“When you said “ORFan”, did you mean “ORFan” – a gene unique to one species that appear to have no relatives in other species, or “OFTen”, frequently?” *

In a previous post about a Expelled Q & A event held at Biola University, I mentioned that Paul Nelson (of the Discovery Institute), who chaired the event, had said something about “orphan genes” in our after event discussions (I now know it is ‘ORFan’ rather than ‘orphan’) . Well he brought them up again in the comments section of that post and now Ian Musgrave has written up a good post on ORFans over at Pandas Thumb in response. Take a look.

[ * My apologies to Gilbert & Sullivan ...and Musgrave.]

In my review of the so called “Leaders Guide” put out by the producers of the movie Expelled I addressed its reference to the Discovery Institute’s “A Scientific Dissent From Darwinism” list.

L.G. More than 700 scientists have signed this statement!

A Scientific Dissent From Darwinism

“We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.” (p.12)

To which I responded: “Yes they have a list of scientists, and many of them are the usual creationist suspects. Still others are scientists whose field of study is not particularly relevant to the subject of evolutionary theory. More importantly they constitute a tiny fraction of the global scientific community.”

DonExodus2 over on YouTube has done a little more digging into this list:

[Via Pharyngula]

Now the Disco Institute might complain that they didn’t intend that the list was necessarily meant to express dissent from the theory of common ancestry but merely for the Darwinian mechanism of random mutation and (non-random) natural selection. But such a complaint would be belied by the fact that both the Expelled Leaders Guide (see my two part posts on the Guide) and the Disco Institutes own web page on their list make statements which make it clear that their problem isn’t merely with Darwinian mechanisms for evolution but with evolution (common ancestry) itself:

During recent decades, new scientific evidence from many scientific disciplines such as cosmology, physics, biology, “artificial intelligence” research, and others have caused scientists to begin questioning Darwinism’s central tenet of natural selection and studying the evidence supporting it in greater detail. [Emphasis mine]

But how could supposed evidence from cosmology and physics cause questions to be raised about natural selection which has nothing to do with cosmology or physics? These statements only make sense if they are questioning not just natural selection but much of the conclusions of the entire scientific endeavor (looking for natural explanations for the natural world).

Yet public TV programs, educational policy statements, and science textbooks have asserted that Darwin’s theory of evolution fully explains the complexity of living things. The public has been assured that all known evidence supports Darwinism and that virtually every scientist in the world believes the theory to be true.

The scientists on this list dispute the first claim and stand as living testimony in contradiction to the second. Since Discovery Institute launched this list in 2001 over 700 scientists have courageously stepped forward to sign their names. The list is growing and includes scientists from the US National Academy of Sciences, Russian, Hungarian and Czech National Academies, as well as from universities such as Yale, Princeton, Stanford, MIT, UC Berkeley, UCLA, and others.

See the DonExodus2 video for a response to the above.

The arguments that ultimately unravel the Darwinian synthesis aren’t terribly difficult to grasp. Anyone who remembers the rudiments of logic they learned in freshman composition can follow the essentials of the argument. Below are three articles to get started:

Fact Sheet: Microevolution vs. Macroevolution
Fact Sheet: The Cambrian Explosion
The Survival of the Fakest

All three of these linked articles attack not just the Darwinian mechanism for evolution but evolution itself. So any complaint that they are only questioning the efficacy of natural selection as a mechanism would be disingenuous at best.

In reality their problem is not just with natural selection or even with evolution itself, it is with any scientific finding that they believe contradicts or casts doubt on their theological beliefs.

With the movie Expelled resurrecting the shopworn creationist guilt by association argument that since Nazis and other racists have used [perversions of] evolutionary theory to rationalize their racism, then there must be something inherently wrong with evolution, I thought it might be enlightening to take a look at some of America’s home grown haters, like the Ku Klux Klan.

Given the ‘irrefutable evidence’ linking evolutionary theory to racism and antisemitism surely Klan groups must inevitably be hotbed of evolutionists right? Well, let’s take a look at what one prominent Klan group, “The Knights Party” has to say about the subject on their web site:

We DO NOT believe in evolution. We believe that God created each race as we see it today and that NO race evolved from any animal.

