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Randomness in Evolution: Valid and Invalid Usage

Firstly I made a mistake in my previous post:



They obviously were seperated by more than one generation. However they were very close in generations (the closest possible would be four generations).


Are you sure it is me that is "twsting this paper" and not you?



OK from later on in Lenski's paper:



The discussion is about whether "replaying the tape" of evolution would produce significantly different results.

This is what is meant by historical contingency in this case. The answer is that replaying the tape needn't always produce the same result.

The experiment did replay the tape many times and sometimes got different results. These differences are due to chance, as the other factors were taken account of, and were shown to be unimportant.

It is misguided, and confusing, to deny the role of chance (or historical contingency) in the evolution of citrate metabolism in these populations.

Nobody denies the role of chance...that's a lovely creationist strawman, though-- Difference in outcome may be due to chance (random mutations), but the outcome that results is DETERMINED by natural selection--the environment selecting over time!

Evolution: Random mutation coupled with natural selection which is "determined".

Easy for everyone to understand-- except those who imagine themselves as explaining it better it seems... and for some odd reason those people seem DETERMINED to describe evolution in a way that makes it sound like scientists think that all this complexity came about by "chance". Scientists don't think that. Creationists love others to think scientists think that.

You guys are embarrassing... really.

Predictably and transparently so.

Can you sum up your point so we can laugh and move on?
 
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Articulett, you have repeatedly stated that you think using the word "random" to describe evolution causes misunderstanding of evolution. Okay, fine, I understand your point and I don't really disagree with it. I think we can all agree that we don't want to encourage muddled thinking about evolution.

What I still don't understand is... What makes the word "random" so special? If we should avoid it because it causes confusion, shouldn't we by the same logic also avoid words and phrases like "theory", "Darwinism", "survival of the fittest", "selfish gene" or for that matter teleological phrases like "For some life forms, they evolved to try something new or different when the old stuff isn't working..." ?

Is "random" uniquely confusing?

It's one that creationists are particular fond of using to confuse. They want to spread the notion that scientists think that life came together by random chance. That sounds impossible. But no scientist actually thinks that. They understand that the appearance of design is not due to any god, but good old natural selection. Creationists aim to obfuscate understanding of natural selection which is the opposite of random-- the de-randomizer, if you will-- the keystone in Darwin's theory. Because as long as people think that they know what scientists think, they can dismiss evolution as implausible and imagine a designer as more plausible.

But once natural selection is understood, that designer looks increasingly implausible... all complex designs are bottom up--emerging properties over time... the internet doesn't need a designer to be complex and amazing... and neither does our biosphere.

And calling this random is a travesty that keeps people from understanding Darwins real genius and how it applies to so much more than just life.
 
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By the way, I have never claimed that the smoke detector is random because radioactive decay is random; that is you putting words in my mouth.

Garbage. You maintained - for years, judging by your posting history - that any function of a random variable was random. A smoke detector is a prime example of how stupid a definition that is, and when I brought it up you just went back into your cave and hid for a while.

Does it make sense to call a process all the component of which are random nonrandom simply because it has orderly large-scale bahavior?

Your definition was utterly useless, since - as has been pointed out tens or possibly hundreds of times to you - it makes everything random. Real grown up people recognize that complex processes cannot always be described by a single word or phrase.

I spent some time reading the entries, and I think this is the key question. Is gas expansion random? It's pretty consistent and predictable, to the point where it obeys laws. But the particle behavior that underlies it is entirely random. Smoke dissipates throughout a room due to random brownian motion, but I can guarantee it will dissipate to fill the room. Entropy is so predictable in many environments that it can be considered a force, but its components are random elements.

The word "random" is very ill-defined for precisely these reasons. That's one of many reasons for the excruciating pointlessness of this thread. If I had to give it a definition it would be something like "fundamentally unpredictable", in which case the expansion of a gas can be either random or non-random, depending on precisely what you want to know about it. Just like evolution (and every other process in the physical world).

Evolution has a similar trend: toward increasing diversity. But the details of how it gets there are unpredictable. The process is neither truly random nor truly directed, but parts of the process are random and the net effect can be argued to be directional, if not actually directed.

Well put, although the trend towards increasing diversity is probably more a consequence of the initial conditions than something intrinsic to the process itself.
 
