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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Splish, Splash, Draw Me an Extrasolar Bath

With all of the hoopla this week surrounding the announcement of the discovery of Gliese 581e (the smallest exoplanet yet discovered at 1.9 Earth-masses) and the refinement of the orbit of Gliese 581d (placing it firmly in the habitable zone of the Gliese 581 stellar system – meaning it may have liquid water at the surface), I thought I’d offer an engineering perspective. A number of sites have discussed the theoretically possible means of getting there. But what about realistic means of getting there?

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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.

I’ll Have the Mayo, Hold the Reuben

The academic blogosphere is buzzing with the recent discovery of a major incident of academic fraud.  Dr. Scott Reuben published 21 papers over the course of 12 years that have been implicated in the fraud, making this one of the largest cases of academic fraud ever discovered.  Worse yet, Dr. Reuben’s research is in medicine, throwing a primary method of post-surgical treatment into disarray.

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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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The Basics – Critical Thinking

A lot of blogs have a category in which they describe basic concepts pertinent to the subject matter.  I think this is a wonderful idea, and will sporadically indulge myself.  Here is the first of my basic concepts: critical thinking.

Critical thinking is once again entering the lexicon of the culture wars.  It is considered the gold standard of teaching, so it is understandable that various ideologies would like to wrap themselves in its mantle.  However, what these ideologists call critical thinking is but a pale ghost of what critical thinking really is.

Back in high school, one of my classmates complained to me that he couldn’t figure out how to solve the homework problems.  So I sat down and asked him to show me what he was doing so I could help him.  When I saw what he was doing, I was speechless.  Instead of solving the problem the way we were taught, he was trying to use the method we were taught to use to check our work.  You need to have an answer before you can check your work.  When I pointed out to him what he wa doing, we looked at me like I had grown two heads.  Why would we solve a problem we already solved?

The answer, of course, is to make sure we solved it correctly.  Checking your work is the least important part of finding a solution, but its vital to making sure that your solution is correct, that you understand how to solve the problem.

Creationists -including people who endorse intelligent design- and other conservative ideologists have made a major push to get “critical thinking” initiatives added to a number of science standards in the United States.  But like my classmate, their concept of critical thinking is limited to the solution check.  They believe (or possibly pretend) that critical thinking means “questioning what you have been taught or have concluded.”  But that is merely the solution check.  Its important to making sure that your answer is correct, but is useless in deriving your answer.

So what is critical thinking?  It is a multi-step, iterative process.  First you identify a problem, trying to discern the relevant questions and known and unkown data.  Then you take the knowledge that you have gained and apply it to the problem, looking to see if there are multiple approaches to take.  You then evaluate what you have done, trying to determine which approach is the most likely to produce a good answer.  You may need to try several approaches.  You then look at your answers to see if they make sense, and whether they suggest other questions to be asked.  Then and only then, do you sit down and ask if the knowledge you were applying can give the answer to the problem.

Ideologists want to skip to the last step.  They want people to conclude that the concept they despise doesn’t give a good answer, without actually going through the beginning steps.  And they want their ideology to get a free pass, for people to conclude that they have the better answer without any of the steps of critical thinking being applied.  In other words, they want rote memorization.

Obviously, in order to teach critical thinking, you have to have a knowledge base.  But how do we select that base?  In the tradition of critical thinking, you let a bunch of people loose on the problems and see if they can reach a general consensus on the solutions by applying critical thinking.  This consensus does not require unanimity.  Those solutions that achieve a general consensus become part of the knowledge base.  You then teach that knowledge base, and show the students how to properly apply all the steps of critical thinking.  Only after they have mastered the art of critical thinking do you start to introduce them to solutions not in the general consensus or that have not been subjected to or have failed rigorous critical thinking.  This level of mastery is not normally reached until college. 

To make it short and to the point, the question we need to be teaching them to answer is not “How does x explain y?” or “How could x possibly explain y?”

The question they should be learning to answer is “How would x explain y?”