Wednesday, August 15, 2007

The importance of scientific rigor...

Once again, David Colquohoun (a noted physiologist at University College London), has a number of important points to make about the decline of logical and scientific rigor in daily discourse and institutions. Read his post in the Guardian, and check out his website.

As we approach science education, at all levels, we need to move away from generating the impression that science is about authoritative statements, and more about a critical, progressive, and self-correcting social process.

The first step is to encourage students to go beyond simple answers, and require them to state explicitly what assumptions they are making or are implied by their answer. They should then have the opportunity to consider which assumptions are well-supported, which are shaky, and where they might like (need) more data. In a way, you are asking them to perform a simple Bayesian analysis, in which they calculate the probability that their assumptions are correct (and so the strength of the data needed to make confident conclusions - weakly probable assumptions required more data!)

The process including making sure that they when they use a scientific term, they can explain what it means.

Tuesday, August 14, 2007

Critical thinking and the nature of science

There is a history of authoritative pronouncements by scientists. In the case of British and American geneticists, these led to the promulgation, particularly in the USA, of rather harsh eugenics (forced sterilization and restricted immigration) laws.

Similarly, there have been claims that educational interventions cannot and should not be used to address sociopolitical and biological inequities (see this link.

Most recently, there has been lots of borderline hysterical discussion about the dangers of global warming, and the need to commit substantial resources to the effort to avoid it reviewed here.

There is a recent post by Freeman Dyson on the need for clarity and balance in these discussion, that is, the need for a critical analysis of what the predictions are based on, what our certainty is in the models used, what the interventions will cost, what their likelihood of producing the desired effects will be, what benefits may in fact come from warming, what programs will suffer from the diversion of resources, and what immediate benefits could be attained with such resources.

This approach, of teaching science and science-based policy decisions through a rational and explicit analysis of assumptions, observation, predictions, confidence levels, and the costs of action and inaction, would go far to break down the illusion of scientific authoritarianism (black and white/right and wrong), and make science more accessible to a wider audience.

Friday, August 10, 2007

Memorizing elements, or proteins or pathways ...

There has been an interesting discussions going on on the NSTA chemistry listserv on ways to encourage students to remember the names of the elements. This reminds me of experiences I have had in teaching introductory molecular and cellular biology at the college level.

In dealing with fundamental issues like energy transformation, cell replication, DNA replication and mRNA translation, it is easy to be seduced into presenting (and testing on) detailed lists of components or steps. I believe there may still be questions on Biology AP exams dealing with the order of compounds in tricitric acid cycle (as if that matters to anyone but a biochemist working on the reactions involved). Similarly, it is possible to spend time on the names of stages of mitosis or meiosis, while leaving the students in the dark about what, of significance, is happening. For example, how can a chromosomal rearrangement (that has no other effect on phenotype) lead to sterility or reproductive isolation? A person who can answer this question correctly really understands meiosis (and how it differs from mitosis).

The end result is that students tend to accumulate a vocabulary, which they and their instructors often mistake for understanding - yet, when placed in a novel situation, they are unable to use that information to think productively about the problem at hand. How many students are asked to learn the genetic code, yet cannot understand how a non-sense suppressor mutation works? And a point coming out of our own research, how many students understand that the genetic code is an algorithm for reading information stored in DNA, and not the information itself? This is a point of great interest from a evolutionary perspective.

Luckily (or unluckily) at the college level, there are few constraints on what I should or should not "cover" (something that I believe is not the case for K-12 teachers.) I have been free to change content at will, and together with a growing understanding of the value of formative assessment, begin to understand whether students are actually getting it.

The end result has been Biofundamentals, a course that replaces the standard major's introductory course and uses interactive engagement methods and virtual laboratories (like this one on working with bacteria). Over the years I have been teaching the course, I have removed more and more superfluous content largely because the inclusion of these topics demands a substantial commitment to presenting background materials necessary for the concepts to be usable by the student.

For example, a discussion of RNA interference or non-sense mutation suppression demands (I would argue) a more thorough understanding of the details of mRNA translation and roles of untranslated regions in RNA turnover than can be attained in the time available in an introductory course - yet now many instructors feel that they must keep their materials "up to the minute" by the inclusion of such topics? As an aside, this appears to be a particular problem in biology, since few introductory physics courses deal with relativity or quantum mechanics.

It must be constantly kept in mind that there are real constraints on effective learning. A curriculum must understand those constraints, otherwise it will inevitably sacrifice conceptual (working) understanding for trivial memorization.

This is of practical importance at the K-12 level, where instructors are being forced to address various unrealistic standards in the teaching of science. Even a cursory analysis suggests that the coverage specified by most state and national standards are extremely over-ambitious, and so actually antithetical to robust learning.

Tuesday, August 07, 2007

Statistics and subjectivity in science

There seems to be a general misunderstanding about statistical significance versus real significance, particularly when it comes to health related issues. In this paper Facts versus Factions: the use and abuse of subjectivity in scientific research, Robert Matthews discusses the problem from an historical and statistical perspective.

Of particular interest is the discussion of Baysian analysis, which implicitly recognizes scientific subjectivity in its characterization of the probability that a particular hypothesis is correct.

A more recent discussion of this phenomena is found in Why Most Published Research Findings Are False by John P. A. Ioannidis.

Monday, August 06, 2007

The mathematics of biology

After some time off, writing grant proposals, papers, and the like, I am back.

A number of interesting issues have emerged, including the role of mathematical literacy in understanding (rather than simply accepting) evolutionary biology and molecular processes.

My thinking has been particularly impacted by the article by Michael Lynch in PNAS, entitled "The frailty of adaptive hypotheses for the origins of organismal complexity"(it is free to download the pdf.)

It is clear that genetic drift has particularly profound effects at the molecular level in small populations, such as typical of speciating metazoans. Similarly, there is a recent paper in PloS One Population bottlenecks promote cooperation in bacterial biofilms provides evidence for the importance of random events (in this case a bottleneck) in bacterial evolution.

Clearly, an important question to consider is "what mathematical topics should be mastered by biology students."