Gene frequencies and evolution

in article [email hidden], William Morse at
[email hidden] wrote on 1/2/04 12:34 PM:

Quoted message said:

But we do get non-contingent results. And in evolution we have had experiments repeated. On three
continents we have had mammals evolve in the presence of the potential food resource of anthills.
The result is spiny anteaters, pangolins, and south american anteaters. They are totally
unrelated, but share numerous features in common. Now they are not identical, because evolution
_is_ contingent. But they are similar, because evolution is also statistical - even with the
confounding factors there is enough equivalent comparison (Fred is 22, Joe is 20, both turned as
the tiger started its charge, often enough that differential speed alone made a difference in
survival) to give evolution some typical directions. These directions represent possible niches -
large size and low reproductive rate, small size and high reproductive rate: speed, armor:
camouflage, toxicity and bright colors: etc. So we cannot talk about an overall direction for
evolution, but we can make predictions despite contingency.

I have no problem with non-contingent evolution. In fact I probably have one of the more extreme
views on this. I believe evolution is very predictable and has a direction. From what I understand
you are talking about traits I am talking about genes as in discrete sequences of DNA and there
change infrequency in response to selection.

--

Phillip Smith phills@(buggger).co.nz replace bugger with ihug applied-evolution.co.nzapplied-evolution.co.nzOpen ↗

"he who is smeared with blubber has the kindest heart" -- a Greenland Eskimo adage

<< TT:- Definitions of evolution involving gene frequenquencies *are* narrow.

Is it possible to do better?

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

JE:- For the above definition to represent a testable theory of evolution and not just a loose non
testable view of evolution it has to be amended to read:

" NON RANDOM changes to the heritable elements of a population "

Quoted message said:

Quoted message said:

But there is no mention of selection in those heritable variants of either def.. Should there be?

phillip smith <[email hidden]> wrote or quoted:

Quoted message said:

Tim Tyler at [email hidden]

Quoted message said:

Quoted message said:

Definitions of evolution involving gene frequenquencies *are* narrow.

Is it possible to do better?

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

What is wrong with simply "change over time"

Such a definition would turn the process of erosion into evolution.
--
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phillip smith said:

in article [email hidden], Anon. at [email hidden] wrote
on 24/1/04 7:51 PM:

Quoted message said:

But you need linkage disequilibrium (LD) as well as epistasis to change the effects of a single
gene. LD is reduced by recombination, so you'd need the interacting genes to be close to each
other, or for the epistasis to be large, for the affect to be appreciable.

This is true of the epistatic interactions are limited to a single allele of a single gene at a
limited stretch of the genome. For this to be true the rest of the genome must be considered
static. I doubt this ever occurs or occurs out side of the lab with sufficient frequency to
matter. To illustrate my point take the rest of the genome save the gene we are interested in and
cinsider it all as being one gene. How many alleles are there and what is the epistatic effects on
that on the coefficent of selection of the gene we are examining?

Well, if we're considering all of the interacting genes, then clearly the epistatic interactions
with the rest of the genome are zero.

Bob

--
Bob O'Hara

Dept. of Mathematics and Statistics
P.O. Box 4 (Yliopistonkatu 5) FIN-00014 University of Helsinki Finland Telephone: +358-9-191 23743
Mobile: +358 50 599 0540 Fax: +358-9-191 22 779 WWW: rni.helsinki.fi~bohOpen ↗

in article [email hidden], John Edser at [email hidden]
wrote on 2/2/04 11:40 PM:

Quoted message said:

TT:- Definitions of evolution involving gene frequenquencies *are* narrow.

Is it possible to do better?

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

JE:- For the above definition to represent a testable theory of evolution and not just a loose non
testable view of evolution it has to be amended to read:

" NON RANDOM changes to the heritable elements of a population "

This would be far too vague, and therefore untestable. You would have to specify "non-random"
with respect to something in particular. It is an empirical fact in a complex universe that any
change will be correlated with some other changes. This would allow someone using the definition
above to choose any reference point they want and claim that evolution either did or did not
occur in any instance.

Guy

<< TT:- Definitions of evolution involving gene frequenquencies *are* narrow.

