PZ, Poutine, and the End of the World

One of the highlights of Eschaton 2012 was taking PZ Myers to the Elgin Street Grill for poutine. He had the plain, ordinary version diluted with a chicken burger. I had the chili poutine.

Other highlights included his two talks. The one on Saturday morning was about the sorry state of science education in the United States. That was depressing.

PZ's talk on Saturday evening was at the Canadian Museum of Natural History, just around the corner from the hotel. There were about 200 people in the audience. He tackled a very difficult topic, the role of chance in evolution. Naturally he covered random genetic drift but most of his talk was about coalescent theory because he wanted to explain some recent results from the sequence of the gorilla genome (Scally et al. 2012).

The authors of that paper report that, "In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other." PZ explained why this is exactly the result you would expect. (See his blog post at: A tiny bit of knowledge is a dangerous thing.)

He also pointed out that the Intelligent Design Creationists got all excited about this result, thinking that it overthrows the theory of evolution and proves the existence of God. (I exaggerate slightly, but you get the point!) What this means if that the IDiots really don't understand evolution.

While we don't expect everyone to see immediately why 30% of our genes could be more similar to gorilla genes than to chimp genes, we do expect those who criticize evolution to have a better understanding. Instead, what we see is that those "experts" who post at Evolution News & Views (sic) don't even have an introductory college level understanding of evolution. Their ignorance of evolution produces some remarkably stupid posts on that blog—the website of the Discovery Institute.

I made a similar point in my talk except that I focused on the IDiot's lack of knowledge of mutation [see Breaking News: IDiots Don't Understand Genomes or Biology].

PZ took on a challenging task but he succeeded better than I could have imagined. While the audience didn't follow all of the explanation, they could see that it was based on solid evidence and theory. Many of them learned for the first time about chance in evolution and that's a plus, in my opinion.

Now let's work on the IDiots.

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Scally, A, Dutheil, J.Y., Hillier, L.W., Jordan, G.E. et al. (2012) Insights into hominid evolution from the gorilla genome sequence. Nature 483:169-175. [PubMed]

Breaking News: IDiots Don't Understand Genomes or Biology

Just when you think they couldn't get more stupid, along comes some IDiot to prove you wrong. Here's the latest from an anonymous contributor at Evolution News & Views [Your Genome? Which One?].

A new finding about DNA differences in somatic cells overthrows a common assumption and might have dramatic implications for evolutionary studies.

Young's Law (from Murphy's catalog of perverse tendencies in nature) states that all great discoveries are made by mistake. A corollary is that the greater the funding, the longer it takes to make the mistake, but we won't go there. Anyway, a team of Yale scientists wasn't looking to overturn a huge assumption in genetics -- but they did. The ripple effects of their discovery remain to be seen.

We've all been told that every cell in our body has a copy of our unique genetic code. That's one of those simplistic beliefs that sounds sensible but is almost impossible to check. Doesn't the whole body arise from cell divisions of a single zygote with its unique genetic code? Yes, but it doesn't necessarily follow that the genes in cells downstream don't get modified. That was just assumed....

"Somatic mosaicism" is jargon for the finding that genomes differ from cell to cell -- not only in copy number variations (CNV's), but in single nucleotide polymorphisms (SNP's). The assumption that you have one genome is thus falsified. You have lots of genomes!

Okay, let's take a poll.

How many of you thought that mutations such as nucleotide substitutions, deletions, and insertions, could never take place during the thousands of generations that give rise to our somatic cells? (How were they supposed to be suppressed?)

How many of you thought that all of our cells, including red blood cells, contain copies of our unmodified genome?

How many of you thought that there were no polyploid cells in our liver?

How many of you thought that B cells, and T cells (and others) contain the same identical copy of our genome that's found in germ cells?

How many of you thought that spermatocytes and ovaries have exactly the same genome as our original zygote?

How many of you thought that cancer-causing gene rearrangements and mutations in somatic cells were impossible?

How many of you are completely ignorant of any medical problems due to genetic mosaicism?

If you answered "yes" to all of those questions then, congratulations!, you're as smart as an IDiot.

Sheeesh!

One thing is clear at this stage: the assumption that each individual has a unique genome has been overthrown to some extent. Think how this might impact common evolutionary studies. For years, evolutionists have claimed small differences between human and chimpanzee genomes. What if the percent difference is a function of the source cells used? Remember, the Yale team found differences between cells in the same organ -- human skin. If the percent difference grows or shrinks depending on the source, any conclusions about human-chimp similarities would prove unreliable.

