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Antievolution.org is the critic's resource on antievolution. The public bulletin board is a lightly moderated place for general discussions, using a set of rules first implemented in 1992 for the Fidonet "Evolution Echo".
Updated: 5 hours 17 min ago

Pssst ... look at the Birthday Calendar!

Thu, 2014-01-23 15:53
Post by Driver
Quote (BillB @ Jan. 23 2014,15:01)Yes, indeed. Happy birthday to you (and also to me, I turned 41 last Sunday)
And to you, and to them, and me (also 41, on Sunday)
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Evolutionary Computation

Thu, 2014-01-23 15:41
Post by Wesley R. Elsberry
Quote (BillB @ Jan. 23 2014,04:32)       Quote (Wesley R. Elsberry @ Jan. 23 2014,09:17)While I did stress that the genomic content of the initial organism, and thus the Avidian population, could only acquire the new instructions via mutation, once an ancestral organism had one or more of those, they would be passed down to offspring with the usual frequency. And any effects they had on the organism could yield a difference in fitness, driving the usual selective processes. I think saying mutation was the only operative process goes too far. Not including the instructions in any way in the initial organism simply eliminates the possibility that I as experimenter set up a particular outcome by whatever arrangement of movement-relevant instructions might be set in that initial organism.

One question I was asked at SSCI in 2009 was why use Avida and not something like Echo. And while the efficient answer is that when one is at the Devolab, one is usually going to be using Avida, I did survey the available software at the time for applicability to the question I was looking at. The software systems allowing for agent movement all treated movement as a primitive property, often requiring some fixed movement strategy be defined for the agents a priori. I was interested in looking at what evolution could do given just the sort of capabilities underlying movement as seen in organisms like E. coli, but without specifying how those capabilities were used. And that kind of question was not what the other software packages could address.
Excellent stuff, and something I'm really interested in despite having no time to work on any more ...

I'm not intimately familiar with Avida but a few things jumped to mind whilst reading the description:
              Quote A facing is always toward another adjacent grid cell, so for an interior grid cell there are eight legal facings, five legal facings on an edge, and three at each corner grid cell.

I would say that there should be no illegal facings, just an inability to move when facing an edge – this would prevent a bias towards movement back to the centre – A bit like breeding E. coli in a jar: They cannot pass through the glass container but they could repeatedly bump against it until they die. By having illegal facings you are, in one sense, providing them with obstacle avoidance behaviour for free.


Avida giveth, and Avida taketh away. Facing is very basic to the software. Illegal facings, when exercised, terminate the program with an ugly "bus error" message.

On the other hand, the world geometry options are (or I should say "were", I haven't checked the latest code) grid, torus, and clique. I have no idea what clique does. Torus, though, wraps the edges of the world grid. Using torus would solve the illegal facing issue, since every cell would then be an interior cell. However, I also thought of torus as giving Avidians something for free, since on a relatively prime grid size I think movement on the diagonal will give the organism access to a lot of the grid, if not all of it.

    Quote (BillB @ Jan. 23 2014,04:32)
              Quote The "sense-diff-facing" instruction puts the difference in the amount of a specified resource between the current grid cell and the faced grid cell into one of the Avida registers.

What if this was expanded to be a “sense X,Y diff” instruction where X and Y can be any of the surrounding cells, or your own cell? The values for X and Y would be heritable. (And I don't know what you do about sensing the cell in front of you when facing the edge of the world)


As I recall it, access to adjoining cells is entirely defined by facing. It would be nice to have X,Y addressable during the run, but as I recall, it doesn't work that way.

I think this issue, among others, led a colleague of mine to give up on modifying the Avida grid system entirely, and instead implemented a separate arena-style system that was instantiated on a per-organism basis, what she referred to in the planning stages as "dream-a-grid". Many of the things that I am describing as constraints would not be in her codebase. (Her Avidians evolved such things as perfect maze-running, but she had a complex system of markers that when correctly sensed and acted upon would lead to that.) The tradeoff, though, is that her movement experiments were all about individual performances, and no interaction between members of the population would be possible. I'm thinking in terms of future experiments possibly having a larger role for competition.

    Quote (BillB @ Jan. 23 2014,04:32)
Perhaps if you wanted to add an interesting twist you could turn that into something like "Z=F(X,Y)" where X and Y are as described above but the function F is a heritable operand (Add, Subtract Multiply Divide or Modulo) - you might even include bit shifting as a possible operand? Z=X<<Y or Z=X>>Y

The point would be to provide multiple pathways for this sensory apparatus to work - and for it to fail to work.

