Sean Carroll's View of Evo-Devo

I'm trying to teach students about different ways of looking at evolution in my course on molecular evolution. One of the myths about molecular evolution is that it applies only at the level of molecules and "real" evolutionary biologists don't have to think about it when they are out in the field studying flowers, fruit flies, or small fish.

This is a profound misunderstanding on many levels but one of the most important is that many biologists don't appreciate the contributions molecular studies have made to our understanding of phenotypic diversity. All biologists need to learn about the way genes produce diversity.

The combination of evolution and developmental biology (evo-devo) has provided considerable insights into the problem of phenotypic diversity. We now understand how a small set of genes can produce drastically different body types. Sean Carroll has written several books on this subject but if you don't have time to read them you can listen to a 37 minute lecture he gave last Fall: How Bugs Get Their Spots: Genetic switches and the evolution of form. Keep in mind that this lecture is partly about how to teach evolution to undergraduates and high school students.

Does evo-devo have to be incorporated into an extended evolutionary synthesis? If you listen to some of the main proponents of evo-devo you'd have to answer "yes" to this question. These proponents think that the Modern Synthesis cannot deal with the discoveries of evo-devo and it needs to be extended to cover the idea that small changes in regulatory genes can have large effects on morphology.

Unfortunately, there are two serious problems with evo-devo when presented as a theory. They both detract from the main message. The most important problem to do with perspective. The fundamentals of evolutionary theory ("extended" or not) have to be broad enough to cover all of biology. Evo-devo doesn't really do that because it focuses almost exclusively on large multicellular animals. To put this into perspective, look at the diagram below. It's from Keeling et al. (2005).


Find the "Kingdom" of "animals" on this tree of eukaryotes. When you see the small branch that defines the most important subject matter of evo-devo you'll begin to appreciate why some of us don't think this generalizes to a major extension of evolutionary theory. (Note that prokaryotes are not included in this tree so the problem is even worse than you imagine.)

The second problem has to do with the unfortunate hype that seems to come with promoting evo-devo. As I said above, much of it detracts from the important and valuable lessons we can learn from developmental biology. Here are some examples from Sean Carroll's talk.

He talks about evo-devo discoveries that "shattered expectations" and gives a few examples.

Expectation: Different Sets of Genes Build Different Body Forms

He claims that his advisers believed you could never learn about furry things from studying fruit flies. He's talking about regulatory genes, especially HOX genes, as though that was a truly shocking discovery.

Maybe it was to some people but I grew up in the world of Jacques Monod and a whole bunch of molecular biologists who were convinced that what we learned about bacteria and bacteriophage would apply to elephants (and fruit flies). And it did.

Sean is talking about a different set of people who, forty years ago, may not have been on top of molecular biology. It's time to stop using these bogeymen to make your field look more revolutionary than it is. He says that the discovery of HOX genes is a finding that no biologist on the planet anticipated as though the idea that you might have similar regulatory genes shared by a small cluster of species (see diagram above) was revolutionary.

Why was that revolutionary? By the time the first HOX genes were sequenced (in the early 1980s) we already knew that all living organisms (prokaryotes and eukaryotes) shared a number of genes in basic metabolic pathways including DNA replication, transcription, and translation. The first homeobox sequences were thought to be similar to the helix-turn-helix motif in bacterial regulatory proteins and none of my friends were shocked. Were yours?

Expectation: Vastly different structures with similar functions such as animal eyes, appendages, etc evolved from scratch via independent genetic paths.

This is mostly correct. We knew in the 1980s that insect legs and vertebrate legs, for example, were not homologous so we expected that some of the genes for these structures would be different.¹ This expectation has been confirmed in spite of what Sean Carroll might imply in his talk. The fact that regulatory genes controlling the expression of these different genes might be conserved is not a surprise.

Insects and mammals needed to evolve separate unique genes (from scratch) for their different appendages. These genes were easily brought under the control of existing regulatory proteins. They did not need to evolve new regulatory proteins, and they didn't.

So, if evo-devo represents a real challenge to evolutionary theory then what, exactly, is being challenged and how does evo-devo provide an answer? It seems to me that evo-devo is helping us understand some of the details about the history of life—especially animal life—but I'm not sure this is the same thing as making a contribution to evolutionary theory.

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1. Nobody expected the muscle and nerve cell genes to be different but we would have been truly shocked to find that insects contained the genes for making bones or that mammals had the genes for making chitinous exoskeletons.

Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J., Gray, M.W. (2005) The tree of eukaryotes. Trends Ecol. Evol. 20:670-676.

Hugh Ross Teaches Us about Evolution

There's been a lot of talk recently about teaching evolution. The IDiots want us to teach the "controversies" in evolution. I'm happy to oblige. For all you students out there, here's an example of the intellectual opposition to evolution. I think we need to expose every university student to this sort of controversy. It would do wonders for science education.