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I Get Mentioned, Again, on an IDiot Blog

The nameless people at Evolution News & Views (sic) didn't like my comments about Michael Behe. Naturally they focus right in on defending the IDiot science (not!) [Giving Thanks for Minority Opinions]. (The reference to "thanks" is in honor of today's American Thanksgiving holiday.)

When in the future they write the history of modern biology, if it turns out that contemporary ID theorists were onto something big, then Michael Behe's name will figure very prominently as one who helped launch the intelligent-design revolution.

When that history is written, whatever fate holds in store for ID, no one thinks that University of Toronto biochemist Larry Moran's name will figure prominently in any account as a thinker of great stature or influence.

So there's some irony in Moran's patronizing three-part series, at his blog Sandwalk blog, about meeting Mike Behe when the latter came to visit and speak recently in Toronto. Moran is full of condescension and, sticking to the science as always, carefully points out the discrepancy in physical stature between himself and Behe where Moran does have the advantage -- "He's a lot shorter than I imagined but otherwise looks just like his photos." Moran includes a photo of himself leaning over Behe with a smirk to prove the point. Well then!

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Is It Science?

I've been having discussion with several of my friends and colleagues about whether the activities of the Intelligent Design Creationists count as "science." My position is that much of what they do is science, especially when they criticize existing scientific explanations. It may not be very good science but that's not the question. After all, there are atheist scientists who don't do much better.

One argument is that simply criticizing current theories doesn't count as science unless you can also offer a plausible, scientific, competing model. I don't think that's a requirement. Here's an example we can discuss ...

One of the latest posts on Evolution News & Views (sic) is an article by Casey Luskin criticizing the old Urey-Miller experiment by pointing out that their origninal conditions didn't mimic the conditions on the primitive Earth [On the Miller-Urey Experiment, Wikipedia Offers a Citation Bluff]. He goes on to say that scientists still haven't shown convincingly that amino acids (and other molecules) could have formed spontaneously on Earth. Furthermore, the "chirality problem" hasn't been solved.¹

Luskin correctly points out that a Wikipedia reference misrepresents the science it reports.

Is this (Luskin's article) scientific? Isn't criticism of current models and hypotheses an example of how science is supposed to work?

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1. I agree that the spontaneous formation on Earth of significant amounts of amino acids, carbohydrates, and, especially, nucleotides, is extremely unlikely. That's why I support "Metabolism First." I disagree about the chirality problem—I think we have a good explanation.

Five Myths (?) About Intelligent Design Creationism

Melissa Travis writes for a blog called Hard-Core Christianity. Her latest post is: Top Five Myths Christians (and Non-Christians) Often Believe About Intelligent Design. It's interesting because it reveals the standard myths that Intelligent Design Creationists believe about themselves.

Here's the list of "myths" along with what Mellisa Travis has to say about them.

MYTH #1: Intelligent Design (ID) is just a fancy name for Creationism.

The true story: Intelligent Design theory is not a form of, nor is it synonymous with “creationism.” Rather, it is an over-arching scientific theory that disputes wholly naturalistic/materialistic accounts of the origin of the universe and the origin of life. As such it is an indispensable ally for those who espouse various creation models. ID makes NO CLAIM about the age of the earth.

FACT: Modern Intelligent Design Creationism evolved from the creationist movement in the 1980s as was proven conclusively in the Dover trial. Intelligent Design Creationism is not a scientific theory. Instead, its a hodgepodge of criticisms of evolution and of scientists and materialism. Just look at the posts on Evolution News & Views (sic) to see what it's all about. Count the number of posts promoting a "scientific" view of Intelligent Design Creationism as opposed to disjointed helter-skelter criticisms of evolution that often contradict each other.

There's no "over-arching" scientific theory in sight.

Another Evolutionary Paradox?

The IDiots are remarkably good at uncritical thinking. When you couple this tendency to ignorance of evolution, you come up with some remarkable conclusions.

Take, for example, the well-known fact that rich people tend to have fewer children than poor people. What this means is that poor people are better at passing on their genes (alleles) to the next generation than rich people. If there is a genetic component to richness and poorness then poor people are "more fit" than rich people and, eventually, the poorness alleles will become fixed in the population. That's just a fact and it doesn't matter what you might think about the genetic advantage of being rich.

Of course there may not be any significant difference in the genetic compositions of rich people and poor people in which case the argument becomes moot.

