NTS LogoSkeptical News for 25 October 2011

Archive of previous NTS Skeptical News listings


Tuesday, October 25, 2011

Evolution education update: October 21, 2011

A new issue of RNCSE for your reading pleasure. NABT issues a 2011 update of its statement on teaching evolution. And a well-deserved honor for long-time NCSE member James Krupa.

RNCSE 31:5 NOW ON-LINE

NCSE is pleased to announce the fifth issue of Reports of the National Center for Science Education in its new on-line format. The issue -- volume 31, number 5 -- features Lorence G. Collins and Barbara J. Collins's article "Pleistocene Continental Glaciers: A Single Ice Age Following a Genesis Flood or Multiple Ice Ages?" and David Morrison's feature "Science Denialism: Evolution and Climate Change," arguing, "There are some interesting common elements in these two cases of science denialism." For his regular People and Places column, Randy Moore discusses the impresario of the Scopes trial, George Rappleyea (1894-1966).

Plus a host of reviews of books on the history of science: J. David Archibald reviews Olivier Rieppel's Evolutionary Theory and the Creation Controversy; John W. Geissman reviews Doug Macdougall's Nature's Clocks; Sara B. Hoot reviews Sheila Ann Dean's Charles Darwin: After the Origin; Sherrie Lyons reviews Natural Selection & Beyond: The Intellectual Legacy of Alfred Russel Wallace, edited by Charles H. Smith and George Beccaloni; Aubrey Manning reviews Sean B. Carroll's Remarkable Creatures, and A. Bowdoin Van Riper reviews Sherrie Lynne Lyons's Species, Serpents, Spirits, and Skulls

All of these articles, features, and reviews are freely available in PDF form from http://reports.ncse.com. Members of NCSE will shortly be receiving in the mail the print supplement to Reports 31:5, which, in addition to summaries of the on-line material, contains news from the membership, a regular column in which NCSE staffers offer personal reports on what they've been doing to defend the teaching of evolution, a new regular column interviewing NCSE's favorite people -- members of NCSE's board of directors, NCSE's Supporters, recipients of NCSE's Friend of Darwin award, and so on -- and more besides. (Not a member? Join today!)

For the table of contents for RNCSE 31:5, visit:
http://reports.ncse.com/index.php/rncse/issue/current/showToc

For information about joining NCSE, visit:
http://ncse.com/join

NABT RENEWS ITS VOICE FOR EVOLUTION

The National Association of Biology Teachers recently issued a 2011 update of its statement on teaching evolution. Like its predecessors dating back to 1995, the statement affirms the scientific and pedagogical necessity of teaching of evolution:

***

Just as nothing in biology makes sense except in the light of evolution, nothing in biology education makes sense without reference to and thorough coverage of the principle and mechanisms provided by the science of evolution. Therefore, teaching biology in an effective, detailed, and scientifically and pedagogically honest manner requires that evolution be a major theme throughout the life science curriculum both in classroom discussions and in laboratory investigations.

***

A new addition is the insistence that evolution "should not be misrepresented as 'controversial,' or in need of 'critical analysis' or special attention for any supposed 'strength or weakness' any more than other scientific ideas are."

The NABT's statement is now reproduced, by permission, on NCSE's website, and will also be contained in the fourth edition of NCSE's Voices for Evolution.

For NABT's statement, visit:
http://www.nabt.org/websites/institution/index.php?p=92

For Voices for Evolution, visit:
http://ncse.com/voices

CONGRATULATIONS TO JAMES KRUPA

NCSE is delighted to congratulate James Krupa on being named the 2011 winner of the Four-Year College & University Section Biology Teaching Award from the National Association of Biology Teachers. The award honors a four-year college faculty member who demonstrates creativity and innovation in his/her teaching. According to a press release from the University of Kentucky, "Krupa's lesson on the ivory-billed woodpecker was considered by the awards committee to be particularly useful in covering evolution with non-biology majors. ... In teaching Darwinian foundations of evolution and the scientific method to his students, there are few stories that Krupa is more passionate about than the ivory-billed woodpecker." Vincent Cassone, the chair of the University of Kentucky's Department of Biology, was quoted as saying, "This award from fellow biology educators is a testament to the quality of instruction Dr. Krupa is inclined to give ... He challenges students' sensibilities and predispositions often, particularly when it involves evidence for evolution, biodiversity and public policy, and sometimes students don't like it. However, this is what a university education is all about -- to challenge people's preconceived notions; and this is what we cherish in the Department of Biology." Krupa is Associate Professor of Biology at the University of Kentucky.

For the press release, visit:
http://uknow.uky.edu/content/uk-biology-professor-wins-teaching-award

Thanks for reading. And don't forget to visit NCSE's website -- http://ncse.com -- where you can always find the latest news on evolution education and threats to it.

Glenn Branch
Deputy Director
National Center for Science Education, Inc.
420 40th Street, Suite 2
Oakland, CA 94609-2509
510-601-7203 x305
fax: 510-601-7204
800-290-6006
branch@ncse.com
http://ncse.com

Read Reports of the NCSE on-line:
http://reports.ncse.com

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NCSE's work is supported by its members. Join today!
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How to examine the evolution of proteins

http://scienceblogs.com/pharyngula/2011/10/how_to_examine_the_evolution_o.php

Category: Evolution • Molecular Biology • Science
Posted on: October 20, 2011 3:00 PM, by PZ Myers

In my previous post, I described the misguided approach Gauger and Axe have taken to criticizing evolution, and one of the peculiarities of their criticism is that they cited another paper by a paper by Carroll, Ortlund, and Thornton which traced (successfully) the evolutionary history of a class of proteins. Big mistake. As I pointed out, one of the failings of the Gauger/Axe approach is that they're asking how one protein evolved into a cousin protein, without considering the ancestral history …they make the error of trying to argue that an extant protein couldn't have directly evolved into another extant protein, when no one argues that they did.

The tactical error is that right there in the very first paragraph of their paper, Carroll, Ortlund, and Thornton point out the fallacy of what the creationists were doing.

Direct comparisons among present-day proteins can sometime yield insights into the sequence and structural mechanisms that underlie functional differences. Such "horizontal" comparisons, however, cannot determine which protein features are ancestral and which are derived, so they are not suited to reconstructing the events that produced functional diversity.

They don't mention Gauger and Axe, of course — this paper was written before the creationists wrote theirs — but a methodological flaw is still spelled out plainly, the creationists reference it so I presume they read it, and they still charged ahead and did their flawed study, and then had the gall to claim their work was superior.

Ah, silly creationists. They just assume their target audience won't bother to read the work they're citing, and isn't competent to understand it anyway. And they're usually right.

The crew doing the work in the Carroll paper did not make the same mistakes. They are doing ancestral sequence reconstruction (ASR), so the effort to work backward to trace ancestral states is implicit. The bulk of the paper describes the sequencing of homologous and paralogous genes in more organisms (in this case, especially cartilaginous fishes), and the analysis of synthesized, reconstructed ancestral proteins, so it's built entirely on an empirical foundation. And their answers actually advance our understanding of the base-by-base changes that led to the evolution of the current set of proteins. I think they were courteous and sensible (and probably, the idea didn't even occur to them) in not comparing their work to that of the creationists — it would have been less than gracious to point out how ugly, cheap, and cheesy the stuff coming out of the Biologic Institute looks.

What the real scientists were studying is a class of receptors that respond to mineralocorticoid and/or glucocorticoid hormones. These proteins are similar in sequence and structure to one another, and are clearly paralogous: they arose by an ancient gene duplication event, somewhere around 450 million years ago. The two copies have since diverged to have different roles in hormone physiology.

The two receptors are called MR, for mineralocorticoid receptor, and GR, for glucocorticoid receptor.

MRs are activated by adrenal hormones, aldosterone and deoxycorticosterone, and to a lesser exent, cortisol. The receptors are extremely sensitive to the hormones. These hormones are important in regulating salt balance, and you might well imagine that in our fishy ancestors, as well as ourselves, regulating the concentrations of salts in our blood and tissues is a very important function. Deviations can cause death, after all.

GRs are activated by high doses of cortisol; these receptors are much less sensitive, requiring high doses of the hormone to trigger a response. They are important in regulating stress responses: they adjust the immune system and sugar metabolism. These aren't 'twitchy', fast response functions like maintaining salt balance is; they are long-term, 'last-ditch' reactions to growing stresses, so functionally it makes sense that activation requires high levels of accumulated hormone.

Using ASR techniques — phylogenetic analysis and estimating the most likely sequence of the ancestral protein — the investigators have put together a picture of the receptor before MR and GR diverged. This protein is called AncCR, for Ancestral Corticosteroid Receptor, and it has been synthesized in the lab, so we know about its properties. AncCR is a lot like MR: it's sensitive to low concentrations of hormone, and it responds to low concentrations of a broad spectrum of hormones.

The pedigree of these proteins is illustrated below.


Simplified phylogeny of corticosteroid receptors. Ancestral sequences are shown at relevant nodes: AncCR, the last common ancestor of all MRs and GRs; AncGR1, the GR ancestor of cartilaginous fishes and bony vertebrates; AncGR2, the GR ancestor of ray- and lobe-finned fishes (including tetrapods); AncMR1, the MR ancestor of cartilaginous fishes and bony vertebrates. (AncGR1.0 and AncGR1.1 are different reconstructions of node AncGR1, inferred from datasets with different taxon sampling.) Black, high sensitivity receptors; gray, low sensitivity receptors. Single and double gray dashes mark functional shifts towards reduced sensitivity and increased specificity, respectively. Support values are the chi-square statistic (1 - p, where p equals the estimated probability that a node could occur by chance alone) calculated from approximate likelihood ratios. The length of branches from AncCR to AncMR1 and to AncGR1, expressed as the mean number of substitutions per site, are indicated in parentheses.

The MRs are similar in function to the AncCR, so they aren't particularly interesting in this context — there's no big question about how the MRs retained similar properties to their ancestor. The interesting questions are all about the GRs: what changed to make GRs different from the ancestral protein? What amino acid changes set AncGR1 apart from AncCR?

The investigators have an answer. The first step was the evolution of reduced hormone sensitivity, so that these receptors only responded to very high concentrations of the hormone, and the second step was a loss of sensitivity to the mineralocorticoids, already handled by the MRs, so that they only respond to high doses of cortisol, which at this point became exclusively a stress hormone. And they know exactly which amino acids changed to confer the reduced sensitivity.

They identified three changes: the conversion of a valine at position 43 into an alanine, called V43A; the conversion of an arginine at position 116 into a histidine, R116H; and the conversion of a cysteine at position 71 into a serine, C71S. They also know the effect of the mutations. V43A and R116H each loosen the structure of the receptor so that it's less sensitive, and when both mutations are present the effect greatly reduces sensitivity about 10,000-fold…too much! They make the mutant hormone too insensitive, and much less insensitive than their reconstructed AncGR1.

The most interesting change is C71S. It basically does nothing to the sensitivity; make the C71S change to AncCR, and you get a receptor protein that is essentially indistinguishable in its response. This is effectively a neutral mutation. It can spread freely through a population with no deleterious or advantageous effect.

C71S does have one significant effect in cooperation with the other two mutations: it buffers both V43A and R116H. When all three mutations are present, the desensitizing effects of V43A and R116H are reduced to produce the level of sensitivity expected for the AncGR1 protein. This means we can reconstruct the order of the amino acid changes in evolution. First came C71S, because it doesn't cause any particular adaptive change, and because if either V43A or R116H came first, the resulting receptor would be generally non-functional. The existence of C71S first means the subsequent V43A/R116H changes produced receptors that are still functional, but simply operate only at higher concentrations of the hormones.

