Michael Behe compares apples to oranges while waiting for two mutations

Plasmodium malariae

Plasmodium malariae

A recent scientific article published in Genetics criticized Michael Behe and “exposed flaws” in his thinking.  The article in question, Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution, provides a mathematical model of the rate for two different mutations to occur in order.  They show that the time for prespecified mutations is within reason and support this by using two real world examples from humans and fruit flies.  Behe doesn’t believe it.

Behe had previously calculated the mutation rate that makes the protozoan P. falciparum (causes malaria) resistant to the antibiotic chloroquine that arose from two prespecified mutations in one protein.  He argued that this would take 1,000,000,000,000,000 years to achieve a similar pair of mutation in humans based on human population numbers and age until reproduction.   He seems to think that this is evidence to support intelligent design.

There are several problems with Behe’s thinking.  The most obvious is that Behe is comparing completely different organisms.  The mutation rate between various organisms can be very different.  In writing this post, I quickly determined from following the links from Wikipedia that the error rate of other protozoan (not specifically P. falciparum) seems to be around 100 fold lower than humans.  Not exactly the best comparison is it?

Other errors in Behe’s thinking include

  • Behe calculated the requirement for prespecified mutations; Evolution is not prespecified
  • These mutations could have arisen many times without our knowledge.  Unless Behe knows the sequence of every single P. faciparum, he can not really know how often these mutations occurred
  • Behe’s calculations seem to make the common statistical error of treating two consecutive events as one event.  For example, the odds of a couple that already have two girls having another girl is still 1 in 2, not 1 in 8 like you would get if you asked what are the odds in the beginning of having 3 girls

The original authors had many other complaints against Behe’s assessment, but they are fairly technical and beyond the scope of this blog.  If your interested, follow the links below.  Even without these criticisms, it is clear that Behe’s mind is being clouded over by the motivation of having an intelligent designer.

One interesting thing to note is that the authors actually call out Michael Behe by name in the abstract. I actually think this is semi-unprofessional. At the same time however, I think it also shows a lot of gumption. They must have known that not only would Behe respond with sharp criticism.

Further reading:

Behe’s blog

Behe’s response to Rick Durrett and Deena Schmidt

Durrett and Schmidt’s response to Behe’s response

Waiting for Two Mutations

Behe’s 2007 paper on the subject

A typical Intelligent Design proponent series of events

Upon examination of the many intelligent design (ID) proponent attempts to spin real science into something that supports ID, I have come up with the equivalent of a business plan for ID:

  1. Real scientific research finds something new
  2. Scientists have different hypotheses on what is going on
  3. Newer research rules out some of the old hypotheses
  4. Discovery institute says scientists were wrong and ID was right
  5. profit

Past examples of such a nonsense view of the progression of science include junk DNA and endogenous retroviruses,  A new example can be seen in a recent blog post by Casey Luskin entitled Nature Paper Shows "Junk-RNA" Going the Same Direction as "Junk-DNA" In this post, Luskin tries to persuade his audience that a recent discovery of a function for some “junk-RNA” supports ID.  It simply doesn’t.  For a nice critique of Luskin’s ideas check out the sandwalk blog, by evolutionary biologist Larry Moran,

Lets look at the series of events according to the ID proponent business plan outlined above::

  1. Scientists find some RNAs that do not have any known function
  2. Some scientists believe these RNAs must have some unknown function, others believe they could just be junk
  3. Recent Nature paper shows some of this RNA has a function (~5%)
  4. Discovery Institute’s Casey Luskin says: see, this is what ID predicted, a function for these RNAs (doesn’t mention that is only 5% of them)
  5. profit

Of course the new research supports evolution. These new small RNA’s have  "over 95% showing clear evolutionary conservation."  Wow, that sure does disprove evolution and prove intelligent design right? Doesn’t it?

Discovery Institute once again shows us that it is all about ideology

Human embryonic stem cell

Human embryonic stem cell colony

The Discovery Institute’s Evolution News and Views blog often leaves the realm of evolution.  Whenever it does, you can be sure that the subject will be politically or religiously motivated.  The fact that the Discovery Institute takes up these subjects not involved with evolution shows that they are not really interested in knowing the real science.  They just want to push their ideology.

In Logan Gage’s recent post entitled New Administration Displays Old, Naïve Understanding of Science, Gage engages in the typical language used in partisan attacks, including references to the “hard Left” and the “anti-Bush mantra.”  In the post, he is arguing how questions of embryonic stem cell research “involves questions of a moral and prudential (political) nature.”  So why is he arguing this in a blog dedicated to the discussion of evolution?  Gage tries to somehow link this to a discussion of evolution education, but it is clear this is a ideologically motivated post.

