November 2009 Archives

Over on the T-urf13 thread we had a request for an open thread for questions and answers. In the spirit of the holiday season, I’m happy to oblige. However, let’s make this an experiment in attempting to increase the signal-to-noise ratio in blog comments. I suggest:

1. This thread is not for arguing, it is for explaining.

2. Thus the issue is not whether or not person X believes viewpoint Y, the only issue is to understand/explain the science relating to Y.

Moraxella bovis

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Photograph by John C. McMichael.

Photography contest, Honorable Mention.

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Moraxella bovis – evolution in a Petri dish.

Scientists point out, quite rightly, that the religio-political charade known as “intelligent design” (ID) is not good science. But how do we know this?

One of the hallmarks of science is that it is fruitful. A good scientific paper will usually lead to much work along the same lines, work that confirms and extends the results, and work that produces more new ideas inspired by the paper. Although citation counts are not completely reliable metrics for evaluating scientific papers, they do give some general information about what papers are considered important.

ID advocates like to point to lists of “peer-reviewed publications” advocating their position. Upon closer examination, their lists are misleading, packed with publications that are either not in scientific journals, or that appeared in venues of questionable quality, or papers whose relationship to ID is tangential at best. Today, however, I’d like to look at a different issue: the fruitfulness of intelligent design. Let’s take a particular ID publication, one that was trumpeted by ID advocates as a “breakthrough”, and see how much further scientific work it inspired.

The paper I have in mind is Stephen Meyer’s paper “The Origin of Biological Information and the Higher Taxonomic Categories”, which was published, amid some controversy, in the relatively obscure journal Proceedings of the Biological Society of Washington in 2004. Critics pointed out that the paper was not suited to the journal, which is usually devoted to taxonomic issues, and that the paper was riddled with mistakes and misleading claims. In response, the editors of the journal issued a disclaimer repudiating the paper.

Putting these considerations aside, what I want to do here is look at every scientific publication that has cited Meyer’s paper to determine whether his work can fairly said to be “fruitful”. I used the ISI Web of Science Database to do a “cited reference” search on his article. This database, which used to be called Science Citation Index, is generally acknowledged to be one of the most comprehensive available. The search I did included Science Citation Index Expanded, Social Sciences Citation Index, and Arts & Humanities Citation Index. Even such a search will miss some papers, of course, but it will still give a general idea of how much the scientific community has been inspired by Meyer’s work.

I found exactly 9 citations to Meyer’s paper in this database. Of these, counting generously, exactly 1 is a scientific research paper that cites Meyer approvingly.

Read more at Recursivity.

Meleagris gallopavo

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Meleagris gallopavo–domesticated turkey.

No, it’s not exactly a bird sanctuary; it’s an egg farm in Brittany, where they don’t actually know from Thanksgiving. The turkey is about to be inseminated (artificially, that is) by the male Homo sapiens.

Hunter vs. Hunt on Turf-13

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As a last treat for the 150th anniversary of the Origin, have a look at young-earth creationist creationist Cornelius Hunter [Update: Hunter has stated he is not a young-earth creationist on his blog, so I guess he’s not, although that position directly follows from his stated theology/philosophy], author of the “Darwin’s God” book and blog. Hunter’s basic argument against virtually any common pro-evolution argument is, basically, “But you evolutionists are claiming that God wouldn’t have done it this way! You’re making an unscientific theological argument!”

Last month I was sent a review copy of one of the most beautiful books I’ve ever read: Charles Darwin’s On the Origin of Species: A Graphic Adaptation by Michael Keller and Nicolle Rager Fuller. Although, I haven’t finished the book yet, I think today, the 150th anniversary of the publication of the Origin, is an appropriate day to talk about it.

