GreyThumb.Blog

An article in this morning's New York Times discusses the trade offs between the capacity to learn versus automatic responses, particularly focusing on insects and their ability to learn.

From the article:

"It takes just 15 generations under these conditions for the flies to become genetically programmed to learn better. At the beginning of the experiment, the flies take many hours to learn the difference between the normal and quinine-spiked jellies. The fast-learning strain of flies needs less than an hour.

"But the flies pay a price for fast learning. [Dr. Tadeusz Kawecki, an evolutionary biologist at the University of Fribourg] and his colleagues pitted smart fly larvae against a different strain of flies, mixing the insects and giving them a meager supply of yeast to see who would survive. The scientists then ran the same experiment, but with the ordinary relatives of the smart flies competing against the new strain. About half the smart flies survived; 80 percent of the ordinary flies did."

And this interesting fact:

"Humans’ oversize brains require 20 percent of all the calories burned at rest."

There's a neat video posted on YouTube of a self organizing robot from the Mod Lab at UPenn that repairs itself after getting kicked apart.

Olivia Judson has a good article in today's New York Times about species that have coevolved to form beneficial associations with one another. The article discusses the mutualisms between shrimp and goby; leaf cutter ants and their harvested fungi; and coral and algae, among others.

This is a reminder that Dr. Carlos Gershenson will be presenting on the design and control of self-organizing systems.

See the Meetings Page for more information.

This video by Dr. Deborah Gordon gives a good overview of task allocation in ants, focusing on how simple, local rules can bring about complex, dynamic behavior without any central organization. It was given at the 2003 TED conference.

There are two articles on the use of ALife themes in video games that I'd like to point out. One is on the autonomy of characters in the game S.T.A.L.K.E.R. and the other is on the living environment and creatures in the game Dwarf Fortress.

S.T.A.L.K.E.R. features up to 1000 non-player characters with independent lives, goals and interactions that exist beyond the realm of the player's vicinity.

Dwarf Fortress is a complex, ASCII graphics based, independent game that features a fractally generated ecosystem, populated with thousands of persistent creatures with a dynamic economy.

In Olivia Judson's latest blog entry, she performs a thought experiment of how evolution would work if suddenly mutation no longer took place. To summarize, evolution would continue (by mixing and matching from the current levels of diversity) for a long, long time.

One interesting anecdote from the article:

"In general, however, it’s hard to know for sure how old an old seed is. But thanks to the foresight of a certain Dr. William James Beal, a seed viability experiment has been going on in East Lansing, Michigan, for more than 120 years. In 1879, Dr. Beal buried 20 bottles each containing sandy soil and a mixture of seeds from 21 different species. At regular intervals, a bottle is dug up, and the sand-seed mix is transferred into a shallow tray of soil and watered. Most recently —the 120th year — 26 seeds from three different species sprouted, and several of the plants went on to produce normal seeds in turn. The next bottle is due to be dug up in 2020."

Tom De Smedt has posted some pretty cool images and information from an evolving ecosystem of plant life called Superfolia. Superfolia is built atop NodeBox, which in turn is built atop Processing. Both Processing and NodeBox are open source and available for download.

Alex Champandard has put together a great collection of papers and web sites regarding evolving virtual creatures.

This is a great first stop for information and has links to research by Karl Sims, Nicolas Lassabe, Gene Ruebsamen, Thomas Miconi, Josh Bongard, Russel Smith, Maciej Komosinski, Szymon Ulatowski, Gregory Hornby and Jordan Pollack.

The creatures featured range from the early Sims creatures to flying creatures and humanoids.

In Today's blog entry by Olivia Judson in the Times, she writes about what we can extrapolate from different types of fossils.

The part of the article that struck me is as follows:

"Genomes are made of DNA, so the bigger the genome an organism has, the more DNA it has in each cell. This, in turn, affects the volume of the cells. And although different types of cells within an organism have different characteristic volumes, all of them are affected by the amount of DNA they contain. So if you compare cells of the same type across a range of related species, you’ll find that differences in sizes reflect differences in how much DNA the cells have. (Some estimates suggest that as much as half of the variation in cell size of a given type can be accounted for by differences in genome size.)

"The volumes of some types of cell can be measured from fossil skeletons or leaves. Which gives a method for estimating the genome sizes of organisms long extinct. For instance, the size of osteocytes — bone cells — can be measured from cross sections of fossil bone. Similarly, in plants, you can measure the size of guard cells in fossil leaves. (Guard cells border the pores, known as stomata, through which plants take up carbon dioxide and excrete oxygen and water vapor.) "

A recent conference, organized by the NCSE and the AAAS, was held to discuss the state of the art in the field of evolution, as well as the misunderstandings of the field by the general public.

I think one of the points made cannot be stressed enough: that the origin of life is not directly part of evolutionary theory, but rather, is a separate field of its own that shares many of the same principles.

