Friday, March 27, 2015

Plant biologists are confused about the meanings of junk DNA and genes

A recent issue of Nature contains a report on plant micro-RNAs (Lauressergues et al., 2015). The authors found that certain genes for plant micro-RNAs encoded short peptides in the micro-RNA presursors and those peptides seemed to have a biological function. What this means is that part of the longer precursor RNA that is cleaved to produce the final micro-RNA may have a function that wasn't recognized. If you thought that the part of the precursor that was thought to be discarded as useless junk was, in fact, junk, then you were wrong—at least for some genes.

This is not a big deal and the authors of the paper don't even mention junk DNA.

The paper was reviewed by Peter M. Waterhouse and Roger P. Hellens in the same issue (Waterhouse and Hellens, 2015). They think it's a big deal. Here's what they say,

Student essays about evolution

Students in my molecular evolution course have to write an essay. They can pick any topic they like as long as it's related to evolution and some controversy in the scientific literature. I have to approve the topic. The idea is that the students have to critically evaluate both sides of an issue and pick a side that they can defend.

The essays tell me a lot about what things are interesting in the course and how well the students understand the topics. Here are this year's topics.

  • Education: Misconceptions in Evolutionary Biology
  • Are Transposable Elements Junk?
  • RNA World Hypothesis
  • Evolutionary Psychology and Biology: A Comparison
  • The End for the Alternative Search for Complexity
  • C-Value Paradox: Why Junk DNA Looks So Good
  • Will Humans Ever Be Perfectly Evolved?
  • Epigenetic Inheritance: A Turning Point in Evolution?
  • Back to Basics (about evolutinary biology eduaction)
  • The Relationship between Natural Selection and Artificial Selection
  • Foreign Gene Incorporation in Agriculture and in the wild: Debunking Anti-GMO Rhetoric and the "Unnatural" Fallacy
  • Enhancers: An Evo-Devo Perspective
  • Will humans stop evolving?
  • Genomic Screening: Currently Not Worth the Trouble
  • The Decade Long Argument Over Junk
  • What Is a Gene?
  • Sex: Is It Really Advantageous?
  • A Critical Analysis of Stephen Meyer's Darwin's Doubt; The Explosive origin of Animal Life and the Case for Intelligent Design
  • The Role of Natural Selection in the Process of Biological Human Evolution
  • The Struggle Between Humans and Bacterial Evolution
  • Drifting Away: Perspectives on Modern Evolution
  • The Continuing Struggle Against Junk DNA
  • The Evolution of Influenza A: Antigenic Drift at Work?

Wednesday, March 25, 2015

Another successful prediction of Intelligent Design Creationism?

The genetic code is redundant. Many amino acids have multiple codons ranging from two to six. The different codons for the same amino acid are called "synonymous" codons.

As sequences of protein-coding genes began to accumulate in the 1980s, it became apparent that different synonymous codons were used preferentially in different species. The phenomenon became known as codon bias. By 1990 it was known that the frequency of codon usage was correlated with tRNA abundance. As a general rule, there is a different tRNA for each codon and if multiple codons exist for a given amino acid then insertion of that amino acid into protein will depend on different tRNAs carrying the same amino acid.

Monday, March 23, 2015

Quantifying the "central dogma"

There was a short article in a recent issue of Science that caught my eye. The title was "Statistics requantitates the central dogma."

As most Sandwalk readers know, The Central Dogma of Molecular Biology says,
... once (sequential) information has passed into protein it cannot get out again (F.H.C. Crick, 1958)
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. (F.H.C. Crick, 1970)
You might wonder how you can quantify the idea that once information gets into protein it can't flow back to nucleic acids. You can't, of course.

The authors are referring to the standard scheme of information flow from DNA to RNA to protein. This is often mistakenly referred to as the Central Dogma by those scientists who haven't read the original papers. In this case, the authors of the Science article are asking whether the levels of protein in different cells are mostly controlled at the level of transcription, translation, mRNA degradation, or protein degradation.

Mary Lyon (1925 - 2014)

Mary Lyon died on Christmas day last December. She was 89 years old.

She was a famous mouse geneticist who spend most of her working career at the MRC labs in Harwell, United Kingdom (near Oxford). The labs are known as an international center for mouse genetics.

Mary Lyon is famous for discovering the phenomenon of X chromosome inactivation. This is when one the the X chromosomes of female mammals is selectively inactivated so that the products of the X chromosome genes are quantitatively similar to the dosage in males where there's only one X chromosome. The phenomenon used to be referred to as Lyonization.