Expanding on this a bit more (if it is worth doing) you could allow for more distal sensing - maybe a Z=F((A,B)(X,Y)) instruction where A and B, and X and Y, are relative cell co-ordinates, perhaps capped to a maximum range of +/- 5. If you did this then I would be tempted to add a cost for longer range sensing (You need more energy to grow those longer whiskers!)


There was already code in Avida for distinguishing resources. This was based on a label system, where several bases in the genome get interpreted as a label, so what the organism gets when it processes a sensory instruction is heritable. All the sensory instruction does is put a value into an Avidian CPU register. What happens to it after that has to evolve, too.

Like I said above, I don't know that distant sensing has an obvious implementation pathway.

    Quote (BillB @ Jan. 23 2014,04:32)
              Quote The environment is defined with a positively rewarding resource, with a peak in the resource set off-center in the world grid.

Can you make this more complex and dynamic? Perhaps try something more akin to a simple hydrothermal vent model:

A source (of the resource) pops up at a random location and begins churning out the ‘resource’, creating a gradient. Eventually the source is exhausted and the gradient disappears. You can have a maximum of x sources in the world at any time and when the number of sources is less than x a new source has some probability of appearing at a new random location.


The current way I define a resource gradient is quite cumbersome. I have a Perl script that set up CELL declarations in the environment config for every cell in the grid. I do have code for a method to establish a resource gradient at runtime, but that's not yet tested. Yes, I'd like to have a moving resource at some point. I don't think it will be the first thing out the gate.

    Quote (BillB @ Jan. 23 2014,04:32)
It would also be nice to have a negative resource – something that causes harm but which is not simply a lack of positive resource – using the same hydrothermal vent model you could have a second resource whose intensity costs or harms an agent. This should result in a much more interesting and dynamic resource landscape for the agents to navigate.

I'm not sure if this should be a sense-able resource (something the agent can sense) of if it just causes harm without the agent realising -- Something I'm not clear on with Avida: can the agent sense its own 'energy' and as a result tell if it is being rewarded or harmed?


The "detrimental resource" is likely the first thing out the gate. There's some issues on how this gets implemented, but I think I see a way forward on that that won't impact what I've already done too much.

As far as the Avidians sensing whether they are doing well or not, I think the answer is "no". The system scheduler assigns cycles based on merit, so poorly performing Avidians are also slowly performing Avidians. As far as I know, permitting an Avidian to have access to some transformation of its own merit would require setting up an instruction to do just that. Plus, an absolute value for merit wouldn't be terribly useful. In the first hundred updates, a merit of 0.29 would be excellent, but then pretty miserable not so much further into the run. What would be useful to the Avidian is some relative number related to their ranking in the population. I don't know of any biological correlate to that, though.

    Quote (BillB @ Jan. 23 2014,04:32)
I am tempted to suggest actually defining a spectrum of resources (some good, some bad) but this would require many more methods for the agent to sense them (and makes for a much more complex research project). What I am thinking of here (and it is a vague thought without any of the important details) is to include potential routes by which an agent can gain an advantage by combining certain resources in certain ratios – it can create a more potent energy source than the ones it absorbs passively – This would, of course, be balanced by the potential for agents to combine resources into fatal concoctions.

Actually, the sensing system is already label-based, so multiplying the resources could be done without any particular hassle for the programmer. What it would do to the Avidians... that's an experiment.

The first experiment was pretty much a stab in the dark. We set up something that hadn't been tried, and we didn't know whether we were posing a challenge outside the scope of what could be evolved in Avida. Now that we know that Avidians can evolve movement strategies, including ones in an optimal class of strategies, we can raise the bar some.
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Uncommonly Dense Thread 5

Thu, 2014-01-23 15:23
Post by Soapy Sam
Quote (olegt @ Jan. 23 2014,14:41)   Quote (Soapy Sam @ Jan. 23 2014,08:33)But surely still, as a shorthand, 'interaction'? Interactions between atoms and molecules in pure form or solution change with energy distribution, number and the properties of the atoms in any surrounding medium. That there are discrete phase transitions doesn't go against the simplistic notion that collective properties arise from summed complex interactions.
A bit too simplistic. Surely, if atoms didn't interact then there would not be any solids. Or liquids, for that matter. But just saying "interactions are responsible for rigidity" misses an essential point. Interactions between atoms exist in both liquids and solids. However, solids keep their shapes and liquids do not. The presence of interactions does not explain this key difference. So alluding to interactions is not an explanation.
It's true - it's no more an explanation than 'emergence' is. I merely regard them as approximately synonymous, and it evades the slightly mystical quality that emergence seems to engender.

