Saturday, April 19, 2014

Core concepts in genetics

I stumbled across an article in Science & Education that caught my eye. The authors discuss the way genetics is taught in introductory university courses (McElhinny et al. 2014). They quote several sources that define the core concepts of genetics that students must learn.

Here's the list ...
  1. DNA is the universal information molecule in living organisms, encoding genes and allowing for genetic variation within and genetic continuity between generations (DNA);
  2. Mendelian patterns of inheritance are directly related to the mechanisms of meiosis (MENDELIAN);
  3. Traits result from the expression of one or more genes working alone or together, with the environment, often in unpredictable ways (GENE EXPRESSION);
  4. The activities of genes and the environment regulate all developmental processes (GENES + ENVIRONMENT);
  5. Genetic variation underlies variation in traits, which is the basis for the differential survival and reproduction that allow populations to evolve (VARIATION); and
  6. The ability to analyze and manipulate genetic information raises a variety of complex issues for individuals and society (GENES + SOCIETY).
These six concepts for genetic literacy will hereafter be referred to as the core genetics concepts.
This is a strange list. Let me explain why.
  1. The structure of DNA and how it is expressed should be covered in other mandatory courses, including introductory biology and biochemistry. You should not have to spend any time at all on these topics in a genetics course. (P.S. DNA does not "encode genes.") You may want to spend some time on the biochemistry of recombination if it's not covered elsewhere. Students should understand Holliday junctions and how they are resolved.
  2. Mendelian genetics is important. Students should learn and understand the three laws he discovered. They should also learn about meiosis and sex. However, it's important for students to understand that simple transmission genetics is not limited to diploid eukaryotes. Bacteria also do genetics.
  3. Traits (phenotype) are due to information in DNA (not just genes) but most of those traits have very little to do with the external environment.
  4. Of course the activities of genes regulate development. They also regulate the citric acid cycle, photosynthesis, and protein synthesis. Surely you don't want undergraduates to think that development is the only thing that's important in genetics?
  5. It's important for students to understand that populations contain genetic variation. That means they have to learn about MUTATION and how it happens. They also have to learn why there's so much variation in populations—one of the most important discoveries in genetics in the last century. The answer is Neutral Theory and random genetic drift. No genetics course should leave out this important concept, especially because so few students will have never heard of it before enrolling in the course.
  6. Discussions about cloning, GM foods, and personal genomes are interesting but, unfortunately, there are very few scientists who can handle those issues in a genetics course. The important core concept is to get the science right and make sure students understand that getting the science right is absolutely essential whenever you discuss controversial issues.
  7. POPULATION GENETICS is an essential core concept in an introductory genetics course. You can't teach students about the genetics of EVOLUTION without it.
The authors discovered that only the first three "core concepts" were taught in every genetics course. Variation and mutation were taught in only 88% of the courses they surveyed. Only 63% covered GENES + ENVIRONMENT and only 9% covered GENES + SOCIETY.

McElhinn et al. (2014) discuss one possible change in the curriculum. It's a suggestion originally made by Dougherty (2009) and echoed by Redfield (2012). The idea is to "invert" genetics courses by beginning with coverage of poplations, variation, and complex traits. I strongly disagree with Rosie Redfield's proposal [see Questions for Genetics Students] but what surprises me in the McElhinny et al (2014) paper is that they can seriously list those core concepts without mentioning mutation and population genetics.


McElhinny, T.L., Dougherty, M.J., Bowling, B.V., and Libarkin, J.C. (2014) The Status of Genetics Curriculum in Higher Education in the United States: Goals and Assessment. Science and Education 23:445-464.
[doi: 10.1007/s11191-012-9566-1]

Redfield, R. J. (2012) "Why do we have to learn this stuff?’’—A new genetics for 21st century students. PLoS Biology, 10, e1001356 [doi: 10.1371/journal.pbio.1001356]

Branko Kozulic responds: Part II

Branko Kozulic has asked me to post some additional comments. I'm happy to do so since it reflects a sincere attempt to learn about evolution and come to grips with the concepts of neutral alleles and random genetic drift. We should encourage the creationists to continue this effort whenever possible.

As usual, my policy is not to comment on posts from guests, especially those that disagree with my views. So here's Branko Kozulic's latest take on the "evidence" as he see it.
I thank Professor Moran for posting my text.

