I don't have much time for blogging these days 'cause I'm in the middle of writing a textbook—trying to be as accurate as possible.
Watch Paul Nelson making comments about the authors of biology textbooks. He sounds very sincere. I think he actually believes that biology textbook authors are deliberately lying. Poor deluded Paul Nelson. That's why we call them IDiots.
"Sosin's address to the 2010 Papyrological Congress in Geneva
The text of Josh Sosin's address, delivered at the 26th Congress of the International Association of Papyrologists, 19 August 2010, in Geneva, has been posted to the Stoa Consortium blog. Gabriel Bodard has added a useful comment collecting bibliography related to the papyrological editor software described therein."
What do you do about all those fake Christians who believe in theistic evolution? You develop a litmus test, of course.
... if you ask me whether someone is a Christian, I say, "Let him recite the Apostle's Creed and affirm that he believes it and renounces contrary doctrines."
Sounds like a plan. I'll quote the English Language Liturgical Consultation (ELLC) version of the Apostle's Creed and we can discuss whether believing it is compatible with science as a way of knowing. Doesn't look like it to me. Denyse is right!
I believe in God, the Father almighty, creator of heaven and earth. I believe in Jesus Christ, God's only Son, our Lord, who was conceived by the Holy Spirit, born of the Virgin Mary, suffered under Pontius Pilate, was crucified, died, and was buried; he descended into hell. On the third day he rose again; he ascended into heaven, he is seated at the right hand of the Father, and he will come to judge the living and the dead. I believe in the Holy Spirit, the holy catholic Church, the communion of saints, the forgiveness of sins, the resurrection of the body, and the life everlasting. Amen.
Jerry Coyne is an expert on speciation. That's why it's always informative to read his latest thoughts on the problem. In spite of what many people might believe, the main cause of reproductive isolation—the actual speciation event according to the biological species concept—is due to accident, not adaptation. It's just one more example of the importance of random genetic drift in evolution.
Genetic barriers aren’t thought to arise for the purpose of keeping species distinct. Rather, they are usually thought to be evolutionary accidents: geographically isolated populations diverge genetically under natural selection or other evolutionary forces like genetic drift, and that divergence leads to the evolution of genetic barriers (mate discrimination, the sterility of hybrids, ecological differences, etc.) as byproducts of evolutionary change. For example, populations could adapt to different environments (one dry, one wet, for example), leading to them becoming genetically different. When these populations meet each other again, this genetic divergence could result in hybrids that don’t develop properly because the parental genomes are sufficiently diverged that they can’t cooperate in building a single individual.
I wish more people would assimilate this message. It seems to be the overwhelming consensus among the experts in speciation but the average scientist still has an adaptationist view of speciation (and of evolution in general).
Speaking of adaptationists, Coyne also likes the idea that some examples of reproductive isolation can be reinforced by natural selection. You can read about those cases on his blog.
Watch the video. Oprah sends very mixed messages. On the one hand she advises following the advice of doctors but at the same time she supports The Secret.
Most of you know that DNA strands have a sugar-phosphate background. The bases in each strand are covalently linked to each other by phosphodiester linkages between the 5′ and 3′ carbon atoms of the deoxyribose sugar.
Recently there has been a claim by NASA-funded scientists that a certain bacterium can replace those phosphates with arsenic. Close examination of the Science paper has revealed that, at most, a few percent of the phosphorus atoms are replaced and even that amount is challenged. It has become abundantly clear from reading the paper that the bacteria absolutely required phosphorus and sufficient quantities were present in the media as contaminants.
Carl raises an issue that has cropped up in many of the comments sections of various blogs. Is criticizing a scientific paper appropriate outside of the peer-reviewed scientific literature? Is it ethical to cast doubt on the integrity of scientists when questioning the quality of their science?
Felisa Wolfe-Simon1 is the lead author of the study and she was the main spokesperson in the video below. Carl Zimmer asked her if she wanted to respond to the criticism of her paper and here's what she said, according to the Slate article,
"Any discourse will have to be peer-reviewed in the same manner as our paper was, and go through a vetting process so that all discussion is properly moderated," wrote Felisa Wolfe-Simon of the NASA Astrobiology Institute. "The items you are presenting do not represent the proper way to engage in a scientific discourse and we will not respond in this manner."
Carl asked some other scientists about this and the best quote comes from Jonathan Eisen,
But Jonathan Eisen of UC-Davis doesn't let the scientists off so easily. "If they say they will not address the responses except in journals, that is absurd," he said. "They carried out science by press release and press conference. Whether they were right or not in their claims, they are now hypocritical if they say that the only response should be in the scientific literature."
