Michael Behe has tried to explain where I'm going wrong and why evolution is highly improbable [Guide of the Perplexed: A Quick Reprise of The Edge of Evolution]. He lists a number of bullet points that are supposed to explain his argument. Let's look at each one ...
- If the development of some particular adaptive biochemical feature requires more than one specific mutation to an organism's genome, and if the intermediate mutations are deleterious (and to a lesser extent even if they are neutral), then the probability of the multiple mutations randomly arising in a population and co-existing in a single individual so as to confer the adaptation will be many orders of magnitude less than for cases in which a single mutation is required.
This is correct. The probability of any single mutation occurring is equal to the mutation rare, which is about 10-10. The probability of an additional specific mutation occurring is also 10-10. The combined probability of any two specific mutations occurring is 10-20.
In spite of what they say, the Intelligent Design Creationist movement is primarily an anti-science, anti-evolution movement. Something like 99% of their efforts and activities are directed toward discrediting scientists and science. The 1% of their effort devoted to promoting scientific evidence for creationism has been a spectacular failure.
Here's a new video produced by John G. West. In case you don't know who John G. West is, here's what Wikipedia [John G. West] says about him ...
John G. West is a Senior Fellow at the Seattle-based Discovery Institute (DI), and Associate Director and Vice President for Public Policy and Legal Affairs of its Center for Science and Culture (CSC), which serves as the main hub of the Intelligent design movement.
The video was posted to YouTube on Aug. 14, 2014 and it is copyrighted by the Discovery Institute. I learned about the video from a post on Evolution News & Views (sic) [Coming to Grips with the Truth About Social Darwinism].
The video has nothing to do with evolution and evolutionary theory but IDiots believe that it does. That's, of course, why we call them IDiots.
One of the most fascinating things about philosophy is the fact that philosophers still can't agree on the major issues even after debating them for hundreds of years. For example, they still can't, as a discipline, agree on whether there are good arguments for the existence of gods. Many universities have theologians who masquerade as philosophers and publish in philosophy journals.
Philosophers are still discussing the mind-body problem. In other words, there actually are legitimate philosophers who call themselves dualists and think that the mind is something more than the workings of matter. Some philosophers think there are moral absolutes while others are ethical relativists and some are something else. Apparently, several hundred years of debate hasn't resolved this issue either.
Recently (last century) the discipline of philosophy has spun off a subdiscipline known as the "History and Philosophy of Science." This is now a separate department in many universities.
I got curious about student debt when I saw a YouTube presentation about the "squeeze generation." The point of the talk was to explain how difficult life is for the under 45 group compared to their baby boomer parents.
The video repeated the common claim that average student debt was about $23,000. I've always been puzzled by this claim since most of my friends were able to help their children get a university education just as our parents helped us. Most of our children were able to graduate from university (undergraduate degree) with no debt.
If about half the graduating class got help from their parents, as we did, then the average debt of those students with debt must be about $46,000 and that's unreasonable.
I was a little bored yesterday so I watched God's Not Dead.
There's good news and bad news.
The bad news is that I wasted almost two hours.
The good news is that if this is the best Christians can do then rational people are not threatened. On the other hand, unbalanced people—like the Christians in this mover—can be unpredictable, so maybe we should be worried.
The most repulsive scene is when a Christian pastor tries to force a dying atheist (car accident) to accept Jesus. The second most repulsive scene is when the hero's Christian girl friend leaves him because he wants to stand up for his faith. If those people are typical Christians then it's no wonder that people are abandoning Christianity.
Let me say, right from the beginning, that Michael Behe's book The Edge of Evolution is very interesting and provocative. Many of my colleagues think that Behe's main argument can be easily dismissed as the work of an uninformed IDiot who is blinded by his religion. There's some truth in that, but only a little.
The main thesis of the book is that there are some combinations of mutations that could theoretically be beyond the reach of evolution during the 3 billion years that life has evolved on Earth. Behe refers to this combination as a double CCC (1040). It's his estimate of the probability of a particular combination of four specific mutations arising by chance. Since we know that such combinations have arisen, Behe concludes that god(s) must have been involved.
