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Creationism reappears in Texas

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Of course, it never really disappeared, as Michael Zimmerman notes in an article in the Huffington Post this past week.

I will not go into detail, but according to Professor Zimmerman, a committee of the Texas State Board of Education had voted 6-2 to remove four standards that had been added in 2009, more or less at the last minute. Suffice it to say that the standards had been supported by Don McLeroy when he was chairman of the SBOE, and the two dissenting votes were by the creationists who, Professor Zimmerman says, were “added” to the current committee.

Now, things get nasty. The committee is not scheduled to present its recommendations to the full Board until November. Nevertheless, Ray Bohlin, one of the two dissenting committee members and vice-president of something known as Probe Ministries, attacked the committee’s recommendation at a recent Board meeting. No one else from the committee had attended the Board meeting, so the Board received an unscheduled and “one-sided perspective on the four anti-science, politically driven standards.”

Kathy Miller, president of the Texas Freedom Network, wrote to the SBOE (as quoted by Professor Zimmerman), complaining that “a number of state board members seemed willing to call into question [the committee’s] objectivity and professionalism based on hearsay from one individual.… Some board members even suggested that the panelists somehow want to prevent students from asking questions.”

It is distressing, then, that Mr. Bohlin in effect went over the head of the committee and directly to the board, and, perhaps more importantly, that some of the Board were sympathetic to his position. Though Don McLeroy lost his position as chairman of the SBOE, I am afraid Texas and we are by no means done with creationist attacks on the schools.

By Gaythia Weis.

An uproar fanned by the right-wing media has left a University of Colorado at Colorado Springs professor and two instructors with quite a tightrope walk. The uproar involves an online humanities and environmental health class at the University of Colorado at Colorado Springs, entitled “Medical Humanities in the Digital Age.” The three faculty members (and others) may have to walk softly when teaching courses that may be a subject of public controversy. In my opinion, statements calling for “balance” (below) by a UC Board of Regents member and UC President Bruce Benson have potentially negative ramifications for academic freedom and the teaching of politically controversial material in a science-appropriate manner.

The controversy here originated with an e-mail sent by the professors indicating that the course would be based on science and would not be a forum for discussing other ideas, as reported by a Colorado Springs TV station:

The point of departure for this course is based on the scientific premise that human-induced climate change is valid and occurring. We will not, at any time, debate the science of climate change, nor will the “other side” of the climate change debate be taught or discussed in this course. This includes discussion among students in the discussion forums. Opening up a debate that 98 percent of climate scientists unequivocally agree to be a non-debate would detract from the central concerns of environment and health addressed in this course. [Excerpt from email.]

It seems from this link that the professors’ response was a specific response to students worried about their grades in the class. (Note that the College Fix advertises itself as offering “right-minded news and commentary from across the nation.”)

This source is not one I’d usually quote, but it does indicate the involvement of one of the conservative UC Board of Regents members in the controversy:

John Carson, a member of the University of Colorado Board of Regents, said he plans to make inquires Thursday about an email from three University of Colorado at Colorado Springs professors who advised students to drop the class if they dispute climate change.

“I have a lot of questions after reading this reported email sent to students,” Mr. Carson told The Washington Times. “We should be encouraging debate and dialogue at the university, not discouraging or forbidding it. Students deserve more respect than this. They come to the university to be educated, not indoctrinated.”

After Googling the professors involved, I see that they are now apparently under attack:

Thus, I offer you their emails along with a request that you politely send them links to information disputing the obvious hoax of man-made climate change:

Then again, you’re probably just pissing into the wind, as these three professors have already declared themselves to be cognitive idiots who are incapable of neuroplasticity (i.e.[,] learning anything new or expanding their knowledge in any way whatsoever). One of them also has a PhD! (I didn’t realize they were handing out PhDs for f–ktardery studies… hmmm…)

Moving forward in time, here is an article dated 9/8 that gives some data on an e-mail apparently sent by UC President Bruce Benson to UCCS Chancellor Pam Shockley-Zalabak. It would be interesting to read the entirety of this e-mail to see more about the context of “a little more balance”:

University of Colorado President Bruce Benson also wanted more “balance” from the professors. In an email The Colorado Independent obtained last week, Benson wrote to the regents about the email controversy. “I talked with Pam [Shockley-Zalabak, Chancellor of UCCS] about a variety of issues on her campus, including the faculty syllabus that has caused a stir recently,” he said. “I am not happy about it[,] and I shared that with Pam. While the issue falls squarely in the realm of academic freedom, it also seems that a little more balance would have helped.”

The Chancellor’s apology seems to me to have been carefully phrased and limited:

I am issuing an apology for the public concern that this has generated.

I can understand why Benson’s apparent e-mail to the Chancellor may have led her to feel the need to apologize. And, moving down the chain of command, she has now apparently told the professors teaching the course that their e-mail was “ill advised.” I frankly do not agree that it was ill advised. Progress in science education coursework cannot be made if time must be continually taken out to rehash basic underlying principles at the instigation of active denialists. Thus, it also seems to me that future directions have at least the potential to stray from remaining “squarely in the realm of academic freedom” and wandering off into denialism and politics. The Chancellor should have stood up for her faculty.

Geology for evangelicals

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In honor of the opening of Ken Ham’s nefarious Ark “replica” today – you know, the one made out of gopher steel and wood – I decided to post this piece about a book written by evangelical scientists who know better than to treat the book of Genesis as history or science, for evangelical laypersons who either know better than to treat the book of Genesis as history or science, or can be taught to know better.

