Junk DNA doesn't exist according to "Conceptual Revolutions in Science"

The blog "Conceptual Revolutions in Science" only publishes "evidence-based, paradigm-shifting scientific news" according to their home page.

The man behind the website is Adam B. Dorfman (@DorfmanAdam). He has an MBA from my university and he currently works at a software company. Here's how he describes himself on the website.

Intelligent Design Creationism and the fine-tuning argument

Michael Denton and the Discovery Institute are promoting his new book, Evolution: Still a Theory in Crisis. I haven't yet read the book. I ordered from Amazon.ca and I won't get it until March.

Denton tries to explain the connection between the fine-tuning argument and structuralism in a recent post on Evolution News & Views: Natural Life: Cosmological Fine-Tuning as an Argument for Structuralism. I've dealt with structuralism already [What is "structuralism"?] so let's think about fine tuning.

The essence of the fine-tuning argument is that the basic laws of physics and chemistry are so precise that even slight changes would result in a universe where life is impossible. The focus is usually on the fundamental constants such as the speed of light and the charge on an electron. I don't know enough about physics to evaluate the argument that these are fine-tuned so I have to rely on physicists to inform me.

Can theology produce true knowledge?

Matthew Cobb wasn't happy with the way Denis Alexander reviewed Jerry Coyne's book. Recall that Denis Alexander is a biochemist at Cambridge University (UK) and we had a little debate a week or so ago [Is there a conflict between science and religion?]. His position is that there's no conflict between science and religion because a person who believes in god can always make their views conform to the discoveries of science. I didn't accept his premise—that gods exist—so we had a discussion about whether there's any evidence to support his belief in god.

If you believe in such a being then that conflicts with science as a way of knowing because you are believing in something without reliable evidence to support your belief. Scientists shouldn't do that and neither should any others who practice the scientific way of knowing. Denis Alexander thinks there are other, equally valid, ways of knowing but he wasn't able to offer any evidence that those other ways produce true knowledge.

Matthew Cob wrote a letter to the editor in which he asked, "I wonder if Dr Alexander, or indeed any reader, could provide an example of knowledge gained through theology, and above all tell us how they know that knowledge is true?" [see Matthew Cobb battles with the faithful over my book].

What is "structuralism"?

The Intelligent Design Creationists are promoting Michael Denton's new book Evolution: Still a Theory in Crisis. The new buzzword is "structuralism" and it's guaranteed to impress the creationist crowd because nobody understands what it means but it sounds very "sciency" and philosophical. Also, it's an attack on "Darwinism" and anything that refutes evolution has to be good.

You can watch Michael Denton explain structuralism ... it only takes a few minutes of your time.

The most intellectual creationists explain why there are still Darwinists when Darwinism has been falsified

You are probably wondering why "Darwinism" persists after the creationists have thoroughly demonstrated that it is a failed theory. Lucky for you, the most intelligent and intellectual of all Intelligent Design Creationists, David Berlinski and Michael Denton, have gotten together to explain it in a short (15 mins) podcast.

It's moderated by David Klinghoffer who introduces it like this ... [Michael Denton and David Berlinski Discuss: How Does Darwinism Hang On?]

If the most brilliant Darwin critics, like David Berlinski and Michael Denton, are right, how then does Darwinism hang on? How does a failed theory maintain its grip on our science and on our culture? Why is there a sense of stalemate? On ID the Future, we posed these questions to Dr. Berlinski and Dr. Denton.

If you are interested in the conflict between Intelligent Design and science you owe it to yourself to see/hear the best they've got on their side.

ID the Future: More Berlinski and Denton.

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Berlinski and Denton challenge Darwinism

It's fun to listen to the "ID the Future" podcasts. It shows us the very best of Intelligent Design Creationists. This time we get a twofer— David Berlinski and Michael Denton posing their most challenging questions to Darwinists. Here's how David Klinghoffer introduces the pair ... [Berlinski and Denton: If You Could Pose One Challenge to a Thoughtful Darwinist, What Would It Be?].

You can always dream. While the evolutionist side in the Darwin debate is long on rhetoric and insults, serious debate or dialogue is woefully rare. But imagine you had the opportunity to sit down with a thoughtful, honest, well-informed Darwinist and pose one question or challenge. What would it be?