There are many ways of exploring Behe's calculations in order to see if he has a point. The first problem is that the meaning of his conclusion is very unclear. Let's think about it this way ...
Apparently I flunked the Behe challenge [Laurence Moran's Sandwalk Evolves Chloroquine Resistance]. Let's review what happened.
In his book, The Edge of Evolution, Michael Behe calculated the odds of a malaria parasite developing resistance to chlorquine by assuming that two separate mutations were necessary. Here's what he said on page 57 ...
How much more difficult is it for malaria to develop resistance to chloroquine than to some other drugs? We can get a good handle on the answer by reversing the logic and counting up the number of malarial cells needed to find one that is immune to the drug. For instance, in the case of atovaquone, a clinical study showed that about one in a trillion cells had spontaneous resistance. In another experiment, it was shown that a single amino acid change at position number 268 in a single protein, was enough to make P. falciparum resistant to the drug. Se we can deduce that the odds of getting that single mutation are roughly one in a trillion.
The debate over the existence of human races has heated up recently with the publication of a book by science writer Nicholas Wade. The book is ridiculous, by all accounts (I haven't read it). In fact, it is so wrong that a group of geneticists have written an open letter refuting the claims [see Geneticists decry book on race and evolution].
There are several aspects of this controversy that interest me greatly. One of them has to do with the reputation of science writers. Nicholas Wade was a science writer for Nature (1967-1971), Science (1972-1982), and the New York Times (1982-2012). I've often heard heard him being referred to as one of the best science writers, particularly by other science writers. That's an opinion that I've never shared and I'm glad to see him get his comeuppance.
Science writers aren't doing so well these days.
Micheal Behe came to Toronto a few years ago and gave three talks on the campus of the University of Toronto. One of them was in the big lecture hall in my building (Medical Science Building). I went to all three lectures and enjoyed them immensely even though I disagreed with what he was saying [Michael Behe in Toronto: "What Are the Limits of Darwinism?"] [Michael Behe in Toronto: "Evidence of Design from Biology" ]. It was fun meeting him again and talking to him about his views. You can learn a lot about what people think by attending a lecture and seeing how they respond to questions and debate.
That's what a university is all about. I also greatly enjoyed a lecture by William Dembski a few years ago. I got to meet him and I got to ask a question at his lecture. It was a very valuable experience. Over the years I've heard several creationists speak on my campus, even Hugh Ross. Attending those lectures has put me in touch with many creationist sympathizers in my area and I've formed a number of friendships. Some of them read my blog.
Vincent Joseph Torley (vjtorley) has several degrees listed on his website. Quoting ...
- Bachelor of Science, completed in 1981, at the Australian National University, Canberra. Major: Pure Mathematics. Other subjects studied: Physics (2 years), Chemistry (2 years), Geology (1 year) and Science German (1 year).
- Bachelor of Arts, completed in 1986, at the Australian National University, Canberra. Majors: Philosophy and Computing Science.
- Bachelor of Economics, completed in 1987, at the Australian National University, Canberra. Majors: Economics and Accounting. Other subjects studied: Statistics (2 years).
- Master of Arts in Philosophy, completed in 1994, at the University of Melbourne, Australia. Thesis topic: Laws of Nature (Scientific Laws). Grade: 2A.
- Ph.D. in philosophy, which I received in August 2007 from the University of Melbourne, Australia. Thesis topic: The Anatomy of a Minimal Mind.
.... end quote.
He hasn't studied much biology and his undergraduate science degree, obtained 26 years ago, was a major in pure mathematics.
That hasn't prevented him from writing extensively about biology and evolution. His latest contribution is a critique of Keith Blanchard's article on Why you should stop believing in evolution: You don't believe in it — you either understand it or you don't. That article has attracted attention from evolution supporters who think he got some things wrong [see Glenn Bransch's Five Quibbles for Blanchard]. I agree with them. Blanchard does not present the best case for evolution and he seems to lack a deep understanding of evolution.