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Sorry I've dropped off a bit, I was away at a conference. Lets see if I can address these points.

orbits with rationally related periods are NOT tori, they are periodic orbits. and they remain in the "chaotic sea" after the tori are gone. thus the destruction of the tori says nothing about the existance of the periodic orbits. no?
1. It is completely legitimate to talk about the period of a KAM torus. It is essentially a shorthand for the winding numbers of orbits around the torus(technically winding numbers are frequencies around the torus). We can think of the periodic orbits you are talking about as winding around either the inner or outer edge of the torus.

2. Periodic orbits are trivially destroyed in a system under small perturbation. Thus they do not exist.

3. Maybe I misunderstand, but I think you might be making a little logical mistake here, from the standpoint of argumentation. You claim that there exist chaotic systems with periodic orbits. I do not dispute this. The existence of chaotic systems with periodic orbits does not disprove my claim that chaotic systems without periodic orbits exist. To disprove my claim you need to show me that no chaotic systems without periodic orbits can exist(in the sub-discussion, that no KAM systems without periodic orbits can exist).

4. To make my claim I only need to show the existence of one system that has no periodic orbits. Here are 3 KAM systems and one non KAM system.
a. A KAM system that is defined over only quasi-periodic orbits(as is typical, because periodic orbits are not interesting in the study of the KAM theorem).
b. A system under small perturbation. Under such a system only quasi-periodic orbits survive, thus this is a system without periodic orbits.
c. A KAM torus with irrationally valued inner and outer diameters.
d. Rule 30

to the extent that we are discussing chaotic mathematical systems (to the extent that KAM is relelevant), it is important not to confuse physical systems and mathematical systems.

if you really want to talk about natural systems, you'll find it hard to establish that they are "ultimately" described by mathematics at all. many of us believe them to be, but that is a religous belief not one based on evidence.
In this topic of discussion we are applying these definitions to natural systems. But it might be more fruitful to talk about systems that dissipate quickly and slowly(orbits of planets vs the friction of snooker balls).

i do not see how that could follow, unless you are suggesting that dissipative systems cannot be chaotic: the most commonly discussed chaotic systems are dissipative (Lorenz's equations, all systems with strange attractors, or any attractor for that matter!)

did i miss something here? what was the "this" in "this seems to exclude"?
At the limit, dissipative systems will fall into a steady state, thus ceasing to be chaotic. Thus, at best, the system will be chaotic within some finite boundary. You can think of it as being a point made in analogy to your argument against computers being chaotic from finite memory. Which is what initiated this discussion. All physical systems, digital or analog face physical limitations. Thus, it is incorrect to exclude one computational modality while including the other.

Here are your quotes arguing we should consider a system only at the limits:
it means digital computers cannot simulate chaotic processes in the long run (as all trajectories eventually fall onto digitally-periodic orbits of finite length).
the hallmarks of chaos are defined in the limit as time goes to infinity; transient behavour is almost always explicitly excluded. (not sure if i need that "almost")

Also, In the Lorenz Equations, you'll find that they dissipate quite quickly if you include a term to allow dissipation.

a little hasty, but not much. a dense set of unstable periodic orbits often features in the various definitions of choas, not just bob devaney's. and some argue that the existance of such a set follows from other definitions of chaos.

Some might argue this, but to claim that this is proven constitutes conjecture. Moreover, some argue the contrary and I've not seen any clear explanation why a dense set of periodic orbits must follow from chaos.

yes, i think that is the main point. no hamiltonian counter example has been provided at this point.

Who cares if a system is Hamiltonian? A non-Hamiltonian example would suffice and I don't think you've presented any objection to Rule 30.

there is no evidence for this in an analogue system, the fact that the observation of the state is quantized by the A/D converter implies we have a limited number of values we can observe, not that the system has a limited number of states.
Now you're arguing that no physical system can be digital. If that is your opinion, then this whole discussion is really superfluous. Personally, I think that we should characterize a physical system by its observables and not by the possibility of an underlying unobserved state. It just feels...unscientific.

