Every non-lethal genome position is variable in the human population

Melissa Wilson Sayres blogs at mathbionerd and Panda's Thumb. A recent post on Panda's Thumb address a tweet from Daniel Wegmann where he said "Every non-lethal genome position is variable in the human population."

She asks "Is this true?" and proceeds to show that it is [How many mutations?]. She assumes that the human mutation rate is 1.2 × 10^-8 per sit per generation. Multiply this by 7.16 billion people on the planet and you get an average of 86 mutations at every single base pair in the human genome.¹

Many of these mutations will be deleterious and they will be quickly eliminated from the population if they are lethal or cause severe problems. Some moderately and slightly deleterious mutations will be present in the population because they haven't yet been eliminated by negative selection. (Some will have no effect if they are present in only one copy of your diploid genome.)

To a first approximation, the statement is pretty accurate. If it's true that most of our genome is junk then the nucleotide sequence is not important.² As we sequence more and more genomes we should see heterogeneity at 90% of the base pairs in the genome. We haven't reached this sort of coverage but all available evidence is consistent with the idea that most positions can be variable.

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1 I prefer a larger mutation rate of 100 new mutations per generation for a total of 112 mutations at every site.

2. This doesn't rule out functions that are not sequence-specific. Such functions are known to exist but there are no reasonable hypotheses that justify such functions for most of the genome.

David Klinghoffer Asks a Serious Question?

Well, maybe not really serious. His latest post on Evolution News & Views (sic) is about something called "Darwinian censorship" ["Shut Up," They Said: On the Medved Show, John West Discusses Darwinian Culture of Censorship].

At the end, he asks ...

When did you last hear of a Darwinist willing to seriously entertain -- not merely condemn and shout down -- counterarguments. The most frequently employed argument in the Darwinian arsenal at the moment is "Shut up."

It seems to me that real scientists and philosophers have spent a considerable amount of time addressing the claims of Intelligent Design Creationism. I could even argue that they have spent too much time given that IDiots rarely pay attention.

In my own area of expertise, I've addressed many of the claims made in Darwin's Black Box, The Edge of Evolution, Icons of Evolution, The Myth of Junk DNA, Science & Human Origins, and Signature in the Cell. I've also discussed dozens of blog posts over the years.

And I'm not alone. There are hundreds of articles and posts by dozens of scientists and philosophers. David Klinghoffer's question is ridiculous. Perhaps he's confused because he demands "seriously entertain" and he's disappointed when we seriously entertain their arguments and conclude that they are silly. Perhaps he will only accept that we have "seriously entertained" their arguments when we agree with them? That wouldn't surprise me, it's perfectly consistent with creationist logic.

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IDiots Don't Understand Punctuated Equilibria

Intelligent Design Creationism is a movement dedicated to discrediting evolution and attacking the rational explanation of nature.¹ The evidence is in the books and blogs and the propaganda distributed to local school boards and state legislators. The attack on science and scientists makes up about 99% of their activities.

Given their dedication to disproving evolution, you'd think that the IDiots must at least understand it. Maybe not all of them—because there are some really, really, stupid IDiots—but certainly some of the most prominent IDiots should know what they're talking about? Right? Doesn't that seem reasonable?

The facts say otherwise. Off hand, I can't think of a single IDiot who has an adequate understanding of the science they attack. Believe me, I've tried harder than most to find an intelligent believer.

Dan Dennett vs. Andrew Brown

I remember meeting Andrew Brown in a London pub seven years ago. He didn't like the New Atheists then and he still doesn't like them. I remember struggling to understand his accommodationist position back in 2006 and failing completely. At the time I attributed it to the beverages we were consuming but later on as I read his articles—when we were both sober—I realized that his position made no sense.

Andrew Brown sat down with Dan Dennett to discuss "Do the New Atheists have any new ideas?.

Andrew Brown challenges philosopher and atheist Daniel Dennett to convince him that the New Atheists have new ideas – and that they have really changed the face of belief in America. Dennett, one of the original 'four horsemen' of new atheism (along with Richard Dawkins, Sam Harris and Christopher Hitchens), has argued that belief in God is not merely mistaken, but dangerous.

Watch the short video and judge for yourself whether Andrew Brown is making sense.

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[Hat Tip: Jerry Coyne]

Ugly Americans

I don't mean to pick on PZ Myers—he's just one of many seemingly intelligent people who think that the American system of government is far superior to the governments of countries like the United Kingdom, Japan, Canada, Australia, Jordan, Spain, Sweden, Malaysia, Belgium, the Netherlands, Norway, and Denmark.

Here's what he posted today [My deepest regrets to the people of the United Kingdom ] ...

