All of science owes debt to Darwin

http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2009/02/07/MNPJ15M1VJ.DTL

All of science owes debt to Darwin
David Perlman, Chronicle Science Editor
Sunday, February 8, 2009

The shy young naturalist Charles Darwin, who voyaged around the world aboard HMS Beagle and became the bearded sage of rational scientific thought, is having a birthday this week - his 200th - and celebrations have already begun throughout the Bay Area, and indeed on every continent.

"No one," says Kevin Padian, a Berkeley biologist and tracker of dinosaur evolution, "has influenced modern thought, modern science, and indeed our modern culture more than Darwin.

"His influence is everywhere, and science would be impossible without him."

Every true scientist at work today is in fact a Darwinian.

They are decoders of the human genome, immunologists battling AIDS, stem cell researchers seeking tomorrow's cures, anthropologists unearthing fossil hominids to define our human ancestry - even the "astrobiologists" seeking life on other planets while they study organisms living in extreme conditions on Earth.

The man who was born just 200 years ago Thursday did not stumble on his theory of natural selection in one blinding insight - as legends that have morphed into quasi-history would have it - when he observed the varied finches and mockingbirds and tortoises of the Galapagos Islands during the Beagle's stopover there.

No, his theories developed long after the observations he had made while adventurously collecting fossils of long-extinct beasts and living plants and animals - largely in South America.

His first insights on evolution and the emergence of new species came to him two years after the Beagle returned to England, and it wasn't until 1859, more than 20 years later, that Darwin, inspired by the writings of Thomas Malthus on population pressures and Charles Lyell on the ancient age of Earth's geology, completed his first great work: "On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life."

To evolution researchers today, the California Academy of Sciences in San Francisco is an important source of information, for the academy maintains the world's largest collection of Galapagos plant, animal and insect life. The Galapagos archipelago and the Darwin Research Station in the tourist-jammed town of Puerto Ayora on the island of Santa Cruz there remain an international monument to his achievement.

Collecting specimens

Darwin, no ornithologist, had collected scores of finches and mockingbirds from different Galapagos islands and noticed how widely varied the finch beaks were. He thought some were not finches at all.

But it was long after the Beagle's return to England that he learned his birds were of widely different species and wondered how they came to be.

"One might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends," he wrote in "The Voyage of the Beagle."

Descent from common ancestors with modification are watchwords for scientists of all stripes today. And Darwin saw more clearly than anyone that the pressure for modification came primarily through natural selection: Beasts or plants or microbes come from common ancestors. They are modified to adapt best to an environment, and produce descendents; those who aren't adapted die by the wayside - just as the Neanderthal people may have died away competing in vain with the first Homo sapiens, our direct ancestors. That's today's version.

Species adaptation

"A steady thread of Darwin's natural selection runs through all our work," says David Mindell, dean of science and curator of ornithology at the California Academy of Sciences in Golden Gate Park who studies the evolution of predatory birds - hawks, eagles, falcons and the like. "Darwin has given us the way to see how species change over time, how new species arise - and that fact remains the real focus of all scientists who study evolution."

The concepts of natural selection and Darwin's later parallel discovery of sexual selection operate at all levels of life, and not just among vertebrate animals that reproduce sexually, Mindell says.

"You can put a culture of bacteria into a laboratory flask, and even though they reproduce by fission, you can see natural selection operating even there - new bacterial species will arise almost instantaneously," he says.

Among his own birds of prey, as Mindell notes, Darwin's concept of sexual selection operates clearly: A bird uses its plumage - or its chirps or raucous cries and whistles - to signal to a potential mate that it has the most desirable genes for producing the best descendants. To Mindell, that means that studying "molecular systematics," or the structure and sequences of genes in his birds, can lead to clues to the evolution of new species.

They are, Mindell says, "molecular clocks" for the history of speciation.

Intelligent design

Padian, the Berkeley biologist, testified as an expert witness during the famed 2005 trial in Dover, Pa., over the school district's decision to order the teaching of intelligent design as an alternative to evolution in explaining the origin of life. Intelligent design is based on the idea that living organisms are too complex to have evolved naturally, and must have required an intelligent designer to create them.

Like virtually all scientists today, Padian equates intelligent design with biblical creationism, a view held also by the judge in the Dover case who ruled that intelligent design "is a religious view, a mere re-labeling of creationism, and not a scientific theory." In Dover, evolution won.

Despite that ruling, efforts to promote intelligent design continue to roil school districts across America, and Darwin's evolution - no more a theory than gravity or the round Earth - is still under legal assault.

