Intelligent Design Creationists Choose ENCODE Results as the #1 Evolution Story of 2012

The folks over at Evolution News & Views (sic) have selected the ENCODE papers as the Number 1 evolution-related story of 2012. Naturally, they fell for the hype of the ENCODE/Nature publicity campaign as you can see from the blog title: Our Top 10 Evolution-Related Stories: #1, ENCODE Project Buries "Junk DNA".

Most of the article is just the reposting of an article by Casey Luskin but some anonymous editor has added ...

Editor's note: For the No. 1 slot among evolution-related news stories of 2012, this one was an easy pick. The publication of the ENCODE project results detonated what had been considered among the sturdiest defenses that Darwinian evolutionary theory could still fall back upon: "Junk DNA." Casey Luskin's initial reporting is featured below. See also our response to the ensuing controversy over ENCODE ("Why the Case for Junk DNA 2.0 Still Fails").

Normally I would make fun of the creationists for misunderstanding the real scientific results in the papers that were published last September but, in this case, there are lots of real scientists who fell into the same trap.

Even Science magazine selected the ENCODE results as a top-ten breakthrough and noted that 80% of the human genome now has a function [Science Magazine Chooses ENCODE Results as One of the Top Ten Breakthroughs in 2012]. Oh well, I guess I'll just have to be content to point out that many scientists are as stupid as many Intelligent Design Creationists!

I can still mock the creationists for claiming that "Darwinian evolutionary theory" supports junk DNA.

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Cornelius Hunter predicts that there's going to be function found for the vast majority of the genome according to the intelligent design paradigm

Listen to this Podcast where Casey Luskin interviews Dr. Cornelius Hunter.¹ It's only 9 minutes long.

Dr. Cornelius Hunter on ENCODE and "Junk" DNA, Part 2

Here's part of the transcript.

Casey Luskin: ... and, as we all know, or many ID the Future listeners probably know, for years Darwinian theorists and evolutionary scientists have said that our genomes ought to be full of junk if evolution is true

.....

Casey Luskin: So, Dr. Hunter, you think, just for the record, that in the long term there is going to be function found for probably the vast majority of the genome and so, maybe, you might call it a prediction you would make coming out of an intelligent design paradigm. Is that correct?

Cornelius Hunter: Yes, that's correct Casey, I'll definitely go on the record on that. Not to say I have a hundred percent confidence and also I wanna be clear that from a metaphysical perspective, from my personal belief, I don't have a problem wherever it lands. It doesn't matter to me whether it's 10% or 90% or any where in between or 100% ... just from the scientific perspective and just from the history of science and the history of what we've found in biology, it really does look like it's gonna be closer to 100 than zero.

Casey Luskin: Okay, great, I always like it when people put clear and concrete predictions out there and and I think that's very helpful.

I predict that about 90% of our genome will turn out to be junk DNA—DNA with no function. I base my prediction on the scientific perspective and the history of what we've found in biology. That's interesting because Cornelius Hunter and I are apparently reaching opposite conclusions based on the same data.

I also love it when people make predictions. Will the intelligent design paradigm be falsified if I turn out to be right?

Does it sound to you that Cornelius Hunter personally doesn't care if the prediction coming out of the intelligent design paradigm is correct or not?

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1. How come in the podcast they never refer to Dan Graur as Dr. Graur? Isn't that strange?

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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The top ten problems with evolution according to Intelligent Design Creationists

Most of Intelligent Design Creationism consists of whining about evolution. Their main goal seems to be to discredit scientists and evolution in order to lay the ground work for a new approach to science, one that demonstrates the existence of an intelligent designer.

Most of their criticisms of evolution are ridiculous but a few of them require a response. So far, after more than 25 years of whining, the creationists have utterly failed to make a convincing case against evolution.

Are they still trying? You bet. Casey Luskin has done us the favor of listing "The Top Ten Scientific Problems with Biological and Chemical Evolution" in a series of blog posts on Evolution News & Views (sic).

Here they are for your amusement.

1. No Viable Mechanism to Generate a Primordial Soup. I think he's right about this one. But then, I don't think a primordial soup plays a role in the origin of life.
2. Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code. This has nothing to do with the origin of the genetic code. It's an argument against "RNA world." Casey Luskin is correct. We don't know how the first information-containing molecules arose and how they came to be self-replicating.
3. Step-by-Step Random Mutations Cannot Generate the Genetic Information Needed for Irreducible Complexity. Luskin is dead wrong about this one.
4. Natural Selection Struggles to Fix Advantageous Traits in Populations. Casey Luskin doesn't understand modern evolutionary theory, and it shows.
5. Abrupt Appearance of Species in the Fossil Record Does Not Support Darwinian Evolution. Casey Luskin doesn't understand modern evolutionary theory, and he doesn't understand the scientific literature. What else is new?
6. Molecular Biology Has Failed to Yield a Grand "Tree of Life". Modern scientific discoveries have revealed that there may not be a universal tree of life common to all genes. Casey Luskin accepts the evidence but rejects the idea that scientific explanations can change when new data comes in.
7. Convergent Evolution Challenges Darwinism and Destroys the Logic Behind Common Ancestry. This is nonsense compounded by wishful thinking.
8. Differences Between Vertebrate Embryos Contradict the Predictions of Common Ancestry. Dead wrong.
9. Neo-Darwinism Struggles to Explain the Biogeographical Distribution of Many Specie. What?
10. Neo-Darwinism's Long History of Inaccurate Predictions about Junk Organs and Junk DNA. You'll have to read that post yourself to see how many different ways Casey Luskin can go wrong and the very few ways he can go right.

