What Is Epigenetics?

 
Berger et al. (2009) attempt to define epigenetics.

"An epigenetic trait is a stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence."

Sounds good to me. Just about anything wold be better than the kitchem sink definition proposed by Eva Jablonka [Epigenetics at SEED].

The main examples are "DNA methylation, histone modifications, histone variants, and nucleosome positioning." These are chromosomal alterations that are passed on to daughter cells following cell division by mitosis or meiosis.

Although the Berger et al. don't mention it, these epigenetic signals are all reversible. I still don't find the term useful. It's far more accurate to refer to each of the individual examples by name and the field is "regulation of gene expression."

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Berger, S.L., Kouzarides, T., Shiekhattar, R., and Shilatifard, A. (2009) An operational definition of epigenetics. Genes & Dev. 23:781-783. [DOI: 10.1101/gad.1787609]

[Hat Tip: Hopeful Monster]

Monday's Molecule #116

 
If you look closely you'll realize that these mouse embryos aren't really "molecules" in any meaningful sense of the word "molecule." That doesn't matter 'cause I still want you to identify what's going on here. This is the first time that I've resorted to using photographs from my previous life—shows you how desperate I'm getting!

The images are supposed to remind you of the work of some Nobel Laureates. See if you can guess who they are.

The first person to identify the photographs and the Nobel Laureates wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are eight ineligible candidates for this week's reward: David Schuller of Cornell University, Adam Santoro of the University of Toronto, Dima Klenchin from the university of Wisconsin, Alex Ling from the University of Toronto, Bill Chaney of the University of Nebraska, Elvis Cela from the University of Toronto, Paul Horwich from Dalhousie University, and Devin Trudeau from the University of Toronto.

Dima and Bill have donated their free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

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Religion Wars: Linux and Mac vs. Rationalism

 
Greg Linux is disappointed that the Confliker virus didn't do more damage on April 1st [Did Conflicker Flop? Yes. Why? Nobody knows].

I wasn't worried because I checked all five of my computers and not one them were infected. If they had been, it was very easy to get rid of the worm. My Linux machine didn't have the worm either.

That doesn't stop Greg from offering this advice ...

Experts expect that the worm is going to re-awaken at some time in the future and possibly actually do something. In the mean time, you may want to get rid of it if is on your system.

If you run Windows, the best way to get rid of the computer is to get a Mac or a Linux computer. There are probably other ways to do this but I don't really care. If you are running Linux, this worm can't directly affect you.

Sheesh, those religious nuts sure can be silly.

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The End of Christian America?

 
The number of Americans who don't identify with a religion has increased from 8% in 1990 to 15% today. This is encouraging but it doesn't quite mean that the battle between rationalism and superstition has been won.

Nevertheless, the fact that a national magazine could publish an article like "The End of Christian America" is an indication that the debate is on.

If North American societies become much less religious—like those in Europe—then most of the major problems with creationism will go away. Maybe then we can concentrate on promoting good science education. That's why some of us would rather put our efforts into promoting rationalism over superstition rather than defending specific creationist attacks on schools.

Both approaches are needed but those who advocate the compatibility of science and superstition are not helping.

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[Hat Tip: Hemant Mehta who has some interesting comment.]

Last Week's Scientific Breakthroughs

 
This are stories from the past week that would make good topics for discussion. I don't have time so I'll leave it up to you.

Scientists Find 'Baffling' Link between Autism and Vinyl Flooring

Masturbation could bring hay fever relief for men

New research shows lower educational outcomes for survivors of childhood cancer

6 out of every 10 university students present mathematical anxiety or fear of this subject

Humanoid Robot Helps Scientists To Understand Intelligence

Omega-3 kills cancer cells

How probiotics can prevent disease

UBC study first to show evolution's impact on ecosystems

UT Southwestern researchers reveal how the brain processes important information

Your oral health is connected to your overall health

Penn researchers demonstrate a new model for drug discovery with a fluorescent anesthetic

Humans May Be Losers If Technological Nature Replaces The Real Thing, Psychologists Warn

Milkshakes Are Medicine For Anorexic Teens In Family-based Outpatient Therapy

Hermit Arthropods 500 Million Years Ago?

Alzheimer's Disease Linked To Mitochondrial Damage

Robot Scientist Becomes First Machine To Discover New Scientific Knowledge

Virus-built Battery Could Power Cars, Electronic Devices

Athletic Ability May Lie in a Single Gene

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Washington D.C.

 
In a few days I'll be on my way to Washington (Bethesda, actually) to attend the Center for Inquiry World Congress 2009. Let me know if you'll be there and we can meet up.

Here are the main events ....

Thursday April 9, evening: Panel: The Influence of Darwin

Friday April 10, afternoon: Science and Public Policy

Friday April 10, 5:45pm: James Randi: Search for the Chimera

Saturday April 11, morning: Skepticism and Science

Saturday April 11, 5pm: Special Feature: Separation of Church and State

Sunday April 12, morning: Secularism Around the World

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Darwin Rocks

 
Watch this video about evolution and see if you can figure out what's going on. You can check your answer here.

In the fight to increase scientific literacy, I'm not sure if this contribution is useful, useless, or counter-productive but I'm leaning toward counter-productive.

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[Hat Tip: John Dennehy, who leans toward the "useful" point of view.]

Will Universities Survive?

 
Believe it or not, there are supposedly intelligent people out there who think the internet will replace universities.¹ It didn't take Sean Caroll very long to come up with some excelent reasons why this ain't gonna happen [Will the Internet Replace Universities?].

Let me add one more—research experience. You can't learn what it's like to work in a research lab if you're sitting at your desk in the suburbs.

Why do I get the feeling that most people don't understand what a university is supposed to be like? Is it true that most people think of universities just as places where you come and listen to lectures and then go home?

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1. Back in 1970 their parents were convinced that television would mean the end of universities as we know them.

Electronic Textbooks

 
There's an article in this week's issue of Nature on The textbook of the future.

Most of the article is about a Kindle version of science textbooks.

Another drawback of current e-readers is that they have small black-and-white displays, just a little larger than 9 by 12 centimetres. This makes them unsuited to most science textbooks, which typically have large pages and colourful graphics. "The market is not likely to expand until the e-readers improve," says Hegarty.

Publishers are experimenting with ways of delivering their textbooks electronically (e.g. CourseSmart) but there are still problems to be solved.

Competing ideas, such as Wiki's that replace textbooks, have a long way to go before they become a threat to the textbook market [Wikibooks: Biochemistry]. Besides, there are other problems that need to be solved.

For now these free textbooks remain a cottage industry, says Esposito. Wikipedia-like volunteer efforts are much better suited to self-contained modules that are small enough for an individual to see through from A to Z. But a textbook demands a coherent overall structure and coordination between sections. That is why creating one has always been a major undertaking, demanding long-term commitments by publishers — who need to make a profit — and by authors who usually want to be paid for their effort.

Still, perhaps 'free' and 'profitable' need not be a contradiction in terms. One group of veteran textbook publishing executives is trying to put open textbooks on a solid commercial footing. In 2007 they created Flat World Knowledge, based in Nyack, New York, and in January 2009 rolled out the first of the 21 textbooks they have in development so far. The texts are written by some 40 domain experts who will be paid 20% of royalties. The company also plans to make its content available via Kindle and other e-readers. All its content will be free to reuse for non-commercial purposes under a creative commons licence.

Eric Frank, Flat World's co-founder, says that the strategy is to attract greater use by giving the e-textbooks away — the initial targets are the high-volume texts for first-year students — and then look for profit from students' purchase of print-on-demand versions at $29.95 for black and white, and $59.95 for colour. Students can copy and use the electronic content in any way they wish, says Frank. "Cheap prices are the most effective digital-rights management," he says. "We want to avoid a digital-rights war with students." The company also hopes to make money by licensing its content to commercial companies, such as distance-learning outfits and course-management software firms.