(Hugh Ross is an Old Earth Creationist. He has a Ph.D. in astronomy from the University of Toronto that qualifies him as an expert on evolution. He is Canadian, but please don't spread that around.)

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[Hat Tip: Pharyngula]

Christianity Today: Unreasonable Doubt

Jim Spiegel is a philosophy professor at Taylor University (a Christian College in Indiana, United States). He has published an article in Christianity Today: Unreasoanble Doubt, "The reasons for unbelief are more complex than many atheists let on."

It's interesting to see what a philosophy professor/Christian apologist has to say about why we have failed to be convinced about the existence of supernatural beings.

Paul provides at least part of the answer in the same Romans passage, noting that some people "suppress the truth by their wickedness" (1:18). We all suffer from intellectual blind spots created by personal vices and immoral desires. To the extent that we succumb to these, we may be tempted to adopt perspectives that enable us to rationalize perverse behavior.

In this regard, scholars are no different from anyone else. The 20th-century ethics philosopher Mortimer Adler (who was baptized quietly at age 81) confessed to rejecting religious commitment for most of his life because it "would require a radical change in my way of life, a basic alteration in the direction of my day-to-day choices as well as in the ultimate objectives to be sought or hoped for …. The simple truth of the matter is that I did not wish to live up to being a genuinely religious person."

Historian Paul Johnson's fascinating if disturbing book Intellectuals exposed this pattern in the lives of some of the most celebrated thinkers in the modern period, including Rousseau, Shelley, Marx, Ibsen, Hemingway, Russell, and Sartre. In their private (and often public) lives, these Western intellectual stars were moral wrecks. Could their rejection of God—and, in particular, Christianity, with its exacting moral standards—have been entirely intellectual and dispassionate? Or might the same desires confessed by Nagel and Adler have played a role in their atheism?

Damn him! He's discovered the secret. My life is a moral wreck and that's why I have to reject God. Can you imagine how my life would be transformed if I ever became a Christian? I'm just not ready for that kind of morality.¹

(I assume this is one of those "sophisticated" arguments for religion that we hear so much about.)

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[Hat Tip: Canadian Atheist]

1. The University expects its members to use discretion and discernment in their choices of entertainment and recreation (some examples include media, Internet usage, and games). Social dancing is not permitted on or away from campus. However, acceptable forms of expression may include sanctioned folk dances, dances that are designed to worship God, dancing at weddings, and the use of choreography in drama, musical productions and athletic events. Activities and entertainment that are of questionable value or diminish a person's moral sensitivity should be avoided.

Happy Valentine's Day!

Who was Saint Valentine and why do we (males) have to buy flowers and chocolates today?¹ Nobody really knows very much about the Saints Valentine (there were about a dozen of them). The whole idea of romantic Valentine's day seems to have been invented by Geoffrey Chaucer sometime around 1380.

It seems like people in England just wanted to enjoy a bit of debauchery fun on February 14th so they connected their frolics with a Roman Catholic saint in order to get the permission of the church! Pretty clever, eh?

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1. And why don't women have to reciprocate?

A New Way of Regulating Human Genes?

ScienceDaily is all over this revolutionary discovery [Primates' Unique Gene Regulation Mechanism: Little-Understood DNA Elements Serve Important Purpose].

Scientists have discovered a new way genes are regulated that is unique to primates, including humans and monkeys. Though the human genome -- all the genes that an individual possesses -- was sequenced 10 years ago, greater understanding of how genes function and are regulated is needed to make advances in medicine, including changing the way we diagnose, treat and prevent a wide range of diseases.

"It's extremely valuable that we've sequenced a large bulk of the human genome, but sequence without function doesn't get us very far, which is why our finding is so important," said Lynne E. Maquat, Ph.D., lead author of the new study published February 9 in the journal Nature.

The actual paper is ...

Gong, C. and Maquat, L.E. (2011) lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature 470:284–288. [doi:10.1038/nature09701]

It's just one more example of how a transcribed Alu sequence can screw up gene expression. There's an outside chance that this is significant and has been selected as a regulatory mechanism but the most probable explanation is that it's just an accident. In any case, there's no reason to generalize from this single example.

This statement is unworthy of a scientist.

"Previously, no one knew what Alu elements and long noncoding RNAs did, whether they were junk or if they had any purpose. Now, we've shown that they actually have important roles in regulating protein production," said Maquat, the J. Lowell Orbison Chair, professor of Biochemistry and Biophysics and director of the Center for RNA Biology at the University of Rochester Medical Center.