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Two Kooks in a Pod

Casey Luskin, the chief IDiot over at Discovery Institute has posted an addendum to his inept article on junk DNA [Follow-up on Junk-DNA]. Luskin has discovered the junkdna.com website of Andras Pellionisz. Those two deserve each other.

Why All the Fuss About Chromosomes?

I've been following the latest kerfluffle on the fusion of two chromosome into one during human evolution. I understand the superficial dispute involving Carl Zimmer. He had the audacity to ask for evidence to back up a claim being made by the IDiots on their Facebook page and they responded by going nuclear [The Mystery of the Missing Chromosomes, Continued: An Update From Your Preening Blogger].

Typical.

Let's step back a bit and ask why the IDiots are so upset. Carl Zimmer posted a really nice summary of the evidence that two smallish chimp chromosomes fused to produce human chromosome 2 [The Mystery of the Missing Chromosome]. That evidence is based on an analysis of the chimp, human, and gorilla genomes and it allows scientists to reconstruct the events that led up to the fusion. All of the DNA sequence around the fusion point are consistent with what we might expect, especially the presence of defective telomeres (sequences at the ends of chromosomes).

Why are the IDiots so bothered by this evidence? It's not as if it's new—the essential evidence has been around for decades. There must be something else going on that causes the IDiots to circle the wagons at this time.

It think it's all about their latest book Science & Human Origins by Ann Gauger, Douglas Axe, and Casey Luskin.¹ The book is published by the Discovery Institute Press. In that book, two of the authors (Gauger and Luskin), apparently argue that science cannot rule out a recent origin of humans descended from Adam and Eve. The chromosome fusion data threatens that bizarre claim and perhaps that's why they are reacting so strongly.

I think I understand this. The IDiots have made bold claims about some of their recent books (e.g. Signature in the Cell: DNA and the Evidence for Intelligent Design , The Myth of Junk DNA) but those books have been met by yawning indifference from the general public and devastating criticism from real scientists. Two of the authors on this latest book (Gauger and Axe) have substantial scientific credentials so the Discovery Institute must have expected that the book would stand up to criticism by other scientists.

Instead, a "mere" graduate student (Paul McBride) has dimantled the book chapter by chapter [Science & Human Origins: Review] and a "mere" science writer, Carl Zimmer, has challenged the integrity of two "scientists" (and a lawyer). No wonder they're upset. All of their wonderful books are scientific embarrassments.

On what grounds do the IDiots want to deny the chromosomal evidence that humans and chimps share a common ancestor? Carl Zimmer supplies a partial answer when he quotes one of the chief IDiot defenders, David Klinhoffer, who says ...

The evidence from chromosomal fusion, for one, is strikingly ambiguous. In the Darwinian presentation, the fact that humans possess 23 chromosome pairs and great apes 24 clearly points to an event in which human chromosome 2 formed from a fusion, leaving in its wake the telltale sign of telomeric DNA — normally appearing as a protective cap at the end of the chromosome — in the middle where it doesn’t belong. Ergo, common descent.

But Casey [Luskin, of the Discovery Institute and co-author of the book] explains, there’s a lot wrong with this inference. Even if there was such an event and humans once had 24 chromosome pairs, it doesn’t at all follow that this happened in some prehuman past. Nothing stands in the way of picturing a human population bottleneck accomplishing the spread of a fused chromosome 2 from part of an early human community to all of it.

But the idea of such an event having occurred at all is itself far from sure. The telomeric DNA parked in the middle of chromosome 2 is not a unique phenomenon. Other mammals have it too, across their own genomes. Even if it were unique, there’s much less of it than you would expect from the amalgamation of two telomeres. Finally, it appears in a “degenerate,” “highly diverged” form that should not be the case if the joining happened in the recent past, circa 6 million years ago, as the Darwinian interpretation holds.

That's it? The fusion event could have happened relatively recently in human evolution so it's no big deal? And if you don't buy that, then maybe it didn't happen at all because the junction sequence isn't exactly what a typical IDiot might expect if evolution were true?

(Carl asked for the evidence that that the junction sequence isn't what one might expect and that's what caused the latest problem.)

I think that even the most stupid IDiots realize that they are in a very weak position on this one. They have been painted into a corner where the only way out is to admit that chromosome fusions happens&mdashbut only in the past 10,000 years—or that solid scientific evidence is wrong and there was no fusion. Neither option is appealing.

That's why you see people like Cornelius Hunter desperately looking for another way out [Carl Zimmer Doubles Down on Chromosome Two Lies and Misdemeanors] and why the people at Uncommon Descent have picked up on a non-scientific way to defend Intelligent Design Creationism [Why no one can confute Darwinism and, consequently, no one should believe it].

My question for Intelligent Design Creationists is, "why all the fuss?" What is there about the figure at the top of the page that really upsets you? Aren't most of you supporters of common descent in some form or another? Are all of you really going to defend the idea that humans have no evolutionary history with the other apes?

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1. I haven't read the book. It's on order but it still hasn't been released in Canada (see Amazon.ca).

Casey Luskin "Explains" Intelligent Design Creationism

Casey Luskin is upset with a philosopher named Christopher Pynes. Paynes had the audacity to suggest that one of the key features of Intelligent Design Creationism is ... creationism. According to Paynes, "supernaturalism is a necessary component of ID: there must be a designer" [AD HOMINEM ARGUMENTS AND INTELLIGENT DESIGN: REPLY TO KOPERSKI].

