July 2010 Archives
Oral arguments on a motion to reconsider the sanctions levied against R. Kelly Hamilton and John Freshwater were heard in federal district court yesterday, July 29, 2010.
[Edit on August 1: See the Addendum in this comment. Hamilton has an interesting conception of what can be true.]
Recall that on June 1, 2010, federal district Judge Gregory Frost issued an order granting the plaintiffs’ (Dennis family) motion to impose sanctions on Freshwater and Hamilton for failure to comply with the requirements of the discovery process in Doe v. Mount Vernon Board of Education, et al.. The sanction was basically to pay the Dennises $29K in attorney fees and costs associated with Freshwater’s and Hamilton’s failure to comply with discovery requests. The order also instructed Freshwater and Hamilton to comply with those requests. The sanctions were imposed following a hearing that Hamilton failed to attend due to two flat tires.
Freshwater and Hamilton subsequently filed a motion to reconsider sanctions, arguing that they had done their best, and the Dennises, via their attorney, Douglas Mansfield, filed a memorandum in opposition. The purpose of the hearing on July 29 was to hear oral arguments and testimony on the dispute. Bear in mind that the focus of the hearing is the discovery issue, and not a general hearing on the larger case.
The principals present in the court were John Freshwater and his attorney R. Kelly Hamilton at the defense table and the Dennis family (Steve, Jenifer and Zachary) and their two attorneys from Jones Day at the plaintiff table, with Douglas Mansfield being the lead attorney and Matt Johnson assisting him. The presiding judge is Gregory L. Frost, appointed to the federal bench by President Clinton in 1999.
More below the fold.
Several years ago, I saw a fantastic talk at the Evolution meeting about Intraspecific macroevolution: variation of cranial shape in dog breeds. The talk was by Abby Drake, then a grad student, and reported on a huge digital morphometric comparison of the skulls of dogs and many representatives from the order Carnivora (dogs, cats, bears, sea lions, etc.).
Morphometrics basically consists of taking digital photos of e.g. bones from different angles, and then marking the same landmarks on homologous bones across a big group. Then you can quantitatively compare the differences in shape, independent of things like body size. This is a much more sophisticated analysis than is possible with just calipers, where you can only get length, width, etc.
Phylogenetic trees are essential tools for representing evolutionary relationships. Unfortunately, they are also a major conceptual stumbling block for budding biologists. Anyone who has taught basic evolutionary concepts to college undergrads (and probably high school students as well) has most likely dealt with students struggling to properly read and draw phylogenies.
Lucky for us, there is also a growing body of literature on the most effective ways to teach what has been dubbed “tree-thinking”. I have summarized this literature in a review due to be published in the journal Evolution: Education and Outreach (doi:10.1007/s12052-010-0254-9). The full text of the article is available at that link, and I have reproduced the abstract below.
Evolution is the unifying principle of all biology, and understanding how evolutionary relationships are represented is critical for a complete understanding of evolution. Phylogenetic trees are the most conventional tool for displaying evolutionary relationships, and “tree-thinking” has been coined as a term to describe the ability to conceptualize evolutionary relationships. Students often lack tree-thinking skills, and developing those skills should be a priority of biology curricula. Many common student misconceptions have been described, and a successful instructor needs a suite of tools for correcting those misconceptions. I review the literature on teaching tree-thinking to undergraduate students and suggest how this material can be presented within an inquiry-based framework.
I just realized/figured out that Lauri Lebo, the reporter of Dover fame, and co-resident at the International Beer Can Museum, has an RSS feed for her posts at Religion Dispatches. Lots of fun stuff there, including the upcoming end of the world. By the way, we’ve got a guy on the Berkeley campus, David Temple, who is regularly out on the quad handing out these weird scrawled predictions of the end of the world starting May 21, 2011. He also hits the Integrative Biology building a couple times a year. I’ve saved a few since I figured this would make for a really good party next year.
I always assumed that the scrawling and Bible-verse quoting meant that David Temple was doing his own Bible-based numerology, but maybe he’s getting it from Harold Camping? Does anyone have any insight? I know a lot more about the literalists who focus on the beginning times than I do about the end-times guys. (Although, as you can see, the two are intimately connected.)
