The Panda's Thumb

"Intraspecific macroevolution" within domestic dog breeds

2010-07-30T00:07:20Z

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.

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A previous study had noted that the skull variation in dogs was bigger than the variation in the family Canidae, but the incredible result of Drake’s study was that the variation in shape of dog skulls was bigger than the variation in shape across the entire order Carnivora, which is 60 million years old and includes even mostly-aquatic forms.

Figure 3: Principal component (PC) analysis for skull shape in the complete data set. A-C, Plots of the PC scores. D, Shape changes associated with the PC axes. For each PC, the shapes corresponding to the observed extremes in the positive and negative directions are shown as a warped surface of a wolf skull (Wiley et al. 2005).

And most of this morphological variation took only a few hundred years to produce. It is true that some of these weird skulls would not be favored in the wild – Drake notes that natural selection is reduced when your food comes from a can rather than stuff you hunt – and artificial selection is greatly enhanced by selective breeding. But this is strong evidence that (a) there is no problem on the genetic variability end of the equation for the kinds of variability that we see in a mammalian order like Carnivores; rather the constraint is natural selection for a particular niche. If the selective pressure is there, the morphological change can happen very quickly; and (b) lack of time isn’t the issue; if the conditions are right, hundreds or thousands of years can be plenty of time.

I didn’t even notice when this study came out and got a bunch of press in January, probably because I actually had a girlfriend at the time (see, rare events do happen in geologic time!). But this is a study that should be in the back pocket of any creationism opponent. You can see an example of its usage on Cornelius Hunter here; it’s kind of like a surprise sack of a quarterback.

The other thing I like about the conclusion of “intraspecific macroevolution” is that it tweaks a lot of standard tropes that even we scientists have about what is meant by the word “macroevolution.” The minimal definition of macroevolution is “evolution above the species level”, but it has become a catchall term encompassing everything from speciation to lineage-diversification and extinction dynamics to “evolution of ‘higher taxa’” (ack! go read “down with phyla!”) to vaguely defined “large” amounts of change to evo-devo changes in development. These things then all get mixed together in people’s heads, resulting in the erroneous presumption that “‘large’ amounts of change” = lots of speciation events = the origin of some big Linnaean ‘taxon’ = lots of action at the lineage-counting level. As a very rough approximation it might be true that these different things are often linked, but as this study shows, it ain’t always true. We would probably be better off using specific terms for each of these different topics, and not trying to lump them all together under “macroevolution” as if they were all intrinsically connected. Questions like “is macroevolution just the result of repeated rounds of microevolution” have almost no meaning if “macroevolution” refers to all of these different things at once.

References

Abby Grace Drake and Christian Peter Klingenberg

Large‐Scale Diversification of Skull Shape in Domestic Dogs: Disparity and Modularity

Am Nat 2010. Vol. 175, pp. 289-301

DOI: 10.1086/650372

Abstract:

The variation among domestic dog breeds offers a unique opportunity to study large‐scale diversification by microevolutionary mechanisms. We use geometric morphometrics to quantify the diversity of skull shape in 106 breeds of domestic dog, in three wild canid species, and across the order Carnivora. The amount of shape variation among domestic dogs far exceeds that in wild species, and it is comparable to the disparity throughout the Carnivora. The greatest shape distances between dog breeds clearly surpass the maximum divergence between species in the Carnivora. Moreover, domestic dogs occupy a range of novel shapes outside the domain of wild carnivorans. The disparity among companion dogs substantially exceeds that of other classes of breeds, suggesting that relaxed functional demands facilitated diversification. Much of the diversity of dog skull shapes stems from variation between short and elongate skulls and from modularity of the face versus that of the neurocranium. These patterns of integration and modularity apply to variation among individuals and breeds, but they also apply to fluctuating asymmetry, indicating they have a shared developmental basis. These patterns of variation are also found for the wolf and across the Carnivora, suggesting that they existed before the domestication of dogs and are not a result of selective breeding.

Robert K. Wayne (1986). “Cranial Morphology of Domestic and Wild Canids: The Influence of Development on Morphological Change.” Evolution, Vol. 40, No. 2 (Mar., 1986), pp. 243-261 * Stable URL: http://www.jstor.org/stable/2408805

Abstract l The domestic dog varies remarkably in cranial morphology. In fact, the differences in size and proportion between some dog breeds are as great as those between many genera of wild canids. In this study, I compare patterns of intracranial allometry and morphologic diversity between the domestic dog and wild canid species. The results demonstrate that the domestic dog is morphologically distinct from all other canids except its close relatives, the wolf-like canids. Following this, I compare patterns of static and ontogenetic scaling. Data on growth of domestic dogs are presented and used to investigate the developmental mechanisms underlying breed evolution. Apparently, most small breeds are paedomorphic with respect to certain morphologic characters. In dogs and other domestic animals, morphologic diversity among adults seems to depend on that expressed during development.

Teaching Tree-Thinking to Undergraduate Biology Students

2010-07-29T20:00:00Z

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.

Lauri Lebo blog and the End of the World

2010-07-29T05:42:21Z

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)

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Darwin Day 2008, cell phone pics:

Scan of poster:

Later in Spring 2008:

And July 2010:

Creationists on the Square in Madison, Wisconsin

2010-07-27T14:17:54Z

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.

If and only if Cornelius Hunter made sense, then...

2010-07-27T03:32:39Z

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.

Via the Discovery Institute Blog/Misinformation Service, I came across this post from Hunter, which is his Monday post. I also read Hunter’s Sunday post and got confused.

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.

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He thinks this is important for evolution because sometimes evolutionists say Y (lanugo, shared errors in pseudogenes, etc.) can “only” be explained by common ancestry. Of course, any fair assessment of these sorts of statements would note that people use such language all the time (“the only explanation for the 20 identical paragraphs in these two students’ term papers is copying from each other or from a common source”), and they don’t mean that they can formally exclude, say, miraculous intervention by Thor or something. All people typically mean by these statements is “this is the only decent explanation of Y that has been put forward to date; if someone else comes up with a better explanation, fine, but until then X is what I’m going with.” But if creationists were fair about such things, they wouldn’t be creationists.

(Parenthetical, Hunter throws in some total bunkum:

Any scientific analysis of the evidence [of pseudogenes] would come up empty handed. Pseudogenes reveal various patterns, some which can be employed to argue for common descent, others which violate common descent (they could be explained, for instance, by common mechanism). Furthermore pseudogenes reveal evidence of mutational hotspots.

