May 2008 Archives
And it must also be time for the 106th edition of the Tangled Bank. Read it!
Check back at Pharyngula later — I've just arrived at the IEDG 2008 conference on Integrating Evolution, Development, and Genomics, and I'll be filling you all in on the latest juicy cool evo-devo stuff.
The PT Crew received an email, announcing a breathtaking website called Exploring Life’s Origins. The website displays in stunning graphics and video how scientists are exploring the origins of life. The graphics were made by an NSF Discovery Corps Postdoctoral Fellow named Janet Iwasa, in collaboration with Jack Szostak, and the Current Science and Technology team at the Museum of Science, under an NSF grant. The resources are available under a Creative Commons License which requires attribution, non-commercial use and no derivative works. The website explains in clear and accessible language how science envisions life arose on earth and explains the RNA world, which, despite the wishful thinking of some creationists, has not lost its relevance.
Allen MacNeill has yet another interesting contribution (as well as an announcement about a new course). Allen MacNeill:It’s very gratifying to see Lynn Margulis finally getting the recognition that she deserves. As the originator of the serial endosymbiosis theory (SET) for the origin of eukaryotes, Lynn’s work provides an excellent example of how ID should (but currently doesn’t) proceed. During the late 1960s, Lynn published a series of revolutionary papers on the evolution of eukaryotic cells, culminating in her landmark book Symbiosis and Cell Evolution, in which she carefully laid out the empirical evidence supporting the theory that mitochondria, choloroplasts, and undulapodia (eukaryotic cilia and flagella) were once free living bacteria (purple sulfur bacteria, cyanobacteria, and spirochaetes, respectively).
Read the rest at Serial Endosymbiosis and Intelligent Design
Allen makes an excellent case how science progresses and that while science may resist change, the only way to change science is to do hard work, research and show how your ideas form scientifically relevant contributions. This is particularly relevant when it comes to Intelligent Design, whose proponents have chosen it to remain scientifically vacuous, without content. And still they whine about being ‘expelled’ when in fact they are ‘exposed’.
Allen is also organizing Seminar in History of Biology: Evolution and Ethics: Is Morality Natural? at Cornell
COURSE LISTING: BioEE 467/B&Soc 447/Hist 415/S&TS 447 Seminar in History of Biology
SEMESTER: Cornell Six-Week Summer Session, 06/24/08 to 07/31/08
On Quintessence of Dust Steve Matheson, a biologist at Calvin College, has back to back posts on the role of gene regulation in the development of ‘novel’ structures. The first, How the bat got its wing, describes the work of Chris Cretekos and colleagues on the regulation of Prx1, a gene influencing bone morphogenetic proteins which are involved in limb elongation. The protein coding regions of Prx1 in bats and mice are virtually identical, but in nearby regions thought to contain elements regulating the local expression of Prx1 there are some substantial sequence differences. Replacing the mouse Prx1 forelimb regulatory region with the bat Prx1 regulatory region resulted in mice with significantly elongated forelimbs. Read Matheson’s post for the rest of the story.
In Finches, bah! What about Darwin’s tomatoes? Matheson describes new genetic research on an old friend, the tomato specimens that Darwin brought back from the Galapagos. Didn’t know Darwin brought tomatoes back from the Galapagos? Again, see Matheson’s post for
… an example of a change in a regulatory region of the DNA, the kind of change that evo-devo theorists have predicted to be fairly common in the evolution of new forms.
The nested hierarchy of DNA/Protein sequence similarity is powerful evidence for common descent. The parallel hierarchy formed by broken genes is more powerful still. Even anti-evolutionist Dr. Michael Behe accepts it as evidence of common descent. Behe’s acceptance of the evidence from broken genes confuses the conventional creationists, as seen in a report of a recent creationist forum. However, the creationists think they have a way out, but wouldn’t you know it, they are wrong.
Don McLeroy is the deranged creationist dentist who was appointed to the chairmanship of the Texas State Board of Education, and who is responsible for the recent purge and intimidation of people who support good biology — he's trouble all the way through. Take a look at his latest stunt.
The State Board of Education's debate on new English and reading standards took another rowdy turn Friday as members approved a never-before-seen version of the lengthy document which materialized less than an hour before the board was to take a final vote.