(HT: John Pieret)
Every Saturday on the square in downtown Madison you can find a big box covered with tired, ridiculous claims of Young Earth Creationism. Standing nearby Larry and Kevin preach the Gospel of Jesus-On-A-Triceratops to the curious and appalled alike. Together they make sort of a “good cop, bad cop” of creationism: Kevin, sort of a naive and basically likeable innocent guy, and Larry, a blustering, know-it-all whose abysmal knowledge of science is only inversely matched by his inflated sense of how much he thinks he knows. With creationists like these, who needs evolutionists.
Read a description of my encounters with them over a few weekends this summer on another server, and post your comments here at Panda’s Thumb.
I consider myself pretty well-educated about creationism, and of course I know it’s all silly, but I pride myself on usually being able to understand what argument the creationists are trying to make, even when they are doing it poorly. But I need help with this one.
Starting on Sunday, we have: Cornelius Hunter, Sunday, July 25, 2010, speaking about shared errors in pseudogenes:
This claim, that such shared errors indicate, or demonstrate, or reveal common ancestry, is the result of an implicit truth claim which does not, and cannot, come from science. It is the claim that evolution and only evolution can explain such evidences. It is the equivalent of what is known as an IF-AND-ONLY-IF claim.
Science makes IF-THEN statements (if evolution is true, then species with recent common ancestors should have similarities between them). IF-AND-ONLY-IF statements (if and only if evolution is true, then species with recent common ancestors should have similarities between them) cannot be known from science. [italics original]
OK, so here he’s saying, I guess, that science can only make if-then statements, and test hypotheses on that basis. Science cannot formally say that X is the ONLY possible explanation of Y, because, I suppose, there always might be some other explanation out there.
Update 2: There is no settlement yet. The start of the trial was postponed for ongoing settlement talks. My best guess is that it all depends now on the outcome of the hearing on sanctions scheduled for July 29. As I noted here, the sanctions requested by the Doe family would eviscerate Freshwater’s defense in the civil suit, so if the judge grants either of the sanctions (adverse evidentiary inference or defaul judgment) on July 29, Freshwater is in deep trouble in that case and the probability of a settlement will go way up.
Update 1: See this comment below. It’s not clear now that this is a “settlement.”
The Mount Vernon News is reporting that Doe v. Mount Vernon, the federal civil suit in which John Freshwater is the sole remaining defendant, has been settled. The trial was due to start today. No details on the settlement are yet available. I’ll update this post as and when I learn more.
The other federal civil suit, Freshwater v. Mount Vernon BOE, is still proceeding as far as I know now.
Photograph by James Wood.
Photography contest, Honorable Mention.
Tachyglossus aculeatus – short-beaked echidna, or spiny anteater, wandering along the edge of the Jordan River, Midlands, Tasmania. One of Australia’s two native monotremes. Echidnas in Tasmania are somewhat hairier than individuals on the mainland and are recognized as subspecies setosus, one of five recognized subspecies.
Most of you don't understand evolution. I mean this in the most charitable way; there's a common conceptual model of how evolution occurs that I find everywhere, and that I particularly find common among bright young students who are just getting enthusiastic about biology. Let me give you the Standard Story, the one that I get all the time from supporters of biology.
Evolution proceeds by mutation and selection. A novel mutation occurs in a gene that gives the individual inheriting it an advantage, and that person passes it on to their children who also gets the advantage and do better than their peers, and leave more offspring. Given time, the advantageous mutation spreads through the population so the entire species has it.
One example is the human brain. An ape man millions of years ago acquired a mutation that made his or her brain slightly larger, and since those individuals were slightly smarter than other ape men, it spread through the population. Then later, other mutations occured and were selected for and so human brains gradually got larger and larger.
You either know what's wrong here or you're feeling a little uneasy—I gave you enough hints that you know I'm going to complain about that story, but if your knowledge is at the Evolutionary Biology 101 level, you may not be sure what it is.
Im sure everyone here is well aware of the fact we have ‘science education issues’ here in Oklahoma. Not only do we have a failing grade of 50% on the State Science Standards report card, we have a plethora of politicians and powerful religious leaders declaring scientists and science itself untrustworthy.
How do you get kids excited by science in this kind of landscape?
A childrens musician in Stillwater has a great idea going. Monty Harper pairs up with local scientists to give sweet presentations for kids at the Stillwater Public Library– Monty writes a catchy song about the scientist/their research, and the scientists talk about their research!