Let's see how an anonymous IDiot deals with this information on their main blog site, Evolution News & Views (sic) ... [Survival of the Poorest: Another Evolutionary Paradox].

Here's another evolutionary paradox: the "demographic transition." We've alluded to this before, but why not recall the point? Darwin notwithstanding, it seems to support the view that the meek shall inherit the earth.

By all accounts, the rich should be, in Darwinian terms, the fittest. They have the most resources, and the most opportunities for advancement. Yet they leave fewer offspring. That's the finding of a large study of Swedish families that's just been completed.

Nature recently recognized that this has been a known contradiction to evolutionary theory.

"Fitness" is defined in all evolutionary biology textbooks as ...

The fitness of a genotype is the average lifetime contribution of individuals of that genotype to the population after one or more generations ... A general term for this number is reproductive success, which includes not simply the average number of offspring produced by the reproductive process, but the number that survive, since survival is prerequisite to reproduction.

Futuyma, D.J. (2009) Evolution p. 306

Do the IDiots ever read basic introductory evolution textbooks or do they just pull out "evolutionary paradoxes" from their nether parts? There's no contradiction with evolutionary theory and there's nothing in "Darwinian terms" that defines fitness as anything but reproductive success.

The only "puzzle" might be the naive presumption that rich people should have more reproductive success than poor people but we've known that this isn't true for over one hundred years.

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[Photo Credit: Ten children of Ethel and Bobby Kennedy (the 11th child was born after Bobby was killed). This is the exception that proves the rule. Prompted by last night's viewing of the remarkable documentary Ethel which also prompts the question, "Why doesn't America have principled politicians like Bobby Kennedy any more?"]

On Attacking the Integrity of Scientists

We are discussing the evolution/creation controversy in my course. One of the issues that comes up frequently is the role of scientific evidence. The importance of science in the 21st century cannot be exaggerated. Everyone wants science to be on their side because if your views conflict directly with scientific evidence then your case is very weak.

So, how do creationists handle this issue? They usually try to present counter-evidence or they cherry-pick the scientific literature looking for papers that lend support to their cause. But that only takes you so far. Creationists are forced to admit that the vast majority of scientists support evolution and that's a real problem for their flock.

The solution is obvious. If you can't attack the science then attack the scientists. By casting doubt on the motives of scientists you can partially neutralize the impact of science.

Here's an excellent example from today's post on Evolution News & Views (sic) [How to Talk About "Evolution"].

Better to think of opinion as sharply divided. The professors, their students and many university-educated people believe one thing (evolution is a fact) and most everyone else is suspicious. They won't believe in evolution if you tell them what the professors believe -- that life in all its complexity assembled itself as a result of a series of lucky hits; that we live in a world of random changes that sometimes "coincide" with the environment (natural selection); and that's how we got here.

To believe that, we first have to be blinded by antagonism to the normal, automatic recognition of purpose and design in nature. And for most people, this blindness has to be inculcated; by teachers, by the academy, by the culture.

As to the possibility of our reaching the professor group, the trouble with my correspondent's design versus "accidental mutation/natural selection" formula is not that it is too wordy but that the professoriate have learned to accept that accidental mutation and natural selection can explain everything under the sun.

I have often wondered: What would it take for a biology professor to see some living organism, study it and then clap his hand to his forehead and say: "Wow, natural selection couldn't possibly have done THAT!"

Answer: Nothing. They are locked into a materialist worldview, and they think that anything outside it is unscientific. They have already accepted Lewontin's Law about the necessity of a "prior commitment to materialism." They will look at any strange organism you may show them and say: "Well, it exists doesn't it? How else did it get here, if not by gradual stages, bit by bit, starting with molecules in motion, finally building up to what we see in front of us? What other choice is there?"

In such a dogmatic environment dissenters wisely keep their mouths shut and upholders of the orthodoxy firmly close their minds.

Of course they don't like it when we refer to them as IDiots or creationists but they have an answer to that one as well.

Going beyond that, some of our better-known adversaries indulge in name-calling so mechanically that they may well have ceased to understand the issues. It's as though they become unable to think about what they don't want to think about. Those who resort to slogans like "ID creationism" often show no sign of understanding what the claims of ID are, sufficiently even to be able to restate them.

Unfortunatly for the IDiots, I actually understand the issues better than they do! Here's the main tenets of Intelligent Design Creationism.