Not only is Gage focusing on something that should not have anything to do with evolution, he is being very mismleading:

President’s decision to have taxpayers (many of whom are morally opposed) fund new embryo-destructive research

As of right now, the Dickey-Wicker Amendment is still in effect, therefore embryos will not be created and destroyed for this research.  Even if this law was repealed, human embryos are destroyed during in vitro fertilization procedures.  The most likely source of new embryonic stem cells will be these discarded embryos.  Gage is not even giving half the story here.

Gage also quotes a Robert George and Eric Cohen article:

It is red meat to his Bush-hating base, yet pays no more than lip service to recent scientific breakthroughs that make possible the production of cells that are biologically equivalent to embryonic stem cells without the need to create or kill human embryos.

First, it is too early to really know if these cells are biologically equivalent to embryonic stem cells.  We shouldn’t shut any doors because of a few new studies.  Secondly, Obama does more than pay “lip service” by making a promise to support

promising research of all kinds, including groundbreaking work to convert ordinary human cells into ones that resemble embryonic stem cells.

No matter where you fall in the embryonic stem cell debate, it is clear that the Discovery Institute is complacent with spreading misinformation on any subject.  How on earth does anyone believe these guys are honestly trying to pursue science?

Repost of deleted New Scientist article critical of creationism

Update: As Tony points out, I do not know the circumstances for the withdrawal of the article.  My best guess was that is was from a creationist group, but it could have been for any reason.

(from Lamda Delta: Tony Sidaway’s blog)

This article was deleted from New Scientist due to pressure from creationists groups.  If you disagree with this censoring, let New Scientist know.

Amanda Gefter

New Scientist

Sat, 28 Feb 2009 22:35 UTC

As a book reviews editor at New Scientist, I often come across so-called science books which after a few pages reveal themselves to be harbouring ulterior motives. I have learned to recognise clues that the author is pushing a religious agenda. As creationists in the US continue to lose court battles over attempts to have intelligent design taught as science in federally funded schools, their strategy has been forced to… well, evolve. That means ensuring that references to pseudoscientific concepts like ID are more heavily veiled. So I thought I’d share a few tips for spotting what may be religion in science’s clothing.

Red flag number one: the term “scientific materialism”. “Materialism” is most often used in contrast to something else – something non-material, or supernatural. Proponents of ID frequently lament the scientific claim that humans are the product of purely material forces. At the same time, they never define how non-material forces might work. I have yet to find a definition that characterises non-materialism by what it is, rather than by what it is not.

The invocation of Cartesian dualism – where the brain and mind are viewed as two distinct entities, one material and the other immaterial – is also a red flag. And if an author describes the mind, or any biological system for that matter, as “irreducibly complex”, let the alarm bells ring.

Misguided interpretations of quantum physics are a classic hallmark of pseudoscience, usually of the New Age variety, but some religious groups are now appealing to aspects of quantum weirdness to account for free will. Beware: this is nonsense.

When you come across the terms “Darwinism” or “Darwinists”, take heed. True scientists rarely use these terms, and instead opt for “evolution” and “biologists”, respectively. When evolution is described as a “blind, random, undirected process”, be warned. While genetic mutations may be random, natural selection is not. When cells are described as “astonishingly complex molecular machines”, it is generally by breathless supporters of ID who take the metaphor literally and assume that such a “machine” requires an “engineer”. If an author wishes for “academic freedom”, it is usually ID code for “the acceptance of creationism”.

Some general sentiments are also red flags. Authors with religious motives make shameless appeals to common sense, from the staid – “There is nothing we can be more certain of than the reality of our sense of self” (James Le Fanu in Why Us?) – to the silly – “Yer granny was an ape!” (creationist blogger Denyse O’Leary). If common sense were a reliable guide, we wouldn’t need science in the first place.

Religiously motivated authors also have a bad habit of linking the cultural implications of a theory to the truth-value of that theory. The ID crowd, for instance, loves to draw a line from Darwin to the Holocaust, as they did in the “documentary” film Expelled: No intelligence allowed. Even if such an absurd link were justified, it would have zero relevance to the question of whether or not the theory of evolution is correct. Similarly, when Le Fanu writes that Darwin’s On the Origin of Species “articulated the desire of many scientists for an exclusively materialist explanation of natural history that would liberate it from the sticky fingers of the theological inference that the beauty and wonder of the natural world was direct evidence for ‘A Designer’”, his statement has no bearing on the scientific merits of evolution.

It is crucial to the public’s intellectual health to know when science really is science. Those with a religious agenda will continue to disguise their true views in their effort to win supporters, so please read between the lines.

Egnor’s response to Jerry Coyne is false, misleading, and deceitful

Michael Egnor has posted a reply to Jerry Coyne’s criticism of him in regards to an article he wrote for Forbes magazine.  His reply is filled with the usual Intelligent Design (ID) tactics that we have grown to know and love.  The post is found on the Discovery Institute’s evolution news and views blog and is entitled: My Reply to Jerry Coyne: Why Darwinism is False.

