Randomness in Evolution: Valid and Invalid Usage [Archive] - Page 5

zosima

17th June 2008, 02:58 PM

read the theorem more carefully. it does not establish that computer simulations are chaotic.

What the shadowing theorem proves is that the computational path has a true analog in the chaotic system, that is the path of the shadow. But I'll agree that It is more accurate to say it proves effective chaos, or as chaotic as is possible in a physical system with finite resources. I don't think any physical system, analog or digital can be truly chaotic in the precise mathematical terminology and I've stated that several different times.

When we're talking about physical systems, we're really talking about effective definitions and approximations.

how could the trajectory of a finite state machine not approach a periodic cycle?
In finite memory a system will definitely approach a finite periodic cycle. I would argue that that it is effectively chaotic up until the cycle begins to repeat. The length of which would be limited by the size of available computational resources. In infinite time&memory( ie an abstract computational machine), you could have a period of infinite length.

In any physical system(analog or digital) there will be finite resources and thus a finite set of possible states(although it might be harder to visualize what these states are in an analog system). Once the system runs out of distinct states, the next step must land in a repeating state by the pigeon hole principle.

I agree that an analog system must be controllable to be a simulation of anything. But I don't think it is the case that no analog system is controllable. Only that the system has finite limitations. After which it will diverge from the theoretical. Often analog systems are limited by the available energy or system noise. It can often be difficult to create a controllable chaotic simulation in an analog system because noise will create stability in the system. So beyond a certain number of iterations the error in the analog system converges.

ETA: An example of one technique for making an analog system controllable is to use a low pass filter. Then your system is an accurate approximation of the mathematical ideal up to the efficiency of the filter.

jimbob

17th June 2008, 03:06 PM

but then the physical componets will not be exactly the same either so the two analogue computers will be simulating different systems.
(and would be expected to diverge even if one could use the same initial condition, no?)

simulations on analogue machines imply structural error so the equations realised (if you believe that corresponding equations exist) will differ from the mathematical target system as well.

Yes, which is why I made the following statement, with highlighting.

An analogue system aims to be a physical analogue of the system that is modelled, so there is no numerical approximation. In other words, a chaotic analogue simulation will be chaotic, but obviously its behaviour will diverge from that of the system it is modelling because it is a different chaotic system.

zosima

17th June 2008, 04:33 PM

Yes, which is why I made the following statement, with highlighting.
An analogue system aims to be a physical analogue of the system that is modelled, so there is no numerical approximation. In other words, a chaotic analogue simulation will be chaotic, but obviously its behaviour will diverge from that of the system it is modelling because it is a different chaotic system.

So you're claiming that to make an 'analog model' of the weather on earth we would have to make a duplicate of earth and copy it down to the highest level of detail, like Slartibartfast in Hitchikers Guide to the Galaxy? But since we couldn't copy the earth perfectly the second time(for example we might use different fjords) it would have a different time evolution?

What system aims to be the physical instantiation of e^x?

Treatment of an analog model like there is some sort of one-to-one correspondence leads to a lot more problems than just initial conditions. Approaching it from the perspective of abstracting a controllable system is much more sensible.

lenny

17th June 2008, 05:17 PM

zosima

19th June 2008, 03:24 AM

Outside of some bounded interval ([0,1] in the case of the logistic, any intial interval will eventually not map into itself.

Nice assertions. Would you care to back them up with some actual examples?
I already showed these claims to be false.

But when r is restricted to the integers, the dynamical system is not chaotic, as there are no periodic orbits and periodic orbits are an essential element of chaos.

But just for the sake of thoroughness, I thought I'd hammer this one home.
Since Mijo seems to value arguments from authority more than ones via reasoning...

http://mathworld.wolfram.com/Chaos.html

They do state the constraints Mijo mentioned as general guidelines. (But neither necessary nor sufficient conditions.)

More importantly note:

"However, it should be noted that despite its "random" appearance, chaos is a deterministic evolution. In addition, there are chaotic systems that do not have periodic orbits (periodic orbits only survive in the boundaries of KAM tori, and for sufficiently strong perturbations from the integrable case, islands do not necessarily survive). Furthermore, in so-called quantum chaos, trajectories do not diverge exponentially because they are constrained by the fact that the entire evolution must be unitary."

We conclude from this:
1. Chaotic systems are deterministic.
2. There are chaotic systems that do not have periodic orbits.

Also:

"Chaos" is a tricky thing to define. In fact, it is much easier to list properties that a system described as "chaotic" has rather than to give a precise definition of chaos.

Gleick (1989, p. 306) notes that "No one [of the chaos scientists he interviewed] could quite agree on [a definition of] the word itself," and so instead gives descriptions from a number of practitioners in the field. For example, he quotes Philip Holmes (apparently defining "chaotic") as, "The complicated aperiodic attracting orbits of certain, usually low-dimensional dynamical systems." Similarly, he quotes Bai-Lin Hao describing chaos (roughly) as "a kind of order without periodicity."

It turns out that even textbooks devoted to chaos do not really define the term. For example, Wiggins (1990, p. 437) says, "A dynamical system displaying sensitive dependence on initial conditions on a closed invariant set (which consists of more than one orbit) will be called chaotic." Tabor (1989, p. 34) says, "By a chaotic solution to a deterministic equation we mean a solution whose outcome is very sensitive to initial conditions (i.e., small changes in initial conditions lead to great differences in outcome) and whose evolution through phase space appears to be quite random." Finally, Rasband (1990, p. 1) says, "The very use of the word 'chaos' implies some observation of a system, perhaps through measurement, and that these observations or measurements vary unpredictably. We often say observations are chaotic when there is no discernible regularity or order."

This puts us in the position of defining chaos. In that context I return to my contention that in the context of evolution a definition of exponential error growth is the most appropriate definition for chaos in this discussion. Insofar as it is possible that there could be unbounded systems without periodic orbits that are models of evolution. If they are behaving in a way that is unpredictable with respect to initial conditions, it seems logical to include them under the aegis of chaos. This is doubly true in the status quo where no reasoning has been proposed for why periodic orbits in a bounded region are necessary and/or relevant.

jimbob

19th June 2008, 03:04 PM

so i think we are close to agreement, but when you say
In other words, a chaotic analogue simulation will be chaotic, but obviously its behaviour will diverge from that of the system it is modelling because it is a different chaotic system.

i would claim all you have evidence for is that the physical analoge is a "different system" not a "different chaotic system." given that it is different from the target mathematical system, we have no evidence that the physical analogue is itself chaotic, only that is it different.

so we can prove digital simulations are NOT chaotic, but we cannot prove analogue simulations are.

do we agree on this?

in fact, i know of no examples where the target equations turn out to be the best model of the output of an analogue computer simualtion, given a large set of obs from the simulation. i find it quite rational to be skeptical that any set of "governing" equations exist. which is a weak link back into evolution...

Maybe I have a slightly different interpretation to you. I would say that you could theoretically produce an anlalogue "computer" that exhibits true chaotic behaviour; one could attempt to model it (and assess whether the idealised components) would produce a chaotic system, Chua's circuit (http://en.wikipedia.org/wiki/Chua's_circuit) for example, could be used as a model for some other physical system.

Of course, the best that you could produce is a different chaotic system so it would be impractical, and except over short timescales, all it would model well would be itself...

Back to your last point.

i find it quite rational to be skeptical that any set of "governing" equations exist. which is a weak link back into evolution...

Agreed. On reflection, I do not think that evolution is a chaotic system, but that it is influenced by many systems that are, and that there are many nonlinear feedback loops which mean that it is equally as affected by small chance events being magnified into significant events, including events due to "disruptive mutations" that skew the whole ecosystem, or fitnes landscape. When these will occur is random, and which occurs first will affect what can come afterwards.

It is probably easiest to talk about viral mutations altering the virulance of diseases. A bird-flu epedemic that affects the number of insect-eating birds could easily affect vegitation cover in a large area, and albedo and transpiration rate, on a scale the is definitely sufficient to affect weather.

Similarly if a pandemic alters human economic activity, this would directly affect the weather. This effect has been shown in the aftermath of September 11th (http://en.wikipedia.org/wiki/Contrail#September_11.2C_2001_climate_impact_study )
The grounding of planes for three days in the United States after September 11, 2001 provided a rare opportunity for scientists to study the effects of contrails on climate forcing. Measurements showed that without contrails, the local diurnal temperature range (difference of day and night temperatures) was about 1 degree Celsius higher than immediately before;[4] however, it has also been suggested that this was due to unusually clear weather during the period.[5]

lenny

19th June 2008, 04:57 PM

We conclude from this:
1. Chaotic systems are deterministic.
2. There are chaotic systems that do not have periodic orbits

By definition, chaotic systems are deterministic. no argument there.

But i know of no chaotic system that does not have a pretty interesting set of (unstable) periodic orbits. can you give us an example (your quote does not suggestion there are no periodic orbits, only that there are no islands.)

i would be very interested to learn of an example!

lenny

19th June 2008, 05:05 PM

and except over short timescales, all it would model well would be itself...

agreed.

and defining chaos requires taking limits in the long time limit. (if Lyapunov exponents are to play a role in defining chaos, and they usually are.)

so without access to the "underlying" equations which "govern" the physical system, which we never have access too, we cannot prove a physical system is chaotic. or periodic for that matter!

ed lorenz used to say that it was reasonable to call a system chaotic if our best model of that system was chaotic, while never forgetting that tomorrow's best model might be rather different from today's best model.

i expect that this is about the best we can do.

lenny

19th June 2008, 05:17 PM

A bird-flu epedemic that affects the number of insect-eating birds could easily affect vegitation cover in a large area, and albedo and transpiration rate, on a scale the is definitely sufficient to affect weather.

i know of quotes illustrating that the atmosphere was sensitive to initial condition which date back to Poe.

this one from Sir Arthur Eddington (1928)

A total eclipse of the sun, visible in Cornwall is prophesied for 11
August 1999... I might venture to predict that 2+2 will be equal to 4 even
in 1999... The prediction of the weather this time next year ... is not
likely to ever become practicable... We should require extremely detailed
knowledge of present conditions, since a small local deviation can exert
an ever-expanding influence. We must examine the state of the sun ... be
forewarned of volcanic eruptions, ..., a coal strike ..., a lighted match
idly thrown away...

and i expect your bird-flu epedemic would qualify to join the list.

zosima

20th June 2008, 09:50 PM

By definition, chaotic systems are deterministic. no argument there.

But i know of no chaotic system that does not have a pretty interesting set of (unstable) periodic orbits. can you give us an example (your quote does not suggestion there are no periodic orbits, only that there are no islands.)

i would be very interested to learn of an example!

Well I think in they use the Kam Tori, because it is considered chaotic even in the regions of parameter space where it is not behaving periodically.

Personally, one of my favorite examples is 'Rule 30'. It has a growth that is approximately: f(x) ~= 4*f(x-1), If its output is plotted with respect to magnitude, it will actually just look like e^x with small deviations. Yet if you look at the patterns occurring in the digits, it has a lot of chaos buried in its output. Its one of the simplest and yet complex and amazing systems that I am aware of. It is actually used as the random number generator in Mathematica(as opposed to the traditional linear congruential generators). 'Rule 110' is even more amazing. It is actually Turing complete. So if you find cellular automata interesting, check 110 out too.

http://mathworld.wolfram.com/Rule30.html

These systems are both discrete time and discrete state systems, nor do they have periodic orbits(well since 110 is universal, technically it can have periodic orbits, although it is chaotic in regions of parameter space that are non-periodic).

Actually, since so much of the work done in chaos theory is experimental rather than deductive, I think that systems with periodic orbits are often studied more frequently out of expediency. In a bounded system the state representation is growing towards more and more insignificant digits rather than more and more significant ones. If you are truncating insignificant digits the shadow theorem tells us that you will not fundamentally change the nature of equation you were modeling. If you start truncating* the significant digits of the state vector, you no longer have such a guarantee. Thus it can be far trickier to simulate a system that is growing exponentially, than one that is more stationary in its most significant digits.

One thing that I think** will always be true of a chaotic system is that it will always have a representation that grows exponentially. This is a necessary precondition for exponential error growth from nearby positions. I think there are probably just as many chaotic systems that grow 'up' as grow 'down'.(Although I can't prove it in any way)

*Truncating the state vector being distinct from truncation only for the purpose of plotting the output.
**Opinion not put forth as fact.

lenny

21st June 2008, 03:45 AM

i would be very interested to learn of an example! Well I think in they use the Kam Tori, because it is considered chaotic even in the regions of parameter space where it is not behaving periodically.

thanks.

for a given dynamical system, some trajectories will be chaotic, others not. initial conditions on a torus are "quasi-periodic" (for a common two dimensional torus, that would correspond to something like the sum of two sinusiods with incommensurate periods, so the trajectory never quite repeats itself). along with the tori are real periodic orbits. proofs here go back to poincare et al.

as you change a parameter in the system, the tori start to "break up", but you never get rid of the periodic orbits; i work more with disipative systems than with the hamiltonian systems that KAM applies too, but i am pretty sure the periodic orbits never go away.

so i don't think this qualifies as example, but remain interested!

zosima

21st June 2008, 03:58 PM

thanks.

so i don't think this qualifies as example, but remain interested!

I guess you'll have to take it up with Mathworld, did you read about rule 30?

lenny

22nd June 2008, 07:28 AM

so i don't think this qualifies as example, but remain interested!
I guess you'll have to take it up with Mathworld,
i'd be happy too. but while i see that they claim the tori are lost, i find no claim that the chaotic sea is not littered with unstable periodic orbits. so as far as i can tell mathworld makes no claim that this is an example. i remain happy to follow up pointers to specific text
did you read about rule 30?
yep. it is a nice CA.

mijopaalmc

22nd June 2008, 09:30 AM

i'd be happy too. but while i see that they claim the tori are lost, i find no claim that the chaotic sea is not littered with unstable periodic orbits. so as far as i can tell mathworld makes no claim that this is an example. i remain happy to follow up pointers to specific text

Is there a standard definition of "island" in dynamical sytems theory or chaos theory?

Does an island have to be a continous interval where all the orbits are periodic? Can it be as subinterval where only isolated, indivdual periodic orbits exits but are "closer" to one another than they are to any other orbits in a larger subinterval?

yep. it is a nice CA.

I think that zosima's point was that the cell's color as a function of its position for each iteration of the CA is aperiodic for every cell in the array. Apparently, there is a proof that no two columns of rule 30 can ever repeat (http://www.springerlink.com/index/V835L14266318810.pdf). Unfortunately, it is not publicly availble (as is the case with the proof that rule 110 is universal (http://www.complex-systems.com/Archive/hierarchy/abstract.cgi?vol=15&iss=1&art=01).

Nonetheless, there does seem to some order in the left-most cells of rule 30 (e.g., repeating left-shifted "L" shapes in the "first" columns of the automaton, but, as this behavior is not described by the defintion of "periodicity" that I am most familiar with I am not sure how relevant it is to the discussion.

lenny

22nd June 2008, 10:04 AM

Is there a standard definition of "island" in dynamical sytems theory
yep. they correspond to a certain type of trajectory in the state space. take a look at the text and figures here (http://amath.colorado.edu/pub/dynamics/papers/StdMap.pdf) for the "standard map". islands correspond to quasi-periodic orbits (two or more incommensurate frequencies) in hamiltonian maps or flows. as a parameter (in this case "k") is increased the islands break up into "cantori" and no longer present barriers to trajectories. of course in dimensions greater than 3, a 2-D torus is not a barrier anyway... but from figures 1 & 2 you can see why they are called islands.
Does an island have to be a continous interval where all the orbits are periodic?
you require a 2-d (or a 3-d flow) or higher dimensional dynamical system.

motion on a circle (in 2-d) or the surface of a torus (in 3-d) is quasi-periodic, not periodic. even after the tori break up, unstable periodic orbits remain.

jimbob

23rd June 2008, 03:09 PM

Back to the OP (you can see why I started a different thread about chaotic systems...)

It is indisputible that there are many highly nonlinear feedback loops in ecosystems. Because of these interactions between organsims, sometimes smalll chance changes in one organism can have a large effect on the whole ecosystem, and thus on the "fitness landscape" and course of evolution for many organisms.

These chance effects are likely to be more important when the fitness landscape is more plastic, which will be when the environment is changing, or has changed recently*. This assertion is borne out by the fossil evidence, where most major "explosions of diversification" occur after mass extinctions, where the environment has changed, and there are many empty niches available.

I'll reiterate the following post (hidden for brevity) because this is the sort of situation that I would expect to occur (infrequently), whereas denying the probabilistic nature seems to make it hard to explain why only one colony in many evolved the ability to metabolise citrate.

With evolution, chance events become more important over time, they don't average out as in "well behaved systems".

Why isn't this an example of a random evolutionary event:

From New Scientist (http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html)
Mostly, the patterns Lenski saw were similar in each separate population. All 12 evolved larger cells, for example, as well as faster growth rates on the glucose they were fed, and lower peak population densities.

But sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use.

Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species. The citrate-using mutants increased in population size and diversity.

In the meantime, the experiment stands as proof that evolution does not always lead to the best possible outcome (http://www.newscientist.com/channel/life/dn13620-evolution-24-myths-and-misconceptions.html). Instead, a chance event can sometimes open evolutionary doors for one population that remain forever closed to other populations with different histories.

That argument that a chance event can open (or close) evoloutionary "doors") has been part of my argument, although I talked about "niches".

I notice that articulett is claiming to have put me on ignore again:

And jimbob... I've explained my point a thousand times. The nuts get to the top through probabilities, I supposed... but that IS irrelevant to understanding how they always seem to end up there. And I have you on ignore. Don't bother asking me leading questions you cannot comprehend the answer to anyhow. That is mijo-esque. I've been there; done that. You can have the last word. I refuse to let you inflict it on me, however.

(Your obfuscation regarding probabilities is fantastic, however, if you don't really want people to understand the basic science that ensures that the big nuts will settle on top... if, instead, you hope that they'll be open to the idea that there is a plot amongst nut sellers to make it look like there are more big nuts then there actually are. kudos.)

I say that Dawkins in the Extended Phenotype uses a probabilistic treatment of natural selection.

What is the alternative "nonprobabilistic" treatment?

That is obviously somehow a dishonest question.

*Because initially, the organisms will not be so optimised to the new environment as before. When near an optimum, random changes would be more likely to move away from the optimum (these are selected against so don't move the organism away from the optimum), whilst if further away, more changes will be likely to move nearer an optimum, maybe a different optimum. Again this is borne out by fossil evidence, where the evolution rate (as measured by acquisition of "modern features") slows over time in new types of molluscs {from memory from Maynard Smith's "Theory of Evolution"}

zosima

24th June 2008, 03:11 PM

I think that zosima's point was that the cell's color as a function of its position for each iteration of the CA is aperiodic for every cell in the array. Apparently, there is a proof that no two columns of rule 30 can ever repeat (http://www.springerlink.com/index/V835L14266318810.pdf). Unfortunately, it is not publicly availble (as is the case with the proof that rule 110 is universal (http://www.complex-systems.com/Archive/hierarchy/abstract.cgi?vol=15&iss=1&art=01).

It is relevant by showing a system that does not show periodic orbits yet is chaotic. It demonstrates that the definition of chaos that you have provided is too restrictive.

Although this spat over the definition of chaos is irrelevant insofar as we're talking about evolution. Whether we call them apples or oranges doesn't matter.

mijopaalmc

24th June 2008, 04:02 PM

It is relevant by showing a system that does not show periodic orbits yet is chaotic. It demonstrates that the definition of chaos that you have provided is too restrictive.

Although this spat over the definition of chaos is irrelevant insofar as we're talking about evolution. Whether we call them apples or oranges doesn't matter.

OK, I was a little hasty in saying that chaos required a dense set of periodic orbits. It was a published definition by an expert in choas theory, Robert Devaney, but, as Devaney himself admits, it is not the only definition of chaos and there is no universally agreed upon definition of chaos. Nonetheless, it seems that you are ignoring that the Kolmogorov–Arnold–Moser theorem (which applies to the KAM tori mentioned in the MathWorld article on chaos) mentions only quasiperiodic orbits and says nothing about periodic orbits themselves.

zosima

24th June 2008, 06:09 PM

i'd be happy too. but while i see that they claim the tori are lost, i find no claim that the chaotic sea is not littered with unstable periodic orbits. so as far as i can tell mathworld makes no claim that this is an example. i remain happy to follow up pointers to specific text

You're splitting the hairs pretty to the point of reinterpreting the English language if you think that they didn't mean that statement as an example. But generally I think systems described by KAM-theorem exclude tori with rational valued periods. Thus KAM-systems are only quasi-periodic. Yet KAM-systems are still considered chaotic. I'm confused as to how you don't consider this sufficient.

@Mijo: I agree with you this only relaxes the definition to periodic or a quasi-periodic systems, but I think rule 30 is probably a good example of a chaotic system that is aperiodic. (Although as you note, not completely disordered)
I'm not sure why we would want our definition of chaos to exclude a system like this. If you read each row of progression in the system off as a binary number it actually grows exponentially and without bound.

Speaking of dissipative systems. Aren't all natural systems ultimately dissipative and only non-dissipative in approximation? This seems to exclude any natural system from being chaotic in theory(not just that we are unsure because we can't model it or measure it sufficiently well).

zosima

24th June 2008, 06:25 PM

OK, I was a little hasty in saying that chaos required a dense set of periodic orbits. It was a published definition by an expert in choas theory, Robert Devaney, but, as Devaney himself admits, it is not the only definition of chaos and there is no universally agreed upon definition of chaos. Nonetheless, it seems that you are ignoring that the Kolmogorov–Arnold–Moser theorem (which applies to the KAM tori mentioned in the MathWorld article on chaos) mentions only quasiperiodic orbits and says nothing about periodic orbits themselves.

I answered this in my response to lenny. :-)

On the topic of evolution I'd like to just agree to disagree. You don't like my definition and I don't like yours. If we define random systems as any system that is non-deterministic then evolution is trivially random. If we define random as uniformly distributed outcomes between uncorrelated trials, then evolution is trivially non-random.

I think we can agree that the true behavior of evolution is somewhere in between,whether we consider it random or not.

If you want to continue this discussion I wouldn't mind talking about some of these issues of convergence and divergence, but I don't think we're gonna make any more progress on this "fundamentally random" definition.

zosima

24th June 2008, 06:34 PM

jimbob

25th June 2008, 11:24 AM

With evolution, chance events become more important over time, they don't average out as in "well behaved systems".
I know you feel that way. Maybe if you close your eyes, click your ruby slippers together, and wish really hard it will come true.

Whether the KT impact was "random" it certainly was arbitary and had a huge effect on evolution.

You could claim that the effects are only pseudoranddom but (surely) you can't deny their importance over long timescales.

jimbob

25th June 2008, 11:47 AM

Can you provide the link to the paper. I trust New Scientist about as far as I can throw it, which quite un-randomly ends up being the distance to the trash bin.

The article quoted the original scientist, quite extensively, so you would expect it to be pretty accurate...

Anyway this has been discussed recently:

From another thread...

Found the whole article in a pdf file.