After a wacky and terse debate on the new curriculum, the board voted 9-6 in favor of the new version, which will remain in place for the next decade and sets standards for state tests and textbooks, as well as classroom teaching.
Experts and teachers have been working on the new curriculum standards for two and a half years.
"I find it's really wild that we can work for three years on a project and then the board is so qualified they can pull it out of their hat overnight," said board member Pat Hardy, a Fort Worth Republican who, like other board members, received the substituted document when it was slipped under her hotel door less than an hour before their meeting was set to convene Friday morning.
Some social conservatives on the board prepared the latest version overnight.
This is similar to what our former education commissioner for Minnesota, Cheri Yecke, tried to pull — she tried to swap in a 'minority report' for the state science standards that was composed behind the back of the official committee … only McLeroy has outdone her by an order of magnitude or so. Why even bring in qualified educators and scientists to do the hard work of a standards committee if you're just going to throw their work away and replace it with some hack job done by ideologues overnight? And to give it to them for review an hour before the meeting is just plain insulting.
This is for the English standards. What kind of circus are we going to see in response to the upcoming science standards?
At least one board of education member is calling for McLeroy's ejection, although it sounds like she doesn't expect anything to come of it. This is what we can expect of creationist conservatives: a dictatorship of the incompetent.
A friend from grad school sent me the following clip from his home town.
Warning: some strong language and stereotypes.
“Intelligent design” creationist Paul Nelson was bragging recently on “Uncommon Descent” about getting a presentation accepted at a conference in the UK, the Ian Ramsey Center for Science and Religion at Oxford’s “God, Nature and Design: Historical and Contemporary Perspectives”. Apparently, the fix is in for IDC advocates, and several openly pro-IDC abstracts have been accepted.
There seem to be about five that have been spotted so far, Paul Nelson’s included. Nelson’s presentation is titled, “The Logic of Dysteleology”. Having attended the 1997 “Naturalism, Theism, and the Scientific Enterprise” conference and heard Nelson’s talk there, if I were attending the Ian Ramsey conference now I could go visit a snack bar during Nelson’s talk and not miss much. It looks to be the same topic, just with a few more recent references tossed in.
Now, as to the rigor of this conference, let’s look at another abstract that was deemed worthy by the reviewers, submitted by one Don Booker of Pace University.
Opposition to evolution is cultural. It isn’t because people are laying awake at night worrying about gaps in the fossil record.
How does this opposition persist and spread in our culture? A new paper in PLoS Biology documents the fact that our public school biology teachers play a significant role. A national survey of high school biology teachers found that about one sixth of them are young earth creationists. Of the remaining 5 sixths, most are in a large muddled middle. I recall another survey (but not the reference) that defined creationists more broadly and more correctly than just YEC’s and found that about one third of science teachers are creationists.
The Washington Post has an excellent editorial on the recent attempts by Intelligent Design Creationists to ‘teach the controversy’ and ‘academic freedom’, observing that
Red-herring arguments about ‘academic freedom’ can’t be allowed to undermine the teaching of evolution.
The editorial points out how these efforts to undermine science are at best misguided.
NO ONE would think it acceptable for a teacher to question the existence of gravity or to suggest that two plus two equals anything but four. It’s mystifying, then, that a movement to undermine the teaching of evolutionary biology is attracting some support. Equally perverse is that this misguided effort is being advanced under the false guise of academic freedom.
The Rockefeller University presents a two day symposium on “From RNA to Humans”
With videos of all the lectures
Session 1: Archaean Chemistry and Earliest Fossils
- The RNA World and the Molecular Origins of Life Gerald F. Joyce, The Scripps Research Institute
- The Origins of Cellular Life Jack W. Szostak, Harvard Medical School
- Can the Distribution of Protein Domains Shed Light on the Tree of Life Russell F. Doolittle, University of California, San Diego
- The Earliest Life on Earth Roger Buick, University of Washington
- Proterozoic Life and Environments Andrew H. Knoll, Harvard University
Session 2: Cells, Cellular Evolution and Protein History
- The Tree of Life and Major Transitions in Cell Evolution Thomas Cavalier-Smith, University of Oxford
- The Origin of Eukaryotes Eugene V. Koonin, National Center for Biotechnology Information, National Institutes of Health
- Barking up the Wrong Tree: The Dangers of Reification in Molecular Phylogenetics and Systematics W. Ford Doolittle, Dalhousie University
- RNA Interference May Provide a Window on the RNA-to-DNA World Transition Phillip A. Sharp, Massachusetts Institute of Technology
Evening Lecture, 6 – 7 p.m.
