Functions of endogenous retroviruses does nothing for intelligent design

Scanning electron micrograph of HIV-1 (in green) budding from cultured lymphocyte.

On August 21, 2008, Casey Luskin wrote Large Scale Function for Endogenous Retroviruses: Intelligent Design Prediction Fulfilled While Another Darwinist Argument Bites the Dust. In this post, Luskin uses a recent article in Bioinformatics by Conley et al. to attack a piece of evidence brought up by Douglas Theobald in his 29+ Evidences for Macroevolution. This article can be found at TalkOrigins, and is a must read for anyone who is interested in the evolution debate.

Short response:

Luskin is not really addressing the evidence provided by Theobald. Luskin says that new evidence shows that endogenous retroviruses have function. Theobald never addressed this issue. Therefore, Luskin’s point is moot and should be disregarded as such.

Full Response:

The piece of evidence in question here concerns the presence of endogenous retroviruses (ERVs) found throughout genomes. When a retrovirus (such as HIV or HPV) infects a person, the virus gets incorporated into the person’s DNA. If a germ cell gets infected by one of these viruses, then it will become part of the offspring’s genome. Once it has become part of the genome, it is endogenous and will be passed down to successive generations.

Because these ERVs are passed down to offspring, one should be able to trace the introduction of different ERVs through evolutionary history by examining phylogenetic trees. As pointed out by Theobald, this is in fact what we see when we look at the ape family or the felines. We never see an ERV in the same position in two different distantly related apes without seeing it in the intervening species. So this provides strong support to evolutionary theory. An excellent overview of this can be found in episode 113 of the Evolution 101 podcast.

So how does Luskin try to disprove this evidence? He discusses the Bioinformatics article that points to ERVs affecting transcription of genes. Luskin states:

Douglas Theobald claims that “Endogenous retroviruses provide yet another example of molecular sequence evidence for universal common descent.” The presumption behind his argument is that endogenous retroviruses (ERVs) are functionless stretches of “junk” DNA that persist because they are “selfish”-but they have no function for the organism… The force of Theobald’s argument thus depends upon the premise that ERVs are selfish genetic “junk” that do not necessarily perform any useful function for their host.

However, this is not at all the point of Theobald’s argument. He says nothing about whether the ERVs are able to affect the function of genes. This is clearly a strawman that Luskin created for his uninformed readers.

The focus here is not if the ERVs have a function, it is do their positions in the genome match what a phylogenetic tree would predict.  The fact that ERVs affect gene expression is not unknown or unexpected. For one thing, retroviruses utilize their host cell’s machinery to express their own genes. So if the retrovirus gets put into the genome near another gene, why wouldn’t it affect the gene?

The real thing to ask yourself, or someone from the Discovery Institute, is why a Designer would need to put the skeletons of retroviruses by genes to effect its expression?  Other genes do not have these remnants of retroviruses and seem to function just fine.  This should really be the focus of someone interested in reality, but we know proponents of intelligent design are not interested in what is going on.

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The History Channel’s Evolve

The History Channel has been running a series called “Evolve.”  The basic premise of the show is to take a subject, such as eyes or skin, and trace its path through evolutionary history.  I can not guarantee its scholarly detail, but the show does seem to be accurate.  The renderings of ancient life is really well done and interesting bits of trivia are sprinkled throughout the show.  If you have not seen the show yet, I highly recommend you checking it out.  Here is a list of upcoming episodes.

The multiverse and evolution, related only in the minds at the Discovery Institute

On August 11, 2008, Casey Luskin veers away from his usual posts of misunderstanding and misreporting of evolution to talk about a subject that is completely unrelated to evolution: the theory of the mulitverse.  This theory states that there might be an infinite number of parallel universes that each differ by small variables.  As he says:

this speculative idea was invented for the purpose of avoiding the conclusion that the cosmos was intelligently designed

Does Luskin really think that scientists (many of whom are religious) sit around thinking of ways to disprove God? Does Luskin have any proof that this is the case? Of course not. This technique of accusing scientists of trying to destroy God by making up theories is ridiculous and has been a talking point against evolutionary theory.

But how did the theory arise? I really don’t know, but it does seem to fall out from what we know of quantum mechanics and the inflation shortly after the big bang.  Michael Clive Price wrote a FAQ explaining how the mulitverse actually resolves many paradoxes found in quantum mechanics.

Luskin continues:

the hypothesis was constructed in order to explain away the improbability of our universe’s physical laws, which are finely-tuned to permit the existence of advanced life.

Ignoring Luskin’s denial that the hypothesis came out scientific observations, another possibility that Luskin does not offer is that there is some fundamental property that forces the physical laws to be compatible with each other. This property would lead to the inevitable values that we currently measure.

