions one might ask at the linked comment.

Alopochen aegyptiaca


Photograph by Alice Levine.


Alopochen aegyptiaca – Egyptian goose, Kirstenbosch Botanical Gardens, Cape Town, South Africa.

William Dembski’s “Catalog of Fundamental Facts”


Scanning past Uncommon Descent this afternoon, I noticed a kairosfocus post pointing to the Internet Archive’s stored version of a (now defunct) website called evolutiondebate.info/ where Eric Anderson provided a “Brief Primer on Intelligent Design.” In the second paragraph we read

Rather, this represents my modest attempt to … outline the fundamental central tenet of intelligent design, which is that some things exhibit characteristics of design that can be objectively and reliably detected.

For some reason that reminded me of something William Dembski proposed years ago, a sort of catalog of designs in biology. More below the fold.

E.O. Wilson says you can be successful as a scientist without math. Well, maybe. But, you can improve your chances of success if you take a breath, let go of your fear of math, and take some time to learn it. I think it is really quite wonderful. Oh, and if you aren’t sure about where to start, there just happens to be a workshop for Mathematics in Biology. Yes, yes, go sign up!!

 2013 Workshop for Young Researchers in Mathematical Biology (WYRMB)

August 26 - 29, 2013

Application deadline: May 1, 2013

The workshop is intended to broaden the scientific perspective of young researchers (primarily junior faculty, postdocs, and senior graduate students) in mathematical biology and to encourage interactions with other scientists.

Workshop activities include plenary talks and poster sessions, as well as group discussions on issues relevant to mathematical biologists. Several abstracts will be chosen for short talks as well as poster presentations. Limited funding is available on a competitive basis.

We cordially invite young mathematical biologists to participate. For full consideration, please apply by May 1, 2013. To apply, click this link http://www.mbi.osu.edu/wyrmb/wyrmb2013.html

Plenary Speakers

Lisa Fauci, Tulane University
Kresimir Josic, University of Houston
Claudia Neuhauser, University of Minnesota
Sebastian Schreiber, UC Davis
Arthur Sherman, Laboratory of Biological Modeling, NIDDK, NIH
John Tyson, Virginia Tech
Lani Wu, Southwestern University

This post has gotten a few questions since yesterday, so I’ll take that as a cue to make it my first one here. I’m starting to get a taste for how interactive it is to be a part of PT, so until I make blogging my day job, I will be alternating between new posts and content I wrote before.

Emu are one of the largest living species of birds:

Awesome emu.

Hello world


I am thrilled to start cross-posting on Panda’s Thumb (from my small corner of the internet at mathbionerd.blogspot.com). I’m an evolutionary biologist studying many things, which generally involve sex-specific processes (sex chromosome evolution, meiosis, male mutation bias: http://cteg.berkeley.edu/~sayres). I am dedicated to communicating science in language that is accessible to general audiences. So, here I’ll be posting “accessible research”, as well as other bits about science careers.

Tips on Lab Meetings


As I prepare for another lab meeting, I realize that I have no idea what I am doing.

Any experienced PIs have any tips about putting together successful lab meetings?

Keep in mind that my lab consists of about 7 undergraduates, a grad student, and a postdoc.

Sula nebouxii


Photograph by Thomas Layton.

Photography contest, Honorable Mention.

Layton_Blue Footed Booby.jpg

Sula nebouxii – blue-footed booby, Espanola Island, Galapagos Islands.

The Times last week ran an article on the implementation of school vouchers in a number of states. My concern here is that the vouchers may be applied to religious schools and possibly home schools that have little oversight.

In response to our post and comments on Stephen Meyer needs your help William Dembski has replied at Evolution News and Views. He is upset that we were “attempting to disparage” Meyer’s book without having seen it. (More on that below).

In the post, I made my suggestion of content for Meyer’s book. I suggested that Meyer acknowledge in his book that Dembski’s Design Inference using Complex Specified Information (CSI) had failed, because the theorem that Dembski needed did not exist. Dembski disagrees:

Felsenstein’s request for clarification could just as well have been addressed to me, so let me respond, making clear why criticisms by Felsenstein, Shallit, et al. don’t hold water.

If Dembski has refuted these criticisms, that is worth careful attention; you would need to understand why Shallit and I were wrong. Were we? Even if we were right, has Dembski supplanted his earlier arguments with newer ones that that do a better job of arguing against the effectiveness of natural selection?

