Discovery Institute has no goal (posts)

One thing you have to love about the Discovery Institute is their constant hypocrisy. Take for example, the recent post by Jonathan Wells, entitled Moving the goalpost.

For those of you unfamiliar with the logical fallacy of moving the goalpost, it describes a situation where one party says that if certain specific goals are met, then something is proven.  However, when those goals are met, the group changes the goals or adds qualifiers.

For clarification I will take an example from this particular post.  Many if not all Intelligent Design proponents (IDers) have said that there are no examples of speciation observed in living organisms.  Scientists have pointed to the speciation of different plants by polyploidy as an example.  Not being satisfied with this, Jonathon Wells now says that such examples do “not produce the major changes required for Darwinian evolution.”

Now that I think about it, maybe hypocritical isn’t the best word to use here.  IDers don’t engage in moving the goalposts, because they do not really have goals or specific ideas. In fact, it has been said that ID is not interested in who, what, where, or why of the intelligent designer. Without any such characteristics, it is impossible to test the idea of ID. This lack of goals is exactly what makes ID a pseudoscience.

Getting back to Wells’ current post, it is obvious that he is not paying attention to current evolutionary theory.  First, he says that the theory of evolution “has only one rule: survival of the fittest.”  This is not what the theory of evolution states. Its actually more about reproductive success than fitness.  Besides, there are other factors involved including genetic drift and geographic isolation.

He then goes on to say that evolution is “unguided.”  No, it is guided by survivability. Calling evolution unguided is like saying that a train is unguided.  Sure, there is no steering wheel to control it, but there is no doubt that the train is steered by the rails that it sits upon.  These are central tenets to evolution and it is really surprising that Wells wouldn’t know them.

Wells claims that the Scientific American’s Steve Mirsky is engaging in moving the goalposts.  He takes a recent tongue-in-cheek example by Mirsky of calling each dog breed as its own species:

face it, the only shot a male Chihuahua has with a female Mastiff involves rock climbing or spelunking equipment.  Biologists clearly continue to include the two types of dogs within the same species out of modesty. But with creationists fighting evolution education throughout the country, the time calls for bold action. Let’s reassign the trembling, bug-eyed Chihuahua to its own species. Voilà, humans have observed speciation.

Wells responds:

Voilà, indeed! If we cannot find evidence for the origin of new species, let’s just call dog breeds separate species. If Darwinism is in danger of losing, let’s just move the goalpost!

Is this post a joke? Mirsky was definitely joking. He even says so in his podcast.  Wells presenting this as a true argument put forth by evolution proponents is dishonest and deceitful.


Luskin can’t see the reality of evolution for the trees (part 3)

Part 3 – Analysis and rebuttal (cont)

This post is the third part of a three-post series aimed at clearing up the misinformation written by the Discovery Institute’s Casey Luskin in regard to phylogenetic trees and  the idea of a complete tree of life (TOL).  In parts 3, 4, and 5 of Luskin’s series, he continues his bastardization of the evidence for evolution.

In part 3, Luskin discusses what he calls “extreme genetic convergence.”  The problem is that he confuses genetic convergence with heredity.

One data-point that might suggest common design rather than common descent is the gene “pax-6.” Pax-6 is one of those pesky instances where extreme genetic similarity popped up in a place totally unexpected and unpredicted by evolutionary biology. In short, scientists have discovered that organisms as diverse as jellyfish, arthropods, mollusks, and vertebrates all use pax-6 to control development of their very distinct types of eyes.

Having the same gene controlling eye development in different organisms is completely compatible with evolutionary theory.  This gene (pax-6) could have controlled the development of a very simple eye, perhaps a patch of photosensitive cells, in a common ancestor.  Subsequent organisms would use the foundation laid by pax-6 and add their own specific modifications to yield different eye types.  Luskin’s assertion here that pax-6 argues against evolution makes no sense, except for someone who is actively looking to twist data to their preconceived notion.