I never met Mary Lyon but from what people say about her, I'm sure I would have liked her. Here's an excerpt from the obituary in Nature: Mary F. Lyon (1925 - 2014).
Lyon was a central figure in twentieth-century mouse genetics. She laid the intellectual foundations and developed the genetic tools for the use of mice as model organisms in molecular medicine, cell and developmental biology and in deciphering the function of the human genome. Lyon was editor of Mouse News Letter from 1956 to 1970, a publication that had a key role in establishing a mouse-focused research community in the pre-Internet age. She also helped to develop a common language for the field by chairing the Committee on Standardised Genetic Nomenclature for Mice from 1975 to 1990. Her pivotal contribution was recognized by the naming of the Mary Lyon Centre, an international facility for mouse-genetic resources, opened at Harwell in 2004, and by the creation of the Mary Lyon Medal by the UK Genetics Society in 2014.

Because everything Mary said was so carefully thought through, she could be difficult to talk to: on the phone, it was easy to think you had been cut off. She did not suffer fools gladly, but was a great supporter of the bright young scientist, often eschewing authorship of publications to enhance the profile of junior collaborators. She was intellectually rigorous but not dictatorial. When I began my PhD with her in 1977, she gave me a handful of papers, showed me the genetic tools — mice carrying the various mutations and chromosomal rearrangements — and said, “do something on X-inactivation”. That degree of academic freedom was exhilarating, coupled as it was with the safety net of robust critique.

... Her first love was mice, although she always had a cat — a tortoiseshell, of course.
X chromosome inactivation is one of the classic examples of epigenetics, sensu stricto. It was the subject of one of my most popular posts of all time: Calico cats. Calico cats almost always have to be female but there are very rare examples of male calico cats. Can anyone figure out why?

Sunday, March 22, 2015

On the handedness of DNA

Double-stranded DNA forms a helical structure where the two strands are twisted into a helical shape. If you think of the base pairs forming a ladder then imagine that the entire ladder could be distorted by rotating the ends relative to each other. The result would be the helical shape of DNA. The twisting results mainly from the attraction between the planar base pairs (rungs of the ladder.) They are "happier" when they are stacked close together right on top of each other. (The "force" is called "stacking interactions.")

This is not how DNA is actually built since there's never a time inside the cell when the DNA forms a ladder-like structure that's not helical, but you get the picture. [The Three-Dimensional Structure of DNA]

The final form of double-stranded DNA on the right is a cartoon used to illustrate certain features. I've deliberately drawn it with about 10-11 base pairs per turn so you can see the shape of the helix.

Saturday, March 21, 2015

Conrad Black attacks the shabby, shallow world of the militant, atheist

Conrad Black, also known as Baron Black of Crossharbour, KSG, was stimulated by a conversation with Christian apologist, and physicist, John Lennox. Black decided to write a column for the National Post (Toronto, Canada): Conrad Black: The shabby, shallow world of the militant atheist.

Richard Dawkins tweeted ...
Conrad Black seems to be at large again. Spot the factual errors, illogicalities and failures to understand.
Good advice. I wonder how many can be packed into a brief diatribe?

Keep in mind that no matter how many strawmen are erected, the important issue is whether gods exist. If you are a Christian, and you are going to attack the "shabby, shallow world" of atheists then the very least you can do is present your strongest case for the existence of gods.

Check out Conrad's Black's evidence for the existence of gods. (Warning: you will have to ignore all the rhetoric about the benefits of religion because it isn't relevant. On the other hand, there's a certain enjoyable irony in reading about how Christians are more moral than atheists.)

How the genome lost its junk according to John Parrington

I really hate it when publishers start to hype a book several months before we can read it, especially when the topic is controversial. In this case, it's Oxford University Press and the book is "The Deeper Genome" Why there is more to the human genome than meets the eye." The author is John Parrington.

The title of the promotion blurb is: How the Genome Lost its Junk on the Canadian version of the Oxford University Press website. It looks like this book is going to be an attack on junk DNA.

We won't know for sure until June or July when the book is published. Until then, the author and the publisher will have free reign to sell their ideas without serious opposition or push back.

Here's the prepublication hype. I'm going to buy this book and read it as soon as it becomes available. Stay tuned for a review.

Junk DNA comments in the New York Times Magazine

It's always fun to be quoted in The New York Times Magazine but there's a more serious issue to discuss. I'm referring to a brief article about online comments after Carl Zimmer published a piece on "Is Most of Our DNA Garbage?" a few weeks ago. If you read the comments under that article you'll discover that we have a lot of work to do if we are going to convince the general public that our genome is full of junk.

Wednesday, March 18, 2015

Richard Lenski answers questions about the long-term evolution experiment (LTEE)

Richard Lenski has a blog called Telliamed Revisited. He's been answering questions about his long-term evolution experiment and the latest answers are at: Questions from Jeremy Fox about the LTEE, part 2.
"Did the LTEE have any hypotheses initially, and if so, how were you going to test them?

