The Obama Presidency, a bright day for science and evolution?

With the winning of the presidency of the United States going to Barack Obama, one wonders if there will be a change in the climate of the U.S. towards a better scientific future.

Former President George W. Bush

Former President George W. Bush

Science and The Bush Presidency

It has become exceedingly clear that the Bush administration has been anti-science.  I don’t mean to say that George W. Bush hates every aspect of science or all scientists (like Ben Stein), but there are certain areas the current administration is morally and intellectually corrupt. The facts of such subjects as climate change and stem cell research were regularly distorted and repressed.  Areas such as space exploration seem to be promoted and presented accurately.  However, having any anti-scientific thought is surely going to dilute reason, critical thinking, and acceptance of scientific fact.

How about the subject of evolution?  Of course, the blatant fundamentalist Christian ideals that underlie the Bush administration’s policies are anti-evolution. He is of the mind that both Intelligent Design and Evolution should be taught together:

Both sides ought to be properly taught . . . so people can understand what the debate is about

2008 Presidential Election

No matter who had one the 2008 election, it is clear that science in the US would take a step forward.  How could it possibly take a step backwards?  Although neither candidate (Barack Obama and John McCain) agreed to a debate concerning science, they did answer these 14 questions relating to science.  Although their answers could just be pandering, it is clear from their answers that the current shameful scientific policies would come to an end.

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Newly Elected President Barack Obama

Obama said some very encouraging things in his response to the questions, but actions speak louder than words.  Over the weekend, Obama did something that should make anyone on the side of science and reason, very happy.  He made a point to say that he would reverse Bush’s “ban” on embryonic stem cell research:

I strongly support expanding research on stem cells. I believe the restrictions that President Bush has placed on funding of human embryonic stem cell research have handcuffed our scientists and hindered our ability to compete with other nations… As president, I will lift the current administration’s ban on federal funding of research on embryonic stem cell lines.

Although this move does not directly affect his view or the U.S.’s direction toward evolutionary belief, it does indicate that Barack Obama is serious about changing scientific policies for the better.

But what do we know specifically about Obama’s view of evolution?  He seems to be keeping pretty quiet on the subject, but he has been quoted as saying:

I believe in evolution, and I believe there’s a difference between science and faith. That doesn’t make faith any less important than science. It just means they’re two different things. And I think it’s a mistake to try to cloud the teaching of science with theories that frankly don’t hold up to scientific inquiry.

I applaud Mr. Obama for this action and hope that he does make a change.  Not one that we can believe in, but one that is based on reality.

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Expelled: Not #1 of Anything

The folks from Ben Stein’s Expelled are busy promoting the DVD version of the film to be released today.  They even go so far as to “Thank you for making Expelled the #1 Documentary of 2008.”  There is only one problem with that statement.  Expelled was not the #1 documentary of 2008.

As far as documentaries go, it has been moderately successful.  According to boxofficemojo.com, it has made just over $7.5 million at the box office.  It is ranked as the 13th most grossing documentary.  Pretty good, but is it really the “#1 documentary of 2008”?  Nope.  By numbers, Religulous has already made over $9 million in its first 3 weeks.  Religulous also opened in fewer theaters than Expelled: 502 vs 1052, respectively.  Looks to me like Religulous is #1 so far this year.

So why is it being called the #1 documentary of 2008?  I am not really sure, but I guess they could mean that it is the #1 documentary with the least reflection of reality.  Maybe it is because the people behind the film have no problems lying about the movie.  Either way, promoting it as #1 is just plain wrong.

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Cichlid speciation and predictable Intelligent Design dismissal

Jewel cichlid

Jewel cichlid

I have split this post into two parts: the actual science and intelligent design response.  Skip down below if you are familiar with the recent Cichlid research.

The Research

African cichlids are a favorite among fish collectors due to the wide variation of species. These species are naturally found in the many isolated lakes in Africa. It is easy to understand how the species that are found in different lakes have evolved differently over time, but cichlid speciation in the same lake is harder to understand. In a recent article in Nature, Ole Seehausen and colleagues seem to have discovered a probable mechanism for this speciation.

