Request for textbook recommendations

"Jim Menegay" <[email hidden]> wrote in message

Quoted message said:

Before I started reading this group, I thought I had a pretty good layman's understanding of
evolutionary theory and terminology. I realize now that my background in the technicalities is
inadequate.

You probably do have a reasonable understanding of the basic issues. Evolution is one of the
simplest scientific theories to understand, however, like any science, a large number of people are
interested in it and try to push our understanding as far as it will go. So just reading "The
Selfish Gene" will only start you on the road to being an evolutionary biologist.

Quoted message said:

Can anyone recommend a good graduate or advanced undergraduate > textbook

on the THEORY of evolution?

Quoted message said:

Matt Ridley, Evolution. (This is quite a big volume, I think there may be a slim popular work by him
of a similar name).

Quoted message said:

I am not allergic to math. I would like to see some kind of treatment of evolution at different
levels; even if the conclusion turns out to be that only one level (gene, organism, whatever) is
important, I would like to see this proved, rather than merely asserted. I want to see treatments
of ESS, kin selection, co-evolution of symbiotes, evolution of signaling mechanisms, evolution of
life histories, etc.

If you really want to be au fait with the issues, you need to look a journals. My favourite journal
is Brain and Behavioural Sciences, because every article is accompanied by critical comments from
the peer reviewers. It often has material on the evolution of behaviour, and often human behaviour.
TREE (Trends in Ecology and Evolution) is maybe a more relevant journal.

Quoted message said:

My primary interest is applying natural selection to origin of life, but it is not obvious just
which ideas may be useful here, so I guess I need to know a little about everything.

These are two separate issues. Evolution is what happens after replicating entities have appeared.
Now all known organisms use the same amino acids, the same gentic code (almost), DNA and RNA,
celular structure. What this means is that the most recent common ancestor was itself a fairly
sophisticated organism. Using evolution, it is difficult to push back our understanding beyond this
ancestor, but it cannot have appeared at a stroke.

Quoted message said:

And, while I have people thinking about textbooks, let me ask for recommendations in some
other fields:

I don't really know much about the biochemical side of things, which is relevant to the origin of
life. I'm just a ball-and-stick biochemist. I doubt that you can learn enough chemistry to make a
contribution to understanding the origin of life simply by reading textbooks, though that may be
more a reflection of my inabilities as a student rather than the difficulty of the subject.

Try Evolutionary Biology, Douglas J. Futuyma.

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

Can anyone recommend a good graduate or advanced undergraduate textbook on the THEORY of
evolution?

I am not allergic to math. I would like to see some kind of treatment of evolution at different
levels; even if the conclusion turns out to be that only one level (gene, organism, whatever) is
important, I would like to see this proved, rather than merely asserted. I want to see treatments
of ESS, kin selection, co-evolution of symbiotes, evolution of signaling mechanisms, evolution of
life histories, etc.

There's:

Evolution - Mark Ridley Evolutionary Biology - Douglas Futuyma

The former book does a good job of the "evolution at different levels" issue - IMO.

Quoted message said:

My primary interest is applying natural selection to origin of life, but it is not obvious just
which ideas may be useful here, so I guess I need to know a little about everything.

I would suggest considering life as being *defined* in terms of being an evolving system.

If you have no living system, there's no evolution.

Quoted message said:

From this point of view, natural selection can only apply *after*

the origin of life - and thus can't really be used to explain it.

Natural selection is relevant to practically every aspect of life - *except* its origin.
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Malcolm <[email hidden]> wrote or quoted:

Quoted message said:

Matt Ridley, Evolution. (This is quite a big volume, I think there may be a slim popular work by
him of a similar name).

There is. One is a text book. The other is a book of collected papers. Make sure you don't get them
muddled up...
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"Malcolm" <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

"Jim Menegay" <[email hidden]> wrote in message

Quoted message said:

[snip]
My primary interest is applying natural selection to origin of life, but it is not obvious just
which ideas may be useful here, so I guess I need to know a little about everything.