Is it possible to do better?

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

JE:- For the above definition to represent a testable theory of evolution and not just a loose non
testable view of evolution it has to be amended to read:

" NON RANDOM changes to the heritable elements of a population "

Quoted message said:

Quoted message said:

TH:- But there is no mention of selection in those heritable variants of either def..
Should there be?

JE:- No, it is not necessary. At the moment the only testable theory of evolution we have was
Darwin's original proposition. This does not mean that other non random causations should be
excluded if and when they are produced as testable theories of nature. Not that Neo Darwinism has
changed nothing re: Darwin's original proposition of evolution as the only testable theory of
_nature_ we have.

Until Neo Darwinians are prepared to open a discussion on possible simplified model misuse within
evolutionary theory, this problem will remain swept under a carpet within an ivory tower. I have
tried to open discussion on this topic for nearly 5 years and have failed.

Best Wishes

John Edser Independent Researcher

PO Box 266 Church Pt NSW 2105 Australia

[email hidden]

Quoted message said:

Quoted message said:

Definitions of evolution involving gene frequenquencies *are* narrow.

Is it possible to do better?

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

Quoted message said:

What is wrong with simply "change over time"

TT:- Such a definition would turn the process of erosion into evolution.

JE:- What is the testable difference between the processes of erosion and genetic drift,
i.e. excluding the difference between dirt and genes and just comparing each process as a logical
structure?

Regards,

John Edser Independent Researcher

PO Box 266 Church t NSW 2105 Australia

[email hidden]

Tim Tyler said:

phillip smith <[email hidden]> wrote or quoted:

Quoted message said:

Tim Tyler at [email hidden]

Quoted message said:

Quoted message said:

Definitions of evolution involving gene frequenquencies *are* narrow.

Is it possible to do better?

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

What is wrong with simply "change over time"

Such a definition would turn the process of erosion into evolution.

I like the definition "changes to the heritable elements of a population". It is broad enough to
encompass changes in our understanding of evolution but also limits the definition such that it only
applies to life.

More specifically, I have the following problems with the "gene frequency" definition.

1) To nitpick the terminology, aren't we really interested in allele frequency, not gene frequency?

2) Genes (and their alleles) are very blunt concepts. They cannot be defined as discrete units in
terms of DNA. So what we are reduced to is tracking the levels of particular DNA sequences in
living organisms.

3) Was there evolution before the emergence of the genetic system? (ribosomes, tRNA, and such) I
have trouble imagine how the genetic system emerged if not by evolution.

4) Similarly, it does not account for evolution of the cellular structure. Proteins often have
localization signals. Is it just the gene-encoded information that causes a protein to be sent to
a particular organelle? I doubt it... there are aspects of that organelle's membrane and the cell
architecture that cannot be reduced to simply being the result of genes.

5) Similarly, it does not account for heritable endosymbiosis, as is believed to have produced
plastids and mitochondria.

6) Similarly, it does not account for inherited ecological interactions. I have never heard of
anyone talk of this, but heritable endosymbiosis would be one extreme of this. Another would be
where a creature picks up an external mutualist/parasite from its parents.

7) Similarly, it does not account for habitat construction. I understand that this is a
controversial concept in E&E circles (if I used the proper term), but it makes sense to me.

8) It does not account for multigenerational prions, which seem to have influenced the
evolution of yeast. There are also other examples of structural inheritance, including the
orientation of cilia.

9) It does not account for how all of the molecules in a living system come together to give
interesting behavior. It doesn't account for phenotypic plasticity. Sure, there might be changes
in gene frequencies but that really isn't the interesting part of life.

The study of evolution should answer the question "How did life get to be as it is?" Any one of the
above objections is enough to sink the "gene frequency" view of evolution as being too narrow.

-adam

to email me, replace SEVEN with the number.

Quoted message said:

TT:-
Definitions of evolution involving gene frequenquencies *are* narrow.
Is it possible to do better?
Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

Quoted message said:

JE:- For the above definition to represent a testable theory of evolution and not just a loose non
testable view of evolution it has to be amended to read:

Quoted message said:

" NON RANDOM changes to the heritable elements of a population "

GH:- This would be far too vague, and therefore untestable. You would have to specify "non-random"
with respect to something in particular.

