Friday, February 28, 2014

Why are the human and chimpanzee/bonobo genomes so similar?

David Klinghoffer isn't impressed by the fact that the DNA of humans and bonobos is 98.6% identical in the areas that can be aligned. Here's what he says at: This Might Be the World's Most Underwhelming Evidence for Darwinian Evolution ...
Oh please. If there are any "creationists" out there who are running scared, they need not do so. The new article [by Chris Mooney] is titled "You Share 98.7 Percent of Your DNA with This Sex-Obsessed Ape," referring, of course, to the precious bonobo, a chimp-like ape famous for its progressive sexual habits. Just by itself, the genetic similarity between us and apes such as the bonobo is supposed to be of knockdown importance.

But what else would anyone expect, whether on a model of Darwinism, intelligent design, or creationism? Apes and humans are similar in many ways, and you don't need Darwinian evolution to see this.
This is a common argument from the IDiots. They assume that the intelligent designer created a model primate and then tweaked it a little bit to give chimps, humans, orangutans, etc. That's why the genomes of these species are so similar.

Unfortunately for them, there's a bit more to it than that. Their model of intelligent design also has to account for the fact that humans are more similar to chimps/bonobos than to gorillas and all three are about the same genetic distance from orangutans. This sequence data correlates with the fossil record over a period of about 10-15 million years.

It gets even worse for the IDiots. Evolutionary theory predicts that the rate of change should correspond to the mutation rate since most of the differences are due to neutral substitutions in junk DNA. We know that the mutation rate is about 130 mutations per generation based on our knowledge of biochemistry. This rate has been confirmed by direct sequencing of parents and children [Estimating the Human Mutation Rate: Biochemical Method] [Estimating the Human Mutation Rate: Direct Method].

If evolutionary theory (population genetics) is correct, and if David Klinhoffer and chimps/bonobos actually evolved from a common ancestor, then we should observe a correspondence between the percent similarity of Klinghoffer and chimps and the predicted number of changes due to evolution.

Let's see if it works.

The human and chimp genomes are 98.6% identical or 1.4% different. That difference amounts to 44.8 million base pairs distributed throughout the entire genome. If this difference is due to evolution then it means that 22.4 million mutations have become fixed in each lineage (humans and chimp) since they diverged about five million years ago.

The average generation time of chimps and humans is 27.5 years. Thus, there have been 185,200 generations since they last shared a common ancestor if the time of divergence is accurate. (It's based on the fossil record.) This corresponds to a substitution rate (fixation) of 121 mutations per generation and that's very close to the mutation rate as predicted by evolutionary theory.

Now, I suppose that this could be just an amazing coincidence. Maybe it's a fluke that the intelligent designer introduced just the right number of changes to make it look like evolution was responsible. Or maybe the IDiots have a good explanation that they haven't revealed?

Or maybe they're just IDiots who don't know what they are talking about.

Thursday, February 27, 2014

Physicians and engineers are not scientists

Creationists are fond of mentioning people who are committed to creationism but still function as successful scientists. We saw an example in the debate between Bill Nye and Ken Ham. These creationist "scientists" are often physicians or engineers.

It seems obvious to most of us that engineers and physicians are not scientists. PZ Myers mentions this on his blog when he discusses the debate as reviewed by William Saletan: Saletan is at it again. Here's what PZ says ...
Engineers can practice real science, but an engineer is not the same thing as a scientist. I agree that creationists can be perfectly good engineers, but how can you trust the scientific acumen of someone who insists that the earth is only 6,000 years old? That says right there that they have no respect for the evidence. How can Saletan ignore Ham’s bogus distinction between historical and observational science, in which he flatly rejects any possibility of inference about the past from the present? This creationism is utterly incompatible with biology, anthropology, geology, astronomy, climate science, geochemistry, cosmology, and any other science that deals with cause and effect and history. These sciences apparently do not matter to Saletan, as long as engineers make satellites and doctors do surgery.

Saletan cites Ham’s videos as falsifying the claim that creationism is incompatible with science. Ken Ham makes a big deal of this, too.
This would be unremarkable except that Jason Rosenhouse disagrees [Saletan vs. Myers on Nye vs. Ham]. Here's what Jason says ...
Oh for heaven’s sake! Engineers are scientists. Full stop. Are you really that desperate to deny that a creationist could ever make a contribution to science that you will sink to this level of insult and idiocy? (Yes, it is insulting to suggest that engineers are not scientists.)
Engineers have a Bachelor's degree in engineering and they typically work for a construction company or in the IT department of a large corporation. They are not scientists. Full stop.

It's true that some engineers do science but usually they have a higher degree in engineering and usually they are academics. There's no possible way you could assume that all engineers are scientists just because they are licensed engineers and wear the ring. I'm sorry, Jason, but you are wrong.

