I can understand why the Intelligent Design Creationists want to label me as a Darwinist, but John Wilkins? What's his motive?
He writes [Closet Darwinism, and definitions],
Larry’s argument is roughly this: modern evolutionary theory includes a host of ideas that do not rely upon the ubiquity of natural selection. "Darwinism" and cognates is basically a focus upon natural selection (and hence adaptationist views of biology). Ergo, modern evolutionary theory is not “Darwinian” in the main. I would say both of these premises are correct (of course – Larry is a very clever and erudite man), but that the conclusion doesn’t follow.
Well, it follows for me. If the term "Darwinist" has become associated with an adaptationist view of evolution then I don't want to be called a "Darwinist."
There are plenty of other terms that are just as suitable. You could refer to everyone who studies evolution as an "evolutionary biologist." What's wrong with that?
Theme
Mutation
-definition
-mutation types
-mutation rates
-phylogeny
-controversies
The Intelligent Design Creationists are remarkably ignorant about evolution so, over the past two decades, we have tried to explain a little bit about modern concepts of evolution. My latest attempt was to describe how modern evolutionary theory (and evidence) is consistent with the differences in DNA sequence between humans and chimpanzees. This required a brief explanation of Neutral Theory, population genetics, and random genetic drift, along with a description of mutation rates.
It didn't work. Creationists like Vincent Torley and Sal Cordova came up with all kinds of reasons why they couldn't believe the explanation. They were joined by Branko Kozulic, a biochemist who decided to help Vincent Torley come up with criticisms that used the right words.
There is no universally agreed upon definition of "Darwinism" but many of us think it refers to a view of evolution that emphasizes natural selection as the dominant mechanism of evolution. That's why I don't call myself a "Darwinist."
What Is Darwinism?
What Is Darwinism?
Jerry Coyne on Darwinism
Don’t Call it "Darwinism"
Let’s Get Rid of Darwinism
I'm not a Darwinist, but I Ain't Signing
Why I'm Not a Darwinist
In our discussion about the differences between the human and chimp genome sequences, we've been talking about Neutral Theory, molecular mutation rates, population genetics, and random genetic drift. These are not traditional Darwinian topics. Nevertheless, the Intelligent Design Creationists over at Uncommon Descent want to make sure that everyone knows I'm a true Darwinist.
The Intelligent Design Creationists tell us repeatedly that they have a valid scientific theory of design. The reality is that 99.9% of everything they say is an attack on science and evolution. They don't have any answers themselves and they desperately want to show their flock that scientists don't have any answers either. That's all they've got.
Salvador Cordova (scordova) is one of those IDiots who think they've got scientists stumped. He's come up with a series of questions that students can ask their college professors: Questions college students should ask science professors.
Remember, the goal is the question will be so powerful, that when the student asks the scientist or other authority figure, and when the scientist is forced to admit the truth, the student will realize the weakness in mainstream claims.
That's pretty scary stuff. I'm guessing that biology professors all over the world are shaking in their boots hoping that one of their IDiot students doesn't stand up in class and ask one of these questions. (Not.)
The questions (see below) aren't very difficult to answer. If Salvador Cordova can put together an audience of biology students at a reputable university (George Mason?) and get an Intelligent Design Creationist to ask these questions, I'll be happy to come and answer them. We'll get the students to vote on whether they want to abandon science and join the nearest fundamentalist Christian church after the class is over.1
As most of you know, I prefer a broad definition of science as a way of knowing. I usually refer to it as a way of knowing based on rational thinking, evidence, and healthy skepticism but there are many other ways of expressing the same idea.
However you say it, the broad definition of the scientific way of knowing covers everything, not just physics, biology, chemistry and geology. Not only that, it appears to be the only way of knowing that has proven to be successful. Thus, I can tentatively conclude that it is the only way of knowing until someone provides an example of knowledge obtained by another way of knowing.
Alan Sokel has posted three articles on Massimo Pigliucci new blog, Scientia Salon [What is science and why should we care? — Part III].
Here's how he describes science in Part III.
We have now travelled a long way from “science,” understood narrowly as physics, chemistry, biology and the like. But the whole point is that any such narrow definition of science is misguided. We live in a single real world; the administrative divisions used for convenience in our universities do not in fact correspond to any natural philosophical boundaries. It makes no sense to use one set of standards of evidence in physics, chemistry and biology, and then suddenly relax your standards when it comes to medicine, religion or politics. Lest this sound to you like a scientist’s imperialism, I want to stress that it is exactly the contrary. As the philosopher Susan Haack lucidly observes:
“Our standards of what constitutes good, honest, thorough inquiry and what constitutes good, strong, supportive evidence are not internal to science. In judging where science has succeeded and where it has failed, in what areas and at what times it has done better and in what worse, we are appealing to the standards by which we judge the solidity of empirical beliefs, or the rigor and thoroughness of empirical inquiry, generally.” [21]
The bottom line is that science is not merely a bag of clever tricks that turn out to be useful in investigating some arcane questions about the inanimate and biological worlds. Rather, the natural sciences are nothing more or less than one particular application — albeit an unusually successful one — of a more general rationalist worldview, centered on the modest insistence that empirical claims must be substantiated by empirical evidence.
Conversely, the philosophical lessons learned from four centuries of work in the natural sciences can be of real value — if properly understood — in other domains of human life. Of course, I am not suggesting that historians or policy-makers should use exactly the same methods as physicists — that would be absurd. But neither do biologists use precisely the same methods as physicists; nor, for that matter, do biochemists use the same methods as ecologists, or solid-state physicists as elementary-particle physicists. The detailed methods of inquiry must of course be adapted to the subject matter at hand. What remains unchanged in all areas of life, however, is the underlying philosophy: namely, to constrain our theories as strongly as possible by empirical evidence, and to modify or reject those theories that fail to conform to the evidence. That is what I mean by the scientific worldview.
Hat Tip: Jerry Coyne: Alan Sokal highlights the incompatibility of science and religion
I just read a couple of papers on teaching evolution. The focus was on common misconceptions and whether teachers share the same misconception as students (Yates and Marek, 2013; Yates and Marek, 2014). The authors are associated with Oklahoma Baptist University. Their survey results cover Oklahoma high school teachers and students taking biology.
