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Author Topic:   Diversification: Random Walk or Biological Determinism?
AnswersInGenitals
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Posts: 518
Joined: 07-20-2006


Message 16 of 35 (488726)
11-15-2008 8:16 PM
Reply to: Message 1 by Fosdick
11-12-2008 12:43 PM


Reducto ad Diversito.
Diversity within a species is a trait that confers a major advantage for survival. Why? Because the environments that species occupy are never constant. They very greatly, not only from place to place, but from time to time. Environments from one time to another can differ like day and night. A species that has a very "tight" genome and very little phenotypic diversity will do well in an environment to which it is well adapted, and will do better than a species with a very "loose" genome and broad phenotypic diversity which will waste a lot of resources producing offspring that are not well adapted to that environment.

But it is inevitable that that environment will change and the "loose" species is far more likely to have some individuals that can thrive in the new environment. We see this in the human species with its great diversity in height, skin color, hair color and hairiness, and hundreds of other traits. We see it in dogs (and wolves, foxes, dingos, and other canids) whose 1500 breeds cover the range from great danes to chihuahuas, from almost all hair to hairless. While most of the diversity in dogs results from environments and selection pressures imposed by humans, the principle still holds.

We even see this principle in non-biological systems. The automobile industry of one country is narrowly focused on high performance and luxury gas guzzlers with only a grudging nod to efficient cars, while that of another diversifies to place major emphasis on fuel and resource efficient cars as well as the large carbon footprint models. Then the environment changes with high fuel prices and constrained budgets. Guess which country's automobile industry is on the verge of extinction. The Japanese and Korean auto makers are also suffering in the current environment, but with a lot of production in the now desirable models, they are well situated to survive this downturn and then fill the niches vacated by failed American makers. There is a great temptation to carry the 'extinction event' analogy beyond its logical usefulness here, but I will resist.

Given that phenotypic diversity within a species is a very beneficial trait in supporting survival in the face of changing environments, an interesting question arises: What is the physical mechanism (down to the molecular level) that enforces such diversity? The most obvious is sex with its reshuffling of genomic components and 'mix and match' production of offspring. Another is that while all organisms have developed DNA proofreading mechanisms to correct most major DNA errors that occur during reproduction, these still allow many numbers and types of mutations to occur. (E. g., the genomes of every one of our ~100 trillion cells differ from the egg we originated from by several dozen to several thousand different mutations. The vast majority of these mutations cause us no problems - they are either neutral or kill the mutated cell which is then just recycled into other cells.) A third and rarely appreciated mechanism that is a major enabler of evolution is fecundity - the production of large numbers of offspring. We consider a couple (of humans) who produce 20 children to be very fecund (as well as very irresponsible), but most members of the plant world produce hundreds of seed or millions of spores each season. Fishes (and, in fact, most species) produce thousands of fertilized eggs. This fecundity permits the species to produce highly diverse offspring, the vast majority of which will not survive, but include enough that are survivable in their current environment to continue the species, but also have "Plan B" offspring deployed in case of severe environment changes.

So, what happens at a major extinction event (or even a very minor localized one for that matter)? The vast majority of the members of most of the species are wiped out, but several of the species will leave a few "out-lier" members who are able to survive in the new conditions. These individuals may not be all that well adapted to these new conditions, but survival and evolution depend on been just good enough, and for a fair period of time, there is little competition for whatever resources the new environment provides. These survivors themselves now thrive and diversify with some of the more diverse forms being divergent enough to be a species distinct form the original (or it might take several of these near-extinction/reemergence events, but new species will be created). Notice that this process favors species with the most intraspecies variability and thus with the built-in mechanisms to effect such variability, i. e., diversity breeds diversity. It is therefore not surprising that major extinction events are followed by major diversity events, an "explosion" of species radiation. We also notice that there is no need to talk about mysterious (mystical?) Emergent Properties - it is all due to simple, basic easily understood processes that are amenable to a reductionist analysis.