But just to avoid blurring the line between the physical and the theoretical, I can't see any reason why a theoretical turing machine with an infinite tape can't constitute a chaotic system.

i know of no cases in the lab where this has been a problem. there are other problems, of course; and i am not sure what you mean by "controlable": you can certainly damp out chaos if you try, but if you do not actively attempt to, then the observations tend to look as if they came from a chaotic process.
There is a whole field of engineering called "Control Systems" that studies controllable systems. These are physical systems that can be made to perform reliably. If you are doing some sort of analog simulation it is important that the system be controllable, at least in the sense that you can make it perform like the system you are simulating and not just like itself.

Noise induced stability, however, is a common phenomenon in chaotic systems. This can cause a chaotic system to perform regularly under perturbation. If you are unfamiliar with this, I'm sure you can find it in the literature. I think I even linked to a tutorial describing it in one of my previous posts.

Whether stability is induced or not, an analog simulation will reach a floor(often a thermal noise) where it is forced to deviate from the trajectory of the system it is simulating. At that point it is just "shadowing" the original system as well.(Insofar as it is following a path in the chaotic system, but not the original one)

agreed, but the point is that that path is not chaotic: the periodic computer trajectory is shawdowed by an unstable periodic orbit of the chaotic system.
As far as I'm aware, the shadowed trajectory does not need to be periodic, at least not theoretically. It seems you are restating the point from the finiteness of computer memory

how does filtering the observations have any effect on the dynamics of the system?

I'm talking about filtering the system itself, not just filtering the observations. So how can it not have an effect on the dynamics of the system?
 
I read the Lenski paper and I thought I'd make two points from the paper that have not yet been stated.

1. Lenski notes that even after the potentiating mutations the probability of mutating citrate is extraordinarily low. (Page 5, right column, top)
This seems to support the alternative to Lenski's theoretical advocacy. Making his results mixed, at best.

2. The mutations did not come without cost. The Cit- population was never forced out of the population even after many generations in coexistence with the Cit+. This indicates a trade-off for Cit+. Thus under an environment with selective pressure and variation in resources(citrate) we can expect the Cit+ to be forced out of the environment.

3. One & Two also clearly correspond with reality. Where with many, many more generations of opportunity for E Coli to generate the potentiating mutations in the natural world, it still has failed to evolve.

Conclusion:
Of course there are mutations that can occur if multiple mutations that would normally have to occur simultaneously are allowed to occur concurrently. (Because the creatures are in an unnatural environment with minimal selective pressure and variability). I don't think many, if any, people on this thread would dispute that. In the presence of selective pressures, however, these improbable branches are pruned away. This essentially leaves a clear demarcation between the possible options(allowed by the environment) and the impossible ones (disallowed by the environment) . It is from this demarcation that the non-randomness of evolution flows
 
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Rerunning the tape of evolution would (given time) produce significantly different results, even if all initial situations were identical.

I actually don't see how this experiment shows that. In fact if anything I think it indicates the opposite. It took a long time for citrate-metabolizing bacteria to evolve in one of the colonies. I would expect that if the experiment goes on for another decade that trait will evolve independently in another colony, and then another, until all the colonies have evolved to more or less the same final state. That would be a good example of one of the non-random aspects of evolution.

In fact, that even one colony evolved in that specific way is a good example of how predictive evolution is. Those bacteria evolved the ability to eat citrate because that's what they were given to eat. That's highly predictable. Precisely when they evolved that way, and through precisely which pathway, is impossible to predict. But the end result it more or less the same. Of course this was a highly controlled and artificial situation, which proves nothing about the actual evolution of life on earth, which took place in a complex and variable environment.

The truth is not so black and white as the posters in this thread seem to want. Evolution is not random, full stop, and it is not non-random or deterministic, full stop. It is a complex and fascinating phenomenon which cannot be described in such simple - and simplistic - terms.

The truth is not so black and white as the posters in this thread seem to want. Evolution is not random, full stop, and it is not non-random or deterministic, full stop. It is a complex and fascinating phenomenon which cannot be described in such simple - and simplistic - terms.

Indeed, I have stated situations where I'd consider "nonrandom" to be adequate, which is "over moderately long limescales in stable environments". In changing environments which organism got which trait first would be important, and over geological timescales "large" random events would become more important. Admittedly those situations are slightly different to the e.coli in the LTE experiment.

