Evolution's Hidden Force

I was really excited (not) when the January 8th edition of New Scientist arrived. The cover story was bound to be something I could use in my course when we discussed modern views of evolution. Even the title was provocative: Uncertainty principle: How evolution hedges its bets.¹

The article was written by freelance science writer Henry Nicholls. He lives in London UK and he has a Ph.D. (2007) in Evolutionary Ecology. Here's how the article begins ...

A man walks into a bar. "I have a new way of looking at evolution," he announces. "Do you have something I could write it down on?" The barman produces a piece of paper and a pen without so much as a smile. But then, the man wasn't joking.

The man in question is Andrew Feinberg, a leading geneticist at Johns Hopkins University in Baltimore; the bar is The Hung, Drawn and Quartered, a pub within the shadow of the Tower of London; and what's written on the piece of paper could fundamentally alter the way we think about ... evolution ....

Let's turn this into a quiz.

What did Andrew Feinberg write about on that piece of paper?

1. the importance of small RNAs
2. random genetic drift
3. epigenetics
4. species sorting
5. hierarchical theory
6. evo-devo
7. evolvability
8. mutationism
9. developmental constraints
10. contingency
11. alternative splicing
12. selfish DNA
13. the demise of the Central Dogma
14. facilitated variation
15. group selection
16. phenotypic plasticity
17. molecular chaperones
18. genome complexity and the myth of junk DNA
19. horizontal gene transfer
20. the death of trees
21. molecular drive
22. endosymbiosis
23. mass extinctions
24. punctuated equilibria
25. genomics
26. proteomics
27. systems biology
28. the high cost of a beer in London

All of these things have been touted as new ways of looking at evolution. Which one did he choose?

Here's a hint ...

Before setting foot in the pub, Feinberg had taken a turn on the London Eye, climbed Big Ben and wandered into Westminster Abbey. There, as you might expect, he sought out the resting place of Isaac Newton and Charles Darwin. He was struck by the contrast between the lavish marble sculpture of a youthful Newton, reclining regally beneath a gold-leafed globe, and Darwin's minimalist floor stone.

As he looked round, Feinberg's eyes came to rest on a nearby plaque commemorating physicist Paul Dirac. This set him thinking about quantum theory and evolution, which led him to the idea that ... XXX ... might inject a Heisenberg-like uncertainty into the expression of genes, which would boost the chances of species surviving. That, more or less, is what he wrote on the piece of paper.

Hmmm ... Hung, Drawn and Quartered ... that gives me an idea. Let me write it down ....

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[Photo Credit: Jaunted]

1. Most of you can't follow the link because it's behind a paywall.

Sing the National Anthem

Ms. Sandwalk has a thing about singing our national anthem, O, Canada. Not only does she think that every Canadian should sing along whenever it's played but they should do so in TWO languages!

It's really not that difficult. The words and the music are widely available on the internet and everyone sings from the same page.

Not so true in the USA as we see below. Christina Aguilera is singing just one of the hundreds of versions that are popular. You'd have to know in advance what version she was going to use if you want to sing along. Ms. Sandwalk is not happy.

Oh, say, can you see, by the dawn's early light,
What so proudly we hail'd at the twilight's last gleaming reaming?
Whose broad stripes and bright stars, thro' the perilous fight,
O'er the ramparts we watch'd, were so gallantly streaming?
Oh so proudly we washed at the twilight's last reaming
And the rockets' red glare, the bombs bursting in air,
Gave proof thro' the night that our a flag was still there.
O say, does that star-spangled banner yet wave
O'er the land of the free and the home of the nuh brave?

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[Hat Tip: Greg Laden's Blog: Sing along with Christina Aguilera]

A Changing Society

This is really funny ... "Name Something That Gets Passed Around."

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[Hat Tip: Friendly Atheist]

A Challenge to Homeopathy

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Evolution Made Us All

This is from Ben Hillman at Vimeo [Evolution Made Us All]. I appreciate the intent but I can't help but wonder whether such videos don't do more harm than good. It makes me very uneasy to see evolution presented in such a manner and I really don't like the glorification of Charles Darwin that we see in popular views on evolution.

