Saturday, May 31, 2008

Darwin in WSJ

I was waiting to meet with a banker today to wire money to Europe, and I picked up the Wall Street Journal. In it, I was surprised to find a book review of Darwin's Voyage of the Beagle. They have a section reviewing classic books, "masterpieces". Embarrassingly, I've never read this Darwin classic, I think I'll take it on my vacation. The review was short and readable, reminding us that young Darwin was a passionate naturalist and geologist. The review also makes a connection with today, pointing out how invasive species and extinction have dramatically changed the planet in the geological blink since Darwin's voyage. I especially liked the illustration of a youthful, vibrant Darwin in the Galapagos.

Coming to grips with common descent

Talk about a bump. Since PZ mentioned this blog, visits are through the roof. I'm not sure I really ever intended to blog for the masses; I was just using a blog as a motivator to write more often, and to collect ideas for a book that I am very slowly writing. But I feel a bit obliged to have something of substance, since so many intelligent people are spending time looking at these pages.

Since I am swamped finishing up our quarter, and preparing for a family vacation to Europe, I'll pull something off my hard drive, which is pretty good. Here is a little set up: Only the most irrational and fundamental creationists object to natural selection, or "microevolution". The real barrier to the acceptance of evolution is recognizing global common descent ("macroevolution"), and especially the inference that humans are not specially created, but a twig in the tree of life. At the same time, natural selection is often directly equated with Darwinism (see this post for example) and evolution itself. I'm very slowly working on a book that explores the implications of common descent (pattern) and the processes that produce it (speciation, gene duplication, and "duplication" of biological units in between genes and species, like gene networks and traits). This post is an excerpt from a draft of one chapter. I've edited it down a bit, but it's perhaps still a little long and technical for a blog post - but pharyngulites are a smart bunch, so I have faith. For what it's worth:

Coming to grips with common descent

One of the most profound insights in the history of human thought is Darwin’s proposal that all species are united by common descent. The idea transformed the view of humankind’s place in the natural world from a self-congratulatory perch atop the Scalae Naturae to an arbitrary outpost alongside other apes as cousins to every palm, gastrotrich, and canary (note the goal here was to rhyme names of organisms with "Tom Dick and Harry", the colloquialism meaning "everyone"; not sure if anyone ever gets that though). We are still coming to grips with the idea that each and every living thing is related through a common evolutionary heritage. Despite being accepted for about a century and a half, I argue that a truly intuitive grasp of common descent remains difficult. Nevertheless, coming to grips with common descent is of fundamental importance for achieving the central goal of evolutionary biology: to understand the origins of biological diversity. Most notably, I argue that a conspicuously missing topic in evolutionary theory is the explicit comparison of hierarchical patterns and processes of lineage splitting and common descent.

[For brevity, I deleted a part describing Mayr's "horizontal processes" - like speciation; and "vertical processes", like natural selection. These are equivalent to cladogenesis and anagenesis. This horizontal is not to be confused with horizontal gene transfer. I first point out that traits, like teeth vertebrae and eyes, can duplicate within a species by mutation. Therefore, these traits can form phylogenetic trees like gene families. This is the subject of the book, so it's only briefly introduced here.]

1. Common descent is non-intuitive

The most formidable obstacle to a fully intuitive grasp of common descent may be the sheer magnitude of differences that life outwardly expresses. An oak tree and a dung beetle are cousins!? Not to mention our more obscure relatives, the oxymonads, slime molds, and E. coli’s of the world! How can it be that such enormous differences in appearance, life style, size, and behavior have evolved? The answer is not difficult to understand logically. For example, to Darwin the immensity of biotic diversity could in large part be explained by time itself. Geological time is so vast as to be practically incomprehensible. Who then could logically argue with time’s ability to allow for the origin of an equally incomprehensible biological variety – even if starting from a single point? Many of the tell tale similarities expected of cousins would logically erode away after so many millions of generations. But logic quite often does not guide intuition. Such is the case with common descent. Even after learning crystal clear indicators, we continue to be surprised by common descent.

