Since the “Hobbit” fossil LB1 was discovered on the Indonesian island of Flores in 2004, debate has raged as to whether it is a new species of hominid (Homo floresiensis), or a pathological modern human specimen. And, if it is a new species, where it should fit in the human family tree - a near-human relative, a dwarf Homo erectus, or something else?

The November issue of the Journal of Human Evolution was devoted to Homo floresiensis, with a number of papers on various aspects of its anatomy and environment.

Argue et al. have performed the first cladistic study of LB1. Cladistics uses comparisons of characteristics of specimens to try and determine their evolutionary relationships. Their results showed that LB1 most likely split from the rest of the genus Homo either after H. rudolfensis but before H. habilis, or after H. habilis. It therefore apparently evolved from an early Homo species, sometime between about 1.5 and 1.9 million years ago. They also tested whether LB1 could have shared a unique common ancestor with either Homo erectus or Homo sapiens, but both of these hypotheses were strongly rejected. Their full conclusion was:

Argue et al. 2009 Wrote:

Based on rigorous cladistic analyses, we propose that H. floresiensis evolved in the Late Pliocene or Early Pleistocene. The first of our two equally parsimonious trees suggests that H. floresiensis branched after H. rudolfensis (represented by KNM-ER 1470) but prior to the divergence of H. habilis (represented by KNM-ER 1813 and OH 24). Alternatively, our results are equally supportive of H. floresiensis branching after the emergence of H. habilis. Our results sustain H. floresiensis as a new species (Brown et al., 2004; Morwood et al., 2005) and favor the hypothesis that H. floresiensis descended from an early species of Homo (Falk et al., 2005; Argue et al., 2006; Larson et al., 2007; Tocheri et al., 2007). We find no evidence of close phylogenetic relations to H. sapiens, and reject the idea that the Liang Bua remains represent a pathological modern human. Importantly, we also are unable to link H. floresiensis phylogenetically to H. erectus, rejecting the hypothesis that the small enigmatic bones resulted from insular dwarfing of H. erectus. It is surely time we accepted the reality of H. floresiensis as a species and seek answers to the questions that this species poses, not least of which is: who were its ancestors?”

Other papers reach similar conclusions:

First, you start with a lizard.

Really, I’m not joking. Snakes didn’t just appear out of nowhere, nor was there simply some massive cosmic zot of a mutation in some primordial legged ancestor that turned their progeny into slithery limbless serpents. One of the tougher lessons to get across to people is that evolution is not about abrupt transmutations of one form into another, but the gradual accumulation of many changes at the genetic level which are typically buffered and have minimal effects on the phenotype, only rarely expanding into a lineage with a marked difference in morphology.

What this means in a practical sense is that if you take a distinct form of a modern clade, such as the snakes, and you look at a distinctly different form in a related clade, such as the lizards, what you may find is that the differences are resting atop a common suite of genetic changes; that snakes, for instance, are extremes in a range of genetic possibilities that are defined by novel attributes shared by all squamates (squamates being the lizards and snakes together). Lizards are not snakes, but they will have inherited some of the shared genetic differences that enabled snakes to arise from the squamate last common ancestor.

The Sacramento Bee has good pictures of the Lianga Bua, Indonesia, site where Homo floriesiensis remains have been found. As you will notice, they’re not just scraping the floor of a nice shallow cave with trowels.

Hat tip to James Kidder.

Photograph by Matt Opel.

Photography contest, Honorable Mention.

Conophytum bachelorum – a desert plant from South Africa, in cultivation. The plant body is a pair of fused, succulent leaves.

How did all those “kinds” of animals survive aboard the Ark during Noah’s Flood? Ken Ham has a novel answer. See below the fold.

Rob Pennock has a new article out in Science and Education. It analyzes how Phillip Johnson brought postmodernist elements to the ID movement, tracing these elements back to Johnson’s midlife crisis, his gradual turn to evangelicalism, and his move into “Critical Legal Studies” in legal studies, wherein he made up the entire “right wing” of that field. Pennock compares Johnson’s 1984 article on critical legal studies to his later arguments against evolution and for a conservative evangelical Christianity (Johnson didn’t actually argue very much for ID!).

The Smithsonian Institution has launched a new web site focused on human origins. It includes a good deal of material on the evidence (behavior, fossils, genetics, and dating) and Smithsonian’s research projects, along with what looks like a very useful set of education resources including lesson plans for teachers, a teachers forum, and student resources including an interactive mystery skull interactive exercise (I had trouble with that in Chrome but not in Firefox; apparently there’s a Flash glitch in the interaction of the site with Chrome).

