The Charlie in question is Darwin, tho I have my doubts that anyone ever called him that, at least, not after he was 10 or 12 years old. According to an e-mail from the developer, Kate Miller, Charlie’s Playhouse is a

Only two weeks remain, and there is a lack of nominations from the Panda’s Thumb. Your mission, readers, is to find our best articles from the last year and nominate them from the Panda’s Thumb. The rumor I’m hearing is that anti-anti-evolution blog posts are going to get the shiv this year, so try to focus on posts that are not responses to the stupidity that is (“intelligent design”) creationism.

Just click the image to nominate some posts of ours.

Last month PvM posted on Casey Luskin’s misconceptions based on some remarks reportedly made by Catherine Boisvert in a news story on the resolution of the distal radials of Tiktaalik.

However, as PvM pointed out, Boisvert’s research using MicroCT scans, discussed in that news article, actually resolved those elements of a Tiktaalik:

The disposition of distal radials in Panderichthys are much more tetrapod-like than in Tiktaalik,” Boisvert wrote. “Combined with fossil evidence from Tiktaalik and genetic evidence from sharks, paddlefish and the Australian lungfish, it is now completely proven that fingers have evolved from distal radials already present in fish that gave rise to the tetrapod.

Now Chris of A Free Man, a geneticist in Australia, has interviewed Boisvert about Luskin’s misuse of her remarks and her work with the specimens. The money quote:

As you know, the “Discovery” Institute tactic is not to go to the primary literature in order to understand it but rather to use quotations from secondary, even tertiary sources, reorganise or use them out of context opportunistically to their own convenience. In this case, they used an article where the journalists unfortunately misunderstood me. Tiktaalik’s material is in fact exquisite, it is very well preserved, basically uncrushed and can be prepared out to be examined in three dimensions. I never said the quality was poor. I have simply explained that the morphology of the fin of Panderichthys is more tetrapod-like than that of Tiktaalik, which has nothing to do with the quality of the material.

That pretty much settles it, I’d say.

As a follow-up to P.Z.’s post on evolution and entropy, I have added some context to the thermodynamics argument in this post over at EvolutionBlog (comments may be left there.)

Oberlin College physicist Daniel Styer has published a brief, but very useful, article in The American Journal of Physics showing that even under very conservative assumptions the change in entropy of the biosphere as the result of evolution is negligible compared to the entropy flux of the Earth that results from the Sun’s heating. Sadly, I know from personal experience that this sort of thing tends to leave creationists unimpressed. This is because their arguments use only the language, but not the substance, of thermodynamics. Their assertion that evolution violates the second law is not really an invitation to carry out entropy calculations. Rather, it is just another incarnation of ye olde argument from incredulity, in which they express the difficulty they have in believing that fully naturalistic processes can explain the growth in complexity in organisms over time.

I provide some details in my post. Enjoy!

Daniel J. Phelps is President of the Kentucky Section of the American Institute of Professional Geologists and Chairman of the Geology Section of the Kentucky Academy of Science. He is also founder and President of the Kentucky Paleontological Society, a well-respected amateur paleontological organization.

Dan is also among the most active scientists in debunking Answers in Genesis’ Creationism Museum, to the point that AIG whines about it. Dan has been tireless in critiquing the museum and the faux “science” it promotes.

Now Dan has been named Distinguished Professional Scientist in a Non-academic Position by the Kentucky Academy of Science. Congratulations to a committed supporter of science and honest science education!

by Mike Zerella, University of Colorado

Sula nebouxii — Blue-Footed Booby, Galápagos Islands.

Aminoacyl-tRNA synthetase ribozyme, an example of the RNA-based catalysts that may have preceded protein enzymmes during the origin of life.

The Museum of Science at Boston has a fantastic interactive web resource on the origins of life. Exploring Lifes Origins has a timeline of lifes evolution (with sliders), and pages on understanding the RNA world and building protocells, with a nice animation of protocell replication. The pages have been made in collaboration with ribozyme guru Jack Szostak and his laboratory, and there is a handy resources page for educators.

If you are interested in our current understanding of the origin of life, this is a very handy starting off point. You can explore ribozymes in more detail with proteopedia.

(Hat tip to Sandra Porter, biology educators should not miss her blog)

The Society of Vertebrate Paleontology has come up with a very well-produced video introduction to the Society.