As the argument needs more than a few lines, I will place most of it below the fold. There I will argue that

  • When Shallit and Elsberry found a hole in Dembski’s theorem, and when I pointed out that the theorem was unable to refute the effectiveness of natural selection (because its specification changed in midstream) we were right.
  • Dembski’s more recent reformulation of his CSI argument in 2005 adds a term that calculates the probability that natural selection and mutation could do the job; this simply made the rest of the Design Inference redundant, and
  • The more recent Search For a Search arguments of Dembski and Marks are arguments about a Designer being needed in order to make the pattern of fitnesses be one in which natural selection does work. Thus they are not arguments against the effectiveness of natural selection.

Let’s see .…

The paper Selective bird predation on the peppered moth: the last experiment of Michael Majerus is one of the most downloaded and cited articles in Biology Letters in 2012. As Bruce Grant, one of the coauthors, said to me privately, “It is encouraging that the Biston evidence, presented by those of us who actually know it, is being widely read.” Biston is the genus of the peppered moth, B. betularia.

PT has covered a controversy concerning the peppered moth here. Michael Majerus, a lepidopterist and expert on melanism and the peppered moth, died suddenly and unexpectedly in 2009. Nick Matzke covered Majerus’s last experiment here.

Happy 9th Paul Nelson Day!


It's a dying holiday, I'm sorry to say -- I completely forgot it last year. But I was reminded this year, so I'll mention it again. I think the proper way to celebrate it is simply to laugh at a creationist today.

The source of the holiday is a remarkable exhibition from Paul Nelson, who like several other creationists, loves to register and present at legitimate science conferences. The barriers are low, and many conferences are intended to give students an opportunity to present, so you'll often find that all you have to do is send in a fee and an abstract and you'll be allowed to put up a poster in an allotted space for a few hours of time. So Nelson showed up at the Developmental Biology meetings in 2004 with a poster titled "Understanding the Cambrian Explosion by Estimating Ontogenetic Depth" in which he and Marcus Ross claimed to have been collecting data measuring some parameter called "ontogenetic depth" in various organisms.

I was at that meeting. I asked him about that in person, and also in blog posts afterwards. How do you measure ontogenetic depth? Share your procedure so I can assess and replicate it, which is what scientists are supposed to do. He hemmed and hawed and hmmphed and in typical Nelsonian fashion babbled and burbled on, and the upshot was that he couldn't tell me just then, but he had something he was writing and he'd polish it up and get it to me the next day, 7 April. He didn't. We've been watching the 7th of April pass by for nine years now.

I think he's felt the sting of mockery. In 2010 he announced that my criticisms were invalid, but he was inventing Ontogenetic Depth 2.0, which still isn't defined and still doesn't have a procedure.

In 2011 he posted some more essays on his fictitious method, in the first of which he announced that ontogenetic depth is A Biological Distance That's Currently Impossible to Measure. Yeah? So why was he presenting a poster at a serious scientific meeting in which he and his colleague claimed to have been measuring it? Sounds like scientific fraud to me.

But then, Intelligent Design creationism has been scientific fraud all along, so I guess he was just following hallowed tradition.

FT Magazine on AIG’s Ark project


Via NCSE’s Facebook page. A snippet:

The ark will sit next to a man-made lake whose waters will erupt sporadically in fiery explosions to simulate the breaking open of the fountains of the deep. But the ark will not set sail. Marsh could build a seaworthy vessel with the same techniques, he said, but non-biblical fire regulations require concrete stairwells and exits that mean his version would sink.

I want to see that wooden ark covered inside and out with pitch riding out those “fiery explosions.” Pitch burns really well.


As we reflect upon the amazing body of work left behind by this giant of the movie scene, readers of the Thumb should know (if they don’t already) that Roger Ebert was a passionate defender of science, and of evolution in particular.

His passion was not un-noticed by creationists (of both young-earth and intelligent design categories). William Dembski had this to say about Ebert in an Uncommon Descent blog from 2006:

Roger Ebert: Film Critic, Expert on Evolution, ID Basher, and Overall Supergenius .….. Or is Ebert just another clueless bonehead whose imagined expertise is in exact disproportion to his actual knowledge …

Here are some memorable comments by Ebert on creationism, evolution, and religion.