And just to stir the pot a little, the page on the Broader Social Impacts Committee will provide some fuel to the accommodationist/hardliner feud. In particular, notice who is not represented on it.

At any rate, I strongly commend the site to your attention.

Hat tip to ASA Voices.

An open access paper just out looks at science blogging. According to the abstract, the paper

… focuses on one of the ICTs [Information and Communication Technologies] that have already been adopted in science communication, on science blogging. The findings from the analysis of eleven blogs are presented in an attempt to understand current practices of science blogging and to provide insight into the role of blogging in the promotion of more interactive forms of science communication.

Bora has a critical look at it, as does Cosmic Variance. Panda’s Thumb is one of the 11 blogs examined in the paper.

One of the main conclusions of the (pretty chancy) analysis is that

To become a tool for non-scientist participation, science blogs need to stabilize as a genre or as a set of subgenres where smaller conversations may facilitate more meaningful participation from members of the public. Science bloggers need to become more aware of their audience, welcome non-scientists, and focus on explanatory, interpretative, and critical modes of communication rather than on reporting and opinionating.

The author goes on to suggest that

An interesting practical experiment would also be to reverse the roles of writers and readers and invite the so called “ordinary persons” to create and publish science blogs, i.e., to engage them in the practices of science blog writing rather than reading or commenting.

Hm? Why would that be interesting? And, for that matter, “ordinary persons” have the same access to blogging software as do scientists; nothing (except disinclination or disinterest) is stopping “ordinary persons” from blogging about anything they wish.

The author clearly has a particular model in mind as a referent, implicit in the title of the paper: “Science blogs and public engagement with science: practices, challenges, and opportunities.” That’s tantamount to “blogs as an extension of science education.” But while many of us are interested in science education, that’s an institutional goal while blogs are, by and large, personal vehicles. It seems to me that institutionalization is not a state to be desired. (After writing this paragraph, I found that Scholarly Kitchen made much the same point.)

(I invite my PT colleagues to comment. This post is based on a fast read-through with contractors waiting to abduct me to force a decision on the color of house siding.)

Photograph by James Rice.

Photography contest, Honorable Mention.

8-meter Rimstone Formation, from the first science and mapping expedition to Haunted Forest Cave in Belize.

Some big stories came out this week.

Science Daily reported on March 3^rd that

A fossil that was celebrated last year as a possible “missing link” between humans and early primates is actually a forebearer of modern-day lemurs and lorises, according to two papers by scientists at The University of Texas at Austin, Duke University and the University of Chicago. In an article now available online in the Journal of Human Evolution, four scientists present evidence that the 47-million-year-old Darwinius masillae is not a haplorhine primate like humans, apes and monkeys, as the 2009 research claimed. They also note that the article on Darwinius published last year in the journal PLoS ONE ignores two decades of published research showing that similar fossils are actually strepsirrhines, the primate group that includes lemurs and lorises. ‘Many lines of evidence indicate that Darwinius has nothing at all to do with human evolution,’ says Chris Kirk, associate professor of anthropology at The University of Texas at Austin. ‘Every year, scientists describe new fossils that contribute to our understanding of primate evolution. What’s amazing about Darwinius is, despite the fact that it’s nearly complete, it tells us very little that we didn’t already know from fossils of closely related species.’ ..

And, the BBC reports on March 4^th that

An international panel of experts has strongly endorsed evidence that a space impact was behind the mass extinction event that killed off the dinosaurs. They reached the consensus after conducting the most wide-ranging analysis yet of the evidence. Writing in Science journal, they rule out alternative theories such as large-scale volcanism. The analysis has been discussed at the 41^st Lunar and Planetary Science Conference (LPSC) in the US. A panel of 41 international experts reviewed 20 years’ worth of research to determine the cause of the Cretaceous-Tertiary (K-T) mass extinction, around 65 million years ago. The extinction wiped out more than half of all species on the planet, including the dinosaurs, bird-like pterosaurs and large marine reptiles, clearing the way for mammals to become the dominant species on Earth. Their review of the evidence shows that the extinction was caused by a massive asteroid or comet smashing into Earth at Chicxulub on Mexico’s Yucatan Peninsula…

While creationists are sure to glom onto these stories as evidence that any change of opinions over time means entire disciplines are simply nonsense, both of these stories show science incorporating new information, and improving with age.

