Critical Thinking Needed in Science Education

Several recent articles noted that students are being dumbed down in science education.  Can this be applied to their learning about evolution?
    PhysOrg reported that critical thinking has been called into question at the university level of education.  “A post-secondary education won’t necessarily guarantee students the critical thinking skills employers have come to expect from university grads,” the article said of a recent study from New York University.  Other academics were surprised at the findings; they said students are motivated and curious as ever, spending a great deal of time on their studies.  But Richard Arum was not speaking of time spent or motivation, but of critical thinking ability.  His book “revealed 45 per cent of students made no significant improvement in critical thinking, reasoning or writing skills during the first two years, and 36 per cent showed no improvement after four years of schooling.”
    Science educators sometimes conflate knowledge with acceptance.  Jon Miller, from the University of Michigan, has tracked scientific literacy from 1998 to 2008, and found that it has actually improved, according to PhysOrg.  “Only 37 percent of American adults accepted the concept of biological evolution in 2008,” the article noted, “and the level of acceptance has declined over the last twenty years.”  It would seem, though, that understanding of evolution should be distinguished from acceptance of evolution – if critical-thinking students are able to judge the evidence and accept or deny the theory on the basis of sound reasoning.  According to his statistics, scientific literacy has grown while acceptance of evolution has declined.
    If applied uniformly, critical thinking should include evaluating claims of religion and science.  Religion is already routinely criticized, of course, but two recent articles on philosophy and history of science show how it might be applied to the latter.  New Scientist posted a short eyebrow-raising article by Jonathon Keats about how a group of four Victorian Englishmen, John Herschel, Charles Babbage, William Whewell and Richard Jones “invented” modern science over eggs and bacon (and ale).  Meeting at the Philosophical Breakfast Club, they reasoned how to take Sir Francis Bacon’s ideas on induction to create a new path to natural knowledge.  While admiring their “boundless curiosity,” Keats recognized that their vision was visionary: they “envisioned a future for science as visionary and elusive as Utopia.”  What’s more, their efforts led to a Big Science that became increasingly divorced from the humanities, he argued.
    Ken Conner, writing for Town Hall Magazine applied even more critical thinking to science.  The paradigm of the brave scientist as unbiased seeker of the truth, using an objective method, with unimpeachable motives, personal integrity, and the best interests of mankind at heart, is “beginning to crumble,” he said.  “As it turns out, scientists are just as fallible and flawed as the rest of humanity, and this fallibility impacts their work.”  Conner argued against the false dichotomy of science and faith, pointing out with examples that one needs faith to do science.  “After centuries of hegemony in an increasingly secular world, it is ironic that faith – faith in the right thing – may be the only thing that can restore credibility to the world of science.”
Case Study: Having a BLAST
An educational tool proposed in PLoS Biology can be evaluated for its effectiveness at teaching critical thinking.  Cheryl A. Kerfeld (Joint Genome Institute, Walnut Creek, California) and Kathleen M. Scott (UC Berkeley) wrote on how to use software to teach evolution: “Using BLAST to Teach ‘E-value-tionary’ Concepts,” they titled their paper.¹  BLAST (Basic Local Alignment Search Tool) is a common genome-comparison tool used by geneticists and evolutionists.  Kerfeld and Scott described ways students can learn evolutionary concepts, such as “molecular evolution (e.g., gene duplication and divergence; orthologs versus paralogs)” using the software.  As for what “E-value-tionary concepts” are, BLAST makes use of E-values, defined as “the number of subject sequences that can be expected to be retrieved from the database that have a bit score equal to or greater than the one calculated from the alignment of the query and subject sequence, based on chance alone.”  E-values calculated from program runs can help students see homologies as evidence of common ancestry, they argued.  In addition, BLAST has a pedagogical benefit, they argued, by providing “an opportunity to illustrate how mathematics functions as a language of biology.”
    But does their teaching tool illustrate or obfuscate?  Does their method teach students to be critical of the method?  Apparently not, because when E-values show common ancestry, the authors assume it supports evolution, but when they do not, critical thinking must be suspended by tweaking the inputs:

Sometimes it is helpful to “mask” parts of the query sequence to prevent them from being aligned with subject sequences.  Masking is helpful when the query sequence has “low-complexity” regions, such as stretches of small hydrophobic amino acids that are commonly present in transmembrane helices of integral membrane proteins.  Because these features arose from convergent evolution, and their inclusion in BLAST searches could result in spurious hits, it is best to set the BLAST search parameters to eliminate these sorts of regions from word generation, as well as alignment scoring.

