(http://robinhanson.typepad.com/photos/uncategorized/2008/10/13/audaxviator_2.jpg)
http://www.overcomingbias.com/2008/10/behold-our-ance.html (http://www.overcomingbias.com/2008/10/behold-our-ance.html)
A community of the bacteria Candidatus Desulforudis audaxviator has been discovered 2.8 kilometres beneath the surface of the Earth in fluid-filled cracks of the Mponeng goldmine in South Africa. Its 60C home is completely isolated from the rest of the world, and devoid of light and oxygen.
D. audaxviator gets its energy from the radioactive decay of uranium in the surrounding rocks. It has genes to extract carbon from dissolved carbon dioxide and other genes to fix nitrogen, which comes from the surrounding rocks. ... D. audaxviator has genes to produce all the amino acids it needs. D. audaxviator can also protect itself from environmental hazards by forming endospores - tough shells that protect its DNA and RNA from drying out, toxic chemicals and from starvation. It has a flagellum to help it navigate.
From http://environment.newscientist.com/channel/earth/dn14906-goldmine-bug-dna-may-be-key-to-alien-life.html (http://new%20scientist)
Also, http://www.sciencemag.org/cgi/content/abstract/322/5899/275 (http://science%20journal)
I thought this organism was worth a second look it its own thread and a different context.
However, why oh WHY do people have to go on and on and on about seeding from outer space? I mean, sure it sounds cool, but isn't it so much cooler to contemplate how life might have arisen on our own planet, that this whole diversity is home grown and endemic? The nearest planets are dead lifeless rock, and even then, why is it more likely that life arose there rather than here? What is it about elsewhere that makes it seem so much more probable than right here on this planet, with so much water, low impact cosmic radiation and relatively happy temperatures? Furthermore, why is it so much more attractive?
I think its because people want to find "intelligent life" elsewhere. They want to be reassured that they we are not alone in this sector of the universe, or want to relive their childhood science fiction fantasies. Besides, saying life came from elsewhere doesn't help us understand how life arose, and unless you buy into a creator deity, it arose somewhere, sometime, somehow, and it arose spontaneously.
As fun as aliens may be sometimes, it is really really TRULY time to use Occam's Razor.
Now, back to the organism. Chemosynthetic, from URANIUM. Thats a new one. Chemosynthetic organisms that make use of sulfur are relatively common. Some of the most ancient of these (we suppose) are those living in deep sea vent environments, mostly because there is very little way that these could have gotten there if they had not arisen there in the first place. This bacteria is doing pretty well for its self too, with a flagellum and full ammino acid ability, plus, it can go cryptobiotic. Lots of bacteria have these abilities, but few have them in this combination, and none that I know of have these characters together, especially the whole Uranium radiation pathway.
So, we have two possible pathways for the metabolisms of the earliest bacteria now. Very cool.
Most perturbatory. It reminds me of that fungus found inside chernobyl's reactor that uses gamma radiation as a food source.
It's amazing how life can be found just about everywhere on earth. Evolution is such a damn powerful process.
Quote from: Felix on October 13, 2008, 10:24:49 PM
Most perturbatory. It reminds me of that fungus found inside chernobyl's reactor that uses gamma radiation as a food source.
I haven't heard of that. Thats pretty cool too. Still, its a fungus, so that was a secondary addition...
Which is a cool thought, too. It means that things like chemosynthesis and radiosynthesis aren't as difficult to derive as we may think.
Quote from: Vene on October 13, 2008, 10:28:10 PM
It's amazing how life can be found just about everywhere on earth. Evolution is such a damn powerful process.
I'm amazed too. I'm amazed and awed at the emergent capacity for life on this planet.
I was reading recently from one of those books I've been gabbing about on here, Reinventing the Sacred. Kauffman was talking about some experiments with self replicating RNA molecules and how when you reach a threshold complexity of the molecules themselves, once the chains have a codon sequence that can independently put proteins together, then all kinds of crazy shit starts happening. Its amazing and exciting stuff, wish I could back it up with some journal articles.
Quote from: Kai on October 13, 2008, 10:29:35 PM
Quote from: Felix on October 13, 2008, 10:24:49 PM
Most perturbatory. It reminds me of that fungus found inside chernobyl's reactor that uses gamma radiation as a food source.
I haven't heard of that. Thats pretty cool too. Still, its a fungus, so that was a secondary addition...
Which is a cool thought, too. It means that things like chemosynthesis and radiosynthesis aren't as difficult to derive as we may think.
I read that the fungus was using melanin the same way plants use chlorophyll. Freaky shit.
Quote from: Felix on October 13, 2008, 10:37:11 PM
Quote from: Kai on October 13, 2008, 10:29:35 PM
Quote from: Felix on October 13, 2008, 10:24:49 PM
Most perturbatory. It reminds me of that fungus found inside chernobyl's reactor that uses gamma radiation as a food source.
I haven't heard of that. Thats pretty cool too. Still, its a fungus, so that was a secondary addition...
Which is a cool thought, too. It means that things like chemosynthesis and radiosynthesis aren't as difficult to derive as we may think.
I read that the fungus was using melanin the same way plants use chlorophyll. Freaky shit.
Okay, the radiosynthetic fungus I can believe, but for this one :cn:.
As far as I know, there are no photosynthetic fungus.
http://unitedcats.wordpress.com/2007/05/29/major-biological-discoveryinside-the-chernobyl-reactor/
Citation Granted.
You make some interesting points Kai, about looking elsewhere for our beginning. I will have to go and contemplate.
Interesting find discovery.
Quote from: Felix on October 13, 2008, 10:42:27 PM
http://unitedcats.wordpress.com/2007/05/29/major-biological-discoveryinside-the-chernobyl-reactor/
Citation Granted.
OFUK Now I see! :fap:
Very very very cool.
That...thats actually more cool that deep cave living radiosynthetic bacterium.
Actually, while that is cool, I am still not completly satisfied. I can't find a link to a peer reviewed journal, and the articles only hint at the possibility of there being a melanin radiosynthetic pathway.