My own impression of this fiasco is that the scientific authors of the paper can be accused of bad science and the lead author, Felisa Wolfe-Simon, is guilty of grossly misrepresenting her work at the press conference. There really can't be any excuse for that behavior if you want to call yourself a scientist. Those who think this is impolite and unethical are dead wrong. It's an absolute requirement of good science that we point out to the general public when scientists are behaving badly, otherwise we lose all credibility.
As you watch this video keep in mind that the bacteria absolutely require phosphate in the media in order to grow and that only a few phosphorus atoms, at most, are replaced by arsenic in DNA. If you think that's what Felisa Wolfe-Simon is telling you then you need to work hard on your listening comprehension skills.
1. The name of the bacterial strain is GFAJ-1. Rumor has it that this stands for "Get Felissa a Job." I wonder how that's working out? Do you think the job offers are pouring in?
John Lennon died on Dec. 8, 1980 when he was shot four times in the back by Mark David Chapman. His ashes were scattered by Yoko Ono in Central Park in New York at the site of the Strawberry Fields Memorial.
That was thirty years ago today. A whole new generation has grown up since then and I fear we are in great danger of forgetting what Lennon and The Beatles did to help change our culture for the better.
Many people have questioned the significance of blogs and bloggers. Some think that science blogs have no useful purpose and that they are undermining the peer review process of publication in scientific journals. Science journalists resent the fact that amateur writers can throw up something on a blog and claim that it's contributing to science education.
Over the years I've come to appreciate that science blogs do at least one thing that's new—they provide instant commentary on science news and that helps to serve as authoritative fact-checking. Science blogs monitor science journalism in the same way that political blogs monitor FOX news and the New York Times.
This role has been illustrated in spades over the past few days as we monitor the response to the NASA hype over bacteria that grow in the presence of arsenic. The weaknesses of the Science paper are now well-known thanks to many science bloggers. In the past, this kind of analysis would have had to wait for the publication of an appropriate critique in a scientific journal and that was very unlikely to happen for a number of very good reasons. Thus, in the past shoddy, over-hyped work got a free pass and science journalists who fell for the hype never even realized that they had been duped.
Read David Dobbs on Wired for a thoughtful analysis of the episode and the lesson we need to learn [Is That Arsenic-Loving Bug — Formerly an Alien — a Dog?]. It's interesting that even Nature News got sucked into promoting the hype. This shows that even journalists at the premier science journals are not very skeptical.
This finding of an alternative biochemistry makeup will alter biology textbooks and expand the scope of the search for life beyond Earth. The research is published in this week's edition of Science Express.
I read the paper (Wolfe-Simon et al., 2010) and I can assure you that nothing in that paper is going into my biochemistry textbook. I predict that a year from now we'll have forgotten about this discovery. I'm not even sure it's going to be confirmed but, if it is, the result is pretty trivial.
For a start, even the title of the paper is misleading. The title says "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus" but all of the data show that there was phosphorus in the media and that the bacteria used it for growth and reproduction. This selected strain of bacteria incorporated more arsenic than non-selected species but it by no means did it replace all phosphate with arsenic. Only a few percent (at most) of the phosphorus atoms in DNA, for example, were replaced by arsenic.
The purpose of this posting it to alert you to a fantastic article by microbiologist Rosie Redfield at the University of British Columbia. I strongly urge that everyone read her take-down of the science paper [Arsenic-associated bacteria (NASA's claims)]. The problem is not just that a bad paper was published in Science—it's that the paper was so heavily promoted in the media. We've got to do better when it comes to educating the general public about science.
Wolfe-Simon, F., Blum, J.S., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D., and Oremland, R.S. (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science Published Online 2 December 2010 [DOI: 10.1126/science.1197258]
I teach in a second year course on "Scientific Misconceptions and Controversies." In my part of the course we discuss creationism and evolution. The object is to learn to think rationally about the controversy.
Students have to read Icons of Evolution and write an essay analyzing the arguments in one of the chapters (their choice). They have no problem recognizing the flaws in the logic and the outright mistruths in that book. For typical university students with a rudimentary understanding of evolution it's like shooting fish in a barrel.
The Discovery Institute sees it differently but they must live on another planet.
A Berkeley PhD in molecular and cell biology, Wells is among the most lucid and accessible scientist-writers devoted to the modern project of critiquing Darwin. When I say the book is sweetly reasoned, I don't only mean that it's well reasoned but that there's an appealing geniality, a sweetness, to the man's writing that stands out in contrast to the donkey-like braying of a Darwinian biologist Jerry Coyne, the sinister coilings of a Richard Dawkins, the ugly "humor" of a P.Z. Myers. Yes, you can get a sense of a person's character, and perhaps too his credibility, from the words he uses.
And here's an example of "sweet geniality" from page 234 of Icons.