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli (http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf)

And here's Behe's comments (http://www.amazon.com/gp/blog/post/PLNK3U696N278Z93O) from his blog.I think the results fit a lot more easily into the viewpoint of The Edge of Evolution. One of the major points of the book was that if only one mutation is needed to confer some ability, then Darwinian evolution has little problem finding it. But if more than one is needed, the probability of getting all the right ones grows exponentially worse. “If two mutations have to occur before there is a net beneficial effect — if an intermediate state is harmful, or less fit than the starting state — then there is already a big evolutionary problem.” (4) And what if more than two are needed? The task quickly gets out of reach of random mutation.Here's your answer about what the Creationists will say. Ha! Talk about being unable to face the fact you have been wrong in a big way.

Behe is saying that the observation of a rare sequence of mutations occurring (needing to occur for species evolution), proves it can't happen. What an idiot.

From the abstract (EDIT: of the original article):

The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit+) variant finally evolved in one population by 31,500 generations, causing an increase in population
size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that ‘‘replayed’’ evolution from different points in that population’s history. We observed no Cit+ mutants among 8.4x1012 ancestral cells, nor among 9x1012 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability. Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

I could highlight many phrases in the abstract, as this supports both my general point, and the New Scientist article.

articulett

25th June 2008, 12:49 PM

jimbob... they are saying that the environment DETERMINES the outcome.

mijopaalmc

25th June 2008, 01:40 PM

jimbob... they are saying that the environment DETERMINES the outcome.

But that is something quite differnt that calling evolution a deterministic process, which pertains to how organisms interact with their environment. The continued conflation of the fact that enviroment determines the probabilities of different phenotypes' ability to produce reproductively viable offspring with the idea that evolution is a deterministic process only causes confusion and seems to be quite deliberate on the part of those who insist that evolution is non-random.

The point of jimbob's posts on Lenski's research is that it demonstrates quite clearly that identical populations* under identical eviromental conditions do in fact evolve differently. In other words, their evolution is random.

This, however, doesn't that the evolution of a Cit+ population was completely unexpected as citrate was in 68-fold excess to glucose, providing an abunant and unutilized resource that would provide some selective advantage to populations who evolved such a trait. Nonetheless, any insistence that evolution is non-random must be accompanied by ab explanation as to why the other 11 populations, which were identical to the Cit+ population at the beginning of the experiment, did not evolve to metabolize exogenous citrate.

*Lenski is quite clear in the cited research describing the Long-Term Evolution Experiment that the 12 populations of E. coli were identical to one another at the beginning to the experiment (i.e., there was no standing interpopulation or intrapopulation variation at the beginning of the experiment).

lenny

28th June 2008, 10:22 PM

But generally I think systems described by KAM-theorem exclude tori with rational valued periods. Thus KAM-systems are only quasi-periodic. Yet KAM-systems are still considered chaotic. I'm confused as to how you don't consider this sufficient.
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?
Speaking of dissipative systems. Aren't all natural systems ultimately dissipative and only non-dissipative in approximation?
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.
This seems to exclude any natural system from being chaotic in theory(not just that we are unsure because we can't model it or measure it sufficiently well).

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"?

lenny

28th June 2008, 10:30 PM

OK, I was a little hasty in saying that chaos required a dense set of periodic orbits.
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.
Nonetheless, it seems that you are ignoring that the Kolmogorov–Arnold–Moser theorem (which applies to the KAM tori mentioned in the MathWorld article on chaos) mentions only quasiperiodic orbits and says nothing about periodic orbits themselves.yes, i think that is the main point. no hamiltonian counter example has been provided at this point.

jimbob

29th June 2008, 04:39 AM

jimbob... they are saying that the environment DETERMINES the outcome.

No they are not, the environment affects the outcome, but it doesn't determine it.

Historical contingency (aka chance) also plays a part:

Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

The conditions weree as close to identical as possible in the twelve groups, and one group only out of the twelve evolved the ability to metabolise citrate. This is the only e.coli population anywhere known to metabolise citrate. This ability evolved after 30,000 generations, but depended on a prior mutation that occured betweeen 15,000 and 20,000 generations in this population.

If the environment determined this, then the other eleven groups would also have evolved this ability.

cyborg

29th June 2008, 05:35 AM

lenny

29th June 2008, 06:31 AM

What the shadowing theorem proves is that the computational path has a true analog in the chaotic system, that is the path of the shadow.
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.
When we're talking about physical systems, we're really talking about effective definitions and approximations.
agreed. and i think there is value in lorenz's suggestoin that we call a physical system chaotic if the best model we have for that system today is chaotic.
In finite memory a system will definitely approach a finite periodic cycle. I would argue that that it is effectively chaotic up until the cycle begins to repeat.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")
The length of which would be limited by the size of available computational resources. In infinite time&memory( ie an abstract computational machine), you could have a period of infinite length.
agreed
In any physical system(analog or digital) there will be finite resources and thus a finite set of possible states(although it might be harder to visualize what these states are in an analog system). Once the system runs out of distinct states, the next step must land in a repeating state by the pigeon hole principle.
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.
It can often be difficult to create a controllable chaotic simulation in an analog system because noise will create stability in the 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.
An example of one technique for making an analog system controllable is to use a low pass filter. Then your system is an accurate approximation of the mathematical ideal up to the efficiency of the filter.
how does filtering the observations have any effect on the dynamics of the system?

jimbob

29th June 2008, 06:41 AM

If the environment determined this, then the other eleven groups would also have evolved this ability.

It's been X number of months are you still insist on getting this wrong and playing semantic games:

No they are not, the environment affects the outcome, but it doesn't determine it.

Because this is a deterministic relationship. You've had this explained. You don't like the words. So you reject it.

No I am not playing semantic games.

The differences in the initial populations and their environments were insignificant*. The differences in the outcomes were significant.

As the difference in the initial populations were insignificant with rewpect to the evolution of this trait, they could have been identical, and there would be no certainty whether the trait would appear or not. Beyond the 20,000th generation (in the particular population), the odds were highly skewed in favour of this trait's emergence.

The evolution of citrate metabolism in e.coli was an unlikely event. It happened onece. Other unlikely events will also happen.

*We know this, because the significant change in the population occured somewhere between the 15,000th generation and the 20,000th generation.

jimbob

29th June 2008, 06:52 AM

No they are not, the environment affects the outcome, but it doesn't determine it.

Because this is a deterministic relationship. You've had this explained. You don't like the words. So you reject it.

So:

The environment affects the outcome but doesn't determine it, "Because this is a deterministic relationship"??

Your addition makes no sense.

Did you mean that the environment does determine the outcome? If this is the case how can significantly identical populations and environments lead to significantly different outcomes?

cyborg

29th June 2008, 09:49 AM

I explained everything months ago. You still refuse to understand.

articulett

29th June 2008, 10:36 AM

Jimbob, the parts that were not identical but adaptive to the population became exponentially multiplied over time... How?-- because the environment DETERMINES which of these minute differences in the DNA works best in whatever environment it finds itself in over time. This really isn't contested amongst anyone but a few people determined to call evolution random no matter how unclear that might be. Multiple peer reviewed articles call evolution "nonrandom" or determined. I haven't seen one call it "random" yet --unless by random, they mean "unpredictable" or "unguided"-- and, when that is the case, they are very clear upon the definition of random. I have seen not a single reputable source look at evolution nor the information on e. coli and refer to it with the muddled terminology you and mijo use. You may be able to extrapolate your "explanations" into that paper... but to the rest of us, it looks like some semantic twisting to call evolution "random".

You guys wanting to call evolution random have not provided a single peer reviewed paper that actually says what you are saying nor one that defines random as you do. Though you think that the e. coli experiment supports your "description of evolution"-- I assure you that the vast majority would disagree and prefer the many definitions already provided by real experts such as Dawkins and Coyne.

lenny

29th June 2008, 11:09 AM

jimbob

29th June 2008, 11:41 AM

Yes Lenny. If the differences were significant. However they weren't:

The initial 12 populations came form the same stock. Because the experiment was well thought-out, they also froze samples of the populations at different generations, part of the abstract quoted below:

We observed no Cit+ mutants among 8.4x1012
ancestral cells, nor among 9x1012 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations.

PDF file of entire pper here (http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf)

articulett

29th June 2008, 12:07 PM

mutations are random in respect to whether an organism benefits, but they are determined by the environment. Translation errors don't happen for "no reason"... the process has high fidelity, but it's prone to errors... these "errors" are the source of our mutations. We can call them random, because we can't predict which will occur and they occur whether they benefit or are a detriment to their host and its' progeny.

But the environment DETERMINES which of these changes is multiplied exponentially... we can say that whatever we see in the final populations was determined by what reproduced best in the prior populations in the respective environments over time.

That, in essence, is what natural selection is about--what evolution is about. Calling this random or "probabilistic" is obfuscating and useless as far as I can tell. If you want to communicate what is going on in the e. coli experiments with any one... I'd suggest you use words that scientists actually use and not the explanations of jimbob or mijo. I find them maddeningly obfuscating, misleading, and biased towards "needing" to call evolution a "random process".

Why not use the words of people who actually teach this stuff to tons of people and who know what the most common errors in understanding are? Why do some people imagine themselves as having expertise on how it should be described when no-one has every intimated that they've gained understanding through their explanations?

jimbob

29th June 2008, 12:13 PM

How about

The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue.

The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population.[/COLOR]

Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

cyborg

29th June 2008, 03:09 PM

As ever you seem to think the people disagreeing with you have reading comprehension difficulties. As I said many months ago you are simply emotionally responding to words you don't like; such as "affect" is okay, but "determines" is not despite the semantic equivalence because of your intense need to argue against anything in evolution being associated with the word. You've had this all explained to you before. You finding new examples of basically the same stuff you've gone over before is not going to change anything.

Is this too difficult a concept for you to grasp? It's not going to work no matter how many quotes you make because our point in response to it isn't going to change.

jimbob

29th June 2008, 03:35 PM

So it is a semantic discussion.

"Determines" in this situation usually implies "determies in its entirety". "Affects" implies that other factors are important.

There is a semantic difference.

[1]"The winner of a game of poker is determined by both the dealing of the cards and the strategies of the players"

[2]"The winner of a game of poker is affected by both the dealing of the cards and the strategies of the players"

[3]"The winner of a game of poker is affected by the dealing of the cards"

[4]"The winner of a game of poker is determined by the dealing of the cards "

#1,# 2, and #3 could be consistent with each other, but #1, and #4 are contradictory, as are #2 and #4.

jimbob

29th June 2008, 03:43 PM

Are you saying that you are using the "determines" and "affects" interchangably?

This is a red herring as far as the question of randomness is concerned.

In the expermient, significantly similar starting conditions produced significantly dissimilar outcomes. The starting conditions could have been identical and they still could have producesd significantly different outcomes.

Why is that not a significant a significant affect* due to chance?

*Note that I did not calim that chance "determined" the outcome, as there are non-chance factors affecting the outcome too.

articulett

29th June 2008, 03:57 PM

No. You are the one making it a semantics argument. Yes, evolution and papers can be twisted so that some in some sense you can describe it as random or probabilistic... However nobody who actually conveys understanding of evolution to others describes it as you do.

Yes, you can twist any article so that it might seem to support your point-- just as Mijo and Behe do.--that people can call evolution random. That doesn't mean that actual people who want people to convey information to other actual people regarding how evolution comes about use language in the muddled way you do, Jim-bob. Nor do Mijo and Behe actually convey information about evolution in a way that others find useful and coherent.

Having random components does does not a random process make.

"contingent upon history" means "determined by the environment over time"

DETERMINED. Opposite of RANDOM.

cyborg

29th June 2008, 04:21 PM

So it is a semantic discussion.

That's the game you like to play:

"Determines" in this situation usually implies "determies in its entirety". "Affects" implies that other factors are important.

Are you saying that you are using the "determines" and "affects" interchangably?

Nope.

Why is that not a significant a significant affect* due to chance?

Significance is irrelevant. An insignificant difference is still a difference and should make no difference to your argument.

I explained this months ago: there is no difference in outcome if the event was purposely induced or not. This is staggeringly simple to grasp.

articulett

29th June 2008, 04:44 PM

you could use "determined by" and "contingent on" interchangeably.

jimbob

29th June 2008, 11:08 PM

The original 12 were clones. Of course there were the usual errors in DNA replication so they were not completely identical, however the differences were only one generation. The environmental conditions were as close to identical as the experimenters could make.

What differences there were, were insgnificant with respect to the outcome. This was proved because there was no increased propensity to evolve citrate metabolism in samples taken from "early" generations of the "interesting" population. Samples taken from "later" generations did show an increased likelyhood of evolving citrate metabolism.

In other words something changed between generation 15,000 and generation 20,000 that made citrate metabolism more likely. This was when the significant difference occured. This significant difference was the occurance of an "enabling" mutation. It took until generation 31,500 (another 11, 500 to 16,500 generations) for citrate matabolism to actually evolve.

In other words the initial conditions could have been completely identical, and the outcomes could still have been significantly different.

That is an example of the sort of randomness that I have been talking about as important in evolution. It also is more important over longer timescales than shorter timescales.

Do you disagree with the following statement?

The evolution was not haphazard, but technically whether the bactreia evolved citrate metabolism was heavily influenced by chance.

articulett

29th June 2008, 11:18 PM

No. I think there are much clearer ways to say things. I opt for the words used by the scientists who actually do describe the evolution of ecoli rather than the way you and those who need to see evolution as "random" describe the process.

But maybe someone somewhere will think you sound less muddled then the experts and teachers and science writers who convey this understanding to others.

jimbob

30th June 2008, 01:43 PM

Firstly I made a mistake in my previous post:

The original 12 were clones. Of course there were the usual errors in DNA replication so they were not completely identical, however the differences were only one generation. The environmental conditions were as close to identical as the experimenters could make.

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?

No. You are the one making it a semantics argument. Yes, evolution and papers can be twisted so that some in some sense you can describe it as random or probabilistic... However nobody who actually conveys understanding of evolution to others describes it as you do.

Yes, you can twist any article so that it might seem to support your point-- just as Mijo and Behe do.--that people can call evolution random. That doesn't mean that actual people who want people to convey information to other actual people regarding how evolution comes about use language in the muddled way you do, Jim-bob. Nor do Mijo and Behe actually convey information about evolution in a way that others find useful and coherent.

Having random components does does not a random process make.

"contingent upon history" means "determined by the environment over time"

DETERMINED. Opposite of RANDOM.

OK from later on in Lenski's paper:

Gould argued that contingency renders evolution fundamentally quirky and unpredictable, and he famously suggested that replaying the ‘‘tape of life’’ from some point in the distant past would yield a living world far different from the one we see today. Simon Conway Morris countered that natural selection constrains organisms to a relatively few highly adaptive options, so that ‘‘the evolutionary routes are many, but the destinations are limited’’ (16). He and others point to numerous examples of convergent evolution as evidence that selection finds the same adaptations despite the vagaries of history. Evolution may thus be broadly repeatable, and multiple replays would reveal striking similarities in important features, with contingency mostly confined to minor details (16–19).

Of course, replaying life’s tape on the planetary scale is impossible, but careful experiments can examine the role of contingency in evolution on a more modest scale (15, 20, 21). To address the repeatability of evolutionary trajectories and outcomes, the long-term evolution experiment (LTEE) with Escherichia coli was started in 1988 with the founding of 12 populations from the same clone (2). These populations were initially identical except for a neutral marker that distinguished six lines from six others.

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.

jimbob

30th June 2008, 02:13 PM

Significance is irrelevant. An insignificant difference is still a difference and should make no difference to your argument.

There are differences, I was conceeding that, however they were shown to be insignificant, so do make no difference to my argument.

Rerunning the tape of evolution would (given time) produce significantly different results, even if all initial situations were identical.

mijopaalmc

30th June 2008, 02:23 PM

sol invictus

30th June 2008, 02:28 PM

sol invictus

30th June 2008, 02:31 PM

Why don't those who are arguing that evolution is non-random see identical clonal populations developing in the same environment and evolving differently (in Lenski's most recent publication, evolving the cit+ phenotype) as contradicting the premise of their argument?

You put some bacteria in a citrate-rich environment, and they evolve the ability to metabolize citrate. That's what you call "random", mijo?

A bit like the smoke detector, isn't it?

Read my previous comment if you want a more nuanced and less annoyed view, but your comment deserves derision, frankly.

Earthborn

30th June 2008, 02:59 PM

cyborg

30th June 2008, 03:06 PM

Rerunning the tape of evolution would (given time) produce significantly different results, even if all initial situations were identical.

And here we go again missing the point. The only way to go from here is me saying, "if the tape rewinds and it plays the same thing, it plays the same thing," and you saying, "QUANTUM MECHANICS FTW!"

mijopaalmc

30th June 2008, 03:39 PM

You put some bacteria in a citrate-rich environment, and they evolve the ability to metabolize citrate. That's what you call "random", mijo?

A bit like the smoke detector, isn't it?

Read my previous comment if you want a more nuanced and less annoyed view, but your comment deserves derision, frankly.

No, it is not at all like the smoke detector. What I call "random" is that only one out of the twelve populations evolved the ability to metabolize citrate despite the fact that the populations were identical at the beginning of the experiment and the fact that they evolved in the same evirnoment. Even if all the populations eventually evolved the ability to metabolize citrate, the evolution of that trait would still be random in so far as the populations evolved that trait at different times. I've said it before, and I'll say it again: convergence does not imply non-randomness.

sol invictus

30th June 2008, 04:19 PM

No, it is not at all like the smoke detector.

Really?

What I call "random" is that only one out of the twelve populations evolved the ability to metabolize citrate despite the fact that the populations were identical at the beginning of the experiment and the fact that they evolved in the same evirnoment.

Yes, evolution takes time.

Even if all the populations eventually evolved the ability to metabolize citrate, the evolution of that trait would still be random in so far as the populations evolved that trait at different times. I've said it before, and I'll say it again: convergence does not imply non-randomness.

So you think the fact that these bacteria evolved the ability to metabolize citrate when put in a citrate rich environment is random.

That is just as ridiculous as your earlier contention that a smoke detector is random because it relies on the (truly random) radioactive decay of unstable atoms. You are using the word in a way no one else does - including mathematicians. You were unable to supply a single reference that defines the word your way, and you never responded when I checked several references - including a standard text on prob. and stats. - none of which define it your way.

The statement that "evolution is random", full stop, is (to be blunt) stupid.

mijopaalmc

30th June 2008, 04:33 PM

blutoski

30th June 2008, 05:45 PM

sol invictus-

I really don't understand what is preventing you from comprehending that fact that orderly large-scale behavior does not imply non-random small-scale behavior. 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. I have, however, maintained that the orderly operation of the smoke detector does in fact arise from the underlying randomness of radioactive decay.

My main objection to the assertions of articulett and others is that all the mechnisms of evolution (i.e., mutation, natural selection, developmental constraints, etc.) can be random, but evolution can still display the orderly behavior that they insist is random.

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

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.

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.

articulett

30th June 2008, 09:56 PM

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?

articulett

30th June 2008, 10:02 PM

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.

sol invictus

30th June 2008, 10:03 PM

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.

zosima

1st July 2008, 12:57 AM

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?

zosima

1st July 2008, 01:50 AM

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

sol invictus

1st July 2008, 06:15 AM

4. To make my claim I only need to show the existence of one system that has no periodic orbits.

All quantum systems have periodic orbits (start in an energy eigenstate). So does rule 30 - start with all zeros, or in many other configurations.

http://www.iwriteiam.nl/Rule30.html

jimbob

1st July 2008, 11:48 AM

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 (http://www.nytimes.com/2007/06/26/science/26lab.html?_r=1&scp=1&sq=evolution+bacteria&st=nyt&oref=slogin)
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 (http://forums.randi.org/showthread.php?t=111832)"

Looky looky, web surfer skeptic girl found the whole paper free online: :D

Rapid large-scale evolutionary divergence in morphology and performance associated with exploitation of a different dietary resource (http://www.bio.umass.edu/biology/irschick/Irs_papers/Herrel%20et%20al%202008%20PNAS.pdf)

Dang, I'm good.

And a possible (but admittedly unlikely) suggestion:

There is another possible explaination that could be investigated:

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"

cyborg

1st July 2008, 12:12 PM

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).

articulett

1st July 2008, 03:53 PM

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.

jimbob

1st July 2008, 04:08 PM

jimbob

1st July 2008, 04:13 PM

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.

cyborg

1st July 2008, 04:32 PM

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.

mijopaalmc

1st July 2008, 04:39 PM

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.

articulett

1st July 2008, 04:41 PM

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.

mijopaalmc

1st July 2008, 04:57 PM

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" (http://books.google.com/books?id=SjpSkzjIzfsC&pg=PA14&dq=tape-of-life&sig=ACfU3U3dNb1xLRmcTGWmw-5dUZ-ltsH9VA).

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".

articulett

1st July 2008, 05:13 PM

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.

articulett

1st July 2008, 05:21 PM

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" (http://books.google.com/books?id=SjpSkzjIzfsC&pg=PA14&dq=tape-of-life&sig=ACfU3U3dNb1xLRmcTGWmw-5dUZ-ltsH9VA).

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.

cyborg

1st July 2008, 05:41 PM

I think it's perfectly clear that I consider a "tape" to be a bad analogy for obvious reasons - no matter who said it.

Herzblut

1st July 2008, 06:05 PM

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.

mijopaalmc

1st July 2008, 06:15 PM

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.

articulett

1st July 2008, 08:28 PM

It sounds like Herzblut and Mijo are in agreement... that's a troll quorum, isn't it.

On planet smart people "random processes" are terms sometimes used to describe stochastic processes... the smart people don't consider the processes themselves random... they are noting that they have random components. Similarly, algebraic problems can be called variable problems because they contain variables. The smart people realize that it would be silly to presume that it means the problems are variable.

tsk.

You guys are made for each other... do run off and play now so the grown ups can talk.

mijopaalmc

1st July 2008, 09:41 PM

zosima

1st July 2008, 09:44 PM

All quantum systems have periodic orbits (start in an energy eigenstate). So does rule 30 - start with all zeros, or in many other configurations.

http://www.iwriteiam.nl/Rule30.html

I'm not sure repeated digits count as a periodic orbit. I guess it depends on what definition of periodic orbit you use.

On the other hand, if you interpret the central column of rule 30 as a binary number, the number will never repeat. That said, I have no doubt that a sub-sequence of its digits will repeat.

Random numbers will have repeated digit sequences as well. In fact, I'm pretty sure* an infinite sequence of random digits should contain all possible finite subs-sequences of digits.

*I haven't proven this, if you have a reason to disagree I'd be genuinely interested in understanding why.

I agree with your claims about QM.

ETA: Is there a finite non-zero starting point on a plane of unlimited width that will cause rule 30 to repeat indefinitely? I think the examples you link only work if they are repeated to fill the entire plane.

mijopaalmc

1st July 2008, 09:59 PM

zosima-

Aren't you talking about rule 30 with a specific initial condition (i.e., one black square and all others white)?

zosima

1st July 2008, 10:19 PM

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.

I think we need to be clear on what you mean by "reran the tape". If you are saying that when we rerun the tape, we start life on earth 4 billion years ago, with asteroid impacts at the same time as they occurred, volcanic eruptions happening as they happened, continents moving the same way, etc...Then things would turn out the same.

What you are trying to claim is that if we start life somewhere else, where the timing, number, and sequence of events is different, then we would get a different result.

Of course, if things are different, then things will be different. This is true of deterministic systems as well. Different initial conditions lead to different outcomes.