Perhaps the clearest signal of globally shared evolutionary heritage is the genetic code. On October 12, 1962, the headlines of the New York Times read “The Genetic Code is Held Universal: All Living Things Are Said to Use Same Chemicals for Heredity Transfers[1]. More than a full century after Darwin’s “Origin”, common descent was again in the public eye. Who could help but marvel at the thought of a universal genetic code, in place nearly since the dawn of life? A code that remained constant through the origins of cells, of gastrulation, of brains and of societies. The few exceptions now known to the universal code have not diminished the significance. The conserved hereditary machinery provides a concrete thread linking every organism in the tree of life.

One might expect that the triumphant generality of the genetic code would have precluded any more surprises relating to common descent. After discovering a “universal code”, perhaps we finally could come to grips with the universal relatedness of living things. But more surprises were in store. The advent of molecular developmental genetics would again cause biologists to re-examine their expectations regarding common descent. This time the papers read, “From worms to cows, one class of genes spells out the blueprint”. “Class of genes” of course refers to the Hox genes, the conserved transcription factors involved in body patterning. Discoveries of other genes with highly conserved roles were to follow. Of the gene Pax-6, the newspapers read, “science outdoes fiction” when a human gene was shown to step in seamlessly for a defective fly gene or to produce eyes in unnatural places.

The lesson in this tripartite sketch of the history of biology is that at three levels of organization – species, genes, and developmental processes – biologists have been surprised to discover common descent. To me, this indicates a rather fundamental lack of intuition for the process. We seem to have to relearn the lessons of common descent at every level of biological organization. In each case, we start with the assumption – or perhaps with the notion (something less formal than an assumption) – that biological entities somehow arise de novo in a massively parallel manner. In Darwin’s time very few biologists considered common descent of species (exceptions include Buffon and Erasmus Darwin), and no one else neared the sweeping generalizations for the relatedness of most or all of life that Charles Darwin suggested. Instead, Darwin’s contemporaries and predecessors believed that each species had a separate origin. Some biologists broke the strictly typological thinking common of the time – to Lamark species transformed and to Cuvier they sometimes went extinct – but no one else had formed anything near a Darwinian concept of a global tree of life. Perhaps it is the strong intellectual roots in creationism, or perhaps it is the conceptual difficulty in linking together the entire enormity of biodiversity, but even long after Darwin’s ideas of common descent have been accepted for species, a biologist’s intuition often falls back on the notion of parallel origins when considering other levels of biological organization.

Current support among biologists for common descent of genes (see also this post) is strong– but this was not always so. The 1960’s and early 1970’s was the time when biologists were learning that common descent holds for genes and proteins as well as species. One telling quote, used recently by both Gould {2002} and Carroll {1999}, can be found in an influential book by Ernst Mayr, Animal Species and Evolution.

"Much that has been learned about gene physiology
makes it evident that the search for homologous
genes is quite futile except in very close relatives. If
there is only one efficient solution for a certain
functional demand, very different gene complexes
will come up with the same solution, no matter how
different the pathway by which it is achieved.”

Ernst Mayr (1963)

I do not think that this was a particularly radical viewpoint of the time. For example, I was struck when reading Walter Fitch’s citation classic defining the terms orthology (descent by speciation) and paralogy (descent by duplication), because almost the entire paper is concerned with a topic rather different from orthology vs. paralogy. Instead, Fitch lays out statistical methods for discriminating homologous from analogous proteins. In other words, a real concern of the time was that proteins might have evolved similar sequences in parallel. This is of course a worthy consideration and is a hypothesis that is tested thousands of times per day using similarity searches of genetic databases. Nevertheless, I find comparison with biologists of Darwin’s time extremely interesting. In both cases, massively parallel and de novo evolution was taken almost as the null expectation, no matter how unparsimonious. To Darwin’s contemporaries, species were created separately and similarly. To Fitch’s biochemist and especially to Neo-Darwinist contemporaries of the 1960’s (e.g. Mayr above), the very real possibility remained that genes were “created” separately and similarly in different species. I don’t mean to imply religious-type creationist leanings in the biologists of the 1960’s. On the contrary, their “creator” was strong (Darwinian) natural selection for a particular function. They imagined natural selection to be so powerful and dominant as to allow multiple re-inventions of genes, thereby erasing most of the historical component of genes. No matter the creative force behind the purported independent origins of species or genes, the point here is that deeply rooted common descent was a hard earned realization, not an immediately obvious intuition of biologists studying the problem.