Grand_Canyon_Cover.jpg

The book is called The Grand Canyon: Monument to an Ancient Earth, and it is an anthology written by competent people and directed at evangelical Christians. Indeed, the subtitle is, “Can Noah’s Flood Explain the Grand Canyon?” The book, which I have not seen, appears to be lavishly illustrated, with 255 photographs and 104 diagrams and sketches, according to Church & State magazine. It is being sold in all 8 bookstores in the Grand Canyon National Park.

I am getting virtually all my information from an article in the latest issue of Church & State magazine. They note that the book has 11 co-authors, 8 of whom are evangelical Christians, and 3 are agnostics. The authors’ specialties include geology, biology, and paleontology. Church & State quotes Steven Newton of the National Center for Science Education to the effect that the book “does a great job of explaining the science of Grand Canyon’s spectacular geology, as well as helping readers understand how the creationist misuse of Grand Canyon finds no support from science.”

Importantly, the publisher of the book is an evangelical firm, Kregel Publications, which, according to co-author Tim Helble, “was a good match for us because they have … published other books dealing with origins issues and would be able to sell the book in venues where evangelicals can be reached.” The last seems very important to me.

The bulk of the Church & State article is an interview with Mr. Helble, a retired hydrologist with the National Weather Service. Mr. Helble states explicitly that the “11 authors wanted to help counter the misleading information being disseminated by the young-Earth creationist (YEC) ministries.” He recognized the problem in 1994 when he found a book, Grand Canyon: Monument to Catastrophe, edited by PhD geologist Steve Austin, and apparently chock full of errors. Here are a few snippets from the interview:

Three things we agreed to before we started writing were (1) our target audience is people who are uncertain about the age of the Earth, (2) a Christian reader shouldn’t feel like he/she is being ridiculed and (3) a college science degree shouldn’t be needed to understand it. …

Of course the Bible has tremendous value – I just think the young Earthers over-globalize the flood account, fail to see the worldview of the ancient Near East people and miss out on the rich poetic devices used in the early parts of Genesis. …

I think those claiming censorship misunderstand how the scientific process works. You can’t write an article about something like a geologic formation that basically says “the Flood did it,” and expect to have it accepted by a scientific journal. There has to be a quantitatively realistic mechanism consistent with the laws of physics behind what you are proposing. …

Creationism is a third rail in public schools, but there are some ways to inoculate students against it without directly addressing the subject. Schools could to do a better job of teaching how we know the Earth is old. For example, instead of just teaching that sedimentary rocks are made of sediments like sand and silt, students can be shown how fossils are found in such rocks of things that take a long time to form like intact reef systems, termite nests, forest communities and orderly nests of unhatched dinosaur eggs. …

By the way, when a student brings up young-Earth arguments, the worst thing to do is attack his or her faith. All you’re doing then is reinforcing the “us-vs.-them” mindset and helping the young-Earth ministries keep a lifetime follower. …

It certainly seems like there is a clash [between science and religion] if you focus on the extremes – the “new atheists” at one end and the YECs at the other. It’s interesting that both of them insist on a wooden, literal interpretation of Genesis 1-11.

I think religion and science can coexist if they don’t tread on each other’s turf where it’s not appropriate. I’ve seen new atheists use some pretty bad theology, and I think religious people should accept that there are some things that you just have to take on faith – stop trying to find “ultimate proofs” of difficult theological ideas like creation.

I am an old atheist (or, as I prefer to put it, a strong agnostic), and I do not know what is wooden about my interpretation of Genesis, but we will let that go. I think that among Mr. Helble’s most important remarks are that people should not feel that they are being ridiculed (yes, I know it is difficult at times, and the line between gentle satire and ridicule is sometimes uncertain), students should not think their faith is being attacked, and religion and science can coexist if they do not “tread on each other’s turf.” That is, as your local accommodationist, I think he is right that we have to accept religious people as they are, but only as long as they do not make claims that are flatly contrary to scientific fact.

Avida-ED is educational software that provides an accessible presentation layer on the Avida artificial life platform. The first version was released nine years ago, and today marks Prof. Rob Pennock’s release of version 3, with a formal presentation at Evolution 2016. Avida-ED is geared toward the needs of undergraduate and advanced high school curriculum use.

The new version, Avida-ED Web 3.0, is a web application: it runs in your browser (Firefox or Chrome currently; Safari, Internet Explorer, and Edge have some compatibility issues). To get it, visit the canonical Avida-ED site, or the mirror site. As a web application, Avida-ED Web 3.0 lowers the barriers to use, restoring the ability for those running Linux to use Avida-ED, and giving Windows users access to the latest feature set. While installation is not required, there are installers for MacOS and Windows that set up a local HTTP server and launch a local copy of Avida-ED Web in the default browser. This latter option may be useful for people who expect to be without internet access when they want to use the program. More discussion below the fold.

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A commenter on an earlier thread directed our attention to an article by Zack Kopplin in the Daily Beast, “School teaching creationism with video from Islamic sex cult.” The headline may be a bit over the top, but the gist of the article is that the school district is employing materials developed by Harun Yahya. To give due credit, here is what the commenter, “Charley Horse,” wrote on the earlier thread:

A bit off topic … but of interest.

School Teaching Creationism With Video From Islamic Sex Cult. An Ohio school district is using a video made by a Holocaust-denying Muslim to undermine evolution in science class.

QUOTE A BIT:

A curriculum map recommends teachers in this public school district show a creationist video, Cambrian Fossils and the Creation of Species as part of 10th grade science education. The video claims that the Cambrian Explosion “totally invalidates the theory of evolution.”

