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Category Archives: Rationalism v Superstition
Posted by in junk DNA, Rationalism v Superstition
Why do Intelligent Design Creationists lie about junk DNA?
A recent post on Evolution News (sic) promotes a a new podcast: Casey Luskin on Junk DNA’s “Kuhnian Paradigm Shift”. You can listen to the podcast here but most Sandwalk readers won't bother because they've heard it all before. [see Paradigm shifting.]
Luskin repeats the now familiar refrain of claiming that scientists used to think that all non-coding DNA was junk. Then he goes on to list recent discoveries showing that some of this non-coding DNA is functional. The truth is that no knowledgeable scientist ever claimed that all non-coding DNA was junk. The original idea of junk DNA was based on evidence that only 10% of the genome is functional and these scientists knew that coding regions occupied only a few percent. Thus, right from the beginning, the experts on genome evolution knew about all sorts of functional non-coding DNA such as regulatory sequences, non-coding genes, and other things.
Read more »Stephen Meyer lies about scientists working on evolutionary theory
I know Stephen Meyer and I have discussed his views on creationism many times. Some of the issues he raises are quite interesting and they aren't easy to refute. In this video from 2020, he presents two standard creationist objections to evolution: the Cambrian explosion, and the probability of evolving a gene.1
Read more »Discovery Institute’s latest video: The Codes of Life
This is a very slick video from the Discovery Institute. It shows you what we are up against. Anyone who thinks they can easily refute the claims in this video hasn't tried.
Intelligent Design Creationists know exactly what they are doing and they are very good at it. There are so many thing wrong with this video that it would take a book to correct them all and, furthermore, you would have to convince people that their entire worldview has to change in order to really understand biology. I bet there are many scientists who couldn't deal with a video like this and that's a problem.
Real biology is messy and sloppy. Things do not look as neatly designed as Richard Dawkins and the creationists would have you believe. I've tried to present the case for a sloppy worldview in my latest book.
How Intelligent Design Creationists try to deal with the similarity between human and chimp genomes
The initial measurement of the difference between the human and chimp genomes was based on aligning 2.4 billion base pairs in the two genomes. This gave a difference of 1.23% by counting base pair substitutions and small deletions and insertions (indels). However, if you look at larger indels, including genes, you can come up with bigger values because you can count the total number of base pairs in each indel; for example, a deletion of 1,000 bp will be equivalent to 1,000 SNPs.
Read more »Posted by in Genome, Rationalism v Superstition
On reasoning with creationists
I've been trying to reason with creationists for more than 30 years, beginning with debates on talk.origins back in the early 1990s. Sometimes we make a little progress but most of the time it's very frustrating.
Over the years, we've encountered a few outstanding examples of creationists whose "reasoning" abilities defy explanation. One of he most famous is Otangelo Grasso - his ability to misunderstand and misconstrue science is legendary. He is one of only a small number of people who are banned from Sandwalk.
Here's an example of his unique unreasoning abiltiies.
Trying to educate a creationist (Otangelo Grasso)
I bring this up because he recently posted an artilce on the Uncommon Descent blog and you just have to read it if you want a good laugh. It shows you that 30 years of attempting to teach science to creationists isn't nearly long enough.
Otangelo Grasso on the difficulties of reasoning with atheists
Science reviews a creationist book
You can't get much more anti-science than a book about Adam and Eve. Nevertheless, Stephen Schaffner—a computational biologist at the Broad Institute of MIT in Boston—decided that such a book was worthy of a mostly favorable review in one of the most prestigious science journals in the world [Adam. Eve, and the evolution of humankind].
Schaffner is reviewing a book by William Lane Craig whom he describes as "a widely published philosopher, theologian, and Christian apologist." There are others who would dispute that laudatory description including Richard Dawkins in a ten-year-old essay published in The Guardian [Why I refuse to debate with William Lane Craig].
I won't bother to mention all of the issues with the review since Jerry Coyne has covered them on his website but I would like to quote part of the second-last paragraph of the review.
Craig’s goal in writing this book, of course, is not a scientific one, and it cannot be judged on scientific grounds. I suspect that for many scientists, including religious ones, the exercise will be seen as misguided or simply incomprehensible.
Having followed Craig's anti-science crusade for several years, I have no difficulty in understanding why he would write such a book. What I find truly misguided and incomprehensible is why Science would publish such a review. Perhaps it's because AAAS, the publisher of Science, has a history of accommodating religion?
Posted by in alternative splicing, Rationalism v Superstition
Religion vs science (junk DNA): a blast from the past
I was checking out the science books in our local bookstore the other day and I came across Evolution 2.0 by Perry Marshall. It was published in 2015 but I don't recall seeing it before.
