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Monday, December 19, 2011

Jonathan McLatchie and Junk DNA


Genomes & Junk DNA
Jonathan McLatchie takes on PZ Myers in a spirited attack on junk DNA [Treasure in the Genetic Goldmine: PZ Myers Fails on "Junk DNA"]. The Intelligent Design Creationists are convinced that most of our genome is functional because that's what a good designer would create. They claim that junk DNA is a myth and their "evidence" is selective quotations from the scientific literature. They ignore the big picture, as they so often due.

I discussed most of the creationist arguments in my review of The Myth of Junk DNA.

Jonathan McLatchie analyzes three argument made by PZ Myers in his presentation at Skepticon IV. In that talk PZ said that introns are junk, telomeres are junk, and transposons are junk. I have already stated that I diasgree with PZ on these points [see PZ Myers Talks About Junk DNA]. Now I want to be clear on why Jonathan McLatchie is wrong.
  1. Introns are mostly junk. I think PZ exaggerated a bit when he dismissed all introns as junk. My position is that we should treat introns as functional elements of a gene even though many (but not all) of them could probably be deleted without affecting the survival of the species. Each intron has about 50-80 bp of essential information that's required for proper splicing [Junk in Your Genome: Protein-Encoding Genes]. The rest of the intron, which can be thousand of base pairs in length, is mostly junk [Junk in Your Genome: Intron Size and Distribution]. Some introns contain essential gene regulatory regions and some contain essential genes. That does not mean that all intron sequences are functional.
  2. Telomeres are not junk. I don't think telomeres are junk [Telomeres]. They are absolutely required for proper DNA replication. PZ Myers agrees that telomeres (and centromeres) are functional DNA (28 minutes into the talk). Jonathan McLatchie claims that PZ describes telomeres as junk DNA, "Myers departs from the facts, however, when he asserts that these telomeric repetitive elements are non-functional." McLatchie is not telling the truth.
  3. Defective Transposons are Junk. PZ Myers talks about transposons as mobile genetic elements and states that transposons make up more than half of our genome. That's all junk according to PZ Myers. My position is that the small number of active transposons are functional selfish genes and the real junk is the defective transposon sequences that make up most of the genome [Transposon Insertions in the Human Genome]. Thus, I differ a bit from PZ's position. Jonathan McLatchie, like Jonathan Wells, argues that because the occasional defective transposon in the odd species has acquired a function, this means that most of the defective transposon sequences (~50% of the genome) are functional. This is nonsense.

[Image Credit: The image shows human chromosomes labelled with a telomere probe (yellow), from Christoher Counter at Duke University.]


PZ Myers said...

1. I agree. I was simplifying for a lay audience.

2. Of course I agree -- I put telomeres into the category of structural elements...they are no more junk than is regulatory DNA.

3. Now we get into tricky distinctions. Active transposons are functional from the transposons perspective...but from the human perspective? There are also known instances of the presence of transposons modulating other genes...but again, I didn't want to get into stuff like position effects for this audience.

Larry Moran said...

PZ says,

Active transposons are functional from the transposons perspective...but from the human perspective?

I'm thinking of it from the perspective of evolution, not what humans might or might not want to happen in their genome! Besides, from the human perspective, a few active parasites in your DNA doesn't make much difference.

Even worse, if you're a religious person then you have to accept that God wants you to have transposons. He designed your genome with that feature.

John Harshman said...

PZ makes the same point about transposons that I made the last time you brought this up. I all depends on how you look at it. Are they conserved by selection? Yes, if you consider the individual to be the individual transposon insertion and the population to be the set of insertions in a genome; transposons without inactivating mutations will reproduce, and others won't. No, if you consider the individual to be, well, the individual and the population to be the population of organisms. The sequences of individual transposon insertions, active or inactive, accumulate mutations at the neutral rate. And I call that junk. It seems to me that your answer doesn't work, since both these perspectives are the perspective of evolution.

Corneel said...

Larry said
I'm thinking of it from the perspective of evolution, not what humans might or might not want to happen in their genome!

That I do not understand. The entire genome is the product of evolution. The only reason to label some of it "junk" is if it is not functional from the perspective of the organism.
What makes defective transposons junk and active transposons not?

The Other Jim said...

Corneel said...
What makes defective transposons junk and active transposons not?

Take someone infected by HIV - are the RT'd chromosomal inserts junk or not? I would suggest they are not, and are functional DNA - but the "property" of the viral parasite.

Now if a defective copy of the genome somehow got into a germcell and was inherited...

Corneel said...

The other Jim said:
I would suggest they are not, and are functional DNA - but the "property" of the viral parasite.

I understand your argument, but I think the issue of "ownership" is a bit tricky. Does a transposon become the property of its host once it is defective? And is it sufficient that the transposase is nonfunctional or should it be completely incapable of transposing?

If you don't mind, I will subscribe to the notion that the chromosomal inserts have become -at least temporarily- part of the genome, and are junk. Otherwise you end up with legal discussions in a biology class ;-)

Bayesian Bouffant, FCD said...

If Jonathan McLatchie is actually learning something about biology, how long will it be before his head explodes, or he stops touting ID?

The whole truth said...

An irritating thing about McLatchie is that he starts his sermon on UD, where opposing comments are severely restricted, and then links to the rest of his sermon on ENV, where no comments are allowed.

He opposes Moran but doesn't have the guts to do it here. In typical IDiot fashion, he just wants to preach, and not engage in open and honest discussion.

The whole truth said...

PZ said:

"I was simplifying for a lay audience."

Oversimplification can be a bad thing, especially if it creates wrong impressions. Of all people you should realize that every word you speak will be scrutinized (and not just by your religious opponents), so you should be very careful with your choice of words, even with a so-called "lay audience".

The Other Jim said...

@ Corneel

Leave it to biology to ignore our human logic and social constructs ;-)

Yahya Snow said...

McLatchie is better off sticking to talking about science. He recently began talking about Islam and has left a trail of blunders: