Evolution: A Course for Educators: Week One

I'm taking a MOOC! It's called Evolution: A Course for Educators. The principle instructors are Joel Cracraft and David Randle of the American Museum of Natural History in New York (USA).

Welcome to Evolution: A Course for Educators! We’re excited to have almost 13,000 students enrolled in the course and look forward to spending the next four weeks together as we learn about the Tree of Life, natural selection, the history of life, and human evolution, as well as how to incorporate an exploration of these issues into your classrooms.

You can earn a "Verified Certificate" by paying $29.00.

Science Journal Blows It Again

This week's issue of Science contains three separate papers analyzing transcription factor binding sites and chromatin modification sites in the genomes of different individuals. If most of these sites are spurious sites that just happen to contain a consensus sequence, then you would expect a lot of variability since the sites are mostly in junk DNA where the sequences make no difference. That's what all three papers found but, of course, they interpret this to mean that the regulatory sites must be responsible for the variation between individuals.

The papers were summarized in the form of a "press release" called a "Perspective." The complete citation is ...

Furey, T.S. and Sethupathy, P. (2013) Genetics Driving Epigenetics. Science 342:705-706. [doi: 10.1126/science.1246755]

These authors are affiliated with several departments at the University of North Carolina in Chapel Hill but, most significantly, they are part of the Carolina Center for Genome Sciences. This strongly suggests that they know something about genomes.

Why Humanists Should Be Vegans

I am not a humanist and I'm not a vegan. Sarah Moglia explains why I don't subscribe to either of those two beliefs. I first saw this on Skepchick: Why Vegan Values are Humanist Values.

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Alfred Russel Wallace (8 January 1823 – 7 November 1913)

Alfred Russel Wallace died¹ on this day in 1913. That's exactly one hundred years ago.

Jerry Coyne has posted a guest article by Andrew Berry that should be required reading for everyone who admires Wallace but wonders why he didn't get much credit for natural selection [A guest post for Wallace Day].

The IDiots over on Evolution News & Views (sic) have, of course, an entirely different version of the truth [Counter the History Deniers: Get Out the Word on Alfred Russel Wallace; We've Got the Resources You Need]. Here's what David Klinghoffer has to say about historical truth.

Today is the 100th anniversary of the death of Alfred Russel Wallace (1823-1913), co-discoverer with Charles Darwin of the theory of evolution by natural selection.

If you follow us at all at ENV you'll already know that the scientific and scholarly communities have done a terrible disservice to Wallace's legacy by airbrushing out the fact that he broke with Darwin over what University of Alabama science historian Michael Flannery calls "intelligent evolution." That is, Wallace's steadily more certain and detailed view that an "overruling intelligence" guided the evolutionary process. He anticipated major elements of the modern theory of intelligent design. Oh, the irony! It burns! It burns!

Well, the massive effort by scientists, journalists, bloggers and others to defend Darwinian theory often proceeds by such airbrushing. You can fight back and counter the censors by passing along the historical truth to friends, students, and teachers, online and in person.

...

It's time everyone agreed to be honest about Wallace -- about the important historical truth that one of the two men to first spell out the modern theory of evolution came to reject that theory as an adequate explanation of life's development, in favor of proto-intelligent design. Toward that end, please join us in refuting the history deniers.

You just can't make this stuff up. Every time you think that the IDiots can't get any worse, along comes one of them to show you that you were being far too optimistic.

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1. I refuse to use the stupid phrase "passed away."

The Adaptation Assessment Probe

I'm taking a MOOC on evolution that's designed for educators [Evolution: A Course for Educators]. One of the things that was covered in the first lecture was a test on "adpatation" taken from a book called "Uncovering Student Ideas in Science, Volume 4: 25 New Formative Assessment Probes. The book is published by the National Science Teachers Association (NSTA).

Let's take the test ...

Adaptation

Three friends were arguing about what would happen if a population of rabbits from a warm, southern climate were moved to a cold, northern climate.¹ This is what they said:

Bernie: "I think all of the rabbits will try to adapt to the change."

Leo: "I think most of the rabbits will try to adapt to the change."

Phoebe: "I think few or none of the rabbits will try to adapt to the change."

Which person do you most agree with and why? Explain your ideas about adaptation.

I agree with Bernie. I think all the rabbits will try to adapt to the colder weather by finding warmer, more cozy, burrows and by cutting down on their activity during the cold nights. I think they will adapt by eating more. If hair growth is related to temperature, as it is in some mammals, then the rabbits will adapt by growing thicker coats.

Let's see how I did.

