Today is the 5th Anniversary of Kitzmiller Trial

On December 20th, 2005, Judge John E. Jones III, ruled that it was unconstitutional to read a statement that discredits evolutionary theory and barred the teaching of intelligent design there.  This was the first, but probably not last, trial that involved the teaching of intelligent design as an alternative to evolution.

Its hard to believe that it has only been 5 years since the details and motives of the Intelligent Design (ID) movement were brought out to the public in a public trial.  We learned from staunch ID supporter Michael Behe that there are no peer reviewed published articles supporting ID.  We learned how the Discovery Institute’s”wedge document” essentially points to the idea that ID was brought up as a way to replace the scientific method with “a science consonant with Christian and theistic convictions”  We also saw how the book in question, Of Pandas and People,  had earlier versions where they simply replaced the word “creation” with “intelligent design.”  Of course there was more damming evidence against the ID proponents in the trial, but these three facts alone provide sufficient evidence that intelligent design is not science and should never be taught in the classroom.

Intelligent Design does not make predictions and is not science.

Since it has been so long since I last wrote a blog post, I thought that I ease back into blogging by attacking the lowest of the low hanging fruit from the Discovery Institute. Namely, the argument that Intelligent Design (ID) is real science.

Recently, Casey Luskin wrote a post discussing how ID proponents test their theory in real world situations.  Luskin provides a short list of four items (is that the most he could come up with?) that are supposed predictions of ID.  Lets take them one at a time:

(1) Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).

This is not a prediction. Life has already been seen to have “intricate patterns that perform specific functions.”  In fact, isn’t the complexity of life what made people believe ID in the first place?

(2) Forms containing large amounts of novel information will appear in the fossil record suddenly and without similar precursors.

It is rare to find any facet of an organism that doesn’t already have a precursor, let alone “large amounts of novel information.”  The prediction of ID should state that there will only be the instant appearance of new structures. Any evidence for a slow, gradual development of a structure would refute ID and prove evolution.  For example, you might see a fully formed tetrapod without any precursors if ID was true.  However, we see in the fossil record myriad examples of transitional forms from fish to tetrapod (Tiktaalik, Panderichthys, etc.).

(3) Convergence will occur routinely. That is, genes and other functional parts will be re-used in different and unrelated organisms.

This prediction seems odd to me. Convergence is a prediction of evolution. Take for example the convergence of the ability to fly. Evolution would predict that different organisms would gain the ability to fly, but they would achieve this ability by slightly different methods.  Luskin is predicting that structures would be re-used by different organisms.  Why do all wings look so different? Does a fly’s wing resemble a bird’s or a bat’s? Not at all.

(4) Much so-called “junk DNA” will turn out to perform valuable functions.

4) “Much?” Luskin should have said “all.” if we are to believe in intelligent design.  Why waste even a single nucleotide if you were to design an organism’s DNA? This sort of ambiguity is what makes these predictions worthless.

I think it is clear to see that the predictions put forth by Luskin are basically worthless for providing support that ID is real science.  What do you expect when you can give the “designer” any attribute, power, or foresight that you desire?

Intelligent Design proponents are not stupid

In talking with some of my colleagues about intelligent design (ID) it has become clear to me that there are some misconceptions about ID.  These misconceptions are not limited to science professionals as these ideas can also be seen when viewing message boards, reading comment sections, or anywhere else the subject arises.

The general consensus seems to be that ID proponents are just not very smart.  Although I do think this is true for some “IDers,” it is not a prerequisite for belief in the pseudoscience.  Just look at the Discovery Institute.  Many of the “fellows” there have PhDs or have achieved other higher levels of education.  Perhaps the most telling is how cogent their arguments appear to be.  I honestly think it takes some kind of weird intelligence to be able to defend a evidence-less theory against the onslaught  of ever increasing evidence for evolution.

Don’t get me wrong, I am not saying ID proponents are geniuses.  I am just saying stupidity is not the source of their belief in ID.  So, what are the sources?  Well, Christian fundamentalism is an obvious one.  These people are going to twist the world around them to their preconceived notion of the universe no matter what evidence is available.

Another source could be a strong reliance on the logical fallacy of personal incongruity (personal disbelief).  This logical fallacy basically says that just because someone has a hard time believing something does not mean it is not true.  People can not accept that we are evolutionarily related to monkeys.  Some people can’t believe that the diversity of life happened on its own.  They say “look how complicated life is. It had to be designed.” The feeling is so strong that they abandon reason and acceptable evidence for pseudoscience.

Willful ignorance is undoubtedly another reason that otherwise intelligent people believe in intelligent design.  Some people just don’t really care about the subject, so they will just go along with what there preacher or friend believes.  Other people are not willing to find out the truth for the fear that it will shatter their world view.

Whatever the reason, simply insulting their intelligence is not going to be an effective way to convince them of reality.  I didn’t write this post to defend ID proponents, I am just hoping that understanding where they are coming from will help during debates.