Do you know of one?
Flores, Graciela. "Radiation: it's what's for dinner.(SAMPLINGS)(black fungus Cladosporium sphaerospermum)(Brief article)." Natural History 116.7 (Sept 2007): 14(1). Expanded Academic ASAP. Gale. Canada Community College. 13 Oct. 2008
Sorry, Natural History, the magazine publication of the National Museum of Natural History, while a good publication, is not peer reviewed.
Huh. My database seems to think it is. Oh well.
Quote from: Felix on October 13, 2008, 11:33:11 PM
Huh. My database seems to think it is. Oh well.
To be completely honest, I had to check some lists myself, because I wasn't sure. Nature is on there, but I couldn't find Natural History on any lists.
Quote from: Kai on October 13, 2008, 11:00:56 PM
Actually, while that is cool, I am still not completly satisfied. I can't find a link to a peer reviewed journal, and the articles only hint at the possibility of there being a melanin radiosynthetic pathway.
Do you know of one?
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000457 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000457)
You ask and you shall receive.
Bad ass, Vene. Good website.
cool! i have to keep an eye on where this is going.
Quote from: Vene on October 13, 2008, 11:53:14 PM
Quote from: Kai on October 13, 2008, 11:00:56 PM
Actually, while that is cool, I am still not completly satisfied. I can't find a link to a peer reviewed journal, and the articles only hint at the possibility of there being a melanin radiosynthetic pathway.
Do you know of one?
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000457 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000457)
You ask and you shall receive.
THAT is what I was looking for! :D :mittens:
Reading articles like this really torque my nice iron bars ;-)
I'm constantly surprised that while I can easily stick my head in models that include egrigores, invocations, aliens and Eris... I seem to have been so inoculated against the idea of abiogenesis that I tend to dismiss evidence out of hand as an initial reaction.
Fucking Prison.
Quote from: Ratatosk on October 14, 2008, 03:18:22 PM
Reading articles like this really torque my nice iron bars ;-)
I'm constantly surprised that while I can easily stick my head in models that include egrigores, invocations, aliens and Eris... I seem to have been so inoculated against the idea of abiogenesis that I tend to dismiss evidence out of hand as an initial reaction.
Fucking Prison.
On the other hand, I have a hard time sticking models in my head that include egrigores, invocations, aliens and Eris, while ideas like evolutionary biology and abiogenesis get stuck in my head hard.
The only difference between the two is that one has more evidence. Its STILL some ideas stuck in your head driving your thoughts.
Quote from: Kai on October 14, 2008, 03:25:04 PM
Quote from: Ratatosk on October 14, 2008, 03:18:22 PM
Reading articles like this really torque my nice iron bars ;-)
I'm constantly surprised that while I can easily stick my head in models that include egrigores, invocations, aliens and Eris... I seem to have been so inoculated against the idea of abiogenesis that I tend to dismiss evidence out of hand as an initial reaction.
Fucking Prison.
On the other hand, I have a hard time sticking models in my head that include egrigores, invocations, aliens and Eris, while ideas like evolutionary biology and abiogenesis get stuck in my head hard.
The only difference between the two is that one has more evidence. Its STILL some ideas stuck in your head driving your thoughts.
Well sure, but my goal is model agnosticism... ANY MODEL, ANY TIME, ANY PLACE. I was inoculated against magic (from the devil!!) and drugs (the demons can possess you if you are on drugs!!) but abiogenesis, the life from unlife model just eludes me still. I know that we're talking about replicating proteins at that point, not frogs and rats and Cramuli, but still... :wink:
Quote from: Ratatosk on October 14, 2008, 03:59:30 PM
Quote from: Kai on October 14, 2008, 03:25:04 PM
Quote from: Ratatosk on October 14, 2008, 03:18:22 PM
Reading articles like this really torque my nice iron bars ;-)
I'm constantly surprised that while I can easily stick my head in models that include egrigores, invocations, aliens and Eris... I seem to have been so inoculated against the idea of abiogenesis that I tend to dismiss evidence out of hand as an initial reaction.
Fucking Prison.
On the other hand, I have a hard time sticking models in my head that include egrigores, invocations, aliens and Eris, while ideas like evolutionary biology and abiogenesis get stuck in my head hard.
The only difference between the two is that one has more evidence. Its STILL some ideas stuck in your head driving your thoughts.
Well sure, but my goal is model agnosticism... ANY MODEL, ANY TIME, ANY PLACE. I was inoculated against magic (from the devil!!) and drugs (the demons can possess you if you are on drugs!!) but abiogenesis, the life from unlife model just eludes me still. I know that we're talking about replicating proteins at that point, not frogs and rats and Cramuli, but still... :wink:
Its alright. No one really knows the how. All we will ever have is some guesses to the how and the where, and we have some models for the what.
No one will ever know the why, if there is one, but lots of people will think they do.
Quote from: Kai on October 14, 2008, 04:59:38 PM
Quote from: Ratatosk on October 14, 2008, 03:59:30 PM
Quote from: Kai on October 14, 2008, 03:25:04 PM
Quote from: Ratatosk on October 14, 2008, 03:18:22 PM
Reading articles like this really torque my nice iron bars ;-)
I'm constantly surprised that while I can easily stick my head in models that include egrigores, invocations, aliens and Eris... I seem to have been so inoculated against the idea of abiogenesis that I tend to dismiss evidence out of hand as an initial reaction.
Fucking Prison.
On the other hand, I have a hard time sticking models in my head that include egrigores, invocations, aliens and Eris, while ideas like evolutionary biology and abiogenesis get stuck in my head hard.
The only difference between the two is that one has more evidence. Its STILL some ideas stuck in your head driving your thoughts.
Well sure, but my goal is model agnosticism... ANY MODEL, ANY TIME, ANY PLACE. I was inoculated against magic (from the devil!!) and drugs (the demons can possess you if you are on drugs!!) but abiogenesis, the life from unlife model just eludes me still. I know that we're talking about replicating proteins at that point, not frogs and rats and Cramuli, but still... :wink:
Its alright. No one really knows the how. All we will ever have is some guesses to the how and the where, and we have some models for the what.
