Monday, December 26, 2016

David Coppedge, Redux

David Klinghoffer has a post for "Evolution, News and Views" in which he defends David Coppedge, the erstwhile NASA technician who claimed he was fired from his job at JPL because of his intelligent design support. Coppedge has a fifteen-minute video in which he recounts the affair.   In typical hystrionic fashion, Klinghoffer writes:
Of all the cases we've covered here where scientists and others have been persecuted for sharing ideas favorable to intelligent design, what happened to David Coppedge is arguably the most reprehensible. That's partly because Coppedge, working at NASA's Jet Propulsion Lab as a team lead on the Cassini Mission to Saturn, wasn't a PhD scientist with the space agency. He was a computer administrator, albeit a senior one, and therefore by definition a less powerful, more vulnerable player in the science world.
Klinghoffer either has not read the trial transcripts or chooses not to remember them. Coppedge sued NASA and it came out during the trial that he was a difficult employee who was hard to get along with.  My original post on this trial, and Klinghoffer's reaction to it, is here.  Newsvine wrote, at the time (link no longer works):
At trial, JPL attorney Cameron Fox contended Coppedge was a stubborn and disconnected employee who decided not to heed warnings to get additional training, even when it became clear the Cassini mission would be downsized and computer specialist positions eliminated.

Coppedge often was confrontational and insensitive to customers and colleagues, who had complained about his behavior and his advocacy of intelligent design, Fox said.
I remarked, then, that Klinghoffer was focusing on the wrong aspects of the trial, a situation in which the Cassini project was being downsized and Coppedge was well aware of this at the time.

As in the case of Richard Sternberg, the details are what matter.

Saturday, December 24, 2016

Pope Francis: Big Bang and Evolution are True

The Toowoomba Chronicle is reporting a story out of the Vatican that Pope Francis has declared evolution and the big bang to be scientifically accurate and not threats to faith.  Andrew Withnall writes:
THE theories of evolution and the Big Bang are real and God is not "a magician with a magic wand", Pope Francis has declared.

Speaking at the Pontifical Academy of Sciences, the Pope made comments which experts said put an end to the "pseudo theories" of creationism and intelligent design that some argue were encouraged by his predecessor, Benedict XVI.

Francis explained that both scientific theories were not incompatible with the existence of a creator - arguing instead that they "require it".

"When we read about Creation in Genesis, we run the risk of imagining God was a magician, with a magic wand able to do everything. But that is not so," Francis said.

"The Big Bang, which today we hold to be the origin of the world, does not contradict the intervention of the divine creator but, rather, requires it.

"Evolution in nature is not inconsistent with the notion of creation, because evolution requires the creation of beings that evolve."
This follows a pattern in recent years of the Popes accepting evolution that goes all the way back to Pope John XXIII.  I am quite sure that if the Hammish one gets wind of this, he will denounce it, forthwith. 

Friday, December 23, 2016

New Indie Film: We Believe in Dinosaurs

Indiewire has a story about a new film soon to be out that follows the construction of the Ark Encounter from blueprint stage to opening and examines the “unsettling and uniquely American conflict between science and religion.”  From the story:
In recent years, believing has not been enough for creationists. Determined to prove that the Bible is historically and scientifically accurate, they have begun building museums based on creation science. Their goal is to debunk evolution and to do that they are starting to think big. A comparison of 34 industrialized countries finds that the United States ranks near the bottom when it comes to public acceptance of evolution.

As creationism moves into the White House, it remains one of the most polarizing forces in the United States. That is why this film is so important right now.
I will be surprised if this comes anywhere near Knoxville but might appear as a Fathom event.

Thursday, December 22, 2016

Petition: Mike Pence Should Ban the Teaching of Evolution

Patheos is pointing to a petition that is being circulated to have incoming vice-President Mike Pence make the teaching of evolution illegal.  Here is part of the petition:
We the undersigned note that, when you were a member of the U.S House of Representatives, you spoke out on the subject of science education and for presenting students with all available information. Recently, we have seen the passage of academic freedom bills in Louisiana and Tennessee which have allowed for critical evaluation in the classroom and improved educational standards. However, whilst an important development, they were only enacted owing to the need to protect students from indoctrination. We object to the teaching of the very controversial theory of evolution as part of the K-12 science curriculum which we regard to be unnecessary and unhelpful.

