Food Trucks

 
I love the food trucks. Today was a special day, there were seven new food trucks visiting our campus.

There were so many choices ....

Two of my favorites ...

Bacon poutine and a cinnamon-sugar BeaverTail. Only in Canada!

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The Reason Rally

 
For all of us who weren't there, here's what The Thinking Atheist saw at the Reason Rally last weekend.

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Monday's Molecule #163

 

You blew it last week because you didn't follow instructions. It's not going to get any easier. This week you have to identify the molecule using TWO different common names AND name the Nobel Prize winner most closely associated with this molecule.

Remember, you need THREE answers or you can't win!

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answers wins. I will only post 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.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is Vitamin B12, also known as cobalamin. The Nobel Laureate is Dorothy Crowfoot Hodgkin. This week's winners are John Runnels and Raul A. Félix de Sousa. Contact me by email to set up a time.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner

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Human Mutation Rates May Be Lower than We Thought

The predicted mutation rate in humans is thought to be about 130 mutations per generation or 10^-10 per nucleotide per generation [Mutation Rates]. About 120 (>90%)of these new mutations occur in males, mostly during spermatogenesis. Only about 10 mutations are contributed by females. These values are based on what we know about the biochemistry of DNA replication and repair.

The evidence from evolution was consistent with this calculation. Nachman and Crowell (2000), for example, calculated that the accumulation of mutations in 18 pseudogenes from humans and chimpanzees yielded a value of 175 mutations per generation.

Up until recently it wasn't possible to get a direct measurement of the mutation rate but I addressed some of the attempts in November 2010: Human Mutation Rates. In that posting I discussed two experimental results that yielded estimates of the mutation rates in humans.

Recently there have been two attempts to verify this calculation. In one, the Y chromosomes of two men separated by 13 generations in a paternal lineage from a common male ancestor were sequenced. The differences correspond to a mutation rate of 0.75 × 10^-10 per generation, or almost the same as theory predicts. This is based on the fact that if most mutations are nearly neutral (they are) then the rate of fixation by random genetic drift should be the same as the mutation rate.

The other study, by Roach et al. (2010), compared the genome sequences of two offspring and their parents. By adding up all the differences in the offspring they arrived at an estimate of 70 mutations in the offspring instead of the expected 130. This is half the expected value but the study is fraught with potential artifacts and it's best not to make a big deal of this discrepancy.

Now there's another paper that sequenced two sets of parents and a child (Conrad et al., 2011). You might think that the calculation is easy because all you have to do is count the number of new alleles in the child. But this doesn't work because you have to account for somatic mutations that arose in the tissue culture cells lines that are being used as a source of DNA. These can be eliminated by comparing the sequence with fresh DNA samples directly from the parents and child. In addition to false positives, you have to allow for some false negatives.

I don't understand all the mathematical manipulations but they are probably trustworthy. (Some of it was done by Reed Cartwright of Panda's Thumb.) The final estimates are 60 mutations in one of the children and 50 in the other. Both of these values are lower than the calculated rate and when you combine them with earlier results, it's beginning to look like the actual mutation rate is about half of the calculated value based on biochemistry. This could easily be due to a two-fold error in our estimate of repair efficiency. It could be that instead of repairing only 99/100 sites of damage the actual repair machinery fixes 199/200 damaged sites, for example.

The surprising result is that 92% of the new mutations in one of the children comes from the father but in the other family only 32% of the mutations were paternal. We expect that most of the mutations will occur during spermatogenesis so that part is not surprising. What's surprising is that in one case the majority come from the mother.

I suspect that this is an artifact of some kind, or a statistical outlier. The authors, however, take this as evidence of natural variation in male and female mutation rates. I'd like to see the estimates for other children of the same family in order to see if the result is reproducible.

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Conrad, D.F., Keebler, J.E., DePristo, M.A., Lindsay, S.J., Zhang, Y., Casals, F., Idaghdour, Y., Hartl, C.L., Torroja, C., Garimella, K.V., Zilversmit, M., Cartwright, R., Rouleau, G.A., Daly, M., Stone, E.A., Hurles, M.E., Awadalla, P.; 1000 Genomes Project. (2011) Variation in genome-wide mutation rates within and between human families. Nat. Genet. 43:712-714. [doi: 10.1038/ng.862]

Nachman, M.W. and Crowell, S.L. (2000) Estimate of the mutation rate per nucleotide in humans. Genetics: 156:297-304.

New Scientist: The Accommodationist Issue

 

I subscribe to New Scientist. Many years ago, I decided that it was the best of the popular science magazines—better than Scientific American, National Geographic, SEED (now defunct), and Discover. Recently, however, I been having second thoughts as the quality of the articles deteriorates and more and more pseudoscience and wrong science is making its way into the magazine. The issue of March 17-23, 2011—The God Issue—is the last straw. This is no longer a science magazine.

It's not because the topic is out-of-bounds. Quite the contrary, I think it's perfectly appropriate to address the conflict between science and religion. There's even a good article in there; it's the one by Victor Stenger. Stenger argues convincingly that science conflicts with the existence of all personal gods. It's possibly compatible with a strictly deist god but nobody believes in such a god.