Oops! That's not the "right" answer. The correct answer is what Phoebe said. Here's what they say on the website ...

The best answer is Phoebe's: "I think few or none of the rabbits will try to adapt to the change." The key word here is try. Biological adaptation involves genetic variation that allows some individuals to survive a particular change, such as a change in the environment, better than others.

I didn't read the question carefully. I didn't notice that what they were asking about was not just "adaptation" but "adaptation by natural selection." Silly me.

We turned our clocks back one hour last weekend and I'm still adapting adjusting to the change.

If this is the kind of nonsense that the National Science Teachers Association thinks is important then it's no wonder that evolution education is in trouble.

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1. Not a good test for Australian students! :-)

Test Your Scientific Skepticism

I once posted a series of articles on Roundup® (glyphosate) explaining how it works and how one makes Roundup®-Ready genetically modified plants.

• How Roundup® Works
• Roundup Ready® Transgenic Plants
• The Molecular Basis of Roundup® Resistance
• Glyphosate-resistant Weeds
• Roundup® Is Safe

A reader has alerted me to a paper published last Spring that purports to show the dangers of glyphosate. This paper has gone viral—as you might have guessed. It led to an interview with the lead author, Anthony Samsel, on Moms Across America [Part 1 Samsel on Glyphosate and Autism, Asthma, COPD, Diabetes and more]. Here's part of what blogger Zen Honeycutt has to say about this paper ...

Stop Using the Term "Noncoding DNA:" It Doesn't Mean What You Think It Means

Axel Visel is a member of the ENCODE Consortium. He is a Staff Scientist at the Lawrence Berkeley National Laboratory in Berkeley, California (USA). Axel Visel is responsible, in part, for the publicity fiasco of September 2012 where the entire ENCODE Consortium gave the impression that most of our genome is functional.

He is also the senior author on a paper I blogged about last week—the one where some journalists made a big deal about junk DNA when there was nothing in the paper about junk DNA [How to Turn a Simple Paper into a Scientific Breakthrough: Mention Junk DNA].

Dan Graur contacted him by email to see if he had any comment about this misrepresentation of his published work and he defended the journalist. Here's the email response from Axel Visel to Dan Gaur.

The Carnival of Evolution #65: Horror Host Edition

The latest issue of Carnival of Evolution is hosted by PZ Myers, a developmental biologist with an interest in evolution (among other things). He's a professor at the University of Minnesota in Morris. PZ blogs at Pharyngula. Perhaps you've heard of it?

Read: The Carnival of Evolution #65: Horror Host Edition.

I prepared for the Carnival of Evolution late at night over the last several days, bracketing the Halloween holiday, and coupled them with my traditional custom of watching horror movies. It wasn’t a good match. The evolutionary stories were far more frightening!

There are several dozen contributions and some of them are very scary.

If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.

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How Many Different Cell Types in an Adult Human?

We're having a little discussion about complexity in the comments from my post of last Friday [Vertebrate Complexity Is Explained by the Evolution of Long-Range Interactions that Regulate Transcription?]. I pointed out that many scientists just can't come to grips with the idea that humans aren't much more complicated than other animals. We are not special. I call this The Deflated Ego Problem.

One of the minor arguments in favor of human exceptionalism is the idea that we (mammals?) have more cell types that other species. Therefore, we are more complex. The number that's often bandied about is 210 cell types. PZ Myers debunks this myth (once again) in Methinks it is like a fox terrier". I love it when people like PZ make oblique references to Stephen Jay Gould as he does in the title. If you don't know what this has to do with fox terriers then you're in for a double treat.

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Vertebrate Complexity Is Explained by the Evolution of Long-Range Interactions that Regulate Transcription?

The Deflated Ego Problem is a very serious problem in molecular biology. It refers to the fact that many molecular biologists were puzzled and upset to learn that humans have about the same number of genes as all other multicellular eukaryotes. The "problem" is often introduced by stating that the experts working on the human genome project expected at least 100,000 genes but were "shocked' when the first draft of the human genome showed only 30,000 genes (now down to about 25,000). This story is a myth as I document in: Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome. Truth is, most knowledgeable experts expected that humans would have about the same number of genes as other animals. They realized that the differences between fruit flies and humans, for example, didn't depend on a host of new human genes but on the timing and expression of a mostly common set of genes.

This isn't good enough for many human chauvinists. They are still looking for something special that sets human apart from all other animals. I listed seven possibilities in my post on the deflated ego problem:

A "Perfect Painting" Proves that Beneficial Mutations Are Impossible and Neutral Mutations Are Impossible

There are times when the stupidity of creationists just makes you gasp. This is one of those times. The creationist is Denyse O'Leary, who holds some kind of record for stupidity.