No one will ever know the why, if there is one, but lots of people will think they do.
And that is why I like Kai. No dogmatic sciencism!
Quote from: Ratatosk on October 14, 2008, 05:31:59 PM
Quote from: Kai on October 14, 2008, 04:59:38 PM
Quote from: Ratatosk on October 14, 2008, 03:59:30 PM
Quote from: Kai on October 14, 2008, 03:25:04 PM
Quote from: Ratatosk on October 14, 2008, 03:18:22 PM
Reading articles like this really torque my nice iron bars ;-)
I'm constantly surprised that while I can easily stick my head in models that include egrigores, invocations, aliens and Eris... I seem to have been so inoculated against the idea of abiogenesis that I tend to dismiss evidence out of hand as an initial reaction.
Fucking Prison.
On the other hand, I have a hard time sticking models in my head that include egrigores, invocations, aliens and Eris, while ideas like evolutionary biology and abiogenesis get stuck in my head hard.
The only difference between the two is that one has more evidence. Its STILL some ideas stuck in your head driving your thoughts.
Well sure, but my goal is model agnosticism... ANY MODEL, ANY TIME, ANY PLACE. I was inoculated against magic (from the devil!!) and drugs (the demons can possess you if you are on drugs!!) but abiogenesis, the life from unlife model just eludes me still. I know that we're talking about replicating proteins at that point, not frogs and rats and Cramuli, but still... :wink:
Its alright. No one really knows the how. All we will ever have is some guesses to the how and the where, and we have some models for the what.
No one will ever know the why, if there is one, but lots of people will think they do.
And that is why I like Kai. No dogmatic sciencism!
I despise the Brights as much as I do the Creationists.
This thread on candidatus desulforudis needs more reptilian agents
Quote from: Thurnez Isa on October 14, 2008, 10:48:07 PM
This thread on Candidatus Desulforudis audaxviator needs more reptilian agents
Fixsthhhhhhhhhhed.
\
(http://img170.imageshack.us/img170/2448/90reptilian1pv4.jpg)
fucking shapeshifting reptilian aliens
spreading their candidatus desulforudis semen all over the universe
Quote from: Thurnez Isa on October 15, 2008, 12:28:56 AM
fucking shapeshifting reptilian aliens
spreading their candidatus desulforudis semen all over the universe
eh....I think my point was, while using a picture of a reptilioid, that candidatus isn't part of the species name, its simply a word that indicates a prokaryotic species as not yet being completly described. Its like a pre-recognition, a candidate for a species, in this case candidate species
Desulforudis audaxviator. Genus names are always capitalized, and there are never two genus names.
This piece of random biological trivia brought to you by Sludge.
(http://www.huntsman.com.au/images/applications/sludge-reduction.jpg)
That bacteria is possibly the most awesome thing on the planet. Not so much the feeding off radiation (I've seen that in the fungii species that were determined to do it in the wake of the chenobyl discovery), but in the sheer robustness of the organism, does it need any organic chemicals in its enviornment at all to survive?
QuoteHowever, why oh WHY do people have to go on and on and on about seeding from outer space?
I was thinking more along the lines of using it to seed other planets than it having been seeded on ours.
Quote from: Requiem on October 16, 2008, 02:23:00 AM
That bacteria is possibly the most awesome thing on the planet. Not so much the feeding off radiation (I've seen that in the fungii species that were determined to do it in the wake of the chenobyl discovery), but in the sheer robustness of the organism, does it need any organic chemicals in its enviornment at all to survive?
QuoteHowever, why oh WHY do people have to go on and on and on about seeding from outer space?
I was thinking more along the lines of using it to seed other planets than it having been seeded on ours.
0_0
You're in SANE.
I like that.
Quote from: Requiem on October 16, 2008, 02:23:00 AM
That bacteria is possibly the most awesome thing on the planet. Not so much the feeding off radiation (I've seen that in the fungii species that were determined to do it in the wake of the chenobyl discovery), but in the sheer robustness of the organism, does it need any organic chemicals in its enviornment at all to survive?
QuoteHowever, why oh WHY do people have to go on and on and on about seeding from outer space?
I was thinking more along the lines of using it to seed other planets than it having been seeded on ours.
You were thinking that. Unfortunately, most of the articles I looked at were going for the whole panspermogenesis angle, or whatever they call it. Your idea is
cool. Their idea needs Occam's Razor.
And the WORST part about the whole pangeospermowhatever (aliens seeded the planet!) is that it puts people in the mindset that abiogenesis is something other, something out there, out in space *gestures towards some imaginary celestial object*making it very dismissive. Since life began elsewhere we don't have need to explore /how/ and what and really try to figure out the where on this planet. Thats dismissal that makes things completely boring.
I also don't understand how it is more likely that life came from elsewhere, especially considering the vast distances in space, the improbability of life escaping a planetary atmosphere and in the minute form of a bacteria, somehow crossing light years worth of space, or at the smallest, billions of miles and somehow ending up on earth. I don't understand how that is more likely. Maybe someone here can explain it to me?
Quote from: Kai on October 16, 2008, 02:42:43 AMAnd the WORST part about the whole pangeospermowhatever (aliens seeded the planet!) is that it puts people in the mindset that abiogenesis is something other, something out there, out in space *gestures towards some imaginary celestial object*making it very dismissive. Since life began elsewhere we don't have need to explore /how/ and what and really try to figure out the where on this planet. Thats dismissal that makes things completely boring.
Exactly. Also it doesn't answer any questions, it just relocates the problem for no reason. Very complicated biomolecules have been shown to spontaneously form in the right conditions. And in conditions that resemble early Earth. (link) (http://www.ncbi.nlm.nih.gov/pubmed/18574710)
QuoteI also don't understand how it is more likely that life came from elsewhere, especially considering the vast distances in space, the improbability of life escaping a planetary atmosphere and in the minute form of a bacteria, somehow crossing light years worth of space, or at the smallest, billions of miles and somehow ending up on earth. I don't understand how that is more likely. Maybe someone here can explain it to me?
