Friday, August 29, 2014

What are students interested in and does it matter?

PZ Myers [Oh, dear] picked up on a tweet from Jeffrey Ros-Ibarra [Tell me botany doesn’t have a recruitment problem]. He posted the result of a survey of 800 first year students.

This shouldn't come as a big surprise to any Sandwalk readers. The question is, what should we do about it?

Most university professors share this bias so they are very comfortable with teaching biochemistry from a strictly animal (mostly human) perspective. When challenged, they point out that students are mostly interested in animals and themselves. They think we should design our courses to accommodate these interests because that's what students want to hear. I call these professors the "caterers."

A minority (that includes me) look upon this data as a challenge. Our goal is to convince students that they should broaden their interests and learn about other species. People like me will emphasize broad principles and concepts that apply to ALL living organisms. We teach comparative biochemistry and talk a lot about evolution. These guys are the "challengers." (They're also the ones with the low student evaluations.)

The easiest way to tell the difference between the two types of professor in introductory biochemistry courses is to see whether they teach photosynthesis or the glyoxylate shunt, and whether they spend as much time on gluconeogenesis (the most ancient pathway) as they do on glycolysis (the derived pathway). It's also informative to observe whether they cover the biosynthesis of amino acids or whether they treat amino acids as food.

It's a really bad sign if they spend any time at all on the difference between "essential" and "nonessential" amino acids.

Thursday, August 28, 2014

The function of IDiots

There aren't very many big questions left to answer. Most ot the great debates have been settled and we're now in a mopping up situation.

One of the few remaining questions concerns the function of IDiots. The Intelligent Design Creationist Movement has been a spectacular failure. The Wedge Document is a joke. They've failed to get creationism into American schools. People are abandoning Christianity. Their books have all been trashed by critics.

One wonders why they're still around. They must be thinking the same thing because David Klinghoffer has put up a recent post on this very issue [You're Welcome: Darwinists Should Thank Us for Quality Control, Fact-Checking]. It turns out that the function of IDiots is to keep real scientists honest by finding flaws in their reasoning and errors of fact.
Casey [Luskin] points out that in any marketplace—whether vendors are promoting consumer products or ideas about evolution—competition improves the products and the service. The absence of competition almost always results in shoddy products and poor consumer service, as anyone who has visited a socialist country can tell you. Darwin advocates should be thanking us.

Of course the flipside to all this is that for every orthodox evolutionist who is made more judicious and truthful in what he argues, there's probably another who prevaricates about the meaning of scientific data, because "What will the creationists say?"

Still, on the whole, they and everyone else who cares about getting at the truth in science ought to be glad we're here.
Who knew?

Wednesday, August 27, 2014

Tim Hortons is seduced by the dark side

I'm not a fan of dark coffee but this is a cute commercial video.

Michael Behe's final thoughts on the edge of evolution

We've been having an interesting discussion about chloroquine resistance and the Edge of Evolution. It began last month when Michael Behe started bragging that his "prediction" had been confirmed by a recent paper [A Key Inference of The Edge of Evolution Has Now Been Experimentally Confirmed]. It didn't take long for Casey Luskin to jump on the bandwagon [So, Michael Behe Was Right After All; What Will the Critics Say Now?]. Luskin demanded an apology from Behe;s critics.

It turns out that Behe and Luskin are wrong and the recent results published by Summers et al. (2014) actually refute most of Micheal Behe's calculations. PZ Myers pointed out that Behe's critics were mostly1 right when they criticized the original calculations in The Edge of Evolution [Quote-mined by Casey Luskin!].

Tuesday, August 26, 2014

Payback for burning Toronto

From British embassy apologizes for cheeky tweet commemorating White House burning.
... in what some considered a cheeky jab, the Washington wing of the British embassy came under fire from some unimpressed Americans for its commemoration tweet. On Aug. 24, 1814, British troops invaded Washington, D.C., setting the White House on fire during the War of 1812. The attack was in response to an American attack on the city of York (present-day Toronto).

The tweet featured a photo of a sheet cake adorned with a miniature White House with the respective countries' flags on each side.

"Only sparklers this time," the embassy wrote to cap off the tweet.

Banning the views of those who disagree with you

The blogosphere is excited about a petition that's being presented to the Scottish Parliament on behalf of the Scottish Secular Society. A chemist, and Nobel Laureate, Sir Harold Kroto, has backed the petition [Nobel prize winner backs Scottish Secular Society petition to exclude creationism in Scottish schools].

