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Sunday, January 13, 2019

Most popular Sandwalk posts of 2018

Blogging was light last year because I was busy with other things and because the popularity of blogs is declining rapidly. The most popular post, based on the number of views, garnered only 9229 views, which is more than the most popular post of 2017 but only half as much as the most popular post of 2016. The post with the most comments (53) has almost 10X fewer comments than posts from a few years ago but that's partly because more people are commenting on Facebook and because I'm restricting blog comments in various ways.

Here's the most popular post by total views. It attracted a number of people who attempted, rather unsuccessfully, to defend evolutionary psychology.
Is evolutionary psychology a deeply flawed enterprise?

You may disagree with these criticisms of evolutionary psychology but there's no denying that the discipline is under attack. In fact, it's hard to think of any other academic discipline whose fundamental validity is being questioned so openly.
The post with the most comments generated a lively discussion about Neutral Theory and Nearly-Neutral Theory and I learned a lot.

Celebrating 50 years of Neutral Theory
The journal of Molecular Biology and Evolution has published a special issue: Celebrating 50 years of the Neutral Theory. The key paper published 50 years ago was Motoo Kimura's paper on “Evolutionary rate at the molecular level” (Kimura, 1968) followed shortly after by a paper from Jack Lester King and Thomas Jukes on "Non-Darwinian Evolution" (King and Jukes, 1969).
One of my posts that took a lot of work is also one that I think is pretty informative.
How many protein-coding genes in the human genome?

There are many ways of predicting protein-coding genes using various algorithms that look for open reading frames. The software is notorious for overpredicting genes leading to many false positives and that's why every new genome sequence contains hundreds of so-called "orphan" genes that lack homologues in other species. When these predicted genes are examined more closely they turn out to be artifacts—they are not functional genes.
I figured out how to do pie charts and how to represent the overlapping categories of junk DNA (e.g. defective transposons within introns). You can see my first attempt in the figure at the top of the page but watch for an update in the post below.
What's In Your Genome? - The Pie Chart

This adds up to 8% of the genome. The remaining 92% is junk.

Most of the junk consists of: (1) very obvious examples of broken genes (pseudogenes 5%); (2) bits and pieces of transposon sequences that used to be capable of transposing but have mutated over time (45%); and (3) ancient viral sequences that have degenerated (9%). That's 59% of the genome that's clearly junk DNA. In addition, there's plenty of evidence that most intron sequences are dispensable. That accounts for another 28% of the genome. The total amount of junk DNA is at least 87%.

Note that protein-coding genes take up about 23% of the genome (1% exons, 22% introns). Genes for functional noncoding RNAs take up an additional 7% of the genome (1% exons, 6% introns). (Much of the functional region of noncoding RNA genes consists of 300 copies of ribosomal RNA genes (0.4%).) The important point is that roughly 30% of the genome is genes when we define a gene as a DNA sequence that's transcribed. A lot of this is junk within introns.


Jass said...

If you hadn't banned all those Darwinists, they could have helped your blog a little...possibly...

John Harshman said...

Looking forward to that book, by the way.

Jass said...

Looking forward to reviewing the book...
Hope there is still some junk left other than the book...

John Harshman said...

Your first name is clearly Hugh.