Ben Stein vs. Darwin: The Movie

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Re: Ben Stein vs. Darwin: The Movie

Postby JoshuaZ » Sat Mar 08, 2008 4:14 am UTC

Malice wrote:
I'm not saying that's what this documentary did, and I'm not saying Creationists are correct. But I do think that it does your own argument, and the culture in general, at risk to dismiss somebody else's criticism as "dogmatic nonsense" put together by idiots.

A true follower of science should welcome others' critical evaluation of current theory.


Up to a point. This is a set of questions that have been settled for more than a hundred years. In 1800 most scientists believed in a global flood and a young earth. By 1900 no one did. That's because the evidence convinced them. Similar comments apply to evolution itself; initially no one accepted it then everyone did. The testable variants of creationism have all been found to insufficient multiple times over; it is from the perspective of scientists largely a waste of time to examine them. There are of course very difficult questions about evolution still open which are vigorously debated such as the roles of neutral drift and genetic bottlenecks in speciation. However, from a scientific perspective this isn't very different than dealing with geocentrists (and yes there are people who are still geocentrists, mainly due to their interpretation of the bible. It is easy to find them online). And note that no intelligent design proponents or such are engaging in actual "critical evaluation" they are repeating tired arguments that have been repeated many times before. Irreducible complexity for example is an idea the basic form of which existed over a hundred years ago. They've simply moved the argument to a smaller scale and thrown in more complicated terminology.

Finally, there's one point about this movie that isn't getting sufficient attention; intelligent design proponents have repeatedly claimed that they are not religiously motivated and have attacked and slimed the judge in the Dover trial who decided otherwise. Yet here they come with a movie which claims that they are being religiously persecuted and which aims itself at Christian schools as part of the target audience. The level of forked-tonguedness here is staggering. Scientists have no good reason to engage in dialogue with people who are repeating old arguments in a manifestly bad-faith fashion.

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Re: Ben Stein vs. Darwin: The Movie

Postby EsotericWombat » Sat Mar 08, 2008 5:08 am UTC

EXACTLY the sort of argument that the ID crowd would somehow spin as religious persecution.

There's a part of me that thinks that if we're going to be accused of persecuting those who ascribe to ID no matter what, perhaps we should get on with the persecutin'.

Though I suppose that's not wise
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Re: Ben Stein vs. Darwin: The Movie

Postby Enneract » Sat Mar 08, 2008 7:25 am UTC

22/7 wrote:
Enneract wrote:In principle, yes - however, religious based arguments are, at the core, nothing more than dogmatic nonsense, in terms of science.
Ok, then. Use science to prove that 100% of all "religious based arguments" are "nothing more than dogmatic nonsense". Completely disregarding a stance because it disagrees with your stance is, at it's very core, unscientific. So is this
Enneract wrote:Evolutionary theory is pretty bloody obvious, as a framework for the development of knowledge - even if 99% of the specific information that we have deduced turns out to be incorrect, the overall concept of speciation change over time due to survival of the fittest is going to be an accurate basis upon which every other biological concept can be built. Simply throwing everything away for the sake of 'goddidit', over any small point which creationists attempt to niggle at is silly... even if that one point is wrong, it does not 'endanger' the theory as a whole.
If the point is wrong, the point is wrong. It doesn't matter who first declares that the point is wrong.



what?

Sorry, but any argument which relies on total disregard of every speck of physical evidence, and a blind assumption to inherently fantastical space-gods is utter bunkum. Sorry, spade-a-spade, and all that.


As to my second point, it went entirely over your head, so I will rephrase - perhaps my communication skills fail.

Evolution is not wrong. Biological creatures become more complex over time due to some traits being more suitable for the survival of said creature than others, and thusly, those creatures with fitter survival traits will propagate more extensively. Aka, survival of the fittest. The specific path that this process has followed in the past, as we have deduced it, may certainly be inaccurate - but the fact that creatures become more complex over time due to survival fitness is undeniable. Unless you are a crazy, or a religio (but I repeat myself)

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Re: Ben Stein vs. Darwin: The Movie

Postby EsotericWombat » Sat Mar 08, 2008 7:59 am UTC

Also, what does ID have to say about the observable evolution of bacteria?
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Re: Ben Stein vs. Darwin: The Movie

Postby alterant » Sat Mar 08, 2008 8:53 am UTC

Too bad... I do enjoy Ben Stein's deadpan. I guess he will now join Bruce Schneier and wear the dunce cap for a while.
I loved the Galileo bit! :)
A quote from Richard Dawkins explains pretty well why secular people are getting pissed off about "intelligent design":

The Rome-deniers, let's imagine, are a well-organised group of nutters, implacably convinced that the Roman empire never existed. The Latin language, for all its rich literature and its romance language grandchildren, is a Victorian fabrication.

The Rome-deniers are, no doubt, harmless wingnuts, more harmless than the Holocaust-deniers whom they resemble. Smile and be tolerant. But your tolerance might wear thin if you are a scholar and teacher of Roman history or literature.

And what if Rome-deniers manage to infiltrate the teaching staff of an otherwise reputable school, and energetically promote their inanities to a susceptible new generation? A normally tolerant person could be forgiven for wanting to see those teachers fired.

http://www.learning-together.org.uk/docs/called12.htm

I'm inspired, though.
I think I'll try making a documentary about the 2nd law of thermo, complete with sobbing perpetual motion machine inventors, driven from their jobs in a McCarthyesque witch-hunt. There'll be impassioned cries of "Keep Energy Free!"
Oh, and Hitler.

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Re: Ben Stein vs. Darwin: The Movie

Postby Robin S » Sat Mar 08, 2008 1:27 pm UTC

EsotericWombat wrote:Also, what does ID have to say about the observable evolution of bacteria?
The people I know who don't believe in macroevolution through natural selection claim that the bacteria aren't naturally evolving into new species - and because they don't reproduce sexually, it's not really possible to argue with them without using a definition of species that they can disagree with. Admittedly they aren't Intelligent Design supporters, but I imagine they'd use a similar argument.
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Re: Ben Stein vs. Darwin: The Movie

Postby iop » Sat Mar 08, 2008 1:49 pm UTC

JoshuaZ wrote:Finally, there's one point about this movie that isn't getting sufficient attention; intelligent design proponents have repeatedly claimed that they are not religiously motivated and have attacked and slimed the judge in the Dover trial who decided otherwise.

It's not that the judge "just decided". One particular piece of evidence was that in the book "Of Pandas and People", which was supposed to be used in teaching intelligent design, the editors had replaced "creation" with "intelligent design", leaving the context intact. This made it hard to argue that (Christian) creationism and ID were unrelated.

Enneract wrote:the fact that creatures become more complex over time due to survival fitness is undeniable.

It is very difficult to make the point that increased complexity would increase fitness. Complexity is actually one of the weakest points of evolution through natural selection. Of course, based on genetic evidence, there is no doubt that complex organisms evolved, but natural selection is unlikely to have been the driving force.

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Re: Ben Stein vs. Darwin: The Movie

Postby Robin S » Sat Mar 08, 2008 1:51 pm UTC

Natural selection is unlikely to have been the driving force.
Why not? If the advantages outweigh the disadvantages, anything can involve, including complexity. Clearly, for many species, they didn't (hence the vast number of microbes still around today) but, for others, they did.
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Re: Ben Stein vs. Darwin: The Movie

Postby iop » Sat Mar 08, 2008 9:05 pm UTC

Robin S wrote:Why not? If the advantages outweigh the disadvantages, anything can involve, including complexity.

If the selective advantage is large given the population size and the mutation rate, then it will be selected for.

The problem with multicellular organisms is that a) there aren't really compelling advantages that come with being complex, and that b) the population size of multicellular organisms tends to be small, thus decreasing the strength of natural selection.

There is quite a bit of danger of circular logic with evolution due to natural selection. If you assume that evolution occurs solely through natural selection, then, obviously, everything that has evolved was advantageous in some way, which is why it evolved.