The book is a wonderful adaptation of the Darwin’s influential original. It beings with a history lesson about his voyage on the HMS Beagle and his return to England. It then follows with abridged text from the Origin and associated graphical adaptations. I could spend a thousand words describing the format to you, but it is more effective to simply share a lo-res sample with you. Although the format is great and beautiful, some of the artwork, especially people, does not look right. I would have preferred a style of artwork more suitable to the graphical novel medium, like The Manga Guide to Molecular Biology.—But doing it in manga form opens up the possibility of Darwin x Wallace dōjinshi, which makes me cower.—But this is probably just due to my taste.

Minor art issues aside, I believe that this book will make a great gift for anyone interested in science and especially biology. I also think that it can serve as a powerful teaching tool in high school and college, due to its uniqueness. For anyone that still has a bad taste in their mouth from Comfort’s bastardization of Darwin’s work, Charles Darwin’s On the Origin of Species: A Graphic Adaptation will make you feel better.

Kirk Cameron on the spot

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Here’s a video from UCLA last week showing some folks getting the opportunity to discuss evolution with Kirk Cameron in person – something the rest of us on the other campuses were hoping for. Who’s the brilliant young woman telling Kirk what’s what down at UCLA? I think I’m in love…

(HT: via TMZ via Huffington post)

The British Council presents E. O. Wilson on Darwin

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Here online. Unfortunately Wilson is recovering from pneumonia and so pre-recorded his talk. Following is a panel discussion with (among others) Peter Bowler.

Darwin reflects on man’s ancestry

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Photograph by Michael Barton.

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Banners for primate hall/exhibit as seen looking from Darwin’s statue. Central Hall, Natural History Museum, London, July 14, 2009. Today is the 150th anniversary of the publication of On the Origin of Species.

Exactly one-hundred and fifty years ago, on November 24, 1859, On the Origin of Species was published. Ever since then, some have been predicting the imminent demise of the theory of evolution. But it’s still here, and better than ever! Let’s make this an open thread, post links to the best Origin-related resources you’ve found, or whatever else you think is a milestone in the 150 years since 1859.

Here’s mine: The evolution of The Origin of Species. And take the National Geographic Darwin quiz.

NSF’s “The Evolution of Evolution”

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The National Science Foundation has announced the opening ot their Evolution of Evolution site. According to the press release,

Going wide and deep, Evolution of Evolution: 150 Years of Darwin’s “On the Origin of Species” provides a uniquely sweeping, at-a-glance explanation of how “Origin” cut an intellectual swath through anthropology, biology, the geosciences, polar sciences and even astronomy, and why it likely will continue to serve as the organizing framework for the sciences into perpetuity.

I’ve not yet gone through the site exhaustively, but I see a number of interesting parts. For example, there’s an interview with Ron Numbers on the impact and interaction of the theory of evolution with astronomy, a nice touch that reminds us that Numbers is an historian of science, not merely of creationism. And it was nice to see David DeVorkin give a shout out in his interview to George Darwin, Charles’ son, who wielded a significant influence on the conception of stellar dynamics in the late 19th and early 20th century. There were more Darwins than just Charles.

I have two minor objections. First, I’m afraid that the ‘silent movie’ conceit in the video interviews might get a little old after the fourth or fifth iteration. And second, the titles/links to video and audio interviews are in ant print, and the whole site seems to be in Flash format, making the text non-magnifiable. Ctrl+ fails. Us old folks will have some trouble with that.

Nevertheless, I recommend it heartily.

Order in Chaos

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Photograph by Francois Malan.

Photography contest, Honorable Mention.

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Incense smoke swirling in quiet air. Negative image.

Mr. Malan writes that his photograph “illustrates how apparent design can be induced in apparently chaotic natural phenomena,” though the smoke is not truly chaotic until it “goes over into true turbulence.” He concludes, “Physics, all there’s to it.”

Essays in Honor of OOS

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Genetics has published three essays in honor of 150th anniversary of the Origin. Allen Orr’s piece provides an interesting historical perspective on the interaction between the science of evolution (or Darwinism) and the impacts on society. The Charlesworths provide an opinion on the importance of Darwin on genetics (note that they get the D-M speciation model wrong by suggesting that it’s anything but apathetic toward the role of natural selection). And Adam Wilkins weighs in on whether Darwin was a genius or a plodder.