Side rant: This is, basically, total crap. Hunter apparently has no idea that, in phylogenetics, it is trivial to test hypotheses like “there is no tree structure in the sequence data” or “these two phylogenies from two different genes agree/disagree with each other”, to quantify the amount of agreement/disagreement, etc. The amount of homoplasy (character states which evolved independently, as might occur occasionally with pseudogenes) can be estimated, and we can tell whether or not we are close or far from a situation in which there is so much homoplasy that no phylogenetic structure is statistically supported. And when this kind of thing is done, the result is typically *massive* statistical support for common ancestry. At least, it would be considered such in any other field of science, but Hunter wants to treat evolution differently from all other parts of science. For evolution, he wants to have the special privilege of pulling out a few characters that disagree with some pattern, and ignore the hundreds/thousands of other characters that support the pattern. Hunter complains and complains about the unscientific nature of evolutionists, but when it comes to doing an actual fair data analysis that actually looks at the statistical support for common ancestry, he’s totally at sea. OK, end of rant.)

(Not quite done. I should add that my first encounter with Hunter was in 2001 or so. Somehow or other we were in an argument about whether or not some genetic sequence data produced a tree structure. He had calculated the pairwise distances between the genes and done a histogram of the distances. The distribution of gene-gene distances had a number of separate humps. He claimed that this falsified tree structure. I pointed out that this pattern was exactly what you would expect from distances produced from a tree. After a lot of arguing, he eventually got it, but then said something irate about how he was sorry but just because he was totally wrong about this (I would say the definition of a surprising successful prediction is one where someone claims their data is good and a good falsification of a hypothesis, but then it turns out that their data has exactly the pattern they claimed it didn’t have), he wasn’t going to “genuflect” to evolution. Sadly I can’t find the email now and the only word I can remember is “genuflect”. Ah well.)

Anyway, so, everyone’s got his argument so far? Evolutionists shouldn’t use “IF-AND-ONLY-IF statements”, they should be real scientists and just use “IF-THEN statements” like other scientists, the good kind of scientists.

(By the way, if Hunter is right, he’s just nuked Stephen Meyer’s argument in Signature in the Cell, which relies almost entirely on the argument that intelligence is the ONLY source of genetic “information”. Oops. Of course, Meyer’s assertion is wrong, but that’s a different story.)

With that, I give you, Cornelius Hunter, Monday, July 26, 2010. He is complaining about an introductory biology textbook by Johnson & Lobos. After saying the authors “rehearse the usual lies”, Hunter really gets going on the fossil record:

Such misrepresentations of science, as damaging as they are, pale in comparison to Johnson’s and Lobos’ next move. The apologists make a pathetic attempt to enlist the fossil record as powerful evidence for evolution, and end up with only the usual religious dogma. They write:

If the theory of evolution is not correct, on the other hand, then such orderly change is not expected.

Very interesting. And how do evolutionary clowns know so much? From where did Johnson and Lobos learn such ultimate truths? If evolution is not correct then such orderly change is not expected? Tell us more.

What are all the possibilities aside from evolution and why do none of them predict “such orderly change”? Why is it that evolution, and only evolution, predicts such an outcome? This is truly fascinating. If and only if evolution is true would we see such orderly change. Johnson and Lobos are real geniuses–they have knowledge of all possible causes.

You cannot make this stuff up. In two and half pages the text’s chapter on evolution has gone from misleading to absurd. What will come next?

But this is nothing new in evolutionary circles. Only evolutionists can make fools of themselves with a straight face and then repeat the process ad nauseam.

But, did they use the word “only”? No! And they said nothing about “ultimate truths”, and nothing about whatever mysterious alternatives Hunter endlessly claims are out there, but which he shockingly, cravenly, scandalously never bothers to elucidate, as any real scientist would have to. All the authors did was make an if-then statement, like Hunter JUST FREAKING SAID scientists were supposed to do the day before! Instead of congratulating them on saying the right thing, Hunter convicts them of vast, grand metaphysical sins.

So I’m at a loss. If I had to guess, I’d say he’s just mad and letting emotion run his argumentation, under the cover of unsupported blather about metaphysics. Maybe this textbook is being used in his home town or something?

Freshwater: One civil suit settled (?: See updates)

2010-07-26T18:04:51Z

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.

Tachyglossus aculeatus

2010-07-26T17:00:00Z

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.

It's more than genes, it's networks and systems

2010-07-24T23:46:57Z

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.

]]> Just to make you even more queasy, the misunderstanding here is one that creationists have, too. If you've ever encountered the cryptic phrase "RM+NS" ("random mutation + natural selection") used as a pejorative on a creationist site, you've found someone with this affliction. They've got it completely wrong.

Here's the problem, and also a brief introduction to Evolutionary Biology 201.

First, it's not exactly wrong — it's more like taking one good explanation of certain kinds of evolution and making it a sweeping claim that that is how all evolution works. By reducing it to this one scheme, though, it makes evolution far too plodding and linear, and reduces it all to a sort of personal narrative. It isn't any of those things. What's left out in the 101 story, and in creationist tales, is that: evolution is about populations, so many changes go on in parallel; selectable traits are usually the product of networks of genes, so there are rarely single alleles that can be categorized as the effector of change; and genes and gene networks are plastic or responsive to the environment. All of these complications make the actual story more complicated and interesting, and also, perhaps to your surprise, make evolutionary change faster and more powerful.

Think populations

Mutations are the root of biological variation, of course, but we often have a naive view of their consequences. Most mutations are neutral. Even advantageous mutations are subject to laws of chance in their propagation, and a positive selection coefficient does not mean there will be an inexorable march to fixation, where every individual has the allele. This is also true of deleterious mutations: chance often dominates, and unless it is a strongly negative allele, like an embryonic lethal mutation, there's also a chance it can spread through the population.

Stop thinking of mutations as unitary events that either get swiftly culled, because they're deleterious, or get swiftly hauled into prominence by the uplifting crane of natural selection. Mutations are usually negligible changes that get tossed into the stewpot of the gene pool, where they simmer mostly unnoticed and invisible to selection. Look at human faces, for instance: they're all different, and unless you're looking at the extremes of beauty or ugliness, the variations simply don't make much difference. Yet all those different faces really are the result of subtly different combinations of mutant forms of genes.

"Combinations" is the magic word. A single mutation rarely has a significant effect on a feature, but the combination of multiple mutations may have a detectable or even novel effect that can be seen by natural selection. And that's what's going on all the time: the population is a huge reservoir of genetic variation, and what we do when we reproduce is sort and mix and generate new combinations that are then tested in the environment.

Compare it to a game of poker. A two of hearts in itself seems to be a pathetic little card, but if it's part of a flush or a straight or three of a kind, it can produce a winning hand. In the game, it's not the card itself that has power, it's its utility in a pattern or combination of other cards. A large population like ours is a great shuffler that is producing millions of new hands every day.

We know that this recombination is essential to the rapid acquisition of new phenotypes. Here are some results from a classic experiment by Waddington. Waddington noted that fruit flies expressed the odd trait of developing four wings (the bithorax phenotype) instead of two if they were exposed to ether early in development. This is not a mutation! This is called a phenocopy, where an environmental factor induces an effect similar to a genetic mutation.