If we're truly interested in advancing the goal of science education then videos such as this are part of the problem, not part of the solution.

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[Hat Tip: RichardDawkins.net]

Former Canadian Prime Minister Kim Campbell Challenges the Teabaggers on Evolution & Climate Change

The Right Honourable Kim Campbell is the former Conservative Prime Minister of Canada. I never voted for her party but I'm proud of her today. She took on Congressman Jack Kingston (R, Georgia) recently on the Bill Maher show and showed him how stupid he was for denying climate change and evolution.

Even intelligent conservatives in Canada know about science. Unfortunately, many of today's leaders of the Conservative Party don't qualify as "intelligent." However, I don't know of any Canadian federal politician who would publicly confess to such ignorance about science as Jack Kingston.

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The Accommodationist War: Josh vs Jerry

Jerry Coyne visited a group of Methodist in Chicago and had an interesting conversation [A confab with the faithful]. Josh Rosenau tried to paint this as a concession to accommodationism by emphasizing that Coyne was being polite [Minor Coyne snark].

Jerry is, quite rightly, having none of this as his comment on his blog indicates.

There's more discussion at "Gnu Atheist" does not mean "nasty"; "accommodationist" does not mean "nice".

The disappointing thing about this incident is that Josh has failed to grasp the point about accommodationism even though we've been trying to explain it to him for four years. If that's what the rest of the people at NCSE believe then the Gnus have been wasting their time.

And Josh isn't backing off in spite of all the criticism he's received: The danger of certainty.

Jerry fires back with Gnus can be gnice!.

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Support Corporations: Wear the Flower

Read about Raffelesia and wear the flower to support free enterprise and profit making.

Support People for Corporate Tax Cuts.

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People for Corporate Tax Cuts

The recent economic downturn was caused by the private sector, especially big banks and investment companies. As an average citizen and public sector employee, I was happy to help out by giving the private sector bundles of taxpayer money in order to rescue them from their own greed. After all, that's what the public sector is for—to support free enterprise with government money.

Private companies need your help more than ever. They need corporate tax cuts. You can't expect them to support corporate welfare payments with high corporate tax rates. That would be like giving money to themselves and they don't teach that in business school, do they?

Support People for Corporate Tax Cuts.

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Out of Africa, but When?

I'm very uncomfortable with popular claims about the migration of modern humans into Asia and Europe. You often see the date as 50,000 years ago and most people seem to think that this was a sudden event associated with the destruction of ancient hominids (Neandertal, Homo erectus) who lived in Asia and Europe at this time.

The recent date was based largely on mitochondrial DNA sequences and it required a reliable time reference that just wasn't there. As other nuclear genes were analyzed the dates indicated much older migrations. Then there's the fossil evidence. I'm not able to judge that evidence but it didn't seem to me to be as neat and tidy as a sudden exodus at 50,000 years ago would require.

Fortunately we have John Hawks, a scientist who's area of expertise covers archeology AND population genetics. He thinks that the date for "Out of Africa" should be older and he can back up his skepticism with evidence. Read his latest posting at: Jebel Faya and early-stage reduction. Will the new date end up being 100,000 years ago—or maybe even 150,000 years ago?

Since John doesn't allow comments on his blog I thought I'd open up some discussion here. John, aside from the question of modern Homo sapiens, when did Neandertals leave Africa and when was the migration of Homo erectus? How secure are those dates?

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P.S. As I was about to publish this post I did a quick check to see when the movie was released. It was 1985. This means that none of the students in my molecular evolution class were alive when it came out. I feel old.

[Image Credit: The map is from The Human Journey.]

Are the "Good Guys" Losing in America?

The battle between science and religion has been going on for centuries. Part of the conflict is over the teaching of evolution in American public schools. Religious parents don't want their children exposed to ungodly evolution and the most vocal of them want creationism taught as part of the science curriculum.