Acknowledgement: Thanks to Richard Meisel for the blurb and the links.

Freshwater: A Bonsell in the offing?

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One of the low points for the defense in Kitzmiller was the testimony of Alan Bonsell, who was President of the Dover Area District Board of Education at the time of the adoption of the policy that provoked the lawsuit. Specifically, his sworn testimony in a pretrial deposition was found to be seriously contradicted by his equally sworn testimony in the court. Though it ultimately came to nothing, Judge Jones went so far as to refer the matter to prosecutors for potential perjury charges. (See here and here for the pertinent testimony.)

Now a roughly similar situation appears to have arisen in the Freshwater affair. It centers around the process by which Zachary Dennis was burned with a Tesla coil, and Freshwater is contradicting himself about it in two sets of sworn testimony and a motion filed in federal court. I’ll describe them in separate sections, reproducing a good deal of the testimony for the flavor of what goes on.

First recall that there are three legal proceedings under way, the administrative hearing on Freshwater’s termination; a federal suit brought against the district, administrators, and Freshwater; and a federal suit brought by Freshwater against the Dennis family, the district, and sundry others (including a number of unidentified John or Jane Does). The first two are the focus here. This is a long post, with lots of quotations from various of the legal venues, but it should give a feeling for the problems Freshwater is creating for himself in his sworn testimony in the several proceedings.

A schedule note: The administrative hearing was supposed to resume November 17, but did not do so and has been postponed to Dec 10.

Comfort’s Tract Meet

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Ray Comfort starting handing out his bastardization of the Origin today. A day earlier than expected.

If any of our readers witnessed it, please feel free to describe your experiences in a comment.

Via John Pieret’s excellent Thoughts in a Haystack blog I learn of an ongoing controversy about the teaching of evolution at Adventist Universities. (See also this Sept. 1 article from Inside Higher Ed.) The latest event is that the board of trustess of La Sierra University in Riverside, California, voted to endorse young-earth creationism:

La Sierra’s board of trustees last week unanimously voted to endorse Adventist beliefs that the world was created in six 24-hour days and said the teaching of evolution must be “within the context of the Adventist belief regarding creation.”

The board also proposed that all 15 North American Adventist universities develop a curriculum that includes a “scientifically rigorous affirmation” of Adventist creation beliefs.

At first glance, it is confusing that this is news. Those of us who are familiar with the history of creationism and have read Ronald Numbers’ classic The Creationists, and learned that the Seventh-Day Adventists were virtually the only fundamentalists who produced major advocates supporting belief in a young earth and global flood in the early 20th century – based on the literalist visions of Adventist founder and prophetess Ellen White. It was only in the 1960s that the young-earth/global view became dominant within American fundamentalism/conservative evangelicalism in general, primarily through the efforts of Henry Morris and John Whitcomb in The Genesis Flood.

Delicate Arch

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Photograph by David Collins.

Photography contest, Honorable Mention.

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Delicate Arch – an Entrada Sandstone formation in Arches National Park, near Moab, Utah.

For some reason or other I got on the email list of Ray Comfort’s mailing list. What can I say, I am a connoisseur of the weird. As I’ve learned a little bit about Comfort’s ministry, I have been beginning to wonder – is this whole “Darwin giveaway” thing actually going to happen? Or is it mostly imaginary – primarily a fundraising stunt? I have seen lots of evidence that Comfort et al. are good at publicity and producing videos – but no evidence that they are strong on the ground. If they were actually organized to distribute hundreds of thousands of books on hundreds of campuses, I kind of think there would be more evidence of that organization. But there is virtually no such evidence, despite there being plenty of fundamentalist student groups on campuses that might serve as the foot soldiers for this sort of thing.