What about scientists who knowingly make false utterances or misleading omissions but believe the overall effect is not misleading because they are teaching "a deeper truth"? Does the commitment to a supposed deeper truth excuse conscious misrepresentations? Such an excuse probably wouldn't help a stock promoter. Under federal law, a stock promoter is not justified in mistating the facts just because he or she deeply believes that a company is destined to prosper. The stock promoter commits fraud by misrepresenting the truth, regardless of his or her underlying beliefs. Shouldn't scientists be held to the same standard?
Fraud is a dirty word, and it should not be used lightly. In the cases described in this book, dogmatic promoters of Darwinism did not see themselves as deceivers. Yet they seriously distorted the evidence—often knowingly. If this is fraud when a stock promoter does it, what is it when a scientist does it?
...
If dogmatic promoters of Darwinian evolution were merely distorting the truth, that would be bad enough. But they haven't stopped there. They now dominate the biological sciences in the English-speaking world, and they use their position of dominance to censor dissenting viewpoints.
Bagnall, Roger S.,The Florida Ostraka: Documents from the Roman Army in Upper Egypt(GRBM7 [1976] Full text Turner, Eric G., The Papyrologist at Work (GRBM 6 [1973]) Full text
I thought Hitchens did a much better job that Tony Blair but it's hard to be unbiased. Here are the results of the poll before and after the debate.
On the question "Is Religion a Force for Good?"
Before the debate ...
Yes (Blair): 22% No (Hitchens): 57% Undecided: 21%
After the debate
Yes (Blair): 32% No (Hitchens): 68%
Both speakers increased their numbers by about 10%. In simplistic terms, the undecided members of the audience split 50:50 on the question.
That's a tie by my calculation. The blogosphere is reporting this as a huge victory for Hitchens but it didn't seem that way in Massey Hall in Toronto. Just because Hitchens started out with 57% of the votes doesn't mean he won the debate. (Although I think he did.)
Rob Day, better known as Canadian Cynic, finally got tired of the malicious defamations posted by Patrick “Patsy” Ross on his blog The Nexus of Assholery. The result was an $85,000 judgment in Rob's favour—$10,000 in legal costs and $75,000 in punitive damages [Another Mudfish Beached]. Let's hope Patsy pays up before the police have to come knocking on his door. This is one way to deal with bloggers and trolls who step over the line. Another way is to press criminal charges against those who post serious threats. I think the second way is better, if it's an option, and I'm looking forward to the time when some of the mentally deranged trolls are locked away in an institution without a computer. There are a few such trolls who may soon be getting a visit from the cops.
I understand, and agree with, the basic sentiment behind this poster but I wish they'd chosen better examples. Charles Darwin was wrong about lots of things.1
1. But he's still the best scientist who ever lived.
I couldn't get tickets to see the actual debate at Massey Hall in Toronto so I'm doing the next best thing by going to the beerparty live streaming of the debate at CFI tomorrow night.
All the cool people will be there (wearing WiFi radiation protection).
Starts: Friday, November 26th 2010 at 7:00 pm Ends: Friday, November 26th 2010 at 9:00 pm Location: Centre for Inquiry, 216 Beverley Street (just south of College and St. George)
Since the debate between well-known atheist and author Christopher Hitchens and former British Prime Minister Tony Blair sold out we will be screening the live video stream of the event at CFI Ontario.
In a world of globalization and rapid social change does religion provide the common values and ethical foundations that diverse societies need to thrive in the 21st century? Or, do deeply held religious beliefs promote intolerance, exacerbate ethnic divisions, and impede social progress in developing and developed nations alike? To encourage a far-ranging discussion on one of human kind's most vexing questions, the 6th semi-annual Munk Debate will tackle the resolution: be it resolved, religion is a force for good in the world.
$5, $4 for students and FREE for CFI Members.
Attendees are invited to stay after the debate to enjoy some food and drinks while they discuss who they thought won the debate!
A study by some Dutch scientists claims to have shown that WiFi kills trees [Study Says Wi-Fi Makes Trees Sick]. Combine that with the widespread myth evidence that WiFi radiation is harming school children [Sometimes School Trustees Make You Proud] and all of a sudden we've got a serious problem.
University campuses are awash with WiFi radiation coming from sites in every building. If you are one of those people who think you're being harmed, I've come up with a simple solution—a tinfoil1 hat to protect your brain. I have carefully researched the shape of this hat in order to maximize the desired effect. Wear it when you are at your desk studying, when you are in class, and when you're taking a break. Get all your friends to wear one too.
Not only will this tinfoil hat protect you, it will also serve as a reminder to others that you are an intelligent person who cares about the environment.
Here's a special note to parents of school age children who are worried about WiFi radiation in the public schools. It's easy to make a protective hat. Just roll up some poster board in the shape of a cone and cover it with tinfoil. Make sure your children keep the hat on while they are in school. Your children will rapidly gain the admiration and respect of the other students for being so scientifically literate.