Padian is a foremost expert on the evolution of dinosaurs, the creatures that ruled the earth for about 160 million years and whose mass extinction an estimated 65 million years ago has given rise to conflicting causes: a meteorite crashing onto Earth or Indian volcanoes erupting in catastrophe.

To Padian, however, the dinosaurs never really went extinct. His studies, and those of many others, have provided overwhelming evidence that dinosaurs evolved in true Darwinian fashion to become today's birds.

Some of the meat-eating fossil dinosaurs that Padian and other scientists have unearthed at ancient sites around the world bore fierce horns, while their more placid plant-eating relatives did not. So Padian today is also studying the evolution of horns in modern animals.

"That's why," he said recently, "I studied a thousand skulls of different antelope species in South Africa - to see how they fit into Darwin's tree of life."

E-mail David Perlman at dperlman@sfchronicle.com.

This article appeared on page A - 1 of the San Francisco Chronicle

Spore, Dividing Cells and Opinions

http://www.washingtonpost.com/wp-dyn/content/story/2008/09/13/ST2008091302271.html

Spore, Dividing Cells and Opinions
By Mike Musgrove
Sunday, September 14, 2008; F01

The Turtok species is trying to kill me. The Katmondo are my allies. I'm trying to befriend the Wurbles, but it might not work out, due to some other interplanetary commitments I'm hoping to maintain. Probably none of these alien species would want anything to do with mine, if they knew we used nuclear weapons as a shortcut to world domination a while back on our home planet of Fiumincino.

The latest computer game from the creator of the Sims lets players design and manage a virtual species from its earliest moments as a cell, all the way up to the era when it builds rockets and begins to venture into space and encounter other virtual lifeforms. It's an ambitious adventure filled with humor and eye candy, but at the end of its first week of release, Spore has already been the subject of much grumbling among game fans.

What has mainly caused a stir -- and some cancelled game purchases, from the looks of it -- is the title's anti-piracy scheme, which publisher Electronic Arts says is designed to keep people from sharing the $50 game disc with all of their friends.

Spore is set up so that owners have to activate the software online to enjoy all of its features, such as access to the online content users can download to fill out the game's virtual universe. Under the terms of the game's built-in "digital rights management" software, one copy of the game can be installed on three computers.

But those who have had a bad experience with this sort of software say the system counts computer upgrades as separate installations. In essence, they argue, EA is making people rent rather than buy the game. Some of the title's potential customers are actively discouraging their friends and anyone who will listen not to buy the game or any game from EA until the company changes its policies.

At Amazon.com, some 2,000 or so people have logged on and given Spore the site's worst possible rating; nearly all cite the DRM software as the reason for their contempt. The game's average review at the site is now a lowly one, out of a possible five, stars.

"I have no interest in paying full price for a game that I will be severely restricted from being able to play at a later point," one commenter wrote. "Imagine applying this to other products. What if you could only watch purchased DVDs on one specific DVD player and once you've played it on that system, you could never play them on another one?"

EA, for its part, says that 90 percent of its customers install PC games on only one machine, and that people with special circumstances requiring additional installations can call the company's customer-support number to plead their case. The publisher defends its antipiracy scheme as "just like online music services that limit the number of machines you can play a song on."

It's too early to tell if this week's flap will have an impact on the game's long-term success. Spore started the week as the top-selling item in Amazon.com's video game store when it went on sale, but by the end of the week it had slipped a couple of notches. A bite-sized version of Spore released for the iPhone for $9.99 was the No. 1 selling application at iTunes last week.

Aside from the DRM complaints, the game's reviews have been generally positive, if not wildly enthusiastic. Many of Spore's early players have complained that the ambitious game that was pitched as "your universe in a box" isn't entirely satisfying.

I nudged three friends into playing it last week, and none of them fell entirely in love with the game. One found Spore's many parts to be all derivative of other games, one had complaints with the game's interface, and one said she simply found the Sims more addictive than the new title.

I've been managing the evolution of my species, a meat-eating-type creature I dubbed Humberticus, for about 9 billion years, according to the game's clock. In real-world time, that's somewhere north of a dozen hours, and I could probably pour another dozen hours traveling through virtual space in order to encounter more of the oddball creations people have designed with the game's nifty tools.

The game's chief designer, Will Wright, told me a couple of weeks ago that he always figured this would be a half-finished game at its launch. That's because the idea was to get users to create the content; the aim was to make the game "like browsing an endless art gallery," he said.

As I peruse the Sporepedia, an online roster that keeps track of what players have designed, I find a series of creatures that users have evolved to look like hamburgers. Another player has spent serious time building a collection of famous fictional spaceships from Star Wars and Star Trek. One of the most popular creatures right now is the Charles Darwin species, a pudgy, bearded bald guy dressed in caveman gear. Already, sort of like on Facebook, I've got my real-world friends and Spore-friends mixed together as I subscribe to content made by the game's early wave of players.

