Cebus capucinus

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Photograph by Daniel Sprockett

Photography contest, Honorable Mention.

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Cebus capucinus – white-faced or white-headed capuchin monkey eating seeds from a tree.

Quote without comment

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Ken Ham, who runs a tax-exempt nonprofit and has received various tax breaks and subsidies from the city and the state, writes,

“The Nation’s T. Rex” will be a centerpiece for the Smithsonian–a museum funded by our tax dollars. In reality, then, the government is imposing the religion of evolution and millions of years on children visiting the Smithsonian, while also claiming a supposed separation of church and state! Our tax dollars are funding the religion of naturalism (atheism) and its evolutionary story to be exhibited in the Smithsonian in the nation’s capital!

Download a PDF copy of this ad.

The Cartwright Lab at Arizona State University in Tempe, AZ is seeking multiple Postdoctoral Research Associates in the areas of Evolutionary Genomics, Statistics, and Bioinformatics to develop methodologies and study evolutionary questions related to mutation and short-read sequencing. Successful applicants will join a rapidly growing and well-funded lab involved on a variety of active research projects and collaborations. Current projects include

  1. the analysis of cilliate mutation accumulation lines,
  2. the development of software for de-novo mutation detection from traditional and single-cell sequencing datasets,
  3. the analysis of non-pathogenic somatic mutation patterns in mammals and plants,
  4. the study of indel patterns across the tree of life,
  5. characterizing mutations and fitness-landscapes of metabolically engineered microbes,
  6. population genetics of malaria parasites,
  7. the construction of phylogenies from short-read, whole genome datasets, and
  8. simulation techniques for molecular evolution research.

The Cartwright Lab is part of the Center for Evolutionary Medicine and Informatics (CEMI), one of 10 research centers in Arizona State University’s Biodesign Institute. Research in the Cartwright Lab covers many different questions in population genetics and molecular evolution, at the interface of biology, statistics, and computer science. A majority of our research involves developing, implementing, and applying novel methodologies to study genomic datasets. Members have the opportunity to develop both dry-lab and wet-lab research programs through interactions with both national and international collaborations.

As part of this project, the Postdoctoral Research Associates are expected to be able to:

  1. Assemble microbial or metazoan genomes from short-read sequences and identify variable sites and regions.
  2. Develop novel, high-throughput methodologies to study mutations from next generation sequencing of related individuals and cells.
  3. Work closely with collaborators to customize methodologies to specific experimental designs.

Required Qualifications:

Ph.D. in genomics, bioinformatics, or a related field

Desired Qualifications:

  1. Experience working with genomes and evolutionary analyses
  2. Knowledge of programming languages including R, Python, and C++
  3. Knowledge of statistical methodologies
  4. Experience with short-read sequencing

Application must contain:

  1. Resume
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  3. Names, addresses, and phone numbers of three professional references

Deadline for applications is May 1, 2014. Applications will continue to be accepted and considered until the job is filled/closed.

For more information see http://cartwrig.ht/lab/ or http://labs.biodesign.asu.edu/cartwright/.

To apply, forward one document that includes a cover letter, detailed CV, and names of 3 references to cartwright@asu.edu. Please put the job title in the subject line of the letter.

Arizona State University is an Equal Opportunity/Affirmative Action employer. A background check is required for employment.

I occasionally get books for review unsolicited, and many of them are not worth noticing. However, Kostas Kampourakis' Understanding Evolution is a wonderful resource for students of all kinds, including biology students.

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Once again, desperately dissing Avida

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One of the characteristics of a pseudoscience is repeating discredited arguments as though they were new. And sure enough, once again an Intelligent Design Creationist is flailing around trying to discredit research in digital evolutionary models that shows that structures displaying IDC’s central concept, irreducible complexity, are evolvable via Darwinian processes. I have previously looked at earlier attempts to discredit that research; see here and here for examples.

Now it’s happening again. This month, Winston Ewert, affiliated (according to the paper) with the Discovery Institute’s Biologic Institute (though he doesn’t appear on their published list of personnel), published a review and critique of several computer models of evolution in the DI’s captive journal Bio-Complexity. Ewert was a graduate student of Robert Marks at Baylor, where he was associated with Marks’ and Dembski’s Evolutionary Bioinformatics Lab. He now has a Ph.D. from Baylor, the first in Baylor’s combined electrical engineering and computer science graduate program.