When we barred the school house door to God, traditional Christian teaching, prayer and Bible reading, and opened the school house door to sexual perversion, condoms, evolution, and abortion counseling, we robbed our kids of their moral foundation.

Adam and Eve were not the progenitors of all races. Isn’t it amusing how on one hand the modern church fights against the idea of evolution and than on the other hand wants us to believe that all races evolved from one source.
…
Now within the last hundred and fifty years a very dangerous idea began circulating in the Church - again brought on by Jewish fables which said that the Black race was the children of Ham who was cursed. I am sure you have heard this; that the whole world was under a flood and only 8 people survived. This causes problems because the church must then explain how all of the other races came into being. So they latch on to the idea that the three sons carried the genes from Adam and Eve which all of a sudden caused the three sons’ offspring to become the different races. We see the church teaching evolution again.

Yep, a bunch of materialistic “Darwinists” right there. How is it that we didn’t hear about this group in Expelled?

I feel like I need to go take a long shower now.

This last Monday (April 28th) I attended a Q & A forum on intelligent design (ID) creationism and the movie Expelled held at Biola University (La Mirada, CA) which I saw advertised over on Uncommon Descent by Paul Nelson (who told me he has my blog bookmarked; hi Paul):

…If you’ve got a burning question or two about the Expelled controversies. Darwin-to-Hitler, doesn’t Sternberg still have his Smithsonian position, the Pepperdine students were extras, the cell animation is plagiarized, Dawkins and P.Z. Myers and all the rest were tricked into granting interviews, Darwin’s Descent of Man was quote-mined, why didn’t Ben Stein just use Google Maps to find the Discovery Institute, ID is religious ’cause Expelled admits it, Yoko Ono is suing…whatevah.

Bring Your Questions for Profs. John Bloom, Mike Keas and Paul Nelson

Joining me to monitor the goings on were my friends Don Frack and Cal. State Fullerton Professor Jim Hofmann. Besides ourselves and the three panel members there were perhaps 20 other people in attendance.

I figured I had to go, if for no other reason than to document what they said, particularly as it related to the movie Expelled and its claims of supposed discrimination against ID proponents like Richard Sternberg. The discussion began on something of a sour note unfortunately (from my POV anyway) as the first thing they did was to request that no one make any private recordings of the session. This was a problem for me since I routinely record such events whenever I attend them.

Now I suppose there could be legitimate reasons for not allowing people to record certain events (like rock concerts etc.) since the material could be bootlegged and sold without permission of the artist. But this wasn’t exactly some big event that they were likely to make a DVD of to sell. It was an informal Q & A with only a handful of people in attendance and only a few of them actively participated in the discussion. Given this, the fact that I have grown more than a bit cynical about how antievolutionists operate, and some of my history with Paul Nelson, I suspect, but cannot prove, that their ban on private recordings was more of a defensive maneuver aimed primarily at me and my companions.

Yours truly with Dr. Paul Nelson,a Fellow of the Discovery Institute’s Center for the Renewal of Science and Culture,at the “Intelligent Design & the Future of Science” event held at Biola University in La Mirada California (4-23-2004).

One of the reasons I suspected this is because the last time I saw Paul was at the Rolling Hills Covenant Church back in May of 2006, where he and John Mark Reynolds (both fellows at Discovery Institute), were there to debate Jim Hofmann and Craig Nelson of Cal. State Fullerton on the subject of ID creationism and evolution.

During the debate, which I recorded, Paul relayed an exchange he had via e-mail with paleontologist (and Christian) Keith Miller on the subject of natural vs. intelligent causation. The position he claimed that Miller had taken during this discussion struck me as rather unlikely so I contacted Miller and asked him if Nelson’s characterization of his position was accurate.

Miller responded saying that he not only did not hold the views that Nelson had claimed for him, but that the e-mail exchange that Nelson had quoted from (before an audience of a thousand or more people) had been private and not intended for public consumption.

Since I didn’t have a blog at the time I handed the material over to my friend Ed Brayton who published an account of what happened over on his popular ScienceBlog, Dispatches from the Culture Wars. This led to several follow-up posts with Nelson even leaving a few comments attempting to defend his actions.

