Mathematical Proof of God

 
Here's Kirk Durston explaining how mathematics can show that evolution is impossible and Intelligent Design Creationism is probable. Durston is a graduate student at the University of Guelph (Guelph Ontario, Canada). At some point he will have to describe his ideas to a group of scientists who will determine whether he should get a Ph.D. Good luck Kirk, you will need it. Unless, of course, if the committee is stacked with IDiots people who don't understand biology.

If this explanation forms any part of Durston's thesis then it would be extremely embarrassing if the University of Guelph awards him a Ph.D. But what if all this is left out of the thesis? Is it still fair game for the Ph.D. oral committee?

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Science Journalists and Junk DNA

The latest issue of SEED magazine concentrates on the idea that "Science Is Culture"—whatever that means.

One of the things it seems to mean is that good, accurate science reporting is not a high priority.

Junk DNA is one of those subjects that seem to bamboozle science journalists. They just can't seem to accept the possibility that much of our genome serves no purpose. One of the most extreme examples of this bias can be found in an article by Veronique Greenwood titled What We Lose.

The point of the article is that scientific models aren't perfect. They often over-simplify and, even more dangerous, they can exclude the very information required to refute the model. The example she uses is the software that will select what data to look at when the Large Hadron Collider (LHC) starts working. Greenwood's point is that the software might ignore the most interesting collisions because they aren't what scientists expect.

Here's how she explains the danger.

It wouldn't be the first time a standing model has excluded data that could revise it. In the 1980's, NASA analyses of the ozone layer flagged a great many data points as errors—values that seemed too low to be real, values that indicated a huge hole in the planet's protective layer. NASA scientists overlooked the possibility until an outside group published its discovery of the ozone hole in 1985. ....

Something similar happened in the 1990's when DNA that didn't code for proteins was labeled "junk." Noncoding DNA, biologist have since found, regulates protein-coding DNA.

THEME

Genomes & Junk DNA
No, Ms. Greenwood, that's not what happened. Junk DNA has been around for 35 years and it is well-established that much of our genome is composed of degenerate transposons and pseudogenes. There's good evidence that up to 90% of our genome may be junk, perhaps more.

Regulatory sequences have been known for over forty years. They cannot account for more than a small fraction of noncoding DNA. You are dead wrong when you claim that a function has been found for most junk DNA.

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Kirk Durston vs PZ Myers

 
PZ Myers has a brief account of his encounter with Kirk Durston in Edmonton (Alberta, Canada) last weekend [An ugly debate in Edmonton].

PZ discovered what many of us already knew about Kirk ...

He's a good debater, because he relies on a powerful tactic: he'll willingly make stuff up and mangle his sources to make his arguments. I'm at a disadvantage because I won't do that.

Exactly. It's hard to debate someone who lies with a straight face, especially if they act like a Christian while doing it.

Here's what I had to say last year about my encounter with Kirk Durston [Kirk Durston's Proof of God].

It was a very frustrating experience. Like most Intelligent Design Creationists, Durston was all over the map in terms of spreading lies and misconceptions about science. This scattergun approach seems to be very successful for them. I assume it's because no one person can address all of the problems with their presentation. Most people will catch one or two flaws but they'll assume that everything else has to be correct.

Sounds like nothing has changed.

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Does God Exist? A Debate

 
It's almost too late but here's an event you should attend it you live in Toronto.¹ Jim Brown is an atheist philosopher and a very, very smart man. I almost feel sorry for William Lane Craig.

This event is co-sponsored by the University of Toronto Secular Alliance and the Campus for Christ at U of T.

Does God Exist? A Debate

Time: Tues Jan 27, 6:00pm
Location: Isabel Bader Theatre (BT), Victoria College, 93 Charles Street West
Tickets: $2 (Student) at the door (Tues) $10 (Non-Student)
Theist: Dr. William Lane Craig
Atheist: Dr. James Robert Brown

This will prove to be an exciting debate between two world-renowned philosophers, including a professor from here at U of T. After a formal debate structure, both debaters will take questions from the audience. We anticipate a full auditorium for this broad topic that appeals to many students, regardless of where they stand on the debate.