Here's what it says ....
Calling on the Scottish Parliament to urge the Scottish Government to issue official guidance to bar the presentation in Scottish publicly funded schools of separate creation and of Young Earth doctrines as viable alternatives to the established science of evolution, common descent, and deep time.
I would never, ever, sign such a petition. I think it's a bad idea for politicians to get involved in the specifics of what should and should not be taught in publicly funded schools. You can see what happens in the USA when you give them that right.

If the teaching of Young Earth Creationism is creeping into Scottish schools then it's time to show students why it is wrong and why science can refute it. Banning it will only make it seem like a genuine threat that can't be confronted by teachers and education.

Is philosophy a waste of time?

John Wilkins tries to show that philosophy is not a waste of time. He describes philosophers who are anti-realists and wonders whether genes actually exist.

Intelligent Design is Stupid: Neil deGrasse Tyson

Another stupid "prediction" by Intelligent Design Creationists

The IDiots are claiming to have "predicted" something that's been known for thirty years.

Let's start by reviewing some basic facts about codons.

Look at the standard genetic code (right). Notice that for some amino acids there are several codons. For example, There are four different codons for alanine (A): GCT (GCU), GCC, GCA, and GCG. These are called "synonymous" codons.

A lot of mutations in coding regions will change one codon into another without changing the amino acid encoded by the mRNA. These are presumably neutral mutations, since they occur frequently in populations and in comparisons between species. What this means is that it mostly doesn't matter which codons are being used.

Monday, August 25, 2014

David Klinghoffer recognizes the problems with authorities and quote mining

We all know the drill by now. Intelligent design Creationists attempt to discredit evolution and science by pointing out what they see as flaws in basic theory. They also spend a considerable amount of time attempting to discredit individual scientists using guilt by association or direct character assaults.

One of their favorite tricks is to lift quotations out of context and present them in a way that makes it look like famous scientists are supporting Intelligent Design Creationism—or, at least, supporting the idea that evolution is flawed.

The tactic is so widespread and despicable that it led to formation of The Quote Mine Project
Or, Lies, Damned Lies and Quote Mines
. That project ran out of steam about eight years ago because the authors just couldn't keep up with all the misinformation coming out of books, lectures, and articles from leading members of the Discovery Institute.

Stephen Meyer is a expert at this. Here are a couple of examples from his book Darwin's Doubt (2013).

Friday, August 22, 2014

Understanding Michael Behe

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.

Does this video have anything to do with the scientific evidence for Intelligent Design Creationism?

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.

Monday, August 18, 2014

John Wilkins discusses the "Demarcation Problem"

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.

Student debt in Canada

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.

Sunday, August 17, 2014

God's Not Dead

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.

Friday, August 15, 2014

CCC's and the edge of evolution

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 ...

Wednesday, August 13, 2014

Flunking the Behe challenge!

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.

What do biologists know about human races?

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.

Monday, August 11, 2014

Who should speak on a university campus?

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.

Sunday, August 10, 2014

What did Vincent Torley say on Uncommon Descent?

Vincent Joseph Torley (vjtorley) has several degrees listed on his website. Quoting ...
  1. 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).
  2. Bachelor of Arts, completed in 1986, at the Australian National University, Canberra. Majors: Philosophy and Computing Science.
  3. Bachelor of Economics, completed in 1987, at the Australian National University, Canberra. Majors: Economics and Accounting. Other subjects studied: Statistics (2 years).
  4. Master of Arts in Philosophy, completed in 1994, at the University of Melbourne, Australia. Thesis topic: Laws of Nature (Scientific Laws). Grade: 2A.
  5. 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?

Friday, August 08, 2014

Refugee camps in Canada (1775-1780)

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 Machoche, 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.

Historical contingency and the evolution of the glucocorticoid receptor

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.

Creationist cartoon

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.)

Thursday, August 07, 2014

The filter problem

Drugmonkey (@drugmonkeyblog) doesn't think there's a filter problem [There is no "filter problem" in science].

He writes,

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 Function Wars: Part IV

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.

Wednesday, August 06, 2014

When will they ever learn?

On most days I'm an optimist. I think that eventually the truth will win out and all you have to do is convince people that they are misguided. That's why I spend so much time discussing the view of Intelligent Design Creationists. On the good days, I firmly believe that if I can show them what science is all about then they will come around to accepting evolution.