Here are links to Ed’s posts in the order in which they appeared:

• Paul Nelson’s Outrageous Lie
• Paul Nelson’s Continued Lie
• The Full Nelson-Miller Exchange
• Nelson’s Larger Misrepresentation
• Paul Nelson’s Sleight of Hand

So my immediate suspicion was that this history might have led to the “no private recordings” business but then again I could be having delusions of grandeur and it had nothing to do with me or my friends being there with recording devices.

As for the Q & A session that followed it wasn’t what I had hoped in that the subject of the supposedly expelled people in Expelled barely came up. Much of the discussion was on ID creationism in general and a lot of that was a red herring diversion into questions about morality and where it supposedly comes from.

What Paul and his compadres do is conflate evolutionary biology with philosophical materialism (atheism) call it “Darwinism” and then argue that since “Darwinism” does not provide moral absolutes. This of course means that believing in “Darwinism” leads to The Inquisition, witch hunts, anti-Semitic pogroms…oh wait, I mean free sex, marijuana smoking, death metal and The Holocaust.

The point is, evolutionary biology is not atheism, it doesn’t provide moral teachings of any kind and isn’t intended to (no scientific theory does or is). And none of this has anything to do with how accurate and productive evolution is as a scientific theory. It is all beside the point but such questions dominate the thinking of many in the antievolutionist camp.

After the talk Paul came over to me and said that he had noticed that I had been shaking my head rather vigorously during the discussion and he asked me what it was I objected to. I told him he was going to have to be more specific as I was shaking my head a lot (not uncommon for me at creationist events). This particular head shaking was prompted by his response to a question about Michael Behe, common descent, humans, chimps and guinea pigs.

You see the faithful in the pews don’t like it when they hear contradictory things from their leaders in the professional antievolutionist ranks. For example I attended a lecture put on by young Earth creationist (YEC) Walt Brown who caused a lot of agitation in the audience by pooh-poohing the idea of a pre-Noah’s Flood vapor canopy surrounding the Earth (a supposed source for much of the Floodwater). The reason this caused so much consternation was because the vapor canopy (ad hoc) hypothesis has been a staple in YEC teachings for decades and was promoted by the Henry Morris and his Institute for Creation Research who many YEC look to as the source of all “true” scientific knowledge. Hearing another “creation scientist” being dismissive of a main tenant of ICR style YEC caused a bit of cognitive dissonance and hence squirming in the seats.

In this case the fact that leading ID creationism proponent Michael Behe has on several occasions stated that he believes in common descent (though not mainstream mechanisms behind it) including the idea that humans and chimpanzees share a common ancestor, and Paul Nelson (who is a YEC) and many others in the ID crowd, disagree with Behe on this.

The problem is the idea that humans share a common ancestor with other primates is perhaps the number one thing that creationists don’t want to accept about evolution since, in their eyes, this would deny humans their special place in the universe etc. etc.

During the Biola discussion a woman a few rows ahead of where we were sitting said she had read in one of Behe’s books about how chimpanzees and humans both have the same malfunctioning gene (a pseudogene), which prevents their bodies from being able to synthesis vitamin C (something most other mammals can do) and how Behe thought that this was good evidence for common descent. She said that this “confused” her because it didn’t make sense considering “everything else” (whatever that is). My perception of this was that she wanted reassurances that despite Behe’s place in the pantheon of ID proponents, his views on humans and chimps sharing a common ancestor weren’t true.

Paul answered her by noting that some in ID creationist camp, like Behe, accept common descent but believe (as Behe apparently does) that God controlled this process in some way. He then talked about how it had been discovered that guinea pigs have a similarly malfunctioning gene for vitamin C synthesis and about how many of the mutations in the gene are the same as those found in humans and chimps. He then seemed to imply that if this mutation could be a genetic coincidence then perhaps the many of the other similarities between the human and chimps were just a coincidence as well.

That is what got my head shaking in this case.

First I wanted to see the material on guinea pig genes (never take an antievolutionists word on anything) for myself and I’m currently waiting on a copy of paper on this. I want to see just how similar the guinea pig pseudogene is to ours and then compare this similarity to that which exists between humans and chimps.