Luskin wants to remind everyone that Intelligent Design Creationism has nothing to do with a creator/designer [Professor Pynes Rails Against the "Straw-Man Fallacy" while Attacking a Straw-Man Version of Intelligent Design]. According to Luskin (a lawyer), Intelligent Design Creationism is a purely scientific theory that relies on: (a) proving that evolution is wrong, (b) detecting the creator/designer by examining nature.

On the primary¹ grounds that it's always good to know your enemy, I present to you the best scientific grounds for Intelligent Design Creationism.

• Studies of physics and cosmology continue to uncover deeper and deeper levels of fine-tuning. Many examples could be given, but this one is striking: the initial entropy of the universe must have been fine-tuned to within 1 part in 10(10^123) to render the universe life-friendly. That blows other fine-tuning constants away. New cosmological theories like string theory or multiverse theories just push back questions about fine-tuning, and would, if true, simply exacerbate the need for fine-tuning. This points to high levels of complex and specified information (CSI) in the cosmid architecture of the universe--information which in our experieince only comes from intelligence.
• Mutational sensitivity tests increasingly show that DNA sequences are highly fine-tuned to generate functional proteins and perform other biological functions. Again, this is high CSI--which in our experience only comes from intelligence.
• Studies of epigenetics and systems biology are revealing more and more how integrated organisms are, from biochemistry to macrobiology, and showing incredible fine-tuned basic cellular functions. The integrated nature of organismal body plans shows CSI throughout biological systems--in our experience, only intelligence can generate tightly intregrated multi-component blueprints.
• Genetic knockout experiments are showing irreducible complexity, such as in the flagellum, or multi-mutation features where many simultaneous mutations would be necessary to gain an advantage. This is more fine-tuning--and in our experience, irreducibly complex machines arise only from intelligence.
• The fossil record shows that species often appear abruptly without similar precursors, which represents mass-explosions of high CSI--something which requires an intelligent cause.
• There have been numerous discoveries of functionality for "junk DNA." Examples include recently discovered functionality in some pseudogenes, microRNAs, introns, LINE and ALU elements. Intelligent design predicted this data.

If all of these things were true, then you'd predict that scientists would be flocking to church on Sundays. You'd also expect that the scientific literature would be full of papers proving the existence of God. It would be the most remarkable discovery in the history of humans.

A key part of Intelligent Design Creationism—the part that Casey Luskin is leaving out—is to explain why it has been so remarkably unsuccessful after 200 years of trying. That part has to do with the huge Darwinist conspiracy that forces scientists to tow the line and stick with atheistic Darwinism in spite of all the scientific evidence against it. If you read the blogs, you'll see that attacking scientists and Darwinism is the dominant theme. The "scientific" "evidence" for Intelligent Design Creationism is almost never mentioned.

Most of us scientists don't realize that we are part of such a conspiracy because we have been brainwashed into believing in evolution. However, a few god-fearing souls have seen the truth. Some of them are lawyers (Casey Luskin, Philip Johnson), some of them are philosophers, some of them claim to be mathematicians, and a few think they are scientists (Michael Behe, Jonathan Wells). The one thing they all have in common is that they are all IDiots.

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1. The secondary grounds are to keep a record of the June 2012 "facts" because they will change soon enough.

Facts Supporting Intelligent Design Creationism?

 
We all know that the Intelligent Design Creationist movement consists almost exclusively of attacks on science. The idea seems to be that if you can cast doubt on evolution then this is evidence in favor of God.

Some unnamed Professor has challenged students to come up with facts that support Intelligent Design Creationism. The only criterion is; "fact can be any observation in biology that is substantiated by publication in a scientific journal,"

Casey Luskin attempts to meet the challenge over on the Discovery Institute propaganda site, Evolution News & Views: Helping Students Answer a Professor's Challenge to "Find a Fact" That Supports Intelligent Design (Part 2).

Here's a list of "scientific" publications submitted by Luskin. I haven't read all of them but, of the ones I've read, there isn't a single one containing a fact that supports the existence of God, let alone evidence that he/she designed anything at all. Furthermore, many of them aren't from a scientific journal. It looks like Casey Luskin has goofed, once again.

Let me know if any of these publications contain evidence of Intelligent Design Creationism. Is this the best they can do? (I've put asterisks in front of the ones I've read.)

*Douglas D. Axe, "Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors," Journal of Molecular Biology, Vol. 301:585-595 (2000)

*Douglas D. Axe, "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds," Journal of Molecular Biology, 1-21 (2004)

*Michael Behe, Darwin's Black Box: The Biochemical Challenge to Evolution (Free Press, 1996)

*Michael J. Behe & David W. Snoke, "Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues," Protein Science, Vol 13:2651-2664 (2004)

Geoff Brumfiel, “Outrageous Fortune,” Nature, Vol. 439: 10-12 (Jan. 5, 2006)

Bract, "Inventions, Algorithms, and Biological Design," in Progress in Complexity, Information, and Design (Vol. 1.1, 2002)

*William A. Dembski, The Design Inference: Eliminating Chance Through Small Probabilities (Cambridge University Press, 1998)

a. William A. Dembski and Robert J. Marks II, “Conservation of Information in Search: Measuring the Cost of Success” (In publication, 2009)

b. William A. Dembski and Robert J. Marks II, “The Search for a Search: Measuring the Information Cost of Higher Level Search” (In publication, 2009)