I don't know how it's more likely either. It seems to me that for something to survive in space makes it ill-suited to survive on Earth.
Quote from: Vene on October 16, 2008, 02:56:52 AM
Quote from: Kai on October 16, 2008, 02:42:43 AMAnd the WORST part about the whole pangeospermowhatever (aliens seeded the planet!) is that it puts people in the mindset that abiogenesis is something other, something out there, out in space *gestures towards some imaginary celestial object*making it very dismissive. Since life began elsewhere we don't have need to explore /how/ and what and really try to figure out the where on this planet. Thats dismissal that makes things completely boring.
Exactly. Also it doesn't answer any questions, it just relocates the problem for no reason. Very complicated biomolecules have been shown to spontaneously form in the right conditions. And in conditions that resemble early Earth. (link) (http://www.ncbi.nlm.nih.gov/pubmed/18574710)
I love you. <3 For that link, specifically. Right there you have all the necessary components for ribonucleic acid chains. Its very likely that the first replicating nucleic acids were RNA, because DNA requires transcription and seems to be a much more derived process. However, RNA does not require transcription for the coding of proteins, it IS the transcription for modern genetic processes.
QuoteQuoteI also don't understand how it is more likely that life came from elsewhere, especially considering the vast distances in space, the improbability of life escaping a planetary atmosphere and in the minute form of a bacteria, somehow crossing light years worth of space, or at the smallest, billions of miles and somehow ending up on earth. I don't understand how that is more likely. Maybe someone here can explain it to me?
I don't know how it's more likely either. It seems to me that for something to survive in space makes it ill-suited to survive on Earth.
That and, we have examples of organisms that seem less derived, more basal, than the hypothetical space seed would have been. If something like
D. audaxivator were the seeds that started life on this planet, then where the hell did Archaea come from?
Oh FUCK I missed the part where they said "hydrothermal systems". :fap: (see signature for reference)
Hmm, anybody have access to the research paper. Trying to figure out what its genetic relationship to other organisms, as well as if its process for absorbing radition is similar to photosythesis or the melatonin method the fungi in chernobyl appear to use.
Quote from: Kai on October 16, 2008, 03:16:22 AM
Quote from: Vene on October 16, 2008, 02:56:52 AM
Quote from: Kai on October 16, 2008, 02:42:43 AMAnd the WORST part about the whole pangeospermowhatever (aliens seeded the planet!) is that it puts people in the mindset that abiogenesis is something other, something out there, out in space *gestures towards some imaginary celestial object*making it very dismissive. Since life began elsewhere we don't have need to explore /how/ and what and really try to figure out the where on this planet. Thats dismissal that makes things completely boring.
Exactly. Also it doesn't answer any questions, it just relocates the problem for no reason. Very complicated biomolecules have been shown to spontaneously form in the right conditions. And in conditions that resemble early Earth. (link) (http://www.ncbi.nlm.nih.gov/pubmed/18574710)
I love you. <3 For that link, specifically. Right there you have all the necessary components for ribonucleic acid chains. Its very likely that the first replicating nucleic acids were RNA, because DNA requires transcription and seems to be a much more derived process. However, RNA does not require transcription for the coding of proteins, it IS the transcription for modern genetic processes.
That's why I like the RNA world hypothesis.
Quote from: Requiem on October 16, 2008, 03:20:28 AM
Hmm, anybody have access to the research paper. Trying to figure out what its genetic relationship to other organisms, as well as if its process for absorbing radition is similar to photosythesis or the melatonin method the fungi in chernobyl appear to use.
http://www.sciencemag.org/cgi/reprint/322/5899/275.pdf (http://www.sciencemag.org/cgi/reprint/322/5899/275.pdf)
Does that work for you? This is the original article, I believe.
It wants money. 10$ per article.
Quote from: Requiem on October 17, 2008, 05:49:35 AM
It wants money. 10$ per article.
I've got a university connection that allows me to download most of these articles for free. Sorry.
:argh!: My university hates Science.
Quote from: Kai on October 13, 2008, 10:33:30 PM
I was reading recently from one of those books I've been gabbing about on here, Reinventing the Sacred. Kauffman was talking about some experiments with self replicating RNA molecules and how when you reach a threshold complexity of the molecules themselves, once the chains have a codon sequence that can independently put proteins together, then all kinds of crazy shit starts happening. Its amazing and exciting stuff, wish I could back it up with some journal articles.
is that the same Kauffman that thought up binary Kauffman networks?
i learned about them in Computational Science class, it was some heavily (and i mean extremely) simplified model of genes decoding into proteins causing other genes to be decoded, or preventing them, inhibiting and exhibiting. It was basically a graph (network) of binary vertices (on or off) with boolean operations on the nodes. Initialized randomly and then they let it run. On a computer you can simulate this really quickly and then discover that such networks will develop cycli, but several of them, depending on the initialization, being some kind of attractors of the system.
the concept was a really big mindfuck for me, in ways that are slightly too complicated to explain without having five pages of thread before you see my point (sorry).
i'm ashamed to say that, however simple, i've never coded a Kauffman network to play with for myself.
Quote from: Triple Zero on November 15, 2008, 12:46:53 AM
Quote from: Kai on October 13, 2008, 10:33:30 PM
I was reading recently from one of those books I've been gabbing about on here, Reinventing the Sacred. Kauffman was talking about some experiments with self replicating RNA molecules and how when you reach a threshold complexity of the molecules themselves, once the chains have a codon sequence that can independently put proteins together, then all kinds of crazy shit starts happening. Its amazing and exciting stuff, wish I could back it up with some journal articles.
is that the same Kauffman that thought up binary Kauffman networks?
i learned about them in Computational Science class, it was some heavily (and i mean extremely) simplified model of genes decoding into proteins causing other genes to be decoded, or preventing them, inhibiting and exhibiting. It was basically a graph (network) of binary vertices (on or off) with boolean operations on the nodes. Initialized randomly and then they let it run. On a computer you can simulate this really quickly and then discover that such networks will develop cycli, but several of them, depending on the initialization, being some kind of attractors of the system.
the concept was a really big mindfuck for me, in ways that are slightly too complicated to explain without having five pages of thread before you see my point (sorry).
i'm ashamed to say that, however simple, i've never coded a Kauffman network to play with for myself.