phoodoo, I'm betting, would waft away any scientific understanding of this or that specific emergent phenomenon because it does not extend to his chosen example - ants, or brain cells. He wants THE scientific explanation for emergence as a phenomenon - everything beyond the naked quark, if such can stand alone. And the fundamental, explains-nothing-by-itself quality of emergent phenomena is that they result from interactions, building onion-like up to and including the level of interest.
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Pssst ... look at the Birthday Calendar&#33;

Thu, 2014-01-23 15:01
Post by BillB
Yes, indeed. Happy birthday to you (and also to me, I turned 41 last Sunday)
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Uncommonly Dense Thread 5

Thu, 2014-01-23 14:41
Post by olegt
Quote (Soapy Sam @ Jan. 23 2014,08:33)But surely still, as a shorthand, 'interaction'? Interactions between atoms and molecules in pure form or solution change with energy distribution, number and the properties of the atoms in any surrounding medium. That there are discrete phase transitions doesn't go against the simplistic notion that collective properties arise from summed complex interactions.
A bit too simplistic. Surely, if atoms didn't interact then there would not be any solids. Or liquids, for that matter. But just saying "interactions are responsible for rigidity" misses an essential point. Interactions between atoms exist in both liquids and solids. However, solids keep their shapes and liquids do not. The presence of interactions does not explain this key difference. So alluding to interactions is not an explanation.
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Pssst ... look at the Birthday Calendar&#33;

Thu, 2014-01-23 14:34
Post by deadman_932
Happy birthday, Phil and Wes.
How does it feel being THAT old?
HAHAHAHAHA.
No, really, you're old
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A Separate Thread for Gary Gaulin

Thu, 2014-01-23 14:33
Post by k.e..
Jesus fucking Christ Gary where is the Hopfield net?
Just a bunch of nested loops, man ur such a bullshitter.
Samsung called and they want their wasted RAM back you fucking turkey.
Go ahead and send that to whomever you like but attach a picture of turkey just to make sure they get the joke. Here's one if you can't find a turkey on the webs.
<img src="http:// http://techjost.com/wp-cont....g" border="0" max-width="560" />
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Uncommonly Dense Thread 5

Thu, 2014-01-23 14:33
Post by Soapy Sam
Quote (olegt @ Jan. 23 2014,12:45)The notion of emergence in science, as I understand it, begins with a negative statement.

For example, the rigidity of a solid is not explained by the properties of atoms that make it up. You can know everything about the atomic structure and energy levels and even about interactions of atoms. But you still don't understand what makes a solid rigid. When you attempt to deform a piece of ice and it resists your efforts, you can't just say "Oh, atoms are hard and so is the solid they make up." Because when that piece of ice melts, you can deform the resulting water easily. And it is made of the same atoms. So it's not about atoms.

But of course making a negative statement does not explain anything. You need a positive theory. The rigidity of crystals is explained by spontaneous breaking of the symmetries of translations and rotations in them. The vacuum is translationally and rotationally invariant: it looks the same if you move by an angstrom left or right or if you turn your head. A liquid is also translationally and rotationally invariant: there are no preferred positions or directions in it. A crystal isn't: atoms form a periodic structure; shifting by an angstrom left or right shifts the periodic lattice; turning your head changes its orientation with respect to the crystal's face.

So the rigidity of a crystal turns out to be a property that is not possessed by the atoms constituting a solid. It only emerges when a large collection of atoms does something entirely new: spontaneously breaks some symmetries of the vacuum. Rigidity is a canonical example of emergence in science. Contrary to phoodoo's ignorant claim, scientists know very well what emergence is. There are well understood cases.
But surely still, as a shorthand, 'interaction'? Interactions between atoms and molecules in pure form or solution change with energy distribution, number and the properties of the atoms in any surrounding medium. That there are discrete phase transitions doesn't go against the simplistic notion that collective properties arise from summed complex interactions.
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Uncommonly Dense Thread 5

Thu, 2014-01-23 13:55
Post by Amadan
Tard goes in, tard goes out.

You can't explain that.
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A Separate Thread for Gary Gaulin

Sat, 2014-01-18 06:48
Post by GaryGaulin
Quote (Alan Fox @ Jan. 16 2014,14:05)Assuming the board has the right info - Happy Birthday to Gary!
Yes, it's correct. Thanks for the friendly words (and JohnW sort of). That helped cheer me up, from the depressing F-bombing, on top of all else.

I had a day to work on the hippocampal system. Around 5% of the time the critter will go around the moving invisible shock zone then wait for it to be safe. I then read some of the latest papers on how the hippocampal system might work which led to Hopfield Neural Network attractors and such:

http://www.youtube.com/watch?v....9OnjoZS

I'm now trying to outdo myself by wiring up a system with the Hopfield Neural Net in mind as how memory is stored (in biology as opposed to computer code that must be stored in electronic RAM) for quickly finding shortest path to food avoiding places in between at a certain current and future angular time (angle of room cue card relative to arena revolving over time around the rat's arena). I have a circuit on paper with a good chance to working, and will try it out. It's just a step up from what I already have that worked well enough to show I next need to try making each place cell in the network a separate memory system working in parallel with others, as opposed to one for each entire lobe. I'll then essentially be modeling (what by theory qualifies as) “cellular intelligence”.

