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Sunday, June 13, 2010

Nicholas Wade Writes about Genomes and Evolution

His fellow science writers often think that Nicholas Wade is among the best of their ilk. Wade writes for the New York Times and his latest article is: A Decade Later, Genetic Map Yields Few New Cures. A couple of paragraphs from that article deserve some kind of award.

But while 10 years of the genome may have produced little for medicine, the story for basic science has been quite different. Research on the genome has transformed biology, producing a steady string of surprises. First was the discovery that the number of human genes is astonishingly small compared with those of lower animals like the laboratory roundworm and fruit fly. The barely visible roundworm needs 20,000 genes that make proteins, the working parts of cells, whereas humans, apparently so much higher on the evolutionary scale, seem to have only 21,000 protein-coding genes.

The slowly emerging explanation is that humans and other animals have much the same set of protein-coding genes, but the human set is regulated in a much more complicated way, through elaborate use of DNA’s companion molecule, RNA.

Thanks to Jonathan Eisen at The Tree of Life, Nicholas Wade can now add the "Twisted Tree of Life Award" to his many others [Twisted tree of life award #5: Nicholas Wade & use of higher, lower, ladders, etc].

You see, Wade makes one of the most fundamental errors of evolutionary thinking when he writes about "higher" and "lower" on the "evolutionary scale."

There are two other flaws in his quoted excerpt. First, it did not come as a big surprise to all scientists that humans had about the same number of genes as other animals. That's a myth based on overemphasizing the opinions of some people and underemphasizing the opinions of the experts [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome]. This is part of what I call The Deflated Ego Problem and it's not endemic. It can be cured by reason.

Second, the explanations for similar numbers of genes in animals come from genetics and developmental biology over the past fifty years. It may have been "slowly emerging" back when I first started teaching but it's now fully emerged and has been for twenty years. Long before the human genome was sequenced we knew that major morphological changes could be caused by small mutations in regulatory sequences. During the 1980s and 1990s it became apparent that animals such as Drosohila and humans shared many important development genes1 and even more of the genes involved in basic metabolism. This was not a surprise.

It may be true that RNA places a much more important role in regulating gene expression than we thought. The jury is still out on that one. However, even if RNA is part of the regulation picture that fact does not change the basic principle that molecular biologist developed over the past thirty years; namely, that the same basic gene set is just regulated differently in different animals. This is the contribution of Evo-Devo.

There's one other logical flaw made by those with deflated egos. What they're looking for is some specific mechanism that explains the marvelous complexity of humans relative to the "lowly" fruit fly or nematode. What they need in order to satisfy this longing is a mechanism that we have and they don't. As far as I know, there isn't (hardly) anyone who claims that regulatory RNAs have only evolved in humans. The genome sequences of all animals is pointing in the same direction. If there are abundant regulatory RNAs then there are lots in nematodes and fruit flies as well. It's not going to solve the pseudoproblem that Nicholas Wade imagines.

1. Perhaps you've heard of homeotic genes and HOX genes?


Jonathan Eisen said...

Nice background - wish I had remembered who had written the discussion of genes in the human genome from years before I wanted to refer to ... now I know it was you. Gonna add it to my post ...

Todd I. Stark said...

This is really fascinating context for the issue.

It amazes me how much of a gap there is between expert knowledge and popular impression of that knowledge. This really speaks to the importance of *good* science writing and the necessity of evaluating science writing and appreciating the good writers.

Psi Wavefunction said...

Funny enough, the ciliate use of non-coding RNA and other epigenetic gymnastics makes that of animals and plants pale in comparison... which makes sense, as I'm convinced ciliates ARE the higher eukaryotes =P

Kat said...

I came across your blog (which I enjoyed, by the way) for the first time today because it was linked to by PZ Meyers. I subscribe to the science blog feeds because I am about to begin transitioning to a bioinformatics major from computer science.
I've read enough on genetics and biology that I found the Times writer's shock at the small gene difference silly, but I didn't know to take issue with the "evolutionary ladder" comment. Perhaps you, Jonathan, or PZ could do a small evolutionary primer to further elucidate the errors in the "evolutionary laddder" comment for those with minimal evolution knowledge?

Psi Wavefunction said...

@Katie (hope you don't mind a response from a random blogger...)

Simple: All extant lifeforms have been evolving the same amount, the same length of time. No life form is 'more' or 'less' evolved than any other. When we say a certain organism is more or less 'derived' or 'modified', it's really a lousy shorthand for saying that a specific, very narrow, feature we are looking at has changed more in one organism than another with respect to the -inferred- ancestral state (which we don't actually ever know, as we were never there).

In fact, if you ever see anyone, including professional biologists, utter things like "species x is more derived/evolved than species y", feel free to give them a dirty look. They should, in theory, know better.

As for extinct species, an argument could be made that they evolved a lesser duration of time than modern ones; though it is a very weak and pointless argument considering the directionless nature of evolution itself.

We're all ~3.5 billion years old.

Disclaimer: Being a protistologist, I do have a strong personal interest against the evolutionary ladder. I'm sick of people referring to my organisms as 'primitive' or 'lower'. From the perspective of cell biology, most protist cells are far more complex and sophisticated* than animal or plant cells could ever dream to be.