They believe that they are observing what is called sensory-driven speciation. The idea here is that slightly different environments lead to slightly different optimal communication systems (visual, olfactory, etc.). These changes lead to reproductive isolation (one definition of species) due to easy to detect characteristics being favored in each environment. The interesting thing is that this can occur within one population with slightly different environment as is seen with the cichlids in the research article.

Lake Victoria is a lake in Africa that has many different species of Cichlids. It is also a lake that has diverse environments that could allow for the creation of many species of cichlids. One example of different environments is depth and turbidity of the water. In some areas the water is relatively clear, but as you get deeper and deeper the water gets more cloudy. This results in two distinct environments: Close to the surface is clear where blue light is more prevalent and close to the bottom where there is mostly red light.

How does this lead to speciation? Seehausen and colleagues caught closely related species of Cichlids at various depths of water. When they looked at the color sensing chemicals in the fish’s eyes, they found that the fish at the surface were more sensitive to blue and the fish at the bottom were more sensitive to red. Since sexual preference in cichlids is believed to be based on how conspicuous the male fish is, blue fish at the surface and red fish at the bottom will be more successful at mating. Interestingly, when the researchers looked around areas where it got cloudy rapidly, they did not see this distinction in red vs blue fish distribution with depth. Furthermore, they did not see any female mating preference based on color at these sites.

Intelligent Design Response

Jonathon Wells posted at the Evolution News and Views blog that this work is “One long Bluff.”

But the researchers did not observe the origin of a new species. They did what biologists have been doing for a long time: They analyzed differences in existing species to find evidence to support a particular hypothesis of speciation.

Since when is finding evidence to support a hypothesis a bad thing?  I guess it is bad if you are stooped in pseudoscience.  What the researches did do is give support to a type of speciation that had only been hypothesized previously.  Wells continues:

Although “genetic mutations helped some fish adapt” might sound as though the researchers induced mutations that helped some fish adapt to new conditions, all they really did was compare existing species and find a correlation between differences in their DNA and differences in their vision.

The authors actually went out in the field and looked to find evidence that supported their hypothesis.  If this had all been done in the lab, Wells would then have complained about how these mutation could never have arisen in the wild.  Either way, the goal posts would have been moved.

British physicist David Tyler had slightly more reasonable assessment of the research, but still had some objections to the findings:

There is no new genetic information – just fine-tuning of existing genetic systems. There is no evidence that these new species lack the potential to interbreed. Indeed, the differences are so slight that hybridisation to produce fertile offspring can be predicted with some confidence.

There is new genetic “information”. The cichlids examined have different chemical sensors in their eyes than other cichlids. One is optimized to see in red and one is optimized to see in blue. The authors noted that the mutation that shifted the red chemical led to an increase in sensitivity by 10%. Surely this is also an example of a gain-of-function change, of which we are led by intelligent design proponents to believe don’t exist .

As to Tyler’s objection that the species can still interbreed, the point of the article is that they are recently or in the process of diverging into new species. If the cichlids were completely unable to breed, then the findings would not be considered as early in a speciation event.

He goes on to say:

These variations allow organisms to diversify and prosper in new ecological niches as they become accessible. However, these variations have nothing to do with the origin of cichlids, eyes or complex specified information.

There were never any claims that this research showed anything involved the “origin of cichlids.” The research here simply showed an example of how a small change in environments could lead to speciation. This diversification is completely in line with evolutionary theory. Small changes over short time periods add up to large changes over long periods.

Self described “journalist and grandmother ” Denyse O’ Leary doesn’t add much to what Tyler said, but did say:

The problem isn’t with the researchers, who sound suitably cautious. It’s the pop science media that jump on something like this and make far more of it than the current state of knowledge would justify.

So journalists are trying to oversell a story. That is their job.  They do it in every story because it is the nature of their business. That doesn’t mean that there isn’t anything important to learn from the research.

I find it interesting how none of the responses that I could find deny the research or even try to spin it into evidence for intelligent design. I guess this new evidence is not a big deal to them since it is just another rock on top of a mountain of evidence.

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Discovery Institute believes pseudoscientific “strengths and weaknesses” should be taught in Texas

Texas_population_map In a recent post from the Discovery Institute, Casey Luskin writes that "Texas Darwinists Reject the Scientific Method of Analyzing “Strengths and Weaknesses” of Scientific Theories." The post argues that it is fundamentally unscientific to not teach the "strengths and weaknesses" of evolution (read: teach the controversy) to students. Luskin’s writing is in regard to the Texas State Board of Education proposal to remove the above language from their academic standards.