If this works then I will have saved myself tons of time, trying to model a hippocampal system. So hopefully none mind my focusing on that, for now. I'll check back to see how things are going here, in case there is something else worth replying to, like your reply. I'm feeling older, but at a time like this your wishing me a happy birthday helped me to none the less be glad to made it to this stage of development, of my everything.
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MHC/HLA immune genome mutation rates question

Sat, 2014-01-18 03:56
Post by qetzal
Keep in mind that each individual can have a mutation. So if you had 100,000 children born in each new generation, you'd expect one new mutation per 3000 bp per generation in the population overall.

I'm sure the actual math is more complicated, but I don't know the details.
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Board Mechanics

Sat, 2014-01-18 00:47
Post by fnxtr
...AND... we're back. Thank yew!
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Board Mechanics

Fri, 2014-01-17 23:02
Post by Wesley R. Elsberry
I'll see about contacting Reed. PT is on his server.
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Board Mechanics

Fri, 2014-01-17 22:19
Post by rossum
http://www.downforeveryoneorjustme.com/....tme....tme.com has PT down for everyone at 22:00 GMT
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Board Mechanics

Fri, 2014-01-17 21:58
Post by fnxtr
Couldn't reach PT at 1:50PST today.
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Thread for Phoodoo

Fri, 2014-01-17 18:12
Post by Friar Broccoli
Quote (Alan Fox @ Jan. 17 2014,10:47)Hi Friar Broccoli

I'm not sure if there is a probationary period. Couple of options. Find an existing thread with a similar topic heading and post in that.

Post it in this thread and I or one of the regulars can set up a thread for you. The thread with the most recent comment comes to the top of the topic list so it should be visible for a while.

Thanks.  As you can see, things seem to be working ok now.
-
-
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MHC/HLA immune genome mutation rates question

Fri, 2014-01-17 18:06
Post by Friar Broccoli
Hi;

I am trying to write up a shorter and clearer (so creationists can read it) version of Lenny Flank's argument about mutation rates as implied by the number of alleles in the MHC complex.  I also want this rewrite because (among other things) the creationist response focuses on his use "beneficial" mutations. (See: http://creation.com/bible-t....versity )


In my first draft I began:

_start_
MHC regions are usually less than 2000 bp long in a genome that is 3,000,000,000 bp long.


Observationally we know there are a 100 mutations per generation over the entire genome.

Therefore in a region that is:

- 300,000,000 bp long we would expect one mutation per generation.
- 3,000,000 bp long we would expect one mutation ever 100 generations.
- 3,000 bp long we would expect one mutation ever 100,000 generations.

Since we sometimes see more than 1000 mutations (alleles) in the 2,000 bp long MHC immune complexes this suggests these areas have been mutating for 100,000,000 generations.
_stop_

Here I said to myself 100,000,000 generations seems like way too many, unless (for example the mouse MHC complex looks fairly similar - does it?).  If it does not, what is a more reasonable estimate of the number of generations to achieve the diversity we see in the human MHC complexes?

Also is the observed generation to generation rate of mutations in the MHC complexes much different from that observed in the rest of the human genome?
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Thread for Phoodoo

Fri, 2014-01-17 16:47
Post by Alan Fox
Hi Friar Broccoli

I'm not sure if there is a probationary period. Couple of options. Find an existing thread with a similar topic heading and post in that.

Post it in this thread and I or one of the regulars can set up a thread for you. The thread with the most recent comment comes to the top of the topic list so it should be visible for a while.
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Thread for Phoodoo

Fri, 2014-01-17 16:23
Post by Friar Broccoli
I just registered hoping to be able to ask a question here.  But when I try "new topic" in:

Antievolution.org Discussion Board > From the Panda's Thumb > After the Bar Closes

(the only place that seems active) I get the message:
"Sorry, you do not have permission to start a topic in this forum. You are currently logged in as Friar Broccoli"

What do I need to do?

it's a slightly technical question about counting generations based on mutation rates.
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A Separate Thread for Gary Gaulin

Thu, 2014-01-16 21:23
Post by JohnW
Quote (Alan Fox @ Jan. 16 2014,12:05)Assuming the board has the right info - Happy Birthday to Gary!
Happy birthday*, Gary!




* assuming the planet you live on has a 365.24-day year...
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