The importance of RNA-Seq and next generation

I want to draw your attention to: Genomics researchers astonished to learn microarrays still exist. I especially like this comment from the author (jovialscientist) ...

In recent years, RNA sequencing (RNA-Seq) has been favoured over microarrays. This new technology, using next-generation sequencing, is slightly more accurate, and nations have recently declared war over which is the best aligner to use.

In a recent poll, 98% of researchers answered "next-generation sequencing" to every single question – even their name, age and job title. The new science of "sequence first, think later" has been coined "nextgenomics".

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The very best argument for the existence of God

The atheists and skeptics had a wonderful time last Friday night. That's because the debate over "Is There a God?" was a tremendous defeat for Roman Catholics who turned out in droves to hear Philip Cleevely make the case for god.

Cleevely's only argument goes like this:

• The world began from nothing.
• That's very mysterious.
• Therefore, god(s) exist.

Justin Trottier did a very good job for the skeptic point of view. In particular, he made it very clear that he was NOT defending the proposition that gods do not exist. That's not what he means by atheism. He made it very clear that the burden of proof was on those making the extraordinary claim (god exists). He had to do this because rather than provide evidence for the existence of god(s), Cleevely kept trying to show that materialism.naturalism could not prove the nonexistence of gods.

I'm pretty sure that Cleevely didn't get it. I think he is committed to the idea that atheism means the denial of god(s) and he couldn't wrap his mind around the idea that he might be wrong.

The other point he (Cleevley) was trying to make was that science absolutely requires "something" in order to work. Since the universe began from "nothing" that means that it's beyond science. Again, this is an argument about the possible limitations of science but it says absolutely nothing at all about the case for the existence of god(s).

I think that most of the audience, even the Christians, realized that the priest was avoiding the question. As I said, Justin did an excellent job of steering the debate back to the main topic whenever possible. Near the end of the debate, Justin pointed out that Phillip Cleevely had not made much of a case and that the only evidence he had presented was not much more than philosophical babble. Justin didn't go on about this—just the right amount of harsh criticism—but it had to be said.

I'm pretty sure I wouldn't have been so kind.

Two other issues came up. Cleevely demanded that Justin explain where morality came from and where rational thought came from. Justin did a pretty good job but added that we don't have all the answers. He then assumed that Cleevely did have the answers but it turns out that Cleevely was not making the case for god based on the origin of morality or rationality. He said that those topics were too complicated—maybe they could be covered in another debate. The point of his questions was to show that science doesn't have all the answers. The implication is that because science doesn't have all the answers then god exists but Cleevely was clever enough (or stupid enough?) to avoid saying this.

Finally, Cleevely is an ordained priest and the moderator kept referring to him as "Father" whereas Justin was addressed as "Justin." There was a big difference between the respect that the moderator showed for Father Cleevely and for atheist Justin Trottier.

I imagine that it's impossible to avoid "Father" in a debate sponsored by Roman Catholics. His opponent should have been addressed as "Mr. Trottier."

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Is There a God? Find out tonight!

There are still a few tickets available. Email me ASAP.

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Why is a brain surgeon afraid of evolution?

Michael Egnor is a brain surgeon who doesn't like evolution. Egnor isn't a scientist so why does it matter so much to him?

Listen to this podcast where Casey Luskin interviews Michael Egnor: Dr. Michael Egnor on Debating Intelligent Design. You may want to turn off your irony meter.

Egnor is afraid of evolution for exactly the right reasons. It's because evolution (and science) threaten his worldview. Science tells us that we don't have free will—at least not the kind of free will that Christians demand. Science tells us that there's no such thing as moral absolutes that are dictated by god(s). Science is materialistic and it may be the only valid way of knowing.

No wonder he's scared. Michael Egnor is a Roman Catholic and he knows that evolution threatens his religion.

You'll probably enjoy hearing Egnor and Luskin talk about atheist blogs and about the high quality of science writing on Evolution News & Views. Casey Luskin (lawyer) and Michael Engor (physician) are responsible for some of that high quality science writing.

David Klinghoffer really likes the podcasts. Here's his review at: Listening to Neurosurgeon Michael Egnor on the Brain and Intelligent Design, Rubik's Cube and Jerry Coyne's Blog.

