Theme: Mutation

This is a collection of Sandwalk posts on mutation starting in 2007. The latest ones are at the bottom of the list.

March 27, 2007
Silent Mutations and Neutral Theory
Neutral Theory and random genetic drift explains variation and it also explains molecular evolution and the (approximate) molecular clock. There are no other explanations that make sense and nobody has offered a competing explanation since Motoo Kimura (1968) or Jack King and Thomas Jukes (1969) published their papers almost fifty years ago. (Aside from occasional nitpicks, of course. There are always scientists who like to show that some mutations that were thought to be neutral are actually beneficial or deleterious. None of them have mounted a serious claim that most variation or most of molecular evolution can be explained by natural selection.)

April 19, 2007
Haldane's Dilemma
This is very interesting. Dembski has teamed up with Walter ReMine, demonstrating once again that the old addage "opposites attract" does not apply to kooks.

ReMine has an article on Uncommon Descent where he pushes his usual whine about evil scientists and how their world-wide conspiracy has kept him from revealing the fatal flaw in evolution [Evolutionist withholds evidence on Haldane’s Dilemma]. I can see how similar this is to Intelligent Design Creationism.

Read more »

Dramatic Irony

From Wikipedia [irony] ...

Irony (from the Ancient Greek εἰρωνεία eirōneía, meaning dissimulation or feigned ignorance) is a rhetorical device, literary technique, or situation in which there is an incongruity between the literal and the implied meaning....

In dramatic irony, the author causes a character to speak or act erroneously, out of ignorance of some portion of the truth of which the audience is aware. In other words, the audience knows the character is making a mistake, even as the character is making it. This technique highlights the importance of a particular truth by portraying a person who is strikingly unaware of it.

The funny thing about irony (and sarcasm) is that there are so many people who are irony-deficient. They just don't get it. They seem to be incapable of recognizing anything other than the literal meaning of a statement. Look at the example given in the Wikipedia article (right figure). Then look at yesterday's Jesus and Mo cartoon (below). Both are excellent examples of intended irony.

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Citation Chart

This is pretty cool. You can ask Google Scholar to collect all citations to your published articles and display them as a chart [Citations]. I don't have a lot of citations but it's still fun to see them.

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[Hat Tip: Ford Denison of This Week in Evolution: A citation a day keeps ideas in play. He has hundreds of citations every year.]

Defending Homeopathy?

Timothy Caulfield published a nice article in The national Post last week where he lambasted naturopathy and homeopathy [Don’t legitimize the witch doctors]. Here's part of what he said ...

Allow me to lay my admittedly love-of-science, rant-tainted cards on the table. In general, the services provided by naturopaths reside either in the realm of commonsense lifestyle advice (get lots of sleep, eat well and stay active) or they have little empirical evidence to support their use. In fact, many naturopathic practices are based on a semi-spiritual theory (the healing power of nature), and have no foundation in science. They reside largely in the realm of pseudoscience.

Am I being too harsh? I recently worked with a University of Alberta colleague on an analysis of the websites for the naturopaths in Alberta and British Columbia. We wanted to get a sense of what is being offered to the public. In Alberta, the number one most commonly advertised service is homeopathy.

Homeopathy has been around for hundreds of years. The basic philosophy behind the practice is the idea of “like cures like.” A homeopathic remedy consists of a natural substance — a bit of herb, root, mineral, you get the idea — that “corresponds” to the ailment you wish to treat. The “active” agent is placed in water and then diluted to the point where it no longer exists in any physical sense.

In fact, practitioners of homeopathy believe that the more diluted a remedy is, the more powerful it is. So, if you subscribe to this particular worldview, ironically, you want your active agents to be not just non-existent, but super non-existent.

The bottom line: For those of us who reside in the material world, where the laws of physics have relevance, a homeopathic remedy is either nothing but water or, if in capsule form, a sugar pill.

There are people who don't live in the material world and they always pop out of the woodwork whenever their favorite superstitions are questioned. In this case, it's a homeopath named Karen Wehrstein who was given space on the newspaper website to respond to Timothy Caulfield [Homeopathy offers hope]. Wehrstein is described as ....

Karen Wehrstein is the executive director of the Canadian Consumers Centre for Homeopathy (homeocentre.ca), an organization formed in 2011 to educate the public about homeopathy and advocate for freedom of choice in health care.

In other words, she's a lobbyist for quackery. She runs the Homeopathy Centre of Muskoka. Here's part of what she has to say ...

Homeopathy’s big stumbling block to acceptance is that its medicines are diluted so much that people outside of the field can’t understand how they can possibly have an effect. There are, however many scientists who do have that expertise. So many, that there is an entire journal devoted to the field, the International Journal of High Dilution Research. And they seem to be getting intriguingly close to providing definitive answers.

Opponents of homeopathy claim that homeopathic medicines are “just plain water” with no medicinal properties. But increasing numbers of scientific findings are making it harder to maintain such as stance. One study has found that solutions prepared in the traditional homeopathic way — through repeated dilutions by mechanical shaking — have properties unlike plain water, with elements of the dissolved material. Another study suggests the solutions have an affect on living cells in vitro. Yet another study shows that solutions can be distinguished from each other, using the right equipment to determine their contents. And emerging research suggests that homeopathic solutions actually contain nanoparticles of the original dissolved material.

Students who have taken my course will recognize this kind of response. Science is so overwhelmingly respected these days that nobody can afford to be on the wrong side of scientific evidence. If you are defending quackery then you only have two choices; either you discredit the evidence against you or you make up scientific evidence to support your position. Most quacks do both. They end up simultaneously disparaging and praising scientists who work in the field.

If you're interested in the scientific truth and why Karen Wehrstein is so very wrong, then you can do no better that read what Diane Sousa has to say on Skeptic North where she takes apart all of Wehrstein's claims [A Response to Karen Wehrstein: Homeopathy Offers Hope but Delivers Only Sweet Nothings].

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Should Chilliwack BC Permit Distribution of Bibles in Public Schools?

Here's a notice from the BC Humanist Association.

Recent secular victories in Chilliwack are at risk.

On November 13th, the Board of the Chilliwack School District deleted Regulation 518 that stated, "The Board approves the distribution of Gideon Youth Testaments to Grade 5 pupils with parental consent." At the same meeting, the Board agreed to draft a new policy to permit the "distribution of materials" by March 2013.

This new policy represents an attempt to use public schools for religious proselytizing in BC public schools.

Superintendent Evelyn Novak intends to gather feedback through February to draft the new policy. While this feedback may not be open to the public, secular voices will be heard.

Please sign the petition below to send the message to the Chilliwack School Districts that BC schools should remain secular.

Sign the Petition. You will have to identify yourself but that shouldn't be a problem if you really believe in a secular school system.

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[Hat Tip: Veronica Abbas at Canadian Atheist.]

Guelph Biology Students

Here are the biology students at the University of Guelph (Guelph, Ontario, Canada) dancing and singing to "Anna Sun" by Walk the Moon.

I love this stuff. Some of these students are going to be scientists some day.

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[Hat Tip: Ryan Gregory, Professor, University of Guelph.]

