The Loom

When it comes to evolution, the nation’s attention is focused these days on Dover, Pennsylvania, where parents are suing the local board of education for introducing creationism into the classroom. It’s certainly an important case, but if you really want to get a sense of what’s at stake in the struggle over evolution, I suggest you turn your attention south, to the sunshine state. Florida is trying to have it both ways when it comes to creationism, and sooner or later something’s going to have to give.

Two weeks ago, governor Jeb Bush broke ground on what he has called “a defining moment in Florida’s future.” The Scripps Research Institute, one of the world’s premier biomedical institutions, has agreed to build a huge east-coast campus in Palm Beach. Bush and his fellow Florida politicians had lobbied hard for Scripps to come to their state, because they expect it to be a vast economic boon. Thousands of people work at Scripps, investigating everything from regenerating nerve cells to potential cures for AIDS. It gets lots of money from the National Institutes of Health and other sources to pay all those taxpayers. On top of these attractions, Scripps has spun off dozens of start-up biotech companies around its main campus near San Diego. At the same time, it has attracted other companies to set up shop nearby, further vitalizing the southern California economy. Governor Bush hopes that Scripps East will do the same for Florida. It’s predicted to bring over three billion dollars to the community.

It’s a simple fact that when you bring such a leading player in biological research to your state, you bring a major dose of evolution as well. Evolution is part of the foundation of modern biological research, and the work at Scripps is no exception.

For years Scripps has fostered some of the most ambitious investigations of evolution. At the lab of Paul Schimmel, for example, scientists investigate the evolution of the genetic code: the way in which the sequence in our DNA gets translated into proteins. Gerald Joyce and his colleagues investigate the theory that DNA-based life evolved from a simpler precursor some 4 billion years ago. Floyd Romesburg studies how the structures and functions of proteins have evolved over billions of years, using rapidly changing antibodies as a model. While these scientists are trying to understand what happened to life in the distant past, their work is also serving as the seeds for new start-up companies that hope to make money on new kinds of biological molecules.

Evolutionary biology also helps guide medical research at Scripps. Some researchers study how resistance to drugs evolves in HIV and bacteria. Last year scientists made some important progress in the fight against antibiotic-resistant bacteria by discovering how to prevent the microbes from evolving.

Claes Wahlestedt, one of the scientists who will be setting up shop on Scripp’s Florida campus, searches for new drugs by understanding how the human genome evolved. Genes only become active in our cells when certain proteins lock onto small stretches of DNA near them called enhancers. The enhancer bends until it meets up with another piece of DNA called a promoter. That bending acts like a switch, turning on the gene, allowing it to produce a protein. The elements of these switches are very hard to pinpoint in the human genome. That’s because they are very short and are located hundreds or thousands of positions away from the gene they control. Making matters worse, they are usually nestled within long stretches of DNA that don’t appear to serve any function. Finding these switch elements could prove very important to medicine. A mutation to a switch may make people prone to certain diseases or respond poorly to certain medicines.

Wahlestedt is finding these promoters, and it’s evolution he’s using as his guide. He and his colleagues described their approach in an open-access paper published earlier this year in the journal BMC Genomics. They lined up the sequences of human genes with their corresponding genes in mice. They then looked near the genes, in the long sequence of non-coding DNA, searching for short stretches of DNA that were similar in both species. Their reasoning was this: if a piece of non-coding DNA in the common ancestor of humans and mice didn’t serve an important function, it might pick up mutations over time without causing any harm. As a result, most non-coding sequences should be noticeably different in humans and mice, because we share an ancestor that lived some 100 million years ago. But switches probably played a vital role in that common ancestor, and most mutations that struck them would have had a devastating effect. Natural selection should have prevented most of these mutations from becoming fixed in both humans and mice. As a result, parts of DNA involved in switching genes on and off should look very similar in humans and mice, unlike the other non-coding DNA.