JE:- Yes, contesting testable theories of causation for an observed non random change re: heritable
elements must be included. This remains "understood" if valid scientific theories are testable. Note
that this means that every testable theory of evolution must define evolution _differently_. LM's
view that evolution can be defined in a very general way that makes sense to science is not
sustained.

My Regards,

John Edser Independent Researcher

PO Box 266 Church Pt NSW 2105 Australia

[email hidden]

John Edser said:

Quoted message said:

Quoted message said:

Definitions of evolution involving gene frequenquencies *are* narrow.

Is it possible to do better?

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

Quoted message said:

What is wrong with simply "change over time"

TT:- Such a definition would turn the process of erosion into evolution.

JE:- What is the testable difference between the processes of erosion and genetic drift,
i.e. excluding the difference between dirt and genes and just comparing each process as a logical
structure?

For starters...

At a particular location, erosion is a one-way process. The only possible consequence is the removal
of material from that location. With genes, genetic drift does not determine in which manner things
will change.

To get more to the point, erosion always removes material and the only way that elevation can
increase on a hill is by tectonic/volcanic activity. This geological activity could be analogous to
mutation, however mutation is going to be inherent to any system that experiences genetic drift,
whereas erosion can occur in a system without tectonic/volcanic activity.

-adam

--
To email me, replace SEVEN with the number.

Adam Retchless said:

Tim Tyler said:

phillip smith <[email hidden]> wrote or quoted:

Quoted message said:

Tim Tyler at [email hidden]

Quoted message said:

> Definitions of evolution involving gene frequenquencies *are* narrow.
>
> Is it possible to do better?
>
> Evolution /could/ be defined as being:
>
> ``Changes to the heritable elements of a population''

What is wrong with simply "change over time"

Such a definition would turn the process of erosion into evolution.

I like the definition "changes to the heritable elements of a population". It is broad enough to
encompass changes in our understanding of evolution but also limits the definition such that it
only applies to life.

Why would you *want* to limit "Evolution" in that way?. The concept of general evolution, i.e. that
that is subject to the Darwinian process of trait generation, trait replication, and trait
selection is very useful outside life. For example, GA (genetic algorithms) for the solution of
mathematical problems.

For me, "evolution" is *any* process subject to those 3 general Darwinian axioms.

Kevin Aylward

anasoft.co.ukanasoft.co.ukOpen ↗ SuperSpice, a very affordable Mixed-Mode Windows Simulator with Schematic
Capture, Waveform Display, FFT's and Filter Design.

"That which is mostly observed, is that which replicates the most"
anasoft.co.ukindex.htmlOpen ↗

"quotes with no meaning, are meaningless" - Kevin Aylward.

in article [email hidden], John Edser at [email hidden]
wrote on 2/3/04 10:18 PM:

Quoted message said:

Quoted message said:

Quoted message said:

Definitions of evolution involving gene frequenquencies *are* narrow.

Is it possible to do better?

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

Quoted message said:

What is wrong with simply "change over time"

TT:- Such a definition would turn the process of erosion into evolution.

JE:- What is the testable difference between the processes of erosion and genetic drift,
i.e. excluding the difference between dirt and genes and just comparing each process as a logical
structure?

That is a very interesting analogy. I'm not sure there is an important difference in the logical
structures of the processes of erosion and evolutionary drift. They certainly share many important
similarities, including that they can both play important roles in changing the "landscape" and
facilitating structural self-organization. While both contribute to the deterioration of existing
structures (e.g., adaptive form in the case of drift), they also play essential roles in the
creation of optimized structure. Erosion, for example, plays a critical role in the process of
optimal drainage system (e.g., stream/river systems that drain surface water from higher to lower
elevations) structural modification. That is, the shape of streams and rivers is constantly
changing, and the process of erosion helps to ensure that each internally generated change maximizes
the rate of flow. The contribution of drift to adaptive biological evolution was one of the most
important points Sewall Wright made during his career.

