Just a day before a handful of candidates dropped out of the race, Science ran an article on the candidates’ positions “on some select science-related issues (keeping in mind that the candidates have yet to sound off on many topics of interest to researchers).” The article was necessarily a little shallow but gives a good idea where most of the candidates stand on critical issues like science policy, the space program, climate change, vaccination, and genetically modified organisms.

Rainbow

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Photograph by Debbie Garelick.

DebbieRainbow_600.jpg

Rainbow. The rainbow is formed from relatively nearby raindrops. It is evidently raining lightly, because you can see a light cloud cover behind the rainbow. Direct backscatter from the clouds probably accounts for much of the brightness of the sky inside the arc and helps make a dramatic picture. See also here.

The Human and Comparative Genomics laboratory at the Biodesign Institute is looking for a Software Application Associate who will work in a collaborative environment to design, construct, test, document and maintain software packages. Typical projects involve implementing high performance algorithms for the statistical analysis of large genomic datasets for studying questions related to evolution and population genetics.

To apply visit http://links.asu.edu/job19991BR or search for ID 19991BR at https://cfo.asu.edu/hr-applicant.

If you have any questions about the opening, please email [Enable javascript to see this email address.] and visit http://cartwrig.ht/. ESSENTIAL DUTIES: Develops and documents requirements of software applications. Participates in on-the-job and formal training sessions concerning the design, writing, and testing of software application programs. Participates in and/or independently performs the design, testing, and documentation phases of programs. Translates predetermined logic into appropriate programming language and operating systems. Utilizes standard reference, resource, and/or procedural materials to resolve problems. Integrates multiple tools into a single, user-friendly software package, as well as providing support for the software. Operates on-line terminals and related computing equipment as required.

MINIMUM QUALIFICATIONS: Bachelor’s degree in Statistics, Mathematics, Computer Science or related field AND two years of experience in software application development, including writing computer code in one or more programming languages; OR, any equivalent combination of experience and/or education from which comparable knowledge, skills and abilities have been achieved.

DESIRED QUALIFICATIONS: Experience in translating software prototypes from Perl, Python, Java, etc into C/C++ preferred. Experience with JavaScript. Experience with databases query tools including, but not limited to, SQL, as well as programming languages including, but not limited to, C++ python, XML, HTML.

DEPARTMENT STATEMENT: The Biodesign Institute addresses today’s critical global challenges in healthcare, sustainability, and security by developing solutions inspired from natural systems and translating those solutions into commercially viable products and clinical practices. The Cartwright Lab is based in the Human and Comparative Genomics Laboratory in the Biodesign Institute at Arizona State University. Our research focuses on various topics in the field of computational evolutionary genetics. We develop methods and software to analyze large genomic datasets and “big data”. The majority of our research is related to the detection and analysis of mutations and variation from next-generation sequencing. We are species-neutral and work on taxa across the tree of life. Recent work involves humans, cancer, bonobos, ciliates, maize, Plasmodium, Leishmania, E. coli, archaea, Solanaceae, strawberries, and Anolis.

A Federal judge ruled yesterday that the Ark Park is entitled to sales tax incentives that had been denied by the state of Kentucky, according to an article by Dylan Lovan. Briefly, District Judge Gregory F. Van Tatenhove ruled that the state cannot exclude the Ark Park from receiving the tax incentive simply because the park has a religious purpose. Further, although Mr. Lovan does not note it, the judge opined that the Ark Park is within its rights to discriminate in employment on the basis of religion (and still receive the tax incentive), because it is clearly a religious organization.

Americans United, in a blog post, called the ruling “radical” and argued that Kentucky would have had a good chance of winning on appeal, based on a 2004 Supreme Court decision, Locke vs. Davey, wherein the court gave states “discretion to exclude religious programs from otherwise neutral funding schemes.” The ruling is unlikely to be appealed, according to the Associated Press, because the newly elected Republican governor is “pleased” with the decision.
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Thanks to Dan Phelps for the tip and for the transcript of the Judge’s ruling.

Rainbow

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Photograph by Gabrielle Hovinen.