Win Ben Stein’s mind, December 3, 2008

The more you know about evolution, or simple logic, the more you are likely to be appalled by the film. No one with an ability for critical thinking could watch more than three minutes without becoming aware of its tactics. It isn’t even subtle. Take its treatment of Dawkins, who throughout his interviews with Stein is honest, plain-spoken, and courteous. As Stein goes to interview him for the last time, we see a makeup artist carefully patting on rouge and dusting Dawkins’ face. After he is prepared and composed, after the shine has been taken off his nose, here comes plain, down-to-earth, workaday Ben Stein. So we get the vain Dawkins with his effete makeup, talking to the ordinary Joe.

I have done television interviews for more than 40 years. I have been on both ends of the questions. I have news for you. Everyone is made up before going on television. If they are not, they will look like death warmed over. There is not a person reading this right now who should go on camera without some kind of makeup. Even the obligatory “shocked neighbors” standing in their front yards after a murder usually have some powder brushed on by the camera person. Was Ben Stein wearing makeup? Of course he was. Did he whisper to his camera crew to roll while Dawkins was being made up? Of course he did. Otherwise, no camera operator on earth would have taped that. That incident dramatizes his approach throughout the film. If you want to study Gotcha! moments, start here.

How I believe in God, April 17, 2009

During in all the endless discussions on several threads of this blog about evolution, intelligent design, God and the afterworld, now numbering altogether around 3,500 comments, I have never said, although readers have freely informed me I am an atheist, an agnostic, or at the very least a secular humanist–which I am. If I were to say I don’t believe God exists, that wouldn’t mean I believe God doesn’t exist. Nor does it mean I don’t know, which implies that I could know.

Let me rule out at once any God who has personally spoken to anyone or issued instructions to men. That some men believe they have been spoken to by God, I am certain. I do not believe Moses came down from the mountain with any tablets he did not go up with. I believe mankind in general evidently has a need to believe in higher powers and an existence not limited to the physical duration of the body. But these needs are hopes, and believing them doesn’t make them true. … No, I am not a Buddhist. I am not a believer, not an atheist, not an agnostic. I am still awake at night, asking how? I am more content with the question than I would be with an answer.

Darwin survives as the fittest, February 11, 2009

The True Believers. Found in both parties. One side declares God without any doubt does exist, and created the universe and everything in it. A much smaller subset of this group is convinced that God did this in fairly recent times–as little as 6,000 years ago, or in any event too recently for Darwin’s evolutionary process to have had enough time to take place. The other side declares that God without any doubt does not exist, and it is equally certain. Both sides frequently quote the Bible, on the one hand citing its truth, on the other side citing its falsity. Christianity is the only religion involved; my blog has readers from all over the world, but apparently those from elsewhere find Intelligent Design a uniquely American notion.

The longest thread evolves, September 4, 2009

The zealots of Creationism are indefatigable. Even now there are attempts to legislate that the pseudo science of Intelligent Design must be taught in school systems as a “debate” with Evolution. In common sense terms, that debate was over a century ago. Yet there are votes out there for politicians who support such legislation, and at the 2008 GOP presidential debate, no less that three candidates said they do not believe in evolution. I suppose I should be gratified that there weren’t more.

New Agers and Creationists should not be President, December 2, 2009

My only purpose today is to state early and often that if a Presidential candidate believes early humans used saddles to ride on the backs of dinosaurs, as they are depicted at the Creation Museum in Petersburg, Kentucky, that candidate should not be elected President.

And if a candidate counts among close friends and advisors anyone in communication with the spirit world, that candidate should not be elected President.

And if a candidate accounts for the fact that humanoid and dinosaur bones are never found at the same level in the fossil record by evoking the action of sediment after the Great Flood, that candidate should not be President.

And if a candidate has a spirit guide, consults his or her Chart and takes more than a passing amusement in the horoscope, that candidate should not be elected President.

There’s a category page linking these and other blogs, appropriately titled “Darwin My Hero”.

Comments about Roger Ebert are welcome. Comments that are nonsequiters, religious rants, or are otherwise irrelevant, will be tossed onto the Bathroom Wall.

Evolution: Education and Outreach articles all available now


Evolution: Education and Outreach, the Springer journal devoted to … em … evolution education and outreach, has made all its articles available online free. Browse and enjoy!

Hat tip to Genie Scott’s Facebook page.

Great Unconformity


Photograph by Jon Woolf.

Photography contest, Honorable Mention.


The Great Unconformity in the Grand Canyon. Mr. Wolf writes that the unconformity “demonstrates geologic time and a number of basic geologic rules that help to destroy YEC.”

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