On the other hand, I may be wrong.


This message is a reply to:
 Message 1 by Fosdick, posted 11-12-2008 12:43 PM Fosdick has responded

Replies to this message:
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NosyNed
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Posts: 8863
From: Canada
Joined: 04-04-2003
Member Rating: 4.6


Message 17 of 35 (488728)
11-15-2008 8:42 PM
Reply to: Message 16 by AnswersInGenitals
11-15-2008 8:16 PM


Re: Reducto ad Diversito ==POTM
I've POTM'd this AiG. I think this is very clear writing and reasoning even if it might be wrong.

Question:
Where did this factino come from:

E. g., the genomes of every one of our ~100 trillion cells differ from the egg we originated from by several dozen to several thousand different mutations. The vast majority of these mutations cause us no problems - they are either neutral or kill the mutated cell which is then just recycled into other cells.)

To tidy up a loose end I think you'd need to add a paragraph that discusses how a species of loose genome can maintain that given your comment that a tight one might be better for a specific condition.

I think the paragraph needs to emphasize the constant micro changes in environments. E.g., somewhere (I'll look later maybe) I read (or my mind is making up) that some (I can't remember ) species undergoes genetic shifts throughout the passage of a couple of seasons as the conditions change.

ABE
http://cat.inist.fr/?aModele=afficheN&cpsidt=17532917
Describes moths (I think) that have genetic changes over a season. This is not the example I was thinking of though.

This one I can only barely read:
http://www.genetics.org/cgi/content/abstract/105/4/935
but it hints at the same thing:

quote:
We propose that Ost probably consists of a finite array of supergenes that are differentially favored in each season by natural selection.

Edited by NosyNed, : No reason given.


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Fosdick 
Suspended Member (Idle past 3785 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 18 of 35 (488743)
11-16-2008 11:20 AM
Reply to: Message 16 by AnswersInGenitals
11-15-2008 8:16 PM


Re: Reducto ad Diversito.
AI writes:

Notice that this process favors species with the most intraspecies variability and thus with the built-in mechanisms to effect such variability, i. e., diversity breeds diversity. It is therefore not surprising that major extinction events are followed by major diversity events, an "explosion" of species radiation. We also notice that there is no need to talk about mysterious (mystical?) Emergent Properties - it is all due to simple, basic easily understood processes that are amenable to a reductionist analysis.


Why do you assume that all emergent properties are either mysterious or mystical? Isn't biological life an emergent property of abiotic nature? How did the genes get here if not by way of an emergent property of chemical systems? How did the eukaryotes evolve if not by way of an emergent property of prokaryotes? How did symbolic language arise if not as an emergent property of humans?

And the bottom-line question is: Does diversification happen randomly or deterministically? To this question you have answered: "diversity breeds diversity." So, why is that true for biological structures like organisms and not true for physical structures like rocks. I've never seen a population of stones diversify into an interstate highway without human intervention. That happens because of human determinism. Therefore, I would argue that "diversity breeds diversity" is evidence of biological determinism.

I get impression that you think biological life emerged on planet Earth by way of reducto ad diversito.

—FTF


I can see Lower Slobovia from my house.

This message is a reply to:
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AnswersInGenitals
Member
Posts: 518
Joined: 07-20-2006


Message 19 of 35 (488752)
11-16-2008 6:45 PM
Reply to: Message 18 by Fosdick
11-16-2008 11:20 AM


An ab initio Reducto ad Diversito.
I really don't think that we are disagreeing about anything, just reacting to different definitions of "emergent property". I had interpreted RADZ's use of the term (and also the direction that StevenFire seems to be going) as being the use that has emerged amongst chaos theorists (such as Stewart Kaufman), i. e., that as a system becomes more complex, certain traits and behaviors emerge that cannot be explained by the basic properties and components of the less complex system. They argue that this inability to describe such systems is not simply due to a lack of understanding or computational power, but is due to the emergence of new phenomena that must be explained with new physical laws ab initio. As I said , I believe that this is the meaning that RADZ was going after, which is why I Capitalized the term.