So in this case, because the authors somehow “know” that certain features are due to convergent evolution, the data have to be masked when they would otherwise falsify evolution.  Evolution itself is protected from critical analysis; it must be assumed.  E-values that seem to indicate divergent evolution, by contrast, are not masked; they are accepted at face value as “meaningful” –

A meaningful alignment will facilitate the comparison of two sequences with a shared evolutionary history by maximizing the juxtaposition of similar and identical residues.  Sequences with a recent shared ancestry will have a high degree of similarity; their alignments will have many identical residues, few substitutions and gaps, and tiny E-values.  Conversely, sequences with an ancient common ancestor will be deeply divergent, with few shared sequence identities, many gaps, and larger E-values.  Furthermore, an alignment of two sequences can clarify which portions are conserved (e.g., active sites), and which are divergent, which helps cultivate students’ understanding of protein structure and function.

They seem to be saying is that sequence comparisons demonstrate common ancestry by evolution, except when they show convergent evolution or conservation.  The search for homologies can therefore whiz right past the genetic evidence that might falsify common ancestry.
    These scientist-educators seemed oblivious to the fact that homology as evidence for common ancestry is a circular argument.  Even creationists accept a hierarchical order of their created kinds, and would expect more divergent traits the more two organisms are distant within the hierarchy, without assuming those differences are due to common ancestry.  Yet Kerfeld and Scott seemed to insist that students be guided against falsifying evolution in the data:

Students (and researchers as well) tend to draw an arbitrary line below which they consider E-values to provide convincing evidence that two sequences are homologs (e.g., E<0.00001). >informative to scrutinize this assumption, and ask the students to consider whether and when more stringent E-values might be appropriate (e.g., to assist in sorting paralogs from orthologs), or when larger E-values do not provide definitive evidence of evolutionary independence (as is the case when two sequences share an ancient ancestor).
    It is also informative for the students to discuss what their alignments “mean”, and whether the pairwise alignments between their query sequence and the subject sequences “prove” whether the sequences are homologs.  Indeed, it can catalyze a larger discussion of whether it is possible to “prove” that two sequences are homologs, and what other approaches (e.g., protein structure, gene context) might be used to strengthen or refute such an assertion.

While the authors appear in this quote to support critical thinking, they have constructed their teaching method to guarantee that evolutionary theory itself is protected from criticism.  Basically, they want students to have a more nuanced way of manipulating the data statistics):

In summary, deconstructing the BLAST algorithm and manipulating parameters systematically and evaluating the results with students helps them understand not only what the scores mean but also how to manipulate parameters to optimize their searches…. Finally, explicating the algorithm in this way allows students to explore research databases thoughtfully and illustrates the critical connection between mathematics and science, showing how numbers can be used to quantify biological relationships from the level of gene to organism….

Dr. Cornelius Hunter, by contrast, had a good laugh over what he perceived as simplistic homology arguments being used to support evolutionary theory at another educational website, Understanding Evolution (produced by UC Berkeley, the same institution where Scott teaches).  “This Just In: Plants Have Leaves—Evolution Must Be True.” his headline quipped.  “As if evolution was not silly enough already evolutionists are now claiming that the fact that different plants all have leaves is a compelling evidence for their belief that all of nature just happened to spontaneously arise, all by itself,” he said.  “I occasionally enjoy a good spoof, but this is no joke.”  Readers can compare Hunter’s view with that of the Understanding Evolution website.
    Students wanting a course on evolution that will teach both sides might look at summer seminars on intelligent design presented by the Discovery Institute.

1.  Cheryl A. Kerfeld and Kathleen M. Scott, “Using BLAST to Teach ‘E-value-tionary’ Concepts,” PLoS Biology, 9(2): e1001014. doi:10.1371/journal.pbio.1001014.

Kerfeld and Scott provide another example of manipulating students’ impressionable heads with the illusion of scientific credibility in order to indoctrinate them into the cult of Charlie worship (cf. David Sloan Wilson’s “Evolution for Everyone” curriculum, 12/21/2005).  Evolution itself is never to be questioned; the objectivity of science itself is never under scrutiny.  This entry provides an opportunity for you to hear several points of view and evaluate which are credible with the fewest fallacies.
Exercise:  Apply your critical thinking skills to the following evolution articles:

• Science Daily: “New Research Changes Understanding of C4 Plant Evolution.”
• Science Daily: “Molecular Link Between Reproduction in Yeast and Humans.”
• Science Daily: “New View of Human Evolution?  3.2 Million-Year-Old Fossil Foot Bone Supports Humanlike Bipedalism in Lucy’s Species.”
• Live Science: “How Dinosaurs Handed Down Their Fingers to Birds.”