Evolutionary/Genetic Algorithms

[Justatruthseeker]

This is the first I've seen it, but it is awesome art.

After having read a bit, it seems to be the issue is mostly ID mutation issues, as in, that mutations cannot create information, which if course is ridiculous.

Still interesting arguments though.

Is it ridiculous? Or just what we observe in actual experiments after 50+ years of research? Not saying none isn't ever, but it's few and far between and averages out, leaving only variation of the same kind.

http://www.weloennig.de/Loennig-Long-Version-of-Law-of-Recurrent-Variation.pdf

Good comic tho AV. Did silver and copper get snuffed?

 

[sfs]

Is it ridiculous?

Yes, it's ridiculous. Flat-out absurdly wrong.

Or just what we observe in actual experiments after 50+ years of research?

What we observe is mutations adding information. (And by "we", I mean the scientists doing the research, not the people reading about them on lunatic-fringe websites.)

Not saying none isn't ever, but it's few and far between

In other words, even you agree that this particular claim is wrong. Good.

and averages out, leaving only variation of the same kind.

http://www.weloennig.de/Loennig-Long-Version-of-Law-of-Recurrent-Variation.pdf

In Lenski's long-term evolution experiment with E. coli, a major new ability (the ability to utilize citrate) didn't evolve until more than 31,000 generations had passed. But it did evolve.

 

[juvenissun]

Yes, it's ridiculous. Flat-out absurdly wrong.

What we observe is mutations adding information. (And by "we", I mean the scientists doing the research, not the people reading about them on lunatic-fringe websites.)

In other words, even you agree that this particular claim is wrong. Good.

In Lenski's long-term evolution experiment with E. coli, a major new ability (the ability to utilize citrate) didn't evolve until more than 31,000 generations had passed. But it did evolve.

I think this experiment only said that evolution in a natural environment is impossible.

 

[sfs]

I think this experiment only said that evolution in a natural environment is impossible.

I think you're making up an answer you like and attaching it to an experiment with no justification.

 

[Justatruthseeker]

Yes, it's ridiculous. Flat-out absurdly wrong.


What we observe is mutations adding information. (And by "we", I mean the scientists doing the research, not the people reading about them on lunatic-fringe websites.)


In other words, even you agree that this particular claim is wrong. Good.


In Lenski's long-term evolution experiment with E. coli, a major new ability (the ability to utilize citrate) didn't evolve until more than 31,000 generations had passed. But it did evolve.

But yet here you have 50+ years of actual mutational research in plant and animal husbandry which does not agree with theories of the mind.

But you are right, let's throw out 50+ years of research because someone in a lab finally got a recessive gene to turn on or off. Citrizate can already be utilized by it, it's just not it's preferred food supply. I'm sure you don't prefer to eat certain foods, but if that's all you had I am sure you would too.

What you didn't tell everybody is that nothing new was done, That all they did was enhance an already existing gene. Variation. Plain and simple, just like the 50+ years of actual mutation research with animals and plants, not bacteria in a jar showed you.

You don't even need to go to a lab to know that e coli can already process citrus.

Coliforms, Escherichia coli and Salmonella serov... [J Food Prot. 1998] - PubMed - NCBI

"Salmonella cells in juice were associated with population levels of fecal coliforms and E. coli above the upper most probable number (MPN) limits of detection (> 110/ml)."

Why you think it is a stunning feat in the lab when they already do it is beyond me, unless you have an agenda?

 

[DogmaHunter]

How do you get the best car on one hand, and also get another best car on the other hand?

Your question doesn't make any sense to me.

If you don't get it, then think about this: Why should chimp evolved into human on one hand

Chimps did not evolve into humans. How can you still not know this?
Chimps and humans share a common ancestor. Which was not a chimp (or a human).

, but also continue to thrive on the other hand?

Is this a rehash of the "if we came from monkeys, why are there still monkeys" nonsense?

It's called genetic isolation. We can do this in GA applications as well, but there's no real use for it. But we sure could do it.