You seem to be railing against the idea of convergence. Convergence in evolution is something that is documented to occur, and something that supports some of the evolutionary determinism arguments that people have been putting forth. But convergence is, at best, ancillary to the central claim that has been made. Moreover, convergence does not occur without qualification.

For example, if you put E. Coli. in citrate for long enough, proponents of convergence would argue that it will eventually evolve a means to metabolize citrate. They would also predict that C. Tetani would develop the ability to metabolize citrate if it were placed in a citrate rich environment. But that does not mean proponents of convergence claim that this will happen in the same way in both species, or that it will take the same amount of time.

The fact the convergence occurs, however, is reason to be skeptical that changes in tiny details like random differences in quantum states will have any effect when we "re-roll the tape".

zosima

1st July 2008, 10:25 PM

zosima-

Aren't you talking about rule 30 with a specific initial condition (i.e., one black square and all others white)?

Generally, that is the case that people like to talk about.

But I'm also pretty sure that if you start rule 30 with any non-zero, finite set of black squares in an unbounded space, it will not repeat. That said, it'd be an interesting exercise to see if we can find an example where that is not the case. I'm trying to find one right now, but I encourage you to beat me to it.

mijopaalmc

1st July 2008, 10:33 PM

Generally, that is the case that people like to talk about.

But I'm also pretty sure that if you start rule 30 with any non-zero, finite set of black squares in an unbounded space, it will not repeat. That said, it'd be an interesting exercise to see if we can find an example where that is not the case. I'm trying to find one right now, but I encourage you to beat me to it.

The page sol invictus supplied provided infinitely repeating patterns (in the initial conditions) that yield periodic orbits.

articulett

1st July 2008, 10:36 PM

Can you provide a source that defines a stochastic process as you do?

Already been done... multiple times. It's not my problem that you are impenetrable to all that goes against what you want to be true.

mijopaalmc

1st July 2008, 10:40 PM

Already been done... multiple times. It's not my problem that you are impenetrable to all that goes against what you want to be true.

No, actually all you have done is repeat your mantra "having random components does not a random process make". This is not the same as present a definition from a mathmatics textbook, dictionary, or encyclopedia.

articulett

1st July 2008, 11:03 PM

Wowbagger

1st July 2008, 11:07 PM

So, now you folks are arguing over the definitions of definitions.

Wonderful. Just wonderful.

mijopaalmc

1st July 2008, 11:14 PM

So, now you folks are arguing over the definitions of definitions.

Wonderful. Just wonderful.

How would you suggest we have a meaningful discussion if we can;t agree on what the therms we are discussing mean?

mijopaalmc

1st July 2008, 11:20 PM

so cute... troll semantics...

They say anything to convince themselves their woo is true and then repeat it to keep their brain washing alive.

See Zosima--I predicted exactly this. Familiarize yourself with the technique. There are some that will demand that you jump through all sorts of hoops asking for evidence that they'll completely deny no matter how much careful effort you go through to provide it. Mijo has been doing this since his first post. His requests are insincere and his thanks for your effort is more of the same nothing... in fact you become a "bad guy" in the woo straw man view for your efforts.

At least you learn whom you can trust and whom to ignore.

The problem with your much totuted evidence was that it was just assertions that evolution was not random based on a definition of "random" that I was not using. Then, to cover your backside, you insisted that my definition of "random" made everything random, blatantly ignoring that it is the defintion of "random" that mathematicians (who you obviously do not consider to be "smart people") use when studying probability theory, stochastic processes, and statistics.

articulett

1st July 2008, 11:34 PM

Nope, not arguing. Just reiterating... Mijo et. have provided no peer reviewed sources defining random as they are and no peer reviewed sources or respected scientist that say "evolution IS random "nor "evolution is a random process." And yet he keeps contending that some scientists somewhere find his explanation useful in some way.

It appears his definition is only being used by him and not by anyone who actually desires to convey understanding to people. Mijo appears impervious to the fact that nobody considers him an expert on the topic nor his special loose definition useful in regards to evolution, smoke detectors, poker, or anything else.

zosima

1st July 2008, 11:42 PM

The page sol invictus supplied provided infinitely repeating patterns (in the initial conditions) that yield periodic orbits.

Yes it did. The question I asked was whether a finite initial condition yield a periodic orbit.

zosima

1st July 2008, 11:53 PM

The problem with your much totuted evidence was that it was just assertions that evolution was not random based on a definition of "random" that I was not using. Then, to cover your backside, you insisted that my definition of "random" made everything random, blatantly ignoring that it is the defintion of "random" that mathematicians (who you obviously do not consider to be "smart people") use when studying probability theory, stochastic processes, and statistics.

Technically the term you defined was 'random variable' not 'random'.

You inferred that 'random' would have the same sense when it was found in other terms. Generally, people rejected your inference for good reason. While it is okay to separate adjective from a phrase with a given sense and apply them with that sense to other phrases in common language, this is not acceptable with technical terms. Each technical term has a specific definition that may not follow from the senses of its constituent parts of speech.

Thus, since you used a technical definition of 'random variable', your inference is invalid. The observation that this inference makes all systems random, is an example of the odd sorts of conclusions you reach when you make false inferences.

jimbob

2nd July 2008, 11:23 AM

I think we need to be clear on what you mean by "reran the tape". If you are saying that when we rerun the tape, we start life on earth 4 billion years ago, with asteroid impacts at the same time as they occurred, volcanic eruptions happening as they happened, continents moving the same way, etc...Then things would turn out the same.

What you are trying to claim is that if we start life somewhere else, where the timing, number, and sequence of events is different, then we would get a different result.

Of course, if things are different, then things will be different. This is true of deterministic systems as well. Different initial conditions lead to different outcomes.

You seem to be railing against the idea of convergence. Convergence in evolution is something that is documented to occur, and something that supports some of the evolutionary determinism arguments that people have been putting forth. But convergence is, at best, ancillary to the central claim that has been made. Moreover, convergence does not occur without qualification.

For example, if you put E. Coli. in citrate for long enough, proponents of convergence would argue that it will eventually evolve a means to metabolize citrate. They would also predict that C. Tetani would develop the ability to metabolize citrate if it were placed in a citrate rich environment. But that does not mean proponents of convergence claim that this will happen in the same way in both species, or that it will take the same amount of time.

The fact the convergence occurs, however, is reason to be skeptical that changes in tiny details like random differences in quantum states will have any effect when we "re-roll the tape".

I am not railing against convergence, often it will happen. However, sometimes something differnet will happen. This could be rare, but significant enough to alter the fitness landscape.

"rerun the tape" was Gould's analogy. What I mean is that we start with the identical initial conditions. Random events that had not been determined at that time would not have been determined so could be different. Mutations would definately be included in this, I would also contend that this might include some asteroid impacts over the 3.8 billion years since life arose (due to the generally accepted chaotic nature of the orbits of many Near Earth Objects).

Also mutations that happened which changed the fitness landscape significantly for other organisms would have a large effect on which organisms are "selected" and which are not. Given that the vast majority of organisms fail to reproduce, most "advantageous" mutations will also die out, again I would argue that these will be affected by arbitary events, and I would argue that many (not all) of these arbitary events are also random.

A slight difference in wind direction, and the founder population of Darwin's Finches might not have made it to the Galaopgos. A slight difference in weather patterns arouond the time of the Toba eruption (70k yrs ago) and no humans might have survives. Ecosystems would look vastly different if that had happened. A slight difference in the rise of the black death, and civilisation might look significantly differnet, which again would affect many ecosystems, and the slelective pressures.

Slightly different timing of mutations, and different niches could have been filled after the KT impact, again leading to a different set of ecosystems, and different selective pressures. Certain features would evolve many times, certain ones wouldn't.

cyborg

2nd July 2008, 02:05 PM

You still seem to think that I don't understand your point: if you execute an algorithm with non-deterministic branching points then yes, if on run one you branch left where on another run you branch right then you will reach a different end point. THIS IS SO TOTALLY AMAZING THAT THERE IS NO WAY I COULD HAVE UNDERSTOOD THIS IF IT WERE NOT FOR THE MONTHS OF EXAMPLES YOU PROVIDED!!!

What you seem to fail to understand is that replacing the non-deterministic branching with deterministic branching one can infact reach the same end points. WOW! THIS IS SO TOTALLY UNEXPECTED!!! IF THE ASTEROID STILL CRASHES AND WIPES OUT THE DINOSAURS THEN DINOSAURS ARE STILL ********** REGARDLESS OF WHETHER OR NOT HUMANS COME ALONG!!!

Herzblut

2nd July 2008, 03:20 PM

It sounds like Herzblut and Mijo are in agreement... that's a troll quorum, isn't it.

I'm in agreement with mathematics.

On planet smart people "random processes" are terms sometimes used to describe stochastic processes... the smart people don't consider the processes themselves random...

Wishful thinking.

jimbob

2nd July 2008, 03:52 PM

Cyborg, so if random events affect the "shape" of ecosystems and evolutionary pressures, the outcome is nonrandom, despite being significantly affected by random factors, and these factors include the results of other organisms evolution.

OR MAYBE YOU WAND ME TO SHOUT AND USE SOME *** ASTERISKS BECASE tat makes it clear?

WOW! THIS IS SO TOTALLY UNEXPECTED!!! IF THE ASTEROID STILL CRASHES AND WIPES OUT THE DINOSAURS THEN DINOSAURS ARE STILL ********** REGARDLESS OF WHETHER OR NOT HUMANS COME ALONG!!!

You seem to be having a problem with causality. If an asteroid didn't wipe out the dinosaurs, humanity wouldn't have arisn. Even though one did, humanity was far from inevitable at that time. It isn't just a minor species, but the entire ecosystem that would be different.

cyborg

2nd July 2008, 04:03 PM

OR MAYBE YOU WAND ME TO SHOUT AND USE SOME *** ASTERISKS BECASE tat makes it clear?

LOLCATS.

I just want you to comprehend the incredibly simple things I'm saying but it doesn't seem to matter how many ways I say it you miss it every single time.

You seem to be having a problem with causality.

No, you seem to be having a problem with causality.

Even though one did, humanity was far from inevitable at that time.

Here is the point -->.

You are at the other end of the universe.

OR MAYBE YOU WAND ME TO SHOUT AND USE SOME *** ASTERISKS BECASE tat makes it clear?

So what that **** I supposed to use to get you to understand what I am saying? Do I have to perform brain surgery before you actually appreciate the concept I am actually trying to communicate rather than you continually making up the one you seem to insist I am communicating? I am seriously thinking that direct manipulation of the neurons is the only way.

Herzblut

2nd July 2008, 04:48 PM

Walter Wayne

2nd July 2008, 07:47 PM

Technically the term you defined was 'random variable' not 'random'.

You inferred that 'random' would have the same sense when it was found in other terms. Generally, people rejected your inference for good reason. While it is okay to separate adjective from a phrase with a given sense and apply them with that sense to other phrases in common language, this is not acceptable with technical terms. Each technical term has a specific definition that may not follow from the senses of its constituent parts of speech.

Thus, since you used a technical definition of 'random variable', your inference is invalid. The observation that this inference makes all systems random, is an example of the odd sorts of conclusions you reach when you make false inferences.
You have indulged in the same tactic. Before I went away, I mentioned a list of areas where random included non-uniform. However, you stuck the definition from computer science ... in spite of the fact it is a specific area of comp sci. that used your definition. The fact is the algorithms I mentioned for generating non-uniform variables come from computer science.

The reality is comp. sci., math, and the physical sciences all support a definition different from the one you insist on. Layman, when they refer to random things often use for those things which aren't of uniform probability.

It is hardly appropriate to accuse others of using a specific term of art to define the term in general, when you choose to define in a manner which is the exception rather than the rule.

Walt

lenny

5th July 2008, 06:55 AM

The UNDERSTANDING of the content of the tape requires reasoning about the CLASS, not the INSTANCE. it.

jargon normalization request:

your "instance" is a particualr realization of a process

your "class" is the dynamical process itself (and thus all possible realizations)

the difference is betwen observing one particular random walk, and the ensemble of all possible random walks under the particualr generating process. right?

lenny

5th July 2008, 07:09 AM

At the limit, dissipative systems will fall into a steady state, thus ceasing to be chaotic.
this is simply false, given the standard definition of dissipative in the dynamical systems theory! (i assume you mean something else by the word).

dissipative dynamcal systems are those where volumes of state space shrink in time: they need not shrink to a point. in conservative systems, state space volume is conserved under the flow, KAM applies only in conservative (aka hamiltonian) systems.

Also, In the Lorenz Equations, you'll find that they dissipate quite quickly if you include a term to allow dissipation.
the lorenz equations, as writen by lorenz in 1963, ARE dissipative!

(and if you add a term to them, they are no longer the Lorenz Equations!)

jimbob

5th July 2008, 10:27 AM

Cyborg,

At the time of the KT impact, was the evolution of something akin to humanity inevitable?

ETA: If not, why it is incorrect to refer to the outcome, or course of evolution as random?

cyborg

5th July 2008, 11:02 AM

Cyborg,

At the time of the KT impact, was the evolution of something akin to humanity inevitable?

Yes or no.

jimbob

5th July 2008, 11:26 AM

And you accuse me of playing semantic games

cyborg

5th July 2008, 12:10 PM

If you can't see why I answered as I did you clearly haven't been reading a damn word I've said.

lenny

5th July 2008, 12:23 PM

And you accuse me of playing semantic games
s/he may not be playing with ya, but perhaps responding to your "akin" and his/her limited omniscience.

4:1 if you ask whether or not at the time of the KT impact this thread on something "akin" to the JREF forum was inevitable you'd get a straightup reply of "no".

10:1 if you ask whether or not at the time of the KT impact someone burning coal for energy about now was inevitable you'd get a reply of "yes, probably". (or something more creative).

(assuming my interpretation of cyborg jargon was accurate; still hoping for an answer there... .)

jimbob

5th July 2008, 12:45 PM

OK, lenny, I'd argue that the emergence of a social, advanced-tool using species was not inevitable at that time. By advanced, I mean consisting of three or more components, for example a stone lashed to a stick.

Wowbagger

6th July 2008, 10:56 AM

Perhaps it was not inevitable, at that particular time and place. But, still inevitable to occur somewhere in the Universe. And, likely in multiple places and times.

(By the way, there are now 1111 replies, in this thread!)

jimbob

8th July 2008, 03:46 PM

But if it was not inevitible for any particular planetary ecosystem, then surely it is entrely appropriate to describe it as "random but not haphazard" for example?

and further to Walter Wayne's comment that this is a common definiton of random, I am using it in the same way that biologists use it in technical discussions, and as statistician do too:

Skeptgirl,
Mijo is not arguing for "random" as "unbiased" or "haphazard". This is a difference between him and Behe that Articulett refuses to accept. (That and mijos repeted assertions that humanity evolved from ape-like ancestors with no guiding supernatural deity, indeed almost a "drunkards walk" and influenced by many chance events. (What would our genome look like if humanity had not got almost wiped out 70k-yrs ago by Tambora's eruption?
Let me second this. Jimbob is correct. Mijo's insisting that by the proper definitions of 'random' and 'deterministic', evolution is random. It is. I'm not interesting in debating the matter. I'm a professional statistician; I know what the word 'random' means! But 'random' is also quite commonly taken to mean things that are properly termed "haphazard" "unbiased" or "uniformly distributed". By that usage, you are correct and evolution is anything but.

Not the agreement that evolution is neither unbiased, nor haphazard, which is what Behe claims.

lenny

18th July 2008, 11:15 AM

On planet smart people "random processes" are terms sometimes used to describe stochastic processes... the smart people don't consider the processes themselves random... they are noting that they have random components.
i would really like to understand all the confusion/argument here.

articulett, statisticians would generally not be "smart people" by your definition. random processes (aka stochastic processes) are indeed considered random, you seem to think this is a very restrictive condition, for the most part they do not.

not all random processes are IID (independent, identically distributed) or Gaussian distributed, "most" are subject to "deterministic" influences; they are random processes merely because there is a random term (in discrete or continuous time) onthe right hand side of the equations that define them.

do we all agree that a classical random walk is a random process?

and that so is a random walk on a tilted surface (that is a random process that contains a deterministic drift?)

if you agree the second is random, i do not see why you reject the idea that evolution is random, (given the typical alternatives: random and deterministic, would you want to say evoluiton is deterministic?)

articulett, you just seem to allergic to the use of the word "random" in connection with evoluiton, would you consider it OK to call a radiation induced mutation random?

cyborg could you tell me which post you explained things in, there are over a thousand on this thread!

thanks.

mijopaalmc

19th July 2008, 12:21 AM

So do any of the people who argue that evolution is non-random have answers to lenny's questions?

articulett

19th July 2008, 12:54 AM

mijopaalmc

19th July 2008, 10:48 AM

jimbob

19th July 2008, 02:36 PM

Yes, lenny, for all practical purposes radiation induced mutations are random... but selection is not-- it is the derandomizer... it is the essence of evolution.. it is what gives it the appearance of design. Selection pulls from the pool of random mutations.

But the odds of selection don't work like that. Most organisms fail to reproducs. Mostvery similar siblings fail to reproduce. Those that do are "lucky" too.

If an "typically fit" organism only has a 10% chance of reproducing, but then typically has 10 offspring per parent, the population would remain stable. Any deleterious mutations would be very quickly removed. Most advantageous mutations would also.

In the example of the e.coli, there was a mutation that was in itself "neutral" that occured between after about 15,000 generations in one population. By chance, this survived (being at the time akin to genetic drift, and having neither positive nor negatve impactson reproduction). This did however allow later generations to evolve citrate-matabiolism after a further 10,000 generations.

The mutation was random. The selection was biased, but random, like a set of loaded dice. The eventual outcome was random, because as well as this, in most environments, the interactions with other organisms would provide complex, nonlinear feedbacks that affect the fitnes landscape for the other organisms.

It was not haphazard. But it was random.

ETA:

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.

*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"

jimbob

19th July 2008, 02:41 PM

In brief: identical situations, or ones where the initial differences are unimportant would give different results; this is what the Long Term Evolution experimnet has shown.

cyborg

19th July 2008, 03:06 PM

In brief: identical situations, or ones where the initial differences are unimportant would give different results; this is what the Long Term Evolution experimnet has shown.

Nope.

mijopaalmc

19th July 2008, 03:28 PM

Nope.

Can you explain why only one of the genetically identical colonies evolved the ability to metabolize citrate under oxic conditions when they were all in the same environment?

mijopaalmc

20th July 2008, 12:24 PM

It is interesting that no-one who think evolution is non-random has answered lenny's questions.

lenny

6th August 2008, 07:50 PM

It is interesting that no-one who think evolution is non-random has answered lenny's questions.

so talking to folks here in oxford (UK), it seems this reflects a tactical choice which, to me at least, seems strategically counterproductive. the central role of randomness is denied rather than explained, even though this role is fully accepted, rather wellunderstood, and poses no fundamental challenge to "natural selection".

i am told dawkin's discusses this often in lectures noting that it can be counterprodutive, but i have only heresay evidence this is the case. surely he himself must have written about it somewhere? no?

perhaps this tactical approach is useful in some places (?the US?) where naysayer confusionist arguements might make shortterm gain (as in "see: they say it is just random"), but in the long run surely this tactic will prove counterproductive. no?

Reality Check

6th August 2008, 08:42 PM

i would really like to understand all the confusion/argument here.

articulett, statisticians would generally not be "smart people" by your definition. random processes (aka stochastic processes) are indeed considered random, you seem to think this is a very restrictive condition, for the most part they do not.

not all random processes are IID (independent, identically distributed) or Gaussian distributed, "most" are subject to "deterministic" influences; they are random processes merely because there is a random term (in discrete or continuous time) onthe right hand side of the equations that define them.

do we all agree that a classical random walk is a random process?

and that so is a random walk on a tilted surface (that is a random process that contains a deterministic drift?)

if you agree the second is random, i do not see why you reject the idea that evolution is random, (given the typical alternatives: random and deterministic, would you want to say evoluiton is deterministic?)

articulett, you just seem to allergic to the use of the word "random" in connection with evoluiton, would you consider it OK to call a radiation induced mutation random?

cyborg could you tell me which post you explained things in, there are over a thousand on this thread!

thanks.
Hi lenny:
The confusion comes because certain posters are trying to apply their interpretation of the word random (which seems to be "non-deterministic") to the entire theory of evolution.

The "random walk on a tilted surface (that is a random process that contains a deterministic drift?)" bit of your posting is actually applicable to a simple description of evolution as a random walk on a fitness landscape.
The random walk part comes from the dozen or so different kinds of mutations (http://en.wikipedia.org/wiki/Mutation) that can happen in genes.
The "fitness landscape" is natural selection.

People tend to object the description of evolution as "random" since that implies that evolution is not predictable or repeatable. But evolution is predictable (e.g. given an environmental niche we can predict that there will be something to fill it; given a gap in the fossil record we can predict that there was something to fill it) and repeatable - see the E. coli long-term evolution experiment (http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment).

I would say that evolution is not random but it is also not deterministic. It is something in-between. You could call evolution "mostly deterministic" given the overwhelming effect of natural selection.

sol invictus

6th August 2008, 08:42 PM

So this stultifyingly idiotic zombie discussion shambles on...

do we all agree that a classical random walk is a random process?

It's a type of random process, yes.

and that so is a random walk on a tilted surface (that is a random process that contains a deterministic drift?)

That's called a "directed random walk". It is not called "random". See the difference?

mijopaalmc

6th August 2008, 08:59 PM

That's called a "directed random walk". It is not called "random". See the difference?

No, and I surprised that you don't see the equivocation (or the internal logical contradiction if you are not equivocating) in your statement.

sol invictus

6th August 2008, 09:07 PM

No, and I surprised that you don't see the equivocation (or the internal logical contradiction if you are not equivocating) in your statement.

Back to this again... how wonderful.

So, mijo, tell me - are smoke detectors random? Yes or no?

Until you say one or the other with no caveats I'm not going to respond to anything else you post. :)

mijopaalmc

6th August 2008, 09:14 PM

Back to this again... how wonderful.

So, mijo, tell me - are smoke detectors random? Yes or no?

Until you say one or the other with no caveats I'm not going to respond to anything else you post. :)

As you have shown quite amply, one cannot answer that question without caveats when the person equivocates on the meaning of "random" one is using. The smoke detector is based on the random process of radioactive decay; however, since there are so many decay events the "no smoke" signal behaves in a predictable fashion, as dictated by the law of large numbers, a property intrinsic to the vast majority of random processes.

lenny

6th August 2008, 09:17 PM

sol invictus

7th August 2008, 06:42 AM

this may be an issue in public presentation of natural selection, but it is not an issue in statistics or in physics (or amongst researchers in natural selection speaking in private).

I'm not sure what issue you're speaking about, but if you think most statisticians and physicists would agree with the statement "evolution is random", I'm pretty sure you're wrong.

nevertheless mathematically (and philosophically) a process is either determinsitic or not determinisitic (sets of measure zero excluded), and eventually i expect biologists will have to declare.

Really? Says who? To make that claim you will need to define "determinism". Please make your definition specific enough to answer the question of whether QM in the many worlds interpretation is deterministic. You should also give examples of at least one deterministic and one non-deterministic real-world process in order to demonstrate that your definition is useful in categorizing them.