Luskin is also outright wrong when he says that pax-6 is used to “control development of their very distinct types of eyes.”  Pax-6 is necessary for eye development, but it does not influence the type of eye made.  For example, if you take the mouse pax-6 gene and put it into a fruit fly, the fruit fly makes fly eyes, not mouse eyes.  It is clear Luskin is either confused or is misrepresenting the facts.

Homology is evidence against evolution?

In part 4, he argues that homology between animals, both at the molecular level and at the physiological level, is a problem for evolution.  Luskin doesn’t really do any of his own work, but instead quotes from the Explore Evolution “textbook”:

To summarize, biologists have made two discoveries that challenge the argument from anatomical homology. The first is that the development of homologous structures can be governed by different genes and can follow different developmental pathways. The second discovery, conversely, is that sometimes the same gene plays a role in producing different adult structures. Both of these discoveries seem to contradict neo-Darwinian expectations

Neither discovery contradicts the theory of evolution.  It doesn’t matter the path that a gene or structure takes to be effective, it just matters that it is effective.  Explore Evolution is trying to take an interesting facet of biology and say it disproves evolution without really showing how common descent precludes these features.

Let’s turn the tables and ask what do these two discoveries mean for intelligent design? Well it means that here is another example of stupid design. I say stupid because what designer would use “different genes” and “different pathways” to come up with the same structure. That would be a monumental waste of time and effort for the designer. How about using the same gene for different functions? Well, that is better design, but it goes completely against the first point.

Morphological vs. phlyogenetic trees

In part 5 of Luskin’s series of posts, he claims that morphological data does not correlate with phylogenetic trees.   Maybe they don’t fit exactly, but the similarities are so common that it is ridiculous to think they are not due to common ancestry.  Like I mentioned in part 1, there is a lot of problems associated with the creation of mathematical models used to predict phylogenetic trees. Likewise, trees based on morphology are subject to their own problems.

To make his point, Luskin actually refers to the gene (cytochrome B) that I had picked in part 1 of my series of posts.  Using the sequence of this gene from different ape species,  I was able to produce the exact same phylogenetic tree as had been done using endogenous retroviruses.   What does Luskin say about cytochrome B?

pro-evolution textbooks often tout the Cytochrome C phylogenetic tree as allegedly matching and confirming the traditional phylogeny of many animal groups. This is said to bolster the case for common descent. However, evolutionists cherry pick this example and rarely talk about the Cytochrome B tree, which has striking differences from the classical animal phylogeny.

I didn’t look throughout all of “classical animal phylogeny,” but I was able to create evidence for common ancestry using cytochrome B that matched both morphological and molecular evidence.  Without common ancestry, this should not have been possible.

One final point. Whenever someone looks up scientific articles, it is best to look at the newest articles for obvious reasons. Yet Luskin did the exact opposite.  To help make his point here, Luskin quotes from several scientific papers that were published around the turn of the century.  One is even from 1993.  These papers came before the genomics era and before automated sequencing was common.  They do not really belong in this discussion.


Through his series of posts, Casey Luskin tries to portray the state of phylogenetic analysis as being counter to the theory of evolution.  I hope that I have showed that the opposite is true.  While we don’t have and may never have a complete tree of life, the data that we obtain creating trees or bushes is points squarely to common descent.

Luskin can’t see the reality of evolution for the trees (part 2)

This post is the second part of a three-post series aimed at clearing up the misinformation written by the Discovery Institute’s Casey Luskin.  In his recent posts, Luskin tries to persuade his readers that the idea of a tree of life (TOL) and the very idea of phylogenetic trees is erroneous and not evidence of common descent.  These trees are created by looking at genetic similarities between organisms to arrange them in terms of relatedness and common ancestry.  In my series of posts, I will expose the weaknesses in the arguments put forth by Luskin.