The authors refer frequently to "the theory of evolution" but none of their questions cover the understanding of what that means. I still don't know whether they looked at misconceptions about the meaning of the phrase.
They did reference a statement by the Oklahoma Academy of Science from 2007 so I thought I'd check it out to see if they define evolution. I was able to find the statement via a link from the National Center for Science Education (NCSE) who endorsed it in 2008 [Oklahoma Academy of Science adds its voice for evolution]. You can find the complete statement at: Science, Religion, and Teaching Evolution – 2007. I reproduce it below.
Before you read it, let me make one thing clear. I do not believe that scientific associations should say anything at all about religion. I do not think they should say that science and religion are incompatible, even though I think that's correct. I also don't think they should say that science and religion are compatible, but not because it's wrong (IMHO).
There is considerable debate about the compatibility of science and religion and the one thing we can say with certainty is that scientists and philosophers do not agree. Therefore, it is wrong for scientific organizations to take one side or the other and pretend that the issue has been decided. They should stay out of the issue. This applies to ALL scientific organizations. I think it should also apply to NCSE.
Here's the statement. What do you think? Is it true that if you are an atheist you will never be able to answer "Who?" or "Why?" questions? There's a growing belief that we need to teach more about the nature of science. Is this statement a good place to start?
Science and religion can coexist harmoniously if people understand the strengths and limitations of each field. Albert Einstein said, “Science without religion is blind and religion without science is lame.” (1) Science and religion can complement each other - each informing the other in the domain where each is knowledgeable. Respected religious and world leaders such as Billy Graham, Jimmy Carter, Pope John Paul II and Pope Benedict XVI have written statements affirming harmony (2).
Strengths of Science – Science is very successful at understanding the tangible, perceivable world; anything that can be weighed, measured, detected, imaged or described objectively is the domain of science. Science can predict future actions of matter, energy, time, and space, based on past observations and experiments, or it can deduce past events, based on observing the results of those events. For example, geology can deduce what physical happenings occurred in the past and how long ago they occurred. Science can answer the HOW? and WHEN? questions about the physical world extremely well. Science is self-correcting; if new data or better interpretations become available, the scientific community will refine or add to its conclusions to reflect the recent findings.
Limitations of Science – Science cannot answer the ultimate WHO? or WHY? questions. Science is restricted to the domain of physically tangible things. Science can explain HOW things work in ever-finer detail. For example, physiology is explained in terms of biology and chemistry, which is further explained in terms of physics. Beyond the most detailed scientific explanation lies another question -- What is the First Cause? Most scientists would argue that the “First Cause” is not knowable by the methods of science.
Teaching of Evolution in Public Schools – The Oklahoma Academy of Science strongly supports thorough teaching of evolution in biology classes. Evolution is one of the most important principles of science. A high school graduate who does not understand evolution is not prepared for college or for life in a technologically advanced world, in which the role of biology and biotechnology will continue to grow. The Academy affirms that the tangible, perceivable world is the domain of science and that science is clearly the discipline to explain HOW and WHEN the universe came into being. There is no credible scientific evidence that the earth came into being recently or that evolution is not the best explanation of the origins of living organisms. Science, by definition, starts with all available evidence, draws conclusions, and generates testable predictions. The content of science courses should be determined by scientists and science educators, and not by political or religious directives. In particular, science teachers should not be required to teach ideas, models, and theories that are extra-scientific (3). "Creationism" and “Intelligent Design” are not science because they do not conform to the testable and falsifiable criteria of science. It is not appropriate for science textbooks or science teachers to teach creation as science. Creation and other matters of faith are topics for religion, philosophy, and humanities courses.
Conclusion – The Academy regards the fundamental unity of life to be evident in the common building blocks and biochemical reactions of cells and in the remarkable conservation of information in DNA sequences across the biological kingdoms. The latter documents the relatedness of all organisms--plants, microorganisms, and animals.
The Academy contends that the acceptance of the general theory of evolution and a belief in God are compatible. A wide diversity of religious faiths and belief systems are celebrated in the community of science, and the overwhelming majority of scientists accept the principles of evolutionary theory. Many do this without compromising their individual faiths in a Creator. This includes many evangelical Christians today and in the past who accepted both the Judeo-Christian Bible and evolutionary theory. One such individual was Harvard botanist Asa Gray, who was also Charles Darwin’s principal and earliest American proponent in the nineteenth century. There is no inconsistency in holding both viewpoints because the practice of science--observation, measurement, forming and testing hypotheses, controlled experimentation, drawing conclusions, and finally establishing an overall theory of how things happen--simply does not address the ultimate questions of purpose. The theory of evolution is our most rational system that explains an enormous number of observations; why or by whom that system was set in motion is not within the bounds of scientific inquiry. (4)
Understanding of the strengths and limitations of both science and religion can alleviate concerns of both scientists and non-scientists. Scientists do not accept the suppression or neglect of well-understood science because non-scientists dispute it for non-scientific reasons. Similarly, science does not speak on issues of purpose and creation, as these are not objectively testable. Science and religion have different perspectives when they address common issues, and recognizing the differences may make it possible for those active in both to realize that their most important goals are not in conflict.
Yates, T.B. and Marek, E.A. (2013) Is Oklahoma really OK? A regional study of the prevalence of biological evolution-related misconceptions held by introductory biology teachers. Evolution: Education and Outreach 6, 1-20. [doi: 10.1186/1936-6434-6-6]
Yates, T.B. and Marek, E.A. (2014) Teachers teaching misconceptions: a study of factors contributing to high school biology students’ acquisition of biological evolution-related misconceptions. Evolution: Education and Outreach 7, 1-18. [doi: 10.1186/s12052-014-0007-2]
Last week's molecule [Monday's Molecule #235] was N-formylmethionyl-tRNAfMet (fMet-tRNAfMet). The polynucleotide has to be specifically identified as the initiator tRNA (tRNAfMet, in bacteria). The winner is Jon Binkley. As I expected, there were very few people who got the right answer—in fact, there was only one other correct answer.
This week's molecules (below) may look very familiar but don't be fooled. You'll have to be very careful in identifying and naming each one of the stereoisomers. (Use common names.)