In many ways, it was history repeating in the 1980’s and 1990’s when biologists began discovering deep homologies in body patterning genes like Hox genes. The prevailing view and intuition of the time, especially of morphologists and systematists, was that many organismal structures like segments, eyes, limbs, and hearts, evolved essentially de novo, multiple times independently in various lineages. Like the pre-Darwinian concept of species or the concept of genes in the days preceding the advent of molecular biology, the dogma was that organismal structures and the developmental processes leading to them often arose separately in different lineages – especially when comparing different phyla, which are considered to have different “body plans”. But the discovery of conserved developmental genetic processes for patterning the bodies of taxonomically different organisms forced biologists again to consider common descent at new levels of biological organization.

Eye evolution provides a canonical example. A comprehensive, and well-cited paper on photoreceptors by Salvini-Plawen and Mayr from 1977 surveyed the morphological types of eyes in all animals, concluding that photoreceptors must have evolved essentially de novo 40-65 times independently. But the 1990’s saw a chain of discoveries that showed many genes involved in eye development are homologous between phyla. That visual pigment genes (opsins) are conserved was known for some time. Instead, the watershed discovery in eye evolution was that similar mutant (disease) eye phenotypes in flies, mice and humans are caused by mutations in homologous genes {Quiring, 1994}. These genes are named Pax-6 in vertebrates and eyeless in flies. Multiple other phyla were subsequently shown to utilize homologous Pax-6 proteins during in eye development. Furthermore, multiple other genes besides Pax-6 and opsin were subsequently shown to have a conserved role in eye development across phyla. Similar stories can be told for limbs, hearts, and segments. Naturally, many biologists began to question the generality of the assumption that organs and especially developmental processes evolved multiple times independently. Just as biologists recognized deep common descent of species in the 1860’s and genes in the 1960’s, they began to recognize a real possibility for deep homology at levels of biological organization in between genes and species. These conserved developmental processes and the genes that code for them have been termed “the genetic toolkit for development”.

There are many possible reasons why common descent is hard to intuit, deep-seated intuitions about ladders of progress, and an overemphasis on natural selection seem to be especially important. Yet once we start thinking about genes, traits, and species in terms of common descent, we can be greatly enlightened about how evolution has produced the enormous complexity that we see every day.

[1] The Genetic Code is Held Universal. Robert K. Plumb New York Times Octocter 12, 1962.

Tuesday, May 27, 2008

Evolution of Random: Random of Evolution

I attended the 2008 Western Evolutionary Biologists (WEB) conference on Sunday, sponsored by NERE. The winner of this year's Western Evolutionary Biologist of the Year (WEBY) was Kevin Padian of UC-Berkeley, in recognition of his many accomplishments in research and outreach in evolutionary biology. Kevin delivered a fun WEBY address, that mentioned his recent research briefly, and also discussed how evolutionists might better communicate with the public. In terms of bettering the abysmal anti-evolution statistics in the USA, Kevin thinks we shouldn't really focus much on the fundamentalists (who in my words are brain washed beyond rescue). Rather we should focus on a huge middle ground of people who may not understand the vast weight of evidence for evolution, and therefore have doubts, owing in large part to the anti-evolution propaganda machine that exists here. One of the topics Kevin brought up, which struck a chord in me because I just mentioned this in my Macroevolution class recently, is the difference between colloquial usage of words, and the meaning of those words in the scientific community.

Language and words, just like species and genes, evolve. Languages have been used to build phylogenetic trees to test hypotheses of human migration, and the meanings and relative usage of words often shift, sometimes radically, over time. An interesting example of this is what I've seen as a rather recent upsurge in colloquial use of the word "random". In fact, this "evolution of random" may have implications for how people understand the "random of evolution", the meaning of the word random in the context of natural selection.