Gabrielle_Rainbow_600.jpg

Rainbow, showing a primary and a secondary rainbow, plus a bevy of Hovinens. The primary rainbow is overexposed, but the photograph clearly shows how the sky is brighter inside the primary rainbow and outside the secondary rainbow. See Figure 6 here.

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As part of the year-end Kitzmas festivities, The Discovery Institute’s PR organ Evolution News and Views re-posted an earlier article titled Following Kitzmiller v. Dover, an Excellent Decade for Intelligent Design.

This uncredited article from September 2015 included the following, which caught my eye:

In fact, the decade since Dover has been an excellent one for ID. Casey Luskin noted some highlights not long ago:… Theoretical peer-reviewed papers taking down alleged computer simulations of evolution, showing that intelligent design is needed to produce new information.

The paper which was linked, hereafter Ewert 2014, is titled “Digital Irreducible Complexity: A Survey of Irreducible Complexity in Computer Simulations”, and was written by Winston Ewert of the Biologic Institute for a 2014 edition of the institute’s open-access journal BIO-Complexity.

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Ewert claims that Michael Behe’s concept of “Irreducible Complexity” is a stumbling block for evolutionary algorithms, and that several computer models of the evolution of irreducibly complex structures all fail to falsify Behe’s concept. Ewert examines five models: Lenski’s Avida, Schneider’s Ev, my own Steiner Trees, Sadedin’s Geometric Model, and Thompson’s Digital Ears program.

I won’t speak for the other models, but I can say this about Ewert’s discussion of Steiner solutions to network problems: it’s a massive strawman fallacy, a desperate “bait and switch” in which the problem my algorithm was solving, Steiner networks, was “replaced” with a much simpler problem, Minimum Spanning Trees. This ruse enabled Ewert to launch a (straw) attack on my genetic algorithm for solving Steiner’s problem.

The Steiner Genetic Algorithm was the subject of a heated blog war, the “War of the Weasels,” occurring between Panda’s Thumb and Uncommon Descent during the summer of 2006. It all began with my post of July 5th, 2006, Target? TARGET? We don’t need no stinkin’ Target! It seemed the War of the Weasels ended in the fall of 2006, after Uncommon Descent’s top programmers were unable to out-design the Steiner genetic algorithm during a public design challenge. But with Ewert’s 2014 article, and an earlier 2012 piece in BIO-Complexity by Ewert, Dembski and Marks, it’s clear that no ceasefire exists.

The War of the Weasels is back! More below the fold.

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Iridescence with wave clouds

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Iridescence with wave clouds, Boulder, Colorado, December, 2015.

Update on the Tree of Birds

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The tree of birds just got a bit more accurate with a study published last October. We first covered the ever-evolving tree in 2014, when we posted about a study in Science magazine that used phylogenomics and thousands of genes sequenced from 48 bird species to produce what was thought to be the most accurate phylogenetic tree of birds to date (Jarvis et. al., 2014; see their tree here). Since then, a different team of scientists published a new phylogeny of birds that it claims is the most comprehensive (Prum et. al., 2015; see their tree below). So what is the difference between these two trees and how they were constructed, and which is more accurate?

The biggest difference between the methods of the two studies is the amount of data used. In the Jarvis et. al. study, the authors sequenced the whole genomes of 48 bird species and aligned thousands of genes. But Prum et. al. criticize this methodology as too “sparse” of a sampling; instead, they used 198 bird species and two crocodile species. Because sequencing that many whole genomes would be costly and time-consuming, Prum et. al. developed genetic markers that targeted highly conserved “anchor” regions of vertebrate genomes – regions did not change much over many years. Using this technology, the new tree of birds could be developed with only about 400 genetic regions instead of the thousands of genes in the previous study.

If there is a tradeoff between analyzing more genes or more species, is it more accurate to compare fewer genes between more species, or more genes between fewer species? One is not inherently better than the other, but rather, the way in which each is used relative to common issues in constructing a phylogenetic tree determines accuracy of the tree.

One such issue is distinguishing important genetic signals from noise. Genomic data contains a certain amount of “phylogenetic signal,” the informative genes that determine lineage. This signal must be differentiated from non-phylogenetic signal–genes that falsely suggest certain relationships. For example, non-phylogenetic signal can arise because species divergence events that happened close together in time are difficult to distinguish, or when species that diverged from a common ancestor a long time ago independently develop similar traits (called homoplasy). A 2011 article in PLOS Biology analyzed published phylogenetic trees and noted that merely adding more genes did not improve their accuracy because adding genes amplifies all signal (non-phylogenetic and phylogenetic alike).