These are two separate issues.

I don't think so, for reasons given below.

Quoted message said:

Evolution is what happens after replicating entities have appeared.

Replicating entities with reproducible variation, yes.

Quoted message said:

Now all known organisms use the same amino acids, the same gentic code (almost), DNA and RNA,
celular structure. What this means is that the most recent common ancestor was itself a fairly
sophisticated organism.

This is well understood.

Quoted message said:

Using evolution, it is difficult to push back our understanding beyond this ancestor, but it
cannot have appeared at a stroke.

Certainly it could not have appeared at a stroke! Therefore, evolution must have been in operation
long before this complex common ancestor. Something much simpler "appeared at a stroke" and then
evolved to the LCA. An evolving "RNA world" is a cliche today, and I suspect that there may have
been other evolving entities before there were RNA sequences.

What I don't understand is your assertion that it is difficult to push back our understanding beyond
the LCA, *using evolution*. It is certainly true that it is impossible to push back our
understanding using phylogenic inference. But an understanding of the processes of evolution must
certainly be useful in pushing our understanding back - after all, it is evolution that provides the
dynamics leading from the "stroke" to the
LCA. Every trait of the LCA must be examined to see whether it could plausibly have evolved, or
whether it must have been primitive.

But perhaps I am overreacting here. I use the phrase OOL to refer to the entire process - the
"stroke" plus the evolution to the LCA. I prefer this usage, because it is far from clear that the
first evolving entities were "alive". If you understand the phrase "origin of life" to refer only
to events leading to the "stroke", then I am simply quibbling about your language. I have no wish
to do that.

Thank you very much for your other recommendations.

Jim

Tim Tyler <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

My primary interest is applying natural selection to origin of life, but it is not obvious just
which ideas may be useful here, so I guess I need to know a little about everything.

I would suggest considering life as being *defined* in terms of being an evolving system.

If you have no living system, there's no evolution.

Quoted message said:

From this point of view, natural selection can only apply *after*

the origin of life - and thus can't really be used to explain it.

Natural selection is relevant to practically every aspect of life - *except* its origin.

Thanks for the textbook recommendations. Regarding LIFE: I think I will assume my "Perplexed"
personna in responding to you, but also see my response to Malcolm ;-)

Dear Mr. Tyler,

My younger son shares your view of the meaning of life. All he wants

misses something important. He must, IMO, go out and get a job and learn how to maintain himself in
some way. His current bountiful environment will not last forever. My friends Varella and Maturana
agree with me.

Perplexed in Peoria.

Jim Menegay <[email hidden]> wrote or quoted:

[Evolution - not very relevant to life's origin?]

Quoted message said:

I think I will assume my "Perplexed" personna in responding to you, but also see my response to
Malcolm ;-)

Malcom is defending this thesis:

``Using evolution, it is difficult to push back our understanding
beyond this ancestor, but it cannot have appeared at a stroke.''

...which is debatable.

It may be *difficult* to look beyond the LCA - but there are two possibilities for reconstruction:

* Fossils;
* Scars and hangovers;

The first may be a bit far out - but the second has its uses.

Your "Perplexed" personna causes me some amusement. However, on usenet, there often is enough
confusion, without deliberately adding more.

In this case the Peorian resident seems to have gone off on quite a tangent - and I see little point
in pursuing them.

What does evolution tell us about the origin of life?

It tells us that there must have been a path from the first organisms to us.

I think the historical details of the early part of that path have been pretty effectively obscured
by the passage of time - and *possible* paths between practically *any* early organism and us are
possible to imagine - so that this clue does not amount to a hill of beans.
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[email hidden] (Jim Menegay) wrote in
:"]news:[email hidden]:

Quoted message said:

"Malcolm" <[email hidden]> wrote in message
news:<[email hidden]>...

Quoted message said:

"Jim Menegay" <[email hidden]> wrote in message

Quoted message said:

Using evolution, it is difficult to push back our understanding beyond this ancestor, but it
cannot have appeared at a stroke.