It is obvious to us that Evolutionism-Darwinism is an anti-Christian atheistic dogma masquerading as science. According to renown philosopher of science, Professor Michael Ruse, himself an ardent evolutionist, there is no doubt that the theory of evolution represents a philosophical worldview: “Evolution is promoted by its practitioners as more than mere science. Evolution is promulgated as an ideology, a secular religion—a full-fledged alternative to Christianity.”
Aside from the fact that when examined, it turns out that Dr. Ruse has an extraordinarily peculiar view of Christianity and the relationship between what Jesus taught and what Paul taught, there is no sound basis for the idea that evolution is a religion.  If it were, organizations like BioLogos would not exist.   BioLogos seeks to understand the workings of the natural world within the context of a God-created universe.  Ruse is projecting his atheism onto his understanding of evolution.  Because some evolutionary biologists are not Christians does not make it impossible (or improbable) for a Christian to be one.

Onward.  The writers of the petition use three examples of recent research to attempt to bolster their case.  The first one is The Demise of the Genetic Blueprint.  They write:
Two researchers, Monteiro and Podlaha, admit that,“the genetic origin of new and complex traits is probably still one of the most pertinent and fundamental unanswered questions in evolution today.” Harvard professor, Peter Park, goes even further to proclaim that,“it's become very clear that DNA sequences are just a building block. They don’t explain higher-order complexity.” Obviously, if organisms are more than just the epiphenomena of their genes, then the gene-centric Neo-Darwinian paradigm cannot at all explain the diversity of form and so fails utterly.
The problem with the first quote is that it is used entirely out of context. Here is an un-quoted part of the abstract:
In the last two decades we have learned that novel traits appear to be built using old genes wired in novel ways [5], but it is still a mystery whether these novel traits evolve when genes are rewired de novo, one at a time, into new developmental networks, or whether clusters of pre-wired genes are co-opted into the development of the new trait. The speed of evolution of novel complex traits is likely to depend greatly on which of these two mechanisms underlies their origin. It is important, thus, to understand how novel complex traits evolve.
These writers have, in no way, undermined the theory of evolution, they have simply highlighted some areas in which our understanding of the processes are unclear.  This is classic young-earth creationist quote-mining.  The Nature paper, of which Dr. Park is an author, is highly technical and deals with how genomic sequences are regulated.  It does, in no way, cast a negative light on evolution as a process, however.  Once again, the question is simply by which path do complex traits evolve, whether by means of accumulated change or in larger steps (no I am not invoking Goldschmidt).

Example number one shot down.  The second one is The Demise of Cumulative Selectionism.  The petitioners write:
The core premise of Darwin's theory of evolution is that biological features have been produced by the cumulative selection of innumerable slight successive modifications. But as renown biologist Dr. Michael Denton has noted, the theory of evolution has been in crisis for the past 30 years because of the abject failure to show that there is a functional continuum in biology that allows for a gradual change leading to complex new features. In his view,“Darwinian theory of evolution is no more nor less than the great cosmogenic myth.”
Here the authors have reached way into the past to grab a book that was written in 1986—an eternity in scientific terms—as their go-to source. Interestingly Denton updated the book much more recently, and retitled it Evolution: Still a Theory in Crisis.  Sy Garte reviewed this book and writes this:
Denton describes his own worldview throughout the book as “structuralism”, which is all about the form that matter (including biological matter) takes. This contrasts with “functionalism” (the basis of Darwinism), which is about how things work, including adaptation. His hero is Richard Owen, a pre-Darwin naturalist who wrote extensively on the concept of natural law as the basis for biological forms. Denton takes the pre-Darwinian 19th-century concept of Types—clades, such as vertebrates and mammals—as his central theme. According to Denton (and Owen), Types are the manifestation of built-in biological laws; and what distinguishes them are structural homologs that cannot be explained by either slow, progressive steps (the gradualism of classical Darwinism) or purely adaptationist natural selection. This philosophical view fits well with the standard anti-evolution paradigm of Intelligent Design.
This approach is almost diametrically opposed to the modern practice of systematics, in which the focus of evolutionary development is on traits, not whole organisms.Using Owen's blueprint, transitional forms are, indeed, rare and macroevolutionary changes cannot be readily explained.  Once the focus is shifted to traits, however, then one can see how certain traits emerge, change and disappear in the fossil record and taxonomic relationships can much more easily be delineated.

With regards to this petition, however, damningly, Denton clearly writes that evolution has happened and that there is universal common ancestry for all life forms.  According to Garte, he mentions Intelligent design exactly once in the book.