In the app I linked, that would mean that we would for example grab the population of generation 100, split it in 2 and have one half stay on the current track while moving the other half to another track without allowing interbreeding between both groups.

After a while, we would have 2 populations of cars that don't really resemble eachother that much anymore. We would have 2 "species" of cars, each "specialised" to ride the track they evolved on. And both groups would share ancestry from before the genetic split.

Why is that so hard to understand?

How do you improve your algorithm to make that happen?

That would not improve the algorithm. When we use GA's, we set fixed parameters for the fitness test, because we actually have a goal in mind that we want to accomplish. We actually have a specific system of which we expect a specific output. And the GA helps us in optimizing that system according to the parameters of our choosing.

In nature, nobody is setting parameters. Nore are the parameters fixed. The parameters are determined by the environment. The total sum of the parameters actually will amount to a description of the niche that the species is filling. It will include its natural enemies, the climate it needs to survive in, the sexual pressures of the species, etc. And all of those are pretty dynamic. Their enemies evolve with them, climate changes from time to time, natural desasters can seriously disrupt the environment etc....

You could say that GA's operate in "controlled environments". In nature, they operate in a far more dynamic world.

 

[DogmaHunter]

I think this experiment only said that evolution in a natural environment is impossible.

Yeah and by the very same "logic" you present here, we can conclude from the ice in the freezer in the kitchen is evidence that ice can't form in a natural environment.

 

[juvenissun]

Is this a rehash of the "if we came from monkeys, why are there still monkeys" nonsense?

It's called genetic isolation. We can do this in GA applications as well, but there's no real use for it. But we sure could do it.

Why is there no real use? I think it is VERY useful.

You write an algorithm which perfects one species, at the same time, produce another perfect species, through the evolution algorithm (process).

How do you program that?

 

[DogmaHunter]

Why is there no real use? I think it is VERY useful.

Why do you think so?

You write an algorithm which perfects one species, at the same time, produce another perfect species, through the evolution algorithm (process).

It's quite clear that after all this time, you still don't understand the use of a GA.

It doesn't evolve systems just for the sake of it.
It's a method of optimization of a system that needs to perform in a specific environment with specific parameters.

It makes no sense to play with genetic isolation. It has no added value to the optimization process.

You could run multiple simulations, sure. But that's not the same thing.

You also don't seem to understand that GA's are used to optimize systems that fill a specific niche. Whereas population splits in nature aren't like that. Both groups don't occupy the same niche. They live in different environments. The environments might be similar, but they would not be the same. Different parameters would result in different selective pressures. And you'll end up with 2 population, each of which would be optimized for its specific niche - not for the niche of the other.

In a GA application, there is only 1 niche to fill.

How do you program that?

You don't, because it's a waste of money.
But in case you have money to waste and want to do it just for the sake of it, you can. And I already explained how to do it in my previous post. Perhaps you should read it all the way through.

I'll repeat it. In the linked car app, you'ld grab half the population of a specific generation and move them to a new track, while leaving the other half on the original track and while not allowing interbreeding between both groups from that point on.

You will have successfully isolated part of the population which would then in turn start to be optimized for that new niche they have to fill (being, the new track).

Moving half the population to another identical track would not result in fitter cars. In fact, it would most probably slow the optimization process down, as you would have successfully eradicated half of the genetic variation of the population.

 

[sfs]

Why is there no real use? I think it is VERY useful.

You write an algorithm which perfects one species, at the same time, produce another perfect species, through the evolution algorithm (process).

How do you program that?

He just told you.

 

[juvenissun]

I think you're making up an answer you like and attaching it to an experiment with no justification.

Of course I have reasons:

1. The environment in the experiment is strictly protected.
2. The concentration of material used in the experiment is un-naturally high.

Take these two conditions off, I would like to see how many generations would it take to make the change. I predict those E Coli would DIE in a few generations.

The experiment "is making up" an answer which evolutionists want to see. The genetic algorithm is of the same nature as it is now.

 

[sfs]

But yet here you have 50+ years of actual mutational research in plant and animal husbandry which does not agree with theories of the mind.