Quoted message said:

Certainly it could not have appeared at a stroke! Therefore, evolution must have been in operation
long before this complex common ancestor. Something much simpler "appeared at a stroke" and then
evolved to the LCA. An evolving "RNA world" is a cliche today, and I suspect that there may have
been other evolving entities before there were RNA sequences.

Daniel Dennett, who is an "evolutionary philosopher" if there is such a thing, would agree with you
( as would others who think evolution only requires replicators).

Quoted message said:

What I don't understand is your assertion that it is difficult to push back our understanding
beyond the LCA, *using evolution*. It is certainly true that it is impossible to push back our
understanding using phylogenic inference. But an understanding of the processes of evolution must
certainly be useful in pushing our understanding back - after all, it is evolution that provides
the dynamics leading from the "stroke" to the LCA.

Given your interest in studying the basics of biochemistry as they apply to evolution, I suspect you
might also be interested in some of the work that attempts to explain the appearance of complexity
as a general phenomenon of non-equilibrium systems. This work attempts to bridge the divide between
chemistry and biology. Stuart Kauffman is a leading expert in the field, but the only book I have by
him - "Investigations" - I have found rather impenetrable. Apparently his "Coming of Age in the
Universe" is more readable, but I have heard that there are better introductions to this subject -
unfortunately I can't remember any names.

Yours,

Bill Morse

William Morse <[email hidden]> wrote or quoted:

Quoted message said:

[email hidden] (Jim Menegay) wrote in

Quoted message said:

"Malcolm" <[email hidden]> wrote in message

Quoted message said:

Quoted message said:

Quoted message said:

Using evolution, it is difficult to push back our understanding beyond this ancestor, but it
cannot have appeared at a stroke.

Certainly it could not have appeared at a stroke! Therefore, evolution must have been in
operation long before this complex common ancestor. Something much simpler "appeared at a stroke"
and then evolved to the LCA. An evolving "RNA world" is a cliche today, and I suspect that there
may have been other evolving entities before there were RNA sequences.

Daniel Dennett, who is an "evolutionary philosopher" if there is such a thing, would agree with
you ( as would others who think evolution only requires replicators).

As does practically everyone else.

Few think RNA was the first genetic medium - since the associated biochemistry is so unlikely and
fantastic.

Quoted message said:

Given your interest in studying the basics of biochemistry as they apply to evolution, I suspect
you might also be interested in some of the work that attempts to explain the appearance of
complexity as a general phenomenon of non-equilibrium systems. This work attempts to bridge the
divide between chemistry and biology. Stuart Kauffman is a leading expert in the field, but the
only book I have by him - "Investigations" - I have found rather impenetrable. Apparently his
"Coming of Age in the Universe" is more readable [...]

You mean "At Home in the Universe".
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William Morse <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

Given your interest in studying the basics of biochemistry as they apply to evolution, I suspect
you might also be interested in some of the work that attempts to explain the appearance of
complexity as a general phenomenon of non-equilibrium systems. This work attempts to bridge the
divide between chemistry and biology. Stuart Kauffman is a leading expert in the field, but the
only book I have by him - "Investigations" - I have found rather impenetrable. Apparently his
"Coming of Age in the Universe" is more readable, but I have heard that there are better
introductions to this subject - unfortunately I can't remember any names.

I've read some Kauffman. The two books you mention, particularly "Investigations", struck me
as things that he turned out under a deadline from his publisher - part of a three book deal
to cash in.

