Wednesday, June 18. 2008
Spore
The free trial of the Creature Creator for Spore has been released. Though not a proper ALife simulation, per se, hopefully Spore may stoke interest in ALife. Either way, I'm looking forward to playing with it.
Thursday, June 12. 2008
the Great 2008 Biota Podcast CD Give-Away
I'm in the process of assembling the masters for the Biota CD that will be distributed at ALIFE XI. Due to the economies of such a press I will have a substantial number of additional CDs (100s in fact) looking for good distribution points.
I think universities and similar institutions should provide good drop points but I need logistical interest and assistance. If you have a good location for 10-plus CDs, please get in contact and I will start assembling postage lists and work out the logistics and costs of getting these CD bundles out.
Please note these are free giveaway CDs intended to be passed on to multiple people to introduce them to the Biota podcast.
I think universities and similar institutions should provide good drop points but I need logistical interest and assistance. If you have a good location for 10-plus CDs, please get in contact and I will start assembling postage lists and work out the logistics and costs of getting these CD bundles out.
Please note these are free giveaway CDs intended to be passed on to multiple people to introduce them to the Biota podcast.
Embedded Journalists?
I talked on the Apologia podcast last night. More on that when the audio is available. One of the ongoing themes through the podcast was the lack of popular information with regards to contemporary artificial life: how the journalists, philosophers and popular authors who write on artificial life Venning topics have failed to get the rich vision of the artificial life community to the general public.
This morning I was listening to ShrinkRapRadio #157 on an embedded journalist in SecondLife.
Perhaps artificial life needs embedded journalists too?
This morning I was listening to ShrinkRapRadio #157 on an embedded journalist in SecondLife.
Perhaps artificial life needs embedded journalists too?
Tuesday, June 10. 2008
Evolution in the lab
From a Science News article:
"[Richard Lenski and his colleagues at Michigan State University] watched 12 colonies of identical E. coli bacteria evolve under carefully controlled lab conditions for 20 years, which equates to more than 40,000 generations of bacteria. After every 500 generations, the researchers froze samples of bacteria. Those bacteria could later be thawed out to 'replay' the evolutionary clock from that point in time."
This type of work is reminiscent of a simulated ALife environment, where replaying scenarios is very common, but this is fascinating to see actually done in a lab.
At around generation 31,500, one of the the E. coli populations evolved the ability to metabolize citrate. E. coli's inability to process citrate is actually one of the ways in which scientists have previously distinguished it from other species.
The trait has only re-emerged when 'replayed' from generation 20,000 onward in that one population. The researchers are now working to determine the mutation that took place around generation 20k which led to the later mutation affecting citrate metabolism -- particularly with respect to whether that earlier mutation offers any advantage in and of itself.
Additional link to a New Scientist article.
"[Richard Lenski and his colleagues at Michigan State University] watched 12 colonies of identical E. coli bacteria evolve under carefully controlled lab conditions for 20 years, which equates to more than 40,000 generations of bacteria. After every 500 generations, the researchers froze samples of bacteria. Those bacteria could later be thawed out to 'replay' the evolutionary clock from that point in time."
This type of work is reminiscent of a simulated ALife environment, where replaying scenarios is very common, but this is fascinating to see actually done in a lab.
At around generation 31,500, one of the the E. coli populations evolved the ability to metabolize citrate. E. coli's inability to process citrate is actually one of the ways in which scientists have previously distinguished it from other species.
The trait has only re-emerged when 'replayed' from generation 20,000 onward in that one population. The researchers are now working to determine the mutation that took place around generation 20k which led to the later mutation affecting citrate metabolism -- particularly with respect to whether that earlier mutation offers any advantage in and of itself.
Additional link to a New Scientist article.
Plants and sensation
From the New York Times article:
"Some plants, for example, have been shown to sense potentially competing neighboring plants by subtle changes in light. That is because plants absorb and reflect particular wavelengths of sunlight, creating signature shifts that other plants can detect...
"Scientists also find plants exhibiting ways to gather information on other plants from chemicals released into the soil and air. A parasitic weed, dodder, has been found to be particularly keen at sensing such chemicals...
"In time-lapse movies, scientists saw dodder sprouts moving in a circular fashion, in what they discovered was a sampling of the airborne chemicals released by nearby plants, a bit like a dog sniffing the air around a dinner buffet.
"Then, using just the hint of the smells and without having touched another plant, the dodder grew toward its preferred victim. That is, the dodder reliably sensed and attacked the species of plant, from among the choices nearby, on which it would grow best."
"Some plants, for example, have been shown to sense potentially competing neighboring plants by subtle changes in light. That is because plants absorb and reflect particular wavelengths of sunlight, creating signature shifts that other plants can detect...