Email your answer to me at: Monday's Molecule #236. The first one with the correct answer wins. I will only post the names of winners to avoid embarrassment. The winner will be treated to a free lunch.
There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)
Theme Genomes & Junk DNAThe American Society of Plant Biologists has put out a press release with the title New functions for 'junk' DNA?.
Non-coding DNA sequences found in all plants may have undiscovered roles in basic plant development and response to the environment.
DNA is the molecule that encodes the genetic instructions enabling a cell to produce the thousands of proteins it typically needs. The linear sequence of the A, T, C, and G bases in what is called coding DNA determines the particular protein that a short segment of DNA, known as a gene, will encode. But in many organisms, there is much more DNA in a cell than is needed to code for all the necessary proteins. This non-coding DNA was often referred to as "junk" DNA because it seemed unnecessary. But in retrospect, we did not yet understand the function of these seemingly unnecessary DNA sequences.
We now know that non-coding DNA can have important functions other than encoding proteins. Many non-coding sequences produce RNA molecules that regulate gene expression by turning them on and off. Others contain enhancer or inhibitory elements. Recent work by the international ENCODE (Encyclopedia of DNA Elements) Project (1, 2) suggested that a large percentage of non-coding DNA, which makes up an estimated 95% of the human genome, has a function in gene regulation. Thus, it is premature to say that "junk" DNA does not have a function—we just need to find out what it is!
I've sent a link to this post to Tyrone Spady [tspady@aspb.org] who is listed as the contact person at The American Society of Plant Biologists and to Gregory Bertoni [gbertoni@aspb.org] who is listed as Science Editor, The Plant Cell.
I'll keep it simple for them.
- "This non-coding DNA was often referred to as "junk" DNA ..." No reputable group of scientists ever said that all non-coding DNA is junk. No scientist who understands genomes would ever say that today. [Stop Using the Term "Noncoding DNA:" It Doesn't Mean What You Think It Means]
- "We now know that non-coding DNA can have important functions other than encoding proteins." We have known that for fifty years. Is that what American plant biologists think of as a recent discovery worthy of mention in a 2014 press release? [What's in Your Genome?]
- "Recent work by the international ENCODE (Encyclopedia of DNA Elements) Project (1, 2) suggested that a large percentage of non-coding DNA, which makes up an estimated 95% of the human genome, has a function in gene regulation." It is true that the ENCODE Consortium claimed that most of our genome is functional. However, good scientists know that this claim is disputed and the best scientists know that it is wrong. Where does that leave American plant biologists? [Science still doesn't get it] [Ford Doolittle's Critique of ENCODE ]
- "Thus, it is premature to say that "junk" DNA does not have a function—we just need to find out what it is!" There is abundant evidence that most of that extra DNA in our genome really is junk. It is not some mysterious black box as you imply. [Non-Darwinian Evolution in 1969: The Case for Junk DNA ] [Five Things You Should Know if You Want to Participate in the Junk DNA Debate]
It's bad enough having to teach biology to creationists but when you also have to teach it to biologists, you know we're in big trouble.
I'm having an interesting discussion with some creationists. They claimed that the differences between the sequences of the human and chimpanzee genomes could not be explained by evolution. Therefore, it had to be due to design.
I wrote up a little post showing that there were about 44 million differences and that they could be accounted for by our understanding of population genetics and Neutral Theory. What his means is that the creationist explanation has to account for the fact that the vast majority of differences look like what we would expect if most of them were neutral and population genetics is correct. It's not good enough to simply invoke design and magic to explain the differences, you have to account for all the data.
Vincent Torley attempted to understand modern evolution theory. Some of these concepts were quite new to him because he doesn't have much of a biology background. We've had an exchange of posts were he expressed his astonishment and I try to explain evolution. You can find the links at: Vincent Torley apologizes and claims that he is not a liar.
I was thinking that this exchange would wind down but I was wrong. Vincent Torley is having second thoughts about accepting my explanation of Neutral Theory, population genetics, and mutation rates. He posted those second thoughts yesterday at: A Short Post on Fixation. My apologies if this is getting boring for Sandwalk readers but I feel an obligation to try and teach creationists about evolution, if for no other reason than being able to say that I tried.
We know why the IDiots use the words "Darwinist" and "Darwinism" to describe evolutionary biologists and modern evolutionary theory. There are three main reasons.
- They want their flocks to believe that modern scientists worship Charles Darwin and his 150 year-old theory so that when they discredit him—as they are constantly trying to do—it reflects on evolution.
- They want to link modern evolutionary biology to social Darwinism and it's easier to do so if they refer to evolutionary biologists as Darwinists.
- They are too stupid to realize that there's a lot more to modern evolutionary biology than natural selection.
Every time you challenge creationists on this point they find some way to defend their use of Darwinism rather than just say "evolutionary biology" or "modern evolutionary theory." There's a reason for this (see above).
Stephen H. Webb is the latest example. Apparently his use of "Darwinism" was challenged so he wrote a blog post on Evolution News & Views (sic) defending it The Strange Mental World of Darwinian Fundamentalists. I hope you appreciate the irony in the title.
I run Adobe Reader on about six different devices so I see that annoying "update required" notice far too often. I've just given in and updated to version 11.0.03 but when I went to the website I saw that you can download version 11.0.06. I assume that means I'm going to be prompted to update three more times in the near future.
None of the other programs I run are so flaky that that the manufacturer needs to issue updates on a regular basis. What's wrong with Adobe? Why can't they get it right after all these years?
I think I may know part of the answer. If you aren't careful when you update the Adobe software it will automatically install "McAffe Security Scan Plus" on your computer. This will screw up a lot of other programs so you must be sure to uncheck the box. I wonder if the purpose of these frequent "updates" isn't to sneak McAffee software on to your computer—and maybe some other things as well?
Oops! I almost forgot. Flash Player is also pretty bad software that needs frequent fixing. I wonder who makes it?
Stop bundling McAfee in Flash updater!
Why Adobe is recommending McAfee security scan during flash player installation?
Adobe Reader installing McAfee Security Scan Plus Scareware
Why does Adobe require DAILY updates? Are they just trying to push McAfee on everyone?