"Theories of the mind"? What are you talking about? Evolutionary biologists are well aware that there are limits to how quickly evolution can change species.

But you are right, let's throw out 50+ years of research because someone in a lab finally got a recessive gene to turn on or off. Citrizate can already be utilized by it, it's just not it's preferred food supply. I'm sure you don't prefer to eat certain foods, but if that's all you had I am sure you would too.

Your response suggests you do not understand either this experiment or genetics in general. First, there are no such thing as recessive genes: there are recessive alleles for particular traits. Second, we're talking about an experiment in E. coli, a haploid bacterium that cannot have either recessive or dominant alleles. Third, when oxygen is present, wild-type E. coli cannot use citrate, because they lack a transporter molecule to get citrate inside the cell that works in the presence of oxygen. (Also, "citrus" is a group of plants; "citrate" is a kind of molecule.)

What you didn't tell everybody is that nothing new was done, That all they did was enhance an already existing gene. Variation. Plain and simple, just like the 50+ years of actual mutation research with animals and plants, not bacteria in a jar showed you.

You don't even need to go to a lab to know that e coli can already process citrus.

Coliforms, Escherichia coli and Salmonella serov... [J Food Prot. 1998] - PubMed - NCBI

"Salmonella cells in juice were associated with population levels of fecal coliforms and E. coli above the upper most probable number (MPN) limits of detection (> 110/ml)."

Why you think it is a stunning feat in the lab when they already do it is beyond me, unless you have an agenda?

"The inability to use citrate as an energy source under oxic conditions has long been a defining characteristic of E. coli as a species (35, 36)." (From the paper on the evolution of cit+ E. coli; you can find the citations here.) In this experiment, E. coli evolved the ability to do something E. coli normally cannot do. The evolution occurred by gene duplication, with one of the copies of the gene acquiring a new regulatory mechanism. This initial development was only weakly advantageous, however, and it was followed by multiple additional mutations that improved the performance of the new ability. This is exactly the process that evolutionary biologists have long suggested as one of the primary mechanisms for the development of new traits.

 

[sfs]

Of course I have reasons:

1. The environment in the experiment is strictly protected.

The environment implies fierce competition between individual bacteria, just like real environments.

2. The concentration of material used in the experiment is un-naturally high.

Is this reason is based on having read the Lenski paper and on your knowledge of citrate concentrations in nature, or is it based on making something up because you don't like this result? The experiment used a citrate concentration of 1.7 mM. Citrate concentrations in common fruit juices are ten to thirty times higher than that.

Take these two conditions off, I would like to see how many generations would it take to make the change. I predict those E Coli would DIE in a few generations.

Of course they'd lose out to native populations in a wild environment: the two populations are adapted to different environments.

The experiment "is making up" an answer which evolutionists want to see. The genetic algorithm is of the same nature as it is now.

This experiment demonstrates conclusively that random mutations and natural selection can produce new functional traits in living species, something many creationists insist absolutely cannot happen.

ETA: Note, by the way, that this experiment was not designed to see the development of citrate-using E. coli. They just happened to be using a growth medium with citrate and little other source of carbon in it (presumably because citrate is needed by the bacteria for iron uptake).

 

[DogmaHunter]

1. The environment in the experiment is strictly protected.

Errr.... yeah. It's called a "controlled environment" for a reason, you know...

Do you have a problem with using controlled environments when conducting experiments? If so, please explain why. So we can have a good laugh.

Off course, anyone familiar with grade school level science, understands why a controlled environment is kind of important when conducting an experiment.

2. The concentration of material used in the experiment is un-naturally high.

Which is irrelevant.

Take these two conditions off, I would like to see how many generations would it take to make the change.

It wouldn't make this change. Do you find that surprising?

Seriously, what gives? Do you understand what "selection pressure" is? Because it sounds like you don't.

You are basically saying that "yes, the trait evolves when the selection pressure will favor those that have the trait... but it does NOT evolve when that pressure isn't present...so, there!!!".

Well ok then, Captain Obvious. It's rather funny that your objection is actually in favor of evolution.

I predict those E Coli would DIE in a few generations.

