New technologies show Panderichthys and Tiktaalik on the way to living on land

In a recent paper in Nature, Catherine A. Boisvert, Elga Mark-Kurik, and Per E. Ahlberg show how a prehistoric fish, Panderichthys who lived 385 million years ago, had bone structure that resembles animal digits instead of typical fin architecture. It appears that there is some debate among paleontologists as to the when “fingers” first arose and this paper pushed the date back. It had previously been hypothesized that digits arose from an extrapolation of prehistoric fin structure. However, fossil evidence of Panderichthys and similar fish had indicated that they do not have any such digit bones. However, more advanced technology used in this paper has revealed that Panderichthys_BWat Panderichthys does in fact have these features.

The authors used CT scanning and analyzed a largely undisturbed fin (except when it got smashed upon excavation!) to be able to see inside the fossil. Previously, imperfect fossils and the remains of the fish’s scales did not allow researches to see these bones.

These early fish having these fingerlike digits is not wholly unexpected. In fact, the presence of these bones in the closely related lobe-finned fish Tiktaalik pointed in this direction. Furthermore, the presence of certain developmental genes (hox genes) that are involved in digit development in related present day fish nearly predicted it.

Changes in the details of our knowledge of evolution are what makes science the best way to understand the world. The scientists here resolved some contradictory evidence of where early digits arose evolutionary. At the same time, they proved other scientists wrong. There is nothing wrong with this and it shows the strength of the scientific approach.

The Discovery Institute does not see it that way. They believe that scientists are now backpedalling to try fix some imaginary mistake that they say scientists made. Take for instance, Casey Luskin’s blog post from September 26, 2008 entitled: The Rise and Fall of Tiktaalik? Darwinists Admit “Quality” of Evolutionary Icon is “Poor” in Retroactive Confession of Ignorance.

The first point I want to make is that scientists are not at all one cohesive group with the same exact goals. In fact, scientists working on similar subjects are actually competitors. They compete for money, resources, talent, and recognition. In many respects and unfortunately, it benefits one group for a competitor to be proven wrong. So when Luskin takes a quote from one scientist that contradicts what another said, it does not mean that scientists are engaging in “Retroactive confessions of ignorance.”

Besides, when the article published in 2006 describing Tiktaalik as an example of a transitional fossil, they plainly stated that they do not know the state of Panderichthys’ limb structure.  From the article:

Unfortunately, the distal region of the best-known pectoral fin of the elpistostegid Panderichthys is covered by lepidotrichia and the complete distal endoskeleton is unknown

Perhaps Luskin should have actually read the article that he is referring to when making such claims.  The paleontologists were upfront and honest with their ignorance at the time.

So what is the big problem with “Retroactive confessions of ignorance” anyway?  Are scientists supposed to know everything from the beginning? New technologies or even new insights can tell us what we thought we knew was wrong. It can also tell us that there are things that we didn’t know we didn’t know.  Unlike intelligent design/ creation proponents, scientists are willing to change their minds when new facts and ideas emerge.

Getting back to Luskin’s post, he states:

My main observation is this: if Panderichthys is dethroning Tiktaalik as the icon of the fish-to-tetrapod transition, what does that say about all the hype we’ve seen surrounding Tiktaalik? It says that “poor” and “primitive” Tiktaalik was never all it was hyped up to be.

Tiktaalik is still a good example of a transitional fossil, but so is Panderichthys. Tiktaalik has other tetrapod features that tiktaalik_f from NSFPanderichthys lacks (including changes in skull and rib structures) pointing to it being closer to a tetrapod.  However, Panderichthys shows that fish may have evolved digit-like structures earlier than we previously thought.  Both a re important for our understanding and there was no “dethroning.”

Luskin did something semi-unethical in the post with his figure that compares Panderichthys with a “real tetrapod”. I can’t show the figures from the research article here because of copyright issues, but Luskin took two separate figures and put them together to show a comparison. However, the authors already had made a similar figure that compared not only Panderichthys to a “real tetrapod,” but includes a comparison to Tiktaalik and a more fishlike ancestor. I can only think that he did this to highlight differences to the untrained eyes, because the original figure is much more compelling. What makes his argument even more egregious is that Luskin does not show the very similar drawing from the original Tiktaalik paper that showed the fin bones of Panderichthys as large flat pieces.  Of course that would have disproved the whole “retroactive confession of ignorance.”

Of course, as is often the case with Luskin, that was not the only instance of questionable writing in his post.  His post was filled with the usual quote mining.  For example, he quotes Catherine A. Boisvert from a New Scientist article:

it is now completely proven that fingers have evolved from distal radials already present in fish that gave rise to the tetrapod.” Boisvert also praised her findings, stating: “The disposition of distal radials in Panderichthys are much more tetrapod-like than in Tiktaalik

Luskin makes it sound like Boisvert is ignoring the evidence brought to light by the discovery and analysis of Tiktaalik. Is this what she meant by her statement?  Lets see the original quote (emphasis is mine):

“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.”