…The district’s curriculum map calls for teaching “an alternative theory called Intelligent Design,” which is another name for creationism. Youngstown suggests teachers show a creationist video, Unlocking the Mystery of Life, produced by the right wing Christian advocacy group, Focus on the Family and by the Discovery Institute, a creationist think tank.…

“Students are reminded how the irreducibly complex system like the flagellum of a bacterial cell could not have evolved slowly, piece by piece and serves as a counter-example to evolution,” says the curriculum, citing another disproven creationist talking point. It also recommends the video Darwin’s Dilemma, also produced by the Discovery Institute. Other materials call evolution a “theory in crisis,” and were created by the All About GOD ministries.

The Daily Beast article directs us to a “curriculum map” and notes,

A curriculum map (PDF) recommends teachers in this public school district show a creationist video, Cambrian Fossils and the Creation of Species as part of 10th grade science education. The video claims that the Cambrian Explosion “totally invalidates the theory of evolution.” The Cambrian Explosion was a time period, nearly 550 million years ago, where, over the next tens of millions of years, the number of species on Earth experienced a (relatively) rapid expansion by evolutionary standards. Christian creationists regularly point to this explosion of life as evidence for creation by God and against evolution.

Blink and you’d miss the Islamic connection in the video. A black screen flashes for less than one second that says “this film is based on the works of Harun Yahya.” In the right corner, there’s a gold bubble that says, “Muhammad is the messenger of Allah” in Arabic.

I followed the link to the curriculum map. I am not a biologist, and I did not read all 24 pages in detail, but, sure enough, on page 3/24, I found,

Dan Phelps just sent us an editorial in the Lexington Herald-Leader. The editorial accuses Kentucky of seeking science jobs while at the same time denying science: not just evolution but also global warming, alternative energy sources, and conservation. The editorial notes that Kentucky is “perennially short of money,” in part because of tax breaks like that for the Ark Park, and concludes,

Kentucky forgoes tax revenue to help deny science while telling students they need to learn it. In homage to coal, Kentucky dumbly stints on alternative energy technologies, or even conservation, while telling young people they need to prepare to work in advanced manufacturing.

The messages aren’t just mixed, they’re in open conflict.

That about sums it up.

By Gaythia Weis.

I want to call attention to the newly enacted legislation, the Every Student Succeeds Act (ESSA), which relinquishes Federal control over many aspects of the education of our nation’s children. In so doing, this law may enable religious activists to exert their influence to a greater extent than previously possible. I need not remind readers of The Panda’s Thumb of the manner in which creationists attempt to subvert the public education system to further their own ideological goals.

ESSA is the latest version of the Elementary and Secondary Education Act (ESEA), which was first enacted in the Lyndon Johnson administration as a means of furthering equality of education in our nation. ESSA is ostensibly directed to address issues, including excessive student testing and ineffective teachers, that many think were problems with the previous No Child Left Behind program. However, the ESSA is the result of bipartisan political compromise and its provisions raise new issues.

Some of these issues ought to be of grave concern to those of us interested in science education. These issues call for our close attention and active monitoring.

I do not know why it is coming to light only now, but a few years ago a Kentucky elementary school rewarded students with “perfect” attendance by taking them on a field trip to the Creation “Museum.” Americans United has reported the story here, and a few days ago we received a press release from Daniel Phelps, a persistent critic of the Ark Park and the Creation Museum. Mr. Phelps has sent his press release to the Associated Press and elsewhere, but he tells us that he cannot get any reporter interested in investigating. We will reproduce his press release below the fold.

Americans United notes that the school’s definition of “perfect” is somewhat flexible, in that one absence counted as perfect. More importantly, they note

And kids have a right to learn about [certain religious concepts] - on their own time or in Sunday school. Such ideas are not appropriate for an official public school field trip, even if that trip was only offered to a handful of students. Instead, kids should be learning sound science - not religious dogma.

Mr. Phelps argues that the trip is “a clear violation of the separation of church and state” and “an act of educational malpractice.” He is concerned that, although this trip happened in 2012, there may be many like it, and he claims that Answers in Genesis “brags that they have stealth missionaries in the public school system.” Mr. Phelps’s entire press release follows.

College internships are like test-driving a new car. They are a great way to get a first-hand look at a specific company and field and see if the work atmosphere is a good fit for you.

Last academic year, I wrote blog posts about evolutionary biology for the Cartwright Lab at ASU. But over the summer, I had an opportunity to learn more about my undergraduate field of study–biomedical engineering–as an intern at a major medical device company in its R&D engineering department.

I had previously worked in academic research labs so I was looking forward to gaining a better understanding of the differences between academia and industry R&D. In my personal experience, academic research involves the discovery and refinement of new technologies that industry can then further develop and market to customers (which are, in the medical device industry, patients, doctors, and hospitals). They have their obvious differences. Industry employees must focus on the company’s bottom line, legal image, and regulatory requirements, while academic researchers must secure grants; at a company, a well-structured 9-to-5 day is standard, while academia offers more flexibility and freedom. But ultimately, early-stage academic research and industry research and development often go hand-in-hand in creating cutting-edge medical care for patients. I enjoyed both for different reasons - academia for its flexibility, and industry for its organization.