As I have written before, terms like "academic freedom" and "strengths and weaknesses" are words that sound innocuous when referring to evolution, but really are a stealth attack on teaching reality. Does it really make sense for the classrooms of elementary and secondary education to critically analyze the strengths and weaknesses of a theory that has withstood 150 years of scientific inquiry by thousand of professional scientists?

So I guess the new bill does not leave any room for flexibility in the students mind about the theory? That is what Casey Luskin and the Discovery Institute imply. Well, here are a few select passages from the proposed standards (emphasis mine):

 

The student knows evolutionary theory is an explanation for the diversity of life…

[students will] evaluate models according to their limitations in representing biological objects or events.

So, evolutionary theory is AN explanation for the diversity of life; it is not THE explanation for the diversity of life. So students can see that there are other options out there, and they also see that these are models that have limitations.  Seems pretty reasonable to me without requiring the bogus “weaknesses” requirement.

Here is another one from the proposal (originally taken from the National Academy of Sciences):

Scientific explanations are open to testing under different conditions, over time, and by independent scientific researchers. Many theories in science are so well established that no new evidence is likely to alter them substantially; however, they are subject to continuing refinement as new areas of science emerge or as new technologies enable observations and experiments that were not possible previously.

Yup, the new standards still say that science is subject to change as new information becomes available. Not nearly as dogmatic as we are led to believe.

Still, is there really any harm with leaving a few criticisms of evolution in the lesson plan? Luskin brings up some of the potential problems as illustrated by the NCSE in a recent article. One is that it will "dilute the treatment of evolution." This seems pretty straight forward to me. More time teaching criticisms means less time teaching the theory. The NCSE also says that teaching evolution will "damage and corrupt science textbooks." This is because it would allow board members to reject any textbook simply because it doesn’t substantially address strengths and weaknesses despite it being the best book in every other regard.

But what does Luskin say about these criticisms by the NCSE?

"Such authoritarian statements have no place in science, and they serve to indoctrinate students rather than teach students how to think critically and skeptically—like scientists. "

Ignoring the point that these students are not qualified to really critically analyze evolutionary theory, the question is then, how much evidence is enough that it wouldn’t be considered indoctrination? Would any amount ever be enough for creation/ intelligent design proponents? A scientific theory can never be really proven; it can only be disproven. Evolution has never been disproven and it has had plenty of chances for it to be wrong. Over the 150 years since its inception, it has only increased in validity with increasing evidence.  Teaching reality is not indoctrination.

Here is an interesting quote from the post:

Discovery Institute believes that if scientists can dispute the core claims of neo-Darwinism (as these scientists do), then students can learn about those views:

Good, something we can agree on. If and/ or when scientists can actually discover something that disputes the core of evolution, then I would be all in favor for it. However, there would need to be some strongly compelling evidence. So far, there is no evidence, let alone compelling evidence. On the other hand, I have seen plenty of pseudoscientific views that are against evolution.

Don’t forget, evolution could be easily disproven. If a precambrian rabbit was found, that would completely disprove evolution. If we found out that the human gene for cytochrome C was more similar to an amoeba’s cytochrome C than to a chimpanzee, then that would disprove evolution. Every new gene sequence and every new fossil find could potentially disprove evolution, but none have. Until that time, we should teach evolution as it is, and not waste student’s time with pseudoscientific criticism that have no basis in reality.

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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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The Discovery Institute is missing something: reality

On, Aug. 5, 2008, Anika Smith writes that “Something is missing: evolution meets reality with Alife.” Smith is writing about a scientific conference on Artificial Life (Alife) being held in Winchester, UK.  Smith writes that the conference, or at least the article he links to, is focused on the “failure of Darwin’s theory to explain complex creatures.”

I am not usually this harsh on ID/creationists, but I just have to say that Anika Smith has no idea what is going on here. She thinks that the article is lending support to the rejection of evolution. In reality, it is showing the weaknesses of the current computer models:

Prof Mark Bedau of Reed College in Portland, Oregon, will argue at this week’s meeting – the 11th International Conference on Artificial Life – that despite the promise that organisms could one day breed in a computer, such systems quickly run out of steam, as genetic possibilities are not open-ended but predefined. Unlike the real world, the outcome of computer evolution is built into its programming.