With respect to biochemistry and genetic diversity, prokaryotes kick our sorry little asses all the way to outer space.

*no real definition of complexity/sophistication exists either, FYI.

Anonymous said...

Psi, I'd like to suggest that we are are actually less evolved than "lower life forms". We're all the same number of years old, but they have both larger population bases and gone through a great many more generations in that time than our esteemed K-selected selves.

Evolution = random mutation + natural selection.

Natural selection is perpetually ongoing, but (persistent Germ-line) mutation happens once per generation.

Geometric Optics said...

Psi, I'd like to suggest that we are are actually less evolved than "lower life forms". We're all the same number of years old, but they have both larger population bases and gone through a great many more generations in that time than our esteemed K-selected selves.

Evolution = random mutation + natural selection.

Natural selection is perpetually ongoing, but (persistent Germ-line) mutation happens once per generation.

Georgi Marinov said...

Another outrageous line:

"chip sequencing, which gives researchers access to the mysterious and essential chromatin, the complex protein machinery that both packages the DNA of the genome and controls access to it"

If you don't know what ChIP stands for, you have no business writing about genomes...

Georgi Marinov said...

Psi, I'd like to suggest that we are are actually less evolved than "lower life forms". We're all the same number of years old, but they have both larger population bases and gone through a great many more generations in that time than our esteemed K-selected selves.

And we also have a lot more non-adaptive and maladaptive traits due to the effects of small population size. Which is also completely left out of the discussion 99% of the time, while it is absolutely essential for understanding the subject

Unknown said...

Assigning a value hierarchy to species in terms of evolution sounds a little like the sort religious thinking that spawned the great chain of being.

Psi Wavefunction said...

Geometric Optics and Georgi:
Yes, I do completely agree that in some [most?] ways we are 'less' evolved - retardedly long generation spans and small eff pop size (Ne) make us quite awkward. In fact, I like to argue that multicellularity as a whole is rather stupid in many ways, and is an example of [constructive] neutral evolution gone mad. Rapid morphological diversification is not necessarily a sign of success, and makes sense for multicel things:

multicellularity leads to larger, more resource-demanding organisms with longer generation spans, which crudely-speaking leads to lower Ne, which leads to more rampant drift and fixation of slightly deleterious alleles; since there are more ways to have complexity bloated than reduced while remaining functional, this tends to lead to more cumbersome lifeforms that can persist due to low Ne and inhabiting a different niche from the more streamlined competition, which enables more drift and such... and we end up with utterly stupidly 'designs' like large metazoa. The positive feedback tendencies of the system would explain how [morphological] diversification and complexity 'bloating' can happen so rapidly in a short period of time.

On a smaller scale, a similar thing must've happened around the time of eukaryogenesis.

Of course, the above view is a bit of a minority one, so I wouldn't really push it onto the public just yet. Many evolutionary biologists still dismiss non-adaptationist views. Step 1 is dispelling the scala naturae myth, and it's still not finished...

For anyone interested, I do have a few posts pertaining to neutral evolution over on my blog... [/shameless advertising]

Georgi Marinov said...

@ Psi Wavefunction:

It may be a minority view, but it neatly explains a lot of observations and will eventually have to adopted widely.

It has some very deep theological implications though (it pretty much completely destroys even Francis Collins' and Ken Miller's claims about evolution and God, or at least it makes them even more obviously equivalent to Old Earth Creationism), so it will be a tough pill to swallow for many. I am actually surprised that no creationists have attacked it yet, but that's probably because they can't understand the science behind it.

Jud said...

On Katie's question, from an absolute amateur (I'm not a geneticist/biologist):

Stephen Jay Gould wrote about conceiving evolution as a bush against a wall.

Evolution begins at a quite simple level - self-replicating molecules, let's say. Now evolution is undirected, so it branches out like a bush from ancestors to progeny. But if the self-replicating molecules get any simpler, they're no longer self-replicating and no longer capable of evolving. That's the "wall." There is no barrier in the other direction (greater complexity).

So multicellular species evolve with multicellular versions of vital systems like respiration, digestion, excretion, reproduction, etc. Meanwhile quite simple virii and unicellular life forms evolve to out-compete or coopt the original self-replicating molecules, and they evolve into lots more species of virii and unicellular life forms.

Some folks look at this situation and see an evolutionary direction from lesser to greater complexity. But that's an illusion caused by the fact that undirected evolution proceeds in all directions, except where evolution toward greater simplicity would produce non-life.

Anonymous said...

Oh knows! The christian isn't going to like being just another form of life, they might even prefer to be lower on the ladder than being totally without.

Christians should be happy that they aren't higher than (non-talking) snakes. However, christians should always bray for talking snakes and thank them for making the christian experience possible.

Monado said...

People who are in an ego-boosting competition with the other organisms to have more genes would do well to remember that onions have about 50,000, if I recall correctly.

Kat said...

What Jud said..that also was my rationale for why I thought there was an evolutionary ladder.
Thanks for the clarification, Jud, and also Psi.