I've exchanged many emails with brain surgeon and ENV contributor Dr. Michael Egnor, but I had never actually heard his voice till now. It's a good voice, which is vital for a physician, mellow yet authoritative, with the correct pitch and timbre. Egnor's stellar academic and medical background aside, I've often thought that, if you had no other information about a healthcare provider, what you don't want is a doctor with the wrong kind of voice.

Now you can hear Egnor as I just did in this fascinating new series of podcasts in which he is interviewed by Casey Luskin. Their themes include evidence of intelligent design in the complexity of the brain, but no less so in the simplest creature, a bacterium. Dr. Egnor compares that design to the solution of a Rubik's Cube. It doesn't happen by chance.

Egnor also talks about the unusual window that Jerry Coyne provides into the mind of a materialist, which is why his name comes up here often. Coyne, unlike many Darwin apologists, doesn't self-censor. You don't have to wonder: What does he really think about, for example, personal responsibility. Because he tells you! Whatever else Coyne may be, he's no weasel. For that, Egnor expresses his gratitude and -- yes, appropriately.

I'm disappointed that Egnor said nothing about me even though he posts quite a few comments on Sandwalk. Guess I don't get much respect.

I wonder why David Klinghoffer didn't mention Casey Luskin's voice?

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Jason Rosenhouse agrees that evolution is a threat to religion

Jason Rosenhouse also read the accommodationist article by Phil Plait [The Creation of Debate] and he also sees the problem.

I argued that, contrary to what Phil Plait believes, evolution is a threat to all superstitious beliefs, including those of theistic evolution creatinists (see my post at: The real war is between rationalism and superstition).

Read Jason Rosenhouse's post at: It’s Not Just Fundamentalist Religion That Has A Problem With Evolution. Here's the important part ....

So, after all, that, let us return to Plait’s argument. He tells us that the problem is too many people perceiving evolution as a threat to their religious beliefs. Indeed, but why do they perceive it that way? Is it a failure of messaging on the part of scientists? Is it because Richard Dawkins or P. Z. Myers make snide remarks about religion? No, those are not the reasons.

It is because these people have noticed all the same problems the scholars of Darwin’s time were writing about. It is because evolution really does conflict with their religious beliefs, but not because of an overly idiosyncratic interpretation of one part of the Bible. It is because the version of evolution that so worried the religious scholars of Darwin’s time, that of a savage, non-teleological process that produced humanity only as an afterthought, is precisely the version that has triumphed among modern scientists. And it is because the objections raised to that version of evolution in the nineteenth century have not lost any of their force today.

So I think the issue is just a tad more complex than Plait suggests. It manifestly is not the case that only the most narrow of fundamentalists has a problem with evolution. Evolution challenges the Bible, refutes the argument from design, exacerbates the problem of evil, and strongly challenges any notion that humanity plays a central role in creation. These are not small points, and Plait needs to acknowledge them.

I hope Phil Plait is listening.

I hope Ken Miller, Francis Collins, and Simon Conway-Morris are listening. They are not on my side in this war.

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Does an understanding of evolution help scientists understand the secrets of biology?

You're probably wondering why I would ask a question like, "Does an understanding of evolution help scientists understand the secrets of biology?" It's not my question. It's a paraphrase of a question asked by someone who goes by the pseudonym "PaV" on Uncommon Descent. Here's the full context from her post: Does Evolutionary Theory Really Help Scientists?

For a number of years, many of us at UD have made the argument that evolutionary theory, in practice, is of almost no help whatsoever in getting at the secrets of biology. I’ve taken the position personally that it actually hurts, and that it is not a matter of indifference to the study of biology whether evolution is employed or not. ID is the way to go.

Now, besides the fact that she is an IDiot, you may be asking why anyone would write such a thing.

Here's the scoop. Someone was looking at unknown RNAs in zebra fish and discovered that one of them encoded a protein that hadn't previously been characterized. This sort of thing happens all the time in various species so why is PaV so excited?

Here's the answer ...