Monty has built up enough of a song-base now, he wants to make an album so he can help kids everywhere get excited about science. It will include songs on topics like phototaxic bacteria, stress hormones, wheat genomics, bacterial biofilms, bat taxonomy, x-ray crystallography, and luminescence dating! For real.
Here is where you can help– If you think this is a neato idea and would like to help it become reality, check out Montys page over at kickstarter.
Look at the donation tiers, and see where you want to help– you can donate and free CDs will be sent to a school of your choice, you can get a CD for yourself for your kids (Im giving mine to my nieces), you can get all kinds of insider exclusives, get your name in the CD booklet as an official donor, or at the highest tier– you can get a custom song of your very own, written about YOUR research or your FAVORITE branch of science if you arent a scientist, and be included on the CD!
Im contacting local freethought groups to see if they want to pitch in to get CDs sent to local rural schools– My parents teach at rural schools, and these kids (and their teachers) would appreciate a way to bring professional scientists and researchers into their classroom, even if its only vicariously. A pro-science, pro-family way to do some good.
If Monty doesnt reach his funding goal by August 21 (HIS BIRTHDAY), you wont be charged anything, Monty loses the window his producer has open, and he has to start all over.
Monty may not be a scientist, but he is using his passion and talent to actually DO something to promote science literacy and getting kids excited about science in a pretty harsh environment. I think thats just awesome.
I'm one of those dreadful animal-centric zoologically inclined biologists. Plants? What are those? Fungi? They're related to metazoans somehow. Lichens? Not even on the radar. The first step in fixing a problem, though, is recognizing that you have one. So I confess to you, O Readers, that my name is PZ, and I am a metazoaphile. But I can get better.
My path to opening up to wider horizons is to focus on what I find most interesting about animals, and that is that they are networks of cells driven by networks of genes that generate patterned responses of expression by cell signaling, or communication. See? I'm already a little weird. Show me a baby bunny, and I don't just see a cute little furry pal with an adorable twitchy nose, I see an organized and coherent array of differentiated tissues that arose by a temporal sequence of cell-cell interactions, and I just wanna open him up and play with his widdle epithelial sheets and dismantle his pwetty ducts and struts and fibers and fluids, oochy coo. And ultimately, I want to take apart each cell and ask why it has its particular assortment of genes switched off and on, and how its state affects its neighbors and the whole of the organism.
Which means, lately, that I've acquired a growing interest in bacteria. If I were 30 years younger, I could probably be seduced into a career in microbiology.
There are a couple of reasons why an animal-centric biologist would be interested in bacteria. One is the principle of it; the mechanisms that animal cells use to build complex arrangements of tissues were all first pioneered in single-celled organisms. We have elaborated and added details to gene- and cell-level phenomena, but it's a collection of significant quantitative differences, with nothing known that is essentially new in metazoan cells. All the cool stuff was worked out by evolution in the 3-4billion years before the Cambrian, a potential that simply blossomed in the past half-billion years into big conglomerations of cells. Understanding how the building blocks of multicellularity work individually ought to be a prerequisite to understanding how the assemblages work.
But there's another reason, too, a difference in perspective. It is our conceit to regard ourselves as individuals of Homo sapiens, a body of cells clonally derived from a single human cell. It's not true. It turns out that each one of us is actually a whole population of species, linked by our evolutionary history and lumbering through the world as a team. Genus Homo is also genera Escherichi and Bacteroidetes and Firmicutes and many others.
Over on the Thinking Christian blog I have been challenged on my assertion in several publications (e.g. in this PNAS article) that “intelligent design” leader Dean Kenyon – a coauthor of Of Pandas and People and a Discovery Institute fellow – is actually a young-earth creationist and “creation scientist.” Usually I get these things right, but I was recently wrong about Cornelius Hunter, and only some of the evidence is on the Dean Kenyon entry on Wikipedia, so it is worth it to review the evidence.