Did Darwin make faulty predictions on evolution?

David Klinghoffer has been interviewing Intelligent Design (ID) proponent and Discovery Institute fellow, Cornelius Hunter. They discuss Hunter’s new website, Darwin’s Predictions. The idea of the website is to illustrate how some of Darwin’s predictions have turned up false.

Before we get into the interview, let’s review a few of Darwin’s predictions and see how they fared:

• Transitional Fossils? Yes
• More closely related, the more similar? Yes
• Tree of life? Yes
• Biogeographic diversity? Yes
• Earth is at least several hundred million years old? Yes

As can be clearly seen by these overarching predictions, Darwin got a lot right.  In fact, he got enough right that any subsequent theory needs to take into account his basic premises.  Unfortunately, many ID proponents choose to ignore these proven ideas in favor of the smaller, more complex details that have yet to be proven.  Details which have not been worked out yet or might not ever be due to the constantly changing earth.  That is exactly what Hunter is doing with his website.  He is actually exploiting the process of science, which involves bad predictions and failed ideas, to illustrate his point.  Therefore, not much stock should be put into these so-called failed predictions.

So, Hunter’s premise is flawed, but let’s go ahead and get into a few examples of what Hunter is calling Darwin’s failed predictions.  One example is where Hunter describes the similarity of the squid eye and the mammalian eye as being a failed Darwin prediction:

dramatic similarities are sometimes found in otherwise distant species. The eye of the squid and the human, for example, are incredibly similar. Such design convergence is rampant in biology, in spite of the evolutionary expectation.

In such a situation, evolutionary theory predicts that they have common ancestor with genes necessary for basic eye development and the final shape will be a result of subsequent modifications.  This doesn’t seem like a failed prediction to me.

Anyway, are the eyes of squid and mammals really that similar?  So similar that they preclude an evolutionary origin?  On the surface, they do seem very similar, but when you delve deeper, the differences become clear and obvious. The most obvious is that the mammalian eyes have the light sensing layers of the retinal inverted compared to the squid eye.  Furthermore, the two eyes develop completely differently with the squid eye arising from a series of invaginations, while the mammalian eye forms from cell signaling.  Besides, how else are you going to make an effective eye?

Another example that Hunter gives of Darwin’s failed prediction comes from the relatedness of very conserved genes:

the finding of long stretches of identical DNA in distant species is a good one. Evolutionists have worked hard to figure out how this could be

Did I miss something? When did conserved stretches of DNA falsify evolution? Of course Hunter is really talking about how they are too conserved to be explained by evolutionary theory.  Since this is the exception rather than the rule, I don’t see how this is a failed prediction.

His next example:

Then there is the evolution of contradictory behavior patterns, such as altruism. Evolution has undergone a big makeover in the past fifty years in trying to explain such behaviors.

Altruism is pretty straight forward.  A social group of organisms helping each other out will survive longer than those that don’t.  Plus, there is also the punishment of those that don’t play by the societies rules.  You can even see altruism in one of the simplest of organisms, Dictyostelium. Some of these amoeba actually kill themselves so that others will be able to live.

These examples that Hunter provided are not very convincing.  None of them really falsify evolutionary theory.  They do show how some ideas of evolution were wrong, but they don’t come anywhere near falsifying the theory.

Since I have been on a roll of calling out the Discovery Institute for its hypocrisy, I might as well end up with another example. At one point, Klinghoffer says:

Darwinists are compelled to mold their interpretations of data to match the preconceived theory.

This comes from the same group that says that once wrote:

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.

Besides, not all evolutionists are atheists. Far from it.  Ever heard of Ken Miller?

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.

Conclusion

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.

Luskin can’t find a fact to support intelligent design (Part 2)

In the first part of my two part blog post addressing Casey Luskin’s assertion of the existence of facts that support intelligent design(ID), I analyzed Luskin’s overview of the framework for ID.  In that post, I concluded that the very ideas that intelligent design are grounded on are completely arbitrary and baseless.  In my second part, I was hoping to analyze real data that ID proponents bring forth when arguing for ID.  Unfortunately, I did not find anything that resembles a scientific argument from Luskin.

The purpose of Luskin’s post was as a response to students seeking to “find a fact” that supports ID.  However,  Luskin does not give any “facts” He gives generalities and provides post hoc explanations.  Phrases like “ID explains why” and “ID encourages” are in places where facts should have been.  References are included, but he never states one solid fact that came from these studies.

Facts would have been something like this:

• The fossils of Tiktaalik show bone structures that are a hybrid of water living and land living animals. They were found in a geological place and time that corresponds to a time shortly before fossils of land animals can be found.
• Genes between closely related species have a high degree of homology.  Less related species have less homology.

How hard would it have been to provide equivalent facts? Not very, provided there are real facts to back up intelligent design.  Since Luskin never provided any real information, I am not going to devote any more time to Luskin’s “facts.”