April 2014 Archives

Gaillardia aestivalis

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Photograph by Lynn Wilhelm.

Photography contest, Honorable Mention.

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Gaillardia aestivalis var. winkleri “Grape Sensation”; common name, Winkler’™s White Firewheel-Purple selection, JC Raulston Arboretum in Raleigh, North Carolina.

Ms. Wilhelm writes, “This cultivar (cultivated variety) is a selection by the Stephen F. Austin State University Mast Arboretum in Nacogdoches, Texas, in honor of the school color. The natural variety is white with a yellow center and is found only in one county in Texas. Gaillardia aestivalis depends on fire to reduce competition in its native habitat (hence the common name).”

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
  2. Cover Letter
  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.

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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.

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