I was also eager to observe the state of the gender gap in the engineering industry. The numbers show that this is a huge problem in STEM (science, technology, engineering, math) disciplines - in 2011, a mere 25% of STEM employees were women, and of that total, only 13% of engineers were female. Moreover, women in STEM jobs make an average of $75,100, compared to $91,000 for men (according to the Census Bureau). But while the numbers are discouraging, I have hope for the future based on my summer experience. I did observe that a slight majority of engineers I interacted with at the company were men, but I met several women in engineering management positions, and of the group of about 50 interns, nearly half were women. I suspect that the gender gap will continue to shrink and might even disappear in my lifetime, as long as we continue to encourage young girls and women to pursue STEM and have the confidence to compete with their male counterparts in these fields.

So what’s your opinion? Do you have a different experience of academia vs. industry or gender issues in STEM disciplines?

Stay tuned for future posts about the exciting evolutionary biology research going on in the Cartwright Lab.

I do not know whether Cope will turn out to be the mouse that roared or the Energizer bunny – or maybe Don Quixote – but the Tenth Circuit Court of Appeals heard oral arguments the other day in Cope’s appeal of a ruling in favor of the Kansas State Board of Education. I am inclined toward the Energizer bunny, but the Appeals Court rejected Cope’s attempt to file a surreply, which I gather is sort of a reply to a rejoinder to a response and is generally prohibited. At any rate, the lawsuit against the Kansas State Board of Education (hereinafter, as your lawyer might say, Kansas) was dismissed in December of last year.

PT first reported on Cope here; you may learn more about them here. According to Charity Navigator, their annual income is less than $50,000 per year, so they do not have to file Form 990 with the IRS. Americans United for the Separation of Church and State quoted Steven Case, director of the science center at the University of Kansas, to the effect that their lawsuit was “about as frivolous as lawsuits get.” Evidently, the Judge, Daniel D. Crabtree, agreed; he dismissed the case in large part because the plaintiffs (Cope and a number of others including parents of children in Kansas schools) lacked standing. You may find the documents in the case here.

Standing seems like a concept that only a lawyer could love, but all it says is that you have to be harmed or imminently harmed in order to sue someone (“injury in fact”). Additionally, if you are harmed, you must sue the entity who harmed you, not a third party. And finally (a new one to me), the harm that was done to you must be redressable by a favorable decision by the Court. Taxpayers, not incidentally, do not have standing to sue a government agency merely because they are taxpayers.

Cope, chugging along tirelessly, appealed Judge Crabtree’s ruling in March of this year, and Kansas replied in June. The Tenth Circuit Court of Appeals heard oral arguments last Wednesday morning, so I hopped on a bus and went down to Denver. To no one’s surprise, John Calvert represented Cope. Kansas was represented by Dwight Carswell, an assistant solicitor general for Kansas. I frankly thought that Calvert was somewhat more effective in his presentation than Carswell.

The discussion centered largely on the harm that may have been done to the plaintiffs. Much of the Judges’ questioning concerned the fact that the standards (Next Generation Science Standards) adopted by Kansas are only advisory, and local school districts are not required to adopt them. Indeed, school districts are required to teach science, but not instructed how to do so. The Judges questioned Carswell closely on the content of Kansas law and the discretion of local school boards on implementing standards adopted by the State Board of Education. Additionally, no evidence has been presented to suggest that any school district has adopted the standards, nor that any plaintiff has been harmed by the standards. I think one of the Judges remarked that the school teaches children, and the children are not the plaintiffs. On another occasion, a Judge rhetorically asked Calvert whether he had jumped the gun, filing his lawsuit before any district had actually adopted the standards. Calvert was also asked why he sued Kansas and not a school district. What precisely does he want the Court to enjoin?

Calvert argued that the NGSS adopted by Kansas establish a religious preference - a nontheistic religious worldview - because they support methodological naturalism, which he described as an orthodoxy. He further opined that “origins science” should not be taught at all to children in K-8, because they are too young to engage in such discussions, which Cope considers to be inherently religious. Asked whether he would be satisfied with a clause requiring creationism to be taught in addition, Calvert replied, “No,” and argued that an objective view of science that included “critical thinking” and provided alternatives to methodological naturalism would suffice.

Other questions posed to Calvert: What is the injury in fact? Is a nontheistic religious worldview really being taught? Where do we find methodological naturalism in the standards? Do not local school districts have discretion whether to adopt the standards? What areas of Kansas law are pertinent? Precisely what do you want us to enjoin? Would you be satisfied with a declaratory judgment?

Carswell, who was somewhat hard to understand, was asked what normative standard the NGSS might establish. Asked whether the law precluded alternate theories, he responded that the law recognized that the curriculum may be extended and school districts may teach alternative scientific theories. Asked whether any districts had actually implemented the NGSS, Carswell responded that he did not know of any. There was also some discussion about whether (presuming that harm had in fact been done) a declaratory judgment would redress that harm.

Other questions posed to Carswell: Why do we have standards if districts have discretion about them? Is not this whole case speculative because NGSS has not been implemented? Does not injury depend on actual implementation of the standards, as opposed to their adoption?

After the hearing, I met Clare Leonard, an education activist and fellow Colorado Citizens for Science member, in the hall. Calvert was holding, um, court surrounded by a half-dozen or more of his minions. If the decision is based on acting ability, Calvert wins. But I had the impression that the Court was much more skeptical of his position than of Carswell’s, particularly of his claim that there was an injury in fact.

Cope takes the position that science is a religion. They may be tilting at windmills; but they can still do real damage.

Acknowledgments. Thanks to Glenn Branch for inciting this whole expedition; to Deanna Young and Clare Leonard for pertinent discussion following the hearing; to Clare Leonard for the coffee; and to all three for numerous emendations, including many of the questions posed by the Court..