I cherish a few modest successes over the years. For example, a few months ago I tried to teach David Klinghoffer and his friends about modern concepts of evolution and genetics. The example I used was the 98% sequence similarity between the human and chimp genomes. I showed him that the similarity is quite consistent with our understanding of Neutral Theory and random genetic drift [Why are the human and chimpanzee/bonobo genomes so similar?].

A remarkable thing happened. Some of the Intelligent Design Creationists on Evolution News & Views (sic) and Uncommon Descent actually agreed with me! They tried to explain to their fanatical friends that chimps and humans really do share a common ancestor and that the differences between them are explained by evolutionary theory. (I've included links to all the posts at the bottom of this post.)

Just when you think you are making some progress, the IDiots prove you wrong. Yesterday on Uncommom Descent there was a post on the topic of the similarity between chimps and humans [At last, a proposed answer re 98% human-chimpanzee similarity claim]. The author was probably Barry Arrington posting as "News." Here's the relevant part of that post ...
From this comment (by Gordon Davisson, in response to this post):
In other words, I’m agreeing with Denyse here:
BUT claimed 98% similarity due to a common ancestor (a claim that hundreds of science writers regularly make, in support of common descent) *undermines anything else they have to say on the subject.*
I do not know how to put the matter more simply than this: A person who does not see the problem is not a credible source of information.
He responds:
…just disagreeing about which side is not credible. Take the 98% similarity figure as an example: one of the basic principles of science is that you must follow the evidence. If the evidence supports the 98% figure, and that conflicts with your intuition, then you either have to throw that intuition into the trash bin, or stop claiming to be doing science.
No. Absolutely not.

One should never discard intuitions formed from experience, especially about vast claims. Chimpanzees are so obviously unlike humans – in any way that matters – that claimed huge similarities only cast doubt on genetic science.
This is called, among other things, wanting to have your cake an eat it too. The IDiots want you to believe that they accept all of modern science and that their "theory" is consistent with the evidence.

On the other hand, if the science of genetics leads to conclusions that contradict your "intuition" then the science must be wrong.

We've known for decades that this is how the IDiots really think but it's interesting to see someone like Barry Arrington express it so openly.

Now all we have to do is sit back and wait for the more intelligent IDiots to point out that we've been through all that a few months ago and Barry's intuition is wrong. Instead, what we're seeing is Barry Arrington doubling down [Sun orbits Earth vs. Chimps are people too – the differences].

This is not a good day. It's hard for me to remain optimistic.

An Intelligent Design Creationist explains why chimpanzees and humans are so similar
IDiots respond to the evidence for evolution of chimpanzees and humans
A creationist illustrates the argument from ignorance while trying to understand population genetics and Neutral Theory
Breaking news: Creationist Vincent Torley lies and moves goalposts
Vincent Torley apologizes and claims that he is not a liar
Vincent Torley tries to understand fixation
On the frustration of trying to educate IDiots
Why creationists think they are more open-minded than scientists
What would happen if Intelligent Design Creationists understood evolution?
Branko Kozulic has questions about fixation
Branko Kozulic responds
Branko Kozulic responds: Part II

Tuesday, August 05, 2014

Stephen Meyer isn't keeping up

There are so many problems with Darwin's Doubt that one hardly knows where to begin. For me, the most important problem is that Meyer dismisses all the evidence for pre-Cambrian ancestors. These ancestors had most of the genes necessary to make all the animals that arose during the Cambrian explosion.

Our current model for evolution and development is that small changes in the regulation and timing of key developmental genes are responsible for big phenotypic differences, including new animal body plans. The data shows that all the animal phyla have similar genes and that there aren't very many genes whose origins can be traced to the Cambrian.

... those ignorant of history are not condemned to repeat it; they are merely destined to be confused.

Stephen Jay Gould
Ontogeny and Phylogeny (1977)
This model was popularized by Stephen Jay Gould in his 1977 book Ontogeny and Phylogeny. Meyer disputes this model. He claims that massive amounts of new information (= new genes) arose at the time of the Cambrian explosion. He claims that this cannot be explained by any naturalistic means; therefore, god(s) must have made those strange Cambrian animals. (Presumably, the gods are also responsible for making them go extinct.)