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Re: Ben Stein vs. Darwin: The Movie

Postby 22/7 » Sat Mar 08, 2008 10:06 pm UTC

Enneract wrote:what?

Sorry, but any argument which relies on total disregard of every speck of physical evidence, and a blind assumption to inherently fantastical space-gods is utter bunkum. Sorry, spade-a-spade, and all that.
Apparently you've never had an intelligent conversation with a religious person, so I'll try this again, since you're having trouble wrapping your head around it. There is 0%/nothing/nada/bumpkis scientific about this statement.
Enneract wrote:
Enneract wrote:In principle, yes - however, religious based arguments are, at the core, nothing more than dogmatic nonsense, in terms of science.
If you cannot listen to the argument and forget about who is making the argument, then you are worthless to science. You can refute the argument all you want, but as soon as you say "this guy's religious, nothing he has to say is worth anything" you have completely invalidated yourself.
Enneract wrote:As to my second point, it went entirely over your head, so I will rephrase - perhaps my communication skills fail.

Evolution is not wrong. Biological creatures become more complex over time due to some traits being more suitable for the survival of said creature than others, and thusly, those creatures with fitter survival traits will propagate more extensively. Aka, survival of the fittest. The specific path that this process has followed in the past, as we have deduced it, may certainly be inaccurate - but the fact that creatures become more complex over time due to survival fitness is undeniable. Unless you are a crazy, or a religio (but I repeat myself)
That's all fine and dandy, but what you said was
Enneract wrote:Simply throwing everything away for the sake of 'goddidit', over any small point which creationists attempt to niggle at is silly... even if that one point is wrong, it does not 'endanger' the theory as a whole.
This, again, has a "you're religious, your point is therefore invalid" theme to it, which, again, is completely and wholly unscientific. Aside from those undertones, you specifically say that "attempt(ing) to niggle at... ("any small point")... is silly", which, again is flat out wrong. If they come up with a legitimate reason why some part of your view is incorrect, it doesn't matter what their motivation is, it doesn't matter who they are. If it's wrong, it's wrong, and you don't get to say "oh, well it doesn't matter if this thing is wrong, we're still right on the whole evolution thing." I'll say it again, because apparently it's going over your head. If it's wrong, it's wrong. Doesn't matter how big the issue is, nor who is bringing the issue to light, nor why they are bringing it to light.
Totally not a hypothetical...

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Re: Ben Stein vs. Darwin: The Movie

Postby Enneract » Sun Mar 09, 2008 12:09 am UTC

Hmm, Again, I think I am failing to communicate, 22\7.

Religion is not based on science, and it has no scientific content to it. Saying that an argument is discounted because it is religious, is, strictly speaking, not entirely correct. More accurately would be to say that an argument or 'theory' is discounted because it is not based on science, but instead on religion. The two concepts are antithetical in every sense of term - only in very select instances, where one world view castrates itself into meaninglessness, can the two coexist 'peacefully' (for instance, those who say that evolution is accurate, that is how species came to be as they are, and the universe was formed by a natural process, most likely the 'big bang', but I believe that god set all that in motion so god still wins!!!... to the scientist, the 'god' portion of this statement is meaningless and irrelevant, and to the religio, the science is meaningless and irrelevant... merely words to placate).

Religious theories are, by definition, unfalisable, and thus, fail to meet the basic criteria of a theory. What does the theory of an intelligent designer predict? Nothing. How could the theory of an intelligent designer, as presented by ID and creationist dogma, be proven incorrect? In no way. Conversely, What does the theory of evolution predict - growing complexity over time, in regards to survival fitness (in the most gross terms, mind you.). How could evolutionary theory be proven incorrect? - by the discovery of another natural method of speciation which more closely fits observed data.


Religious theories are not wrong simply because they are religious. Religious theories are *not theories* because the concept of religion is incompatible with the concept of reason.

I, or any other man, has no metric by which to judge the world around him other than his mind and his senses. Maybe these are insufficient to understand the world, as theologians would tell you - but they are all we have. Ignoring the percieveable world (of which science is the most powerful tool we have to make sense of it), out of fear, uncertainty, and doubt... well, thats just silly :)

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Re: Ben Stein vs. Darwin: The Movie

Postby JoshuaZ » Sun Mar 09, 2008 12:36 am UTC

Enneract wrote:Hmm, Again, I think I am failing to communicate, 22\7.

Religion is not based on science, and it has no scientific content to it. Saying that an argument is discounted because it is religious, is, strictly speaking, not entirely correct. More accurately would be to say that an argument or 'theory' is discounted because it is not based on science, but instead on religion. The two concepts are antithetical in every sense of term - only in very select instances, where one world view castrates itself into meaninglessness, can the two coexist 'peacefully' (for instance, those who say that evolution is accurate, that is how species came to be as they are, and the universe was formed by a natural process, most likely the 'big bang', but I believe that god set all that in motion so god still wins!!!... to the scientist, the 'god' portion of this statement is meaningless and irrelevant, and to the religio, the science is meaningless and irrelevant... merely words to placate).

Religious theories are, by definition, unfalisable, and thus, fail to meet the basic criteria of a theory. What does the theory of an intelligent designer predict? Nothing. How could the theory of an intelligent designer, as presented by ID and creationist dogma, be proven incorrect? In no way. Conversely, What does the theory of evolution predict - growing complexity over time, in regards to survival fitness (in the most gross terms, mind you.). How could evolutionary theory be proven incorrect? - by the discovery of another natural method of speciation which more closely fits observed data.


Religious theories are not wrong simply because they are religious. Religious theories are *not theories* because the concept of religion is incompatible with the concept of reason.

I, or any other man, has no metric by which to judge the world around him other than his mind and his senses. Maybe these are insufficient to understand the world, as theologians would tell you - but they are all we have. Ignoring the percieveable world (of which science is the most powerful tool we have to make sense of it), out of fear, uncertainty, and doubt... well, thats just silly :)


Er, please look up non-overlapping magisteria and theistic evolution. Certain classes of questions are not scientific because they are untestable. That doesn't make them wrong or not worth thinking about. It simply means that science cannot examine them. This applies to a variety of different classes of questions not just the strictly religious but also statements about morality or aesthetics. Please don't turn this into a science v. religion claim; that's exactly what many of the ID and YEC proponents want it to be. That's not what this is about.

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Re: Ben Stein vs. Darwin: The Movie

Postby Enneract » Sun Mar 09, 2008 12:43 am UTC

JoshuaZ wrote:
Enneract wrote:...


Er, please look up non-overlapping magisteria and theistic evolution. Certain classes of questions are not scientific because they are untestable. That doesn't make them wrong or not worth thinking about. It simply means that science cannot examine them. This applies to a variety of different classes of questions not just the strictly religious but also statements about morality or aesthetics. Please don't turn this into a science v. religion claim; that's exactly what many of the ID and YEC proponents want it to be. That's not what this is about.


Exactly~ There are domains of thought in which science really doesn't help. If religion belongs anywhere, it is there (although, religious morality is kinda a joke). What this movie is about is the incursion of religion into the realm of hard fact.

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Re: Ben Stein vs. Darwin: The Movie

Postby iop » Sun Mar 09, 2008 2:38 am UTC

Enneract wrote:Conversely, What does the theory of evolution predict - growing complexity over time, in regards to survival fitness (in the most gross terms, mind you.)

If "gross" means "wrong".

Evolution cannot predict complexity. Natural selection ("survival fitness") can predicts that given environmental challenges, certain alleles will increase in frequency within a population.
Evolution through natural selection could at best explain why complexity grew, but it doesn't even do that (since complexity doesn't really bring advantages). Note that in that regard, evolution isn't actually falsifiable, and it was thus originally not counted as scientific by Popper.

Please choose another example than complexity to cite in support for evolution by natural selection.

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Re: Ben Stein vs. Darwin: The Movie

Postby Enneract » Sun Mar 09, 2008 3:17 am UTC

iop wrote:
Enneract wrote:Conversely, What does the theory of evolution predict - growing complexity over time, in regards to survival fitness (in the most gross terms, mind you.)

If "gross" means "wrong".

Evolution cannot predict complexity. Natural selection ("survival fitness") can predicts that given environmental challenges, certain alleles will increase in frequency within a population.
Evolution through natural selection could at best explain why complexity grew, but it doesn't even do that (since complexity doesn't really bring advantages). Note that in that regard, evolution isn't actually falsifiable, and it was thus originally not counted as scientific by Popper.

Please choose another example than complexity to cite in support for evolution by natural selection.


I'm not a biologist, poor choice of words then.

Perhaps this is an opportunity for my own edification - I was under the impression that evolutionary process resulted in a great deal of genetic material that is not neccessarily 'used' (ie, junk\dormant dna). This would, in the mind of this layman, at least, count as 'complexity'. Sort of a reverse entropy (not a good analogy) effect with regards to the accumulation of genetic information?

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Re: Ben Stein vs. Darwin: The Movie

Postby Jay Jay » Sun Mar 09, 2008 4:40 pm UTC

I don't understand what the issue is here. I'm an atheist evolutionist, I guess. I studied a couple of subjects at university on History and Philosophy of Science, am by no means an expert on the topic... I'm not claiming that ID isn't a valid belief - if you believe in god, then ID probably makes sense - but in the end, the ID model relies on faith. Although there may be scientific components, the model fundamentally requires a belief in a higher being without proof (although I'm somewhat hazy about what some consider proof - things that are irreducibly complex now may be better under stood later with advances in technology and knowledge, if you compare the list of irreducibly complex things from when the theory came out compared to now, you'll see what I mean), and I think that makes it non-scientific. ID cannot be answered by science from what I have seen. It belongs in another realm. Please note, not claiming its not true, just not scientific. Thus, it has no place in scientific journals. So yeh, I can see why people would jack up about this kinda stuff in the scientific community.

I suspect these kinds of movies/tv shows/radio programs who play the "teach the controversy" card are simply vying for air time and exposure.

That's just my opinion and I certainly don't claim to be any kind of expert, sorry if I've offended anyone, and if it doesn't make sense. Its late (early?), can't sleep, but tired ^_^

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Re: Ben Stein vs. Darwin: The Movie

Postby EsotericWombat » Sun Mar 09, 2008 8:16 pm UTC

I offer a link: http://csicop.org/si/2005-11/id.html

Mark Perakh asserts that the notion of Irreducible Complexity as an argument for design is a fallacy.

Simply stated, the definitions given for IC all stem from the idea that a system is likely to have been designed if it is (a) improbable and (b) only able to function with all of its components in place. The problem with that notion is that any engineer will tell you that IC is shitty design.

Imagine a pile of stones. Each stone has some irregular shape that resulted from a series of chance events. Among these irregularly shaped stones, we find a perfectly rectangular brick. It has a simple shape that can be described by a simple equation containing only three numbers—width, length, and height. On the other hand, each of the irregularly shaped stones can be described only by a more complex program containing many numbers. However, the probability of a rectangular brick being produced as a result of chance is low; the brick can reasonably (with a high probability) be assumed to be a product of design. For irregularly shaped stones, the opposite is true—the probability of their having been created by chance is larger than the probability of their having been created by design. Here, the relationship between probability and complexity is the opposite of the one prescribed by Dembski’s definition
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Re: Ben Stein vs. Darwin: The Movie

Postby JoshuaZ » Sun Mar 09, 2008 8:32 pm UTC

EsotericWombat wrote:I offer a link: http://csicop.org/si/2005-11/id.html

Mark Perakh asserts that the notion of Irreducible Complexity as an argument for design is a fallacy.

Simply stated, the definitions given for IC all stem from the idea that a system is likely to have been designed if it is (a) improbable and (b) only able to function with all of its components in place. The problem with that notion is that any engineer will tell you that IC is shitty design.


There are additional problems with irreducible complexity as a barrier to evolution; they aren't one. In fact, the existence of apparently irreducible systems was predicted by as a consequence of evolution over 50 years ago (iirc by Haldane). We have a very good understanding of how such systems could evolve and pretty good ideas about how some of those did evolve. I strongly recommend that anyone interested in this topic read the cross-examination of Behe in the Dover trial in which Behe was confronted with many journals and books discussing the evolution of the systems which he claimed could not evolve. See the section of the cross-ex at http://www.talkorigins.org/faqs/dover/day12pm.html .

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Re: Ben Stein vs. Darwin: The Movie

Postby mazzilliu » Mon Mar 10, 2008 2:59 am UTC

it says it comes out on april 18th, i plan on watching this two days after it comes out in theaters and i plan to have an extremely good time with it.


also this:
http://www.expelledthemovie.com/

In yet another crippling blow to science, Ben Stein has singlehandedly disproved evolution and years of supportive "evidence" with his new movie, "expelled", wherein intelligence is indeed not allowed. Portraying himself as a rebel against the tyranny of Big Science, Ben Stein shows off his knees and his megaphone, supposedly used to express his superior point of view all the better; most likely in a very loud monotone drawl. the movie website opens with a quote from Richard Dawkins, one of the most intolerant people ever when it comes to fresh new ideas, for example the popular innovative idea, "God did it". By portraying Dawkins' statement in a negative fashion, i (and therefore everyone else) am instantly inclined to believe whatever point of view the movie is trying to portray.

This movie claims to "blow the horn on suppression", which is a great thing. Science has had a long history of suppressing good ideas for no better reason then the so-called "facts" disagree with the perfectly good idea being suppressed. Galileo oppressed the Catholic Church with bigotry great enough in magnitude to rearrange the heavens. Promethius was the exemplary suppressive bastard of the ages when he directly took power away from the gods. Newton's hatred of freedom caused trees to spontaneously pummel him with apples! Darwin got away scot free, however, and we should not let such a thing pass unhindered. We should oppose Darwin's ideas like any free thinking individual would do.

You know, without science, the world would be a better place, because then we could have all sorts of great ideas and there would be no big bully to shoot them down at every opportunity. We would live in flying houses and fight each other with light sabers, but science steps in and ruins our day saying we can't do those things.

Check out this preposterous letter, straight from DARWIN HIMSELF! It proves exactly how much Big Science is bad.
http://www.expelledthemovie.com/bigscienceacademy.php
that's one school I am definitely not going to.

This movie argues that Big Science has suppressed free speech in the classrooms and those monopolizing nerds have shut out equally sound alternative theories such as Intelligent Design, creationism, and flying spaghetti monsterism, along with a large number of lesser believed -isms. I am glad that people like Ben Stein have the courage to step up against those scientists who are against progress and hate truth.
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Re: Ben Stein vs. Darwin: The Movie

Postby AndyG314 » Tue Mar 11, 2008 4:05 pm UTC

EsotericWombat wrote:He isn't really a hell of a lot better than Tom Cruise. And worse, people actually respect him.


Nobody respects Ben Stein, I mean have you seen him in the Alaska seafood commercials? You can't respect a man after that.
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Re: Ben Stein vs. Darwin: The Movie

Postby iop » Tue Mar 11, 2008 4:53 pm UTC

Enneract wrote:Perhaps this is an opportunity for my own edification - I was under the impression that evolutionary process resulted in a great deal of genetic material that is not neccessarily 'used' (ie, junk\dormant dna). This would, in the mind of this layman, at least, count as 'complexity'. Sort of a reverse entropy (not a good analogy) effect with regards to the accumulation of genetic information?

You are right that only a few percent of the DNA in humans code for proteins, as opposed to nearly 100% in bacteria. However, the rest of the DNA is not "old" genes that are no longer being used. It consists in part of regulatory sequences (stretches of DNA to which proteins bind to turn a gene on or off - incidentially, it is mutations in regulatory sequences, not proteins, that account for a large amount of evolutionary change in multicellular organisms), sequences that are being read but that are never actually turned into protein (at least some code for regulatory RNA), probably some structural elements (spacers, etc.), and to a large part of "transposons" - DNA elements that code for just the tools to ensure that they are copied and inserted somewhere else in the DNA - possibly related to retroviruses that lost the ability to make virus particles. Also, some of the non-coding DNA has no known purpose or function yet.