Evolution of Random

In his best California-surfer-valley-girl accent, Padian illustrated current colloquial usage of the word random, "I, like, met this random guy in the mall the other day who...." (I actually can't remember the exact line Kevin used, but it was something like that). Kevin also defined current usage of random as identifying a non-sequitur, something that doesn't follow. I've certainly noticed this type of usage, and it seems to have surged tremendously in the past 5 years or so (perhaps because that is when I moved to California?) I've also thought of the colloquial use of random as meaning "unexpected", or even "unknown". For example, a "random" guy at the mall means to me that the speaker doesn't know the person. It also means that the reason the person was there is unimportant to the story, or unknown to the speaker. These colloquial meanings of random are quite different from statistical meanings, which is how I often think of its use in evolution.

Random of evolution
When I use the word random, I use the statistical meaning. Statistical randomness might mean that one possible outcome usually has an equal chance of being observed compared to another defined possibility. This is quite different than the colloquial usage that I mentioned above. A "random guy at the mall", according to the meaning often implied, does not include someone known to the speaker. So the speaker's dad is not included in the set of possibilities, which might be considered a decidedly non-random subset of all possible people, based on the statistical definition I presented above.

Kevin also made an interesting analogy, illustrating yet another subtlety in the statistical meaning of random. House fires may be modeled as random events. Given no prior information about one's house, there is a given probability that one's house will burn down. But if we have more information, we find out that most fires are caused by smoking in bed and arson. So, if a person is not a smoker, and has no pyromanical enemies, the chance of their house burning down is much lower than "average". Here, we are defining a random event (house fire) as stochastic, happening "by chance", yet recognizing that specific factors can alter the probability in specific instances. As Padian mentioned, if John Doe has an angry ex-spouse looking to torch the house lost in a divorce, the probability of Doe's house burning down goes up.

Given these sometimes subtly different usages of the word random, it's no wonder that sometimes people misunderstand natural selection, which has a "random" element. For natural selection to act, heritable variation must be introduced into a population. Evolutionists conceive of mutations as random events, and just as a certain prior knowledge of house fire risk can guide our estimation of probabilities, so can our prior knowledge of mutation. For example, flies exposed to UV light show a much increased rate of mutation. We might expect whole genome duplication events to be rarer than some other forms of mutation. But we don't mean that a mutation is a non-sequitur, or that a mutation is (necessarily) unknown to us or unspecified. And this is just a part of the entire process of natural selection!

Kevin's point in this is that we must be very careful about language. We must consider who is our audience, and what is their exposure and typical usage of different words. We must define clearly what we mean, and how our usage might differ from theirs. None of this is easy. As I grade exams, I see that understanding natural selection can be difficult for people; a difficulty probably caused by one random misunderstanding after another.

Saturday, May 24, 2008

Gould: Pluralism by monism

Well, I saw that Ryan Gregory mentioned this blog on Genomicron, giving me the “Gregory Bump” (that makes the most sense to fans of the Colbert Report). So, I figured I should add something of substance to my blog, which I haven’t done in a while – we’re still in session here at UCSB, on the quarter system. Here ‘tis, for what it’s worth:

One of my life goals is to have an original idea – since I’m an evolutionist by passion, it’s difficult, because Darwin has already claimed most of the original ideas in my field. But here is an insight I’ve had that might be somewhat original. The field is history of science, so that explains why Darwin didn’t already think of it. History of science is also not my field, which could explain my perception of novelty: Chances are someone already thought of this, and I just don’t know it, because it’s outside my field.

The idea, in a phrase, is that the controversial evolutionist, Stephen Jay Gould, practiced “pluralism by monism”. This is a fun idea in many ways. First, I’ll explain in a little more detail what I mean by “pluralism by monism”. Then I’ll explore some of the fun implications and ironies of this idea.

