Flame war in the Durango Herald!

A while back, a reader mentioned that my name (or some permutation thereof) was being taken in vain in the letters pages of the Durango Herald. Nothing new there, it’s just the usual half-truths of the Discovery Institute being disseminated.

Challenges to evolution met with scorn

I find that some of the brightest people in the world today (as with some of the brightest people throughout history) disbelieve the theory of evolution.

As Paul Bynum correctly noted in his letter (Herald, Nov. 20), it is true that folks who dare to challenge some of evolution’s claims are, indeed, often ridiculed and maligned. Note the remarks of University of Minnesota biology P.Z. Meyers: that opponents of Darwinism need to be subject to “some form of righteous fury, much butt kicking and the firing and humiliation of some teachers, many school board members and vast numbers of sleazy far right politicians.”

Gary Andersen, Durango

There was more in the letter; the usual protestation that “Darwinists” are afraid, that there are “volumes of evidence of design all around us” (backed up by mentioning that birds fly and cats take naps), and that chance is a “dreary thought.” I responded with a short note pointing out that my quote was taken out of context, and that I’m not against challenging evolution, but am against incompetent teaching.

Creationists weaken science teaching

In a letter by Gary Andersen on 1 Jan 2006, I was quoted misleadingly, in a way that the Discovery Institute has consciously propagated. Yes, I have called for the firing of teachers and politicians, but not because they are “opponents of Darwinism”–but for incompetence. If a science teacher cannot grasp basic concepts of biology, he or she has no place teaching our children in the classroom. We are not afraid of Intelligent Design creationists, but we are getting increasingly angry at the disservice they are doing to our kids by weakening the science curricula in our high schools.

Mr Andersen claims there are weaknesses in the theory of evolution. Yes, there are, but the fact of evolution is not in doubt; there is active argument and research on specific details and mechanisms. Intelligent Design creationists are not participants in that work, and are actively promoting discredited ideas that are not supported by any evidence. Science class is not a place for garbled anecdotes and wishful thinking, yet that is all Mr Andersen has to offer—I think we can do better by our children.

Oh, and the name is Myers. One “e”. It’s bad enough to be misrepresented by the likes of the Discovery Institute and their minions, but they could at least spell the name correctly.

I am amused to see that the Durango Herald has published a reply. It shows the same level of incomprehension as the first letter.

Reaction shows evolutionists scared

In his letter (“Creationists weaken science teaching, Herald, Jan. 10) associate professor P.Z. Myers of Morris, Minn., suggested that anyone believing God created the universe “has no place teaching science in our classrooms.”

What an arrogant statement! Statements such as this reinforce the feeling that evolutionists are indeed quivering in fear.

Paul Bynum, Durango

Of course there is more ranting. I’m accused of “indoctrination and propaganda, and told that “All tyrants, Hitler, Stalin, etc., approve of and use this type of ‘education.'”

I think his argument is greatly weakened by the blatant quote mining of his very first sentence. You can rummage through the entire archive of my site, you can chase down every word I’ve ever said, and you can give me a Vulcan mind-meld and probe all of my thoughts, and you will not find me expressing or thinking that ridiculous sentiment anywhere. But of course, readers of the Durango Herald are most unlikely to even open up a week-old copy of their paper to assess the accuracy of the creationist’s claims. The creationists know their lies can spread faster than the truth, and they will continue to spout that kind of dishonesty shamelessly.

At least they learned how to spell my name properly.

Deficiencies in modern evolutionary theory

This is a post originally made on the old Pharyngula website; I’ll be reposting some of these now and then to bring them aboard the new site.

There are a number of reasons why the current theory of evolution should be regarded as incomplete. The central one is that while “nothing in biology makes sense except in the light of evolution”, some important disciplines within biology, development and physiology, have only been weakly integrated into the theory.