This reply to the comments has grown in size much more than initially anticipated. At the outset, to prevent misunderstandings, I declare my complete ignorance of paleontology and, in general, that my ignorance is by far larger than my knowledge. And I am prepared to repeat this as many times as the readers are willing to read it.

From this discussion up to date, it seems that we do not have a simple model that could show the fixation of 22,000,000 mutations. And that no simple model will work becomes evident, for example, with just a glance at the Beerli & Felsenstein paper.

The referring of our colleague McBride to the Li & Durbin paper provides an opportunity to touch upon two other topics. In addition to the Li & Durbin article, I have carefully read also the paper by Gronau et al., dealing with the same topic. Both research groups started with the data derived from the sequenced genomes of several humans (7 and 6, respectively) from various sub-populations, with the goal of illuminating past fluctuations of the effective population size. Both groups arrived at similar results: thus the first paper reports for the Yoruba population the Ne of 15,313 ± 559, while the second paper gives the range of 7,500 to 10,500. Given this congruence of the results and the quality of the journals in which the results are published, I have no doubts about correctness of the results: I trust in internal consistency of these results. But they depend on certain starting assumptions, like all other results that are an outcome of scientific models. Now it´s time to look closer at the starting assumptions of these models because there is an external inconsistency – with another set of experimental data – as will become apparent in view of other three papers.

Figure 1 of Nielsen et al., paper shows multiple (up to 21) synonymous and non-synonymous substitutions in thousands of chimp proteins compared to the related human proteins. In the second paper Behe & Snoke conclude that in order to generate a new function that requires mutations of two amino acids, like forming a disulfide bridge, 108 generations are needed with a population size of at least 109. In the third paper, Lynch countered that much smaller populations could reach this goal in less time. Now, if we take the human population size from the above two studies (Ne about 104) for the population size in Figure 3 of the Lynch article, we can see that it would take 108 generations for the arrival of a new function, even if the two changed amino acid were any 2 of 50 (with a high s = 0.01). For humans, 108 generations mean 2 Billion years: an impossibly long period. Needless to say, a new function requiring 3, 4 … up to 21 amino acid changes would take much longer than 108 generations. And yet there about 3,000 proteins with 3 amino acid substitutions, over 1,000 proteins with 5 substitutions, etc. A contradiction is thus evident between the experimental data on the one side and the Lynch model plus Li & Durbin and Gronau et al., modeled results on the other, by a wide margin. Therefore, either the starting assumptions of the Lynch model, or of the human population size models, or of both, are false.

Furthermore, we should not lose sight of singletons/orphans found in all sequenced genomes. Population genetics – which deals with changes of allele frequencies in populations – necessarily will remain “agnostic” in relation to the singletons: they are, simply put, beyond its horizon.

Some of the comments referred to religious implications. I deny the existence of direct contact between scientific conclusions and religion. In my view, each particular scientific conclusions must pass through the filter of philosophy and exit at the other side as part of a general statement (universal); then universals are incorporated into a philosophical system, and that philosophical system may or may not be in accordance with philosophy (or theology) of a religion. The only level at which the implications of scientific conclusions can be meaningfully discussed is the philosophical level, in my opinion.

Allow me to conclude with additional philosophical thoughts. Science is no democracy, but a dictatorship. A dictatorship of experimental data: and only of experimental data. Can a scientist ignore the experimental data that contradict his favorite theory without betraying his vocation of scientist? I do not think so.

Moreover, I do not expect other scientists to provide answers to all my questions; nor can I answer all their questions: this is the normal state of affairs.

I wish to extend my thanks to all participants, especially Professor Felsenstein, for their courtesy shown during this discussion.
Beerli, P. and Felsenstein, J. (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natl, Acad. Sci. (USA) 98:4563–4568. [doi:10.1073/pnas.081068098]

Behe, M.J. and Snoke, D.W. (2009) Simulating evolution by gene duplication of protein features that require multiple amino acid residues. Protein Science 13:2651–2664. [doi: 10.1110/ps.04802904]

Gronau, I., Hubisz, M.J., Gulko, B., Danko, C.G., and Siepel, A. (2011) Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics 43:1031–1034. [doi: 10.1038/ng.937]

Li, H. and Durbin, R. (2011) Inference of human population history from individual whole-genome sequences. Nature 475:493–496. [doi: 10.1038/nature10231]