Basically, as eloquently presented by Michael Shermer in “In Darwin’s Shadow”, Gould (like many great scientists), pursued deep philosophical themes that permeate western thinking, and all of science. Shermer named several “thematic pairs”, such as theory versus data, contingency versus necessity, punctuationism versus gradualism, etc. I won’t go into here what all these mean, in detail, but the general idea is that these are opposing concepts that color how people view the world. I like to think of them in light of the Taoist philosophy of the “unity of opposites”. One cannot fully understand one concept without understanding it’s opposite. Opposites are in fact one thing, two sides of a single coin, that grade into each other, yin and yang. Pluralists, then, are those who see both sides of the coin, those who see the unity of opposites, and see the falseness of dichotomies.

My thesis here is that Gould tried to elicit pluralism in the field of evolutionary biology by taking a monistic stance that opposed most of the field. He would find cases where the field had gone too far to one side of a false dichotomy, and bravely, forcefully, and egotistically argue for the exact opposite. If evolution was all about arguing for yin – Gould would stand up, and say, “what about yang?” His ego was large enough, and his intellect sharp enough, that he believed (and often achieved) that he could bring the entire Force into balance by going – often alone - to the Dark Side.

Perhaps some explicit examples will help. Let’s start with Shermer’s pair “Adaptationism – Nonadaptationism”. The field of evolution pre-1979 had skewed toward Adaptationism, leading Gould and Lewontin to coin the phrases “adaptationist program” and “Panglossian Paradigm” (all for the best). T. rex’s reduced limbs were adapted for titillating females, Aztec sacrifice and cannibalism were adaptive for a protein shortage, and architectural spandrels were adapted as an artist’s canvas. There was a disturbance in The Force - it was in extreme imbalance - until Gould and Lewontin stepped over to the Dark Side to try to restore balance. It’s not all adaptive, they said, there are constraints, historical and structural, and most of all we cannot simply assume something is adaptive before testing it.

When I mention Gould to some of my colleagues (who lean toward being adaptationists, as far as I am concerned), they loathe Gould, saying he was against natural selection (adaptationism). To some, he was a monist on this issue, taking a stand against natural selection. Not at all, he knew the strength and frequency of natural selection. He was only arguing for pluralism.

Another case in point is Shermer’s punctuationism versus gradualism. The field of evolution was focused only on excruciatingly gradual modes of evolution, explaining away other patterns, like phenotypic gaps in the fossil record, as missing data. In response, Eldredge and Gould proposed punctuated equilibrium. They argued that stasis and discrete jumps are a common mode of evolution, such that the fossil record might more often be an accurate record of the evolutionary process than once appreciated. Here again, the field had gone too far to one side of a false dichotomy. Punctuated equilibrium acted as a pull toward a more central tendency that considered other modes, besides pure gradualism. Again, taking a contrary stance inflamed some people (for example, Punctuated Equilibrium is sometimes referred to as "Evolution by Jerks".)

A final example that I will mention here was aimed at humankind more than at the field of evolution. Humans have long held the view that our species is a pinnacle. Either humans are specially created in the image of God (e.g. perhaps She looks like Whoopi Goldberg). Even after Darwin introduced the idea of global common descent, and tree thinking, many people still shoehorned humans at the top of a ladder of progress (see my post Iconography of an Expectation). The key dichotomy here is “contingency versus determinism”. Many people think of human evolution as destined, determined either by the supernatural (think Whoppi) or the natural progression of evolution gradually increasing complexity until the summit of human perfection was achieved. Enter Gould’s Wonderful Life (and similarly themed short essays), where SJ entertained the mostly monistic thesis that contingency dominates the history of human and in fact all evolution. Replay the tape of evolution (an interesting linear, non tree-thinking analogy) and humans only evolve one out of a trillion times. Nothing special about us, just dumb luck; we’re just lucky to have been part of one of the clades that survived a decimation after a Cambrian Explosion. By taking this stance, Gould could take on religious fundamentalists and wrong-headed evolutionists in one fell swoop aimed at putting paleontology at the center of a new revolution in human understanding.