The Society’s website says

WE ARE SVP is a 33-minute video that tells the inside story of the Society of Vertebrate Paleontology – who we are, what we do, and why our work is important for science and society. The video is introduced and narrated by Sam Waterston, the long-time star of “LAW & ORDER.”

While the whole video is worthwhile, some of you may want to go straight to Chapter 4, “Evolution Vs. Creationism.” It’s got Kevin Padian and more., Go ahead - you know you want to.

Cheers, Dave

I made reference to this in a comment, but thought I’d promote it. The Guardian has a video up on innovative approaches to teaching evolution to secondary school students in Great Britain. It also interviews Martin Reiss, the recently resigned/ousted Education Officer of the Royal Society.

Added in edit: John Pieret has a post on a survey associated with the show. (Though I apparently can’t send a trackback there.)

Over on UD Denyse O’Leary is complimenting Alfred Russel Wallace for his 1907 critique of Percival Lowell’s claims that Mars was inhabited by intelligent, canal-building Martians. She says:

What made Wallace so unpopular compared to Darwin is that he insisted that in science, evidence matters. Carl Sagan-style proclamations like “They’re out there! How could we be so arrogant as to think we are all alone!” do not become science just because they are proclaimed by scientists.

First, the idea that Wallace was ever wildly unpopular is ridiculous, he was a grand old man of evolution and British science when he died. Second, if Wallace insisted that evidence matters and O’Leary likes this, then I guess she considers this a strong vote for common ancestry and natural selection, both of which Wallace defended as vigorously as anyone. We evolutionists win I guess. Third, let’s have a look at what Wallace actually said about Lowell’s hypothesis that intelligent designers were the best explanations for the patterns he thought he saw on Mars:

The site of Dmanisi in the Republic of Georgia has produced four superb hominid skulls ranging in size from 600 cm³ to 780 cm³. These sizes range from the lower end of Homo erectus downwards into the Homo habilis range. The fossils contain a mixture of anatomical features from erectus and habilis. They could arguably be considered to belong either to primitive H. erectus (or H. ergaster), or to a new species, Homo georgicus. Vekua et al 2002 concluded:

The Dmanisi hominids are among the most primitive individuals so far attributed to H. erectus or to any species that is indisputably Homo, and it can be argued that this population is closely related to Homo habilis (sensu stricto) as known from Olduvai Gorge in Tanzania, Koobi Fora in northern Kenya, and possibly Hadar in Ethiopia.

These skulls are intermediate in both anatomy and size between Homo erectus and H. habilis, and as a result are exceedingly difficult for creationists to classify. Creationists therefore either ignored them (the usual reaction), or were forced into the absurdity of claiming that the biggest skull is human but the smallest two are apes (Lubenow 2004), or the almost equally implausible suggestion that all of them are human (Line 2005).

In 2007, further light was thrown on the Dmanisi hominids with the announcement that a substantial number of bones from below the skull had been discovered (Lordkipanidze et al 2007). These included a right femur, tibia and kneecap (the most complete known lower limb of early Homo); an ankle bone, part of a shoulder blade, three collar bones, three upper arm bones, five vertebrae, and a few other small bones. Some of these bones were associated with some of the previously discovered skulls.

Analysis of the bones shows that the Dmanisi hominids definitely walked bipedally and upright. However, the bones show a number of differences from modern humans and have some features associated with Homo habilis. The upper body differences lead the authors to suggest, with some caution, that “the Dmanisi hominins would have had a more australopith-like than human-like upper limb morphology”.

Their final conclusion was:

Day 6 of the Freshwater administrative hearing was on October 31, 2008. Testifying were Paul Souhrada, an editor of the Columbus Dispatch and the parent of a student in Freshwater’s class; Souhrada’s son Simon; Richard Cunningham, chairman of the high school science department; Katie Beach, a middle school intervention specialist; Kerri Mahan, a middle school special education teacher; and Katherine Button, a former student in Freshwater’s 8^th grade science class.

Important note: I did not get to the hearing in time to get a seat for the morning session. My summary of the morning (Paul and Simon Souhrada, Cunningham, and Beach) is based on an hour-long interview later that day with two people who were at the morning session and who took notes. So it’s second-hand information to me and third-hand to you. I did have a seat for the afternoon session (Mahan and Button). For another view on that morning’s testimony see the Columbus Dispatch story. I’ve used that story and the Mount Vernon News story as additional sources for the Friday morning session. Reporters Dean Narcisco (Dispatch) and Pam Schehl (News) were at the morning session.