In his critique Ewert looks at five programs: Avida, Tom Schneider’s Ev, Dave Thomas’s Steiner tree GA, Suzanne Sadedin’s geometric model, and Adrian Thompson’s “digital ears”, a program realized in field programmable gate arrays. Here I will analyze Ewert’s critique of Avida; I am less familiar with the other models Ewert discusses. However, given the errors I find in his discussion of Avida, I am very dubious with respect to his analysis of the other programs. If he does so badly with something I know pretty well, why should I trust his judgement in areas I don’t know so well?

After repeating an introduction to Avida that I wrote some years ago, I will follow (roughly) Ewert’s analysis, in which he first describes all five programs and then criticizes them. Hence, I’ll look at Ewert’s description of Avida, and in particular note several errors in it, and then I’ll evaluate his criticisms. I find that his description is faulty and his critique ill-founded.

Branta canadensis

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Branta canadensis – Canada goose on nest, Walden Ponds, Boulder, Colorado, 2014. The nest is on a small island in the middle of a pond. The goose sat on her (?) nest for most of the hour or so that we hung around. Then she got up, apparently cleaned the nest, and took off for a tryst or something with her boyfriend. We could see no sign of eggs or babies, but we thought we heard a high-pitched chirping coming from the nest when the parents were gone. The geese came back a little while later, and one of them immediately sat down on the nest. We plan to check on our newfound friends every week or so and will report back if there is anything to report.

It’s a 3-part series with Neil Shubin, the paleontologist who discovered Tiktaalik. The series begins tomorrow, Wednesday, April 9, at 10 p.m. Eastern Daylight Time. You can see a preview here.

Rocky Mountain PBS says about the series

Anatomist and paleontologist Neil Shubin sees evidence of our ancient past in our anatomy and in our DNA. Join him as he journeys to meet our ancient animal ancestors, while revealing the impact those animals have had on our bodies

and they have an interactive webpage here.

The second and third episodes are called “Your Inner Reptile” and “Your Inner Monkey.”

Update, April 9: An AP release yesterday afternoon notes that PBS will also premiere a 3-part Nova series tonight. Tonight’s episode: “Inside Animal Minds.” These 2 series, along with Nature, exemplify PBS’s new “Think Wednesday” schedule, which AP characterizes as “a three-hour prime-time block of nature, science and technology programs” anchored by Nature and Nova.

My, how time flies.

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PZ reminds us that today is the 10th anniversary of Paul Nelson’s promise to deliver an operational definition of “ontogenetic depth.” Nelson said it would be forthcoming “tomorrow.” When I was about four years old it struck me that tomorrow never comes.

And I can’t resist re-publishing this:

Concerning Richard B. Hoppe and his requests for Paul Nelson to provide support for his Intelligent Design claims about Ontogenetic Depth:

Paul Nelson’s “depth” tales sounded tall.
Richard Hoppe thought, “it’s past time to call
Nelson’s ontogenetic-
clad apologetic.”
Quoth Richard, “So where’s the beef, Paul?”

I doubt that he’ll find satisfaction,
nor even a lucid reaction.
Behind the smoke screen
there’s an ID machine
building weapons of media distraction.

A meal of Intelligent Design
when served with the fruit of divine
is lacking in beef,
which supports my belief
that it’s tripe marinating in whine.

Edestus jaw

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Photograph by Daniel Phelps.

Photography contest, Honorable Mention.

Phelps-EdestusJaw_600.jpg

Edestus jaw – Upper Carboniferous, Henderson County, Kentucky. Found in an underground coal mine earlier this year. On display at the Kentucky Geological Survey.

Yeah, yeah, I know: Schizophrenia is a specific medical diagnosis, and it does not mean holding two views at the same time. But its etymology does imply something like split mind, and I cannot think of a better way to describe this:

The Creation “Museum” has put on display the Allosaurus fossil that we reported on here. And they are tickled pink. Their house geologist, Andrew Snelling, who used to do real geology (or his doppelgänger did) said of their Allosaurus,

From the website of the Schilling School, “A Nationally Recognized K-12 [Charter] School for the Gifted in Cincinnati, Ohio”:

Dr. Michael Behe to present at Schilling. Mark your calendar for Sunday, April 6th from 7:00 pm - 9:00 pm to hear him present, “ Feeling left out by the Ham-Nye Debate? The Reasonable Middle Ground of Intelligent Design.” Call 489-8940 for ticket prices and group rates.