All of these changes are perfectly compatible with an evolutionary model of their origin. No sudden leaps, no deleterious intermediates are required — everything hangs together beautifully and is backed up by solid empirical evidence. In addition, the work explains the mechanics of receptor-hormone interactions, stuff I haven't explained here, but if you're a biochemist, there's much to savor in the paper.

It's an amazing contrast to the Gauger and Axe paper, too. No wonder I'm not a creationist!

Carroll SM, Ortlund EA, Thornton JW (2011) Mechanisms for the evolution of a derived function in the ancestral glucocorticoid receptor. PLoS Genet.7(6):e1002117. Epub 2011 Jun 16.

Stand for Science: Confront Homeopathy

http://scienceblogs.com/pharyngula/2011/10/stand_for_science_confront_hom.php

Category: Skepticism
Posted on: October 24, 2011 2:00 PM, by PZ Myers

Aww, the students of Campus Atheists, Skeptics, and Humanists have warmed the frigid, friable cockles of my black heart. They're having a protest of homeopathy on the Twin Cities campus this Friday! They're hosting a lecture debunking that nonsense, and are planning to poison themselves with homeopathic dilutions.

Take that, Center for Spirituality and Healing! We all see right through you.

Homeopathy is renowned for both its popularity and the overwhelmingly incorrect pseudoscientific tenets it purports. In the UK, the growing 10/23 protest has called for the end of government support of such unsupported blather. It's about time the United States joined her sibling. This October 28th, join CASH at the University of Minnesota- Twin Cities and the Center for Inquiry at Michigan State in protesting the pseudoscience of homeopathy and its faulty 'regulation' by the FDA.

The Food and Drug Administration regulates the homeopathic industry not to lend credibility to such products, but to supposedly protect consumers from products that can kill them. This is not enough. Just like with actual medications (as homeopaths liken their products to), testing of the claims made by such companies must be both accurate and rigorous. Without such standards, homeopaths openly use the stamp of FDA approval to advertise for the effectiveness of homeopathic remedies.

Join the growing numbers who are taking a stand for science-based medicine. Join us on October 28th in confronting homeopathy and demanding that the FDA require peer-reviewed, scientific research in order to garner its approval. Participation is easy!

Protest on October 28th at your local university, hospital, or drugstore that dispenses homeopathic remedies. Conduct an 'overdose'. Give a statement to your local media. Write a letter. Sign the petition. Take a stand for science.

The following materials may be of interest as well:

CFI's industry-wide petition (no signatures):
http://www.centerforinquiry.net/media/newsroom/pdf/petition_to_fda_re_standards_for_homeopathic_drugs.pdf

CFI's Walmart-directed petition (signature-based):
https://secure3.convio.net/cfi/site/Advocacy?cmd=display&page=UserAction&id=251

Secular Student Alliance activity packet:
http://www.secularstudents.org/node/4015

More information from CFI:
http://www.centerforinquiry.net/news/cfi_and_csi_petition_fda_to_take_action_on_homeopathic_drugs/

Updated information from CASH:
http://cashumn.org/main/index.php?option=com_content&view=article&id=146&Itemid=100167

Join CASH and CFI in taking a stand for science-based medicine on October 28th. Making evidence-based thinking a movement and not a counterculture requires effort, and the efforts of many hands can move more mountains than the faith of a few.

Sincerely,

Chelsea Du Fresne
Campus Atheists, Skeptics, and Humanists
University of Minnesota- Twin Cities
cashumn.org

Perry Officials Censored Climate Change Report

http://motherjones.com/politics/2011/10/perry-officials-censored-climate-report

The Texas Commission on Environmental Quality doesn't want you to know that climate change is causing sea level rise in Galveston Bay.

—By Kate Sheppard
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Wed Oct. 12, 2011 9:30 AM PDT

Rick Perry takes Texas pride in being a climate change denier—and his administration acts accordingly.

Top environmental officials under Perry have gutted a recent report on sea level rise in Galveston Bay, removing all mentions of climate change. For the past decade, the Texas Commission on Environmental Quality (TCEQ), which is run by Perry political appointees, including famed global warming denier Bryan Shaw, has contracted with the Houston Advanced Research Center to produce regular reports on the state of the Bay. But when HARC submitted its most recent State of the Bay publication to the commission earlier this year, officials decided they couldn't accept a report that said climate change is caused by human activity and is causing the sea level to rise. Top officials at the commission proceeded to edit the paper to censor its references to human-induced climate change or future projections on how much the bay will rise.

John Anderson, the oceanographer at Rice University who wrote the chapter, provided Mother Jones with a copy of the edited document, complete with tracked changes from top TCEQ officials. You can see the cuts—which include how much sea level rise has increased over the years, as well as the statement that this rise "is one of the main impacts of global climate change"—here and embedded at the end of this story. As the document shows, most of the tracked changes came from Katherine Nelson, the assistant director in the water quality planning division. Her boss, Kelly Holligan, is listed as a reviewer on the document as well.

Holligan and Nelson are top managers at Perry's commission; lower-ranking staff at the agency had already approved the document, according to the publication's editor. The changes came only after the two managers reviewed the issue. TCEQ's commissioners, who are direct political appointees of the governor, select the top managers at TCEQ. Although the director and assistant director jobs aren't technically political appointments, those hires are usually vetted by the governor's office.

Anderson, whose complaints were first reported by the Houston Chronicle on Monday, says that the cuts to his paper were political and had nothing to do with science. The research underlying the study was peer-reviewed and is part of a decadelong study Anderson has conducted in partnership with other scientists. The Geological Society of America published the scientists' results in 2008. "I was a bit astonished," Anderson tells Mother Jones. "Really this paper is just a review of papers we published previously. There's no denying the fact that sea level rise has significantly accelerated. The scientific community is not at all divided on that issue."

TCEQ even deleted a reference to the fact that the bay is currently rising by 3 millimeters a year—five times faster than the long-term average. The edited version that TCEQ sent back also killed a line noting that the bay's "future will be strongly regulated by the now rising sea," as well as the factual assertion that the disappearance of the wetlands is "due mainly to direct human intervention." The officials also cut out the statement that the water level rise "is one of the main impacts of global climate change."

Anderson has refused to let TCEQ publish the heavily edited version of his work. "It would not have been a worthwhile paper," he says. "It would not have said anything."

Jim Lester, the co-editor of the State of the Bay and vice president of the Houston Advanced Research Center, notes that the scientists self-censored before submitting the paper to TCEQ, removing references to the Intergovernmental Panel on Climate Change (a favorite target of climate skeptics) and largely avoiding the question of whether humans were causing the climate to change. But that wasn't enough to keep the paper out of the commission's crosshairs. The report was supposed to be published in 2010, as the title of it suggests, but it has been delayed. Lester and his co-editor have also said they don't want their names attached to something that is factually inaccurate. "It damages our scientific credibility," Lester said.

It's not surprising that people appointed by Perry, the climate deniers' favorite climate denier, would excise references to climate change from a scientific paper. But the commission's response to the Chronicle's request for a comment was pretty classic:

TCEQ spokeswoman Andrea Morrow gave no reason for the deletions in an e-mail response, saying only that the agency disagreed with information in the article.

"It would be irresponsible to take whatever is sent to us and publish it," she said.

The commission's edit is reminiscent of efforts by the George W. Bush administration to suppress climate science. Top political appointees at the White House edited documents to downplay link between greenhouse gas emissions and global warming and to make the science sound more uncertain. In another instance, the Bush administration edited the congressional testimony of the director of the Centers for Disease Control and Prevention to remove references to public health concerns tied to climate change.

Anderson says his chapter and the entire publication were written to provide accurate, useful information to Texas state policymakers. He pointed to neighboring Louisiana, where coastal erosion has reached a crisis point and decision makers are struggling to deal with it.

"Sea level doesn't just go up in Louisiana. We're the next in line," he says. "We are in fact starting to see many of the changes that Louisiana was seeing 20 years ago, yet we still have a state government that refuses to accept this is happening."

Rick Perry officials spark revolt after doctoring environment report

http://www.guardian.co.uk/environment/2011/oct/14/rick-perry-texas-censorship-environment-report

Scientists ask for names to be removed after mentions of climate change and sea-level rise taken out by Texas officials

Suzanne Goldenberg, US environment correspondent
guardian.co.uk, Friday 14 October 2011 08.05 EDT

Rick Perry's administration deleted references to climate change and sea-level rise from the report. Photograph: Evan Vucci/AP

Officials in Rick Perry's home state of Texas have set off a scientists' revolt after purging mentions of climate change and sea-level rise from what was supposed to be a landmark environmental report. The scientists said they were disowning the report on the state of Galveston Bay because of political interference and censorship from Perry appointees at the state's environmental agency.

By academic standards, the protest amounts to the beginnings of a rebellion: every single scientist associated with the 200-page report has demanded their names be struck from the document. "None of us can be party to scientific censorship so we would all have our names removed," said Jim Lester, a co-author of the report and vice-president of the Houston Advanced Research Centre.

"To me it is simply a question of maintaining scientific credibility. This is simply antithetical to what a scientist does," Lester said. "We can't be censored." Scientists see Texas as at high risk because of climate change, from the increased exposure to hurricanes and extreme weather on its long coastline to this summer's season of wildfires and drought.

However, Perry, in his run for the Republican nomination, has elevated denial of science, from climate change to evolution, to an art form. He opposes any regulation of industry, and has repeatedly challenged the authority of the Environmental Protection Agency.

Texas is the only state to refuse to sign on to the federal government's new regulations on greenhouse gas emissions. "I like to tell people we live in a state of denial in the state of Texas," said John Anderson, an oceanography at Rice University, and author of the chapter targeted by the government censors.

That state of denial percolated down to the leadership of the Texas Commission on Environmental Quality. The agency chief, who was appointed by Perry, is known to doubt the science of climate change. "The current chair of the commission, Bryan Shaw, commonly talks about how human-induced climate change is a hoax," said Anderson.

But scientists said they still hoped to avoid a clash by simply avoiding direct reference to human causes of climate change and by sticking to materials from peer-reviewed journals. However, that plan began to unravel when officials from the agency made numerous unauthorised changes to Anderson's chapter, deleting references to climate change, sea-level rise and wetlands destruction.

"It is basically saying that the state of Texas doesn't accept science results published in Science magazine," Anderson said. "That's going pretty far."

Officials even deleted a reference to the sea level at Galveston Bay rising five times faster than the long-term average – 3mm a year compared to .5mm a year – which Anderson noted was a scientific fact. "They just simply went through and summarily struck out any reference to climate change, any reference to sea level rise, any reference to human influence – it was edited or eliminated," said Anderson. "That's not scientific review that's just straight forward censorship."

Mother Jones has tracked the changes. The agency has defended its actions. "It would be irresponsible to take whatever is sent to us and publish it," Andrea Morrow, a spokeswoman said in an emailed statement. "Information was included in a report that we disagree with."

She said Anderson's report had been "inconsistent with current agency policy", and that he had refused to change it. She refused to answer any questions. Campaigners said the censorship by the Texas state authorities was a throwback to the George Bush era when White House officials also interfered with scientific reports on climate change.

In the last few years, however, such politicisation of science has spread to the states. In the most notorious case, Virginia's attorney general Ken Cuccinelli, who is a professed doubter of climate science, has spent a year investigating grants made to a prominent climate scientist Michael Mann, when he was at a state university in Virginia.

Several courts have rejected Cuccinelli's demands for a subpoena for the emails. In Utah, meanwhile, Mike Noel, a Republican member of the Utah state legislature called on the state university to sack a physicist who had criticised climate science doubters.

The university rejected Noel's demand, but the physicist, Robert Davies said such actions had had a chilling effect on the state of climate science. "We do have very accomplished scientists in this state who are quite fearful of retribution from lawmakers, and who consequently refuse to speak up on this very important topic. And the loser is the public," Davies said in an email.