Feeding and Gloating for More: The Challenge of the New Creationism Jerry A. Coyne, The University of Chicago
Session 3: Development of Eukaryotic Genetic Capacity and Multicellularity
- The Deep Evolutionary History of Eukaryotes Andrew Roger, Dalhousie University
- Demonstrating the Sufficiency of Microevolutionary Processes David Penny, Massey University
- Genes and Development: A Comparison of Human and Amphioxus Genomes Peter W.H. Holland, University of Oxford
- Cnidaria and the Evolution of the Bilaterian Body Plans: Insights from an Outgroup Ulrich Technau, University of Vienna
Session 4: Human Evolution through the Lens of DNA Sequences
- Evolution of Human Populations L. Luca Cavalli-Sforza, Stanford University School of Medicine
- Accelerated Evolution in the Human Genome Katherine S. Pollard, University of California, Davis
- Probing Human Brain Evolution at the Genetic Level Bruce T. Lahn, The University of Chicago
- A Neanderthal Perspective on Human Origins Fairfield Osborn Memorial Lecture , Svante Pääbo, Max Planck Institute for Evolutionary Anthropology
NCSE’s staff worked behind the scenes in the archives to find the missing links tying “intelligent design” to its creationist ancestry.
An outstanding video explaining how through hard work, the NCSE staff uncovered the missing link “cdesign proponentist” (oops they already mutated from their native form “cdesign proponentsists”).
According to the charts at Box Office Mojo the data for expelled for the weekend have gone missing. Although we know that in the 5th week, the theatre count drop almost 50 % from 402 to 210.
In other news, the United Methodist Church passed several relevant resolutions, one apologizing repenting for eugenics, and the other one expressing their displeasure with intelligent design and public schools
THEREFORE BE IT RESOLVED that the General Conference of the United Methodist Church go on record as opposing the introduction of any faith-based theories such as Creationism or Intelligent Design into the science curriculum of our public schools.
No updates on the lawsuit by Yoko Ono against Premise Media.
And despite the efforts by the Discovery Institute and Premise Media it was reported that
Despite the fanfare over Expelled in Missouri, the antievolution House Bill 2554 has died
The score so far: “academic freedom” antievolution bills have died in Florida, Alabama, and Missouri, and South Carolina’s looks poised to die as well.
The study was published in the Journal Science. It’s a good week for science and faith.
Falls Church, VA – May 17, 2008. The non-profit Alliance for Science announced the results this week of its second annual National High School Essay Contest. Students were asked to write a 1,000 word essay on either “Agriculture and Evolution” or “Climate and Evolution”. Neal Desai, a 10th grader at the Pembroke Hill School in Kansas City, Missouri won the top prize. Neal’s insightful essay addressed the tradeoffs between the benefits obtained from genetically modified crops and the potential risks.…
For more information, please visit The Alliance for Science. From there you can find out more details about the winning essays, download the press release, learn about next year’s topic, and how to donate to the prize fund.
In the creationist literature of various kinds an assertion is often made that Einstein was a believer in God, and this assertion is often suggested as allegedly an argument favoring religious faith. However such statements are contrary to what can be found in various documents, for example in Einstein’s letters to various people. The fate of one more such letter is revealed by Associated Press in the following message:
Einstein letter dismissing ‘childish’ religion sells for 200,000 pounds.
By The Associated Press
The letter was written to philosopher Eric Gutkind in January 1954, a year before Einstein’s death. In it, the Einstein said that
“the word God is for me nothing more than the expression and product of human weaknesses, the Bible a collection of honorable but still primitive legends which are nevertheless pretty childish.”
Einstein also said he saw nothing “chosen” about the Jews, and that they were no better than other peoples “although they are protected from the worst cancers by a lack of power.”