1. It's actually aluminum foil but who's counting?
The photos were taken by Alex Palazzo who wishes to remain anonymous.
This poster is from Rock Stars of Science. There are six people in the photo: one of them is a rock star (I'm told) and five of them are famous scientists (I'm told).
I could be wrong. Maybe this is a good way of reaching out to people. Maybe GQ's readers are getting out their dictionaries and picking through those descriptions, stopping occasionally to stare at the blurry, bearded interloper in the background of Bob's photograph. And maybe those readers are now more inspired by science as a result. If so, I'd like to see some evidence of it - maybe a poll of readers?
But I still can't help but feel that if you have to resort to rockstars make science cool, you're really not very good at communicating science. Because science is way cooler than rock stars.
You won't be surprised to learn that Chris Mooney likes this campaign and ERV doesn't. Jerry Coyne doesn't like it either. Does anyone notice a pattern here? ... The one person who isn't a scientist is the one who thinks he knows how to promote science.
So, who's behind this promotion? It's a company called GEOFFREY BEENE that I've never heard of. But don't take that lack of knowledge seriously because I'm a scientist and I'm definitely not cool.
Here's a video put out by the company. Is this mostly about science or is it mostly about the company exploiting their support for medical technology?
Yesterday Age of Autism and SafeMinds released the following statement as reported in the latest posting on Skepchick [Good guys win!]. Congratulations Skepchick!
SafeMinds was notified late yesterday afternoon that AMC Theaters has decided to block the SafeMinds Public Service Announcement (PSA) on influenza vaccines with mercury. The PSA alerts parents and pregnant women of the presence of mercury in most influenza vaccines and the ample availability of mercury-free alternatives. The CDC has declined to give a preference for the mercury-free versions, so it is important that the public is aware of its options. AMC’s advertising representative had reviewed and approved the PSA to run in AMC cinemas over the Thanksgiving weekend. A small group of vocal vaccine proponents dismissive of mercury concerns learned of the PSA and bombarded the AMC website, leading to the company’s decision to prevent its release. SafeMinds thanks its supporters who viewed the PSA and contributed to its efforts to educate the public to avoid unnecessary mercury exposure. Mercury in all forms is dangerous, especially to the developing fetus and infants, as referenced on the PSA website www.safemindsflu.org. SafeMinds will continue its mission to educate the public on this important healthcare topic.
BTW, the ad was NOT a public service announcement by any stretch of the imagination.
There are several well-known examples of Nobel Laureates in science who later become enamored with quackery. Orac mentions a few on his blog in The Nobel disease strikes again.
Can you guess who holds the record for the swiftest turn around from getting the Nobel Prize to endorsing quackery? (Hint: mentor of Richard Dawkins).
Of course this record only applies to scientists who became quacks after getting the Nobel Prize. That lets Kary Mullis off the hook.
(Flu shots are perfectly safe, but I don't need to tell YOU that, do I?)
Here's a list of theaters that will be showing the video. Boycott them if you live near by.
* Empire 25 in New York City * Long Beach 26 in Long Beach, California * River East 21 in Chicago, IL * Boston Common 19 in Boston * Phipps Plaza 14 in Atlanta * Tyson’s Corner 16 in McLean, VA * Northpark Center 15 in Dallas, TX * Rosedale 14 in Saint Paul, MN * Pavillions 15 in Denver, CO
PZ Myers reports from Skepticon III in Missouri that some people are upset because there's too much atheism at a skeptical meeting. This leads naturally to a discussion about the difference between being a skeptic and being an atheist. Can you be a theist and still be genuinely skeptical?
Jim Lippard has an interesting point of view on this question. You should read his blog posting [What to think vs. how to think] and join the discussion on The Lippard Blog.
Sergio Daris, Dizionario dei nomi geografici e topografici dell'Egitto greco-romano, supplemento 5 (2006-2009), Biblioteca degli «Studi di Egittologia e di Papirologia», 8, Fabrizio Serra Editore, Pisa-Roma 2010, pp. 124. Fabrizio Serra editore, Pisa · Roma
La pubblicazione del Dizionario dei nomi geografici e topografici dell'Egitto greco-romano nella collana 'Biblioteca degli «Studi di egittologia e di papirologia»' era iniziata nel 2003, con l'edizione delle voci uscite fra il 1935 e il 1996, dando in questo modo continuazione all'iniziativa di Aristide Calderini (1935), che rappresenta ancora oggi il repertorio più completo del settore, strumento essenziale di lavoro per il papirologo, l'egittologo e, più in generale, lo studioso del mondo antico. Nel quarto supplemento, edito nel 2007, sono stati poi raccolti i testi apparsi negli anni 2002-2005. Questo quinto supplemento, la cui impostazione editoriale segue quella adottata nei volumi precedenti, raccoglie invece il materiale pubblicato negli anni 2006-2009, con aggiunte e correzioni relative a voci già precedentemente prese in considerazione: alcune sono state in parte o totalmente rielaborate. Oltre ad esse, naturalmente, ci sono voci del tutto nuove, dato il continuo incremento di dati, l'ampliamento delle ricerche e il conseguente arricchimento del quadro delle informazioni: le voci nuove, di regola, sono immediatamente riconoscibili per la presenza delle sezioni fondamentali, Cit(azione), Den(ominazione), Loc(alizzazione), mentre le aggiunte e le correzioni riguardano, di norma, singole sezioni. Per tutte le voci già registrate nei volumi precedenti è sempre segnalato, nella bibliografia, il rinvio interno alDizionario per facilitarne il rapido reperimento.
