Saturday, February 18, 2006

 

[evomech] Mutation and adaptation: the directed mutation controversy in evolutionary perspective

[Lenski & Sniegowski, Annual Review of Systematics, Nov '95]

Abstract:

A central tenet of evolutionary theory is that mutation is random with
respect to its adaptive consequences for individual organisms; that is,
the production of variation precedes and does not cause adaptation.
Several recent experimental reports have challenged this tenet by
suggesting that bacteria (and yeast) ''may have mechanisms for choosing
which mutations will occur'' (6, p. 142). The phenomenon of nonrandom
mutation claimed in these experiments was initially called ''directed
mutation'' but has undergone several name changes during its brief and
controversial history. The directed mutation hypothesis has not fared
well; many examples of apparently directed mutation have been rejected
in favor of more conventional explanations, and several reviews
questioning the validity of directed mutation have appeared (53, 54,
59-61, 79, 80). Nonetheless, directed mutation has recently been
reincarnated under the confusing label ''adaptive mutation'' (5, 23, 24,
27, 35, 74). Here we discuss the many experimental and conceptual
problems with directed/adaptive mutation, and we argue that the most
plausible molecular models proposed to explain ''adaptive mutation'' are
entirely consistent with the modern Darwinian concept of adaptation by
natural selection on randomly occurring variation. In the concluding
section of the paper, we discuss the importance of an informed
evolutionary approach in the study of the potential adaptive
significance of mutational phenomena. Knowledge of the molecular bases
of mutation is increasing rapidly, but rigorous evolutionary
understanding lags behind. We note that ascribing adaptive significance
to mutational phenomena (for example, ''adaptive mutation'') is beset
with some of the same difficulties as ascribing adaptive significance to
features of whole organisms (29). We consider some examples of
mutational phenomena along with possible adaptive and nonadaptive
explanations.

Full text at:

https://vnet.uh.edu/vrecord_data/vclass/resource/sniegowski_9211.pdf
http://myxo.css.msu.edu/lenski/pdf/1995,%20ARES,%20Sniegowski%20&%20Lenski.pdf

John Latter

*Model of an Internal Evolutionary Mechanism* [Evolution]:
http://members.aol.com/jorolat/index.html

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Friday, February 17, 2006

 

[evomech] Evolution at two levels in humans and chimpanzees (Classic Paper)

[King & Wilson, Science, Apr '75]

"Their macromolecules are so alike that regulatory mutations may account for their biological differences"

(No Abstract. Related keywords include Marie-Claire King, human and chimpanzee, dna and genetics, genome, Wilson)

Scanned PDF file available at:

http://www.mun.ca/biology/scarr/King_&_Wilson_1975.pdf

John Latter

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Thursday, February 16, 2006

 

[evomech] Info wanted on two intriguing 'Lamarckian' experiments

On pages 48 and 49 of "The Great Evolution Mystery" (Secker & Warburg version - page numbers may be different in Abacus or MacDonald editions) Gordon Rattray Taylor wrote:

"Fifty years ago, for instance, one Harry Schroeder conducted an intriguing experiment with the willow-moth caterpillar. This caterpillar places itself on a leaf and rolls the leaf around itself before pupating, fastening it down with a web.

Normally, it starts by drawing the tip of the leaf over itself, but Schroeder, with fiendish cunning, systematically cut off the tips of all the leaves on which caterpillars had taken up position. Sensibly enough, they responded by drawing the side of the leaf over instead.

When these caterpillars had produced another generation, Schroeder found that, of nineteen offspring, four drew the side of the leaf over, not the tip, when their time to pupate came around.

It may be said that this was inheritance of an acquired behavior, not a structure, but there may not be much difference from a genetic point of view, as we shall see.

Perhaps the same might be said of an unique series of experiments by Frederick Griffiths, who placed rats on slowly revolving turntables for periods of up to one and a half years. When the wretched animals were freed their heads constantly flicked in the direction in which they had been rotated, and their eyes flicked also. This flicking automatism reappeared in their progeny."

Both of the above experiments exhibit characteristics consistent with the proposed homeostatic internal evolutionary mechanism I am currently researching. Unfortunately, however, Taylor gives no citations and there are no further references to Schroeder and Griffiths in either the Bibliography or the Sources.