Wahlestedt and his colleagues used this method to identify a number of candidate switches. Further tests confirmed that most of them actually did affect the way genes work. And still more tests showed that humans carry different versions of these switches, and that these differences affect the way that these genes make proteins. If Wahlestedt had used creationism as his guide, he’d still be floundering in an ocean of DNA.

In other words, Jeb Bush is bringing evolution into Florida. But you have to wonder if he knows what he’s doing. That’s because in addition to bringing Scripps to Florida, he’s bringing in a creationist to run his schools.

In August, Bush appointed Cheryl Yecke as his state chancellor of K-12 education. In her previous job, Yecke had served as Minnesota’s state education commissioner. A self-proclaimed creationist, she had said she wanted to get science classes to discuss “a higher power creating life alongside evolution.” Major science organizations, such as the American Institute of Biological Sciences were appalled. Yecke lost the post after a year, but Bush decided she was the right woman for the job in Florida.

Yecke has company in the sunshine state. The chair of the state House Education Council favors teaching intelligent design, and recently introduced a bill that he said would allow students to sue their professors if they didn’t consider it in class. Science standards are up for review next year in Florida, and as this article in yesterday’s Palm Beach Post explains, some observers won’t be surprised if a Kansas-style battle erupts.

How does Jeb Bush handle this contradiction? How does he explain simultaneously embracing evolution-based cutting edge biology and hiring a creationist to run his schools? Florida newspapers are discovering that his solution is simply to avoid the issue altogether.

This summer, for example, reporters approached the governor after he attended a meeting about Florida’s science standards. They asked him if intelligent design should be taught. As the Saint Petersburg Times reported in August, he declined to comment. Later, the Times asked his education commissioner, and he declined too.

Last week Bush was asked again about whether he believes, like his brother, that intelligent design belongs in science classes.

“I don’t know…I don’t know,” he said. “It’s not part of our standards. Nor is creationism. Nor is Darwinism or evolution either.”

That’s wrong. Natural selection and other evolutionary processes are part of the science standards. When Bush was informed of this, he blamed his education commissioner for misleading him. ”I like what we have right now,” he added. “And I don’t think there needs to be any changes. I don’t think we need to restrict discussion, but it doesn’t need to be required, either.”

When pressed further about these contradictions, Bush simply clammed up, as the Miami Herald reported yesterday:

“That is so loaded. That’s like, you’ve already written the article, why do you want me in it? It’s not fair,” Bush told a reporter when asked.

So that’s a ”no” then?

”No, that’s nothing,” Bush said. “That’s no comment. The governor refused to comment. That’s what it is in the article: The governor refused to comment.”

It’s possible that Bush is trying to run out the clock before he’s forced to say something coherent about evolution and creationism. After all, his term ends next year, so any fallout from a fight over school standards may just wind up as the next governor’s problem.

Claes Wahlestedt is frankly baffled by the hostility to evolution in his newly adopted home of Florida. “All our work at Scripps gives evidence of the existence of evolution,” he told the Palm Beach Post yesterday.

I don’t know how long Florida will be able to go on this way, trying to attract the biotech industry while its leading state officials try to teach its students that creationism is an equally valid way of understanding life. Sooner or later, something’s got to give.

Update: 10/9 6:30 pm Fixed description of promoters. Thanks to John TImmer for sending me back to my bio textbook.

Comments

  1. #1 John Timmer
    October 10, 2005

    Good description, but you missed slightly on the terminology. The long-distance gene regulatory elements are called either enhancers (if they increase gene expression) or silencers (if they decrease it). The promoter is the region that’s immediately proximal to the start of where the mRNA is transcribed.

    And enhancers are conserved beyond simply within mammals – putting mouse enhancers into a chicken generally works well, also.

  2. #2 Skeptico
    October 10, 2005

    Great explanation of how evolutionaly theory is a necessary part of much ongoing research – and how useless ID would be. This is a much needed explanation of why evolution is important – thanks.

