Recently in Evolution Category

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.

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.

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.

Geranium richardsonii

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Photograph by Andrew Freeman.

Photography contest, Honorable Mention.

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Geranium richardsonii – wild geranium, Pearl Lake, Colorado.

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.

Gaillardia aestivalis

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Photograph by Lynn Wilhelm.

Photography contest, Honorable Mention.

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Gaillardia aestivalis var. winkleri ‘Grape Sensation’ – Winkler’s White Firewheel-Purple selection, JC Raulston Arboretum Raleigh, North Carolina. Ms. Wilhelm adds, “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).

Cupressus macrocarpa

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Photograph by Tom Gillespie.

Photography contest, Honorable Mention.

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Cupressus macrocarpa – Monterey cypress, just off the 17-Mile Drive near Pebble Beach, California, looking north from the pedestrian walkway to the Lone Cypress, December, 1995. Mr. Gillespie wonders “how much erosion has taken place since.”

Sarcodes sanguinea

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Photograph by Jim Norton.

Photography contest, Honorable Mention.

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Sarcodes sanguinea – snow plant, a saprophytic plant with no chlorophyll. King’s Canyon National Park, California, July 3, 2010.

Coccinella septempunctata

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Photograph by Buddhini Samarasinghe.

Photography contest, Honorable Mention.

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Coccinella septempunctata – seven-spotted ladybird beetle. Also, ladybug, lady beetle. Scotland, UK.

Sterna antillarum browni

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Photograph by Marschal Fazio.

Photography contest, Honorable Mention.

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Sterna antillarum browni – California least tern. Mr. Fazio writes, “This species is listed as endangered under the Federal Endangered Species Act. It nests along the California coast on sandy shorelines; as humans have encroached, the tern has lost much of its nesting habitat and now nests in overcrowded sites or mudflats, making them more prone to predation.”

Nye-Ham debate an hour away

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And you may watch it here on NBC or here on WCPO, Cincinnati.

Piers Morgan will interview the debaters on CNN at 9:45 EST, and MSNBC will interview Bill Nye during the 10:00 hour, EST. C-Span will rebroadcast the event Wednesday, February 19 at 8 p.m. EST, according to WCPO.

If you cannot wait till the end of the debate, you may leave comments below at any time. I suggest that we allow comments from (many of) our creationist trolls, as long as they are coherent. I will not allow comments that are merely insulting.

Petroica macrocephala

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Photograph by Erik Duerr.

Photography contest, Honorable Mention.

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Petroica macrocephala – South Island tomtit, New Zealand. Mr. Duerr writes, “I would never have been able to get such a close up photo of such a small bird if it weren’t for the fact that birds in NZ are designed not to be afraid of humans.”

Dan Phelps, president of the Kentucky Paleontological Society, will participate in an “extended interview” with Terry Mortenson of Answers in Genesis. The participants will discuss the question, “Is teaching creationism harmful to children, society?” at 11:00 a.m., Eastern Standard Time, Thursday, January 30, on WEKU of Richmond, Kentucky. It looks like you can get it streaming. I will refrain from noting that modern journalism thinks there are two sides to every question, even when there are not.

Does any reader know of any other, similar warm-ups or “extended interviews”?

Panthera pardus

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Photograph by Ed Neubaum.

Photography contest, Honorable Mention.

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Panthera pardus – African leopard, Kruger park, South Africa.

Agkistrodon contortrix

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Photograph by Nicholas Plummer.

Photography contest, Honorable Mention.

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Agkistrodon contortrix – juvenile copperhead snake.

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