Here’s the latest odd thing along these lines –

PRESS RELEASE - 5 of 7 - Militant Atheists Seek Details

Militant Atheists Seek Details of Darwin Book Giveaway

When 170,000 copies of Charles Darwin’s On the Origin of Species with Ray Comfort’s Introduction are given away at universities around the country, atheists plan to be waiting for them. But they don’t know the identity of the universities the books will be given out. Comfort said. “The reason atheists are finding nothing is because every school that is being visited is a closely guarded secret. We don’t want to cause a disturbance. We simply want to get books into the hands of students across the country.” Others advised those who see the books being handed out said, “Cut out the intro in front of them, leave it on the table and take the book.” Another said, “Get them to sign [the] book, thank them, and then make some devastating point that will shatter them forever.” See http://www.livingwaters.com/origin “Press kit” for textual, audio, and video sound bites.

What? The list of schools being visited is a closely-guarded secret? Then why what it on their website at one point (if I recall correctly – here’s a copy from September), and why did they proudly announce in the original video that the top 50 American universities would be targeted? In that video, they also said they were working with Campus Crusade, Answers in Genesis, and the Alliance Defense Fund – but I haven’t heard anything about the Origin-into-schools project from those groups.

Anyway, it doesn’t make much sense and I don’t have any firsthand information, but at the moment I’m wondering if this Origin-into-schools thing will poke above the background noise of random crazies who hand out stuff on the quads of college campuses every day. (You can be sure, though, that there will be one place with Ray Comfort and his camera crew, since in some arenas, a video is worth more than 1,000,000 words and 1,000 on-the-ground volunteers.)

I’ve received a letter from Iowa written by Dr. Hector Avalos, which, I think, may be of interest to many readers of this blog. In his letter Dr. Avalos reports about a defeat of ID advocates in one of the school boards in Iowa. The full text of Dr. Avalos’s letter can be seen here. I hope most of the PT’s denizens will join me in expressing our gratitude to Dr. Avalos for his letter.

Turdus migratorius

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Turdus migratorius – American robin, feathering his nest.

One of the (many) things that drive me bats

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From Nova’s Becoming Human, Part 1 at -9:00 (Nova uses a countdown timer). Discussing the hypothesis that short-term (hundreds to thousands of years) extreme climate variability drove human evolution, and particularly increases in brain size, in the ramp-up from 400 cc or so to Homo habilis’s 600 or 700 cc, and maybe on to larger brained successors, the film says:


Narrator: “This observation led [Rick Potts] to an amazing new idea: Rapid [climate] change as a catalyst for our evolution.”
Rick Potts: “And I began to think that well maybe it’s not the particular environment of a savanna that was important, but the tendency of the environment to change.”

[Here it is]

Narrator: “Could it be that the need to survive violent swings of climate made our ancestors more adaptable?”

Right. And it was the need of giraffes to reach higher branches with yummier leaves that made them grow longer f***ing necks. Gaaaaah!!! Lamarck is dead! And so is Bergson.

That locution, that phraseology, that notion that a “need” somehow drives evolution, drives me bats. “Needs” don’t make populations evolve anything. Now, properties of an environment may select for traits in a population if appropriate variants occur, and as a result of that selective process the population may be more adapted to that selective environment. And it’s not necessarily implausible that an environment that varies irregularly on an appropriate time grain (bunches of generations) could select for some sort of generalized adaptability on the part of a population provided there’s some genetic basis for that adaptability that gives individuals a reproductive advantage, but a “need” doesn’t “make” the trait evolve. If that were the case we’d have wings and gills.

Don’t Diss Darwin

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As everyone in the science blogosphere knows by now, banana man Ray Comfort, he who cannot understand sex, is planning to distribute on the order of 170,000 (his claim) copies of Darwin’s On the Origin of Species in late November on various U.S. and Canadian university campuses. The book is prefaced by an introduction (2 Meg PDF) by Ray that contains the standard creationist argle bargle.

NCSE has created a page in response called Don’t Diss Darwin that has a variety of resources and suggestions. It has an appropriate flier, posters, and a lovely banana bookmark ready for downloading.