New Premier of Ontario: Kathleen Wynne

Last night the Liberal Party of Ontario selected a new leader, Kathleen Wynne. Since it's the governing party, she automatically becomes the Premier of Ontario.¹ I was hoping she would be chosen but in the last few weeks it looked like her opponent, Sandra Pupatello, was going to win.

Kathleen Wynne represents the leftish wing of the Liberal Party of Ontario and that's the view I support. Wynne becomes the first women Premier of Ontario and she joins five other women who lead provincial/territorial governments in Canada. As of today, almost 90% of Canadians live in provinces headed by a woman!

Kathleen Wynne is also the first openly gay person to head a provincial government. She is married to Jane Rounthwaite.² Her sexual orientation wasn't really much of an issue during the campaign. Here she is, thanking her partner Jane during the acceptance speech last night.

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1. Subject to approval by the Lieutenant Governor.
2. Same-sex marriage has been legal in Ontario since 2002.

How Many Genomes Have Been Sequenced?

There are several types of genome sequence. Some are relatively incomplete and they don't really count. Others have been thoroughly sequenced and we have a good permanent draft sequence. The best ones are the "finished" genome sequences where the preliminary drafts have been checked and gaps have been filled.

How many "finished" or permanent draft complete genome sequences have been published?

How many of them are eukaryotes?

Here are the answers from: GOLD

(Apologies for the Three Domain influence.)

Archaea: 181
Bacteria: 3762
Eukaryotes: 183

Why are there so few eukaryotes? Because many eukaryotic genomes are very large and it takes a lot more work to sequence that much DNA. Furthermore, many eukaryotic genomes are full of junk DNA and it's difficult to sequence and assemble repetitive regions in order to get a complete chromosome. The bottom line is money—for most labs it's too expensive to sequence the genome of their favorite eukaryote but it can be quite cheap these days to sequence a bacterial genome.

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[Hat Tip: Jonathan Eisen]

Why You Should Become a Postdoc Instead of Taking a Job in the Private Sector

Eric Lewellyn is an enthusiastic postdoc in the Drubin/Barnes Lab at US Berkeley. (They work on membrane trafficking.)

Eric tries to convince you to stay in university using song and dance. He describes all the good things about slaving away enjoying science in a research lab. I don't know Eric but I have met his mother—she's the cousin of one of our best friends.

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What Does the Liberal Party of Canada Stand For?

I've long been a supporter of the Federal Liberal Party of Canada. It's the party of Mike Pearson and Pierre Elliot Trudeau—two Prime Ministers that I greatly admire. I even like Jean Chrétien!

Lately I'm having trouble understanding what the Liberal Party stands for. They've just had two leaders (Michael Ignatieff, and Bob Rae) who are complete mysteries to me. I really don't know what they stand for, or what they're passionate about.

Apparently I'm not alone. Here's the view of Thomas Walkom from a column in the Toronto Star a few days ago [Do Canada’s, or Ontario’s, Liberals matter any more?].

On the other hand, it’s not clear what the Liberals represent any more. They would like voters to think of them as the non-Conservatives — the alternative to Stephen Harper federally or to Tim Hudak in Ontario.

But are they?

Paul Adams, an astute political observer writing in iPolitics, argues that the federal Liberals have transformed themselves into the old Progressive Conservatives, socially progressive but fiscally to the right.

I’d go further. I reckon the old PCs of Joe Clark would find federal Liberal leadership candidate Martha Hall Findlay’s talk of dismantling farm marketing boards a bit too right-wing for their tastes

Similarly, Liberal front-runner Justin Trudeau’s enthusiastic embrace of the Alberta oilsands would probably be seen as a tad naive by the Red Tories of former Ontario premier Bill Davis, most of whom believed that strong business required equally strong regulation.

As a party, the Liberals haven’t had a new idea since the 1980s. Individual party members have (Stéphane Dion’s green shift comes to mind).

But the party, as a whole never signed onto Dion’s environmental agenda. Nor has it signed onto anything else.

The Liberals talk of holding policy conventions that would replicate that golden period of the 1960s, when the party embraced medicare, public pensions and welfare reform.

But they never do. Former federal leader Michael Ignatieff hosted a thinkers’ conference that headlined prominent conservatives. Nothing came of it.

The conventional wisdom among Liberals is that strong policy positions should be avoided at all costs in order to avoid alienating voters. Instead, Liberals prefer to talk about what they call values.

We've been discussing this issue with our former Liberal MP, Omar Alghabra, who happens to be a member of Justin Trudeau's team. Justin, for those of you who don't follow Canadian politics, it the son of Pierre Elliot Trudeau and he's running for the leadership of the Federal Liberal Party. We want Justin, and all the other candidates, to speak out on what the Liberal Party stands for.

Omar sent us a link to this video. It's obvious that Justin is avoiding the question. He stands for some trivial issues like legalizing marijuana but what about the bigger issues? How do I tell the difference between the Liberal Party and Conservative Party or the New Democratic Party? I don't think I can vote for Justin Trudeau or for any of the other leadership candidates. In fact, I'm not sure I can vote for the Liberal in the next election. The NDP is looking very attractive.

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What Is Science? - Still No Answer!

We had a fun meeting last night thanks to Rufina Kim [WTF Is Science?]. A bunch of students showed up along with Steve Livingston, the new co-Chair of CASS (Committee for the Advancement of Scientific Skepticism), and David Bailly, Chair of The Association for Science and Reason (Skeptics Canada).

Unfortunately we were not able to come to an agreement on "What Is Science."

Now we have to meet again in a couple of weeks!

We talked about whether there was a scientific method and whether falsifiability is part of the definition of science. The Wikipedia article on falsifiability is a good place to look for background information. Here are two sections from that article to get you started.

Paul Feyerabend examined the history of science with a more critical eye, and ultimately rejected any prescriptive methodology at all. He rejected Lakatos' argument for ad hoc hypothesis, arguing that science would not have progressed without making use of any and all available methods to support new theories. He rejected any reliance on a scientific method, along with any special authority for science that might derive from such a method. Rather, he claimed that if one is keen to have a universally valid methodological rule, epistemological anarchism or anything goes would be the only candidate. For Feyerabend, any special status that science might have derives from the social and physical value of the results of science rather than its method.

...

In their book Fashionable Nonsense (published in the UK as Intellectual Impostures) the physicists Alan Sokal and Jean Bricmont criticized falsifiability on the grounds that it does not accurately describe the way science really works. They argue that theories are used because of their successes, not because of the failures of other theories. Their discussion of Popper, falsifiability and the philosophy of science comes in a chapter entitled "Intermezzo," which contains an attempt to make clear their own views of what constitutes truth, in contrast with the extreme epistemological relativism of postmodernism.

Sokal and Bricmont write, "When a theory successfully withstands an attempt at falsification, a scientist will, quite naturally, consider the theory to be partially confirmed and will accord it a greater likelihood or a higher subjective probability. ... But Popper will have none of this: throughout his life he was a stubborn opponent of any idea of 'confirmation' of a theory, or even of its 'probability'. ... [but] the history of science teaches us that scientific theories come to be accepted above all because of their successes." (Sokal and Bricmont 1997, 62f)

They further argue that falsifiability cannot distinguish between astrology and astronomy, as both make technical predictions that are sometimes incorrect.

There's no such thing as a universal scientific method and falsifiability doesn't describe how the scientific way of knowing actually works.