Unfortunately for creationists, using the authority of Einstein as a supposed argument in favor of their beliefs is based on a distortion of the views of the great scientist. Of course, argument from authority is anyway of little value.
By now, everyone must be familiar with the inside out organization of the cephalopod eye relative to ours: they have photoreceptors that face towards the light, while we have photoreceptors that are facing away from the light. There are other important differences, though, some of which came out in a recent Nature podcast with Adam Rutherford (which you can listen to here), which was prompted by a recent publication on the structure of squid rhodopsin.
Continue reading “The subtly different squid eye” (on Pharyngula)
J.B.S. Haldane, when asked “What has the study of biology taught you about the Creator, Dr. Haldane?”, replied
“I’m not sure, but He seems to be inordinately fond of beetles.”
Discovery Institute Fellow Dr. Paul Nelson is inordinately fond of ORFans, genes unique to one species that appear to have no relatives in other species. He feels that these unique genes represent a significant challenge to evolutionary biology. However, he has not noticed that the distribution of ORFans implies that the designer is more enamoured of viruses than humans.
There are many excellent resources available online and I recently ran across a conference organized by John C. Avise and Francisco J. Ayala called In the Light of Evolution I: Adaptation and Complex Design
In the presentation that caught my initial interest, Robert Hazen explains the various steps necessary for the origin of life and defines complexity and shows how complexity can increase. I have combined notes on his lecture with additional papers and presentations by Robert Hazen, in order to outline that which many creationists insist, does not exist: a scientific explanation of the origins of life.
I predict that ID creationists will be quick to argue that these are just so stories, and yet, these are stories which present testable hypotheses. And thus I invited ID creationists to present the best explanation as to how ID explains these data?
Seems fair enough.
Read more at ID Exposes where comments may be left.
Sneer Review reports on an in-depth investigation into “The Wedgwood Document” which outlines how the teapot from the famous atheist Bertrand Russell was acquired to undermine the recent successes from atheists.
Remember that Bertrand Russell had stated
“If I were to suggest that between the Earth and Mars there is a china teapot revolving about the sun in an elliptical orbit, nobody would be able to disprove my assertion .….….….. But if I were to go on to say that, since my assertion cannot be disproved, it is an intolerable presumption on the part of human reason to doubt it, I should rightly be thought to be talking nonsense. If, however, the existence of such a teapot were affirmed in ancient books, taught as the sacred truth every Sunday, and instilled into the minds of children at school, hesitation to believe in its existence would become a mark of eccentricity and entitle the doubter to the attentions of the psychiatrist in an enlightened age or of the Inquisitor in an earlier time.”
This simple statement set in motion a series of events which will reverberate in history.
Intelligent Design advocates are fond of using the bacterial flagellum as, in Dembski’s words, a “mascot” of the Intelligent Design movement. In particular, during the recent TV debate between Behe and myself, Behe showed pictures of flagella and triumphantly asserted that they looked exactly like man-made machines, and therefore they must be designed. What ID advocates, including Behe, fail to mention is that the images of flagella they endlessly demonstrate are heavily doctored, and that the real observed flagella do not look like “machines” at all. In fact the structure of flagella is more typical of a bacteriophage virus. Seeing the actual cryogenic electron micrographs of flagella, as well as the images derived from X-rays analysis immediately reveals that showing artificial machine-like images of flagella, without explaining the degree of idealization applied, is sometimes perilously close to committing a fraud.
Read Flagella – Real and Fictional, at Talk Reason.
It seems that the evolution of thorns and plants is seen by some creationists as evidence against evolution and in favour of an Intelligent Designer. While I hate to spend time on debunking creationist foolishness on demand, I found the issue quite fascinating and relatively straightforward to rebut.
Read further at Plants that defy evolution: Datura stramonium (Jimson Weed) where also comments can be left.
PS: Joseph Alden and Gary McGuire are the same person. So any future postings by Joseph should continue under one of the two names as the use of multiple names is in violation of the board’s rules and can be grounds for moderation or removal. Jospeh Alden is Gary McGuire’s uncle and the two were sharing a similar email address and IP connection.
