Kent Hovind in trouble again

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I haven’t got time to investigate further, but Hovind watchers might be interested that Mr, Hovind (Dr. Dino) has been charged with filing a lien on property that had already been forfeited. Or something. A Forbes columnist, Peter Reilly, suggests that the government is piling on, and I suspect he is right; you may read about it here.

Acknowledgement. Link provided by the truly indefatigable Dan Phelps.

The Family Tree of Life

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In the next few weeks, we’ll be posting a series of articles for the general public focused on understanding how species are related and how genomic data is used in research. We start with a background on phylogenetic trees.

Imagine you could go back in time and meet your great grandmother or even your great-great-great-great-great grandmother, when they were your age. Would they look like you? Or would they look more like your siblings or cousins? Maybe you would all look a little different. Scientists try to figure out how the distant ancestors of apes, other animals, plants, and all organisms living today looked and behaved, much in the same way that people use a family tree to trace their ancestry.

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The common ancestor of great apes lived about 18 million years ago. Source: Smithsonian National Museum of Natural History http://humanorigins.si.edu/evidence/genetics

In evolutionary biology scientists use a type of tree called a “phylogenetic tree” to organize the history of how species descended from common ancestors. The closer two species are to a common ancestor on the phylogenetic tree, the more closely the two are related.

Take the phylogenetic tree of primates, for example. The common ancestor of apes lived about 18 million years ago. But over time, this one group branched off to form many different species, including humans, which have their own separate branch on this tree.

How did so many unique species develop from one ancestor? New branches formed by a process known as divergence. When groups of ancient organisms became geographically isolated from one another, either through migration or geologic events like earthquakes, each group began to develop its own unique set of physical attributes. Sometimes, by chance, a change in a characteristic enabled an individual to survive better in its environment and produce more offspring.

Perhaps individuals in one group with larger arms were better able to break open the hard-shelled fruits that were common in one region, while some individuals in another group had the ability to travel more easily through tall trees that offered protection from predators. Whatever the reason may have been, selection favored genetic differences that improved survival. Over time, this gradual process of isolation and selection produced distinct species, which in turn branched into more species.

The end result of divergence is many species, related in a tree-like fashion, and we display these relationships using phylogenetic trees. Scientists now use increasingly sophisticated methods to determine how species were related and build phylogenetic trees. In the past, scientists built these trees simply by comparing physical traits, like how many limbs an organism has or whether it has a tail. But with the recent surge in fast and affordable gene sequencing technologies, researchers today can directly compare species’ DNA to determine how they are related.

But analyzing entire genomes, with billions of DNA base pairs, presents its own unique set of challenges, and researchers often struggle to determine if the DNA differences they find between species are truly significant or are simply due to common variability. As computer software and statistical analysis become more adept at handling these challenges, our understanding of species’ relationships could change — providing exciting new insights into our family tree of life.

Check back next week when we discuss the differences between studying small and large datasets, and the challenges associated with big data analysis. This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

According to an article in Science today, a creationist group has booked a room for a conference at Michigan State University. Science is more discreet than I have to be, but it appears that they duped a student group into booking a room for them, and they are scheming to hold another conference at the University of Texas at Arlington.

Science writes that the conference, scheduled for November 1 and

called the Origins Summit, is sponsored by Creation Summit, an Oklahoma-based nonprofit Christian group that believes in a literal interpretation of the Bible and was founded to “challenge evolution and all such theories predicated on chance.” The one-day conference will include eight workshops, according the event’s website, including discussion of how evolutionary theory influenced Adolf Hitler’s worldview, why “the Big Bang is fake,” and why “natural selection is NOT evolution.” Another talk targets the work of MSU biologist Richard Lenski, who has conducted an influential, decades-long study of evolution in bacterial populations.

All that old familiar nonsense.

Acknowledgment. Thanks to the indefatigable Dan Phelps for the tip.

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Pinhole-camera images of solar eclipse formed by spaces between leaves in canopy. According to Jon Grepstad, this phenomenon was explained by Aristotle. The eclipse is just ending; the picture was as close to total as it got here (Boulder, Colorado).

Aeshna cyanea

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Photograph by Marilyn Susek.

Photography contest, Honorable Mention.

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Aeshna cyanea – southern hawker.

Beginning this week, we will run photographs every other Monday, so no picture next week; we no longer have enough honorable mentions and other miscellaneous photographs to continue posting a photograph every week. But polish your lenses (very carefully) and keep an eye out for the contest in the summer.

Case Western steps up, rejects House Bill 597

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As I noted a few weeks ago (see here and here), Ohio House Bill 579 cuts the guts out of science education in the public schools by emphasizing “scientific knowledge” and eliminating the teaching of “science processes”. As I argued, the process of science is central to how one justifies claims about the world in science, and eliminating reference to those processes eviscerates science education.

