Mechanisms of Evolution – Philipp Dettmer (2013)

This is a video that's specifically designed to teach the mechanisms (plural) of evolution. It's produced by Philipp Dettmer who, as near as I can tell, is an expert on video presentations but not on evolution. A perfect example of style trumping substance.

How many errors can you spot?

---

They're Firing Cannons Across the Street!

Today is November 11th and the cannons started blasting at 11am in Queen's Park just across the street from the building where my office is located. It's a day when we should remember the horrors of war and the waste of lives, both civilian and military. It's a day when we should resolve never to let army generals run the world. It's a day to reflect on the many times that we failed to keep the peace and the terrible cost of those mistakes.

So how do we celebrate peace and remember the evils of armies, guns, and bombs? In Toronto we do it by a public display of soldiers dressed in their finest uniforms bedecked with medals. And the army brings its cannons. It's all very glorious.

I long for the day when we don't even have an army and all the cannons are rusting in some junk heap. That will be the day when we have truly learned about the evils of war and the purpose of November 11th.

I agree with PZ Myers when he asks Who deserves honor?

---

I'm Related to a Philosopher! Edwin Proctor Robins (1872-1899)

I'm been filing and organizing my mother's genealogical data and I came across a list of people buried in various Prince Edward Island (Canada) cemeteries. One of the tombstones in the Lower Bedeque United Church Cemetery says, "In Memory Of / Edwin Proctor Robins, / Born At / Central Bedeque / July 2, 1872. / Died at / Cornell University, Ithaca, N. Y. / April 19 1899. / Mors Janua Vitae [Death is the gate of [everlasting] life]" [Edwin Proctor Robins].

This was intriguing. I know I am related to all the Robins (Robbins) descendents from Prince Edward Island but I'd never heard of Edwin Proctor Robins. His great-grandfather, Robert Robbins, is a United Empire Loyalist who came to PEI from New Jersey when the American Revolution ended. Edwin Proctor Robins and I are fourth cousins, three times removed. Why did he die at Cornell University?

I still don't know how he died and why he was so young (26 years old) but I did find a book he published on Some Problems of Lotze's Theory of Knowledge. I think the book was first published in 1900—a year after he died. Sounds like Edwin Proctor Robins might have been an epistemologist. Does anyone know anything about my relative or about Lotz's Theory of Knowledge?

---

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.

---

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.

---

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.

---

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.

CoE on Facebook
CoE on Twitter

---

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.

---

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.

---

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.

---