The problem is with all the other articles which are accommodationist to various degrees. Several of them flatly contradict science (and common sense). One of them (by Alain de Botton) advocates that atheists adopt some of the practices of religion as if religion has a monopoly on being nice.

You only have to read the editorial to see how bad things have become ....

"GIVE me the child until he is seven, and I will show you the man." This Jesuit maxim epitomises how many of us perceive religion: as something that must be imprinted on young minds.

The new science of religion begs to differ. Children are born primed to see god at work all around them and don't need to be indoctrinated to believe in him (see "The God issue: We are all born believers").

This is just one of many recent findings that are challenging standard critiques of religious belief. As we learn more about religion's biological roots, it is becoming clear that secularists are often tilting at windmills and need to rethink.

Another such finding is that belief in a god or gods does appear to encourage people to be nice to one another. Humans clearly don't need religion to be moral, but it helps (see "The God issue: Religion is the key to civilisation").

An interesting corollary of this is a deeply held mistrust of atheists (see "In atheists we distrust"). In fact, atheists might consider themselves as unrecognised victims of discrimination. In a recent opinion poll, Americans identified atheists as the group they would most disapprove of their children marrying and the one least likely to share their own vision of American society. Self-declared atheists are now the only sizeable minority group considered unelectable as president.

Such antipathy poses a dilemma for opponents of religion, and may explain why "militant atheism" has failed to make headway.

Secularists would also do well to recognise the distinction between the "popular religion" that comes easily to people's minds and the convoluted intellectual gymnastics that is theology. Attacking the latter is easy but will do little to undermine religion's grip (see "The God issue: Science won't loosen religion's grip").

This is not an apologia for god. Religious claims still wither under rational scrutiny and deserve no special place in public life. But it is a call for those who aspire to a secular society to approach it rationally - which means making more effort to understand what they are dealing with. Religion is deeply etched in human nature and cannot be dismissed as a product of ignorance, indoctrination or stupidity. Until secularists recognise that, they are fighting a losing battle.

The editors seem to have been completely bamboozled by the article entitled Born Believers. The author is Justin L. Barrett of Fullier Theologial Seminary in Pasadena, California (USA). Barrett argues ....

Drawing upon research in developmental psychology, cognitive anthropology and particularly the cognitive science of religion, I argue that religion comes nearly as naturally to us as language. The vast majority of humans are "born believers", naturally inclined to find religious claims and explanations attractive and easily acquired, and to attain fluency in using them. This attraction to religion is an evolutionary by-product of our ordinary cognitive equipment, and while it tells us nothing about the truth or otherwise of religious claims it does help us see religion in an interesting new light.

Barrett quotes a few studies in support of his claim but those studies don't really say what he thinks they say. It makes no sense to say that young children find religious claims and expectations attractive unless they have heard these explanations from adults.

I don't remember a time in my childhood when I spontaneously created a supernatural being who expected me to behave in certain ways. I never saw any evidence that my children needed to create gods and I don't see any evidence that my two-year-old granddaughter needs to imagine sky daddies in order to understand the world around her.

There are millions of children in Europe who are growing up as second and third generation atheists and I can't imagine that their parents are upset because the children are turning out to be "born believers." The idea is ridiculous. It could only come from a culture where young children are being constantly brainwashed by stories about gods. There's no such thing as an innate attraction to religion in a culture with no religion in the first place.

Oh, and one other thing, it's not true that belief in one of the gods makes you a nicer person. If that were true then America would be one of the kindest, nicest, societies among all Western industrialized nations. And Saudi Arabia would take the prize for the nicest society in the world. And you sure as hell wouldn't want to live in evil, crime-ridden Sweden or Holland.

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Richard Dawkins Defends the Reason Rally

 

Richard Dawkins writes in yesterday's Washington Post [Who would rally against reason?].

March 24th is a landmark date for Washington, D.C. Thousands will converge on the world’s leading capital city to celebrate the crowning human virtue of reason.

How have we come to the point where reason needs a rally to defend it? To base your life on reason means to base it on evidence and logic. Evidence is the only way we know to discover what’s true about the real world. Logic is how we deduce the consequences that follow from evidence. Who could be against either? Alas, plenty of people, which is why we need the Reason Rally.

I agree with Dawkins. "Reason" and rationality is what we should be promoting. If we are successful, then religion will disappear and atheism will be the default position. As Dawkins puts it in The God Delusion, the real battle is between rationalism and superstition or between reason and superstition.

Dawkins has a series of videos called The Enemies of Reason. They are promoted as: "Professor Richard Dawkins confronts the epidemic of irrational, superstitious thinking with logic, observation and evidence - in other words, through reason." Here's the episode on superstitious beliefs in health and medicine.



It's obvious that anyone who opposes vaccination and/or promotes alternative medicine is an enemy of reason. It's difficult to imagine how such a person could be invited to speak at the Reason Rally in Washington, right?

So why are Senator Tom Harkin and Bill Maher speaking if they are clearly enemies of reason [The Reason Rally ought to have some standards]?

It's because some of the organizers of the Reason Rally do not agree with Richard Dawkins. They see this event as an atheist rally and the speakers are being invited because they are prominent atheists, not necessarily rationalists. Hemant Mehta of Friendly Atheist is one of those people [Plan Your Own Reason Rally and Then Tell Me How It Goes].