What Waddington did next was to select for individuals that expressed the bithorax phenotype most robustly, or that were better at resisting the ether, and found that he could get a progressive strengthening of the response.

The progress of selection for or against a bithorax-like response to ether treatment in two wild-type populations. Experiments 1 and 2 initially showed about 25 and 48% of the bithorax (He) phenotype.

This occurred over 10s of generations — far, far too fast for this to be a consequence of the generation of new mutations. What Waddington was doing was selecting for more potent combinations of alleles already extant in the gene pool.

This was confirmed in a cool way with a simple experiment: the results in the graph above were obtained from wild-caught populations. Using highly inbred laboratory strains that have greatly reduced genetic variation abolishes the outcome.

Jonathan Bard sees this as a powerful potential factor in evolution.

Waddington's results have excited considerable controversy over the years, for example as to whether they reflect threshold effects or hidden variation. In my view, these arguments are irrelevant to the key point: within a population of organisms, there is enough intrinsic variability that, given strong selection pressures, minor but existing variants in a trait that are not normally noticeable can rapidly become the majority phenotype without new mutations. The implications for evolution are obvious: normally silent mutations in a population can lead to adaptation if selection pressures are high enough. This view provides a sensible explanation of the relatively rapid origins of the different beak morphologies of Darwin's various finches and of species flocks.

Think networks

One question you might have at this point is that the model above suggests that mutations are constantly being thrown into the population's gene pool and are steadily accumulating — it means that there must be a remarkable amount of genetic variation between individuals (and there is! It's been measured), yet we generally don't see most people as weird and obvious mutants. That variation is largely invisible, or represents mere minor variations that we don't regard as at all remarkable. How can that be?

One important reason is that most traits are not the product of single genes, but of combinations of genes working together in complex ways. The unit producing the phenotype is most often a network of genes and gene products, such at this lovely example of the network supporting expression and regulation of the epidermal growth factor (EGF) pathway.

The EGF pathway (from www.sabiosciences.com/pathwaycentral.php)

That is awesomely complex, and yes, if you're a creationist you're probably wrongly thinking there is no way that can evolve. The curious thing is, though, that the more elaborate the network, the more pieces tangled into the pathway, the smaller the effect of any individual component (in general, of course). What we find over and over again is that many mutations to any one component may have a completely indetectable effect on the output. The system is buffered to produce a reliable yield.

This is the way networks often work. Consider the internet, for example: a complex network with many components and many different routes to get a single from Point A to Point B. What happens if you take out a single node, or even a set of nodes? The system routes automatically around any damage, without any intelligent agency required to consciously reroute messages.

But further, consider the nature of most mutations in a biological network. Simple knockouts of a whole component are possible, but often what will happen are smaller effects. These gene products are typically enzymes; what happens is a shift in kinetics that will more subtly modify expression. The challenge is to measure and compute these effects.

Graph analysis is showing how networks can be partitioned and analysed, while work on the kinetics of networks has shown first that it is possible to simplify the mathematics of the differential equation models and, second, that the detailed output of a network is relatively insensitive to changes in most of the reaction parameters. What this latter work means is that most gene mutations will have relatively minor effects on the networks in which their proteins are involved, and some will have none, perhaps because they are part of secondary pathways and so redundant under normal circumstances. Indirect evidence for this comes from the surprising observation that many gene knockouts in mice result in an apparently normal phenotype. Within an evolutionary context, it would thus be expected that, across a population of organisms, most mutations in a network would effectively be silent, in that they would give no selective advantage under normal conditions. It is one of the tasks of systems biologists to understand how and where mutations can lead to sufficient variation in networks properties for selection to have something on which to act.

Combine this with population effects. The population can accumulate many of these sneaky variants that have no significant effect on most individuals, but under conditions of strong selection, combinations of these variants, that together can have detectable effects, can be exposed to selection.

Think flexible genes

Another factor in this process (one that Bard does not touch on) is that the individual genes themselves are not invariant units. Mutations can affect how genes contribute to the network, but in addition, the same allele can have different consequences in different genetic backgrounds — it is affected by the other genes in the network — and also has different consquences in different external environments.

Everything is fluid. Biology isn't about fixed and rigidly invariant processes — it's about squishy, dynamic, and interactive stuff making do.

Now do you see what's wrong with the simplistic caricature of evolution at the top of this article? It's superficial; it ignores the richness of real biology; it limits and constrains the potential of evolution unrealistically. The concept of evolution as a change in allele frequencies over time is one small part of the whole of evolutionary processes. You've got to include network theory and gene and environmental interactions to really understand the phenomena. And the cool thing is that all of these perspectives make evolution an even more powerful force.

Bard J (2010) A systems biology view of evolutionary genetics. Bioessays 32: 559-563.

"Songs From the Science Frontier" - YOU can help kids get excited about science!

2010-07-23T21:00:42Z

(earlier draft @ ERV)

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.

The lyrics on his song about how scientists study bat evolution are hysterical and awesome.

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.

No metazoan is an island

2010-07-22T01:04:28Z

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.

]]> Physiology

Let's begin with the most widely known factor: we're mostly bacterial in cell numbers, with about ten times as many bacterial cells as human cells. Most of these are nestled deep in our guts, where they are indispensible. In mammals, they help break down complex polysaccharides which we can then absorb through the wall of the digestive tract — these are compounds that would be simply lost without bacterial assistance. Even more dramatically, termite guts contain colonies of bacteria that produce enzymes to break down cellulose. Another insect, aphids, live in plant saps which have negligible protein components, and they rely on gut bacteria that can synthesize nine essential amino acids. One cool feature is that the bacteria can't complete the synthesis of leucine; the last step is carried out by aphid enzymes. The synthetic pathway is split acros two different species!

Another weird twist is that gut bacteria can affect morphology (or vice versa; physiology influences which gut bacteria thrive). Mice with a genetic predisposition to obesity were found to have a different distribution of gut bacteria; fat mice are full of Firmicutes, while lean mice are loaded with Bacteroidetes. Something in the genetics of the obese mice seems to favor the proliferation of that one species. Cause and effect is not so easily separated, though, since doing a fecal transplant and inoculating the guts of germ free mice with the bacteria from obese mice vs. lean mice has a surprising effect: the mice given obese mouse fecal enemas subsequently increased their body fat by 60%. The bacteria promoted more fat storage in the host animal.

So what, you may be thinking, it's mice. However, it turns out that obese humans tend to have reduced amounts of Bacteroidetes species in their guts than lean people, and weight loss is accompanied by an increase in Bacteroidetes. Fecal transplants are not recommended as a weight loss technique…at least not yet.