Part 2 – Analysis and rebuttal

In this second part of my three-part series on the realities of the TOL, I will provide rebuttals to Luskin’s points.  These points were written in Luskin’s part 1 and part 2.

One of Luskin’s points in his post is to question the motives and biases of scientists.  Here, Casey Luskin claims that scientists assume there is a tree of life so their findings will support their preconceived notions:

the first assumption that goes into tree-building is the basic assumption that similarity between different organisms is the result of inheritance from a common ancestor

Of course this is a ridiculous proposition.  I guess Luskin has completely forgotten all about Charles Darwin and all the study into evolution since that time.  Prior to Darwin, common ancestry was not an idea that had any credence.  Sine the time of Darwin, more and more evidence keeps adding to Darwin’s idea basic ideas of common descent.  Basing ideas on evidence is not the same thing as assuming.

Luskin also contents that scientists engage in ad hoc reasoning:

whenever data contradicts expectations of common descent, evolutionists resort to a variety of different ad hoc rationalizations to save common descent from being falsified

No. What scientists do is to take this new information and form new hypothesis and alter the details of evolution. Science is always changing.  Finding unexpected things is what makes science interesting and nothing is gained in science by keeping ideas that have been proven wrong.

As far as saving “common descent from being falsified,” evolution is easily falsifiable.  Find a rabbit in the precambrian and all of evolution will fall apart.  Find genes in humans that more resemble cockroach genes than any mammal.  However, one result like this would need to be critically analyzed to go against years of research and thousands of experiments.

I find it hilarious that he uses the idea of “ad hoc reasoning” to criticize evolution. The whole idea of intelligent design (ID) is ad hoc reasoning. Any result or any piece of data can be simply said to have been designed that way. There are no predictions or testable hypothesis in ID.

In his second post, Luskin draws heavily on the false idea that scientists are abandoning the tree of life.  A lot of his all comes from the dreaded New Scientist article, “Darwin was wrong.”  I am not going to go into the details as many others have shown that the article was inaccurate to say the least here, here, here , and here.

In addition to heavily quoting the New Scientist article, Luskin “quote mines” from several different scientific papers.  One of the more egregious examples comes from a 2005 science paper by Rokas et al.  Luskin says:

Other scientists agree with the conclusions of the New Scientist article. Looking higher up the tree, a recent study published in Science tried to construct a phylogeny of animal relationships but concluded that “[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.”

Luskin neglects to mention that the next couple sentences:

In contrast, the same genes robustly resolved phylogenetic relationships within a major clade of Fungi of approximately the same age as the Metazoa. The differences in resolution within the two kingdoms suggest that the early history of metazoans was a radiation compressed in time, a finding that is in agreement with paleontological inferences.

Luskin fails to mention a few critical points in the article.  He ignores the fact that a well constructed tree based on Fungi can be made.  Also missing is the fact that the authors came up with a hypothesis to explain the previous data. Finally, Luskin fails to mention that the authors provide for a better way to look create phylogenetic trees when problems arise, rare genomic changes.

Luskin continues the quote mining throughout the post, but he never really says anything favors an intelligent design perspective.  He is just using the tried and true method of ID proponents, namely to find the currently unresolved issues in the scientific literature and omit the overwhelming number of successful findings.

The Story of Jesse Kilgore and his exploitation by the Discovery Institute


On the Discovery Institute’s podcast, ID the future, there is a tragic story of how Jesse Kilgore took his own life.  Jesse was a college student who had spent most of his life as a devout and involved Christian who loved to debate people about his beliefs.  He was even had a couple of of blogs to his credit.  He had already spent some time in the military and by all accounts appeared to have a great life ahead of him.

According to the podcast, he was challenged with reading Richard Dawkin’s The God Delusion by one of his professors.  His studies into the theory of evolution, as well as Dawkin’s book, appeared to have changed his worldview.  Jesse stopped believing in god, which led to him questioning everything he had previously believed.  Although he left no suicide note, many believe that this change is what led to his death.