The correct statement is that we've known for decades that the vast majority of Alu elements in the genome do absolutely nothing. However, there are a dozen examples already in the scientific literature of Alu sequences that affect transcription, RNA processing, mRNA, or translation. They've all proven to be unique, rare, cases. We strongly suspect that most long noncoding RNAs are junk but there are some excellent examples of ones that are functional.

Lynne Maquat has shown an effect of a transcribed Alu sequence but it's simply not true that every obscure phenomenon reveals an important role in regulating protein production. And it's simply not true that this example has any implications for the vast majority of Alu sequences in the genome. Save the hype for your grant application.

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[Hat Tip: Ryan Gregory at Genomicron: Grumble grumble… media… evolution… junk DNA… grumble.]

iPhone App

I have friends and relatives who love iPhone and Blackberry apps. Here's just the gift for someone who has everything and it's only $1.99.

This app is sanctioned by the Pope and it will guide you through confession by helping to list all your sins [Catholic church gives blessing to iPhone app].

There's something a little troubling about the screen shot. Do you see that box beside "Have I been involved with superstitious practices ..."? Isn't there something strange about leaving it unchecked while filling out a form like this?

I wonder how many sins there are and whether they have a box for "check all."

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[Hat Tip: RichardDawkins.net]

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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Inciting Hatred

 
This video is making the rounds. I'm including it here because so many people have been discussing "civility" and "politeness" in the wake of the Tuscon mass killing. In my opinion, it's not lack of civility that's the problem. The problem arises when you start treating your opponents as anti-American and unpatriotic and their ideas as illegitimate (not just a difference of opinion). That's when it becomes reasonable to consider using force to prevent your enemy from destroying the country. You are protecting America against dictatorial traitors and that's exactly what reasonable citizens should do.

Glen Beck is a master of this technique. He should not be surprised if some of his followers jump to the obvious conclusion. Indeed, CUNY professor Frances Fox Piven (78 years old) has been receiving death threats ever since Beck's rant aired on television last November [Glenn Beck's Ranting Sparks Death Threats Against 78-Year-Old Sociologist]. Is anyone surprised?

Why does Glen Beck still have a job?

A note to Canadian readers. Pay attention. This is the real problem, not simple lack of politeness.

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What Did You Learn at University?

What did you learn at university? Not much, it seems, according to the data in a new book titled Academically Adrift. The book is reviewed in the latest issue if Inside Higher Ed [Academically Adrift].

The data aren't surprising. The authors of the book show that 36% of students failed to learn anything after four years of college. Of those who did learn something, the gains were very modest.

Why don't students learn?

The main culprit for lack of academic progress of students, according to the authors, is a lack of rigor. They review data from student surveys to show, for example, that 32 percent of students each semester do not take any courses with more than 40 pages of reading assigned a week, and that half don't take a single course in which they must write more than 20 pages over the course of a semester. Further, the authors note that students spend, on average, only about 12-14 hours a week studying, and that much of this time is studying in groups.

Who's to blame for this sorry state of affairs?

Debra Humphreys, vice president for communications and public affairs of AAC&U, said that she viewed the book as "devastating" in its critique of higher education. Faculty members and administrators (not to mention students and parents) should be alarmed by how little learning the authors found to be taking place, she said. Humphreys also said that the findings should give pause to those anxious to push students through and award more degrees -- without perhaps giving enough attention to what happens during a college education.

"In the race to completion, there is this assumption that a credit is a credit is a credit, and when you get to the magic number of credits, you will have learned what you need to learn," she said. What this book shows, Humphreys added, is that "you can accumulate an awful lot of credits and not learn anything."

None of this is news my colleagues and me. Problem is, there's not much we can do about it. If we increase the rigor of our biochemistry courses and start demanding more of our students then the result won't be increased learning. It will simply mean that undergraduates will avoid biochemistry courses. In fact, that's already happening since the University of Toronto has developed dozens of new programs that will award degrees in the biological sciences without ever forcing students to take a rigorous course.

This brings up a question that I often ask my students. If university is supposed to be difficult (rigorous) then it's likely that some students won't be capable of completing a degree. In an ideal setting with expertly taught, challenging, programs, what percentage of the incoming class of students should expect to complete a degree? Clearly the answer can't be 100% because that bar is way too low. Should it be 50% as it was in many universities in the past? Lower?

The graduation rate at the University of Toronto has been pretty constant over the past decade at 73-75%. I assume that many of the students who drop out do so for reasons other than the rigor of university courses (e.g., personal problems, financial problems, transfers, changing goals etc.). Let's assume that this accounts for 15% of the drop-outs.