  3. #3 Wesley R. Elsberry
    October 10, 2005

    In the Palm Beach Post article, Yecke tried to blow off the experiences reported by members of the Minnesota science standards writing committee, especially as those related to the continued push to include the failed “Santorum amendment” as the guiding legal outlook for the standards.

    For those residents of Florida who don’t want to play “trust me” roulette with science education for K-12 students, please drop by the Florida Citizens for Science web site and let us know that you want to get involved.

  4. #4 Joel
    October 10, 2005

    “If Wahlestedt had used creationism as his guide, he’d still be floundering in an ocean of DNA.”

    Why is this? In the paper referenced here’s the main assumption:

    “Currently the most successful approach to overcome this information gap is based on the assumption that sequences conserved between species (here human and mouse) would most likely mediate biological function.”

    A creationist, attempting to “predict functionally relevant SNPs in silico”, could also
    assume the sequences similiar between species are conserved because of functional
    design, and get similar results.

  5. #5 Ed Darrell
    October 10, 2005

    One can hope that the leaders of the Scripps branch in Florida will consider it their duty to bring Ms. Yecke in for a tour, early, and emphasize to her the importance of having kids coming out of high school fully equipped with an understanding of evolution in order to hit the ground running when they get to biology classes at college or university. They may want to enlist former HHS Secretary Donna Shalala, who has a stake in both the research and the education parts of the equation.

    Then they need to do the same for the governor, and for the chairs of the relevant committees in the state legislature (health, research, and education, including higher education if it’s separate from primary and secondary education.

    And while they’re at it, they should invite in the reporters from the Miami Herald especially, with their links to the national Knight-Ridder chain, and from all the other major daily newspapers in Florida.

  6. #6 Carl Zimmer
    October 10, 2005

    Joel–This is a hard question to answer, since we have no paper to look at written by a creationist actually using creationism as a theory to guide the search for regulatory sequences. So it’s all a bit hypothetical. But I would respond to your question with two questions of my own. First, why would regulatory sequences be conserved in two species, if they were both designed independently? Second, why would the vast majority of DNA outside of genes not be so different? If you use conserved sequences as evidence of design, then all the rest of the unconserved DNA is not designed. Evolutionary theory gives clear guidance as to how these patterns emerge. Creationism does not.

  7. #7 Carl Zimmer
    October 10, 2005

    Oops. I meant to say “why would the vast majority of DNA outside of genes be so different,” not “not so different.”

  8. #8 Joseph Poliakon
    October 11, 2005

    I assume you may have heard of the Grand Unified Theory: Wave Theory. Dr. Chaim H. Tejman writes in Chapter 10: Wave Theory and Life of his book entitled United Nature Theory: Wave Theory (Grand Unified Theory) that “Life is not an accidental event. Where methane, ethane, propane and other similar compounds are present organic creations can easily be created without further assistance.”

    Dr. Tejman writes, “The essential matter from which our universe is created is energetic matter. It behaves like living matter, creating every known entity, including living objects and even thought (which occurs through energetic matter-wave interaction). The essential structure of energetic matter is high-energy (concentrated energetic matter) electro-magnetic waves. This simple structure is the basis of everything: every energetic formation and the universe…The DNA (double helix) of all living formations has the same structure as waves: two loops of the same energetic matter, behaving according to the same rules.”

    Is it possible there exists a Grand Unified Theory of Intelligent Evolutionary Bio-Design that is still beyond our imagination and deep understanding which will seamlessly merge the tenets of the Evolutionists with those of the Creationists?

  9. #9 Ann
    October 11, 2005

    I don’t understand why evolution and intelligent design are considered incompatible. Granted, I don’t know much about intelligent design, but wouldn’t it be a good way to teach probabilities to our children? There’s little doubt that evolution is occurring, so the big question is whether life, the universe and everything happened 100% through chance, or whether there was a “guiding hand” of some sort.