The fun part of this idea is the irony. Achieving pluralism through monism seems impossible. Yet at the same time it highlights the theme of false dichotomies so deliciously. There can be no pluralism without monism, just as we cannot understand adaptationism without understanding what is not adaptationism, etc. All this highlights the philosophical underpinnings of evolutionary biology. Rather than being built upon fundamental laws, natural history presents myriad possibilities, forcing arguments about what is most important. Echoing this sentiment, I’ll end with a quote from Gould and Lewontin (1979):

“In natural history, all possible things happen sometimes; you generally do not support your favored phenomenon by declaring rivals impossible in theory. Rather, you acknowledge the rival but circumscribe its domain of action so narrowly that it cannot have any importance in the affairs of nature. Then, you often congratulate yourself for being such an undogmatic and ecumenical chap."

Tuesday, May 6, 2008

Interview by student

I got these questions from a student, and decided to post them here.

> Hi, I'm currently doing a general research paper on evolutionary biology for my >writing class. I would really appreciate it if you could answer a few questions for >my paper. My main focus is on natural selection.
> 1. Besides natural selection, are there any other mechanisms observed in the evolution of a species?

Although natural selection is an important driving force in evolution, there are many other factors that influence the evolution of species, often in concert with natural selection. A primary consideration is genetic drift, which is related to the idea of "neutral evolution". In the field of population genetics, genetic drift is known to result from "sampling error", which is especially likely in very small populations. To understand what I mean by sampling error, first consider what we might expect if we were examining one gene in a population, and if we expect no evolution to happen to that gene in a population of individuals. Without evolution, we'd expect the different copies of a gene to stay at an equilibrium proportion. So, if we had two different types of a gene (types of a gene are called alleles), each occurring at 50% frequency, we'd expect the frequencies to stay the same over time without evolution. But if the population of individual organisms is very small, we might expect some "sampling bias". Sampling bias can occur in coin tosses. If we toss a fair coin 1000 times, we expect that pretty close to 50% of the time, the coin will land on heads. But if we toss the coin only 4 times, we wouldn't be too surprised to find that the coin landed on heads 100% of the time. The same can happen to alleles in small populations. Even though the alleles described above are equally prevalent, and we'd expect them to equally prevalent in offspring (without evolution), we could discover the result that the prevalence of alleles changes from 50% just by chance possibility. Just as we can obtain biased results in a few tosses of a fair coin, alleles can be passed on in a biased fashion by chance, especially in small populations. This is called genetic drift, and it is a mechanism for evolution other than natural selection.

Related to genetic drift is neutral evolution. Neutral evolution is the idea that some mutations in genes do not influence the phenotype of the organism. "Nearly neutral" means that some mutations have only a tiny effect on the phenotype of the organism. Neutral and nearly neutral mutations can enter into species in the absence of natural selection. Since the organismal phenotype is barely changed, there is very little cost to the organisms that maintain these mutations. Some have argued that major features of the genomes of species have been shaped by neutral and nearly neutral evolution. For example, genes can duplicate, and might be maintained in genomes simply because there is little cost to maintaining it.

Another mechanism that has a major influence on evolution, but has nothing to do with natural selection, is catastrophic events. For example, at several points in Earth's history, meteors have struck Earth, and are implicated in massive extinction of many species. Such massive extinction changes the interactions among species entirely, and has a profound effect on how evolution proceeds. Mass extinctions have little to do with how "fit" species are: most any species could be wiped out if a meteor drops on them.

A final consideration is constraints, which may channel or restrict the action of natural selection. Many traits are linked together genetically and/or developmentally. As such, changing one trait (perhaps by natural selection) can indirectly change other traits. Developmental evidence suggests that cavefish without eyes lost eyes through natural selection on increased jaw size. While selection changes jaw size, the direct arbiter of change in the eyes is thought to be the link with jaws. Selection may not have acted directly on eyes, but rather through a developmental constraint that ties jaw size and eye size together.

> 2. I’ve often heard that while natural selection is represented by the phrase “survival of the fittest,” it is not a correct way to describe the process. What are your thoughts on this statement?

The epitome "survival of the fittest" is in fact misleading. Instead, natural selection is better defined by some specific postulates. Namely, heritable variation exists, and there is differential survival of that heritable variation. So one thing missing in "survival of the fittest" is a mention of heritability.