Vince Torley's article is worth reading because it illustrates some of the confusions in the minds of IDiots as they struggle to catch up with 21st century biology [see Why Keith Blanchard really doesn’t understand evolution]. However, that's not the point I want to make today. Instead, I want to quote a paragraph from near the end of Vincent Torley's article ....
I could go on, but I’d like to conclude this article with a final observation: Keith Blanchard doesn’t have a science degree. His LinkedIn profile lists him as having a two year tech degree in Electronic Technology, which he obtained in 1975. Let us freely grant that the man’s skill set looks quite impressive. Nevertheless, the fact remains that a man without a science degree has no place writing an article on evolution in a popular online magazine like The Week. It’s simply presumptuous.
I wonder if there are any prominent Intelligent Design Creationists who don't have real science degrees?
I love watching "Who Do You Think You Are." The latest episode features Rachel McAdams and her sister Kayleen who search for their Canadian ancestors. They discover a family who settled on the shores of Lake Champlain in the mid-1700s and got caught up in the Revolutionary War. Their ancestors supported the government (Great Britain) against the revolutionaries and when General Burgoyne's invasion from Canada was stopped at the Battles of Saratoga (1777) the loyalists had to flee to Canada with the retreating army.
The McAdams ancestors spent a year or so at a refugee camp near St. Johns in Quebec, near the American border. The sisters visit the site during the show. It looks like one of the young sons of their ancestors died during the stay in the refugee camp—probably because the conditions were pretty horrible.
One of my ancestral families was Isaac Montras and his wife Tamar Betts. They had a farm near Saratoga and they supported the British side during the revolution. They also had to leave their farm and flee to Canada after the Battles of Saragota. They were settled at another refugee camp in Machiche, Quebec where they stayed for a year before moving on to settle in Nova Scotia.
Tens of thousands of United Empire Loyalists came to Canada after the Thirteen Colonies gained their independence from Great Britain. Nobody knows how many of the residents of the Thirteen Colonies remained loyal to the government in Great Britain but it may have been as much as one-third of the total population. Only a small percentage of them left after the war was over.
You can watch a clip from "Who Do You Think You Are" featuring the McAdams sisters at: Rachel McAdams Learns Her Ancestors' Loyalties. If you want to watch an entire show, I recommend the British version that's been around for ten seasons. Here's one on J.K. Rowling.
Michael Behe is at it again. He has a freaky knack of taking scientific results that directly contradict his views and twisting them into confirmation that only god can explain the result.
This time he is revisiting an old issue. Joe Thornton's lab has published a series of papers showing that the evolution of the glucocorticoid receptor involved a number of neutral steps that were absolutely required before the receptor could acquire the ability to bind to cortisol. Each of the steps was contingent on earlier steps. This is evolution by accident.
This conflicts with Michael Behe's view of evolution because he maintains that there's an edge of evolution defined by pathways that involve multiple steps. According to Behe, all the multiple mutations have to take place at the same time because none of the intermediates are beneficial and most of them are detrimental.
I visited the Institute for Creation Research back in 1992 when it was still based in Santee, California (USA). I toured the museum and bought this wonderful poster in the gift shop. It now hangs on the wall outside my office. I relate to the pirates.
A much simpler black and white version (below) was shown to a high school class in Atlanta, Georgia, USA and it caused quite a stir [Flap over creationist cartoon shown in high-school class]. I can understand why. The color poster that I bought twenty years ago is much better. I can see why the Atlanta high school students weren't impressed with the pirates.
Seriously, I don't think evolution supporters should make a fuss about this [see Evolution vs. creationism: Does this cartoon belong in Grady High School biology class? ]. It may provide some comfort to the diehard fundamentalist Christian students in the class but lots of students are going to make fun of the cartoon and that may have a beneficial effect in the long run. We should be careful about putting up obstacles that prevent creationists from shooting themselves in the foot.
(I know about the so-called "separation of church and state" provision in the American Constitution. You don't need to lecture me on the legality of showing a religious cartoon in a public high school.)
Drugmonkey (@drugmonkeyblog) doesn't think there's a filter problem [There is no "filter problem" in science].
He writes,
Seriously.