The author is an engineer (The Salem Conjecture) who's a big fan of Intelligent Design. The book is an attempt to prove that evolution is a fraud.I checked to see if junk DNA was mentioned and came across the following passages on pages 273-275. It's interesting to read them in light of what's happened in the past four years. I think that the view represented in this book is still the standard view in the ID community in spite of the fact that it is factually incorrect and scientifically indefensible.
Take the issue of so-called junk DNA, or "non-coding DNA" as it's known today.1 We are aware that 3 percent of the human genome codes for proteins.2 In 1972, a scientist coined the term junk DNA to describe the 97 percent of DNA with no known function.3 Some scientists still maintain that large portions of the genome are useless accretions of evolutionary garbage.4
The ENCODE project ("Encyclopedia of DNA Elements") was started in 2003 to find all the functional elements of the human genome. The 'New York Times' announced, "Bits of Mystery DNA, Far from 'Junk,' Play Crucial Role," and went on to say.The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as "junk" but that turns out to play critical roles in controlling how cells, organs and other tissues behave. The discovery, considered a major medical and scientific breakthrough, has enormous implications for human health because many complex diseases appear to be caused by tiny changes in hundreds of gene switches.5Science magazine's report was entitled. "ENCODE Project Writes Eulogy for Junk DNA." There is no such thing as junk in the trunk when it comes to DNA.6
A tiny contingent of diehard junk-DNA advocates, such as Larry Moran of the University of Toronto, insisted that the ENCODE announcement was a "media fiasco."7 ENCODE found over 80 percent of the genome is involved in RNA production, DNA expression, or replication, for at least one cell type. ENCODE has expanded into a family of investigations into noncoding DNA functions. 8
Do Larry Moran and other junk-DNA advocates also happen to share any particular bias with respect to religion? Check and see for yourself.
If we assume purposelessness in evolution, as is done in the 1.0 version, it's logical to expect a lot of junk. If we assume a designer, we assume there's a purpose to its inclusion, and therefore, look into it until we discover it's not really junk after all. 9
...
The people who say parts of DNA are junk say so out of ignorance, not knowledge. They don't know how to build a cell or a genome. They don't know what everything does. The burden of proof that junk DNA is truly junk is on them. Until they understand everything and can explain every nuance of the genome's operation in precise detail—until they can build a cell from scratch—their job is not done.... 10
Any scientist who takes his work seriously has no choice but to say, "I don't know what it function is, but my job is to fully engage in the systematic study of the structure and behavior of this until I do. So until I have a complete working model that describes the entire system in exact detail, I have no right to assume these stretches of DNA are junk.
1. Stop Using the Term "Noncoding DNA:" It Doesn't Mean What You Think It Means
2. It's no more than 1%. [What's In Your Genome? - The Pie Chart] [How many protein-coding genes in the human genome?]
3. He's referring to the paper by Susumu Ohno (1972). Ohno did not say that 97% of our genome is junk and he did not say or imply that all noncoding DNA was junk. He estimated that no more than 6% of our genome could be devoted to genes and he knew that some of the noncoding parts include promoters, regulatory sequences, and centromeres. [Required reading for the junk DNA debate]
4. Today, a majority of knowledgeable scientists agree that most of our genome is junk and the number is growing every year as more and more scientists become aware of the overwhelming evidence for junk DNA. [What is the dominant view of junk DNA?]
5. The New York Times is not a reliable source of information about science.
6. Science is usually a reliable source of scientific information but in this case Elizabeth Pennisi gets it all wrong [Science Writes Eulogy for Junk DNA ].
7. [The ENCODE publicity campaign of 2007] [The truth about ENCODE]
8. [ENCODE's false claims about the number of regulatory sites per gene] [What did the ENCODE Consortium say in 2012?]
9. Atheism does not predict anything about the composition of our genome or any other genome. From our knowledge of biochemistry and evolution, we might have guessed that most genomes would be packed with functional sequences because junk DNA is likely to be deleterious. Natural selection should eliminate junk DNA in populations undergoing strong selection. That's what we see in bacterial populations. The discovery of massive amounts of junk DNA in mammals conflicted with this simple understanding of evolution but it was consistent with the view of evolution that was developed in the late 1960s. That view allowed for the expansion of the genome by adding junk DNA in populations that were not under strong selection. With respect to the existence of junk DNA, it doesn't matter whether you are a believer or not. What matters is whether you accept scientific evidence or reject it. Many believers reject science because of their religious bias.
10. Only one side of this debate is basing their view on ignorance and lack of knowledge and it's not the scientists. There is plenty of evidence for junk DNA [Five Things You Should Know if You Want to Participate in the Junk DNA Debate].
Posted by in junk DNA, Rationalism v Superstition, Science and Religion
Michael Behe’s third book
This will be Behe's third book. The first one was Darwin's Black Box (1996) where he argued against evolution by suggesting that some cellular complexes (e.g. bacterial flagella) are irreducibly complex and could not possibly have evolved by natural means. His second book was The Edge of Evolution (2007) where the theme was that there are limits to evolution preventing it from accomplishing significant beneficial changes.