The Faculty Senate of Case Western Reserve University agrees. It has adopted a resolution that speaks directly to that issue. The resolution is below the fold.

Cupido comyntas

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Photograph by Robin Lee-Thorp.

Photography contest, Honorable Mention.

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Cupido comyntas – eastern tailed-blue butterfly.

According to reports by Linda B. Blackford in the Lexington Herald-Leader and Tom Loftus in the Louisville Courier-Journal, here and here, Kentucky authorities have noticed the apparently deceptive hiring practices of AIG and Ark Encounter, and sent a letter informing the proprietors of the Ark Park,

Therefore we are not prepared to move forward with consideration of the application for final approval [of a tax incentive] without the assurance of Ark Encounter LLC that it will not discriminate in any way on the basis of religion in hiring for the project and will revise its postings accordingly.

Update, October 9, 2014, noonish. According to a Reuters dispatch, AIG has said that it will fight for its “religious rights after state officials warned he could lose millions in potential tax credits if he hires only people who believe in the biblical flood.” In a not entirely veiled threat, Mike Zovath told Reuters, “We’re hoping the state takes a hard look at their position, and changes their position so it doesn’t go further than this,” and argued that the state had added a requirement by prohibiting religious discrimination. The state has responded by saying, “We expect all of the companies that get tax incentives to obey the law.”

Larus delawarensis

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Larus delawarensis – ring-billed gull, Boulder, Colorado. There is right now a fairly large flock at Walden Ponds east of Boulder. They are too far away to get a picture, unless you like snapshots of an array of gray-and-white ellipses. But this one very kindly landed in a parking lot and posed long enough to enable this portrait.

Freshwater: It is finished

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The Supreme Court of the U.S. today denied John Freshwater’s request (PDF) for a writ of certiorari. In other words, the Court declined to hear his case. After a legal saga that spanned more than six years and involved a two year long administrative hearing, a Court of Common Pleas review, an appeal to the state Court of Appeals, and an appeal to the Ohio Supreme Court, we are finally done. After an administrative hearing that generated over 6,000 pages of transcript, and after costing the school district on the order of $1m in direct costs (not counting the indirect costs of teacher and administrator time), the case is finally at an end.

One of these days I may write a retrospective piece on the case, but for now I’m simply glad that the damned thing is over.

On August 14, William Dembski spoke at the Computations in Science Seminar at the University of Chicago. Was this a sign that Dembski’s arguments for intelligent design were being taken seriously by computational scientists? Did he present new evidence? There was no new evidence, and the invitation seems to have come from Dembski’s Ph.D. advisor Leo Kadanoff. I wasn’t present, and you probably weren’t either, but fortunately we can all view the seminar, as a video of it has been posted here on Youtube.

It turns out that Dembski’s current argument is based on two of his previous papers with Robert Marks (available here and here) so the arguments are not new. They involve considering a simple model of evolution in which we have all possible genotypes, each of which has a fitness. It’s a simple model of evolution moving uphill on a fitness surface. Dembski and Marks argue that substantial evolutionary progress can only be made if the fitness surface is smooth enough, and that setting up a smooth enough fitness surface requires a Designer.

Briefly, here’s why I find their argument unconvincing:

  1. They conside all possible ways that the set of fitnesses can be assigned to the set of genotypes. Almost all of these look like random assigments of fitnesses to genotypes.
  2. Given that there is a random association of genotypes and fitnesses, Dembski is right to assert that it is very hard to make much progress in evolution. The fitness surface is a “white noise” surface that has a vast number of very sharp peaks. Evolution will make progress only until it climbs the nearest peak, and then it will stall. But …
  3. That is a very bad model for real biology, because in that case one mutation is as bad for you as changing all sites in your genome at the same time!
  4. Also, in such a model all parts of the genome interact extremely strongly, much more than they do in real organisms.
  5. Dembski and Marks acknowledge that if the fitness surface is smoother than that, progress can be made.
  6. They then argue that choosing a smooth enough fitness surface out of all possible ways of associating the fitnesses with the genotypes requires a Designer.
  7. But I argue that the ordinary laws of physics actually imply a surface a lot smoother than a random map of sequences to fitnesses. In particular if gene expression is separated in time and space, the genes are much less likely to interact strongly, and the fitness surface will be much smoother than the “white noise” surface.
  8. Dembski and Marks implicitly acknowledge, though perhaps just for the sake of argument, that natural selection can create adaptation. Their argument does not require design to occur once the fitness surface is chosen. It is thus a Theistic Evolution argument rather than one that argues for Design Intervention.