I had the opportunity to pose that question to two of the most brilliant minds in the intelligent design community -- Michael Denton and David Berlinski. Take a well-spent 15 minutes and listen to their answers -- focusing respectively on the insect body plan and the enigma of whale evolution -- recorded as an episode of ID the Future.

Berlinski wants a detailed mathematical estimate of the number of mutations required to go from a land animal to a whale. Denton wants details on the formation of insect body plans.

It's important to note that these are questions about the history of life. You could easily answer "I don't know" to both questions and it would not affect our understanding of evolution and common descent one iota. The answers have nothing to do with "Darwinism" per se and nothing to do with evolutionary theory (which is not Darwinism).

Listen to the very best minds in the Intelligent Design Creationist community ... and weep for them. This is all they've got.

Id the Future: Berlinski and Denton

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Is there a conflict between science and religion?

Some of you may not be able to come to our little "dialogue" tomorrow night. Don't worry, you can watch it on YouTube: Is There a Conflict Between Science and Religion?.

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James McGrath disproves atheism

James McGrath is a professor of religion at Butler University in Indianapolis, Indiana, USA.

He is one of those "sophisticated theologians" who dismiss modern atheists because we haven't spent years studying theology and because we haven't experienced the true existential angst of Jean-Paul Sartre. As a group, they hold to the position that the "New Atheists" are amateurs in the study of religion and their arguments can be easily dismissed.

Richard Dawkins makes a mistake when describing why gene trees are evidence of evolution

Back in 2010, Richard Dawkins was answering questions on Reddit and one of the questions was "Out of all the evidence used to support the theory of evolution, what would you say is the strongest, most irrefutable single piece of evidence in support of the theory."

There are several ways to answer this question. Personally, I would take a minute to explain the difference between the "theory of evolution" and the history of life. I would point out that evolutionary theory includes things like Darwin's natural selection and there is overwhelming evidence proving that natural selection exists and operates today. The entire field of population genetics, which included other mechanisms of evolution such as random genetic drift, is massively supported by thousands of published papers in the scientific literature. There is absolutely no doubt at all that the current basic tenets of evolutionary theory are correct.

Confirmation bias

Confirmation bias is one of the major logical fallacies. When philosopher Chris DiCarlo and I were teaching a course on critical thinking we used to spend quite a bit of time on it because it's a very common trap. We are all guilty, from time to time, of focusing on just the evidence that confirms our belief and ignoring all the evidence that refutes it.

Some examples of confirmation bias are a bit more complicated than others and people typically mix together several different fallacious forms of argument. Here's an example from Denis Alexander's book Creation or Evolution (p. 213) that combines begging the question and confirmation bias.

An undergraduate biochemistry lecture converts an atheist to Christianity

I'm reading Creation or Evolution: Do we have to choose? by Denis Alexander in preparation for our discussion next Friday at Wycliffe College on the University of Toronto downtown campus [Discussing the conflict between science and religion with Denis Alexander].

Denis Alexander is a biochemist at the University of Cambridge (UK). I thought I'd share one of the stories in his book.

At the church I attend in Cambridge we baptised an undergraduate in the natural sciences who had come to a personal, saving faith in Christ from a completely atheistic background. As is usual in our church, just before being baptised she explained publicly to the whole congregation how she had become a Christian, telling us she had become convinced there must be a God while sitting through a standard biochemistry lecture, hearing the amazing story of how two meters (about six feet) of DNA are packaged into a single cell. Of course the lecturer was not talking in religious terms at all, but she described to us how the beauty of that engineering feat overwhelmed her as she listened, giving her the deep intuition there must be a God, so leading her onward in he personal pilgrimage to put her trust in this creator God through Christ. Truly natural theology at work!

That got me thinking. I've been describing chromatin and packing in my textbooks since the first version in 1987. There must have been several hundred thousand students who have read my descriptions since then.

I wonder how many I've converted?

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Massimo Pigliucci tries to defend accommodationism (again): result is predictable

Massimo Pigliucci is an atheist who thinks that science and religion are compatible because they rule in different domains. He takes a very narrow view of "science"— one that excludes the work of historians and philosophers who are presumably using some other way of knowing. (He doesn't tell us what that is.)

I prefer the broad view of science as a way of knowing that relies on evidence, rational thinking, and healthy skepticism. This broad view of science is not universal—but it's not uncommon. In fact, Alan Sokel has defended this view of Massimo Pigiucci's own blog: [What is science and why should we care? — Part III]. According to this view, any attempt to gain knowledge should employ the scientific worldview. Historian and philosophers should follow this path if they hope to be successful. Pigliucci should know that there are different definitions and any discussion of the compatibility of science and religion must take these differences into account.

