Teaching Evolution in Tennessee

The state of Tennessee is about to have a new law that impacts the teaching of science in their public schools. Here's how the National Center for Science Education (NCSE) describes the law.

Nicknamed the "monkey bill," HB 368 would, if enacted, encourage teachers to present the "scientific strengths and scientific weaknesses" of topics that arouse "debate and disputation" such as "biological evolution, the chemical origins of life, global warming, and human cloning."

It doesn't take a mental giant to see where the Tennessee legislators are coming from. They want to support teachers who challenge evolution in the classroom. Most of those teachers will, of course, be creationists of one form or another.

But here's the problem. Those ignorant legislators have been very clever to avoid mentioning religion or creationism. On the surface, the new law looks perfectly reasonable.After all, who wouldn't want students to learn both the scientific strengths and weaknesses of current theories of biological evolution?

Winners

Here are three winners having lunch. On the left is David Schuller (Monday's Molecule #156) and that's Joseph Somody (Monday's Molecule #159) on the right.

(Thank-you David for the photo.)

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Monday's Molecule #`165

Name this molecule. You don't need the full IUPAC name but you do need to be specific since there are several different molecules with very similar structures. You also have to tell us why this molecule is important in biochemistry.

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 kanamycin C (not A or B). It binds to the small subunit of the prokaryotic ribosome and inhibits translation. It is/was widely used in cloning experiments since there are several plasmids with kanamycin resistance alleles. I posted all three of the responses that recognized kanamycin but only one named this variant as kanamycin C. That person didn't mention that this was a translation inhibitor so there are no winners 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
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 10: no winner

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The Toronto Transit Commission Stands for Freedom of Speech

The Toronto Transit Commission (TTC) has resisted attempts to have a controversial ad removed from their buses, streetcars, and subways as reported in The Toronto Star [TTC won’t remove controversial ads].

But a review that is automatically triggered whenever the TTC gets at least five complaints about an ad found there were no grounds to pull either advertisement.

That review was by TTC chair Karen Stintz and TTC commissioner Maria Augimeri.

“Although I would not personally condone the comportment outlined in the advertisement, I feel that I do not have the jurisdiction nor the authority to promote its cancellation; particularly because the TTC would not fare well in a court challenge should the promoter of the advertisement choose to make this issue one of rights and freedoms,” Augimeri said of the ... ad.

“There is nothing that violates any of our policies, and we do have policies around our advertising (based on) the Ontario Human Rights Code, not promoting hate or violence,” said TTC spokesman Brad Ross.

“You don’t have to agree with the message, you don’t have to like the message of the advertiser. Our suggestion would be that if somebody takes issue with the ad they take it up with the advertiser,” he said.

Congratulations TTC! That's exactly right.

It doesn't matter what sort of ad triggered the complaints but just in case you're interested, here it is. The first paragraph says, "Dear Jesus, My mom and dad do drugs at home and it scares me. Will you help them stop? Thank you for hearing my prayer." The second paragraph is, "Don’t worry about anything; instead, pray about everything. Tell God what you need, and thank him for all he has done. If you do this you will experience God’s peace, which is far more wonderful than the human mind can understand." The ad is sponsored by Bus Stop Bible Studies.

Note: Hemant Mehta has a slightly different take on the issue [Christian Bus Ad Advises Child with Druggie Parents to Pray, Not Call for Help].

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[Hat Tip: Canadian Atheist]

Evo Devo and Giants

Anything found to be true of E. coli must also be true of elephants.

-Jacques Monod (1954)While preparing for the last lecture in my molecular evolution course I came across this quotation that explains Evo Devo.

The key to understanding form is development, the process through which a single-celled egg gives rise to a complex, multi-billion-celled animal. This amazing spectacle stood as one of the great unsolved mysteries of biology for nearly two centuries. And development is intimately connected to evolution because it is through changes in embryos that changes in form arise. Over the past two decades, a new revolution has unfolded in biology. Advances in developmental biology and evolutionary developmental biology (dubbed “Evo Devo”) have revealed a great deal about the invisible genes and some simple rules that shape animal form and function. Much of what we have learned has been so stunning and unexpected that it has profoundly reshaped our picture of how evolution works. Not a single biologist, for example, ever anticipated that the same genes that control the making of an insect’s body and organs also control the making of our bodies.

Sean B. Carroll “Endless Forms Most Beautiful: The New Science of Evo Devo” W.W. Norton & Co., New York (2005)

I've already criticized this point of view several times [Things You Didn't Know] [Sean Carroll's View of Evo-Devo] and I won't repeat them here. Read those posts to see what's wrong with Evo Devo.

If I have seen further it is by standing on ye sholders of Giants.

Isaac Newton, 1676I want to emphasize another point. I come from a culture that praised and admired the important work that formed the background to modern discoveries. My mentors were proud of the fact that they stood on the shoulders of giants.

Someone named anthrosciguy commented on my earlier post [Sean Carroll's View of Evo-Devo] by saying ...

No one wants to stand on the shoulders of giants anymore.

That struck me as a profound commentary on much of modern biological science so I thought I'd share it with you. These days it seems like everyone wants to claim credit for discovering something that nobody anticipated. You can't be standing on the shoulders of giants if you're proclaiming a revolution. That would look silly.

I'm pretty sure I know anthrosciguy's real identity but I'll leave it to him to out himself and take credit for a very clever statement.

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Carnival of Evolution #46

 

This month's Carnival of Evolution (46th version) is hosted by Bradly Alicea of Synthetic Daisies: Carnival of Evolution, Number 46 -- The Tree (structures) of Life

Welcome to Carnival of Evolution, Number 46. I am your host, Bradly Alicea. This month's theme is: the Tree (structures) of Life. Since this blog covers a mix of both biological and computational content, it is fitting that we explore this month's submissions in the context of trees (the computational kind) and biological classification (the biological kind). I will indulge in a historical and technical overview of trees used in evolutionary analysis, then present this month's posts.

The next Carnival of Evolution (May) will be hosted by John Wilkins and the one after that by PZ Myers. You can send articles directly to them or you can submit your articles at Carnival of Evolution. Bjørn is looking for someone to host the July edition. He would prefer someone who has not hosted before. Contact him at the Carnival of Evolution blog.

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Monday's Molecule #164

 

What is this structure and what is its significance? You don't need to come up with a chemical name but you do need to be as specific as possible.

Don't forget to tell us why this structure exists.

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 the cap structure on the 5′ end of eukaryotic mRNAs. It's actually a CAP 2 structure with methyl groups at the 2′ positions of the last two nucleotides but that terminology seems to be outdated so I won't insist that you specify. (Thanks to Bill Chaney for getting it right.) The winner is Sean Ridout. (Please contact me by email.)

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
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout

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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.