Composto in carattere Dante Monotype. Formato 21,5 x 29,7. Legatura in tela. Sovraccoperta in cartoncino Murillo Fabriano castagna con stampa a due colori. ISBN: 978-88-6227-363-3 E-ISBN: 978-88-6227-365-7 ISSN: 1828-874X SKU: 2519
Sommario: C.Balconi, Orsolina Montevecchi K.Jaros, Ein Fragment des Lukasevangeliums aus der Privatsammlung De Hamel in Cambridge: Gk MS 386 A.Martano, Note di esegesi anacreontea antica: P.Oxy. 3722 e Anacreonte, fr.82 Gentili M.C.Scappaticcio, PL III/504: Virgilio, la dialysis e un'ignota Ars Grammatica M.Stroppa, Lista di codici tardoantichi contenenti hypomnemata K.Jaros, Zur Textueberlieferung des Markusevangeliums nach der Handschrift P.Chester Beatty I (P45), zu 7Q5 und zum "Geheimen Markusevangelium" D.Minutoli, Ordine di pagamento: PL III/343 R.Pintaudi, SB V 7633: registro di terreni G.Casanova, "A caval donato ...": P.Hib. II 274 riesaminato D.Colomo, Proposte di integrazione a P.Laur. IV 167: frammento di resoconto sulla manutenzione delle dighe G.Nachtergael, Une stèle funéraire d'Alexandrie L.Migliardi Zingale, Sui papiri "ravennati", punto di incontro tra Occidente ed Oriente: alcune riflessioni E.Lucchesi, Hymnes de Sévère et sur Sévère A.Delattre, Un ostracon copte d'Antinoé E.Lucchesi, "Nachtrag" à l'édition du "P.Vat.Copt.Doresse 7" P.Grossmann, Antinoopolis Oktober 2007. Vorlaeufiger Bericht ueber die Arbeiten im Herbst 2007 P.Grossmann, Antinoopolis Januar/Februar 2008. Vorlaeufiger Bericht ueber die Arbeiten im Fruehjahr 2008 R.Sousa, The Papyrus of Nesipautitaui (SR 1025): an iconographical reading J.R.Aja Sanchez, El "rio de Nun" y el "(César) Nilo de Egipto": del mito egipcio a la concordia politica romana. La insercion de JE 48862 y P:Brooklyn 47.218.84 en el tema
Several bloggers have discussed the letter.1 Petsko is defending a traditional liberal education that includes literature and language and I agree with the gist of what he is saying. However, I wish we could have more of a conversation about "liberal science" instead of always referring to "liberal arts." It's not enough to insist that every student be exposed to philosophy and literature—they must also be exposed to science or you can't say that they are getting a truly liberal education. And I'm not just talking about a token science course for humanities students called "Astronomy for Dummies."
But let's leave that conversation for another time. I want to discuss another issue. Here's what Petsko said,
Let's examine these and your other reasons in detail, because I think if one does, it becomes clear that the facts on which they are based have some important aspects that are not covered in your statement. First, the matter of enrollment. I'm sure that relatively few students take classes in these subjects nowadays, just as you say. There wouldn't have been many in my day, either, if universities hadn't required students to take a distribution of courses in many different parts of the academy: humanities, social sciences, the fine arts, the physical and natural sciences, and to attain minimal proficiency in at least one foreign language. You see, the reason that humanities classes have low enrollment is not because students these days are clamoring for more relevant courses; it's because administrators like you, and spineless faculty, have stopped setting distribution requirements and started allowing students to choose their own academic programs - something I feel is a complete abrogation of the duty of university faculty as teachers and mentors. You could fix the enrollment problem tomorrow by instituting a mandatory core curriculum that included a wide range of courses.
Young people haven't, for the most part, yet attained the wisdom to have that kind of freedom without making poor decisions. In fact, without wisdom, it's hard for most people.