They have worked for some other problems. Crohn's disease and ulcerative colitis are diseases that involve intestinal inflammation, and they're also associated with imbalances in the species distribution of gut bacteria. Some promising treatments have involved collecting feces from healthy individuals, and using a nasogastric tube to inoculate the guts of Crohn's patients with the stuff. Ick, I know, but it seems to have worked surprisingly well in a small number of patients.

Development

Bacteria are present in the gut from a very early age, and populate the digestive epithelia. There must be interactions going on, and it appears that the bacteria are actually regulating the growth of the gut lining.

Germ-free zebrafish lines have no gut bacteria, and they also have problems. The intestinal lining arrests its development and fails to fully differentiate; the lining also grows much more slowly. They also have difficulty absorbing some nutrients. Add bacteria, though, and growth and differentiation resume. This is a case where the developmental program and the bacterial influences are interdependent, and it makes sense — they've co-evolved.

It's not just fish, either — these are conserved interactions across the vertebrates. Mice exhibit the same dependence on gut flora for development of the intestinal lining.

The very best example of a developmental dependence on bacteria, though, is in squid. The bobtail squid has a light-emitting organ that relies on colonization by a luminescent bacterium, Vibrio fischeri. The animal gleans the bacteria from the water with a special ciliated epithelium and secreted mucus that seems to be just the right flavor for Vibrio, and the bacteria migrate deep into the light-emitting organ. Once colonized, the squid dismantles the harvesting cilia and downregulates the secretion of mucus. If no bacteria of the right species are present, it maintains the cilia. If the bacteria in the organ die, resumes mucus production.

Bacterial symbionts induce light-organ morphogenesis in squid. A Adult squid (E scolopes). SEM images of epithelial fields before B and after C regression of ciliated appendage. Scale bar, 50 mm. Ciliated appendages are marked by an orange dashed line.

Evolution

If something affects development and physiology, it affects evolution, so evolutionary importance is simply rather unavoidable. However, there's also one somewhat surprising observation (to me, at least — microbiologists probably expect it): different species of related organisms can have different microbial populations, even when raised in identical conditions. Different Hydra species in the lab under controlled conditions have recognizably different populations of bacteria living on their epithelia, and Hydra of the same species collected in the wild have similar distributions of species. The properties of each Hydra species uniquely favor different distributions of bacteria, and the bacteria are also preferentially colonizing particular species of Hydra.

Hydra are wonderful experimental animals in that one can ablate stem cells for a particular tissue type, and still get an animal that develops and lives; do the same thing to a vertebrate, for instance knocking out the mesodermal lineage in the embryo, and you get an aborted blob. In Hydra, you get a tissue that survives and is colonized by bacteria…but the kinds of bacteria populating it is different from the populations in the intact animal. The animal and the bacteria are swapping molecular signals that specify favored relationships. Again, these are coevolved populations that recognize molecular properties of the host and symbiont.

This is all getting very complicated. I'm used to thinking in terms of networks of genes: there are regulatory interactions between genes in a single cell that establish cell-type specific patterns of gene activity; all express a common core of genes, but different cell types, such as a neuron vs. a cell of the digestive epithelia, will also have their own unique special-purpose genes switched on. I'm also comfortable thinking of networks of cells: cells are in constant negotiations with their neighbors, mainting a common pattern of expression within a tissue, and defining interacting edges with other tissues. Cells are continually sending out messages about their state into the system and responding to local and global signals. All this is part of the normal process of thinking developmentally.

Now, though, there's another layer: we have to think in terms of networks of species that cooperate in the development and physiology of individual multi-cellular organisms. Purity is compromised. My precious animalia — they're inconceivable without bringing bacteria into the picture.

Fraune S, Bosch TCG (2010) Why bacteria matter in animal development and evolution. Bioessays 32:571-580.

Dean Kenyon: a young-earth creation scientist who was later relabeled an intelligent design proponent

2010-07-21T00:13:50Z

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.)

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It’s not quite clear how this revolution happened – I suspect there was more to it than what happened in 1976. For example, in the early 1970s Kenyon published some weird stuff for an OOL researcher, for example several short review articles on acupuncture, on the idea that viruses may originate de novo when environmental pollution stresses the body (see also the 1972 newspaper article I found on the article by Adolphe Smith and Dean Kenyon, quoted below), and on the idea that new life was originating through self-organization in the present day. This stuff is not necessarily crazy (however, I have the articles, and they seem to be quite a ways from vaguely similar modern ideas – e.g. it looks like he is not talking about the idea that genome-encoded viruses could re-activate). However, it is a long ways from the technical chemistry and experimental work on which he did his Ph.D. in the 1960s, and which petered out in the 1970s.

In 1974 Kenyon spent his sabattical at Trinity College in Oxford on science/religion issues:

Then, during the 1970s, I began to rethink my Christian faith. I had been raised as a Christian, but I now began to take a fresh look at my beliefs and they began to have a greater personal significance. In 1974, I went to Oxford University as part of a sabbatical leave and spent the time reading and interviewing people on the relation between science and Christian faith. At that time, most of the people I talked to were theistic evolutionists. I went through a period for a couple of years of being quite intrigued with the works of Teilhard de Chardin. His writings were very popular in Oxford at the time.

Kenyon, Dean, and Pearcey, Nancy (1989). “Up From Materialism: An Interview with Dean Kenyon.” Bible-Science Newsletter, 27(9), 6-9. September 1989.

(note: this paragraph comes just before the previous paragraph I quoted)

Before that, “Kenyon spent the 1969-1970 academic year on a fellowship at the Graduate Theological Union in Berkeley, where he reviewed the contemporary literature on the relationship of science and religion. As an Episcopalian, he was not inclined to see any conflict between God and Darwinism. Yet this was for him a season of intellectual doubt. [goes on to discuss the Wilder-Smith book]” (Witham 2002, p. 163).

And finally, the early 1970s were not exactly a placid time in the U.S., especially on college campuses, and very especially at San Francisco State. There is no specific evidence for this having an effect on Dean Kenyon, but it wouldn’t be surprising if the general chaos of the times had an influence.

Anyway, to summarize some of the evidence for Dean Kenyon being a young-earther:

* Kenyon was scheduled to testify in defense of the “creation science” laws in the McLean and Edwards cases.

* In 1982, Kenyon wrote the forward to Henry Morris’s YEC book What is Creation Science?

* Through the 1980s, there was a variety of “creation science” literature which cited Kenyon as an example of an evolutionist who saw the light and adopted creation science.

* Of Pandas and People was derived from an explicitly “creation science” text, and even the published version explicitly depicted the young-earth view as reasonable, along with the old-earth view. (see also: Matzke 2009, “But Isn’t It Creationism?”, in But Is It Science?, edited by Pennock and Ruse)

* Kenyon is a speaker, writer, and board member for the Kolbe Center, a Catholic fringe group which, unlike most modern Catholics, lobbies for the young-earth view.

* In fairly recent history, Kenyon has attended/presented at some of the International Conferences on Creationism, a well-known YEC series of conferences.