I made up an example of a Professor of English whose research focuses on how the English language actually sounded in the time of Geoffrey Chaucer (about 1370)¹. Is she doing science? If not, what kind of way of knowing is she using?

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1. This is roughly the time of World Without End. If the characters actually spoke in 14th century dialect we probably wouldn't have understood a word.

e-sequence: Musical Mss.

e-sequence
Audiovisuelle digitale Repräsentation von Sequenzen Notkers des Stammlers († 912) aufgrund ausgewählter Handschriften.

Im Zeitalter der Karolinger im 9. Jahrhundert wurde mit den Neumen eine Notenschrift entwickelt, die den liturgischen Gesang, den so genannten Gregorianischen Choral und seine Erweiterungen wie die Sequenz, erstmals in entscheidend neuer Weise, nämlich dem genauen agogischen Verlauf entsprechend, aufzeichnen konnte. Obwohl die Musik, die im 9. und 10. Jahrhundert das Kloster St. Gallen erfüllte, längst verklungen ist, bieten die St. Galler Handschriften wertvolle Anhaltspunkte, diese heute wieder zum Leben zu erwecken. Durch ein sorgfältiges Studium der Handschriften zusammen mit den neuen digitalen Techniken ist es möglich, die Musik des Gallusklosters so weit als möglich zu rekonstruieren, die velorenen „soni“ wieder zu finden.

Teaching Developmental Biology

PZ Myers posted some lecture notes from his developmental biology course [What I taught today: molecular genetics and basic concepts ]. Here's part of what he said ...

Think about that. In the early days of developmental biology, we didn’t even know whether there was differential gene activity or not; it was considered a reasonable possibility that all the genes were just doing their work, whatever it was, all the time in every cell, and that differences between cells emerged farther downstream, in biochemical interactions. But they knew this was an important question. They knew that we had to look at the activity of individual genes…they just didn’t have the tools yet. So it was back to hacking up embryos and trying to infer causes from aberrations.

The change emerged gradually, but there were a couple of watershed moments where everyone looked up and noticed that hey, we do have ways of looking at genes directly. One was the work of Ed Lewis, a most excellent geneticist who used the tools of genetics to look directly at mutations that caused changes in fly morphology, in the 1960s. This was amazing stuff — the papers he wrote were beautiful and complex and very, very genetical — but it was written in a language that most developmental biologists of the day were unprepared to read. They were genetics papers. But I think they laid a foundation: if you want to do development, you’d better learn about genetics.

The second big event was the saturation mutagenesis screen of Christiane Nusslein-Volhard and Eric Wieschaus, about 20 years later. This work was also built on an understanding of genetics, but also used the tools of molecular biology. It was another lesson: if you want to do development, you’d better learn about molecular biology.

I used to teach this stuff in the 1980s and I certainly agree with PZ that you need to understand molecular biology and gene expression.

When it came time to write my first textbook I incorporated the examples I had used in class. The first ones I described were: the early to late switch in gene expression in bacteriophage T4, sporulation in Bacillus subtilis, and the genetic switch in bacteriophage lambda. These were well-studied examples from experiments carried out in the 1970s. They teach fundamental concepts in developmental biology and they have an additional advantage; namely, they get students thinking about species that aren't animals.

These are still excellent examples that are well-understood at the molecular level. They are much easier to understand than Drosophila or plants. Unfortunately, we've educated an entire generation of developmental biologists who have never heard of these elegant examples.

Is this a good thing or a bad thing? Do students need to know the real history of developmental gene expression as worked out by scientists who studied phage and bacteria?

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What's Wrong with These Sentences?

Here's a short paragraph containing three sentences from my textbook (page 584). Is there anything wrong with any of these sentences?

Under physiological conditions, double-stranded DNA is thermodynamically much more stable than the separated strands and that explains why the double-stranded form predominates in vivo. However, the structure of localized regions of the double helix can sometimes be disrupted by unwinding. Such disruption occurs during DNA replication, repair, recombination, and transcription.

Having trouble seeing where I went wrong, according to some people? Check out this and this.

Oh, and don't forget this.

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Onion Talks: Social Media

Everyone knows about TED talks (Ideas Worth Spreading). They know that TED talks are "riveting talks by remarkable people." Or at least that's what they would like to believe [TED Tries to Clean Up Its Act].

Here's some worthy competition to TED talks from The Onion. It's title is Using Social Media To Cover For Lack Of Original Thought.

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[Hat Tip: Mike the Mad Biologist]

The Revisionaries Is Coming to Television

The Revisionaries is a documentary about the Texas state board of education and their attempt to suppress science in Texas public schools.

It will be aired on PBS starting January 28th. It's due to be broadcast in my area (WNED) on Feb. 3, 2013 at 11pm and on Feb. 8, 2013 at 4am.

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[Hat Tip: Mike the Mad Biologist]

DM: Dr. Mohamed El-Ashery (العشيري)

Prof. Magdy Ali sent out this obituary:

We have lost a very nice, decent and good friend on Tuesday night, January 15th Dr. Mohamed El-Ashery was born August 26 1961. He was working in Helwan University, Cairo. Mohamed was very helpful colleague and very respected friend. It is really a big loss. May ALLAH have mercy on his soul. Mohamed was buried yesterday in Cairo. We already miss him. To the colleagues of our list who do not know Mohamed El-Ashery, he was the third generation of the Egyptian papyrologists after Prof. Zaki Aly then Prof. Sayed Omar, Prof. Alia Hanafi and of course the late Prof. Abd Allah el-Mosallamy. He was extraordinary Greek papyri reader.

Monday's Molecule #198

The last "Monday's Molecule" was 2R,3S-isocitre [Monday's Molecule #197]. The winner was Evey Salara. She's probably too far away to come for lunch.

This week's molecule is very strange looking but it serves a very important role in some species. What is the molecule, what species have it, and what does it do?

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Read more »

Vote for Your Favorite Theory of Evolution!

I'm conducting a poll on topics that some people would like to add to modern evolutionary theory in order to create an "extended" modern synthesis [Which subjects need to be added to current evolutionary theory to create a new extended synthesis?].

So far there are almost 200 votes and "EvoDevo" is leading the pack (Boo!). I'm delighted to see that "Nonadaptive Evolution of Complexity" is getting a substantial number of votes. It suggests that there are people who really do understand Michael Lynch and Eugene Koonin (among others).

"Epigenetics" is way too popular. It is NOT an addition to evolutionary theory, in my humble opinion.

Nobody has voted for "Theistic Evolution."

VOTE NOW!

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WTF Is Science?

Join us for a discussion about science and its relevance in the real world. This group will meet regularly every few weeks and it's open to everyone.

The topic for the first meeting is "What Is Science?" Check out the facebook page at: WTF Is Science?.

Wednesday, January 23, 2013 at 6pm.
Room 5243, Medical Sciences Building (5th floor)

You are welcome to bring food and (non-alcoholic) drinks.

Here are some definitions of science from the Oxford English dictionary.