Simon Brown of Americans United reports that 2 Kentucky lawmakers plan to introduce a bill that would prohibit local public schools from beginning the fall term before late August. The avowed purpose of the legislation is to support the Ark Park. One of the legislators, Damon Thayer, explained,

Grant County is set to become a major tourist destination due to the presence of the Ark. But there won’t be many families from Kentucky visiting in August if we continue with the current calendar

Mr. Brown points out in his article, however, that if the Ark Park will truly get 2 million visitors in its first year, the vast majority will not come from Grant County and thereabout. Local school officials are not so keen on the idea either.

In addition, and not entirely off topic, Dan Phelps notifies us of another editorial (available in hardcopy only) by Mark Looy of Answers in Genesis. Mr. Phelps writes that Mr. Looy

will not admit that AIG’s loss of the tax incentive is because of their discriminatory hiring practices. He ignores the advertisement for Computer Assisted Design technician from a year ago that got them in trouble. If you recall, the advertisement required adherence to AiG’s statement of faith, salvation history, and membership in very specific types of Christian churches. Furthermore, when Ark Encounter originally received the tax incentive in 2010/2011 they specifically said they would not discriminate in hiring.

Ark Encounter is a for-profit corporation, and Mr. Looy knows perfectly well how to get his tax incentives restored; as I noted recently,

… Ark Encounter’s tax incentives will be restored, if only they pledge in writing that they will not discriminate in employment. Ark Encounter has so far declined to give such assurance, which makes a body speculate that they just might be thinking of laundering all Ark Encounter employment through Answers in Genesis in order to circumvent the law.

The Washington Post reported the other day that Justice Antonin Scalia, in a commencement address, said,

Humanity has been around for at least some 5,000 years or so, and I doubt that the basic challenges as confronted are any worse now, or alas even much different, from what they ever were.

I suppose that “at least 5000 years” gives you some wiggle room, but I would hardly call, say, 200,000 years “at least 5000 years.” That is a bit like saying, “The trip from Boulder to New York is at least 20 kilometers.”

Jerry Coyne, who is much nicer than I am, thinks that it might have been “just an offhand remark that’s been blown out of proportion.” Well, maybe, but I watched most of the speech on Professor Coyne’s website, and I could not help but notice that Justice Scalia was reading that text: he did not misspeak.

Justice Scalia dissented in Edwards vs. Aguillar, but he seemed more concerned with whether the legislature intended creation “science” as a religious doctrine than with its scientific merit. He also supported the “balanced treatment” argument to the effect that students who learn evolution are entitled to the opposing view as well. His argument was well reasoned but depended on the assumption that creation science is not a religious doctrine if its supporters think it is not.

Contrary to some reports, Justice Scalia did not say, “The body of scientific evidence supporting creation science is as strong as that supporting evolution”; rather, he was paraphrasing the testimony of witnesses and states explicitly “that I by no means intend to endorse its accuracy” but that “what is crucial is not [the legislature’s] wisdom in believing that [a certain secular] purpose would be achieved by the bill, but their sincerity in believing it would be” [italics in original].

Still, Justice Scalia generally comes across as an authoritarian, uncomfortable with ambiguity and guided by literalist interpretations. If he takes the Bible as literally as he takes the Constitution, then it is easy to see that he might well believe in a young Earth. I hope I am wrong and Professor Coyne is right.

The majority of U.S. medical schools do not require evolutionary biology as a prerequisite for acceptance and do not offer courses dedicated to the subject. But as we talked about last time, adopting an evolutionary perspective on medical issues can potentially give new insights into disease treatment, prevention, and diagnosis. Where do we and should we begin to teach this kind of thinking? What resources are available to teachers and students to learn about evolution and its application to modern day problems?

Evolutionary training can help doctors look at diseases in a different light (Nesse et al, 2006). Take, for instance, sickle cell anemia: carriers of the sickle cell trait, a disease which is highly prevalent in tropical regions, are resistant to malaria, likely as a result of natural selection. This knowledge is helpful in developing ways to prevent malaria and perhaps similar evolutionary links between other diseases or infections and protective traits exist, but examining this hypothesis requires a thorough understanding of evolution and population genetics. Based on examples like this proponents of evolutionary medicine believe evolutionary biology should be considered a core subject for medical students, side by side with anatomy, physiology, biochemistry, and embryology, and that medical license exams should include questions about evolutionary biology.

People with sickle-cell anemia, whose bodies produce abnormal, crescent-shaped red blood cells, also carry genes that protect against malaria. This is most likely the reason sickle cell anemia is so common in areas where malaria is highly prevalent.

Image source: National Health Service

But while most medical schools do not offer much in the way of evolutionary education, there are some resources available for K-12 students and teachers as well as college undergraduates and graduates. One example is the BEACON Center for the Study of Evolution in Action at Michigan State, an interdisciplinary research team working on applying evolutionary principles to a wide range of problems in fields such as medicine, computer science, ecology, and engineering. Along with research, BEACON is focused on evolution outreach and education: researchers are conducting studies to see if integrating undergraduate cellular and molecular biology courses with evolution improves evolutionary understanding. The center also organizes K-12 summer programs, activities for K-12 teachers, and undergraduate and graduate-level courses.

While BEACON is enjoying great success, the NESCent (National Evolutionary Synthesis) Center, a center in North Carolina promoting multidisciplinary evolutionary research, will be closing this year after a decade of operation. Like BEACON, NEScent was also active in public outreach and education, organizing events like Darwin Day for K-12 students and training workshops for graduate students and teachers. But a new center is opening in the wake of NESCent: the Triangle Center for Evolutionary Medicine (TriCEM), which will focus on the partnership of evolutionary biology with human and veterinary medicine.