Raff (1996) in his book The Shape of Life(amzn/b&n/abe/pwll) gives some of the historical reasons for the divorce of evolution and development. One is that embryologists were badly burned in the late 19th century by Haeckel, who led them along the long and unproductive detour of the false biogenetic “law”. That was a negative reaction; there was also a positive stimulus, the incentive of Roux’s new Entwicklungsmechanik, a model of experimental study of development that focused exclusively on immediate and proximate causes and effects. Embryology had a Golden Age of experimentation that discouraged any speculation about ultimate causes that just happened to coincide with the time that the Neo-Darwinian Synthesis was being formulated. Another unfortunate instance of focusing at cross-purposes was that the Neo-Darwinian Synthesis was fueled by the incorporation of genetics into evolutionary biology…and at the time, developmental biologists had only the vaguest ideas about how the phenomena they were studying were connected to the genome. It was going to be another 50 years before developmental biology fully embraced genetics.

The evolutionary biologists dismissed the embryologists as irrelevant to the field; furthermore, one of the rare embryologists who tried to address evolutionary concerns, Richard Goldschmidt, was derided as little more than a crackpot. It’s an attitude that persists today. Of course, the problem is mutual: Raff mentions how often he sees talks in developmental genetics that end with a single slide to discuss evolutionary implications, which usually consist of nothing but a sequence comparison between a couple of species. Evolution is richer than that, just as development is much more complex and sophisticated than the irrelevant pigeonhole into which it is squeezed.

In her book, Developmental Plasticity and Evolution(amzn/b&n/abe/pwll), West-Eberhard (2003) titles her first chapter “Gaps and Inconsistencies in Modern Evolutionary Thought”. It summarizes the case she makes in the rest of her 700 page book in 20 pages; I’ll summarize her summary here, and do it even less justice.

She lists 6 general problems in evolutionary biology that could be corrected with a better assimilation of modern developmental biology.

  1. The problem of unimodal adaptation. You can see this in any textbook of population genetics: the effect of selection is to impose a gradual shift in the mode of a pattern of continuous variation. Stabilizing selection chops off both tails of the distribution, directional selection works against one or the other tail, and disruptive selection favors the extremes. This is a useful, productive simplification, but it ignores too much. Organisms are capable of changing their specializations either physiologically, in the form of different behaviors, morphologies, or functional states, developmentally in the form of changing life histories, or behaviorally. Evolution is too often a “theory of adults”, and rather unrealistically inflexible adults at that.
  2. Cohesiveness. There is a long-standing bias in the evolutionary view of development, that of development imposing constraints on the organism. We can see that in the early favor of ideas like canalization, and the later vision of the gene pool as being cohesive and coadapted, which limits the magnitude of change that can be permitted. It’s a view of development as an exclusively conservative force. This is not how modern developmental biologists view the process. The emerging picture is one of flexibility, plasticity, and modularity, where development is an innovative force. Change in developmental genes isn’t destructive—one of the properties of developmental systems is that they readily accommodate novelty.
  3. Proximate and ultimate causation. One of the radical secrets of Darwin’s success was the abstraction of the process away from a remote and unaccessible ultimate teleological cause and to a more approachable set of proximate causes. This has been a good strategy for science in general, and has long been one of the mantras of evolutionary biology. Organisms are selected in the here and now, and not for some advantage many generations down the line. Evolutionary biology seems to have a blind spot, though. The most proximate features that affect the fitness of an organism are a) behavioral, b) physiological, and c) developmental. These are the causes upon which selection can act, yet the focus in evolutionary biology has been on an abstraction at least once removed, genetics.
  4. Continuous vs. discrete change. This is an old problem, and one that had to be resolved in a somewhat unsatisfactory manner in order for Mendelian genetics (an inherently discrete process) to be incorporated into neo-Darwinian thought (where gradualism was all). Many traits can be dealt with effectively by quantitative genetics, and are expressed in a graded form within populations, and these are typically the subject of study by population geneticists. We often see studies of graded phenotypes where we blithely accept that these are driven by underlying sets of graded distributions of genes, such as the studies of Darwin’s finches by the Grants, yet those genes are unidentified. Conversely, the characters that taxonomists use to distinguish species are usually qualitatively distinct are at least abruptly discontinuous. There is a gap in our thinking about these things, a gap that really requires developmental biology. Wouldn’t it be useful to know the molecular mechanisms that regulate beak size in Darwin’s finches?
  5. Problematic metaphors. One painful thing for developmental biologists reading the literature of evolutionary biology is the way development is often reduced to a metaphor, and usually it is a metaphor that minimizes the role of development. West-Eberhard discusses the familiar model of the “epigenetic landscape” by Waddington, which portrays development as a set of grooves worn in a flat table, with the organism as a billiard ball rolling down the deepest series. This is a model that completely obliterates the dynamism inherent in development. Even worse, because it is the current metaphor that seems to have utterly conquered the imaginations of most molecular biologists, is the notion of the “genetic program”. Again, this cripples our view of development by removing the dynamic and replacing it with instructions that are fixed in the genome. This is bad developmental biology, and as we get a clearer picture of the actual contents of the genome, it is becoming obviously bad molecular biology as well.
  6. The genotype-phenotype problem. Listen to how evolutionary explanations are given: they are almost always expressed in the language of genes. Genes, however, are a distant secondary or tertiary cause of evolutionary solutions. Fitness is a collective product of success at different stages of development, of different physiological adaptations, and of extremely labile interactions with the environment. Additionally, a gene alone is rarely traceable as the source of an adaptive state; epigenetic interactions are paramount. We are rarely going to be able to find that a specific allele has a discrete adaptive value. It’s always going to be an allele in a particular genetic background in a particular environment with a particular pattern of expression at particular stages of the life history.