Look, the organizers spent a long time listening to the suggestions of dozens of people (representing tens of thousands of atheists) regarding who should speak at the Rally. They did everything in their power to contact all the “big names” that people said they wanted to hear at the Rally. They rustled up and managed the hundreds of thousands of dollars in funding needed to put on an event of this magnitude. They got every major organization in our movement to work together to make this work — and that’s not an easy thing to do. They had to deal with the speakers complaining about their prominence on our website (yep, it happened).

Just about everyone believes in something irrational. Including atheists. So, yes, you’re going to hear people at the Rally who hold ideas we think are completely unreasonable. Maybe even harmful.

If we got rid of every speaker who held an irrational belief, there would be no one left on that stage.

So deal with it.

I’m not saying you shouldn’t call them out where they’re wrong. Have at it. I did it, too. In many cases, they deserve it. But to suggest the organizers are at fault for inviting really famous atheists who hold some view you don’t agree with is absurd. Almost as ridiculous as faulting them for accepting a greeting from a sitting U.S. senator who stands to lose a lot more than he’ll gain for addressing our crowd.

This is going to be confusing. Who's right? Is this a Reason Rally as Dawkins and PZ Myers think or is it an Atheist Rally as Hemant believes?

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I Rank Number One on Google

 
I was searching through some old posts today and I came across I Rank Number One on Google from October 2007. The idea was to come up with five words or phrases where Google would return something by you at the top of the page.

Back then I picked ...

• Larry Moran
• Sandwalk
• Three Domain Hypothesis
• adaptationist-pluralist
• is there a genetic component to intelligence

All five of them worked in 2007 but today the last one has Sandwalk in 4th position. The list that works today is ....

• Larry Moran
• Sandwalk
• Three Domain Hypothesis
• adaptationist-pluralist
• random genetic drift

How easy is this? Can every blogger come up with a list where they rank number one on the Google search? I tried it with a few blog names and it always seems to work. The names of some bloggers don't always work. We already know about a more famous "John Wilkins" for example and "Paul Myers" doesn't even mention the Pharyngula blogger in the top ten!¹

I'm giving a lecture tomorrow on the Three Domain Hypothesis and why it is no longer valid. I still have the top three hits for this topic on Google. In case you've forgotten, you can read about it at: Theme: The Three Domain Hypothesis.

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1. "Paul Zachary Myers" works, but that's cheating.

Dynamics and Sloppiness in Protein Synthesis

 

Protein synthesis can be divided into three stages.

First, there's the initiation stage when a ribosome binds to the initiation codon in messenger RNA (mRNA) and the translation initiation complex forms by recruiting additional components.

Second, there's the elongation stage when the elongation complex moves along the mRNA translating the coding region and producing a polypeptide chain. The elongation rate is relatively constant but from time to time the elongation complex pauses at particular sites that are difficult to translate.

Finally, the elongation complex encounters a termination site where it disassembles and the ribosome with its various factors is released from the mRNA.

Read more »

We Are All Apes

 
Richard Dawkins created a bit of a stir among the theists by claiming that he is an African ape.

Someone named Vasko Kohlmayer was partularly upset so he wrote up a "rebuttal" for the Moonie newspaper The Washington Times: Is Richard Dawkins an Ape?.

I don't much care about the opinions of theists like Vasko Kohlmayer because they have an obvious agenda. Scientific arguments are meaningless to them.

But I do care about the opinions of other scientists and philosophers. Jerry Coyne explains why we are apes and why it's not a good idea to say that people living in Oxford or Chicago are African apes [Washington Times denies that Richard Dawkins is an ape]. I agree with Jerry.

John Hawks disagrees [Humans aren't monkeys. We aren't apes, either.]. He claims that the term "ape" is not a legitimate phylogenetic term and therefore is doesn't have to refer to a monophyletic group.

Chimpanzees are apes. Gorillas are apes, as are bonobos, orangutans, and gibbons. We routinely differentiate the "great apes" from the "lesser apes", where the latter are gibbons and siamangs. Humans are not apes. Humans are hominoids, and all hominoids are anthropoids. So are Old World monkeys like baboons and New World monkeys like marmosets. All of us anthropoids. But humans aren't monkeys.

I don't agree with this distinction. There's nothing to be gained by saying that our closest relatives are apes but we aren't.

John Wilkins thinks we are apes [Are humans, apes, monkeys, primates, or hominoids?]. John argues like a philosopher but, in this case, he's right.

It is not possible to stem the tide of linguistic change, as the Académie Française has found out repeatedly. If experts can redefine terms influentially, then there is nothing wrong with that so long as it doesn’t confuse the experts. Using paraphyletic terms (that is, group names that denote what is left of the group once a subset has been removed) is a Very Bad Idea that hangs on in science, but it need not hang on in folk usage. And there’s nothing wrong with saying “humans are apes”, because, on the best construal of what those terms denote, they are.

Neil Shubin’s excellent book Your Inner Fish makes a similar point. Where once a “fish” was anything that lived in water (including swans, geese, alligators and crocodiles, whales, and water snakes), it came to mean a vertebrate that had gills and fins and scales. Shubin shows how the Gnathostomes (jawed fishes) includes land vertebrates, including mammals and ultimately us, as well. Language can change…

UPDATE: Brian Switek of Laepaps weighs in with: I’m an Ape, and I’m Also a Fish.