1. Darwin is evil and gave rise to Hilter. Evolutionists are wedded to atheism and materialism. Most scientists are too stupid to interpret evidence correctly. Evolution cannot account for life as we know it.
2. Life can only be explained by invoking an Intelligent Designer but we're not going to tell you how or when he/she/it did it.
3. The Intelligent Designer is not necessarily a god. We never said that so you can't accuse us of being creationists.
4. The general public is being prevented from learning the truth about creationism anti-evolutionary theory by a vast conspiracy of dogmatic scientists who control higher education (and almost everything else in some secular "foreign" countries like France or Japan).

Do you think I got it right?

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A Dishonest Intelligent Design Proponent?

Most IDiots are ignorant about evolution and they let their religious biases interfere with the proper interpretation of scientific data. We excuse their mistakes on the grounds that they don't know any better.

However, some IDiots clearly should know better. They have advanced degrees in relevant fields and they have received considerable feedback on the claims they post or the books they write. We know they have read the critiques so when they persist in repeating falsehoods, there must be another explanation. They must be lying.

Jonathan Wells has a Ph.D. in molecular biology. He has posted numerous articles about junk DNA and he was written a book on the subject (The Myth of Junk DNA). Lots of people have made comments about his blog posts and his book has been widely critiqued. Many of his claims have been shown to be false.

So what do we make of his recent post on Evolution News & Views) (sic) entitled Why All the Fuss Over Some Junk?. We are forced to conclude that Wells is dishonest. Perhaps with the caveat expressed by Peter Medawar many years ago in his review of Père Teihard's The Phenomenon of Man.

Yet the greatest part of it, I shall show, is nonsense, tricked out with a variety of metaphysical conceits, and its author can be excused of dishonesty only on the grounds that he has taken great pains to deceive himself.

An Honest Intelligent Design Proponent?

It's unusual to find a proponent of Intelligent Design Creationism who makes an honest attempt to evaluate scientific facts. Jonathan McLatchie (Jonathan M) seems to be one of those rare birds. I'm not going to refer to him as an IDiot.

Here's a bit from his latest post on Evolution News & Views (sic [Perspectives on ENCODE and Junk DNA].

The debate thus hinges on whether activity such as transcription, transcription factor association, and histone modification are signs of true function. My own view is that such activity is suggestive of functionality, but not proof. Therefore I would be cautious about claiming that these results show 80% of the genome to have function in the sense that we normally use that word.

On the other hand, the observation that the genome is buzzing with activity underscores what proponents of ID have been saying for years: not knowing what something does doesn't constitute evidence that it's doing nothing. Moreover, it wasn't long ago that Laurence Moran and PZ Myers were telling us that the genome is not even pervasively transcribed and that this amounted to evidence that the majority of our DNA is junk.

That's pretty good for someone who posts on a blog that also publishes stuff from Jonathan Wells and Casey Luskin. I wonder if they talk to each other?

On the other hand, it's not perfect. I've been arguing for years that there is good solid evidence that most of our genome is junk. I have never used the argument from ignorance that Jonathan attributes to me.

Also, I have never denied that the genome is pervasively transcribed. Instead, I have argued that pervasive transcription is something that one expects given what we know about DNA binding proteins and transcription. I've pointed out that the vast majority of our genome is transcribed very rarely—about one transcript per day in 100 cells—and this is consistent with accidental transcription. This is noise. The product is junk RNA and is has no function [Useful RNAs?] [Junk RNA] [Pervasive Transcription] [How to Frame a Null Hypothesis] [How to Evaluate Genome Level Transcription Papers ].

I discussed this thoroughly when I reviewed Jonathan Wells' book The Myth of Junk DNA [Junk & Jonathan: Part 6—Chapter 3]. Perhaps Jonathan McLatchie hasn't read my earlier posts?

Contrast McLatchie's post with that of Jonathan Wells [A Dishonest Intelligent Design Proponent?].

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Douglas Axe Explains Molecular Evolution

There are several dozen scientists and graduate students in my department studying various aspects of protein evolution, structure, and folding. They've published dozens of papers but, apparently, they never realized that what they're studying is impossible. Douglas Axe, a leading Intelligent Design Creationist, sets them straight.

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[Hat Tip: Evolution News & Views: Axe: Vive la Différence]

Are All IDiots Irony Deficient?

As I'm sure you can imagine, the Intelligent Design Creationists are delighted with the ENCODE publicity. This is a case where some expert scientists support one of their pet beliefs; namely, that there's no such thing as junk DNA. The IDiots tend not to talk about other expert evolutionary biologists who disagree with them—those experts are biased Darwinists or are part of a vast conspiracy to mislead the public.