Lynch, M. (2009) Simple evolutionary pathways to complex proteins. Protein Science 14:2217–2225. [doi: 10.1110/ps.041171805]

Nielsen, R., Bustamante, C., Clark, A.G., Glanowski, S., Sackton, T.B., Hubisz, M.J., Fledel-Alon, A., Tanenbaum, D.M., Civello, D., White, T.J., Sninsky, J.J., Adams, M.D., and Cargill, M. (2005) A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees. PLoS Biology doi: 10.1371/journal.pbio.0030170


Thursday, April 17, 2014

Branko Kozulic responds

Branko Kozulic has asked me to post his reply to Branko Kozulic has questions about fixation. My policy is to post letters like this without comment. We can discuss it in the comments.

I think it's an excellent example of the difficulties that many creationists will face when they try to come to grips with modern evolutionary biology.

Here's what he wants to say ...
Since Professor Moran has kindly addressed the questions I have raised, I feel obliged to respond here. But I must add that my response will be restricted to one topic only, and therefore this reply should not be construed to have the same purpose as the earlier discussion.

I find only a few minor contentious issues in Professor Moran´s post, so I prefer not to bother the readers with details about them. In my opinion, it is important that we have started to look at the core issue – the average fixation of about 100 mutations per generation, or 22,000,000 in 5,000,000 years, according to the genetic drift model - in terms of close to real-life conditions. Now we see that the simple genetic drift model needs extension, to include population splitting and recombining that leads to the postponement of fixation (I thank Professor Felsenstein for improving the clarity of this point). Furthermore, we see that in expanding populations the fixation rate is lower than the average. Thus, in today´s human population, the fixation rate per generation is close to zero. In order to compensate for the lower than the average fixation rates in some generations, it is necessary to postulate higher than the average fixation rates in other generations, if one wishes to account for the 22,000,000 fixed mutations in 5,000,000 years.

Let us consider the most dramatic case, mentioned in the comments, leading to the maximal fixation rate: the shrinking of a whole population to just a single couple, 2Ne = 2. Today we know that two unrelated human individuals differ in 1 nucleotide per about 1,000 nucleotides, so that each one of us carries about 3,000,000 SNPs. This is the maximal number (actually the maximal number is smaller because a fraction of SNPs is always in the heterozygous state) that can be fixed in this dramatic case. An interesting thing comes out to light now: the average of 100 fixed mutations per generation may result from the values that span a range of over six orders of magnitude, from less than 1, to over 1,000,000.

This raises the question of the meaning of the term “genetic drift model”. Can we maintain to be talking about the genetic drift model if the essential postulate of that model – mutation rate equals fixation rate – does not hold, because while the mutation rate changes little, the fixation rate can vary over six orders of magnitude? I think not. Drastic scenarios, known as “bottlenecks”, do not belong to the genetic drift model, in my opinion.

Now the important question is this: During the 5,000,000 years, what is the number of mutations that would have been “delayed to fix” because of the expansion of the human population, and/or due to the splitting-recombining, so that we must postulate dramatic events (“bottlenecks”) to account for their fixation? In other words, how many mutations were fixed in “bottlenecks” and how many by the ordinary course of genetic drift, in percentage? I doubt anyone can provide a verifiable answer (I kindly ask Professor Felsenstein to correct me if I am wrong). If for a “bottleneck” we take 2Ne significantly larger than 2, then many more “bottlenecks” need to be postulated in order to account for the same number of “delayed to fix” mutations. Is it possible to account for all the fixed synonymous mutations found in the human and chimp genomes by invoking fewer than two “bottlenecks” with 2Ne = 2? So that only 6 Million mutations are fixed in the “bottlenecks”, while 16 Million are fixed by genetic drift? I do not know.