I haven't read his third book but it looks like it will continue the pattern of trying to show that evolution is flawed rather than trying to show evidence of intelligent design. David Klinhoffer has posted a quotation from the new book indicating that the main approach is to argue that evolution can break things but not construct things [For #GivingTuesday, Help Michael Behe Demonstrate that Darwin Devolves].
This book…concentrates on completely unexpected, devastating new problems that could only have come to light after major recent advances in technical methods for probing the molecular level of life. With surpassing irony it turns out that, as with the polar bear, Darwinian evolution proceeds mainly by damaging or breaking genes, which, counter-intuitively, sometimes helps survival. In other words, the mechanism is powerfully de-volutionary.This is standard propaganda for the Discovery Institute whenever a new book is about to be published. We are subjected to months of promotion including dire warnings about the imminent collapse of evolution because some ID intellectual has finally come up with an irrefutable argument that the scientific community can't ignore [Michael Behe’s Darwin Devolves Topples Foundational Claim of Evolutionary Theory]. None of us can respond because we haven' read the book but when we suggest, based on our knowledge of chicken little and the boy who cried wolf, that there's no reason to fear the collapse of science then we are accused of dishonesty for not reading the book! [Evolutionist Attacks Behe Book’s Title]
You might imagine that Behe would take on his YEC colleagues as fiercely as he fights evolutionary biologists, but he doesn't. I find it very strange that ID proponents who still believe in a young Earth are fans of Michael Behe but I suppose they are happy because Behe is attacking evolution and as long as he keeps the focus on attacking a common enemy they are happy.1
Those of you who read the first two books will recall that they were also about "devastating problems" with evolution that only came to light with new research revealed in 1996 and 2007. For some strange reason the textbooks have not been re-written and the churches have not filled up with new converts. What happened?
Refuting his first book was pretty straightforward because Behe based his argument on his inability to imagine how an irreducibly complex system could have evolved by natural means. All we had to do was show that irreducibly complex systems could evolve without the help of a designer and this turned out to be relatively easy.2
Refuting his second book was much harder—not because he was making a valid scientific argument but because showing where he goes wrong requires a fairly deep understanding of modern evolution. Behe was arguing that many presumed examples of evolution required three or more mutations in order to produce a beneficial effect. He claims that in many cases none of the individual steps are beneficial and some of them might even be detrimental. Thus, three mutations have to occur simultaneously and that's not possible—it's beyond the edge of evolution.
Behe would be correct if the only way to fix mutations was by positive natural selection. That's the old-fashioned, adaptationist view of evolution from the 1960s and it's the view that dominates the thinking of ID proponents. But with the development of Neutral Theory and it's off-shoot, Nearly-Neutral Theory, we now know that neutral and detrimental alleles can be maintained in a population for a long time because random genetic drift is often as potent a mechanism as natural selection.3
Thus, it's relatively simple to imagine how a new system requiring several mutations can evolve under modern evolutionary theory and this extends the edge of evolution far beyond the limits postulated by Michael Behe.4 In fact, it's easy to show that this is exactly how Behe's favorite example, chloroquine resistance to malaria, evolved. But, while such ideas are easy for most of us, they are still very difficult for most creationists, including Behe. You can see for yourself how he resists any explanation involving random genetic drift [Revisiting Michael Behe's challenge and revealing a closed mind].
It's kinda cute to see that the Discovery Institute is still under the illusion that they can discredit evolution and convince the world that a creator god exists. It's been more than 20 years since Intelligent Design became a popular creationist idea and the predictions from back then were that by now we would all be creationists. Instead, evolution is as strong as ever and people all over the world are abandoning religion.
I'm 100% certain that I can refute Behe's latest claim because I've seen it all before. Nevertheless, I will wait until I've read the book so the creationists can enjoy their yearly round of gloating and premature celebration. It's just about the only thing they have going for them these days.
1. Things can go very badly for any creationist who disagrees with their fellow creationist. Look what happened to Sal Cordova [What would happen if Intelligent Design Creationists understood evolution?]
2. [The meaning of "irreducible complexity"] [Blown Out of the Water]
3. see [Evolutionary biochemistry and the importance of random genetic drift] [Learning about modern evolutionary theory: the drift-barrier hypothesis]
4. [Understanding Michael Behe's edge of evolution] [Understanding Mutation Rates and Evolution] [Historical evolution is determined by chance events]
Test your irony meter
The irony meter was a running joke on the newsgroup talk.origins back in the last century. Our irony meters were supposed to protect us from the craziness of creationists but as soon as we built a really good irony meter a new bit of creationist crazy came along and fried it. Apparently Jesus and Mo have the same problem.
Posted by in Rationalism v Superstition