Example number two shot down.  On to number three.  This one is the Demise of the Last Universal Common Ancestor:
The Last Universal Common Ancestor (LUCA) is the hypothetical organism, that lived 4 billion years ago, for which there is no actual physical evidence of at all. It is only inferred because all life shares essentially the same genetic code. Recent scientific research indicates there is no reason to believe that it ever existed. As Professor Ford Doolittle states, “We do doubt that there ever was a single universal common ancestor.” Indeed, the idea that all living organisms are descended from a single ancestor is as preposterous as the discredited hypothesis that all human languages are descended from a prototypical tongue.
Once again, the writers of the petition have not done even the most rudimentary research into the position of the paper that they quote. Lets look at the abstract of the paper:
If the tree of life (TOL) was the thesis and the web of life (WOL) its antithesis, then we are now in the period of disciplinary synthesis. A more realistic (less idealistic and dogmatic) microbial systematics and evolutionary theory will inevitably emerge. WOL advocates (WOLers) will be unable to claim total victory, however, and TOLers will be tempted to redefine what it was they were defending in order to avoid the appearance of defeat (e.g. Galtier & Daubin 2008). Preferable to this, epistemologically and ontologically, would be the adoption of a pluralist perspective, from which this controversy can be seen as but a stage in the development of a more powerful and general reading of Darwin's theory.
A more powerful and general reading of Darwin's theory. That does not sound like anti-evolutionary writing to me. Doolitle, further, writes: “I will propose a more general and relaxed evolutionary theory and point out why anti-evolutionists should take no comfort from disproof of the TOL hypothesis.”

Example number three shot down.  So what we have here is a petition to have the theory of evolution banned by an organization that uses examples from the literature in which the theory of evolution is universally supported.  This does not sound like a winning strategy to me. The salient feature of all of the quoted articles is that the theory of evolution is remarkably strong, explains a great amount of diversity in past and present life but that it is having growing pains and that new ideas are emerging that need to be examined in light of the traditional evolutionary synthesis.

This petition needs to be pitched into the circular file as yet another example of how  anti-evolutionists cannot even take the time to do basic research into what it is that they wish to ban.  No wonder nobody in the scientific world takes these people seriously.

Friday, December 09, 2016

Dinosaur Feathers Found in Amber

Many outlets are reporting the find in Myanmar of perfectly-preserved dinosaur feathers in Amber.  From the Washington Post:
The amber hunters who dug up the segment in Burma (Myanmar) assumed the encased remains were vegetation, making the amber valuable when carved into jewelry. It probably did not occur to them that their discovery could be a dinosaur tail with secrets to tell. But a Chinese paleontologist named Xing Lida, perusing a Burmese amber market in 2015 for objects of scientific interest, recognized the amber’s true value.

“With the new specimen from Myanmar, we finally get that association between identifiable bones and feathers preserved in exquisite detail,” said Ryan McKellar of the Royal Saskatchewan Museum in Canada, a paleontologist and an author of the study, in an email to The Washington Post. Lida, McKellar and their Chinese and Canadian colleagues published an analysis of the tail on Thursday in the journal Current Biology.
How do we know it is from a dinosaur and not a bird?
X-ray images revealed that no ancient bird grew this tail. The tail tip belonged to a two-legged dinosaur called a theropod. “We can tell that this specimen came from a theropod dinosaur because the tail is flexible and the vertebrae articulate with each other, instead of being fused together to form a solid rod — which is a characteristic of modern birds and their closest relatives,” McKellar said. Specifically, the researchers hypothesized the animal was a type of dinosaur called a coelurosaur, and likely a juvenile.

Image Credit: A rendition of the coelurosaur. (Chung-tat Cheung and Yi Liu)

This further cements the link between the late Cretaceous theropods and early birds. More pieces of the puzzle.

More Bad News...

After the death of Keith Emerson in March of this year, Greg Lake, of ELP has died after a long battle with cancer.  NPR has a glowing tribute to the lyricist for both King Crimson and ELP. 
Greg Lake spent much of his musical life as the "L" in ELP. He was the band's singer, played guitar (both acoustic and electric) and bass, and wrote lyrics for the beloved 1970s progressive rock band. He often acted as the quiet, contemplative counterpoint to the thunder of drummer Carl Palmer and keyboardist Keith Emerson.

Most people came to know Greg Lake through ELP's first "hit" song "Lucky Man," with its images of white horses, white lace and feathers, and (somewhere in there) the tale of a king and a man who goes off to war to die for his country. These phantasmagoric songs were a pleasant shift in rock music, from the often literal tales and endless songs of love that streamed across the airwaves. The world of wild song structures Greg Lake and his bandmates pioneered was liberating and literate — and it was his sonorous tones that led the charge.
He had a distinctive and powerful voice and, even though I did not care for his philosophical take on life, often angrily anti-religious, the voice dovetailed with the other two members of the band and he was a consummate bassist. Another prog rocker gone. Rest in Peace.