Adobe Please Stop Including Bloatware Like McAfee Security Scan and Toolbars With Free Downloads
Trust Nobody – Especially Adobe and McAfee
This YouTube video is described as "The most ignorant 82 seconds you'll ever see." I don't know about that. I been around IDiots for quite a long time. It may not be the "most ignorant" but it's surely in the top ten.
Remember, this is the best they've got. Really. Trust me on this.
Today is the last day of classes at the University of Toronto and I have to submit a copy of the final exam to the Examination Supervisor. Actually, I have to submit a copy for each student PLUS 11 extra copies AND the "original." They have to be in two separate sealed packages with specified labels on the outside.
There's a set of rules and regulations that must be followed, including specific formatting rules. Some of the rules make sense and some don't.
Rule #12 is interesting. Here's what it says ...
Instructors and departmental offices should take stringent measures to prevent unauthorized persons from having access to the examinations. NO COPY OF AN EXAMINATION IS TO BE KEPT IN THE DEPARTMENT BEFORE THE FINAL EXAMINATION IS WRITTEN. This applies to electronic storage as well as to flash drives/usb key and paper copies.
Those of you who know me well will be able to imagine how much effort I have taken to erase everything from my hard drive and the automated backup drive attached to my computers. They will understand exactly how difficult it was for me to check my flash drive to make sure that no copy of the exam was stored there or in dropbox. They'll also know just how scrupulous I've been about not having a copy of my exam anywhere in my files. They can imagine that I've stored a copy safely at home so I can print out a version the day after the exam is written and put if back on my desktop hard drive.
I wonder how many of my colleagues will follow this rule? What do you think the penalty is if you don't?
Thank the gods for bureaucrats.
The President of the University of Toronto recently published an article about undergraduate education. I questioned whether my university really is committed to the ideals of undergraduate education (critical thinking etc.) [Does the University of Toronto really care about undergraduate education?]. The answer, IMHO, is "no."
Now I want to bring up something else from the article by President Meric Gertler. It's not a major point—more like a motherhood throwaway line—but I think it raises an interesting question. Gertler said,
U of T reaffirms the value of a broad liberal arts education at the undergraduate level, and we are working to help our graduates extract the full benefit from that education.
I suppose there are as many definitions of "liberal arts education" as there are teachers but I think we can agree on a few points. A "liberal arts education" does not put much emphasis on math and science courses. In fact, I'm pretty sure that there are many who would be happy with a "liberal arts education" that didn't include a single math or science course.
I think that there are some extremely important humanities courses that every student should take. Philosophy (logic and reasoning) is the most obvious one but there's also history and maybe even sociology. I think university students should be familiar with great literature and many other topics in the humanities programs. But I also think that every single university student needs to take (and pass) some math and science courses in order to call themselves university-educated.
This is the 21st century. Surely we can agree that science is at least as important as "liberal arts"? Maybe we should be talking about a "broad science and humanities" education as the important value that we are trying to achieve?1
I'm not sure where that leaves the thousands of students who are getting degrees in commerce and business. Perhaps we should admit that those undergraduate programs, like engineering, are not really education programs. They are job training programs.
1. I'm not talking about "astronomy for poets" and other watered-down science courses. Humanities majors should take the same courses that science majors take just as science majors take the same courses that humanities students take.
My university, the University of Toronto (Toronto, Canada), is huge. We have 60,000 undergraduates making it one of the biggest universities in North America. You'd think that undergraduate education should be a very high priority.
The university publishes an online "newspaper" called the Bulletin every Tuesday and Thursday. It's basically a PR ploy to advertise everything that's great about the University of Toronto. There was a time in the past when the Bulletin had editorials that were critical of university practice and policies but I haven't seen anything like that in years.
The latest issue has a link to an article by the President of the University, Meric Gertler. The title of the article is: Job Ready: U of T is developing new programs to help students succeed after graduation. I want to discuss two things in that article. The first is whether the university really is committed to the goals of undergraduate education (this post). The second is What does "liberal arts education" mean in the 21st century?.
I was very upset when Vincent Torley suggested that I attributed all of the evolution of chimpanzees and humans to the fixation of nearly neutral alleles by random genetic drift. He tried to convince his audience that I was rejecting natural selection as a component of that evolution. I corrected him at: Breaking news: Creationist Vincent Torley lies and moves goalposts.
When he said, "Professor Moran’s view: 22.4 million neutral mutations were what made us human," I concluded that this was so ridiculous that it had to be a deliberate misrepresentation, i.e. a lie.
Later on in the post I admitted that there was another possibility, he may just be stupid and not a liar.
He has now posted an "update" on his original post: Can the neutral theory of evolution explain what makes us human?. Here's what he says ....
A couple of years ago I posted an article on How Did the Zebra Get Its Stripes?.
I pointed out that this wasn't a Rudyard Kipling story but that many of the explanations had strong ties to just-so stories. I noted that everyone just assumed that there had to be an adaptive explanation for zebra stripes so they kept looking and looking. Every time one of the adaptive explanations was ruled out, they invented another one.
The best explanation back in 2012 was that zebra stripes evolved to protect zebras from horseflies and there was some experimental support for the idea that horseflies tended to avoid stripes. However, there was no evidence that avoiding some horseflies actually conferred enough selective advantage to drive the evolution of stripes.
Now we have a press release that announces the final solution: Scientists solve the riddle of zebras' stripes.
Why zebras have black and white stripes is a question that has intrigued scientists and spectators for centuries. A research team led by the University of California, Davis, has now examined this riddle systematically. Their answer is published April 1 in the online journal Nature Communications.
The scientists found that biting flies, including horseflies and tsetse flies, are the evolutionary driver for zebra's stripes. Experimental work had previously shown that such flies tend to avoid black-and-white striped surfaces, but many other hypotheses for zebra stripes have been proposed since Alfred Russel Wallace and Charles Darwin debated the problem 120 years ago.
Sounds like old news to me. And I'm still not convinced that you need an adaptive explanation.
Here's the paper ...