There are many lines of evidence for the proposition that Kenyon is/was a young-earther. It is true that he wasn’t always like this – in the late 1960s he was a young origin-of-life researcher, and he coauthored the book Biochemical Predestination which accepted the standard view on evolution and the age of the Earth. But in the late 1970s he changed his mind:
“Then in 1976, a student gave me a book by A.E. Wilder-Smith, The Creation of Life: A Cybernetic Approach to Evolution. Many pages of that book deal with arguments against Biochemical Predestination, and I found myself hard-pressed to come up with a counter-rebuttal. Eventually, several other books and articles by neo-creationists came to my attention. I read some of Henry Morris’ books, in particular, The Genesis Flood. I’m not a geologist, and I don’t agree with everything in that book, but what stood out was that here was a scientific statement giving a very different view of earth history. Though the book doesn’t deal with the subject of the origin of life per se, it had the effect of suggesting that it is possible to have a rational alternative explanation of the past.”
Kenyon, Dean, and Pearcey, Nancy (1989). “Up From Materialism: An Interview with Dean Kenyon.” Bible-Science Newsletter, 27(9), 6-9. September 1989.
(Note: both A.E. Wilder-Smith and Henry Morris are famous young-earther creation scientists. Nancy Pearcey is a young-earther too – she once wrote that humans were contemporaneous with dinosaurs. And the Bible-Science Newsletter was a famously rabid young-earth publication that sometimes even flirted with geocentrism.)
Photograph by Kari Tikannen.
Photography contest, Honorable Mention.
Fraunhofer lines appear in sunlight reflected off a CD. The Fraunhofer lines are the dark absorption lines superimposed upon the colored spectrum.
A lot of people have been writing to me about this free webgame, CellCraft. In it, you control a cell and build up all these complex organelles in order to gather resources and fight off viruses; it's cute, it does throw in a lot of useful jargon, but the few minutes I spent trying it were also a bit odd — there was something off about it all.
R. Kelly Hamilton and John Freshwater have filed responses to the Dennis family’s memorandum of opposition to reconsideration of the sanctions against Hamilton and Freshwater ordered by the judge in Doe v. Mount Vernon BOE, et al.. I recently described the memorandum in Tightening the vise. The responses are masterpieces of misdirection. See Hamilton’s (pdf) and Freshwater’s (large pdf).
Recall that the memorandum of opposition made two principal allegations:
1. Hamilton and Freshwater claimed that they spent many hours in May 2008 preparing 15 affidavits to give the independent investigators. However, Hamilton’s billing records for the period from mid-April through the end of May 2008, obtained pursuant to a federal court order to the Board of Education’s attorney, show no evidence of affidavit-related activity.
2. Freshwater has been unresponsive to discovery requests and unresponsive to a court order to compel compliance with those requests.
More commentary below the fold
For some strange reason, CNN’s iReport website wants people to post photos of church signs. Given the existence of websites to create fake church signs, this seems ripe for abuse. While looking at an article today, one of the signs popped up in the side bar, and it was a “deep” insight into evolution. From Venice, Florida:
Five years of grad school destroyed by the “wisdom” of this church’s sign!
(Note: I got off on some tangents in this post – big tangents, not having written a Luskin-rebuttal in awhile. In some cases – most of them, probably – I may be the only person in the world who would bother to rebut these points. But, hey, everyone needs a summer vacation, and Luskin usually takes lack of response as evidence that he must be right. This is hilarious, but it’s funniest when he relies on an argument for many years, getting more and more confident in it. But, eventually someone has to pop the bubble. I really have to stop now so please point out errors, which must exist, and I will fix when I get a chance.)
Casey Luskin has responded to my recent article “The Evolution of Creationist Movements” in Evolution: Education and Outreach. My article is freely online, so you should read it and all of the other great pieces in that issue, which was a festschrift for Eugenie C. Scott (only a few of the articles are currently open access, however).
Luskin raises 3 issues. I will answer in 3 parts:
Possibly stimulated by Jerry Coyne’s post, there’s a spate of web attention to a survey concerning evolution, science, and religion performed by the Center for Public Policy of Virginia Commonwealth University (pdf here). The survey was purportedly performed in collaboration with VCU Life Sciences. I seriously wonder who they consulted in the Life Sciences. It surely could not have been an evolutionary biologist, because like so many such surveys, this one asks a stupid question, and commenter Kevin on Coyne’s blog nails it:
I have a HUGE problem with question 1.
“Which of these statements comes closest to your views on the origin of biological life:”
What? Are you talking about abiogenesis? How am I to know whether it happened all at once or gradually over time?