* And apparently just last year, Kenyon endorsed this explicitly YEC book:

Kolbe Center for the Study of Creation 952 Kelly Rd., Mt. Jackson, VA 22842 Tel: 540-856-8453 E-Mail: [Enable javascript to see this email address.]

For me You have created the skies scattered with stars … and all the beautiful things on earth

(St. Maximilian Kolbe) http://www.kolbecenter.org

Dear Friends of the Kolbe Center,

Pax Christi!

As Christmas rapidly approaches, I am happy to announce a new breakthrough for our apostolate. Fr. Victor Warkulwiz, our chief theological advisor, has written a major work on the doctrines of Genesis 1-11, which has just been published with a foreword by Bishop Robert Vasa of the Baker Diocese in Oregon. Bishop Vasa has this to say about Fr. Victor’s work:

The Doctrines of Genesis 1-11: A Compendium and Defense of Traditional Catholic Theology on Origins, by Reverend Victor P. Warkulwiz, M.S.S., is a wonderfully researched and thoroughly stimulating work. Father Warkulwiz, drawing on his very substantial scientific background, walks us through the early chapters of Genesis showing and giving testimony to the essential compatibility between the literal account of Genesis, the understanding of the Fathers of the Church and the modern day observations of natural science.

He very cogently points out that many of the accepted scientific conclusions which contradict the days of creation and the great flood are based on a variety of unproven premises which are pillars set firmly on sand. Father very adeptly tackles the complex issues of cosmogony, astronomy, astrophysics, mathematics, nuclear science, evolutionary theory, geological uniformitarianism, radiocarbon dating, big bang theory, and others to show that the observed phenomena which they try to explain are just as readily, properly and easily explained by such Genesis factors as direct creation by God and the Genesis Flood. In doing so he opens a clear path for dedicated Christians to read the Book of Genesis with a renewed and, to a certain extent, unencumbered faith.

Dr. Dean Kenyon, Ph.D. Biophysics, and formerly one of the leading evolutionary biologists in the world, writes that Fr. Victor “brilliantly demonstrates that the relevant results of modern science, rightly interpreted, are much more consistent with the traditional Catholic view of origins than they are with macro-evolutionary theory.” And Fr. James Anderson, Ph.D., Philosophy, and former Academic Dean of Holy Apostles College and Seminary, writes that Fr. Victor’s “scholarship is first rate and his argument is incisive. This book is a must for scholars, students and laymen.”

This is a book that can change the way that Catholic bishops, pastors, and teachers think about origins. It is a book that can do more to restore the traditional Catholic understanding of origins and human history than perhaps any book written in the past 60 years. Although expensive (roughly 560 pages, $32.95 + shipping), it is a book that ought to become a standard reference for every Catholic home, seminary, college, and high school. Please help to promote this book in your parish and community. Please pray that through the prayers of the Blessed Virgin Mary and St. Maximilian Kolbe, Fr. Victor’s book will cause great numbers of bishops, priests and lay people to return to the traditional Catholic understanding of Genesis, the foundation of the Gospel.

May the Lord Jesus find a blessed home in your hearts this Christmas and always!

Yours in Christ,

Hugh Owen, Director Kolbe Center for the Study of Creation

Anyway, all of this stuff makes a darn good case. But it’s not alone. Back in 2006 I tracked down in the microfiche the original source of a series of short 1980 newspaper articles on a controversy at San Francisco State about Dean Kenyon teaching creationism in his evolution class. The first story (and the longest) appears to be a December 17, 1980 story in the San Francisco Examiner (now a free daily, but back then a standard newspaper).

And the article is – well, by itself it proves the case. Strangely, though, this history was never mentioned in any of the 1990s ID movement literature glorifying Kenyon as a scientists who saw the light and became an ID proponent, leaving out the 10+ years of his being a creation-science proponent before that. The only mention of this anywhere in ID-sympathetic literature is the following oblique mention by Larry Witham, a journalist who wrote a rosy and pretty naive history of ID in 2002 (which nevertheless dropped many interesting tidbits derived from interviews):

As Biochemical Predestination was published, Kenyon spent the 1969-1970 academic year on a fellowship at the Graduate Theological Union in Berkeley, where he reviewed the contemporary literature on the relationship of science and religion. As an Episcopalian, he was not inclined to see any conflict between God and Darwinism. Yet this was for him a season of intellectual doubt. In the mid-1970s, a student gave him a book that challenged the idea of purely chemical origins of life: The Creation of Life: A Cybernetic Approach to Evolution, by European creationist A.E. Wilder-Smith. Kenyon made time during the summer for what he thought would be a handy refutation of the work. “I found out, in fact, I could not answer the arguments,” he says. Thus began a period of “serious personal rearrangement of thought and anguish of the soul” that took him up to the 1980 fall term. He was a tenured professor [he got tenure in 1970 – Witham 2002, p. 163], and he had to make a decision.

“Just go public with my doubts? Take my chances?” He asked himself that question, then proceeded to do just that, perhaps naive about the consequences that would follow when a few students complained about his comments in class. The story would make the San Francisco Examiner. “Well,” Kenyon says, “I had no idea of the fallout.” He was summoned to three faculty hearings to testify on what he taught in his courses. Department chairman William Wu responded by laying down the “5 percent doctrine”: no more than 5 percent of a course could include criticism of or doubts about Darwinian theory, and that was how Kenyon proceeded through the 1980s.

(Witham 2002, Where Darwin Meets the Bible, pp. 163-164).

Hmm, so the controversy in 1980 was about “criticism of or doubts about Darwinian theory”, and throughout this passage and the book, Witham takes pains to make it seem like ID is disconnected from creationism.

But check out the actual article in the SF Examiner. The photo is particularly good. PDF download. Text below for posterity. Posting this is fair-use under copyright law, as I recently learned at a talk on copyright that not only is this academic, nonprofit use, but posting a single article is reproducing only a portion of the work (the “work” in copyright law being e.g. an entire journal, volume, etc.)

[Reference]

Salner, Rebecca (1980). “Professor teaches a supernatural creation of world.” San Francisco Examiner, p. zA-9. Wednesday, December 17, 1980.

[Article text]

[transcribed by Nick Matzke, 10/29/06]

‘The. better scientific model is the creationist one. Evolutionary view has too many inconsistencies’

Professor teaches a supernatural creation of world

By Rebecca Salner

Dean Kenyon is a soft-spoken, serious and sincere man who teaches evolution at San Francisco State University.

But he doesn’t believe in evolution. He believes in God and scientific creationism – an alternative theory which parallels the biblical story of creation.

Kenyon has taught the biology department’s only evolution class for 12 years. For eight of those 12, he was a believer in macro evolutionary theory as were the vast majority of his colleagues.