My argument is mainly against the fatwa against describing anything in evolution* or natural selection as probabilistic or random. If evolution was nonrandom, then that would imply that something similar to humanity was inevitible from the time that life first arose on Earth. This seems to be incredibly self-centred, as well as wrong. (Also many of the more reasonable CoE Christians that I know have some idea that "God just set creation in motion with the conditions so that worshipers would eventually evolve". I think that this misunderstanding is particularly likely if you deny the role that chance has played in evolution.


Back to the E.Coli experiment: The "enabling mutation" arose in one population say after 15,000 generations. It took about another 10,000 generations for citrate matabolism to evolve.

A "neutral" mutation can sometimes later have positive (or negative) effects on selection if the environment changes. The was a related case of that in e.coli too, inspired by earlier work of Lenski, and with his collaboration) NY times article
Hidden for bervity

Dr. Bennett was particularly curious about how organisms adapt to different temperatures. He wondered if adapting to low temperatures meant organisms would fare worse at higher ones, a long-standing question. Working with Dr. Lenski, Dr. Bennett allowed 24 lines of E. coli to adapt to a relatively chilly 68 degrees for 2,000 generations. They then measured how quickly these cold-adapted microbes reproduced at a simmering 104 degrees.

Two-thirds of the lines did worse at high temperatures than their ancestors, experiencing the expected trade-off. “If you’re a betting person, that’s the way you’d better bet,” Dr. Bennett said. But the pattern was not universal. The bacteria that reproduced fastest in the cold did not do the worst job of breeding in the heat. A third of the cold-adapted lines did as well or better in the heat than the ancestor. Dr. Bennett and Dr. Lenski published their latest findings last month in The Proceedings of the National Academy of Sciences.

Given that so far only one population out of the 12 has evolved this citrate metabolism, the best least bad bet is that this is a rare occurance with a roughly 1/12 chance of arising in 15,000 generations of that population size. If you scaled up to larger organisms with longer generational length you are begining to get into timescales of thousands of years. They will probably have the advantage of sexual selection whcih might speed up evolution (but not if the mutation doesn't yet exist) but against that, the mutation rate tends to be lower.

If the environment remains constant, for long enough, you should expect more to evolve citrate metabolism, but in real situations, you are quite likely to see other factors altering the selective landscape over this timescale.

Should there be two different types of bacteria in the jars, neither of which could metabolise citrate, the one that evolves citrate metabolism first would tend to prevent the other from evolving this.

One organism acquiring a trait can hinder other organisms from acquiring similar traits, because they will be better adapted for that particular niche. It closes the door to competitors.

There was a situation described earlier this year, where this situation "might" have been seen, based on the fact that the two environments seemed very similar:

From the thread "Lizards Undergo Rapid Evolution After Introduction To A New Home"



And a possible (but admittedly unlikely) suggestion:

There is another possible explaination that could be investigated:

Devil's Advocate: "

As the islands seem very similar,

Maybe this was a random mutation that was highly beneficial, and allowed spread throughout the lizard population on the island where it occured, as it enabled a slight change in lifestyle, and a greater population density.

This could be investigated by placing some of the "new" lizards back onto the original island, and seeing if they spread. If they do, then it can't have be due to the differences in the external environment, but a "benefical" mutation opening up a slightly different niche...


"

*ETA: For example the idea that the fitness landscape is subject to arbitary (and I would argue sometimes random) changes, thus altering the selective "directions"
 
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My argument is mainly against the fatwa against describing anything in evolution* or natural selection as probabilistic or random.

And as I've pointed out before and you choose to ignore this misses the point entirely (i.e. it is not what is being argued).
 
And as I've pointed out before and you choose to ignore this misses the point entirely (i.e. it is not what is being argued).

Indeed it's what we call a straw man.

Scientists use the term random when describing evolution all the time-- but having random components does not a random process make.



We don't dash about attempting to insert the word "random" or "probabilistic" into a discussion about how the game of poker is played... and we would never do it for natural selection for the exact same reasons. It's misleading, unnecessary, and obfuscating. Yet creationists MUST do it... and apparently some other folks for some unnamed reason must do so as well. My bet is that it's because they learned evolution from a creationist.
 
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Articulett, I understand your point about random components. However my contention is that there was nothing inevitable about the course of evolution, it was significantly affected (i.e. altered) by chance events, and that if you "reran the tape of evolution" you would be likely to get significantly different ecosystems and have a significantly different course of evolution.