It is your job as a scientist to read the literature, keep abreast of findings of interest and integrate this knowledge with your own work.
We have amazing tools for doing so that were not available in times past, everything gets fantastically better all the time.
If you are a PI you even have minions to help you! And colleagues! And manuscripts and grants to review which catch you up.
So I ask you, people who spout off about the "filter" problem.....
What IS the nature of this problem? How does it affect your working day?
I'm trying to keep up with a number of very broad and diverse fields. For example, as a textbook author, I need to keep abreast of just about everything that might be covered in an introductory biochemistry course. I'm also trying to keep informed about evolutionary biology; especially molecular evolution because I teach a course on that topic and I blog about it. I don't want to miss exciting developments in pedagogy (teaching) and the philosophy of science. Finally, I like to be up-to-date on the latest advances in other disciplines.
Here's the problem. There's a lot of junk out there. It's a waste of time to scan all of the science journals that might possibly have something of interest to me and it's a waste of time to get any "tools" to do it for me. Most of the time I wouldn't even know what to ask for. For example, I don't want to see all the papers on photosynthesis but I need to see the one that's going to change my textbook. I don't want to see all the papers on mutation rates but I do want to see the ones that are worth blogging about.
There were times when I could sit down for a few hours every week and scan the tables of contents of the leading journals in my field. Those days are long gone and my "field" has expanded enormously. I need to filter but I'm pretty sure I'm missing some important papers. In fact, I know this because just about every month I hear from others about things that I've missed months, or even years, ago.
I have a filter problem. I'm filtering out some important things and reading far too much junk. My filter problem can't be solved. If it wasn't for blogs, I'd be in bigger trouble.
We're in the middle of a discussion about the function wars. It's obvious to me that members of the ENCODE Consortium also have a filter problem. They've filtered out all kinds of information about the organization of the human genome. They don't understand the evidence for junk DNA, for example, and they don't have a good grasp of evolution. On the other hand, they've probably read every recent paper on the methodology of RNA-Seq, ChIP, and data analysis algorithms.
I'm glad that drugmonkey doesn't have a filter problem. Or, should I say, I'm glad that he THINKS he doesn't have a filter problem. It must be comforting to believe that he's keeping abreast of everything relating to his interests. I've never felt like that.
The world is not inhabited exclusively by fools and when a subject arouses intense interest and debate, as this one has, something other than semantics is usually at stake.
Stephan Jay Gould (1982)This is my fourth post on the function wars.
The first post in this series covered the various definitions of "function" [Quibbling about the meaning of the word "function"]. In the second post I tried to create a working definition of "function" and I discussed whether active transposons count as functional regions of the genome or junk [The Function Wars: Part II]. I claim that junk DNA is DNA that is nonfunctional and it can be deleted from the genome of an organism without affecting its survival, or the survival of its descendants.
In the third post I discussed a paper by Rands et al. (2014) presenting evidence that about 8% of the human genome is conserved [The Function Wars: Part III]. This is important since many workers equate sequence conservation with function. It suggests that only 8% of our genome is functional and the rest is junk. The paper is confusing and I'm still not sure what they did in spite of the fact that the lead author (Chris Rands) helped us out in the comments. I don't know what level of sequence similarity they counted as "constrained." (Was it something like 35% identity over 100 bp?)
My position if is that there's no simple definition of function but sequence conservation is a good proxy. It's theoretically possible to have selection for functional bulk DNA that doesn't depend on sequence but, so far, there are no believable hypothesis that make the case. It is wrong to arbitrarily DEFINE function in terms of selection (for sequence) because that rules out all bulk DNA hypotheses by fiat and that's not a good way to do science.
So, if the Rands et al. results hold up, it looks like more that 90% of our genome is junk.
Let's see how a typical science writer deals with these issues. The article I'm selecting is from Nature. It was published online yesterday (Aug. 6, 2014) (Woolston, 2014). The author is Chris Woolston, a freelance writer with a biology background. Keep in mind that it was Nature that started the modern functions wars by falling hook-line-and-sinker for the ENCODE publicity hype. As far as I know, the senior editors have not admitted that they, and their reviewers, were duped.