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Monday's Molecule #162

 

The last few challenges have been too easy so I'm going to make this week's molecule a bit more difficult. Not only do you have to identify the molecule but you also have to identify each of the four residues that are sugar derivatives. What is the molecule in blue and what are the other three sugary-looking residues?

Be sure to give a complete unambiguous name—that means getting the stereochemistry correct.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment. The winner will be treated to a free lunch. I'll be setting up a lunch for this Thursday so expect an email message. If I owe you a lunch, it wouldn't hurt to remind me in case I forget you.

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.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is ganglioside G_M2. The residues are N-acetyl-α-neuraminic acid (blue), N-acetyl-β-D-galactosamide, β-D-galactose, and β-D-glucose (left to right). You were asked to be specific in naming the sugar residues. Several people got the molecule correct but nobody named the sugar residues in a completely unambiguous manner, although the correct names are implied in the formal name of the molecule. There is no winner this week.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner

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The "Reason Rally" Will Have Everything But Reason.

 

A lot of people are going to Washington next Saturday to stand¹ near the reflecting pool for eight hours listening to short speeches and videos during the Reason Rally.

One of the speakers will be PZ Myers and he is rightly upset about some of the other speakers who don't exactly fit the criterion of "reason." Read what he has to say about Senator Tom Harkin and Bill Maher [The Reason Rally ought to have some standards].

Was Deepak Chopra busy on 24 March? Did Oprah have a hair appointment? Maybe it’s not too late to sign up John Edward — he could channel Ingersoll and Russell and Sagan for us, although of course we’d have to be content with him guessing at their words one letter at a time.

So what's the point of having a "Reason Rally" if you schedule talks from known kooks who oppose reason?

I suspect that a lot of people will be wandering off to look at the cherry blossoms behind the Jefferson Memorial. I hope the size of the crowd isn't an embarrassment.

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You can buy a ticket for the seating area in front of the stage if you're willing to pay $500, $1000, or $5000 [VIP Seating].

A. Monson, From the Ptolemies to the Romans Political and Economic Change in Egypt

From the Ptolemies to the Romans
Political and Economic Change in Egypt
Andrew Monson, New York University
Hardback 9781107014411
GBP 60.00

This book gives a structured account of Egypt's transition from Ptolemaic to Roman rule by identifying key relationships between ecology, land tenure, taxation, administration and politics. It introduces theoretical perspectives from the social sciences and subjects them to empirical scrutiny using data from Greek and Demotic papyri as well as comparative evidence. Although building on recent scholarship, it offers some provocative arguments that challenge prevailing views. For example,  patterns of land ownership are linked to population density and are seen as one aspect of continuity between the Ptolemaic and Roman period. Fiscal reform, by contrast, emerges as a significant mechanism of change not only in the agrarian economy but also in the administrative system and the  whole social structure. Anyone seeking to understand the impact of Roman rule in the Hellenistic east must consider the well-attested processes in Egypt that this book seeks to explain.
Sample


Contents
Preface;
Part I.
Introduction:
1. The political economy of Egypt;
2. Geography and population;
Geography and population;
Part II. The Land Tenure Regime:
3. The regionalism of land tenure;
4. The continuity of agrarian institutions;
Part III. Fiscal and Administrative Reforms:
5. Land taxation and the economy;
6. Administration and redistribution;
Part IV. The Politics of Economic Change:
7. The impact of empire;
8. Conclusion.

L.H. Blumell, Lettered Christians : Christians, letters, and late antique Oxyrhynchus

Lettered Christians
Christians, Letters, and Late Antique Oxyrhynchus

Lincoln H. Blumell

With the discovery of the Oxyrhynchus Papyri just over a century ago a number of important texts directly relating to ancient Christianity have come to light. While certain literary texts have received considerable attention in scholarship by comparison the documentary evidence relating to Christianity has received far less attention and remains rather obscure. To help redress this imbalance, and to lend some context to the Christian literary materials, this book examines the extant Christian epistolary remains from Oxyrhynchus between the third and seventh centuries CE. Drawing upon this unique corpus of evidence, which until this point has never been collectively nor systematically treated, this book breaks new ground as it employs the letters to consider various questions relating to Christianity in the Oxyrhynchite. Not only does this lucid study fill a void in scholarship, it also gives a number of insights that have larger implications on Christianity in late antiquity.