One unfortunate problem with discussing these issues in venues frequented by lay people is, you guessed it, creationism. Any criticism of a theory is seized upon as evidence that the theory is wrong, rather than as a sign of a healthy, growing theory. The Neo-Darwinian Synthesis is not wrong, but neither is it dogma. It was set up roughly 70 years ago with the knowledge that was available at the time, and it is not at all surprising that the explosion of new knowledge, especially in molecular biology, genetics, and developmental biology, means that there are radically different new ideas clamoring to be accommodated in the old framework. The theory is going to change. This isn’t cause for creationists to rejoice, though, because the way it is changing is to become stronger.

MLK on fighting the fight

Hey, Norbizness is supposed to be a funny guy. So what’s he doing posting an excellent excerpt from a Martin Luther King letter?

I must confess that over the past few years I have been gravely disappointed with the white moderate. I have almost reached the regrettable conclusion that the Negro’s great stumbling block in his stride toward freedom is not the White Citizen’s Councilor or the Ku Klux Klanner, but the white moderate, who is more devoted to “order” than to justice; who prefers a negative peace which is the absence of tension to a positive peace which is the presence of justice; who constantly says: “I agree with you in the goal you seek, but I cannot agree with your methods of direct action”; who paternalistically believes he can set the timetable for another man’s freedom; who lives by a mythical concept of time and who constantly advises the Negro to wait for a “more convenient season.” Shallow understanding from people of good will is more frustrating than absolute misunderstanding from people of ill will. Lukewarm acceptance is much more bewildering than outright rejection.

If only he were alive today, I’d have to politely toss that one back in his face and remind him of what freethinkers think of the progressive Christian community. Confrontation and forthright expression is always going to be preferable to meek appeasement by a minority to an oblivious majority.

Let’s all pretend New Orleans will be OK!

Chris Clarke sees that we’re Abandoning NOLA in Orion:

“[W]hile encouraging city residents to return home and declaring for the media audience that “we will do whatever it takes” to save the city, the President… formally refused the one thing New Orleans simply cannot live without: A restored network of barrier islands and coastal wetlands.”

Leiter reports on the human catastrophe and the same shortsightedness:

The Army Corps of Engineers is still not doing anything on stopping the loss of the coastal littoral. Before Katrina, Louisiana lost some 40 miles of coastline over the last three decades. Congress has only appropriated $200 million for a coastal restoration study when $14 billion is required for coastal restoration and another $25 billion is needed for Category 5 hurricane levee preparation.