*William Dembski and Jonathan Wells, The Design of Life: Discovering Signs of Intelligence in Living Systems, (FTE, 2008) (see www.thedesignoflife.net)

*Wayt T. Gibbs, “The Unseen Genome: Gems among the Junk,” Scientific American (November, 2003)

Guillermo Gonzalez and Jay Wesley Richards, The Privileged Planet: How our Place in the Cosmos is Designed for Discovery, (Regnery, 2004)

*Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009)

Hiroaki Kitano, ”Systems Biology: A Brief Overview,” Science, Vol. 295: 1662-1664 (March 1, 2002)

Wolf-Ekkehard Lönnig, "Dynamic genomes, morphological stasis, and the origin of irreducible complexity," in Dynamical Genetics pp. 101-119 (Valerio Parisi, Valeria De Fonzo, and Filippo Aluffi-Pentini eds., 2004)

Casey Luskin, “Human Origins and Intelligent Design,” Progress in Complexity and Design, (Vol 4.1, November, 2005)

Casey Luskin, "Intelligent Design Has Scientific Merit in Paleontology," part of the "Does Intelligent Design Have Merit?" debate at OpposingViews.com (September, 2008)

*Wojciech Makalowski, “Not Junk After All,” Science, Vol. 300(5623) (May 23, 2003)

Stephen C. Meyer, Marcus Ross, Paul Nelson & Paul Chien, "The Cambrian Explosion: Biology's Big Bang," in Darwinism, Design, and Public Education (John A. Campbell and Stephen C. Meyer eds., Michigan State University Press, 2003)

*a. Stephen C. Meyer, “The Cambrian Information Explosion,” in Debating Design (edited by Michael Ruse and William Dembski; Cambridge University Press 2004)

b. Stephen C. Meyer, “The origin of biological information and the higher taxonomic categories,” Proceedings of the Biological Society of Washington, Vol. 117(2):213-239 (2004)

Scott A. Minnich & Stephen C. Meyer, “Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic bacteria,” in Proceedings of the Second International Conference on Design & Nature, Rhodes Greece (M.W. Collins & C.A. Brebbia eds., 2004)

Paul Nelson and Jonathan Wells, “Homology in Biology,” in Darwinism, Design, and Public Education, (Michigan State University Press, 2003)

*Richard v. Sternberg, "On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic– Epigenetic System," Annals of the New York Academy of Sciences, Vol. 981: 154–188 (2002)

J.T. Trevors and D.L. Abel, "Chance and necessity do not explain the origin of life," Cell Biology International, Vol. 28: 729-739 (2004)

D. L. Abel & J. T. Trevors, “Self-organization vs. self-ordering events in life-origin models," Physics of Life Reviews, Vol. 3: 211–228 (2006)

Øyvind Albert Voie, "Biological function and the genetic code are interdependent," Chaos, Solitons and Fractals, Vol. 28:1000–1004 (2006)

Jonathan Wells, "Using Intelligent Design Theory to Guide Scientific Research" Progress in Complexity, Information, and Design (Vol. 3.1.2, November 2004)

Jonathan Wells, "Do Centrioles Generate a Polar Ejection Force?," Rivista di Biologia / Biology Forum, Vol. 98:71-96 (2005)

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Detecting God's Signature

Stephen Meyer has two main objectives. He wants to prove that Intelligent Design Creationism is the best explanation for the origin of information in the cell and he wants to prove that Intelligent Design Creationism is genuine science.

Let's look at the form of argument he uses in Signature in the Cell: DNA and the Evidence for Intelligent Design. This is from Chapter 17 where he's trying to refute the accusation that Intelligent Design Creationism is nothing more than an argument from ignorance.

... the argument made in this book ... takes the following form:

Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.
Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information.
Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for information in the cell.

Or, to put it more formally, the case for intelligent design made here has the form:

Premise One: Causes A through X do not produce evidence E.
Premise Two: Cause Y can produce E.
Conclusion: Y explains E better that A through X.

In addition to a premise about how material causes lack demonstrated causal adequacy, the argument for intelligent design as the best explanation also affirms the demonstrated causal adequacy of an alternative cause, namely, intelligence. This argument does not omit a premise providing positive evidence or reasons for preferring an alternative cause or proposition. Instead, it specifically includes such a premise. Therefore, it does not commit the informal fallacy or arguing from ignorance. It's really as simple as that.

Scientist are often accused of picking on the most idiotic of the IDiots and avoiding the really big guns who have all the best arguments for Intelligent Design Creationism.¹ See A Reason to Doubt the Real, Rather than Pretended, Confidence of Darwin Advocates, where David Klinghoffer asks,

How about answering the arguments of a real scientist who advocates intelligent design on scientific rather than Bible-thumping grounds -- a Douglas Axe or Ann Gauger, for example? How about a thoughtful critique of The Myth of Junk DNA or Signature in the Cell? A response to serious science bloggers like ENV's Casey Luskin or Jonathan M.?

So, here's my response to the very best that the IDiots can offer.

Premise One

Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.

On the surface this looks like a purely scientific statement. I'm sure that most creationists accept it at face value since the leaders of the movement have been saying for years that evolution can't account for specified complexity or irreducible complexity.

Stephen Meyer is a philosopher but he's confident that his knowledge of biology is sufficient to establish the truth of this claim. He says on page 341 ...