Caro, T., Izzo, A., Reiner Jr, R.C., Walker, H. and Stankowich, T. (2014) The function of zebra stripes. Nature Communications 5, Article number: 3535 [doi: 10.1038/ncomms4535]
Despite over a century of interest, the function of zebra stripes has never been examined systematically. Here we match variation in striping of equid species and subspecies to geographic range overlap of environmental variables in multifactor models controlling for phylogeny to simultaneously test the five major explanations for this infamous colouration. For subspecies, there are significant associations between our proxy for tabanid biting fly annoyance and most striping measures (facial and neck stripe number, flank and rump striping, leg stripe intensity and shadow striping), and between belly stripe number and tsetse fly distribution, several of which are replicated at the species level. Conversely, there is no consistent support for camouflage, predator avoidance, heat management or social interaction hypotheses. Susceptibility to ectoparasite attack is discussed in relation to short coat hair, disease transmission and blood loss. A solution to the riddle of zebra stripes, discussed by Wallace and Darwin, is at hand.
I'm betting that in five years there will be papers examining the SIX major adaptive explanations and five of them will be ruled out in favor of the latest one.
Although all types of creationists are anti-science to some degree,1 the Intelligent Design Creationists are unusual because they don't just ignore science, they try to use science to show that science is wrong!
When dealing with the similarities between closely related species, they claim that the similarities (and differences) are due to design and not evolution. They claim that evolution cannot account for the differences between, say, humans and chimps. Only intelligent design can do that.
In an attempt2 to show them that evolution CAN account for the differences between humans and chimps/bonobos, I wrote up a description of how Neutral Theory and random genetic drift produce genomes that differ by 22 million positions if we take the fossil evidence at face value and assume that chimps and humans last shared a common ancestor about 5 million years ago [Why are the human and chimpanzee/bonobo genomes so similar?].
Apparently there are some creationists who are slightly embarrassed that they don't understand evolution. First, there was Vincent Torley who made an attempt to understand population genetics (from the 1920s and 1930s) and Neutral Theory, which is only 45 years old. You can read his attempt at: Fixation: the neutral theory’s Achilles’ heel?. See my attempt to correct his errors at: A creationist illustrates the argument from ignorance while trying to understand population genetics and Neutral Theory.
I appear to have been partially successful because if you scroll down to the bottom of Vincent Torley's post you'll see an "update" that pretty much refutes his entire post.
The comments on Torley's post reveal that there are very few creationists who have ever heard of population genetics and Neutral Theory. Now that they've been exposed, their response is to reject it because they don't understand it. Salvador Cordova (scordova) pops up in those comments to explain that modern evolutionary theory is all wrong because of "unfixing." Apparently, evolutionary biologists have missed something important that only creationists can see. This happens a lot.
Sal is so proud of himself that he puts up another post at Uncommon Descent: Fixation rate, what about breaking rate?. One gets the impression that some of the creationists are a bit worried.
The irony is that the vast majority of creationists will have absolutely no idea what Cordova is talking about. To them, it's like he's speaking gibberish. In this case, it means that the average IDiot isn't even posting comments under Cordova's post because they don't know what to say. This is all news to them.
So, what is the great discovery that refutes population genetics and Neutral Theory? It's got something to do with the idea that for neutral alleles the rate of fixation is equal to the mutation rate. Cordova agrees with the math but thinks it is "flawed from a functional standpoint." Why? Because ...
Ok, so let’s do an experiment. Let’s subject bacteria or plants or any organism to radiation and thus increase the mutation rate mutation rate by a factor of 1 million or 1 billion. Do you think the above formula will still hold? We tried it in the lab, it killed the plants, and at some point rather than speeding evolution we are doing sterilization.
Cordova is correct. An organism will die if you subject it to massive amounts of radiation. This blast doesn't have much to do with mutation rate but later on Cordova comes closer to a serious discussion of evolutionary theory.
Here's what upsets him ...
... even with moderate rates of mutation per individual per generation, genetic deterioration will happen. Further, this claim is reinforced by the work of Nobel Prize winner Hermann Muller who said a deleterious mutation rate of even 0.5 per individual per generation would be sufficient to eventually terminate humanity. So the simple model I present is actually more generous than Muller’s. Current estimates of the number of bad mutations are well over 1.0 per human per individual. There could be hundreds, perhaps thousands of bad mutations per individual per generation according to John Sanford. Larry Moran estimates 56-160 mutations per individual per generation. Using Larry’s low figure of 56 and generously granting that only about 11% of those are bad, we end up with 6 bad mutation per individual per generation, 6 times more than the cartoon model presented, and 12 times more than Muller’s figure that ensures the eventual end of the human race.
He's talking about genetic load although he goes out of his way to avoid using that term.
Sal Cordova is correct that if the deleterious mutation rate is too high, the species will go extinct. We don't know the exact minimum number of deleterious mutations that have to happen per generation in order to cause a problem. It's probably less than two (2). It's probably not as low as 0.5. It should be no more than 1 or 2 deleterious mutations per generation.
Genetic load arguments have been around for over forty years [Non-Darwinian Evolution in 1969: The Case for Junk DNA]. Back then, they were used to explain that most of our genome is junk and mutations in that part of the genome have no effect. We now know that those arguments were correct and 90% of our genome is junk.
Imagine that there are 130 new mutations per generation. Since only 10% of our genome is functional DNA, this means that only 13 of these mutations occur in DNA that has a biological function. We know that in a typical coding region about 25% of all mutations are seriously detrimental so if all the functional region of the genome were coding region that would mean 3.25 detrimental mutations per generation.1 However, less than 2% of our genome encodes protein. The remaining functional regions are much less constrained so they can tolerate more mutations. It's likely that there are fewer than 2 detrimental mutations per generation and this is an acceptable genetic load.
All of this information is readily available in textbooks and scientific papers. It's basic evolutionary theory and facts about the human genome.
Cordova is correct to raise the point about genetic load but he is quite wrong in his calculation.
Still, we seem to be making a bit of progress because at least the creationists are talking about evolutionary theory from the 100 years after Darwin died.
Better late than never. Now all they have to do is get the facts right and they'll be ready to move into the 21st century.