Most important for our immediate purposes, it contains a list of universities currently targeted. That list is reproduced below the fold. (I note that Lehigh is on the list; I wonder if Michael Behe will avail himself of the opportunity to learn some evolution.)

I urge scientists and interested folks on the infected campuses to seek immunization from the NCSE page.

Hat tip to Florida Citizens for Science.

Freshwater: Oct 30, 2009

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This was the last of three October hearing sessions. The next sessions are scheduled for November 17-19.

The highlight of today was testimony by Taylor Strack, a student in Freshwater’s class, who corroborated Zach Dennis’ testimony about how the students’ arms were positioned and what stopped the shock that Freshwater was supplying via the Tesla coil.

Taylor Strack Direct testimony

Taylor Strack was a student in the 8th grade science class at the time the alleged burning of Zachary Dennis’ arm occurred, and she saw the procedure followed. That came out in cross examination; first is her direct testimony by R. Kelly Hamilton, Freshwater’s attorney.

Postmodernism versus Religion

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The Education Life supplement of last Sunday’s New York Times contained a little blurb that claimed college students who majored in the humanities and social sciences were apt to become less religiously observant after college. According to the Times, you may credit or blame postmodernism because it stresses that truth is relative rather than absolute. Small solace, as far as I am concerned.

New Nova Series, Evolution Website

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First things first. The 3-part series is called Becoming Human, and it begins tonight at 8 p.m. Eastern time (and 7 p.m. my time, so check your local schedule).

The website, which is in a beta edition right now, is called simply “Evolution.” Today, it features articles on Becoming Human, Evo-Devo, and The Evolution of Motherhood, among others. It looks as though a regular feature will include links to recent news articles, and there are also links to apparently original material by Neil Shubin, Sean Carroll, and Carl Zimmer. There are additional links to a number of relevant books and websites. Finally, you can watch “Intelligent Design on Trial” and “Darwin’s Darkest Hour” just by following links prominently displayed on the “Evolution” website.

Sean Carroll live web talk

As part of a year-long Darwin Lecture Series, evo-devo guy Sean Carroll will be giving a webcast talk based around his Making of the Fittest. The talk is on Wednesday, November 4, and you can sign up for the live webcast here.

Mt. Vernon School Board Election (with results!)

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With all precincts reporting, the two new Board of Education members are Paula Barone and Steve Thompson, who finished in what was nearly a dead heat, 3,476 votes for Barone and 3,477 votes for Thompson, or 25% each. The two incumbents, Watson (19.6%) and Hughes (7.4%) , came in 4th and 5th, respectively, with Robert Kirk in third place with 23%.

It’s a little hard to interpret this outcome. On the one hand, the two incumbents (Watson and Hughes) were defeated, but on the other hand the ‘ticket’ of Thompson and Kirk, who closely associated themselves in the campaign, was split. From the point of view of the handling of the Freshwater affair the results are inconclusive. Barone was perceived as supporting the Board’s handling, and in fact her son Joe testified for the Board in the administrative hearing and Paula addressed a Board of Education meeting about it last year. So I can’t clearly interpret it in either direction if it’s taken as a referendum on the issue of Freshwater’s situation. If one adds what might be crudely interpreted as the pro- vs. anti-Freshwater vote (Thompson+Kirk vs Barone+Watson+Hughes), the split is 48% pro to 52% anti. That’s torturing the data a fair amount–“pro” and “anti” are crude designations and there were other issues in the campaign. But it’s suggestive of the kind of split there is in the community.

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Mt. Vernon voters elect two members of the five-member Board of Education tomorrow, and I’ll be very interested to see the results. Two incumbents, current Board President Ian Watson and Steve Hughes, are running, as are Paula Barone, a former teacher and Mt. Vernon City Council member; Steve Thompson, a vice president in a major local company; and Robert Kirk, an administrator at the Knox County Career Center (formerly Joint Vocational School). To the extent that the election is interpreted as a referendum on the handling of the Freshwater situation, Watson, Hughes, and Barone are generally perceived as supporting the current Board’s actions and Thompson and Kirk are seen as opposing the current Board’s handling of the affair.