Finals week is upon me, and I should be working on piles of paper work right now, but I need a break … and I have to vent some frustration with the popular press coverage of an important scientific event this week, the publication of a draft of the platypus genome. Over and over again, the newspaper lead is that the platypus is "weird" or "odd" or worse, they imply that the animal is a chimera — "the egg-laying critter is a genetic potpourri — part bird, part reptile and part lactating mammal". No, no, no, a thousand times no; this is the wrong message. The platypus is not part bird, as birds are an independent and (directly) unrelated lineage; you can say it is part reptile, but that is because it is a member of a great reptilian clade that includes prototherians, marsupials, birds, lizards and snakes, dinosaurs, and us eutherian mammals. We can say with equal justification that we are part reptile, too. What's interesting about the platypus is that it belongs to a lineage that separated from ours approximately 166 million years ago, deep in the Mesozoic, and it has independently lost different elements of our last common ancestor, and by comparing bits, we can get a clearer picture of what the Jurassic mammals were like, and what we contemporary mammals have gained and lost genetically over the course of evolution.
We can see that the journalistic convention of emphasizing the platypus as an odd duck of a composite creature is missing the whole point if we just look at the title of the paper: "Genome analysis of the platypus reveals unique signatures of evolution." This is work that is describing the evidence for evolution in a comparative analysis of the genomes of multiple organisms, with emphasis on the newly revealed data from the platypus.
Continue reading "The platypus genome" (on Pharyngula)
Intelligent Design advocates regularly claim that Intelligent Design is science. However, a recent paper on the lamprey genome demonstrates the sharp gulf between science and ID. One of the key icons of ID is Michael Behe’s “irreducibly complex” clotting system. In 1996 he claimed that the clotting system was unevolvable, and no simpler clotting system could exist. In contrast, in 1987 evolutionary biologist Russell Doolittle hypothesised that the clotting system had been built up by co-option of duplicated genes. Doolittle specifically predicted that fish would lack key elements of the Mammalian clotting system (elements of the intrinsic or contact clotting system). Let’s see how those predictions fared.
- Alabama Kills Evolution Bill
- Ono gains temporary injunction against “Expelled”
- Kenneth Miller reviews “Expelled”
- Jeffrey Schloss reviews “Expelled at ASA
- Percival Reviews “Expelled”
And in late breaking news:
Oktar’s teachings echo those of Christian fundamentalists in the United States. He has publicly denounced Darwinism and Freemasonry in high-profile attacks.
Expelled Theatre count
While legislatures focus on antievolution bills, a new video at Expelled Exposed helps students see how evolution works.
Oakland, California, May 6, 2008 As attacks on evolution education remain in the news, with proposed antievolution legislation in Alabama, Florida, Louisiana, Michigan, and Missouri in the headlines, a new video rebutting the basic premise of intelligent design creationism is now available on www.ExpelledExposed.com.
by Joe Felsenstein
Over at Uncommon Descent Sal Cordova has opened a dramatic new thread “Gambler’s Ruin is Darwin’s Ruin”. Apparently improvement of a population by natural selection is now shown to be essentially impossible. He invokes the example of Edward Thorp, who developed the winning system for blackjack fictionalized in the movie 21.
Cordova uses the stochastic theory of gene frequency change of citing Motoo Kimura and Tomoko Ohta’s well-known 1971 monograph “Theoretical Aspects of Population Genetics”, and argues that
Fast political action is needed to stop another anti-science bill in Louisiana. Below is a message from Barbara Forrest, who says it all better than I can.
Friends, fellow educators, and concerned citizens,
First, please accept my thanks to those of you who helped in the effort to stop SB 561, especially those who went to the Capitol to testify. Second, action is needed IMMEDIATELY to ask members of the House Education Committee to kill HB 1168, which is the House twin of SB 561. As far as I know, no newspapers have carried the story of its being filed on Monday, April 21. The bill could be heard in the House Education Committee as early as this week of April 28, so immediate action is crucial.
As you may know, SB 561 was amended to SB 733, the "Louisiana Science Education Act," in which form it is less pernicious but still bad because it contains code language that creationists can exploit. However, the creationists were unhappy with the amendments, so Rep. Frank Hoffman of West Monroe has introduced HB 1168 in the House of Representatives. HB 1168 is identical to the original SB 561. (Mr. Hoffman was the Asst. Supt. of the Ouachita Parish school system in 2006. He helped persuade the the Ouachita Parish School Board to pass its creationist "science curriculum policy" that is the basis for both SB 561 and HB 1168.)