Second and much more importantly this particular pseudogene is hardly the only similarity between humans and chimps. There are a whole host of genetic, physiological, anatomical and even behavioral similarities between humans and chimps. So casting aspersions about this single similarity is like bailing water out of the Titanic with a teaspoon and the implication that all these other similarities might be coincidental in a similar fashion really strains credulity.

For example here is another bit of genetic evidence supporting the common ancestry of humans and chimps from Ken Miller (not to be confused with Keith Miller mentioned earlier):

I told Paul that this (the second part) was why I had a problem with his comments. He denied that his telling the woman about guinea pig’s and their pseudogenes was intended to cast doubt on other similarities between humans and chimps, but when my friend Don agreed with my perception of what Paul had said he rather quickly changed the subject to something called ‘orphan genes’ in microorganisms.

From there it devolved into a random discussion, mostly between Don and Paul about the history and philosophy of science as it pertains to evolution.

Ah well…

Via Pharyngula

This is from a piece on 60 Minutes last Sunday and it is both depressing and frightening as hell:

The mind boggles that a member of the SCOTUS can, with a straight face, argue that the use of torture by government agents would not be prohibited by the Eighth Amendment’s proscription against cruel and unusual punishment as long as it is done to someone before they are convicted of anything. Well if the 8th doesn’t cover it how about due process your Honor?

I dare you to find anyone (anyone not wearing a tin-foil hat to keep the aliens from reading his thoughts, that is) who can look at the U.S. Constitution and come to the conclusions this man has about the original intents of the Founders.

Oh sure, the Founders thought that there should not be “unreasonable searches and seizures”, that people shouldn’t be compelled to be a witness against themselves, and that there shouldn’t be excessive bail, but if the govt. wants to hook a car battery up to your genitals for a few hours that would be just fine as long as it is only to get information out of you and not as a punishment for a crime.

Yeah, right. “Originalism” my ass.

I’m moving this up from comments because it involves a particular interest of mine, embryology as it relates to evolution and the controversies over various embryo illustrations. Here is the comment by “1wmcaw” in full:

Glazius - I may be a lay person. I am not, however, ill-informed.

Darwin disproved: Take a look at his drawings of in utero creatures. He constantly compared the early embryo and fetus’ of human beings to that of pigs and other animals.

I’m here to tell you that medical science has roundly disproved those drawings/pictures/whatever you want to call them. I’ve seen them with my own eyes, as a lay person. Medical professionals, biologists, anthropologists, abortionists, all of them will concede that the embryo and early human fetus looks absolutely nothing like Darwin’s crude drawing and compares nothing to a fetal pig. We were able to distinguish my son’s genitalia at 13 weeks in utero. He did not possess any “tail” as so classically drawn. Many scientists will admit that human beings do not develop a tail at all in the womb, but that it fits the theory of evolution nicely and so it is still promoted in popular scientific literature.

Oh, and plenty of people understand how God’s creation works. Simply because you do not does not make it untrue.

This is the sort of thing I talked about in my page explaining the title of this blog. An antievolutionist presents an argument, which they apparently half-remembered from some creationist web site, that I am going to have to try to reconstruct for them before I can even address it.

I may be a lay person. I am not, however, ill-informed.

Right of the bat we know we’re probably in trouble. It’s like when someone starts a sentence with “I’m not a racist but…” you know that what is to follow is likely to be racist as hell.

Darwin disproved: Take a look at his drawings of in utero creatures. He constantly compared the early embryo and fetus’ of human beings to that of pigs and other animals.

“1wmcaw” has apparently confused Darwin with another creationist whipping boy from the history of biology, Ernst Haeckel, who did publish numerous comparative illustrations of various vertebrate embryos (including humans and pigs). Here is his most (in)famous illustration from earlier editions of his book (Anthropogenie AKA The Evolution of Man 1874). These illustrations have been attacked for over a hundred years by creationists (as well as some mainstream scientists) and I could write a short book about that but I won’t right now since this is ostensibly about “Darwin’s” embryo drawings.