Guy

John Edser <[email hidden]> wrote or quoted:

Quoted message said:

Quoted message said:

Quoted message said:

Definitions of evolution involving gene frequenquencies *are* narrow.

Is it possible to do better?

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

Quoted message said:

What is wrong with simply "change over time"

TT:- Such a definition would turn the process of erosion into evolution.

JE:- What is the testable difference between the processes of erosion and genetic drift,
i.e. excluding the difference between dirt and genes and just comparing each process as a logical
structure?

The *main* difference is:

* erosion acts on non-reproducing, dead rocks ...and...
* evolution acts on self-reproducting living organisms.

*If* the rocks were self-reproducting, then their erosion *would* be a type of evolution (or maybe
devolution) - but they are not: so it isn't.
--
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John Edser <[email hidden]> wrote or quoted:

Quoted message said:

TT:-

Quoted message said:

Quoted message said:

Definitions of evolution involving gene frequenquencies *are* narrow.

Is it possible to do better?

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

JE:- For the above definition to represent a testable theory of evolution and not just a loose non
testable view of evolution it has to be amended to read:

" NON RANDOM changes to the heritable elements of a population "

I disagree - but then none of your views about whether stochastic processes can be part of
"testable" scientific theories have ever made any sense to me :-(
--
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John Edser said:

Quoted message said:

Quoted message said:

Definitions of evolution involving gene frequenquencies *are* narrow.

Is it possible to do better?

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

Quoted message said:

What is wrong with simply "change over time"

TT:- Such a definition would turn the process of erosion into evolution.

JE:- What is the testable difference between the processes of erosion and genetic drift,
i.e. excluding the difference between dirt and genes and just comparing each process as a logical
structure?

The difference is exactly the difference between dirt and genes. Evolution is a change in the
heritable elements of a population. To the extent that we believe that these lie in the genes, then
evolution is a change in the allele frequencies of a population.

Period. End of story. That is what all biologists and, more partcularly, what all evolutionary
biologists say. What you, John Edser, say is quite irrelevant. You are entitled to your opinion.
Just don't call it "evolution."

Someday, also, you are going to have to face up to the simple fact that you are the only person in
the entire universe who does not accept genetic drift as a mechanism of evolution.

Quoted message said:

Quoted message said:

Quoted message said:

Definitions of evolution involving gene frequenquencies *are* narrow.

Is it possible to do better?

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

Quoted message said:

Quoted message said:

What is wrong with simply "change over time"

Quoted message said:

TT:- Such a definition would turn the process of erosion into evolution.

Quoted message said:

JE:- What is the testable difference between the processes of erosion and genetic drift,
i.e. excluding the difference between dirt and genes and just comparing each process as a logical
structure?

GH:- That is a very interesting analogy. I'm not sure there is an important difference in the
logical structures of the processes of erosion and evolutionary drift. They certainly share many
important similarities, including that they can both play important roles in changing the
"landscape" and facilitating structural self-organization. While both contribute to the
deterioration of existing structures (e.g., adaptive form in the case of drift), they also play
essential roles in the creation of optimized structure. Erosion, for example, plays a critical role
in the process of optimal drainage system (e.g., stream/river systems that drain surface water from
higher to lower elevations) structural modification. That is, the shape of streams and rivers is
constantly changing, and the process of erosion helps to ensure that each internally generated
change maximizes the rate of flow. The contribution of drift to adaptive biological evolution was
one of the most important points Sewall Wright made during his career.

JE:- If you assume erosion as causative to building houses, then you can see my point! Neo
Darwinists assume that evolution (nature building houses) can be supposed to be caused by just a
supposed random process. It can't. All erosion can do is provide variation and _not_ evolution. If
it was supposed that erosion could build houses, but this supposition was non testable, then it
would be absurd to consider such a view within a scientific framework. All genetic drift can be
supposed to do is provide a temporal variation in gene freq.

Best Wishes,

John Edser Independent Researcher

PO Box 266 Church Pt NSW 2105 Australia

[email hidden]

Quoted message said:

Quoted message said:

Quoted message said:

Definitions of evolution involving gene frequenquencies *are* narrow.