Rather than bore you with more examples of quote mining, I will just finish with a couple questions:  Are there tetrapods located present at this time in history? Do Intelligent Design proponents have a better theory for the presence of these transitional fossils?

hat tip: JLT

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Academic freedom: should religous students learn other religions?

The Discovery Institute is all up in arms about an editorial that appeared in American Society for Biochemistry and Molecular Biology Today. The writing in question is by Gregory A. Petsko, the president of ASBMB, on the state of evolution denial. He discusses the propaganda film Expelled and the Trojan horse legislative activities given the label “academic freedom.”

One interesting point that Petsko makes is drawing a parallel between having “academic freedom” to teach competing ideas on the evolution of man and on having “academic freedom” in religious institutions. He argues that if teaching competing views is such a good idea when teaching evolution, then it should be helpful for students in religious institutions to learn about other religious ideas, including the idea of no religion.

It has been the mantra of Intelligent Design(ID) proponents that students should be exposed to differing ideas and opinions. They say that his will only improve student’s understanding and critical thinking skills. Based on their logic, you would have thought that they would support such a move in religious schools. The fact that they got so offended by Petsko suggestion implies that they are not really interested in student’s overall education. The Discovery Institute is just interested in pushing ID on students.

I do not think that we should force students at religious schools to learn about other religions no more than I think a evidence-less theory like intelligent design should be forced on kids. The fact is that the ID proponents are cherry picking a few ideas that they want to promote. Nearly every subject in school could be taught in the guise of “academic freedom.” For example, holocaust denial should be brought up as well as the “faked” moon landings. Astrology, alchemy, and numerology would also need to be taught. Such ideas are ridiculous and like ID should be ignored. Students have enough to learn as it is.

Angela Hvitved, in another editorial in ASBMB Today, summarizes what is really at the heart of these “academic freedom” bills:

at best, these bills are unnecessary and do not provide any additional legitimate protection and, at worst, provide cover for introducing intelligent design and other nonscientific topics into the science classroom

They bring up the old argument that there are quite a few scientists who do not accept evolution. It is clear that these scientists are in such a minority that bringing them up is ridiculous. I wonder if they has ever heard of ‘project steve’? This idea shows that there are so many more scientists that accept evolution that the number of scientists with just the name Steve (or Stephanie) will outnumber all the scientists that reject it. Well, the count is now up to 958 (as of September 25th), compared to their 700+. Besides, only a small percentage of these scientists have anything to do with biology.

To end, I am going to quote Petsko’s editorial, where he gives a nice summary of why intelligent design (and creation) should not be given any credence:

The fact that some people believe nonsense does not give that nonsense scientific credibility. A challenge to existing scientific principles must be based on evidence, not on belief, and there isn’t a shred of evidence to support either creationism or intelligent design.

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Discovery Institute, primate limbs, and “junk DNA”

In his September 24, 2008 post entitled “Study Challenges Two Icons of Evolution: Functional Junk DNA Shows “Surprising” Genetic Differences Between Humans and Apes,” Casey Luskin shows us just how much he really is out of touch with molecular biology and modern evolutionary theory.  He refers to an interesting study that seems to have found at least one of the reasons why there is such a difference in human limbs compared to other primates.  This article was published in the September 5th issue of Science.  Luskin somehow thinks these findings go against evolutionary theory.  They are perfectly consistent with the theory, as you will see below.

Luskin promotes the idea that scientists still believe that all the sequence that does not directly code for a protein is “junk.” The article of which he refers made a discovery in a region which may have once been considered “junk,” but not for a long time.  Scientists have known that DNA that is far away from a gene (thousands of base pairs) can directly regulate its function for decades. Other regions are believed to provide structural functions or regulate a gene that is nowhere nearby (see siRNA). This stuff widely known and Luskin is either lying or is willfully ignorant.  I also want to put some blame on the people who are responsible for the Yale press release. They are helping perpetuate this myth of “junk DNA,” but Luskin should know better as a person heavily involved in the evolution/ intelligent design debate.

To make his point about how “junk DNA” is still used as an “icon” for evolution, Luskin quotes a human physiology textbook by Willam McArdle et al. (emphasis mine):

“junk DNA” “is considered defective” and are “inherited sequences [that] perform no currently known ‘genetically useful’ purpose, yet they remain part of the chromosomes.”