The bottom row represents a more or less fetal stage and the different organisms are pretty readily distinguishable compared to the same animals on the rows above (that was sort of the point). Most of the criticisms of Haeckel’s drawing have been applied to the top row in the illustration rather than the middle or bottom row, so I don’t see how “1wmcaw” could be talking about them.

Darwin did publish a comparative illustration of two embryos in his book The Descent of Man (1871), but they are of a human and dog embryo. Here they are (below) next to a photographs of a human (top) at approximately the same stage (perhaps slightly earlier), and a cat embryo (bottom). I couldn’t find picture of a dog at this stage but I would imagine they don’t look all that different (most mammals don’t).

I’m here to tell you that medical science has roundly disproved those drawings/pictures/whatever you want to call them. I’ve seen them with my own eyes, as a lay person. Medical professionals, biologists, anthropologists, abortionists, all of them will concede that the embryo and early human fetus looks absolutely nothing like Darwin’s crude drawing and compares nothing to a fetal pig.

No, a fetal pig doesn’t look much like a fetal human but then I don’t know of anyone (including Darwin and Haeckel) who ever claimed otherwise. Nor am I aware of any drawings purporting to be of fetuses that attempt to make them look overly similar.

Human and pig embryos, now that’s another story:

Here we have illustrations of two embryos at about the same point in development, one of a pig and the other of a human. Both are taken from embryology texts (by the same author). Who can tell me which is which?

We were able to distinguish my son’s genitalia at 13 weeks in utero. He did not possess any “tail” as so classically drawn.

That’s because 13 weeks (about 3 months) is much farther into the developmental process than when you’d have to look to see the tail (around the 5th and 6th week). Did your son look something like the picture below?

Many scientists will admit that human beings do not develop a tail at all in the womb, but that it fits the theory of evolution nicely and so it is still promoted in popular scientific literature.

To “admit” such a thing would be to express either dishonesty or ignorance of the subject. Humans and all other members of the phylum Chordata have at some point in their lives a post anal tail. In fact it is one of the defining characteristics of chordates.

A stage 15 human embryo with a clear tail.

While humans normally only have tails as embryos occasionally children are born with tails still intact.

Similar pictures can be found in medical textbooks. Usually the tail is just soft tissue but occasionally children are even born with tails that have extra vertebral bones in them. The re-expression of an ancestral character is known as an atavism. The existence of atavisms is easy to understand under evolutionary theory but difficult to explain under creationism.

So, Darwin not disproved.

This bit of wackiness which comes from a site called California Catholic Daily (which is odd since most Catholics don’t have a problem with evolution):

Now that Darwinists rule academia, they will brook no contradiction, and they will happily commit employment assassination even against tenured professors who dare even to mention intelligent design. The Darwinists even have their own Gestapo in the National Center for Science Education led by a modern day Heinrich Himmler named Eugenie Scott.

The NCSE is like the Gestapo and Genie Scott is comparable to Himmler, really?

I’m not sure how to even respond to such irrationality, I mean ye gods people get a grip. The claim that there is an epidemic of people losing their jobs for questioning Darwinism evolution is, at best a gross exaggeration. Trying to draw a comparison between the NCSE and the Gestapo is just plain idiotic, and comparing Genie to Himmler is, well, there really are no words to adequately express the mind numbing stupidity of that.

Here I am (on the right) with the notorious Dr. Eugenie Scott (Executive Director of the NCSE, center), and Professor Jim Hofmann (who teaches a class on the C/E issue at Cal State Fullerton on the left), prior to a lecture by Dr. Scott at CSF (4/17/03). (Photo by Don Frack).

You can almost see the evil radiating off of us can you not?

Perhaps I should withhold judgment as to whether it will be the most hysterical nonsense of the week (the week has barely started after all), but I think it would be hard to top this one.

We’ll see.

[Thanks to Jason Spaceman on the Talk Origins Newsgroup for the heads up on this.]

I recently picked up the March/April issue of a new magazine, Science Illustrated which is sort of like Discover Magazine-lite. Lots of pretty pictures (as the name suggests) but the actual information content is somewhat limited and in some cases it is more than limited, it is simply wrong.