You might think that distinguishing between these two types of expert scientists would be a real challenge and you would be right. Let's watch how David Klinghoffer manoeuvres through this logical minefield at: ENCODE Results Separate Science Advocates from Propagandists. He begins with ....

"I must say," observes an email correspondent of ours, who is also a biologist, "I'm getting a kick out of watching evolutionary biologists attack molecular biologists for 'hyping' the ENCODE results."

True, and equally enjoyable -- in the sense of confirming something you strongly suspected already -- is seeing the way the ENCODE news has drawn a bright line between voices in the science world that care about science and those that are more focussed on the politics of science, even as they profess otherwise.

How Do Intelligent Design Creationists Define "Creationism"?

David Klinghoffer showed up in the comments on James Shapiro Claims Credit for Predicting That Junk DNA Is Actually Part of a "highly sophisticated information storage organelle" to ask about creationism.

He didn't like the fact that I define "creationism" as belief in a creator and anyone who believes in a creator is a creationist. I identified several flavors of creationism including Young Earth Creationism, Intelligent Design Creationism, and Theistic Evolution Creationism. This is exactly the same sort of definition used by many people and it's the one described in the Wikipedia article on creationism. (It has even more flavors.)

David Klinghoffer didn't like that so he decided to make an issue of it by posting on Evolution News & Views: What Is a "Creationist"? Let's take a look at what he says in order to learn a little more about the creationist mindset.

Groupthink Science And That 'Junk DNA'

The IDiots (e.g. Tom Bethell) over at Evolution News & Views are gloating about a comment made on The Wall Street Journal website [Why ENCODE Is a Significant Defeat for Darwinism].

The WSJ article is: Groupthink Science And That 'Junk DNA'.

Anyone with even the slightest understanding of the evolutionary process knows that evolution is too relentlessly efficient to have allowed most, or even large sections, of DNA to be "junk" ("'Junk DNA' Theory Debunked," U.S. News, Sept. 6). Any intelligent scientist would have simply said, "I don't know."

Unfortunately, this says something important about the quality of contemporary Ph.Ds. Groupthink has become pervasive in part because of how research is now financed: grants. The disillusioning sociological aspects of scientific research that Thomas Kuhn identified more than four decades ago have become more pronounced, not less.

Tom Shillock

Portland, Ore.

This is exactly backwards, in my opinion. The real problem is that many scientists think, incorrectly, that natural selection would have removed all junk DNA so they are looking for reasons why it isn't junk. If they can't find evidence then they just make up a story or re-define the word "function." They don't have even the slightest understanding of evolution, just like Tom Shillock.

UPDATE: Shapiro and Sternberg Anticipated the Fall of Junk DNA.

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James Shapiro Claims Credit for Predicting That Junk DNA Is Actually Part of a "highly sophisticated information storage organelle"

Do you remember James Shaprio? He's the University of Chicago scientist who claims to have discovered a new theory of evolution in his book evolution: A View from the 21st Century [see my review in NCSE Reports]. The book criticizes the old hardened version of the Modern Synthesis and never mentions things like random genetic drift or Nearly-Neutral Theory. It's difficult to imagine how someone could criticize evolutionary theory without understanding population genetics but he managed to pull it off.

You might also recall that he's the scientist who criticized the Central Dogma of Molecular Biology when he clearly didn't understand it [Revisiting the Central Dogma in the 21st Century]. I was shocked to learn that he had published a paper with the title "Revisiting the Central Dogma in the 21st Century" without ever bothering to read the literature to find out how Francis Crick actually defined the Central Dogma. (In fact, Shapiro misrepresented Crick's view.) It goes to show you how silly you look when you criticize something you don't understand.

ENCODE/Junk DNA Fiasco: The IDiots Don't Like Me

Casey Luskin has devoted an entire post to discussing my views on junk DNA. I'm flattered. Read it at: What an Evolution Advocate's Response to the ENCODE Project Tells Us about the Evolution Debate.

Let's look at how the IDiots are responding to this publicity fiasco. Casey Luskin begins with ...

University of Toronto biochemistry professor Larry Moran is not happy with the results of the ENCODE project, which report evidence of "biochemical functions for 80% of the genome." Other evolution-defenders are trying to dismiss this paper as mere "hype".