"By employing these intimidation tactics, these policymakers are, in fact, successful in censoring the message coming from the very institutions whose expertise we need."


Monday, October 24, 2011

David Barton and Ken Ham aren't mistaken, they're just lying

http://www.patheos.com/blogs/slacktivist/2011/10/18/david-barton-and-ken-ham-arent-mistaken-theyre-just-lying/

By Fred Clark, October 18, 2011 3:59 pm

Karl Giberson and Randall J. Stephens, who we discussed a few weeks ago in "Evangelicals vs. Science," have an op-ed column in today's New York Times on "The Evangelical Rejection of Reason."

The Republican presidential field has become a showcase of evangelical anti-intellectualism. Herman Cain, Rick Perry and Michele Bachmann deny that climate change is real and caused by humans. Mr. Perry and Mrs. Bachmann dismiss evolution as an unproven theory. …

The rejection of science seems to be part of a politically monolithic red-state fundamentalism, textbook evidence of an unyielding ignorance on the part of the religious. As one fundamentalist slogan puts it, "The Bible says it, I believe it, that settles it." But evangelical Christianity need not be defined by the simplistic theology, cultural isolationism and stubborn anti-intellectualism that most of the Republican candidates have embraced.

This is a real phenomenon and Giberson and Stephens are right to be concerned — both for their own evangelical Christian community and for the nation as a whole, given that this "rejection of science" has become a prerequisite for seeking the Republican nomination for president.

Some Republicans have been — quietly, and without much success so far — pushing back against the anti-science, anti-reality ideology dominant in their party's primary campaign.

[Former Republican Sen. John] Warner, a former Navy secretary, now travels the country for the Pew project, making speeches and appearances at military bases, and calling attention to the national-security concerns of climate change and fossil-fuel dependence.

Working with Warner on the Pew climate-change project is George Shultz, President Reagan's secretary of State, who helped advise George W. Bush's 2000 presidential campaign and who remains an influential Republican voice. Last year, Shultz, who now serves as a distinguished fellow at Stanford University, cochaired the "No on Prop. 23" campaign in California, which successfully defended California's pioneering climate-change cap-and-trade law against an oil-industry-led effort to overturn it.

"My own opinion is that this problem is very real," Shultz told National Journal. "I recognize there's a lot of people pooh-poohing it. Whether they like the science or not, there's a huge problem coming at us. There's a huge melt coming in the Arctic regions. There's melting taking place." Of Republicans like Perry who deny climate science, he said, "They're entitled to their opinion, but they're not entitled to the facts."

That — from Coral Davenport's National Journal article, "Retired Republicans Quietly Try to Shift GOP Climate-Change Focus" (see also this from Phil Plait) — is a positive sign. George Shultz is a significant figure. Unfortunately, though, he's a significant figure from the past. In the present, people like Bachmann, Cain and Perry have much more influence in the Republican Party and, despite what Shultz says, they seem to think they're entitled to their own facts.

Herman Cain's proud ignorance about sexuality, Michele Bachmann's endorsement of anti-vaxxer hysteria, and Rick Perry's repeated assertions that climate change is a hoax cannot be separated from their shared embrace of the anti-science ideology of "creationism" and dismissal of evolution.

Creationism is indefensible on the evidence. The facts are against it. That leaves its proponents with no option except to go meta, attacking the very idea of "evidence" and "facts" by following Pilate's example and shrugging off the evidence by asking "What is 'truth'?" Opposed and refuted by overwhelming scientific evidence, they are forced to attack science itself, suggesting that the whole endeavor and the very possibility of learning about the natural world is somehow illegitimate.

Once you've taken that leap and made that ideological claim, there's no reason not to apply the same no-standards standard to sexuality, medicine, climate science or economics. You're no longer bound by science, by facts, by reality, by what is. And once that's the case, you're free to assert whatever foolish absurdities you calculate will be most politically expedient. You can say that you chose to be heterosexual. You can say that vaccines cause autism. You can say that carbon doesn't trap heat. You can say that reducing demand leads to economic growth.

And since hermeneutics is also a kind of science — a way of seeking after the truth and determining, as best as possible, the facts and reality of the matter — embracing the ideology of anti-science also means you're free to say that any text means anything you want it to say. To be unbound by facts is to be unbound by texts as well.

Again, the issue here is not questions of belief in things which simply have not been proved. It's perfectly reasonable to believe in something despite a lack of compelling proof or evidence that it is certainly true. But it is not reasonable to believe in something in spite of compelling proof and evidence that it is certainly not true. To do that is to say that reality itself does not matter.

And once you've said that — as Bachmann, Cain and Perry all have, in public, on television — then you have, as Giberson and Stephens say, "rejected reason." You've left your senses and no longer make sense, only non-sense.

I cannot know or guess whether Bachmann, Cain and Perry have truly embraced the nonsense they claim to believe or if those nonsensical claims are something more cynical. I cannot know for sure if they are deceived or deceivers. But I think we can know which is the case with two of the evangelical leaders discussed by Giberson and Stephens: David Barton and Ken Ham. Barton and Ham, they say, "have been particularly effective orchestrators — and beneficiaries" of the evangelical "parallel culture" that rejects science and reason:

Mr. Ham built his organization, Answers in Genesis, on the premise that biblical truth trumps all other knowledge. His Creation Museum, in Petersburg, Ky., contrasts "God's Word," timeless and eternal, with the fleeting notions of "human reason." This is how he knows that the earth is 10,000 years old, that humans and dinosaurs lived together, and that women are subordinate to men. Evangelicals who disagree, like Francis S. Collins, the director of the National Institutes of Health, are excoriated on the group's website. …

Mr. Barton heads an organization called WallBuilders, dedicated to the proposition that the founders were evangelicals who intended America to be a Christian nation. He has emerged as a highly influential Republican leader, a favorite of Mr. Perry, Mrs. Bachmann and members of the Tea Party. Though his education consists of a B.A. in religious education from Oral Roberts University and his scholarly blunders have drawn criticism from evangelical historians like John Fea, Mr. Barton has seen his version of history reflected in everything from the Republican Party platform to the social science curriculum in Texas.

Barton and Ham are not deceived. They are deceivers. They tell lies that they know to be lies. They tell lies for money.

Barton doesn't merely misread and misquote the founding fathers due to careless scholarship and ideological blindness. His misreadings and misquotations reveal too much care and craft for that to be the case. His distortions are composed with painstaking care. They are deliberate, intentional and knowing. He devises and markets conscious falsehoods — false claims that he knows to be false. He does not believe what he says. He does not mean what he says. He says what he says only in order to deceive others and thereby to separate them from their money.

The same is true for Ken Ham. Ken Ham is a liar, a charlatan, a con-man, a bearer of false witness. He lies for money. Like Barton, he has been personally and publicly corrected innumerable times over many years, confronted again and again with the demonstrable, undeniable falsehood of his statements. And like Barton he makes no correction and offers no apology for those false statements. With an astonishingly cynical contempt for his audience, he simply assumes that his critics have no influence among those he has been fleecing, and he willfully continues fleecing them, continuing to make the very same claims and statements that he has been shown are false, continuing to say things that he knows are not true. Because he can get away with it and because it's profitable.

David Barton and Ken Ham are not fundamentalists. They are not in denial, defensively retreating from a bewildering world they do not understand except as a vague threat to their faith. No. Fundamentalists in denial are their prey, their mark — the goose that provides them with golden eggs.

It's considered rude to state this so bluntly. That's what they're counting on. Their ability to continue this lucrative con depends on a misplaced notion of civility that mistakenly presumes that the presumption of good faith is absolute and impervious to evidence. That warped idea of civility is what creates the space in which they are free to act in bad faith with impunity, to lie without any danger of ever being called to account for lying. Refusing to call liars to account is not civility, it's aiding and abetting — becoming an accomplice in their scam.

Parents face inquiry for treating son with alternative medicine

http://www.telegraph.co.uk/health/alternativemedicine/8844461/Parents-face-inquiry-for-treating-son-with-alternative-medicine.html

Alternative Medicine

A couple who treated their sick four-year-old son with alternative medicine are being investigated for manslaughter, Italian police have said.

By Nick Pisa

7:40PM BST 23 Oct 2011

Luca Monsellato was taken to hospital with a high fever and cold symptoms but failed to respond to emergency medical treatment and died.

His parents, Marcello and Giovanna Pantaleo, told doctors they had been treating his apparent three-week cold with fennel tea – a popular homeopathic remedy for coughs – in an attempt to keep his fever under control. They eventually took him to hospital when his condition worsened.

Staff at the hospital described Luca as looking "pale, thin and breathless".

Mr Monsellato, 52, of the southern Italian town of Tricase, close to Lecce, has been a doctor of alternative medicine for more than 20 years. He is honorary president of Italy's Homeopathic Sinergy Association and an expert on acupuncture.

He told staff at the hospital how his son had been suffering from the effects of a cold for three weeks and they had given him fennel tea instead of other medical treatment.

Prosecutor Alberto Santacatterina said: "A manslaughter investigation has been opened against the parents of little Luca. We are looking into the events that surrounded his death and whether they were responsible by not giving him proper medical treatment when he was ill."

The couple, who have been bailed, have denied any wrongdoing through their lawyer, Alfredo Cardigliano, who said the family were thinking of bringing negligent charges against doctors at the hospital for not looking after their son properly.

A message on the website of the Homeopathic Sinergy Association said: "We are united in our condolences to honorary president Dr Marcello Monsellato and his family for the loss of little Luca.

"We fully support Dr Monsellato who in 30 years of practice has worked with love and professionalism with thousands of patients who have turned to him for help in dealing with the difficulties of their illnesses.

"His figure incarnates the image of a doctor, whose only objective is the wellbeing of his patient."

An autopsy performed by forensic pathologist Alberto Tortorella ruled that Luca had died from natural causes but police said they were still investigating his parents actions.

Italy's Bioethics Committee also spoke out and in a statement said that ''medical practices that were not scientifically based could not substitute those that were scientifically proven.''

However Fausto Panni, head of Omeoimpresse, the association which overseas the supply of homeopathic remedies said:''The latest statistics show that during the last five years just 21 people have had side effects from homeopathic medicine with no fatalities.

''That compares to many who have died as a result of medical malpractice or adverse reactions to medicine.''

Homeopathy is popular in Italy with more than 5,000 homeopathic doctors treating more than three million people a year but it has no legal entity and there is no formal register of those who practice the treatment.

Steve Jobs, Alternative Medicine and Cancer

http://www.care2.com/causes/steve-jobs-alternative-medicine-and-cancer.html

by Kristina Chew
October 23, 2011
4:39 pm

Did alternative medicine kill Steve Jobs? This question has been circulating around the internet since the visionary co-founder of Apple died on October 5. Ramzi Amri, a research associate at Harvard Medical School who says he has been studying the type of cancer Jobs had for a year and a half, has argued that the type of pancreatic tumor Jobs had was "treatable" and that by initially relying on alternative medical treatments, he cut short his chances for survival. Others including Brian Dunning in a post entitled A Lesson in Treating Illness have decried Jobs's decision to treat a terminal disease "with woo rather than with medicine."

The publication tomorrow, October 24, of Walter Isaacson's biography of Jobs could provide more information. In a Sunday evening 60 Minutes interview, Isaacson has said that Jobs came to regret his initial decision to treat a neuroendocrine tumor in his pancreas that was detected in 2004 with an alternative diet instead of medically recommended surgery. The Apple CEO — "so used to swimming against the tide of popular opinion" — had been intrigued by Eastern mysticism as a young man and, according to an ABC News report, "believed in alternative herbal treatments." An AP report also says that Jobs ate a vegan diet and used "acupuncture, herbal remedies and other treatments he found online, and even consulted a psychic." He was also "influenced by a doctor who ran a clinic that advised juice fasts, bowel cleansings and other unproven approaches .. before finally having surgery in July 2004."