They’ve studied this embryonic stage for 20 years, and couldn’t figure out the decisive signals for initiation of the gastrula. They had to look to “non-coding” RNA, i.e., “junk DNA,” in order to solve their new found secret.

And why didn’t they study “junk DNA” before? Well, evolutionary theory posits that it is “junk” (their word, not ours), so why investigate.

See? Evolutionary theory actually impedes scientific progress. And you wonder why we call them ....

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The real war is between rationalism and superstition

Phil Plait of Bad Astronomy watched the debate between Bill Nye and Ken Ham. He decided that both of them are wrong because the debate was framed as a war between evolution and religion. Like a long list of accommodationists before him, Phil Plait thinks he has the answer in his post: The Creation of Debate.

I can’t stress this enough. The conflict over the teaching of evolution is based on the false assumption that evolution is antagonistic to religion. This is why, I think, evolution is so vehemently opposed by so many in the United States. The attacks on the specifics of evolution—the claims about irreducibility of the eye, for example, or other such incorrect statements—are a symptom, not a cause. I can talk about how we know the Universe is old until the Universe is substantially older and not convince someone whose heels are dug in. But if we can show them that the idea of evolution is not contrary to their faith, then we will make far, far more progress.

That’s not to say I’ll stop talking about the science itself. That still needs to be discussed! But simply saying science is right and faith is wrong will never, ever fix the problem.

And this won’t be easy. As long as this discussion is framed as “science versus religion” there will never be a resolution. A religious person who doesn’t necessarily think the Bible is literal, but who is a very faithful Christian, will more likely be sympathetic to the Ken Hams than the Bill Nyes, as long as science is cast as an atheistic dogma. For example, on the Catholic Online website, the argument is made that both Ham and Nye are wrong, and casts science as an atheistic venture.

That must change for progress to be made.

This is the classic accommodationist position. Problem is, it's been tried and it doesn't work in the United States. And the reason it doesn't work is that Americans aren't that stupid. They realize that these debates really are about science vs. religion. They know that evolution is, in fact, antagonistic to religion.

Jerry Coyne points this out rather forcibly in his response to Phil Plait. Read Coyne's article: Debate postmortem II: Phil Plait goes all accommodationist. I'll get back to Jerry Coyne in a minute but first let me quote Phill Plait's "solution."

And who should do this? The answer to me is clear: Religious people who understand the reality of science. They have a huge advantage over someone who is not a believer. Because atheism is so reviled in America, someone with faith will have a much more sympathetic soapbox from which to speak to those who are more rigid in their beliefs.

It's possible that "religious people who understand the reality of science" is a very small group and it's even more possible that they will be opposed to science and evolution precisely because they DO understand the reality of science. Plait is probably thinking about Ken Miller and Francis Collins but it's not clear to me that they truly understand what science is telling us. Science is telling us that there's no need for god(s) in order to understand the world around us. Evolution tells us that life has no purpose.

What Phil Plait is saying is that the best people to defend evolution are those who think that there really is a creator god but he/she/it mostly used evolution as a method of creation. In other words, we atheists should rely on theistic evolution creationists to convince other creationists to adopt a somewhat different view of creationism! That probably means we should keep quiet unless we are willing to make the case for one version of supernaturalism. Why would we do that?

That may be acceptable to some people but it misses the point of the conflict as far as many atheists are concerned. Jerry Coyne said it best in response to the accommodationist views of Micheal Ruse some years ago. Coyne's letter, which appeared in Playboy after Ruse's article was published, said ...

[Ruse] fails to grasp the real nature of the conflict. It's not just about evolution versus creationism. To scientists like Dawkins and Wilson, the real war is between rationalism and superstition. [my emphasis, LAM] Science is but one form of rationalism, while religion is the most common form of superstition. Creationism is just a symptom of what they see as the greater enemy: religion. While religion can exist without creationism, creationism cannot exist without religion.

This passage has been widely quoted and I wholeheartedly agree with Coyne's view.¹

For many of us the real war is between rationalism and superstition and the battle over evolution is just a minor skirmish in that war. What this means is that New Atheists are not inclined to recruit people who believe in superstition in order to fight a war against superstition.