Yes that's right -- we're supposed to ignore the intentionally unambiguous abstract of an 18-page Nature paper, the lead out of 30 other simultaneous papers from this project, co-authored by literally hundreds of leading scientists worldwide, because it's "hype." (Read the last two or so pages of the main Nature paper to see the uncommonly long list of international scientists who were involved with this project, and co-authored this paper.) Larry Moran and other vocal Internet evolution-activists are welcome to disagree and protest these conclusions, but it's clear that the consensus of molecular biologists -- people who actually study how the genome works -- now believe that the idea of "junk DNA" is essentially wrong.

More Expert Opinion on Junk DNA from Scientists

The Nature issue containing the latest ENCODE Consortium papers also has a New & Views article called "Genomics: ENCODE explained" (Ecker et al., 2012). Some of these scientist comment on junk DNA.

For exampleshere's what Joseph Ecker says,

One of the more remarkable findings described in the consortium's 'entrée' paper is that 80% of the genome contains elements linked to biochemical functions, dispatching the widely held view that the human genome is mostly 'junk DNA'. The authors report that the space between genes is filled with enhancers (regulatory DNA elements), promoters (the sites at which DNA's transcription into RNA is initiated) and numerous previously overlooked regions that encode RNA transcripts that are not translated into proteins but might have regulatory roles.

And here's what Inês Barroso, says,

The vast majority of the human genome does not code for proteins and, until now, did not seem to contain defined gene-regulatory elements. Why evolution would maintain large amounts of 'useless' DNA had remained a mystery, and seemed wasteful. It turns out, however, that there are good reasons to keep this DNA. Results from the ENCODE project show that most of these stretches of DNA harbour regions that bind proteins and RNA molecules, bringing these into positions from which they cooperate with each other to regulate the function and level of expression of protein-coding genes. In addition, it seems that widespread transcription from non-coding DNA potentially acts as a reservoir for the creation of new functional molecules, such as regulatory RNAs.

If this were an undergraduate course I would ask for a show of hands in response to the question, "How many of you thought that there did not seem to be "defined gene-regulatory elements" in noncoding DNA?"

I would also ask, "How many of you have no idea how evolution could retain "useless" DNA in our genome?" Undergraduates who don't understand evolution should not graduate in a biological science program. It's too bad we don't have similar restrictions on senor scientists who write News & Views articles for Nature.

Jonathan Pritchard and Yoav Gilad write,

One of the great challenges in evolutionary biology is to understand how differences in DNA sequence between species determine differences in their phenotypes. Evolutionary change may occur both through changes in protein-coding sequences and through sequence changes that alter gene regulation.

There is growing recognition of the importance of this regulatory evolution, on the basis of numerous specific examples as well as on theoretical grounds. It has been argued that potentially adaptive changes to protein-coding sequences may often be prevented by natural selection because, even if they are beneficial in one cell type or tissue, they may be detrimental elsewhere in the organism. By contrast, because gene-regulatory sequences are frequently associated with temporally and spatially specific gene-expression patterns, changes in these regions may modify the function of only certain cell types at specific times, making it more likely that they will confer an evolutionary advantage.

However, until now there has been little information about which genomic regions have regulatory activity. The ENCODE project has provided a first draft of a 'parts list' of these regulatory elements, in a wide range of cell types, and moves us considerably closer to one of the key goals of genomics: understanding the functional roles (if any) of every position in the human genome.

The problem here is the hype. While it's true that the ENCODE project has produced massive amounts of data on transcription binding sites etc., it's a bit of an exaggeration to say that "until now there has been little information about which genomic regions have regulatory activity." Twenty-five years ago, my lab published some pretty precise information about the parts of the genome regulating activity of a mouse hsp70 gene. There have been thousands of other papers on the the subject of gene regulatory sequences since then. I think we actually have a pretty good understanding of gene regulation in eukaryotes. It's a model that seems to work well for most genes.

The real challenge from the ENCODE Consortium is that they question that understanding. They are proposing that huge amounts of the genome are devoted to fine-tuning the expression of most genes in a vast network of binding sites and small RNAs. That's not the picture we have developed over the past four decades. If true, it would not only mean that a lot less DNA is junk but it would also mean that the regulation of gene expression is fundamentally different than it is in E. coli.

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[Image Credit: ScienceDaily: In Massive Genome Analysis ENCODE Data Suggests 'Gene' Redefinition.

