Wednesday, September 13, 2017

Sequencing human diploid genomes

Most eukaryotes are diploid, including humans. They have two copies of each autosome. Thousands of human genomes have been sequenced but in almost all cases the resulting genome sequence is a mixture of sequences from homologous chromosomes. If a site is heterogeneous—different alleles on each chromosome—then these are entered as variants.

Monday, September 11, 2017

What's in Your Genome?: Chapter 4: Pervasive Transcription (revised)

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! The first chapter is an introduction to genomes and DNA [What's in Your Genome? Chapter 1: Introducing Genomes ]. Chapter 2 is an overview of the human genome. It's a summary of known functional sequences and known junk DNA [What's in Your Genome? Chapter 2: The Big Picture]. Chapter 3 defines "genes" and describes protein-coding genes and alternative splicing [What's in Your Genome? Chapter 3: What Is a Gene?].

Chapter 4 is all about pervasive transcription and genes for functional noncoding RNAs. I've finally got a respectable draft of this chapter. This is an updated summary—the first version is at: What's in Your Genome? Chapter 4: Pervasive Transcription.

Saturday, September 09, 2017

Cold Spring Harbor tells us about the "dark matter" of the genome (Part I)

This is a podcast from Cold Spring Harbor [Dark Matter of the Genome, Pt. 1 (Base Pairs Episode 8)]. The authors try to convince us that most of the genome is mysterious "dark matter," not junk. The main theme is that the genome contains transposons that could play an important role in evolution and disease.

Wednesday, August 30, 2017

Experts meet to discuss non-coding RNAs - fail to answer the important question

The human genome is pervasively transcribed. More than 80% of the genome is complementary to transcripts that have been detected in some tissue or cell type. The important question is whether most of these transcripts have a biological function. How many genes are there that produce functional non-coding RNA?

There's a reason why this question is important. It's because we have every reason to believe that spurious transcription is common in large genomes like ours. Spurious, or accidental, transcription occurs when the transcription initiation complex binds nonspecifically to sites in the genome that are not real promoters. Spurious transcription also occurs when the initiation complex (RNA plymerase plus factors) fires in the wrong direction from real promoters. Binding and inappropriate transcription are aided by the binding of transcription factors to nonpromoter regions of the genome—a well-known feature of all DNA binding proteins [see Are most transcription factor binding sites functional?].

Sunday, August 27, 2017

The Extended Evolutionary Synthesis - papers from the Royal Society meeting

I went to London last November to attend the Royal Society meeting on New trends in evolutionary biology: biological, philosophical and social science perspectives [New Trends in Evolutionary Biology: The Program].

The meeting was a huge disappointment [Kevin Laland's new view of evolution]. It was dominated by talks that were so abstract and obtuse that it was difficult to mount any serious discussion. The one thing that was crystal clear is that almost all of the speakers had an old-fashioned view of the current status of evolutionary theory. Thus, they were for the most part arguing against a strawman version of evolutionary theory.

The Royal Society has now published the papers that were presented at the meeting [Theme issue ‘New trends in evolutionary biology: biological, philosophical and social science perspectives’ organized by Denis Noble, Nancy Cartwright, Patrick Bateson, John Dupré and Kevin Laland]. I'll list the Table of Contents below.

Most of these papers are locked behind a paywall and that's a good thing because you won't be tempted to read them. The overall quality is atrocious—the Royal Society should be embarrassed to publish them.1 The only good thing about the meeting was that I got to meet a few friends and acquaintances who were supporters of evolution. There was also a sizable contingent of Intelligent Design Creationists at the meeting and I enjoyed talking to them as well2 [see Intelligent Design Creationists reveal their top story of 2016].

Friday, August 25, 2017

Niles Eldredge explains punctuated equilibria

Lots of people misunderstand punctuated equilibria. It's a theory about small changes leading to speciation. In many cases the changes are so slight that you and I might not notice the difference. These are not leaps or saltations and there are no intermediates or missing links. The changes may be due to changes in the frequency of one or two alleles.

Punctuated equilibria are when these speciation events take place relatively quickly and are followed by much longer periods of stasis (no change). Niles Eldredge explains how the theory is derived from his studies of thousands of trilobite fossils.

Niles Eldredge explains hierarchy theory

You may not agree but you should at least know what some evolutionary biologists are thinking.

How much of the human genome is devoted to regulation?

All available evidence suggests that about 90% of our genome is junk DNA. Many scientists are reluctant to accept this evidence—some of them are even unaware of the evidence [Five Things You Should Know if You Want to Participate in the Junk DNA Debate]. Many opponents of junk DNA suffer from what I call The Deflated Ego Problem. They are reluctant to concede that humans have about the same number of genes as all other mammals and only a few more than insects.

