It's going up to +1 next week!

I stole this from Ms. Sandwalk's blog. I'm pretty sure she'll mind.

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What is epigenetics?

Several students in my class decided to write essays on epigenetics. This was very brave of them since nobody seems to have a good definition of epigenetics and much of the hype about epigenetics is not very scientific. I'm also more than a little skeptical about some of the claims that have been made.

Here's a video. What do you think? Is this a useful contribution to our understanding of a complex issue? Is the inheritance of methylation sites at restriction/modification loci in bacteria an example of epigenetics? After E. coli divides, both cells inherit some lac repressor molecules and the lac operon is not expressed provided the parent wasn't exposed to lactose. Is this epigenetics?

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Monday's Molecule #234

Last week's molecules [Monday's Molecule #233] were oxaloacetate, ethanol, lactate, alanine, and acetyl-CoA. All of them can be synthesized in a reaction using pyruvate as a substrate (two steps to make ethanol). All of them are precursors to pyruvate and hence glucose. The winner is Jean-Marc Neuhaus. I will be buying him four meals next time I visit Switzerland. I'm thinking it will be two raclettes and two fondues with lots of wine.

This week's molecule (left) is probably not very familiar to most of you so I don't anticipate many correct answers. You can use the common name. Email your answer to me at: Monday's Molecule #234. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)

Thesis defense - 40th anniversary

Today is the 40th anniversary of my Ph.D. oral defense.¹ The event took place in the Department of Biochemical Sciences at Princeton University back in 1974.

It began with a departmental seminar. When the seminar was over I retired with my committee to a small classroom for the oral exam.

I don't remember everyone who was on my committee. My Ph.D. supervisor (Bruce Alberts) was there, as was my second reader, Abe Worcel. I know Uli Laemmli was there and so was Arnie Levine. I'm pretty sure the external member of the committee was Nancy Nossal from NIH in Bethesda, MD (USA). It's a bit of a blur after all these years.

I remember being fairly confident about the exam. After five and a half years I was pretty sure that everyone on my committee wanted to get rid of me and the easiest way to do that was to let me pass. Bruce stood to gain $3000 per year of research money and Uli was going to get back the basement of his house where Ms. Sandwalk and I had been living for the past month.

The toughest questions were from Uli Laemmli, which should not come as a surprise to anyone who knows him. He has this annoying habit of expecting people to understand the basic physics and chemistry behind the biochemical sciences. Fortunately, my inability to answer most of his questions didn't deter him from voting to pass me.

This photograph was taken at a party that evening. I look pretty calm at that point but this may have had a lot to do with the various refreshments that were being served.

The amazing thing about the photograph—as I'm sure you all agree—is how little I've changed since then—apart from a haircut.

Back in those days we didn't spend a lot of time writing a thesis. I started in the middle of January and the entire process of writing and defending took nine weeks. My thesis was bound and delivered to the library about one week after the Ph.D. oral.

The second page of my thesis has only three words on it. It says, "To Leslie Jane." This is Ms. Sandwalk. She really should have her name on the cover 'cause I couldn't have graduated without her. Typing my thesis was only one of her many contributions. There are 257 pages in my thesis and she typed every one. As a matter of fact, she typed them twice, one draft and then the final version.

The figures in my thesis were all hand drawn. I've included one (below) to illustrate what I was doing during those five and a half years.

The Alberts lab was interested in DNA replication during bacteriophage T4 infections of E. coli. We knew that replication was carried out by a complex protein machine that assembled at a replication fork but we didn't know all the players or what they did.

The T4 proteins required for DNA replication were known from genetic studies. The most important genes were genes 30 (ligase), 32 (single-stand DNA binding protein), 41, 43 (DNA polymerase), 44, 45, and 62. The products of the unknown genes were called 41P, 44P, 45P and 62P.

We wanted to purify and characterize those proteins; my target was the product of gene 41, or 41P.

We had a cool assay, developed mostly by a postdoc in the lab named Jack Berry. What we did was to prepare a cell lysate from cells that had been infected by bacteriophage carrying an amber mutation in one of the genes. This lysate could not support DNA synthesis, as measured by incorporation of ³²P nucleotides, unless we added back the missing component. This is the basis of an in vitro complementation assay that worked for each of the unknown proteins.

In my case, I used traditional protein purification methods to isolate fractions of proteins and them tested them for activity in the complementation assay. The figure below shows the elution profile of proteins bound to a hydroxylapatite column. The peak centered on fraction 61 is the activity of the complementation assay. It indicates that 41P elutes early as a sharp peak in the elution profile.


The complementation assay doesn't tell us anything about the function of 41-protein, only that it complements an extract that's deficient in 41P. Strictly speaking, it doesn't even tell us that the activity is due to the product of gene 41 since it could be something else that complements in vitro.