So, the real world is open-ended and computer models are not. Got that? well Anika Smith doesn’t. We need to work on the programming, not turn away from evolutionary theory as Smith suggests.  Of course these types of computer models are beneficial to our understanding of biology, and the real focus of this article:

Although natural selection is necessary for life, something is missing in our understanding of how evolution produced complex creatures. By this, he [Bedau] doesn’t mean intelligent design

What does he mean? Dr. Richard Watson, co-organizer of the meeting, thinks it may be self-organization. The basic idea here is that atoms or chemicals can make complex arrangements without an outside force simply due to attraction and repulsion. I am sure that self-organization plays an important role in life, but I don’t know if these programs for evolution simulations include everything we already know about evolution.  Does it include such factors as genetic drift, bottle-necks, changes in available nutrients and/or toxins, isolation, etc.?

Smith falls back on the old argument that no one is taking intelligent design seriously (cry me a river):

Of course, no one would dare consider the possibility of design (especially not with that straw-man description), but it looks like a few brave souls may be willing to admit, in the face of the evidence, that Darwin’s theory really is not sufficient to explain life.

First, Darwin’s theory as it stood 150 years ago is dead and has been replaced by modern evolutionary theory. For crying out loud, Darwin did not even know of DNA or genes.  Yes, there are gaps in our knowledge, but there are problems with every theory. Second, evolution does not deal with the beginnings of life (abiogenesis). A fact that has been repeated numerous times, but ID/creationists still use this relic of a talking point. Finally, the evidence for evolution is continuing to pile up, not go the opposite way. Unless of course, you have your head buried in the sand, like so many at the Discovery Institute.

Really, Anika Smith dropped the ball on this one. Unless of course she completely understands the point of the article and is just trying to spin it to her liking. It is not like the Discovery Institute hasn’t done such a thing before.

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One step closer to a complete Tree of Life

The inability of scientists to create a complete Tree of Life (TOL) has been a talking point of ID proponents for some time. Indeed, a complete TOL based on DNA sequence alignments has yet to be completed. Instead of a single tree, usually ‘bushes’ of different clades are about as close as we have gotten. I don’t believe this is because it is impossible to make a complete tree that encompasses all known living organisms, it is simply another example of where the science is a work in progress. Molecular biology is in its infancy and the era of bioinformatics has just started. Nonetheless, IDers take our incomplete understanding as evidence against evolution (For the Discovery Institute’s take, see here and here).


These phylogenetic trees are made by taking DNA sequences from different organisms and aligning them with each other. Organisms that are closer evolutionarily will have more DNA in common and therefore the sequences will mostly match and be easily aligned. Organisms that are distantly related will have less similarities in their sequences. This is not an easy task and is fraught with error due to mutations that lead to an insertion of a piece of DNA, deletion of pieces of DNA, substitutions of DNA, etc.


In the June 20, 2008 issue of Science, Ari Löytynoja and Nick Goldman report a new and better way to align DNA sequences thereby creating better phylogenetic trees. Aligning DNA sequences is a mathematically complex process with several different algorithms designed to take into account small changes in the sequence. Don’t be scared, I am not going to bore you with the mathematical details (mostly because I don’t understand it).

According to the authors, the biggest problem with the current algorithms is that:

Traditional multiple sequence alignment methods disregard the phylogenetic implications of gap patterns that they create and infer systematically biased alignments with excess deletions and substitutions, too few insertions, and implausible insertion deletion–event histories”

Surprisingly, they found that simply adding more and more sequences from similar organisms did not increase the accuracy due to every additional sequence adding evolutionary time to the analysis and therefore more DNA deletions, insertions, or substitutions. This is where the authors say that their new method really shines due to its ability to utilize the phylogenetic relationship of sequences.


What does this all mean for the theory of evolution? Hopefully this will lead to better phylogenetic trees and bring us one step closer to that all important TOL. On the more technical side, the authors think that their new method will allow for a better understanding of the frequency of DNA insertions, deletions, and substitutions.