Even more damaging to Luskin’s argument comes from a recent paper published in Journal of Cosmology and Astroparticle Physics. Fred Adams, a physicists from the University of Michigan have come up with new calculations that seem to indicate that nearly a 1/4 of combinations of physical constant values results in universes that contain the stars and planets.

Of course Luskin’s post about the multiverse has nothing to do with evolution. Evolutionary theory does not deal with the beginning of the universe. It doesn’t even deal with the beginnings of life on Earth. So why is Luskin posting this on an evolution blog? Because many ID proponents equate evolution with atheism. Therefore, any topic that equates science with atheism is a win for intelligent design.

Rejecting Evolution, a path back to the dark ages

Journalist Denyse O’Leary wrote an op-ed in the Calgary Herald defending “Albertans right to reject Darwinian evolution.” It really should have been called “Albertans right to be ignorant of modern biology and medicine and a small step back towards the Dark Ages.” She is attacking a column by Rob Breakenridge where he is disturbed by the lack of belief in evolution in Alberta, Canada.  She says that he should not have written “about big topics without basic research.” O’Leary should take her own advice.

She starts by giving us her take on the 2005 Kitzmiller trial. This is the trial where it was ruled that Intelligent Design was essentially creationism and therefore violated the Establishment Clause of the US Constitution.

The 2005 Judge Jones decision in Pennsylvania, to which Breakenridge devotes much of his column, has not crimped the worldwide growth of interest in intelligent design. That is no surprise. A judge is not a scientist, and Jones cannot plug gaping holes in Darwin’s theory of evolution.

O’Leary is using one of ID proponents newest arguments to deflate the impact of the Kitzmiller trial. They are fond of pointing out that Jones isn’t a scientist. Well guess who else isn’t a scientist? That is right, Denyse O’Leary.  Instead, she is a “Toronto-based journalist; grandmother; Roman Catholic Christian.”  Don’t you just love the hypocrisy?

O’Leary then makes some audacious comments:

Evolution is—contrary to its (largely) publicly funded zealots— in deep trouble, for a number of reasons….Textbook examples of evolution often evaporate when researchers actually study them

And who do you think brought us these results that contradict earlier findings? Yes, scientists. Scientists who supposedly are stuck in the dogma of Darwinian evolution. Challenges to what we thought we knew is what makes Science the best way we have of looking at the world. But lets look at a few of the examples that O’Leary gives that supposedly “evaporate.”

One example that O’leary points to is the disappearance of eyes in the blind cave fish. As PZ Myers pointed out, this adaptation to living in a lightless environment is actually due to an increase in the expression of a particular developmental gene, sonic hedgehog.  This change leads to a stronger jaw with better sensory structures.  Both these changes are quite advantagous for searching for food in dark caves where eyes are useless.

O’Leary even has the gall to make a reference to Michael Behe’s Edge of Evolution (2007) where he

notes that for decades scientists have observed many thousands of generations of bacteria in the lab. And how did they evolve?  Well, they didn’t.

Apparently, O’Leary doesn’t mind lying here saying that no evolution has been observed. As many of you will recall, evolution was observed in one such experiment by Richard Lenski’s group. They observed the gain of the ability of E. coli to utilize a food source (citric acid) that it could not use before. This story was all over the evolution and intelligent design circles. We can forgive Behe here because his book was published before Lenski’s paper, but O’Leary is just being dishonest.

O’Leary goes on to quote polls that show that only 37% of Albertans accept evolution. She even says “Well, good, let’s drive the numbers lower still.” Not only does O’Leary ignore evidence contrary to her position, misconstrue scientific findings related to evolution, and outright lie about recent findings, but she wants people to be scientifically illiterate.

Picking sides: Evolution or Intelligent Design

In a scientific debate such as Intelligent Design vs. Evolution, it is important to know each side’s qualifications. Since the discussion is largely based on scientific principles, it seems prudent to determine the level of science education and accomplishment on each side. It is also important to look into each side’s possible motivation. Finally, it may be important to see what each side gains if their side wins or how much they lose if their side loses.

Lets start with the most important aspect: qualifications. Not every evolution proponent is a practicing scientist, but there is a substantial number of them that are. Without a doubt, the discoveries that are made to further evolutionary theory come from well-trained scientists. These scientists all have PhDs in the respective fields (paleontology, botany, biology, molecular biology) and publish articles in peer-reviewed scientific journals. They spend their whole lives devoted to finding out the reality that underlies the world around us.

Intelligent design proponents, like those from the Discovery Institute, are rarely scientists. Have a look for yourself here. Most either specialize in philosophy/religion or in government/public policy. Even in their most scientific blog, Evolution News and Views, there are only three PhDs in fields related to evolution out of the 15 contributors.