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[Hat Tip: Uncertain Principles]

Extraordinary Claims: Psychics, Homeopathy and Christ

 

This Friday night at 7:30 p.m. CFI Canada launches the much awaited Extraordinary Claims campaign with three lectures, a panel discussion and an audience question-and-answer session, for a critical analysis of Psychics, Homeopathy and Christ. The invitation has also been respectfully extended to hundreds in the Toronto area who support one or more of these claims. The night promises to be an exciting and fascinating experience. Don't miss out!

Professor James Alcock of York University will address Psychics, Dr. Iain Martel of the Committee for the Advancement of Scientific Skepticism (CASS) will analyze Homeopathy and John Loftus, a former Christian Minister and apologist, will take on Christ. The night will be moderated by Michael Kruse, co-chair of CASS.

Date and time: Friday, January 21, 7:30 p.m. to 10:00 p.m. CFI members have advance access to seating beginning at 6:45 p.m. Non-members will be seated shortly before the presentation begins.

Location: University of Toronto - MacLeod Auditorium - 1 King's College Circle, Room 2158 Google Map

Admission prices: $8 general, $5 students and FREE for CFI members. Become a CFI member or renew.

Prepaying admission by PayPal is offered HERE. Please print out your PayPal receipt and bring it with you.

CFI members please bring your membership card and check the expiration date to ensure you can get in for FREE. If you are unsure then call Centre for Inquiry Ontario at (416) 971-5676 or e-mail info@cficanada.ca

A members-only reception is being held at 5:30 p.m. at CFI Ontario (216 Beverly St.).

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Comments Allowed at Evolution News & Views!

 
Evolution News & View is one of the main blogs for promoting Intelligent Design Creationism. Up 'till now it has not allowed comments but that has changed. Here's the new policy ...

Of course, you might want to discuss it with the scientists and scholars themselves. To that end, comments will be allowed on selected articles. All comments are held for moderation. The debate over evolution and intelligent design attracts all kinds, including those who detract from the conversation by their obnoxious behavior. In order to maintain a higher level of discourse, we will not publish comments that use foul language, ad hominem attacks, threats, or are otherwise uncivil.

By way of contrast, this blog and many others run by defenders of evolution will allow all comments except spam. We're not afraid of contrary opinions or uncivil behavior from creationists. We get them all the time.

I wonder what they're really afraid of?

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[Image Credit: Institute for Creationist Strategies: Show pride in your anti-scientific beliefs]

The Bankruptcy of Evolutionary Psychology

Evolutionary psychologists never seem to give up. Their latest folly is to pretend that women have a series of evolved behaviors to avoid rape during the time that they're ovulating.

Jerry Coyne has already commented on the study and his follow-up posting is worth reading because it highlights the responses of others who have dissected the papers [The women of Slate take on evolutionary psychology].

The bottom line is that the entire field of evolutionary psychology is in big trouble and it is bound to become a major laughing stock unless evolutionary psychologists clean up their act [Evolutionary Psychology as Maladapted Psychology].

One of Jerry Coyne's comments caught my eye because we've just been reading the Gould & Lewontin Spandrels paper in class. Coyne said,

Like the stories of the Bible, there’s no evolutionary psychology hypothesis that can be disconfirmed by data. If your story doesn’t hold up, simply concoct another story. Of course, there’s no evidence for the alternative stories, either.

In 1979 Gould and Lewontin wrote,

The admission of alternatives in principle does not imply their serious consideration in daily practice. We all say that not everything is adaptive; yet, faced with an organism, we tend to break it into parts and tell adaptive stories as if trade-offs among competing, well designed parts were the only constraint upon perfection for each trait. It is an old habit. As Romanes complained about A.R. Wallace in 1900: "Mr. Wallace does not expressly maintain the abstract impossibility of laws and causes other than those of utility and natural selection... Nevertheless, as he nowhere recognizes any other law or cause... he practically concludes that, on inductive or empirical grounds, there is no such other law or cause to be entertained. The adaptationist programme can be traced through common styles of argument. We illustrate just a few; we trust they will be recognized by all:

(1) If one adaptive argument fails, try another. Zig-zag commissures of clams and brachiopods, once widely regarded as devices for strengthening the shell, become sieves for restricting particles above a given size (Rudwick, 1964). A suite of external structures (horns, antlers, tusks) once viewed as weapons against predators, become symbols of intra-specific competition among males (Davitashvili, 1961). The eskimo face, once depicted as "cold engineered" (Coon, et al., 1950), becomes an adaptation to generate and withstand large masticatory forces (Shea, 1977). We do not attack these newer interpretations; they may all be right. We do wonder, though, whether the failure of one adaptive explanation should always simply inspire a search for another of the same general form, rather than a consideration of alternatives to the proposition that each part is "for" some specific purpose.

Plus ça change, plus c'est la même chose.