Apparently, your antiquated monarchy is going to continue, and the birth of a child of extraordinary privilege warrants far more attention than the birth of thousands who will live in poverty. I hope you get over it soon, and I hope it doesn’t infect my country; despite fighting a revolution to get out from under a king, there are a lot of conservatives with a bizarre sentimental attachment to the idea of a hereditary aristocracy.

There's a certain irony in this statement since Americans are fond of celebrating babies born into extraordinary privilege, especially if they are movie stars. Furthermore, the percentage of children born into poverty in the USA exceeds that of many of the European monarchies. I'm reminded of pots and kettles.

But, more importantly, the condescending attitude of superiority is totally unjustified. The UK is a democracy with a parliamentary system of government and a ceremonial Head of State who happens to be a monarch. It's a system of government that is vastly superior to the American system, in my opinion. The people of the United Kingdom (and all other democratic monarchies) are perfectly capable of abolishing the monarchy if they choose. The fact that they haven't must mean that they like it that way.¹ Why can't Americans respect that? They certainly demand that the rest of the world respect their choices!

Why do Americans have so much trouble seeing the world as non-Americans see it?

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1. Of course there are many citizens of monarchies who wish to abolish the monarchy. You can be sure that quite a few of them will show up in the comments below.

Donald Prothero Reviews Darwin's Doubt

Donald Prothero is a paleontologist. He has reviewed Darwin's Doubt [ Stephen Meyer's Fumbling Bumbling Cambrian Amateur Follies]. The reason why this is important is because the IDiots want a "real expert" to review the book [see IDiot Ironly.

Well, they got their wish. It's a long, detained review but here's the fun part.

The entire literature of creationism (and of its recent offspring, "intelligent design" creationism) works entirely on that principle: they don't like any science that disagrees with their view of religion, so they pick tiny bits out of context that seem to support what they want to believe, and cherry-pick individual cases which fits their bias. In their writings, they are legendary for "quote-mining": taking a quote out of context to mean the exact opposite of what the author clearly intended (sometimes unintentionally, but often deliberately and maliciously). They either cannot understand the scientific meaning of many fields from genetics to paleontology to geochronology, or their bias filters out all but tiny bits of a research subject that seems to comfort them, and they ignore all the rest.

Another common tactic of creationists is credential mongering. They love to flaunt their Ph.D.'s on their book covers, giving the uninitiated the impression that they are all-purpose experts in every topic. As anyone who has earned a Ph.D. knows, the opposite is true: the doctoral degree forces you to focus on one narrow research problem for a long time, so you tend to lose your breadth of training in other sciences. Nevertheless, they flaunt their doctorates in hydrology or biochemistry, then talk about paleontology or geochronology, subjects they have zero qualification to discuss. Their Ph.D. is only relevant in the field where they have specialized training. It's comparable to asking a Ph.D. to fix your car or write a symphony--they may be smart, but they don't have the appropriate specialized training to do a competent job based on their Ph.D. alone.

Stephen Meyer's first demonstration of these biases was his atrociously incompetent book Signature in the Cell (2009, HarperOne), which was universally lambasted by molecular biologists as an amateurish effort by someone with no firsthand training or research experience in molecular biology. (Meyer's Ph.D. is in history of science, and his undergrad degree is in geophysics, which give him absolutely no background to talk about molecular evolution). Undaunted by this debacle, Meyer now blunders into another field in which he has no research experience or advanced training: my own profession, paleontology. I can now report that he's just as incompetent in my field as he was in molecular biology. Almost every page of this book is riddled by errors of fact or interpretation that could only result from someone writing in a subject way over his head, abetted by the creationist tendency to pluck facts out of context and get their meaning completely backwards. But as one of the few people in the entire creationist movement who has actually taken a few geology classes (but apparently no paleontology classes), he is their "expert" in this area, and is happy to mislead the creationist audience that knows no science at all with his slick but completely false understanding of the subject.

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Stop Taking Vitamin Supplements!

Here's a post for all my friends and acquaintances who think they have to load up on vitamin supplements ever day. You don't need them (unless you are ill or pregnant).

If you think you do, then chances are you've fallen victim to one of the biggest scams of modern times. It's not much different than the pitches made by snake oil salesmen over one hundred years ago. There are people making big money by convincing gullible citizens that they have vitamin deficiencies. Some of those people are doctors and many of the enablers are family physicians who don't know the scientific evidence behind vitamin supplements.

"There's a sucker born every minute."

David Hannum
(frequently attributed to P.T. Barnum)The Atlantic has published a nice summary of the current evidence: The Vitamin Myth: Why We Think We Need Supplements. Most of the article is about Linus Pauling and why he was spectacularly wrong about vitamin supplements. Here's the bottom line ...