The main publicly debated issue in the election is finances, with Thompson and Kirk charging fiscal mismanagement on the part of the current Board and Watson in particular defending the record of the current Board.

Thompson and Kirk are out-spending the others by a large margin, as much as an 8-1 margin according to mid-October filings, and there are indications that the disparity has grown since then. Kirk has had to return some illegal corporate donations to his campaign, and questions have been raised about his having possibly commingled personal and campaign funds. So far no official body is acting on the allegations to my knowledge.

I won’t venture to predict the outcome, though I know what I’m hoping for. I’ll post an addendum to this post tomorrow night when the outcome is clear.

Kilauea Volcano

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Photograph by Michael Klaas.

Photography contest, Honorable Mention.

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Cloud birth – an eruption of Kilauea Volcano, Hawaii.

Freshwater: October 29, 2009.

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On Thursday, October 29, the morning saw Tim Keib, former assistant principal and for a time interim principal of the middle school, continue his direct examination. R. Kelly Hamilton, John Freshwater’s attorney, introduced into evidence an affidavit Keib had signed and walked Keib through it. Keib is a graduate of Cedarville University, a very conservative Christian school in Ohio.

Keib testified that he was in Freshwater’s classroom for a number of 30+ minute observations for evaluation and perhaps 60 to 100 times for a few minutes over the years.

Over the years Keib did a number of evaluations of Freshwater, and testified that he never saw any problematic behavior in Freshwater’s classroom. Asked if he ever saw Freshwater teach creationism, Keib replied that there was “never any direct instruction pertaining to creationism that I heard.” Interesting locution there.

In a series of questions Hamilton pushed the case that Freshwater was using suspect materials in order to teach analysis and objective consideration of multiple hypotheses per the Academic Content Standards, using those materials to see whether students could use the scientific method.

Keib testified that he never saw Freshwater try to push his faith or proselytize students. He never heard Freshwater put down another person’s faith, though he voiced concerns about that to Keib privately. He testified that he never saw Freshwater teaching intelligent design.

Freshwater: October 28 hearing notes

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The administrative hearing on the termination of John Freshwater resumed Wednesday, October 28, and also met Thursday and Friday. I missed most of Wednesday, but hope to have a summary from another spectator sometime soon. This is a summary of the testimony I heard Wednesday morning.

“Coach” David Daubenmire Direct Examination

The first witness Wednesday was “Coach” David Daubenmire. Daubenmire once taught and coached in the MT. Vernon school system, and then left to teach and coach in London, Ohio, where he and the district were sued by the ACLU for praying with his football players. That case was settled out of court just before going to trial, with the district paying costs. Daubenmire left teaching in 2000 to found Pass the Salt Ministries. He claims a Ph.D. in “scriptural psychology” from some school – possibly Faith Bible College in Missouri. He also claims to be an adjunct professor at Mt. Vernon Nazarene University, where he taught a couple of continuing education classes for teachers, one a two-day workshop on religion in the classroom that Freshwater attended in the early 2000s. That class used a text called Finding Common Ground, which appears to be an eminently respectable guide to religion in public schools and First Amendment issues. A copy was introduced as an exhibit in the hearing.

Daubenmire was also the organizer of “Minutemen United” (whose web site now appears to be defunct; see the pages preserved in the Internet Archive) through which he coordinated picketing at abortion clinics (he testified to that); allegedly photographed license plates of patrons of a nearby strip club and posted them on the web somewhere (I haven’t been able to find documentation of that; see note at the end of this post); and disrupting services at a Baptist church that is accepting of the LGBT community. According to Daubenmire’s testimony, Freshwater joined the Minutemen United Saturday morning picketing at a Columbus abortion clinic several times.

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