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Additionally, a phylogeny will only be accurate if the orthologous genes–those genes shared between species that were inherited from a common ancestor–are correctly identified. And that depends on the ability of software to distinguish orthologous genes from similar genetic sequences between species that code for genes that are not orthologous but rather are xenologous (transferred via horizontal gene transfer instead of inherited from the common ancestor) or paralogous (resulting from duplication of a gene). (Read more about orthologous, xenologous, and paralogous genes here.)

The model of evolution that researchers choose to use in their analysis can also greatly influence phylogeny accuracy. The PLOS article authors analyzed models and found some have difficulty detecting nucleotide substitutions, resulting in trees that are dominated by non-phylogenetic signal.

While analyzing a larger set of species won’t help when a model of evolution is inadequate or software has issues identifying orthologous genes, it can help with the issue of non-phylogenetic signal. Increasing the number of species in a study generally increases the phylogenetic signal-to-noise ratio, making it easier to detect substitutions that can lead to homoplasy, and also can improve accuracy by breaking up long branches. But the PLOS article states that it is not enough to just add more species; researchers should analyze more species that evolve slowly and comprise outgroups closely related to the group of interest.

Thus, including more species to construct a phylogenetic tree may be beneficial for tree accuracy, but only as long as methods for determining orthologous structures and modeling evolution are sufficient, and the chosen species are appropriate. Because Prum et. al. looked at more species while keeping these important factors in mind, and developed quality genetic markers that analyze enough genetic regions to determine phylogenetic relationships, they argue their tree is the most accurate yet. It is a convincing argument for the moment, but phylogenetic analysis can always be improved with better software and models, and the tree of birds (and the tree of life in general) will be constantly revised in the future as these methods improve.

The latest tree of birds presents a few differences from the Jarvis et. al. tree, some of which Prum et. al. suggest resulted from their larger sample size. One of the most striking differences is in the classification of the major bird groups. Jarvis et. al. propose that the initial divergence of a highly debated branch of birds, called Neoaves, resulted in two main groups: Columbea, containing birds like doves and flamingoes, and Passerea, containing a wide variety of species (parrots, falcons, penguins, and eagles, to name a few). But Prum et. al.’s tree instead splits Neoaves into five groups: Strisores (nightjars, hummingbirds, and frogmouths), Columbaves (cuckoos, pigeons, and sandgrouse), Gruiformes (cranes, coots, and rails), Aequorlitornithes (grebes, flamingoes, and shorebirds), and finally the very diverse Inopinaves (owls, vultures, and parrots). Also, Jarvis et. al. place pigeons, mesites, and sandgrouse in their own branch (Columbea) apart from the rest of Neoaves, while Prum et. al. rejected that for their five-group system. The Prum et. al. classification of Neoaves is likely the most accurate because they included more species that diverged close to speciation events (called nodes), which is especially important when the time between multiple nodes is short.

These findings bring up some new ideas about bird evolution and also support some old ones. For one, the new tree of birds developed by Prum et.al. supports a previous theory that swifts and hummingbirds, neither of which is nocturnal, evolved from a group of birds that had been nocturnal for 10 million years (Jarvis et. al. finds a similar relationship). Also, the new finding of the group consisting of waterbirds and shorebirds (Aequorlithornithes) suggests that the divergence of birds into different environments occurred with some level of restriction, known as evolutionary constraint. But as interesting and exciting as the new tree and its implications for bird evolution are, it is unlikely to be the final word on bird evolution. Other studies have also been published examining parts of the bird tree (like Rocha et. al. on the bird genus containing woodcreepers and Bell et. al. on an extinct group of Cretaceous birds). A new, more accurate complete tree of birds that supports or rejects these theories may be only another year away. Such is the nature of scientific research.