SB 733 will probably pass the Senate and be sent to the House, where it could be merged with HB 1168, which means that we are back where we started with SB 561. So HB 1168 must be killed in the House Education Committee, which means that we must generate as much opposition to the House Education Committee **NOW.** The bill could come up in the House Education Committee this week, but we are not sure. We need to act immediately to request that House Education Committee members kill HB 1168. And please also contact everyone else you know INSIDE LOUISIANA to do the same. We want opposition from inside the state, not outside. We want the House Education Committee members to hear from people who live here and vote here. We may need to generate outside opposition later, but not at this time.
I have written a revised backgrounder for HB 1168 based on the one I wrote for SB 561. You may download it here:
There are talking points, contact information, and some instructions for you at the end of this document.
A shorter set of talking points, also with contact information, is here:
The contact information in these is for ten members of the House Education Committee who may be receptive to our contact based on what we have been able to learn. If you personally know another member who is approachable, please also contact that person.
I have talked personally to three committee members and found those three very nice and very interested. Some of the committee members have been teachers and served on their parish school boards. Some are attorneys. The three to whom I talked were aware of the Dover trial, Kitzmiller et al. v. Dover Area School District (2005), in which I served as an expert witness for the plaintiffs, a case that cost the Dover school board one million dollars. This seemed to resonate with them. You may wish to keep that in mind as you contact them. If I may make a suggestion: remember that this is a political problem, not a scientific one. Please try to avoid "science talk." As Eugenie Scott, our executive director at the National Center for Science Education says, we will not solve this problem by throwing science at it. We must appeal to the legislators as fellow citizens, parents, and educators. No academic-speak! :)
The children and teachers of Louisiana are being used as pawns by the Louisiana Family Forum and, most likely, the Discovery Institute, about which I have written so extensively. These people will assuredly not be around to clean up the wreckage they will leave in their wake if we don't stop them. We have to stop them.
The Florida legislature failed to pass either of two forms of the Discovery Institute’s draft “academic freedom” bills, and adjourned Friday evening. We have until the legislative session next year to make sure that those in the legislature know exactly what the history and intent of bills like that are. But it doesn’t feel like a “win”; those of us who invested our time in advocating for good science education in Florida essentially got lucky this time.
Some good news from Florida Citizens of Science
Let us take a moment of silence for House Bill 1483 and Senate Bill 2692, the deceptively named “academic freedom” bills. Time of death: 6 p.m. I doubt they will rest in peace, though.
In other hopeful news: According to Box Office Mojo, the theatre count for Expelled in its third week has dropped by 386 to 655 and the daily numbers have dropped to $157,191 or $151/theatre for Monday, $162,396 or $156/theatre for Tuesday and $159,273 or $153/theatre for Wednesday.
Farewell to bad arguments about good science.
We all know that Ben Stein thinks that “science leads you to killing people”. The following is a quote from a 2002 article Stein wrote for Forbes magazine, in which he offers “a few suggestions on how we can ruin American competitiveness and innovation in the course of this century”. Forbes’ readers probably thought that Stein’s “suggestions” were meant as satire, but in light of recent events, it is clear that he was in fact serious about doing his part to tank America’s economic future (presumably to avoid all the people-killing caused by sound science education).
12) Elevate mysticism, tribalism, shamanism and fundamentalism–and be sure to exclude educated, hardworking men and women–to an equal status with technology in the public mind. Make sure that, in order to pay proper (and politically correct) respect to all different ethnic groups in America, you act as if science were on an equal footing with voodoo and history with ethnic fable.
Ben Stein, “How to Ruin American Enterprise”, Forbes 12/23/2002
EDIT: Someone in the comments has argued that Ben Stein’s Youtube snippet and quote above must have been taken out of context. You can actually watch the entire TBN interview here. If anything, the thing is even more embarrassing in context, with Stein exposing his abysmal scientific ignorance for half an hour before casually condemning half a century of scientific progress as murderous. If you don’t have the stomach for the whole thing (and I don’t blame you), you can go to the quote itself just after minute 28.