Now you might think that that this particular battle has been decisively won by the "good guys" because of all the court victories. Not so. The results in the classroom reveal that evolution is not being taught except in the most liberal states and a substantial number of teachers are teaching creationism in spite of the law.

You can read postings on The Panda's Thumb [Who controls America’s schools? Who should?] and on Pharyngula [Bad science education in the US]. Each of these authors has their own take on the issue.

I want to raise another question. What good has it done to win all the court cases? Has it prevented an even worse disaster? Has relying on lawyers to defend evolution been the right strategy or should more emphasis have been placed on promoting good science instead of the American Constitution?

There's one point that few people raise. Evolution is taught badly even in universities—and so is everything else. You might think that by the time a student graduates with a degree from university he or she will be knowledgeable enough to reject superstition and rely on critical thinking. If we can't even do a good job of teaching adults in university then how can we expect public school teachers to do any better? In an ideal world every parent who is a university graduate should be an ally of their child's teacher when it comes to supporting good science education.

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PZ Myers on TVOntario

PZ Myers gave a talk at the Atheist Alliance International meeting in Montreal last October. It was taped for TVOntario's "Big Ideas" show and it will air tomorrow (Sunday, January 30, 2011) at 5:30 pm.

Or, you can watch it right now on the TVO website at PZ Myers on Science and Atheism: Natural Allies. Even better, here's the YouTube version for your immediate viewing pleasure.

WARNING: PZ Myers is one of those Gnu Atheists and some people may find it offensive to have their cherished beliefs questioned.¹

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1. As Ricky Gervais said recently, "Just because you're offended doesn't mean you are right."

Zoë Walks

I hope you all appreciate the fact that I've not been inundating you with photos and videos of my granddaughter, Zoë. You probably don't share my view that she's the third most wonderful girl in the world.

Anyway, just in case you were feeling neglected, here's Zoë taking her first steps. She was almost walking during her visit at Christmas but now she's really a toddler.

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More Prebiotic Soup Nonsense

There's another round of nonsense under way, fueled by the discovery that chemical trickery can lead to a slight excess of L-amino acids over D-amino acids. There's a BBC News story about it at: 'Life chemicals' may have formed around far-flung star. The story is reproduced without comment on RichardDawkins.net.

The press reports refer to an article published in The Astrophysical Journal Letters [NON-RACEMIC AMINO ACID PRODUCTION BY ULTRAVIOLET IRRADIATION OF ACHIRAL INTERSTELLAR ICE ANALOGS WITH CIRCULARLY POLARIZED LIGHT]. Here's the abstract.

The delivery of organic matter to the primitive Earth via comets and meteorites has long been hypothesized to be an important source for prebiotic compounds such as amino acids or their chemical precursors that contributed to the development of prebiotic chemistry leading, on Earth, to the emergence of life. Photochemistry of inter/circumstellar ices around protostellar objects is a potential process leading to complex organic species, although difficult to establish from limited infrared observations only. Here we report the first abiotic cosmic ice simulation experiments that produce species with enantiomeric excesses (e.e.'s). Circularly polarized ultraviolet light (UV-CPL) from a synchrotron source induces asymmetric photochemistry on initially achiral inter/circumstellar ice analogs. Enantioselective multidimensional gas chromatography measurements show significant e.e.'s of up to 1.34% for (13C)-alanine, for which the signs and absolute values are related to the helicity and number of CPL photons per deposited molecule. This result, directly comparable with some L excesses measured in meteorites, supports a scenario in which exogenous delivery of organics displaying a slight L excess, produced in an extraterrestrial environment by an asymmetric astrophysical process, is at the origin of biomolecular asymmetry on Earth. As a consequence, a fraction of the meteoritic organic material consisting of non-racemic compounds may well have been formed outside the solar system. Finally, following this hypothesis, we support the idea that the protosolar nebula has indeed been formed in a region of massive star formation, regions where UV-CPL of the same helicity is actually observed over large spatial areas.