1. The state or fact of knowing; knowledge or cognizance of something specified or implied; also, with wider reference, knowledge (more or less extensive) as a personal attribute.
2. Knowledge acquired by study; acquaintance with or mastery of any department of learning. Also +pl. (a person's) various kinds of knowledge.
3. A particular branch of knowledge or study; a recognized department of learning.
4. In a more restricted sense: A branch of study which is concerned either with a connected body of demonstrated truths or with observed facts systematically classified and more or less colligated by being brought under general laws, and which includes trustworthy methods for the discovery of new truth within its own domain.
5. The kind of knowledge or of intellectual activity of which the various `sciences' are examples. In early use, with reference to sense 3: What is taught in the schools or may be learned by study. In mod. use chiefly: The sciences (in sense 4) as distinguished from other departments of learning; scientific doctrine or investigation. Often with defining adj. as in 4 b.

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"Multispectral documentation and image processing analysis of the papyrus of tomb II at Daphne, Greece"

Multispectral documentation and image processing analysis of the papyrus of tomb II at Daphne, Greece
Journal of Archaeological Science (February 2013), 40 (2), pg. 1242-1249 
Athina A. Alexopoulou; Agathi-Anthoula Kaminari; Athanasios Panagopoulos; Egert Pöhlmann



Abstract
This paper refers to the study of an ancient papyrus, dated ca. 420/430 BC, found in 1981 during an excavation at Daphne, Athens, Greece, using multispectral imaging combined with image processing analysis. It was assumed that the papyrus contained ancient Greek musical notation but the condition of the object hindered the drawing of any conclusion based only on visual examination. This fact, combined with the significance of the object itself, as it is the oldest papyrus which carries Greek text, pointed to the application of non-invasive techniques to enhance its readability. The multispectral imaging carried out in the range of 420–1000 nm enabled the detection of more letters on surface layers, at various places and orientations. False colour imaging proved to yield better results in distinguishing the letters compared to single wavelength recording. In some cases, letters from several layers underneath are revealed in the infrared. The letters present different greylevels according to the layer they belong. An interesting result coming from a simple subtraction of the infrared image at 1000 nm from the visible one at 660 nm is that different layers of the papyrus can be distinguished. The Application of Principal Component Analysis (PCA) showed that the best results, as far as the extraction of the letters from the background is concerned, are obtained when the second and the third images are merged. The automatic extraction of the letters is feasible to some extent but there is a certain amount of noise with similar characteristics that cannot be removed.

Highlights
► Deteriorated papyrus from ancient Greek tomb was studied using non-invasive methods. ► Visible–infrared multispectral- and infrared false colour imaging were applied. ► Text from underlayers was detected and legibility was overall improved. ► Image processing helped in distinguishing letters and differentiate script layers.

See also Musical finds from the Tomb of the Poet, and their interpretation

A significant archaeological find came to light some thirty years ago in Daphne, Attica. The so-called Tomb of the Poet dates back to the classical era (around 430 BC) and the excellent condition of the grave goods yielded valuable information to archaeologists – especially concerning music and musical instruments in ancient times.

Herd Immunity

Have you ever heard anyone say that they don't need to get a vaccination because they never get the disease and, even if they do, it's never very serious?

That's fine if the only person you care about is you. Maybe you live in a cave. Maybe you never visit old people in a retirement home. Maybe you are never near babies. Maybe you don't have a spouse or a partner. (I can't imagine why such a self-centered person would not have a partner.)

Or maybe you just don't understand the concept of herd immunity. Ignorance can be cured ....

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[Hat Tip: Mike's Weekly Skeptic Rant]

That's Extraordinary! Homeopathy

Here's a new video from Centre for Inquiry, Canada. Homeopathy is ridiculous, pseudoscientific, nonsense. It's about time that all intelligent people recognized this fact. Tell your friends.

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The NRA Anti-Obama Ad

If you live outside of the USA you may not have seen this television ad paid for by the National Rifle Association.

It's tantamount to a declaration of war on the issue of gun control. What this means is that there is no compromise or middle ground with these people. I hope Obama accepts the challenge and takes on the gun lobby. Last I heard, they were not a democratically elected part of the legislature.


BTW, if members of the NRA are really interested in protecting their children from the risk of being killed by guns then they should send them to school in the UK. Even Canada would be better.

Here's another version of the ad.

NRA - Stand and Fight Parody - watch more funny videos

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[Hat Tip: Pharyngula]

Which subjects need to be added to current evolutionary theory to create a new extended synthesis?

Here's a list of subjects that have been proposed as extensions to the so-called "Modern Synthesis" of evolution. Some of them are radical changes and others are more subtle.

I'm not going to explain all of them because that would take many posts and a lot of time. Besides, most of them have been openly debated on numerous blogs over the past decade or so.

Choose the one(s) that you think are the most important.

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«Papyrologica Lupiensia» 20-21 (2011-2012)

Nuova pubblicazione del Centro di Studi Papirologici dell’Università del Salento, Lecce

«Papyrologica Lupiensia» 20-21 (2011-2012), Pensa Multimedia, Lecce 2013, pp. 266.

INDICE GENERALE

MARIO CAPASSO, Per Paolo Radiciotti.

MARIO CAPASSO, La noia di Jacqueline.

GIANLUCA DEL MASTRO, Il PHerc 566: L’Echelao di Epicuro.

DARIO INTERNULLO, Cicerone latino-greco. Corpus dei papiri bilingui delle Catilinarie di Cicerone.

NATASCIA PELLÉ, Il restauro dei papiri ossirinchiti greci della Sackler Library di Oxford. Prima campagna (2012).

ELINE SCHEERLINCK, Inheritance disputes and violence in women’s petitions from Ptolemaic Egypt.


Schede bibliografiche e recensioni

Mario Capasso, Scrinia curva. VIII.

Serena Ammirati-Paolo Radiciotti, Palaeographia Papyrologica. X (2011).

Paola Gagliardi, Rassegna bibliografica sul papiro di Gallo (anni 2004-2012).

Libri ricevuti
Notiziario

ISSN 1591-2140
Prezzo:
Euro 32,00


Distribuzione:
Pensa Multimedia s.r.l.
Via A.M. Caprioli, 8
 73100 Lecce
Tel. 0832.230435
Fax 0832.230896
info@pensamultimedia.it


Per cambi rivolgersi a
Centro di Studi Papirologici dell’Università del Salento
Via V.M. Stampacchia, 45
73100 Lecce
cspapiri@unisalento.it

50th Anniversary of Ramachandran Plots

This year marks the 50th anniversary of the publication of Ramachandran plots (Ramachandran 1963).

Don't know what I'm talking about? Read Ramachandran Plots.



THEME:

More posts on
Protein StructureChirag Vora was kind enough to alert me to this anniversary. Check out his blog at: Golden Jubilee of Ramachandran Plot.

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Ramachandran, G. N., Ramakrishnan, C. T., and Sasisekharan, V. (1963) Stereochemistry of polypeptide chain configurations. Journal of molecular biology, 7:95-99.