That’s a lot of argument to bite off in one chew. Let’s go into more detail below the fold …

Schrödinger’s cat is, famously, both dead and alive, simultaneously. There has been doubt as to whether macroscopic objects could be prepared in cat states, but Answers in Genesis has done it! As Ed Hensley of the Kentucky Secular Society observes below, AIG is both a nonprofit and a for-profit entity, simultaneously (a condition that we noted earlier on PT). Following up on material that Dan Phelps acquired under the Freedom of Information Act, Mr. Hensley sent the following (lightly edited) press release to a number of interested journalists:

Freshwater: Tick, tock, tick, tock …

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John Freshwater’s application to the Supreme Court of the U.S. for a writ of certiorari was placed on the Court’s docket for Sept 29, 2014, yesterday. According to the Court’s web site

Scheduled order lists are posted on this Website on the day of their issuance, while miscellaneous orders are posted on the day of issuance or the next day.

It’s now Sept 30, but no order list for the 29th has yet been posted. Two Miscellaneous Orders are posted (one granting a stay of a lower court’s ruling on the Ohio (Republican) Secretary of State’s election finagling of early voting), but nothing on Freshwater is up.

Apis mellifera

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Apis mellifera – western or European honeybee, dining along with others on a milkweed flower. Apparently a melanic form, because Bugguide assures me that it is “just a dark one.”

Noctilucent clouds

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Photograph by Kari Tikkanen.

Photography contest, Honorable Mention.

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Noctilucent clouds. Mr Tikkanen writes that these “are bluish clouds located in the mesosphere at altitudes of around 80 kilometers. Relative recent appearance and their gradual increase may be linked to climate change.”

Brachystola magna

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Photograph by Ralph Arvesen.

Photography contest, Honorable Mention.

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Brachystola magna – plains lubber, or western lubber..

Science is not about certainty

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That is the title of an interesting article in The New Republic by the theoretical physicist Carlo Rovelli. I read it mostly because it had been quote-mined by Elizabeth Mitchell here. Professor Rovelli’s article was perhaps a bit windy, and I could take issue with some of his discussion, but it was not all that hard to understand. One of his main points is that science has been extremely successful and any new theory will have to reduce to existing theory in the appropriate limit:

Happy Jason Lisle Day!

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Note: This is a guest-post by DiogenesLamp. He has cross-posted it at WordPress and Blogger versions of his blog. I have BLEEPed a few things as PT is supposed to be in part an educational resource. – Nick Matzke

Happy Jason Lisle Day! Today is the second anniversary of the day when Jason Lisle, director of what passes for research at ICR (Institute for Creation Research), promised he would explain why his alleged solution to the creationist “Starlight Problem” wasn’t really demolished by the math of Einstein’s General Relativity– in spite of much proof to the contrary that had been shoved right in his face. Lisle had whipped up a convoluted, technical explanation for why Young Earth creationists [YECs] are right about the universe being created only 6,000 years ago, even though we can see galaxies that are millions of light years away, and their starlight must have been traveling towards us for much longer than 6,000 years. Subsequently critics confronted Lisle with a handful of different mathematical and observational arguments that refuted his alleged solution to the Starlight Problem, which he calls “ASC” [Anisotropic Synchrony Convention]– one point being that his ASC would in fact require a gravitational field that ought to be observable, but isn’t observed. In his only response, two years ago today, Lisle promised to explain why we’re all stupid and maths are all wrong and his BLEEPy model actually rules.

A friend brought this 2012 news article about the evolution of the rhesus monkey Y chromosome to my attention. The primary work itself is about characterizing the gene content of the rhesus Y chromosome (a laborious, and necessary task). This particular write-up, however, is slightly frustrating for some of the (wrong) assumptions it makes, but most noticable is the image:


The picture of the “X and Y” chromosomes where the X chromosome, presumably, looks like an X, and the Y chromosome looks like a Y. If this were true, we might then assume that chromosome 1 looks like a “1” and chromsome 22 looks like a “22”. None of these are true. 


All human chromosomes, even the six acrocentric chromosomes (13, 14, 15, 21, 22, and Y), look kind of like “X’s” when they are duplicating, having sister chromatids (see this karyotype, a picture of chromosomes: https://www.mun.ca/biology/scarr/Hu[…]ryotype.html). And none of the chromosomes look like X’s when they are not in the duplication process (see this image from the J. Craig Venter Institute: http://www.jcvi.org/cms/fileadmin/s[…]figure2a.jpg).


Alluvial fan

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Alluvial fan created by the torrential rainfall 1 year ago, as seen from the Visitor Center, Trail Ridge Road, Rocky Mountain National Park, Colorado, September, 2014. The meander at the bottom of the screen passes through the bed of Fan Lake, which was formed in 1982 when the Lawn Lake Dam burst and inundated the City of Estes Park.

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