The alternatives offered were
– Biological life developed over time from simple substances, but God guided this process,
– Biological life developed over time from simple substances but God did not guide this process,
– God directly created biological life in its present form at one point in time?
[Note: the order of answers was randomized among people]
Kevin went on:
Now, if you’re talking EVOLUTION, that’s a different kettle of fish. That can be defined as “diversity of life forms on this planet.” That we know a LOT more about.
But “origins of life”? Not so much.
Bad poll question. Horridly bad. Almost designed to allow theists to wedge a god into a gap.
Exactly right. This poll in fact tells us precisely nothing about acceptance of evolution because of the sloppy wording of that question. Worse, asking the question that way merely propagates the creationist conflation of the question of abiogenesis and the reality of evolution. So again, I wonder who in the VCU Life Sciences they actually consulted on that question.
A Chinese man who saved a one-armed, one-legged monkey says the primate has paid him back - by killing all of his chickens.
Good thing the monkey didn’t see the farmer choke his chicken.
by Mark Farmer, http://www.uga.edu/cellbio/people/farmer.html
Intelligent Design Creationism has evolved yet again. In preparing for a discussion last month (May) with Charles Thaxton I went to the DI’s site to see what their definition of ID was. What I found was this:
Intelligent design is a scientific theory which holds that certain features of the universe and living things are best explained by an intelligent cause, and are not the result of an undirected, chance-based process such as Darwinian evolution.
OK so what does the same site say today, a month later?
Intelligent design refers to a scientific research program as well as a community of scientists, philosophers and other scholars who seek evidence of design in nature. The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.
Notice the two important differences? 1) Apparently ID is no longer a “scientific theory” instead it now refers to “a scientific research program” and 2) ID is no longer contrasted with “chance-based process such as Darwinian evolution.” but rather is now compared to “an undirected process such as natural selection.”
It makes one wonder whether this is simply the natural evolution of ID as it continually adapts to an ever changing environment or whether recent court defeats, rejections by state school boards, and continued lack of intellectual advancement have brought about their own form of punctuated equilibria for intelligent design.
Daily Kos has posted the best of their Q2 hate mail, and number 2 concerns evolution:
Evolution is a LIE!
You are a LIAR and a FRAUD for spreading your bullshit evolution prpaganda! evolution has never been proven to work and it’s not even logical. Let me tell you a fun story. My friend’s seven year old nephew died of cancer two months ago. How the fuck is that evolution? Evolution is supposed to guarantee that all individuals get to procreate: this is called “fitness” (your word, not mine)! If someone dies at 7, he doesn’t get to procreate. This happens all the time. It also proves that evoution doesn’t work EVEN BY YOUR OWN FUCKED UP STANDARDS! Why would evolution make people have cancer? what “advantage “ do you get from having cancer? Evolutionists have got to be the dumbest fucking retards this side of scientology. Need more proof? How’s this: if birds “evolved” magically from dinosaurs (tyranosaurus?), then there should be a creature that’s 99% dinosaur and 1% bird, then another thats 98% dinosaur and 2% bird and so on. Am I going too fast for you? It’s called basic logic, you shitbrain retard. Now, show me a fossil of a 82/18 dinosaur/bird? Or 61/39? Wait! Maybe they don’t exist! How fucking stupid do you have to be to believe something that’s obviously bullshit? Did your mommy drop you on your head? You mock people’s faith in God when you yourselves have faith in stuff that’s not even remotely reasonable. Your probably not really evil, just really fucking stupid and brainwashed. So why dont you pull your head from your ass and look at how retarded your evolution cult really is.
and maybe you’l wake up and realize you’ve been fucked over and defrauded.
I want to call “Poe”, but a Poe should make more sense.
We received the following announcement from the National Center for Science Education and reproduce it with permission:
I’ve been informed that I’ve been negligent in keeping the dramatis personae and various legal actions in the Freshwater affair clearly distinguished. Let me summarize below the fold.