If Spore becomes wildly popular, like Wright's last game, I can only imagine that the game will follow the rest of the Web's development and we'll soon see a new equivalent of spam species, with creatures trying to sell Viagra or promote online dating sites.

Already, I'm a little tickled to see that people are using the game to poke fun at itself. Some joker, for example, has created a species named EA's DRM Policy. While I can't tell for sure what it's supposed to be, it looks kind of like a creature with its head parked up in its hindparts.

Six Things Ben Stein Doesn't Want You to Know...

http://www.sciam.com/article.cfm?id=six-things-ben-stein-doesnt-want-you-to-know

April 16, 2008
Six Things in Expelled That Ben Stein Doesn't Want You to Know...
...about intelligent design and evolution
By John Rennie and Steve Mirsky

In the film Expelled: No Intelligence Allowed, narrator Ben Stein poses as a "rebel" willing to stand up to the scientific establishment in defense of freedom and honest, open discussion of controversial ideas like intelligent design (ID). But Expelled has some problems of its own with honest, open presentations of the facts about evolution, ID—and with its own agenda. Here are a few examples—add your own with a comment, and we may add it to another draft of this story. For our complete coverage, see "Expelled: No Intelligence Allowed—Scientific American's Take.

1) Expelled quotes Charles Darwin selectively to connect his ideas to eugenics and the Holocaust.

When the film is building its case that Darwin and the theory of evolution bear some responsibility for the Holocaust, Ben Stein's narration quotes from Darwin's The Descent of Man thusly:

With savages, the weak in body or mind are soon eliminated. We civilized men, on the other hand, do our utmost to check the process of elimination. We build asylums for the imbecile, the maimed and the sick. Thus the weak members of civilized societies propagate their kind. No one who has attended to the breeding of domestic animals will doubt that this must be highly injurious to the race of man. Hardly anyone is so ignorant as to allow his worst animals to breed.

This is how the original passage in The Descent of Man reads:

With savages, the weak in body or mind are soon eliminated; and those that survive commonly exhibit a vigorous state of health. We civilized men, on the other hand, do our utmost to check the process of elimination. We build asylums for the imbecile, the maimed and the sick; we institute poor-laws; and our medical men exert their utmost skill to save the life of every one to the last moment. There is reason to believe that vaccination has preserved thousands, who from a weak constitution would formerly have succumbed to small-pox. Thus the weak members of civilized societies propagate their kind. No one who has attended to the breeding of domestic animals will doubt that this must be highly injurious to the race of man. It is surprising how soon a want of care, or care wrongly directed, leads to the degeneration of a domestic race; but excepting in the case of man himself, hardly anyone is so ignorant as to allow his worst animals to breed.

The producers of the film did not mention the very next sentences in the book:

The aid which we feel impelled to give to the helpless is mainly an incidental result of the instinct of sympathy, which was originally acquired as part of the social instincts, but subsequently rendered, in the manner previously indicated, more tender and more widely diffused. Nor could we check our sympathy, even at the urging of hard reason, without deterioration in the noblest part of our nature. The surgeon may harden himself whilst performing an operation, for he knows that he is acting for the good of his patient; but if we were intentionally to neglect the weak and helpless, it could only be for a contingent benefit, with an overwhelming present evil.

Darwin explicitly rejected the idea of eliminating the "weak" as dehumanizing and evil. Those words falsify Expelled's argument. The filmmakers had to be aware of the full Darwin passage, but they chose to quote only the sections that suited their purposes.

2) Ben Stein's speech to a crowded auditorium in the film was a setup.

"Viewers of Expelled might think that Ben Stein has been giving speeches on college campuses and at other public venues in support of ID and against "big science." But if he has, the producers did not include one. The speech shown at the beginning and end was staged solely for the sake of the movie. Michael Shermer learned as much by speaking to officials at Pepperdine University, where those scenes were filmed. Only a few of the audience members were students; most were extras brought in by the producers. Judge the ovation Ben Stein receives accordingly.

3) Scientists in the film thought they were being interviewed for a different movie.

As Richard Dawkins, PZ Myers, Eugenie Scott, Michael Shermer and other proponents of evolution appearing in Expelled have publicly remarked, the producers first arranged to interview them for a film that was to be called Crossroads, which was allegedly a documentary on "the intersection of science and religion." They were subsequently surprised to learn that they were appearing in Expelled, which "exposes the widespread persecution of scientists and educators who are pursuing legitimate, opposing scientific views to the reigning orthodoxy," to quote from the film's press kit.