My university is run by spineless faculty who think that we should structure the university according to what the students want to take. We are evolving into a university that promotes a wide range of options and degrees that have no major focus of study. This is all in the names of "breadth," "diversity," and "interdisciplinary." It's the smörgåsbord approach to education.
The problem with Petsko's analysis is that the very faculty he assumes to possess the "wisdom" to set curricula are the ones promoting student choice and abrogating responsibility—at least at the University of Toronto.
So, here's the question: Should universities be mandating required courses in order to assure a minimal standard of liberal education or should we be allowing students to choose whatever courses they are interested in taking?2
1. John Pierot [Knowing Ways] thinks that humanities represent a different way of knowing. Jerry Coyne also has a humanities background [Keeping the humanities alive].
2. Knowing full well that some students will often choose courses on the basis to expected grades rather than interest.
Today marks the official launch of the Extraordinary Claims campaign by the Centre for Inquiry, Canada. A lot of the work behind this campaign was done by members of the Committee for the Advancement of Scientific Skepticism (CASS). While I'm listed as a member of that committee I haven't been very active for the past six months while I've been working on my book. The credit goes to Michael Kruse and Iain Martel and all the other members who worked so hard.
If you're a CFI member, support CFI by attending the Official Launch Part this evening at the Centre for Inquiry, 216 Beverley Street, Toronto (just south of the St. George campus of the University of Toronto).1 If you're not a member then go anyway and join up!
1. I wish I could be there but a prior commitment got in the way.
Much of Collins’s case for Darwinian evolution is based on so-called “junk DNA.” This is the part of the genome that does not appear to code for the production of proteins. In mammals, the vast majority of DNA has been dismissed as “junk.”
Junk DNA, according to Darwinists like Collins, gives evidence of common descent—the idea that all life, including human life, branches off from a common evolutionary tree. As life evolved, according to this view, garbled, useless genetic information accumulated and has remained fixed—like dirt swept under a carpet—even as mammals, for example, diversified from a common ancestor.
But the argument from junk DNA—also called “ancient repetitive elements” (AREs)— depends on the premise that no function will ever be discovered for AREs. Collins’s faith in Darwinian theory would be severely hamstrung if the premise were shown to be wrong. It is a faith based on gaps in scientific knowledge. Hence, “Darwin of the gaps.”
I don't want to defend Francis Collins. I want to emphasize something else; namely that the concept of junk DNA is about as far removed from "Darwinism" as you can possibly be and still be an evolutionary biologist. If it has any meaning at all, "Darwinism" has to be a synonym for the belief in natural selection as the most potent mechanism of evolution. Junk DNA is completely non-Darwinian and there's no way you could describe it as compatible with "Darwinian theory."
Why do creationists have so much trouble understanding this? It's not that hard.
Now, here comes the fun part. Over on Uncommon Descent Barry Arrington asked the Intelligent Design Creationists to define "Darwinism". The contrast between what they're saying in the comments and what the modern textbooks say about evolution is truly astonishing.
Everyday Writing in the Graeco-Roman East Roger S. Bagnall
Available worldwide Sather Classical Lectures A Joan Palevsky Book in Classical Literature Hardcover, 192 pages ISBN: 9780520267022 December 2010 $49.95, £34.95
Most of the everyday writing from the ancient world—that is, informal writing not intended for a long life or wide public distribution—has perished. Reinterpreting the silences and blanks of the historical record, leading papyrologist Roger S. Bagnall convincingly argues, however, that ordinary people—from Britain to Egypt to Afghanistan—used writing in their daily lives far more extensively than has been recognized. Marshalling new and little-known evidence, including remarkable graffiti recently discovered in Smyrna, Bagnall presents a fascinating analysis of writing in different segments of society. His book offers a new picture of literacy in the ancient world in which Aramaic rivals Greek and Latin as a great international language, and in which many other local languages develop means of written expression alongside these metropolitan tongues.