Lynch, M. (2010) Rate, molecular spectrum, and consequences of human mutation. Proceedings of the National Academy of Sciences 107, 961-968. [doi: 10.1073/pnas.0912629107]
Keightley, P.D. (2012) Rates and fitness consequences of new mutations in humans. Genetics 190, 295-304. [doi: 10.1534/genetics.111.134668]
Kondrashov, A.S. (2002) Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Human mutation 21, 12-27. [doi: 10.1002/humu.10147]
1. Estimates of the percentage of deleterious mutations in coding regions are all over the map. I figure that most distantly related genes are only 30% identical in amino acid sequence. Some mutations in the conserved amino acid codons will be synonymous. But even if this value is 50% instead of 25%, the total number of deleterious mutations in coding regions would only be 50% × 2% × 130 = 1.3 deleterious mutations.
I know I've said this before, but I continue to be astonished at the ignorance of creationists. Those who oppose evolution most vehemently don't understand it in spite of the fact that they are convinced it has to be wrong.
This is most obvious with the Intelligent Design Creationists because they like to use science-sounding jargon to convince us that they know what they are talking about. They claim that they can refute evolutionary biology using scientific evidence. Instead they just reveal their ignorance.
They've been doing it for decades in spite of the fact that many people have tried to educate them. I don't get it.
Recently, I tried to explain how the difference between the chimpanzee and human genomes is consistent with what we know about population genetics, mutation rates, and Neutral Theory. I was aware of the fact that this stuff would all be news to most Intelligent Design Creationists but it was still an opportunity to try, once again, to teach them about modern evolutionary theory.
Last week's molecule [Monday's Molecule #234] was insect juvenile hormone. The winners are Frank Schmidt and Raul Félix de Sousa (still an undergraduate?). They live in foreign countries so they won't be coming to lunch.
This week's molecule (right) is very common. You have to identify the entire molecule including the specific polynucleotide. Emphasis is on the word "specific"—there's only one possibility. I'm betting that there won't be very many correct answers for this one.
Email your answer to me at: Monday's Molecule #235. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.
There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)
God's not dead is a movie that's gaining some notoriety in the USA. Here's a synopsis ...
Present-day college freshman and devout Christian, Josh Wheaton (Shane Harper), finds his faith challenged on his first day of Philosophy class by the dogmatic and argumentative Professor Radisson (Kevin Sorbo). Radisson assigns him a daunting task: if Josh will not admit that "God Is Dead," he must prove God's existence by presenting well-researched, intellectual arguments and evidence over the course of the semester, and engage Radisson in a head-to-head debate in front of the class. GOD'S NOT DEAD weaves together multiple stories of faith, doubt and disbelief, culminating in a dramatic call to action.
I haven't seen the movie (yet) but I'm guessing that the 18 year-old Christian student wins the debate against his "dogmatic" professor.
This sort of thing happens quite a bit in the movies. It's pretty rare to find a university professor portrayed as a good person, or even a smart person who knows their stuff. If you are one of those university students who watch the movie and are convinced that you can win a debate with a professor on the subject "Do gods exist?" then please contact me and we'll set up a time and place for you to make the attempt. I'm pretty sure I can find a smart professor at most major universities.
Yesterday afternoon I attended a forum on Science and Mathematics teaching in Ontario schools. It was put on by The Centre for Science, Mathematics and Technology (SMT) Education at the Ontario Institute for Studies in Education (OISE) at the University of Toronto (Toronto, Canada).
OISE is one of the places responsible for training teachers in Ontario. It offers advanced degrees (Masters. Ph.D.) in education. I thought this might be a good opportunity to network with the people responsible for teaching science in our high schools.
Here's a description of the forum ...
The Canadian Secular Alliance is hosting a talk by Lauren Forbes tomorrow evening in rm 4171 of the Medical Sciences Building at the University of Toronto. (My building, one floor below my office.) Contact me if you want to meet up before the talk.
It's important to note that Ms. Forbes is going to DEFEND things like prayer at city council meetings. Come out and hear the other side of the issue. She is a Master's student at the University of Ottawa.
Read her article: To Pray or Not to Pray, is that the Question?: How the Increasing Desire for State Neutrality Affects Prayer Before Council Meetings in Canada. Here's the abstract ...
Historically, in western liberal democratic states, Christian prayers have often been recited at the opening of various public institutions' meetings. However, the recitation of such prayers is now being questioned on the grounds of being too particular in promoting specific religious denominations; of promoting a particular religion over another; and even of promoting religion in states where no longer everyone subscribes to one. Many such disputes spring from the growing desire for equality and neutrality in increasingly diverse and secular societies. This paper focuses on the recent legal disputes in Canada, concerning the recitation of prayers before the commencement of primarily council meetings. It examines Canadian tenets of neutrality and consequently secularism, questioning what each looks like (or could look like) and whether they require public spaces to be religion-free in order to hold true, or whether they can be inclusive to both religious and worldviews of non-belief in these public spaces (i. e. council meetings in this context). In this paper the relevant legal cases are analyzed and current solutions to the disputes are discussed. Concerns are raised and finally, solutions that may be more neutral and that equally do justice to both freedom of religion and freedom of conscience are considered.
I stole this from Ms. Sandwalk's blog. I'm pretty sure she'll mind.
Several students in my class decided to write essays on epigenetics. This was very brave of them since nobody seems to have a good definition of epigenetics and much of the hype about epigenetics is not very scientific. I'm also more than a little skeptical about some of the claims that have been made.
Here's a video. What do you think? Is this a useful contribution to our understanding of a complex issue? Is the inheritance of methylation sites at restriction/modification loci in bacteria an example of epigenetics? After E. coli divides, both cells inherit some lac repressor molecules and the lac operon is not expressed provided the parent wasn't exposed to lactose. Is this epigenetics?
Last week's molecules [Monday's Molecule #233] were oxaloacetate, ethanol, lactate, alanine, and acetyl-CoA. All of them can be synthesized in a reaction using pyruvate as a substrate (two steps to make ethanol). All of them are precursors to pyruvate and hence glucose. The winner is Jean-Marc Neuhaus. I will be buying him four meals next time I visit Switzerland. I'm thinking it will be two raclettes and two fondues with lots of wine.