This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

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From yesterday’s announcement on ENV:

It is with a mixture of sadness and excitement that I write this to announce that, as the year 2015 closes, I am leaving Discovery Institute. I am doing so in order to fulfill a lifelong goal of furthering my studies. My colleagues, who entirely support this decision, are people of the utmost integrity and they have been incredibly generous and welcoming to me and my family. I know we will miss each other. Working here over the past ten years has been a wonderful experience for which I am extremely grateful.

I think this will be good for Casey. Who knows, next time he reviews a show on TV about the science of evolution, he’ll now have time to actually watch the entire episode before writing a critique.

Discuss.

By David MacMillan.

David has been fascinated by the creation/evolution controversy for many years. Growing up, he was fully committed to creationist apologetics. He purchased a lifetime charter membership to the Creation Museum and even had blog posts featured on the Answers in Genesis website. During college, he continued to actively pursue creation apologism as he earned a degree in physics, but began to recognize the mounting religious and scientific problems with young-earth creationism. His renewed investigation uncovered more and more misconceptions implicit in creationism, and he eventually rejected it as both theologically indefensible and scientifically baseless. He now writes extensively about young-earth creationism for several websites.

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Note added December 30, 2015: This article has been cross-posted at Naturalis Historia, the blog of Joel Duff. As David MacMillan notes below, in a comment, “He gets a slightly different readership and has attracted the attention of AiG before so it will be neat to see whether they deign to reply.”
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As the strict young-earth creationists at Answers in Genesis work to complete their Ark Encounter “theme park”, they have expended an impressive amount of energy organizing the millions of species of land animals alive today into a handful of small groups they call “baramins”. They claim these groups represent the original created kinds of which Noah would have brought pairs onto the ark. This consolidation of numerous species into single “baramin” groups is driven primarily by the space on Noah’s purported vessel. The smaller the menagerie the Ark was purported to have contained, the more feasible it seems, and so the “baraminologists” at Answers in Genesis have gone to great lengths to explain how the vast array of species today could have been represented by a relatively low number of ancestral pairs.

One well-known hallmark of modern young-earth creationism is the dogma of separation between “microevolution” and “macroevolution”. Although early opponents of Darwinian evolution categorically denied that speciation or natural selection were possible at all, advances in genetics and biology made this position completely untenable. In response, creationists (particularly the young-earth crowd) protested that while “microevolution” was a viable, observable process in biology which they accept as “change or speciation within a kind”, the notion of “macroevolution”, or “change between kinds”, remains impossible. These definitions beg the question by presuming such things as discrete “kinds” exist, but creationists are nonetheless insistent that while adaptation or speciation within a particular “baramin” is observable (and, indeed, necessary in order to account for the present observed diversity of life), there is never any overlap between separate kinds. Their most well-known example of “kinds” is the difference between cats and dogs, where they explain that the diversity of dog breeds is the result of “microevolution” from some original dog/wolf kind, but that dogs will never “macroevolve” into cats.

Unfortunately for the young-earth model, the push to minimize the number of animals riding on the Ark has exposed a major problem with this view. Ironically, this problem is perhaps nowhere more apparent than with the very clade (the technical/evolutionary equivalent of the term “kind”) to which cats and dogs belong: Order Carnivora.

The Answers in Genesis website has repeatedly posted large, detailed lists of various species, families, and orders with attempts to organize them into baramins. One of the largest such postings, by retired veterinarian Jean Lightner, organizes the majority of Order Carnivora into eight distinct “baramins”: felines, civets, dogs, hyenas, bears, weasels, mongooses, and red pandas.

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Figure 1. The eight major carnivorous “baramins”, as claimed by young-earth creationists at Answers in Genesis.

Zack Kopplin, who has been opposing the antievolution nonsense in Louisiana since 2008, has an interesting new article in The Daily Beast:

Kopplin, Zack (2015). Creationism Whistleblower: ‘Academic Freedom’ Is Sneak Attack on Evolution. The Daily Beast. December 28, 2015. http://www.thedailybeast.com/articl[…]olution.html

Kopplin has really gotten the goods on what these “stealth creationism” bills mean on the ground – of course, what they mean is straight-up creationism taught in the public schools. Kopplin quotes from documents he has obtained from Louisiana school districts.