It’s all a hollow shell. The Bush administration throws a pittance at a problem, enough to put up a façade of actually caring, while letting the infrastructure rot and the underlying problems grow. They’re all bluster, and why should they care? They’ll reap their profits now, and let future generations pay for it.

Open Thread

This is the place to bring up any old thing that strikes your fancy. I’m also asking some of the commenters from The Panda’s Thumb to bring their gripes about the ludicrous management of Uncommon Descent, that bastion of Intelligent Design close-mindedness, over here, just because the outrage is spilling over into far too many irrelevant threads.

But don’t let that stop you from mentioning anything else of far more interest than Dembskian dogmatism…

Textbook vs. Frontier

The Hwang Woo Suk stem cell research scandal has triggered quite a bit of concerned introspection in the scientific community. Orac has some useful comments on a good article in the NY Times that makes the distinction between “frontier science” and “textbook science”, where much of the current stem cell research is clearly on the frontier.

Much of science at the very frontiers turns out not to be correct. However, the way it is all too often reported in the press is that it is correct. We in science understand the difference between textbook science and the sort of frontier science that makes it into journals like Science. Indeed, we often lament that the very highest tier journals, such as Nature, Science, and Cell, tend to be too enamored of publishing what seems to be “sexy science,” exciting or counterintuitive results that really grab the attention of scientists–in other words “cutting edge” or frontier science. Such journals seem to pride themselves on publishing primarily such work, while more solid, less “sexy” results seem to end up in second-tier journals, which is why they are so widely read and cited.

I would add another factor, though: Hwang Woo Suk’s results were not at all unexpected, did not contradict any accepted scientific concepts, and were dramatic because they represented a methodological breakthrough. In a way, it was almost a “safe” category in which to cheat: lots of people are trying to transform adult cell nuclei into totipotent stem cells, it looks like a problem that’s just going to require a lot of trial-and-error hammering to resolve, and what Dr Hwang did was steal priority on a result he could anticipate would be “replicated” (or more accurately, done for the first time) in short order. This is one of the hardest categories of science to police, I would think. It’s frontier science all right, but it’s only one step beyond the textbook.

Orac’s comments about those sexy hot scientific results that get into the top-ranked journals also applies to weblogs. I’m guilty of the same thing: the articles I tend to summarize here are the ones that push at the edges of what we know, rather than the ones that consolidate what we already knew, which actually represent the majority of what I read. The solid stuff that is packed with gobs of detailed data on expression patterns of a single gene, for instance, is hard to make exciting to a general audience—when the conclusion of a long paper is that Hox1 represses transcription of Pax1/9 in the endoderm, it takes an awful lot of background exposition to try and make that interesting.

For the creationists out there, by the way, most of evolutionary biology is solidly in the “textbook science” category, which is one of the reasons biologists are so baffled about why the general public embraces criticisms of it.

Journey to the other side

Lya Kahlo carried out an
informal atheistical survey of Christian forums—she visited 35 online religious forums as an openly atheist but friendly visitor, to sample their attitudes. The results aren’t pretty. Her summary:

The entire experience can be summed up fairly easily. Generally speaking, they know next to nothing about atheists, they are extremely emotionally attached to their deities, and they are just people looking for truth as we are. The animosity that sparks between atheists and theists seems to stem from the two camps speaking two different languages – atheists speak in terms of empirical evidence and logic; theists speak in terms of faith, emotion, and the unknown. An atheist expects proof before acceptance, a theists sees acceptance as proof.

Do I see it as a waste of time? On some of the boards (*cough*HolyCultureRadio*cough*) it was a waste of time. On boards frequented by a large teenage population or a way-out-there new-agey element, it was a waste of time. But this is not the case overall—surprisingly some of the more useful conversations happened on some fairly conservative forums.

Lastly, I think there are some allies to be made out there in the fight against an impending American Theocracy (okay, that’s a little dramatic), women’s rights and anti-war activism. There are plenty of good, decent xtians out there. However, we are never going to understand each other. We speak different languages.

I don’t doubt that the majority of Christians have good intentions. That language barrier, though…that’s a killer, especially since there’s little mutual interest in learning to speak each other’s language.