We’ve made the case for why an evolutionary understanding can improve research in medicine. But if we want to shift the paradigm of medical thought to one that emphasizes evolutionary biology, we need to reevaluate how we teach evolution from the earliest levels of education through medical school.

This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

Teachers first, scientists second

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That is one of the disquieting results of a new survey, Enablers of doubt, by Michael Berkman and Eric Plutzer. The two Penn State professors interviewed a total of 35 students on 4 Pennsylvania campuses in 2013. All the students were training to be biology teachers; many were not comfortable with the theory of evolution, and many were “concerned about their ability to navigate controversy initiated by a student, parent, administrator, or other members of the community.” Indeed, instead of relying on their knowledge of biology, they intended to fall back on classroom-management techniques to deal with creationist students. Notably, these were not education students, but rather biology students who “take a set of required courses in educational psychology, classroom management, and methods of instruction.” Their lack of expertise in science seems not to concern them; to the contrary, they thought they would use their skills at avoiding controversy to avoid any controversies.

PT readers may remember Professors Berkman and Plutzer for their book, Evolution, Creationism, and the Battle to Control America’s Classrooms, which we reviewed here a few years ago. The disquieting conclusion of that book was that only about 28 % of biology teachers actually teach evolution according to recognized standards. The present study may help explain why.

The students, who attended a large research university, an institution that granted degrees at the master’s level, a Catholic college, or a historically Black university (all unnamed), were interviewed in focus groups. The interviews lasted 50-65 min and were conducted by the authors. The focus groups do not provide a statistical sample, but the authors attempted to include several different kinds of educational institution, and they consider the findings “suggestive.” Below the fold, some representative comments.

Q&A in the WASP nest

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By Steven Mahone.

What would happen if a dyed-in-the-wool secularist was given the opportunity to speak with students from one of the most religiously conservative school districts in the country? Well, I had the privilege of finding out first hand.

The Classical Academy (TCA) is an affluent, public charter high school in north Colorado Springs, so imagine my surprise at receiving an invitation to represent the secular and scientific viewpoint for a week-long seminar titled “Worldviews: The Scientific, Religious, and Cultural Underpinnings of Our Society”. The school is situated two miles from Focus on the Family (an evangelical stronghold for 19th century Christian “values”) and New Life Church, a 10,000-member mega-church that was once pastored by Ted Haggard. (You might recall that Haggard had a parking lot “altercation” with Richard Dawkins when Dawkins attempted to interview him for a BBC special. You can’t help but appreciate the irony when six months after he admonished Dawkins for living a lie behind the veil of science, Haggard was caught with methamphetamines and a male prostitute.) Also sharing the same zip code with the school are the corporate headquarters for Compassion International, The Association of Christian Schools International, and Cook Ministries. I bring this up only to set the stage for my mindset before I ever arrived at the school’s parking lot.

Phylogenomic Fallacies

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This is the fourth in a series of articles for the general public focused on understanding how species are related and how genomic data is used in research. Today, we talk about some common fallacies in phylogenomics.

Where do humans fit on the evolutionary tree of life? This is an important topic in evolutionary biology. A lot of people believe humans are the most important and highly-evolved organisms, but in reality, all modern species are equally evolved. Our natural tendency to assume that humans are evolutionarily superior has led to a few misconceptions about phylogenetic trees.

plants.png

To understand the first misconception, let’s look at a phylogenetic tree of plants (from “The Amborella Genome and the Evolution of Flowering Plants”). Eudicots and monocots are two classes of flowering plants, or angiosperms, and the plants in black are non-flowering plants. The term “basal” refers to the base of a phylogenetic tree, and a basal group is a species that branches closer to that base. The authors chose to label the angiosperms that are not eudicots or monocots as “basal angiosperms.” But this label is arbitrary; all the angiosperms are equidistant from the common ancestor and thus equally evolved. We sometimes tend to give more weight to branches that contain the species of interest and call other branches basal, almost assigning them a lesser importance. In this case, the species of interest is plants that consist of many foods that humans eat; a species is often deemed more important as it relates to humans. But modern species are equally evolved from a root common ancestor regardless of when their branch diverged from the common ancestor. To avoid confusion, it might be best to eliminate the “basal” term altogether.

This type of thinking also leads us to place humans at the end of phylogenetic trees. However, this placement is arbitrary and trees can be drawn in many equivalent ways. For example, compare a tree of primates with the branches rotated. The tree on the left, with humans at the top of the tree, is one you might see more often. But both of these trees are actually identical, and the relationships between species that can be inferred from the tree on the right is the same as the relationships in the tree on the left. Species at the tip of a tree are equidistant from the root common ancestor, so they can be considered evolutionarily equivalent.

primate tree 1.png

primate tree 2.png

Similarly, a common misconception is that humans evolved directly from monkeys. Monkeys, though, are modern species just like we are and have been evolving and changing over time. The common ancestor we share with monkeys may have looked much different than monkeys do now. This assumption that modern species represent an ancestral state of human evolution is what T. Ryan Gregory calls the platypus fallacy. Gregory uses the example that we can’t examine the traits of platypuses and think that humans at one point in their evolution possessed these same traits. We can no more infer the traits of human ancestor species from platypuses than platypuses can infer the traits of their ancestors from us.

Human-centered thinking is very prevalent in our society, affecting our laws, religions, and customs. While it probably influences all of us on a personal level, it can lead to false conclusions and misconceptions in science, like thinking that humans are the most highly evolved species. But all modern species are evolutionarily equivalent because they have been evolving for the same amount of time. Eliminating this fallacy will enable us to better understand the evolutionary process.