I believe you are using the term in the common colloquial sense of convenient or simplified terms to summarize complex systems or behavior. It is much easier to say that a glass of water is 62 degrees F than to describe the instantaneous velocities of several trillion trillion molecules.

I must admit that I react to the term 'emergent property' about the same way that Richard Dawkins reacts to the term 'irreducible complexity'. It's not that I doubt that the chaos theorists, who are certainly much smarter and more knowledgeable about such matters than I am, are on to something important. It's more that complex things are so far over my head, beyond my reach, and out of my limited depth, that I am driven to seek simpler answers. If the Pew Research Group were ever to contact me during one of their surveys of religious beliefs in America, I would declare myself to be an Absolute Reductionist. Our main tenet is that anyone who disagrees with us is condemned to eternal complexity.

I've never seen a population of stones diversify...

Since I seem to be in an argumentative mood, I will point out that if you were to look long enough, you would see your population of stones diversify into pebbles, gravel, sand, and dust through the processes of erosion and weathering. But such unlimited generalization of the term would just be, I think, spreading too little butter over too much toast.


This message is a reply to:
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Coyote
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Posts: 6117
Joined: 01-12-2008


Message 20 of 35 (488753)
11-16-2008 7:05 PM
Reply to: Message 19 by AnswersInGenitals
11-16-2008 6:45 PM


Interlude
But such unlimited generalization of the term would just be, I think, spreading too little butter over too much toast.

Reacting to your colloquialism--

I knew a professor once who used, where you are using butter & toast, the term "slicing the baloney thinner."

We now return you to your regularly scheduled thread.


Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.

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Fosdick 
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Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 21 of 35 (488756)
11-16-2008 7:43 PM
Reply to: Message 19 by AnswersInGenitals
11-16-2008 6:45 PM


Re: An ab initio Reducto ad Diversito.
AIG writes:

I really don't think that we are disagreeing about anything, just reacting to different definitions of "emergent property". I had interpreted RADZ's use of the term (and also the direction that StevenFire seems to be going) as being the use that has emerged amongst chaos theorists (such as Stewart Kaufman), i. e., that as a system becomes more complex, certain traits and behaviors emerge that cannot be explained by the basic properties and components of the less complex system...


Yes, I can agree with that, more or less. We're talking about the same meaning of "emergent property," I think.

I believe you are using the term in the common colloquial sense of convenient or simplified terms to summarize complex systems or behavior.

Well, just how does your understanding of EP differ from mine? You mentioned Stewart Kauffman in support of your argument. Was he speaking in the colloquial sense when he said (in At Home In The Universe, 1995, p. 45)?:

quote:
There are compelling reasons to believe that whenever a collection of chemicals contains enough different kinds of molecules, a metabolism will crystalize from the broth. If this argument is correct, metabolic networks need not be built one component at a time; they can spring full-grown from a primordial soup. Order for free, I call it. If I am right, the motto of life is not We the improbably, but We the expected.

To me, Kauffan's statment is one place you can go to find mystery and mysticism. (I'd never say anything as reckless as that, and I've been known to say reckless things.)

Since I seem to be in an argumentative mood, I will point out that if you were to look long enough, you would see your population of stones diversify into pebbles, gravel, sand, and dust through the processes of erosion and weathering. But such unlimited generalization of the term would just be, I think, spreading too little butter over too much toast.

Is biological diversification like erosion? If so, then it would be a random walk. If not, it would have to be either fundamentally deterministic or an emergent property, or both.

—FTF

Edited by Fosdick The Fearless, : tidy, tidy


I can see Lower Slobovia from my house.