The Discovery Institute wasted no time in blaming Jesse’s death on the belief in evolution.  This is another example of their use of fear-mongering to persuade people that evolution is evil.  They have even blamed the horrors of the Nazis on evolution. Yet, their exploitation of Jesse or even the holocaust victims does nothing to show that evolution did not happen.  Besides, there are hundreds of millions of people that believe in evolution that have not taken their own lives or become evil because of it.  Furtherore, Jesse had already made references to committing suicide well before his new encounters with evolution and Dawkin’s book.  Putting the blame on the theory of evolution and its proponents is simply wrong.

On a personal note, I also had a relative take his own life.  I understand the pain that Jesse’s family must be feeling.  I also understand the need to blame anyone and everyone for his death.  This is why it angers me to see the Discovery Institute use this tragedy for some small gain in pushing their pseudoscientific fairy tale. They should be ashamed.

Egnor still insists eugenics is based on evolution

Over at Space City Skeptics, I wrote a blog post criticizing Discovery Institute fellow Michael Egnor’s claim that the only thing evolutionary theory has given medicine is eugenics.  Several other blogs were also critical of this ludicrous idea. Now, Egnor has responded to blogs such as Respectful Insolence, Pharyngula, and my Space City Skeptics post.

In his post, Egnor still still claims that the theory of evolution led to eugenics.  He even goes so far as to call eugenics, “Darwinian medicine 1.0.”  The whole idea is ridiculous.  Eugenics is essentially human breeding, and we all know that animal breeding preceded Darwin by thousands of years.

Egnor implies in his first post that a conference on evolution and medicine was somehow being kept a secret. He said that he is “having trouble finding the program.”  However, details of the conference were are already available on Pharyngula:

(P.Z.) Myers notes that he had posted the conference schedule a while back, which I missed. Sometimes my Internet Content Filter screens out Pharyngula, so it’s not always easy keeping up. I’ll have to dial down the ‘bigotry’ and ‘casual obscenity’ settings.

Notice how Egnor puts the blame for his own ignorance on someone else?  Shouldn’t he have accepted some blame, or better yet, have actually done some research before coming to the conclusion that the conference was being hidden?  This is typical of the Discovery Institute and similar Intelligent Design proponents.  They want to have their conclusion first without finding out the reality.  It is called willful ignorance and is at the core of many of the ID talking points (i.e there are no transitional fossils).

In order to exert some sort of authority on the subject, Egnor goes on and on about how he is a professor of neurosurgery and has a lot of experience in medicine.  However, he is too far removed from basic science to really see how the ideas and knowledge obtained through evolutionary theory really effect his work.  I know this from my own personal experience. I used to work in a neurobiology lab and took a medical neuroscience class. The med class wasn’t anywhere near the level of depth where evolution would be important.  There is just too much other information that is more relevant to being a doctor. It wasn’t until I started studying microbes and their relation to each other and higher life forms that it became obvious of that evolutionary theory permeates nearly everything one does at that level even if it isn’t explicitly stated.

Egnor goes on to say:

My own experience with medical research and education is that medical practice is a very effective check on b.s., because in medicine ideas often have immediately obvious consequences.

If this were true, we wouldn’t need large randomized, double-blind studies for the evaluation of medicines.  We also wouldn’t need to show any result by several different methods before they can be taken seriously.  There are just too many uncontrolled and unknown variables that can’t be accounted for in experiments.  The fact that Egnor doesn’t understand this fundamental property of doing proper science is an example of the improper mindset that ID proponents have.

Of course he doesn’t really address the myriad of reasons why evolutionary theory benefits modern medicine that I and others pointed out.  He does however argue that medicine is just fine with only knowing the “proximate” explanations for diseases, etc. In other words, he believes that doctors and research scientists only need to know the “what” of biology.  Again, Egnor misses the fact that we would not have the knowledge that we have today if it weren’t for evolutionary theory.