The authors assume that the primodial soup speculation about the origin of life is the most reasonable explanation. According to this widely believed scenario, life originated in a soup of organic molecules that supplied most of the molecules of metabolism such as glucose and amino acids (and nucleotides?). Presumably once life got underway these molecules were used up and only then did metabolic pathways evolve to synthesize these molecules.

The competing hypothesis is Metabolism First [Metabolism First and the Origin of Life]. In this scenario, the first steps involved the establishment of simple oxidation-reduction reactions across a "membrane" using inorganic molecules. Once this supply of energy was in place the first pathways led to synthesis of simple organic molecules like acetate and glycine.

What's wrong with the Primordial Soup model? Well, for one thing, it's awfully hard to imagine how incoming asteroids could supply enough material to make a difference. The maximum concentration of all amino acids in the ocean, for example, could never have been more than 10-100 pM and that's optimistic [Can watery asteroids explain why life is 'left-handed'?].¹

Instead of trying to prove that asteroids could carry a slight excess of L-amino acids, I wish these workers would apply a bit of healthy skepticism to the subsequent steps of the scenario. It's not reasonable to assume that minute quantities of amino acids could ever fuel the origin of life. Incidentally, the Primordial Soup Hypothesis also imagines that early cells used exogenous glucose as a fuel. This implies that the glycolysis pathway is more primitive that the gluconeogenesis pathway for synthesis of glucose. Unfortunately the data disproves this prediction. Gluconeogenesis is more ancient and glycolysis evolved later [Aldolase in Gluconeogenesis & Glycolysis]. A nasty little fact.

The real problem is not that metabolism firstists such as Bill Martin are right and soupists are wrong—although that's a very real possibility. The problem is that most scientists are not thinking critically about the origin of life. There are several possibilities and none of them are particularly convincing. However, the Primordial Soup Hypothesis has a number of glaring weaknesses that need to be addressed honestly and it doesn't do anyone any good if scientists sweep these weaknesses under the rug.

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1. We're talking about a primordial soup where the concentration of L-alanine might be 0.50 pM and the concentration of D-alanine might be 0.49 pM. That's supposed to be enough for life based on amino acids to evolve and to lead to the subsequent preference for synthesizing exclusively L-amino acids. How, exactly, does that work?

What Should Replace Religion?

Here's Daniel Dennett speaking in Montreal last October. He addresses the "problem" of what should replace religion once we get rid of it. You may wonder what "problem" he's referring to. After all, when you visit countries in Europe you don't see a pressing need to come up with some institutions that replace religion.

Here's a list of good things that religion provides according to Dennett: hope, love, beauty, joy, and moral teamwork. These are the things we get from organized religion.

Really? I haven't noticed that these things are missing in the lives of my atheist friends. Nor have I noticed that the people of Denmark or Belgium are loveless, joyless and incapable of moral teamwork. What the heck is he talking about? What he's talking about is the idea that a church is "the place where if you have to go there they have to take you in."

... churches do that very well. They are a safety net of last resort for many people, and not just poor people, ... churches open their doors to these people and they can do a better job at this than government agencies.

He's talking about churches as safety nets and sources of social support. What he's talking about is the (possible) necessity of churches in a country that rejects socialism. He's talking about America but he doesn't admit it.

You can watch the faces of this mostly Canadian audience, as I did, to see how well Dennet's ideas are being received. There's a lot of puzzled looks as you might expect in a country where socialized medicine is a universal right. Why do you need churches for those things that any just society must provide? Why do you need churches when you have publicly funded community centers where you can hang out with your friends and neighbors?

Things go rapidly downhill from that point on (about 12 minutes into the talk). The next part of the talk is about religious music. It includes some truly excruciating atheist gospel songs that the audience is subjected to. (They cut out a large part of that from the video.) The remainder of the talk has very little to do with the necessity of religion.

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