This post really bugged me. Almost every single sentence in this piece of garbage is wrong.  It is filled with logical fallacies, misrepresentations of evolutionists point of view, and denial of evidence.  Jerry Coyne astutely pointed to the evidence for evolution and the reasons not to believe in this repackaged creationism called intelligent design.  Egnor is really grasping at straws to come up with decent counter arguments.  He fails.

Lets start by reviewing Coyne’s excellent points in support of evolution (as illustrated by Egnor):

  • basic tenants of evolution are undeniable to genuine scientists
  • ID proponents are decades out of date on research
  • ID proponents are blinded by faith
  • Fossil record shows transitional fossils, like those predicted by Darwin
  • Dead genes illustrate a record of evolution 

Of course there is more to Coyne’s article than what I have listed, and I suggest you read it.  For the rest of this post, I am going to quote directly from Egnor’s post and respond appropriately.

As evidence for Darwinism, Coyne cites the fossil record. But the fossil record lacks the innumerable transitional forms predicted by Darwin’s theory.

The dozens of transitional forms found already is not enough for Egnor  The fact that these fossils are found in predicted paleo-geographic regions is fantastic evidence to support evolution.  This is simple denial of the evidence.

Coyne cites the existence of “dead genes” as evidence for Darwin’s unguided process and evidence against intelligent design. But data from the genome projects show that most—perhaps all—of what was previously thought to be “junk DNA” is in fact functional.  Following Coyne’s logic, the recent scientific literature actually provides evidence against Darwinism and for intelligent design.

No. There are still "dead genes" There is still a lot of "junk DNA" that still has no known function. Much of the DNA that ID proponents call “junk DNA” has had known functions for decades.  Besides, even if every single molecule of DNA had a beneficial function, that would not disprove evolution in the slightest.  How does this provide evidence for intelligent design? I guess because the only supposed evidence for intelligent design is when there are perceived weaknesses in evolutionary theory.

But ID claims only that we can infer from evidence that some features of living things are better explained by an intelligent cause than by unguided natural processes. ID is not an argument from ignorance, and it does not explain things by saying “God did it.”

They “infer”?  So essentially he is saying is that they have a gut feeling that things are designed but no evidence.  They are essentially saying, we don’t understand how something could have arisen without being designed.  Isn’t that an argument from ignorance?  Besides, how is describing poorly-designed systems a better explanation than evolution?

biomolecules translate the DNA code into functional proteins such as enzymes. Still other molecules are motors, or energy-producing factories, or intricate surface channels that regulate the cell’s interactions with the outside world. Darwinists claim that all of this originated from random mutations and unguided natural selection, without design.

NO! it is not unguided. it is guided by survival and reproduction. Is their a stronger mode of selection? I don’t think so.

Yet there isn’t a single detailed, evidence-based explanation for the evolution of any biomolecule from primordial precursors. All Darwinists have to offer are “just-so” stories about how biomolecules might have originated.

If that isn’t the definition of an argument from ignorance than I don’t know what is.

We have extensive knowledge of computer codes, motors and energy-producing factories. All of them are designed. The more we learn about living cells, the more they look like things that can only be made by design

As someone who studies the internal workings of living cells, I disagree. The more we look at living cells, the more it looks like a haphazard collection of molecules. It has to work or it would be either dead or out-competed by a better system.

Modern cell biology implicitly accepts this and consists essentially of reverse engineering.

How else are we going to figure something out? Besides, it actually isn’t true. There is a whole new field of biology where the scientists are trying to artificially synthetic cells.

Darwinists detest intelligent design theory because it is compatible with belief in God

No, we detest intelligent design because it is pseudoscience with the only thing backing it up is this gut feeling that things look "designed."  Even if every single person studying evolution were Satanists, the data is still points to evolution..

Putting words in scientist’s mouths like only the Discovery Institute can

The Discovery Institute’s evolution news and views blog has a post by Casey Luskin entitled "Science Paper admits evolution mechanism of ‘adaptive radiation’ lacks empirical evidence." The post is referring to a review article published in the February 6, 2009 issue of Science by Sergey Gavrilets and Jonathan Losos. The review, in actuality, is calling for more studies to be undertaken to look at adaptive radiation.  Nowhere in the article does it say that there is no empirical evidence for adaptive radiation.

Adaptive radiation is when an ancestral group undergoes rapid diversification into different ecological niches leading to groups with great diversity. After a period of time, these new groups become different species.  Typical examples include the Anolis lizards, African cichlids, and Hawaiian silverswords.  Darwin’s finches are considered a group in the earliest stages of adaptive radiation.  Unfortunately, the triggers for adaptive radiation are not fully understood and varying modes of adaptive radiation have been proposed.