Ecker, J.R., Bickmore, W.A., Barroso, I., Pritchard, J.K. (2012) Genomics: ENCODE explained. Nature 489:52-55. [doi:10.1038/489052a]
Yoav Gilad
& Eran Segal

More Creationist Objections to Unguided Evolution

Maybe it's just my imagination, but I think I detect a change on Evolution News & View and on Uncommon Descent. For years these blogs have been attacking evolution without paying the least attention to what their opponents are saying. Lately, however, there seem to be some authors who are actually listening to their opponents and trying to address the main criticisms of the IDiot position.

Sometimes you even see articles that are close to being scientifically correct and I've even seen articles that recognize the existence of modern evolutionary theory (i.e. not Darwinism).

The good articles are still quite rare but I'm encouraged by the fact that they are listening.

The latest contribution is by Stephen A. Batzer, a contributor to Evolution News & Views since May 10, 2012. Batzer has a Ph.D. in Mechanical Engineering (see The Salem Conjecture). He's responding to an earlier post of mine where I attempted to explain to Casey Luskin why he was wrong about evolutionary theory [Is "Unguided" Part of Modern Evolutionary Theory?]. Recall that Luskin was saying that the "unguided" nature of evolution was a core part of the theory of Darwinian evolution.

Advice to New Creationist Students

We're getting close to the beginning of the semester in the northern hemisphere. That means a lot of high school students will be experiencing university for the first time.

In many cases, students will have graduated from high school with only a rudimentary knowledge of some important topics. This isn't necessarily a bad thing as long as they realize that they still have lots to learn. It becomes a bad thing when they think they know the subject but what they know is wrong.

Universities are places that challenge your beliefs and force you to think. New students should embrace this challenge and look forward to giving up misconceptions and ideas that can't stand up to critical analysis. The last thing you want to do as a new student is to begin university with the idea that your high school ideas are always right.

Which brings us to creationism. A large number of students enter university with little or no knowledge of evolution but they are convinced that it's wrong. They will soon encounter teachers who try to convince them that evolution is true. How should students react to this challenge?

David Klinghoffer¹ proposes one solution on the Intelligent Design Creationist blog Evolution News & Views. Here's his advice [A Piece of Unsolicited Advice to Students].

The practical question is nearly self-answering. You should be very, very circumspect about even hinting at your views to people who will end up giving you grades. But beyond that fairly obvious and uninteresting advice, I wanted to add that you should, in your own mind, strive to give respect to your Darwinist teachers no matter how firmly convinced you are that they are wrong.

If I were a professor and had a student who walked into my class intending to inform me that my fundamental views on the subject of my professional training were in error, I can well imagine thinking the kid deserved a good smack. Unfair? Yes, but true. Overturning scientific theories is not the job of an undergraduate student. A student's job is to learn what his teacher has to teach him, so that perhaps later when the student is intellectually ripened, he can lead or participate in a revolution. It's not at all that you need a PhD to hold a dissenting view, but age, thought and experience count for a lot.

At an emotional and personal level, I can sympathize with the Darwinist prof who resents his openly Darwin-doubting student. What arrogance, it must seem, to imagine that what I spent decades mastering, you a little pipsqueak think you're ready to discard half-way into the semester. Imagine yourself in your teacher's place. To him, this is about you, in your ignorance and arrogance or at best innocence, sitting in judgment of the system to which he's devoted his professional life.

In other words, hide your views because your professor might punish you. Recognize that your professor thinks he/she knows more than you do but be confident that they're wrong. Realize that when you encounter professors in class they probably don't understand their subject even though they've devoted their lives to studying it. They might be a bit angry if you exposed them so keep you mouth shut.

Above all, resist the temptation to learn and to question your beliefs. You already know the right answer. University is not the a place for learning.

Here's my advice. It you don't want to learn then don't go to university. If your belief in creationism is really strong then don't ever take a biology class—it might turn you into an atheist and your parents will be very upset. If you need the grade, then take the class, but be prepared to fail. It takes courage to openly stand up for what you believe, especially if there might be consequences. But it's the Christian thing to do.

Most professors love it when students challenge their ideas in class. We prefer those kind of students even if they are wrong. You will never fail a course because of your ideas and beliefs as long as they don't conflict directly with scientific facts. If you believe that the Earth is 6000 years old then you will not pass a geology course or a biology, unless you lie. If you dispute the existence of junk DNA then you could get an excellent grade as long as you get your facts correct.

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1. I don't think Klinghoffer has ever been to university. None of the creationist websites mention any university degrees.