There was this whole chapter about boolean operations and binary and stuff. I understood about a quarter of it.
basically, the cycli are yet another example of emergence happening in complex systems. you got a network with lots (hundreds) of simple boolean operations, yet none of them really explains on its own why the network in state X returns to exactly the same state after, say, 17523 iterations. unless you initialize it to state Y, when it gets caught in a loop of just 3125 iterations.
the cycli could be likened to cycli in a cell, like the reproduction cell splitting cycle or such.
one of the things i got from it was an immense respect for the biologists trying to figure out these things in actual cells, which are a lot more complicated (okay, actually instead of respect i got a very distinct feeling of hopelessness, but apparently they still try).
another likeness would be the heart, which is a huge network of all sorts of little muscles inhibiting and exhibiting eachother. usually it's stuck in a really big cycle that makes it pump around blood properly. but when something goes wrong, it can get stuck in a smaller cycle, which is called fibrillating. fortunately the big cycle is a rather strong attractor in the system (i say fortunately, but of course it's because of better fitness for the organism not luck), and that's why defibrilating works, you give the thing a big electric kick, re-initializing it to some semi-random state, and hope this time it gets caught in the big cycle again.
before you jump on me for comparing it like that, know that it is of course a gross over-simplification (yet when i explained it to a medical student friend of mine, after explaining for an hour how such a network works, and learning a lot about how the heart works, she did agree with the similarity, though).
Quote from: Triple Zero on November 15, 2008, 01:06:14 AM
basically, the cycli are yet another example of emergence happening in complex systems. you got a network with lots (hundreds) of simple boolean operations, yet none of them really explains on its own why the network in state X returns to exactly the same state after, say, 17523 iterations. unless you initialize it to state Y, when it gets caught in a loop of just 3125 iterations.
the cycli could be likened to cycli in a cell, like the reproduction cell splitting cycle or such.
one of the things i got from it was an immense respect for the biologists trying to figure out these things in actual cells, which are a lot more complicated (okay, actually instead of respect i got a very distinct feeling of hopelessness, but apparently they still try).
another likeness would be the heart, which is a huge network of all sorts of little muscles inhibiting and exhibiting eachother. usually it's stuck in a really big cycle that makes it pump around blood properly. but when something goes wrong, it can get stuck in a smaller cycle, which is called fibrillating. fortunately the big cycle is a rather strong attractor in the system (i say fortunately, but of course it's because of better fitness for the organism not luck), and that's why defibrilating works, you give the thing a big electric kick, re-initializing it to some semi-random state, and hope this time it gets caught in the big cycle again.
before you jump on me for comparing it like that, know that it is of course a gross over-simplification (yet when i explained it to a medical student friend of mine, after explaining for an hour how such a network works, and learning a lot about how the heart works, she did agree with the similarity, though).
No no! I liked the heart example. The whole pacemaker system is so complex that I don't remember how it works exactly anymore. I do know it works independent of the brain, except for the speed of pace which is set by neurotransmitters. The steadyness of the pace, meaning the syncronization is this big cycle like you said with cardiac muscle in coordination by the pacemaker cells. If it gets stuck out of cycle, or shuts down for whatever reason, you have to reboot it and hope it catches the sync again (by electric shock in most cases, though CPR can do it too). I thought it was good.
Yeah, I'm so stuck on emergence after reading that book now. If you liked that in class you really should read it, prolly would understand it better than I do too.
000, I have honestly never thought of living systems that way. But it does seem to fit what I know about them (er..us, whatever).
well, i'm honestly surprised, because i've tried to explain this idea to people loads of times and never had them "get it" so quickly :D
about the emergence book, I have trouble reading books from the screen, but I hope i can print it at university (even though i'm no longer a student, there's a good chance my acct still works), cause i really really want to read it.
I had a discussion about Emergence with someone recently, and it led me to believe that Emergence may in fact be Divinity, seeing that it's this .. thing, or concept, a process, that is so obvious, nearly tautological ("that which survives, survives" as Douglas Adams called it, in the Salmon of Doubt), it can be said to hardly "really exist", yet it's everywhere, and it causes new things to come into existence out of nothing (or out of chaos, if you like). but my idea about it isn't entirely hatched properly yet, i think. yet synchronicity has it that shortly after that discussion the topic started popping up (again) here and there on this forum :)
Quote from: Triple Zero on November 15, 2008, 01:48:15 AM
well, i'm honestly surprised, because i've tried to explain this idea to people loads of times and never had them "get it" so quickly :D
Really? Because enzymes tend to be either "on" or "off." When there are a lot of them present you get a gradient, but the individual components are a switch. That's also true of nervous and muscle impulses. A single nerve cell either sends an impulse or it doesn't, a single muscle cell either contracts or it doesn't. And it looks like it works at the genetic level too, a particular gene is either transcribed or it isn't (regulated by proteins that are either "on" or "off"). But, I have no problems with looking at organisms as machines and this is all very machine-like.
Quote from: Triple Zero on November 15, 2008, 01:48:15 AM
well, i'm honestly surprised, because i've tried to explain this idea to people loads of times and never had them "get it" so quickly :D
about the emergence book, I have trouble reading books from the screen, but I hope i can print it at university (even though i'm no longer a student, there's a good chance my acct still works), cause i really really want to read it.