Having done that, you will need to specify the definition of "random", which was the topic of this thread. Presumably that definition will explain why you have brought up the term determinism.

sol invictus

7th August 2008, 07:23 AM

but i have no desire to add fuel to the confusionist argument.

On the issue of strategy - that's largely a question of how best to communicate the concepts underlying evolution. I think the answer is to explain that there are random elements, like a large meteor hitting earth, and that there are non-random elements, like the effects on species of the climate resulting from that meteor strike.

In the case of those bacteria, which petri dish first evolved the ability to metabolize citrate was totally unpredictable, but the fact that that particular ability might evolve (out of an infinity of possibilities) was predictable.

I don't think anyone above chimpanzee level will have trouble understanding that a process can have both random and non-random elements. But when you say "evolution is random", you are communicating to most people the claim that there are no non-random elements, which is simply false.

mijopaalmc

7th August 2008, 11:43 PM

I know it's probably futile for me to think that those who argue that evolution is non-random will think that anything I say clarifies my argument but I thought the following post clearly explains my thoughts about the "meaninglessness" of the definition of "random" that I use:

Essentially, everything is random according to your definition of what "random" is.

In principle, yes.

And by the way, this is not "my" definition. This is the standard definition.

You've basically made the term "random" meaningless.

Not at all. Just because everything is in principle "random" does not in any way mean that the term is without meaning. Many, many processes can be predicted using deterministic models with far, far more accuracy than we can possibly measure. It makes sense in these cases to speak of these processes as "deterministic", since it is beyond our ability to tell otherwise.

So, in practice, there is a kind of subjective "degree of randomness" that a process must have in order for it to be utilitarian to refer to it as "random", even if all processes are random according to the technical definition of the word. In other words, we can make a conceptual distinction between the two concepts which is very useful in practice, in much the same way that we can make a distinction between "circles" and "squares", even though no absolutely perfect circles or squares may exist in real life.

As for your drive to work, I think it does make sense to refer to it as random. Take car accidents, for example. There are good statistics available on the incidence of such accidents per car per trip. We can measure the probabilities involved, and they are not negligibly small. Assuming you have the same probability as anyone else of getting into an accident, then your successful arrival at work is indeed the result of random chance.

I can think of 2 or 3 times in the last year when I started driving to work and for whatever reason ended up not getting there that day. So - if we stipulate that the factors that kept me from getting there are random - then my probability of not getting to work each day is on the order of 1 in 100. To me, this is non-negligible.

And as for evolution, It seems clear to me that it is significantly more random than whether or not you get to work safely. Walter Wayne made a good point in the other thread:

A question for the "non-randomites". Do you think that the rise of humanity was inevitable, given the conditions when life first crawled onto land?

Again, to re-re-re-iterate: Saying that "evolution is random" is in no way a criticism of evolutionary theory.

articulett

8th August 2008, 04:18 AM

Ha-- Mijo is shopping his "evolution is random" around other skeptic forums including IIDB and Richard Dawkins net... and getting his butt handed to him on a platter as he did here.

Mijo needs to "believe" that it somehow makes sense to call evolution "random"-- but no one is buying it.

Mutations are generally considered random in that they happen whether they benefit an organism or not-- SELECTION chooses from that randomess--it is the derandomizer and the best of the randomness is multiplied exponentially.

To quote Dawkins reveiw of Behe's book again:

The crucial passage in “The Edge of Evolution” is this: “By far the most critical aspect of Darwin’s multifaceted theory is the role of random mutation. Almost all of what is novel and important in Darwinian thought is concentrated in this third concept.”

What a bizarre thing to say! Leave aside the history: unacquainted with genetics, Darwin set no store by randomness. New variants might arise at random, or they might be acquired characteristics induced by food, for all Darwin knew. Far more important for Darwin was the nonrandom process whereby some survived but others perished. Natural selection is arguably the most momentous idea ever to occur to a human mind, because it — alone as far as we know — explains the elegant illusion of design that pervades the living kingdoms and explains, in passing, us. Whatever else it is, natural selection is not a “modest” idea, nor is descent with modification. http://www.nytimes.com/2007/07/01/books/review/Dawkins-t.html

Ha ha ha ha ha

No biologist is defiining random like Mijo is.... if you are going to use random in evolution, you better define as the peer reviewed scientists in the articles do if you want to convey understanding. In fact, in biology there are degrees of randomness. Of course this has been explained to Mijo in thread after thread for years and now on different forums because he's tired out the people here.

Mijo's goal is to prove to himself and others that evolution is random just like the creationist canard says -- which is exactly what as Behe is doing.

Kleinman, another creationist who needs to prove that "evolution is mathematically is impossible" is also shopping his same story across skeptic forums.

Myself, I'll stick with those who teach many and ARE successful at conveying understanding of evolution--not the self-appointed experts.

MG1962

8th August 2008, 04:35 AM

Just a quick question from the sideline, is there a scientific or mathematical name for the type of biased randomness we find in nature?

articulett

8th August 2008, 04:52 AM

"natural selection"... Dawkins et. al. consider this the opposite of random-- the derandomizer. It DETERMINES what evolves and how. It is responsible for the appearance of design.

When a dice is biased, we call it a loaded dice.

Mijo's definition would call such a dice "random".

Not very explanatory.

MG1962

8th August 2008, 05:39 AM

The more I think about this, the more complex the question becomes. The history of life on the planet does seem to point to a bias towards greater complexity. In my mind the more complex an organism, the lesser the chance an individual mutation can make the particular animal unviable. Yet with a less complex creature, a single mutation could do the reverse.

So then is complexity a genetic insurance policy against genetic coding errors? If the answer becomes yes, then is correct to say that life is activily attempting to lessen acummulated randomness?

Or am I just over tired lol

articulett

8th August 2008, 06:03 AM

Actually that's pretty good... life become more "efficient" like technology does in a way. However most of life on this planet is very very simple life... so that's a great strategy too-- but not the only way to get DNA passed on. Sexual recombination happens to be a super way to pass on huge amounts of DNA data into increasingly "complex" and efficient "DNA processors"... It ups the variety from which natural selection can act on... and just like the information in evolving technology is cumulative and more efficient (it doesn't go backwards) neither do genomes--the only way is "forward".

sol invictus

8th August 2008, 08:14 AM

So then is complexity a genetic insurance policy against genetic coding errors? If the answer becomes yes, then is correct to say that life is activily attempting to lessen acummulated randomness?

It's more complex and interesting than that. To a large extent organisms are able to control how many mutations they undergo (search p53 and cancer, for example). If there are too few mutations the species is at a disadvantage. For example a virus which cannot mutate rapidly to overcome immune defenses would quickly go extinct. On the other hand if there are too many mutations, not enough offspring survive and the species goes extinct. So there is an optimal rate.

articulett

8th August 2008, 04:04 PM

Yes, parts of our genome and others are highly conserved (very resistant to change) and other parts are hot-spots for crossovers and mutations because because it's proven a good gamble evolutionarily.

A clever virus strategy is to evolve just enough to encourage your host to pass you on--but not so much as to kill your host. Colds are "clever" virus because they cause a reaction (coughing, sneezing, runny noses, etc. that make them very easy to pass on... and they don't harm their vector so that it can keep on passing colds in the future). But because the immune system recognizes old viruses and protects against them, they need to keep altering themselves a wee bit to sneak by and cause their vector to sneeze, cough, etc. again.

lenny

8th August 2008, 07:16 PM

Just a quick question from the sideline, is there a scientific or mathematical name for the type of biased randomness we find in nature?
mathematically, one usually just speaks of random processes (or equivalently stochastic processes), "pure randomness" being a special case.

almost all modelling involves what you called "biased randomness", since the "pure randomness" (for example, where a variable takes on random values which are independent and identically distributed (IID) draws from some given distribution.) is a very special case.

a standard text is:
The Theory of Stochastic Processes by D.R. Cox & H.D. Miller

and you can read the first page at:

http://www.amazon.com/gp/reader/0412151707/ref=sib_fs_bod?ie=UTF8&p=S00D&checkSum=5FGm4DnCQXSRdH9yhvrAbt5YyOBQpNr3PA4nm8dBw 0A%3D#reader-link

here the random walk variable is X, and since it has a memory it is arguably already a case of "biased randomness", but the steps in the random walk (the Z's on this page) are IID (that is "pure random"). as you might guess, most of the 407 other pages in this book focus on more interesting varieties of "biased randomness" - referred collectively as "stochastic processes".

so the biased/pure distinction fails to attract the same attention inside mathematical biology that it does in public discussions of evolution.

note that this is undergraduate mathematics, not rocket science:
From http://www.stats.ox.ac.uk/prospective_students/bammath_maths__and__statistics/course_details
In the third year, all Mathematics and Statistics students take the
compulsory Applied Statistics course, and at least one of Statistical
Inference and Stochastic Modelling

to argue that the fact evolution is best modelled as a stochastic process (aka random process) implies "evolution is random" in the pure random sense is just silly.

i can see that it might be an effective tactic if someone aims only to confuse the issue. i am not sure what the best tactical response is.

(hope that helped at the sidelines)

Herzblut

8th August 2008, 09:34 PM

here the random walk variable is X, and since it has a memory it is arguably already a case of "biased randomness", but the steps in the random walk (the Z's on this page) are IID (that is "pure random"). as you might guess, most of the 407 other pages in this book focus on more interesting varieties of "biased randomness" - referred collectively as "stochastic processes".

This simple random walk has interesting features already.

For instance, the random walker will find himself almost always on the right-hand-side (X>0) or almost always on the left-hand-side (X<0).

The case where he finds himself more or less equally often left or right, is the least likely of all cases.

jimbob

9th August 2008, 02:42 PM

thanks Reality Check

The confusion comes because certain posters are trying to apply their interpretation of the word random (which seems to be "non-deterministic") to the entire theory of evolution.

yes, i see this. i introduced the "random walk on a tilted surface" as a step toward stocahstic motion on a fitness landscape, naively assuming both sides would agree.

but i see why, for tactical reasons, one side goes quiet.

this may be an issue in public presentation of natural selection, but it is not an issue in statistics or in physics (or amongst researchers in natural selection speaking in private). from a pedagogical point of view it seems a high risk strategy not to simply explain that stochastic dynamics does not mean "utterly random".

but i have no desire to add fuel to the confusionist argument.

I would say that evolution is not random but it is also not deterministic.

i understand. and i may understand why you would say that. nevertheless mathematically (and philosophically) a process is either determinsitic or not determinisitic (sets of measure zero excluded), and eventually i expect biologists will have to declare. i personally believe declaring early is better, but you guys are the ones fighting the fight. i hope understanding prevails in the end!

thanks for your reply.

I'd prefer "random" but not haphazard". For many situations, I would have thought that the analogy of a bent game of dice where the randomness affects the score, but not who wins.

Furthermore, Lenny, in my experience in the UK, I mostly (although not always) come across religious people who "accept evolution" but think that it is somehow predetermined and that God could have set the ball rolling, with the inevitable consequence of something akin to humanity arising.

This is not what we see evidence for at all. Obviously it was not impossible, but there were a myriad of (almost unimagnible) other possible ecosystems, it was merely chance that led to the current ecosystem...

On the issue of strategy - that's largely a question of how best to communicate the concepts underlying evolution. I think the answer is to explain that there are random elements, like a large meteor hitting earth, and that there are non-random elements, like the effects on species of the climate resulting from that meteor strike.

In the case of those bacteria, which petri dish first evolved the ability to metabolize citrate was totally unpredictable, but the fact that that particular ability might evolve (out of an infinity of possibilities) was predictable.

I don't think anyone above chimpanzee level will have trouble understanding that a process can have both random and non-random elements. But when you say "evolution is random", you are communicating to most people the claim that there are no non-random elements, which is simply false.

I differ with this analysis of the long term evolution experiment, and the evolution of citrate metabolism.

Especially:

but the fact that that particular ability might evolve (out of an infinity of possibilities) was predictable.

Adaptations to environments will occur; what form these adaptations will take is affected by historical contingency and the history of the previously "neutatral" mutations.

With a more complex original ecosystem replicated in different expeiments, the effect of a chance mutation affecting the evolutionary path of the other types of organisms would be amplified.

If a citrate-metabolising bacterium was introduced to these populations around generation 30,000 in some flasks it might be able to establish itself, having no competition, whilst in others it might not, depending on the effeciancy of citrate metabolism of the established e.coli populations.

As soon as you introduce different competing types of organisms into the mix, the whols fitnes landscape is subject to random alteration when "disruptive" mutations occur. This change is also random, as well as the actual mutations themselves.

mijopaalmc

29th September 2008, 02:23 PM

Reality Check

29th September 2008, 03:35 PM

It looks like you win: Evolution is random.
So what?

mijopaalmc

29th September 2008, 03:42 PM

It looks like you win: Evolution is random.
So what?

If you are agreeing (rather than conceding to stop the argument), why is there such antipathy to a simple statement of fact?

It is as if I had "evolution is an observable fact" to a creationist.

Reality Check

29th September 2008, 04:11 PM

If you are agreeing (rather than conceding to stop the argument), why is there such antipathy to a simple statement of fact?

It is as if I had "evolution is an observable fact" to a creationist.
The problem is that you did not define what you mean by random. So everyone thought that you mean random as in unpredictable. Now everyone knows that you (probably) mean random as in a stochastic process (i.e. a process with predictable outcomes).
So evolution is a random, predictable process.

mijopaalmc

29th September 2008, 04:17 PM

The problem is that you did not define what you mean by random. So everyone thought that you mean random as in unpredictable. Now everyone knows that you (probably) mean random as in a stochastic process (i.e. a process with predictable outcomes).
So evolution is a random, predictable process.

Actually I did define "random" from the outset of the discussion and have repeated that definition several time of its course, but people rejected it saying that it "makes everything 'random'" and fell back upon the non-technical definition.

Reality Check

29th September 2008, 04:32 PM

Actually I did define "random" from the outset of the discussion and have repeated that definition several time of its course, but people rejected it saying that it "makes everything 'random'" and fell back upon the non-technical definition.
From memory, that was a result of you using non-deterministic as part of the definition of random. So that makes a lot random (not everything) including the example of a smoke detector (IMHO not a good example).

mijopaalmc

29th September 2008, 04:52 PM

From memory, that was a result of you using non-deterministic as part of the definition of random. So that makes a lot random (not everything) including the example of a smoke detector (IMHO not a good example).

But scientists do often use "random" to mean "non-deterministic". In fact, the deterministic/non-deterministic distinction often makes much more sense for the usage of "random" than the uniformly distributed/non-uniformly distributed distinction. This is because any non-uniform probability distribution can be transformed in the appropriate uniform probability distribution, whic means the same thing is both random and non-random, if "random" means "non-uniformly distributed".

Reality Check

29th September 2008, 05:15 PM

But scientists do often use "random" to mean "non-deterministic". In fact, the deterministic/non-deterministic distinction often makes much more sense for the usage of "random" than the uniformly distributed/non-uniformly distributed distinction. This is because any non-uniform probability distribution can be transformed in the appropriate uniform probability distribution, whic means the same thing is both random and non-random, if "random" means "non-uniformly distributed".
That is correct. Using non-deterministic for the random parts of the process of evolution is also correct. Using non-deterministic (or random) for the entire process of evolution is confusing since there are deterministic parts within the process (natural selection).

mijopaalmc

29th September 2008, 05:22 PM

That is correct. Using non-deterministic for the random parts of the process of evolution is also correct. Using non-deterministic (or random) for the entire process of evolution is confusing since there are deterministic parts within the process (natural selection).

You last statement is incorrect. If any part of the process is random, the process is random as a whole. By the way, the vasat majority of the discussion seems to be predicated on the idea that mutation is random and natural selection is not while presenting very little evidence that natural selection is not in fact random and seemingly ignoring the fact that the empirical evidence (i.e., Lenski's Long-Term Evolution Experiment) contradict that assumption.

Reality Check

29th September 2008, 05:48 PM

You last statement is incorrect. If any part of the process is random, the process is random as a whole. By the way, the vasat majority of the discussion seems to be predicated on the idea that mutation is random and natural selection is not while presenting very little evidence that natural selection is not in fact random and seemingly ignoring the fact that the empirical evidence (i.e., Lenski's Long-Term Evolution Experiment) contradict that assumption.
Your second statement is incorrect. If a random process is followed by a deterministic process then the process as a whole is not random. For example throwing a die is random but then selecting a specific number from the throws makes it deterministic (whatever you throw you always get that number).
Evolution is the highly random process of mutation followed by the less random process of natural selection. The overall process is somewhere between random and deterministic. The usual term used for such processes is stochastic.
The empirical evidence is that evoloution is stochastic (random by your definition), predictable and repeatable (as in Lenski's Long-Term Evolution Experiment).

sol invictus

29th September 2008, 08:20 PM

Actually I did define "random" from the outset of the discussion and have repeated that definition several time of its course, but people rejected it saying that it "makes everything 'random'" and fell back upon the non-technical definition.

And those people were absolutely correct. According to your silly definition, either everything in the world is random, or everything in the world is not (depending on something we don't know now and will probably never know, namely the fundamental nature of quantum mechanics).

That makes it totally useless, and it renders this whole idiotic rotting zombie discussion even more pointless, absurd, and stultifyingly ridiculous than it otherwise would have been.

Everyone that participated in this thread had had their IQ permanently reduced by at least 5 points. Congratulations.

All I can say is, "Wake up, you cardboard!"

jimbob

30th September 2008, 11:28 AM

What about defining something as random if random factors cause a significant (to be defined) alteration to the state of the system?

In this case I would argue that evolution wouold still be random, because if the tape was rewound, and evolution replayed, there is no reason to suppose that similar organisms would re-evolve. At the time of the KT impact, there was no inevitiability in the eventual evolution of humanit, nor of any similar organism occupying similar niches. Gibven the effect that organisms have on the ecosystems, there was not even any inevitibility in the general "shape" of the ecosystem 65-million years later. Although several niches whould have been highly probable.

sol invictus

30th September 2008, 12:31 PM

What about defining something as random if random factors cause a significant (to be defined) alteration to the state of the system?

Defining terms in terms of themselves isn't usually helpful.

jimbob

5th October 2008, 01:09 PM

It depends on your point of view. An analogy:

In the second world war balistic missiles were aimed at London.

It was predictible that the missiles would land in London, it wasn't predictible which particular houses would get hit. From the point of view of someone interested in the number of hits on London it was predictible. Form the viewpoint of a householder, it was random whether the missiles would hit their particular house.

Brownian motion might have an infinietessimal effect on the tragectory, but this would not ususally be considered significant.

there wouldn't be a hard and fast rule, but if random factors caused 20% uncertainty, they would be more significant than if they had caused 5% uncertainty. Above 50% uncertainty due to random factors, and I think it is always acceptableto call the system "random".

Supposing you released a ballon into the atmosphere. And at the end of each day, you recorded its position. With a knowledge of weather systems its initial behaviour would be predictible, but it would be impossible to predict where the balloon would be in a year's time*, because random factors would have played a significant part.

*It's a magic balloon that doesn't deflate, and has neutral buoyancy in air.

Walter Wayne

5th October 2008, 01:38 PM

Since this thread is on the front page, I thought I would mention that the new Skeptic (Vol 14, No 2), might be of some interest to people here. A couple of articles are loosely related to some things brought up in this thread.

Predicting Evolution
How Likely is it that Human-level Intelligence will Evolve Again?

by David Zeigler

The Chain of Accidents & the Rule of Law
The Role of Contingency & Necessity in the Evolution of Higher Intelligence

by Michael Shermer

Walt

P.S. I haven't read the articles, just thought I would pass it on.

sol invictus

5th October 2008, 01:59 PM

It depends on your point of view.

The point seems to have gone whizzing over your head. You defined "random" in terms of "random". That's really not useful.

jimbob

5th October 2008, 02:50 PM

No, I defined a random system as one where random differences played a significant part in determining the state of the system. With a smoke detector, the radioactive decay might be random, but because of the rate of decay events, random differences do not cause a significant part in determing the state of the system. You can average these out.

It is my contention that you can't with evolution.

If a cosmic ray can cause a seeding event that is of a scale to affect cloud formation, and that this becomes "significant" for a particular defintion of "significant", then weather would be random over timescales greater than this. Especially if a cosmic ray a few millimetres/miliseconds away would cause a "significantly" different outome.

I thought we had already decided what random was.

I'm happy with quantum uncertainty and anything "significantly" affected by that as being random.

My contention is that quantum decay events are random and they can affect the survival of individual organisms, both directly, and (more importantly) indirectly, therefore natural selection is "probabilistic" (a skewed game of chance) and evolution itself*, by the multiple feedbacks and simple malthusian reasoning (most "beneficial" mutations will also fail) is also random although often predictible for long timescales.

*Every so often the fitness landscape will be changed by e.g. a disruptive mutation that alters the rules for many organisms, for example.

Wowbagger

5th October 2008, 10:34 PM

My monster! It's still growing! Ahhhhhhhhhh!!!!!!!!!!

Dancing David

6th October 2008, 05:31 AM

Come see articulett embarrass herself when she discusses the stochasticity of evolution with real evolutionary biologists. (http://www.richarddawkins.net/forum/viewtopic.php?f=4&t=7428&p=1184351#p1184351)

So did they agree with you when you posted?

From looking at the last page, I would say it is undecided, are you MJPAM?

millwallfan

6th October 2008, 07:22 AM

huh??

cyborg

11th October 2008, 02:56 PM

This is pointless anyway. Let us grant you that "randomness" equates to "acausal". What does this get us? It means nothing to evolution by natural selection - the acausal element only creates variation, variation which could arise by any means at all and evolution would still occur.

What is your point with all this?

Just because my entire point was answered right before I even got started in the thread. But it seems too difficult a point to grasp for some where chasing acausal relationships somehow makes sense.

articulett

11th October 2008, 03:43 PM

So did they agree with you when you posted?

From looking at the last page, I would say it is undecided, are you MJPAM?

He started another thread on it... he is embarrassing himself there like he did here. It's not undecided by Dawkins et. al. or any of the professional biologists. Most are pretty clear that it's a 2 part process, with the emphasis on "natural selection" which selects from the "randomness". As far as I can tell, only those who don't really understand natural selection are hung up on defining evolution as " wholly random" or a "theory of chance" (and creationists like Behe.) Mjpam thinks that because you can model evolution "stochastically", it makes sense to call it "random"- but, by his vague definition, smoke alarms work "randomly", and poker is random, and so is whether seat belts save lives. In fact, if it has any randomness whatsoever, Mijo insists on calling it "random"--so this thread is "random". This is not informative for explaining what evolution is nor for addressing the OP--but it's something creationists are oddly fond of doing.

Mijo lives to convince himself (by trying to convince others) that it's informative or useful to call evolution random. I think that on the Dawkins forum they just think he (mjpam) is daft and dishonest...

I think he's a creationist, because all his arguments on all his threads are rehashes of creationist arguments... but he'll pretend he wants to know "for a friend" or "a date" or some people he "ran into". He also tried the same argument at Internet Infidels and who knows where else... --everyone pretty much realizes he's not really saying anything coherent after a bit.

As far as I can tell, the only person buying what he's saying is himself.

(BTW, Happy Birthday Cyborg!)

