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.

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?

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.

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.

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.

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?”

2nd Summary Judgment – Followup

This is a brief followup to my previous post.  In addition to the numerical error, there was some confusion from my readers about the use of the original expert witness reports.  The original expert witness reports, which were timely, covered the seven courses named in the complaint.  However, they did not address the as-applied challenges to the individual course rejections, only the facial challenges to the policies.  When the plaintiffs finally identified the 41 course rejections they were challenging, they dropped two of the original seven from the list, and then three more after UC objected.  This left 33 new courses (not offered by Calvary Chapel), four original courses offered by Calvary Chapel, and one original course not offered by Calvary Chapel.  ACSI submitted supplemental reports/affadavits (they submitted them as both types of documents just in case one type was precluded) for all 38 of the courses, this time arguing specifically for the as-applied challenge (and specifically for unreasonableness).  The judge rejected the supplemental reports, leaving only the original reports for the 5 remaining courses named in the Complaint.

As I noted, these original reports only addressed the facial policies.  The evidence offered in a facial challenge can be used to demonstrate that the policy, on its face, is unreasonable.  But once that policy is determined to be reasonable (as was determined in the first partial summary judgment), the evidence offered must demonstrate that the course would not have been rejected by a reasonable person working under the guidelines of the policy.  In other words, did the course meet the requirements listed by the policy?  That is an entirely different kettle of fish.

So the plaintiffs tried to shoehorn their old evidence into the new standard of review.  The problem was, for each course, the evidence they provided failed to demonstrate that they had met the listed requirements for that type of course.  For example, one of the requirements for a literature course is that whole works be used as the primary text, not anthologies or short stories.  Rather than argue that they met the “whole works” req, ACSI argued that the other courses approved by UC had used texts by the same authors in the anthology ACSI used.  This analysis also failed to address whether the works of those authors in the approved courses were whole works or part of anthologies.

Of particular interest to many of my readers is the biology course.  Although UC challenged this course based on standing*, the judge declined to address the standing issue for this course (and since it was based on prudential standing, not constitutional standing, the judge could use his discretion on the issue).  Dr. Behe, a familiar face to those following creationism, provided the expert report. The portion of his report that ACSI offered up tried to demonstrate that the Christian textbooks met the state BOE standards as well as certain secular textbooks.  He did this by analyizing whether a topic was mentioned in the books (even going so far as to include misreperesenting a scientific claim as mentioning a topic, because a teacher could use that as a launching point for further discussion! – though he didn’t quite word it that way, of course).  His criteria was merely a mention of the concept, openly admitting “I did not consider how much detail or depth a text went into on a given standard.”  See pages 2-3.  The problem, aside from using a standard that UC is not obligated to accept, is that doesn’t meet the requirement for content – and Behe acknowledged what that requirement was.  Behe cites the requirements on page 17-18:

Certification Categories.  Generally, courses that are suitable for satisfying the minimum requirement will fall into one of three categories: 

1. College preparatory courses in biology, chemistry, or physics.
2. College preparatory courses which may incorporate applications in some other scientific or career-technical subject area, but which nonetheless cover the core concepts that would be expected in one of the three foundational subjects.  A few examples could include some courses in marine biology or agricultural biology, which may qualify as providing appropriate content in basic biology; and some advanced courses in earth and space sciences, which may provide suitable coverage of chemistry or physics.  These are only examples; other possibilities exist.  Hoever, it is emphasized that courses in this second category must cover, with sufficient depth and rigor, the essential material in one of the foundational subjects in order to qualify for “d” certification.

Behe then follows with the following observation: “It seems clear from this description that the university’s prime concern is that the “essential material in one of the foundational subjects” must be covered…”  Correct, but Behe neglected to mention the part about “with sufficient depth and rigor” – which he previously admitting not having evaluated.  Behe failed to produce evidence that the rejection was unreasonable because he abdicated the discussion of whether the course met the stated requirements.

In a similar vein, ACSI had no evidence for the unreasonableness of other course rejections.  The evidence ACSI produced was merely “a thin veneer” quickly destroyed by the judge.

 

*Allowing myself to get distracted tracking down whether UC objected to the course is the root cause of why I made the numerical error in the previous post.

-Edited for wordpress display issues (stupid indents not working with numbered lists)

2nd Summary Judgment In ACSI v. Stearns

On Friday, August 8, 2008, Judge Otero entered summary judgment against plaintiff ACSI in the Christian course evaluation case.  This resolved the remaining claims made by ACSI; the judge had entered partial summary judgment back in late March.  In a subsequent posting, I will analyze the earlier summary judgment.  This post is for last Friday’s ruling.

I have uploaded the ruling from the PACER online casefile (the only change being to rename the computer file) for the reader’s convenience.

acsivuc-ruling

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.