Some of his earlier stuff had some substance, but not enough thermodynamic realism to suit me.
Prigogene, on the other hand, has the thermodynamics, but not the information theory. Brooks and
Wiley attempt both, but there are so many errors in their concept and in their details that it is
impossible to take them seriously. I wish there were a good tutorial on this whole thing of
information, thermodynamics, evolution, and systems theory that spelled out the foundations properly
before going on to speculation about the possible applications. I haven't come across any thing like
that yet. Though I noticed some recommendations on another thread recently.

in article [email hidden], Jim Menegay at
[email hidden] wrote on 12/19/03 8:43 AM:

Quoted message said:

William Morse <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

Given your interest in studying the basics of biochemistry as they apply to evolution, I suspect
you might also be interested in some of the work that attempts to explain the appearance of
complexity as a general phenomenon of non-equilibrium systems. This work attempts to bridge the
divide between chemistry and biology. Stuart Kauffman is a leading expert in the field, but the
only book I have by him - "Investigations" - I have found rather impenetrable. Apparently his
"Coming of Age in the Universe" is more readable, but I have heard that there are better
introductions to this subject - unfortunately I can't remember any names.

I've read some Kauffman. The two books you mention, particularly "Investigations", struck me as
things that he turned out under a deadline from his publisher - part of a three book deal to
cash in.

Some of his earlier stuff had some substance, but not enough thermodynamic realism to suit me.
Prigogene, on the other hand, has the thermodynamics, but not the information theory. Brooks and
Wiley attempt both, but there are so many errors in their concept and in their details that it is
impossible to take them seriously. I wish there were a good tutorial on this whole thing of
information, thermodynamics, evolution, and systems theory that spelled out the foundations
properly before going on to speculation about the possible applications. I haven't come across any
thing like that yet. Though I noticed some recommendations on another thread recently.

You might want to take a look at a book called "Darwinism Evolving" by Depew and Weber.

Cheers,

Guy

[email hidden] (Jim Menegay) wrote in
:"]news:[email hidden]:

Quoted message said:

William Morse <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

Given your interest in studying the basics of biochemistry as they apply to evolution, I suspect
you might also be interested in some of the work that attempts to explain the appearance of
complexity as a general phenomenon of non-equilibrium systems. This work attempts to bridge the
divide between chemistry and biology. Stuart Kauffman is a leading expert in the field, but the
only book I have by him - "Investigations" - I have found rather impenetrable. Apparently his
"Coming of Age in the Universe" is more readable, but I have heard that there are better
introductions to this subject - unfortunately I can't remember any names.

I've read some Kauffman. The two books you mention, particularly "Investigations", struck me as
things that he turned out under a deadline from his publisher - part of a three book deal to
cash in.

Some of his earlier stuff had some substance, but not enough thermodynamic realism to suit me.
Prigogene, on the other hand, has the thermodynamics, but not the information theory. Brooks and
Wiley attempt both, but there are so many errors in their concept and in their details that it is
impossible to take them seriously. I wish there were a good tutorial on this whole thing of
information, thermodynamics, evolution, and systems theory that spelled out the foundations
properly before going on to speculation about the possible applications. I haven't come across any
thing like that yet. Though I noticed some recommendations on another thread recently.

You seem to be ahead of me on this end of evolution. It is only recently that I realized I would
have to be able to understand Boltzmann, Prigogene, and Shannon along with pid control if I was
serious about figuring out how life started - and my ability to follow the details of the math stops
right about at Maxwell. Unfortunately I have also not found the tutorial you are looking for. You
may want to check out Howard Odum's " Environment, Power, and Society" for an early attempt at
"consilience".I would think someone has done a similar synthesis recently, but I don't know of one.
Wilson does a reasonably nice job of defining the benefits of consilience, but he doesn't fill in
the details.

Yours,

Bill Morse

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

Some of his earlier stuff had some substance, but not enough thermodynamic realism to suit me.
Prigogene, on the other hand, has the thermodynamics, but not the information theory. Brooks and
Wiley attempt both, but there are so many errors in their concept and in their details that it is
impossible to take them seriously.

Amazon has a review - which offers the following comments:

``As useless as the book cited above is the book 'Evolution as Entropy'by Brooks and Wiley. The
basic proposition in this work is that speciation is controlled by the stochastic premises of the
second law of thermodynamics. One may only regret that in the 43 years since the publication of
Schrodinger's work [the book 'What is Life?'] a book has appeared whose authors do not understand
the role of the second law of thermodynamics in living nature...the authors are concerned only with
the amount of information and, hence, with entropy. But, by confining oneself to these concepts
alone, one can hardly say anything about evolution...in the world of living things the quality or
value of information is often of decisive importance...''