For example while flipping through this issue I ran across a little two paragraph editorial piece on a small (non-avian) dinosaur fossil known as Sinosauropteryx: “Researchers Pluck “Feathered Dinosaur” Theory”.

A new analysis of fossils raises doubts about when feather first emerged. Previously, researchers believed that Sinosauropteryx, a turkey-sized beast that lived about 140 million years ago, was clad in ‘protofeathers’ that had evolved to keep it warm.

South African researchers have reexamined the fossil and now posit that the characteristic marks on the skin are not feather remains, but are instead collagen fibers. (Collagen is a protein found in connective tissue.) If true, this means that dinosaurs didn’t develop feathers as early as previously thought, and that birds evolved from a later group of dinosaurs.

The first problem is that this isn’t exactly new. The most recent place I can find (via a web search) a reference to someone from South Africa publishing on this in the scientific literature is from an article in the Proceedings of the Royal Society B from last year:

Theagarten Lingham-Soliar, Alan Feduccia, Xiaolin Wang (2007) “A new Chinese specimen indicates that ‘protofeathers’ in the Early Cretaceous theropod dinosaur Sinosauropteryx are degraded collagen fibres”, Proceedings of the Royal Society B: Biological Sciences, 274(1620):1823-1829

But it wasn’t even a new suggestion then. I heard this being argued 10 years ago, not long after Sinosauropteryx was discovered, by some in the anti-dino/bird crowd at the third DinoFest International Symposium in Philadelphia (1998). Nor is the idea that the ‘protofeathers’ on the Sinosauropteryx fossils are merely collagen fibbers widely accepted by other paleontologists.

The second problem is the conclusion that the S.I. editorial comes to. Because even if the collagen fiber hypothesis was accepted, it doesn’t change the fact that there are numerous other dinosaur fossils from the same area of China that Sinosauropteryx comes from which show clear impressions of unquestionable feathers.

These other fossils date from the early Cretaceous (as does Sinosauropteryx), whereas the oldest known ‘bird’ fossil, Archaeopteryx, dates from late Jurassic. So regardless of what the skin of Sinosauropteryx was covered with, the ancestor of birds is to be found among dinosaurs older than Archaeopteryx.

While many of the fossils from China are morphological intermediates between dinosaurs and birds they are not their actual ancestors. They are cousins to the actual ancestors who lived earlier, likely in the early or mid-Jurassic period.

So Science Illustrated does have lots of nice pictures (can’t wait for the swimsuit edition) but they’re going to have to work a little harder on the accuracy of their information content.

For more:

Brian Switek over at Laelaps posted a more detailed look at the Proceedings article referenced above.

I highly recommend that anyone interested in the evolution of birds from dinosaurs check out Luis Chiappe’s excellent book on the subject: Glorified Dinosaurs: The origin and early evolution of birds.

Just ran across this on the science section of the NY Times web site:

Tests Confirm T. Rex Kinship With Birds

The article, by science writer John Noble Wilford, reports on results from a Harvard study to be reported in the next edition of the journal Science.

In the first analysis of proteins extracted from dinosaur bones, scientists say they have established more firmly than ever that the closest living relatives of the mighty predator Tyrannosaurus rex are modern birds.

The research, being published Friday in the journal Science, yielded the first molecular data confirming the widely held hypothesis of a close dinosaur-bird ancestry, the American scientific team reported. The link was previously suggested by anatomical similarities.

This, if it bears out, it is further evidence supporting the evolutionary relationship between theropodcomparative anatomy. dinosaurs and birds that has been strongly suggested by the evidence from

The anti-dino/bird faction amongst scientists (Martin, Feduccia etc.) will no doubt claim that this is merely yet another example of the many (supposed) convergences between dinosaurs and birds. Creationists will probably deny, deny, deny.

Remember to stay tuned on this though. This is only the popular level report, the peer reviewed material is yet to be seen; and it is only the first such study. More studies, if possible, will be needed to confirm this finding.

They apparently did some similar tests on mastodon bones:

Similar molecular tests on tissues from the extinct mastodon confirmed its close genetic link to the elephant, as had been suspected from skeletal affinities.

Perhaps not terribly surprising, but still interesting nonetheless.