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The Science Hall of Fame

 
Science has published the Science Hall of Fame, a list of the most famous scientists of the past few hundred years. They compiled the list by counting the number of times that a scientist was mentioned in books published since 1800. The standard is Charles Darwin whose citations are set at 1000 milliDarwins. The only one who ranked higher was Bertrand Russell at 1500 milliDarwins.

Here are the top 25. The ones on the bottom have scores of 152. One remarkable thing about this list is how few of them are really famous for doing science. Many of them are cited in popular books for other reasons. Another remarkable thing about the list is that all of the scientists in the top 25 are dead.

Bertrand Russell (1872-1970) (1500mD)
Charles Darwin (1809-1882) (1000mD)
Albert Einstein (1879-1955) (878mD)
Lewis Carroll (1832-1898) (479mD)
Claude Bernard (1813-1878) (429mD)
Oliver Lodge (1851-1940) (394mD)
Julian Huxley (1887-1975) (350mD)
Karl Pearson (1857-1936) (346mD)
Niels Bohr (1885-1962) (289mD)
Alexander Graham Bell (1847-1922) (274mD)
Max Planck (1858-1947) (256mD)
Francis Galton (1822-1911) (255mD)
Robert Oppenheimer (1904-1967) (252mD)
Louis Pasteur (1822-1895) (237mD)
Chaim Weizmann (1874-1952) (236mD)
Alfred North Whitehead (1861-1947) (229mD)
Marie Curie (1867-1934) (189mD)
Robert Koch (1843-1910) (185mD)
Isaac Asimov (1920-1992) (183mD)
James Jeans (1877-1946) (182mD)
Ray Lankester (1847-1929) (175mD)
Stephen Jay Gould (1941-2002) (169mD)
Norbert Wiener (1894-1964) (163mD)
Rachel Carson (1907-1964) (152mD)
Carl Sagan (1934-1996) (152mD)

The website has an interactive table that links you to Wikipedia articles. If you click on "Karl Pearson," for example, you'll learn about his science. You can also click on the citation score to see how their citations vary over time. I've copied the charts for Dawkins and Gould so you can see how they compare.

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Homeopathy: Cue or Con?

 
Check out the Marketplace show. If you live in Canada, go to Cure or Con?, otherwise watch it on YouTube (below). Our Center for Inquiry friends in Vancouver overdose at the beginning of the show. Will they survive?

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Homeopathy on Marketplace

 
We've known about this upcoming show for several months because the producers have been contacting skeptical groups to get both sides of the story. Watch it tonight on CBC (Canada) at 8 PM.

Our Vancouver members of the Centre for Inquiry get to have all the fun!

Cure or Con?

Erica Johnson investigates one of the fastest growing alternative health treatments in the country: homeopathy. Ontario homeopaths are about to become the first province in Canada to regulate homeopathy — lending credibility to this unproven practice.

Canada's leading consumer ally takes a long hard look at the theories, and the remedies. For the first time in Canada, we conduct a test of homeopathic medicines, investigating the science behind these so-called medicines. In light of our results, we ask both the Ontario government and Health Canada why they are lending credibility to the homeopathic industry. Johnson also meets up with a rep from the world's leading manufacturer of homeopathic medicines, who admits that even the company doesn't know how homeopathy is supposed to work.

Watch, as we witness a Vancouver group of skeptics taking part in a group overdose of homeopathic remedies. Perhaps most disturbing we learn that some homeopaths are treating cancer patients with homeopathic remedies — this despite a leading cancer specialist saying there is no role for homeopathy in the treatment of cancer, that it is a "scam that is not evidence-based".

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25 Influential Atheists

 
Here's a list of The 25 Most Influential Living Atheists. How many do you recognize? Are they good people or are they all morally degenerate because they're not scared of God?

Why isn't Hemant Mehta on the list?

Here's a better list 'cause it includes some people who are much more interesting than Daniel Dennett [The 50 Most Brilliant Atheists of All Time].

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A Challenge to Fans of Alternative Splicing

There are many well-known examples of alternative splicing. These examples have been taught in undergraduate courses for 30 years and they are prominently featured in textbooks. Alternative splicing exists.

Here's the problem. The explosion of EST data in the 1990's resulted in detection of many sequences suggesting that alternative splicing was much more widespread that previously suspected. The vast majority of these claims have not been verified and many of them have been removed from the annotated genomes published in the past few years.

Now we have a whole new set of claims based on high throughput analysis of transcripts from a variety of organisms and tissues. Many workers believe that the majority of human genes are alternatively spliced and some even publish articles stating that 95% of humans genes exhibit alternative splicing. One of my colleagues who makes such a claim says that just because a gene is alternatively spliced doesn't mean that the various isoforms of RNA are functional but I think that's disingenuous. If it's going to be a meaningful term then "alternative splicing" has to imply that that at least two different versions of RNA have some biological function.