T'ai Chi

11th October 2008, 04:07 PM

Just in case anybody missed it, I have a great article that started this discussion at

http://www.statisticool.com/main.htm

It is funny those that say evolution is not random. Because they essentially are either denying the scientific definition of random for whatever reason (usually because they are afraid of creationists misuing the term, or they are catering to the general layman's understanding of random), or are saying everything is deterministic.

So it is fun popping in every few months to see some strange denials.

sol invictus

11th October 2008, 04:22 PM

Just in case anybody missed it, I have a great article that started this discussion at

http://www.statisticool.com/main.htm.

That's a silly article. The argument given there immediately implies that all physical processes are random (for exactly the same reason Mijo's did), making it equally pointless.

The whole debate is utterly useless.

articulett

11th October 2008, 05:16 PM

I think Tai Chi and Mijo are of the same "bent" and taken about as seriously as each other around these parts. Tai Chi (along with Behe) are examples of the "sorts of people" I think of when I hear folks bent on playing semantic games so that they can think it's informative or useful to refer to evolution as a "theory of chance" (the creationist straw man).

As far as I can tell, their expertise is in their own minds. After a while, they all blend together to me.

T'ai Chi

11th October 2008, 06:32 PM

That's a silly article. The argument given there immediately implies that all physical processes are random (for exactly the same reason Mijo's did), making it equally pointless.

That's a silly response.

Let's forget about "all physical processes" and just focus on evolution. Either it is random or it isn't. Now what is your answer?

Say what you mean and mean what you say.

articulett

11th October 2008, 06:47 PM

Either poker is random or it isn't. Either smoke alarms are random or they aren't. Either this thread is random or it isn't.

Now, whether it's informative or useful or descriptive to say such a thing is an entirely different matter.

(But that is a conversation that is beyond those who need to believe it makes sense to call evolution "random".)

Dancing David

13th October 2008, 05:48 AM

That's a silly response.

Let's forget about "all physical processes" and just focus on evolution. Either it is random or it isn't. Now what is your answer?

Say what you mean and mean what you say.

Don't focus on the errors in my logic, just look exactly at what I want you to look at.

Variation in expression can be somewhat random, selection is not.

articulett

13th October 2008, 06:05 PM

And variation doesn't need to be random at all for evolution to work. Sexual recombination is a great way for making new varieties--no "random mutation" is needed... the genes are just shuffled.

Natural selection is the key to understanding evolution, and it is no more "random" than any other iterative, cumulative, process connected through time-- the formation of canyons, ecosystems, the internet, languages, technology, and science, itself.

Having random components does not a random process make.

The only people I know who insist on calling evolution "random" are creationists, like T'ai (and Behe). Doing so shows a profound lack of understanding regarding natural selection as well as a need to "obfuscate" understanding so that evolution sounds akin to the creationist straw man --rather than the fairly easy to understand process that Darwin (and later, Dawkins) brilliantly clarified.

sol invictus

13th October 2008, 06:15 PM

Let's forget about "all physical processes" and just focus on evolution. Either it is random or it isn't. Now what is your answer?

Either that blue and red shirt is blue or it isn't. Now what is your answer?

It's a stupid question, and stupid questions have only stupid answers.

Wowbagger

13th October 2008, 06:18 PM

We can demonstrate that a system with some random inputs or components are not necessarily completely random systems, with a simple model:

Let's say some child ONLY likes blue M&Ms. He builds a machine that can detect the color of M&Ms that are poured into it. Blue ones come out, intact, into a bin. And, other colors are sent to another bin to be given away or disposed of.

What goes into the system? An unpredictable, random assortment of M&M colors.
What comes out? Only the blue ones.

The entire system is NOT random, because we can predict important aspects of its output, with very high reliablility, even though the input was completely randomized.

Evolution via Natural Selection is kinda, sorta like that.

T'ai Chi

14th October 2008, 12:23 PM

Either that blue and red shirt is blue or it isn't. Now what is your answer?

It's a stupid question, and stupid questions have only stupid answers.

All you did, like others have, is just avoid it again, or appeal to humor to hide your ignorance of the science.

Do you believe evolution can be modelled accurately by mathematics? Yes or No?

sol invictus

14th October 2008, 12:46 PM

All you did, like others have, is just avoid it again, or appeal to humor to hide your ignorance of the science.

No, actually, I showed that your statement (that evolution "is random or isn't") is idiotic. Complex processes cannot necessarily be accurately characterized with one term, particularly one as ill-defined as "random".

Do you believe evolution can be modelled accurately by mathematics? Yes or No?

No, not accurately and in full detail. However one can easily build models in which some type of evolution by selection occurs, using either random, pseudo-random, or non-random algorithms.

CFLarsen

14th October 2008, 12:54 PM

Vorticity

14th October 2008, 02:42 PM

Stephen Jay Gould - certainly not one who would avoid explaining Evolution, had this to say about randomness. (http://www.pbs.org/newshour/gergen/november96/gould.htm)

From the link:

...
STEPHEN JAY GOULD: So in its random motion back and forth occasionally a species staggers over towards greater complexity, but it arises within an effectively random system.
...

The "system" Gould refers to here is the process of evolution itself. With his drunkard's walk analogy, he is actually reiterating the very point that the "randomites" in this thread have been making: Just because a process is random does not preclude some (or even most!) aspects of its behavior from being predictable. In the same way, just because some aspects of a process' behavior are predictable does not necessarily make it a non-random process.

Look again at Gould's description of the drunkard's walk:

...
DAVID GERGEN: You used an analogy, which I found quite helpful to me, in thinking about the randomness of it all. You talked about the drunk coming out of a bar and staggering. Could you--

STEPHEN JAY GOULD: Yeah. It’s an old statistical paradigm called the drunkard’s walk, which is a wonderful way of illustrating how you can get directional and predictable motion within a totally random system. All right. Here’s the story. A drunk staggers out of a bar. Here’s the bar, and he’s leaning right against the wall of the bar. Now, he’s staggering completely at random, back and forth. There’s a gutter 30 feet away. He staggers five feet every time he staggers, completely at random, goes towards the bar as often as he goes away, except if he hits the bar wall, he can’t go through it, so he just stands there until he staggers away. Now, where does he end up every time? Of course, he ends up in the gutter. He falls down in the gutter, the thing’s over. We understand that very easily.

DAVID GERGEN: Right.

STEPHEN JAY GOULD: He’s going to lend up in the gutter every time.

DAVID GERGEN: Right.
...

Now if we imagine the data set which consists of the drunkard's position as a function of time, this data set clearly describes a random process (by construction). However, we can impose a "filter" on the data which yields a deterministic outcome. In Gould's example the filter would be the "Where the drunkard winds up" filter. With probability 1, this filter always yields "gutter". And yet the original process itself is still random. I can design other filters that yield a random outcome from this data set. For example the "How many steps until the drunkard ends up in the gutter" filter, or the "How many times does the drunkard hit the wall" filter.

Despite the fact that we can construct a non-random filter on the drunkard's walk process does not make it "the exact opposite of random".

jimbob

14th October 2008, 02:57 PM

Stephen Jay Gould - certainly not one who would avoid explaining Evolution, had this to say about randomness. (http://www.pbs.org/newshour/gergen/november96/gould.htm)

It is false to say that Evolution is random, period.

We've been over this, again and again. Repetition of a falsehood does not make it true; It is only done because it works: The same way people are indoctrinated within religious circles and totalitarian societies, the same way it is hoped that we will simply accept dogma - and not question it - by repeating it over and over and over again.

From your link.

I don't think I am taking him out of context:

As far as they’re concerned, we’re just little islands of mobile resources which they can exploit for a while. They’re happy to let us strut this little hour on the stage because they’ll still be here when we’re gone. But, you see, you don’t see that unless you’re willing to look at the history of life as the full range of its variation through time. I mean, it is true the most complex thing has gotten more complex. Once there were only bacteria. Now there are humans, but that’s not the result of an intrinsic defining central drive. It’s just a kind of random movement away from a necessary beginning at maximal bacterial simplicity. That’s all it is.

STEPHEN JAY GOULD: So in its random motion back and forth occasionally a species staggers over towards greater complexity, but it arises within an effectively random system.

I agree it is misleading to talk about random as if that meant that everything was equally possible, but it doesn't usually mean that. I would prefer to say Natural Selection is not haphazard. But technically I would say it is random.

It is certainly not nonrandom.

If it was nonrandom, then all Lenski's results in the Long Term Evolution Experiment would produce cultures with only insignifcant differences, as the external environment differed insignificantly*.

We know that they haven't and that the differences between the ewternally imposed environment were insignificant, so the differences in the outcome must be due to the differences that arose within the bacteria themselves.

It is a classic example of what I have been arguing, that it is inevitable that adaptations will occur, but as changes in organisms affect the evolutionary landscape for other organisms, it is possible for rare events to totally disrupt the selective landscape for other organisms. A chance mutation in HIV could have a vast effect on selective pressures in many populations. Without medicine such mutations would have even greater effects.

Remember that the Long Term Evolution experiment is in a pretty simple environment, most of the competition comes from descendants of the original culture, there are not really other organisms in a dynamic ecological equilibrium within these jars. As soon as these are added into the equation (in a more complex environment or over billions of years), then the scope for random mutations affecting the fitness landscape becomes far greater.

*We know this because Lenski kept freeze-dired cultures at different stages, and can identify which strain developed the initial "facilitating" mutation even though citrate metabolism didn't evolve until thousands of generations later.

ImaginalDisc

14th October 2008, 04:06 PM

From your link.

I don't think I am taking him out of context:

I agree it is misleading to talk about random as if that meant that everything was equally possible, but it doesn't usually mean that. I would prefer to say Natural Selection is not haphazard. But technically I would say it is random.

It is certainly not nonrandom.

If it was nonrandom, then all Lenski's results in the Long Term Evolution Experiment would produce cultures with only insignifcant differences, as the external environment differed insignificantly*.

We know that they haven't and that the differences between the ewternally imposed environment were insignificant, so the differences in the outcome must be due to the differences that arose within the bacteria themselves.

It is a classic example of what I have been arguing, that it is inevitable that adaptations will occur, but as changes in organisms affect the evolutionary landscape for other organisms, it is possible for rare events to totally disrupt the selective landscape for other organisms. A chance mutation in HIV could have a vast effect on selective pressures in many populations. Without medicine such mutations would have even greater effects.

Remember that the Long Term Evolution experiment is in a pretty simple environment, most of the competition comes from descendants of the original culture, there are not really other organisms in a dynamic ecological equilibrium within these jars. As soon as these are added into the equation (in a more complex environment or over billions of years), then the scope for random mutations affecting the fitness landscape becomes far greater.

*We know this because Lenski kept freeze-dired cultures at different stages, and can identify which strain developed the initial "facilitating" mutation even though citrate metabolism didn't evolve until thousands of generations later.

That's because, unsurprisingly, Gould was talking out of his ass.

Describing bacteria as the simplest possible organisms is false. Bacteria are, in thunderf00t's words, "grizzled heavyweights." The "simple" bacterium has sophisticated mechanisms for coating itself, protecting itself, mobility, and digestion.

Complexity isn't a drunkard's walk, it's an emergent property and certain features of complexity are selected for or against at different times.

jimbob

7th November 2009, 12:18 PM

From another thread to rerail both...

This is interesting discussion material jimbob. Feel free to start a thread and PM me, or set up a diversion here (beep beep!). Meantime, I'm a little confused as to what you mean by "usual scientific definition", "neither of the options Richard Dawkins stated" and "inputs"? See, you've already managed to obscure matters beyond the pre-existing confusion mentioned by Dawkins! ;)

An update:

In this thread (http://forum.richarddawkins.net/viewtopic.php?f=14&t=97719&p=2414686#p2414686) on his forum, Richard Dawkins has now stated that he is not using the technical definition for random

Words, as Twatsworth rightly says, often have more than one meaning, sometimes related meanings. Confusion, and even patronizing abuse, can result when somebody adopts one meaning and presumes that another person is using the same meaning. The Shorter Oxford Dictionary gives two definitions of the adjective 'random'. In this order:

1. Not sent or guided in a special direction; having no definite aim or purpose.

2. (statistics) Governed by or involving equal chances for each of the actual or hypothetical members of a population.

Meaning 2 is the one adopted by statistically-minded members of this Forum, not surprisingly since that is the technical definition used in their profession.

Meaning 1 is the one used and assumed by everybody except professional statisticians. It is the one I have consistently followed in all my books, and the one understood by the kinds of people I am trying to communicate with: the kinds of people who need to be convinced of the truth of evolution, or who need better comprehension of what evolution means.

The two halves of Meaning 1 are themselves open to confusion. Meaning 1b ('having no definite aim or purpose') is the meaning assumed by creationists, who therefore regard evolution by natural selection as random, because it has no definite aim or purpose (which they assume to mean intelligently designed aim or purpose). Meaning 1a ('not sent or guided in a special direction') is the meaning adopted by most biologists, who therefore regard natural selection, but not mutation or drift to fixation, as nonrandom because it sends or guides evolution in the direction of adaptive improvement. It has been a large part of my life's work to dispel the confusion between 1a and 1b. So engrossed was I in the battle between 1a and 1b, I was momentarily taken aback by a sudden outflanking manoeuvre from an unexpected source, namely Meaning 2 (which I was aware of but had largely ignored and even forgotten about).

After some reflection, I shall continue to use Meaning 1, and shall continue my efforts to disentangle the confusion between 1a and 1b. I might think about possible ways to clarify the side issue of the confusion with Meaning 2. I don't think it is unkind to say that the postings to this forum by partisans of Meaning 2 are not well-adapted to enlighten laypeople. I can't help wondering whether it would be wise even to attempt to explain Meaning 2 to laypeople, while the more important confusion between 1a and 1b remains the dominant barrier to general understanding of evolution.

And now, I don't know about the rest of you but I've had enough of this. I'm going back to work. Goodbye.

Richard

I would argue, as marios does four posts down, that it is still wrong and the usual scientific definition of a random event fulfills neither of the options Richard Dawkins stated, but that a random event is an event that is not predetermined, where where identical inputs do not produce identical outcomes. (This is what marios refers to as "meaning #3").

In other words the "opposite of random" is "predetermined", or "predestined", or "preordained"; thus using the incorrect definition of random so that claiming that natural selection is the opposite of random is claiming that natural selection is predetermined, so it doesn't matter what else happens, but that the evolution of particular collections of traits were inevitable as they were driven by an already predetermined natural selection, a bit like dropping marbles onto a slope with a track running along the bottom, where the marbles will all end up running downhill along the track, wherever they started.

Talking about natural selection as though it is preordained is (a) wrong, and (b) playing into the hands of ID proponents.

Southwind17

7th November 2009, 11:35 PM

I would argue, as marios does four posts down, that it is still wrong and the usual scientific definition of a random event fulfills neither of the options Richard Dawkins stated, but that a random event is an event that is not predetermined, where where identical inputs do not produce identical outcomes. (This is what marios refers to as "meaning #3").

In other words the "opposite of random" is "predetermined", or "predestined", or "preordained"; thus using the incorrect definition of random so that claiming that natural selection is the opposite of random is claiming that natural selection is predetermined, so it doesn't matter what else happens, but that the evolution of particular collections of traits were inevitable as they were driven by an already predetermined natural selection, a bit like dropping marbles onto a slope with a track running along the bottom, where the marbles will all end up running downhill along the track, wherever they started.

Talking about natural selection as though it is preordained is (a) wrong, and (b) playing into the hands of ID proponents.

I'm a little confused as to what you mean by "usual scientific definition", "neither of the options Richard Dawkins stated" and "inputs"? See, you've already managed to obscure matters beyond the pre-existing confusion mentioned by Dawkins! ;)

sol invictus

8th November 2009, 02:50 AM

I would argue, as marios does four posts down, that it is still wrong and the usual scientific definition of a random event fulfills neither of the options Richard Dawkins stated

There is no "usual scientific definition" of random. It's used in different ways in different fields, and even in different contexts within the same field. That's what makes this debate so utterly pointless.

"Random" simply isn't a precise term, and scientists don't use it as one. When there is the possibility of confusion, they either use a different term or qualify it.

In other words the "opposite of random" is "predetermined", or "predestined", or "preordained";

No, because again - "random" doesn't have a single definition, and therefore it doesn't have a definite opposite. FYI "predetermined", "predestined" etc. are not really technical terms. The term you're presumably looking for is "deterministic" (or "determined by initial conditions"). Its opposite is "non-deterministic". Those are specific terms with unambiguous meanings, unlike "random".

Dancing David

9th November 2009, 05:32 AM

Eeeeek!

Super zombie thread!

posted by JimBob
In other words the "opposite of random" is "predetermined", or "predestined", or "preordained"; thus using the incorrect definition of random so that claiming that natural selection is the opposite of random is claiming that natural selection is predetermined,

Major fallacy, fallacy of construction, the defintion of the opposite of random is inderterminate, then this is an overgeneralization.

aggle-rithm

9th November 2009, 06:11 AM

And variation doesn't need to be random at all for evolution to work. Sexual recombination is a great way for making new varieties--no "random mutation" is needed... the genes are just shuffled.

This also, neatly, allows evolvability, a key requirement for evolution to work. Sexual recombination covers a multitude of genetic "sins", which arise inevitably as mutation takes place. These sins might later become assets, but in the meantime they are kept hidden so as not to do any damage.

jimbob

9th November 2009, 01:40 PM

Eeeeek!

Super zombie thread!

Major fallacy, fallacy of construction, the defintion of the opposite of random is inderterminate, then this is an overgeneralization.

Why?

The overgenralisation is in the statment "opposite of random". I would accept "Opposite of the frequently used definition of random as 'directionless' "... even though it is ugly. "Natural Selection has direction, but no intelligent guidence".

I believe you are an engineer, so what problem do you the statement that a random system can have different outcomes for identical inputs, whilst a nonrandom system can't. In other words a nonrandom output is predetermined, whilst a nonrandom output isn't.

It is the statement "Opposite of random" that I object to.

That is equivalent to a boolean NOT function, and implies (to me) that natural selection has no important features of randomness. Furthermore, I would argue, and there are evolutionary biologists on that thread who agree that the definition as used by me, is a workable definition in their field of evolutionary biology. A statistician on this forum has also agreed that my definition of random is how statisticians define "random".

I would say that it fits the definition of randomness in physics, so that definition is pretty common in many disparate scientific disciplines.

As I have said several times before, the problem I have is that it is perfectly reasonable, and indeed in many respects technically more correct to describe Natural Selection as a random process, or probabilistic, whilst it is only nonrandom i a particular colloquial definition. Attacking people for technical accuracy is itself misleading and confusing.

I would argue that sometimes in complex systems nonrandom variables are treated as random to help analysis, but these are actually pseudorandom rather than actually random.

Paul C. Anagnostopoulos

9th November 2009, 04:54 PM

The term you're presumably looking for is "deterministic" (or "determined by initial conditions"). Its opposite is "non-deterministic". Those are specific terms with unambiguous meanings, unlike "random".
I agree that random is a slippery term that's best avoided. However, it seems to me that as far as processes are concerned, there is no logical room left after we include deterministic and random factors. That makes random a synonym for nondeterministic. Am I missing something?

I presume we agree that a stochastic process is one that has some random generators. Here is the definition from the Penguin Dictionary of Mathematics:

stochastic process. A random process. Common usage excludes essentially deterministic processes that are subject only to random errors.

~~ Paul

Dancing David

9th November 2009, 05:49 PM

lenny

10th November 2009, 02:24 PM

I agree that random is a slippery term that's best avoided.

in fact it is used regularly and with little confusion in statistics, physics, and (slightly less so, like all concepts) philosophy.

why it causes such recurrent gnashing of teeth in discussions of evolution ... there must be several psychology dissertations in there...

However, it seems to me that as far as processes are concerned, there is no logical room left after we include deterministic and random factors. That makes random a synonym for nondeterministic. Am I missing something?

I presume we agree that a stochastic process is one that has some random generators. Here is the definition from the Penguin Dictionary of Mathematics:

stochastic process. A random process. Common usage excludes essentially deterministic processes that are subject only to random errors.

~~ Paul

i do not think you are missing anything.

perhaps a note that "subject only to random errors." is intended to refer to observational noise, not dynamic noise.

and the idea of including "deterministic and random factors" is tricky in nonlinear systems (where we cannot invoke linear superposition). not a problem in defining dynamical systems, but fundamental in terms of identifying a dynamical system.

sol invictus

10th November 2009, 05:32 PM

I agree that random is a slippery term that's best avoided. However, it seems to me that as far as processes are concerned, there is no logical room left after we include deterministic and random factors. That makes random a synonym for nondeterministic. Am I missing something?

Yes - the way the term "random" is used, it is not synonymous with "non-deterministic". "Random" often implies "flat distribution", "directionless", or "equiprobable". As one example, consider the lottery where the numbers are drawn from bouncing balls. Is that process "random"? Certainly most people would agree that it generates random numbers, and yet the process itself might be deterministic.

Another example is suggested by your dictionary definition. Consider a measurement in a physics experiment, say of the length of some object. The length is not precisely defined due to quantum fluctuations, and therefore the result of the measurement is, strictly speaking, non-deterministic. And of course in addition there are the usual types of measurement errors, which may or may not be deterministic.

And yet, no one in their right mind would say that the results of measuring something with a tape measure are "random". They might say the errors are random (even though they may be deterministic), but they would never say the result is. Why not? Because the result has a non-zero mean and small fluctuations around that mean. We don't usually characterize distributions like that, distributions that are fairly sharply peaked around some non-zero value, as "random".

I presume we agree that a stochastic process is one that has some random generators.

"Stochastic" is close to synonymous with non-deterministic, but carries a slightly different connotation. In physics it's often used for systems in which the non-deterministic element is some kind of noise, thermal or otherwise. More generally it usually implies the presence of some kind of direction, force, or tendency, one that is perturbed but not destroyed by the noise. I'd say it's the best term to describe evolution.

Wowbagger

10th November 2009, 08:51 PM

More generally it usually implies the presence of some kind of direction, force, or tendency, one that is perturbed but not destroyed by the noise. I'd say it's the best term to describe evolution.That does sound like a nice, succinct summary of evolution, to me.

jimbob

12th November 2009, 01:51 PM

Why?

The overgenralisation is in the statment "opposite of random". I would accept "Opposite of the frequently used definition of random as 'directionless' "... even though it is ugly. "Natural Selection has direction, but no intelligent guidence".

I believe you are an engineer, so what problem do you the statement that a random system can have different outcomes for identical inputs, whilst a nonrandom system can't.

Hardly, I am a computer aide, with a psych degree and social work as a former profession.

Sorry, I must have been confusing you for someone with a similar name/location or posting style

In other words a nonrandom output is predetermined, whilst a nonrandom output isn't.

Now that is also a statement I don't agree with, you mean a closed system with known inputs and responses to inputs?

Schrödinger's Cat (http://en.wikipedia.org/wiki/Schrödinger's_cat) could be a closed system that is random (if the radioactive source is placed in the box next to the cat.

If you don't like cruelty to imaginary cats, you could change the response of the detector to maybe multiply an input by a factor that depended on the number of radiation counts in the preceding five seconds, or something akin to that. The external inputs will be known , and even how it responds to particular random events, but it will still produce a random output, because it has its own modification of the inputs according to some random number.

Many statistical techniques are often based on assuming not that something is *actually* random, on other confounding factors that are too complex to model.

