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April 14, 2008

Dumbing down intelligent design

'No practical biologist interested in sexual reproduction would be led to work out the detailed consequences experienced by organisms having three or more sexes; yet what else should he do if he wishes to understand why sexes are, in fact always two?' -- R. A. Fisher (1930).

The scientific definition of "theory" is very different from its popular meaning of "wild speculation." The Theory of Evolution, like the Germ Theory of Disease, or the Atomic Theory that forms the foundation of chemistry, is solidly based in observations and experiments. The "theoretical" part, in each case, is a collection of well-tested principles that make sense of the masses of data and let us make predictions. For example, Germ Theory led to measures to limit the spread of AIDS, where the Divine Punishment Theory failed. The Theory of Evolution has been equally successful, with slowing the spread of insecticide resistance in insect pests among its recent contributions.

But is there a place for speculation in biology? I think there is, so long as we don't confuse it with fact or well-grounded theory. For example, life as we know it uses nucleic acids for heredity and makes much of its cellular machinery from proteins, but can we think of other possibilities? If so, can we design experiments that would detect such alien lifeforms, if they exist, on Mars or perhaps even on Earth?

Similarly, what if some alien life-form -- any sufficiently advanced life-form is indistinguishable from a god -- has intervened in evolution here on earth? Could we develop quantitative methods to measure this effect, as we now do for natural selection and gene flow? Or, suppose we had an old bloodstain purported to be from a demigod; could we extract DNA, look for alleles that don't match anything in the human genome, and (if we found any) clone them into E. coli? A gene for smiting might have military applications. Perhaps others could be reverse-engineered for flood control. (Hey, mixing religion and science was their idea, not mine!)

The topics in the last paragraph may be too speculative to be competitive for tax-supported research grants -- success rates for many NSF programs are around 10% -- but private foundations could certainly fund such research, if they chose. To be taken seriously, however, researchers looking for evidence of intelligent design would need, as in all of science, to design experiments that have the potential to disprove their hypotheses, if those hypotheses turn out to be wrong. And they would need to publish their results in peer-reviewed journals, so that other scientists have a chance to catch any logical fallacies or methodological problems they may have missed.

This is what the advocates of intelligent design have failed to do. Put all the intelligent design papers ever published in a pile and you don't match the productivity of one good graduate student. Whining, as in the much-discussed film, Expelled, is no substitute for science.

March 01, 2008

Knowing when not to cheat

This week’s paper is Facultative cheater mutants reveal the genetic complexity of cooperation in social amoebae published in Nature by Lorenzo Santorelli and colleagues at Rice University and Baylor College of Medicine, both in Texas.

The evolution of cooperation is a central problem in the history of life. Darwin explained how sophisticated adaptations -- “the structure of the beetle which dives through the water… the plumed seed which is wafted by the gentlest breeze” -- can evolve in a series of small improvements over generations. But some of the major transitions in evolution are harder to explain, because It seems that they should have been opposed, rather than supported, by natural selection. The origin of multicellular life is a good example. It’s not that hard to imagine independent cells working together in loose groups for mutual benefit – huddling together for defense, say – but why would a cell give up the ability to reproduce, as most of the cells in our bodies have done?

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February 03, 2008

Natural ecosystems as a source of ideas

This week I want to share some thoughts on “ecosystem services”, starting with this recent paper:
Proximity to forest edge does not affect crop production despite pollen limitation
They found that the closer grapefruit trees were to forest edges, the more visits they got from pollinating bees, but this trend had no effect on fruit production. There’s more to the paper than that, but I want to commend the authors for actually measuring effects on yield. It’s surprisingly common to measure variables that are hypothesized to have some effect on yield, without measuring yield itself. For example, Risch et al. noted that, out of 150 studies on how intercropping affects insect pests, only 19 bothered to measure yield, and only one study determined how much the pests actually affected yield (Environ. Entomol. 12:625). This would be like medical researchers measuring the effect of some treatment on cholesterol but not checking whether there was any effect on the frequency of heart attacks.