And here is an additional complication. According to Wikipedia (since Professor Moran has relied on that source in his post, I follow suit):
Early humans (before Homo sapiens)

Early members of the Homo genus, i.e. Homo ergaster, Homo erectus and Homo heidelbergensis, migrated from Africa during the Early Pleistocene, possibly as a result of the operation of the Saharan pump, around 1.9 million years ago, and dispersed throughout most of the Old World, reaching as far as Southeast Asia. The date of original dispersal beyond Africa virtually coincides with the appearance of Homo ergaster in the fossil record, and the associated first emergence of full bipedalism, and about half a million years after the appearance of the Homo genus itself and the first stone tools of the Oldowan industry. Key sites for this early migration out of Africa are Riwat in Pakistan (1.9 Mya), Ubeidiya in the Levant (1.5 Mya) and Dmanisi in the Caucasus (1.7 Mya).
If correct, this information means that the time available for fixation of 22,000,000 mutations is reduced by about 2 Million years - to just about 3 Million years - because after migrating out of Africa different human sub-populations fixed different neutral mutations, due to the stochastic nature of the process. All specific human-chimp genetic differences (= all humans have them, no chimp has them, or vice versa) must have been fixed before the out of Africa migration. Is it possible to construct a genetic drift model (without “bottlenecks, with reasonable numbers) able to account for all the fixations, now within 3 Million years? I doubt it, but am willing to review a model that could dispel my doubts.

Let´s suppose that there are indeed 22 Million fixed synonymous mutations between the two genomes. I have no principal problem with that, or any other, experimentally established number. Whatever the exact number may turn out to be, scientists will continue looking for a model that fits the data best. In my opinion, no model should be rejected a priori. In order to contribute more constructively to this discussion, I ask: Why not test a model that uses 2Ne = 2 for the starting human population? With this model, for example, in the first generation 15 Million synonymous mutations might be fixed. Therefore, this model does not require multiple “bottlenecks” (perhaps just one) to account for a large fraction of the fixed mutations; while a smaller fraction - the 7 Million remaining mutations – could then be fixed in many subsequent generations in an expanding and splitting-recombining human population according to the population genetics theory.

One could argue that the starting Ne = 2 model is preferable in view of the principle known as Occham´s razor. But I would be the first one to disagree with such argumentation. Only in view of other experimental data found in the sequenced genomes one should decide which model is the preferred one; if the genome sequence data contradict one of any two models, the bad model should be rejected; and if the data contradict both, both models should be rejected.

I hope the above makes clear my thinking on this topic.


Wednesday, April 16, 2014

Jesus and Mo on Wednesday

This one is from five years ago, reposted today at eggs2.



What would happen if Intelligent Design Creationists understood evolution?

There's an interesting phenomenon taking place over on one of the main Intelligent Design Creationist websites. It started when a philosphopher, Vincent Torley, tried to understand how the sequences differences between chimpanzees and humans could be explained by evolution. In the beginning, he was skeptical of the explanation I offered and he was supported by a biochemist creationist named Branko Kozulic. Kozilic assured him that his skpeticism was justified and the population geneticists were wrong.

Then an amazing thing happened. Salvador Cordova, another well-known creationist, posted a comment on one of Torley's blog posts. You can see it as comment #39 on Branko Kozulic responds to Professor Moran. Cordova was responding to comments posted by Nick Matzke and "WD400" on that same post. Here's what Sal Cordova said,

Tuesday, April 15, 2014

Branko Kozulic has questions about fixation

Branko Kozulic is trying to understand how so many neutral alleles could be fixed in the human and chimpanzee populations (species) over the past five million years. He's not happy that Vincent Torley conceded the point that it was possible.

There are two relevant posts on Uncommon Descent: Branko Kozulic Responds and Branko Kozulic responds to Professor Moran, Part II.

I'll respond to the second one since it is more specific. He begins with ...
The idea of 100 mutations being fixed in the human population in each generation over a period of 185,000 generations, or 5,000,000 years, has always appeared intuitively unrealistic to me, possibly because I am primarily a practical scientist.
Many things in science seem counter-intuitive. That's why you have to make an effort to understand the science. In this case, you've been arguing against evolution for many years so you've had plenty of opportunity to get beyond intuition.

Monday, April 14, 2014

Why creationists think they are more open-minded than scientists

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.

Critical thinking and standardized tests

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.


Saturday, April 12, 2014

On being outed as a closet Darwinist, again

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?

Friday, April 11, 2014

On the frustration of trying to educate IDiots

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.

On being "outed" as a closet Darwinist

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.

Tuesday, April 08, 2014

How can IDiot students stump science professors?

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

Monday, April 07, 2014

Alan Sokal explains the scientific worldview

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

The Oklahoma Academy of Sciences says, "The Academy contends that the acceptance of the general theory of evolution and a belief in God are compatible."

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]

Monday's Molecule #236

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.)