ISBN 9789004180956

Volume 39

Series: 

New Testament Tools, Studies and Documents

ISSN: 

0077-8842

Table of contents
1. Introduction
a. Scholarship and the Christian Remains of Oxyrhynchus
b. The Study: Argument and Structure
c. Caveats
2. Writing Christian
a. Scholarship and Papyrus Letters Written by Christians
b. Markers of Christian Identity within the Letters
3. Mapping Christians: Travel and Epistolary Networks in Christian Letters from Oxyrhynchus
a. Travel and Communication in Roman and Byzantine Egypt
b. Detectable Travel Motives in the Letters
c. Patterns of Travel and Epistolary Networks
d. Conclusions
4. Christians of the Book?
a. Christians and their Texts
b. Learned Christians?
c. The Use of “Scripture” in the Letters
d. Conclusions
5. What’s in a Name?
a. Onomastic Data and Religious Adherence in Antiquity
b. Nomina Christiana
6. Reading Someone Else’s Mail
Epilogue. The Demise of Christian Oxyrhynchus

John Mattick Wins Chen Award for Distinguished Academic Achievement in Human Genetic and Genomic Research

Shame on the Human Genome Organization (HUGO). It has awarded a prestigious prize (US $10,000) to John Mattick, director of the Centre for Molecular Biology and Biotechnology at the University of Queensland in Brisbane, Australia. Here's the report from the Sydney Morning Herald.

Making something of junk earns geneticist top award

WHEN Sydney geneticist John Mattick suggested junk DNA was anything but rubbish he was challenging an assumption that had underpinned genetics for 50 years.

''The ideas I put forward 10 years ago were quite radical but I thought I was right,'' Professor Mattick said.

He was. And tomorrow he will become the first Australian honoured with the Chen Award for distinguished academic achievement in human genetic and genomic research, awarded by the Human Genome Organisation.

For decades after James Watson and Francis Crick discovered DNA was a double helix, scientists believed most genes were the written instructions for proteins, the building blocks of all body processes. The assumption was true for bacteria but not complex organisms like humans, said Professor Mattick, the new executive director of the Garvan Institute.

In humans, more than 95 per cent of the genome contains billions of letters that do not make proteins, called non-coding DNA. ''When people bumped into all this DNA that didn't make proteins they thought it must be junk,'' he said. But Professor Mattick felt it was unlikely that useless material would survive hundreds of millions of years of evolution.

He found that the non-protein-coding sections of DNA had a function, to produce RNA.

"The obvious and very exciting possibility was that there is another layer of information being expressed by the genome - that the non-coding RNAs form a massive and previously unrecognised regulatory network that controls human development.''

Many scientists now believe this RNA is the basis of the brain's plasticity and learning, and may hold the secret to understanding many complex diseases.

Read more »

Happy Ides!

 

Today is the Ides of March a famous day in European history because of Brutus, Cassius and a bunch of other Roman dudes.

Did you ever wonder what an "ide" was. Here's the explanation from Wikipedia [Ides of March].

The word Ides comes from the Latin word "Idus" and means "half division" especially in relation to a month. It is a word that was used widely in the Roman calendar indicating the approximate day that was the middle of the month. The term was used for the 15th day of the months of March, May, July, and October, and the 13th day of the other months.

I think you have to be more than 50 years old to appreciate this skit. You might have to be Canadian.¹

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1. Wayne & Shuster are graduates of the University of Toronto.

What Does a Eukaryotic Ribosome Look Like?

 

There's a picture of a yeast (Saccharomyces cerevisiae) ribosome on the cover of the Dec. 16, 2011 issue of Science. The paper inside by Ben-Sham et al. (2011) describes the structure at 3Å resolution.

There's nothing revolutionary here but I thought I would show you the structure just to emphasize a particular point. You can see the same image below without the distracting orange background.

Most of the ribosome is composed of RNA (silver-gray strands). You can see that a lot of this single-stranded RNA forms short double-helical regions when the RNA folds back on itself. Small ribosomal proteins (various colors) decorate the surface of the ribosome by binding to specific regions of the ribosomal RNA.

The overall impression is that the ribosome is a big ball of RNA with a small amount of protein. The actual site of translation, where messenger RNA is translated into a polypeptide, takes place in the middle of the ribosome near the hole you see in this structure. Translation is catalzyed by the RNA component of the ribosome, not by the ribosomal proteins.

I don't know about the rest of you but I grew up with an electron-micrographic image of a ribosome in my head and I just assumed that what I was seeing was a large glob of protein. If course I realized that there was a huge amount or RNA in there somewhere but I didn't think it contributed very much to the dark blobs in the cell.

When the first crystal structures of ribosomes were published I had to stare at them for quite some time in order to purge the old images from my mind and adopt a new perspective.

Eukaryotes have 79 ribosomal proteins and prokaryotic ribosomes have only 52 proteins. There are prokaryotic ribosomal proteins that have no homoogues in eukaryotes and 33 of the eukaryotic ribosomal proteins have no homologues in bacteria—they are eukaryotic specific. Furthermore, many of the eukaryotic proteins differ considerably from their bacterial homologues. (Mostly by extensions of the poly peptide chain.)

The protein components of ribosomes are not highly conserved. One gets the impression that they don't contribute much to the function of a ribosome—an impression confirmed by the fact that the RNA by itself can catalyze polypeptide synthesis. They may help stabilize the three-dimensional structure of the ribosome.

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[Image credit: The bottom image is "courtesy of Prof Marat Yusupov (IGBMC, Strasbourg)" from The 9th international Conference on Ribosome Synthesis that takes place this summer in Banff, Alberta, Canada.]

Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M. (2011) The structure of the eukaryotic ribosome at 3.0 Å resolution. Science 334:1524-1529. (Epub 2011 Nov 17). [doi: 10.1126/science.1212642]

Monday's Molecule #161

 

Some species make this molecule for a very special reason. Identify the molecule using the common name and the IUPAC name. You must also say why it's important for some species.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment. The winner will be treated to a free lunch with a famous Nobel Laureate, or with me if the Nobel Laureate isn't available.