CONFERENCE: Observing the Scribe at Work: Knowledge Transfer and Scribal Professionalism in Pre-Typographic Societies

Observing the Scribe at Work: Knowledge Transfer and Scribal
Professionalism in Pre-Typographic Societies
Macquarie University, Sydney
27-28 September 2013

Prior to the typographic revolution of the 15th century, the figure of the scribe was one of the keys by which civilisations were able to disseminate their power, culture and beliefs beyond their geographic, temporal, and even linguistic limits. Our access to the pre-modern world is mediated by the material and technological remains of scribal activity, the manuscript as an artefact of culture and administration. Every text preserved prior to the advent of printing bears witness to the activities of scribes. Yet as a social and professional group they are frequently elusive, obscured by other professional titles, reduced to mention in a colophon, or existing within a private sphere into which our sources do not reach. While much attention has been given to the scribe as a literary figure, the manuscripts offer a unique point of access to this group without the distortions of the literary tradition. This perspective, however, has frequently been restricted to a catalogue of errors, reducing the scribe to the transmission of an acceptable text, without recourse to the physical characteristics of the manuscript itself.

This workshop is built around the Australian Research Council funded project ‘Knowledge Transfer and Administrative Professionalism in a Pre-Typographic Society: Observing the Scribe at work in Roman and Early Islamic Egypt’. The project sets aside the often futile search for the historical figures of the scribe in favour of a focus on observable phenomena: the evidence of their activity in the texts themselves. Recognizing that the act of writing can be a quotidian and vernacular practice, it explicitly includes the documents of everyday life as well as the realms of the copying of literature, seeking paths back to an improved understanding of the role and place of scribes in pre-modern societies.

‘Observing the Scribe at Work’ will bring together specialists in pre-modern societies of the Mediterranean world and adjoining cultures, from the ancient Near East, through the Egyptian and Classical worlds to Byzantium and Renaissance Europe. The papers will contribute to a deeper understanding of the processes that drive the operation of pre-printing cultures, and transmit knowledge and traditions forward in human societies.

The workshop will be held at Macquarie University on 27-28 September 2013. Macquarie University cannot offer full funding for all participants traveling to Australia from overseas, but partial financial assistance will be awarded to select abstracts which closely address the themes of the workshop. Decisions to this
effect will be made by the end of April. 

We call for abstracts of up to 300 words that address the objectives of this workshop. These should be sent to jennifer.cromwell@mq.edu.au by 31 March 2013.

Inquiries: Malcolm Choat (malcolm.choat@mq.edu.au); Jennifer Cromwell (jennifer.cromwell@mq.edu.au)

Organising Committee
Malcolm Choat, Jennifer Cromwell, Korshi Dosoo, Rachel Yuen-Collingridge

Sponsors:
Australian Research Council
Macquarie University
Faculty of Arts, Macquarie University
Macquarie University Ancient Cultures Research Centre 

Drive-Thru at Timmy's

It's been ages since I've posted anything about the Canadian institution known as Tim Hortons. Here's a photo from cheezeburger.

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[Hat Tip: David Schuller.]

Why Do the IDiots Have So Much Trouble Understanding Introns?

Most eukaryotic genes have introns. Introns make up about 18% of the DNA sequences in our genome. Most of these sequences are junk but introns are functional and up to 80bp of each intron is required for proper splicing. The essential sequences contain the 5′ splice site (~10 bp); the 3′ splice site (~30 bp): the branch site (~10 bp); and enough additional RNA to form a loop (~30 bp). The branch site and the splice sites are where specific proteins bind to the mRNA precursor [Junk in Your Genome: Protein-Encoding Genes]. It turns out that within introns about 0.37% of the genome is essential and about 17% is junk.


Read more »

What? Me Worry?

Alfred E. Neuman may not have had a care in the world but most of us worry about something. John Brockman of The Edge asks his bevy of followers this question for 2013: 2013: WHAT *SHOULD* WE BE WORRIED ABOUT?.

You'd think that most of the responses would be along the lines of global climate change, poverty, disease, crime, war, or the possibility that Earth might be destroyed by an asteroid impact. You'd think that the treatment of women in third (and second) world countries and the fanaticism of religious extremists might generate more than a few responses.

You would be wrong.

Here's what the best minds in the Western world came up with. I read most of them and I don't think I'll lose any sleep over any of these worries. I will, however, continue to lose sleep over women being raped in India and young children being shot to death in Connecticut.

Chinese Eugenics
What We Learn From Firefighters
That We Won't Make Use Of The Error Catastrophe Threshold
A Fearful Asymmetry: The Worrying World Of A Would-Be 'Science'
Misplaced Worries
We Are In Denial About Catastrophic Risks
The Disconnect
Unfriendly Physics, Monsters From The Id, And Self-Organizing Collective Delusions
Worry About Internet Drivel
We Don't Do Politics
The Black Hole Of Finance
The Opinions Of Search Engines
The Mating Wars
Computer-Generated Fascism
Who's Afraid Of The Big Bad Words?
Data Disenfranchisement
The Patience Deficit
The Underpopulation Bomb
Big Experiments Won't Happen
"Smart"
What—Me Worry? by Craig Venter (one of the few decent responses)
The Promise Of Catharsis
I've Given Up Asking Questions
The Anthropocebo Effect
The Relative Obscurity Of The Writings Of Édouard Glissant
The Danger Of Inadvertently Praising Zygomatic Arches
The Loss Of Death
One Universe
The Rise Of Anti-Intellectualism And The End Of Progress
Applying Classic Science To Understand "Modern States" Shaped By Crime
Lamplight Probabilities
What Is Conscious?
Men
Science By (Social) Media
Unmitigated Arrogance
Technology May Endanger Democracy
"The Singularity": There's No There There
MADness
Blown Opportunities
The Power Of Bad Incentives
Quantum Mechanics
Are We Homogenizing The Global View Of A Normal Mind?
Science Publishing
Is The New Public Sphere... Public?
World As We Know It
Stress by Arianna Huffington, who is one of the important causes of stress
Science Has Not Brought Us Closer To Understanding Cancer
Losing Touch
The Human-Nature Divide
Are We Becoming Too Connected?
Putting Our Anxieties To Work
Incompetent Systems
Too Much Coupling
Power And The Internet
Close To The Edge
The End Of Fundamental Science?
The Paradox Of Material Progress
The Fragility Of Complex Systems by Randolph Nesse, worth a read
Rats In A Spherical Trap
Close Observation And Description
Global Greying
The Fourth Culture
The Coming Fight Between Engineers And Druids
Impact
The Complex, Consequential, Not-So-Easy Decisions About Our Water Resources
Children Of Newton And Modernity
The Teenage Brain
Augmented Reality
Where Did You Get That Fact?
Social Media: The More Together, The More Alone
Is Idiocracy Looming?
The Disconnect Between News And Understanding
Objects Of Desire
Say It Ain't So
Being Told That Our Destiny Is Among The Stars
Global Cooperation Is Failing And We Don't Know Why
Morbid Anxiety
Worrying About Children
A Synthetic World
The Death Of Mathematics
Losing Our Hands
Internet Silos
The New Age Of Anxiety
Does The Human Species Have The Will To Survive?
All The T In China
Neural Data Privacy Rights
Armageddon
No Surprises From The LHC: No Worries For Theoretical Physics
Losing Completeness
Worries On The Mystery Of Worry
The Growing Gap Between The Scientific Elite And The Vast "Scientifically
       Challenged" Majority
Presentism
Metaworry
Do We Understand The Dynamics Of Our Emerging Global Culture?
The Loss Of Lust
We Worry Too Much About Fictional Violence
The Consequences Of Our Increasing Knowledge Of What Causes Disease,
       And Its Consequences For Human Freedom
Natural Death
C.P. Snow's 'Two Cultures': The Nature-Nurture Debate
The Demise Of The Scholar
The Unavoidable Intrusion Of Sociopolitical Forces Into Science
Who Gets to Play in the Science Ballpark
Communities Of Fate
Working with Others?
Working with Others?
Super-A.I.s Won't Rule The World (Unless They Get Culture First)
Posthuman Geography
The Danger From Aliens by Seth Shostak, way, way down on my list
The Role Of Microorganisms In Cancer Is Being Ignored By The Current Sequencing
       Strategies
Human Intuitions Will Stifle Technological Progress
Illusions Of Understanding And The Loss Of Intellectual Humility
The End Of Hardship Inoculation
An Exploding Number Of New Illegal Drugs
Superstition by Matt Ridley, important but not in the top ten
History And Contingency
The Triumph Of The Virtual, And Its Consequences
There Is Nothing To Worry About, And There Never Was
The Cultural And Cognitive Consequences Of Electronics
Failure Of Genomics For Mental Disorders
Crisis At The Foundations Of Physics
The Behavior Of Normal People
Democracy
Human Population, Prosperity Growth: One I Fear, One I Don't
Magic
The Rise In Genomic Instability by Eric J. Topol, gimme a break
Can They Read My Brain? by Stanislas Dehaene, who would want to?
A World Without Growth?
The Dangerous Fascination Of Imagination
Worrying
The Gift Of Worry
Not Enough Robots
Safe Mode For The Internet?
Life As We Know I
Unknown Unknowns
Our Blindspots
The Is-Ought Fallacy Of Science And Morality
The Loss Of Our Collective Cognition And Awareness
The Decline Of The Scientific Hero by Roger Highfield, what's a
       "scientific hero"?
What Is A Good Life?
Digital Tat ...
Capture
Society's Parlous Inability To Reason About Uncertainty
Fast Knowledge
The "Nightmare Scenario" For Fundamental Physics
Homogenization Of The Human Experience
We Won't Be Able To Understand Everything by Clifford Pickover,
       really? that worries you?
Systematic Thinking About How We *Package* Our Worries
The Real Risk Factors For War by Steven Pinker, yes, we should be
       worried about war
Worrying About Stupid
The Belief Or Lack Of Belief In Free Will Is Not A Scientific Matter
Science Is In Danger Of Becoming The Enemy Of Humankind
Living Without The Internet For A Couple Of Weeks by Daniel Dennett,
       not in my top ten