This event is co-sponsored by Campus for Christ at U of T and University of Toronto Secular Alliance.

We expect this debate to be full and will prioritize seating for university students. If you are not a student at this university, please attend the Thursday debate at York University as there will be more room there. Cost is $10 for non-students.

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1. I can't make it. My mid-term is tonight. Please post a message telling us how it went.

The Power of Darwin

 
Richard Dawkins has published an article in Free Enquiry titled The Power of Darwin. Here are the opening paragraphs.

Charles Darwin had a big idea, arguably the most powerful idea ever. A powerful idea assumes little to explain much. It does a lot of explanatory “heavy lifting” while expending little in the way of assumption or postulation. It gives you plenty of bang for your explanatory buck. Its Explanation Ratio—what it explains divided by what it needs to assume in order to do the explaining—is large.

Power of a theory = That which it explains/That which it needs to assume in order to do the explaining

If any reader knows of an idea that has a larger explanation ratio than Darwin’s, let’s hear it. Darwin’s big idea explains all of life and its consequences, and that means everything that possesses more than minimal complexity. That’s the numerator of the Explanation Ratio, and it is huge. Yet the denominator is spectacularly small and simple: natural selection, the non-random survival of genes in gene pools (to put it in neo-Darwinian terms rather than Darwin’s own).

Power of Darwin’s theory = The diverse complexity of life/Non-random survival

Natural selection is an improbability pump—a process that generates statistical improbability. It systematically seizes the minority of random changes that have what it takes to survive and accumulates them, step by tiny step over unimaginable timescales, until evolution eventually scales mountains of improbability and diversity whose height and range seem to know no limit.

Natural selection does NOT explain all of life and its consequences. A great deal of what we see in modern species is a consequence of accident and happenstance where contingency rules over natural selection. Natural selection does NOT explain diversity.

Darwin's big idea was to convince us that life has evolved rather than being created. That's a simple concept that explains a lot.

Natural selection explains adaptation. That's extremely important and extremely interesting but it's only a small part of evolution. Random genetic drift, which Darwin does not get credit for, explains much more because more of evolution is due to drift than to adaptation.

The contributions of Charles Darwin are enormous. That's why he gets credit for being the greatest scientist who ever lived. It does a disservice to his achievements to exaggerate them in celebration of the 150th anniversary of the publication of Origin of Species.

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Lower Animals and Higher Animals

 
Here's an article from ScienceDaily.

New Tree Of Life Divides All Lower Metazoans From Higher Animals, Molecular Research Confirms

ScienceDaily (Jan. 27, 2009) — A new and comprehensive analysis confirms that the evolutionary relationships among animals are not as simple as previously thought. The traditional idea that animal evolution has followed a trajectory from simple to complex—from sponge to chordate—meets a dramatic exception in the metazoan tree of life.

New work suggests that the so-called "lower" metazoans (including Placozoa, corals, and jellyfish) evolved in parallel to "higher" animals (all other metazoans, from flatworms to chordates). It also appears that Placozoans—large amoeba-shaped, multi-cellular animals—have passed over sponges and other organisms as an animal that most closely mirrors the root of this tree of life.

There's so much wrong with this description that one hardly knows where to begin. Ryan Gregory highlighted the worst parts at Lower and basal.

Do NOT use the words "higher" and "lower" to describe biological species. This is a mistake that many scientists make so we can't blame the journalists¹ for this one.

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1. I wonder what Graham Lawton thinks about this tree of life?

Monday's Molecule #105

 
Monday's molecule is on Tuesday this week. Sorry for the delay, I've been busy with a mid-term test in my introductory biochemistry course.

You have to identify this molecule. The role of this molecule in a particular species was elucidated by a Nobel Laureate in the second half of the 20th century. We need the name of the Nobel Laureate who first isolated and characterized the protein.

Your task is to correctly identify the molecule and the species from which it was purified. You also need to name the Nobel Laureate. The first one to do so wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize.

There are five ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin, Bill Chaney of the University of Nebraska, Maria Altshuler of the university of Toronto, Ramon, address unknown, and Jason Oakley of the University of Toronto.