In such cases "randomness" might be illusory, but that is not the situation in evolution.

For example, a collection of random mutations in a flu virus suddenly can make it far more lethal, so these few mutations can exert a large evolutionary pressure on birds.

A different set of mutations, and you get a different set of evolutionary pressures exerted on the host population. Just because we can't *see* proteins generated by the immune system doesn't make this evolution any less important than running ability for gazelles, for example.

It is the statement "Opposite of random" that I object to.

Now that i can understand.

Furthermore, it means that if you learn that Natural Selection is nonrandom, then if you want to study population genetics and its interaction with evolution, you will have to unlearn this "fact".

Evolution can be simply approximated as nonrandom if you are considering sufficiently large populations in a stable environment and the environment remains stable for sufficient time. This is the easiest situation to understand, and is probably what is often implicitly assumed in discussions about how evolution works in theory. This is not what happens in real environments though. Not even in simple environments like flasks of e-coli with no other bacteria present.

Southwind17

13th November 2009, 10:40 AM

Sorry, I must have been confusing you for someone with a similar name/location or posting style
Ivor the Engineer comes to mind!

sphenisc

11th March 2010, 03:58 AM

Stochasticity and speciation events

http://www.nature.com/nature/journal/v463/n7279/full/nature08630.html

jimbob

12th March 2010, 07:41 AM

Stochasticity and speciation events

http://www.nature.com/nature/journal/v463/n7279/full/nature08630.html

And new scientist's article and interview about this:

http://www.newscientist.com/article/mg20527511.400-accidental-origins-where-species-come-from.html?full=true

(I don't know about the blocking for registering in that site now)

anyway, form my viewpoint here are the key paragraphs:

The key point emerging from the statistical evidence, Pagel stresses, is that the trigger for speciation must be some single, sharp kick of fate that is, in an evolutionary sense, unpredictable. "We're not saying that natural selection is wrong, that Darwin got it wrong," Pagel adds. Once one species has split into two, natural selection will presumably adapt each to the particular conditions it experiences. The point is that this adaptation follows as a consequence of speciation, rather than contributing as a cause. "I think what our paper points to - and it would be disingenuous for very many other people to say they had ever written about it - is what could be, quite frequently, the utter arbitrariness of speciation. It removes speciation from the gradual tug of natural selection drawing you into a new niche," he says.

This has implications for one of the most contentious aspects of evolution: whether it is predictable or not. If Pagel is correct, natural selection shapes existing species in a gradual and somewhat predictable way, but the accidental nature of speciation means that the grand sweep of evolutionary change is unpredictable. In that sense his findings seem to fit with the famous metaphor of the late Stephen Jay Gould, who argued that if you were able to rewind history and replay the evolution of life on Earth, it would turn out differently every time.

That is why I dislike descriptions of evolution as "nonrandom".

Wowbagger

14th March 2010, 11:05 AM

That is why I dislike descriptions of evolution as "nonrandom".Almost the same reason the climate shouldn't be called "nonrandom".

mijopaalmc

16th March 2010, 09:52 PM

recursive prophet

16th March 2010, 10:48 PM

"Stochastic" is close to synonymous with non-deterministic, but carries a slightly different connotation. In physics it's often used for systems in which the non-deterministic element is some kind of noise, thermal or otherwise. More generally it usually implies the presence of some kind of direction, force, or tendency, one that is perturbed but not destroyed by the noise. I'd say it's the best term to describe evolution.

And I'd say this is one of the more succinct deconstructions of the semantics involved that I've seen, sol. Remember when we discussed an applicable definition for stochastic back on that other thread? It began with a question I asked in the evo-facts stickey? Is evolution stochastic? That thread went on for 10 pages after it was split, and I'm having a deja vous moment. Did I already tell you about this? :D

Anyway, hail, hail, the gangs all here! Hi mijo, jimbob. ;) I don't think Articulett or Dr. Adequate will be joining us; indisposed, what? Here's a link to that other quite similar thread-http://forums.randi.org/showthread.php?t=131514 Perhaps some of the replies from there can be recycled. :rolleyes:

Wowbagger

16th March 2010, 11:11 PM

As I recall, two of the most commonly advanced arguments about how evolution is non-random that:

Evolution is predictable in the long term.

Natural selection makes evolution non-random.

Doesn't this study cast doubt on both?

To address the first one: It is a little like the difference between weather and climate. Climate is predictable in the long run. The more specifics of weather conditions are not.
The general directions of evolution are predictable, in the long run. The specific details are usually not.

I believe this applies to what the study is saying, also. Since specific occurrences of speciation are dependent on the little details, we would expect to have difficulty knowing in advance when they will occur, and which features it will involve. But, we can figure out many of the general directions they would take, to survive in their niches, when they do.

The study says nothing about the second one. The influence that is Natural Selection is still nonrandom.

mijopaalmc

16th March 2010, 11:37 PM

To address the first one: It is a little like the difference between weather and climate. Climate is predictable in the long run. The more specifics of weather conditions are not.
The general directions of evolution are predictable, in the long run. The specific details are usually not.

I believe this applies to what the study is saying, also. Since specific occurrences of speciation are dependent on the little details, we would expect to have difficulty knowing in advance when they will occur, and which features it will involve. But, we can figure out many of the general directions they would take, to survive in their niches, when they do.

The study says nothing about the second one. The influence that is Natural Selection is still nonrandom.

Did you read the abstract of the article?

Phylogenies reveal new interpretation of speciation and the Red Queen (http://ntserver1.wsulibs.wsu.edu:2138/nature/journal/v463/n7279/full/nature08630.html)

The Red Queen1 describes a view of nature in which species continually evolve but do not become better adapted. It is one of the more distinctive metaphors of evolutionary biology, but no test of its claim that speciation occurs at a constant rate2 has ever been made against competing models that can predict virtually identical outcomes, nor has any mechanism been proposed that could cause the constant-rate phenomenon. Here we use 101 phylogenies of animal, plant and fungal taxa to test the constant-rate claim against four competing models. Phylogenetic branch lengths record the amount of time or evolutionary change between successive events of speciation. The models predict the distribution of these lengths by specifying how factors combine to bring about speciation, or by describing how rates of speciation vary throughout a tree. We find that the hypotheses that speciation follows the accumulation of many small events that act either multiplicatively or additively found support in 8% and none of the trees, respectively. A further 8% of trees hinted that the probability of speciation changes according to the amount of divergence from the ancestral species, and 6% suggested speciation rates vary among taxa. By comparison, 78% of the trees fit the simplest model in which new species emerge from single events, each rare but individually sufficient to cause speciation. This model predicts a constant rate of speciation, and provides a new interpretation of the Red Queen: the metaphor of species losing a race against a deteriorating environment is replaced by a view linking speciation to rare stochastic events that cause reproductive isolation. Attempts to understand species-radiations3 or why some groups have more or fewer species should look to the size of the catalogue of potential causes of speciation shared by a group of closely related organisms rather than to how those causes combine.(emphasis added)

Wowbagger

17th March 2010, 12:54 AM

Did you read the abstract of the article?Yes. Do you think anything I said contradicts anything it said?

mijopaalmc

17th March 2010, 01:30 AM

Yes. Do you think anything I said contradicts anything it said?

Perhaps you could explain how the finding that speciation is dominated stochastic events is consistent with your assertion that evolution is predictable in the long run, given that the overall direction of evolution after speciation is dependent on the genetic background left by the speciation.

sol invictus

17th March 2010, 06:34 AM

OH MY GOD, IT'S ALIVE!!

Perhaps you could explain how the finding that speciation is dominated stochastic events is consistent with your assertion that evolution is predictable in the long run, given that the overall direction of evolution after speciation is dependent on the genetic background left by the speciation.

What the heck....

I see your level of comprehension of this discussion hasn't changed at all.

"Evolution is predictable in the long run" - what does that mean to you? To me, it means that certain things can be reliably predicted in the long run (weird that it would mean that, huh?). That paper doesn't affect that conclusion.

For example: bacteria in petri dishes with some citrate. At the start of the experiment, none of the bacteria can metabolize citrate. The ability to metabolize citrate would be a strong advantage given the environment. So, let multiple colonies in multiple petri dishes live and reproduce for a long time.

Again: the claim at issue is that the theory of evolution by natural selection is predictive in the long term; that is, that it can predict some results of some experiments. So let's apply it to this. According to the theory, there is some non-zero probability per generation that a bacterium will mutate in such a way that it can metabolize citrate. Moreover, the theory tells us that that bacterium and its descendants will have an advantage in the sense that they will reproduce more rapidly than bacteria without that ability. More specifically, the theory predicts that eventually, all bacteria in that petri dish - and therefore eventually, in all petri dishes - should have the ability to metabolize citrate (modulo a few details, like that said ability doesn't come at a cost so significant it cancels out the benefit).

In principle the theory will also tell us how long we need to wait on average before that happens in a given petri dish, but to extract that prediction requires knowledge of the probability I mentioned, and that's hard to estimate (although one can certainly try). Regardless, the above is a definite, solid prediction for the long term, and we can test it.

So someone tested it. Guess what the result was (after a decade or so)?

Wowbagger

17th March 2010, 09:07 AM

Perhaps you could explain how the finding that speciation is dominated stochastic events is consistent with your assertion that evolution is predictable in the long run, given that the overall direction of evolution after speciation is dependent on the genetic background left by the speciation.Climate is also dependent on the background left by the weather. And, yet, we can predict larger trends in climate.

Perhaps an analogy of traffic patterns is easier. You can predict how bad the traffic is going to be around sports stadiums, by looking at the schedule of games. But, you can't predict, in advance, exactly which car is going to be on what part of the road, at any given time - even though the traffic patterns are highly dependent on which cars are on which parts of what roads.

This was NOT A PERFECT ANALOGY to biology, for several reasons. But, hopefully, it will illustrate the general idea of how something can be nonrandom, yet dependent on some random elements.

mijopaalmc

17th March 2010, 09:55 AM

jimbob

17th March 2010, 10:52 AM

Wowbagger, This is the crux of the debate as far as I can see.

There is one view that evolution is generally predictable over the long term. In other words natural selection dominates, and the selection pressures are stable. If you reran the tape of evolution, you would come up with pretty similar organisms.

The other view is that there are enough complex nonlinear feedbacks in the system so that the selection pressures are subject to "random*" change over time, so that over a long enough timescale you can't make many useful predictions about what the ecosystem would look like, to say nothing about the organisms that have evolved within it.

Taken to its extreme, there might be a case for saying that the evolution of multicellular life was a fortuitous occurrence, which only occurs in a small proportion of planets where life arises. Of course there is currently no way of finding this out, at the moment, but we do know that the vast majority of biomass on Earth is not multicellular.

*And I would argue truly random as opposed to pesudorandom.

Wowbagger

17th March 2010, 10:54 AM

Uh...it's not even a good analogy.

As the study that was posted demonstrates, evolution is dependent of stschatic elements the majority of the time and is therefore, in general not predictable, especially over time scales over which speciation becomes important. In other words, the study study the exact opposit exact opposite of ehat you have been saying about that predictability of evolution and its resulting non-randomness.Read it carefully. The study is NOT the exact opposite of what I was saying. It is basically offering an adjusted framework by which evolution can be predicted to work.

It seems to indicate that evolution is predictable, over timescales that speciation occurs. It's just that the precise circumstances are less predictable, since (according the study) they are triggered by rare events of reproductive isolation, rather than in a "race" against the enviornment. (It even predicts a constant rate of speciation.)

Does anyone else disagree with my interpretation?

It really doesn't impact the overall statement that Natural Selection is nonrandom, one way or the other.

Wowbagger

17th March 2010, 11:12 AM

There is one view that evolution is generally predictable over the long term. In other words natural selection dominates, and the selection pressures are stable. If you reran the tape of evolution, you would come up with pretty similar organisms.

The other view is that there are enough complex nonlinear feedbacks in the system so that the selection pressures are subject to "random*" change over time, so that over a long enough timescale you can't make many useful predictions about what the ecosystem would look like, to say nothing about the organisms that have evolved within it. Both are correct, to certain degrees.

The ULTIMATE, broader causes and effects of evolution would be the same, if you reran the the tape of evolution. In a broad sense, you would likely get organisms that fill relatively similar niches in relatively similar manners.

There are just sooo many different ways one can fill a niche, and physics restricts the sorts of niches we would find in any given ecosystem.

However, this implies that the PROXIMATE, more specific causes and effects will likely be very different. (Though, we would also expect a certain amount of "coincidental convergence" of some superficial features, too.)

If we looked at the life forms of an alternative "run" of evolution, we would find that they would look very different from what we are used to, but will probably function and behave, in a broad sense, in recognizable ways.

For example, host/parasite relationships would probably work the same. Though, the existence of a parasite might not be recognized until it is spotted moving to a new host. (As is usual for novel parasites, even on Earth.)

Given enough time, multicellular life would likely develop, since its occurrence follows from host/parasite and other related models. Though, the exact manner in which it happens could differ, as we see in the variety of ways that sponges work.

Wowbagger

17th March 2010, 11:19 AM

This thread will come to a bad end.
Looks like you were wrong. This thread will come to NO end.

sol invictus

17th March 2010, 12:29 PM

And I'd say this is one of the more succinct deconstructions of the semantics involved that I've seen, sol.

Thanks.

Doesn't look like it did much good, though.

recursive prophet

17th March 2010, 02:34 PM

Originally Posted by recursive prophet
And I'd say this is one of the more succinct deconstructions of the semantics involved that I've seen, sol.

Thanks.

Doesn't look like it did much good, though.

Planted seeds take a while to blossom sol. It took me 10 pages on that other thread to concede you were right in your analysis of the terminology on page one. Remember your smoke detector analogy? That planted the seed for me, but it took 10 pages for me to know what I knew after pondering your multiple choice questions.

I hope to soon send a PM to susu.exp and Marios at RDF before they turn out the lights there, suggesting they join the discussion here. I can't begin to remember all the arguments, but there were a passel of very bright people that basically agreed with mijo (mjpam there) wrt the non-deterministic overall nature of NS, and why it is important to view it from that perspective. Allele drift in small groups and reproduction success were two of the major factors they mentioned, as I recall. My_wan was the only one from here that jumped the fence, and he put on quite a show. Very compelling; many new rebuttals that resonated, but to little effect. He had-not sure if it's still ongoing-a challenge to the wikinition of random that was pretty awesome. Really made a lot of very new slants on this ambiguous concept. Wittgenstein's 'beetle in a box' came to mind reading it.

As always I'm far from certain which POV is more; relevant; pragmatic; or accurate. But it does seem to stimulate a lot of interesting discussion, and I'm glad this thread did a Lazarus even be it all pure glasperlenspiel.

If you have a chance I'd enjoy reading your comments on jimbob's last entry. And again, I'd really appreciate your thoughts on the XpoTurbine.

mijopaalmc

18th March 2010, 02:34 PM

OH MY GOD, IT'S ALIVE!!

What the heck....

I see your level of comprehension of this discussion hasn't changed at all.

"Evolution is predictable in the long run" - what does that mean to you? To me, it means that certain things can be reliably predicted in the long run (weird that it would mean that, huh?). That paper doesn't affect that conclusion.

For example: bacteria in petri dishes with some citrate. At the start of the experiment, none of the bacteria can metabolize citrate. The ability to metabolize citrate would be a strong advantage given the environment. So, let multiple colonies in multiple petri dishes live and reproduce for a long time.

Again: the claim at issue is that the theory of evolution by natural selection is predictive in the long term; that is, that it can predict some results of some experiments. So let's apply it to this. According to the theory, there is some non-zero probability per generation that a bacterium will mutate in such a way that it can metabolize citrate. Moreover, the theory tells us that that bacterium and its descendants will have an advantage in the sense that they will reproduce more rapidly than bacteria without that ability. More specifically, the theory predicts that eventually, all bacteria in that petri dish - and therefore eventually, in all petri dishes - should have the ability to metabolize citrate (modulo a few details, like that said ability doesn't come at a cost so significant it cancels out the benefit).

In principle the theory will also tell us how long we need to wait on average before that happens in a given petri dish, but to extract that prediction requires knowledge of the probability I mentioned, and that's hard to estimate (although one can certainly try). Regardless, the above is a definite, solid prediction for the long term, and we can test it.

So someone tested it. Guess what the result was (after a decade or so)?

I'm not sure why those who argue that evolution is non-random keep holding up Lenski's research as a demostration that evolution is non-random. Only one of the twelve original, identical, replicate populations evolved the cit+ phenotype, and the vast majority of replicate populations taken from different generations failed to re-evolve the cit+ phenotype.

How exactly do these results demonstrate that evolution is in general predictable over the long-run?

sol invictus

18th March 2010, 02:50 PM

I'm not sure why those who argue that evolution is non-random keep holding up Lenski's research as a demostration that evolution is non-random.

I suppose that's because, despite literally years of discussing this, you still fail to comprehend the most fundamental aspects of it.

Only one of the twelve original, identical, replicate populations evolved the cit+ phenotype, and the vast majority of replicate populations taken from different generations failed to re-evolve the cit+ phenotype.

How exactly do these results demonstrate that evolution is in general predictable over the long-run?

Did you read what I wrote? I described precisely how Lenski's results demonstrate that. Is there something in there that wasn't sufficiently clear?

The fact that one population evolved and fixed the cit+ phenotype is an massive success of the theory, because the odds of such a thing happening by chance (or in any other theory) are essentially zero. That experimentally tested successful prediction by itself proves - to the extent proof is possible in science - that evolution is both predictive and correct, and predictable in the sense I described.

Of course there are mountains of other experiments and fossil records that prove the same thing.

As a side note: why did only one population out of twelve evolve that trait over the course of the experiment? As I said that's something one could predict too (as a probability distribution, obviously) given knowledge of the time-scale for the mutation and/or the probability per generation for it to occur. As I described in my previous post, such probabilities are difficult to estimate a priori, but in any case they aren't necessary for and do not affect the success of the prediction that the trait will eventually evolve and fixate.

mijopaalmc

18th March 2010, 03:14 PM

I suppose that's because, despite literally years of discussing this, you still fail to comprehend the most fundamental aspects of it.

Such a bold assertion with absolutely no evidence.

Did you read what I wrote? I described precisely how Lenski's results demonstrate that. Is there something in there that wasn't sufficiently clear?

Yes, I read what you wrote.

The thing that is not sufficiently clear is how you get from "there is some non-zero probability" to "non-random". The existence of probabilities is, by definition, sufficient grounds for calling evolution a stochastic (or random) process.

The fact that one population evolved and fixed the cit+ phenotype is an massive success of the theory, because the odds of such a thing happening by chance (or in any other theory) are essentially zero. That experimentally tested successful prediction by itself proves - to the extent proof is possible in science - that evolution is both predictive and correct, and predictable in the sense I described.

And, once again, "predictable" doesn't mean "non-random". If it did, processes where events are independent, identically and uniformly distributed wouldn't be random, as the proportion of successes to total trials can be predicted (with error).

Of course there are mountains of other experiments and fossil records that prove the same thing.

And I don't dispute the evidence. I just dispute the redefinition of widely accepted scientific term in order to get the evidence to conform to your preferred philosophical opinion.

As a side note: why did only one population out of twelve evolve that trait over the course of the experiment? As I said that's something one could predict too (as a probability distribution, obviously) given knowledge of the time-scale for the mutation and/or the probability per generation for it to occur. As I described in my previous post, such probabilities are difficult to estimate a priori, but in any case they aren't necessary for and do not affect the success of the prediction that the trait will eventually evolve and fixate.

So stating predictions in terms of probabilities is now how "non-random" is defined?

Uncayimmy

18th March 2010, 03:19 PM

As a side note: why did only one population out of twelve evolve that trait over the course of the experiment? As I said that's something one could predict too (as a probability distribution, obviously) given knowledge of the time-scale for the mutation and/or the probability per generation for it to occur. As I described in my previous post, such probabilities are difficult to estimate a priori, but in any case they aren't necessary for and do not affect the success of the prediction that the trait will eventually evolve and fixate.

If I understand you correctly, what I think you are saying is this:

In any given species there are existing variations as well as new mutations. They have some probability of happening. Let's say the variation is a resistance to a toxin that normally kills most people. We know such variations exist in humans because we all don't react the same way to bee stings, snake bites or ingesting poisons.

One way to detect the prevalence of these variations in a species such as bacteria would be to isolate the gene responsible and then sample a buttload of bacteria looking for this gene. That's time consuming and expensive I would think.

Another way to do it is pretty much like the experiment described. Try to grow colonies of the bacteria in the presence of the toxin with other control colonies growing in the "normal" environment. The controls will reproduce and grow at a certain rate. Those colonies in the toxic environment with no resistance will die off. Those colonies with a variation that allows them to survive in the toxic environment will experience a dying off of the unlucky bacteria while the lucky ones survive to reproduce. The overall population will drop followed by an increase as the bacteria with the variation grow in numbers.

Mathematically I'm sure you could figure out the prevalence of the variation/mutation. What's interesting is at the same time you are also demonstrating evolution at work. It also demonstrates that evolution is random. There's no guarantee that the variation will appear before the population has died off.

As a simple example think of rolling a "population" of three dice. The "toxin" is a hammer that smashes any die that doesn't land with the two dots facing up. If the three die are 4, 5, and 1, then the entire population of three dice is wiped out when the hammer arrives. If the population is 2, 2, and 2, that entire population survives to reproduce.

Mathematically we can predict that given N populations of three dice with the number of dots appearing equally just how many populations have one or more 2s in them. So while it's predictable, it's still random. At any given time there might be no populations with a 2 in them, so the whole species gets wiped out.

Then again, I'm just a layman trying to explain what might be an oversimplified way of looking at this.

sol invictus

18th March 2010, 03:29 PM

Such a bold assertion with absolutely no evidence.

The evidence is in your posts.

Yes, I read what you wrote.

The thing that is not sufficiently clear is how you get from "there is some non-zero probability" to "non-random".

If you read what I wrote, why are you asking that? Do you see anywhere in my post where I even used the term "non-random" or "random"?

And, once again, "predictable" doesn't mean "non-random". If it did, processes where events are independent, identically and uniformly distributed wouldn't be random, as the proportion of successes to total trials can be predicted (with error).

And once again, did you read what I wrote? If so, what are you talking about?

And I don't dispute the evidence. I just dispute the redefinition of widely accepted scientific term in order to get the evidence to conform to your preferred philosophical opinion.

Frankly, I don't give a **** about semantics - and I will not waste my time arguing over the definitions of terms.

So stating predictions in terms of probabilities is now how "non-random" is defined?

Once again....

sol invictus

18th March 2010, 03:49 PM

If I understand you correctly, what I think you are saying is this:

In any given species there are existing variations as well as new mutations. They have some probability of happening. Let's say the variation is a resistance to a toxin that normally kills most people. We know such variations exist in humans because we all don't react the same way to bee stings, snake bites or ingesting poisons.

One way to detect the prevalence of these variations in a species such as bacteria would be to isolate the gene responsible and then sample a buttload of bacteria looking for this gene. That's time consuming and expensive I would think.

Another way to do it is pretty much like the experiment described. Try to grow colonies of the bacteria in the presence of the toxin with other control colonies growing in the "normal" environment. The controls will reproduce and grow at a certain rate. Those colonies in the toxic environment with no resistance will die off. Those colonies with a variation that allows them to survive in the toxic environment will experience a dying off of the unlucky bacteria while the lucky ones survive to reproduce. The overall population will drop followed by an increase as the bacteria with the variation grow in numbers.