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straightree
Member (Idle past 3036 days)
Posts: 57
From: Near Olot, Spain
Joined: 09-26-2008


Message 22 of 35 (488791)
11-17-2008 3:29 PM
Reply to: Message 21 by Fosdick
11-16-2008 7:43 PM


Re: An ab initio Reducto ad Diversito.
I expect not to stride out of subject. I find refferences to non biological evolution interesting, because they broaden the view. They may be particularly pertinent when talking about determinism and randomness. I, therefore would like to expand a little bit your refference to rocks and erosion.
quote:
Is biological diversification like erosion? If so, then it would be a random walk.

It could seem that erosion is just the destruction of rocks, but, at least in planet earth, it has been the starting point for soil building, that produced forests, and arable earth. So seen in that way, maybe it could be considered as rather deterministic.

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 Message 21 by Fosdick, posted 11-16-2008 7:43 PM Fosdick has responded

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AnswersInGenitals
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Posts: 518
Joined: 07-20-2006


Message 23 of 35 (488792)
11-17-2008 4:14 PM
Reply to: Message 21 by Fosdick
11-16-2008 7:43 PM


Re: An ab initio Reducto ad Diversito.
Is biological diversification like erosion? If so, then it would be a random walk.

You are making the mistake so commonly found in creationist diatribes: If something is partly random, then it must be completely random. They accept the randomness of mutations but ignore the deterministic aspect of natural selection. Yes, erosion has a random component, but it also has a deterministic component due to the environment in which the erosion occurs. Wind (and wind blown sand) and rain will erode rocks into fine particles, sand and dust. Freeze cracking, mechanical failure due to cyclic temperature changes, and differential erosion along faults, veins and inclusions will break big rocks into smaller rocks. Chemical erosion, due to fore example sulphuric emissions from volcanoes, will cause erosion at the molecular level.

The more we explore this, the closer this erosion thing seems to get to biological evolution, but I still think the analogy is more strained than productive and is just diverting us off course from the very interesting OP you introduced (Straightree's Post#22 notwithstanding.) I'm probably most at fault for this and duly apologize.

As to your questions about my understanding of the term 'emergent properties', I'd rather not show my ignorance of this issue by commenting further. I don't think it's pertinent to the discussion anyway.


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Brad McFall
Member (Idle past 3317 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 24 of 35 (488797)
11-17-2008 5:39 PM
Reply to: Message 21 by Fosdick
11-16-2008 7:43 PM


Re: notion of emergence
I consider it a disservice when Mayr, in "What Makes Biology Unique", equated his organcist notion of emergence with Bohr's reference to water, as this tore at my own reading of the same literature.

It is hard for me to imagine that you have captured some sufficient and necessary understanding of the term beyond Mayr.

What makes the notion (emergence) difficult, for me, and it should send up flags at least for others, is that actual infinity in the sense that the parts equal the whole and yet the whole is more than the sum of the parts if applied without contradiction (others simply assume without evidence that that must be in this case) covers the place emergence seeks to carve out linguistically and yet it might still argue against reductionism nonetheless. There is no recognition of this in the literature and yet the lit. goes lightly over the original discussion of upward and downward causation given by Campbell.

Thus Russell(Principles of Mathematics page 145),

quote:
If a unity is infinite, it is possible to find a constituent unity, which again contains a constituent unity, and so on without end. If there are any unities of this nature, two cases are prima faciepossible. (1)There may be simple constituents of our unity but these must be infinite in number.(2)There may be no simple constituents at all, but all constituents, without exception, may be complex; or to take a slightly more complicated case, it may happen that, although there are some simple constituents, yet these and the unities composed of them do not constitute all the constituents of the original unity. A unity of either of these two kinds will be called infinite.

It is through the differences of upward and downward causation that implicate the possibility. We tend to polarize around the dualism instead. Reframing evolutionary space in terms ofAckerman functions(see link to WolframScience here) (I have not thought this yet) seems to offer up a way to cognize the possibility raised logically by Russell but conflated in Mayr's notion of emergence.