Christians against dinosaurs

This is Kristen Auclair of Christians Against Dinosaurs. It is mind-boggling.

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Discussing the conflict between science and religion with Denis Alexander

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Targets, arrows, and the lottery fallacy

Sandwalk readers have been discussing the way Intelligent Design Creationists have been calculating probabilities [see Intelligent Design Creationists are very confused about epigenetics and Waiting for multiple mutations: Michael Lynch v. Michael Behe].

We've known for a long time that the most common mistake is assuming that there's only one solution to a problem. They see an end result, like a bacterial flagellum, or resistance to malaria, or the binding of two proteins, and assume that a few very specific mutations had to occur in a specific sequence in order to produce that result.

judmarc calls this the "lottery fallacy" and I think it's a good term [see lottery fallacy],

This is of course what I like to call the "lottery fallacy." It's used by virtually every ID proponent to produce erroneously inflated probabilities against evolution.

Lottery fallacy: The odds against any *particular individual* winning the PowerBall lottery are ~175 million to 1. But there were three winners just last night. That's because *someone* winning the PowerBall is not an especially rare occurrence. It happens every few weeks throughout the year.

In exactly the same way, Axe, Gauger, Behe, and the rest of the ID folks always base their math on the chances that a *particular* neutral or beneficial mutation will occur, and just as with the lottery, the chances of a *particular* outcome are utterly minuscule. The occurrence of *some* neutral or beneficial mutation, however, is, as with the lottery, so relatively common as to be completely unremarkable.

To summarize: ID proponents misuse probability math to make the common appear impossible.

As it turns out, someone on Evolution News & Views (sic) just posted an excellent example of this fallacy [Intelligent Design on Target]. Here's what he/she/it says,

In his second major treatise on design theory, No Free Lunch: Why Specified Complexity Cannot Be Purchased without Intelligence, William Dembski discusses searches and targets. One of his main points is that the ability to reach a target in a vast space of possibilities is an indicator of design. A sufficiently complex target that satisfies an independent specification, he argues, creates a pattern that, when observed, satisfies the Design Filter. There are rigorous mathematical and logical proofs of this concept in the book, but at one point, he uses an illustration even a child can understand.

Consider the case of an archer. Suppose an archer stands fifty meters from a large wall with a bow and arrow in hand. The wall, let us say, is sufficiently large that the archer cannot help but hit it. Now suppose each time the archer shoots an arrow at the wall, the archer paints a target around the arrow so that the arrow sits squarely in the bull's-eye. What can be concluded from this scenario? Absolutely nothing about the archer's ability as an archer. Yes, a pattern is being matched; but it is a pattern fixed only after the arrow has been shot. The pattern is thus purely ad hoc. [No Free Lunch, pp. 9-10, emphasis added.]

Most people have experience with target shooting of some kind, whether with bows and arrows, guns (including squirt guns), snowballs, darts, or most sports like baseball, soccer, basketball, hockey, and football. Children laugh when they picture an archer who "couldn't even hit the broadside of a barn" and rushes up to the arrow and paints a bull's-eye around it. Grown-ups might compare that to a biologist looking at an irreducibly complex biological system and simply stating, "It evolved." In each of these cases, Dembski would say that since the pattern was not independently specified, therefore it is ad hoc.

The unknown author included the image shown above in order to illustrate the point (Image: © Kagenmi / Dollar Photo Club).

Do you see the fallacy? Just because we observe a complex adaptation or structure does NOT mean that it was specified or pre-ordained. There are certainly many different structures that could have evolved—most of them we never see because they didn't happen. And when a particular result is observed it doesn't mean that there was only one pathway (target) to producing that structure.

To continue the analogy—at the risk of abusing it—there may be hundreds of targets in the woods and most of them have very large bullseyes. Imagine you're out for a walk in the woods and you see that almost every tree has a big target with a large bullseye. You find an arrow stuck at the edge of one of the bullseyes and lots of arrows stuck in the trees, the ground, and parts of most of the targets outside of the central bullseyes. Would you write a book about how good the archer must have been?