No. They'ld just not be subject to selection pressures favoring those that can metabolise citrate.

The experiment "is making up" an answer which evolutionists want to see. The genetic algorithm is of the same nature as it is now.

The experiment is testing the MECHANISMS of evolution. It's not trying to get to a specific outcome. It's just testing to see what happens with the DNA of identical cultures after many generations in isolated populations.

And what happened was exactly what evolution theory is all about. It responded to environmental selection pressures. A single mutation caused a population explosion because it gave them an edge over all others. The ones with the mutation outcompeted those that didn't have it and very quickly dominated the population.

This is exactly what we would expect. Nobody "gave" E Coli the ability to metabolise citrate. They accomplished that on their own through mutation and selection, through the process and mechanism of evolution.

 

[juvenissun]

The environment implies fierce competition between individual bacteria, just like real environments.


Is this reason is based on having read the Lenski paper and on your knowledge of citrate concentrations in nature, or is it based on making something up because you don't like this result? The experiment used a citrate concentration of 1.7 mM. Citrate concentrations in common fruit juices are ten to thirty times higher than that.


Of course they'd lose out to native populations in a wild environment: the two populations are adapted to different environments.


This experiment demonstrates conclusively that random mutations and natural selection can produce new functional traits in living species, something many creationists insist absolutely cannot happen.

ETA: Note, by the way, that this experiment was not designed to see the development of citrate-using E. coli. They just happened to be using a growth medium with citrate and little other source of carbon in it (presumably because citrate is needed by the bacteria for iron uptake).

I did not read the paper. But my arguments are valid:

The environment is protected from natural elements. It is easily to name a few.
The concentration of whatever media can NOT be maintained for such a long time on the surface of the earth.

As I said, this is a experiment that "makes up" data for evolution argument. Whatever the results show, they are not real. I am not saying this experiment is not meaningful. Further better study can be designed according to this one. But until then, the result of this one can not be used to support evolution.

 

[juvenissun]

Errr.... yeah. It's called a "controlled environment" for a reason, you know...

Do you have a problem with using controlled environments when conducting experiments? If so, please explain why. So we can have a good laugh.

Off course, anyone familiar with grade school level science, understands why a controlled environment is kind of important when conducting an experiment.



Which is irrelevant.



It wouldn't make this change. Do you find that surprising?

Seriously, what gives? Do you understand what "selection pressure" is? Because it sounds like you don't.

You are basically saying that "yes, the trait evolves when the selection pressure will favor those that have the trait... but it does NOT evolve when that pressure isn't present...so, there!!!".

Well ok then, Captain Obvious. It's rather funny that your objection is actually in favor of evolution.




No. They'ld just not be subject to selection pressures favoring those that can metabolise citrate.



The experiment is testing the MECHANISMS of evolution. It's not trying to get to a specific outcome. It's just testing to see what happens with the DNA of identical cultures after many generations in isolated populations.

And what happened was exactly what evolution theory is all about. It responded to environmental selection pressures. A single mutation caused a population explosion because it gave them an edge over all others. The ones with the mutation outcompeted those that didn't have it and very quickly dominated the population.

This is exactly what we would expect. Nobody "gave" E Coli the ability to metabolise citrate. They accomplished that on their own through mutation and selection, through the process and mechanism of evolution.

I suggest you to save all the energy in making junk reply like this. It won't do you any good.

Why don't you say something on my comment to your GE algorithm argument?

Is it possible to let the algorithm make two or more equally fit results?

 

[Justatruthseeker]

The environment implies fierce competition between individual bacteria, just like real environments.


Is this reason is based on having read the Lenski paper and on your knowledge of citrate concentrations in nature, or is it based on making something up because you don't like this result? The experiment used a citrate concentration of 1.7 mM. Citrate concentrations in common fruit juices are ten to thirty times higher than that.


Of course they'd lose out to native populations in a wild environment: the two populations are adapted to different environments.


This experiment demonstrates conclusively that random mutations and natural selection can produce new functional traits in living species, something many creationists insist absolutely cannot happen.