The "junk" DNA can only arise in organisms that are under low selective pressure, because it's a big waste of energy. Thus, it is unlikely to have arisen through natural selection. I am not sure whether you can call that complexity.

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Re: Ben Stein vs. Darwin: The Movie

Postby Indon » Tue Mar 11, 2008 5:45 pm UTC

iop wrote:The problem with multicellular organisms is that a) there aren't really compelling advantages that come with being complex, and that b) the population size of multicellular organisms tends to be small, thus decreasing the strength of natural selection.


Well, let's look at an example. Algae!

Algae are a fascinating class of organism - they range from single-celled to multicellular, with differrent variations in-between to include communal single-cellular structures.

Among algae is a good example of the advantage of complexity - seaweed. Many kinds of algae may normally compete with each other for resources, but seaweed does not need to - it exists in what is essentially an entirely different niche of an ecosystem, and could grow rampantly if not for the dangers in its' own ecosystem (namely, things eating it).

The biggest contributor to complexity in the development of life is the filling of new ecological niches - the first organism to adapt to an environment can become prolific within that environment. Since each new organism in an environment change that environment, new potential niches are continually being made: The development of seaweed, and its' becoming prolific, just begs for a fish to develop the ability to eat seaweed, which leaves an opening for a fish developed with the abilities to eat that fish, and so on.
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Re: Ben Stein vs. Darwin: The Movie

Postby JoshuaZ » Tue Mar 11, 2008 6:15 pm UTC

iop wrote:
Enneract wrote:Perhaps this is an opportunity for my own edification - I was under the impression that evolutionary process resulted in a great deal of genetic material that is not neccessarily 'used' (ie, junk\dormant dna). This would, in the mind of this layman, at least, count as 'complexity'. Sort of a reverse entropy (not a good analogy) effect with regards to the accumulation of genetic information?

You are right that only a few percent of the DNA in humans code for proteins, as opposed to nearly 100% in bacteria. However, the rest of the DNA is not "old" genes that are no longer being used. It consists in part of regulatory sequences (stretches of DNA to which proteins bind to turn a gene on or off - incidentially, it is mutations in regulatory sequences, not proteins, that account for a large amount of evolutionary change in multicellular organisms), sequences that are being read but that are never actually turned into protein (at least some code for regulatory RNA), probably some structural elements (spacers, etc.), and to a large part of "transposons" - DNA elements that code for just the tools to ensure that they are copied and inserted somewhere else in the DNA - possibly related to retroviruses that lost the ability to make virus particles. Also, some of the non-coding DNA has no known purpose or function yet.

The "junk" DNA can only arise in organisms that are under low selective pressure, because it's a big waste of energy. Thus, it is unlikely to have arisen through natural selection. I am not sure whether you can call that complexity.


This ignores two major points. First, regulatory sections make up a substantial fraction of the non-coding DNA but are still a minority. Second, this ignores the way we tell if sections are doing something or not: we see if they are subject to neutral drift at about the rate expected from recombination and mutation; if so, there's no selection pressure on them. So in fact the entire method of telling which junk DNA does and does not have active roles is based on natural selection and common descent.

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Re: Ben Stein vs. Darwin: The Movie

Postby Yakk » Tue Mar 11, 2008 8:16 pm UTC

diotimajsh wrote:Did anyone else watch the trailer and seriously crack up when Stein said, "publishing Dr. Meyer's paper would not have been an issue if we were living in the time of Galileo or Einstein," (emphasis mine) and then went on about how in the contemporary era of Darwin, "those who challenge the status quo seldom go unpunished"?


Heh. And the funny part? Publishing the paper isn't the problem. Getting a reputable scientific journal to give it the time of day is the problem.

Malice wrote:A true follower of science should welcome others' critical evaluation of current theory.


You mean "quality critical evaluation"? Someone complaining about the font the published paper was in, and that it proves that the theory is wrong, is just annoying.

22/7 wrote:Ok, then. Use science to prove that 100% of all "religious based arguments" are "nothing more than dogmatic nonsense". Completely disregarding a stance because it disagrees with your stance is, at it's very core, unscientific.


Dogma is a word used to describe the beliefs of a religious organization. So religious based arguments are dogmatic arguments: based off of the dogma of the religion. There are two common tests to determine if an argument is scientific nonsense. The first is the positivist test: can the argument be proven wrong. The second is Occam's Razor: does the argument include extra entities or causes or parts that aren't needed to explain the situation.

An argument based in faith is non-positivist: it cannot be proven wrong, so it is scientific nonsense.

An argument that presumes the existence of an entity, such as God, that is not required by observations is scientific nonsense.

So any religious based arguments that are based off of faith are, scientifically, dogmatic nonsense.
Any religious based arguments that presume the existence of god are, scientifically, dogmatic nonsense.

You disregard a stance because it doesn't have a history or producing positive claims and predictions that are distinct from your existing model's positive claims and predictions. This is the right thing to do with junk science, really it is.

Does this prove that 100% of X has quality Y? No: but that requirement is silly. All you need to know is that it has a history of generating crap results. If it starts generating good predictions (ie, both surprising and distinct from the existing model, and true predictions not hindsight), then it starts gaining credibility. But time is a limited resource, and the number of crack-pot theories that generate crap results is unbounded: one cannot waste time looking at all of them just because they really really want you to!

Malice wrote:"Hi, I'm a scientist and I think I see some inaccuracies in your geological dating methods" people


Sure. Build a model that generates better predictions. :) There are decades of work into making the dating methods work: there is plenty of room to work on repairing errors in the dating methods.

Note, however, that many of the geological dating methods used cross-correlate with other ones which use quite different methods. So when you propose an error in one dating method, in order to be credible you also have to track down the cross-correlations and explain how they are wrong as well...

There is a mountain of evidence, not just a pebble, that one has to deal with. Centuries of documented research and testing and checking...

...

There are people trying to cause life to form in labs. I've seen dozens of them: none of them have access to the ability to run biology for millions of years over millions of sites.

iop wrote:It is very difficult to make the point that increased complexity would increase fitness. Complexity is actually one of the weakest points of evolution through natural selection. Of course, based on genetic evidence, there is no doubt that complex organisms evolved, but natural selection is unlikely to have been the driving force.


Huh? The creation of complexity when you apply natural selection to a population is an observed effect. We can see complexity emerge in computer simulations that use reproduction with variation and selection against test functions.

Useful complexity isn't cheap, no. But useful complexity is, by definition, useful. Note that there isn't a "tide towards complexity" -- the vast majority of biomass on the planet earth is bacteria who are not as complex as human beings. But to build up a complex system that is useful, you need more natural selection than building up a simple system that is useful.

Thus one should expect complex solutions to the selection function to occur after more time applying natural selection than the simpler solutions. If you graph "max complexity" vs "time", you end up with a graph with peaks that form an upward slope.

The problem with multicellular organisms is that a) there aren't really compelling advantages that come with being complex,


Being a multicellular organism is very useful!

and that b) the population size of multicellular organisms tends to be small, thus decreasing the strength of natural selection.


Note that sexual reproduction is very common among multicellular organisms. This increases the strength of natural selection. :)

Second, a decrease in "strength" doesn't mean anything if you don't specify what the baseline strength is.

There is quite a bit of danger of circular logic with evolution due to natural selection. If you assume that evolution occurs solely through natural selection, then, obviously, everything that has evolved was advantageous in some way, which is why it evolved.


We can see natural selection occurs. If we assume it occurs, it is sufficient to explain the observations. Some surprising things, such as the existence of DNA, are predicted by it, lending credence to the assumption.

Species models based off of form and species models based off of DNA seem to match up pretty damn well. When they don't match up, further investigation demonstrates that the form is less of a match up than it appeared superficially.

Rather inefficient systems in an organism are examined, and (together with DNA-based family trees and still living relatives along a branch) one can produce decent models that explain how the inefficient hacks came about. (Like the human salt management system).