I think there's going to be a way to make cheaper electronic versions of textbooks and still compensate the people who do all the work. I'm not sure how it's going to work but I'd love to put my book on a website where I can make changes quickly and get instant feedback from the users.

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James Lunney: Creationist, Chiropractor, Conservative

 
Meet Dr. James Lunney a chiropractor and a Conservative Party Member of Parliament for Nanaimo-Alberni in British Columbia.

"Dr." Lunney recently made a fool of himself by making the following statement in the House of Commons as reported in Maclean's magazine [James Lunney v. Evolution].

Mr. Speaker, recently we saw an attempt to ridicule the presumed beliefs of a member of this House and the belief of millions of Canadians in a creator. Certain individuals in the media and the scientific community have exposed their own arrogance and intolerance of beliefs contrary to their own. Any scientist who declares that the theory of evolution is a fact has already abandoned the foundations of science. For science establishes fact through the study of things observable and reproducible. Since origins can neither be reproduced nor observed, they remain the realm of hypothesis.

In science, it is perfectly acceptable to make assumptions when we do not have all the facts, but it is never acceptable to forget our assumptions. Given the modern evidence unavailable to Darwin, advanced models of plate techtonics, polonium radiohalos, polystratic fossils, I am prepared to believe that Darwin would be willing to re-examine his assumptions.

The evolutionists may disagree, but neither can produce Darwin as a witness to prove his point. The evolutionists may genuinely see his ancestor in a monkey, but many modern scientists interpret the same evidence in favour of creation and a creator.

PZ Myers is making fun of Canada by posting Lunney's remarks on Pharyngula. He's right. We deserve it. Lunney is a genuine kook who quite obviously wouldn't know real science if it bit him on the backbone.

Listen up, all you people who live on Vancouver Island! Don't send this guy back to Ottawa after the next election or you're going to look very silly.

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March on Sandwalk

 
Bora's doing it and Greg Laden is doing it. They're revisiting their posts from last month.

Now I'm doing it too.

Last month Sandwalk attracted 107,747 page views and 75,156 visits from all over the world. That's a new record. I posted 123 times.



The month began with an account of my streetcar ride and the atheist sign campaign in Toronto [The Streetcar We Desire]. I also celebrated the 35th anniversary of my thesis defense.

There were three debates that took up a lot of posting time.

One of them was about positive selection in humans, especially the idea that human evolution might have accelerated in the past 10,000 years. I tried to explain why some of the data looks suspicious in Signals of Positive Selection in Humans?.

We also talked a lot about the quality of science journalism. The two topics were combined when I reviewed SEED magazine's coverage of a recent book on accelerated human evolution [SEED Reviews The 10,000 Year Explosion].

The third debate was about Canada's science minister, Gary Goodyear, and the fact that he is a creationist [Gary Goodyear "Clarifies" His Stance on Evolution].

I'm pretty proud of this posting: Casey Luskin on Junk DNA and Junk RNA. It generated some comments and got a mention on several blogs.

Speaking of comments, one other posting caught the attention of Sandwalk readers and stimulated comments. You were interested to know why I Hate Cilantro/Coriander!.

In terms of most popular postings there was nothing in March that's going to make the top 20 postings. I still get a lot of traffic from people who want to learn about The Genetics of Eye Color from a posting in February 2007. Another popular posting is The Genetics of ABO Blood Types, also from February 2007.

As usual, there were lots of people who tried to guess Monday's molecule. There are a small number of regulars who get most of the prizes, The rest of you are going to have to be faster. I think I'll try and post much earlier in the day to give my European readers a better chance. We don't need to worry about giving the Australians a chance 'cause they probably wouldn't win anyway! :-)

We had an interesting group of Nobel Laureates. These postings always get looked at but nobody leaves comments. I guess there isn't much to say. The most interesting Nobel Laureates from my perspective were Frederick Banting and J.J.R. Macleod because they're from the University of Toronto. Several of the recent prize winners were controvesial, especially Selman Waksman.

Does anyone have suggestions for future postings?

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A field guide to misunderstandings about open access

 
Want to find out what Open Access is really all about? Read A field guide to misunderstandings about open access.

