Friday, August 28, 2015

Open Worm Project

“Isn’t it true,” he asks, “ that Darwin preserved a piece of vermicelli in a glass case, until by some extraordinary means it actually began to move with a voluntary motion?”
“Are you speaking of the worm,” asks Dr. Frankenstein snidely, hoping to crush the inquisitor with sarcasm, “or the spaghetti?”

 - Young Frankenstein

The empirical and the computational are coming together in the OpenWorm Project.  how easily and effectively can something as simple as a roundworm be modeled?
OpenWorm aims to build the first comprehensive computational model of the Caenorhabditis elegans (C. elegans), a microscopic roundworm. With only a thousand cells, it solves basic problems such as feeding, mate-finding and predator avoidance. Despite being extremely well studied in biology, this organism still eludes a deep, principled understanding of its biology. [emphasis mine]

A deep, principled understanding of a creature's biology would certainly be nice to have.

Thursday, August 27, 2015

Placentas Love Horizontal Gene Transfer

From a report titled "Mammals Made By Viruses":
What made syncytin peculiar was that it was not a human gene. It bore all the hallmarks of a gene from a virus.
Viruses have insinuated themselves into the genome of our ancestors for hundreds of millions of years. They typically have gotten there by infecting eggs or sperm, inserting their own DNA into ours. There are 100,000 known fragments of viruses in the human genome,  making up over 8% of our DNA. Most of this virus DNA has been hit by so many mutations that it’s nothing but baggage our species carries along from one generation to the next. Yet there are some viral genes that still make proteins in our bodies. Syncytin appeared to be a hugely important one to our own biology. Originally, syncytin allowed viruses to fuse host cells together so they could spread from one cell to another. Now the protein allowed babies to fuse to their mothers.
It could be that syncytin actually appears in viruses and is utilized for this purpose.  The article is really vague on this point, which would be interesting to know one way or the other.  The article seems to be saying that 8% of the human genome bears "all the hallmarks" of viral genes and are presumed on this basis to be viral in origin. Do the "so many mutations" refer to the differences between the animals that share the viral "junk" or between the viral "junk" and known ancestor genes in known viruses.  Toward the end:
The big picture that’s now emerging is quite amazing. Viruses have rained down on mammals, and on at least six occasions, they’ve gotten snagged in their hosts and started carrying out the same function: building placentas
Lightning has struck at least 6 times.  Curious and curiouser.  You'd think selection would work against tampering with essential reproductive tissues.  Well, think again.  Why is a breakdown of cells into multi-nucleate tissue is important for some animals and not for others?  There should be as much interest in what purpose is served by the difference than speculating on the mechanism for the difference.  The article says there are "all sorts of explanations for why that may be"... Why is it so hard to figure out why natural selection favored it?  What heuristic provides the predictive power for where the true explanation lies?

a theory so obvious

"Neo-Darwinian evolution is one of those theories that are so obvious, it must be protected from any criticism, lest it not seem so obvious."

Sunday, August 16, 2015

Jerry Coyne Demonstrates the Real Power of Selection

Jerry looking very evolved.
Just a quick post here, since it is too easy to dig deeply into these silly exercises of Coynage, but Jerry Coyne wrote a blog post in response to an email from Paul Nelson discussing the limits of natural selection as the explanatory show pony of the evolutionary circus, citing the work of various biologists.

Coyne frames this a "McLuhan moment" (Annie Hall reference) since he is such a big mucky-muck in the speculative science of squishy things that, unlike the Woody Allen character, he can in real life pull these great biologists "from behind the sign" and have them comment on whether Nelson understands their fine work.

But first, the relevant claim by Paul Nelson:
So when you [Jerry Coyne] tell your WEIT audience that natural selection is the only game in town for building complex adaptations, . . .  Readers who already know about the thinking of workers such as Eric Davidson, Michael Lynch, Andreas Wagner, John Gerhart & Marc Kirschner, or Scott Gilbert (all of whom, among many others, have recently expressed frank doubts about selection) must discount what you say about the centrality of natural selection to evolutionary theory . . .
To sum up, even though Coyne hollers loud and long that natural selection is the central, driving, omnipotent core of evolution, various noted biologists have "frank doubts" about the centrality of natural selection and/or unrestricted appeals to its creative power--specifically relevant to the alleged claim of Coyne (which he appears not to deny) that selection is by-and-large omnipotent and all-sufficient even if there are other evolutionary processes interfering along the way.  This counter-claim by Nelson is what Coyne will supposedly debunk.

Monday, August 10, 2015

Freeman Dyson, also a Secular Creationist

Freeman Dyson is a Christian in the same way that many Jewish people practice their religious traditions without believing their scriptures:
I am a practicing Christian but not a believing Christian. To me, to worship God means to recognize that mind and intelligence are woven into the fabric of our universe in a way that altogether surpasses our comprehension.
His point of view seems comparable to Paul Davies', Michael Denton's, Thomas Nagel's, and Rupert Sheldrake.

Watch it there, Freeman.  You are officially a secular creationist.  And a crank.