- amazon.com0226075745Open ↗
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Tim Tyler <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

Some of his earlier stuff had some substance, but not enough thermodynamic realism to suit me.
Prigogine, on the other hand, has the thermodynamics, but not the information theory. Brooks and
Wiley attempt both, but there are so many errors in their concept and in their details that it
is impossible to take them seriously.

Amazon has a review - which offers the following comments:

``As useless as the book cited above is the book 'Evolution as Entropy'by Brooks and Wiley. The
basic proposition in this work is that speciation is controlled by the stochastic premises of the
second law of thermodynamics. One may only regret that in the 43 years since the publication of
Schrodinger's work [the book 'What is Life?'] a book has appeared whose authors do not understand
the role of the second law of thermodynamics in living nature...the authors are concerned only
with the amount of information and, hence, with entropy. But, by confining oneself to these
concepts alone, one can hardly say anything about evolution...in the world of living things the
quality or value of information is often of decisive importance...''

- amazon.com0226075745Open ↗

Ouch! And I thought *I* was being harsh. There is a kernel of truth in their ideas though - that
evolution can be thought of as the accumulation of information. The completely silly thing about it
is that they seem to think that since Shannon said "Information = Entropy", therefore the fact that
information accumulates is a consequence of the 2nd Law.

But they do attempt to apply "Evolution = Information Accumulation" to various non-Darwinian kinds
of evolution (ecosystem evolution, for example) with occasionally provocative results.

Guy Hoelzer <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

in article [email hidden], Jim Menegay at [email hidden] wrote on
12/19/03 8:43 AM:

Quoted message said:

Quoted message said:

I wish there were a good tutorial on this whole thing of information, thermodynamics, evolution,
and systems theory that spelled out the foundations properly before going on to speculation
about the possible applications. I haven't come across any thing like that yet. Though I noticed
some recommendations on another thread recently.

You might want to take a look at a book called "Darwinism Evolving" by Depew and Weber.

Cheers,

Guy

The jacket blurb reported at Amazon makes it sound like it is not the tutorial I was looking for,
but interesting nonetheless. Thx, Guy.

I dug up the "recommendations on another thread" that I had mentioned. The request was:

Quoted message said:

Could anyone recommend me some readings on the topic of evolution as entropy (or as negentropy, I
would think)? I think that the notion of complexity to explain evolution has been largely used by
people such as Stuart Kauffman and Brian Goodwin, but I couldn't find references of writing
referring to entropy.

The request received 5 interesting responses.

1. [moderator's note: Call me crazy, but how about Brooks and Wiley's book, "Evolution as Entropy"?
(Univ. Chicago Press, 1988, I think). Worth a look, although my recollection is that it's
extremely dense writing. - JAH]

2. [Guy Holtzer] ... I would add "Darwinism Evolving" by Depew and Weber, and "Signs of Life" by
Sole and Goodwin.

3. [John Wilkins] Chaisson, Eric L. 2001. Cosmic evolution: The rise of complexity in nature.
Cambridge MA: Harvard University Press. The entropy in B&W is Shannon entropy, or the
informational entropy of a signal. The entropy in Chaisson is thermodynamic entropy. Personally,
I prefer the latter account.

4. [r_norman] Evolution is not ordinarily considered in the context of entropy except. That is why
there are not "standard" works in this area. There are specific somewhat speculative treatises
like the Brooks book already mentioned, as well as things like Weber, Bruce: ed. (1988) Entropy,
Information, and Evolution, MIT Press, Cambridge. You should also look at works in information
theory and complexity theory. Still, none of these areas are main-line evolution. They usually
represent physicists or mathematicians attempts at developing some sort of synthetic theory
applicable to evolution.

and finally

5. [TomHendricks474 who offers to email a collection of his own writings on heat cycles.]

I don't know whether this confirms Edser or refutes him.