Charles Marshall, a paleontologist at UC Berkeley (USA) wrote a critical review of Darwin's Doubt [When Prior Belief Trumps Scholarship]. Here's part of what Marshal wrote in September 2012.

Monday, August 04, 2014

Why don't scientists believe in a creator?

Gordon E. Mullings ("kairosfocus") just can't understand why scientists haven't become believers in a creator who designs life [BA77′s observation: "many influential people in academia simply don’t want Design to be true no matter what evidence . . ."]. He quotes BA77 (really!) ...
The inimitable BA77 observes:
I [used] to think that if ID could only get its evidence to the right people in the right places then they would change their mind about Darwinian evolution and we would have a fundamental ‘paradigm shift’ from the ‘top down’. But after a few years of banging my head on that wall to no avail, I realized that it is not a head problem with these people so much as it is a heart problem. i.e. many influential people in academia simply don’t want Design to be true no matter what evidence you present to them. Indeed, in many educational institutions, there is a systematic effort in academia to Expel anyone who does not toe the Darwinian party line.
He concludes: "Thus the growth in popular support for ID has been more of a ‘bottom up’ affair."
Mullings presents a diagram that's supposed to demonstrate the evidence for Intelligent Design Creationism (right, above).

There are many reasons why "people in academia" have not been convinced by "evidence" like that presented by Bill Dembski. The most important reason is that the "evidence" isn't really evidence at all. It has been refuted repeatedly by people who know what they are talking about. There is no evidence for the existence of a creator who meddles in the affairs of living organisms.

But the real reason why people like BA77 and kairosfocus are puzzled has nothing to do with evidence. They believe in the existence of gods(s); therefore; they already believe in a creator so it's no big leap to "make sense" of biology in the light of god(s). What they don't understand is that for nonbelievers the "evidence" of Intelligent Design Creationism (if it existed) is only a small part of the path towards believing in a divine creator.

It's a heart problem. Intelligent Design Creationists are absolutely convinced that god(s) exist so they don't realize that Dembski's argument falls into category of "extraordinary claim" since it requires the existence of creators. It's not sufficient just to cast doubt on evolution and question scientific evidence. You also have to propose an alternative explanation and that hypothesis includes evidence for the designer. That kind of extraordinary claim requires extraordinary evidence and the IDiots haven't even come close to providing it.1

People like Gordon E. Mullings and BA77 have been trying to convince "infuential people in academia" for over 200 years. Generation after generation of academics have rejected their "evidence" and their logic. It's about time that the IDiots came to grips with the truth; namely, that they don't have any proof of the existence of god(s) and they never will.

They also need to stop fooling themselves about their "success" among the general public. Belief in god(s) is declining all over the world.

1. As most of you already know, the IDiots try to avoid talking about the Intelligent Design Creator. They claim that the "evidence" for his/her/their existence stands on it's own. All they want is for you to accept the "evidence" for the existence of god(s). What you do with that "evidence" is up to you. They aren't concerned about that part because they've already taken the leap.

Friday, August 01, 2014

Atheists really do believe in god!!!

Last year at this time I was in Copenhagean, Denmark. This is a country full of people who don't believe in god(s). At least they think they don't believe in gods. Turns out they are probably wrong according to Casey Luskin [Evolutionary Studies Suggest that Atheists, Whatever They Say to the Contrary, Really Do Believe in God].

Luskin thinks that evolution is true after all, especially when it supports his prejudices beliefs. He quotes some really silly articles that make a really silly claim; namely, that it's impossible for all those Danes to have abandoned belief in gods because lack of belief in gods is psychologically impossible. We have evolved to believe in Loki and Freyr and there's no escaping our evolutionary destiny.

Just when you think that the IDiots can't get any stupider, they come up with something like this.

Taking the Behe challenge!

Michael Behe thinks the main thesis of his book, The Edge of Evolution, has been vindicated by a recent paper (Summers et al., 2014). He is wrong, as I discussed in a previous post [Michael Behe and the edge of evolution].

PZ Myers and Ken Miller have already made the same points that I make but the IDiots never listen when their view are challenged. Instead, they go on the attack and claim that the latest publications refute evolution and support Intelligent Design Creationism.

Behe is certain that he's right. He's so certain that he has issued a challenge to Myers and Miller [An Open Letter to Kenneth Miller and PZ Myers]. I'm going to try and do some calculations to meet his challenge but I'm not certain if I'm doing them correctly. Please help me find any mistakes.