Short answer: Yes, the LTEE had many hypotheses, some pretty clear and explicit, some less so. (What, did you think I was swimming completely naked?)"

Well worth reading ....

Economist Stephen Moore explains why we should mistrust science.

Stephen Moore is an conservative economist who writes for the Wall Street Journal. Here's a quote from the Wikipedia article ...
In a February 2, 2011 appearance on HBO's Real Time with Bill Maher, Moore stated "I say the Reagan tax cuts were the greatest economic policy of the last 50 years" and added "the lowest income people had the biggest gains" during the 1980s. found Moore's assertion to be false.
Moore thinks he's in a position to explain why scientists should not be trusted [The myth of ‘settled science’].
The magazine [National Geographic] is incredulous that so many skeptics "believe that climate activists are using the threat of global warming to attack the free market and industrial society generally."

Wait. Climate change activists are using the issue as a means of attacking free-market capitalism. This past summer major environmental groups gathered in Venezuela to solve leading environmental problems like global warming, concluding: “The structural causes of climate change are linked to the current capitalist hegemonic system.”

How is it paranoia to believe that the climate change industry wants to shut down capitalism when the movement plainly states that this is its objective? And how can a movement be driven by science when its very agenda violates basic laws of economics? I am no scientist, but I’m highly skeptical of a movement whose first advice is to steer the U.S. economy off a cliff toward financial ruin.
Well, there you have it. According to Stephen "I am no scientist" Moore, science can't be trusted because it violates the basic laws of economics, like those laws that Ronald Reagan must have obeyed when he instituted the greatest economic policy of the last 50 years.


Are gods a delusion?

John Lennox is a mathematician from Oxford (UK). He likes to attack the so-called "new atheists" and defend the idea that Christianity is rational. He is just finishing up a tour of North America. This video is a recording of a talk he gave at a church in the Toronto suburbs on March 14, 2015.

It's quite similar to the presentation he gave a few days later at the University of Waterloo (Waterloo, Ontario, Canada). Jeffrey Shallit went to that talk (bless his heart) and reports on the major fallacies and distortions [John Lennox - Talk #1: "Do Science and God Mix?"]. As you watch the video you'll see that John Lennox is a very good speaker. He sounds very, very, convincing in the tradition of many other religious Oxford professors and even atheist ones like Richard Dawkins.

As you listen and watch, you gradually come to the realization that the lecture is all about Irish charm and humor. Most of his arguments don't make any sense as we know from listening to them many times over the past few decades. How many times have we heard the argument that so-and-so Nobel Laureates were Christians so science and religion must be compatible?

Tuesday, March 17, 2015

Apparently it really is impossible to teach Intelligent Design Creationists about evolutionary theory

Last week I asked an important question, "Is it impossible to educate Intelligent Design Creationists on evolutionary theory?.

The reason I asked is because in spite of our best efforts over several decades, the Intelligent Design Creationists still don't understand modern evolutionary theory. We see this all the time whenever they start criticizing evolution. It gets them into all sorts of trouble, especially when we debate junk DNA.

Many of their objections to evolution would be easily answered if they only understood that there's more to evolution than natural selection and the appearance of design. They would understand why Michael Behe is wrong about the edge of evolution, for example, and why their pseudoscientific probability calculations are nonsense. They can't possibly understand molecular evolution and phylogenetic trees based on sequences unless they understand that it has almost nothing to do with "Darwinism" and the appearance of design.

Monday, March 16, 2015

Do offensive pictures justify violence?

This video raises many complicated issues. It's a confrontation between students and anti-abortion protestors on the University of Oregon campus on March 10, 2015.

Most of the buzz on the internet is about the first policeman who tried to defuse a potentially violent confrontation by telling the main protestor that he did not have the right to free speech on a private university campus. He almost succeeded in getting the protestor to hide his offensive signs.

When the sargeant showed up, he overruled his officer and told the protestor he could display his signs and stay on the campus. I agree with the sergeant but I have a great deal of sympathy with what the first policeman was trying to do.

How do Intelligent Design Creationists interpret "extraordinary evidence"?

Marcello Truzzi was one of the founding members of the Committee for the Scientific Investigation of Claims of the Paranormal (CSICOP). Back in 1978 he said, "An extraordinary claim requires extraordinary proof." Carl Sagan popularized this idea as "Extraordinary claims require extraordinary evidence."

The basic idea has been around for centuries.

We often use this saying when we encounter gullible creationists making extraordinary claims. For example, a few weeks ago Vincent Torley claimed that back in the 1600s a monk named St. Cupertino was routinely seen to fly through the air on numerous occasions [see What counts as "evidence"?].