Congratulations to our 2014 U.C. Science Fair winners. All of our students won a cash prize. Two of our students Salma and Daniel have been invited to participate at the state science fair in Columbus next month. Good luck to the both of them!

And may they not be seduced by pseudoscience.

Acknowledgment. Thanks to an alert reader for sending us the link.

Geranium richardsonii

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Photograph by Andrew Freeman.

Photography contest, Honorable Mention.

Freeman.Geranium_richardsonii.jpg

Geranium richardsonii – wild geranium, Pearl Lake, Colorado.

Since everyone is all het up about Noah, I thought I would resurrect (sorry) a narrative I wrote 15 years ago for my book on science and religion. The “Friedman” I cite is Richard Elliott Friedman, author of Who Wrote the Bible? I used the section primarily to explain why scholars are convinced that the Hebrew Bible is a composite of two different but related methodologies (the documentary hypothesis), but it also shows the utter incoherence of the Bible when read as a literal history. The excerpt may be found below the fold.

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Well, AiG’s Ken Ham has seen the movie “Noah” starring Russell Crowe, and boy, is he steamed!

Friends, I just arrived home after seeing the Hollywood (Paramount) movie NOAH tonight. It is MUCH much worse than I thought it would be. Much worse.

The Director of the movie, Darren Aronofsky has been quoted in the media as saying NOAH is ‘the least biblical biblical film ever made’, I agree wholeheartedly with him.

I am disgusted. I am going to come right out and say it-it is disgusting and evil-paganism! Do you really want your family to see a pagan movie the has Noah as some psychopath who says if his daughter-in-law’s baby is a girl, he will kill it as soon as it’s born. And then when two girls are born, bloodstained Noah (the man the Bible calls righteous Noah-Genesis 7:1), brings a knife down to one of the baby’s heads to kill it and at the last minute doesn’t do it-and then a bit later says he failed because he didn’t kill the babies. How can we recommend this movie and then speak against abortion! Psychopathic Noah sees humans as a blight on the planet and wants to rid the world of people.

I feel dirty-as if I have to somehow wash the evil off me.

Aythya americana

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Aythya americana – redhead, Walden Ponds, Boulder, Colorado, 2014. A stray widgeon insisted on getting into the picture. (The person with the biggest binoculars told me that they were cinnamon teals, but that does not look right. Someone with a good pattern-recognition system please correct me if necessary.)

Cygnus columbianus

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Cygnus columbianus – tundra swan, Walden Ponds, Boulder, Colorado, March, 2014. A single swan, presumably the same one, has been showing up here for the last few years. I looked for the people with the biggest binoculars and the longest focal-length camera lenses and asked how come there was only one? I got several answers, all of which begged the question why the bird is not in a flock: (1) They mate for life, and maybe this one lost its mate. (2) They mate for life, but maybe they don’t always hang around together. (3) Maybe this one is a juvenile, not old enough to have a mate.

I finally watched a tape of the first installment of the new “Cosmos” series the other day. I thought it was a bit overdone and maybe a little slow, and I thought the cartoons were ghastly. (Also, there were gobs of commercials; why oh why is this series not showing on PBS?) Never once did I imagine that anyone would accuse such a completely innocuous television program of being propaganda for materialism. Yet according to a Salon article by Andrew Leonard, the far right has accused the program of being precisely that. Ironic that is showing on the Fox network!

I have not looked at the primary sources, so I will have to take Leonard’s word for it, but they may be right about Giordano Bruno. The conventional wisdom is that Bruno was burned for supporting the heliocentric theory, but the historian Alberto Martinez, in his book Science Secrets, thinks that it may as well have been because of his theological views: doubting that Jesus was born of a virgin and denying that he was actually God. Bruno was, nevertheless, an early and vigorous supporter of the Copernican theory, and only an idiot or a conspiracy theorist (but I repeat myself) would think that Bruno was introduced into the program for nefarious reasons.

Acknowledgment. Thanks to Walter Plywaski for showing me the Salon article.

Paabo_2014_Neanderthal_Man_cover.jpgPeople have been sending me this, so I might as well blog it. In February 2014, Svante Pääbo, who led the Neanderthal genome project, published a popular book on the sequencing of the Neanderthal genome, and reactions to it.