    Given how rare life appears to be in our universe, and given the odds that it wouldn’t have occurred here if things had been only slightly different, we could discuss with our children in schools how likely it is that the entire process occurred randomly. Such a discussion would be better than having students memorize only one set of theories that are never questioned at all, in terms of preparing children for future careers as scientists. We could honestly tell children that not everything has been explained, and that we don’t know whether or not there was a ‘creator’. Done right, it could give them a better feel for what science can and cannot tell us, and for which questions are still open. Surely the Scripps Institute wouldn’t be offended by that, would it?

    I’ve only seen this debate from the outside, and the news media tends to give emotions rather than clear arguments from either side. Are you against any mention that life is so improbable that some consider it unlikely to have occurred by chance, or are you simply against the way that intelligent design has been packaged in practice?

  10. #10 John Timmer
    October 11, 2005

    Ann says “Are you against any mention that life is so improbable that some consider it unlikely to have occurred by chance, or are you simply against the way that intelligent design has been packaged in practice?”

    The problem with this is that there is no scientifically valid measurement for the probability of life. It’s an interesting question, and one that’s fine to discuss, but not one that belongs in a science class until we know more – science currently has nothing to say about it. In a similar way, there is absolutely no scientific evidence for intelligent design, leading many of those arguing for it to distort or mislead about actual scientific knowledge. Many of its assumptions (some unidentified designer has intervened in life using methods we cannot understand) are also profoundly unscientific. As a biologist, i mostly object to it being called scientific, and the distortions of its proponents.

    Incidentally, if i sent Carl Zimmer back to his text book, i think i owe him an apology, rather than him owing me thanks. I’d just covered gene regulation in a class i’m teaching, though, so even if i didn’t work on this stuff, i wouldn’t have been able to help myself.

  11. #11 John
    October 12, 2005

    For Ann:
    1) It is good to teach probability to students, in fact, in some ways, that might be more useful to more students than trig or calculus … but that’s a math class.

    2) Students need to understand, not just memorize theories, but they have to to understand the current state of scientific knowledge. A theory is a model or approximation to reality. A new theory may replace the old one if it 1) is consistent with existing data, 2) fits the data better than the old theory, and often 3) makes predictions that are confirmed by observations made later. And if you’re lucky, the theory has practical applications that are beneficial. A theory makes predictions that can be falsified by evidence, but if evidence continues to pile up in its favor, it remains the best current explanation.

    ID is not a falsifiable theory, and it does none of these. If one believes in ID, a non-hypocritical position would be to eschew any food or drugs based on biology-based-on-evolution, and use only those of biology-based-on-ID. Of course, about the only food that hasn’t evolved strongly in the last 10,000 years is wild fish and game, and since there are no drugs based on ID research, there being no useful ID research results, going without most food or modern medicine might be awkward.

    3) For any theory, there are always arguments amongst scientists around the edges of the theory, even if they absolutely agree on the basics. Any student who wants to work in science or engineering has a huge amount to learn. One can waste plenty of time teaching non-science, or trying to take students to the edge of debates by experts, before they’ve learned the basics.

    For example, people once believed the world was flat, and the Flat-Earth Society may well still exist. [In fact, Flat-Earth was actually a theory, although wrong, but ID isn't even a theory, in the scientific use of the term (not the day-to-day use).] Then, they believed the world was a sphere, and the Sun and planets revolved around the Earth in circles, but that didn’t fit the observations, so they added circles onto circles, or “epicycles” to fit better. (Of course, the Earth is better described as an “oblate spheroid”, but it took a while to know that.) Eventually, they realized all planets revolved around the Sun, but it still took a while to understand that orbits were elliptical, not just circular. Newton’s Laws helped explain why, and were a great approximation, and are still good enough for many Earthly uses. Einstein’s Relativity gave an even better approximation, made terrific predictions verified decades later: for GPS satellites to work, you need Einstein, not just Newton. But, Relativity doesn’t explain everything, and people till search for a grand unification of relativity and quantum theory, and there are all sorts of hypotheses (not yet supported theories) flying around. NOBODY prefaces a a first exposure to Relativity by saying “there are all sorts of unexplained gaps” and then pointing people at random other ideas that have zero scientific evidence.