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.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is taurocholate (2-{[(3α,5β,7α,12α)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}ethanesulfonate). Taurocholate is a bile salt in mammals. This week's winners are Bill Chaney and Raul A. Félix de Sousa.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj

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On the Sandwalk

 
Here's a panoramic view of what it's like to be on the Sandwalk behind Down House (Darwin's Home). This is the stretch along the very back of the property at the top of the image in the header for this blog.

360 Panoramic - Sandwalk

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[Hat Tip: Michael Fisher]

How to Control Pesky Scientists

 
This is from Rick Mercer, a Canadian comedian [The Rick Mercer Report].

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[Hat Tip: Craig Smibert]

Dorothy J. Thompson, Memphis Under the Ptolemies (2nd edition)

Memphis Under the Ptolemies
(Second Edition)
Dorothy J. Thompson

Drawing on archaeological findings and an unusual combination of Greek and Egyptian evidence, Dorothy Thompson examines the economic life and multicultural society of the ancient Egyptian city of Memphis in the era between Alexander and Augustus. Now thoroughly revised and updated, this masterful account is essential reading for anyone interested in ancient Egypt or the Hellenistic world.

The relationship of the native population with the Greek-speaking immigrants is illustrated in Thompson's analysis of the position of Memphite priests within the Ptolemaic state. Egyptians continued to control mummification and the cult of the dead; the undertakers of the Memphite necropolis were barely touched by things Greek. The cult of the living Apis bull also remained primarily Egyptian; yet on death the bull, deified as Osorapis, became Sarapis for the Greeks. Within this god's sacred enclosure, the Sarapieion, is found a strange amalgam of Greek and Egyptian cultures.

Dorothy J. Thompson is a fellow of Girton College, University of Cambridge, and a member of the faculty of classics at the University of Cambridge. She is a fellow of the British Academy and an honorary president of the International Association of Papyrologists.

Reviews:

"[A] masterful analysis of the surviving evidence for ancient Memphis."--John F. Oates, American Journal of Philology

"[T]his book greatly enhances understanding of Egyptian history in the Ptolemaic period and the author is to be congratulated on her skill in welding the disparate sources into such an attractive whole."--Amélie Kuhrt,History

"[A] book of utmost importance to all readers interested in ancient civilizations. . . . Thompson's concentration on the Hellenistic period provides a penetrating study of all aspects of this city from the time of Alexander to Augustus."--C. C. Lamberg-Karlovsky, Choice

Endorsement:

"This thoroughly revised and updated account presents a clear picture of one of the most important cities of Ptolemaic Egypt, but it also takes the reader deep into the world of Egyptian temples, the priests who served the various cults, and the religious, economic, and social practices of the diverse communities who lived in and around Memphis. Memphis Under the Ptolemies is one of the greatest studies of an ancient city and a true testament to one of the finest scholars of the Hellenistic world."--J. G. Manning, Yale University

Table of Contents:

List of Illustrations and Tables ... viii
Prefaces  ... ix

Acknowledgments  ... xv

Abbreviations  ... xvi

A Note on Transliteration ...  xix

Chapter 1: The Second City ...  1

Chapter 2: Economic Life in Memphis ...  29

Chapter 3: Ethnic Minorities ...  76

Chapter 4: Ptolemies and Temples ...  99

Chapter 5: The Undertakers ...  144

Chapter 6: Apis and Other Cults ...  177

Chapter 7: Between Two Worlds: The Sarapieion ...  197

Chapter 8: Roman Memphis: An Epilogue ...  247

Appendixes
A. Memphite Professions Additional to Those Recorded in the Zenon Archive 259
B. The Undertakers' Archive ...  260

C. A Property Settlement in 197 B.C. ...  262

D. Apis Bulls of the Ptolemaic Period ...  263

Bibliography ...  285

Index  ... 319

Paper: $35.00 ISBN: 9780691140339
Cloth: $75.00 ISBN: 9780691152172

Should We Challenge the Beliefs of Our Students?

 

Is it part of our role as university educators to challenge the beliefs of our students? You're damn right it is! That's what university is all about.

Here's what Peter Boghossian says in Should We Challenge Student Beliefs?.

Until two weeks ago, I had been laboring under the naïve assumption that one of the primary goals of every academic was to change students’ beliefs when they were based on inaccurate information. I was awakened from this dogmatic slumber at an interdisciplinary faculty meeting by colleagues who reacted with dismay to my confession that I had tried and failed to disabuse one of my students of Creationist beliefs.

The conversation became more heated when I read to the group what the student had written on her final exam: "I wrote what I had to ‘agree’ with what was said in class, but in truth I believe ABSOLUTELY that there is an amazing, savior GOD, who created the universe, lives among us, and loves us more than anything. That is my ABSOLUTE, and no amount of ‘philosophy’ will change that."

Two of my colleagues, one in the language arts and one in psychology, argued that it was an inappropriate use of my authority to attempt to change this student’s belief; rather, my role should have been to provide her with data so that she could make better decisions.

