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Extended Phenotype as Adaptive Niche 
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Post Extended Phenotype as Adaptive Niche
I haven't managed to read all of The Extended Phenotype and hope someone who has can help me out.

What is the extended phenotype?

Is is the environmental context of the gene as it is affected by the genome? For example, termites in a forest make hollows in trees which birds nest in and bring fertiliser for more trees to grow and more termites. So are the birds and trees and soil part of the extended phenotype of the termite?

As such, the factors of reality into which the genome adapts provide boundaries for its evolution. These boundaries may be defined as the niche of the genome. These boundaries are also affected by the phenotypic behaviour of the organism. Hence the niche is a function of the genome and its adaptation to its possibilities.



Sun Dec 06, 2009 9:51 am
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Post Re: Extended Phenotype as Adaptive Niche
Robert Tulip wrote:
What is the extended phenotype? Is is the environmental context of the gene as it is affected by the genome? For example, termites in a forest make hollows in trees which birds nest in and bring fertiliser for more trees to grow and more termites. So are the birds and trees and soil part of the extended phenotype of the termite?


I'm a bit more than halfway through The Extended Phenotype, but I'll take a stab at your question, Robert.

Normally when you talk about phenotype, it's the expression of genes or observable characteristics of an individual related to its interaction with the environment.

Wikipedia: - Phenotypes result from the expression of an organism's genes as well as the influence of environmental factors and possible interactions between the two. The genotype of an organism is the inherited instructions it carries within its genetic code. Not all organisms with the same genotype look or act the same way because appearance and behavior are modified by environmental and developmental conditions.

But this definition is individual-centric. As you know, Dawkins promotes the idea of seeing things from a gene's perspective which changes things profoundly. If you look at it this way, the gene's environment includes other genes. InThe Selfish Gene, Dawkins presents the idea that a gene's success frequently depends on how it interacts with other genes. Remember the analogy of the rowers in a boat, and how a gene can be affected by both its position in the boat and how it's output can be affected by the positions of other rowers? But the gene's environment is also the body in which it sits, a concept Dawkins explains quite well in the added on last chapter of The Selfish Gene, "The Long Reach of the Gene." The italics in the quoted passage are Dawkins'.

"The phenotypic effects of a gene are normally seen as all the effects that it has on the body in which it sits. This is the conventional definition. But we shall now see that the phenotypic effects of a gene need to be thought of as all the effects that it has on the world. It may be that a gene's effect, as a matter of fact, turn out to be confined to the succession of bodies in which the gene sits. But, if so, it will be just as matter of fact. It will not be something that ought to be part of our very definition. In all this, remember that the phenotypic effects of a gene are the tools by which it levers itself into the next generation. All that I'm going to add is that the tools may reach outside the individual body wall. What might it mean in practice to speak of a gene as having an extended phenotypic effect on the world outside the body in which it sits? Examples that spring to mind are artefacts like beaver dams, bird nests, and caddis houses." (pg. 238)

These are obvious examples, but i think Dawkins is also suggesting that the shape of a caddis house is not really different than the shape of a leg or antenna of the individual caddis. Both are phenotypic effects that a gene has on the world (from a gene's perspective). It doesn't matter so much whether that phenotypic effect takes place in the body in which the gene sits or in the world at large. I think what Dawkins means by "extended phenotype" is a gene's reach into the environment outside of the body in which it sits. So Robert provides some good examples. A spider's web or a tree that creates a canopy and creates a shaded area which limits other types of plant growth are others. Also the way some parasites actively affect the DNA of its host organism is yet another.


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Sun Dec 06, 2009 2:16 pm
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Post Re: Extended Phenotype as Adaptive Niche
geo wrote:
..Dawkins explains quite well in the added on last chapter of The Selfish Gene, "The Long Reach of the Gene." The italics in the quoted passage are Dawkins'... the phenotypic effects of a gene need to be thought of as all the effects that it has on the world.


Let me give a further example, a quick history of the world. Earth's orbit was stabilised with the moon following the massive cosmic bombardment of four billion years ago caused by Neptune moving outside the orbit of Uranus. Since then, life was microbial for 3.5 billion years, gradually adding oxygen to the atmosphere to create the point at which macrobial life could emerge 500 million years ago in the Cambrian Explosion. Of our sixteen orbits of the galaxy since life evolved, only the last two have had multicellular animals.

So, the oxygen we breath is the extended phenotype of billions of years of one cell organisms converting CO2 into carbon and oxygen.