Orac, a scientist who blogs at Respectful Insolence on ScienceBlogs, has long countered, and debunked, the "woo" of alternative medical treatments with science. He has previously written about Jobs's 2009 liver transplant. In weighing the available evidence about whether Jobs's "flirtation" with alternative medicine might have killed him, Orac writes:

…it appears likely that Jobs did indeed decrease his chances of survival through his nine month sojourn into woo. On the other hand, it still remains very unclear by just how much he decreased his chances of survival. My best guesstimate is that, thanks to the indolent nature of functional insulinomas and lead time bias, it was probably only by a relatively small percentage. This leads me to point out that accepting that Jobs' choice probably decreased somewhat his chances of of surving his cancer is a very different thing than concluding that "alternative medicine killed Steve Jobs." The first statement is a nuanced assessment of probabilities; the latter statement is black-and-white thinking…

What is revealed from these accounts about Jobs's initial treatment of his cancer with alternative remedies is that "even someone as brilliant as Steve Jobs can be prone to denial, and, yes, even magical thinking." It's possible that Jobs could have had what Orac terms a "medical reality distortion field that allowed him to come to think that he might be able to reverse his cancer with diet plus various 'alternative" modalities."'

Others have used the term "reality distortion field" in a "part joking, part derogatory, part admiring" sense to describe Jobs's "combination of personal charisma, bravado, hyperbole, marketing, and persistence" that enabled him to persuade and convince anyone, from engineers to Wynton Marsalis, about Apple products. It might be possible that the very qualities that enabled Jobs to make Apple and its products what they are — to be the innovator the world will remember him as — also contributed to his demise. But with cancer, "biology is king and queen," and there is only so much we humans — even visionaries like Jobs whose insights have radically changed our lives — can do to fight that biology.

De mortuis nil nisi bonum. "About the dead, say nothing except good." What we can say is that, after those initial months using alternative treatments, Jobs sought out science-based treatments for his cancer and certainly the best available. It is commendable that, as Isaacson said on 60 Minutes, Jobs wanted to inform the world about his regret regarding his decision not to have been operated on sooner; about having made the wrong decision. How many public figures are willing to say that they have made a mistake?

Knowing this, I feel even more sorrow that Steve Jobs is gone.

The heat is on

http://www.economist.com/node/21533360

Climate change

A new analysis of the temperature record leaves little room for the doubters. The world is warming

Oct 22nd 2011 | from the print edition

FOR those who question whether global warming is really happening, it is necessary to believe that the instrumental temperature record is wrong. That is a bit easier than you might think.

There are three compilations of mean global temperatures, each one based on readings from thousands of thermometers, kept in weather stations and aboard ships, going back over 150 years. Two are American, provided by NASA and the National Oceanic and Atmospheric Administration (NOAA), one is a collaboration between Britain's Met Office and the University of East Anglia's Climate Research Unit (known as Hadley CRU). And all suggest a similar pattern of warming: amounting to about 0.9°C over land in the past half century.

To most scientists, that is consistent with the manifold other indicators of warming—rising sea-levels, melting glaciers, warmer ocean depths and so forth—and convincing. Yet the consistency among the three compilations masks large uncertainties in the raw data on which they are based. Hence the doubts, husbanded by many eager sceptics, about their accuracy. A new study, however, provides further evidence that the numbers are probably about right.

The uncertainty arises mainly because weather stations were never intended to provide a climatic record. The temperature series they give tend therefore to be patchy and even where the stations are relatively abundant, as in western Europe and America, they often contain inconsistencies. They may have gaps, or readings taken at different times of day, or with different kinds of thermometer. The local environment may have changed. Extrapolating a global average from such data involves an amount of tinkering—or homogenisation.

It might involve omitting especially awkward readings; or where, for example, a heat source like an airport has sprung up alongside a weather station, inputting a lower temperature than the data show. As such cases are mostly in the earlier portions of the records, this will exaggerate the long-term warming trend. That is at best imperfect. And for those—including Rick Perry, the Republican governor of Texas and would-be president —who claim to see global warming as a hoax by grant-hungry scientists, it may look like a smoking gun.


To build confidence in their methodologies, NASA and NOAA already publish their data and algorithms. Hadley CRU is now doing so. A grander solution, outlined in a forthcoming Bulletin of the American Meteorological Society, would be to provide a single online databank of all temperature data and analysis. Part of the point would be to encourage more scientists and statisticians to test the existing analyses—and a group backed by Novim, a research outfit in Santa Barbara, California, has recently done just that.

Inconvenient data

Marshalled by an astrophysicist, Richard Muller, this group, which calls itself the Berkeley Earth Surface Temperature, is notable in several ways. When embarking on the project 18 months ago, its members (including Saul Perlmutter, who won the Nobel prize for physics this month for his work on dark energy) were mostly new to climate science. And Dr Muller, for one, was mildly sceptical of its findings. This was partly, he says, because of "climategate": the 2009 revelation of e-mails from scientists at CRU which suggested they had sometimes taken steps to disguise their adjustments of inconvenient palaeo-data. With this reputation, the Berkeley Earth team found it unusually easy to attract sponsors, including a donation of $150,000 from the Koch Foundation.

Yet Berkeley Earth's results, as described in four papers currently undergoing peer review, but which were nonetheless released on October 20th, offer strong support to the existing temperature compilations. The group estimates that over the past 50 years the land surface warmed by 0.911°C: a mere 2% less than NOAA's estimate. That is despite its use of a novel methodology—designed, at least in part, to address the concerns of what Dr Muller terms "legitimate sceptics".

Most important, Berkeley Earth sought an alternative way to deal with awkward data. Its algorithm attaches an automatic weighting to every data point, according to its consistency with comparable readings. That should allow for the inclusion of outlandish readings without distorting the result. (Except where there seems to be straightforward confusion between Celsius and Fahrenheit, which is corrected.) By avoiding traditional procedures that require long, continuous data segments, the Berkeley Earth methodology can also accommodate unusually short sequences: for example, those provided by temporary weather stations. This is another innovation that allows it to work with both more and less data than the existing compilations, with varying degrees of certainty. It is therefore able to compile an earlier record than its predecessors, starting from 1800. (As there were only two weather stations in America, a handful in Europe and one in Asia for some of that time, it has a high degree of uncertainty.) To test the new technique, however, much of the analysis uses the same data as NOAA and NASA.

Heat maps

In another apparent innovation, the Berkeley team has written into its analysis a geospatial technique, known as kriging, which uses the basic spatial correlations in weather to estimate the temperature at points between weather stations. This promises to provide a more nuanced heat map than presented in the existing compilations, which either consign an average temperature to an area defined by a grid square or, in the case of NASA, attempt a less ambitious interpolation.

It will be interesting to see whether this makes it past the review process. Peter Thorne, a climatologist at the Co-operative Institute for Climate and Satellites, in North Carolina, describes it as "quite a hard sell in periods that are data sparse". He adds: "That doesn't mean you can't do it. It means you've got to prove it works."

Two of the Berkeley Earth papers address narrower concerns. One is the poor location of many weather stations. A crowd-sourcing campaign by a meteorologist and blogger, Anthony Watts, established that most of America's stations are close enough to asphalt, buildings or other heat sources to give artificially high readings. The other is the additional warming seen in built-up areas, known as the "urban heat-island effect". Many sceptics fear that, because roughly half of all weather stations are in built-up areas, this may have inflated estimates of a temperature rise.

The Berkeley Earth papers suggest their analysis is able to accommodate these biases. That is a notable, though not original, achievement. Previous peer-reviewed studies—including one on the location of weather stations co-authored by Mr Watts—have suggested the mean surface temperatures provided by NOAA, NASA and Hadley CRU are also not significantly affected by them.

Yet the Berkeley Earth study promises to be valuable. It is due to be published online with a vast trove of supporting data, merged from 15 separate sources, with duplications and other errors clearly signalled. At a time of exaggerated doubts about the instrumental temperature record, this should help promulgate its main conclusion: that the existing mean estimates are in the right ballpark. That means the world is warming fast.

Severing the link between Darwin and Nazism

http://www.philly.com/philly/blogs/evolution/132422123.html

Monday, October 24, 2011

To some creationists, Darwin was not only wrong but poisonous - his evolutionary theory, they say, directly influenced Hitler's genocidal ideology.

Historian Richard Weikart appeared in the anti-evolution film Expelled, promoting this alleged Darwin-Hitler link. Weikart has written extensively on this, arguing that Darwinian evolution destroyed Judeo-Christian morality, especially the notion of reverence for life.

Weikart does not try to push the idea that this invalidates evolution as a scientific idea. But he is openly creationist - a fellow at the Intelligent Design-promoting Discovery Institute in Seattle.

His message is that evolution kills morality. "If everything is a product of chance - purposeless - which is widespread in biology textbooks . . . then I don't think you have any grounds to criticize Hitler."

Those are fighting words, and a number of thinkers have challenged them. Most recently University of Chicago historian Robert Richards took Weikart to task in a paper titled "Was Hitler a Darwinian?", to which he answers a definitive no.

Weikart said he began exploring the topic when he wrote his dissertation on the influence of Darwin on German socialism in the 19th century. There, he said, Darwinism was used to justify eugenics - the attempt to influence selection in the human race, usually by killing or sterilizing anyone considered "unfit."

As Weikart learned more, he said, "the connection to Nazism leapt out at me." Darwin's second evolution book, The Descent of Man, is rife with racist statements about "higher" and "lower" races, said Weikart, and Darwin viewed the extermination of native people in Tasmania and Australia as part of natural selection.

Darwin, Weikart admits, didn't advocate such killings, and he abhorred slavery. Darwin also disavowed the more extreme eugenicist views, instead saying that helping those in need exercised the better part of our nature.

But Darwinian thinkers of Hilter's time were trying to use evolution to justify racism, said Weikart, and this influenced Hitler. "Hitler spoke and wrote incessantly about evolution, natural selection and the struggle for existence, especially the struggle between races," he wrote in one of his books.

Richards calls this all a desperate tactic to undermine evolution. Creationism and Intelligent Design don't hold up scientifically, he said, so people like Weikart are trying to show that evolution is somehow morally dangerous.

"There's not the slightest shred of evidence that Hitler read Darwin," he said. Some of the biggest influences on Hitler's anti-Semitism were opposed to evolution, such as British writer Houston Stewart Chamberlain, whose racial theory became incorporated into Nazi doctrine. Hitler uses language with "a Darwinian flavor," said Richards, but if you look at the ideas behind it they have nothing to do with Darwin.

Hitler often used the word Entwicklungslehre, Richards said, which can mean evolution but is a much more general term meaning development, and Hitler most often employed it to refer to economic development. "It's quite unfair to translate this as evolution," he said, as Weikart does.

While some of Darwin's writings contain racist notions of a hierarchy of races, Richards said, this was inherited from much earlier work and was part of the then-current mode of thinking.

Daniel Gasman, a historian at City University of New York's John Jay College, has also written that Darwin wasn't a major influence on Hitler but he does see a connection with German biologist Ernst Haeckel, who was one of Darwin's fiercest disciples.

Gasman wrote a book called Scientific Origins of National Socialism connecting Haeckel's influence to Hitler and Nazi ideology. Stephen Jay Gould read it and popularized the idea further in his own writings.

Haeckel was Germany's most famous scientist, said Gasman. He advocated evolution but his conception of it was different from Darwin's - he saw progress and advancement where Darwin noted only change. "Haeckel's Darwinism is a vast transformation of what Darwin wrote and stood for," Gasman said.

Haeckel also created his own religion, called monism, which tried to replace the Judeo-Christian idea of separate spiritual and physical worlds with a more integrated view.