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Intelligent Design Creationists are very confused about epigenetics

I've been trying to figure out why Intelligent Design Creationists are so excited about epigenetics. They seem to think it's going to overthrow everything we know about evolution (= "Darwinism"). That means, in their minds, that "naturalism" and "materialism" aren't sufficient to explain biology.

The logic escapes me.

Denyse O'Leary has added a new wrinkle in her latest post (as "News") on Uncomon Descent. She reveals a profound misunderstanding of epigenetics [Could epigenetics change perspectives on adoption?].

I'll just quote the relevant part and let you try and figure out whether Denyse represents mainstream Intelligent Design Creationism. 'Cause if she does, the movement is in far worse shape than even I imagined.

I remember one adoptive mother, taunted by a rebellious teenager who wanted to find her “real” mother, taking the girl by the shoulders and saying, “Look, I raised you from when you were seven days old; I supported you, sat with you in emergency rooms and juvenile court, laughed and cried with you, … and got you into a good school in the end. I don’t know who or where your birth mother is. But I do know this: I am the only ‘real mother’ you have ever had or ever will have. Look at me. Get used to it. It doesn’t GET better than this.”

I hope the kid smartened up. Meanwhile what if she discovers, when she has children, that their genome reflects in part traits she acquired growing up in the adoptive home? Maybe that would allay some of the sense of alienation.

Might epigenetics could provide some basis for understanding? Time will tell.

See also: Epigenetic change: Lamarck, wake up, you’re wanted in the conference room!

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Answering two questions from Vincent Torley

Vincent Torley read a post by Jerry Coyne where Jerry wondered if Intelligent Design Creationism was in trouble because the Discovery Institute has lost Bill Dembski and Casey Luskin [Is the Discovery Institute falling apart?].

Torley disagrees, obviously, but he focuses on a couple of the scientific statements in Jerry Coyne's post and comes up with Two quick questions for Professor Coyne.

I hope Professor Coyne won't mind if I answer.

Before answering, let's take note of the fact that Vincent Torley has been convinced by the evidence that most of our genome is junk. I wonder how that will go over in the ID community?

Here's question #1 ...

Waiting for multiple mutations: Michael Lynch v. Michael Behe

Casey Luskin is trying to help out a university student by describing some important ID contributions to science [No ID Research? Let's Help Out This Iowa State Student].

One of those contributions is a paper by Michael Behe and David Snoke published eleven years ago in Protein Science (Behe and Snoke, 2004). I described the result in a previous post: Waiting for multiple mutations: Intelligent Design Creationism v. population genetics.

If Behe & Snoke are correct then modern evolutionary theory cannot explain the formation of new functions that require multiple mutations.

Cassey Luskin is aware of the fact that this result has not been widely accepted. He mentions one specific criticism:

In 2008, Behe and Snoke's would-be critics tried to refute them in the journal Genetics, but found that to obtain only two specific mutations via Darwinian evolution "for humans with a much smaller effective population size, this type of change would take > 100 million years." The critics admitted this was "very unlikely to occur on a reasonable timescale."

He's referring to a paper by Durrett and Schmidt (2008). Those authors examined the situation where one transcription factor binding site was disrupted by mutation and another one nearby is created by mutation. The event requires two prespecified coordinated mutations.

Did Michael Behe say that astrology was scientific in Kitzmiller v. Dover?

Yes he did. But it doesn't mean what you think it means according to Casey Luskin [Ten Myths About Dover: #8, "Michael Behe Admitted that ID Is No More Scientific than Astrology"

I agree with Casey Luskin. During the trial, Behe was asked to define scientific theory and of course he adopted the broad view of science. He said, "Under my definition, a scientific theory is a proposed explanation which focuses or points to physical, observable data and logical inferences."

Here's the exchange that took place during the trial [Dover: Day 11].