ETA: Note, by the way, that this experiment was not designed to see the development of citrate-using E. coli. They just happened to be using a growth medium with citrate and little other source of carbon in it (presumably because citrate is needed by the bacteria for iron uptake).

No, no, no, the experiment claimed to be able to show evolution from breeding a strain of e-coli that could "live" on citrus, when normally they don't thrive there. But they do and can already metabolize citrus. They created nothing new, no new gene to synthesize citrus, That gene already existed, it was not needed as their exists many more food sources. Only when you gave them no other food source, did that gene that allows them to breed in citrus environments right now anyways, turn on completely. It is mere variation. And what are they still? E-coli. And always will be.

 

[sfs]

I did not read the paper. But my arguments are valid:

No, they're really not.

The environment is protected from natural elements. It is easily to name a few.

So what? Many environments are protected from lots of natural elements, e.g. bacteria living in the human gut (like E. coli, in fact) have a quite sheltered life. Regardless, what difference does it make? This isn't an experiment about how life evolves in any particular environment: it's an experiment showing how evolution can work when an organism is placed into a new environment.

The concentration of whatever media can NOT be maintained for such a long time on the surface of the earth.

?? Are you arguing that, say, orange juice (and therefore oranges) don't exist? I don't even know what this argument is supposed to show.

As I said, this is a experiment that "makes up" data for evolution argument.

That's simply false, and slanderous to boot. No one made up anything.

Whatever the results show, they are not real. I am not saying this experiment is not meaningful. Further better study can be designed according to this one. But until then, the result of this one can not be used to support evolution.

This is just nuts, I'm afraid. Scientists aren't doing these experiments (as DogmaHunter noted) to see whether evolution is true -- the truth of evolution was established long, long ago, to the satisfaction of everyone who matters. (And most of the rest will ignore any evidence, anyway.) They're investigating the process(es) of evolution, and their findings are fascinating.

 

[sfs]

No, no, no, the experiment claimed to be able to show evolution from breeding a strain of e-coli that could "live" on citrus, when normally they don't thrive there.

Right -- and that's exactly what they showed. And it's still citrate, not citrus.

But they do and can already metabolize citrus.

I know. Who claimed that they evolved the ability to metabolize citrate? They developed the ability to import citrate without oxygen present, an ability that took a very long time to appear -- which was why I introduced them in the first place.

They created nothing new, no new gene to synthesize citrus,

Nothing new except for the new ability -- the one they didn't have before and that they evolved through mutation and natural selection. Something you seem to believe doesn't happen.

That gene already existed, it was not needed as their exists many more food sources. Only when you gave them no other food source, did that gene that allows them to breed in citrus environments right now anyways, turn on completely.

This would be irrelevant even if it were true, and it's not. The existing gene does not simply turn on completely; instead, a new copy of the gene had to be created -- by mutation -- so that it could be controlled independently. In creationist terms, this is the introduction of new information into the genome.

It is mere variation.

Mere variation that didn't exist before, that created a new, useful trait, and that was produced by evolution.

 

[juvenissun]

No, they're really not.


So what? Many environments are protected from lots of natural elements, e.g. bacteria living in the human gut (like E. coli, in fact) have a quite sheltered life. Regardless, what difference does it make? This isn't an experiment about how life evolves in any particular environment: it's an experiment showing how evolution can work when an organism is placed into a new environment.


?? Are you arguing that, say, orange juice (and therefore oranges) don't exist? I don't even know what this argument is supposed to show.


That's simply false, and slanderous to boot. No one made up anything.


This is just nuts, I'm afraid. Scientists aren't doing these experiments (as DogmaHunter noted) to see whether evolution is true -- the truth of evolution was established long, long ago, to the satisfaction of everyone who matters. (And most of the rest will ignore any evidence, anyway.) They're investigating the process(es) of evolution, and their findings are fascinating.

The picture I am talking about is E. Coli lived in exposed air at "outside". We are talking about E. Coli, not about a pig, or a croc. I am talking about reality, not an experiment, or an algorithm.

If we can clone a human cell, it certainly does not say we can clone a human.