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Post Re: Extended Phenotype as Adaptive Niche
Robert Tulip wrote:

Let me give a further example, a quick history of the world. Earth's orbit was stabilised with the moon following the massive cosmic bombardment of four billion years ago caused by Neptune moving outside the orbit of Uranus. Since then, life was microbial for 3.5 billion years, gradually adding oxygen to the atmosphere to create the point at which macrobial life could emerge 500 million years ago in the Cambrian Explosion. Of our sixteen orbits of the galaxy since life evolved, only the last two have had multicellular animals.

So, the oxygen we breath is the extended phenotype of billions of years of one cell organisms converting CO2 into carbon and oxygen


I wasn't aware that the change of Neptune's orbit would have caused a massive cosmic bombardment. On earth, you mean?

By sixteen orbits, I guess you mean Great Years? I'm not sure of the significance of that except to say this vast time scale always underscores to me how small we are and how recently we came to be on our planet. We homo sapiens have a tendency to overestimate our importance in the grand scheme of things.

That's an interesting concept about oxygen being an extended phenotype of unicellular animals. I would almost suggest extended phenotypic "remnants" although microbial life continues to pump oxygen into the atmosphere. I wonder, is it necessary for unicellular life forms to precede multicellular ones on planets capable of harboring life?


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Post Re: Extended Phenotype as Adaptive Niche
geo wrote:
I wasn't aware that the change of Neptune's orbit would have caused a massive cosmic bombardment. On earth, you mean?
Check out http://en.wikipedia.org/wiki/Late_Heavy ... _migration and especially the superb dynamic graphic at http://www.psrd.hawaii.edu/Aug06/cataclysmDynamics.html

Quote:
By sixteen orbits, I guess you mean Great Years? I'm not sure of the significance of that except to say this vast time scale always underscores to me how small we are and how recently we came to be on our planet. We homo sapiens have a tendency to overestimate our importance in the grand scheme of things.
Ha, this is funny. Howard Bloom says in Genius of the Beast that the earth takes 250 million miles to go around the galaxy, when he means 250 million years. There are ten thousand great years in one galactic orbit, and about sixteen galactic orbits since life began, so about 170,000 Great Years in the history of time.
Quote:
That's an interesting concept about oxygen being an extended phenotype of unicellular animals. I would almost suggest extended phenotypic "remnants" although microbial life continues to pump oxygen into the atmosphere. I wonder, is it necessary for unicellular life forms to precede multicellular ones on planets capable of harboring life?

My favourite book on this Topic is Rare Earth, Why Complex Life is Uncommon in the Universe. Yes, there may be dozens of microbial living worlds out there, but how many share our accidents of protection from comets by Jupiter, season regulation by the moon, a radioactive core to drive plate tectonics, several billion cubic kilometres of surface water, a goldilocks temperature where water is liquid, and all that stable for four billion years. But for the grace of God in enabling macrobial complexity, we would still be microbes. Microbes precede macrobes as the simple precedes the complex.



Last edited by Robert Tulip on Wed Dec 23, 2009 6:02 pm, edited 1 time in total.



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Post Re: Extended Phenotype as Adaptive Niche
Robert, I've noticed you're getting your Blooms mixed up :? . Harold is the lit crit, while Howard is your man.

I suppose that even with billions of candidate sites for life, around the universe, it is just barely conceivable that the conditions that ended up producing us are unique and that therefore we are as well.


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Mon Dec 07, 2009 8:41 am
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Post Re: Extended Phenotype as Adaptive Niche
Robert Tulip wrote:
Microbes precede macrobes as the simple precedes the complex.


I meant in terms of creating oxygen. Must the requisite amount of oxygen come from microbial life forms over a vast time period? We evolved from the conditions that exist on earth and other complex life forms on other planets might very well spring up in an environment that's quite different. A world with a smaller percentage of oxygen, for example. Then again, my question seems skewed. Evolution by its very nature starts simple and get more complex, the simpler forms always paving the way for more complex life forms.

DWill wrote:
Robert, I've noticed you're getting your Blooms mixed up :? . Harold is the lit crit, while Howard is your man.


I remember Robert did that in the chat room once with yet another Bloom—Alan Bloom, who wrote The Closing of the American Mind. He confused Alan with Harold, I believe. Robert, you simply must get your Blooms straight. :lol:


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Post Re: Extended Phenotype as Adaptive Niche
geo wrote:
Robert Tulip wrote:
Microbes precede macrobes as the simple precedes the complex.


I meant in terms of creating oxygen. Must complex forms of life be preceded by eons of microbial oxygenation?