For more information on basal groups, check out: “Which side of the tree is more basal?, Krell, Frank et al. Systematic Entomology (2004).

This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

This is the third in a series of articles for the general public focused on understanding how species are related and how genomic data is used in research. Today, we talk about the challenges of using statistics to analyze phylogenomic data.

Suppose you were a door manufacturer trying to figure out the average height of a population living in a certain country. You might conduct an experiment where you ask a group of people to report their height. You would then assemble those measurements in a data set. But in order to study this data set and draw conclusions you would need to analyze it using statistics. For example, how tall should your door be in order to fit 95% of people in the country? How many people do you need to survey to accurately represent the total population? These questions can be answered with statistical analysis.

Because acquiring data from experiments can be costly and time-consuming, we often use small data sets to represent a larger population of interest. In our height experiment, we would not be able to ask every single person in the country his or her height. We would choose a group of people under the assumption that they accurately reflect the population as a whole. However, when we are trying to map out the evolutionary history of organisms using data from sequenced genomes (phylogenomics, which we talked about last time), we need to change our method of analysis.

Let’s look at the treeshrew, for instance. It looks like a rodent but actually shares some internal similarities with primates (studied by Sir Wilfrid Le Gros Clark in the 1920s), like brain anatomy and reproductive traits. To figure out if the treeshrew is more similar to rodents or primates, we could sequence its genome and, using statistics, compare its genes to those of rodents and primates. But typical statistical models are based on subsets of populations, while by definition, genomic sequencing gives us a complete data set - all of the treeshrew’s genes. These typical models may not be suitable for interpreting genomic data.

The treeshrew. Source: Wikipedia

Before reaching a conclusion about the tree shrew, or any set of data, scientists must consider precision and accuracy. Multiple measurements of the same quantity are precise if they are similar to each other. Another way of saying this is that their variance is small. On the other hand, measurements are accurate if they are close to the true value of what they are trying to measure. For genomic data, we need better statistical tools to ensure that the accuracy of our conclusions matches the precision characteristic of these huge data sets.

Larger data sets provide more precise conclusions than smaller ones. For example, when we ask more people to report their height, we are more confident that our sample represents the variability of the actual population. Similarly, we analyze more genes in the treeshrew’s genome to increase our confidence that our conclusion is precise. However, our results might not necessarily be accurate; big data sets may lead us to draw incorrect conclusions with high confidence. The treeshrew’s genome contains some genes that are more similar to rodents’ genes and some that are more similar to primates’ genes (Fan et al., Nie et al., and Xu et al.), and with so much data we could find that the treeshrew is most similar to either group with high confidence. We need analysis tools that will tell us which genes give the correct answer.

Why are conclusions from data sometimes inaccurate? Statistical biases are external factors that produce consistent error in our measurements. Biases have many sources, including faulty experimental design, violation of assumptions made in analyzing the data, and errors in the data collection process. Bias in our height experiment might arise if we unintentionally ask the height of more women than men, causing our estimate of the average height to be lower. But in the case of phylogenomics, we are likely to have biases because of our relative lack of knowledge about the genome: we don’t always know which genes to analyze or the correct way to model the data. For example, some models assume that evolution followed the same pattern throughout all time, but this most likely was not the case.

Furthermore, the process of genome sequencing and analysis itself may create error, especially in the reconstruction of the genome and the alignment of genes for comparison. If we are comparing the genome of the treeshrew to the genomes of primates and rodents, it is difficult for us to know which genes are correlated between species when we are looking at a data set of billions of points. We might use a probability model to determine correlated genes, but all models are at least somewhat incorrect and introduce bias. In smaller data sets, biases are offset by a low precision and relatively small confidence in reaching conclusions. However, in genomic-size data sets, even small biases can be amplified and lead to high confidence in the wrong answer and incorrect phylogenetic trees.

When analyzing phylogenomic datasets, we need to use analyses that are appropriate for large data sets. This will unlock the potential of phylogenomic research to draw unbiased conclusions, like figuring out the correct phylogenetic classification of the treeshrew (still a topic of controversy among evolutionary biologists). However, phylogenomics is such a young field that these tools do not yet exist. When they are developed, we can increase our chances of correctly classifying species’ relationships and discovering the true history of evolution.

For more detail, check out: “Statistics and Truth in Phylogenomics”, Kumar, Sudhir et al. Molecular Biology and Evolution (2011).

References:

Fan, Yu, et al. “Genome of the Chinese tree shrew.” Nature communications 4 (2013): 1426.

Nie, Wenhui, et al. “Flying lemurs-The’flying tree shrews’? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade.” BMC biology 6.1 (2008): 18.

Xu, Ling, et al. “Evaluating the Phylogenetic Position of Chinese Tree Shrew ( Tupaia belangeri chinensis) Based on Complete Mitochondrial Genome: Implication for Using Tree Shrew as an Alternative Experimental Animal to Primates in Biomedical Research.” Journal of Genetics and Genomics 39.3 (2012): 131-137.

Our next installment will cover some misused terminology in phylogenomics. This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

… because it (gasp!) uses the word, “abortion.” But wait – there is a glimmer of hope: The new superintendent, who was ordered to offer a plan for redacting the textbooks, says that the books comply with the law already and instead plans to hold a public discussion.

Meanwhile, as a service to the affected high-school students, Rachel Maddow has posted the offending page on a blog, ArizonaHonorsBiology.com, which her show apparently owns. If you are curious or have a prurient interest, you may also see the verso of The Page, as well as several other pages on human reproduction.