Should anyone comes across any information regarding these experiments - or others of a similar nature - I would be very grateful if you could let me know: jorolat@gmail.com

"The Great Evolution Mystery" is no longer in print although used copies are still listed at:

http://www.amazon.com/gp/product/0349129177/104-1772918-1947930?st=%2A&v=glance&n=283155

and

http://www.amazon.co.uk/exec/obidos/ASIN/0349129177/026-0583169-2213244

John Latter

Related terms include: Lamarck and Lamarckian

*This is an update of evomech message #43:
http://groups.yahoo.com/group/evomech/message/43
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[evomech] 'Turned On': A revolution in the field of evolution? (Book Review)

[Orr, The New Yorker, Oct '05]

"If you read much popular science, you'd be forgiven for thinking that biology has become something of a banana republic. A seemingly endless series of books and newspaper articles reports that biology is being roiled by any number of revolutions. Take your pick: genomics, proteomics, medical genetics, and, now, something called evo devo. Some of the revolutionary rhetoric is surely hype, but these are, undeniably, exciting times in biology. Entire genomes are being decoded at an astounding rate (nearly three hundred species have been done, and more than seven hundred others are in the works), and new high-tech approaches to old problems seem to appear by the week. The result of all this has been some genuinely surprising scientific findings. And some of the biggest have come from the new science of evo devo."

Full text at:

http://www.newyorker.com/critics/books/articles/051024crbo_books1

John

Model of an Internal Evolutionary Mechanism
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Wednesday, February 15, 2006

 

Re: [evomech] The main thrust of the group

On 15/02/2006 johnhewitt22 wrote:
> Dear John Latter and other regular contributors to this group,
>
> I have been a member of the group for just a couple of weeks now and I
> have looked at the web site from which it draws inspiration.

> I understand that what is being advanced is the idea of some kind of
> internal mechanism for evolution but I am not too clear about how this
> translates into a general programme or what exact mechanism is being
> advanced.

> Could I ask that a simple, slimmed down version of the group's basic
> ideas and objectives be given? Something so bare as to be suitable for
> a bear with very little brain.
>
> Sincerely
>
> John Hewitt
> http://www.sexandphilosophy.co.uk

John,

The group homepage contains a description of the group's 'aims/interests' at:

http://groups.yahoo.com/group/evomech/

My website reflects only my area of interest: Cliff, for example, has a homepage at:

http://www.zainar.com/segment/tablecon.html

And Warren has posted his views on a number of occasions - these can be found using the search facility on the group homepage.

Currently I'm engaged in researching material for a rewrite of a proposed testable homeostatic internal mechanism - I'm pretty sure group members are busy in other areas!

Hope this makes things a little clearer,

John
-- 
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[evomech] The main thrust of the group

Dear John Latter and other regular contributors to this group,

I have been a member of the group for just a couple of weeks now and I
have looked at the web site from which it draws inspiration.

I understand that what is being advanced is the idea of some kind of
internal mechanism for evolution but I am not too clear about how this
translates into a general programme or what exact mechanism is being
advanced.

Could I ask that a simple, slimmed down version of the group's basic
ideas and objectives be given? Something so bare as to be suitable for
a bear with very little brain.

Sincerely

John Hewitt
http://www.sexandphilosophy.co.uk

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[evomech] Confessions of a Darwinist (Virginia Quarterly Review)

"Confessions of a Darwinist" Niles Eldredge

[Editor's note: This essay will be published in the Spring 2006 issue of VQR in a special portfolio on Darwin, evolution, and intelligent design. The portfolio will also feature essays by Michael Ruse, Thomas Eisner, and Robert M. Sapolsky, and an excerpt from David Quammen's forthcoming book The Reluctant Mr. Darwin: An Intimate Portrait of Charles Darwin and the Making of His Theory of Evolution. To pre-order the Spring issue, click here.]

"I came to evolution in a roundabout way. Sure, as a kid I had seen the dinosaurs at the American Museum of Natural History - and had heard a bit about evolution in high school. But I was intent on studying Latin and maybe going to law school.

But evolution got in the way... "

Full text at:

http://www.vqronline.org/viewmedia.php/prmMID/9209


John

Model of an Internal Evolutionary Mechanism
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Tuesday, February 14, 2006

 

Re: [evomech] Re: Gene Regulatory Networks and the Evolution of Animal Body Plans

Can you put your name on your posts please Warren.

John

> warrenbergerson wrote: A Gene Regulatory Network, it will be noted, consists of a set of pit- loops.

Model of an Internal Evolutionary Mechanism:
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[evomech] Re: Gene Regulatory Networks and the Evolution of Animal Body Plans

A Gene Regulatory Network, it will be noted, consists of a set of pit-loops.