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How Atheists Cope with Death

There are millions and millions of atheists around the world. Whether it's in Brussels or Beijing these atheists cope with deaths in the family in a variety of ways. None of them require the false comfort of god(s) or heaven.

I live in a (relatively) secular society. Most of my friends are nonbelievers. We are at the age where the deaths of friends and family members are not uncommon. In many cases, the memorial services are completely non-religious but even in those cases where the service takes place in a church my friends are not troubled by their lack of belief in god(s).

However, problems arise in societies where the vast majority of people are religious and where the believers have no concept of what it might be like to be an atheist. The problems aren't caused by the inability to cope with death in the absence of god, they are caused by intolerant and insensitive believers who can't, or won't, recognize that their false beliefs provide no comfort to an atheist. That's why there's so much talk these days about how atheists cope with death in the USA [After Tragedy, Nonbelievers Find Other Ways To Cope].

If you read the examples in that article, you will realize that the problems they face would not exist in non-religious societies. Their "problems" all stem from feelings of guilt about not believing or from interfering Christians. You won't see articles like this published in Brussels or Beijing.

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What Exactly Is Evolution? Stated Clearly Gets It Mostly Right

Stated Clearly posts videos on YouTube. It is dedicated to "spreading the love of science to the world" [Stated Clearly, YouTube] [Stated Clearly, Website].

The video below, narrated by Jon Perry, answers the question, What Exactly Is Evolution. It starts with an excellent definition of evolution that closely resembles my own preferred, minimal, defintion of evolution at What Is Evolution?. Here's the definition in the video ...

(Evolution is defined as) any change in the heritable traits within a population across generations.

The first example involves a new mutation that arises in an amoeba-like organism. Because this new mutation in inherited by a daughter cell, the video declares that "evolution has officially occurred."

What this means is that mutation becomes a mechanism of evolution. I prefer to think of evolution as "heritable changes in a population spread over many generations" in order to make it clear that change in a single generation doesn't qualify. I also prefer to think of mutation as a mechanism for generating variation and not a mechanism for causing evolution but this can be legitimately debated.

The second example is two badgers mating to produce an offspring that has a different combination of characteristics than either parent. According to the video "evolution ... has officially occurred." This is incorrect. Populations evolve, not individuals. It's quite possible for the individuals in a given generation to have different combinations of traits than either of their parents while the frequency of alleles in the population remains unchanged. Thus, evolution has NOT occurred.

The idea that it's populations that evolve and not individuals is crucial to a correct understanding of evolution and it's a shame that the video promotes a common misconception.

Bug_girl at Skepchick liked this video and so did PZ Myers at Pharyngula.

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WTF Is Science?

Rufina is a student at the University of Toronto and she's interested in setting up a group/club to discuss science. Here's what she has in mind.

The goal of this group is to meet regularly (~biweekly) to discuss/debate the hot topics in scientific controversy and their implications in the sociopolitical world. My personal aim in founding this group is to refine the art of delivering articulate and diplomatic scientific explanations to those who don't "believe" in science. In addition, I would like to expand our efforts to somehow elucidating to the general public/non-science students the importance of science in the progress of society.

I'm in.

The first meeting will be Wednesday, January 1623, 2013 at 6pm at a location to be decided. (Probably in my building.) The topic of the first meeting is "What Is Science."

Anyone else want to join us?

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PSI Online

PSI-online Project


Papiri della Società Italiana 
Direzione scientifica
• Guido Bastianini (Università di Firenze - Istituto Papirologico "G.Vitelli")
• Edoardo Crisci (Università di Cassino - Dipartimento di Filologia e Storia)
• Rosario Pintaudi (Biblioteca Medicea Laurenziana; Accademia Fiorentina di Papirologia e di Studi sul mondo antico - Firenze)

Progetto
PSI-online nasce dalla collaborazione scientifica e progettuale fra l’Università degli Studi di Cassino-Dipartimento di Filologia e Storia, la Biblioteca Medicea Laurenziana di Firenze (http://www.bml.firenze.sbn.it/), l’Istituto Papirologico ‘G. Vitelli’ (http://vitelli.ifnet.it/) e l’Accademia Fiorentina di Papirologia e di Studi sul mondo antico (http://www.accademiafiorentina.it/). Esso si propone l’obiettivo di rendere disponibili online tutti i papiri sino ad oggi editi della Società Italiana per la ricerca dei papiri greci e latini (PSI), conservati in massima parte presso la Biblioteca Laurenziana, l’Istituto papirologico ‘G. Vitelli’, il Museo archeologico del Cairo e il Museo greco-romano di Alessandria d’Egitto.