Do you think that articles in open access journals aren't peer reviewed? Think again.

Do you think that all open access journals charge huge publication fees? Wrong.

Do you think that open access journals are lower quality? Nope.

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[Hat Tip: Bora Zivkovic: A Blog Around the Clock]

Dynamic Genomes

There may have been a time in the past when scientists imagined a static genome that only changed slowly over millions of years. However, beginning in the 1960's we began to see the genome as a much more dynamic entity. The first evidence of this kind of genome came with the discovery of huge amounts of variation between individuals in a species.

This was followed by the discovery of transposons and junk DNA. We began to see genomes as rather sloppy DNA molecules with lots of pieces hopping in and out on a timescales of generations. We began to realize that many genomes were full of pseudogenes.

Chromosomal rearrangements such as inversions, duplications, and translocations were documented. In mammals, many of them were associated with cancer, thalassemias, and other diseases but the general impression was that these rearrangements of genetic material were quite common. Indeed, some non-disease examples began to accumulate in the literature. Clear evidence of normal rearrangements associated with regulation and development—including mating type switching in yeast, immunoglobulin rearrangements in mammals, chorion gene amplification in Drosophila, and antigenic variation in trypanosomes—reinforced the idea that the genome was not static.

Most of this information was incorporated into the textbooks. For example, by the early 1980's Benjamin Lewin' textbook Genes had an entire group of chapters under the heading "The Dynamic Genome: DNA in Flux."

We soon learned about the expansion and contraction of repetitive sequences in the human genome. These observations eventually gave rise to DNA fingerprinting whereby every individual could be uniquely identified by variations in the genome.

By the early 1990's the concept of the dynamic genome had become so widely entrenched among molecular biologists that when Singer and Berg published "Genes and Genomes" they felt obliged to inject a note of caution. While genomes are dynamic at the scale of species evolution, the typical genome of an individual is not subject to significant rearrangements.

Outside of molecular biology, the idea that genomes were flexible never seemed to catch on. Most people thought of genomes as relatively static entities that didn't change much over millions of years. In part, they adopted this position because they still placed a great deal of emphasis on the power of natural selection. If genomes were well-adapted then why would they change? Part of the skepticism about junk DNA stems from the belief that selection will eliminate useless DNA.

Recent developments have stirred many people to re-think their concept of genomes. For example, Sandra Porter of Discovering Biology in a Digital World recently asked, "What if everything you thought you knew about the genome was wrong?."

To the extent that such questions acquaint people with the concept of a dynamic genome, they are good. On the other hand, if such questions lead to the unthinking acceptance of alternative splicing, superabundant transcription, and a plethora ot RNAs, they are bad.

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Handel's Messiah

 
One year Ms. Sandwalk took the entire family to see a full performance of Handel's Messiah. It was agony, except for one brief part of the performance where we all got to stand up. Ms. Sandwalk thought it was wonderful but, remember, she also likes some country music.

My children still talk about it. I guess it's one of those "experiences" that contribute to character building, or something.

Now there's an explanation in New Scientist: How misery inspired Handel's Messiah. I knew there had to be a reason.

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Monday's Molecule #115: Winners

 
UPDATE: The molecule is indigotin or indigo dye [2,2’-Bis(2,3-dihydro-3- oxoindolyliden)]. The Nobel Laureate is Johann Friedrich Wilhelm Adolf von Baeyer.

This week's only winner is Alex Ling from the University of Toronto.

The winners this week are Pete Horwich from Dalhousie University and Devin Trudeau from the University of Toronto.

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Identify this molecule and explain why it is useful. You must supply the common name and the formal IUPAC name.

I'm looking for the Nobel Laureate whose name is associated with this molecule.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Maria Altshuler of the University of Toronto, David Schuller of Cornell University, Adam Santoro of the University of Toronto, Dima Klenchin from the university of Wisconsin, Alex Ling from the University of Toronto, Bill Chaney of the University of Nebraska, and Elvis Cela from the University of Toronto.

Dima and Bill have donated their free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

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