That may be acceptable to people like Phil Plait because they're not interested in fighting a war against all forms of superstition, including religion. Instead, they seem content to promote some forms of superstition over others. The accommodationists should not expect all atheists to agree with them and they should acknowledge the fact that many of us think science and religion are incompatible.²

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1. There's some doubt about whether Coyne actually said this in his letter. I'm quoting a second-hand source: Dawkins in The God Delusion.

2. I'm not saying we are correct. I'm just saying that after all these years it's disappointing to see so many accommodationists who just don't get it.

Creationist scientists and bottoms of barrels

One of the interesting quirks of creationists is their intense desire to gain credibility by finding religious scientists who agree with them about god(s) and creation. We saw a good example in the Ken Ham vs Bill Nye debate where Ken Ham managed to find several people who are Young Earth Creationists but nevertheless made a contribution to science or technology. Some were physicians and some were engineers but some were actually scientists [see the debate at: Bill Nye Debates Ken Ham].

I'm reminded of a passage in The God Delusion (p. 100) where Richard Dawkins says ...

The efforts of apologists to find genuinely distinguished modern scientists who are religious have an air of desperation, generating the unmistakably hollow sound or bottoms of barrels being scraped.

Dawkins goes on to point out that efforts to find creationist Nobel Prize winners in Physics, Chemistry, or Physiology & Medicine have been largely unsuccessful.

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IDiots discover that RNA has secondary structure

I suppose we should be happy whenever some IDiots manage to educate themselves but somehow I find it quite sad when it takes thirty or forty years. Here's an example of a somewhat late-blossoming IDiot who posts on Evolution News & Views (sic): RNA Shows Design, Too. She doesn't sign her name to the post—I think I know why.

Here's what she just discovered ...

RNA differs from DNA in one of the sugars that makes up its backbone and one of the bases that makes up its side branches (uracil instead of thymine); it is also usually found in single strands instead of DNA's double helix. New discoveries, though, are showing RNA does far more than passively transfer DNA's information to other places. It, too, is a masterpiece of intelligent design and function.

A paper in Nature describes how information is stored not only in RNA's base sequence, but in its folds. Because RNA has more degrees of freedom, it can take on a wide variety of forms not possible for DNA. "RNA has a dual role as an informational molecule and a direct effector of biological tasks. The latter function is enabled by RNA's ability to adopt complex secondary and tertiary folds and thus has motivated extensive computational and experimental efforts for determining RNA structures," the authors begin (emphasis added). In their conclusion, they say, "We identify hundreds of specific mRNA regions that are highly structured in vivo, and we show for three examples that these structures affect protein expression."

The paper by Rouskin et al. (2014) reports on the development of new software to detect secondary structure in RNA. This is news for IDiots who think that "new discoveries" show that RNA is capable of catalysis and other functions.

Think about that for a minute. This is 2014, it's 25 years since Sidney Altman and Tom Cech were awarded the 1989 Nobel Prize in Chemistry and more that 30 years since undergraduates were routinely taught about catalytic RNAs in introductory biochemistry courses. Those IDiots sure are slow learners.

In other words, the structure, not just the sequence, carries functional information.

Amazing. Sounds like they've never heard of the idea that ribosomal RNA catalyzes peptide bond formation and that it does so through secondary structure. They've never heard of self-splicing introns. All they have to do is read an introductory textbook of biochemistry or molecular biology.

Now if you connect this amazing new bit of information to the equally astonishing (not!) news that some lincRNAs have a function, you get this ....

More design found in what was formerly called junk; more information found parallel to existing information in RNA; more power found in the collective energy of intelligent agents. Why are you not surprised?

The real question is why are IDiots surprised by routine information that even high school students know?

And what does this have to do with intelligent agents? Has this person answered the quiz?

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Another day in New York

Our flight was canceled. We're spending another day in New York. Anyone want to meet for a beer or dinner?

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A quiz for those of you who think you understand Intelligent Design Creationism

One of the great ironies of the Intelligent Design Creationist movement is that its proponents don't understand evolution and they don't understand what their movement stands for. They can't agree on the meaning of intelligent design.