Gasman said examples abound showing that Haeckel was a leader in anti-Semitic thought. Richards said his research shows Haeckel was militantly atheistic but not anti-Semitic - he disliked both Judaism and Christianity in equal measures.

They both agree that any whiff of Darwinism in Hitler's speech or writing was merely window-dressing. The Nazis did try to look scientifically sophisticated, Gasman said. "They took anti-Semitism and gave it a scientific character that propelled them forward," he said. "That's why it was so murderous."

The historians also agree that evolution's validity as a scientific concept is unaffected by this controversy. "Even if Hitler said all his inspiration for persecuting the Jews derived from Darwin, it would say nothing about the validity of evolution," Richards said.

Weikart's view that evolution's proponents lack the moral grounds to criticize Hitler raises this question: Why should we hold evolution responsible for providing a complete moral framework? We don't ask that of Galileo or Newton or Einstein. Weikert replies that evolution is different because various thinkers have applied it to morality.

But there are many ways to spin the moral influence of Darwin. Perhaps instead of creating chaos, it might be helping us construct a more informed and less rigid morality. Darwin himself wrote that violence, selfishness, charity, and goodwill are all part of human nature. He hoped we would choose to act on the better parts.

And the element of chance to which we owe our existence could provide inspiration rather than moral decay. If our lives really did hinge on countless accidents, couldn't that notion make life ever more precious?

Contact staff writer Faye Flam at 215-854-4977 or fflam@phillynews.com. Read her evolution blog at www.philly.com/evolution, or follow her on twitter @darwins_hellcat.

Doing Good Science

Is being a good scientist a matter of what you do or of what you feel in your heart?

By Janet D. Stemwedel | October 19, 2011

If the question posed in the title of the post seems to you to have an obvious answer, sit tight while I offer a situation in which it might be less obvious.

We recently discussed philosopher Karl Popper's efforts to find the line of demarcation between science and pseudo-science. In that discussion, one of the things you may have noticed is that Popper's story is as much about a distinctive scientific attitude as it is about the details of scientific methodology. I wrote:

Popper has this picture of the scientific attitude that involves taking risks: making bold claims, then gathering all the evidence you can think of that might knock them down. If they stand up to your attempts to falsify them, the claims are still in play. But, you keep that hard-headed attitude and keep you eyes open for further evidence that could falsify the claims. If you decide not to watch for such evidence — deciding, in effect, that because the claim hasn't been falsified in however many attempts you've made to falsify it, it must be true — you've crossed the line to pseudo-science.

And, my sense from scientists is that Popper's description of their characteristic attitude is what they like best about his account. Hardly any scientist goes into the lab Monday morning with the firm intention of trying (yet again) to falsify the central hypotheses which she and the other scientists in her field have been using successfully (to predict and to explain and to create new phenomena) for years. Hardly any scientist will toss out hypotheses on the basis of a single experimental result that does not match the predictions of the hypotheses. But scientists agree that when they're following the better angels of their scientific nature, their eyes are open to evidence that might conflict with even their most trusted hypotheses, and they are ready to kiss those hypotheses goodbye if the facts in the world line up against them.

An attitude is something that's in your heart.

Certainly, an attitude may exert a strong influence on what you do, but if having the right attitude is something that matters to us over and above doing the right thing, we can ask why that is. My best hunch is that an attitude may act as a robust driver of behavior — in other words, having the right attitude may be a reliable mechanism that gets you to do the right thing, at least more than you might in the absence of that attitude.

So, what should we say about a scientist who appears to practice the methodology as he should, but who reveals himself as having something else in his heart?

This question came up back in 2007, when the New York Times reported on the curious case of Marcus R. Ross. Ross had written and defended an "impeccable" dissertation on the abundance and spread of marine reptiles called mosasaurs which (as his dissertation noted) vanished about 65 million years ago, earning a Ph.D. in geosciences from the University of Rhode Island. Then, he accepted a faculty position at Liberty University, where he is an Assistant Director of the Center for Creation Studies.

Ross is a young earth creationist, and as such believes that the earth is no older than 10,000 years. He was a young earth creationist when he wrote the impeccable dissertation in which he noted the disappearance of mosasaurs about 65 millions years ago. Indeed, he was a young earth creationist when he applied to the geosciences Ph.D. program at the University of Rhode Island, and did not conceal this information from the admissions committee.

Some details from the New York Times article:

For him, Dr. Ross said, the methods and theories of paleontology are one "paradigm" for studying the past, and Scripture is another. In the paleontological paradigm, he said, the dates in his dissertation are entirely appropriate. The fact that as a young earth creationist he has a different view just means, he said, "that I am separating the different paradigms."

He likened his situation to that of a socialist studying economics in a department with a supply-side bent. "People hold all sorts of opinions different from the department in which they graduate," he said. "What's that to anybody else?" …

In theory, scientists look to nature for answers to questions about nature, and test those answers with experiment and observation. For Biblical literalists, Scripture is the final authority. As a creationist raised in an evangelical household and a paleontologist who said he was "just captivated" as a child by dinosaurs and fossils, Dr. Ross embodies conflicts between these two approaches. The conflicts arise often these days, particularly as people debate the teaching of evolution. …

In a telephone interview, Dr. Ross said his goal in studying at secular institutions "was to acquire the training that would make me a good paleontologist, regardless of which paradigm I was using." …

He would not say whether he shared the view of some young earth creationists that flaws in paleontological dating techniques erroneously suggest that the fossils are far older than they really are.

Asked whether it was intellectually honest to write a dissertation so at odds with his religious views, he said: "I was working within a particular paradigm of earth history. I accepted that philosophy of science for the purpose of working with the people" at Rhode Island.

And though his dissertation repeatedly described events as occurring tens of millions of years ago, Dr. Ross added, "I did not imply or deny any endorsement of the dates."

Ross pursued an education that gave him detailed knowledge of the theories the geoscience community uses, the questions geoscientists take to be interesting ones to pursue, the methods they use to make observations, to analyze data, and to draw inferences. He showed sufficient mastery of the "paleontological paradigm" that he was able to use it to build an additional piece of knowledge (the work contained in his dissertation) that was judged a contribution to his scientific community.

But, if he believed in his heart that the earth was thousands, not millions, of years old as he built this piece of knowledge, was he really a part of that scientific community? Was he essentially lying in his interactions with its members?

It looks like Ross saw his dissertation as an exercise in presenting the inferences one could draw from the available data using the recognized methods of geoscience. In other words, here's what we would conclude if all the assumptions about the age of the earth, deposition of fossils, isotope dating methods, etc., were true. His caginess about the dates in the interview quoted above, and his professed belief in young earth creationism, suggest that Ross thinks at least some of these scientific assumptions are false.

However, assuming his rejection of the scientific assumptions flows primarily from his commitments as a young earth creationist, the rejection of the claims other geoscientists agree on is based in religious reasons, not scientific reasons. If there were scientific reasons to doubt these assumptions, it seems like examining those could only lead to a stronger body of knowledge in geosciences, and that Ross could have contributed to the field by making such an examination the focus of his doctoral research.

Is it an obligation for a scientist who has concerns about the goodness of an assumption on which people in his field rest their inferences to voice that concern? Is it an obligation for that scientist to gather data to test that hypothesis, or to work out an alternative hypothesis that is better supported by the data? Or is it OK to keep your doubts to your self and just use the inferential machinery everyone else is using?

Maybe people will answer this differently if the scientist in question is planning an ongoing engagement with the other members of this field, or if he is just passing through on the way to somewhere else. More on this in just a moment.

Here's a shorter version of my question about the scientist's obligations here: Does intellectual honesty in scientific knowledge-building just cover the way you use the inferential structure and the inputs (i.e., data) from which you draw your inferences? Or does it require disclosure of which assumptions you really accept (not just for the sake of argument, but in your heart of hearts) when drawing your inferences and which you are inclined to think are mistaken?

Does intellectual honesty require that you disclose as well the fact that you don't actually accept the inferential structure of science as a good way to build knowledge?

Because ultimately, a commitment to young earth creationism seems to be a commitment that the data cannot properly be used to infer any claims that are at odds with scripture.

And here's where scientists who might be willing to accept Ross's dissertation as a legitimate chunk of scientific knowledge may have serious concerns with Ross as a credible member of the scientific community. The dissertation may stand (or fall) as a scientific argument that presents a particular array of data, describes accepted inferential strategies (perhaps even defending some such strategies that are themselves new contributions), and uses these strategies to draw conclusions form the data. Even if the person who assembled this argument was wracked with doubts about all the central premises of the argument, the argument itself could still function perfectly well in the ongoing scientific discourse, and other scientists in the community could judge that argument on its strengths and weaknesses — not on what might be in the heart of the person who constructed the argument.

But, if, ultimately, Marcus Ross rejects the "paleontological paradigm" — and the possibility that the data could properly support inferences at odds with scripture — can he function as a member of a community that makes, and evaluates, inferences using this paradigm?

Maybe he could, but his career trajectory makes it look like he has chosen not to be a member of the larger community of geoscientists. Instead, he has positioned himself as a member of a community of "creation scientists". Whether Ross's ongoing work on extinct marine reptiles is of any scientific interest to the scientific field that trained him will probably depend on the methodology and inferential structure on display in his manuscripts.

Because methodology and inferential structure are much easier to evaluate in the peer review process than what is in the author's heart.


Sunday, October 23, 2011

Ninth Circuit Uses Outcome-Based Jurisprudence to Deny Justice to Darwin-Doubting Student

http://www.evolutionnews.org/2011/10/ninth_circuit_uses_outcome-bas052071.html

Casey Luskin October 19, 2011 6:10 PM | Permalink

Back in August, the Ninth Circuit Court of Appeals denied justice to a Darwin-doubting student by refusing to rule on the merits of a lawsuit. A lower court had previously found a public high school teacher violated a student's First Amendment rights by disparaging creationist religious views in the classroom. In the lawsuit, C.F. v. Capistrano Unified School District, the student/parent plaintiffs, "Farnan," filed suit after the history teacher in question, James Corbett, made various statements during in-class instruction that Farnan felt disparaged their religious beliefs. In 2009, the lower federal court found that Corbett had violated the U.S. Constitution by "disparaging" those beliefs. What did the teacher say, exactly? He called creationism "superstitious nonsense." Both sides then appealed.

There's an extensive body of case law from both the U.S. Supreme Court and the Ninth Circuit holding that it is illegal for the state to "inhibit," "disapprove of," "oppose," "evince a hostility to," show an "an attitude antagonistic to theistic belief" or attempt to "discredit" religion. We also know that federal courts have firmly ruled it is illegal to promote creationism in public schools. But this case shows that as soon as a teacher actually starts up disparaging and inhibiting creationist religious views in public schools, federal courts turn a blind eye and let it go unchecked.

It's been said that selective enforcement of the law is a hallmark of tyranny. Is that what's going on here?

Ninth Circuit Ducks the Issue

On August 19 the court ruled that in bashing creationism, the teacher had "qualified immunity." This got the court off a hook, obviating the need to rule that an evolutionist public high school teacher had violated the 1st Amendment's Establishment Clause by attacking religion. Various repugnant statements in the ruling show a court refusing to do its job because it doesn't like the outcome of an analysis on the merits of a lawsuit. The Ninth Circuit Court of Appeals wrote:

Mindful that there has never been any prior reported case holding that a teacher violated the Constitution under comparable circumstances, we affirm the district court's conclusion that the teacher is entitled to qualified immunity. Because it is readily apparent that the law was not clearly established at the time of the events in question, and because we may resolve the appeal on that basis alone, we decline to pass upon the constitutionality of the teacher's challenged statements. ... "[T]he Establishment Clause presents especially difficult questions of interpretation and application," and we cannot expect Corbett to have divined the law without the guidance of any prior case on point.