More below the fold.

The last two days of this installment of the hearing on John Freshwater’s appeal of the decision of the Mt. Vernon City Board of Education were on October 30 and 31. Once again I’ll summarize rather than try to present a sequential account of questions and answers. This post is Day 5; the next will be Day 6. I hope to have Day 6 written and posted sometime tonight.

Previous posts on the hearing: Days 1 & 2 and Day 3 and Day 4.

See also the coverage of Day 5 in the Mount Vernon News.

Day 5 saw the completion of cross examination of Bill White, Principal of the middle school in 2007-2008, and the testimony of Kathy Kasler, the high school Principal; David Levy, M.D., an expert witness; and Bonnie Schutte, a high school science teacher.

More below the fold.

Updated: Disclaimer appears below. Link to journal endorsement is here.

This journal does not have a vote, and does not claim any particular standing from which to instruct those who do. But if it did, it would cast its vote for Barack Obama.

Politics impacts science. From which research emphases get funded to which school board member to vote for, science and politics often cross paths. PT’s supporters come from all walks of life and bring to the pro-evolution discussion opinions on other matters that span everything from conservative to liberal. To the extent possible, PT tries to avoid overtly being political, partly because we don’t want to needlessly alienate those supporters, but mainly because it’s beyond the charter of this website and that there are many other blogs that serve that purpose better than ours. Occasionally, though, this blog encounters a crossroads between science and politics, entailing posts that necessarily make political statements. This is one.

During this election, there is a difference between the candidates running for president. Palin is a creationist of the first water. Her disbelief that money spent in support of autism research was going to labs in France that used fruit fly models, reported at Pharyngula, speaks volumes.

At least from the standpoint of science advocacy and at least to this PT contributor, the decision during this election appears straightforward. Nature’s endorsement is timely and appropriate.

BCH

PS - And novel! According to this post from DailyKos.com, it would appear that this is first time Nature has endorsed a candidate.

Day 5 of the Freshwater hearing was today, but my post on it won’t be up until tomorrow night at the earliest. Tonight my seminar on the history of the controversies surrounding the theory of evolution is going to a Chautauqua performance about Clarence Darrow, and then I’m going to bed.

As a consolation prize read Glenn Branch’s Zombie Jamboree in Texas in the Beacon Broadside. Texas is heading for a potential disaster in science education.

Preceding posts: Day 3 and Days 1 & 2. This summarizes Day 4, October 29, 2008.

I’ll take a slightly different approach in this post for several reasons. First, I’m short of time and sleep. Second, much of the day was given over to cross examination of the middle school principal by Kelly Hamilton, Freshwater’s attorney, and Hamilton’s approach to cross examination does not lend itself to any sort of narrative flow. Therefore I’ll summarize the main themes of the testimony with some examples of Q&A rather than attempting to reproduce the exact sequence of questions through hours.

The bulk of the testimony today was from Bill White, Principal of the Mt. Vernon Middle School. Another student, a former student of Freshwater who is currently a senior at Mt. Vernon High School, also testified.

More below the fold.

This is a summary of Day 3 of the administrative hearing to determine whether John Freshwater will be terminated as a middle school science teacher in the Mt. Vernon, Ohio, City Schools. Days 1 and 2 are here.

Three witnesses testified today, Zachary Dennis, the boy who was (allegedly) burned with a Tesla coil, his mother Jenifer Dennis, and Freshwater. We’re still in the stage where the Board of Education is presenting its case for termination; later Freshwater will be allowed to put on a defense.

Summaries below the fold.

The mother of the boy at the center of the Freshwater affair, Jenifer Dennis, has given her first interview to the Columbus Dispatch. Two excerpts:

Zachary Dennis, now a high-school freshman, told his mother that his eighth-grade teacher, John Freshwater, held his arm down Dec. 6 and used an electrical device used to test gases to burn a cross on his forearm during a science class demonstration.

“He said ‘Mr. Freshwater said this cross will be here for awhile; it’s like a temporary tattoo,’ “ recalled Jenifer Dennis, Zachary’s mother.

and

“We never intended to go in to get Mr. Freshwater in trouble,” said Mrs. Dennis. “I send my child to school and expect my child not to come home with an injury to his arm.”