You might think I'm exaggerating about not understanding their own goals but just think about it for a moment. The movement encompasses people like Michael Denton who promote a deist version of creation and it also welcomes huge numbers of Young Earth Creationists who believe in the literal truth of the biblical creation myth. Many proponents are somewhere in between these extremes but the vast majority think that there's something seriously wrong with evolution that demands the intervention of an intelligent designer. The designer may have just made bacterial flagella and a few other complex molecular machines or he/she may have stepped in to make all the animal phyla. Almost every proponent of Intelligent Design Creationism thinks that the designer intervened in the human lineage to make humans special.

Someone named "nullasalus" thinks that it's only critics of Intelligent Design Creationism who are confused. He tries to set us straight at: A Quiz for Intelligent Design Critics.

In the near decade that I’ve been watching the Intelligent Design movement, one thing has consistently amazed me: the pathological inability of many ID critics to accurately represent what ID actually is, what claims and assumptions are made on the part of the most noteworthy ID proponents, and so on. Even ID critics who have been repeatedly informed about what ID is seem to have a knack for forgetting this in later exchanges. It’s frustrating – and this from a guy who’s not even a defender of ID as science.

I try really hard not to misrepresent the Intelligent Design Creationist movement. That includes my preference for adding the word "Creationist" to their label. What they're talking about is creationism—a being who creates the universe and who creates some aspects of living organisms.

It's never easy to say exactly what "the most noteworthy ID proponents" mean by intelligent design. That's because they can't agree among themselves. The most common characteristic is that they are all anti-evolution in one way of another. Some of them accept microevolution and some accept common descent but almost all of their writings focus on some aspect of evolution that they don't accept. It could be the idea of junk DNA, or the evolution of animals in the Cambrian, or any one of a long list of "icons of evolution" that scientists get wrong.

A great many prominent ID proponents are opposed to "materialism"—that means they support non-materialism, otherwise known as supernaturalism (e.g. founder Phillip Johnson). A great many prominent ID proponents try to paint all supporters of evolution as social Darwinists. They try to link us to Nazis and they go out of their way to denigrate Charles Darwin. This seems to be an integral part of the Intelligent Design Creationist movement and it can't be ignored.

Just read the titles of the major ID books. They are all about attacking evolution.

New friends in New York

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Pete Seeger (1919 - 2014)

Pete Seeger is dead. That means something to those of us who grew up in the 1960s. It was a time when opposition to war was so strong and so powerful that we thought it might bring an end to all wars.

We were so naive.

Peter Seeger wrote one of the most famous anti-war songs of all time, "Where have all the flowers gone." Peter, Paul, and Mary made it a big hit—and so did others. Here's Pete Seeger singing with them for the last time. This should be the anthem that marks the 100th anniversary of the beginning of World War I.

When will we ever learn?


We will be in Greenwich Village this weekend and I'll be thinking of Pete Seeger. Seeger also wrote "Turn! Turn! Turn!" Here's the best version by the Byrds: "A time for peace, I swear it's not too late."

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Hat Tip: Jerry Coyne

Seven things you need to know about evolution

John Hawks is a pretty cool guy. He studies anthropology with a special emphasis on the genetics of human evolution over the past million years or so. Right now he's in Ethiopia looking at fossils. I visited him a year ago at his lab in Madison, Wisconsin.

He written a summary of seven things about evolution. You should read what he has to say to see if you know enough about evolution. Here's a list of the seven things but each one requires a bit of explanation.

1. Evolution is change in a population
2. Evolution is genetic change
3. Many kinds of genetic changes are important to evolution
4. Evolution can be non-random
5. Evolution can be random, too
6. Populations evolve all the time
7. Evolutionary theory has changed a lot since Darwin's day

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Monday's Molecule #230

Last week's molecule was cholesterol [Monday's Molecule #229]. The figure shows how the molecule would look in a lipid bilayer (membrane). The winner was Tommy Stuleanu.

This week's molecule (below) is going to be hard. I won't be surprised if nobody gets the right answer. It's a key intermediate in an extremely important reaction. You need to give the common name AND the the overall reaction. Name the enzyme as well.

Email your answer to me at: Monday's Molecule #230. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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.)