It is possible there is no actual infinity through upward causation, in which case we would only have empirically the second of Russell's categories. Current thinking on emergence constrains scientists to logically stay restricted to a part/phrase of the second clause. That is why infinite creationism is sometimes a fresh breeze or a snowflake. Emergence keeps one away from this notion of infinity of Russell.

That's how I think it. I think you could have asked your question without bringing emergence into it.

Edited by Brad McFall, : wrong word


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AnswersInGenitals
Member
Posts: 518
Joined: 07-20-2006


Message 25 of 35 (488798)
11-17-2008 5:49 PM
Reply to: Message 17 by NosyNed
11-15-2008 8:42 PM


Re: Reducto ad Diversito ==POTM
I've POTM'd this AiG. I think this is very clear writing and reasoning even if it might be wrong.

Question:
Where did this factino come from:

E. g., the genomes of every one of our ~100 trillion cells differ from the egg we originated from by several dozen to several thousand different mutations. The vast majority of these mutations cause us no problems - they are either neutral or kill the mutated cell which is then just recycled into other cells.)

First, let me apologize for taking so long to respond to your very kind words. I have never been POTM'd before and am curious as to when I will be informed of the time and place of the awards ceremony. Am I expected to wear a tux and give an acceptance speech? You raise some interesting issues in your post and I'm trying to reconcile the work required to discuss them effectively and concisely with my innate laziness, so far without success.

As to your question, there was a thread a few months ago that discussed mutation rates for various types of mutations and referenced some of the original work that addressed this question I haven't figured out the key words to search on to get to that thread. As I remember, there was a range of results depending on which researcher was referenced and their experimental method, but for point mutations (base substitution, deletion, or addition) it came out to few mutations per cell division for a human size genome, i. e., about 6 billion base pairs. In that thread, iI presented an brief and simplistic analysis that indicated about one mutation per 400 million base pairs per cell division, but to repeat it here I think would be off topic. If all else fails, I'll review all my previous posts and see if I can find that thread and its references.

A 100 trillion cell organism, typical of adult humans, can be produced by 47 cell divisions, which would give the several dozen to several hundred point mutations for the cells. But this is far to simple a model of how we acquire all our cells. First, most of our cells are destined to die before we do - we replace 10% to 20% of our cells every year and produce several times that 100 trillion number of cells in our life time. Second, most of our cells are not produced by a simple cascade of cell devisions - we have specialized stem cells that do most of the cell production. I don't recall all the detailed analysis, but when all this is tallied up, most of our cells have resulted from about 100 devisions on average, giving the range of average mutations stated in my post.

The important thing to remember is that the vast, vast majority of mutations in the cells of individuals are inconsequential to the species. The vast majority of those mutations are even inconsequential to the individual, and because of the fecundity issue I discussed, the species can thrive even if some fraction of is members are disadvantage or non-viable. It is because of this high (but not complete) insensitivity to mutation that species experience intra-species diversity (what geneticists refer to as 'genetic drift', but I prefer the term 'genetic diffusion') and that I think this post is not off-topic for this thread.

To tidy up a loose end I think you'd need to add a paragraph that discusses how a species of loose genome can maintain that given your comment that a tight one might be better for a specific condition.

I will try to get back to this with a more detailed discussion, but the bottom line is that survival does not demand perfection, only that the species and its individual members be 'good enough'. (Please see Post #24 for some evidentiary support of this point.) The short term small changes to the environment would certainly be a factor in blurring out the meaning. of perfection and broadening the range of good enough.

Again, thank you for your kind words and for the great job you and other moderators have done in making this the best conceived and managed forum on the web.

Edited by AnswersInGenitals, : No reason given.


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Fosdick 
Suspended Member (Idle past 3785 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 26 of 35 (488805)
11-17-2008 7:47 PM
Reply to: Message 22 by straightree
11-17-2008 3:29 PM


Re: An ab initio Reducto ad Diversito.
straightree writes:

It could seem that erosion is just the destruction of rocks, but, at least in planet earth, it has been the starting point for soil building, that produced forests, and arable earth. So seen in that way, maybe it could be considered as rather deterministic.