In this case she can be partially excused since she seems to be quoting someone named Laszlo Bencze. You can read the whole thing at: Is there no such thing as a neutral mutation? Art explains why there probably isn’t.

Denyse quotes Laszlo Bencze (I think) talking about a painting by French artist Jean-Auguste-Dominique Ingres (1780-1867).

Here is a famous and gorgeous painting by Ingres which I just saw in person at the Frick Museum in New York.

Let’s imagine we can improve it by adding a dot of paint 1mm in diameter to it. In evolutionary terms we will give it a “point mutation,” the smallest possible change. If we add this dot randomly, the odds are pretty high it will damage the painting by creating an obvious, intrusive speck. So let’s give evolution every advantage. Let’s make the process far more likely to succeed by having the great contemporary painter, David Hockney, add the speck wherever he thinks it will “do the most good.”

Now I happen to know that Hockney is a great admirer of Ingres and would be shocked and dismayed at any such request. But if a cruel tyrant under pain of death forced him to do it, Hockney would understand that there is no place he could possibly place a dot of paint that would improve the painting. Like a living thing, the painting is so well crafted that anything he might add to it could only be neutral at best. So Hockney would strive to place the most neutral dot he could by choosing a pigment that matched some dark portion of the painting and hope to hide his speck there.

But would such a speck be truly neutral? No matter how well it matched the color, wouldn’t it be visible as a raised dot under the right lighting conditions? And wouldn’t that actually damage the painting even if ever so slightly? And this is precisely Sanford’s point. In the world of biology it is impossible to create a neutral mutation. The change may be extremely slight, even invisible, yet always a degradation no matter how small.

When you think about it, it's really very sad this this is the best the Intelligent Design Creationists can offer. They are so ignorant that you can almost feel sorry for them.

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Time to Re-Write the Textbooks! Nature Publishes a New Version of the Citric Acid Cycle

I was looking through my copy of Nature the other day trying to take seriously all the special reviews on "Transcription and Epigenetics." One article caught my eye ...

Gut, P. and Verdin, E. (2013) The nexus of chromatin regulation and intermediary metabolism. Nature 502:489-498. [doi: 10.1038/nature12752]

Living organisms and individual cells continuously adapt to changes in their environment. Those changes are particularly sensitive to fluctuations in the availability of energy substrates. The cellular transcriptional machinery and its chromatin-associated proteins integrate environmental inputs to mediate homeostatic responses through gene regulation. Numerous connections between products of intermediary metabolism and chromatin proteins have recently been identified. Chromatin modifications that occur in response to metabolic signals are dynamic or stable and might even be inherited transgenerationally. These emerging concepts have biological relevance to tissue homeostasis, disease and ageing.

The authors argue that, among other things, methylation of histones is regulated by changes in the concentrations of some citric acid cycle metabolites. I find it difficult to imagine that the concentrations of the citric acid cycle intermediates could change significantly enough to act as allosteric effectors but that's not what grabbed my attention.

It's the figure showing the citric acid cycle (TCA cycle) that shocked me.

Textbooks show that the products of the citric acid cycle are ...

That's three NADH, one QH₂, and one GTP (or ATP) for a total of ten ATP equivalents. The new version, published last week in the most prestigious science journal in the world, shows that there are six NADH produced per cycle for a total of 15 ATP equivalents. It must be correct because this is a paper about intermediary metabolism and it was reviewed by experts in the field. Unfortunately, the authors don't give a reference to this new information. I assume that it's common knowledge among the top metabolism researchers so they didn't bother citing the papers.

Can anyone out there direct me to the revolutionary papers that I missed?

P.S. I'm not even going to mention that FADH₂ is NOT a product of enzyme-catalyzed β-oxidation.

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I Just Signed Up for an Evolution MOOC!

I'm not a big fan of MOOCs but I just couldn't resist a course called "Evolution: A Course for Educators". The instructors are two Ph.D. employees from the American Museum of Natural History in New York (USA). As you probably know, the American Museum of Natural History is very proud of its tradition in education. Here's what they say on their website.

The American Museum of Natural History is one of the world’s preeminent scientific, educational and cultural institutions. Since its founding in 1869, the Museum has advanced its global mission to discover, interpret, and disseminate information about human cultures, the natural world, and the universe through a wide-ranging program of scientific research, education, and exhibition.

This is a course for educators and that's right up my alley. You may want to sign up as well. Here's the description and the video.