This week's molecule (left) is probably not very familiar to most of you so I don't anticipate many correct answers. You can use the common name. Email your answer to me at: Monday's Molecule #234. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.
There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)
Today is the 40th anniversary of my Ph.D. oral defense.1 The event took place in the Department of Biochemical Sciences at Princeton University back in 1974.
It began with a departmental seminar. When the seminar was over I retired with my committee to a small classroom for the oral exam.
I don't remember everyone who was on my committee. My Ph.D. supervisor (Bruce Alberts) was there, as was my second reader, Abe Worcel. I know Uli Laemmli was there and so was Arnie Levine. I'm pretty sure the external member of the committee was Nancy Nossal from NIH in Bethesda, MD (USA). It's a bit of a blur after all these years.
I remember being fairly confident about the exam. After five and a half years I was pretty sure that everyone on my committee wanted to get rid of me and the easiest way to do that was to let me pass. Bruce stood to gain $3000 per year of research money and Uli was going to get back the basement of his house where Ms. Sandwalk and I had been living for the past month.
The toughest questions were from Uli Laemmli, which should not come as a surprise to anyone who knows him. He has this annoying habit of expecting people to understand the basic physics and chemistry behind the biochemical sciences. Fortunately, my inability to answer most of his questions didn't deter him from voting to pass me.
This photograph was taken at a party that evening. I look pretty calm at that point but this may have had a lot to do with the various refreshments that were being served.
The amazing thing about the photograph—as I'm sure you all agree—is how little I've changed since then—apart from a haircut.
Back in those days we didn't spend a lot of time writing a thesis. I started in the middle of January and the entire process of writing and defending took nine weeks. My thesis was bound and delivered to the library about one week after the Ph.D. oral.
The second page of my thesis has only three words on it. It says, "To Leslie Jane." This is Ms. Sandwalk. She really should have her name on the cover 'cause I couldn't have graduated without her. Typing my thesis was only one of her many contributions. There are 257 pages in my thesis and she typed every one. As a matter of fact, she typed them twice, one draft and then the final version.
The figures in my thesis were all hand drawn. I've included one (below) to illustrate what I was doing during those five and a half years.
The Alberts lab was interested in DNA replication during bacteriophage T4 infections of E. coli. We knew that replication was carried out by a complex protein machine that assembled at a replication fork but we didn't know all the players or what they did.
The T4 proteins required for DNA replication were known from genetic studies. The most important genes were genes 30 (ligase), 32 (single-stand DNA binding protein), 41, 43 (DNA polymerase), 44, 45, and 62. The products of the unknown genes were called 41P, 44P, 45P and 62P.
We wanted to purify and characterize those proteins; my target was the product of gene 41, or 41P.
We had a cool assay, developed mostly by a postdoc in the lab named Jack Berry. What we did was to prepare a cell lysate from cells that had been infected by bacteriophage carrying an amber mutation in one of the genes. This lysate could not support DNA synthesis, as measured by incorporation of 32P nucleotides, unless we added back the missing component. This is the basis of an in vitro complementation assay that worked for each of the unknown proteins.
In my case, I used traditional protein purification methods to isolate fractions of proteins and them tested them for activity in the complementation assay. The figure below shows the elution profile of proteins bound to a hydroxylapatite column. The peak centered on fraction 61 is the activity of the complementation assay. It indicates that 41P elutes early as a sharp peak in the elution profile.
The complementation assay doesn't tell us anything about the function of 41-protein, only that it complements an extract that's deficient in 41P. Strictly speaking, it doesn't even tell us that the activity is due to the product of gene 41 since it could be something else that complements in vitro.
Fortunately we had another way of identifying 41P. I started my purification with extracts from 17 liters of infected cells. To this I added extracts from cells that had been labeled with radiaoctive amino acids. One batch was from a wild-type infection where all T4 proteins are labeled with 14C amino acids. The other batch is from an infection with an amber mutation in gene 41. In this case every protein except 41P is labeled with 3H amino acids.
You can adjust the settings on a scintillation counter so they distinguish between 14C and 3H but there's some overlap. The equations for calculating the contribution of each isotope in each window are relatively simple. All you need are good standards to get the distribution. One of the most fun things I did as a graduate student was to write a computer program (in Fortran) that did these calculations automatically and plotted them on a plotter. This was back in the time when computers were housed in large separate buildings and required dozens of people to look after them.
If you look of the elution profile in the figure you'll see there's an excess of 14C over 3H in the same fractions where the complementation activity is located. What this means is that the wild-type extract has a protein at that position that's not found in the am41 extract. It's another way of identifying the product of gene 41.
The double label technique was useful 35 years ago but nobody does it anymore. It was fun while it lasted.
(I never did figure out what 41P did during DNA replication but a few years after I left a postdoc identified 41P as a helicase—an enzyme that unwinds DNA ahead of the replication fork. The enzyme is now called gp41 for "gene product.")
1. This post is an almost identical copy of one that was posted five years ago. You'll probably see another in 2019, and especially 2024.
The genomes of chimpanzees and bonobos are remarkably similar to the human genome. In terms of sequence similarity, they are more than 98% identical in the regions that can be aligned. This, of course, is due to the fact that they descend from a common ancestor in the recent past (about 5 million years ago).
Intelligent Design Creationists don't agree. Many of them do not accent common descent and macroevolution so they make up stories that account for the similarity based on what they think god might have been thinking when he created chimps and humans.
But the scientific evidence for evolution is much stronger than just overall sequence similarity. The number of differences (about 50 million substitutions) corresponds pretty closely with what we expect from evolutionary theory (population genetics) and known mutation rates [Why are the human and chimpanzee/bonobo genomes so similar?]. If the Intelligent Design Creationists are going to dismiss this confirmation of evolutionary theory then they are going to have to be much more inventive.
Intelligent Design Creationism is a huge tent that shelters all sorts of creationists ranging from Young Earth Creationists to those who could be called Theistic Evolution Creationists.1 Many of them accept common descent so they clearly don't have much of a problem with most of macroevolution.
On the other hand, there are a lot of Intelligent Design Creationists who don't accept macroevolution. It seems to me that this could only be because they are Young Earth Creationists or they believe in some other strange idea where god(s) make every species.