On October 10, 2011, researchers from the University of Minnesota found that women who took supplemental multivitamins died at rates higher than those who didn't. Two days later, researchers from the Cleveland Clinic found that men who took vitamin E had an increased risk of prostate cancer. "It's been a tough week for vitamins," said Carrie Gann of ABC News.

These findings weren't new. Seven previous studies had already shown that vitamins increased the risk of cancer and heart disease and shortened lives. Still, in 2012, more than half of all Americans took some form of vitamin supplements.

I'm not convinced that moderate amounts of vitamin supplements will actually cause you much harm—the jury's still out on that IMHO. However, it's now abundantly clear that, for the average healthy person, spending money on vitamin supplements is no different that flushing that money down the toilet, which, coincidentally, is where most of the vitamins you take will eventually end up.

See also: What Kind of People Take Vitamins?.

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Re-learning Russian

Ms. Sandwalk and I are going to be in St. Petersburg (Russia) in a few weeks. We plan on spending four hours in the building on the right (and adjacent buildings) although I'm told that's not nearly enough time.

I'm trying to remember my Russian. I last studied it in high school 50 years ago. We've been watching videos of the main tourist spots in St. Petersburg and I can usually figure out what the signs are saying. For example, it was pretty easy to recognize the sign below. In fact, most of you could probably figure it out even if you haven't taken Russian.

Here's the problem. The language in most Western European cities is quite casual compared to the way it was in the past. A typical greeting might be similar to "hi" instead of "How are you?" The comparable words in Russian are Привет and Здравствуйте. Which one is more appropriate in Russia today? And which pronunciation of Здравствуйте should I use?

Similarly, I was taught to say Как вы поживаете (How are you?) but that's a very formal phrase. I get the impression that it's now thought to be archaic and you can easily skip the pronoun by saying Как поживаете. Can you get away with addressing a stranger using the informal first person version of "you," e.g. Как поживаешь?

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Monday's Molecule #210

Last week's molecule was the "go" conformation of the leader sequence in the E. coli trp operon. The winners were Rosie Redfield and Quyen Huynh. [Monday's Molecule #209].

Today's molecule isn't very complicated but it has a big effect. You need to be very specific in identifying the exact molecule shown in the figure. I won't accept answers that are ambiguous.

Email your answers to me at: Monday's Molecule #210. I'll hold off posting your answers for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

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

The Many Faces of Sal Cordova

The IDiots are getting all excited about Nick Matzke because he dared to criticize Darwin's Doubt, a book about evolution written by a philosopher.

The latest post is by Salvador Cordova (scordova) on Uncommon Descent [Two-faced Nick Matzke].

I don't think I can do full justice to the stupidity in this post, you have to read it yourself. Here's the gist ...

Matzke said, quite correctly, that phylogenetic methods can only detect sister groups, not ancestors. This is pretty obvious in the case of sequences because, in most cases, we don't have access to DNA or proteins from extinct ancestors.

Salvador Cordova thinks he was the first one to realize this ...

Not much difference between what Matzke said and I said! I’ve been telling him that since 2006, and now he finally acknowledges it publicly.

Now that's good for a laugh at the expense of IDiots but it gets even funnier. The IDiots think that the absence of living ancestors proves that god(s) created modern species.

I’ve said that it was creationists (like Linnaeus) before Darwin’s time who lumped humans along with the primates, and the primates along with the mammals, etc. The creationists perceived the “sister groups” with no physical ancestor (which suggests the “parent” was an idea in the mind of God, not a physical common ancestor).

The reason Darwinists have all these phylogenetic conflicts is that the ancestors which would resolve all the conflicts are the very ones they will not admit a priori because those ancestors are conceptual, not physical, and conceptual ancestors are anathema to Darwinsits because conceptual ancestors imply ID.

Like I said, you have to read the whole thing ... if you can stomach it.

I wonder why we call them IDiots?

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Bill Maher Shows Us that "Smart" People Can Believe Really Stupid Things

Bill Maher thinks he's a smart person ... maybe even an intellectual. Here's a video of him attacking smart people who believe really stupid things. It drips with sarcasm and mockery. At the end of the video you wonder how in the world people could be so stupid. Maher is upset about the resurgence of the "smart-stupid person." One of his targets is a former Prime Minister of Canada.

Hermant Mehta liked this video [Bill Maher Goes After Dr. Eben Alexander and Other Brilliant Scholars Who Believe in Complete Nonsense].