Contrast that with creationism or “intelligent design,” for which nothing becomes clearer or better understood over time. Hmm - what is the actual mechanism by which the Designer infuses new designs into actual, living organisms? Search me!

Discuss.

The Austin American-Statesman reports that Thomas Ratliff has narrowly defeated Don McLeroy in the Republican primary race for Texas State Board of Education. McLeroy is the right-wing extremist who wants to doctor the state science standards so they reflect his own disbelief in the theory of evolution. Since there is no Democratic candidate, Ratliff will automatically assume McLeroy’s seat.

The Dallas Morning News reports that Ratliff had received the support of “mainstream public education groups” and quotes him as saying, “I want to take politics out of our public schools,” and added that Ratliff

told gatherings across the district that Texans are tired of political posturing on the board as the social conservative [sic] bloc – led by McLeroy – tries to impose its views in history, science and other areas of the curriculum.

“Our kids don’t go to red schools. They don’t go to blue schools. They go to local schools,” he said, also criticizing attempts by some board members to inject their religious beliefs into what children are taught.

The News reports further that McLeroy was “unapologetic about the actions of the social conservatives” and bragged about the “incredible accomplishments that will help our children.”

Thanks to a commenter known to me only as Aagcobb for the tip.

Photograph by Peter Psyhos Burns.

Photography contest, Honorable Mention.

Agelaius phoeniceus – red-winged blackbird, Falmouth, Massachusetts.

Update: Full text of Thompson’s letter below the fold.

In an update to my recent post on Board members recusing themselves from participating in the Board’s decision-making on the Freshwater matter I said that Steve Thompson, Freshwater supporter and former (apparently) fund-raiser, had decided to recuse himself in the same manner as Paula Barone. That now appears to be false. In a Feb 25 story in the Mt. Vernon News we learned that

Board member Steve Thompson also recused himself from discussing and voting on existing litigation.

He did not recuse himself from the administrative proceedings relating to Freshwater’s contract termination.

In other words, he’s planning to participate in the Board’s action on the outcome of the administrative hearing. That puts him squarely back in the conflict of interest soup and puts the Board at considerable litigation risk.

Hat tip to phred on mvohio.net.

We often argue that saying that “God did it” is a science stopper. That claim is typically countered by pointing to numerous examples of scientists who were (Newton) or are (Kenneth Miller) Christians (though as we know, Newton was a peculiar sort of Christian, even for his time).

The Disco ‘Tute, of course, doesn’t think that positing an Intelligent Designer is a science-stopper. Their ‘solution,’ embodied in the Wedge strategy, is to redefine science to include God an unnamed intelligent designer with inscrutable goals and skills as an “explanation.”

One variety of Christian “science,” however, is clearly willing to stop science in its tracks, and Todd C. Wood, faculty member at Bryan College, has provided a stark illustration of that. While Wood has shocked his creationist peers on occasion, for example for saying that

Evolution is not a theory in crisis. It is not teetering on the verge of collapse. It has not failed as a scientific explanation. There is evidence for evolution, gobs and gobs of it. It is not just speculation or a faith choice or an assumption or a religion. It is a productive framework for lots of biological research, and it has amazing explanatory power. There is no conspiracy to hide the truth about the failure of evolution. There has really been no failure of evolution as a scientific theory. It works, and it works well. (All bolding original)

However, Wood has clear boundaries. Writing on his blog more recently Wood says

That’s why I don’t care about the origin of life (and why I’ll probably never finish reading Meyer’s book). I already know where life came from. I open the book of Genesis, and the Bible tells me exactly where life came from. Speculating on how it might have happened in a naturalistic scenario seems like a waste of time to me. Just like it would seem like a waste of time to an atheist to study the logistics of Noah’s Ark.

Can’t get any clearer than that.

Update: Thompson has done the right thing and elected to recuse himself in the same manner as Barone.

Paula Barone, a newly elected member of the Mt. Vernon Board of Education, has decided to recuse herself from participating in executive sessions and voting on the Freshwater matter when it comes before the Board again. Her decision is based on advice from the Ohio School Boards Association, the Ohio Ethics Commission, and David Millstone, the Board’s attorney in the matter. While all three advised her that there was no legal conflict of interest associated with her participation in decisions on Freshwater, nevertheless her participation could give Freshwater’s legal team a pretext for further litigation. She therefore is recusing herself–at this time, anyway–from participation in the decision-making process.