Forget that the book is not an evolutionary biology textbook or even a molecular biology textbook. Did you notice the qualifier “not currently known?” Once a stretch of DNA is found to have a function, then it isn’t considered “junk” anymore.  Yet, Luskin still takes the stand that finding anything important in what he calls “junk DNA” discredits evolution.  Nothing could be further from the truth.

Here is the meat of Luskin’s argument:

Most studies that have claimed that humans and apes have nearly identical genomes have primarily looked at the gene-coding portions of the genome, not the non-coding DNA (formerly claimed to be “junk”). Perhaps as biologists study the non-coding portions of our genome, they will find evidence that challenges two Darwinists icons: Not only does “junk” DNA have function, but humans aren’t as genetically similar to apes as was once thought.

We have already convered that “junk DNA” is a misnomer and he even says that it was “formerly claimed.”  So this being an “icon” of evolution doesn’t really make any sense.  But what about his argument that we “aren’t as genetically similar to apes?”

The article in question seems to promote the idea (or at least Luskin’s take on it) that humans and chimpanzees aren’t as similar as once thought due to the press release saying that the finding“was especially surprising, as the human and chimpanzee genomes are extremely similar overall.”

Lets do some overly simplified math to see if these findings contradict evolution. The region in question (HACNS1) is 546 bases long. They found 16 differences between humans and chimpanzees. So if we do the math (16/546), we find that there is approximately a 3% difference between the human and chimpanzee HACNS1 region. This percentage is exactly the same as the overall difference between the two organisms and matches nicely with the rate of mutation predicted by evolutionary theory since the time of human-chimpanzee split (~6 million years ago).

If the math all lines up, why is this finding surprising? It turns out that there are certain regions of DNA that are so critical that mutations in these regions would be devastating for their function. Only rare and beneficial mutations would be allowed to persist. In fact, this region is highly conserved throughout land animals and it has 4X as any mutations as would be expected based on this evolutionary constraint.

Tracer showing human expression in mouse

Tracer showing human expression by HACNS1 in mouse limb

The end result of these mutation seems to effect the way humans thumbs, wrists, and other limb characteristics develop. In fact, when the scientists put the human DNA region in question in mice with a tracer (see image) and compared it to chimpanzee region, they saw a stark contrast in the levels of the tracer between the two organism’s DNA. The regions where the tracer was observed corresponds to areas that seem to be responsible for both the greater flexibility of the human thumb and wrist. Of course more study needs to be done on the subject, but It does show that this small region could be important.

Everything in the report is consistent with evolutionary theory, despite what Luskin says. If anything it strengthens the argument that small changes (12 changes in 3 billion) between humans and chimpanzees can go a long way. Remember that the “icons” that Luskin speaks of are really strawmen created to divert unsuspecting readers away from the real arguments and evidences.

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Hurricane Ike

Over the last week, I have been busy recovering from Hurricane Ike.  I am hoping things will return to normal soon.  Meanwhile, here is a picture taken shortly after the storm.

Intelligent design lacks evolution’s web of evidence

Multiple lines of evidence converge towards evolution

Multiple lines of evidence converge towards evolution

I have been studying evolutionary theory and debating anti-evolutionists for quite awhile. One thing that continually impresses me is the overwhelming amount of evidence that points to evolution. Each piece of evidence can almost stand on its own for the credence of evolution, but the real power comes from their combination. These evidences even come from such diverse disciplines as molecular biology to paleontology. Although not perfect (but what really is), these forms of evidence compliment each other so strongly that it is nearly inconceivable that evolution is not real.

So what about intelligent design? Surely it also has evidence pointing towards it, right? After all, the Discovery Institute was founded on the idea, and it was the focus of Ben Stein’s Expelled. Well, the simple and accurate answer is a resounding “No”. There is not one piece of evidence that supports the idea. Irreducible complexity is just an argument from personal incredulity. Plus, the structures that are often pointed to as examples of irreducible complexity have had their evolutionary origins identified. The idea of complex specified information theory proposed by William Dembski is simple pseudoscience. Even the ideas that do not directly contradict intelligent design are neutral to the idea.

Take a look at the figure that I have included in this post. It is by no means a complete representation of all the lines of evidence for evolution, but it does show the abundance of evidence. Why do intelligent design proponents ignore all this evidence? Willful ignorance? Distrust for Science and scientists? Either way, it should be obvious that no more time or brain power should be wasted on the idea. And for crying out loud, this pipe dream should not be taught in schools.

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Edward Sisson is the Discovery Institute’s newest nonscientist and anti-evolutionist

Edward Sisson is the newest contributor to the Evolution News and Views blog at the Discovery Institute (DI). I would like to take this opportunity to address the DI’s choice of contributors. I am also going to examine Sisson, himself.  I do not want to personally attack him, but I will address some of the comments that he has made in the past.