What you just read is deliberate evasion on the part of a court that didn't want to rule on the merits of a case because it disagreed with the likely outcome. The reason the court refuses to rule is purportedly because "the law was not clearly established" and these are "difficult questions." But isn't it a court's job to establish what the law is, whether the question is difficult or not? Yes. In the foundational U.S. Supreme Court case Marbury v. Madison, Justice Marshall instructed future generations of jurists that "[i]t is emphatically the province and duty of the judicial department to say what the law is."1

By refusing to say "what the law is," the Ninth Circuit abdicated its responsibility to assess and protect the rights of both students and teachers in public schools. The Appeals Court let the teacher off the hook because he supposedly lacked "guidance" from the case law, but imagine if all courts behaved like this one--it would lead to absurd results: By refusing to rule on the merits of this case, the Ninth Circuit has perpetuated an environment where teachers lacks such "guidance." To put it another way, if every time a new issue arises a court rules that "we cannot expect [the accused] to have divined the law without the guidance of any prior case on point," then no new case law could ever be created. Justice Marshall was right when he exhorted the judicial system that the court's job is to give "guidance"; if the court finds that the teacher ran afoul of the law, so be it.

In short, the Ninth Circuit copped out because it didn't want to issue a politically incorrect ruling against an evolutionist public school teacher who had clearly violated the Establishment Clause. It's a convenient arrangement: courts refuse to rule on these cases to provide "guidance" for teachers, but when teachers get sued for violating the Establishment Clause, courts let them off the hook due to a supposed lack of "guidance."

We've covered the C.F. v. Capistrano Unified School District case in the past here on ENV, but it's worth briefly reviewing what happened. In the lower court ruling, Judge James E. Selna recognized that there comes a point where it is illegal under the U.S. Constitution for a public school teacher to "affirmatively show hostility to religion" or make "statements in class that were improperly hostile to or disapproving of religion in general, or of Christianity in particular." The court's analysis thus asked "whether, when looking at the context as a whole, a reasonable observer would perceive the primary effect of Corbett's statements as disapproving of religion in general or of Christianity in particular."

When Corbett stated "an unequivocal belief that creationism is 'superstitious nonsense,'" the lower court held that this "primarily sends a message of disapproval of religion or creationism" and "therefore constitutes improper disapproval of religion in violation of the Establishment Clause." The lower court found that Corbett could have criticized another teacher who had taught creationism "without disparaging those views," and thus what he did was unconstitutional.2

Given the religious nature of creationism, by the way, I agree that such religious creationist views about life's origins should not be advocated in public school science classrooms. In fact, in my job at Discovery Institute advising educators, I regularly tell teachers that it is illegal to do so. For some reason the National Center for Science Education has yet to send me a thank you note. But, as I argue in this law review article, if it is illegal to promote creationism in public schools, then it should be equally illegal to bash it in such a venue.)

Unfortunately, on appeal to the Ninth Circuit, the appellate judges apparently feared the outcome of Judge Selna's analysis, and decided it was best to turn a blind eye and let the violation of the Establishment Clause go unchecked.

References Cited:

[1.] Marbury v. Madison, 5 U.S. 137, 177 (1803).

[2.] C.F. v. Capistrano Unified School District, 615 F. Supp. 2d 1137 (C.D. Cal. 2009).

Steve Jobs Regretted Trying Alternative Medicine

http://sfist.com/2011/10/20/steve_jobs_regretted_trying_alterna.php

Before he died, Apple co-founder Steve Jobs wanted to world to know that he deeply regretted "wasting time" on alternative medicine while trying to combat his pancreatic cancer. During a recent interview with 60 Minutes, Jobs' biographer Walter Isaacson said:

"We talked about this a lot...He wanted to talk about it, how he regretted it....I think he felt he should have been operated on sooner... He said, 'I didn't want my body to be opened...I didn't want to be violated in that way.'"

Ryan Tate of Gawker goes on to point out that Jobs had a survivable cancer, one that could've been treated with immediate medical attention:

To understand Jobs's prognosis, it is necessary to appreciate the precise type of cancer he had, and the subtype he is believed to have had. First, Jobs's neuroendocrine tumor, also called an islet cell tumor, put him outside the 95 percent of pancreatic cancer victims who have highly fatal adenocarcinoma.

Second, Jobs is believed to have contracted one of the more survivable neuroendocrine tumors. It had several characteristics weighing the initial prognosis favorably, had Jobs acted as doctors recommended:
Sunday, October 23, 2011

No, Ninth Circuit, the Relevant Law in C.F. v. Capistrano Unified School District Was Indeed "Clearly Established"

http://www.evolutionnews.org/2011/10/no_ninth_circuit_the_relevant_052081.html

Casey Luskin October 20, 2011 8:35 AM | Permalink

In August, the Ninth Circuit Court of Appeals denied justice to a creationist student in the case C.F. v. Capistrano Unified School District. The court claimed it was justified in refusing to rule because "the law was not clearly established." In a previous article, we saw that the court thus failed in its job to establish what the law is. In fact the relevant law on this issue is not nearly as murky as the Ninth Circuit made it out to be.

While many questions about academic freedom for public high school teachers are still up in the air, those questions generally pertain to instances where the administration wants the teacher to do X, but the teacher wants to do Y. As far as the question of whether a public school teacher can violate the Establishment Clause, this is settled law: public school teachers cannot establish religion in the classroom. This does not just mean a ban on advocating religion. There is plenty of case law from both the U.S. Supreme Court and the Ninth Circuit holding that it is illegal for the state to "inhibit," "disapprove of," "oppose," "evince a hostility to," show an "an attitude antagonistic to theistic belief" or attempt to "discredit" religion.

The Lemon test requires that the "principal or primary effect" of a law "be one that neither advances nor inhibits religion."1 The test prohibits government inhibition of religion with the same measure of force with which it bans the advancement of religion, for "[t]he government neutrality required under the Establishment Clause is . . . violated as much by government disapproval of religion as it is by government approval of religion."2 While "it is far more typical for an Establishment Clause case to challenge instances in which the government has done something that favors religion or a particular religious group," that same Ninth Circuit ruling observed that the "[Lemon] test also accommodates the analysis of a claim brought under a hostility to religion theory."3

The doctrine prohibiting government inhibition of religion can be traced through some significant U.S. Supreme Court cases. In the landmark case School District of Abington Township v. Schempp, the Supreme Court recognized that "the State may not establish a 'religion of secularism' in the sense of affirmatively opposing or showing hostility to religion, thus 'preferring those who believe in no religion over those who do believe.'"4 In Epperson v. Arkansas the Court likewise held that "The First Amendment mandates governmental neutrality between religion and religion, and between religion and nonreligion" and "the State may not adopt programs or practices in its public schools or colleges which 'aid or oppose' any religion. This prohibition is absolute."5 Consistent with this principle, in Board of Education of the Westside Community Schools v. Mergens, the Court ruled state action is impermissible when it "would demonstrate not neutrality but hostility toward religion."6 Likewise, the endorsement test prohibits "disapproval" of religion.7

As noted, in Schempp the U.S. Supreme Court equated "opposing or showing hostility to religion" with establishing a "religion of secularism" and "preferring those who believe in no religion over those who do believe." In this instance, the Supreme Court held that "[t]he clearest command of the Establishment Clause is that one religious denomination cannot be officially preferred over another."8 The Court gave further guidance regarding the treatment of "denominational preference," stating that "when we are presented with a state law granting a denominational preference, our precedents demand that we treat the law as suspect and that we apply strict scrutiny in adjudging its constitutionality."9

There is case law that extends the principle prohibiting the preference of one religion over another in the public school context. In Hansen v. Ann Arbor Public Schools, a federal district court in Michigan held that a school district's program was unconstitutional because "[a]ny contrary or differing religious view was deemed 'negative,' and summarily excluded" and thus , "the principal effect of the panel was to suggest preference for a particular religious view."10 Similarly, in Citizens for a Responsible Curriculum (CRC) v. Montgomery County Public Schools, a federal court in Maryland issued a preliminary injunction barring implementation of a curriculum on the grounds that it "paints certain Christian sects ... as unenlightened and Biblically misguided."11

In C.F. v. Capistrano Unified School District, the Ninth Circuit Court of Appeals stated that "we cannot expect Corbett to have divined the law without the guidance of any prior case on point. Yet in cases dealing with the teaching of evolution or creationism, the U.S. Supreme Court has given guidance explaining how importance it is to protect constitutional freedoms in public schools. In Epperson v. Arkansas (a case dealing with the teaching of evolution), the Court stated that "the vigilant protection of constitutional freedoms is nowhere more vital than in the community of American schools."12 Likewise, in Edwards v. Aguillard (a case dealing with the teaching of creationism), the Court explained:

The Court has been particularly vigilant in monitoring compliance with the Establishment Clause in elementary and secondary schools. Families entrust public schools with the education of their children, but condition their trust on the understanding that the classroom will not purposely be used to advance religious views that may conflict with the private beliefs of the student and his or her family. Students in such institutions are impressionable and their attendance is involuntary. The State exerts great authority and coercive power through mandatory attendance requirements, and because of the students' emulation of teachers as role models and the children's susceptibility to peer pressure. Furthermore, "the public school is at once the symbol of our democracy and the most pervasive means for promoting our common destiny. In no activity of the State is it more vital to keep out divisive forces than in its schools ....13

But in C.F. v. Capistrano Unified School District, the Ninth Circuit chose not to be vigilant in preventing violations of the Establishment Clause. Apparently the need to vigilantly monitor compliance with the Establishment Clause only applies when it is a "creationist" who is violating the law, rather than an evolutionist. We see a double standard at work, with the Ninth Circuit eagerly enforcing constitutional rights when they cut against "creationists," but refusing to do so against evolutionists.

The Supreme Court has held that the "clearest command" of the Establishment Clause is that one religious denomination cannot be officially preferred over another, and when the state opposes or shows hostility towards religion, it is preferring a "religion of secularism" over other religious beliefs. Moreover, the Court has held that "the vigilant protection of constitutional freedoms is nowhere more vital than in the community of American schools" and courts must be "particularly vigilant in monitoring compliance with the Establishment Clause in elementary and secondary schools." Yet in this case the Ninth Circuit had the gall to expect us to believe their claim that the case law is insufficiently clear to warrant even attempting to address the issues.

The practical implication of the holding in the C.F. v. Capistrano School District is that public school teachers may denigrate, disparage, attack, and oppose the religious beliefs of students however they please, because those teachers have "qualified immunity" and won't be held accountable by the courts. Perhaps it was putting religion in such an unfavorable position that the Ninth Circuit Court intended all along. When it comes to being "vigilant in monitoring compliance with the Establishment Clause in elementary and secondary schools," apparently the Ninth Circuit only engages in such monitoring to stop actions that might benefit religion, and turns a blind eye when the actions would harm religion.

References Cited:

[1.] Lemon v. Kurtzman, 403 U.S. 602, 612 (1971) (emphasis added). See also Smith v. Bd. of Sch. Comm'rs of Mobile County, 827 F.2d 684, 690, 692 (11th Cir. 1987) (equating "inhibiting religion" with exhibiting "an attitude antagonistic to theistic belief" or attempting to "discredit it").

[2.] Vernon v. City of Los Angeles, 27 F.3d 1385, 1396 (9th Cir. 1994).

[3.] Vasquez v. Los Angeles ("LA") County, 487 F.3d 1246, 1256 (9th Cir. 2007) (citing Am. Family Ass'n., Inc. v. City & County of San Francisco, 277 F.3d 1114, 1122 (9th Cir. 2002), cert. denied, 537 U.S. 886 (2002)).

[4.] School District of Abington Township v. Schempp, 374 U.S. 203, 225 (1963) (citations and internal quotation marks omitted).

[5.] Epperson v. Arkansas, 393 U.S. 97, 104, 106 (1968) (emphasis added) (citations and internal quotation marks omitted).