These qualification alone should be enough to give someone interested in the intelligent design debate reason to swing towards the evolution side. However, we shouldn’t stop there. What about each side’s motivation? Both groups claim to want to find the truth of life’s origins and complexity. However, if we look again at the backgrounds of the contributors to the Discovery Institute’s evolution blog, other motivations become clear. Ignoring the fact that nearly a third of the contributors are outright theologians, we see that even the scientists mentioned above have religious motivations. For example, Jonathon Wells has a PhD in religious studies. Cornelius G. Hunter, another of the scientists mentioned above, wrote the book Darwin’s Proof: The Triumph of Religion Over Science. I think it is pretty clear that many intelligent design proponents have religious motivations and are not simply looking for reality.

Finally, let us look at what each side gains or loses if their side wins. If intelligent design is clearly and forever proved wrong, the Discovery Institute and similar intelligent design proponents will have to find new jobs. This is clearly a strong motivator to persuade people to their side. If evolution is proven wrong, intelligent design proponents will enjoy wider recognition and the vindication they lust after. Evolution proponents will have to shift focus to studying ID principles, but likely will keep their research positions. These two scenarios show how ID proponents have a bigger stake in this debate.

From the above comparisons, I think it is pretty clear that the evolution side should be the side to trust.

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I thought it was called “intelligent design”

In his August 13, 2008 post entitled The Proper Rebuttal to the Flying Spaghetti Monster: Cartoon Satire on South Park, Casey Luskin attacks the use of the Flying Spaghetti Monster (FSM) as a way of disproving intelligent design. He uses a scene from Southpark to prove his point, but somehow I don’t think that he really gets it. FSM was used in the Kansas evolution hearings as an argument that it could just as likely be FSM behind intelligent design as God. The FSM argument, at least in my opinion, is more about religion vs. atheism.

The theory is called intelligent design, not God design. So why does Luskin talk about God in a blog about evolution and intelligent design? For one, we know that almost every person in the intelligent design movement believes that God is the intelligent designer, but they can’t say so because it would preclude teaching ID in schools. It also gives them the talking point that they are really doing science and not religion because they do not usually state that God is the designer. They also try to invoke fear in their readers. Reading between the lines, they are stating that if you believe in evolution, then you do not believe in God. Of course the two ideas are not mutually exclusive (unless you believe the every word in the bible is literal). They should start calling their pet theory God design. If they do, at least they will finally be honest about it.

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Top 10 Intelligent Design Tactics

Note:This post is written with respect to Poe’s Law.

Here are the top ten ways that ID proponents can further the cause of elevating Intelligent Design to a level where it is accepted at or above Darwinism.

  1. Teach the controversy – Contrary to what Darwinists say, there are still gaps in the theory of evolution.  These areas that have not been fully explored create gaps in the theory and are perfect for intelligent design to fill.  Don’t mention the fact that these gaps are getting smaller and smaller with each new experiment.
  2. Ignore evidence – When a new study supporting evolution comes out, simply ignore this new evidence.  If you never talk about it, people might not know it exists!  Also, pretend old lines of evidence don’t exist either.  A good example would be if someone asks about transitional fossils.  Don’t acknowledge the myriad of examples, just say that there aren’t any.
  3. Spin evidence – Whether or not new evidence supports evolution, it should be considered as evidence of design.  Although ignoring evidence is still preferable.
  4. Evolution is just a theory – Remind people that Darwin’s theory of evolution is just that: a theory.  Since it is just a theory, then it has not been proven 100%.  Do not mention that it is a strong theory that has withstood 150 years of scrutiny.
  5. Science is a religion – Tell people that science requires as much faith as religion.  Scientists don’t question, they just blindly trust what other Darwinists are saying.
  6. The designer is not necessarily God – If intelligent design is ever to be taught in schools, it has to be distanced from religion.  Tell people you don’t know who is the “Designer.”  Say it could be God, but could also be aliens or someone else entirely.  Do not mention how nearly every organization promoting ID is full of Christians.
  7. Confusing people with math – People have a hard time with large numbers.  Simply say that the odds of life beginning on earth by itself are something like 1 in 100 trillion.  Don’t worry about there being absolutely no basis for these numbers.
  8. Academic freedom – Take advantage of the politically correct times in which we live.  Everybody loves freedom! Disguising your motives to teach intelligent design as science under the sign of freedom.  They wouldn’t want to deny you any freedom would they?
  9. Promote analogies – With analogies, one can convey an idea or convince another person without having any real evidence.  Plus you can twist any analogy to look like it supports any conclusion you want.  For example, you can say that the eye looks exactly like a camera even though the eye has a blind spot and the detectors are located underneath layers of cells.
  10. Do not generate hypotheses – If you make a hypothesis, then that will open the door to actual experiments being done.  This is undesirable due to the odds of success being so low.  Stick with using the above propagandist techniques.

If i have missed any techniques that should be added to the list, please let me know.  If you need to learn more about Poe’s law, find out here.

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