Mathematically I'm sure you could figure out the prevalence of the variation/mutation. What's interesting is at the same time you are also demonstrating evolution at work. It also demonstrates that evolution is random. There's no guarantee that the variation will appear before the population has died off.

As a simple example think of rolling a "population" of three dice. The "toxin" is a hammer that smashes any die that doesn't land with the two dots facing up. If the three die are 4, 5, and 1, then the entire population of three dice is wiped out when the hammer arrives. If the population is 2, 2, and 2, that entire population survives to reproduce.

Mathematically we can predict that given N populations of three dice with the number of dots appearing equally just how many populations have one or more 2s in them. So while it's predictable, it's still random. At any given time there might be no populations with a 2 in them, so the whole species gets wiped out.

Then again, I'm just a layman trying to explain what might be an oversimplified way of looking at this.

I'll repeat what I said long ago: if "random" is synonymous with "probabilistic", or if it simply means that some aspects of the process in question are not deterministic or cannot be predicted with 100% certainty, then it is random that smoke detectors go off when smoke pours into a room(most smoke detectors rely on the decay of radioactive atoms, which is about as truly "random" - at least by those definitions - as you can get).

I'm pretty sure that vast majority of people, including scientists, would agree that that statement is totally absurd. Since I'm not very interested in writing a dictionary entry (I'm interested in the science of evolution), I'd rather just avoid the term "random" entirely.

Here are some (very) old posts of mine on that:

So mijo - are smoke detectors random?

You realize this simple question totally demolishes any lame vestige of a point you might have had, right?

You have three choices:

a) you agree with the statement "smoke detectors are random" (totally absurd), or

b) you agree with the statement "smoke detectors aren't random" (then neither is evolution), or

c) you argue that neither statement suffices because smoke detectors have both random and non-random elements, in which case it is crushingly obvious to everyone that the same applies to the vastly more varied and complicated phenomenon of evolution.

Pick your poison, mijo.

sol invictus

18th March 2010, 04:02 PM

Oh, and one more since I was looking back:

No, it is not at all like the smoke detector.

Really?

What I call "random" is that only one out of the twelve populations evolved the ability to metabolize citrate despite the fact that the populations were identical at the beginning of the experiment and the fact that they evolved in the same evirnoment.

Yes, evolution takes time.

Even if all the populations eventually evolved the ability to metabolize citrate, the evolution of that trait would still be random in so far as the populations evolved that trait at different times. I've said it before, and I'll say it again: convergence does not imply non-randomness.

So you think the fact that these bacteria evolved the ability to metabolize citrate when put in a citrate rich environment is random.

That is just as ridiculous as your earlier contention that a smoke detector is random because it relies on the (truly random) radioactive decay of unstable atoms. You are using the word in a way no one else does - including mathematicians. You were unable to supply a single reference that defines the word your way, and you never responded when I checked several references - including a standard text on prob. and stats. - none of which define it your way.

The statement that "evolution is random", full stop, is (to be blunt) stupid.

Vorticity

18th March 2010, 04:29 PM

My long response to this thread:

Although I've been having this argument on these forums for a number of years now, I haven't participated much in this thread, mostly due to my firm belief that it is futile.

There are two groups of people here that have fundamentally different sets of axioms about the meaning of the word random. These two groups will never see eye-to-eye since they are coming from completely different reference frames, from which each of their assertions ("evolution is random", "evolution is non-random") are true by definition.

I'm not going to get into the argument again, except to note my (doubtless controversial) observation that, in these arguments, people (like myself) who have graduate or undergraduate level educations in probability theory and/or statistics (statisticians, mathematicians, mathematical physicists, etc) generally tend to agree that evolution is "random" by the mathematical definition of the word. Everyone else tends to disagree. Doubtless individual exceptions could be found, but this is my observation of the general trend.

For a look at a thread that ended up going the other way, see this thread: http://forums.randi.org/showthread.php?t=50550 in which it is noted (for example):

If Tai said "Mathematically speaking, evolution is a random process.", then few of us would seriously disagree.

My short response to this thread:

KILL IT WITH FIRE!

mijopaalmc

18th March 2010, 04:37 PM

sol invictus-

Your assertion "that eventually, all bacteria in that petri dish - and therefore eventually, in all petri dishes - should have the ability to metabolize citrate" is unfalsifiable, because you can always claim that we simply haven't waited long enough. In fact, you essentially have when you responded, "Yes, evolution takes time" to my observation that not all of the cultures had evolved the cit+ phenotype. The crucial thing that you are seemingly ignoring is that it take an infinite amount of time for you to be certain that all the cultures will have evolved the cit+ phenotype. Thus, in any finite universe and for any finite experiment, there is a non-zero probability that you will observe at least one of the cultures will not have evolved the cit+ phenotype. This is, of course, perfectly consistent with evolution being a random (stochastic) process and completely inconsistent with evolution being a non-random (deterministic) process.

As to your obsession with smoke detectors, it may be absurd to assert that "it is random that smoke detectors go off when smoke pours into a room" without further explanation. It is perfectly acceptable, and possibly preferable, to make such a statement if you wanted explore why, for instance, americium-241 is used instead a nucleide with a longer half-life (e.g., uranium-238). Such an explanation may not be appropriate for a "how things work" talk on smoke detectors at a science museum, but it maybe perfectly suited for a lecture on the non-medical applications of radioactive decay in an advanced undergraduate engineering seminar. In essence, my answer to your question is "it depends on the context", which, while not the most satisfying answer, is the most straight-forward answer I can give.

Vorticity

18th March 2010, 05:02 PM

sol invictus-

Your assertion "that eventually, all bacteria in that petri dish - and therefore eventually, in all petri dishes - should have the ability to metabolize citrate" is unfalsifiable...

But there is a greater issue here.

Even if it were the case that eventually, all petri dish populations develop the ability to metabolize citrate (which would not surprise me), this would in no way prevent evolution from being a random process by the technical definition of the term. Given any stochastic process, you can almost always apply a filter to its random output that yields non-random results.

(See my previous response (http://forums.randi.org/showpost.php?p=4123348&postcount=1177) in this thread which touches upon this issue.)

sol is applying a filter to the output of the "petri dish evolution" stochastic process. Specifically, he's applying the "Does every petri dish develop the ability to metabolize citrate" filter. This may very well yield a non-random result ("Yes"). The fact that this particular filter yields a predictable outcome in no way implies that the original, unfiltered process is non-random. One could just as easily apply the "On which generation does the first dish develop the ability to metabolize citrate?" filter. Is there any doubt that the output of such a filter is a profoundly random variable?

There is more to the definition of what constitutes a random process than just what the long term trend or outcome is, even if that particular final state happens to be non-random.

Vorticity

18th March 2010, 05:07 PM

In essence, my answer to your question is "it depends on the context", which, while not the most satisfying answer, is the most straight-forward answer I can give.

And this is the essence of these arguments.

Recall that this whole thing started way back when Richard Dawkins asserted that "Evolution is the exact opposite of random." Really? The exact opposite of random? There's nothing less random than evolution? Really?

sol invictus

18th March 2010, 05:08 PM

mike3

18th March 2010, 05:09 PM

Any more blind assertions?

Would you care to elaborate on your totally unscientific statement?

Although the really disquieting the terminological debate about is that it show how willing some scientists and science popularizers are to commit the same abuses that creationists do, while deceiving themselves that they are actually helping.

The problem is that the term "random" would seem to "vindicate" or "fuel" criticisms of evolution that criticize it by attacking this "randomness". But I tend to think what many nonscientist evolution critics really mean by the term "random" is "atheist", or more specifically that "God has nothing to do with it", even though of course the theory of evolution is a theory of physics not meta-physics or religion(*), and so it simply doesn't say anything about God having anything to do with it, either confirmation or denial, in the same way as the theory of gravity doesn't say such things. People accept the theory of gravity, yet they don't accept the theory of evolution as much, interesting... (and I'm using that "theory" moniker on both to show that it _doesn't_ mean "unproven guess" in science. That is the colloquial use of the term, not the scientific one. And since it's the scientists who came up with the term "theory of evolution", the scientific usage is the correct one for interpreting that term correctly.) If anything, Gravity is more mysterious than Evolution! We have a good mechanism for the latter but the theory on the former still doesn't give us a mechanism! (And I don't think "string theory" is the right route since there seems to be no good way to test it.)

This I don't get:

NEWTON vs DARWIN.

NEWTON is a household name for his science.
DARWIN is a blasphemer for his science.

WTF? It's science, silly!

(*) YES, I know evolution does not belong to the formal scientific field of physics, but here I mean "physics" in a more general sense as "dealing with the physical world", in contrast to religion and meta-physics and other philosophical areas that deal with "transcendental" questions (e.g. does God exist, does life after death exist, what's the "meaning", if any, to life or existence, etc.).

sol invictus

18th March 2010, 05:14 PM

Even if it were the case that eventually, all petri dish populations develop the ability to metabolize citrate (which would not surprise me), this would in no way prevent evolution from being a random process by the technical definition of the term. Given any stochastic process, you can almost always apply a filter to its random output that yields non-random results.

(See my previous response (http://forums.randi.org/showpost.php?p=4123348&postcount=1177) in this thread which touches upon this issue.)

sol is applying a filter to the output of the "petri dish evolution" stochastic process. Specifically, he's applying the "Does every petri dish develop the ability to metabolize citrate" filter. This may very well yield a non-random result ("Yes"). The fact that this particular filter yields a predictable outcome in no way implies that the original, unfiltered process is non-random. One could just as easily apply the "On which generation does the first dish develop the ability to metabolize citrate?" filter. Is there any doubt that the output of such a filter is a profoundly random variable?

There is more to the definition of what constitutes a random process than just what the long term trend or outcome is, even if that particular final state happens to be non-random.

I refuse to argue over semantics, it is a miserable waste of time. Kill it with fire.

But I will say that I think you are incorrect that most people with training in mathematics would agree with you, that I certainly constitute a counterexample, and you are also incorrect about the "mathematical definition". "Random" is almost never defined, and when it is, the definition doesn't correspond to the one you have in mind ("random variable" might be, but that's something else). I know - I wasted my time and looked in several probability and stats textbooks, as well as at other sources.

When I posted the definitions I found mijo ran away, and he never posted any source that supported his (absurd and idiosyncratic) definition.

mijopaalmc

18th March 2010, 05:31 PM

Your assertion "that eventually, all bacteria in that petri dish - and therefore eventually, in all petri dishes - should have the ability to metabolize citrate" is unfalsifiable, because you can always claim that we simply haven't waited long enough.

So freaking what?

If a statement is unfalsifiable, then it is not scientific.

If you're asserting that evolution as a theory isn't falsifiable, you're just as wrong there as you are here, but that's another topic entirely.

Where did you ever get the idea that I was "asserting" that evolution was unfalsifiable?

Your statement "that eventually, all bacteria in that petri dish - and therefore eventually, in all petri dishes - should have the ability to metabolize citrate" because there is no empirical observation that can possibly falsify it, at least if you want results in finite time.

If you're asserting that this particular specific prediction isn't falsifiable, again, so freaking what? It was confirmed.

If a statement is unfalsifiable, it cannot be confirmed.

Aside from the impossibility of confirming an unfalsifiable statement, the statement "that eventually, all bacteria in that petri dish - and therefore eventually, in all petri dishes - should have the ability to metabolize citrate" was not confirmed. As you will recall, only one culture evolved the cit+ phenotype. You have yet to justify your leap from that single culture to "all bacteria in that petri dish - and therefore eventually, in all petri dishes ".

The crucial thing that you are seemingly ignoring is that it take an infinite amount of time for you to be certain that all the cultures will have evolved the cit+ phenotype. Thus, in any finite universe and for any finite experiment, there is a non-zero probability that you will observe at least one of the cultures will not have evolved the cit+ phenotype. This is, of course, perfectly consistent with evolution being a random (stochastic) process and completely inconsistent with evolution being a non-random (deterministic) process.

The same is true of every experiment ever performed, and every experiment that will ever be performed. That's the nature of science itself, everything is like that.

To cop a phrase from you:

So freaking what?

As to your obsession with smoke detectors, it may be absurd to assert that "it is random that smoke detectors go off when smoke pours into a room" without further explanation. It is perfectly acceptable, and possibly preferable, to make such a statement if you wanted explore why, for instance, americium-241 is used instead a nucleide with a longer half-life (e.g., uranium-238). Such an explanation may not be appropriate for a "how things work" talk on smoke detectors at a science museum, but it maybe perfectly suited for a lecture on the non-medical applications of radioactive decay in an advanced undergraduate engineering seminar. In essence, my answer to your question is "it depends on the context", which, while not the most satisfying answer, is the most straight-forward answer I can give.

You're chosen option c):
c) you argue that neither statement suffices because smoke detectors have both random and non-random elements, in which case it is crushingly obvious to everyone that the same applies to the vastly more varied and complicated phenomenon of evolution.

Uh...no!

As far as I have argued there are no non-random (deterministic) elements in evolution, and, even if there were, having a random (stochastic) element makes the whole process random (stochastic).

sol invictus

18th March 2010, 05:44 PM

If a statement is unfalsifiable, then it is not scientific.

Nonsense. If a theory is unfalsifiable it is unscientific. The same obviously does not apply to statements, because nearly all predictions made by any scientific theory you care to name are unfalsifiable.

Your statement "that eventually, all bacteria in that petri dish - and therefore eventually, in all petri dishes - should have the ability to metabolize citrate" because there is no empirical observation that can possibly falsify it, at least if you want results in finite time.

But there is an observation that can confirm it, and that's exactly what happened.

If a statement is unfalsifiable, it cannot be confirmed.

Utter nonsense. Laughable nonsense in fact, since we are in the process of discussing an explicit counterexample.

Statement: the bacteria in this petri dish will eventually mutate and fixate the ability to metabolize citrate.
Experimental Result: the bacteria in that petri dish mutate and fixate the ability to metabolize citrate.

Statement confirmed.

Uh...no!

Uh....yes!

mijopaalmc

18th March 2010, 06:00 PM

Nonsense. If a theory is unfalsifiable it is unscientific. The same obviously does not apply to statements, because nearly all predictions made by any scientific theory you care to name are unfalsifiable.

Examples?

But there is an observation that can confirm it, and that's exactly what happened.

No, it didn't, at least it didn't confirm the state that you made in the post that you keep asking me if I read.

Utter nonsense. Laughable nonsense in fact, since we are in the process of discussing an explicit counterexample.

Statement: the bacteria in this petri dish will eventually mutate and fixate the ability to metabolize citrate.
Experimental Result: the bacteria in that petri dish mutate and fixate the ability to metabolize citrate.

Statement confirmed.

That's not the statement that you made.

You said:

More specifically, the theory predicts that eventually, all bacteria in that petri dish - and therefore eventually, in all petri dishes - should have the ability to metabolize citrate (modulo a few details, like that said ability doesn't come at a cost so significant it cancels out the benefit).

This statement (which you claim is a prediction of evolution) would have been confirmed had all of the colonies evolved the cit+ phenotype. Since only one did, the evidence from this experiment is insufficient to confirm what you claim evolution would predict.

Uh....yes!

No! Since I have said that I do not consider any of evolution's constituent processes to be non-random, how exactly does (3) apply?

sol invictus

18th March 2010, 06:13 PM

Examples?

Nearly every statement in any scientific theory ever. For example, general relativity predicts that if the universe is homogeneous and isotropic, it will have one of three final fates. That's unfalsifiable - the universe is not homogeneous and isotropic, and two of those fates take infinite time.

This statement (which you claim is a prediction of evolution) would have been confirmed had all of the colonies evolved the cit+ phenotype. Since only one did, the evidence from this experiment is insufficient to confirm what you claim evolution would predict.

"Conversing" with you is an utter waste of time.

That statement is obviously confirmable by exactly the same reasoning - the experiment could have resulted in all 12 petri dishes fixating that trait.

Moreover, the statement that all 12 colonies will eventually fixate is only one of several closely related predictions the theory makes. I wouldn't have thought it necessary to spell out the rest to any sentient life-form, but I guess I was wrong. Here are some of them:

eventually, all bacteria in petri dish 1 should have the ability to metabolize citrate

eventually, all bacteria in petri dish 2 should have the ability to metabolize citrate

eventually, all bacteria in petri dish 3 should have the ability to metabolize citrate

eventually, all bacteria in petri dish 4 should have the ability to metabolize citrate

eventually, all bacteria in petri dish 5 should have the ability to metabolize citrate

eventually, all bacteria in petri dish 6 should have the ability to metabolize citrate

eventually, all bacteria in petri dish 7 should have the ability to metabolize citrate

eventually, all bacteria in petri dish 8 should have the ability to metabolize citrate

eventually, all bacteria in petri dish 9 should have the ability to metabolize citrate

eventually, all bacteria in petri dish 10 should have the ability to metabolize citrate

eventually, all bacteria in petri dish 11 should have the ability to metabolize citrate

eventually, all bacteria in petri dish 12 should have the ability to metabolize citrate

eventually, all bacteria in petri dishes 1 and 2 should have the ability to metabolize citrate

eventually, all bacteria in petri dishes 1 and 3 should have the ability to metabolize citrate

....

No! Since I have said that I do not consider any of evolution's constituent processes to be non-random, how exactly does (3) apply?

Kill it with fire. Now.

Uncayimmy

18th March 2010, 08:00 PM

I'll repeat what I said long ago: if "random" is synonymous with "probabilistic", or if it simply means that some aspects of the process in question are not deterministic or cannot be predicted with 100% certainty, then it is random that smoke detectors go off when smoke pours into a room(most smoke detectors rely on the decay of radioactive atoms, which is about as truly "random" - at least by those definitions - as you can get).

I'm pretty sure that vast majority of people, including scientists, would agree that that statement is totally absurd. Since I'm not very interested in writing a dictionary entry (I'm interested in the science of evolution), I'd rather just avoid the term "random" entirely.

Here are some (very) old posts of mine on that:

Unfortunately, you can't avoid the term random. Unfortunately, language evolved to where words have multiple meanings. Unfortunately, if you're going to discuss things like this with non-scientists on public discussion boards, you're going to have to find a way to deal with it without getting your panties in a bunch.

All you're doing is setting up a scenario where the contextual meaning of the word matches what you want it to mean while arguing that the other guy is wrong for doing the same thing. We could make a daily game show out of doing this with words in the dictionary that have more than one definition. Hell, we could do with some words that have only one definition listed.

But, hey, if you want to ignore my attempt at checking for understanding to rant about your love-hate relationship with the word random, go for it.

Wowbagger

18th March 2010, 08:41 PM

I'm not going to get into the argument again, except to note my (doubtless controversial) observation that, in these arguments, people (like myself) who have graduate or undergraduate level educations in probability theory and/or statistics (statisticians, mathematicians, mathematical physicists, etc) generally tend to agree that evolution is "random" by the mathematical definition of the word. It depends on what definition of "random" you are using, and that was the original point of this thread!

It is perfectly valid to say that evolution is random, as long as you mean it in a way this really is applicable to evolution.

Examples of inapplicable usage includes "blind chance" and special appeals to quantum fluctuations. There are probably others.

If "stochastic" can be called "random" also seems to depend on how you view it.

I prefer to avoid using both "random" and "non-random", when describing evolution, to avoid these things. Mutations are functionally indifferent, natural selection is a fitness-based filtering process, and the whole process obviously has a lot of predictive power.

But, that still won't shut everyone up, I'll bet.

sol invictus

18th March 2010, 09:24 PM

Unfortunately, you can't avoid the term random.

I can and do avoid using it in situations like this.

Unfortunately, language evolved to where words have multiple meanings. Unfortunately, if you're going to discuss things like this with non-scientists on public discussion boards, you're going to have to find a way to deal with it without getting your panties in a bunch.

I have no problem dealing with it under ordinary circumstances. But when a thread has gone on for two years, with some participants having been involved in the same debate in other threads and for for several years before that... something is deeply, deeply wrong.

All you're doing is setting up a scenario where the contextual meaning of the word matches what you want it to mean while arguing that the other guy is wrong for doing the same thing. We could make a daily game show out of doing this with words in the dictionary that have more than one definition. Hell, we could do with some words that have only one definition listed.

I have no idea what you're talking about.

But, hey, if you want to ignore my attempt at checking for understanding to rant about your love-hate relationship with the word random, go for it.

What you said in your previous post was more or less fine. It's fine to say that "evolution is random, meaning that..." and fill in the ... with examples, illustrations of how some things are predictable and some aren't, etc. - just as you did. What is not fine is to assert "evolution is random", full stop. That gives nearly everyone the wrong idea. And if you define "random" in the non-standard way mijo proposes, then you can immediately see that every process in the physical world is random - making the statement "evolution is random" true but tautological (i.e. logically implied by "evolution is a process in the physical world").

Words are labels for reality. Labels are really boring. We might as well argue over whose handwriting is a more accurate description of the world.

Earthborn

18th March 2010, 10:03 PM

What is not fine is to assert "evolution is random", full stop. That gives nearly everyone the wrong idea.Good thing no one appears to be doing that, then. The discussion started because some have argued that "evolution is the exact opposite of random" and that is just not true.

And if you define "random" in the non-standard way mijo proposes, then you can immediately see that every process in the physical world is random - making the statement "evolution is random" true but tautological (i.e. logically implied by "evolution is a process in the physical world").Just because the term "random" may apply to all physical processes does not necessarily mean the term is tautological. A tautology is something that is true by definition, and can't be logically untrue. If scientists in the 19th century had discovered that at a deep fundamental level all physical processes were completely deterministic, it would have meant that all physical processes are non-random. Physical processes are not random by definition; they are likely random because we discovered them to be.

sol invictus

18th March 2010, 10:13 PM

Good thing no one appears to be doing that, then.

Except those that are.

The discussion started because some have argued that "evolution is the exact opposite of random" and that is just not true.

It's as true as "evolution is random".

Just because the term "random" may apply to all physical processes does not necessarily mean the term is tautological. A tautology is something that is true by definition, and can't be logically untrue.

Evolution is a theory about processes that take place in the real world. So if your definition of "random" makes all such processes random, as mijo's does, then the statement is a tautology.

Why do I need to explain things like this? Why do I bother?

Physical processes are not random by definition

How can you possibly claim that? It obviously depends on your definition, and they are by mijo's definition. By a more sensible definition, we actually don't know - we certainly did not "discover" them to be as you wrongly assert. Quantum mechanics is probably deterministic... but that's another topic.

Wowbagger

18th March 2010, 10:24 PM

Good thing no one appears to be doing that, then. The discussion started because some have argued that "evolution is the exact opposite of random" and that is just not true.It depends on how you define "random". In many cases, it is perfectly valid to say that "evolution is the exact opposite of random".

For example: Natural Selection is an algorithm. Therefore, it is the exact opposite of completely random (as in dice-rolling) chance and "happy accidents".

mijopaalmc

18th March 2010, 10:33 PM

And if you define "random" in the non-standard way mijo proposes, then you can immediately see that every process in the physical world is random - making the statement "evolution is random" true but tautological (i.e. logically implied by "evolution is a process in the physical world").

The bold is one of the most persistent and aggravating lies told by those who argue that evolution in non-random (right behind "no reputable scientist would say that evolution is a random process" and "mijopaalmc is saying 'evolution is random full stop").