Egnor finishes his post with more of his anti-scientific and anti-intellectual prejudice.  He says:

The purpose of the evolutionary explanations is to provide jobs and grant money for evolutionary biologists — a kind of academic workfare for Darwinists-still-seeking-relevance.

This kind of statement would be really funny, if this type of attitude didn’t lead to the general decline of science.  We can see these negative attitudes effect on education, on basic research, and even the perception of the United States.

The Discovery Institute’s Wedge Document Revisited

It has been almost 10 years since the Discovery Institute (DI) created a fundraising proposal called the “Wedge Document.” This proposal included 5 and 20 year plans by the DI for its “Center for the Renewal of Science and Culture.”  The proposal was somehow released on the internet without consent from the DI.  Since then, many people have used this as a smoking gun to show that the DI is promoting religion in not only science but other areas of society.  Books have even been written on the subject.

To be honest, I had not given much credence to the accounts of the wedge document.  However, I decided to read the document to see what the fuss was about.  What I found in the proposal actually shocked me.  I was expecting to find some hints of religious undertones, but with the majority being focused on fleshing out intelligent design as a science.  This is what I found:

Design theory promises to reverse the stifling dominance of the materialist worldview, and to replace it with a science consonant with Christian and theistic convictions.

Alongside a focus on influential opinion-makers, we also seek to build up a popular base of support among our natural constituency, namely, Christians. We will do this primarily through apologetics seminars. We intend these to encourage and equip believers with new scientific evidences that support the faith, as well as to popularize our ideas in the broader culture.

They really spelled it out in those two passages:  The Discovery Institute is focused on pushing a particular Christian view and not on discovering the reality of life on Earth.  It couldn’t be any more clear.

Despite their transparency, the DI has released several documents and blog posts that can only be described as damage control.  One is simply named “The Wedge document: So what?”

In this document, they make the argument that the Wedge document was innocuous and saying otherwise is simple paranoia:

For many the scandal of the Wedge Document is nothing more and nothing less than its mention of “Christian and theistic convictions” and our stated intention to support scientific research that is “consonant” with such convictions.  But why should this be upsetting?”

It is not that it is upsetting to those of us on trying to push an unbiased view of science, it is that they are admitting that they are not impartial to the science.  It shows that they are incapable or unwilling to not let the data take them in whatever direction it will. Their thinking has to fit into a box based on their preconceived notion of reality.  A better approach, and an intellectually honest one, is to say that they will support the science no matter what information it yields.

They continue:

Recent developments in physics, cosmology, biochemistry, and related sciences may lead to a new harmony between science and religion.  Many of us happen to think that they will, and we are not alone in that.  But that doesn’t mean we think religion and science are the same thing.  We don’t. Nor do we want to impose a religious agenda on the practice of science.

Fair enough, they don’t want to impose a theocracy on science, but it does not matter what your intentions are if you are starting from a biased position.  If they want a real harmony between science and religion, they should just keep the two separate.  Or better yet, take the advice of Abdu’l-Bahá:

There is no contradiction between true religion and science. When a religion is opposed to science it becomes mere superstition: that which is contrary to knowledge is ignorance

In light of this new information, I find it hard to believe that so many at the DI still deny the association of intelligent design and religious underpinnings.  It also shows that their science can never be fully trusted until they divorce themselves from their boxed in view of reality.

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Discovery Institute’s award for best indoctrinator

Randy Moore, Ph.D.

Randy Moore, Ph.D.

The Discovery Institute has given an “award” for “Most Dogmatic Indoctrinator In An Evolutionary Biology Course.” Personally, I think that this post deserves an award for “stupidest pretend award.”  Since when is teaching reality indoctrination?  Seriously, an intelligent design proponent talking about indoctrination makes my head hurt.