I countered that both the process that allows one to arrive at Creationist conclusions, and the conclusions themselves, are completely divorced from reality, and that my role was not simply to provide evidence and counterexamples and hope for the best, but to help her overcome a false belief and supplant it with a true one.

Their unanimous reaction to this declaration temporarily made me question one of my basic assumptions about the responsibilities of college educators: Should professors attempt to change students’ beliefs by consistently challenging false beliefs with facts?

I share his frustration. There are far too many university professors who think that the "beliefs" of a student are off limits as long as they have something to do with religion. Those same professors would not hesitate to challenge belief in the superiority of whites over blacks or the efficacy of homeopathy or the validity of supply-side economics.

But it's a different story if a student says that God created the universe 6000 years ago. That belief mustn't be directly challenged because the foolishness of religious beliefs is off limits.

Isn't that strange?

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[Hat Tip: RichardDawkins.net]

Is Science Restricted to Methodologial Naturalism?

Maarten Boudry, Stefaan Blancke, and Johan Braeckman have an article coming out in Science & Education on "Grist to the Mill of Anti-evolutionism: The Failed Strategy of Ruling the Supernatural out of Science by Philosophical Fiat."

It relates to the idea that science is limited by its insistence on adhering to methodological naturalism. According to this view, science cannot investigate the supernatural. The view is popular among some who oppose creationism since it means that creationism can't be scientific, by fiat. It's also important for accommodationists because it allows science and religion to co-exist in separate magisteria.

I oppose such a definition of science but, up until a few years ago, I was always told that my opinion is irrelevant since all philosophers, and many scientists, agree that science is limited by methodological naturalism. That's why I was so delighted to meet the philosophers from Gent. Finally there was another point of view opposed to the methodological naturalism limitation. Now those who promote this limitation on science have to honestly admit that it's just their opinion and not a universally accepted definition of science.¹

Good News from Gent
Methodological Naturalism
Methodological Naturalism - How Not to Attack Intelligent Design Creationism
Here Be Dragons
An Interview with Maarten Boudry

Here's the abstract of the Science & Education paper.

According to a widespread philosophical opinion, science is strictly limited to investigating natural causes and putting forth natural explanations. Lacking the tools to evaluate supernatural claims, science must remain studiously neutral on questions of metaphysics. This (self-imposed) stricture, which goes under the name of ‘methodological naturalism’, allows science to be divorced from metaphysical naturalism or atheism, which many people tend to associate with it. However, ruling the supernatural out of science by fiat is not only philosophically untenable, it actually provides grist to the mill of anti-evolutionism. The philosophical flaws in this conception of methodological naturalism have been gratefully exploited by advocates of intelligent design creationism to bolster their false accusations of naturalistic bias and dogmatism on the part of modern science. We argue that it promotes a misleading view of the scientific endeavor and is at odds with the foremost arguments for evolution by natural selection. Reconciling science and religion on the basis of such methodological strictures is therefore misguided.

And here's a brief summary of their position ...

A widespread philosophical opinion conceives of methodological naturalism as an intrinsic and self-imposed limitation of science, as part and parcel of the scientific enterprise by definition. According to this view (Intrinsic Methodological Naturalism or IMN) – which is the official position of both the National Center for Science Education and the National Academy of Sciences and has been adopted in the ruling of Judge John E. Jones III in the Kitzmiller vs. Dover case – science is simply not equipped to deal with the supernatural and hence has no authority on the issue.3

In our view, however, methodological naturalism is a provisory and empirically anchored commitment to naturalistic causes and explanations, which is in principle revocable in light of extraordinary evidence (Provisory or Pragmatic Methodological Naturalism – PMN). Methodological naturalism thus conceived derives its rationale from the impressive dividends of naturalistic explanations and the consistent failure of supernatural explanations throughout the history of science.4

The distinction between Intrinsic Methodological naturalism (IMN) and Pragmatic Methodological Naturalism (PMN) is important. PMN is a conclusion based on centuries of scientific evidence strongly suggesting that natural explanations are sufficient to explain all phenomena. Those investigations include looking onto possible supernatural explanations.

Scientists have actually investigated possible miracles and found no evidence for them. Scientist have actually investigated the supernatural explanation for a world-wide deluge and refuted it. And if someone says that God made bacterial flagella, real scientists will try and find out whether that's true instead of just throwing up their hands and claiming that such an explanation is outside of science.

The implications of PMN are profound. It means that science and religion really are in conflict.

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1. Of course the accommodationists will admit no such thing as I'm sure you are about to see in the comments. Such an admission would require them to say that they mislead Judge Jones in the Dover trial.