Undirected materialistic causes have not demonstrated the capacity to generate significant amounts of specified information.

This is an important point since the logic of his argument depends on establishing that specified complexity can never arise from natural (materialistic) causes. You might think that a large part of this book would be devoted to backing up his premise. You would be wrong. Turns out, the real premise isn't exactly how it appears above.

Dennis Venema has written a critical review of Signature in the Cell and one of his criticisms is that there are many excellent examples of new information evolving by entirely materialistic mechansims that not violate the laws of physics and chemistry [Seeking a Signature]. We're all familiar with the examples of gene duplication and divergence but he might just as well have used dozens of other examples where specified complexity evolved. The wings of birds are for flying but they evolved from legs and fins. The irreducibly complex citric acid cycle evolved from simpler pathways.

These examples establish beyond a shadow of a doubt that there are perfectly reasonable, materialistic explanations for the evolution of specified complexity. That seems to negate Premise One.

Hang on. Meyer responds to the Venema criticism by pointing out that he was not referring to the origin just any specified information. He was only referring to the kind of specified information that appeared when life first formed. It's an origin of life problem.

The balance of [Venema's] review is spent refuting an argument that Signature in the Cell does not make and, thus, the evidence he cites is irrelevant to the main argument of the book; in short, Venema "refutes" a straw man. ... I happen to think -- but do not argue in Signature in the Cell -- that there are significant grounds for doubting that mutation and selection can add enough new information to account for various macroevolutionary innovations. Nevertheless, the book that Venema was reviewing, Signature in the Cell, does not address the issue of biological evolution, nor does it challenge whether mutation and selection can add new information to DNA. That is simply not what the book is about. Instead, it argues that no undirected chemical process has demonstrated the capacity to produce the information necessary to generate life in the first place. The book addresses the subject of chemical evolution and the origin of life, not biological evolution and its subsequent diversification. To imply otherwise, as Venema does, is simply to critique a straw man. [Stephen Meyer Resonds]

Meyer is correct. The book is about the origin of life and the problem of getting information into DNA 3.5 billion years ago, before there were cells, and before evolution. Meyer isn't always clear about this distinction but the argument that he frames above is about the origin of life.

Here's how he should have expressed Premise One ...

After decades of research, biologists have good explanations of how specified information can arise by evolution but they do not have a good explanation of how life began 3.5 billion years ago.

Premise Two

Intelligent causes have demonstrated the power to produce large amounts of specified information.

He's referring, of course, to the fact that bees make beehives and beavers make dams. There are hundreds of examples where animals produce complex structures full of specified information. That's what he means by "intelligent causes." All of this creation obeys the laws of physics and chemistry, therefore the explanation is entirely materialistic.

Don't forget that the argument is not about the creation of specified information throughout the history of life. It's about the ultimate origin of the information. Animals can create complex structures just as living cells can create new genes. What Meyer really wants to know is where do animals get this ability? Where did the information to create more information come from?

Animals evolved from more primitive ancestors. It's quite reasonable to postulate that all animals evolved from a common ancestor that had very rudimentary intelligence and that intelligence evolved from primitive neurons. Thus, the ability of intelligent animals to create complex structures—like pocket watches—ultimately traces back to the origin of life.

We can re-word Premise Two ...

Intelligent animals can produce large amounts of specified information by purely materialistic means. The ability to do this depends on the evolution of animals from the first living cells that arose 3.5 billion years ago.

Conclusion

Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.

This conclusion does not follow from either of the corrected premises.

Here's a better conclusion.

All of the information we see in biology, including the ability of beavers to make dams, can be traced back to the information present in the first cells. We don't currently have a good explanation for how DNA and cells arose.

It's difficult to see how you can squeeze a supernatural intelligent designer into this conclusion. Whenever we have good explanations for the origin of specified complexity, those explanations involve materialistic actions and not actions that require violation of the known laws of physics and chemistry. Beavers do not wave a wand to poof their dams into existance and bees don't get their beehives by praying for them

Therefore, it seems quite reasonable to assume that all examples of biological information arise by natural means, including the very earliest examples of DNA in the first cell.

(I don't address information theory, which takes up a significant part of the book for some unknown reason. See Jeffrey Shallit's take-down on Stephen Meyer in: More on Signature in the Cell.)

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1. Atheists have the same problem. We're always going after the most stupid theists and avoiding the really sophisticated arguments for the existence of God. You'll find a list of those arguments at: A Challenge to Theists and their Accommodationist Supporters.

March on Sandwalk

 
Bora's doing it and Greg Laden is doing it. They're revisiting their posts from last month.

Now I'm doing it too.

Last month Sandwalk attracted 107,747 page views and 75,156 visits from all over the world. That's a new record. I posted 123 times.



The month began with an account of my streetcar ride and the atheist sign campaign in Toronto [The Streetcar We Desire]. I also celebrated the 35th anniversary of my thesis defense.

There were three debates that took up a lot of posting time.

One of them was about positive selection in humans, especially the idea that human evolution might have accelerated in the past 10,000 years. I tried to explain why some of the data looks suspicious in Signals of Positive Selection in Humans?.

We also talked a lot about the quality of science journalism. The two topics were combined when I reviewed SEED magazine's coverage of a recent book on accelerated human evolution [SEED Reviews The 10,000 Year Explosion].