I had a discussion about Emergence with someone recently, and it led me to believe that Emergence may in fact be Divinity, seeing that it's this .. thing, or concept, a process, that is so obvious, nearly tautological ("that which survives, survives" as Douglas Adams called it, in the Salmon of Doubt), it can be said to hardly "really exist", yet it's everywhere, and it causes new things to come into existence out of nothing (or out of chaos, if you like). but my idea about it isn't entirely hatched properly yet, i think. yet synchronicity has it that shortly after that discussion the topic started popping up (again) here and there on this forum :)
LOL QUIT READING MY FUCKING MIND! :lulz:
No, srsly, thats what Kauffman talks about, how the medieval concept of god or the divine should be shifted to a modern concept that compliments science, that the emergent creativity in the universe like divinity.
Quote from: Vene on November 15, 2008, 01:55:16 AM
Quote from: Triple Zero on November 15, 2008, 01:48:15 AM
well, i'm honestly surprised, because i've tried to explain this idea to people loads of times and never had them "get it" so quickly :D
Really? Because enzymes tend to be either "on" or "off." When there are a lot of them present you get a gradient, but the individual components are a switch. That's also true of nervous and muscle impulses. A single nerve cell either sends an impulse or it doesn't, a single muscle cell either contracts or it doesn't. And it looks like it works at the genetic level too, a particular gene is either transcribed or it isn't (regulated by proteins that are either "on" or "off"). But, I have no problems with looking at organisms as machines and this is all very machine-like.
Impulse was good, muscle wasn't, because muscles fibers can contract to different degrees.
I have a problem with people thinking of organisms as machines because A) they are so so so so much more emergent than a machine is, they have agency, and B) because it spawns all kinds of intelligent design type arguments.
Vene: maybe it helps that i really didn't go into the details and kept it short, then :) i can be a bit longwinded sometimes and talk about preambles and details for half an hour before (if you're lucky), getting to the point. i'm trying to avoid doing that as much as possible (i know it's annoying), but it requires concentration :)
in Steven Pinker's book "the language instinct", he argued that complexity such as life is there because of combinatorics. that is, the discrete nature of, say, DNA (A/T/G/C) makes it possible to get really complex stuff, cause you have to pick "one or the other", whereas if you mix two chemicals, you get a mixture. and if you throw more stuff at it, you just get more equally distributed stuff of the same.
Kai: zomg unbelievable :) one thing that kinda blew my mind was when the other person remarked "that may be why they say Man was created in the image of God" (because humans making/creating things are kind of like emergence-catalysts)
and Kai, about machines, i was talking about computer simulations, which run in machines, but can be way more emergent than a mere mechanical device. the trick seems to lie in having lots of semi-independent parts that act upon relatively simple rules. it's more like a bottom-up-and-see-what-happens approach than a really designed and thought out top-down architecture.
Quote from: Kai on November 15, 2008, 02:07:51 AMImpulse was good, muscle wasn't, because muscles fibers can contract to different degrees.
I guess I should have said each myosin protein instead of referring to the whole cell.
QuoteI have a problem with people thinking of organisms as machines because A) they are so so so so much more emergent than a machine is, they have agency, and B) because it spawns all kinds of intelligent design type arguments.
I think of it like stimulus-response than anything else. Like going to muscle contraction, how is the addition of Ca
2+ leading to a conformational change of the protein not a machine-like action? I look at life at the molecular level more than as a whole system. It does make me biased in a different way than those that look at individuals or groups. I know I'm ignoring the ability to make choices, but can a plant make a decision? Can a bacterium make a decision?
And fuck intelligent design. Fuck those fuckers with rusty barbed wire.
Quote from: Triple Zero on November 15, 2008, 02:15:30 AM
Vene: maybe it helps that i really didn't go into the details and kept it short, then :) i can be a bit longwinded sometimes and talk about preambles and details for half an hour before (if you're lucky), getting to the point. i'm trying to avoid doing that as much as possible (i know it's annoying), but it requires concentration :)
in Steven Pinker's book "the language instinct", he argued that complexity such as life is there because of combinatorics. that is, the discrete nature of, say, DNA (A/T/G/C) makes it possible to get really complex stuff, cause you have to pick "one or the other", whereas if you mix two chemicals, you get a mixture. and if you throw more stuff at it, you just get more equally distributed stuff of the same.
Kai: zomg unbelievable :) one thing that kinda blew my mind was when the other person remarked "that may be why they say Man was created in the image of God" (because humans making/creating things are kind of like emergence-catalysts)
and Kai, about machines, i was talking about computer simulations, which run in machines, but can be way more emergent than a mere mechanical device. the trick seems to lie in having lots of semi-independent parts that act upon relatively simple rules. it's more like a bottom-up-and-see-what-happens approach than a really designed and thought out top-down architecture.
YES YES YES! Thats exactly what he talks about. He relates it back to the Properties of Fluid Behavior and how they can't be derived from quantum mechanics. When you have a couple molecules they function very basically from a physics standpoint. However, when you have a whole shittonne of molecules in fluid medium, the interactions between molecules becomes emergent from the basic physics. It doesn't violate physical laws, but it can't be derived from them either. Moving onwards, biology is emergent from that, and consciousness is an emergent state from biology. Some might say ecology is emergent.
Because of emergent systems, you can't just transplant system language between different systems. They each operate under different rules which don't violate but can't be derived from the emergent system below that. Then you factor in creativity, things like the near infinite possibilities of combinations in DNA and how there are so many combinations that the possibility of having a new combination (that is, having creative combinations) is a probability with a limit near 1.
Quote from: Vene on November 15, 2008, 02:18:58 AM
Quote from: Kai on November 15, 2008, 02:07:51 AMImpulse was good, muscle wasn't, because muscles fibers can contract to different degrees.
I guess I should have said each myosin protein instead of referring to the whole cell.
QuoteI have a problem with people thinking of organisms as machines because A) they are so so so so much more emergent than a machine is, they have agency, and B) because it spawns all kinds of intelligent design type arguments.
I think of it like stimulus-response than anything else. Like going to muscle contraction, how is the addition of Ca2+ leading to a conformational change of the protein not a machine-like action? I look at life at the molecular level more than as a whole system. It does make me biased in a different way than those that look at individuals or groups. I know I'm ignoring the ability to make choices, but can a plant make a decision? Can a bacterium make a decision?