Comparing Barone’s situation with that of Steve Thompson, the other newly elected member of the Board, it’s apparent that Thompson is in a substantially worse conflict of interest situation than Barone, and is doubly obliged to recuse himself.

More below the fold.

A new story is making the rounds now, to the effect that R. Kelly Hamilton, Freshwater’s attorney, has been in contact with the anonymous source of the black bag in the parking lot. That source, it is said, is willing to testify in the hearing but not in public because of fears for his/her safety. So Hamilton has asked the referee to hear testimony from that person with the hearing closed to spectators and press and the referee is considering whether to do so.

As I noted earlier, this has gone past strange and is well into bizarro territory. Does the anonymous source fear that the Evil Atheist Conspiracy is going to take revenge on him/her? Are there mobs of evolutionists with torches and pitchforks waiting outside the walls of the hearing room? Not hardly, not in this county. The one slight justification I can see is if the anonymous source is a school employee and fears being fired for removing the black bag and its contents from the school without authorization (assuming it actually came from the school and not Freshwater’s garage, which is not established). But as far as I know the hearing referee has no power to grant immunity from prosecution for theft, so taking the testimony in private won’t solve that problem for him/her.

Bear in mind that this is the same R. Kelly Hamilton who brought pressure to make the names of the Dennis family public after a federal court had granted them anonymity to protect them, particularly Zachary, from reprisals. And note that the Dennis family finally felt it necessary to move away from this community because their children were being subjected to harassment from other students and school staff – teachers and at least one coach. So why is Hamilton so hot to protect an adult’s anonymity now?

After the B.S. story Don Matolyak offered to justify taking an armed escort with him to retrieve the black bag while deciding he didn’t need the cops, I am of the opinion that this is just more of the smokescreen and is intended to amp up the drama casting John Freshwater as the poor persecuted Christian man in heathen Knox County, Ohio. It’s designed solely to bring more pressure on the Board of Education to settle on Freshwater’s terms. But Hamilton, Matolyak, and Freshwater appear to be becoming so enamored of their delusional fantasies of persecution that I fear for their ever more tenuous grasp on reality.

Photograph by Susan Bello.

Photography contest, Honorable Mention.

Sarracenia purpurea – pitcher plant blossom, Kejimkujik National Park, Nova Scotia.

A common bleat from creationists is “Where are the millions of transitional fossils Darwin said there should be?” Martin Brazeau has an excellent post on taphonomy at The Lancelet reporting a paper in which folks let poor innocent critters rot in order to ascertain which anatomical features are likely to be preserved and which are likely to be lost before fossilization, and the implications for interpreting fossils of ‘soft’ tissues for phylogenetics. Comment there, please.

by Joe Felsenstein, http://evolution.gs.washington.edu/felsenstein.html

The Discovery Institute Press has published a book by Granville Sewell, a mathematician at the University of Texas at El Paso. Under the title of In The Beginning And Other Essays on Intelligent Design, it apparently consists of previous writings of Sewell, some in revised versions. I hasten to say that I do not have a copy of the book, and have not read it. However Sewell makes it clear that its basic arguments can also be found online in earlier versions of these essays. The one that interests me is his argument that evolution contradicts the Second Law of Thermodynamics, which will be found online here, here, here, and here.

Now the statement that evolution can’t have occurred because it contradicts the Second Law is one of the hoariest old creationist myths. When you hear it you know you are dealing either with someone who does not understand science, or else someone who does understand science but is actively, and dishonestly, trying to get you not to understand science. It is easily answered, and has been, many times: in a closed system entropy does increase, but the biosphere is not a closed system — it is utterly dependent on inflows of energy, mostly from the sun, and the entropy increase from the outflow of energy from the sun far exceeds the decrease of entropy by reproduction and by evolution.

Me on the A Pair of Continents podcast talking about the Freshwater affair. The interview starts around 17:00 of Episode 39. Fat Steve and Dany are fun and interesting folks and I recommend their other podcasts, especially the two featuring PZ Myers (“Easy PZ” to Dany; episode 36) and Richard Wiseman (Episode 20). Well, actually, they’re the only two I’ve listened to so far and I hope to get to their interviews with John Horgan and Skepchick Rebecca Watson soon. But again, highly recommended. After all, they interviewed me! :)