Klaus Marsch, Ptolemäische Bankpapyri aus dem Herakleopolites (P.Herakl.Bank)

Ptolemäische Bankpapyri aus dem Herakleopolites (P.Herakl.Bank).
Papyri der Sammlungen in Heidelberg, Köln und Wien,
bearbeitet von Klaus Maresch
(Papyrologica Coloniensia Vol. XXXV)
Paderborn, Verlag F. Schöningh 2012,
XIV + 339 Seiten + DVD-Rom,
ISBN: 978-3-506-77543-6

1. Aufl. 2012, XIV + 339 Seiten + DVD-Rom, Engl. Broschur

ISBN: 978-3-506-77543-6

EUR 64.90 / CHF 86.90
Inhaltverzeichnis

Aegyptus LXXXIX (2009)

SOMMARIO

RACCOLTA DI SCRITTI DEDICATI A ORSOLINA MONTEVECCHI – II

Egitto terra di papiri
Atti del XIII Convegno Nazionale di Egittologia e Papirologia (Siracusa, 17 - 20 giugno 2010)

pag. C. BALCONI, Premessa  …  7

G. ROSATI, Il Libro dei morti di Takerheb ritrovato  … 9

M.C. GUIDOTTI, Il corredo della defunta Takerheb nel Museo Egizio di Firenze . .. 21

F. BOTTIGLIENGO, Il Libro dell’Amduat di Djedmut: uno studio preliminare … .27

S. MUSSO, S. PETACCHI, La collezione egizia del Museo dell’Accademia dei Concordi in Rovigo. Studi recenti e progetti in corso  … 37

C. ADRIANO, La collezione egizia di Salvatore Pugliatti: un resoconto sullo
stato dei lavori  … 55

M. NUZZOLO, R. PIRELLI, Nuove ricerche archeologiche nel tempio solare di Niuserra ad Abu Ghurab … 67

B. GILLI, The Past in the Present: the Reuse of Ancient Material in the 12th Dynasty … 89

R. CZERNER, Ricostruzione teorica degli edifici monumentali di Marina el- Alamein  …  111

G. BA ̨KOWSKA-CZERNER, Divinità egizie nella città greco-romana di Marina el-Alamein … 125

C. BASILE, A. DI NATALE, Restauro dei papiri e indagini preliminari agli in- terventi di restauro  … 141

G. PURPURA, I papiri e le costituzioni imperiali in Egitto … 155

A. SOFIA, Sopatro di Pafo ad Alessandria e i suoi legami con la commedia
fliacica in Magna Grecia … 22

C. GIUFFRÉ SCIBONA, Ricordo di Giacomo Scibona … 233

G. MESSERI, P.Flor. III 324 recto/verso e la famiglia del kôm Kâssûm … 239

G. MESSERI, Noterelle onomastiche  … 253

P. GROSSMANN, Antinoopolis Januar/Februar 2009. Vorläufiger Bericht über die Arbeiten im Frühjahr 2009 … 257

Pikaia is most primitive vertebrate known

 

Yesterday I was talking to one of my colleagues and she asked me if I'd heard the latest news about the Burgess Shale. I confessed ignorance so she told me that scientists had just discovered a primitive vertebrate fossil in the Burgess Shale.

Hmmm ... I was aware of possible primitive vertebrates ("Craniates" is a better term) in the deposits from China (e.g. Myllokunmingia) but I'd never heard of a vertebrate fossil in the Burgess Shale so I thought I'd check out the press release.

It's from my university!!! [Pikaia is most primitive vertebrate known]

Researchers from the University of Toronto, the Royal Ontario Museum (ROM) and the University of Cambridge have confirmed that a 505 million-year-old creature, found only in the Burgess Shale fossil beds in Canada’s Yoho National Park, is the most primitive known vertebrate and therefore the ancestor of all descendant vertebrates, including humans.

The research team’s analysis proves the extinct Pikaia gracilens is the most primitive member of the chordate family, the group of animals that today includes fish, amphibians, birds, reptiles and mammals. Their study is based on the analysis of 114 specimens and is published in the British scientific journal Biological Reviews.

The headline is wrong. Pikaia is a chordate but not a vertebrate as the quotations from the researchers make clear. The press release from Cambridge is only a bit better [Humans' ancient ancestor revealed - as a 505 million-year-old 'eel']

“The discovery of myomeres is the smoking gun that we have long been seeking,” said the study’s lead author, Professor Simon Conway Morris of the University of Cambridge. “Now with myomeres, a nerve chord, a notochord and a vascular system all identified, this study clearly places Pikaia as the planet’s most primitive chordate. So, next time we put the family photograph on the mantle-piece, there in the background will be Pikaia."

Furthermore, this really isn't news. Pikaia was featured in Stephen Jay Gould's book Wonderful Life published in 1989. Even then, Pikaia gracilens was thought to be a chordate similar in broad features to the cephalochordate (non-vertebrate chordate) Amphioxus. This classification was attributed to Simon Conway Morris in 1979. The Wikipedia article [Pikaia] points out that this classification was not universally accepted.

The important points are: (1) that Pikaia is a primitive chordate but not a primitive vertebrate and the press release is just dead wrong about that and, (2) this is old news.

BTW, is Conway-Morris right about Pikaia being the oldest chordate? I thought the fossils from China were older and some of those might even be vertebrates. If that's true then Pikaia lived after the divergence of cephalochordates and vertebrates and it's not even remotely possible that it's our ancestor.

There ought to be a new rule about press releases. Each one should have a statement at the end saying the the press release has been read by the authors of the study and they approve its content.

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Conway Morris, S. and Caron, J-B (2012) Pikaia gracilens Walcott, a stem-group chordate from the Middle Cambrian of British Columbia. Biological Reviews. Article first published online: 4 MAR 2012 [doi: 10.1111/j.1469-185X.2012.00220.x]