In typical anti-science/pro-intelligent design style, Luskin completely misrepresent the authors’ intent. The Science review never admitted that "adaptive radiation lacks empirical evidence." This is just a fabrication by Luskin.  It even says in the abstract that there is empirical data (emphasis mine):

Some of these[modes of adaptive radiation] are strongly supported by empirical work, whereas for others, empirical support is more tentative. In almost all cases, more data are needed. Future progress in our understanding of adaptive radiation will be most successful if theoretical and empirical approaches are integrated, as has happened in other areas of evolutionary biology.

As you can plainly see, the authors are not saying that there is a lack of empirical evidence, but that there are many areas that still require more data.   The review even lists the sources of empirical data, which include fossils, phylogenetic comparisons, microevolutionary studies, and the use of model organisms in the lab.  Luskin really just made this whole lack of data thing up.  I guess since intelligent design has no empirical evidence to support it, he wants everyone to think the same thing about evolution. 

The review article does claim that there is a real lack of effort in studying adaptive radiation, as can be seen in the above quote,  However, Luskin seems to think that this lack of studies equals a deficiency in positive data for adaptive radiation and therefore evolution.  Lack of studies and a lack of data are two completely different things. If the studies have never been undertaken, then we won’t have data either way.

I am not really going to go into it, but this post by Luskin is filled with quote mining.  He literally takes a conclusion to a single idea and says that it applies to adaptive radiation as a whole.  Compare for yourself (if you have access) and you will see just how disingenuous Luskin is being.

A couple of times, Luskin refers to adaptive radiation as a “magic wand that can be waved over the history of life.”talk about the pot calling the kettle black, How can Luskin have a problem with the magic wand idea when the whole theory of intelligent design is based on it?

Intelligent design really is creationism

When I first started to read about intelligent design, I bought into their story about how creation and intelligent design (ID) are different.  They said that ID is a scientific theory based on the idea that their is apparent design throughout nature, while creation is an unscientific viewpoint based on religion.  They argued that certain aspects of biology are irreducibly complex and the amount of information present could not have arisen by chance.  Thee factors all show the trademarks of an intelligent agent, but that they did not know who this intelligent agent is or was. 

My gut feeling was that nearly every ID proponent thought that the designer was in fact God, but I was willing to give them the benefit of doubt.  However, after following the movement for some time,there is no question that it is in fact creationism repackaged.  ID is unscientific and based on religion.  Below I have listed some of the evidences that made me come to this conclusion.

Of Pandas and People

In order to understand a movement such as ID, it is important to look at its beginning.  The textbook, Of Pandas and People, is one of the earliest examples of where the ideas of ID are laid out.  The textbook, first published in 1989 includes both ID and evolution.  This sounds perfectly reasonable until you look at the history of the book. 

During the 2005 Kitzmiller v. Dover trial, the history of the book was unveiled by Barbara Forrest.  It was clearly shown that the book was originally written as a book based on classic creationism.  The trail from creation to intelligent design in Of Pandas and People is clearly laid out.  One of the most damning (and funny) pieces of evidence came from one of the early versions of the book.  In that version, it was apparent that the authors had simply replaced the word creationists with design proponents.  Forrest found a place where the words ‘design proponents” were put into the middle of the word “creationists.”  This botched cut and paste job resulted in the words “cdesign proponentsists.”  For a more detailed discussion and other pieces of evidence check out Barbara Forrest’s testimony.

The Wedge Document

In 1999, the Discovery Institute wrote up a funding proposal called “the wedge document”  This document made in no uncertain terms that they were creating a “science” that is “consonant with Christian and theistic convictions.”  The motivation of ID proponents has become clear.  They don’t want to seek truth; they want to wedge their world view into science.   

Anti-materialism

Many ID proponents are aggressively attacking materialism, the philosophy that everything can be explained by physical causes without the need for the supernatural.  If we took intelligent design at face value, then there should not be any problem with there only being the material world around us.  Remember that we are told by ID proponents that the designer is not necessarily God.  It is only when you assume that a supernatural being such as god had his fingers in the creation of life on earth that materialism is excluded. 

Anti-atheism

Similar to the anti-materialism stance mentioned above, intelligent design as they have sold it should accommodate a world view without God.  Yet, there is a steady anti-atheist presence throughout the movement.  If they were true to their word and be truly independent of creation and God’s influence, then the atheistic view would be as welcomed at the religious view. 

Conclusion

Above is just a short list of the evidences linking creation and ID.  More can be found at the NCSE or from Barbara Forrest’s site.  I am still unsure of whether or not the proponents of ID realize that it is simply creation.  Maybe they realize it, or maybe they don’t.  It doesn’t really matter.  As someone from the outside looking in, intelligent design is creation evolved.