Dima and Bill have offered to donate their free lunch to a deserving undergraduate so the next two undergraduates to win and collect a free lunch can also invite a friend. Since undergraduates from the Toronto region are doing better in this contest, I'm going to continue to award an additional free lunch to the first undergraduate student who can accept a free lunch. Please indicate in your email message whether you are an undergraduate and whether you came make it for your free lunch (with a friend).

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours.

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Good Science Writing

 

Good Science Writing
David Suzuki
Helena Curtis
David Raup
Niles Eldredge
Richard Lewontin
Steven Vogel
Jacques Monod
G. Brent Dalrymple
Eugenie Scott
Sean B. Carroll
Richard Dawkins
Albert Lehninger
Stephen J. Gould
Douglas Futuyma
Just to remind everyone that there is such a thing as a good science writer, here's a list.

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Saturday Morning Music

 
Ms. Sandwalk and I have facing desks in our basement study. Many of her blog postings involve music. For the past hour I've been listening to her singing along to all kinds of songs. Some good, and some not so good.

Here's the result. The best ones made it to her blog [Music this week].

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Jerry Coyne on Science vs. Religion

 
Many people have written about the conflict between science and religion but most get it wrong, especially the apologists for religion. Jerry Coyne is an exception. I don't always agree with his views about evolution but when it comes to the conflict between science and religion he has hit the nail on the head.

Read his article in The New Republic—it's disguised as a review of Ken Miller's book Only a Theory and Karl Giberson's book Saving Darwin: How to be a Christian and Believe in Evolution [Seeing and Believing].

Coyne exposes the fallacy of theistic evolution, a theme close to my own views [Theistic Evolution: The Fallacy of the Middle Ground], ... only Coyne says it so much better ...

True, there are religious scientists and Darwinian churchgoers. But this does not mean that faith and science are compatible, except in the trivial sense that both attitudes can be simultaneously embraced by a single human mind. (It is like saying that marriage and adultery are compatible because some married people are adulterers. ) It is also true that some of the tensions disappear when the literal reading of the Bible is renounced, as it is by all but the most primitive of JudeoChristian sensibilities. But tension remains. The real question is whether there is a philosophical incompatibility between religion and science. Does the empirical nature of science contradict the revelatory nature of faith? Are the gaps between them so great that the two institutions must be considered essentially antagonistic? The incessant stream of books dealing with this question suggests that the answer is not straightforward.

The easiest way to harmonize science and religion is simply to re-define one so that it includes the other. We may claim, for example, that "God" is simply the name we give to the order and harmony of the universe, the laws of physics and chemistry, the beauty of nature, and so on. This is the naturalistic pantheism of Spinoza. Its most famous advocate was Einstein, often (and wrongly) described as believing in a personal God ...

But the big problem with this "reconciliation," in which science does not marry religion so much as digest it, is that it leaves out God completely--or at least the God of the monotheistic faiths, who has an interest in the universe. And this is unacceptable to most religious people. Look at the numbers: 90 percent of Americans believe in a personal God who interacts with the world, 79 percent believe in miracles, 75 percent in heaven, and 72 percent in the divinity of Jesus. In his first popular book, Finding Darwin's God, Kenneth Miller attacked pantheism because it "dilutes religion to the point of meaninglessness." He was right.

A meaningful effort to reconcile science and faith must start by recognizing them as they are actually understood and practiced by human beings. You cannot re-define science so that it includes the supernatural, as Kansas's board of education did in 2005. Nor can you take "religion" to be the philosophy of liberal theologians, which, frowning on a personal God, is often just a hairsbreadth away from pantheism. After all, the goal is not to turn the faithful into liberal theologians, but to show them a way to align their actual beliefs with scientific truths. Theologians sometimes suggest a reconciliation by means of naturalistic deism, the idea that the creation of the universe--and perhaps the laws of physics--was the direct handiwork of a deity who then left things alone as they unfolded, never interfering in nature or history again. For the faithful, this has been even more problematic than pantheism: it not only denies miracles, virgin births, answered prayers, and the entire cosmological apparatus of Christianity, Judaism, Islam, Hinduism, and much of Buddhism, but also raises the question of where God came from in the first place

I've met many "liberal theologians" who claim to believe in some version of "process theology"— a wishy-washy concept that, as Coyne correctly points out, is just a hairsbreadth away from pantheism. The catch is that when you follow these so-called "liberal theologians" back to the safety of their church you'll find that they quickly revert to another form of religion altogether. The "sophisticated" version of Christianity that they proclaim in public is just a sham designed to make them look as though they accept science and all its implications.