I think this is fundamental to the Gaiaist philosophy.

—FTF


I can see Lower Slobovia from my house.

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Fosdick 
Suspended Member (Idle past 3785 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 27 of 35 (488807)
11-17-2008 8:10 PM
Reply to: Message 23 by AnswersInGenitals
11-17-2008 4:14 PM


Re: An ab initio Reducto ad Diversito.
AIG writes:

You are making the mistake so commonly found in creationist diatribes: If something is partly random, then it must be completely random. They accept the randomness of mutations but ignore the deterministic aspect of natural selection.


Ah, I didn't know there was one—the orange one. If natural selection is deterministic then you are saying that a population is predisposed one way or another to "differential reproductive success amongst individuals across the population" (E. O. Wilson et al.) THAT is all that NS really is. It's not some Selector who is out to pick His favorites. Perhaps you are a closet Creatin (just kidding).

Yes, erosion has a random component, but it also has a deterministic component due to the environment in which the erosion occurs.

But that is not really what determinism is. What you are speaking of is only mechanical, like a river carving out a gorge. The river has no determinism to do that, and neither does gravity.

—FTF


I can see Lower Slobovia from my house.

This message is a reply to:
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New Cat's Eye
Inactive Member


Message 28 of 35 (488808)
11-17-2008 9:58 PM
Reply to: Message 27 by Fosdick
11-17-2008 8:10 PM


Re: An ab initio Reducto ad Diversito.
Yes, erosion has a random component, but it also has a deterministic component due to the environment in which the erosion occurs.

But that is not really what determinism is. What you are speaking of is only mechanical, like a river carving out a gorge. The river has no determinism to do that, and neither does gravity.

Isn't that how he's using the word "deterministic", then?

AIG writes:

You are making the mistake so commonly found in creationist diatribes: If something is partly random, then it must be completely random. They accept the randomness of mutations but ignore the deterministic aspect of natural selection.

Ah, I didn't know there was one—the orange one. If natural selection is deterministic then you are saying that a population is predisposed one way or another to "differential reproductive success amongst individuals across the population" (E. O. Wilson et al.) THAT is all that NS really is. It's not some Selector who is out to pick His favorites. Perhaps you are a closet Creatin (just kidding).

I think if you use your "mechanical definition" rather than the "predisposed" one, then you'll be more on to his point.


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RAZD
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Posts: 20156
From: the other end of the sidewalk
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Message 29 of 35 (488814)
11-17-2008 11:15 PM
Reply to: Message 27 by Fosdick
11-17-2008 8:10 PM


back up the creek
What you are speaking of is only mechanical, like a river carving out a gorge. The river has no determinism to do that, and neither does gravity.

So is the gorge an emergent property of water flow and the random actions of erosion?

Enjoy.


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This message is a reply to:
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Fosdick 
Suspended Member (Idle past 3785 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 30 of 35 (488832)
11-18-2008 10:44 AM
Reply to: Message 29 by RAZD
11-17-2008 11:15 PM


Re: back up the creek
RAZD writes:

FTF writes:

What you are speaking of is only mechanical, like a river carving out a gorge. The river has no determinism to do that, and neither does gravity.


So is the gorge an emergent property of water flow and the random actions of erosion?

A very good question. I've heard people out here speak of the Columbia River gorge as the work of God, which might qualify it as an emergent property. That would be a act of Divine Hydraulics. But I personally don't think so. Mechanical things like that don't need to be glorified. When a rock falls to ground and leaves a divot, I don't think that divot is an EP.

—FTF


I can see Lower Slobovia from my house.

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 Message 29 by RAZD, posted 11-17-2008 11:15 PM RAZD has acknowledged this reply

    
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