I haven’t yet read the book, although I’m sure it’s great, based on talks I have seen by Pääbo. However, there is one passage that PT readers may find particularly interesting:

Svante Pääbo (2014). Neanderthal Man: In Search of Lost Genomes. Basic Books; First Edition (February 11, 2014), 288 pages http://www.amazon.com/Svante-P%C3%A[…]e/B00GJ9XR7O

p. 221:

There were many others who were interested in the Neanderthal genome – perhaps most surprisingly, some fundamentalist Christians in the United States. A few months after our paper appeared, I met Nicholas J. Matzke, a doctoral candidate at the Center for Theoretical Evolutionary Genomics at UC Berkeley. Unbeknownst to me and the other authors, our paper had apparently caused quite a flurry of discussion in the creationist community. Nick explained to me that creationists come in two varieties. First, there are “young-earth creationists,” who believe that the earth, the heavens, and all life were created by direct acts of God sometime between 5,700 and 10,000 years ago. They tend to consider Neanderthals as “fully human,” sometimes saying they were another, now extinct “race” that was scattered after the fall of the Tower of Babel. As a consequence, young-earth creationists had no problem with our finding that Neanderthals and modern humans had mixed. Then there are “old-earth creationists,” who accept that the earth is old but reject evolution by natural, nondivine means. One major old-earth ministry is “Reasons to Believe,” headed by a Hugh Ross. He believes that modern humans were specially created around 50,000 years ago and that Neanderthals weren’t humans, but animals. Ross and other old-earth creationists didn’t like the finding that Neanderthals and modern humans had mixed. Nick sent me a transcript from a radio show in which he [meaning Hugh Ross] commented on our work, saying interbreeding was predictable “because the story of Genesis is early humanity getting into exceptionally wicked behavior practices,” and that God may have had to “forcibly scatter humanity over the face of the Earth” to stop this kind of interbreeding, which he compared to “animal bestiality.”

Clearly our paper was reaching a broader audience than we had ever imagined.

Imagine that. anecdotal-oops.jpg

The above is the copy I got in an email.

Somebody spilled the beans, alas, and the corrected version with “antidote” has been posted.

Too late, we’ve gotten our belly laugh! Nyah Nyah, Discovery Institute, no memory hole is big enough to make this laughable faux pas go away.

I occasionally receive a request to print or post a photograph that has appeared on Panda’s Thumb, but this one takes the cake: A magazine called Creation Illustrated, which bills itself as “The Christian answer to National Geographic,” requested permission to publish this photograph

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in its magazine. Fat chance!

Their e-mail was datelined, “URGENT - Matt Young’s photo of Table Mountain needed.” Needed, eh? I am afraid I was not very kind to them:

Thank you; I am glad you liked my photograph. Unfortunately, under no conditions will I allow this photograph (or any other to which I own the copyright) to be published in any creationist publication. So my answer is, “No.” Did you not notice that the website, Panda’s Thumb, where the photograph was published, is devoted to scientific reality, that is, evolutionary science? “Christian answer to National Geographic,” indeed!

Until now, I was blissfully unaware that National Geographic needed an answer of any kind.

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Recent Comments

  • prongs: One counter-example destroys the hypothesis. Consider Alchemy (turning lead into gold). Thousands of practitioners, throughout the centuries, sought the magic formula to transform lead into gold. Science undiscovered? Nay. Alchemy read more
  • harold: That’s nice of David “Koch Brothers” Koch to give that $35M for a new dinosaur room. Unfortunately, David Koch does far more harm than good to science. He’s a read more
  • Helena Constantine: Are you in a contest with Byers to be the stupidest poster here? My core professional competence is the history of magic int he Roman Empire. I do not read more
  • Scott F: Your question, and both statements are false. The statement about airplanes could only be true if you believe that birds fly by using “magic”. Even the ancient Greeks knew read more
  • eric: Please do visit the museum(s), however, be aware that the Natural History Museum’s dinosaur exhibit hall will be closed for renovations, starting this Monday, and probably won’t reopen for read more
  • gregpeterson144: So we have a National T. Rex?! Cool. I’ll have to go see it when I’m at my daughter’s wedding in D.C. in a few months. Thanks, Ken Ham, for read more
  • eric: Yeah I agree. Props to the designer. read more
  • eric: And let’s not forget Peter Delly’s literal takedown of Yellow Bamboo chi fighting, or Sanal Edamaruku laughing on camera while a tantric magician attacks him with a “death curse.” read more
  • eric: I am not sure equating ignorance of mechanism with “magic” saves the concept of God. If you’re implying that God manipulates forces and materials using/by obeying the laws of read more
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