Fortunately we had another way of identifying 41P. I started my purification with extracts from 17 liters of infected cells. To this I added extracts from cells that had been labeled with radiaoctive amino acids. One batch was from a wild-type infection where all T4 proteins are labeled with ¹⁴C amino acids. The other batch is from an infection with an amber mutation in gene 41. In this case every protein except 41P is labeled with ³H amino acids.

You can adjust the settings on a scintillation counter so they distinguish between ¹⁴C and ³H but there's some overlap. The equations for calculating the contribution of each isotope in each window are relatively simple. All you need are good standards to get the distribution. One of the most fun things I did as a graduate student was to write a computer program (in Fortran) that did these calculations automatically and plotted them on a plotter. This was back in the time when computers were housed in large separate buildings and required dozens of people to look after them.

If you look of the elution profile in the figure you'll see there's an excess of ¹⁴C over ³H in the same fractions where the complementation activity is located. What this means is that the wild-type extract has a protein at that position that's not found in the am41 extract. It's another way of identifying the product of gene 41.

The double label technique was useful 35 years ago but nobody does it anymore. It was fun while it lasted.

(I never did figure out what 41P did during DNA replication but a few years after I left a postdoc identified 41P as a helicase—an enzyme that unwinds DNA ahead of the replication fork. The enzyme is now called gp41 for "gene product.")

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1. This post is an almost identical copy of one that was posted five years ago. You'll probably see another in 2019, and especially 2024.

IDiots respond to the evidence for evolution of chimpanzees and humans

Last month I explained how the difference in DNA sequence between chimps and humans corresponds to what we would predict from evolutionary theory. I challenged the Intelligent Design Creationists to explain not only that the sequences are similar but that the degree of similarity is evidence of evolution.

None of the "scientists" on the creationist websites responded to my challenge but eventually—after being prodded—Vincent Torley (a philospher) picked up the challenge. I tried to explain why his response was inadequate.

Here are the three relevant posts.

Why are the human and chimpanzee/bonobo genomes so similar?
So, why are the human and chimpanzee/bonobo genomes so similar? A reply to Professor Larry Moran
An Intelligent Design Creationist explains why chimpanzees and humans are so similar

An Intelligent Design Creationist explains why chimpanzees and humans are so similar

The genomes of chimpanzees and bonobos are remarkably similar to the human genome. In terms of sequence similarity, they are more than 98% identical in the regions that can be aligned. This, of course, is due to the fact that they descend from a common ancestor in the recent past (about 5 million years ago).

Intelligent Design Creationists don't agree. Many of them do not accent common descent and macroevolution so they make up stories that account for the similarity based on what they think god might have been thinking when he created chimps and humans.

But the scientific evidence for evolution is much stronger than just overall sequence similarity. The number of differences (about 50 million substitutions) corresponds pretty closely with what we expect from evolutionary theory (population genetics) and known mutation rates [Why are the human and chimpanzee/bonobo genomes so similar?]. If the Intelligent Design Creationists are going to dismiss this confirmation of evolutionary theory then they are going to have to be much more inventive.

John Wilkins writes about accommodationism

John Wilkins has written a series of posts about the war between science and religion.

Accommodating Science overview

I find the arguments confusing because I'm never quite sure what John defines as "science." I think he's referring to the things that scientists do. This is the narrow definition of science and I think it explains why he claims that there are aspects of religion that do not conflict with science.

ASBMB Core Concepts in Biochemistry and Molecular Biology: Homeostasis

Theme

Better BiochemistryThe American Society for Biochemistry and Molecular Biology (ASBMB) has decided that the best way to teach undergraduate biochemistry is to concentrate on fundamental principles rather than facts and details. This is an admirable goal—one that I strongly support.

Last October I discussed the core concepts proposed by Tansey et al. (2013) [see Fundamental Concepts in Biochemistry and Molecular Biology]. The five concepts are:

1. evolution [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution ]
2. matter and energy transformation [ASBMB Core Concepts in Biochemistry and Molecular Biology: Matter and Energy Transformation]
3. homeostasis [ASBMB Core Concepts in Biochemistry and Molecular Biology: Homeostasis]
4. biological information [ASBMB Core Concepts in Biochemistry and Molecular Biology: Biological Information]
5. macromolecular structure and function [ASBMB Core Concepts in Biochemistry and Molecular Biology: Molecular Structure and Function]

Science still doesn't get it

The latest issue of Science contains an article by Yudhijit Bhattacharjee about Dan Graur and his critique of the ENCODE publicity disaster of September 2012. The focus of the article is on whether Dan's tone is appropriate when discussing science.

Let me remind you what Science published back on September 7, 2012. Elizabeth Pennisi announced that ENCODE had written the eulogy for junk DNA. She quoted one of the leading researchers ...

What do Intelligent Design Creationists really think about macroevolution?

Intelligent Design Creationism is a huge tent that shelters all sorts of creationists ranging from Young Earth Creationists to those who could be called Theistic Evolution Creationists.¹ Many of them accept common descent so they clearly don't have much of a problem with most of macroevolution.