“Ecosystem services” have been a hot topic since Constanza et al. published a paper on the topic ten years ago (Nature 387:253). They estimated that nature provides services (pollination, purifying water, etc.) worth $33 trillion per year, exceeding the value of human economic activity. As an argument for conserving nature, it made me wonder how many of those services are or could be provided by managed ecosystems (including properly managed farms), and how many are provided by species that we couldn’t get rid of if we tried (microbes that break down crop residues, for example). Since then, the ecosystem services meme has spread so much that we rarely hear about all the other reasons to preserve wild species and natural ecosystems. One notable exception is a recent paper by D.J. McCauley titled “Selling out nature” (Nature 443:27).

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January 10, 2008

Ants en't ents

Science advances by disproving previously-tenable hypotheses. For example, "The earth is <10,000 years old" was disproved by annual sediment layers long before we were able to estimate the actual age. Actually, Tom Kinraide and I argued in "Strong inference -- the way of science" that a hypothesis needs to be explanatory as well as falsifiable. So for a young earth to ever have qualified as a hypothesis, it would first have needed to explain at least some real world observations. Right off hand, I can't think of any actual data that an unbiased person would look at and say, "Well, these data would make sense, but only if we assume the earth is <10,000 years old."

Similarly, if someone wanted to convert "intelligent design" from religious whining into a scientific discipline, we'd need some falsifiable hypotheses. Suppose, for example, we hypothesized that current features of plants and animals (not just their single-celled, distant ancestors) were supernaturally-imposed designs to maximize their success. That hypothesis is consistent with the many examples of sophisticated adaptations (err, "design"), but what can we conclude from the many examples of maladaptation ("bad design")? Maladaptation is predicted by evolutionary theory (when current conditions don't match those under which past selection occurred, for example) but if some design team is continuously intervening in evolution, do maladaptations imply that they had a busy week? If so, should we expect the problem to instantly disappear, once they get around to it?

This week's paper is another example of the pattern we see repeatedly in biology: many sophisticated adaptations, but also serious "design flaws." In particular, Acacia trees can be fooled into feeding and housing ants that are harming them.

Breakdown of an Ant-Plant Mutualism Follows the Loss of Large Herbivores from an African Savanna was published this week in Science by Todd Palmer and five coauthors, three of whom I know from my years at UC Davis.

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December 26, 2007

This year in intelligent design

Intelligent design and evolution both have definitions not related to biology. Therefore, as in past analyses, I’ve included “species” as an additional search term. A Google Scholar search for articles mentioning “evolution” and “species”, in publications with “journal” in the title – this eliminates some journals, of course -- gave 17,200 hits for 2007. Substituting “intelligent design” for “evolution” reduced this to 51 hits.

This was few enough that I could check each title individually, looking for papers claiming to provide data showing that living things were designed rather than evolving. I was hoping to find at least one such paper to critique in my usual way, but no luck.

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September 11, 2007

Evolving enzymes in the lab

This week's paper is another example of how nonrandom selection from among random variants can solve problems so difficult that we are unable to "design" a solution. As in an earlier post, the selection process was automated, not requiring the human judgement used in breeding crops or dogs.

"Selection and evolution of enzymes from a partially randomized non-catalytic scaffold" was written by Burckhard Seelig and Jack Szostak, both of Boston, and published in Nature (448:828). Their goal was to evolve an enzyme to link two RNA bases together in a particular way, a reaction not found in nature.

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July 09, 2007

Selection beats design, again

This week's paper is "HIV-1 proviral DNA excision using an evolved recombinase" by Indrani Sarkar and others, published in Science (vol.316, p.1912). This paper is yet another example showing that selection (natural or artificial) can outperform design.

To illustrate the point, let me start with a well-known example from plant breeding. Suppose you wanted to make broccoli, starting with its ancestor, wild kale? You could cross them, identify which genetic differences are most responsible for the large edible inflorescence, and transfer those genes to the wild kale. But what if broccoli didn't exist?

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April 19, 2007

This year in intelligent design

There are hundreds of papers published each month whose authors find evolution useful in explaining their results. One would think that, if "intelligent design" has any scientific merit, there would be a significant number of papers each month presenting evidence of supernatural intervention by an intelligent designer. Surely the many religious scientists, in particular, wouldn't fail to publish results that turn out to support intelligent design, even if that wasn't the original focus of their research.

However, I haven't seen even one paper on intelligent design so far this year that meets the basic scientific criteria in my first post. Maybe I've missed some? Let's check the Discovery Institute web site.

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