(1) The Andrew W. Mellon foundation has very kindly agreed to bring our proposal for “Integrating Digital Papyrology 3” to its Board on 10 December. Nothing is certain or guaranteed, but we are hopeful that the proposal will be funded. Should it be, we shall post the proposal online (as we have done with the previous two efforts (see www.duke.edu/~jds15/DDbDP-APIS-HGV_propRedacted.pdf <http://www.duke.edu/%7Ejds15/DDbDP-APIS-HGV_propRedacted.pdf> and www.duke.edu/~jds15/IDP2-FinalProposalRedacted.pdf) <http://www.duke.edu/%7Ejds15/IDP2-FinalProposalRedacted.pdf%29> . (2) As I mentioned in Geneva, the Papyrological Navigator is in process of being overhauled. The new version is now live atpapyri.info <http://papyri.info/> . It features a great many enhancements, including much improved browse features, and concurrent metadata-and-text searching. Optimization of the interface will be part of the work we shall conduct under IDP3. Papyri.info <http://Papyri.info/> is the single home of both the search interface and the new editing interface. We are fixing bugs as they are reported. If you encounter problems, please alert Hugh Cayless (hugh.cayless@nyu.edu); best also to copy Rodney Ast, James Cowey, and Josh Sosin. (3) Apart from the new initiatives that we shall push forward under IDP3, we are very pleased to announce that, based on the generous and excited input of colleagues who attended the session in Geneva (especially Alain Delattre), we are now in the first stages of embarking on a pilot project to add Coptic material to the DDbDP/HGV. We shall begin with those Greek/Coptic bilingual texts, whose Greek is already in the DDbDP and whose metadata is already recorded in HGV. We’ll see what happens! (4) As promised in Geneva, this message will be followed with invitations to senior scholars to serve as Senior Editors for the newly collaborative DDbDP. We shall alert papyList to the outcome. We shall be in touch as developments arise. Now, on to the new editing platform for the DDbDP. The following is a lightly edited version of the talk delivered at the Congress in August. First some background. I don’t need to tell you very much about the history of the Duke Data Bank of Documentary Papyri. It was founded nearly 30 years ago, as a collaboration between William H. Willis and John F. Oates of Duke University, and the Packard Humanities Institute. Some 14 years later, around the time, as it happens, that APIS was also starting, the Perseus Project, from Tufts University, very kindly agreed to host a new online DDbDP, to develop a search interface, to convert the data from old Beta code to a markup language called SGML. The new home was great, free to the user. But the change meant the end of regular revenues to support data entry and proofreading, and also the end of internal control over the search interface. Within a few years the DDbDP was behind in data entry and the search interface was not growing and maturing as papyrologists wanted. So, in 2003/4, I started a process meant to fix this problem. In 2005 The Andrew W. Mellon Foundation awarded us a modest grant to discuss possible solutions with small groups of papyrologists and technologists. Shortly thereafter James Cowey and I began mapping the HGV and DDbDP to each other, with a view to creating the possibility of technical integration of the two databases. A year later, we began working on a proposal to Mellon to implement the results of those earlier discussions and the new collaboration with HGV. Now, in the meantime, a separate initiative, under the leadership of Roger Bagnall, had begun to develop the Papyrological Navigator, as a tool for searching and browsing the DDbDP, HGV, and APIS. Mellon very generously supported our proposal and we spent 2007/8 (1) converting the DDbDP from the by-then outdated SGML to an open and transparent markup standard known as EpiDoc <http://epidoc.sourceforge.net/> —devised for use with inscriptions, but easily extensible to cover papyrologists’ needs, (2) creating a technical framework for assembling HGV records with the corresponding Duke texts and, where they exist, APIS records—I want to say here, that absolutely critical task was made much easier by the very generous collaboration of Mark Depauw and the entire Trismegistos team, whose TM numbers are in an important sense the glue that holds our software together, and (3) finish the work started on the Papyrological Navigator. We had begun to solve the puzzle. The DDbDP had a powerful search interface. HGV and DDbDP were on a path to technical integration; APIS records could now be displayed alongside Greek texts; Greek texts could be displayed alongside images. So there was progress. But we had not solved all of the puzzle. The DDbDP was slipping farther behind on data entry, and new rules made it difficult to hire students to enter texts. So, how were we to solve this problem? We proposed to build an online environment that would allow the worldwide community of scholars to enter texts into the DDbDP. The system would allow them paste in Word files, make some alterations, and then submit the texts to a board of editors who would proofread them and then push the texts into the database. This began as an economic problem: we could not afford to pay for data entry. But once we started thinking about a new group-based platform a whole new vista of ideas and questions opened up to us. Why should Duke be the sole authority of what goes into the databank? Couldn’t the community do this? Why should the DDbDP only reflect scholarship that had already appeared in print publications? Could it become a forum in which, for example, emendations are