    The Web is full of people who claim that Relativity is Wrong. Most physicists think it is a very good approximation, and it would take a really powerful theory to replace it. Then, the first people could claim there was a “controversy”, and every textbook should have a sticker to show their reservations. This doesn’t seem to happen with any well-accepted theory other than evolution.

    ID is like *really* wanting to go back to the flat-Earth model, by saying there are arguments within modern physics (there are always arguments at the leading edge), and therefore modern physics isn’t right. The history makes it clear that the main ID textbook was edited to convert creationism to ID.

    4) You may have noticed that the world standing of US students in science is not high. From firsthand experience there are a lot of smart, hardworking students in Asia who badly want good jobs in science, and would rather those jobs be *there*, not here. Do you think they teach ID in Singapore? or Japan? or Korea? or China? or India? (I doubt it) Do you think they teach probability and statistics? (yes) The USA has done very well by inward brain drain, but nothing guarantees that will last forever, or even very long. We *can* guarantee American kids won’t get those jobs, that biotech companies won’t be formed here, and that we’ll need to buy the resulting products from other countries. Some school boards are trying hard to achieve this.

    Here in California, UC Berkeley has many more applicants than it can accept. It is being sued because it doesn’t accept ID-oriented biology courses for credit. Of course, California is generally high-tech, and very strong in biosciences, so I don’t expect UCB to change.

    5) Many thoughtful people believe that both science and religion have their own domains, but mixing them is bad for both. My father was a devout Christian, but as an educated farmer, knew evolution worked, and as a 20-year President/VP of the school board, would have been appalled at the thought of teaching ID in our schools. He would also have wondered about the quality of faith that required being shored up by distortion of science.

  12. #12 Anonymous
    October 12, 2005

    not sure what the hubbub re: Ms. Yecke is all about — it appears from what you have written that she espoused teaching that evolution is not a proven fact but a theory, and that there are other theories. sounds like the teaching of science to me. bottom line – if you insist that children must be taught evolution as the origin of the species, then you are relying on only one thing – faith. science is what can be observed and repeated — there is a significant record demonstrating adaptation and survival techniques resulting from evolution — there is not a single instance of one species becoming another (i.e., biological diversity arising from evolution). to make that leap requires faith. how is that more scientific than a “guiding hand??”

  13. #13 John Timmer
    October 12, 2005

    RE: anonymous

    For starters, can you name an alternative scientific theory regarding the diversity of species? I’m a biologist, and i sure can’t. If there was one that was supported by any scientific evidence, we’d know about it by now (as described above, Intelligent Design is not scientific). Given the absence of scientific alternatives, there is nothing to teach other than evolution in science classes.

    Incidentally, if you doubt that the generation of new species has been observed, and for more detail on the above, i recommend you check out http://www.talkorigins.org/faqs/comdesc/. You should be able to see that it’s all pretty scientific, and very little faith is involved.

  14. #14 AntiID
    October 12, 2005

    The most straightforward challenge to ID can be reduced to this:

    Name one example of research in which ID ‘theory’ has played a pivotal role in generating new knowledge, technology, or productive lines of inquiry. What, if anything, is reproducible in any sort of lab which ID propounds?

    ID is simply a game of “give up searching for a natural explanation, and just believe God used supernatural power” there will never be useful scientific outcomes or lines of investigation leading from it.