JoshuaZ wrote:Er, please look up non-overlapping magisteria and theistic evolution. Certain classes of questions are not scientific because they are untestable. That doesn't make them wrong or not worth thinking about. It simply means that science cannot examine them. This applies to a variety of different classes of questions not just the strictly religious but also statements about morality or aesthetics. Please don't turn this into a science v. religion claim; that's exactly what many of the ID and YEC proponents want it to be. That's not what this is about.


But a scientist should dismiss them (those non-scientific claims) when working on science. And when they attempt to insert themselves into "I'm science to", they should be laughed out of the house.

iop wrote:The "junk" DNA can only arise in organisms that are under low selective pressure, because it's a big waste of energy. Thus, it is unlikely to have arisen through natural selection. I am not sure whether you can call that complexity.


Note that the cost of eliminating the "junk" DNA has to be factored in, as well as benefits from having that "junk" DNA around, and the cost of keeping the "junk" DNA around.

Determining what DNA is "junk" is not easy -- let's suppose the organism just deletes 1% of it's DNA on 1% of it's children. It is good enough at this that 25% of the time the DNA deleted was actually junk, and the kid lives!

Deleting 1% of the DNA saves 0.1% of the metabolic load of the critter.

So in exchange for 0.75% reduction in reproduction, your kids have 0.1% more efficient metabolisms. That might not be worth it even when you are under intense selective pressure!

On top of that, having "old" DNA around can be useful when you mutate. That protean that you aren't using any more can be reactivated with a simple mutation -- which might turn out to be useful. Heck, maybe you where a creature that wandered into the sea and had it's legs turned into flippers: being able to roll back those changes through random mutation means that your future offspring might be able to colonize a land mass at some point in the future faster than if they had to reevolve the legs from scratch.

Heck, even if they don't code for anything, by letting it random walk and pick up stuff from elsewhere in our genome (or heck, get overwritten by a virus), it allows for a future small mutation to generate a larger change than it would otherwise.

As JoshuaZ mentioned, these sections might be under zero immediate selective pressure if they are just old stuff. They could still have some small advantage, and it could still be too expensive to do a genetic audit to get rid of them.
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Re: Ben Stein vs. Darwin: The Movie

Postby iop » Tue Mar 11, 2008 9:28 pm UTC

Yakk wrote:We can see natural selection occurs. If we assume it occurs, it is sufficient to explain the observations.

Yakk wrote:useful complexity is, by definition, useful

And because it is useful, it is selected for, which is why complexity has evolved through natural selection.
Also, it is circular logic.

Yakk wrote:The creation of complexity when you apply natural selection to a population is an observed effect. We can see complexity emerge in computer simulations that use reproduction with variation and selection against test functions.

I'm always wary of computer simulations. At best they say that the mechanisms that we think are operating lead to the result we think they should produce.

Yakk wrote:Being a multicellular organism is very useful!

I was thinking of multicellularity when I spoke of complexity. So, what is so useful about being multicellular?


JoshuaZ wrote:This ignores two major points. First, regulatory sections make up a substantial fraction of the non-coding DNA but are still a minority. Second, this ignores the way we tell if sections are doing something or not: we see if they are subject to neutral drift at about the rate expected from recombination and mutation; if so, there's no selection pressure on them. So in fact the entire method of telling which junk DNA does and does not have active roles is based on natural selection and common descent.

First: I did mention that non-coding DNA is made up of more than just regulatory sections. I assume you must have missed that.
Second: I didn't mention how to determine whether something is non-coding or not (I didn't see how that was relevant to Enneract's question), but if you're being picky, you should at least mention that to find out whether a stretch of DNA has a function you can test for whether it is being transcribed, and you can delete it and check whether the organism lives.

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Re: Ben Stein vs. Darwin: The Movie

Postby Yakk » Tue Mar 11, 2008 9:41 pm UTC

iop wrote:
Yakk wrote:We can see natural selection occurs. If we assume it occurs, it is sufficient to explain the observations.

Yakk wrote:useful complexity is, by definition, useful

And because it is useful, it is selected for, which is why complexity has evolved through natural selection.
Also, it is circular logic.


No, I said useful complexity. Useful complexity is a subset of complexity. One can demonstrate that useful complexity exists, independent of any theory of evolution.

I did not say that "useful complexity implies the theory of evolution", I simply said that the theory of evolution uses known, detectable effects that is sufficient to explain observations.

Yakk wrote:The creation of complexity when you apply natural selection to a population is an observed effect. We can see complexity emerge in computer simulations that use reproduction with variation and selection against test functions.

I'm always wary of computer simulations. At best they say that the mechanisms that we think are operating lead to the result we think they should produce.


I'm happy for your wariness.

We can detect reproduction in life. We can detect variation in the reproduction with life. We can detect this variation being inherited. These are mechanism we know are operating.

You can build a simulation that contains these mechanisms that generates results that are more complex than what you started with. This complexity can even be useful and solve problems that are non-trivial.

As such, we have demonstrated that (known properties of life), when isolated in another environment, can produce (useful complexity). It does not prove that the useful complexity that we see was produced by those properties, but it does demonstrate that those properties are sufficient, as far as we can tell, to produce useful complexity.

Yakk wrote:Being a multicellular organism is very useful!

I was thinking of multicellularity when I spoke of complexity. So, what is so useful about being multicellular?


A tree can grow tall and move the photosynthesis organs closer to the sky, shading out other critters? :)

Or do you mean more directly? Algae are an example of a multi-species multi-cellular, and they can survive in areas where their component parts cannot.

Biofilms can form out of bacteria, producing a temporary multicellular life form, which turns out to be useful to them.

At what level of granularity are you asking about it's usefulness? There are millions of things that multicellular organisms can do that cells acting alone cannot do as well.

And if you want to see possible reasons why the first few cells would act together, you should look at some of the 'primitive' multicellular life, and examine what advantage each cell gains from the others. You can also (as I did above) use cooperation between single cellular life as a possible reason to coordinate resources.

I didn't find your question that narrow or clear -- so I tried to answer multiple variations of it.
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Re: Ben Stein vs. Darwin: The Movie

Postby iop » Tue Mar 11, 2008 10:18 pm UTC

Yakk wrote:I didn't find your question that narrow or clear -- so I tried to answer multiple variations of it.

I'll try to be clearer:

"Useful" in the context of evolution is "leading to high reproductive fitness".
Compared to bacteria, multicellular organisms (say, animals) reproduce many orders of magnitude more slowly. Thus, low reproductive fitness.
"Useful" can also mean that an organism can easily adapt.
Compared to bacteria, multicellular organisms have a much harder time adapting. There is of course the issue of much slower generation cycles. In addition, gene networks in multicellular organisms are much more complex, and thus they are much less able to undergo massive changes than bacteria. Also, bacteria can use horizontal gene transfer which allows them to even faster exchange genetic information. A thus unsurprising observation is that multicellular organisms cannot live in an environment where bacteria cannot live.

As you pointed out, bacteria do cooperate (there is also a lot of inter-bacterial signaling going on, for example). From that, it should be only a small step to form multicellular organisms. Why does multicellular life not arise all the time?

The only sensible explanation I have seen for that so far is that multicellularity does not confer a noticeable selective advantage. What is your explanation?

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Re: Ben Stein vs. Darwin: The Movie

Postby Yakk » Tue Mar 11, 2008 11:01 pm UTC

iop wrote:
Yakk wrote:I didn't find your question that narrow or clear -- so I tried to answer multiple variations of it.

I'll try to be clearer:

"Useful" in the context of evolution is "leading to high reproductive fitness".
Compared to bacteria, multicellular organisms (say, animals) reproduce many orders of magnitude more slowly. Thus, low reproductive fitness.


High reproductive fitness is not required to be useful in the context of evolution. Something is useful, evolution wise, if it lets you reproduce, period. The traits that let you become multi-cellular do not prevent your continued reproduction.

As you pointed out, bacteria do cooperate (there is also a lot of inter-bacterial signaling going on, for example). From that, it should be only a small step to form multicellular organisms. Why does multicellular life not arise all the time?