The real value of Coyne's review is the dismantling of Ken Miller's version of theistic evolution. Miller, like most theists, wants to have his cake and eat it too. He wants to accept science and evolution but, at the same time, he wants to sneak God into the picture so that humans are special. This is a recognition of the fundamental conflict between science and religion; namely, that according to what we know about the natural world, humans are not special in any way and life does not have a purpose. There are very few believers who can stomach those ideas, hence their science and their religion are in conflict.

Miller opts for theology. Although his new book does not say how God ensured the arrival of Homo sapiens, Miller was more explicit in Finding Darwin's God. There he suggested that the indeterminacy of quantum mechanics allows God to intervene at the level of atoms, influencing events on a larger scale:

"The indeterminate nature of quantum events would allow a clever and subtle God to influence events in ways that are profound, but scientifically undetectable to us. Those events could include the appearance of mutations, the activation of individual neurons in the brain, and even the survival of individual cells and organisms affected by the chance processes of radioactive decay."

In other words, God is a Mover of Electrons, deliberately keeping his incursions into nature so subtle that they're invisible. It is baffling that Miller, who comes up with the most technically astute arguments against irreducible complexity, can in the end wind up touting God's micro-editing of DNA. This argument is in fact identical to that of Michael Behe, the ID advocate against whom Miller testified in the Harrisburg trial. It is another God-of-the-gaps argument, except that this time the gaps are tiny.

Exactly. The difference between Ken Miller and Michael Behe is trivial compared to the difference between Ken Miller and Richard Dawkins. Coyne is not the only one who has trouble seeing why Behe isn't a theistic evolutionist and Miller isn't an intelligent design creationist.

Coyne has written a great article and you must read all of it. Here are two more teasers that I hope will entice you to learn more ...

Giberson and Miller are thoughtful men of good will. Reading them, you get a sense of conviction and sincerity absent from the writings of many creationists, who blatantly deny the most obvious facts about nature in the cause of their faith. Both of their books are worth reading: Giberson for the history of the creation/ evolution debate, and Miller for his lucid arguments against intelligent design. Yet in the end they fail to achieve their longed-for union between faith and evolution. And they fail for the same reason that people always fail: a true harmony between science and religion requires either doing away with most people's religion and replacing it with a watered-down deism, or polluting science with unnecessary, untestable, and unreasonable spiritual claims.

Although Giberson and Miller see themselves as opponents of creationism, in devising a compatibility between science and religion they finally converge with their opponents. In fact, they exhibit at least three of the four distinguishing traits of creationists: belief in God, the intervention of God in nature, and a special role for God in the evolution of humans. They may even show the fourth trait, a belief in irreducible complexity, by proposing that a soul could not have evolved, but was inserted by God.

This disharmony is a dirty little secret in scientific circles. It is in our personal and professional interest to proclaim that science and religion are perfectly harmonious. After all, we want our grants funded by the government, and our schoolchildren exposed to real science instead of creationism. Liberal religious people have been important allies in our struggle against creationism, and it is not pleasant to alienate them by declaring how we feel. This is why, as a tactical matter, groups such as the National Academy of Sciences claim that religion and science do not conflict. But their main evidence--the existence of religious scientists--is wearing thin as scientists grow ever more vociferous about their lack of faith. Now Darwin Year is upon us, and we can expect more books like those by Kenneth Miller and Karl Giberson. Attempts to reconcile God and evolution keep rolling off the intellectual assembly line. It never stops, because the reconciliation never works.

Visit The Edge to see how otherwise intelligent men and women respond to Coyne's argument. Some of them make the kindergarten error of confusing disagreement with intolerance.

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It took Ricky Gervais only one hour to become an atheist

 
Watch the full story in this clip from Inside the Actors Studio, which, incidentally, is one of my favorite shows.