Having an outcome that is significantly dependent on chance does make the process random
 
Actually the game of poker might be a useful analogy to explain my contention that when the environment has hcanged recently, or is changing that randomness becomes more important.

Should most poker players be playing a game of poker against me, the outcome would be highly predictible.

Should players of equal skill play against each other, the fall of cards would become important in determing the outcome.
 
However my contention is that there was nothing inevitable about the course of evolution, it was significantly affected (i.e. altered) by chance events, and that if you "reran the tape of evolution" you would be likely to get significantly different ecosystems and have a significantly different course of evolution.

And yet again you miss the point that if you "reran the TAPE of evolution," the playback would be the SAME - that is what a tape achieves.

The UNDERSTANDING of the content of the tape requires reasoning about the CLASS, not the INSTANCE. This has also been explained before and you refuse to acknowledge it.
 
Scientists use the term random when describing evolution all the time-- but having random components does not a random process make.

Evidence?

Keep in mind that the mere existence of convergence under constant conditions is not in and of itself evidence of non-randomness. If it were, even the simplest mathematical models of probability (i.e., idenpendent and identically distributed random variables) would not be be random.
 
Yes, we all know that if you did it again there would be change... but the result would be DETERMINED by the random changes in the environment and whatever it was that caused those changes.

It's so simple Jim. It's the part that is NOT identical that results in the differing outcome! The outcome is determined by whatever random factor alters the "replay". You are thinking circularly, jimbob, because you want to believe that someone other than you thinks that it makes sense to describe evolution as you do. No one does.
 
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And yet again you miss the point that if you "reran the TAPE of evolution," the playback would be the SAME - that is what a tape achieves.

Uh...that is most certainly not what Gould (the source of the quote in the Lenski article) meant when he said: "Wind back the tape of life to the early days on the Burgess Shale; let it run from an identical starting point, and the chance becomes vanishingly small that anything like human intelligence would grace the replay".

It should be painfully clear that Gould (and, by extention, Lenski) is saying the exact opposite of what your are when he speak of the "tape of life".
 
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Evidence?

Multiply provided... you are a laughingstock. You've made the term random so broad as to be useless... except of course for furthering your behesque need to call evolution random.

Sorry, Claus...er... mijo-- I don't indulge insincere requests of evidence from those I consider trolls. When has any amount of evidence carefully provided by multiple people ever made an inroad in your impenetrable brain? I see NO EVIDENCE that it ever will. You'll just have to wait for some new unsuspecting JREF member to play this BS game.
 
Uh...that is most certainly not what Gould (the source of the quote in the Lenski article) meant when he said: "Wind back the tape of life to the early days on the Burgess Shale; let it run from an identical starting point, and the chance becomes vanishingly small that anything like human intelligence would grace the replay".

It should be painfully clear that Gould (and, by extention, Lenski) is saying the exact opposite of what your are when he speak of the "tape of life".

It's painfully clear that you are the only one who thinks this. I think you may be the only one in the world who thinks you understand Gould and the only one on this thread who thinks you are smarter than cyborg or that you have understood what he said.

Moreover, Gould would find your arguments utterly buffoonish... to quote him in support of your insane assertion that "evolution is random" (however non descriptive or misleading that is) is just astonishingly dishonest. In your head they may all be supporting your viewpoint per your magical head games... in the real world real scientists communicate so much better than you and nothing you are saying is recognizable in their explanations. The extrapolations are all in your head... and all due to your need to believe that scientists think life came about "randomly"-- just like the creationist straw man says it does.
 
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I think it's perfectly clear that I consider a "tape" to be a bad analogy for obvious reasons - no matter who said it.
 
Yes, we all know that if you did it again there would be change... but the result would be DETERMINED by the random changes in the environment and whatever it was that caused those changes.
Like the path of a random walk is "determined" by the random changes each step? Fine, that's a so called "random process".

I'm glad I could finish this nonsensical debate.
 
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Like the path of a random walk is "determined" by the random changes each step? Fine, that's a so called "random process".

Yeah, I only thought that it was creationists who equviocated and obfuscated, but articulett seems to be giving them a run for their money.
 

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