Jim Menegay <[email hidden]> wrote or quoted:

[Brooks and Wiley's book, Evolution as Entropy]

Quoted message said:

There is a kernel of truth in their ideas though - that evolution can be thought of as the
accumulation of information. The completely silly thing about it is that they seem to think that
since Shannon said "Information = Entropy", therefore the fact that information accumulates is a
consequence of the 2nd Law. [...]

The main link between evolution and thermodynamics which I have considered is the one that regards
evoultion as a dissipative structure that maximises the level of energy degradation in a system.

The idea asks much the same question that Richard Dawkins is famous for asking - namely:

What is it that natural systems are best though of as optimising?

Dawkins pinned the blame on gene frequencies - but this idea identifies a "gross" thermodynamic
concept as the agent responsible - and claims that the action of living systems on an ecosystem is
to dissipate and degrade energy and maximise entropy.

The idea has been floating around for a long while now. I was first alerted to it by:

"Life as a Manifestation of the Second Law of Thermodynamics" - Schneider,
E.D, Kay, J.J., 1994, Mathematical and Computer Modelling, Vol 19, No. 6-8, pp.25-48. [link in
references on site below]

I have my own expression of the idea - at:

originoflife.netbright lightOpen ↗
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Tim Tyler <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

Jim Menegay <[email hidden]> wrote or quoted:

[Brooks and Wiley's book, Evolution as Entropy]

Quoted message said:

There is a kernel of truth in their ideas though - that evolution can be thought of as the
accumulation of information. The completely silly thing about it is that they seem to think that
since Shannon said "Information = Entropy", therefore the fact that information accumulates is a
consequence of the 2nd Law. [...]

The main link between evolution and thermodynamics which I have considered is the one that regards
evoultion as a dissipative structure that maximises the level of energy degradation in a system.

The idea asks much the same question that Richard Dawkins is famous for asking - namely:

What is it that natural systems are best though of as optimising?

Dawkins pinned the blame on gene frequencies - but this idea identifies a "gross" thermodynamic
concept as the agent responsible - and claims that the action of living systems on an ecosystem is
to dissipate and degrade energy and maximise entropy.

The idea has been floating around for a long while now. I was first alerted to it by:

"Life as a Manifestation of the Second Law of Thermodynamics" - Schneider,
E.D, Kay, J.J., 1994, Mathematical and Computer Modelling, Vol 19, No. 6-8, pp.25-48. [link in
references on site below]

I have my own expression of the idea - at:

originoflife.netbright lightOpen ↗

The thing is, though, that Prigogine's "dissipative structures" are claimed to *minimize* the
generation of entropy, at least as measured per unit volume. Your ecosystems are claimed to
*maximize* entropy generation. No one that I have read has ever reconciled these ideas to my
satisfaction.

One idea might be that life is economical in its dissipation of neg-entropy locally (K-selection?),
but that it tends to increase the volume of the dissipative structure (r-selection?). I just wish
that someone would tie together all of these ideas that are floating around out there into some kind
of explanatory framework!

Jim

<< Natural selection is relevant to practically every aspect of life - *except* its origin. >>

Then there is no such thing as 'chemical selection'?

TomHendricks474 <[email hidden]> wrote or quoted me as saying:

Quoted message said:

<< Natural selection is relevant to practically every aspect of life - *except* its origin. >>

Quoted message said:

Then there is no such thing as 'chemical selection'?

"Chemical selection" appears to be a pretty useless term.

It seems to refer to a lot of nonsense about chemicals groping towards life without having any
system of inheritance.

Either there's a system of inheritance - (in which case the thing is alive - and "chemicals" seems a
bit disparaging, since the evolution is biological in nature) - or there isn't - in which case,
selection has no heritable variation to work on.

Some of the autocatalytic set folk use the term in what I suppose is a borderline-acceptable manner
- to refer to simple organisms before any advanced biological molecules or a template replication
system existed. They use it to refer to living, evolving organisms - *after* life's origin.
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