The good bit comes at four and a half minutes.

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[Hat Tip: Friendly Atheist]

Explaining the New Scientist Cover

 
Yesterday I criticized the cover of the latest issue of New Scientist [Darwin Was Wrong?]. There's a good discussion going on at EvolutionBlog [The Trouble With Science Journalism].

I pointed out that the cover was, "an egregious example of journalistic hype and it's unacceptable in a magazine like New Scientist." I also mentioned that the article itself, written by Graham Lawton, contained some interesting—and mostly correct—information about the early history of life.

Graham Lawton posted a comment to my earlier posting where he critized Sandwalk readers because they (we?), "lack a fundamental understanding of how the media works." He was asked to explain. This is how Graham Lawton replied.

The way we work here is that the writer of the piece generally has almost no say over the headline, standfirst and other bits of "page furniture". These are the resonsibility of the copy editor and the sub-editors. The online version often has its own headline, which again is out of the control of the writer (in this case the magazine headline is "Uprooting Darwin's Tree").

Coverlines, similarly, are written not by the writer but by senior editors with the express purpose of selling the magazine (the line between marketing and journalism blurs a little here).

As I'm a senior editor too, however, I can't and won't claim that the coverline was entirely beyond my control. Not my ultimate decision, but I was in on the discussions. We knew we were courting controversy but the feeling was that the story was solid enough to allow us to be provocative and, in any case, the statement is true.

So I feel very strong ownership of the article itself, particularly the print version (and I totally stand by the story, which is the product of weeks of hard work, extensive interviews with scientists, a stack of journal papers and much thought, despite what some bloggers are saying). I feel some ownership of the front cover "sell", though as always I'm acutely aware that it is 50% journalism, 50% sales pitch.

I, for one, am not surprised by this "revelation." I have known for some time that decisions on titles and covers are not made by authors. I've known for some time that decisions about titles and covers can be based on "sales pitch" and "hype" and that scientific accuracy can play a minor role in those decisions.

I'd like to thank Graham Lawton for explaining the process in case there are some people who still don't understand the basics.

The fact that I knew how covers were selected does not affect my criticism of the decision in spite of what Lawton might think. As a matter of fact, now that I know how he was involved as senior editor I can put some of the blame on him. The fact that he defends the cover title ("Darwin Was Wrong") by saying that, "... in any case, the statement is true" is revealing.

It's unusual for a science journalist to be so candid about the trade-off between scientific accuracy and "sales pitch."

As for the article itself, Graham Lawton is quite proud of it. He seems to be implying that the title of the article was not his fault, thereby shifting the blame somewhat to other editors. That position is not going to stand up to close examination of the article.

The first four paragraphs talk about Darwin and what he thought in 1837 and 1859 [Why Darwin was wrong about the tree of life. It will be clear to every reader that this is not just ancient history, the strong implication is that up until recently most evolutionary biologists thought just like Darwin must have thought 150 years ago. They were stuck in the late nineteenth century Victorian mindset. That's why Lawton begins the next paragraph with, "For much of the past 150 years, biology has largely concerned itself with filling in the details of the tree."

That's nonsense, of course. There's a lot more that's been happening in evolutionary biology than just filling in the details of trees. Is it any wonder that the editors picked up on this false notion and created the headline "Darwin Was Wrong"? Graham Lawton, as author of the article, seems to be making exactly that point.

The article would have been much better if Darwin's name had never been mentioned. Darwin knew nothing about molecular evolution and he knew almost nothing about bacteria or the last common ancestor. Dragging Darwin's name into the article serves only to confuse the readers. It's probably another example of "sales pitch" designed to sell the magazine. It may not be only editors who are guilty.

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44 Presidents?

 
This video is very popular these days. The title is "44 US Presidents from George Washington to Barack Obama." There's only one small problem .... there are only 43 different Presidents shown in the video. Can you spot the "missing" President?



How many can you name without watching the video? Please indicate whether you are American or a "foreigner."

Do Americans agree on who the best President was, and on who was the worst President? It seems to me that there are several excellent choices in each category.