Descrizione
Ideato e organizzato con l’apporto tecnico e finanziario dell’Università di Cassino, grazie alla disponibilità delle Istituzioni coinvolte e dei rispettivi responsabili, il progetto prevede la redazione di sintetiche schede descrittive dei materiali, strutturate in forma di database, e la digitalizzazione ad alta definizione delle immagini dei papiri. La scelta di organizzare e presentare il materiale in forma di schede autonome ne consente la versatilità d’uso e la facilità di gestione. Superando la concezione dei tradizionali database disponibili in rete, PSI-online si pone l’obiettivo di riproporre sul web l’esperienza tipica della consultazione diretta di un archivio di testi ed immagini, proponendo all’utente un modello innovativo di raccolta e gestione dei dati e l’opportunità di una nuova esperienza di lavoro online.
L’interfaccia presenta un ambiente operativo racchiuso in un’unica pagina digitale, in cui tutti gli elementi, informativi e operativi, si presentano e si muovono all’interno di un contesto unico e stabile. La dinamica di rappresentazione dell’informazione rinvia ad un ambiente basato su relazioni di tipo oggettuale: un unico elemento base, l’oggetto, si moltiplica e si modifica nelle forme, realizzando le funzioni di ruolo e complementarietà necessarie all’identificazione delle azioni-domanda poste al modello.
L’interazione dell’utente con i contenuti avviene attraverso la gestione di oggetti: ogni richiesta formulata al modello PSI-online produce un oggetto, che a sua volta – oltre all’informazione richiesta – offre la possibilità di operare azioni ulteriori, intervenendo sullo stato dell'oggetto stesso o producendone uno nuovo. All’avvio PSI-online presenta una maschera – oggetto login – in cui è richiesto il riconoscimento per accedere alla sessione di lavoro. Assolta la registrazione o il login, una seconda maschera – oggetto ricerca – permette di indagare il database: è possibile attivare contemporaneamente più percorsi di ricerca, conservando la disponibilità di accesso parallelo a ciascuno di essi. I dati risultanti dall’interrogazione producono ulteriori oggetti – schede segnature – contenenti informazioni di tipo testuale. Le schede di testo possono inoltre prevedere un legame diretto ad una o più immagini – scheda immagine – il cui contenuto può essere ingrandito ed indagato attraverso il ricorso a confronti con altre immagini significativamente collegate. Non solo le immagini, ma anche tutti gli altri oggetti possono essere posizionati liberamente sulla pagina secondo le esigenze dell’utenza e possono essere gradatamente ingranditi per permettere una migliore lettura dei contenuti. L’interazione può essere volontariamente interrotta o sospesa, depositando l’oggetto sul bordo della pagina, sotto forma di etichetta titolata. Da questo stato l’oggetto potrà essere richiamato in qualsiasi momento. I campi previsti nel database, e visualizzati nelle schede, riguardano i seguenti dati: segnatura, numero di inventario, luogo di provenienza, datazione, contenuto, materiale e tipologia del supporto, bibliografia sintetica; appositi simboli riportati su ciascuna scheda segnalano: la direzione delle fibre (nel caso di supporto papiraceo), la riutilizzazione del reperto (papiri opistografi) e l’eventuale ricongiungimento con altri frammenti. L’idea di concentrare in un unico archivio virtuale una collezione fisicamente dislocata presso diversi Istituti di conservazione; la possibilità di attivare, consultare e conservare un numero di schede e di ricerche teoricamente infinito; l’eventualità di confrontare due o più immagini fin nei minimi dettagli, con un ingrandimento medio leggibile di 8x rispetto alla dimensione reale del documento, sono segni tangibili dello sforzo tecnico e concettuale attuato a supporto della migrazione in rete della collezione PSI.

BOEP 2.1 Jan 15 2013

 Bulletin of Online Emendations to Papyri

Is It Time for All Religions to Accept Evolution?

This is a BBC One program posted to YouTube on Jan. 13, 2013. The question is whether it's time for all regions to accept evolution. The answer is "yes" of course, but some religions are going to resist for a bit longer. Because this is Britain, it's not so much the Christians that are the problem but Muslims.

You will recognize some of the people on this program. Matt Ridley, for example, gives a pretty good answer to the question about whether there's a scientific debate about the fact of evolution. It's amusing to read the response of Cornelius Hunter who claims that everything Ridley says is a lie [Here is How Evolutionists Lie to the Public].

Hunter says,

That was such a dizzying flurry of big lies we, frankly, lost count. Those lies are so absurd, so unequivocally false, and spoken with such conviction, that the average person is sure to believe them.

Unfortunately such lies are the rule rather than the exception. This evolution propaganda segment was no mistake—it is unfortunately typical.

Of course one can make truthful arguments for evolution. And one can try to find scientific evidence to support it. It is not easy, but it can be done. But that is not what evolutionists do. They mandate evolution. They insist evolution is a fact in spite of the evidence. And that is a big lie.

I don't think we're ever going to succeed in teaching the Cornelius Hunter's of this world the difference between truth and lies but TV shows like this one are having an impact and I'm glad to see that some Muslims are willing to speak out.

Shows like this one were very rare in the 20th century. It's now become much more acceptable to challenge religious beliefs that conflict with science and I think that's because of outspoken atheists like Richard Dawkins, Daniel Dennett, Christopher Hitchens, and Sam Harris, along with many other so-called "New Atheists."

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Monday's Molecule #197

The last "Monday's Molecule" was β-D-mannopyranose, shown in boat and chair configurations [Monday's Molecule #196]. The winners were Bill Chaney, Dima Klenchin, and Bill Gunn. Bill Gunn should contact me if he is within range of Toronto.

Students often find it very difficult to distinguish between various stereoisomers. For example, many of you thought that the last molecule was glucose. This week's molecule should present a real challenge for most of you. It's a common molecule, present in all cells and it has a common name by which it is identified in most textbooks. However, the common name isn't good enough because there are several different conformations. The conformation shown in the figure is the only one that's synthesized in the normal reaction. Name this molecule using whatever conventions you have to employ to identify it correctly. [Hydrogen atoms are omitted for clarity. You should be able to infer their positions.]

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Read more »

EpiDoc Workshop, London, April 22-25, 2013

EpiDoc Workshop, London, April 22-25, 2013

We invite applications for a 4-day training workshop on digital text-markup for epigraphic and papyrological editing, to be held in the Institute for Classical Studies, London. The workshop will be taught by Gabriel Bodard (KCL), James Cowey (Heidelberg) and Charlotte Tupman (KCL). There will be no charge for the teaching, but participants will have to arrange their own travel and accommodation.

EpiDoc (epidoc.sf.net) is a set of guidelines for using TEI XML (tei-c.org) for the encoding of inscriptions, papyri and other ancient documentary texts. It has been used to publish digital projects including the Inscriptions of Aphrodisias and Tripolitania, the US Epigraphy Project, Vindolanda Tablets Online and Curse Tablets from Roman Britain, Pandektis (inscriptions of Macedonia and Thrace), and the Duke Databank of Documentary Papyri. The workshop will introduce participants to the basics of XML and markup and give hands-on experience of tagging textual features and object description in EpiDoc as well as use of the tags-free Papyrological Editor (papyri.info/editor).

No technical skills are required to apply, but a working knowledge of Greek or Latin, epigraphy or papyrology and the Leiden Conventions will be assumed. The workshop is open to participants of all levels, from graduate students to professors or professionals.