From a write up of the conference by Ars Technica:
"Evolutionary theory, both as proposed by Darwin and elaborated since, deals with the diversification of modern living organisms from a limited number of ancestral living organisms. But the lack of a strong theory for the origin of life is actually treated as an argument against evolution by many of the opponents of teaching the theory. Many of the principles of evolution, including heritable variations and selective pressures, are also applied by origin of life researchers. As such, the two topics appear inextricably linked."

Another researcher, Ted Daeschler, spoke about gaps in the fossil record regarding the transition from water to land some 400 million years ago. Many of those gaps have been filled in in recent decades, though largely out of sight to the public at large. Based upon theory, paleontologists have targeted areas that have been very fruitful in yielding new specimens.

The main subjects of discussion were the following: the origin of life (with recent understandings of RNA), the Cambrian explosion, vanishing gaps in the fossil record, the origins of modern humans, and finally, getting the message to the public. Each of these is detailed in the article.

There is an article in this morning's Times about the research of Dr. Kay Holekamp, of Michigan State University. Dr. Holekamp studies the complex interactions within spotted hyena societies. Apparently, primates are not the only ones with complex, hierarchical social dynamics in large groups.

"Spotted hyena societies have one dominant female at the top, and a series of hyenas below her. Each cub learns exactly where it fits into the hierarchy, and where all the other spotted hyenas fit as well...

"There are times, however, when the entire group of hyenas comes together. Spotted hyena clans patrol the borders of their territory together, marking it with their urine. A kill near a border can provoke a conflict with a neighboring clan. 'When the whole group territory is on the line,' Dr. Holekamp said, 'all these unrelated individuals join forces and engage in a clan war.'”

From the BBC article:

"Within hours of their creation, the nucleus, containing DNA from the mother and father, was removed from the embryo, and implanted into a donor egg whose DNA had been largely removed.

"The only genetic information remaining from the donor egg was the tiny bit that controls production of mitochondria - around 16,000 of the 3billion component parts that make up the human genome."

Olivia Judson's latest blog entry examines how mutations to the switches that affect when and if a protein is created may play a more important role than mutations that actually affect the protein itself.

From the article:

"We know that some of that 98 percent [of the genome] is involved not in making proteins, but in regulating where and when the genes they are made from will get switched on. The biology of this gets pretty complicated — but what it amounts to is that most genes have an elaborate control region — a set of on/off switches officially known as cis-regulatory elements. When the right switches are on, the protein gets made; when they are off, it doesn’t. So mutations to the switches can alter how the protein is deployed. Then, the protein stays the same shape as it was before, but instead of being made in, say, just the liver, it starts being made somewhere else as well."

From the article:

"Yet when the Venter team began sampling the [deep mid-ocean] waters for the most basic evidence of life, the presence of genetic material, they found themselves practically awash in novel DNA. 'From our random sequencing in the ocean, we uncovered six million new genes,' he said, genes, that is, unlike any yet seen in any of the mammals, reptiles, worms, fish, insects, fungi, microbes or narcissists that have been genetically analyzed so far. With just that first-pass act of nautical sequencing, Dr. Venter said, 'we doubled the number of all genes characterized to date.'"

Also, the Endy Lab's BioBricks project is mentioned.

From the article:

"Over a quarter-century, the frozen ammonia-cyanide blend had coalesced into the molecules of life: nucleobases, the building blocks of RNA and DNA, and amino acids, the building blocks of proteins...

"But strange things happen when you freeze chemicals in ice. Some reactions slow down, but others actually speed up—especially reactions that involve joining small molecules into larger ones. This seeming paradox is caused by a process called eutectic freezing. As an ice crystal forms, it stays pure: Only molecules of water join the growing crystal, while impurities like salt or cyanide are excluded. These impurities become crowded in microscopic pockets of liquid within the ice, and this crowding causes the molecules to collide more often. Chemically speaking, it transforms a tepid seventh-grade school dance into a raging molecular mosh pit...

"Freezing also helps preserve fragile molecules like nucleobases, extending their lifetime from days to centuries and giving them time to accumulate and perhaps organize into something more interesting—like life...

"For decades researchers had tried to coax RNA chains to form under all sorts of conditions without using enzymes; the longest chain formed, which Orgel accomplished in 1982, consisted of about 40 nucleobases. So when Biebricher analyzed his own samples, he was amazed to see RNA molecules up to 400 bases long...

New research suggests that flocking birds (in this case starlings) keep track of a fixed number of their nearest neighbors regardless of distance, not just those within a given radius.

From the article:

"Current computer models assume that each bird interacts with all birds within a certain distance. But the new observations, however, show that each bird keeps under control a fixed number of neighbours - seven other starlings - irrespective of their distance, which is the secret of how they stick together."