When exactly did Crossroads become Expelled? The producers have said that the shift in the film's title and message occurred after the interviews with the scientists, as the accumulating evidence gradually persuaded them that ID believers were oppressed. Yet as blogger Wesley Elsberry discovered when he searched domain registrations, the producers registered the URL "expelledthemovie.com" on March 1, 2007—more than a month (and in some cases, several months) before the scientists were interviewed. The producers never registered the URL "crossroadsthemovie.com". Those facts raise doubt that Crossroads was still the working title for the movie when the scientists were interviewed.

4) The ID-sympathetic researcher whom the film paints as having lost his job at the Smithsonian Institution was never an employee there.

One section of Expelled relates the case of Richard Sternberg, who was a researcher at the Smithsonian Institution's National Museum of Natural History and editor of the journal Proceedings of the Biological Society of Washington. According to the film, after Sternberg approved the publication of a pro-ID paper by Stephen C. Meyer of the Discovery Institute, he lost his editorship, was demoted at the Smithsonian, was moved to a more remote office, and suffered other professional setbacks. The film mentions a 2006 House Committee on Oversight and Government Reform report prepared for Rep. Mark Souder (R–Ind.), "Intolerance and the Politicization of Science at the Smithsonian," that denounced Sternberg's mistreatment.

This selective retelling of the Sternberg affair omits details that are awkward for the movie's case, however. Sternberg was never an employee of the Smithsonian: his term as a research associate always had a limited duration, and when it ended he was offered a new position as a research collaborator. As editor, Sternberg's decision to "peer-review" and approve Meyer's paper by himself was highly questionable on several grounds, which was why the scientific society that published the journal later repudiated it. Sternberg had always been planning to step down as the journal's editor—the issue in which he published the paper was already scheduled to be his last.

The report prepared by Rep. Souder, who had previously expressed pro-ID views, was never officially accepted into the Congressional Record. Notwithstanding the report's conclusions, its appendix contains copies of e-mails and other documents in which Sternberg's superiors and others specifically argued against penalizing him for his ID views. (More detailed descriptions of the Sternberg case can be found on Ed Brayton's blog Dispatches from the Culture Wars and on Wikipedia.)

5) Science does not reject religious or "design-based" explanations because of dogmatic atheism.

Expelled frequently repeats that design-based explanations (not to mention religious ones) are "forbidden" by "big science." It never explains why, however. Evolution and the rest of "big science" are just described as having an atheistic preference.

Actually, science avoids design explanations for natural phenomena out of logical necessity. The scientific method involves rigorously observing and experimenting on the material world. It accepts as evidence only what can be measured or otherwise empirically validated (a requirement called methodological naturalism). That requirement prevents scientific theories from becoming untestable and overcomplicated.

By those standards, design-based explanations rapidly lose their rigor without independent scientific proof that validates and defines the nature of the designer. Without it, design-based explanations rapidly become unhelpful and tautological: "This looks like it was designed, so there must be a designer; we know there is a designer because this looks designed."

A major scientific problem with proposed ID explanations for life is that their proponents cannot suggest any good way to disprove them. ID "theories" are so vague that even if specific explanations are disproved, believers can simply search for new signs of design. Consequently, investigators do not generally consider ID to be a productive or useful approach to science.

6) Many evolutionary biologists are religious and many religious people accept evolution.

Expelled includes many clips of scientists such as Richard Dawkins, Daniel Dennett, William Provine and PZ Myers who are also well known as atheists. They talk about how their knowledge of science confirms their convictions and how in some cases science led them to atheism. And indeed, surveys do indicate that atheism is more common among scientists than in the general population.

Nevertheless, the film is wrong to imply that understanding of evolution inevitably or necessarily leads to a rejection of religious belief. Francisco Ayala of the University of California, Irvine, a leading neuroscientist who used to be a Dominican priest, continues to be a devout Catholic, as does the evolutionary biologist Ken Miller of Brown University. Thousands of other biologists across the U.S. who all know evolution to be true are also still religious. Moreover, billions of other people around the world simultaneously accept evolution and keep faith with their religion. The late Pope John Paul II said that evolution was compatible with Roman Catholicism as an explanation for mankind's physical origins.

During Scientific American's post-screening conversation with Expelled associate producer Mark Mathis, we asked him why Ken Miller was not included in the film. Mathis explained that his presence would have "confused" viewers. But the reality is that showing Miller would have invalidated the film's major premise that evolutionary biologists all reject God.

Inside and outside the scientific community, people will no doubt continue to debate rationalism and religion and disagree about who has the better part of that argument. Evidence from evolution will probably remain at most a small part of that conflict, however.