To apply for a place on this workshop please email gabriel.bodard@kcl.ac.uk with a brief description of your reason for interest and summarising your relevant skills and background, by Friday March 1st, 2013.
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(Or link to http://www.icls.sas.ac.uk/about-us/news/epidoc-workshop-22-25-april-2013 for the text, if you prefer.)

A New Year

Here's a photo of my granddaughter, Zoë, flying her kite on Santa Monica beach on New Year's Eve. The kite was a present from Santa Claus.

Zoë turned three years old on January 5th.

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The Great Wrinkled Finger Debate

The students in my Molecular Evolution class have to read the Spandrels paper by next Tuesday.

Ryan Gregory explains why this 35-year-old paper is just as relevant and important today as it was when it was first presented in 1978 (published in 1979). Read aall about it at: The great wrinkled finger debate.

Please leave comments on Genomicron and not here.

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The Problem with Selling the Homeopathic Product Oscillococcinum

A group of skeptics have banded together to sue Shoppers Drug Mart for selling the homeopathic product Oscillococcinum. Watch the video on Think Again! TV produced by Centre for Inquiry, Canada. This is a class action lawsuit and anyone who has purchased Oscillococcinum from Shoppers Drug Mart may join the plaintiffs.

CFI is not a plaintiff but it has agreed to provide the court with "accurate scientific data on the efficacy and substance of the product."

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Jim Yeager Shows Americans Why Banning Assault Guns Is Necessary

My American friends need to watch this video. Be afraid, be very afraid.

I don't know how many people think like this but if it's more than a few thousand there's going to be trouble.

Isn't threatening to kill somebody a crime? Isn't he advocating the overthrow of the democratically elected American government by force? I don't think that's in the Constitution.

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Goodbye, Anonymous, It's Been Nice Knowing You

There are very few anonymous comments these days and those few that persist will not be missed. I've stopped accepting comments from people who won't identify themselves in some way.

I'd prefer if your identifier leads me to an actual name but for now I'll tolerate posting under a pseudonym as long as it's unique.

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I Have the Least Stressful Job!!!

According to Careercast.com, I have the least stressful job of all jobs.¹ Here's how it's reported in Forbes magazine by web staff writer Susan Adams: The Least Stressful Jobs Of 2013.

University professors have a lot less stress than most of us. Unless they teach summer school, they are off between May and September and they enjoy long breaks during the school year, including a month over Christmas and New Year’s and another chunk of time in the spring. Even when school is in session they don’t spend too many hours in the classroom. For tenure-track professors, there is some pressure to publish books and articles, but deadlines are few. Working conditions tend to be cozy and civilized and there are minimal travel demands, except perhaps a non-mandatory conference or two. As for compensation, according to the Bureau of Labor Statistics, the median salary for professors is $62,000, not a huge amount of money but enough to live on, especially in a university town.

Another boon for professors: Universities are expected to add 305,700 adjunct and tenure-track professors by 2020, according to the BLS. All of those attributes land university professor in the number one slot on Careercast.com’s list of the least stressful jobs of 2013. The ranking comes from an annual best and worst jobs list that began in 1995 under the auspices of the Wall Street Journal.

Ironically, this article comes out just as some of my colleagues are getting the bad news about their grant applications. Those who weren't funded face the end of their research career while they are still in their 40s. It also comes out at a time when two of my colleagues are starting to think about their applications for tenure. If they are unsuccessful, they will be out of a job in their late 30s with a family to support.

None of my colleagues took a month off at Christmas and I can assure you that all of my colleagues are here for almost the entire summer running a lab full of graduate students, post-docs, technicians, and summer students. The stress of running what amounts to a small business and getting papers published on things that nobody else has ever discovered is a lot more than most people could stand.

Read to the end of the Forbes article to see how the author responds to the many comments she received. The real problem here is that a prominent journalist could actually believe what she wrote in the first place!

I love the comment from Thomas Epps ...

Given your comment above indicating that you realize the source of your article was poor at best. I think you should consider retracting this article. I know that I would be severely sanctioned for writing this type of article with such questionable sourcing in my academic job. If the same is not the case in your job, then clearly your career is not a terribly stressful one. Maybe, "web staff writer" should be on the top of the "least-stressful jobs" list?

See ...
Do College Professors Have Less Stress?
Top 10 Reasons Being a University Professor is a Stressful Job
Before Professor comes Postdoc: Lower career rung, just as much job stress

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1. I have no intention of supplying specific information about MY job but I'm happy to explain why every one of my younger colleagues is under a tremendous amount of stress every single day.

Proof of God #42: Laminin

No comment is necessary except to say that this man, Louie Giglio, was all set to deliver the benediction at Obama's upcoming inauguration until it was discovered that he hates homosexuals. For me, this video would have been enough to disqualify him.

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[Hat Tip: Hermant Mehta at Friendly Atheist: Louie Giglio, Who Thinks Laminin Molecules Prove Christianity is True, Will Deliver Obama’s Inauguration Benediction]

A New Era at Centre for Inquiry Canada

The Board of Directors of the Centre for Inquiry, Canada has mailed out the following press release. Unfortunately, nothing has been posted on the website [The Centre for Inquiry].

The Board of Directors would like to thank Justin for launching CFI Canada, growing it from one location in Toronto to across the country in short order. There are few individuals who possess the dedication, passion and tenacity to accomplish this. Justin was instrumental in making CFI the premier voice for reason, secularism and skepticism in Canada. We were fortunate to have him. Justin leaves CFI in good hands with our National Director, Michael Payton, and our incredible branch leaders and volunteers who are committed to continuing our growth and influence.

Justin, we look forward to watching you make further positive and lasting contributions to society, as no doubt you will.

Board of Directors, Centre for Inquiry Canada

I'm delighted that The Board and Justin were able to reach agreement on a new direction for CFI and usher in a new era under new leadership. I agree with the Board that Justin did an excellent job of creating CFI Canada and leading it through its formative years. I was happy to work with Justin and support him during those early years of building an organization (see photo).

In the past year I've been very critical of the CFI Board of Directors because I think they mishandled the firings and re-hirings that took place in 2011 and 2012. This time I think they've done the right thing during recent negotiations. Congratulations to Kevin Smith (President) and all the Board members for working hard to ensure the future success of CFI.

The email announcement also contained a letter from Justin Trottier to the Freehthinker members of CRI. It begins ....

Special Note from Justin Trottier, Founding National Executive Director, Centre for Inquiry Canada
To My Fellow Freethinkers,

It is with mixed emotions that I take this opportunity to announce the upcoming end of my leadership role with CFI Canada. March 15, 2013 will mark the end of my full-time position as National Communications Director; however, I will consider, if I am asked, continuing in part time or other status until no later than July 31. I am immensely proud of the contributions I've made to the organization over the last six years and plan to continue as a volunteer and active participant in CFI events and initiatives, but now it is time to start making the transition from CFI and pursue other interests and employment.

It has been a pleasure working with so many amazing people to form a unique Canadian educational charity and expand it into a national voice for atheists, humanists and skeptics from coast to coast. Leading CFI as it came to establish itself as the most visible, active and professional freethought organization in Canada, with employees, infrastructure and a growing budget will stand as one of the most important and certainly, matchless accomplishments of my life.

...

I'm looking forward to rejoining CFI Canada in just a few months.

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