I know the Dennis family, and know that they originally wanted only to assure the safety of Zach and the other children in Freshwater’s classes. Freshwater’s other behaviors at issue came to light in the aftermath of his burning the child and his subsequent publicity seeking via demonstrations outside the schools and on the Mt. Vernon public square.

The termination hearing on Freshwater resumes tomorrow (Tuesday). I’ll be there.

The information content of DNA is much harder to determine than merely looking at the number of base pairs and multiplying it by 2 to get the size in bits (remember that each site can have up to 4 different nucleotides, or 2 bits). However, this approach can provide us with a zeroth order estimate of the maximum possible information that can be stored in said sequence which for the human genome with 3 billion base pairs would amount to 6 billion bits or 750 Mbytes.

After 20 days, Religulous has grossed more than Expelled during its six months in US theatres.

Funny how despite give aways, pre-screenings and discounts, and much marketing to the religious, Expelled did not manage to attract more audience than Religulous. What is even more ironic is that Religulous outperformed Expelled from the opening weekend with half the theatre count.

In a hilarious posting on UcD, our dear friend Davescot, who is best known for his failed predictions ¹, explains why recent research into the Lactose digestion of E. coli, undermines the findings of Lenski regarding E. coli evolving the ability to digest citrate. The reason? Our friend Davescot confused citrate with the Lac Operon

Davescot Wrote:

This is contrary to Lenski’s hypothesis that a series of dice throws, each making a small change towards ability to digest lactose citrate, accumulate until lactose citrate digestion is fully switched on. Darwinian gradualism is denied once again and we see a front loaded genome switch to a new mode of operation through a saltational event.

In other words, Davescot made two mistakes in a single posting: first he confused citrate with the Lac operon and secondly, he incorrectly claims that ‘Darwinian gradualism’ is denied once again, because, after all, a stochastic event affects whether E. coli can digest lactose versus glucose.

According to the ID ‘argument’, since chance and regularity can in fact explain the Lac Operon’s switch, any design inference has been prevented. Which is why Davescot, calls it ‘front loading’ or a ‘saltational’ event.

By Dave Wisker, Graduate Student in Molecular Ecology at the University of Central Missouri.

Creationists The Discovery Institute must have drooled when they heard a paper had been published by the respected journal, Animal Behaviour, which apparently reported that peahens did not prefer peacocks with more elaborate trains. Takahashi et al. (2008) appears to contradict several well-known studies that reported the opposite, and which have been cited as evidence for sexual selection in peafowl. Since the peacock’s tail is a venerable symbol of runaway selection for a secondary sexual trait, the DI ARN jumped on the story, crowing, with breathless excitement:

The alleged amazing powers of natural selection are much diminished as a result of these findings. The argument that it is “powerful enough” to maintain the feather display against the negative effects of attracting predators must be dropped. Furthermore, it appears not powerful enough to remove the display when it becomes an “obsolete signal”. Darwinists need to think very hard about the way they do science. This is a clear example of how a Darwinian hypothesis has become accepted as scientific fact, yet now has been disproved by some rigorous empirical research. This is a falsified prediction. This means that numerous textbooks and web sites need to be revised. More importantly, Darwinists should cease giving the impression that they have the keys to understand the natural world. So much of this ‘understanding’ is like peacock feathers - lots of show and no substance. Richard Dawkins extols Darwinism as a beautiful theory, but whenever we look closely, it fails to account for the observed data.

Unfortunately for the DI ARN, their enthusiasm for this paper may be premature, as I noted in a guest entry on Denis Ford’s “This Week in Evolution”. Essentially, the paper has two major problems (my article deals with some other minor ones as well):

1. The authors used a different methodology to determine male reproductive success than the other studies, which makes comparing them very difficult. While the British and French studies measured male reproductive success by observed successful copulations, the Japanese one estimated the number of successful copulations, based on female pre-copulatory behavior.
2. The genetic variance in tail morphology in all of the studies was very low (Takahashi et al.’s study had the lowest), which only magnifies the differences in methodology. Small differences in number of successful copulations have greater weight because the very low variation makes determining any kind of selection very difficult.

The main thrust of my article is that the differences in methodology for determining male reproductive success were magnified by the very low variance in the trait, invalidating comparison between the studies. It should be noted that Marion Petrie and Adriane Loyau, primary authors of two of the three major studies confirming peahen’s preference for more elaborate male trains, are in the process of publishing a reply to Takahashi et al’s paper. One wonders if the DI ARN will mention that.