[6.] Board of Education of Westside Community Schools v. Mergens, 496 U.S. 226, 248 (1990). See also Van Orden v. Perry, 545 U.S. 677, 683-84 (2005) (stating that the First Amendment "requires that we neither abdicate our responsibility to maintain a division between church and state nor evince a hostility to religion by disabling the government from in some ways recognizing our religious heritage"); Rosenberger v. Rector and Visitors of Univ. of Va., 515 U.S. 819, 845-46 (1995) (warning against state actions that "would risk fostering a pervasive bias or hostility to religion, which could undermine the very neutrality the Establishment Clause requires").

[7.] Lynch v. Donnelly, 465 U.S. 668, 690 (1984) (O'Connor, J., concurring). See also Mergens, 496 U.S. at 249 ("the Act's purpose was not to 'endorse or disapprove of religion'") (quoting Wallace v. Jaffree, 472 U.S. 38, 56 (1985)).

[8.] Larson v. Valente, 456 U.S. 228, 244 (1982) (emphasis added).

[9.] Id. at 246.

[10.] Hansen v. Ann Arbor Public Schools, 293 F. Supp. 2d 780, 805 (E.D. Mich. 2003).

[11.] Citizens for a Responsible Curriculum v. Montgomery County Public Schools, No. Civ.A. AW-05-1194, 2005 WL 1075634, * 10 (D. Md. May 5, 2005).

[12.] Epperson v. Arkansas, 393 U.S. at 104 (quoting Shelton v. Tucker, 364 U.S. 479, 487 (1960)).

[13.] Edwards v. Aguillard, 482 U.S. 578, 584 (1987) (citations omitted).

Evangelical: Why Do Many Evangelicals Get Science From a Creationist?

http://www.religiondispatches.org/dispatches/guest_bloggers/5299/evangelical%3A_why_do_many_evangelicals_get_science_from_a_creationist/

October 20, 2011 10:36PM
Post by Paul Wallace

Lately, Karl Giberson and Randall J. Stephens have spilled some ink trying to convince the world that there is a distinction to be drawn between evangelicalism and fundamentalism. "Fundamentalism appeals to evangelicals who have become convinced that their country has been overrun by a vast secular conspiracy; denial is the simplest and most attractive response to change," they write in this week's Times. "Evangelicalism at its best seeks a biblically grounded expression of Christianity that is intellectually engaged, humble and forward-looking. In contrast, fundamentalism is literalistic, overconfident and reactionary." So fundamentalism is, in their view, spiritually and intellectually stagnant evangelicalism.

In their view evangelicalism has been hijacked (my word) by fundamentalists such as James Dobson, David Barton, and Ken Ham. Dobson and Barton maintain overly-narrow and even demonstrably false notions about human sexuality and US history, while Ham holds to scientific ideas — such as a young earth creationism — that were discredited before Charles Darwin was born.

Although I am neither a fundamentalist nor an evangelical (and although I have not read their recent book on the subject), Giberson's and Stephens' distinction strikes me as fair and well-drawn. I know and have known a number of evangelical Christians who do not deny evolution. There is some evidence that the evangelical world may be softening their views on homosexuality. And economic justice can no longer be considered solely the interest of mainline Christianity.

Therefore, on his website Giberson asks, "Why do tens of millions of Americans prefer to get their science from Ken Ham, founder of the creationist Answers in Genesis, who has no scientific expertise, rather than from his fellow evangelical Francis Collins, current Director of the National Institutes of Health?"

I can think of a few possible answers to this question.

Several prominent atheists have pointed out that some mental gymnastics is required to reconcile anything like traditional Christianity with modern science. And although I don't agree that Christians who actually reconcile the two are simply being disingenuous, I do think they're on to something: real reconciliation is not easy. If it were, more people would have done it.

I have taught several church courses on religion and science and so I have some experience talking to (mostly religiously moderate) parishioners about their views on this issue. And I think that most people simply don't think about it. (One asked me, "Religion and science? Is that a thing?") Beyond this, the responses tend to fall into two groups. The first group assumes that science is just wrong; their opinion basically amounts to asking, "If we evolved from apes, why are there still apes?" The second group sees no problem at all. "I see no contradiction," they say, "Religion tells us why and science tells us how." My skeptical reflex: Is this true reconciliation, or is it just a more culturally acceptable way of not thinking about it?

And then there's the fact that even casual observers of religion and politics know that simple sells. Simple works. And so, for most politicians and religious leaders, the question becomes not, "How can both theology and science be right," but, "How can I use this question to not only gain votes, but to establish clear markers for distinguishing my group from others?" And it is far easier to latch onto the simplicity (and spectacle) of Ken Ham and his posse than to the more shaded opinion of Giberson, Stephens, and Collins. (Plus, evangelical or not, Collins is an Obama-appointed member of the federal bureaucracy. This cannot but hurt his case among the Republican-heavy evangelical population.)

Finally, the success of public atheists like Richard Dawkins has made it more difficult for some to see science as compatible with Christianity. This is in line with atheists' intentions, and is in fact part of their success. The nonbelievers didn't start it, of course; there was boring theology before there was boring atheism. But if ever there was a wedge strategy, Dawkins et al. have found it. By painting science as the enemy of all religion, they have drawn artificial dividing lines and transformed many people's attitudes toward mainstream science from curiosity and mild suspicion into distrust and even hostility.

One can't really blame the atheists. They're just using what they have so freely been given. But the irony of it all is that Ham (who is just a wee bit miffed at Giberson and Stephens) would not have been successful in the first place if it were not for the success of mainstream science. Overawed by real science, Ham cloaks his work in its language and bamboozles those who know virtually nothing about it. His and other creationist organizations (like the Discovery Institute) have played directly into the hands of those who would destroy all religion.

Back in my physics days I would have called this a positive feedback cycle. The whole thing goes around and around and gets louder and louder and more and more distracting.

My answer to Giberson's question? Such a circus makes it hard for moderate voices like his and Stephen's and Collins' to be heard, much less taken seriously.

How not to examine the evolution of proteins

Category: Creationism
Posted on: October 20, 2011 3:00 PM, by PZ Myers

The Discovery Institute has me on a mailing list for their newsletter, Nota Bene. That's probably unwise: usually I just glance at it, see another ignorant bit of fluff from Luskin or Nelson or one of the other usual suspects, and I snigger and hit 'delete', but sometimes they brag about how they're really doing science, and I look a little closer. And then I might feel motivated to take a slap at them.

The latest issue contains an article by Ann Gauger, babbling about her recent publication disproving Darwinism, written with her colleague Douglas Axe, published in their tame 'science' journal, Bio-complexity, and edited by Michael Behe. It's not work that could survive in a real journal, I'm afraid.

The work focuses on a diverse family of enzymes, the PLP-dependent transferases. These are all paralogs, or genes produced by duplication and divergence, as determined by their similar sequences. They picked two members of this family that use different substrates and catalyzed different reactions, and asked how they could possibly have evolved from each other…and they did it all wrong. The mistakes they made were fundamental, obvious, and amazingly stupid.

The cousin problem. You should have picked up on the key problem from my short description above: they picked two extant proteins and then asked how they could have evolved from each other. Imagine if I picked one of my many cousins — say, the tall, red-headed Mormon fellow from Oregon, or the slender fan of horses in California — and started enumerating our many differences and declared that I couldn't possibly have evolved from either of them. You would rightly stop me and suggest that maybe my problem is that I didn't evolve from my cousins — that maybe the smarter approach would be to look at our respective parents, and the grandparents we have in common, and trace the lines of descent.

And you'd be right, of course. A more sensible way of looking at this problem is to start with a valid premise, and examine parental and grandparental states. Gauger and Axe don't do that at all. They speculate about the huge number of possible intermediate states between two cousins, and decide that there are so many possibilities that the path from one to another is so improbable that it couldn't have happened in the history of the planet. You might be able to say the same thing about me and my very different cousin, if you disregarded the fact that there actually were known intermediates.

The bridge hand problem. Creationists pull this one all the time. Here's the situation: you are dealt 13 cards in a hand of bridge. What's the probability that you'll get the hand you've got? Obviously, the probability of getting a hand is 1.0, but the probability of getting any one specific arrangement of 13 cards is less than one in 635 billion. The silliness of the creationists is to point at a number like that and announce that the arrangement must have been designed. Gauger pulls this same stunt.

…we calculate that the waiting time for a bacterial population to acquire seven specific mutations in a duplicated gene, none of which provide any functional benefit until all seven are present, is something like 1027 years. That's a ten with 27 zeros after it. To put this in perspective, the age of the universe is believed to be on the order of 1010 years.

If I played bridge very, very fast, dealing out one hand every minute, that means I'd still have to wait 1.1 million years to get any particular hand you might specify ahead of time…and my life expectancy is only on the order of 102 years. Therefore, bridge is impossible. Similarly, if you add up all the nucleotide differences between me and my cousin, the likelihoods of these particular individuals is infinitesimally small…but so what? We're here.

The talentless critic problem. Let's pretend that the prior problems don't exist (I know, that's an awfully big hypothetical leap to make, but try). Let's pretend therefore that the Gauger and Axe paper actually accomplishes what they claim: that neo-Darwinian mechanisms are inadequate to explain the origin of the family of PLP-dependent transferases. Now what? They're here, obviously — how did they get here? They don't say. They don't even speculate; "intelligent design" is a phrase studiously avoided. Lord knows, their experiments and simulations aren't even designed to reveal alternative mechanisms. This is their conclusion:

…answers to the most interesting origins questions will probably remain elusive until the full range of explanatory alternatives is considered.

Yeah, but…if Ann and Doug aren't considering them in their papers, let alone putting together experiments to test them, why should I? And given that their protocols are so deeply flawed and built on faulty premises, I don't think they've ruled out natural evolutionary mechanisms at all. I'll be much more interested when they actually try to explore their unstated "explanatory alternatives" and show me a novel mechanism.

The much more attractive friend problem. I was surprised at one thing: usually creationists assiduously avoid the possibility of comparisons by, for instance, shutting off comments and not bothering to cite their critics, but in this case, Gauger actually links to a paper by Carroll*, Ortlund, and Thornton. It's a terrible tactical mistake. Gauger and Axe are saying, "Ooh, we shit in a pot and we couldn't even get mushrooms to grow in it," and then pointing to the flourishing, hugely productive garden that Thornton has cultivated and saying, "…and they're doing it all wrong." It's crazy. It just tells me my time is much better spent reading PLoS than Bio-complexity.

That other paper is so much better than the creationist paper, let's talk about it.

*Sean Michael Carroll. No, not the physicist Sean M. Carroll who works at CalTech, and not the developmental biologist Sean B. Carroll at Madison, but another Sean Carroll at Harvard. It's so confusing. If there was a secret research project decades ago to clone a set of hot scientists, you'd think they'd have at least had the decency to append a plate and well number to the ends of their names.

Steve Jobs' alternative medicine choices: The risk of magical medical thinking

http://www.examiner.com/women-s-health-in-los-angeles/steve-jobs-alternative-medicine-choices-the-risk-of-magical-medical-thinking

Monika Woolsey, Beverly Hills Women's Health Examiner
October 21, 2011

Steve Jobs' biography hits the bookstores next week, and tops on the list of topics pre-reviewers are sharing are Jobs' choices with regards to his cancer. Rather than choose to undergo a potentially life-saving surgery with a documented high rate of successful cure, he chose to experiment with a variety of unproven natural treatments, including juicing, supplements, and herbs.

What would make one of the smartest men in history, with unlimited funds available for medical treatments, impose such a high-risk experiment on his own body when a proven medical cure was available?