Speaking of smart-stupid people. Here's a video of Bill Maher talking complete nonsense about vaccines. He is corrected by a really smart person, Bill Frist. This is an example of irony and an example of hypocrisy. The hypocrisy is worse than the irony.

IDiot Irony

Sometimes I really wonder what goes on at the Discovery Institute.

As most of you know by now, Stephen Meyer has written a new anti-evolution book where he criticizes the expert scientific opinion on the Cambrian Explosion. He says that the experts are all wrong and the evidence shows that evolution is impossible. The only reasonable alternative is that god(s) made the primitive animals. Meyer has an undergraduate degree in physics and earth science (1981) and got a Ph.D. in history and philosophy of science ten years later (1991). He is not a scientist and he is not an expert on evolution.

Casey Luskin has a Master's degree in earth sciences but later on he got a law degree and he is primarliy a lawyer. He is not a scientist and he is not an expert on evolution.

David Klinghoffer is a writer. He is not a scientist and he is not an expert on evolution.

Nick Matzke is a graduate student who is finishing up his Ph.D. in evolutionary biology. He is a scientist and he is an expert on evolution. He is also an expert on Intelligent Design Creationism.

Nick Matzke wrote a long review of Darwin's Doubt—a book written by a philosopher [Meyer’s Hopeless Monster, Part II].

Casey Luskin, a lawyer, took it upon himself to critique Matzke's review [How "Sudden" Was the Cambrian Explosion? Nick Matzke Misreads Stephen Meyer and the Paleontological Literature; New Yorker Recycles Misrepresentation]. Luskin says,

Since Matzke published his review, The New Yorker reviewed Meyer's book. Gareth Cook, the science writer who wrote the piece, relied heavily on Matzke's critical evaluation, even though Matzke is a graduate student and not an established Cambrian expert. Cook uncritically recycled Matzke's claim that the Cambrian explosion took "many tens of millions of years," ...

Do you see the irony? Meyer is a philosopher and Luskin is a lawyer but poor old Nick is just a graduate student about to get a Ph.D. in evolutionary biology. Matzke is not an established Cambrian expert. Neither are Meyer or Luskin but that doesn't seem to stop them from criticizing Matzke and all other evolutionary biologists and all paleontologists.¹

David Klinghoffer just can't wait to contribute his two cents. Klinghoffer isn't a scientist and he certainly isn't an expert on paleontology but that doesn't mean he can't have an opinion [Regarding Matzke, Coyne, and Darwin's Doubt, a Reader Asks].

That is a good question. Casey Luskin has already demonstrated what a non-paleontologist Matzke is.

How could non-scientist Klinghoffer possibly know whether lawyer Casey Luskin had made a good case against evolutionary biologist Nick Matzke? Does Klinhoffer realize that Luskin is a lawyer, not a paleontologist?

Do you wonder why we call them IDiots?

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1. My irony meter survived but it was touch-and-go for a minute or two.

Can You Name These Famous People?

I was cleaning up my files and I came across this photo from seven years ago. It's one of those vanity photos¹ where I try to impress you by having my picture taken with famous people.

Can you name all the people in the photo (hint, I'm the one on the right). You're not allowed to guess if you are one of the people in the photo.

Are you impressed? (You should be.)

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1. That's what Jerry Coyne calls them

Speaking of Trees

My friends and colleagues, David Isenman and Jacqueline Segall, used to have a big tree in their back yard. On Monday July 8th it rained ... a lot. The ground became very soggy and the tree tipped over.

So much for the life of this tree. They need a new shed.

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What Is Humanism?

What the heck is humanism? The short answer is ... I have no idea.

If someone tells me they're a humanist then I can guess that they have some kind of ethical standards that have nothing to do with religion but that's about all I can guess. They might as well have told me that they are an atheist and leave it at that.

Are humanists socialists? Do they all favor socialized medicine and support unions? Do they oppose the death penalty? Are they in favor of gun control and abortion on demand? Do humanists oppose the American war in Afghanistan? Did they support the invasion of Iraq?

Are humanists willing to vote for a Republican or a Conservative? How about a Communist? Do all humanists think gay marriage should be legal? Would they legalize prostitution and pornography? Would they legalize drugs like cocaine and marijuana? How do they feel about euthanasia?

Do humanists support a public school system or are some in favor of vouchers and private schools? Do they all have the same position on immigration? on welfare?

I don't know the answer to any of these questions. I don't know what it means to be a humanist.

Hermant Mehta thinks that Humanism tells us what he believes. Watch this video to see what that means.


Still confused? Go to the American Humanist Association website and you'll be even more confused. Read the Humanist Manifesto and the essays by Fred Edwords. They don't answer any of the questions I asked.

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