I've asked repeatedly for evidence that some particular genes are alternatively spliced to give rise to two or more functional products. It should be possible to get this information from the databases used by these researchers—the ones that support their claim of widespread alternative splicing. Unfortunately, this has proven to be difficult. Whenever I search common alternative splicing databases I'm told that those databases aren't very good and the results aren't reliable.

Here's the challenge to all researchers who believe that a majority of human genes are alternatively spliced (in a biologically relevant manner). Show me your data. Pick one of the following sets of genes and demonstrate that most of them have functional alternatively spliced transcripts. If none of the genes in the set qualifies then explain why you reject the presumed alternative transcripts shown in popular databases. This shouldn't be much of a challenge if your claim is correct.

Note that this is a two part challenge. You have to first present evidence that there are functional alternative splicing events and then you also have to present the reasons why you reject some of the data from sequenced RNAs.

Here's an example from the human gene for triose phosphate isomerase (TPI1). The Entrez Gene entry is Gene ID: 7167. The primary entry shows one alternatively spliced transcript that removes the N-terminal coding region of the protein and creates an new larger N-terminal sequence. What is the evidence that this is biologically relevant? Now check out the known transcripts that have been detected according to UCSC Genome Browser, AceView, and Model Maker. These show additional variants affecting the splice junction sequences around exons 2, 4, and 6. Are these also examples of alternative splicing? Are they functional? If you reject these variants then what's the rationale for accepting some possible transcripts as real but rejecting others? Are some of them artifacts?

The three gene sets are ...

1. Human genes for the enzymes of glycolysis.
2. Human genes for the subunits of RNA polymerase with an emphasis on the large conserved subunits [Two Examples of Alternative Splicing]
3. Human genes for ribosomal proteins.

I selected these examples because we know the structures of the proteins so we can evaluate the possibility that an alternatively spliced message might produce a novel polypeptide chain. Of course there might be other reasons (regulation?) for producing alternatively spliced transcripts. Feel free to present the evidence.

Now it's possible that I've accidentally chosen sets of genes that do not exhibit alternative splicing. If that's the case then pick any other set of genes with a common function where the structure of the protein product is known. Meanwhile, you can explain why you reject all the putative splice variants for these genes.

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What Does San Marco Basilica Have to do with Evolution?

Everyone interested in evolution should read the famous critique of the adaptationist program by Stephen Jay Gould (1941-2002) and Richard Lewontin (1929 - ). Whether you agree with them or not, it's essential that you become informed about the adpatationist-pluralist controversy—also known as the neutral-selectionist controversy. That controversy is still very much a part of the debates over evolution, although the adaptationist side tends to argue that the controversy has been settled.

It's no secret that I'm a huge fan of Gould and if I had my druthers I'd make students read every one of his books, including, The Structure of Evolutionary Theory. I'm a pluralist.

My friend John Wilkins, a philosopher, visited St. Mark's Square and the Basilica last year. He's on the opposite side of this debate and he offers the best defense of adaptationism that I've seen in recent years. You should keep an eye on his blog, Evolving Thoughts, it's a must-read for anyone who's serious about evolution. I blogged about John's version of adaptationism [An Adaptationist in Piazza San Marco].

This is a rich topic for undergraduates and there are many potential essay topics.

Michael Ruse Defends Adaptationism
Richard Dawkins' View of Random Genetic Drift
Naked Adaptationism

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Gould, S.J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme. Proceedings of the Royal Society of London. Series B, Biological Sciences, Vol. 205, No. 1161, The Evolution of Adaptation by Natural Selection (Sep. 21, 1979), pp. 581-598. [AAAS reprint] [printable version]

Secret Alien Messages in Your Genome

 
Today is the first day of my course on molecular evolution and I want the students to experience the give-and-take of scientific—and not so scientific—debate in the blogosphere.

Their first assignment is to read the following quotation from an article by Paul Davies and answer the question that follows.

Paul Davies is a professor at Arizona State University. He was trained as a physicist and he lists his interests as cosmology, quantum field theory, and astrobiology. The quotation is from an article he wrote last April in the Wall Street Journal [Is Anybody Out There?: After 50 years, astronomers haven't found any signs of intelligent life beyond Earth. They could be looking in the wrong places.]

Another physical object with enormous longevity is DNA. Our bodies contain some genes that have remained little changed in 100 million years. An alien expedition to Earth might have used biotechnology to assist with mineral processing, agriculture or environmental projects. If they modified the genomes of some terrestrial organisms for this purpose, or created their own micro-organisms from scratch, the legacy of this tampering might endure to this day, hidden in the biological record.