Is it possible to do better?

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

Quoted message said:

Quoted message said:

What is wrong with simply "change over time"

Quoted message said:

TT:- Such a definition would turn the process of erosion into evolution.

Quoted message said:

JE:- What is the testable difference between the processes of erosion and genetic drift,
i.e. excluding the difference between dirt and genes and just comparing each process as a logical
structure?

A:- For starters... At a particular location, erosion is a one-way process.

JE:- Yes, and genetic drift can also cause the extinction of a gene which is a one way process.

B:- The only possible consequence is the removal of material from that location. With genes, genetic
drift does not determine in which manner things will change.

To get more to the point, erosion always removes material and the only way that elevation can
increase on a hill is by tectonic/volcanic activity. This geological activity could be analogous to
mutation, however mutation is going to be inherent to any system that experiences genetic drift,
whereas erosion can occur in a system without tectonic/volcanic activity.

JE:- The question is can both erosion and drift be regarded as random processes and/or
random patterns?

Best Wishes,

John Edser Independent Researcher

PO Box 266 Church Pt NSW 2105 Australia

[email hidden]

TomHendricks474 <[email hidden]> wrote or quoted:

Quoted message said:

J.E.:

Quoted message said:

T.T.:

Quoted message said:

Quoted message said:

Quoted message said:

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

" NON RANDOM changes to the heritable elements of a population "

But there is no mention of selection in those heritable variants of either def.. Should there be?

No - or Larry will berate us ;-)
--
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Guy Hoelzer <[email hidden]> wrote or quoted:

Quoted message said:

in article [email hidden], John Edser at [email hidden] wrote on 2/2/04
11:40 PM:

Quoted message said:

Quoted message said:

TT:- Definitions of evolution involving gene frequenquencies *are* narrow.

Is it possible to do better?

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

JE:- For the above definition to represent a testable theory of evolution and not just a loose
non testable view of evolution it has to be amended to read:

" NON RANDOM changes to the heritable elements of a population "

This would be far too vague, and therefore untestable. You would have to specify "non-random" with
respect to something in particular. It is an empirical fact in a complex universe that any change
will be correlated with some other changes. This would allow someone using the definition above to
choose any reference point they want and claim that evolution either did or did not occur in any
instance.

That seems like an argument for rejecting the whole notion of randomness from scientific theories.

It seems like taking things too far to me.

In practice you can do things like getting the participants to agree in advance which tests for
randomness they were going to apply to the results.

E.g. you could define "random" as being that which passes the "DIEHARD" randomness test suite.

Not a perfect definition - but good enough to be usable in practice.
--
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Tim Tyler <[email hidden]> wrote or quoted:

Quoted message said:

Definitions of evolution involving gene frequenquencies *are* narrow.

Is it possible to do better?

Evolution /could/ be defined as being:

``Changes to the heritable elements of a population''

From: talkorigins.orgevolution definition.htmlOpen ↗

``The changes in populations that are considered evolutionary are those that are inheritable via the
genetic material from one generation to the next.''

- Douglas J. Futuyma in Evolutionary Biology, Sinauer Associates 1986

Mr Futuyma agrees, it seems - though he implicitly rules out multiple genetic materials :-(

Another:

``Evolution is a process that results in heritable changes in a population spread over many
generations.''

Yes - seems OK.

Another:

``In fact, evolution can be precisely defined as any change in the frequency of alleles within a
gene pool from one generation to the next.''

- Helena Curtis and N. Sue Barnes, Biology, 5th ed. 1989;

That's a bad definition.

The page notes:

``One can quibble about the accuracy of such a definition (and we have often quibbled on these
newsgroups) but it also conveys the essence of what evolution really is. When biologists say that
they have observed evolution, they mean that they have detected a change in the frequency of genes
in a population.''

We /are/ quibbling here. *Most* sorts of evolution will involve a change in gene frequencies.

However, definitions should be good - and this one is not - since it disqualifies certain sorts of
rare change in a population from representing evolution - when "clearly" that's what they are.

Still: two out of three isn't too bad.
--
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