Similarly, the typical physician has a private practice at a strip mall in the suburbs. They have an M.D. degree that can be earned right out of high school (in Europe). They are not scientists.

There are some physicians who are scientists and some of them have earned Nobel Prizes. They are the exceptions, not the rule. It's ridiculous to assume that everyone with an M.D. is a scientist.

A mind like that is a disgrace to the human species

Here's a five year old video where Richard Dawkins points to molecular phylogenies as powerful evidence of evolution. He wonders how any creationist could deny the evidence of evolution and suggest that "a mind like that is a disgrace to the human species."

He must have been thinking about Cornelius Hunter because Hunter has resurrected the video in order to show why Dawkins is wrong [Richard Dawkins: How Could Anyone "Possibly Doubt the Fact of Evolution"]. Watch the video and then read what Cornelius Hunter says. You'll recognize some elements of truth in his criticism but you'll also recognize a common creationist fallacy; namely, an inability to see the forest because you've been staring too long at the bark on trees.

What is amazing is the evolutionist’s high confidence and self-assuredness in such a blatant misrepresentation of science. It would be difficult to imagine a bigger falsehood. Phylogenetic incongruence is rampant in evolutionary studies. Conflicts exist at all levels of the evolutionary tree and throughout both morphological and molecular traits. This paper reports on incongruent gene trees in bats. That is one example of many. These incongruences are caused by just about every kind of contradiction possible. Molecular sequences in one or a few species may be out of place amongst similar species. Or sequences in distant species may be strangely similar. As one paper admitted, there is “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.” Or as another evolutionist admitted, the many examples of nearly identical molecular sequences of totally unrelated animals are “astonishing.”

An even more severe problem is that in many cases no comparison is even possible. The molecular sequence is found in one species but not its neighbors. When this problem first became apparent evolutionists thought it would be resolved as the genomes of more species were decoded. No such luck—the problem just became worse. Not surprisingly evolutionists carefully prefilter their data. As one paper explained, “data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.”

Short genes that produce what are known as microRNA also contradict Dawkins’ high claim. In fact one evolutionist, who has studied thousands of microRNA genes, explained that he has not found “a single example that would support the traditional tree.” It is, another evolutionist admitted, “a very serious incongruence.”

Another paper admits that “the more molecular data is analysed, the more difficult it is to interpret straightforwardly the evolutionary histories of those molecules.”

And yet in public presentations of their theory, evolutionists present a very different story. As Dawkins explained, gene comparisons “fall in a perfect hierarchy, a perfect family tree.” This statement is so false it isn’t even wrong—it is absurd. And then Dawkins chastises anyone who “could possibly doubt the fact of evolution.” Unfortunately this sentiment is typical. Evolutionists have no credibility.

On the absurdity of an atheist using the argument from evil

Gary Gutting interviews atheist Louise Antony in the New York Times [Arguments Against God]. Here's part of the interview ...
L.A.: Knowledge in the real world does not entail either certainty or infallibility. When I claim to know that there is no God, I mean that the question is settled to my satisfaction. I don’t have any doubts. I don’t say that I’m agnostic, because I disagree with those who say it’s not possible to know whether or not God exists. I think it’s possible to know. And I think the balance of evidence and argument has a definite tilt.

G.G.: What sort of evidence do you have in mind?

L.A.: I find the "argument from evil" overwhelming — that is, I think the probability that the world we experience was designed by an omnipotent and benevolent being is a zillion times lower than that it is the product of mindless natural laws acting on mindless matter. (There are minds in the universe, but they’re all finite and material.)
The argument from evil goes like this ...
  1. Assume that supernatural, omnipotent beings exist.
  2. Assume that they are kind and benevolent and they have the power and desire to create human societies that will be kind and good.
  3. Therefore, because evil is commonplace, one of the assumptions must be wrong.
An atheist is concerned about whether supernatural beings exist so why in the world would they pay any attention to the premises of this argument? If I were to accept the premise that supernatural omnipotent beings exist then the argument from evil simply leads to the conclusion that the supernatural beings are evil (like Satan) or they don't much care about us, like the Greek gods.

The argument from evil says nothing about whether gods exist or not. It only refers to particular kinds of gods and the only way an atheist should pay any attention to it at all is if they are willing to concede that some sort of gods must exist. Then, and only then, can they enter into a discussion about what kinds of gods exist. In that sense, the argument from evil is about as useful as the Courtier's Reply.

I wish atheists would stop discussing the argument from evil because all it does is show that some gods are possible while others are unlikely. I do not see why Louise Anthony finds the argument convincing because it's perfectly consistent with the existence of Satan.

It's also perfectly consistent the god of the Old Testament (see above). That god is exactly the sort of god that that would create a human society full of evil. Humans are behaving just like the god they worship. What's the problem?