It's hard to figure out what they mean.
Let's look at a recent post by philosopher Vincent Torley. He didn't like my posts about macroevolution [What is "macroevolution"? ] [A chemist who doesn't understand evolution] so he decided to set me straight: Does Professor Larry Moran (or anyone else) understand macroevolution?.
The second episode of the new Cosmos series is Some of the Things That Molecules Do.
It's about evolution and it's not bad. I have four comments.
A missed opportunity. Natural selection is important and Neil deGrasse Tyson did a pretty good job of explaining it. It wouldn't have taken a big effort to mention that there's more to evolution than natural selection. He could, for example, have pointed out that some breeds of dogs are prone to certain genetic diseases or health problems because some bad mutations were accidentally fixed alone with the good ones. He could have pointed out that our eyes have a blind spot.
The Theory of Evolution is not a fact. Neil deGrasse Tyson said that the theory of evolution is a fact. This is not correct. Evolution is a fact. Evolutionary theory attempts to explain how evolution occurs. Some of the explanations, like natural selection, are facts but many aspects of modern evolutionary theory are still hotly debated in the scientific community.
We don't understand the origin of life. The episode closed with deGrasse Tyson saying the we don't understand how life began and there's nothing wrong with admitting that we don't know something. Excellent!
There are better ways of drawing DNA. I don't like the way DNA is pictured in the first two episodes, especially in the opening sequence. It looks like the bases grow out of the backbone and fuse to form base pairs. They could have drawn a more accurate representation without losing any visual appeal.
I give the episode a B+.
The winner is Philip Johnson from Switzerland.
This week's molecule (left) is actually a collection of molecules. Name all five molecules and tell me what they have in common from a biochemical perspective. Common names will do.
Email your answer to me at: Monday's Molecule #233. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.
There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)
Yesterday we watched two episodes of House of Cards and two of our favorite TV shows; Amazing Race and The Good Wife. We also watched a show about working on a Tudor farm and I watched the second episode of Cosmos.
According to Veronica Abbas, I wasted valuable time when I could have been reading [Recommended Reading]. She links to an article by Erin Kelley who says, Reading Books Doesn't Just Make You Literate: It Reduces Stress, Promotes Good Health, and Makes You More Empathetic. I haven't read a book in over four months and I haven't read a novel in years.
I'm doomed to be illiterate, stressed, in poor health, and the opposite of empathetic.1 It also explains why I don't volunteer to work for a non-profit organization.
1. I'm pretty sure Veronica would agree with "illiterate."
I think that universities are places where diversity of opinion should be encouraged and where fringe ideas should be protected. I'm very much opposed to letting outside interests (i.e. politicians and lawyers) decide what should and should not be taught on a university campus.
Clearly there are limits but those should be decided by faculty who understand the concept of academic freedom. It's not a good idea to offer astronomy courses on an Earth-centered solar system or geology courses based on the idea that the Earth is only 6000 years old. Those ideas are just too far out on the fringe. You're unlikely to find any university professors who want to teach such courses.
However, there are lots of other controversies that aren't so easily dismissed. If some of the more enlightened Intelligent Design Creationists want to teach a science course at my university, I would not try to prevent them. Just as I didn't try to prevent Michael Behe and Bill Dembski from speaking on my campus.
James Tour is an organic chemist. He is a Professor of Chemistry and Professor, Professor of Mechanical Engineering & Materials Science, and Professor of Computer Science at Rice University (Houston, United States). James Tour is attracting a lot of attention on the Intelligent Design Creationist websites because he is sympathetic to their main claim; namely, that evolution is wrong [see A world-famous chemist tells the truth: there’s no scientist alive today who understands macroevolution].
Tour is one of the few genuine scientists who signed the Discovery Institute’s "A Scientific Dissent from Darwinism" (2001) that stated, "We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged." (There are very,very, few biologists who signed.)
What exactly, does Jame Tour mean? He wrote an article on his website that explains his position: Layman’s Reflections on Evolution and Creation. An Insider’s View of the Academy. I think it's interesting to discuss what he said.
He begins with ...
It's been almost a year since I commented on an Nature article by Philip Ball [see DNA: Nature Celebrates Ignorance]. Here's part of what I wrote back then ...
The main premise of the article is revealed in the short blurb under the title: "On the 60th anniversary of the double helix, we should admit that we don't fully understand how evolution works at the molecular level, suggests Philip Ball."
What nonsense! We understand a great deal about how evolution works at the molecular level.
The worst thing about the Nature article was the misuse of the Central Dogma of Molecular Biology. The second worst thing was the "revelation" that genes are regulated by regulatory sequences as if that was a new discovery. (He mentions the ENCODE results.)
I think the hardened version of the Modern Synthesis is inadequate to describe 21st century evolutionary biology. I think that it didn't adequately recognize Neutral Theory and random genetic drift and it didn't place enough emphasis on macroevolution and the possibility of hierarchical modes of evolution.
There are a whole host of scientists who want to overthrow the Modern Synthesis for a variety of other (stupid) reasons. Most of them have no idea that the Modern Synthesis has (or should have) been replaced 40 years ago.
Here's another example from last week's issue Science (March 7, 2014). Susan M. Rosenberg and Christine Queitsch have an article entitled "Combating Evolution
to Fight Disease" (Rosenberg and Queitsch, 2014). They begin with ....
The war between science and religion is fought on many fronts. One of the most remarkable campaigns is the attempt by religious zealots to discredit evolution (and science). We see this played out on creationist websites ranging from the most absurd Young Earth Creationist sites to the somewhat more subtle websites of the Intelligent Design Creationists.1
I can understand why believers want to defend their beliefs—we all do that. The part I don't get is the incredible stupidity of the main defenders of Intelligent Design Creationism and Young Earth Creationism. Not all of them, of course, but enough to make me slap my head.
Let's take Michael Egnor as an example. He is perfectly entitled to defend his Roman Catholic beliefs and to try and poke holes in evolution. But why does he have to use such stupid arguments? Why is such a person promoted on the main Intelligent Design Creationist website, Evolution News & Views (sic). Is he really the best they've got?
Let's look at his latest post: Clueless in Toronto. He begins with ....