Q In any event, in your expert report, and in your testimony over the last two days, you used a looser definition of "theory," correct?
A I think I used a broader definition, which is more reflective of how the word is actually used in the scientific community.
Q But the way you define scientific theory, you said it's just based on your own experience; it's not a dictionary definition, it's not one issued by a scientific organization.
A It is based on my experience of how the word is used in the scientific community.
Q And as you said, your definition is a lot broader than the NAS definition?
A That's right, intentionally broader to encompass the way that the word is used in the scientific community.
Q Sweeps in a lot more propositions.
A It recognizes that the word is used a lot more broadly than the National Academy of Sciences defined it.
Q In fact, your definition of scientific theory is synonymous with hypothesis, correct?
A Partly -- it can be synonymous with hypothesis, it can also include the National Academy's definition. But in fact, the scientific community uses the word "theory" in many times as synonymous with the word "hypothesis," other times it uses the word as a synonym for the definition reached by the National Academy, and at other times it uses it in other ways.
Q But the way you are using it is synonymous with the definition of hypothesis?
A No, I would disagree. It can be used to cover hypotheses, but it can also include ideas that are in fact well substantiated and so on. So while it does include ideas that are synonymous or in fact are hypotheses, it also includes stronger senses of that term.
Q And using your definition, intelligent design is a scientific theory, correct?
A Yes.
Q Under that same definition astrology is a scientific theory under your definition, correct?
A Under my definition, a scientific theory is a proposed explanation which focuses or points to physical, observable data and logical inferences. There are many things throughout the history of science which we now think to be incorrect which nonetheless would fit that -- which would fit that definition. Yes, astrology is in fact one, and so is the ether theory of the propagation of light, and many other -- many other theories as well.
Q The ether theory of light has been discarded, correct?
A That is correct.
Q But you are clear, under your definition, the definition that sweeps in intelligent design, astrology is also a scientific theory, correct?
A Yes, that's correct. And let me explain under my definition of the word "theory," it is -- a sense of the word "theory" does not include the theory being true, it means a proposition based on physical evidence to explain some facts by logical inferences. There have been many theories throughout the history of science which looked good at the time which further progress has shown to be incorrect. Nonetheless, we can't go back and say that because they were incorrect they were not theories. So many many things that we now realized to be incorrect, incorrect theories, are nonetheless theories.
Q Has there ever been a time when astrology has been accepted as a correct or valid scientific theory, Professor Behe?
A Well, I am not a historian of science. And certainly nobody -- well, not nobody, but certainly the educated community has not accepted astrology as a science for a long long time. But if you go back, you know, Middle Ages and before that, when people were struggling to describe the natural world, some people might indeed think that it is not a priori -- a priori ruled out that what we -- that motions in the earth could affect things on the earth, or motions in the sky could affect things on the earth.

I mostly agree with Behe.¹ Astrology was an attempt to explain human behaviors by relating them to the position of the Earth on the day you were born. There is no connection. So today we think of astrology as bad science. It's not true that the stars determine your behavior and whenever we make this claim to an astologist we make sure to point out that the evidence is against it.

What we don't do is tell astrologers that they are entitled to believe whatever they want because astrology is not science and therefore we can't make a scientific statement about whether it's correct or not.

Intelligent Design Creationism is bad science. So is most of evolutionary psychology and some of genomics. So is the attempt to find god in a football helmet [The God Helmet: Your Brain on Religion].

It's disingenuous to make fun of Behe's testimony without understanding that the real issue is epistemology and the demarcation problem. Behe's view of science is perfectly legitimate but it didn't jibe with what the plaintiffs were trying to establish during the trial. They wanted to prove that ID isn't science and the best way to do that was to show that something can't be science unless it's true. In other words, science isn't a "way of knowing," it's the end result.

What does this mean? It means that every discredited attempt to explain something using science as a way of knowing becomes "not science" with hindsight. All those people who tried to show that genes were proteins were wrong so it means that what they were doing is not science. It means that of the two sides arguing about junk DNA, one of them will be wrong so, at some time in the future, their current activities will be seen as "not science."

Isn't that bizarre?

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1. He should have been defining "science" not "scientific theory." That's the fault of his lawyers who failed to make this point during his direct testimony.

Did Kitzmiller v. Dover kill Intelligent Design Creationism?

The 10th anniversary of Judge Jone's decision in Kitzmiller v. Dover is coming up on Dec. 20, 2015. See the post at Panda's Thumb: Kitzmas is Coming!.

ID proponents are also marking the event in various ways. If you are interested in the discussion, you should read the posts on Evolution News & Views covering the Ten Myths about Dover. The first one (#10) is Ten Myths About Dover: #10, "The Intelligent Design Movement Died After the Dover Decision".

Of course the ID movement didn't die after Kitzmiller v. Dover. From the outside (i.e. not in the USA) it seems to be as strong as ever. State legislatures all over America are still trying to suppress the teaching of evolution and promote creationist perspectives. The movement has captured the attention of many (most?) prominent politicians and much of the American public still believes that scientists are wrong about evolution.