Sisson graduated MIT with a B.S. in architectural design (1977) and received his law degree from Georgetown (1991). He is an accomplished lawyer who focuses on suing the U.S. government. He has also done a large amount of pro bono work. The DI became interested in Sisson due to his pro-intelligent design advocacy. He was supposed to cross examine the scientists at the 2005 Kansas “evolution hearings,” but could not due to the scientists boycotting the event.

Notice anything missing from Sisson’s resume?  Sisson does not have any real biological training. He doesn’t even have any real scientific training. With the addition of Sisson, the number of trained scientists contributing to the blog is 3 out of 16.

There seems to me to be two reasons why the DI would keep bringing nonscientists aboard. The first is that lawyers are really good at arguing and debating. It is what they are trained in and critical for job performance. If you want to win an argument without having reality on your side, your best hope is with a lawyer or perhaps a radio talk show host (see: Medved).

The second reason is that qualified scientists that are willing to support intelligent design are few and far between. This is quite obvious when you look at the lists of scientists who support intelligent design. Not a lot of biological scientists on those lists.  So the DI is stuck with recruiting unqualified participants.

There is a series of you tube videos showing an interview of Sisson. Most of the interview addresses the trial in Kansas, but he does make some comments that I think need addressing.

The first is where he brings up the overused ID talking point that the world around us is too complex to have arisen naturally:

“such complexity and such code in the DNA …it seems to me that the proponents that it all came about by natural chemical processes have a very tough case to make. They have to present a lot of observational data and a lot of mathematical analysis of that data, and they haven’t done it.”

He is using the logical fallacy of personal disbelief. Just because he doesn’t see how it could have happened doesn’t mean it did not happen. He wants data supporting evolution? I guess 150 years of scientific analysis and thousands of peer-reviewed scientific papers isn’t enough for him. This type of willful ignorance is characteristic of the DI and he will be a good fit there.

Sisson goes on a rant about how the proevolution side does not engage in debates that are fair. He says that they only agree on their own terms. The thing is, evolution is a strictly scientific issue. Scientific issues are not decided in a 1 hour debate, they are decided with theories, experiments, and data.

Another point he makes is about how evolution is entrenched in our culture:

The other side has 100 soe years where its doctrines have been promulgated through all the schools and they have a foundation of public acceptance and public awareness.

I guess Sisson is forgetting that teaching evolution was banned in areas of the U.S. during the early parts of the 20th century.  Remember the Scopes mokey trial that found scopes guilty of teaching evolution? Besides, Sisson apparently is unaware that only ~40% of U.S. citizens think evolution is true. You call that a foundation of acceptance?

I will be honest; I could only make it through 3 of the 6 parts of his interview. If anyone else could stomach the rest of the interviews, please feel free to let me know what you think.

Well, I hope I have given you a taste of what the thought processes are at the DI in deciding who will contribute to their organization. I also hope that I have given you a taste of what Edward Sisson is like as I am sure we will be hearing more from him in the future.

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Randomness and natural selection, two peas in a pod

On August 29, 2008, Casey Luskin writes that:

This tactic to push evolution to the public as “non-random” appears to be part of an ongoing campaign on the part of Darwinists to make neo-Darwinism appear more appealing to the public (which tends to be religious). While there are non-random components to natural selection, evolutionary biology textbooks have made it clear that other aspects of Darwinian evolution are quite random

Luskin utterly and completely misses this aspect of evolution. Here it is simply: Underlying causes are random, while the overall effect is not. For example, a random mutation makes a predator run faster. Being able to run faster means more food, better health, more mates, etc. Therefore, this mutation that was initially random resulted in a non-random selection for this mutation. See how it can be random and directed at the same time? Well, Luskin doesn’t.

Perhaps you are thinking that this is somehow a complex aspect of evolution that is rarely talked about and that is why Luskin is confused.  It isn’t.  It is however on a list that the PBS put out about the basics of evolution.

7. Is evolution a random process?
Evolution is not a random process. The genetic variation on which natural selection acts may occur randomly, but natural selection itself is not random at all. The survival and reproductive success of an individual is directly related to the ways its inherited traits function in the context of its local environment. Whether or not an individual survives and reproduces depends on whether it has genes that produce traits that are well adapted to its environment.

What is really going on here is that Luskin is trying to pull a “gotcha!” moment. He claims that this is some sort of “tactic” that is used by evolution proponents to trick the public. In reality, pointing out how evolution is directed is used to combat the arguments of groups like the Discovery Institute and the general poplulous.  How many times have you heard someone say (or type) “I don’t see how randomness could ever produce the complex forms of life we see around us.”  Complete randomness would not, but random mutation plus natural selection would.

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