As to the definition and usage of "random", its synonymy with "stochastic" and its application to evolutionary biology, the whole discussion is that it is pretty much a nonstarter, because the participants won't agree on the meaning of the terms being discussed. I have in the past granted that "random" can and (most often in nonacademic discourse) does mean "[o]f or relating to an event in which all outcomes are equally likely (http://www.answers.com/random)". There is ample evidence from many dictionaries (see: e.g., The American Heritage Dictionary, def. 3 (http://www.answers.com/random); Merriam-Webster Online, def. 2b (http://www.merriam-webster.com/dictionary/random%5B2%5D); The Oxford English Dictionary, def. 1b (http://dictionary.oed.com/cgi/entry/50197140)). However, most dictionaries also list a definition or usage of "random" as "[o]f or relating to a type of circumstance or event that is described by a probability distribution (http://www.answers.com/random)" (see: e.g., The American Heritage Dictionary, def. 2 (http://www.answers.com/random); Merriam-Webster Online, defs. 2a (http://www.merriam-webster.com/dictionary/random%5B2%5D); The Oxford English Dictionary, Special Uses (http://dictionary.oed.com/cgi/entry/50197140)). It is interesting to note that, with the exception of the The Oxford English Dictionary, the latter definition actually precedes the former, suggesting that it is the primary definition of "random", and the OED actually lists some "Special Uses" of "random" that contradict in general definition provided therein, implying that "random" does mean something more than "equiprobable". In fact, the latter definition coincides nicely with the definition of "stochastic" as "[ı]nvolving or containing a random variable or variables (http://www.answers.com/stochastic)" and "[ı]nvolving chance or probability (http://www.answers.com/stochastic)" (see: e.g., The American Heritage Dictionary, def. 2 (http://www.answers.com/stochastic); Merriam-Webster Online, defs. 1 & 2 (http://www.merriam-webster.com/dictionary/stochastic); The Oxford English Dictionary, def. 2a (http://dictionary.oed.com/cgi/entry/50238045)).

The specialist literature presents a even more explicit case for the synonymy of "random" and "stochastic". There are many books (http://books.google.com/books?q=%22stochastic+or+random%22+|+%22random+or+ stochastic%22&btnG=Search+Books) and scholarly articles (http://scholar.google.com/scholar?q=%22stochastic%20or%20random%22%20|%20%22 random%20or%20stochastic%22&sa=N&hl=en&tab=ps) that use the phrases "random (or stochastic)" or "stochastic (or random)". The CRC Encyclopedia of Mathematics explicitly states, "Stochastic is synonymous with 'random'." The National Research Council similarly glosses "stochastic" in its guideline for teaching and research:

Inspired by biology: from molecules to materials to machines (http://books.google.com/books?id=WxQhVsraqBQC&pg=PA154)

Opposite of a deterministic process in probability theory. Instead of dealing only one possible "reality" for how a process might evolve under time (as is the case with the solution to an ordinary differential equation), in a stochastic or random process there is some indeterminacy in its future evolution described by a probability distribution. This means that even if the initial condition (or starting point) is known, there are many possibilities the process might go to, but some paths are more probable and others less.

Bio 2010: transforming undergraduate education for future research biologists (http://books.google.com/books?id=w4r3Q28KcNsC&pg=PA45)

In a stochastic process,individual outcomes cannot be predicted with certainty. Rather, they are determined randomly according to a probability distribution that arises from the underlying mechanisms of the process.

Finally, there are number of evolutionary biologists who explicitly state that natural selection is a stochastic process:

Selection: The Mechanism of Evolution (http://books.google.com/books?id=sdllt_xU-cYC&pg=PA93)

In every generation better-adapted individuals will bee more likely to survive and reproduce. This is only a tendency, however, not a deterministic rule. A snail living in an English hedgerow is less likely to be eaten of its shell is striped rather than plain.But it is not very likely to survive in any case; it may be eaten by a shrew, or die of heatstroke or starvation; it may even be eaten by a bird after all. Selection is a process of sampling. The variation of characters among individuals ensures that the sample that reproduces is a biased sample of the population as a whole, but its composition cannot be precisely specified in advance. But there is nobody responsible for selecting snail at the bottom of hedgerow, and no individuals, no matter how well-endowed has any guarantee of success, only a greater or lesser chance. Richard Lewontin once prefaced a lecture on this topic with a quote from Ecclesiastes: the race is not alway to the swift, nor the battle to the strong; but time and chance happen to both.

The nature of evolution as sampling implies that evolution is a stochastic process that is subject to sampling error. The composition of a population at any point in time will be determined by three factors. One is historical, the composition of the generation from which it descends. The second is selection, which tends to increase some kinds of individual and decrease others. The third is chance. The actual composition of the population will inevitably differ from what we expected based on descent and selection, because the life of each individual is a historically unique succession of events who eventual outcome is influenced by a multitude of factors. The next generation is formed in a stochastic, or probabilistic, fashion from the success and failure of many such lives. We may be able to predict its average properties with some assurance, but its composition will fluctuate to a greater or lesser extent in ways we cannot predict or account for.

Toward a New Philosophy of Biology: Observations of an Evolutionist (http://books.google.com/books?id=5f5kg_w2dJ4C&pg=PA110)

Selection is often described as a deterministic process, indeed sometimes even as a teleological process, because it seems to result in long-term evolutionary trends. These designations are, however, quite misleading. First of all, a close analysis of long-term evolutionary trends has shown almost invariably that they are actually quite irregular and often even terminated by reversals. Also, how could a process be deterministic in which there is no actual continuity because the genes of a population are returned in each generation to the common gene pool, and are thoroughly reassembled, with an entirely new start being made through the random production of new zygotes.

The importance of chance during evolution has been stressed by certain authors for more than 100 years (Mayr 1963:204). As early as 1871 Gulick insisted that the differences among snail populations on Oahu Island in the Hawaiian Islands were due to random variation and not to selection. Since that time no one has stressed the role of chance factors more emphatically than Sewall Wright. Chance operates at every level of the process of reproduction, from crossing-over to the survival of newly formed zygotes (Mayr 1962). This includes the locus at which mutations occur, the location of chiasmata involved in crossing-over, the segregation of chromosomes during the reduction the survival of the millions or billions of gametes, the meeting of two gametes of opposite sex prior to fertilization, and finally the untold interactions of a zygote with its environment (in the widest sense of the word). There is also genetic drift in all of its forms, particularly significant in small populations, and all the effects of linkage. There is also genetic drift in all of its forms, particularly significant in small populations, and all the effects of linkage. (Beatty 1984; 1987). Chance is also introduced by the phenomenon of pleiotropy. If a gene has multiple expressions, it will be selected for the most important of these,and other expressions of the gene will be carried along incidentally.

The large number of stochastic processes in populations of finite size, as well as the constraints which operate during selection, prevent selection from prevent selection from ever being a deterministic process. Rather, it must be remembered at all times that selection is probabilistic. This is true even for the success of the zygote. Each individual encounters in its environment numerous unpredictable adverse forces, such as catastrophes, epidemics, and unexpected encounters with enemies in which the outcome is largely probabilistic.

Finally, survival may depend on aspects of population structure. A certain genotype may have a high survival probability in a small founder population, while it is clearly inferior in a very large, widespread population.

It should be evident from this discussion how misleading the picture of natural selection is which some authors have. A careful reading of Darwin's version shows that his concept of natural selection was far more mature than that of most of his opponents.

Nevertheless, even he did not fully appreciate the power of the constraints and of chance. The modern concept of natural selection has been rather essentialist-deterministic philosophers. And yet who could question that the study of natural selection is a legitimate component of science? A philosopher thus has three choices: he can close his eyes to the existence of natural selection, or he can claim that, lacking the attributes of the phenomena of inanimate nature, it has to be excluded from science, or, finally, he can revise his view of what science is and enlarge his vocabulary and inventory of principles. and enlarge his vocabulary and inventory of principles.

Uncayimmy

18th March 2010, 10:49 PM

It depends on how you define "random". In many cases, it is perfectly valid to say that "evolution is the exact opposite of random".

For example: Natural Selection is an algorithm. Therefore, it is the exact opposite of completely random (as in dice-rolling) chance and "happy accidents".

So, what do programmers write to simulate dice rolls? ;)

I think one of the downfalls of the Internet and especially discussion boards is that people faced with simple terms or phrases describing a body of knowledge for which hundreds of thousands of words are needed to fully explain will write literally hundreds of thousands of words as to why their particular simple terms or phrases are better than the other guy's. The obvious conclusion is that we need a new word.

Wowbagger

18th March 2010, 11:01 PM

The bold is one of the most persistent and aggravating lies told by those who argue that evolution in non-random (right behind "no reputable scientist would say that evolution is a random process" and "mijopaalmc is saying 'evolution is random full stop").Well, I for one, think your use of "random" has its uses. Perhaps even in describing some parts of evolution. Though, probably not the whole thing.

If "stochastic" is supposed to imply "non-predictable", then clearly the term does not match the entire process of Evolution via Natural Selection. Some parts and aspects of it might be more stochastic and/or unpredictable, than others. It depends on which part or aspect you are looking at.

Though, in the end, I suspect that thinking of Evolution in terms of "randomness" is not going to be terribly useful to evolutionary biologists. It might for statisticians who do not need to iron out any of the empirical details of the process. But, to the biology expert who is bent on unraveling as much as possible: The fewer random elements, the better.

Wowbagger

18th March 2010, 11:04 PM

So, what do programmers write to simulate dice rolls? ;) In computers, it would be a simulation, not an actual dice roll. Although there is always work being done to try to introduce a "true random number generator" for computers, we do have to put up with pseudo-random numbers, for now.

The obvious conclusion is that we need a new word.Evolution is... supercalafragalisticexpialadoshus!

Uncayimmy

18th March 2010, 11:11 PM

In computers, it would be a simulation, not an actual dice roll. Although there is always work being done to try to introduce a "true random number generator" for computers, we do have to put up with pseudo-random numbers, for now.
You haven't seen my version. For each roll requested, it sends an e-mail back to me, and I roll the dice and respond accordingly. Games run a bit slowly, but randomness is assured.

sol invictus

19th March 2010, 05:38 AM

<intellectually dishonest semantic polemics snipped>

This:

I agree that random is a slippery term that's best avoided. However, it seems to me that as far as processes are concerned, there is no logical room left after we include deterministic and random factors. That makes random a synonym for nondeterministic. Am I missing something?

Yes - the way the term "random" is used, it is not synonymous with "non-deterministic". "Random" often implies "flat distribution", "directionless", or "equiprobable". As one example, consider the lottery where the numbers are drawn from bouncing balls. Is that process "random"? Certainly most people would agree that it generates random numbers, and yet the process itself might be deterministic.

Another example is suggested by your dictionary definition. Consider a measurement in a physics experiment, say of the length of some object. The length is not precisely defined due to quantum fluctuations, and therefore the result of the measurement is, strictly speaking, non-deterministic. And of course in addition there are the usual types of measurement errors, which may or may not be deterministic.

And yet, no one in their right mind would say that the results of measuring something with a tape measure are "random". They might say the errors are random (even though they may be deterministic), but they would never say the result is. Why not? Because the result has a non-zero mean and small fluctuations around that mean. We don't usually characterize distributions like that, distributions that are fairly sharply peaked around some non-zero value, as "random".

I presume we agree that a stochastic process is one that has some random generators.

"Stochastic" is close to synonymous with non-deterministic, but carries a slightly different connotation. In physics it's often used for systems in which the non-deterministic element is some kind of noise, thermal or otherwise. More generally it usually implies the presence of some kind of direction, force, or tendency, one that is perturbed but not destroyed by the noise. I'd say it's the best term to describe evolution.

mijopaalmc

19th March 2010, 12:24 PM

Earthborn

19th March 2010, 12:59 PM

It depends on how you define "random".Yes, pretty much everything depends on how you define it.

For example: Natural Selection is an algorithm.Depends on how you define "algorithm". If you define it meaningfully let's say (http://en.wikipedia.org/wiki/Algorithm) as "an effective method (http://en.wikipedia.org/wiki/Effective_method) for solving a problem using a finite sequence of instructions." then no. It isn't.

Therefore, it is the exact opposite of completely random (as in dice-rolling) chance and "happy accidents".Even if natural selection was an algorithm, it would not mean it is "the exact opposite of random". Algorithms can use random elements.

Wowbagger

19th March 2010, 01:13 PM

Every word really depends on how you define it, if you think about it.

Depends on how you define "algorithm". If you define it meaningfully let's say (http://en.wikipedia.org/wiki/Algorithm) as "an effective method (http://en.wikipedia.org/wiki/Effective_method) for solving a problem using a finite sequence of instructions." then no. It isn't.Well, it is a farily finite sequence of steps, though in this case, it happens to occur naturally.

It would not be "solving a problem", except (perhaps) in how reproductive success could be abstracted as a "problem".

Snowflakes also build according to a naturally occuring algorithm, that is a finite series of steps, though it is more difficult to say that they are "solving a problem".

Even if natural selection was an algorithm, it would not mean it is "the exact opposite of random". Algorithms can use random elements.Yes, but the steps would not be random. That is what I mean.

The predictive power of evloution rests on the idea that the steps of natural selection are not random, even if some of the elements in it, such as the units it selects from, are.

sol invictus

19th March 2010, 01:24 PM

Why don't you actually respond to evidence that I provided that "stochastic" and "random" are used as synonyms by the very people whom you insist do not use them as such?

The only true intellectual dishonesty here is your own continued willful ignorance of the fact that "stochastic" is used by scientist to mean what I have said it means.

1) If "random" means ""[o]f or relating to a type of circumstance or event that is described by a probability distribution", then all processes in the physical world are random, and the statement "Darwinian evolution is random" is a tautology.

2) The dictionary definitions you gave include another definition - that outcomes are equiprobable - which does not apply to evolution. Therefore if you insist on using it, you must qualify the term "random" to make it clear which definition you mean. If the options are 1) or 2), the statement "evolution is random" is either tautological or false.

3) Technical books may define "random variable" or "random process", but they rarely if ever define "random".

4) Every time a substantive issue arises in these threads, such as your false assertion that unfalsifiable statements cannot be confirmed, you lose the argument and resort to the same tactic: you retreat back to semantics. It's extremely boring, and I've had enough of it.

mijopaalmc

19th March 2010, 01:44 PM

Wowbagger-

The issue here is that, even if an allele has a selective advantage, the odds against its eventually becoming fixed in a population are enormous. For instance, if an allele allows individuals possessing it to produce on average 1.000001 offspring for every offspring produced by individuals not possessing the allele, the probability that the allele* will become fixed is ~.000002, or 1 in 500000, hardly an efficient process.

For calculations of fixation probabilities see Haldane (1927) (http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=2024552) and Kimura (1974) (http://www.pnas.org/content/71/9/3377.full.pdf).

For the distributions of selective advantages in natural populations see Nielsen (2003) (http://mbe.oxfordjournals.org/cgi/reprint/20/8/1231.pdf).

*despite being more likely to become fixed than the disadvantageous allele that allele allows individuals possessing it to produce on average .999999 offspring for every offspring produced by individuals not possessing the allele

sol invictus

19th March 2010, 01:54 PM

Wowbagger-

The issue here is that, even if an allele has a selective advantage, the odds against its eventually becoming fixed in a population are enormous.

Wrong as usual. The odds are 1.

For instance, if an allele allows individuals possessing it to produce on average 1.000001 offspring for every offspring produced by individuals not possessing the allele, the probability that the allele* will become fixed is ~.000002, or 1 in 500000, hardly an efficient process.

If the selective advantage of a mutation is tiny, obviously the odds any given instance of it will end up fixed are small, at least in a large population. But in a fixed population model taking into account mutation, the allele is certain to be fixed eventually (unless something alters the genome in such a way that it ceases to exist, or so that its rate of mutation goes to zero or its advantage vanishes).

mijopaalmc

19th March 2010, 02:29 PM

Wrong as usual. The odds are 1.

No, they aren't. This has been know for the past 36 years.

If the selective advantage of a mutation is tiny, obviously the odds any given instance of it will end up fixed are small, at least in a large population. But in a fixed population model taking into account mutation, the allele is certain to be fixed eventually (unless something alters the genome in such a way that it ceases to exist, or so that its rate of mutation goes to zero or its advantage vanishes).

Merely reasserting a falsehood does not make it true. Not only is your assertion contradicted by theory (http://www.pnas.org/content/71/9/3377.full.pdf), it is also contradicted by experiment (http://mbe.oxfordjournals.org/cgi/reprint/14/9/914.pdf).

sol invictus

19th March 2010, 03:06 PM

No, they aren't.

Yes, they are. Obviously so.

This has been know for the past 36 years.

Something has been known for the past 36 years, but you've badly misunderstood what it is.

Merely reasserting a falsehood does not make it true. Not only is your assertion contradicted by theory (http://www.pnas.org/content/71/9/3377.full.pdf)

The results of that paper (which I'm familiar with) are fully consistent with what I said, and in fact with a small (and obvious) extension contradict what you asserted.

it is also contradicted by experiment (http://mbe.oxfordjournals.org/cgi/reprint/14/9/914.pdf).

This is especially rich. A few posts back you were claiming that precisely this point is unfalsifiable. Now you are claiming it is falsified.

jimbob

19th March 2010, 03:54 PM

Please let's cut out the pointless insults.

I take issue with several points in the following post.

Firstly, the bit where I think we have common ground:

I would say that over "moderate" timescales, with "sufficient" populations, in environments with constant section pressures, then the effect of any randomness would be minimised, or could be ignored.

This is the situation that is easiest to comprehend, and is used most often in discussing how evolution works. Unfortunately it is not appropriate when discussing what has happened in the history of life on Earth, which is of significant interest in the context of evolution. This is because over long enough timescales, catastrophic events completely alter the environment. Even if you ignored these, individual organisms are co-evolving, and constantly altering the environment for other organisms in the ecosystem

Again, we don't notice a lot of this because it is microscopic, but the "battle" between pathogens and immune systems is certainly *not* predictable, except in the pretty trivial observation that one or another will get the upper hand for a while (and this might sometimes wipe out one set of organisms).

Post hidden for brevity below:

OH MY GOD, IT'S ALIVE!!

What the heck....

I see your level of comprehension of this discussion hasn't changed at all.

"Evolution is predictable in the long run" - what does that mean to you? To me, it means that certain things can be reliably predicted in the long run (weird that it would mean that, huh?). That paper doesn't affect that conclusion.

For example: bacteria in petri dishes with some citrate. At the start of the experiment, none of the bacteria can metabolize citrate. The ability to metabolize citrate would be a strong advantage given the environment. So, let multiple colonies in multiple petri dishes live and reproduce for a long time.

Again: the claim at issue is that the theory of evolution by natural selection is predictive in the long term; that is, that it can predict some results of some experiments. So let's apply it to this. According to the theory, there is some non-zero probability per generation that a bacterium will mutate in such a way that it can metabolize citrate. Moreover, the theory tells us that that bacterium and its descendants will have an advantage in the sense that they will reproduce more rapidly than bacteria without that ability. More specifically, the theory predicts that eventually, all bacteria in that petri dish - and therefore eventually, in all petri dishes - should have the ability to metabolize citrate (modulo a few details, like that said ability doesn't come at a cost so significant it cancels out the benefit).

In principle the theory will also tell us how long we need to wait on average before that happens in a given petri dish, but to extract that prediction requires knowledge of the probability I mentioned, and that's hard to estimate (although one can certainly try). Regardless, the above is a definite, solid prediction for the long term, and we can test it.

So someone tested it. Guess what the result was (after a decade or so)?

"Evolution is predictable in the long run" - what does that mean to you? To me, it means that certain things can be reliably predicted in the long run (weird that it would mean that, huh?). That paper doesn't affect that conclusion.

But that is not what the paper is saying, the authors are saying that this experiment is support for the idea that if one could "rerun the tape of evolution" one would get (significantly) different outcomes. How is this "predictable"? The experiment also supports my point that evolution is less predictable over long timescales than short timescales, as there is more chance that an important random event will alter the outcomes. In the case of citrate+ metabolism, nothing interesting happened for 15,000 generations, and nothing *observable* happened for the first 30,000 generations.

http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf

More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

At its core, evolution involves a profound tension between random and deterministic processes. Natural selection works systematically to adapt populations to their prevailing environments. However, selection requires heritable variation generated by random mutation, and even beneficial mutations may be lost by random drift. Moreover, random and deterministic
processes become intertwined over time such that future alternatives may be contingent on the prior history of an evolving population.

These accidents of history may even determine the survival or extinction of entire lineages, given the capricious and sudden nature of some environmental changes.

Stephen Jay Gould maintained that these historical contingencies make evolution largely unpredictable. Although each change on an evolutionary path has some causal relation to the circumstances in which it arose, outcomes must eventually depend on the details of long chains of antecedent states, small changes in which may have enormous long-term repercussions.

I read the bit below as being the position that you are taking.

Simon Conway Morris countered that natural selection constrains organisms to a relatively few highly adaptive options, so that ‘‘the evolutionary routes are many, but the destinations are limited’’ (16). He and others point to numerous examples of convergent evolution as evidence that selection finds
the same adaptations despite the vagaries of history. Evolution may thus be broadly repeatable, and multiple replays would reveal striking similarities in important features, with contingency mostly confined to minor details

Again: the claim at issue is that the theory of evolution by natural selection is predictive in the long term; that is, that it can predict some results of some experiments. So let's apply it to this. According to the theory, there is some non-zero probability per generation that a bacterium will mutate in such a way that it can metabolize citrate. Moreover, the theory tells us that that bacterium and its descendants will have an advantage in the sense that they will reproduce more rapidly than bacteria without that ability. More specifically, the theory predicts that eventually, all bacteria in that petri dish - and therefore eventually, in all petri dishes - should have the ability to metabolize citrate (modulo a few
details, like that said ability doesn't come at a cost so significant it cancels
out the benefit).

Citrate+ metabolism was (virtually) unknown in E.Coli, so much so that the inability to metabolise citrate+ was considered to be an identifying feature of E.Coli. This was a very rare event, in fact the paper calculates the upper bound for this mutation rate:

With no more than three mutations among the 8.4 x 1012 cells tested here and in the third replay experiment, the upper bound on the ancestral mutation rate to Cit+ is 3.6 x 10-13 per cell per generation (Fig. 4). To the best of our knowledge, this value is the lowest upper bound ever reported for a mutation rate that has been experimentally measured. It is also probably far too high because no mutations were actually observed for the ancestor, nor were any found among another 9.0 x 1012 cells of 60 clones sampled through 15,000 generations; and because some cell turnover and other DNA activity probably occurred during the many days that plates were incubated.

You are missing out the fact that *eventually* this trait would evolve, if the population hadn't been wiped out in the meantime, or the environment hadn't changed, or if another incompatible trait hadn't evolved first. This is also a very simple ecosystem. With more different types of interactions, and with longer time, there would be more scope for more random events to alter the course of evolution.

As soon as you are talking about real organisms outside laboratory environments, you can make predictions, but over sufficiently long timescales apart from "the organsims will be adapted to their environment" the predictions won't be valid. Not because of any inaccuracy in your initial data, but because subsequent random events will have affected the course of evolution, and the whole ecosystem.