And fuck intelligent design. Fuck those fuckers with rusty barbed wire.
I and Kauffman both would argue agency does not require consciousness. Bacteria are self containing self replicating organisms that interact with their environment. Even if this is just triggers, the genes are still there enacting the triggers. Thats where the agency comes from, its an intrinsic property of living things as a consequence of the biology. Its not like a decision as we would think of it in consciousness, but it is still agency.
Quote from: Kai on November 15, 2008, 02:29:01 AM
Quote from: Vene on November 15, 2008, 02:18:58 AM
Quote from: Kai on November 15, 2008, 02:07:51 AMImpulse was good, muscle wasn't, because muscles fibers can contract to different degrees.
I guess I should have said each myosin protein instead of referring to the whole cell.
QuoteI have a problem with people thinking of organisms as machines because A) they are so so so so much more emergent than a machine is, they have agency, and B) because it spawns all kinds of intelligent design type arguments.
I think of it like stimulus-response than anything else. Like going to muscle contraction, how is the addition of Ca2+ leading to a conformational change of the protein not a machine-like action? I look at life at the molecular level more than as a whole system. It does make me biased in a different way than those that look at individuals or groups. I know I'm ignoring the ability to make choices, but can a plant make a decision? Can a bacterium make a decision?
And fuck intelligent design. Fuck those fuckers with rusty barbed wire.
I and Kauffman both would argue agency does not require consciousness. Bacteria are self containing self replicating organisms that interact with their environment. Even if this is just triggers, the genes are still there enacting the triggers. Thats where the agency comes from, its an intrinsic property of living things as a consequence of the biology. Its not like a decision as we would think of it in consciousness, but it is still agency.
Ah, then I have no argument. I also have to find Kauffman's book.
yup, that's pretty much the reason why i don't worry about the problem of Free Will too much. even if we can explain all the mechanics, there's these huge "jumps" in complexity between different scales, where emergent properties of systems build on top of eachother into new emergent properties. there's one between quantum and atoms/molecules (i think), another one between molecules and cells, then one between cells (neurons) and our brain. and i probably left some steps out of that. but i severely doubt we can ever "really" bridge those gaps, even if we understood all the mechanics that lie beneath the elements.
also, i'd like to claim that certain computer programs are in fact able to exhibit creativity (in some sense). i'm talking again here about the emergent "artificial life" like simulations.
like Thomas Ray's "Tierra", which is a simulation of a virtual computer, little 80 instructions computer programs running concurrently in the simulated memory, written in a special simple language that was designed to be kind of robust against mutations, doing nothing but replicating themselves (and artificially dying off after some amount of time). when run, predictably, they'd fill up the memory quickly in a nice limited growth curve. but then Ray added random "mistakes", every once in a while an instruction would fail, or a bit would be flipped. suddenly, an evolutionary arms race developed. since shorter programs could replicate more quickly (less clockticks needed to make an instruction-by-instruction copy of themselves), a 45 instruction "parasite" evolved, that hijacked the copying subroutine of a nearby 80 instruction program! for a while the populations of the two "species" followed a very recognizable "predator-prey" curve/cycle, but after a while a third species appeared, evolutionary optimized to 78 instructions and resistant to the parasite, on having its subroutine hijacked, the parasite would be forced to make a copy of the 78 instruction program instead ..
another example is in evolutionary computing, where they used an FPGA, a computer chip that has programmable transistors. they used an evolutionary scheme, generated a few thousand random configurations, measured the output, and the ones that looked most like a sinus curve would be allowed to continue to the next generation. after some 10,000s of generations, they had evolved a reasonable sinus curve. but upon inspecting the circuit, they found that 90% of the transistors were not used at all [an incredible optimization]! however, cutting out this 90% of "junk" resulted in a non-working chip. after puzzling about it for quite some time, they found out what was going on, the 90% "junk" transistors had evolved not into a computing circuit but were aligned into a physical antenna ... picking up the 50Hz sinus curve of some nearby electrical equipment... sorry but if that's not creativity/out-of-the-box-thinking, i don't know what is.
Quote from: Triple Zero on November 15, 2008, 02:47:22 AM
yup, that's pretty much the reason why i don't worry about the problem of Free Will too much. even if we can explain all the mechanics, there's these huge "jumps" in complexity between different scales, where emergent properties of systems build on top of eachother into new emergent properties. there's one between quantum and atoms/molecules (i think), another one between molecules and cells, then one between cells (neurons) and our brain. and i probably left some steps out of that. but i severely doubt we can ever "really" bridge those gaps, even if we understood all the mechanics that lie beneath the elements.
also, i'd like to claim that certain computer programs are in fact able to exhibit creativity (in some sense). i'm talking again here about the emergent "artificial life" like simulations.
like Thomas Ray's "Tierra", which is a simulation of a virtual computer, little 80 instructions computer programs running concurrently in the simulated memory, written in a special simple language that was designed to be kind of robust against mutations, doing nothing but replicating themselves (and artificially dying off after some amount of time). when run, predictably, they'd fill up the memory quickly in a nice limited growth curve. but then Ray added random "mistakes", every once in a while an instruction would fail, or a bit would be flipped. suddenly, an evolutionary arms race developed. since shorter programs could replicate more quickly (less clockticks needed to make an instruction-by-instruction copy of themselves), a 45 instruction "parasite" evolved, that hijacked the copying subroutine of a nearby 80 instruction program! for a while the populations of the two "species" followed a very recognizable "predator-prey" curve/cycle, but after a while a third species appeared, evolutionary optimized to 78 instructions and resistant to the parasite, on having its subroutine hijacked, the parasite would be forced to make a copy of the 78 instruction program instead ..
another example is in evolutionary computing, where they used an FPGA, a computer chip that has programmable transistors. they used an evolutionary scheme, generated a few thousand random configurations, measured the output, and the ones that looked most like a sinus curve would be allowed to continue to the next generation. after some 10,000s of generations, they had evolved a reasonable sinus curve. but upon inspecting the circuit, they found that 90% of the transistors were not used at all [an incredible optimization]! however, cutting out this 90% of "junk" resulted in a non-working chip. after puzzling about it for quite some time, they found out what was going on, the 90% "junk" transistors had evolved not into a computing circuit but were aligned into a physical antenna ... picking up the 50Hz sinus curve of some nearby electrical equipment... sorry but if that's not creativity/out-of-the-box-thinking, i don't know what is.