They haven’t changed. He has. Four years ago, after “technical evidence” convinced him that evolutionary theory was incorrect, he began including scientific creationism in his course and drawing criticism from those whose beliefs he once shared.

Kenyon defines the main tenet of scientific creationism this way:

“In the relatively recent past – 10,000 to 20,000 years ago – the entire cosmos was brought into existence out of nothing at all by supernatural creation.”

According to Kenyon, gaps in the fossil record and the lack of evidence documenting transmutation of species strongly support creationist views.

The fossil record is posing the greatest problem for today’s evolutionists, says Kenyon:

“Rather than exhibiting trends, the fossil record gives a picture of stasis and then gaps.” (Stasis is the existence of species over long periods of time without change.)

Creationists theorize that fossils and rock strata formed during a worldwide flood, not over billions of years as evolutionists believe.

“Holes are characteristic of evolutionary theory,” he says. “The better scientific model is the creationist one. Evolutionary view has too many inconsistencies.”

One of Kenyon’s most outspoken critics on campus is Professor Lawrence Swan, who calls creationism “embarrassing.”

“How can an institution of higher learning permit the teaching of an aberrant misinterpretation and what I would consider an intolerable representation of the truth?” asks Swan. “What we’re faced with is a very interesting intellectual morass. What do you do with a professor who has gone wrong?”

For Swan, academic freedom is no defense for teaching creationism.

“If this is academic freedom, almost any bucket will go in. I can talk absolute nonsense to my class.”

“Do geologists allow a flat-earth advocate to teach? Would astronomers like astrologists? But this (creationism) differs because the evidence for it is not scientific, it is religious. Does a professor have the right to teach anything he wants? Can society afford to deny science?”

Creationists’ attacks on the holes in evolutionary theory enrage Swan who claims they employ a “You don’t know, therefore God” argument.

Douglas Post, professor of ecological and systematic biology, agrees, saying, “I don’t think there is any positive evidence to prove creationism. They rely on negative evidence. Their main argument is that you can’t prove that Darwin is correct. But I don’t think that just because you can’t prove Darwin you can automatically conclude that creationism is correct.”

Kenyon denies the religious base of his group’s evidence and says creationism is not a “God of the gaps” theory.

[photo] [Photo of Dean Kenyon holding up the book Scientific Creationism by Henry Morris (looks like the General Edition).]

[/photo]

[caption] Biology professor Dean Kenyon’s controversial course seems to be well-supported among the students [/caption]

“Our evidence is of the same status as that used by evolutionists. We talk about fossils, rocks, animal species…”

“One of the creationist’s points is to say this is not religious,” says Swan. “That’s malarky. The major premise is the first chapter of Genesis. It’s an argument, an old argument, between trying to understand what’s natural versus the miraculous.”

None of the professors in the department have expressed much support for creationism, although a few have said the issue is “interesting.”

Department Chairman William Wu also believes the theory is religiously based.

“Having listened to Dr. Kenyon on one side of the coin and some of our evolutionists on the other, I have to tend to agree with it being biblical. It fits.

“Any person who has gone to Sunday school will immediately grasp the similarity. But in fairness to scientific creationism and to Dr. Kenyon, Dr. Kenyon believes that the Bible should not be brought into it.”

Kenyon admits a connection between religion and creationism but holds fast to the belief that religion does not enter the classroom.

“If you’re not familiar with the technical literature you may think that Genesis is being taught. It is quite a radical departure from what most of our faculty learned in graduate school. It takes a lot of effort to change that. Any line of thought which tries to figure out ultimate origins will come into areas of religious thought,” says Kenyon.

Although he may not bring religion into the classroom, Kenyon personally is religious and believes there are “no errors in the Bible.”

In 1969, he took a leave of absence from the university to attend the University of California at Berkeley’s graduate theological union. Five years later he attended Trinity College at Oxford to work on a project titled “The Reception of Darwinism by the Church of England.” On his desk is a plaque proclaiming, “In Christ are hid all the treasures and knowledge.”

Kenyon, 40, is a quiet, scholarly man customarily clad in a professorial tweed blazer and conservative gray slacks. His students like him and even circulated a petition supporting his inclusion of creationism in the course.

He seems genuinely surprised at the violent reaction of some faculty and one or two students. And though he appears to be the only creationist under fire, he claims there are others on campus – three at least, but he won’t say who.

Even Swan, his critic, says Kenyon is “a very sweet, gentle, quiet, somewhat convincing man.”

Only two professors contacted were remotely supportive of Kenyon’s theory.

Sarane Bowen, a specialist in cell and molecular biology, said the issue makes the department’s course offerings more interesting.

Charles Hagar, physics and astronomy, said, “I think it’s very nice to shake up the basket and see what goes on. I’m always in favor of controversy. I think that’s how science progresses. All too often, evolution has been presented as fact and it’s kind of interesting to see that challenged by alternative theories. If they’re wrong, let the scientists knock them down.”

Kenyon has been asked to hold discussions of creationism to 5 percent of class time – a guideline developed by Chairman Wu, who said Kenyon is not policed, although a faculty member is auditing the class.

Wu believes the issue of Kenyon teaching creationism is resolved.

Swan and Kenyon want further discussion of the matter, and believe it is unresolved.

Swan would prefer that Kenyon not teach creationism, or, if he must, at another university.

Kenyon wants more time given to creationism.

“If I were to dream about it, I would say a 50-50 split” between evolution and creationism, says Kenyon.

PS: Here is the 1972 article I found (also back in 2006 I think) on Smith & Kenyon’s idea about de novo origin of viruses:

Winnipeg Free Press, Wednesday, March 22, 1972. p. 43

Prof Flips Theory Coin About Virus Production

MONTREAL (CP) - Man may be a walking virus-maker, says Adolphe Smith, a 43-year-old biophysicist and professor at Montreal’s Sir George Williams University.

In an article to be published in an international journal of microbiology, he and Dean Kenyon of San Francisco State University flip the coin of the current theory that viral infections are caused solely by germs invading the body when resistance is low.

At least some of these infections are caused by viruses produced within, the body after it has undergone damage or stress from the environment, they contend.

Viruses are infectious agents that reproduce in living cells.

“Since Pasteur, man has gone overboard in thinking germs come from outside,” said Dr. Smith in a recent interview.

However, he and his colleague do not discount external factors in the cause of viral infections such as influenza and apply their theory only to “latent” or non-contagious viruses.

He used the example of a cold sore.

“You have a recurrent infection at the same place but in between occurrences it is impossible to detect the presence of a virus – so the virus must come from within.”

According to Dr. Smith’s theory, environmental stress causes some cells to change into viruses and under certain conditions these viruses appear.

“This stress could come from poor living conditions or polluted air which damage the lungs,” he said.

That points to a need for a cleaner world.

“If stress from the environment does produce viruses in the body, then we must reduce this stress by cleaning up the environment,” said Dr. Smith.