    Scientists who pray and believe in God don’t pray, let’s just find that God did it and give up and go home. They pray for new insight into the operations and laws of Nature. They pray for the insight to penetrate the natural mystery and to understand the mechanims and processes at work. They hope to find the formulas and math that describes the processes. They hope to find the experiments which disproves or supports a hypothesis. They may care about a hypothesis, but they expect to find improved and better ones as the scientific efforts by many smart, disciplined people progress.

  15. #15 Nortcliff
    October 12, 2005

    Very interesting and factual post that highlights blatant Republican hypocrisy.

  16. #16 Bob Faulkner
    October 12, 2005

    Think back to 4th century Rome and substitute, respectively, ‘Christian’ and ‘Pagan’ for ‘Intelligent Design’ (Creationism) and ‘Darwinian Evolution’ (Science), and you’ll have the historical equivalent which began with the ‘equal opportunity’ for Christianity, encouraged by Constantine, and the ensuing closure of all Pagan centers of learning, enforced by Theodosius.

    Though science is not a religion, religion is politics, and religionists treat any challenge to their absolutist dogma as a political equivalent and rival. The context and motivation of the current confrontation is politically congruent with that of the historical former. As long as scientists delude themselves that the ‘man on the street’ can be swayed by logical argument, they fight a losing battle. Who, then, is to save the world from another ‘Dark Ages’ of inane mysticism?

  17. #17 david
    October 15, 2005

    It is obvious from reading the above comments that most of you have no clue as to what ID/Creationists really believe as far as the differences between mirco-evolution (natural selection) and macro-evolution (goo to you by way of the zoo). Therefore you are arguing against a point of view from a position of ignorance by not researching what the otherside really believes. Oh sure, you can parrot the same old tripe that the NCSE claims that IDer’s believe, but that is not really accurate.
    I understand that what I am doing would be considered an exercise in futility since most of you will not even consider taking a look at what the other side truly believes.
    If evolution is the answer that unequivocally explains it all, from abiogenesis to modern man, then why do over 60% of our people believe that we were created? They have all studied the same evolutionist textbooks for the last 50-60 years. Here comes some elitist remark about the ignorant masses not having the intellegence to understand the true science behind it, so they have to fall back to religion!

  18. #18 Carl Zimmer
    October 15, 2005

    My response to David’s comment is here

  19. #19 Tom Bartlett
    October 20, 2005

    It makes me sick that our nation is run by inbred morons.

  20. #20 Caineisable
    October 25, 2005

    Honestly I don’t see any contridiction in encouraging scientific biomedical research in a state and having Science teachers mention ID is an option in the classroom. I’m not getting it.

    Many people (most in the Scientific community) who believe in ID believe that God created many if not all things via evolution. The thing that I find most offensive about only teaching evoluation is only when its done in a way to exclude faith in God. Evolutionist cannot explain ultimate orgins and so it’s fair to at least acknowledge the possibility if not the necessity of a higher power at some point in the process.

  21. #21 John Mashey
    October 28, 2005

    It would be a fine thing if Florida went ID. California would certainly welcome more Scripps effort back here, and ID in Florida would help that.

    I’ve spoken at Scripps (and many other bioscience research places), and I doubt that researchers there would welcome ID in the schools, regardless of any personal beliefs.

    My father was a devout Christian, Deacon of the local church, and a 20-year President/VP of the local public school board. He would have been rather scornful of ID, but for reasons of both science and faith. As an educated farmer, he perfectly well knew that evolution worked, having studied genetics, plant & animal breeding.

    Regarding faith, he’d say: “God gave us brains to think with, and the parable of the talents says we’d better use them. If someone’s faith is so weak they need to distort the evidence of science to maintain their faith, they might want to think about their faith some more.” Our schools had fine science programs, no trace of creationism. I don’t know if anyone ever tried to introduce it, but it certainly didn’t get very far.

    Too bad Dad wasn’t leading the Dover effort, in place of William Buckingham, who seemed to have read the Bible rather selectively. He seems to have missed the ninth commandment (not bearing false witness), an unwise move in a videotape era.

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