I pose that as a genuine question; I have no inside information. But I got to thinking this morning about the legal representation situation in Doe v. Mount Vernon Board of Education, et al in which Freshwater is the sole remaining defendant. Recall that in late April the two insurance company lawyers representing Freshwater in that case, Jason Deschler and Robert Stoffers, petitioned the court to withdraw from representing him. (Freshwater claimed that he fired them.) Two new lawyers, Steven C. Findley and Sandra R. McIntosh, were retained by the insurance company to replace them. Now this billing records mess gets dropped in their laps. One wonders how they’re thinking now that there’s documentary evidence of the shenanigans Hamilton and Freshwater have been pulling on the federal court in that case and how long the insurance company will hold out in settlement talks under these circumstances. Recall that the case is to go to trial July 26.
As I understand the process, Freshwater and Hamilton have to respond to the memorandum in opposition very soon–I think this week–and the judge will make a decision based on the documents submitted. (I was hoping for an oral hearing: I’d be willing to drive 1.5 hours in rush hour traffic to see that!) But this has to put pressure on Freshwater’s insurance company lawyers to reach a settlement before the judge rules, since if the judge grants either of the Dennises’ requests for sanctions (default judgment in their favor or an adverse evidentiary inference against Freshwater regarding the missing material), it will result in the crippling of any defense they might try to put on, and they have to know that. This is speculative, but it now would not surprise me to see a sudden settlement of Doe v. Mount Vernon Board of Education, possibly even this week.
The pressure on John Freshwater and his attorney R. Kelly Hamilton was ratcheted up last Friday, July 2, when the attorney for the Dennis family in Doe v. Mount Vernon Board of Education et al. filed a memorandum in opposition (pdf) to Freshwater and Hamilton’s motion for reconsideration of the federal court’s ruling that the two are liable for sanctions–attorney fees–due to non-compliance with discovery requests. That memorandum, written by Douglas Mansfield, the Dennises’ attorney, is full of bad news for Freshwater and Hamilton.
Details below the fold
I’ve said in several venues that should the theocrats win, the next day blood will flow down the aisles and under the pews (one hopes only metaphorically, though that’s by no means guaranteed). We see that metaphor scenario playing out in a number of venues in contemporary Christianity. Ken Ham rails against theistic evolution, arguing that its acceptance of an old earth/universe erodes the authority of scripture, and now Albert Mohler, President of Southern Baptist Theological Seminary (William Dembski’s former employer), all but accuses Francis Collins’ BioLogos Forum of apostasy (or so Darrell Falk interprets it) on much the same grounds, while endorsing the venerable appearance of age notion to account for the data of physics, geology, paleontology, and evolutionary biology.
More below the fold
I guess I’ll have to watch beautiful explosions in the night sky to feel better.
HT: Troy Britain
Katie Haggerty, a woman who lives near Lyons, Colorado, thinks it is a possibility. Ms. Haggerty, who claims no academic or scientific credentials whatsoever, has performed some experiments to test this hypothesis.
According to an article by Bruce Leaf in today’s Boulder Daily Camera, Ms. Haggerty has thought for years that radio waves might be harming her geraniums. So she put some plants inside a Faraday cage, an enclosure that blocks radio waves, and thought she saw improvement in the growth of plants.
A few years ago, she graduated to aspen trees, which are dying in Colorado. Thinking that the cause might be radio waves, not drought, she performed a controlled experiment in which she placed some aspen seedlings into a Faraday cage and some in a fiberglass cage (which will not block radio waves), and also grew some seedlings in the absence of a cage.
Today’s Times has a (possibly unwittingly) amusing article on apps designed for iPhones by Christian publishers attempting to fight “what they view as a new strain of strident atheism.” Nonbelievers are, naturally, responding.
Here is an example of the level of debate:
“Say someone calls you narrow-minded because you think Jesus is the only way to God,” says one top-selling application introduced in March by a Christian publishing company. “Your first answer should be: ‘What do you mean by narrow-minded?’”
Of interest to our fellow defenders of science: Steven Barrett, the proprietor of Quackwatch, is being sued for $10 million for criticizing pseudoscience, and he’s asking for donations to help in his legal defense.
The second PT photography contest is accepting entries now through July 15. Please read and follow the rules here and pay particular attention to Rule 12.
Update, July 8: Just to clarify, we give preference to photographs of endangered species, but general entries are welcome as well. If we receive enough endangered species, we will establish a separate category. Entries in the animal, mineral, and vegetable categories are also welcome.
Update, July 15: The deadline for submissions is tonight at 10:00 Mountain Daylight Time. MDT is UTC(GMT) - 6 h.