“What I am saying, in effect, is that the environment is not just a factor, but the factor.”

Anti-pollution groups are making a great stride in preventive medicine because they are trying to improve the environment which plays such a great role in determining man’s health, he said.

Note: I had to hand-transcribe these articles to text; I caught a few mistakes today, but some typos may remain.

Divergence

2010-07-20T19:16:04Z

This is a sweet little story of evolutionary divergence, and a reunion. Of sorts.

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Fraunhofer lines on CD

2010-07-19T17:00:00Z

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.

CellCraft, a subversive little game

2010-07-15T16:39:51Z

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.

]]> Where do you get these organelles? A species of intelligent platypus just poofs them into existence for you when you need them. What is the goal? The cells have a lot of room in their genomes, so the platypuses are going to put platypus DNA in there, so they can launch them off to planet E4R1H to colonize it with more platypuses. Uh-oh. These are Intelligent Design creationist superstitions: that organelles didn't evolve, but were created for a purpose; that ancient cells were 'front-loaded' with the information to produced more complex species; and that there must be a purpose to all that excess DNA other than that it is junk.

Suspicions confirmed. Look in the credits.

Also thanks to Dr. Jed Macosko at Wake Forest University and Dr. David Dewitt at Liberty University for providing lots of support and biological guidance.

Those two are notorious creationists and advocates for intelligent design creationism. Yep. It's a creationist game. It was intelligently designed, and it's not bad as a game, but as a tool for teaching anyone about biology, it sucks. It is not an educational game, it is a miseducational game. I hope no one is planning on using it in their classroom. (Dang. Too late. I see in their forums that some teachers are enthusiastic about it — they shouldn't be).

Freshwater: Unresponsive responses

2010-07-15T03:40:13Z

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

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The billing records

Both Hamilton and Freshwater claim that Hamilton was operating in two distinct roles in April-May 2008, an “investigative” role for the investigation conducted on the Board’s behalf and a “legal” role for other work. In his response Freshwater wrote

That bill Kelly [Hamilton] gave Sarah Moore [BOE attorney] for May 2008 is accurate because Kelly billed me and I paid for the investigative interview preparation separately. Let me say it this way. I have two bills for May 2008. Actually I may have received three bills because I may have gotten one from Roger Weaver [an attorney who was briefly employed by Freshwater in April-May 2008] too. The two bills I got from Kelly were for two different processes. One bill was for the investigative interview and the other bill was for the legal works other than the interview preparation. I have never hidden the fact that I had separate legal billings. I testified on December 8, 2009 in the state hearing that I had separate legal bills. I read the transcript on page 4212 and am including a copy of it with this statement. Page 4212 of the transcript is accurate and it shows I spoke about the separate legal billings long before this recent mess started. So if anybody accuses me of being untruthful I say how would I know back then that this matter would come up now. Look the difference between the fee agreement of May 19, 2008 and the fee agreement of June 26, 2008 are (sic) as big as the difference between $175.00 per hour and $275.00 per hour. The difference between the two agreements are (sic) as different as night and day, as different as right versus wrong and as different as the truth versus these allegations. (pp 1-2)

So Freshwater is claiming that he employed Hamilton in two separate roles in May 2008, investigative interview preparation (the affidavit preparation), and some other unspecified “legal works” during the same period, the two being invoiced separately and at different rates.

Hamilton echoes Freshwater:

Any billing records obtained by Plaintiff’s counsel indicating any billing activity to John Freshwater during May 2008 are based on a separate fee agreement reflecting work completed for John Freshwater but not relating to the preparation of the fifteen (15) affidavits. (Exhibit 1 - Affidavit of John Freshwater at 3 and 4) Again, truth sometimes is a poor competitor as truth can be complicated and always vulnerable to misinterpretation–but truth is truth. The truth is John Freshwater and his family have had four (4) different fee agreements for legal counsel (Exhibit 1 - Affidavit of John Freshwater at 3) The billing record possessed by Plaintiff’s counsel is reflective of a fee agreement signed by John Freshwater on June 26, 2008–the third fee agreement–that permitted the undersigned [Hamilton] to re-bill or receive payment for legal work done since the inception of John Freshwater’s legal need which began on April 17, 2008 (Exhibit 1 - Affidavit of John Freshwater at 3).

So the implicit claim is that Hamilton’s billing records for work associated with the independent investigation is irrelevant to the federal case, and that only the billing for other unspecified “legal works” qualifies as responsive to the present issue. Bear in mind that at that time, April-May 2008, Freshwater was involved in no other legal issues associated with his troubles vis a vis the Board of Education–Doe v. Mount Vernon Board of Education, et al. was not filed until June 13, 2008 and the resolution to terminate him was not passed until June 20, 2008.

Hamilton claims in his response that

John Freshwater and the undersigned assert the legal invoices and billings for the fifteen (15) affidavits are and were completely different from the legal invoices and billings for the legal work related to John Freshwater’s state hearing and subsequent legal cases.

That’s very strange, since at that time–May 2008–Freshwater could not know there would be a state hearing. There was no foreshadowing of a potential need for a hearing prior to the issuance of the investigators’ report (pdf) dated June 19, 2008. He had to have made that decision after the report was released and the Board of Education passed its resolution of intent to consider termination on June 20, 2008. So what is Hamilton talking about when he claims to have been working in May on legal matters related to the state hearing? It simply doesn’t add up. All the other matters–anything other than the investigation–that would have required Freshwater to have legal advice were initiated well after Hamilton claims he was working on those matters.

Look at the Freshwater quotation more closely. The first claim is that “I have two bills for May 2008.” I found that interesting because I have a distinct memory of a statement by Freshwater that he no longer has those invoices. I don’t recall whether it was in a deposition or in testimony in the hearing, but I have a faint memory that I posted on it somewhere. Anyone else’s Google-fu better than mine?

I also found this claim interesting:

I [Freshwater] read the transcript on page 4212 and am including a copy of it with this statement. Page 4212 of the transcript is accurate and it shows I spoke about the separate legal billings long before this recent mess started.

In the transcript (attached to Freshwater’s response) that comes out of the blue–Hamilton is questioning Freshwater about the preparation of the 15 affidavits–how Hamilton asked questions and Freshwater answered them, and how Freshwater could make corrections or amendments in the drafts Hamilton prepared, and how Hamilton had Freshwater swear to the truth of them. Then in the midst of that, there’s this sequence:

Q. Did I – you’ve come to have an understanding now of the importance of of an affidavit?
A. Yes.
Q. What’s your understanding?
A. Wow. That, one, I know that you’re very good at that. You’re very thorough at that. It’s important so you get the words down on paper in that time period.
Q. Now, you have an awareness of my background. Correct?
A. Yes.
Q. And what was part of my background?
A. Your background–we’ve gotten to know each other very well–Columbus police officer. And you are very good.
Q. When we first hired on together, did I tell you there was a legal component and a legal investigative component?
A. Yes.
Q, And we actually had an arrangement that I would say treated you pretty nicely financially that we separated the legal expertise versus the investigative legal expertise, right?
A. Yes.
Q. And we took care of those on separate billing statements. Right?
A. Yes.