The only sensible explanation I have seen for that so far is that multicellularity does not confer a noticeable selective advantage. What is your explanation?


I can think of a few reasons.

First, the first attempt to build complex multicellular life seemed to take billions of years, to the best of our ability to tell. The probability of it occuring might not be that high.

Second, the already existing multicellular life might occupy the niches that new multicellular life could move into. The areas best suited to multicellular life tend to be occupied by multicellular life, and might not leave a colony of proto-multi-cellular life alone for the 1 to 100 million years of adaptation that it might take to reach full blown multicellular life.

Do remember that evolution is primarily away from extinction. Anything that doesn't go extinct is adaptive. :) Becoming better adapted in ways that <A> reduce your chance to become extinct, and <B> increase your chance to contribute to those who don't go extinct, is also selected for -- but that is not the primary selection mechanism of natural selection.

The primary selection mechanism of natural selection is extinction.

If two cells stick to each other, and this causes no extinction level disadvantage, then we shouldn't expect it to go away. The only thing that can cause a trait to go away is extinction of every line that carries that trait, or a mutation that wipes the trait out in the only remaining lines.

Things have to be insufficiently maladaptive to continue to exist. This is the "variation" part of the theory of evolution -- everything is not perfectly efficient and adapted to it's environment, things vary between each other.

And why doesn't it 'arise all of the time'? On what time scale? First, the gap between evidence of life in the geological record and the evidence of complex multicellular life on the geological record is billions of years long.

Plus there is evidence that various branches of life evolved it independently: on geological time scales, it does happen "all of the time". Heck, today there are existing creatures that spread the "fuzzy boundry" of multicellularity, with greater or lesser degrees of specialization and permanence.

So we have genetic evidence that it didn't happen just once.

We have organisms scattered over the single to multicellular life "barrier".

I don't see what evidence is missing? One shouldn't expect all life to be multicellular, because being multicellular isn't useful in every situation -- all that is required for multicellular life to exist is for it to be useful in some situations.
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Re: Ben Stein vs. Darwin: The Movie

Postby JoshuaZ » Wed Mar 12, 2008 1:50 am UTC

iop wrote:
JoshuaZ wrote:This ignores two major points. First, regulatory sections make up a substantial fraction of the non-coding DNA but are still a minority. Second, this ignores the way we tell if sections are doing something or not: we see if they are subject to neutral drift at about the rate expected from recombination and mutation; if so, there's no selection pressure on them. So in fact the entire method of telling which junk DNA does and does not have active roles is based on natural selection and common descent.

First: I did mention that non-coding DNA is made up of more than just regulatory sections. I assume you must have missed that.
Second: I didn't mention how to determine whether something is non-coding or not (I didn't see how that was relevant to Enneract's question), but if you're being picky, you should at least mention that to find out whether a stretch of DNA has a function you can test for whether it is being transcribed, and you can delete it and check whether the organism lives.


Er yes, my language was too strong; I think the first time I read what you were saying as a more general attack on evolution rather than a strict answer to the Enneract's question, hence my comments about what important qualifiers were relevant in that context.

iop wrote:
Yakk wrote:I didn't find your question that narrow or clear -- so I tried to answer multiple variations of it.

I'll try to be clearer:

"Useful" in the context of evolution is "leading to high reproductive fitness".
Compared to bacteria, multicellular organisms (say, animals) reproduce many orders of magnitude more slowly. Thus, low reproductive fitness.
"Useful" can also mean that an organism can easily adapt.
Compared to bacteria, multicellular organisms have a much harder time adapting. There is of course the issue of much slower generation cycles. In addition, gene networks in multicellular organisms are much more complex, and thus they are much less able to undergo massive changes than bacteria. Also, bacteria can use horizontal gene transfer which allows them to even faster exchange genetic information. A thus unsurprising observation is that multicellular organisms cannot live in an environment where bacteria cannot live.

As you pointed out, bacteria do cooperate (there is also a lot of inter-bacterial signaling going on, for example). From that, it should be only a small step to form multicellular organisms. Why does multicellular life not arise all the time?

The only sensible explanation I have seen for that so far is that multicellularity does not confer a noticeable selective advantage. What is your explanation?


As I understand it, multicellularitity does arise but a) most of the good niches for multicelled life are already taken and b) the line between multicelled and single-celled organisms is not as clear as one might think. See for example: Rainey, P. and Rainey, K. "Evolution of cooperation and conflict in experimental bacterial populations" Nature 425: 72-74 (2003) as well as the paper by Velicer and Yu which is literally right after that one (which I don't unfortunately have access to now, so I don't have the full citation).

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Re: Ben Stein vs. Darwin: The Movie

Postby iop » Wed Mar 12, 2008 2:06 am UTC

Yakk wrote:High reproductive fitness is not required to be useful in the context of evolution. Something is useful, evolution wise, if it lets you reproduce, period.

That is... not wrong, though I wouldn't call vestigial structures "useful", even though they still allow reproduction. I guess I should have written "more useful", i.e. "A trait is more useful if it increases reproductive fitness. Multicellularity is not a trait that is more useful than unicellularity".

The traits that let you become multi-cellular do not prevent your continued reproduction.

I do not dispute that.

Yakk wrote:If two cells stick to each other, and this causes no extinction level disadvantage, then we shouldn't expect it to go away.

If natural selection is at work, then we should expect it to go away if it confers no selective advantage.

What I argue is that multicellularity doesn't confer an inherent selective advantage, and that it was able to stick around because there was no strong selective pressure - i.e. two cells happened to stick to each other, and they didn't die, so they continued sticking to each other. In more technical terms, multicellularity arose through a nonadaptive process.

Yakk wrote:Do remember that evolution is primarily away from extinction. Anything that doesn't go extinct is adaptive.

I don't remember this. What I remember is that there are four drivers of evolution (i.e. of changes in allele frequencies in population)
- Natural selection
- Mutation
- Genetic drift
- Recombination
Natural selection is the only adaptive process. The other three are nonadaptive, but don't necessarily mean that the changes caused by them lead to extinction. They are probably what you'd call "the 'variation' part of the theory of evolution".

Maybe if you read[url=http://www.pnas.org/cgi/reprint/0702207104v1]M. Lynch (2007): The frailty of adaptive hypotheses for the origins
of organismal complexity. PNAS 104:8597–8604[/url], you understand better what I mean.
/Edit: sorry, url tags are somehow not working.

JoshuaZ wrote:I think the first time I read what you were saying as a more general attack on evolution rather than a strict answer to the Enneract's question

I guess one of the problems discussing evolution is that anyone who challenges other people's convictions about evolution is seen as an evolution-denier. I am not denying evolution. I am just getting annoyed when people talk about evolution and get it wrong (especially if they do that while mocking their opponents). "Humans aren't evolving anymore", or "natural selection is the mechanism of evolution" are two of my pet peeves.
It is sad that the authors of the movie get it right that you will get attacked bad as soon as you say something "against" evolution.


EDIT: I have read the articles. They show that cooperation can be useful. However, the cooperating bacteria keep replicating individually and at the same speed. The articles do not address the issue how the organisms would become truly multicellular, i.e. where most of them abandon reproduction, and where the reproduction is slowed down tremendously.

JoshuaZ wrote:a) most of the good niches for multicelled life are already taken and b) the line between multicelled and single-celled organisms is not as clear as one might think

a) This argument fails for two reasons
- If multicellular life was inherently advantageous over unicellular life, there should be multicellular life forms in more environments than there are bacteria. The reverse is true.
- If our ecosystems were such that all the niches are filled, and no other organism can survive, there shouldn't be invasive species, something that is widely observed. Thus, a new multicellular organism should have the possibility to take over another organism's niche.
b) Yes, single celled organisms cooperate. However, if this boundary is so fluid, why do we have so much ancestral diversity in multicellular life compared to the enormous diversity of unicellular life? A fluid boundary should keep producing multicellular organisms if there is an inherent advantage.
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Re: Ben Stein vs. Darwin: The Movie

Postby Yakk » Wed Mar 12, 2008 5:39 pm UTC

iop wrote:
Yakk wrote:High reproductive fitness is not required to be useful in the context of evolution. Something is useful, evolution wise, if it lets you reproduce, period.

