Kenneth Miller’s unrelenting attack on creationism

Kenneth Miller is a professor of biology at Brown University. He is also a widely published author (co-author of high school and college biology textbooks used by millions of students). He is also a practicing Roman Catholic who has served as an expert in several court cases concerning creationist school boards that have tried to muzzle classroom science. In his most recent book, Only a Theory: Evolution and the Battle for America's Soul, Miller makes an unrelentingly strong case against creationists of all stripes, including those who advocate "intelligent design." I did not realize the strength of the scientific case based upon the analysis of the genomes of human beings and other animals. How strong is it? It is at least as strong as the fossil record, arguably much stronger. I already knew a few things about the arguments based on genome analyses. For instance, I had often read that the genomes of chimpanzees and humans were 99% the same (or, at least, 96% the same). I also knew that all animals possessed Hox genes, essentially "toolkits for generating body form." Miller reminds us that "it is the same kit whether that animal is a honey bee, a fish or an elephant." The Hox genes prove "deep connections between animal groups." Miller points out that these similarities are even much more striking than Haeckel's (admittedly exaggerated) embryonic drawings. In fact, Haeckel "actually understated the evolutionary case each of these embryos possesses the same developmental toolkit, revealing both are common ancestry and the similarity of form and function produced by the workings of the evolutionary process." These profound Evo-Devo findings (the combination of development and the study of evolution) show that we "no longer need to make a distinction between the two types of change known as macro evolution and micro evolution. We don't need to attribute special mechanisms for large-scale changes. Evo-devo "reveals that macro evolution is the product of microevolution writ large." According to Miller, these should be "chilling words" to the ID crowd.

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Bacteria that talk to each other

Bonnie Bassler, who teaches molecular biology at Princeton, explains that bacteria don't just grow and divide, grow and divide. They speak to each other and with other species of bacteria through their chemicals. Bassler studies how bacteria use chemical signals to act as coordinated social units. In this delightful TED talk, Bassler discusses how her research group has studied the manner in which bacteria talk to each other. They make chemical "words" to enable group activities (such as triggering the timing for effective virulence attacks), sensing each other through their "quorum-sensing molecules." They can also sense the difference between themselves and other bacteria. Note that each of us is 99% bacterial. Our human body consists of about one trillion of "our own" cells, but ten trillion bacteria. We have about 30,000 of "our own" genes, but we carry about 100 times more bacterial DNA than human DNA. Bacteria live as "mutualists" with us. They help us digest our food, make our vitamins, protects us from other pathogens and help us survive in numerous other ways. Rather than using antibiotics to kill bacteria (which inevitably selects for more virulent strains), Bassler suggests that a better understanding of the communications schemes used by bacteria is allowing scientists to develop potent new medicines. This is an upbeat and informative talk regarding a most ancient form of life.

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Gray Matter at Wolfram Research

As I promised, I have visited the Periodic Table Table on the penultimate floor of the Wolfram Research building. This is a fairly tall building for Champaign, IL and contains some serious brains. We walked in, rode up to the top floor, and asked to see "The Elementary Mr. Gray." The receptionist chuckled, made sure that I claimed to have an appointment, and called down to the co-founder and interface designer for Mathematica Software, Theodore Gray. We were escorted down to his spacious office area, in which samples of every element in the universe are kept. Many on open display. One Corner of the Office Big SamplesI had budgeted 2 hours, and had to tear myself away after 3. There were huge samples of some things like 99.999999% pure silicon and a massive block of magnesium. There were pretty and ingenious samples of others. The pictures he took for PeriodicTable.com are excellent, but seeing them and holding them is an order of magnitude more impressive. I got to hold a nice chunk of depleted Uranium (kept in the safe with the gold and platinum and antique samples). Heavy stuff, and almost as big as my sample of equally heavy tungsten. Maybe I should mention the layers of security and cameras, in case anyone gets acquisitive. PeriodicTableTable and its creator Notice the lead pipe over by Hydrogen? It was last seen on my patio, and now is part of this collection. I hadn't realized that this brain trust is where Hollywood went to get correct math for the TV show Numb3rs. Wolfram staff may not criticize the inaccurate applications, but at least they make sure the formulas written by the actors match what they say they are doing and look cool. I often regret not having gotten a job at a brain trust back when I was young and quick. It was nice to visit such a place and to be made to feel a collegue. So, how shall I spin this as a serious post? Real science is a matter of playing with reality and seeing what makes it tick. To understand matter, one should see what there is of it. To understand the mathematical models on which our standard of living depends, it is good to know some real math. I find comfort in knowning that those who really know the math have fun with it.

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The not-simple question of defining “species”?

There are a lot of simple things out there that aren't really simple once you start trying to understand and explain them. The concept of "species" is one of those non-simple concepts. I had assumed that I had a good gut understanding of "species" until I read an article called "Speciation," by Andrew P. Hendry, published in the March 12, 2009 edition of Nature (available online only to subscribers). Hendry suggests that the term "species" as a technical classification in the field of biology is "ambiguous and amorphous." He starts by quoting Darwin, from on the origin of species: In short, we shall have to treat species in the same manner as those naturalists treat genera, who admit that genera are merrily artificial combinations made for convenience. This may not be a cheering prospect; but we shall at least be free from the vain search for the undiscovered and undiscoverable essence of the term species. Hendry suggests that modern biological research has proved Darwin. No universal easily applicable concept of "species" exists; instead, more than two dozen approaches exist with regard to "species." The most common version is the "biological species concept" (BSC). This definition holds that species are "groups of actually or potentially interbreeding individuals that are reproductively isolated from other such groups (that is, they exchange few genes). Hendry elaborates: The BSC is sometimes interpreted to imply the extreme situation where two groups are separate species only when successful hybrids cannot ever be produced-and any two such groups certainly are separate species. But many other groups that are widely accepted to represent separate species frequently violate the strict criteria; for example, some estimates hold that 25% of all plant species and 10% of all animal species hybridize successfully with at least one other species. Probably for this reason, the BSC is often relaxed to the point that different groups are considered separate species if they can maintain their genetic integrity and nature. This more useful, albeit more ambiguous, criterion allows for some genetic exchange (gene flow) between species as long as they do not become homogenized. Hendry then goes on to discuss various challenges to BSC.

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Flooded With Data

I had an urge to think through some implications of a world-wide flood, such as the one Biblical Literalists claim happened a few thousand years ago. Let's suppose that it happened, that the entire world was inundated all at once to cover the highest mountain, and that all surviving land animals and short-range birds were preserved in a single boat. What would the ecological landscape look like? gray worldFirst, all land animals would only be found on a single connected land mass. There is no way that any crawling creature could have reached Australia or the Americas from the Middle East. Most especially tropical animals. Secondly, we expect to see floral panspermia. That is, the waters would have carried every species of seed to every land mass all at once. Vanilla and cocoa and peppercorns should all be found growing in the same places throughout human history. Same for and chile peppers and coffee and potatoes. Wheat and maize should also be seen as combined staples of every ancient diet. Or the opposite: The flood waters killed off all the seeds except what was carried on the ark. Therefore, only the plants found in the middle east could exist anywhere in the world. Also, all modern animal species should be represented in every geological flood stratum. After all, a single massive drowning event doesn't distinguish between creatures of comparable size like an allosaur and an elephant or a trilobite and a mouse. Surely there must be abundant examples of these combined fossils. So it is easy to prove that such a flood actually happened. In fact, it must have been proven beyond a shadow of a doubt when Europeans first sailed to the Americas and found everything there to be just the same as back home.

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