The third debate was about Canada's science minister, Gary Goodyear, and the fact that he is a creationist [Gary Goodyear "Clarifies" His Stance on Evolution].

I'm pretty proud of this posting: Casey Luskin on Junk DNA and Junk RNA. It generated some comments and got a mention on several blogs.

Speaking of comments, one other posting caught the attention of Sandwalk readers and stimulated comments. You were interested to know why I Hate Cilantro/Coriander!.

In terms of most popular postings there was nothing in March that's going to make the top 20 postings. I still get a lot of traffic from people who want to learn about The Genetics of Eye Color from a posting in February 2007. Another popular posting is The Genetics of ABO Blood Types, also from February 2007.

As usual, there were lots of people who tried to guess Monday's molecule. There are a small number of regulars who get most of the prizes, The rest of you are going to have to be faster. I think I'll try and post much earlier in the day to give my European readers a better chance. We don't need to worry about giving the Australians a chance 'cause they probably wouldn't win anyway! :-)

We had an interesting group of Nobel Laureates. These postings always get looked at but nobody leaves comments. I guess there isn't much to say. The most interesting Nobel Laureates from my perspective were Frederick Banting and J.J.R. Macleod because they're from the University of Toronto. Several of the recent prize winners were controvesial, especially Selman Waksman.

Does anyone have suggestions for future postings?

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Predictions of Intelligent Design Creationism

I love it when they make predictions. Here's what Casey Luskin just posted over on Evoluton News & Views (sic) [A Response to Questions from a Biology Teacher: How Do We Test Intelligent Design?]

Regarding testability, ID makes the following testable predictions:

(1) Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).

Such natural structures exist. They are perfectly compatible with evolution. This prediction does not distinguish between Intelligent Design Creationism and real science.

(2) Forms containing large amounts of novel information will appear in the fossil record suddenly and without similar precursors.

The vast majority of of species with novel information have arisen gradually with plenty of transitional fossils to document their evolution. In a small number of cases (e.g. Cambrian Explosion) the evidence for evolution from known precursors is too sophisticated for creationists to follow. This prediction is not supported; therefore, Intelligent Design Creationism is falsified for all species where we have lots of data.

(3) Convergence will occur routinely. That is, genes and other functional parts will be re-used in different and unrelated organisms.

Convergence is perfectly consistent with evolution. This prediction is meaningless.

(4) Much so-called “junk DNA” will turn out to perform valuable functions.

Most of our genome is junk. The evidence for this is overwhelming. Intelligent Design Creationism has been falsified.

That was easy.

In this regard, ID is falsifiable. When we test these predictions, ID passes those tests.

No it doesn't. Two of the "tests" are consistent with evolution so the "test" is meaningless. Intelligent Design Creationism fails the other two tests.

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Fishing for Creationists

Fishing for creationists is not a sport. All you need to do is dangle a bit of bait and dozens of creationists will fight for the right to impale themselves on the hook. The latest victim is Jonathan McLatchie who responded to criticism of Phillip Johnson [Maligning Phil Johnson, with Lots of Rhetoric but Little Substance]. I'm sure the other bloggers on Evolution News & Views don't see him as a fishy victim, they probably think of him as the designated hitter. (You could use "sacrificial lamb" if you want a Biblical metaphor.)

Jonathan M, as he prefers to be known, is studying in Scotland for a Master's degree in evolutionary biology. He's upset with Jeffrey Shallit for criticizing Phillip Johnson's 1993 video (see This Video Should Be Shown to all Biology Students). He's also upset with my critiques of the same video (see Phillip Johnson, One of the Very Best Intelligent Design Creationists).

James Shapiro Responds to My Review of His Book

I reviewed Shapiro's book, Evolution: A View from the 21st Century for NCSE reports. (NCSE = National Center for Science Education.) You can read it here.

James Shapiro has responded to my review in the latest issue of NCSE reports: Reply to Laurence A Moran’s review of Evolution: A View
from the 21st Century.

Shapiro seems to be really upset that NCSE would choose someone like me to review his book. He opens his rebuttal with ...

Before I saw Laurence A Moran’s book review (Moran 2012), I wrote the following: “It is a shame that NCSE chose Larry Moran to review my book; not because of anything he said in the review but because he is hostile to new ideas and perspectives.”

A year ago, Moran posted a piece entitled “Physicists and biologists” on his Sandwalk blog [Physicists and Biologists¹]. In this post, he ridiculed the enthusiasm I expressed in the book for physicists coming into evolutionary studies and bringing new skills and new ideas.

Meanwhile, I welcome all those physicists who know nothing about evolution, protein structure, genetics, physiology, metabolism and ecology. That’s just what we need in the biological sciences to go along with all the contributions made by equally ignorant creationists.

What a great way to make new friends for evolution science—equating physicists with creationists and calling them “equally ignorant”!

Are IDiots Creationists?

 
I have complained about misuse of the term "Darwinism" by the Intelligent Design Creationists. They seem to be unable to grasp the fact that not all evolutionary biologists are Darwinists.

Having complained about that, it's only fair to consider their complaint that not all Intelligent Design advocates are Creationists. Casey Luskin raises the issue today on the Discovery Institute website [Another Way to Defeat the ID = Creationism MemeM].