proposed, discussed, approved by Editors just as, say, journal articles are? And so, we proposed to the Mellon Foundation to, among other things, build a web-based platform that allows users to add texts to the DDbDP, correct typos, add or change translations, propose additions or emendations to HGV records, add emendations found in the BL or in other publications, even propose emendations directly to the databank, so that control of this central scholarly dataset would grow to reside with the community. Mellon generously funded the project and we spent 2008 to 2010 building it. We have tested it with small groups of colleagues; it is now live. To get started Feel free to consult the very brief guide <https://docs.google.com/document/edit?id=1w0TXTq5VuIzQxGYq9vO0CJRER3JJr6tKmwwaCzyGrXs&authkey=CKnGk_ML&hl=en#> , prepared by our colleague Paul Heilporn and others:https://docs.google.com/document/edit?id=1w0TXTq5VuIzQxGYq9vO0CJRER3JJr6tKmwwaCzyGrXs&authkey=CKnGk_ML&hl=en# <https://docs.google.com/document/edit?id=1w0TXTq5VuIzQxGYq9vO0CJRER3JJr6tKmwwaCzyGrXs&authkey=CKnGk_ML&hl=en#> By 31 December 2010, there will be a much more exhaustive online presentation to consult. But in the meantime: (1) Go to http://papyri.info/editor/signin <http://papyri.info/editor/signin> and sign in (you will be presented with instructions). (2) You will be brought to your ‘dashboard’, where you will see options allowing you to emend an existing publication (say, correct / emend a text already in the DDbDP, or add a text where there is now only an HGV record, but no DDbDP text) or create a new publication (to publish directly to the DDbDP, or add records for newly published texts that are not yet even in HGV). (2b). to add a text where an HGV record exists but the DDbDP text does not yet. Under ‘Emend Existing Publication: select HGV, select series name, enter volume number (leave blank if no volume), enter text number. Click ‘Emend.’ This will open a view of the HGV record. Click on ‘Overview’; on the overview page, click ‘create new text’. (To see whether anyone has already decided to enter this text, check the ‘Overview’ page; please request also access to the googleDoc <https://spreadsheets1.google.com/ccc?key=t89MG70BXJ_dgGhUlfYrgCg&hl=en#gid=0> to help us keep track of progress: https://spreadsheets1.google.com/ccc?key=t89MG70BXJ_dgGhUlfYrgCg&hl=en#gid=0 <https://spreadsheets1.google.com/ccc?key=t89MG70BXJ_dgGhUlfYrgCg&hl=en#gid=0> . In this page we are keeping track of what needs to be entered and what is being entered ... even now, via SoSOL). (3) You will be brought to a window containing a slightly strange looking representation of the Greek text. Much will look normal (say, ἐπιμ[ελὲς δέ σ]οι); some will look odd (say, <:πεπονηκέναι|orth|πεπονεκέναι:>). This unusual syntax is called Leiden+, since it is basically the standard Leiden sigla, plus a number of others that are necessary in order to mark up the DDbDP more fully. (3a) Why do we need Leiden+? In order to be able to display, say, πεπονηκέναι in a text followed by a footnote and accompanying apparatus entry indicating that the scribe wrote πεπονεκεναι, the computer needs to be fed quite a lot of information. The underlying markup for this bit of papyrological logic is “πεπονηκέναιπεπονεκεναι.” Now, we assume that no DDbDP user will want to enter all of that, and so we use Leiden+ as a kind of shorthand, to facilitate entry: <:πεπονηκέναι|orth|πεπονεκέναι:>. So under Leiden+
(ἰσιεί(ου)) is the shorthand for ἰσιείου and is displayed by the PN as ἰσιεί(ου)
κ.2[.8] is the shorthand for κ and is displayed by the PN as κ ̣ ̣[ ̣ ̣ ̣ ̣ ̣ ̣ ̣ ̣]
<#κϛ=26#> is the shorthand for κϛ is displayed by the PN as κϛ.
(3b) Comprehensive documentation of the Leiden+ conventions can be found online: http://papyri.info/editor/documentation <http://papyri.info/editor/documentation> . (4) Once you have added your new text or proposed an emendation or correction to an existing one, and have saved your changes, you may submit it to the Editorial Board by clicking on “Overview” justifying the changes/additions that you have made, and clicking “Submit to Boards.” Then the rotating DDbDP Editorial Board (currently Rodney Ast, James Cowey, Paul Heilporn, Todd Hickey, Cisca Hoogendijk, Josh Sosin) will vote on the change and either add it to the canonical copy of the publication, or else return it to the submitter (in case of error). A Board of Senior Editors (still in formulation) will be consulted in case of especially puzzling problems in texts, on the model of journal referees. (5) Similar processes can be followed in the case of HGV metadata records and translations of documents. Rather than continue at length, I’ll just offer the following invitation: next time you spot a typo in the DDbDP, log on to SoSOL, call up the text, make the correction, and submit it to the editors. If you aren’t quite sure whether you have used Leiden+ correctly, just let us know in your submission comments. We’ll have a look, and the system will automatically send you our comments. The first few times are a bit confusing, but the fastest way to get comfortable with the system is just to use it. It is pretty intuitive once you are familiar with it. If you need help, feel free to email any or all of the editors. If the demand is sufficient, we shall be more than happy to hold web seminars or the like. And, as part of IDP3 we shall hold 2 training sessions in London in the Spring/Summer of 2011. -- Associate Professor, Classical Studies, Duke University Director of Undergraduate Studies Associate Editor, Greek, Roman and Byzantine Studies Co-Director, Duke Data Bank of Documentary Papyri