Wednesday, February 26, 2014

Why the creationists love the 1980 Chicago meeting on macroevolution

A meeting on macroevolution was held at the Field Museum of Natural History in Chicago in October 1980. Normally these meetings would not attract much attention from the press but in this case there was an article published in Discover a month before the meeting took place that suggested something revolutionary was in the wind. Stephen Jay Gould discusses the episode in The Structure of Evolutionary Theory (pp. 981-986).

The article in Discover referred to "growing dissent from the prevailing view of Darwinism" and mentioned that there would be a meeting in Chicago. As a result of this article, a bunch of journalists turned up at the Chicago Macroevolution meeting expecting fireworks.

There was a lot of talk about punctuated equilibria at the Chicago meeting and how the ideas of Eldredge and Gould conflicted with the gradualism that was part of traditional Darwinian evolution. This is complicated stuff so it's no wonder that many journalists misinterpreted the discussion as support for the idea that evolution was being challenged as the creationists claimed.

Tuesday, February 25, 2014

My molecular evolution midterm test

My students wrote the midterm test today. Here are the questions. They had to answer the first question and 4 other questions (out of 5). How would you do?
  1. What’s the most important new thing about molecular evolution that you have learned in this course so far? Explain your answer by describing your "important new thing."
  2. If mutation rates are relatively constant then why does the molecular clock tick at different rates in different proteins?
  3. Many evolutionary biologists think that population genetics is the key concept in understanding evolution but biology students often complete several years of courses without ever learning about effective population sizes, mutation rates and the importance of random genetic drift. Why? Is it because population genetics is not a necessary key concept in evolution?
  4. Grad students at this university publish a journal called Hypothesis. A few years ago (2005) there was a student who wrote ...
    I am a grad student, and long hours at the bench have got me thinking of other things lately, including the idea of marriage. I came up with a few criteria to direct me on my quest for a wife, and near the top of the list was that she needs to know what a gene is. I thought that this would be a reasonable thing to ask for. I like learning about how we and the rest of life work, and knowing how, in a general sense, cells are programmed to do what they do is a pretty good indicator of similar interest. My friends, however, disagreed with me, and on several occasions, as I shared my list, I feared that things were going to get violent. They argued that I will never get married with such a short-sighted and elitist attitude.
    Imagine that you would only seek partners who knew what a gene was. What definition would you require and why?
  5. What’s the best evidence that a substantial amount of our genome is junk?
  6. Imagine that you are teaching a class and you ask students to calculate a mutation rate in humans based on what they know about biochemistry. What mistakes are they most likely to make and why?

Saturday, February 22, 2014

On moral absolutes and ethical relativism

Last week I commented on whether bigots should be given permission to discriminate against gays just because the bigots belong to a religion that promotes bigotry [The Kansas anti-gay bill]. My opinion is that societies should not tolerate bigotry no matter what motivates people to discriminate. I said ...
I read some newspaper articles, and some blog posts, that stated the obvious. It is totally wrong, all the time, to discriminate against someone based on their sexual preferences. If they use religion as an excuse then they should re-evaluate their religion. There is NEVER a time when an enlightened society should tolerate, let alone legalize, bigotry. I guess it's almost impossible to come out and say this on television, or maybe I'm just watching the wrong channels (mostly FOX and CNN).
What I mean is that enlightened societies will almost always reach a consensus on discrimination against minorities. They will decide that society functions best when all types of discrimination are bad and should not be tolerated.

Sunday, February 16, 2014

The Kansas anti-gay bill

I'm currently in Los Angeles visiting the grandchildren so I'm a bit more exposed to American culture than normal. I watched several discussions on the Kansas anti-gay bill on television and one thing struck me as highly unusual.

For the sake of non-Americans, let's begin with a description of the bill passed by the Kansas House, which is dominated by Republicans. Here's what Bill 2453 says ...
Notwithstanding any other provision of law, no individual or religious entity shall be required by any governmental entity to do any of the following, if it would be contrary to the sincerely held religious beliefs of the individual or religious entity regarding sex or gender: (a) Provide any services, accommodations, advantages, facilities, goods, or privileges; provide counseling, adoption, foster care and other social services; or provide employment or employment benefits, related to, or related to the celebration of, any marriage, domestic partnership, civil union or similar arrangement; (b) solemnize any marriage, domestic partnership, civil union or similar arrangement; or (c) treat any marriage, domestic partnership, civil union or similar arrangement as valid.
In other words, if you are a bigot then the state will protect you from prosecution as long as you claim that your bigotry is based on religion.

The bill was expected to pass through the Kansas Senate and signed into law by a redneck governor. Fortunately for Kansas, the Republican-dominated senate decided that Kansas should drop out of the competition for most stupid state and they declined to pass the bill [Kansas Senate Comes To It’s Senses And Nixes Extreme Anti-Gay Legislation ].