That is... not wrong, though I wouldn't call vestigial structures "useful", even though they still allow reproduction. I guess I should have written "more useful", i.e. "A trait is more useful if it increases reproductive fitness. Multicellularity is not a trait that is more useful than unicellularity".


Then evolution does not select against traits with are not useful should be something you can agree with?

The traits that let you become multi-cellular do not prevent your continued reproduction.

I do not dispute that.

Yakk wrote:If two cells stick to each other, and this causes no extinction level disadvantage, then we shouldn't expect it to go away.

If natural selection is at work, then we should expect it to go away if it confers no selective advantage.


Why would it go away? Unless it causes a disadvantage sufficient to make the organism go extinct that is.

What I argue is that multicellularity doesn't confer an inherent selective advantage, and that it was able to stick around because there was no strong selective pressure - i.e. two cells happened to stick to each other, and they didn't die, so they continued sticking to each other. In more technical terms, multicellularity arose through a nonadaptive process.


Yes, but the theory of evolution assumes "variation" and then "selection". The variation occurs not because it is advantageous, but rather because it isn't sufficiently non-advantageous.

The existence of this variation, by the way, is a selective advantage, even if any given variation is not a selective advantage. Because without it you wouldn't have variation to select on. :)

Once such a variation exists and persists, selective pressure on (those with that feature) can occur. As they are competing for resources against those without that feature, one can naively expect that this selective pressure would push the feature-laden organisms into a domain where they can generate an advantage over those without that feature.

The feature doesn't have to be a universal advantage -- it just has to not suck so much that it causes the critter to be wiped out.

Yakk wrote:Do remember that evolution is primarily away from extinction. Anything that doesn't go extinct is adaptive.

I don't remember this. What I remember is that there are four drivers of evolution (i.e. of changes in allele frequencies in population)
- Natural selection
- Mutation
- Genetic drift
- Recombination
Natural selection is the only adaptive process. The other three are nonadaptive, but don't necessarily mean that the changes caused by them lead to extinction. They are probably what you'd call "the 'variation' part of the theory of evolution".


First, the fit are those who survive. If sticking together doesn't screw you, the feature is fit. It doesn't have to be "more fit" to continue to exist, just sufficiently not "less fit"?

Second, you are missing at least one categories of selective pressure and sources of variation. You also don't mention Speciation? On top of that, population-based evolution theories tend to presume sexual gene trading to be common: if there isn't (or there is less) genetic exchange between the members of a population, the populations aren't really populations?

Ie, take a petri dish. In it, there is one small area with cyanide, and a huge area without cyanide. Some little critter is introduced.

A genetically nearby adaptation exists which makes you worse at dealing with "no cyanide" but better when you deal with "cyanide" (however, you still are worse off in the cyanide area compared to the no-cyanide area, even with the feature). Is this adaptive? If you get the "no cyanide" adaptation, even in the best spot for you, you are worse off than if you have the "no-cyanide" version.

Yet one should expect the area with cyanide to contain large numbers of critters with the "cyanide" adaptation, even though this reduces their biomass, and lowers their ability to reproduce. These critters could even trade genetic material using whatever means -- so they aren't isolated populations.

There is just a 'niche' in which there is a marginal advantage to the "cyanide" over the "no cyanide" feature. That is sufficient for the "cyanide" variation to continue on with a stable population. You can view the niche as geographical or not -- the situation is similar.

So long as there is a niche in which increased complexity can generate a marginal advantage, then if that increased complexity arises one should not expect it to go away.

Maybe if you readM. Lynch (2007): The frailty of adaptive hypotheses for the origins of organismal complexity. PNAS 104:8597–8604, you understand better what I mean.
/Edit: sorry, url tags are somehow not working.


Ah -- so by non-adaptive change, you mean "does not generate sufficient benefit to cause the competing options to go extinct within the population due to the improved reproductive success"?

And if you kill off any organism that isn't the best adapted to a situation, then mutation away from local optima is difficult?

.. there is a very strange statement. "The evidence for the operation of group selection is weak". When a species or population becomes extinct, that is an example of an entire group being selected against? We have seen species become extinct... so how is that not strong evidence for group selection?

The paper seems to be arguing that random genetic drift, together with mechanisms that make back-mutation less common than forward-mutation, might be more than sufficient to explain a lot of things that where previously explained by natural selection of features that increase fitness?
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Re: Ben Stein vs. Darwin: The Movie

Postby iop » Fri Mar 14, 2008 9:47 pm UTC

Yakk wrote:Why would it go away? Unless [the feature] causes a disadvantage sufficient to make the organism go extinct that is.

Natural selection means that if a feature causes a decrease in reproductive fitness, this feature will eventually disappear from a population. Conversely, if a feature confers a large advantage, it should take over the population.
Natural selection is weaker the smaller the population, however, and the feature may reappear again through mutations.

Yakk wrote:So long as there is a niche in which increased complexity can generate a marginal advantage, then if that increased complexity arises one should not expect it to go away.

Exactly. From what I know, increased complexity has not been shown to generate an advantage, but there are several arguments why it wouldn't generate an advantage. So you can either argue that these arguments are bad (which you haven't), or you can argue that there may be a special, very rare situation that may possibly be advantageous for increased complexity, and that we just haven't found it yet. But then you could also argue for a designer.
I argue that it is most likely that there just never was a selective advantage of complexity.

Yakk wrote:Ah -- so by non-adaptive change, you mean "does not generate sufficient benefit to cause the competing options to go extinct within the population due to the improved reproductive success"?

I'm not sure I understand your definition.
Non-adaptive change means change that is neither under positive nor negative selection (because population sizes are too small, because mutation rates are too high, or because the changes just don't make a difference).

Yakk wrote:And if you kill off any organism that isn't the best adapted to a situation, then mutation away from local optima is difficult?

That would be the case if there was only natural selection.

Yakk wrote:The paper seems to be arguing that random genetic drift, together with mechanisms that make back-mutation less common than forward-mutation, might be more than sufficient to explain a lot of things that where previously explained by natural selection of features that increase fitness?

It argues that there are people who only think of natural selection when they think about evolution. They then try to come up with bad arguments how something may confer an advantage even though it clearly doesn't. Lynch, being not the nicest person, claims this "dogmatic belief in natural selection" is about as scientific as ID.
He then goes on to explain that non-adaptive evolution can explain a lot of observations (such as the emergence of complexity) that make little sense if only natural selection was considered.

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Re: Ben Stein vs. Darwin: The Movie

Postby Indon » Fri Mar 14, 2008 10:03 pm UTC

Nobody likes algae, I guess...

iop wrote:I'm always wary of computer simulations. At best they say that the mechanisms that we think are operating lead to the result we think they should produce.


Funny thing you mention evolution in the context of computers.

Aside from simulations of evolution, programmers use evolutionary mechanics in order to design actual, working programs!

Programs generated through evolutionary computing tend to manifest a few things in common:

-These programs generate code that is never used by the program (debugging methods can be used to verify what code is used in a program) - as a result these programs are much larger than they would need to be if they were generated by another method due to the 'junk' code.
-They're very, very hard for a person to understand by reading the code.
-They generally function surprisingly fast, and well.

All of these are things that are similar to most living beings on Earth today.

I wonder why there would be a concept like "non-adaptive evolution". Differentiated equilibrium, if I recall, postulates continual increase in diversity - to presumably include complexity - when there is no, or weak, selective pressure on a population. What would this non-adaptive evolution explain that that mechanic doesn't already cover?
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Re: Ben Stein vs. Darwin: The Movie

Postby iop » Sat Mar 15, 2008 12:51 am UTC

Indon wrote:
iop wrote:I'm always wary of computer simulations. At best they say that the mechanisms that we think are operating lead to the result we think they should produce.