One of the common rationalizations is to speculate that while humans may have "only" 25,000 genes they are regulated and controlled in a much more sophisticated manner than the genes in other species. It's this extra level of control that makes humans special. Such speculations have been around for almost fifty years but they have gained in popularity since publication of the human genome sequence.

In some cases, the extra level of regulation is thought to be due to abundant regulatory RNAs. This means there must be tens of thousand of extra genes expressing these regulatory RNAs. John Mattick is the most vocal proponent of this idea and he won an award from the Human Genome Organization for "proving" that his speculation is correct! [John Mattick Wins Chen Award for Distinguished Academic Achievement in Human Genetic and Genomic Research]. Knowledgeable scientists know that Mattick is probably wrong. They believe that most of those transcripts are junk RNAs produced by accidental transcription at very low levels from non-conserved sequences.

Monday, August 07, 2017

A philosopher defends agnosticism

Paul Draper is a philosopher at Purdue University (West Lafayette, Indiana, USA). He has just (Aug. 2, 2017) posted an article on Atheism and Agnosticism on the Stanford Encyclopedia of Philosophy website.

Many philosphers use a different definition of atheism than many atheists. Philosophers tend to define atheism as the proposition that god(s) do not exist. Many atheists (I am one) define atheism as the lack of belief in god(s). The distinction is important but for now I want to discuss Draper's defense of agnosticism.

Keep in mind that Draper defines atheism as "god(s) don't exist." He argues, convincingly, that this proposition cannot be proven. He also argues that theism—the proposition that god(s) exist—can also not be proven. Therefore, the only defensible position for a philosopher like him is agnosticism.

Friday, August 04, 2017

To toss or not to toss?

Now that I'm officially retired I've been cleaning out my office at the university and transferring all the important stuff to my home office. I'm taking advantage of this opportunity to throw out everything that I don't want any more. Eventually I'll have to vacate my university office because it's due to be renovated and transferred to another department.

Some stuff is easy to toss out and some stuff is easy to keep. It's the other stuff that causes a problem. Here's an example ....

These are the manuals that came with my very first PC back in 1981. I know I'll never use them but I'm kinda attached to them. Are they antiques yet?

Thursday, July 27, 2017 evolves

The newsgroup was created more than 30 years ago. It's been a moderated newsgroup for the past twenty years. The moderator is David Greig and the server, named "Darwin," has been sitting in my office for most of that time. I retired on June 30th and my office is scheduled for renovation so Darwin had to move. Another complication is that the moderator is moving from Toronto to Copenhagen, Denmark.

So evolves and the server is moving elsewhere. Goodby Darwin.

Friday, July 14, 2017

Bastille Day 2017

Today is the Fête Nationale in France known also as "le quatorze juillet" or Bastille Day.

This is the day in 1789 when French citizens stormed and captured the Bastille—a Royalist fortress in Paris. It marks the symbolic beginning of the French revolution although the real beginning is when the Third Estate transformed itself into the National Assembly on June 17, 1789 [Tennis Court Oath].

Ms. Sandwalk and I visited the site of the Bastille (Place de la Bastille) when we were in Paris in 2008. There's nothing left of the former castle but the site still resonates with meaning and history.

One of my wife's ancestors is William Playfair, the inventor of pie charts and bar graphs [Bar Graphs, Pie Charts, and Darwin]. His work attracted the attention of the French King so he moved to Paris in 1787 to set up an engineering business. He is said to have participated in the storming of the Bastille but he has a history of exaggeration and untruths so it's more likely that he just witnessed the event. He definitely lived nearby and was in Paris on the day in question. (His son, my wife's ancestor, was born in Paris in 1790.)

In honor of the French national day I invite you to sing the French national anthem, La Marseillaise. An English translation is provided so you can see that La Marseillaise is truly a revolutionary call to arms. (A much better translation can be found here.)1

1. I wonder if President Trump sang La Marseillaise while he was at the ceremonies today?

Check out Uncertain Principles for another version of La Marseillaise—this is the famous scene in Casablanca.

Reposted and modified from 2016.

Revisiting the genetic load argument with Dan Graur

The genetic load argument is one of the oldest arguments for junk DNA and it's one of the most powerful arguments that most of our genome must be junk. The concept dates back to J.B.S. Haldane in the late 1930s but the modern argument traditionally begins with Hermann Muller's classic paper from 1950. It has been extended and refined by him and many others since then (Muller, 1950; Muller, 1966).

Thursday, July 06, 2017

Scientists say "sloppy science" more serious than fraud

An article on Nature: INDEX reports on a recent survey of scientists: Cutting corners a bigger problem than research fraud. The subtitle says it all: Scientists are more concerned about the impact of sloppy science than outright scientific fraud.

The survey was published on BioMed Central.