Which leads to an even more radical proposal. Life on Earth stores genetic information in DNA. A lot of DNA seems to be junk, however. If aliens, or their robotic surrogates, long ago wanted to leave us a message, they need not have used radio waves. They could have uploaded the data into the junk DNA of terrestrial organisms. It would be the modern equivalent of a message in a bottle, with the message being encoded digitally in nucleic acid and the bottle being a living, replicating cell. (It is possible—scientists today have successfully implanted messages of as many as 100 words into the genome of bacteria.) A systematic search for gerrymandered genomes would be relatively cheap and simple. Incredibly, a handful of (unsuccessful) computer searches have already been made for the tell-tale signs of an alien greeting.

Here's the question. Assume that the aliens inserted a 1000 bp message in the same place in the genomes of every member of our ancestral population from five million years ago. At that point every organism in the species had exactly the same message in a region of junk DNA.

If you were to sequence that very same region of your own genome what would the message look like today? Would it be different from the original message of five million years ago? Is there a way of reconstructing the original message and interpreting it?

Comments will be held until tomorrow evening in order to give everyone a fair shot at coming up with an answer.

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Photo Credit: Lieutenant Ellen Ripley communicates with aliens.

How to Do Good Science

Richard Feynman (1918–1988) was a very smart American physicist who's words are often quoted ... for good reason.

Here's one quotation where he describes how good scientists should behave. It's a point I make in my class on scientific controversies and it's worth emphasizing because so many modern scientists ignore it.

Feynman is specifically referrring to "cargo cult science" but his advice applies to a lot of of modern biology as well.

There is one feature I notice that is generally missing in "cargo cult science." It's a kind of scientific integrity, a principle of scientific thought that corresponds to a kind of utter honesty — a kind of leaning over backwards. For example, if you're doing an experiment, you should report everything that you think might make it invalid — not only what you think is right about it; other causes that could possibly explain your results; and things you thought of that you've eliminated by some other experiment, and how they worked — to make sure the other fellow can tell they have been eliminated.

Details that could throw doubt on your interpretation must be given, if you know them. You must do the best you can — if you know anything at all wrong, or possibly wrong — to explain it. If you make a theory, for example, and advertise it, or put it out, then you must also put down all the facts that disagree with it, as well as those that agree with it. There is also a more subtle problem. When you have put a lot of ideas together to make an elaborate theory, you want to make sure, when explaining what it fits, that those things it fits are not just the things that gave you the idea for the theory; but that the finished theory makes something else come out right, in addition.

In summary, the idea is to try to give all of the information to help others to judge the value of your contribution; not just the information that leads to judgment in one particular direction or another.

Richard Feynman, "Cargo Cult Science" in Surely You're Joking, Mr. Feynman!

Think about Feynman's words next time you read a paper on the importance of alternative splicing, the disappearance of junk DNA, or anything about evolutionary psychology.

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Splicing Error Rate May Be Close to 1%

Alex Ling alerted me to an important paper in last month's issue of PLoS Genetics. Pickrell et al. (2010) looked at low abundance RNAs in order to determine how many transcripts showed evidence of possible splicing errors. They found a lot of "alternative" spliced transcripts where the new splice junction was not conserved in other species and was used rarely. They attribute this to splicing errors. Their calculation suggests that the splicing apparatus makes a mistake 0.7% of the time.

This has profound implication for the interpretation of alternative splicing data. If Pickerell et al. are correct—and they aren't the only ones to raise this issue—then claims about alternative splicing being a common phenomenon are wrong. At the very least, those claims are controversial and every time you see such a claim in the scientific literature it should be accompanied by a statement about possible artifacts due to splicing errors. If you don't see that mentioned in the paper then you know you aren't dealing with a real scientist.

Here's the abstract and the author summary ..

Abstract

While the majority of multiexonic human genes show some evidence of alternative splicing, it is unclear what fraction of observed splice forms is functionally relevant. In this study, we examine the extent of alternative splicing in human cells using deep RNA sequencing and de novo identification of splice junctions. We demonstrate the existence of a large class of low abundance isoforms, encompassing approximately 150,000 previously unannotated splice junctions in our data. Newly-identified splice sites show little evidence of evolutionary conservation, suggesting that the majority are due to erroneous splice site choice. We show that sequence motifs involved in the recognition of exons are enriched in the vicinity of unconserved splice sites. We estimate that the average intron has a splicing error rate of approximately 0.7% and show that introns in highly expressed genes are spliced more accurately, likely due to their shorter length. These results implicate noisy splicing as an important property of genome evolution.

