Friday Fisking: WW and ERVs

Yes, it’s the return of Friday Fisking. My first target is a chap calling himself William Wallace over at ERV. Some time ago, William left a comment in which he expressed skepticism that ERV data is justifiably used to support common descent. About a week later, he announced that he had made a model based on random insertion, and then asked for some help in creating an equivalent common descent model, with an aside that the results of the random model “doesn’t look good for your side.” This announcement was met with great derision, with calls for William to explain his conclusion. I directly addressed his question about his common descent model, pointing out where his assumption was incorrect. Even so, I remained puzzled as to how he achieved the results he claimed for both models.

Recently, it was brought up in relation to another post about ERVs. Although William refused to give any details about his model, he claimed that his results were unsurprising if you understood that math. He eventually offered to give me details via email. After a series of exchanges, I received enough information to be confident about the basics of his model.

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Caldwell Denied, Caldwell Wins

The most recent Establishment Clause lawsuit presented to the Supreme Court, Caldwell v. Caldwell (no relation), was denied a writ of certiorari by the Court today. The suit was filed by Jeanne Caldwell, wife of the infamous Larry Caldwell (who is known for filing frivolous lawsuits against teaching evolution). The defendant was UC Berkeley (coincidentally, the lead defendant is also named Caldwell), which maintains the Understanding Evolution website. The lawsuit was previously dismissed at the District and Circuit Court levels due to lack of standing. This denial of cert officially ends the lawsuit.

Gradualism, Contingency, and Punctuated Equilibria

Since Ed is in Vegas again, I offered to put up some guest posts to help alleviate the terrible burden being placed on him.  And today being Darwin Day, I thought I’d put up a post on evolution.

As a consequence of lacking data supporting their own explanations, creationists, like other denialists, have to rely on attacking perceived weaknesses in the mainstream theories.  A popular target arises whenever disagreements between scientists over aspects of the theory crop up.  These disagreements are then exaggerated so as to makeit seem as if the whole edifice is crumbling, when in reality it is just a minor difference in opinions, both of which can be explained by the theory.

In evolution, one such disagreement is between gradualism and punctuated equilibria.  Broadly speaking, gradualism is the idea that changes accumulate over time, while punctuated equilibria is the idea that there are short periods of lots of change interspersed among long periods of little change.  Since these two ideas appear to be contradictory, creationists love to use the debate over the two concepts as evidence that evolution is wrong.  However, the two concepts are not only not contradictory, under the right circumstances gradualism results in punctuated equilibria.

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And Now for Something Completely Different

Let’s take a break from litigation and turn our eyes on ligation. The type of ligation I am talking about is connecting two strands of nucleic acids (RNA in this case; a similar process with the same name takes place with amino acids) to make a longer strand. This is an important concept in origins-of-life research (and in biology), because it allows long strands with high information content to be assembled in shorter segments, kind of like a chemical assembly line. (Note that I am using “information content” in the sense of compressibility). In essence this allows Nature to reduce the odds against producing the right sequence of bases in a long strand. It’s generally much easier to reliably produce short strands than it is to reliably produce long strands.

Of course, it doesn’t do you any good if the shorter strands are simply connecting at random – this doesn’t reduce the probability. So what you want is a process that reliably connects the correct strands in the correct order. The process doesn’t have to be perfect, just better than random. One way to do this is by speeding up the ligation process for the right strands in the right order – in other words, use a catalyst. RNA has an interesting property – it has a “backbone” that strongly connects linearly, as well as matching base pairs that connect weakly. This means that RNA can act as a catalyst for itself – an autocatalyst. Are there combinations of short RNA strands that reliably catalyze into longer strands?

What would be even cooler is if the longer strand could act as a catalyst that takes the short strands and makes another long strand just like itself. That’s self-replication, the first step towards life.

Chemists at the Scripps Research Institute did just that.
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Sign the Petition!

As many of you may be aware, the Florida Science Standards are up for final review this month.  Many school districts have been passing resolutions in opposition to the proposed standards, because the standards are forthright about the role evolution and Big Bang cosmology play in biology and astronomy, respectively.  The Florida Citizens for Science have created an online petition in support of the standards.  You can view it here.  One good thing about the petition is that you can add your comments.  Note that the donations are requested only after your signature has been added – close the page if you do not wish to donate.  The following are my comments:

Many Florida school boards are crafting resolutions in oppostion to the proposed standards.  The opposition takes form in three major arguments.  The first is that evolution is no longer being taught as theory, but rather as “the fundamental concept underlying all of biology and is supported by multiple forms of scientific evidence.”  However, according to Benchmark SC.6.N.3.1, that is the definition of a scientific theory.  In fact, these school boards are promulgating the very misconception that benchmark is trying to avoid when it continues on to explain that “the use of the term theory in science is very different than how it is used in everyday life.”

The second argument is that if we are to teach evolution and Big Bang theory, we should teach other theories as well.  To which I respond, “Go ahead.”  But we must use only teach theories that meet the definition given in the standards – that is, scientific theories.  When pressed, these school boards either can’t provide alternate scientific theories, or else provide “theories” that do not meet the criteria set forth in the standards, but rather are theories only in the sense used in everyday life.  How do you teach a non-existent theory?  These alternate “theories” would be quickly exposed under Benchmarks SC.912.N.2.1-3 – imagine the hue and cry if they were included under those benchmarks!  It should also be pointed out that several benchmarks require students to understand the role alternative explanations play in developing science (e.g., SC.912.N.1.3).

The final argument is that we should “teach both the strengths and weaknesses” of the challenged theories, with thte implication that only the strengths are taught.  But the standards already do that.  The weaknesses of the challenged theories are no different than the weaknesses of the other theories in the standards that haven’t been challenged.  All one has to do is read through the Nature of Science standards to find these weaknesses.  Even within the Life Science standards, specific examples are given (e.g., SC.912.L.15.12).

It is apparent that these school boards are either not familiar with the standards they are purporting to improve, or that they are ignoring them in pursuit of an ideological goal.  This shows a disturbing contempt for the educational standards of Florida.  I urge the BoE to treat these resolutions with the same respect shown by the school boards – none at all.

I am also posting this as a comment at Panda’s Thumb.