Randy Crowther starts off the post with this outlandish statement:

It seems that dogmatic Darwinists will now applaud efforts to consistently suppress scientific criticism of modern evolutionary theory.

No. Evolutionists applaud efforts to suppress pseudoscientific criticisms of evolutionary theory, but real criticisms and unanswered questions are welcomed. Pretending that unanswered questions, logical fallacies, and willfully ignorant remarks are valid criticisms is preposterous.  Yet that is all that intelligent design proponents bring to the conversation

The Discovery Institute gave this “award” to Randy Moore, Ph.D.  Besides a quote from Dr. Moore, Crowther doesn’t really state why he is guilty of indoctrination.  Here is the quote:

“The evidence supporting evolution is overwhelming and comes from diverse disciplines, such as molecular biology, paleontology, comparative anatomy, ethology, and biochemistry. There is no controversy among biologists about whether evolution occurs, nor are there science-based alternative theories,” states Dr. Moore. “Evolution is a unifying theme in biology; teaching it as such is the best way to show students what biology is about and how they can use evolution as a tool to understand our world. [Evolution] is as important an idea as there is in science – it is a great gift to give to students,” says Dr. Moore.

I wanted to include the quote because he made a couple of really important points.  The first is how so many different disciplines provide support for evolution.   Having evidence coming from so many different directions makes a strong theory.  Moore also brings up how there is no controversy among scientists.  Also good for a theory when so many people support it.  Finally, he talks about how using evolution to explain how certain aspects in biology arose leads to a deeper understanding of the world around us.

Obviously, the Discovery Institute disagrees:

First the evidence supporting evolution isn’t as overwhelming or mountianous as Moore claims. Jonathan Wells proved this with Icons of Evolution which still causes conniption fits for Darwinists. More recently, the new supplementary biology text from Hill House Publishers, Explore Evolution,

Is he seriously going to say that two unscientific books (Icons of Evolution and Explore Evolution) can discredit the work of thousands of scientists?  There is a mountain of evidence for evolution, despite Crowther’s willful ignorance.

Crowther continues:

Second, there’s no knowing what Moore means when he says there’s “no controversy … Obviously there is no controversy over microevolution, change over time. But there is huge controversy among scientists over evolution if you mean macroevolution. Witness the Dissent from Darwin list where hundreds of scientists proclaim their skepticism.

A fraction of scientists in unrelated fields saying they don’t believe in evolution is meaningless.  The vast majority of relevant scientists do believe in evolution (see Project Steve).  Does the fact that people literally believe in astrology, aliens living among us, or a hollow earth mean that there isn’t a consensus against those things?  Of course not and the same is true for evolution.

Besides, there is no real difference between micro- and macroevolution in evolutionary theory.  Small changes over short periods equals large changes over long periods.  It is an artificial distinction made for convenience similar to microeconomics vs. macroeconomics.  What happens at the micro scale effects what happens at the macro scale.

Crowther’s last point:

Third, Darwinian evolution is not a theory of everything. To claim it the unifying theory of all biology is laughable.

Moore did not say that it was a theory of everything.  He said “Evolution is a “unifying theme in biology.”  Just like supply and demand in economics, evolution can explain a good deal of the aspects of biology: included but not limited to antibiotic resistance, vestigial organs, gene homology, phylogenetic trees, and geographically isolated species.

Crowther concludes with:

It’s pretty pathetic when a scientific theory like Darwinism has to be propped up through indoctrination. Worse, those who lie to their students will now be rewarded for doing so. Orwellian isn’t it.

What is pathetic is that there is a group of people so desperate for evolution not to be true that they are willing to deny the most logical theory and the evidence that supports it while supporting a theory based on absolutely no evidence.  It is pathetic to call someone a liar for teaching the only theory with evidence to support it.

I personally don’t know Dr. Moore, but after seeing him get this award from the Discovery Institute, I would love to meet him and shake his hand.

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