Darwinian logic often contends that because a given proportion of ID proponents are creationists, ID must therefore be creationism. It's a twist on the genetic fallacy, one I like to call the Darwinist "Genesis Genetic Argument." As noted, it implies that each any and every argument made by a creationist must be equivalent to arguing for full-blooded creationism. This fallacious argument is easy to defeat on logical grounds by pointing out that some ID proponents are not creationists, and in fact have been persuaded to support ID in the absence of religion. Thus something other than creationism or religion must be fundamental to the set of views underlying ID (big hint: it's the scientific data indicating real design in nature)!

First off, it's ridiculous to pretend that some IDiots view the intelligent designer as anyone other than God. While I've no doubt that they might dig someone like this out of the woodwork, the fact remains that 99.999% of all intelligent design advocates see God as the designer. The term "creationist" refers to someone who postulates a role for a Creator (i.e., God) in creating life. Any IDiot who says they were persuaded to support intelligent design in the absence of belief in a Creator is, well, an idiot. But I repeat myself.

Second, there is no scientific data to indicate real design in nature. In fact, there's plenty of evidence to suggest a lack of "design" in much of nature (e.g., junk DNA). (Admittedly, many evolutionists are reluctant to accept this evidence.) The entire Intelligent Design Creationist movement is dedicated to disproving evolution. That's the extent of their "data." You don't become an Intelligent Design Creationist just because you've been brainwashed into rejecting evolution. You become an Intelligent Design Creationist because you've been brainwashed to believe in a Creator God and that, in turn, leads to the rejection of the other alternative, evolution.

There are many different kinds of creationist. They include Young Earth Creationists, Old Earth Creationists, and Theistic Evolutionists. The Theistic Evolutionists restrict the role of the Creator to setting up natural laws and then operating mostly within these natural laws to guide evolution. The Intelligent Design Creationists are a special group of creationists who argue against evolution and who claim (falsely) to have discovered evidence for supernatural creation (i.e., intelligent design). It is quite legitimate to refer to them as Intelligent Design Creationists because it distinguishes their form of creationism from the other forms of creationism.

Robert Pennock discusses this in his anthology Intelligent Design Creationism and Its Critics.

Dembski chides me for never using the term "intelligent design" without conjoining it to "creationism." He implies (though never explicitly asserts) that he and others in his movement are not creationists and that it is incorrect to discuss them in such terms, suggesting that doing so is merely a rhetorical ploy to "rally the troops." Am I (and the many others who see Dembski's movement in the same way) misrepresenting their position? The basic notion of creationism is the rejection of biological evolution in favor of special creation, where the latter is understood to be supernatural. Beyond this there is considerable variability. Some creationists think the world is young while a fewer number accept that it is ancient.

Pennock then goes on to show that Dembski is a creationist and so are most (all?) of his followers.

In spite of Luskin's whining (and Dembski's) it is quite appropriate to refer to Intelligent Design Creationism since the advocates of this superstitious nonsense are creationists by definition.

Another IDiot Book: Science and Human Origins

The IDiots at Disco (Discovery Institute) have published another book. This time the authors are Ann Gauger, Douglas Axe, and Casey Luskin. Gauger and Axe are scientists so this book is supposed to be about science. Unfortunately, Casey Luskin is a lawyer which pretty much negates the authority of Gauger and Axe.

The book has been thoroughly reviewed by Paul McBride on Still Monkeys. McBride is a graduate student studying evolution in New Zealand. Read the reviews at ...

Science and Human Origins - Chapter 1 review
Science and Human Origins - Chapter 2 review
Science and Human Origins - Chapter 3 review
Science and Human Origins - Chapter 4 review
Science and Human Origins - Chapter 4 review: Part 2
Science and Human Origins - Chapter 5 review

Wanna know the bottom line?

1. Common descent is still alive and well.
2. Natural selection still works.
3. The human fossil record still demonstrates evolution.
4. Junk DNA still exists.
5. There's no evidence for Adam and Eve.

Here's how Paul McBride sums up his review.

Science and Human Origins has to be described first and foremost as being anti-evolution rather than pro-intelligent-design, or pro-science. If it offers solace to those seeking evidence against evolution for their faith, the solace should be as incomplete as the arguments made in the book.

This is a common criticism. Most IDiot literature is nothing more than a misguided attack on evolution. It's increasingly rare to see any defense of intelligent design. Perhaps that's because it's indefensible?

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Intelligent design explanations and speculations have all been refuted, discredited, or shown to be unnecessary

Intelligent Design Creationism is a movement based on bad science. Every single one of their positive, science-like, claims about ID have been refuted, or discredited, or shown to be completely unnecessary in the face of robust evolutionary explanations. Some of them have the distinction of being unnecessary AND refuted AND discredited (e.g irreducible complexity).

In addition to a small number of claims in support of ID, the proponents of Intelligent Design Creationism also advance dozens and dozens of arguments against evolution. In fact, this is by far the main activity of most adherents to the movement. Some of their arguments focus on legitimate scientific controversies. They are legitimate criticisms of some aspects of evolution but, even then, ID proponents often misrepresent and/or misunderstand the science behind the controversy (e.g. junk DNA).

However, the vast majority of their attacks on evolution are just as bad as their attempts to build a positive case for intelligent design. A disturbingly large number of such attacks exhibit a profound ignorance of science and how it works. In particular—surprisingly—they are ignorant of evolution. The movement is full of kooks. It will never become a credible source of information unless it purges itself by getting rid of the kooks.

Speaking of kooks,¹ Casey Luskin has been publishing a series of articles on the Kitzmiller v. Dover trial that was decided ten years ago. Some of the articles make valid points but the latest one is a joke: Ten Myths About Dover: #4, "The Dover Ruling Refuted Intelligent Design".

