Vincent Torley was initially very skeptical when I described the differences between human and chimpanzee genomes and explained that those differences could be accounted for by evolution. He didn't want to believe that was true because it didn't fit into his views of how humans came to be.
After resisting for a week or so, he finally came to the realization that what the scientists are saying is correct [When I’m wrong].
Professor Moran and I disagree on many things, and I’m sure we’ll have many lively exchanges in the future, but it would be downright churlish of me not to acknowledge that my attempts to show that the neutral theory could not account for 22.4 million mutations arising in the human lineage over the last five million years have failed. I also wish to state that I had no intention of giving any offense to Professor Moran in our exchange of views, and that I have always striven to remain as polite as possible, while publicly disagreeing with him. The next time I’m dining out, I shall order a glass of red wine and silently toast him.
Thank-you Vincent Torley. I greatly respect you for taking the time to understand evolution and to listen to the explanations of evolutionary biologists.
I think you can see how your initial biases affected your ability to understand evolution. That's why you tried so hard to prove that population genetics was wrong when you didn't understand it and had only heard of the explanation for the first time a few days earlier.
Now Torley wants to address a different point. He wants to show us that creationists are more open-minded and less biased than evolutionary biologists [A question of bias].
In today’s post, I’d like to explain why I believe that evolutionary biologists who regard evolution as an unguided process are more ideologically biased than people who believe that God made us – whether through a process of (a) direct creation or (b) guided evolution. The distinction between the latter two positions is totally irrelevant, from Professor Moran’s perspective ...
It's a long post. Torley describes seven different arguments in support of his position.
Lawyer Barry Arrington has posted a link to an article that compares scores on standardized tests (LSAT) with undergraduate discipline. It also looked at university GPA. That article is: The best prospective law students read Homer. Look at the chart below.
It's not a big shock to see that the average GPA of religion and classics students is higher than that of biology and engineering students (Y-axis). It's interesting that students specializing in biology perform slightly better than religion students on the LSAT (X-axis) but these differences aren't very significant.
Barry Arrington thinks they are significant. His post at Biology Students Score Below Religion and Classics Students on Test of Critical Thinking makes the following claim ...
One wonders why biology students do so poorly while classics and religion students do so well. One hypothesis: classics and religion students learn critical thinking skills while biology students are taught to parrot the central dogma. The chart is from a study of which undergraduate majors correlated most highly with success on the LSAT.
Barry is making the false assumption that scores on the LSAT correlate with the ability to think critically. I suppose it's natural for a lawyer to think like this.
My experience indicates that one of the serious downsides to teaching critical thinking is that it hurts the students' chances of doing well on standardized tests such as the LSAT, MCAT, and GRE. Those tests are usually set up to encourage memorization and regurgitation even though some of the questions look like "think" questions. That's why I tell students to always give the standard, expected, answer on the MCAT even if they know it's wrong or misleading.
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.