"Scientists also find plants exhibiting ways to gather information on other plants from chemicals released into the soil and air. A parasitic weed, dodder, has been found to be particularly keen at sensing such chemicals...
"In time-lapse movies, scientists saw dodder sprouts moving in a circular fashion, in what they discovered was a sampling of the airborne chemicals released by nearby plants, a bit like a dog sniffing the air around a dinner buffet.
"Then, using just the hint of the smells and without having touched another plant, the dodder grew toward its preferred victim. That is, the dodder reliably sensed and attacked the species of plant, from among the choices nearby, on which it would grow best."
Monday, June 9. 2008
GreyThumb Netherlands
I heard from Gerald de Jong recently that the first GreyThumb Netherlands meeting would be on June 24th.
Wednesday, June 4. 2008
More on Rotifers
Olivia Judson's latest blog entry discusses the bdelloid rotifers blogged about below.
Sunday, June 1. 2008
Video from GreyThumb Silicon Valley meeting
Thanks to Alan Lundell, the video of the first official meeting of GreyThumb Silicon Valley from May 27th, 2008 is now available here. Enjoy!
Rotifers are Genetic Borg
Over at ScienceBlogs there's a post about a new finding about the genome of a very strange species: Rotifers.
Rotifers are a complex single celled organism that lives in fresh water lakes, ponds, and rivers. They are quite well diversified and very common, and have a number of odd characteristics: they are asexual (apparently having abandoned sex at some point in their history), can survive being fully dried out and rehydrated, and are amazingly resistant to toxins and radiation.
Their asexuality was perhaps the most baffling of their characteristics. Most complex asexual animals are not particularly successful or well diversified; their asexual nature causes them to hyper-specialize (over-fit?) to a particular niche and they aren't very robust in the face of evolutionary challenges. That's because sex is an evolvability adaptation in higher animals to permit gene exchange and reshuffling.
In simple cells like bacteria, there's another process that dominates: horizontal gene transfer. Bacteria swap genes quite often, but such gene swapping is rare in eukaryotes. The eukaryotic cell structure with a complex nucleus, multiple layers, and DNA organized on chromosomes presents both a physical barrier and a complexity barrier to horizontal gene transfer.
(I've often wondered if eukaryotic sexual reproduction co-evolved with eukaryotic cell structure as a way of maintaining the evolvability benefits of horizontal gene transfer as the increasing complexity of eukaryotes made this basic process more difficult.)
But rotifers, like many other single celled protists, are weird. They've found a new solution: instead of sex, they incorporate genes from all sorts of other living things in their environments: plants, bacteria, other protists, and even multicellular animals. They're genetic "borg": they assimilate other creatures' genes.
Pretty interesting, and somewhat relevant to evolutionary computation research. We used to think that most simple animals like bacteria and asexual protists were trees that didn't branch... mutate, select, repeat. We now know that what I might call "elementary Darwinian evolution" is quite rare in nature. Most living things swap genes somehow.
Rotifers are a complex single celled organism that lives in fresh water lakes, ponds, and rivers. They are quite well diversified and very common, and have a number of odd characteristics: they are asexual (apparently having abandoned sex at some point in their history), can survive being fully dried out and rehydrated, and are amazingly resistant to toxins and radiation.
Their asexuality was perhaps the most baffling of their characteristics. Most complex asexual animals are not particularly successful or well diversified; their asexual nature causes them to hyper-specialize (over-fit?) to a particular niche and they aren't very robust in the face of evolutionary challenges. That's because sex is an evolvability adaptation in higher animals to permit gene exchange and reshuffling.
In simple cells like bacteria, there's another process that dominates: horizontal gene transfer. Bacteria swap genes quite often, but such gene swapping is rare in eukaryotes. The eukaryotic cell structure with a complex nucleus, multiple layers, and DNA organized on chromosomes presents both a physical barrier and a complexity barrier to horizontal gene transfer.
(I've often wondered if eukaryotic sexual reproduction co-evolved with eukaryotic cell structure as a way of maintaining the evolvability benefits of horizontal gene transfer as the increasing complexity of eukaryotes made this basic process more difficult.)
But rotifers, like many other single celled protists, are weird. They've found a new solution: instead of sex, they incorporate genes from all sorts of other living things in their environments: plants, bacteria, other protists, and even multicellular animals. They're genetic "borg": they assimilate other creatures' genes.
Pretty interesting, and somewhat relevant to evolutionary computation research. We used to think that most simple animals like bacteria and asexual protists were trees that didn't branch... mutate, select, repeat. We now know that what I might call "elementary Darwinian evolution" is quite rare in nature. Most living things swap genes somehow.