For the record, the book is Reece, et al., Biology: Concepts and Connections.

This is the second in a series of articles for the general public focused on understanding how species are related and how genomic data is used in research. Today, we talk about phylogenomics, the application of whole genome sequencing to understand evolutionary relationships among species.

DNA Chemical Structure. Source: Madeleine Price Ball

The haploid human genome is 3.2 billion DNA bases long, and each base can be one of four nucleotides: A, T, C, and G. Uncoiled, the DNA in a single human cell would be 2 meters long, and the DNA in a human body would stretch from the sun to Pluto multiple times. With 3.2 billion bases, each person’s genome is unique, and this plays an essential role in shaping our physical and mental individuality. However, despite being unique, each human genome is very very similar, due to our shared ancestral heritage. Similarly, species that share a recent ancestral heritage also have similar genomes. Species that are distantly related are likely to demonstrate significant differences in their genomes. This is why, as we discussed last week, evolutionary biologists compare traits and genes to determine the relationships of different species.

Unfortunately, some genes give us the wrong answer about how species are related. A section of a gene can be identical for two species due to independent mutations. After all, any given base can only mutate into one of three other bases. Chances are the same mutation could happen twice, or multiple mutations can produce the same sequence. Consider two species that are distantly related; one contains an AGA fragment, while the corresponding fragment in the other species is TGT, i.e. they differ in 2 out of 3 positions. As these species evolve, by chance the first species may experience a change in the first position such that AGATGA, and the second species may experience a change in the third position such that TGTTGA. Now, these two sequences look the same so you might think the species share a recent common ancestor; however, it is only an accident of biology that they appear closely related. Because some fragments may be identical due to independent mutations and not shared ancestry, estimating species relationships with using whole genomes is better than just a few genes. The more information we have, the more likely we are to figure out species’ relationships correctly.

The cost to sequence whole genomes has fallen from $100 million to $1000 in just the past twelve years. It now takes days to sequence a genome compared to the 13 years it took for the first human genome. The challenge now is not to obtain the data but to compare all the billions of base pairs in one genome to those in another. Current sequencing methods, while fast, can only read the genome by dividing it into millions of short fragments, which must be reassembled like an enormous puzzle. Researchers then have to figure out which genes correspond to one another in different species’ genomes. These comparisons are challenging because genes in one genome might be in a different order, on different chromosomes, or missing completely in another species’ genome.

Biologists are beginning to use genomic information to understand how species are related and measure how fast or slowly different genes evolve. Then in turn allows us to understand how evolution happens. For example, using genomic information we can figure out how genes mutate, characterize and diagnose genetic diseases, and track harmful pathogens. But before that can happen, we need to address the difficulties of analyzing these large genomic datasets. You might think that more data is always better, but having a lot of data can lead us to have very high confidence in the wrong answer. In a pool of thousands of genes, we need to find the ones that tell us the right answer.

Next week, we’ll discuss statistical challenges associated with big data analysis, especially as it relates to phylogenomics. This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

The Family Tree of Life

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In the next few weeks, we’ll be posting a series of articles for the general public focused on understanding how species are related and how genomic data is used in research. We start with a background on phylogenetic trees.

Imagine you could go back in time and meet your great grandmother or even your great-great-great-great-great grandmother, when they were your age. Would they look like you? Or would they look more like your siblings or cousins? Maybe you would all look a little different. Scientists try to figure out how the distant ancestors of apes, other animals, plants, and all organisms living today looked and behaved, much in the same way that people use a family tree to trace their ancestry.

primate-family-tree-780x520_0.gif

The common ancestor of great apes lived about 18 million years ago. Source: Smithsonian National Museum of Natural History http://humanorigins.si.edu/evidence/genetics

In evolutionary biology scientists use a type of tree called a “phylogenetic tree” to organize the history of how species descended from common ancestors. The closer two species are to a common ancestor on the phylogenetic tree, the more closely the two are related.

Take the phylogenetic tree of primates, for example. The common ancestor of apes lived about 18 million years ago. But over time, this one group branched off to form many different species, including humans, which have their own separate branch on this tree.

How did so many unique species develop from one ancestor? New branches formed by a process known as divergence. When groups of ancient organisms became geographically isolated from one another, either through migration or geologic events like earthquakes, each group began to develop its own unique set of physical attributes. Sometimes, by chance, a change in a characteristic enabled an individual to survive better in its environment and produce more offspring.

Perhaps individuals in one group with larger arms were better able to break open the hard-shelled fruits that were common in one region, while some individuals in another group had the ability to travel more easily through tall trees that offered protection from predators. Whatever the reason may have been, selection favored genetic differences that improved survival. Over time, this gradual process of isolation and selection produced distinct species, which in turn branched into more species.

The end result of divergence is many species, related in a tree-like fashion, and we display these relationships using phylogenetic trees. Scientists now use increasingly sophisticated methods to determine how species were related and build phylogenetic trees. In the past, scientists built these trees simply by comparing physical traits, like how many limbs an organism has or whether it has a tail. But with the recent surge in fast and affordable gene sequencing technologies, researchers today can directly compare species’ DNA to determine how they are related.

But analyzing entire genomes, with billions of DNA base pairs, presents its own unique set of challenges, and researchers often struggle to determine if the DNA differences they find between species are truly significant or are simply due to common variability. As computer software and statistical analysis become more adept at handling these challenges, our understanding of species’ relationships could change — providing exciting new insights into our family tree of life.

Check back next week when we discuss the differences between studying small and large datasets, and the challenges associated with big data analysis. This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

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