On the other hand, there are a lot of Intelligent Design Creationists who don't accept macroevolution. It seems to me that this could only be because they are Young Earth Creationists or they believe in some other strange idea where god(s) make every species.

It's hard to figure out what they mean.

Let's look at a recent post by philosopher Vincent Torley. He didn't like my posts about macroevolution [What is "macroevolution"? ] [A chemist who doesn't understand evolution] so he decided to set me straight: Does Professor Larry Moran (or anyone else) understand macroevolution?.

Cosmos presents evolution

The second episode of the new Cosmos series is Some of the Things That Molecules Do.

It's about evolution and it's not bad. I have four comments.

A missed opportunity. Natural selection is important and Neil deGrasse Tyson did a pretty good job of explaining it. It wouldn't have taken a big effort to mention that there's more to evolution than natural selection. He could, for example, have pointed out that some breeds of dogs are prone to certain genetic diseases or health problems because some bad mutations were accidentally fixed alone with the good ones. He could have pointed out that our eyes have a blind spot.

The Theory of Evolution is not a fact. Neil deGrasse Tyson said that the theory of evolution is a fact. This is not correct. Evolution is a fact. Evolutionary theory attempts to explain how evolution occurs. Some of the explanations, like natural selection, are facts but many aspects of modern evolutionary theory are still hotly debated in the scientific community.

We don't understand the origin of life. The episode closed with deGrasse Tyson saying the we don't understand how life began and there's nothing wrong with admitting that we don't know something. Excellent!

There are better ways of drawing DNA. I don't like the way DNA is pictured in the first two episodes, especially in the opening sequence. It looks like the bases grow out of the backbone and fuse to form base pairs. They could have drawn a more accurate representation without losing any visual appeal.

I give the episode a B⁺.

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Monday's Molecule #233

Last week's molecules [Monday's Molecule #232] were all-trans and 13-cis retinal. Retinal is the active protein donor/acceptor in bacteriorhodopsin. The all-trans form is shifted to the 13-cis form when a photon of light is absorbed. The retinal molecules are arranged within the membrane-bound bacteriorhodpsin in a way that binding and release of a proton results in transport from the cytoplasm to the exterior. The creation of a proton gradient drives ATP synthesis.

The winner is Philip Johnson from Switzerland.

This week's molecule (left) is actually a collection of molecules. Name all five molecules and tell me what they have in common from a biochemical perspective. Common names will do.

Email your answer to me at: Monday's Molecule #233. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)

Reading Books

Yesterday we watched two episodes of House of Cards and two of our favorite TV shows; Amazing Race and The Good Wife. We also watched a show about working on a Tudor farm and I watched the second episode of Cosmos.

According to Veronica Abbas, I wasted valuable time when I could have been reading [Recommended Reading]. She links to an article by Erin Kelley who says, Reading Books Doesn't Just Make You Literate: It Reduces Stress, Promotes Good Health, and Makes You More Empathetic. I haven't read a book in over four months and I haven't read a novel in years.

I'm doomed to be illiterate, stressed, in poor health, and the opposite of empathetic.¹ It also explains why I don't volunteer to work for a non-profit organization.

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1. I'm pretty sure Veronica would agree with "illiterate."

On teaching creationism in American public universities

I think that universities are places where diversity of opinion should be encouraged and where fringe ideas should be protected. I'm very much opposed to letting outside interests (i.e. politicians and lawyers) decide what should and should not be taught on a university campus.

Clearly there are limits but those should be decided by faculty who understand the concept of academic freedom. It's not a good idea to offer astronomy courses on an Earth-centered solar system or geology courses based on the idea that the Earth is only 6000 years old. Those ideas are just too far out on the fringe. You're unlikely to find any university professors who want to teach such courses.

However, there are lots of other controversies that aren't so easily dismissed. If some of the more enlightened Intelligent Design Creationists want to teach a science course at my university, I would not try to prevent them. Just as I didn't try to prevent Michael Behe and Bill Dembski from speaking on my campus.

A chemist who doesn't understand evolution

James Tour is an organic chemist. He is a Professor of Chemistry and Professor, Professor of Mechanical Engineering & Materials Science, and Professor of Computer Science at Rice University (Houston, United States). James Tour is attracting a lot of attention on the Intelligent Design Creationist websites because he is sympathetic to their main claim; namely, that evolution is wrong [see A world-famous chemist tells the truth: there’s no scientist alive today who understands macroevolution].

Tour is one of the few genuine scientists who signed the Discovery Institute’s "A Scientific Dissent from Darwinism" (2001) that stated, "We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged." (There are very,very, few biologists who signed.)

What exactly, does Jame Tour mean? He wrote an article on his website that explains his position: Layman’s Reflections on Evolution and Creation. An Insider’s View of the Academy. I think it's interesting to discuss what he said.

He begins with ...