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Advice for Prospective Graduate Students: Letters of Recommendation

 
Mark, of Cosmic Variance has some advice about Letters of Recommendation. There's lots of useful information in the posting but here's something that bears repeating.

Perhaps the most important thing for prospective graduate students in particular to keep in mind is that admissions committees, while certainly holding great power over individuals’ futures, are in fact desperately seeking good candidates, and are willing to overlook all kinds of blemishes, indiscretions, and specific weaknesses if they feel that they’re getting a fundamentally good candidate. A single specific fact about an application is very unlikely to ruin a person’s chances (you’d be amazed at the GRE scores of some students admitted to even the top programs). Rather, the committee tries to get an overall picture of the candidate, and then to rank them relative to other candidates (also taking into account the department’s research needs at a given time). Only then are admissions decision taken.

I have certainly missed some issues and subtleties here. But the basic idea should be clear and, if my own experience is anything like typical, then it should help some of you, particularly prospective graduate students, to understand what really goes on with letters. It is quite terrifying to ask people for letters and not to know precisely what’s said in them. Hopefully it helps to know that mostly, by far, you can rely on people to do what they can for you, without being dishonest (and this is important - you can’t expect them to write that you’re one of the best students they’ve ever seen if they don’t think that is the case).

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Darwin Was Wrong?

The cover is this week's issue of New Scientist is sure to get your attention.

I happen to believe that the science of evolutionary biology has moved on since 1859, and I happen to be a proponent of evolutionary processes that Darwin new nothing about. Nevertheless, proclaiming that "Darwin was wrong" is a different story. That's an egregious example of journalistic hype and it's unacceptable in a magazine like New Scientist.

The main article is Why Darwin was wrong about the tree of life. The author is science journalist Graham Lawton.

The essence of the story is that the early history of evolution is probably characterized by a net of life and not a traditional tree. The "net" metaphor is due to many example of lateral gene transfer.

Ever since Darwin the tree has been the unifying principle for understanding the history of life on Earth. At its base is LUCA, the Last Universal Common Ancestor of all living things, and out of LUCA grows a trunk, which splits again and again to create a vast, bifurcating tree. Each branch represents a single species; branching points are where one species becomes two. Most branches eventually come to a dead end as species go extinct, but some reach right to the top - these are living species. The tree is thus a record of how every species that ever lived is related to all others right back to the origin of life.

For much of the past 150 years, biology has largely concerned itself with filling in the details of the tree. "For a long time the holy grail was to build a tree of life," says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. "We have no evidence at all that the tree of life is a reality," says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.

As it happens, I was at a function last night with Jan Sapp of York University (Toronto, Canada). Loyal Sandwalk readers might recall a series of articles on the Three Domain Hypothesis. The articles were based on a book edited by Jan Sapp. Sapp is a supporter, as am I, of the scheme advocated by Ford Doolittle (see below).


This net, or web, of life is characteristic of the earliest stages of evolution when all organisms were single cells and the distinction between eukaryotes and prokaryotes was barely discernible. Once the main groups rose out of the web, they evolved pretty much as you light expect by binary speciation events. This gives rise to a traditional tree-like pattern.

As Jan and I discussed, for the last three billion years of evolution the tree of life is a very good metaphor for evolution. Darwin was mostly right about that. On the other hand, the New Scientist article discusses some problems with the tree of life that extend beyond the early history. It makes several valid points that should make everyone skeptical of claims about evolution that are too simple. The tree isn't perfect.

The bottom line is that it's unfair to say that Darwin was wrong. It's as unfair as saying the Newton was wrong because of Einstein. We need to recognize that modern evolutionary biology is an improvement over the view of the Victorian founder of the field, but a cover saying that Darwin was wrong conveys the wrong message. It suggests that up until recently scientists believed that Darwin was right about everything.

A better headline might be: "More evidence that Charles Darwin didn't know everything there is to be known about evolution when he published his book in 1859."

UPDATE: In a surprising development, the IDiots at Uncommon Descent have picked up on these recent (sic) developments in evolutionary theory. Paul Nelson, a Young Earth Creationist philosopher, writes: “The tree of life is being politely buried”.

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