Funny thing you mention evolution in the context of computers.

Aside from simulations of evolution, programmers use evolutionary mechanics in order to design actual, working programs!


Maybe I should clarify why I am wary of computer simulations:
1. Models are only as good as the assumptions. If you get the right result, but use a completely wrong assumption, you have not actually modeled reality, you just showed that your solution is not unique. Yet, if a model produces "excellent agreement" with the data (see 2.), it is often taken as validation of the assumptions. This is not the case as long as you cannot show that the solution is not unique.
2. Simulations more often than not produce qualitative, not quantitative agreement (at least in biology). Qualitative agreement is nice and all, but it is not actually reproduction of experimental results.
3. Models include both explicit and implicit assumptions. Both may constrain the model such that the outcome is more a function of the assumption, and not an emergent property of the model, but this is rarely considered for the implicit assumption.

Of all the modeling papers I reviewed, one was good IMO (the authors actually thanked me for telling them to try and be more quantitative. It improved the model). Unfortunately, that paper got hated out by the other reviewer because of the assumptions.


Indon wrote:I wonder why there would be a concept like "non-adaptive evolution". Differentiated equilibrium, if I recall, postulates continual increase in diversity - to presumably include complexity - when there is no, or weak, selective pressure on a population. What would this non-adaptive evolution explain that that mechanic doesn't already cover?

I think you mean punctuated equilibrium.
Punctuated equilibrium does not worry about what happens at the genomic scale, or what the conditions are for non-adaptive evolution (which is what is at work when there is no, or weak selective pressure). Also, low selective pressure doesn't necessarily mean increase in diversity. Genetic drift may lead to fixation of neutral mutations in a population, which can, for example manifest as cryptic evolution that isn't taken into account by the punctuated equilibrium model. Furthermore, punctuated equilibrium implicitly assumes there is no selective pressure at all for a while, and then suddenly high selective pressure, when there may be both high and low pressure at the same time on different features.

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Re: Ben Stein vs. Darwin: The Movie

Postby Indon » Sat Mar 15, 2008 1:44 am UTC

iop wrote:3. Models include both explicit and implicit assumptions. Both may constrain the model such that the outcome is more a function of the assumption, and not an emergent property of the model, but this is rarely considered for the implicit assumption.


I wasn't talking about modeling evolution - I understand your reasons for being leery of them.

Evolutionary programs are distinct from models of evolution. A model of evolution may simulate genetics - an evolutionary program applies the principles of evolution in an abstract form to make a system that solves a real problem. It is a literal proof of concept for many of the more basic underlying concepts of biological evolution (though, many of them you probably already agree with, it still deserves mentioning).

iop wrote:I think you mean punctuated equilibrium.
Punctuated equilibrium does not worry about what happens at the genomic scale, or what the conditions are for non-adaptive evolution (which is what is at work when there is no, or weak selective pressure). Also, low selective pressure doesn't necessarily mean increase in diversity. Genetic drift may lead to fixation of neutral mutations in a population, which can, for example manifest as cryptic evolution that isn't taken into account by the punctuated equilibrium model. Furthermore, punctuated equilibrium implicitly assumes there is no selective pressure at all for a while, and then suddenly high selective pressure, when there may be both high and low pressure at the same time on different features.


Yeah, that'd be it. I didn't know that about the genetic drift, though, and I'll admit to very much a layman's understanding of the non-algorithmic nature of evolutionary functions. One thought, though: wouldn't it be a simple extention of the framework to describe selective pressure as operating independently on different features?
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Re: Ben Stein vs. Darwin: The Movie

Postby iop » Sat Mar 15, 2008 1:54 am UTC

Indon wrote:I wasn't talking about modeling evolution - I understand your reasons for being leery of them.

Ah, ok. I had been in the post that you quoted, which was why I assumed you would be, too.

Indon wrote:Evolutionary programs are distinct from models of evolution.

Agreed.

iop wrote:One thought, though: wouldn't it be a simple extention of the framework to describe selective pressure as operating independently on different features?

Yes, probably. Except that punctuated equilibrium wouldn't quite be punctuated equilibrium anymore, but a smoother, gradual process of evolution.

I should mention that punctuated equilibrium and the driving forces of evolution I mentioned above are two different approaches of describing evolution - punctuated equilibrium is top-down, i.e. it is concerned with large-scale changes such as speciation. The genomic-level driving forces are about how the genome changes over time. These changes may lead to speciation (and there really is no reason "macroevolution" should involve different mechanisms that "microevolution"), but they also explain recent human evolution such as lactose-tolerance, or high-altitude adaptation.

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Re: Ben Stein vs. Darwin: The Movie

Postby Yakk » Sat Mar 15, 2008 2:54 am UTC

iop wrote:
Indon wrote:I wasn't talking about modeling evolution - I understand your reasons for being leery of them.

Ah, ok. I had been in the post that you quoted, which was why I assumed you would be, too.


Well, your original statement was in response to my:
The creation of complexity when you apply natural selection to a population is an observed effect. We can see complexity emerge in computer simulations that use reproduction with variation and selection against test functions.

which was NOT referring to simulating the real world either. The use of "test functions" to use variation and natural selection can generate complex algorithms. I can't think of a way to use "test functions" to simulate anything other than a crap model of the real world. :)

The emergence of adaptive complexity from natural selection effects has been proven to occur. It is used by computer programmers to produce algorithms to solve problems. It may not happen in life, but the mechanism of natural selection can generate it in some problem domains.

So you could understand how someone could be confused. :)

...

Something else somewhat interesting: in some cases, an additional level of complexity can be shown to allow an organism to live in an area it could not have otherwise? That ... seems adaptive. The original organism couldn't survive in area X, but the modified one can. (As an example, the multiple levels of salt pump that seem to correspond to migration between fresh and salt water environments).

Now, the modified ones cannot survive in the old environment -- but that still increases the range of the two populations compared to the original one population?

The claim that another complexity -- an additional system on top of an existing system -- is never adaptive seems like a rather strong statement.
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Re: Ben Stein vs. Darwin: The Movie

Postby 22/7 » Sat Mar 15, 2008 4:14 pm UTC

Yakk wrote:
22/7 wrote:Ok, then. Use science to prove that 100% of all "religious based arguments" are "nothing more than dogmatic nonsense". Completely disregarding a stance because it disagrees with your stance is, at it's very core, unscientific.


Dogma is a word used to describe the beliefs of a religious organization. So religious based arguments are dogmatic arguments: based off of the dogma of the religion. There are two common tests to determine if an argument is scientific nonsense. The first is the positivist test: can the argument be proven wrong. The second is Occam's Razor: does the argument include extra entities or causes or parts that aren't needed to explain the situation.
First, you're using the word dogma in a different way than we were using it, so this explanation isn't particularly helpful. I agree with it, but as it applies to what we were talking about, well, it doesn't really. He was using "dogmatic" in a "bullshit beliefs that I don't hold" kind of way, and I was quoting him. Secondly, and far more importantly, the second sentence is the one you should be responding to, as it's the one that's actually saying something. And the point that it makes still stands.
Totally not a hypothetical...

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Re: Ben Stein vs. Darwin: The Movie

Postby iop » Sun Mar 16, 2008 2:11 am UTC

Yakk wrote:The claim that another complexity -- an additional system on top of an existing system -- is never adaptive seems like a rather strong statement.

"Never" is most likely too strong a term. "Rarely" sounds much better.

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Pharyngula and Dawkins walk into a theatre

Postby genewitch » Fri Mar 21, 2008 4:28 pm UTC

Ok guys, there was a screening of the movie: Expelled last night.
PZ Myers was there. He gave a write up about it that you HAVE to read.

I am not going to spoil his fantastic write-up of what happened, but here is the Follow Up - there are various other links to what happened there too.

Just remember, PZ Myers is one of the biologists IN the movie. Dawkins is also in the movie. (i'll post a link to his video as soon as it gets released!)

hahahahahahahahahahaha !

PS mods if this warrants it's own thread, can i get a PM if it gets moved? this is Good Stuff.
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