Then again, my question seems skewed. We evolved from the conditions that exist on earth and other complex life forms on other planets might very well spring up in an environment that's quite different. A world with a smaller percentage of oxygen, for example. And, yet, evolution by its very nature would start simple and get more complex, the simpler forms paving the way in important ways.

DWill wrote:
Robert, I've noticed you're getting your Blooms mixed up :? . Harold is the lit crit, while Howard is your man.


I remember Robert did that in the chat room once with yet another Bloom—Alan Bloom, who wrote The Closing of the American Mind. He confused Alan with Harold, I believe. Robert, you simply must get your Blooms straight. :lol:


I've now put the three books beside themselves on my shelf - Alan, Harold and Howard Bloom. All I need is Ulysses by Joyce and I will be ready for Tulips Day.

The theme of simple to complex is basic to evolution, as the genome gradually oozes like molten lava into every nook and cranny of the available niche, becoming steadily more complex until a catastrophe, with the next rise then generally starting from a more complex base. When all its crannies are full, an ecosystem is complex, when it has plenty of empty nooks it is simple. Algae made the niche for animals by oxygenating the air over billions of years. Animals are part of the extended phenotype of algae, evolving into the niche that algae has created.

Can I again recommend a look at the superb dynamic graphic at http://www.psrd.hawaii.edu/Aug06/cataclysmDynamics.html of Neptune setting up the current rhythm of the solar system. This is true! Basically, Saturn was drifting out further from Jupiter, and when Saturn reached the double Jupiter orbit 3.9 billion years ago they set up a resonance which tossed Neptune out from its location as number three gas giant to its present position as number four, behind Uranus at number three. This caused the late cosmic bombardment that put the man in the moon. Earth also got smashed, but our tectonic surface has long since removed all trace.

This gas giant story has the makings of an interesting myth. For the Greeks, Zeus (Jupiter), Chronos (Saturn) and Uranus were successive lords of earth and sky, while Neptune ruled the ocean. Saturn and his father Uranus had a tiff, involving castration and the furies, and then Jupiter/Zeus Pater replaced his six brothers and sisters in their dad Saturn's belly with rocks, as old father time had eaten all the gods at birth except wily Zeus. That is the myth of time (Chronos/Saturn).



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Post Re: Extended Phenotype as Adaptive Niche
Robert Tulip wrote:

So, the oxygen we breath is the extended phenotype of billions of years of one cell organisms converting CO2 into carbon and oxygen.


I'm on Ch. 11, The Genetic Evolution of Animal Artefacts, and I would be remiss not to mention this. Since an actual discussion of this book is not in the cards, I'll just post this here. And rather than try to paraphrase Dawkins, I'll just quote this passage:

"The analysis of artefacts given in this chapter might seem, at first sight, vulnerable to reductio ad absurdum. Isn't there a sense, it may be asked, in which every effect that an animal has upon the world is an extended phenotype? What about the footprints left in the mud by an osytercatcher, the paths worn through the grass by sheep, the luxuriant tussock that marks the spot of last year's cowpat? . . . To answer this we must recall the fundamental reason why we are interested in the phenotypic expression of genes in the first place. Of all the many possible reasons, the one which concerns us in this book is as follows. We are fundamentally interested in natural selection, therefore in the differential survival of replicating entities such as genes. Genes are favored or disfavored relative to their alleles as a consequence of their phenotypic effects upon the world. Some of these phenotypic effects may be incidental consequences of others, and have no bearing on the survival chances, one way or another, of the genes concerned."

Dawkins hypothesizes a mutation that changes the shape of the oystercatcher's feet, which might affect the oystercatcher's survival chances by slightly reducing the bird's risk of sinking into mud. The mutation would also change the shape of the footprints the oystercatcher leaves in the mud, but while this is arguably an extended phenotypic effect, it is of no interest to the student of natural selection . . .

". . . and there is no point in bothering to discuss it under the heading of the extended phenotype, though it would be formally correct to do so. If on the other hand the changed footprint did influence survival of the oystercatcher, say by making it harder for predators to track the bird, I would want it to regard it as an extended phenotype of the gene. Phenotypic effects of genes, whether at the level of intracellular biochemistry, gross bodily morphology or extended phenotype, are potentially devices by which genes lever themselves into the next generation, or barriers to their doing so." (pg. 206-207)

The one-celled organisms' oxygen-producing effect is technically an extended phenotype, but I'd say for purposes of discussion it's more of a phenotypic byproduct. The oxygen produced by the one-celled organism paves the way for more complex animals to come, but presumably at the time it was produced the oxygen didn't affect the survival chances of the genes that produced it.


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