Author Summary

Most human genes are split into pieces, such that the protein-coding parts (exons) are separated in the genome by large tracts of non-coding DNA (introns) that must be transcribed and spliced out to create a functional transcript. Variation in splicing reactions can create multiple transcripts from the same gene, yet the function for many of these alternative transcripts is unknown. In this study, we show that many of these transcripts are due to splicing errors which are not preserved over evolutionary time. We estimate that the error rate in the splicing of an intron is about 0.7% and demonstrate that there are two major types of splicing error: errors in the recognition of exons and errors in the precise choice of splice site. These results raise the possibility that variation in levels of alternative splicing across species may in part be to variation in splicing error rate.

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Pickrell, J.K., Pai, A.A., and Gilad, Y., Pritchard, J.P. (2010) Noisy Splicing Drives mRNA Isoform Diversity in Human Cells. PLoS Genet 6(12): e1001236. doi:10.1371/journal.pgen.1001236

Extraordinary Claims about Human Genes

Sandra Porter of Discovering Biology in a Digital World has recently attended a talk by Chris Mason of Cornell University. According to Sandra, Chris Mason made the following claims based on his analysis of RNAs from various tissues (human? mammal?). [Next Generation Sequencing adds thousands of new genes]

1. A large fraction of the existing genome annotation is wrong.
2. We have far more than 30,000 genes, perhaps as many as 88,000.
3. About ten thousand genes use over 6 different sites for polyadenylation.
4. 98% of all genes are alternatively spliced.
5. Several thousand genes are transcribed from the "anti-sense"strand.
6. Lots of genes don't code for proteins. In fact, most genes don't code for proteins.

I bet that every one of those claims is wrong.

There's a saying about extraordinary claims—they require extraordinary evidence. In this case, I'm pretty sure the "evidence" is the detection of low abundance transcripts using highly sensitive sequencing technology. Anyone who's ever learned about DNA binding proteins knows about non-specific binding and they know that spurious transcription is inevitable. In order to overthrow our view of the number of genes and how they behave, you will have to convince me that you've ruled out accidental spurious transcription (junk RNA).

I think it's somewhat disingenuous to be giving a talk where you claim we have 88,000 genes and 98% of them are alternatively spliced. (The term "alternative splicing" implies biological significance and not just splicing errors.)

In order to evaluate transcriptome data we need to know the abundance of the transcript. It's not sufficient to simply report that such-and-such region of the genome was transcribed. Researchers have got to report the average number of transcripts per cell in the tissue they are analyzing. I'm betting that if we saw that data we would instantly recognize that the so-called new "genes" are producing less than one transcript per cell. If that's the case it can't be biologically significant in a large mammalian cell.

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How Similar Are Humans and Chimpanzees?

 
When it comes to comparing DNA sequences of individual genes, the human and chimp versions are almost identical in sequence. They differ by only 1-2%. That result gave rise to the oft-quoted similarity of 98-99%.

But that's not the whole story. Outside of the genes there's a large amount of DNA that's less similar. We know this because we now have the sequences of both the human and chimp genomes. Furthermore, there are sequences present in the human genome that are absent in the chimp genome and vice versa. If you look at the whole genomes, the overall similarity is about 95% or so depending on how you do the calculation.

Creationists make a big deal about this. They claim that the newest data proves that evolutionists are wrong and chimps aren't necessarily our cousins. The latest debate is between Fazale Rana on the Reasons to Believe (RTB) website and Dennis Venema on the BioLogos website. The important scientific point is about the actual similarity and how is it calculated?

Fortunately for us, Todd Wood of the Center for Origins Research at Bryan College in Dayton, Tennessee, USA is on the case. Todd belongs to a young-Earth creation study group [BSG] but don't let that fool you. He's doing a pretty good job of sorting out the facts in the case.

RTB and the chimp genome Part 1
RTB and the chimp genome Part 2
RTB and the chimp genome Part 3
RTB and the chimp genome Part 4
RTB and the chimp genome Part 5

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Photo Credit: chimpanzee.net

A Defense of the "Theistic Evolution" Version of Creationism

 
Conor Cunningham¹ has just published a defense of Christianity against the attack of Darwinism. I've ordered his book, Darwin's Pious Idea: Why the Ultra-Darwinists and Creationists Both Get it Wrong, and I look forward to commenting on it in future posts.

Meanwhile, here's an excerpt from his BBC series Did Darwin Kill God? You can see right away that there's going to be problem with someone who equates Darwin with modern evolutionary theory. It means that Cunningham lacks scientific credibility making his arguments mostly moot.

There might be a problem with his theology as well but that's not something I'm very interested in. Perhaps some theist can answer a question? If Genesis has always been taken metaphorically and not literally by the Christian church, then what about the rest of the Bible? Specifically, are Christian supposed to take the stories of Jesus as metaphor and not fact? Is the death and resurrection of Jesus something that never actually happened? Is it just a metaphor? What the official Christian view of this?

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Conor Cunningham is a lecturer in theology and religious studies at the University of Nottingham in the United Kingdom.