You should read the article. It's a remarkable example of apologetics and why lawyers shouldn't try and explain science. While it's true that Judge Jones said lots of things we could quibble about, the big-picture take-home lesson from the trial is correct. No ID explanation stood up to the scrutiny of science. They were all shown to be either irrelevant or wrong.

That's why none of them should be presented in science class except as examples of bad science and faulty scientific reasoning.²

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1. Luskin won't even admit that Young Earth Creationism is absurd.

2. In my opinion, they SHOULD be discussed in class since it's important to teach critical thinking and that requires that you directly confront common misconceptions.

What would happen if Intelligent Design Creationists understood evolution?

There's an interesting phenomenon taking place over on one of the main Intelligent Design Creationist websites. It started when a philosphopher, Vincent Torley, tried to understand how the sequences differences between chimpanzees and humans could be explained by evolution. In the beginning, he was skeptical of the explanation I offered and he was supported by a biochemist creationist named Branko Kozulic. Kozilic assured him that his skpeticism was justified and the population geneticists were wrong.

Then an amazing thing happened. Salvador Cordova, another well-known creationist, posted a comment on one of Torley's blog posts. You can see it as comment #39 on Branko Kozulic responds to Professor Moran. Cordova was responding to comments posted by Nick Matzke and "WD400" on that same post. Here's what Sal Cordova said,

Is Creationism Anti-Science?

 

It's very hard to define science—it's the demarcation problem and, in spite of what you've been told, philosophers don't agree on how to define science.

A lot of the activities of Intelligent Design Creationists qualify as science, as far as I'm concerned. That's why I spend so much time arguing against their attacks on evolution. Many of the IDiots accept common descent. Their attacks on other aspects of evolution aren't much different than similar attacks from legitimate, non-theistic scientists (e.g. objecting to junk DNA, questioning the Cambrian explosion, challenging strict Darwinism). It counts as "science" but it's very bad science and it's wrong.

All IDiots are anti-evolution but some go farther than others. If you are a Young Earth Creationist who believes that the universe was created less than 10,000 years ago, then you are not just anti-evolution, you are anti-physics, anti-chemistry, anti-geology, anti-astronomy, and anti-biology. I think it's fair to say that Young Earth Creationists are anti-science. This includes most (all?) of the Republican Presidential candidates in the United States and more than half the citizens of that country.

The only way YECs can possibly justify their strange beliefs is to assume that all the experts in all those fields are completely wrong about the fundamental concepts in their discipline. How could they possibly trust anything else those scientists have to say about their areas of expertise?

Let me introduce you to a "new voice" in the Intelligent Design Creationist world. Here's what Evolution News & Views says about him [A New Voice in the Debate Over Evolution and Intelligent Design].

There is literally a new voice in the debate over evolution and intelligent design. If you're a regular listener to the Center for Science & Culture's very popular and thrice weekly podcast, ID The Future, you have probably come to recognize familiar personalities, like ENV's Casey Luskin. (If you're not yet a listener, then you should be.) Now you will be hearing more often from radio broadcaster David Boze of Seattle's KTTH.

I assume David Boze is a heavy-weight and it's okay to criticize him.

Listen to the Discovery Institute podcast where Boze defends Young Earth Creationism against the charge that it's anti-science ["Anti-Science": Unpacking a Vague & Distorted Label]. (You can click on the embedded copy below.) Note the sleight of hand where he lumps together the Young Earth Creationists with all other IDiots. His point is that just because you're opposed to "atheistic Darwinian evolution" does not mean you're anti-science.

Perhaps not. But if you believe in the literal truth of the Bible then you are definitely anti-science. You are a genuine idiot. Does David Boze do a good job of defending Republican Presidential candidates against the charge of being anti-science? Will a YEC President harm the reputation of the United States? You be the judge.

Personally, I don't think the new kid on the block is much of a threat. Is this the best they can do?

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

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

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

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

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

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

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

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

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

The Top Ten Problems with Darwinism

It was only a few months ago that lawyer Casey Luskin presented us with The Top Three Flaws in Evolutionary Theory. Now he's back with the top ten problems with Darwinian evolution. Here they are, read 'em and weep.

1. Lack of a viable mechanism for producing high levels of complex and specified information.
2. The failure of the fossil record to provide support for Darwinian evolution.
3. The failure of molecular biology to provide evidence for a grand "tree of life."
4. Natural selection is an extremely inefficient method of spreading traits in populations unless a trait has an extremely high selection coefficient.
5. The problem that convergent evolution appears rampant -- at both the genetic and morphological levels, even though under Darwinian theory this is highly unlikely.
6. The failure of chemistry to explain the origin of the genetic code.
7. The failure of developmental biology to explain why vertebrate embryos diverge from the beginning of development.
8. The failure of neo-Darwinian evolution to explain the biogeographical distribution of many species.
9. A long history of inaccurate predictions inspired by neo-Darwinism regarding vestigial organs or so-called "junk" DNA.
10. Humans show many behavioral and cognitive traits and abilities that offer no apparent survival advantage (e.g. music, art, religion, ability to ponder the nature of the universe).

I started to work on the top 1000 problems with Intelligent Design Creationism but then I realized that it was a waste of time. There are only two essential problems with Intelligent Design Creationism: (1) There's no evidence for supernatural design in nature, and (2) There's no evidence for a supernatural designer.

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