Hamilton also quoted a few lines of that testimony in his response. That’s just plunked into the sequence of questions and led nowhere. It seemed to me at the time, and seems to me now, that it was a device to get the claim of Hamilton’s two roles on the record. Another sequence of testimony late in the hearing, in June 2010, struck me the same way when Hamilton asked Freshwater whether he (Hamilton) carried a printer with him:

Hamilton asked if Freshwater had ever seen Hamilton carrying a portable printer, and Freshwater said he had. Asked, he agreed that meant that Hamilton was not restricted to using the church’s printer. (I suspect-but do not know-that these questions are related to the question of the date of preparation of the 15 affidavits Freshwater claims to have put together after his first interview with the investigators, to be used at the second interview.

…

It may not be a coincidence that this particular testimony, with no connection to anything in prior testimony in the hearing, was elicited the day before a computer forensics analyst was scheduled to testify for the Board. To forestall speculation in the comments, that analyst did not testify about the printer provenance of those affidavits.)

One speculative hypothesis that could account for those two bits of strange questioning is that knowing the Board of Education’s counsel had a set of Hamilton’s billing records for April-May 2008 obtained in March 2009, and knowing by then that there were questions about the provenance of the 15 affidavits that the billing records were relevant to, in both the December 2009 and June 2010 questioning Hamilton may have laying the groundwork for a defense for not providing all his billing records along the lines of the “two roles” laid out in Freshwater’s and his documents filed yesterday. I repeat: that’s speculation. But it’s how it struck me on both occasions as I listened to the testimony: ‘this has something to do with the affidavits.’

In any case, none of this speaks to the central question for Hamilton, which is if his computer had been “totally destroyed” in the Flood as he has claimed, how could he have supplied any billing records at all to the Board’s attorney in March 2009? One set of invoices or two, one role or two, those records were wiped in January 2009 according to Hamilton. He does not address that question at all in his response. That’s what I mean by a “masterpiece of misdirection.” Hamilton and Freshwater generated a slew of words about his two roles and about the fragility of “truth” (that word appears 20 times in Hamilton’s response), but the central question is not addressed nor even hinted at in either response.

Discovery issues

Hamilton’s and Freshwater’s response to the assertion that they have not fully complied with the discovery process amounts to two words: “Did too!”

An impending settlement?

Finally, Hamilton uses this paragraph four times in his response:

On Tuesday, July 6, 2010, the undersigned learned from communications with Attorney Sandra McIntosh that a resolution in this matter occurred on Friday, July 2, 2010, which will include resolving any concerns against John Freshwater alleged in Plaintiff’s Memorandum of Opposition (Doc. 114)

McIntosh is one of the two attorneys retained by the school’s insurance company to defend Freshwater in Doe b. Mount Vernon Board of Education, et al. I have been unable to find out if that means there’s a tentative settlement with Freshwater. (Recall that Hamilton is no longer Freshwater’s attorney of record in that action.) It’s unclear what the antecedent of “this matter” is, so we don’t (yet) know whether it refers to the Doe suit or just to something about the sanctions imposed on Hamilton and Freshwater.

It’s perhaps relevant that the federal judge has scheduled an oral hearing on Hamilton’s motion to reconsider the sanctions for July 29, 2010. But the federal trial is scheduled to begin July 26. I don’t know the protocol in these things, but the two additional sanctions requested by the Dennises, a default judgment in their favor, or failing that, an adverse evidentiary inference against Freshwater, are both associated with how (or even whether) Freshwater’s lawyers can defend his case. As I suggested in my ‘Quick settlement’ post, that may have put enough pressure on to settle. (I see now that post would have been better titled “Sudden” settlement, not quick!)

Miscellany

There are some things in both Hamilton’s and Freshwater’s responses that I simply can’t parse. For example, consider this sentence from Hamilton’s response:

On May 15, 2008, the date John Freshwater was interviewed by HR on Call, Inc., John Freshwater made personal perceptions subsequent to personal interaction he had with a previous attorney who originally served as co-counsel.

WTF does that mean?

On a note related to fees, Hamilton wrote

John Freshwater and the undersigned made every reasonable effort to scrabble together that which was possible to comply with the Court’s Order. John Freshwater and the undersigned continue to dispute the reasonableness of the fees asserted by Plaintiff’s counsel. As the undersigned holds unfiled liens and a deed to the Freshwater Family farm both Freshwater and the undersigned complied as best they could with the resources they have available.

Italics added. Freshwater’s effort at compliance was to send a lien on his farm to Doug Mansfield, the Dennises’ attorney, to satisfy the Court’s Order to pay the lawyer fees associated with the extra work required to compel compliance with the various discovery orders. As noted in the memorandum of opposition, however, that lien was not filed with the Clerk of Courts in Knox County and is thus invalid (as, apparently, are Hamilton’s liens). In any case, Freshwater has apparently truly bet his farm on this. And it’s also interesting that Hamilton associates himself with the offer, even though he’s not mentioned in Freshwater’s affidavit of lien. Hamilton has no skin in that game: the “undersigned” offered precisely nothing in fulfillment of the Court’s Order for sanctions except to prepare and forward Freshwater’s Affidavit for Lien. I wouldn’t be surprised to learn that he charged Freshwater for doing so.

Finally, the word “truth” is used liberally in Hamilton’s response. “Truth” and “truthful” together appear 22 times in Hamilton’s response-there’s even a two paragraph section with “Truth” as a title. And the last paragraph of Hamilton’s response emphatically preaches about it:

Truth is everything, truth shall set one free and both John Freshwater and the undersigned will follow truth wherever it may lead. Truth can be complicated and vulnerable to misinterpretation. John Freshwater and the undersigned have been castigated unfairly and unjustly despite simply telling the truth and it is requested by both, that the truth be investigated and determined with as much zeal as has been invested in speculation. Accordingly, reconsideration of this Court’s Opinion and Order are requested.

Somehow I don’t think quoting John 8:32 (“truth shall set one free”) in support of an argument will favorably affect Judge Frost’s judgment on an issue in an Establishment Clause case. Thomas Jefferson (“follow truth wherever it may lead”) might carry a little weight though the full quote doesn’t seem to be consonant with Freshwater’s and Hamilton’s worldview:

This institution [University of Virginia] will be based on the illimitable freedom of the human mind. For here we are not afraid to follow truth wherever it may lead, nor to tolerate any error so long as reason is left free to combat it.

Recall that Jefferson forbade the inclusion of a theology department or divinity school in UVA.