How are all of the species living on Earth today related? How does understanding evolutionary science contribute to our well-being? In this course, participants will learn about evolutionary relationships, population genetics, and natural and artificial selection. Participants will explore evolutionary science and learn how to integrate it into their classrooms.

....

The AMNH course Evolution: A Course for Educators provides an overview of biological evolution for educators. Informed by the recently released Next Generation Science Standards, the course explores the history of evolutionary theory and the evidence that supports it. We will learn about patterns of human evolution and societal implications of modern evolutionary biology, and how scientists determine relatedness among living and extinct organisms. Course participants will bring their understanding of course themes - along with content resources, discussion questions, and assignments - into their own teaching.

It's a bit disturbing that the Next Generation Science Standards don't mention random genetic drift, Neutral Theory, speciation, or population genetics [Natural Selection and Evolution] but the course promises to cover population genetics and I assume that it will also cover all mechanisms of evolution since it's being taught by an evolutionary biologist (Joel Cracraft).

The purpose of the course is to train the next generation of high school (and university) teachers. One of the instructors, David Randle, is an expect on education. We all know that teachers need to be updated on modern evolutionary theory.

It starts next Monday. I'll let you know how I'm doing when I write the first test.

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The Khan Academy and AAMC Teach Evolution in Preparation for the MCAT

Ross Firestone is a 2nd year MD/PhD student at the Albert Einstein College of Medicine. He is one of the winners of the MCAT Video Competition. Apparently the Khan Academy and the Association of American Medical Colleges were impressed with his presentations on evolution. You can see all six videos at Evolution and population dynamics.

I'm posting the first one on Evolution and Natural Selection. It's all about natural selection but it's a very strange kind of natural selection. The organisms are parthenogenic and each individual is genetically programed to have a certain probability of reproducing. One type has a 50% probability of reproducing and another type has only a 25% probability of reproducing. These probabilities seem to be independent of any competition between them. Each successful individual produces four offspring. After some time the number of one type remains constant (25% probability) but the number of the other type (50% probability) doubles with each generation. This is natural selection according to Ross Firestone.

"Naturally," I was disappointed that natural selection was the only mechanism mentioned. There's nothing about random genetic drift in this video and nothing about the stochastic nature of natural selection. But my face lit up when I saw that there was another video on "Alternative Selection: Learn about driving forces of evolution other than natural selection." This could almost make up for screwing up the description of natural selection.

Alas, the second video is even worse. The "alternatives" are group selection and artificial selection. It gets even more worse. The example of group selection is the grandmother hypothesis. According to Ross Firestone, the fact that grandmothers help their grandchildren survive is group selection.

The video on "Bottlenecks and the environment" is also quite interesting. I didn't know that that the peppered moth story is an example of a bottleneck. Did you?


I think these videos are horrible—so horrible, in fact, that the Khan Academy should take them down. What do you think?

Are you wondering why a 2nd year med student feels so confident that he knows enough about evolution to teach it to pre-med students? Me too.

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The Khan Academy and AAMC Teach the Central Dogma of Molecular Biology in Preparation for the MCAT

Here's a presentation by Tracy Kovach, a 3rd year medical student at the University of Virginia School of Medicine. Sandwalk readers will be familiar with my view of Basic Concepts: The Central Dogma of Molecular Biology and the widespread misunderstanding of Crick's original idea. It won't be a surprise to learn that a 3rd year medical student is repeating the old DNA to RNA to protein mantra.

I suppose that's excusable, especially since that's what is likely to be tested on the MCAT. I wonder if students who take my course, or similar courses that correctly teach the Central Dogma, will be at a disadvantage on the MCAT?

The video is posted on the Khan Academy website at: Central dogma of molecular biology. What I found so astonishing about the video presentation is that Tracy Kovach spends so much time explaining how to remember "transcription" and "translation" and get them in the right order. Recall that this video is for students who are about to graduate from university and apply to medical school. I expect high school students to have mastered the terms "transcription" and "translation." I'm pretty sure that students in my undergraduate class would be insulted if I showed them this video. They would be able to describe the biochemistry of transcription and translation in considerable detail.


There are people who think that the Central Dogma is misunderstood to an even greater extent than I claim. They say that the Central Dogma is widely interpreted to mean that the only role of DNA information is to make RNA which makes protein. In other words, they fear that belief in that version of the Central Dogma rules out any other role for DNA. This is the view of John Mattick. He says that the Central Dogma has been overthrown by the discovery of genes that make functional RNA but not protein.

I wonder if students actually think that this is what the Central Dogma means? Watch the first few minutes of the video and give me your opinion. Is this what she is saying?

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