Monday, May 19. 2008
Programming Challenge from Dick Gordon
Gerald de Jong and I spoke with Natalie and Dick Gordon on Friday's Biota Live. Following the recording Dick emailed me a paper which will be the concluding chapter to his Divine Action and Natural Selection: Questions of Science and Faith in Biological Evolution book (aka the Dick Gordon book project for frequent Biota Live listeners. Dick begins the paper;
Dick is interested in feedback/dialogue by May 21st, 2008. He can be contacted directly.
The origin of life is one of the outstanding conundrums of modern biology, which has been tackled mostly from a chemical point of view. It is also the playground of creationists who use probability arguments to deny that life could ever have begun "at random". The latter (Babuna, 2008; Gotfryd, 2008; Gundogdu, 2008) especially like to quote scientists who express doubt, such as:
"In a popular lecture I once unflatteringly described the thinking of these scientists as a 'junkyard mentality'. Since this reference became widely and not quite accurately quoted I will repeat it here. A junkyard contains all the bits and pieces of a Boeing 747, dismembered and in disarray. A whirlwind happens to blow through the yard. What is the chance that after its passage a fully assembled 747, ready to fly, will be found standing there? So small as to be negligible, even if a tornado were to blow through enough junkyards to fill the whole Universe" (Hoyle, 1984).
I would like to suggest that artificial life (Alife) enthusiasts take up Fred Hoyle's challenge, that in a way they simulate a tornado going through a junkyard of parts, and come up with something we would all agree is alive, in the Alife sense, from components that are not alive in the Alife sense (Pennock, 2001; Pennock, 2007).
Dick is interested in feedback/dialogue by May 21st, 2008. He can be contacted directly.
Saturday, May 10. 2008
Chris Hecker (Spore dev) on Biota Live
We had Chris Hecker on Biota Live last night. A fantastic chat and a great opportunity to see the fastest route to get artificial life into games. Enjoy!
Tuesday, May 6. 2008
Costs of learning
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."
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."
Thursday, May 1. 2008
Self organizing robots
Friday, April 25. 2008
GreyThumb Silicon Valley meets for the first time
Bruce Damer emailed me some snaps from the GreyThumb Silicon Valley meeting last night.
Jeffrey Ventrella demoed the new version of GenePool.
Jeffrey Ventrella demoed the new version of GenePool.
Monday, April 21. 2008
UK Grey Thumb!
If you live in the United Kingdom and are interested in attending the next Grey Thumb, please take a few moments to join the Grey Thumb - London mailing list!
Wednesday, April 9. 2008
Mutualisms
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.
Monday, April 7. 2008
Grey Thumb Boston Meeting Tonight
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.
See the Meetings Page for more information.
Tuesday, April 1. 2008
GreyThumb Chapters
Based on the response from GreyThumb London, Gerald de Jong contacted me today about the GreyThumb Netherlands chapter. There are already mailing list associated with Silicon Valley and Los Angeles chapters. If you are in those areas, now is the time to get involved!
Sunday, March 23. 2008
Brian Peltonen in a Biota Chat
I have just published a chat with Brian Peltonen last Sunday. Brian and Adam Ierymenko also featured in today's Biota Live recording on the EvoGrid which I hope to have clean and published in the next day or so. Stay tuned!
Tuesday, March 18. 2008
Deborah Gordon on Task Allocation in Ants
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.
Friday, March 14. 2008
Local Boston Folks: Math and Art tonight at Axiom Gallery
For those of you in the Boston metro area, some friends of mine who operate a gallery locally are putting on an exhibit that many of you would find very interesting. Check out the Axiom Gallery site for more information. From the site:
The opening reception starts at 6pm tonight and runs until 9. I'll probably be there around 7-8pm.
The gallery is located within the Green Street T stop on the MBTA orange line. Pretty much everyone in Boston should be able to find that. :) If you're driving, check the site for the address and map it.
(P.S. We're currently setting up a very nice CMS system to get the rest of greythumb.org back online. The site should return in much greater glory shortly.)
Co-Curated by Axiom Gallery Founding Director, Heidi Kayser, and The Boston Cyberarts Festival Executive Director, George Fifeild, and advised by Director of the Clay Mathematics Institute, Jim Carlson, Art and Math explores the artists use of mathematical concepts in sculpture, photography, and new media. The show will also examine how, through the use of mathematical thought artist can make the journey from awe to beauty to humor.
The opening reception starts at 6pm tonight and runs until 9. I'll probably be there around 7-8pm.
The gallery is located within the Green Street T stop on the MBTA orange line. Pretty much everyone in Boston should be able to find that. :) If you're driving, check the site for the address and map it.
(P.S. We're currently setting up a very nice CMS system to get the rest of greythumb.org back online. The site should return in much greater glory shortly.)
Wednesday, March 12. 2008
Two Video Games
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.
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.
Evolution without Mutation
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."
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."
Tuesday, March 11. 2008
Superfolia
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.
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