Yeah. Its awesome how when you take many many individual pieces (whether they be molecules in a fluid system, RNA, or transistors in this case) and put them together in a semirandom system, over time the interactions between the pieces emerge into something beyond the individuality with each piece. I think its a general property of the universe for this sort of thing to happen.
And that Terra system looks like it works exactly how the first selfreplicating molecular systems worked.
So then, the right set of memes, metaphors, rituals and symbols... we could start ourselves a new religion!
Quote from: Ratatosk on November 15, 2008, 06:21:30 PM
So then, the right set of memes, metaphors, rituals and symbols... we could start ourselves a new religion!
at first i was like :| , but then i :lol:
Quote from: Ratatosk on November 15, 2008, 06:21:30 PM
So then, the right set of memes, metaphors, rituals and symbols... we could start ourselves a new religion!
Or not.
No, I think Rat's got a point (and I keep hearing "If Telarus had the inclination, he could start a cult to rival Scientology" from my cabal-mates).
Memes are an emergent behavior of the lower substrate of abstract concepts (previously limited to one mind, or to the 'clan memory' that verbal communication provides) that have found a path to replication (on a multi-node human-based network, now using external memory in the forms of books and computer systems), and thus a competitive ecology.
BTW, this whole thread is full of win.
Quote from: Telarus on November 15, 2008, 10:26:45 PM
No, I think Rat's got a point (and I keep hearing "If Telarus had the inclination, he could start a cult to rival Scientology" from my cabal-mates).
Memes are an emergent behavior of the lower substrate of abstract concepts (previously limited to one mind, or to the 'clan memory' that verbal communication provides) that have found a path to replication (on a multi-node human-based network, now using external memory in the forms of books and computer systems), and thus a competitive ecology.
BTW, this whole thread is full of win.
Dammit.
I just realized Dawkins coined the term meme. :argh!:
telarus, just a bit of definition, memes do not necessarily replicate. they are any "idea-sort-of-thing". it's just that the ones that do not replicate usually don't get very far or widespread, and usually aren't very interesting to consider, either.
and yeah, of course Rat is right, but that doesn't mean I have to be very enthousiastic about the idea :)
good point, 000. replication probably shouldn't be a requirement for the definition of 'meme'.
Now, a bit tangentially, I've recently been considering the Genesis accounts as an attempt by that tribe to narrativise the events that lead up to acquiring the whole 'abstract communicable thought' function. This makes Adam not 'the first dude', but the first dude who could go, "DUDE!". This also makes Lilith a crafty girl who jacked the skill of Naming and the social power that came with it, and got booted from the tribe as a result. A lot of the other language idiosyncrasies there seem to make a bit more sense with this grid on.
[/tangent]
Quote from: Telarus on November 17, 2008, 01:58:35 AM
good point, 000. replication probably shouldn't be a requirement for the definition of 'meme'.
Now, a bit tangentially, I've recently been considering the Genesis accounts as an attempt by that tribe to narrativise the events that lead up to acquiring the whole 'abstract communicable thought' function. This makes Adam not 'the first dude', but the first dude who could go, "DUDE!". This also makes Lilith a crafty girl who jacked the skill of Naming and the social power that came with it, and got booted from the tribe as a result. A lot of the other language idiosyncrasies there seem to make a bit more sense with this grid on.
[/tangent]
Do you really think those pastoralists thought that deeply about this stuff?
Quote from: Telarus on November 17, 2008, 01:58:35 AM
good point, 000. replication probably shouldn't be a requirement for the definition of 'meme'.
Now, a bit tangentially, I've recently been considering the Genesis accounts as an attempt by that tribe to narrativise the events that lead up to acquiring the whole 'abstract communicable thought' function. This makes Adam not 'the first dude', but the first dude who could go, "DUDE!". This also makes Lilith a crafty girl who jacked the skill of Naming and the social power that came with it, and got booted from the tribe as a result. A lot of the other language idiosyncrasies there seem to make a bit more sense with this grid on.
[/tangent]
The story was written thousands of years after language. Seems that not very many people there would have been around to remember the first spoken sentence.
Quote from: Telarus on November 17, 2008, 01:58:35 AM
good point, 000. replication probably shouldn't be a requirement for the definition of 'meme'.
Now, a bit tangentially, I've recently been considering the Genesis accounts as an attempt by that tribe to narrativise the events that lead up to acquiring the whole 'abstract communicable thought' function. This makes Adam not 'the first dude', but the first dude who could go, "DUDE!". This also makes Lilith a crafty girl who jacked the skill of Naming and the social power that came with it, and got booted from the tribe as a result. A lot of the other language idiosyncrasies there seem to make a bit more sense with this grid on.
[/tangent]
If you'd like my interpretation of Genesis... I'll start by making a very key point that Creationists always ignore: "Adam" means "MAN" and "Eve" means "WOMAN". They are the prototypical perfect human beings. The Garden of Eden is a metaphor for the Olden Times when "nothing bad ever happened ever"and humans were still nomadic hunter-gatherers. Eventually though the humans get bored of the "perfection" and develop curiosity. They trade in their simplistic ways for knowledge/technology. They give up the hunter/gatherer lifestyle and develop agrarian societies with all of it's positives and negatives.
It has the whole cause and effect backwards though. Humans weren't punished to toil the land because of our quest for knowledge. We chose to toil the land and found knowledge as a result. Farming caused people to stay in one place for longer. This, in turn, led to the development of towns and markets. This eventually led to trade routes, organized religion, government, schools, philosophy, modern science, etc, etc, etc.
The serpent gets a raw deal in the whole thing. All he wanted was just a little piece.