Also – it looks like Kopplin somehow got an interview with a former employee of the Discovery Institute – evidently someone who eventually saw that what was really going on there was apologetics for a very specific sectarian view, rather than actual science.

Here’s one of the good quotes from Kopplin’s article:

Lenticular cloud

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Lenticular clouds, Golden, Colorado, November, 2012. The camera was facing east, with its back toward the foothills of the Rocky Mountains. The clouds looked as if they may have formed on the leeward side of South Table Mountain.

Well, I can’t believe it’s been 10 years, but the anniversary of the Kitzmiller v. Dover decision is finally upon us. Looking at the Discovery Institute’s posts over the last few days, and comparing them to the discussion that was going on in December 2005 (see the Panda’s Thumb archive for 2005 – John West is all over that feed as well!), I guess the main thought I have is: just like 2 days after the decision, 10 years later, the ID guys still don’t get it.

The last ten years have been one long bout of the following:

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Professor Steve Steve’s cousin, Dr. Steffi Steffi, a lesser giant panda (Ailuropoda melanoleuca minor), was in Peru on December 21, 2005, and she read about the previous day’s decision in the Times Digest. Here she looks with pleasure at the announcement by Wesley Elsberry in The Panda’s Thumb on December 20 and a longer article by Laurie Goodstein in the Times the following day.

PhyloWiki_Matzke_2015.pngOn PhyloWiki, I have just posted a page of bonus material on the Science paper “The Evolution of Antievolution Policies After Kitzmiller v. Dover.”

Highlights include:

  • pre-print text (for those without university access to Science or ScienceExpress)
  • supplemental material & data (also archived at Science, but may not be generally available until the article moves from ScienceExpress to Science
  • A version of the phylogeny that is CC BY-SA 4.0 licensed (for those of you who want to make t-shirts; or conceivably, other uses)
  • A Frequently Asked Questions (FAQ) section that aims to be introductory
  • Bonus graphics: PDFs of character maps for all characters and traits
  • List of media links
  • List of blog links

(Update: paper preprint and bonus material available free here)

It appears that John West and the Discovery Institute skipped past reading the Science paper and went straight to accusing the author of misconduct. So much for “Academic Freedom”! I don’t even think they read the Supplemental Material, and I’m pretty sure they wouldn’t understand if if they did. It’s conceivable they aren’t up on the latest in phylogenetic methods and their applications.

In any event, though, I welcome any opportunity to explain why my research is in the public interest and how this work connects to my other work scientifically. It’s very late here in Australia, so I will give the short version.

The Israeli newspaper Haaretz reported yesterday that the University of Salzburg has posthumously rescinded an honorary doctorate it had awarded to the ethologist Konrad Lorenz because of what Haaretz called “his fervent embrace of Nazism.” Some people consider Lorenz, the man who famously got a gaggle of geese to imprint on him, to be the father of ethology. Haaretz says,

Lorenz describes himself as “always a National Socialist.” He says his work “stands to serve National Socialist thought.”

The university says Lorenz spread “basic elements of the racist ideology of National Socialism” in his work.

(Update: paper preprint and bonus material available free here)

It is 7 am in Australia, but this is finally out on Thursday afternoon in the U.S.…just in time for the tenth anniversary of Kitzmiller v. Dover! I will do a longer post a little later, but for now - be sure to check out the Supplemental Material!

Matzke, Nicholas J. (2015). “The evolution of antievolution policies after Kitzmiller v. Dover. Science, Published online Dec. 17, 2015. (http://www.sciencemag.org/content/e[…]057.abstract | http://dx.doi.org/10.1126/science.aad4057)

See also: PDF of character maps for characters 1-111 of the Matzke (2015) phylogeny of antievolution bills. These are the presence-absence characters; there are more characters but in a larger file, we’ll see how PT handles this one first

The War Before Kitzmas

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Over at Elizabeth Liddle’s “The Skeptical Zone” (TSZ) blog, Salvador Cordova had something to say about being banned from the “Uncommon Descent” (UD) blog, now being managed (loosely speaking) by Barry K. Arrington.

Arrington did something for Cordova that he doesn’t do for most people banned from UD, which was to send Sal an explanatory letter, which Sal included in his TSZ post. I’ll quote it below the fold.

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