We Called Out IDiot Jonathan Wells, and He Folded

Carl Zimmer had the audacity to post something about the fusion of two ancestral chromosomes in primitive apes. The data is unequivocal. It shows why humans have one less chromosome than modern chimps [The Mystery of the Missing Chromosome (With A Special Guest Appearance from Facebook Creationists)].

Observations like this lend strong support to the idea that humans and chimps share a common ancestor. This doesn't sit well with the IDiots because they are in the midst of hyping their latest book, Science & Human Origins where they try to counter the overwhelming evidence that humans evolved.

So, what did they do? David Klinghoffer challenged Carl Zimmer to pop on over to Evolution News & Views (sic) and debate one of the authors. Carl refused, as would any sane person since that creationist blog is edited by IDiots and no comments are allowed. It would be embarrassing to have one's name on an article at Evolution News & Views [The Mystery of the Missing Chromosomes, Continued: An Update From Your Preening Blogger].

Here's what Carl said,

I thought the question I asked was pretty simple. I wasn’t asking to hold a Lincoln-Douglas debate. I just asked what the evidence was for one of the claims made by the creationists.

Now it seems that in order to get that answer, I can either buy a book–which apparently is based on no peer-reviewed research of the authors, but just cherry-picked quotes from a ten-year old paper–or I can donate my time to write several thousands words for free for a creationist web site.

Making this offer even richer is Klinghoffer’s ground rules about focusing “strictly on the ideas, not on the personalities.” Klinghoffer himself has used Evolution News & Views to call people pathetic, a worthless bully, cowards, illiterate, and “a tyranny of the unemployed” (referring to Wikipedia editors). In one piece he wrote for Evolution New and Views, Klinhoffer mocked a post by a science blogger as “preening and self-congratulatory.”

That blogger happened to be me.

I will answer Mr. Klinghoffer publicly: no thanks. I never asked for a debate, and your arbitrary decrees, such as a mysterious thousand-word cutoff (my blog post on the chromosomes alone clocked in at over 2,000 words) make it even less appealing. I am particularly opposed to web sites that do not allow readers to comment. That’s how I ended up on Facebook in the first place–because the Discovery Institute’s web sites do not permit commenting. You, on the other hand, are more than welcome to leave a comment on my blog. My comment policy is very lax: I only throw out commenters who curse uncontrollably, hawk their own wares, or can’t stay on topic after repeated warnings. We have a thriving, fascinating discussion here, one from which I regularly learn new things from my readers. You might too.

David Klinghoffer, being David Klinghoffer, responded with a blog posting on Evolution News & Views: We Called Out Darwinist Critic Carl Zimmer, and He Folded.

"Reasoning with a Lynch Mob"

This reminded me of an incident that took place last November. You might remember that I spent a great deal of time and effort reviewing Jonathan Wells' book, The Myth of Junk DNA (see The Myth of Junk DNA by Jonathan Wells). I invited Wells to discuss and debate the issue of junk DNA and my extensive criticism of his book.

Wells declined [Jonathan Wells Sends His Regrets]. Here's what he said ...

Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.

Sort of makes you wonder, doesn't it? Do you think the IDiots really are interested in debating science or is it only on their own terms, on their own blog, with no comments, and moderated by their own kind?

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Delusions

I know I shouldn't pick on David Klinghoffer and the other IDiots at Evolution News & Views but, believe it or not, this is the best the IDiots have to offer.

I just can't resist posting this quotation from his latest post at: The Stubbornness of Their Ignorance.

Forget for a moment about who, Darwinists or Design advocates, is actually right. If you took a sample of ID folks and a sample of Darwin people, specifically those who have felt confident enough in their views to write about them for publication, and then quizzed each group about what arguments their opponents offer, there's no question that those from the ID community would know better what their opposites in the debate say.

Just look at ENV as a convenient illustration. We strive to keep up with toughest challenges, such as they are, from evolutionists. Now look at the competing Darwin blogs. Guys like PZ Myers & Co. concentrate their fire on naïve young-earth creationists. Jerry Coyne and his colleagues in the Darwin-defending business are careful to stay unaware of the very serious challenges to Darwinism from ID.

Wrong!

As it turns out, most of us know more about Intelligent Design Creationism than the average IDiot. As for evolution, I've yet to meet an IDiot who even comes close to understanding it, although Michael Behe and Michael Denton come pretty close.

Klinghoffer and his friends are deluding themselves if they think we don't know what they are saying and they are even more delusional if they think they understand evolution. We've proven time and time again that they don't.

Are we surprised? No, because the one thing all IDiots have in common is the God delusion—the biggest one of all.

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