Magical thinking likely played a huge part in the story. Magical thinking is a type of logic that often takes hold over normally rational people who are faced with a seemingly uncontrollable circumstance. Choices providing some sense of control over a situation that has no clear solution, provide an outlet for the stress of feeling boxed into an undesirable fate. Magical thinking is extremely common in medical diagnoses such as cancer, infertility and AIDS, as well as with inevitable life events such as aging. Advertisement

Suzanne Somers' self-administration of bioidentical hormones and reporting responses to those hormones too immediate to realistically be accurate, is another example of magical thinking. In my specialty, infertility, I frequently see women self-administer mixes of unproven herbs and supplements that may dangerously interact with prescribed medications, even cause harm to the babies they may conceive. Mental health diagnoses such as bipolar disorder are also accompanied with much magical thinking, due to their associated cultural stigma.

It's not that alternative and complementary cures have no place in these diagnoses. Nontraditional treatments have worked wonders in helping infertile couples finally achieve the baby they want, for example. The problem is that a very high percentage of people promoting these treatments are not scientists. They are salesmen, and a desperate customer is an easy sale. Physicians promise to "first do no harm," on entering their profession. Supplement salesmen do not. A skilled physician, (and plenty do exist) can help a stressed and desperate patient evaluate which complementary therapies may actually help the outcome of a high-tech Western treatment.

A person pitching his treatment in a way that positions physicians as "bad guys", or who discourages an intelligent blend of proven Western modalities and other supportive options, is likely promoting magical thinking for his own personal gain. I was recently in a raw food establishment in Santa Monica where an employee was sharing all kinds of health benefits that ran counter to any science I'd read about raw eating. When asked where I could learn more, I was told, "It's just what the owner teaches us." That's not what you should be hearing when you're fighting a dangerous terminal illness!

In Steve Jobs' situation, it would make sense on the surface that cutting out certain foods and piling on the antioxidants would be helpful. However, what appears to have been overlooked is that the high carbohydrate/sugar intake of a typical juicing diet is tough on an already stressed out pancreas. The fatal error here was an all-or-nothing approach, in which the perceived choice was Western medicine or "natural" alternatives. One put the patient's fate into the hands of doctors, which for a highly intelligent man accustomed to being the smartest person in any peer group he was in, was new, different, and frightening. The other allowed him to stay in the comfort zone of being in control. Though looking back, it's clear he was in control of the process, but not his ultimate fate.

Steve Jobs learned the hard way, and that lesson may be one of our most important gifts he left us. That is, that in life-threatening situations, not matter how smart you may be about other things, if you're not a trained medical professional, it's important to not succumb to magical thinking. Let those who are trained listeners as well as practitioners, help guide you through the maze of options and chart a course that is based on what is most likely to heal, not what is most likely to benefit another person's wallet.

The Ninth Circuit's Pattern of Double Standards and Denying Justice to Darwin-Skeptics

http://www.evolutionnews.org/2011/10/the_ninth_circuits_pattern_of_052091.html

Casey Luskin October 21, 2011 11:30 AM | Permalink

The Ninth Circuit's recent refusal to rule on the merits of a case where a student alleged his teacher was disparaging creationist religious beliefs isn't the first time it has denied Darwin-skeptics their day in court. In the past here on ENV, we've written about how the Ninth Circuit dismissed the Caldwell v. Caldwell lawsuit for lack of standing.

In the Caldwell case, Jeanne Caldwell, a parent of public school students in Roseville, California, filed suit against the director of UC Berkeley's Museum of Paleontology, who oversaw the production of a website for teachers called "Understanding Evolution." Caldwell's complaint alleged that the website "advocat[es] that teachers use public school science classrooms to proselytize minor students to adopt the government's preferred religious beliefs and doctrines regarding evolutionary theory."

The Understanding Evolution website was funded with a $500,000+ government-sponsored National Science Foundation grant awarded to UC Berkeley staff, with various National Center for Science Education staff members helping to develop the site. The website states that it is a "misconception" to believe "[e]volution and religion are incompatible" or that "one always has to choose between [evolution] and religion." Clearly preferring religious sects that accept evolution, the site asserts that "[m]ost Christian and Jewish religious groups have no conflict with the theory of evolution." The Caldwell complaint also lists the example that "the 'Misconceptions' web page includes a cartoon depicting a scientist shaking hands with a religious pastor holding a Bible with a cross on it, intended to convey the message that there is no conflict between religious beliefs and the theory of evolution."

The website links to pages discussing religious groups that have issued theological statements accepting and endorsing evolution. The list only contains statements from such organizations that support pro-evolution theology, revealing an agenda to promote a particular brand of theology in the science classroom. As John West explains here, the website also contains a link to a lesson plan where NCSE's Eugenie Scott encourages teachers to read pro-evolution theological statements to students in public schools.

The outcome in the Caldwell lawsuit was very similar to the outcome of this present case. As we reported here and here, the Ninth Circuit dismissed Caldwell's lawsuit without regard to its merits. The court did so by holding that Jeanne Caldwell had no right to sue. As we wrote: "The court managed to avoid ruling on the merits of the case by dismissing the lawsuit due to an alleged lack of standing, thus avoiding a politically unpopular holding that [Pro-Darwin] academics had violated the establishment clause."

Note the pattern: When the Ninth Circuit is confronted with a fact pattern that would hold evolutionists accountable for violating the Establishment Clause when promoting evolution, they take the easy way out and refuse to rule on the merits of the case.

Double Standards and Double Hypocrisy from the Darwin lobby

The Caldwell and Corbett cases illustrate two forms of hypocrisy on the part of the Darwin lobby:

First, Darwin lobbyists continuously try to censor scientific evidence that challenges Darwinian evolution on the false grounds that it's religion, but the Caldwell case shows they encourage pushing religion into public schools when those religious viewpoints support evolution.

Second, Darwin lobbyists claim to defend the First Amendment's Establishment Clause by trying to prevent teachers from advocating religion in the classroom, but don't mind when religion that isn't evolution-friendly is unconstitutionally disparaged in the classroom.

As noted in my recent article, case law shows the Establishment Clause likewise makes it illegal for the government to "inhibit," "disapprove of," "oppose," "evince a hostility to," show an "an attitude antagonistic to theistic belief," or attempt to "discredit" religion. But at the Huffington Post, Steve Newton of the National Center for Science Education (NCSE) defends the teacher James Corbett stating, "If teachers are at risk of being sued every time they make a factual statement, it may have a chilling effect." Of course Newton is correct, but that's nothing like what happened in the C.F. v. Capistrano case. The C.F. v. Capistrano lawsuit suit is not about preventing teachers from making factual statements. As Judge Selna rightly ruled at the lower court level, teachers need to find ways to make factual statements "without disparaging" the religious beliefs of students.

Corbett's purpose was to argue that creationism is not scientifically testable; his purpose was valid but his execution was grossly flawed. There's no problem with public school teachers explaining that creationism is not scientific, so long as they make that point without disparaging the religious beliefs of students by using labels like "superstitious nonsense." Steve Newton, known for promoting scientism in public education, defends Corbett's "superstitious nonsense" statement, so apparently he would defend unconstitutional disparagement of religion in public schools.

The reaction from the NCSE to the C.F. v. Capistrano lawsuit shows that the Darwin lobby is concerned with Establishment Clause violations only when they challenge evolution, and not when they benefit evolution.

The practical implication of the Ninth Circuit's ruling is that public school teachers may denigrate, disparage, attack, and oppose the creationist religious beliefs of students however they want, because those teachers supposedly have "qualified immunity" and won't be held accountable by the courts. But as soon as you start to critique Darwinism, you're accused or promoting religion and doing something illegal. The double standard is astounding.

Ending the Double-Standard

I discuss both the C.F. v. Capistrano Unified School District case and the Caldwell v. Caldwell case in my law review article published last year, "Zeal for Darwin's House Consumes Them: How Supporters of Evolution Encourage Violations of the Establishment Clause." The conclusion of that article helps provide a solution to the double-standards problem discussed here:

[C]ourts have consistently held that advocating creationism in public schools is unconstitutional. In this regard, this present author agrees with courts that there are certain core tenets of creationism -- namely its adherence to supernatural or divine forces -- which make it an unscientific and untestable religious viewpoint that cannot be constitutionally advocated in public schools. That having been said, there is a glaring asymmetry in the law when courts hold on the one hand that creationism cannot be advocated in public schools because it is not science, but on the other hand that it can be disparaged as "scientifically . . . nonsense," also because it is not science. To put it another way, those who desire legal symmetry will find the law sorely lacking if advocating creationism is prohibited on the grounds that it is religion, but nonetheless courts permit public schools to critique, attack, and oppose these views as false. When the government takes an affirmative position on the truth or falsity of a religious viewpoint, it is on dangerous constitutional ground. As the U.S. Supreme Court unequivocally held, "If there is any fixed star in our constitutional constellation, it is that no official, high or petty, can prescribe what shall be orthodox in politics, nationalism, religion, or other matters of opinion. . . ."1 In other words, it is one thing to explain why a (purported) religious viewpoint is unfalsifiable (and thereby unscientific), but quite another to state or imply that the viewpoint is objectively and scientifically false. Yet as documented [in the article], this latter offense is precisely what many [Darwin lobbyists and textbooks] do with regards to intelligent design or creationism.

Courts cannot treat these viewpoints like religion in order to strike down their advocacy, but then treat them like science (or ignore thinly veiled attempts like Corbett's to paint them as false) when they are being critiqued in order to sanction their disapproval. Either a viewpoint is religious and thereby unconstitutional to advocate as correct or critique as false in public schools, or it is scientific and fair game for both advocacy and critique in public schools. Creationism is properly considered a religious viewpoint that can be neither advocated as true nor critiqued as false in public schools, and intelligent design should be considered a scientific viewpoint that is fair game for both advocacy and critique in public schools.

Whatever the solution may be, there is presently a gross lack of legal symmetry, and an overabundance of jurisprudential hypocrisy, if a public school teacher cannot legally say that creationism or intelligent design are scientifically correct, but can call these views scientifically incorrect, or "nonsense."

(Casey Luskin, "Zeal for Darwin's House Consumes Them: How Supporters of Evolution Encourage Violations of the Establishment Clause," Liberty University Law Review, Vol. 3(2):403-489 (Spring, 2009).)

In Edwards v. Aguillard, the U.S. Supreme Court held that "families entrust public schools with the education of their children . . . on the understanding that the classroom will not purposely be used to advance religious views that may conflict with the private beliefs of the student and his or her family." But how can parents trust the Ninth Circuit when the court uses double standards, eagerly dispensing justice when it benefits evolutionists, but then refusing to address the merits of cases that might cut against the Darwin lobby?

The Ninth Circuit is showing a pattern where it uses double-standards to deny justice to Darwin-skeptics. Let's hope this pattern comes to an end.

Case Cited:

[1.] West Virginia State Board of Education v. Barnette, 319 U.S. 624, 642 (1943); see also United States v. Ballard, 322 U.S. 78, 86-87 (1944):

The law knows no heresy, and is committed to the support of no dogma, the establishment of no sect. . . . Freedom of thought, which includes freedom of religious belief, is basic in a society of free men. It embraces the right to maintain theories of life and of death and of the hereafter which are rank heresy to followers of the orthodox faiths. Heresy trials are foreign to our Constitution. Men may believe what they cannot prove. They may not be put to the proof of their religious doctrines or beliefs. Religious experiences which are as real as life to some may be incomprehensible to others. Yet the fact that they may be beyond the ken of mortals does not mean that they can be made suspect before the law. . . . The religious views espoused by respondents might seem incredible, if not preposterous, to most people. But if those doctrines are subject to trial before a jury charged with finding their truth or falsity, then the same can be done with the religious beliefs of any sect. When the triers of fact undertake that task, they enter a forbidden domain. The First Amendment does not select any one group or any one type of religion for preferred treatment. It puts them all in that position. Id. (citations and internal quotation marks omitted).