That's not what I want to talk about. What I witnessed on the American TV channels was a debate over the legality of discrimination of gays. The discussion hinged on whether it was legal for an anti-gay bigot to refuse to serve a gay couple in a restaurant or whether an anti-gay bigot could refuse to bake a wedding cake for a gay couple. Almost everyone I saw on TV agreed that it was perfectly okay for Americans to be anti-gay bigots, especially if their bigotry was related to their belief in God. The only serious question seemed to be whether there were legitimate times when anti-gay bigots could express their bigotry in public.

I read some newspaper articles, and some blog posts, that stated the obvious. It is totally wrong, all the time, to discriminate against someone based on their sexual preferences. If they use religion as an excuse then they should re-evaluate their religion. There is NEVER a time when an enlightened society should tolerate, let alone legalize, bigotry. I guess it's almost impossible to come out and say this on television, or maybe I'm just watching the wrong channels (mostly FOX and CNN).

I'm reminded of a statement by Winston Churchill about Russia; "Russia is a riddle wrapped in a mystery inside an enigma." That's the way I feel about the United States. There's such a huge difference between Boston and Texas that I wonder how they can both continue to exist in the same country.

A Darwin Day rap video

An old high school friend of Ms Sandwalk sent me the link to this video by Dirk Murray "Baba" Brinkman, Jr. He is the son of my friend's local MP, Joyce Murray (Liberal, British Columbia).

I hesitated to post in on Darwin Day but now that other blogs have linked to it, I want to use this opportunity to raise two important questions.
  1. The video promotes "Darwinism" as the only solution to evolution. This is wrong, but is there value in lying about this for a greater cause? Is it possible to make an effective video like this without distorting the science?
  2. I'm very uneasy about promoting Darwin worship, partly for the reason that there's more to evolution than what Darwin wrote in 1859 and partly for the reason that it smacks of religion. What do you think? Should we be pushing "Darwin Day"?

Saturday, February 15, 2014

On the difference between Neutral Theory and random genetic drift

PZ Myers posted an interesting article on The state of modern evolutionary theory may not be what you think it is. He makes the point that there's more to evolution than natural selection.

I think this is an important point but I would not explain it the same way as PZ. He focuses attention on Neutral Theory and the fact that neutral, or nearly neutral, mutations are fixed by random genetic drift. Here's how he describes it ...
First thing you have to know: the revolution is over. Neutral and nearly neutral theory won. The neutral theory states that most of the variation found in evolutionary lineages is a product of random genetic drift. Nearly neutral theory is an expansion of that idea that basically says that even slightly advantageous or deleterious mutations will escape selection — they’ll be overwhelmed by effects dependent on population size. This does not in any way imply that selection is unimportant, but only that most molecular differences will not be a product of adaptive, selective changes.
The debate over adaptationism is a debate over mechanisms of evolution. Random genetic drift is a mechanism of evolution that results in fixation or elimination of alleles independently of natural selection. If there was no such thing as neutral mutations then random genetic drift would still be an important mechanism.

Let's say you have a clearly beneficial mutation with a huge selection coefficient of 0.1 (s = 0.1). Population genetics tells us that the probability of fixation is 2s or, in this case, 20%. That means that the allele will be eliminated from the population 80% of the time. That's random genetic drift. Similarly, some fairly deleterious mutations can sometimes be fixed by random genetic drift.

Random genetic drift is a mechanism of evolution that was discovered and described over 30 years before Neutral Theory came on the scene.

What Neutral Theory tells us is that a huge number of mutations are neutral and there are far more neutral mutations fixed by random genetic drift that there are beneficial mutations fixed by natural selection. The conclusion is inescapable. Random genetic drift is, by far, the dominant mechanism of evolution.

Many people seem to equate Neutral Theory with random genetic drift. They think that random genetic drift is only important when the alleles are neutral (or nearly neutral). Then they use this false equivalency as a way of dismissing random genetic drift because it only deals with "background noise" while natural selection is the mechanism for all the interesting parts of evolution. I think we should work toward correcting this idea by separating the mechanisms of evolution (natural selection, random genetic drift, and others) from the quality of alleles being produced by mutation (beneficial, detrimental, neutral).

The revolution is over and strict Darwinism lost. We now know that random genetic drift is an important mechanism of evolution and there's more to evolution than natural selection. Unfortunately, this blatantly obvious fact is not understood by the vast majority of people and teachers. There are even many scientists who don't understand evolution.

Monday, February 10, 2014

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".

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."

Friday, February 07, 2014

Is There a God? Find out tonight!

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

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?

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.

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 ....

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

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.

Tuesday, February 04, 2014

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?

Monday, February 03, 2014

Sunday, February 02, 2014

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.