> 3. Could you give an example of natural selection at work in the recent past?

There are many, many examples of recent natural selection. A textbook example is beak evolution in Galapagos finches, with examples based on decades of field work by Peter and Rosemary Grant and colleagues, which is chronicled in the Pulitzer Prize winning book The Beak of the Finch. As one specific example, they witnessed increased survival of larger beaked ground finches during times of drought because those birds could eat larger and harder seeds. The emergence of pesticide resistance and antibiotic resistance are two practically important examples of recent evolution by selection (although some may not consider these "natural", because humans have impacted the systems).

> 4. Can you point out some results of natural selection in our own natural areas around the UCSB campus?

Natural selection has influenced the evolution of every living thing on earth, including every living thing on the UCSB campus, in natural areas or otherwise.

> 5. What are your views concerning evolution versus creation?

I am very embarrassed and concerned by recent polls showing that the US is second only to Turkey in the proportion of citizens who reject the science of evolution. This reflects a general lack of critical thinking among a large portion of Americans, which is dangerous to our way of life, to American values and freedoms, and to the success of our country in economics and as global citizens. Much of this lack of critical thinking among Americans is rooted in fundamentalist Christian anti-evolutionism. Large institutes (e.g. Discovery Institute) have formed a strategy to impose their religious beliefs on the people of the US through a plan called the "wedge strategy". They see evolution as the easiest target for anti-intellectualism. Once the wedge pierces evolution, the plan is to proceed to other fields of science, until their religious perspective dominates how Americans learn science. This is a fundamentally unconstitutional, and anti-American.

Despite the tired nature of anti-evolution arguments, like Intelligent Design, that were refuted already in Darwin's time, many Americans reject evolution. This is despite the fact that evolutionary biology has thrived as a predictive, and well-established science for 150 years, amassing huge amounts of supportive and consistent evidence supporting the fact that evolution is the causal agent of the diversity of life we see on Earth.

Some people have a less fundamentalist view of religion, and accept the established science of evolution within their faith.

My own personal view is that I have no doubt that evolutionary processes have created all of the diversity of life on Earth. It is also quite clear to me that documents like the Bible are internally inconsistent, and contain many claims that have been disproved - I therefore see little reason to put much stock in such documents. I also believe that religion can be dangerous because it is often co-opted as a means to control the masses, especially by promoting a lack of critical thinking. I do believe that religion can be beneficial to some people, for example by establishing a sense of tradition, connection, and community in some people.

After all that, I still haven't addressed my views on the "creation" question, which is whether I think some sort of creative force is responsible for setting up the universe. I just don't see how anyone could know that - one way or the other - so I call myself an agnostic. And except when someone tries to impose their religious views upon me (for example the Discovery Institute wedge strategy), I don't see any reason why it matters whether there is some creative force or not. Evolution does just fine in explaining where humans came from and when, and evolution does not impinge negatively upon morality or eithics. Humans are an inherent part of nature - I spiritually do not need to know any more than that.

> 6. How does human activity interfere with natural selection among other species?

First, I found interesting your use of the word "interfere" in the question, which sometimes has a connotation of hampering or hindering. I would say that nothing humans could ever do will hinder natural selection, in general. But there is no doubt that human activities impact the course of natural selection. Some examples I already mentioned (the evolution antibiotic resistance in bacteria, and pesticide resistance in insects). Humans are also causing a mass extinction event that is changing the specific interactions among species. Finally, global climate change, and other environmental impacts are influencing how natural selection will act in different species.

Thursday, May 1, 2008

Where a lack of critical thinking can get you

I am all for tradition. I am not religious, but celebrate Christmas, and listen to Christmas carols. I watch the Packers on Sunday, and think back to my earliest memories, growing up in Wisconsin with the Pack.

But there are also traditions that should not persist. For example, I no longer fry up polish sausage to drizzle the grease with Karo Syrup on Wonder bread , as my family used to do during Packers games. Critical thinking has alerted me to the fact that this may not be a healthy tradition.

Here is a tradition that should die: a ritual exists whereby babies are dropped from a building 50 feet high. Video is available at the link below:

News Story