'Warren'

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[evomech] Gene Regulatory Networks and the Evolution of Animal Body Plans

[Davidson & Erwin, Science, Feb '06]

Abstract:

Development of the animal body plan is controlled by large gene regulatory networks (GRNs), and hence evolution of body plans must depend upon change in the architecture of developmental GRNs. However, these networks are composed of diverse components that evolve at different rates and in different ways. Because of the hierarchical organization of developmental GRNs, some kinds of change affect terminal properties of the body plan such as occur in speciation, whereas others affect major aspects of body plan morphology. A notable feature of the paleontological record of animal evolution is the establishment by the Early Cambrian of virtually all phylum-level body plans. We identify a class of GRN component, the 'kernels' of the network, which, because of their developmental role and their particular internal structure, are most impervious to change. Conservation of phyletic body plans may have been due to the retention since pre-Cambrian time of GRN kernels, which underlie development of major body parts.

Reprints available from Eric Davidson at the email address on the following link (or contact jorolat@gmail.com):

http://www.sciencemag.org/cgi/content/abstract/311/5762/796

John

Model of an Internal Evolutionary Mechanism
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[evomech] Viva Lamarck: A Brief History of the Inheritance of Acquired Characteristics

[Cochrane, Aeon 2:2, '91]

A leading evolutionist recently observed that the great questions in evolutionary theory
remain much the same today as they were in Darwin’s time. Certainly this observation
applies to the debate over the inheritance of acquired characters, commonly known as
Lamarckism, after Jean Lamarck, author of the first systematic theory of evolution. The
debate over the reality of Lamarckian ideas has raged for the better part of a century and
a half and shows no signs of abating. Indeed, as I write, the controversy has been
rekindled over the announcement of new experiments allegedly supporting the possibility
of inheritance of acquired characters.

In an attempt to understand the historical background and theoretical significance of this
controversy we will offer here a brief outline of the history of the inheritance of acquired
characters. This outline will include a summary of Lamarck’s theory of evolution; an
assessment of the validity of its rejection by Weismann and Neo-Darwinism; and a
discussion of recent developments including the modern revival of the inheritance of
acquired characters by Steele and Gorczynski.

Full text at:

http://www.maverickscience.com/Lamarck%20Vindicated.pdf

John

Model of an Internal Evolutionary Mechanism
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Monday, February 13, 2006

 

[evomech] Evolution of phenotypic plasticity: where are we going now? (TREE)

[Puglicci, Trends in Ecology and Evolution, Sept '05]

Abstract:

The study of phenotypic plasticity has progressed significantly over the past few decades. We have moved from variation for plasticity being considered as a nuisance in evolutionary studies to it being the primary target of investigations that use an array of methods, including quantitative and molecular genetics, as well as of several approaches that model the evolution of plastic responses. Here, I consider some of the major aspects of research on phenotypic plasticity, assessing where progress has been made and where additional effort is required. I suggest that some areas of research, such the study of the quantitative genetic underpinning of plasticity, have been either settled in broad outline or superseded by new approaches and questions. Other issues, such as the costs of plasticity are currently at the forefront of research in this field, and are likely to be areas of major future development.

Full text at:

http://www.science.siu.edu/plant-biology/EvolDiscGroup/EDG_PDFs/Piggliucci2005TREE.pdf

John
--
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Re: [evomech] Pit-Loops

On 13/02/2006 warrenbergerson wrote:
> In response to comments on another thread, here is another attempt
> to explain pit-loops.
>
> I kind of thought the pit-loop concept would be easy to visualize at
> least for people like yourself that understands systems design. Most
> likely I am not explaining the concept very well.
>
> Start with something like a neuron or a gene that needs to be
> activated or inhibited. The process or program that activates the
> neuron or gene can be described in terms of feedback loops or for
> complex processes as a set of feedback loops. Any computer program
> can be expressed as a set of input-output relationships, and any
> input output relationship can be characterized as a feedback loop.
>
> If the feedback loops are dynamic, programmable or self programming,
> and if the feedback loops serve a purpose or function, then the
> feedback loops fit my definition for pit-loops. Pit-loops are thus
> little more than an effective gimmick for reverse engineering the
> programs that control the development and operations of cells and
> complex organisms. If you analyze cells and organisms in terms of
> pit-loops, you quickly learn that evolution of living systems must
> involve the evolution or modification of pit-loops, not changes in
> genes.
>
> I clearly don't have all the answers to what are all the pit-loops
> ultimately responsible for reprogramming other pit-loops, but
> following the results of pit-loop analysis might eventually lead to
> resolving the issue.
>
> Again, undoubtedly a most of the problem is that I am not expressing
> the concept clearly.
>
> Warren

Although this is a discussion forum at the moment I don't have much time to 'discuss'! My enthusiasm at having more internet time has been somewhat dampened by persistent computer problems and this has led to a certain degree of frustration because I really want to get on with researching a rewrite of the area I'm interested in.

I do, however, read every post - and I'm sure that others do too - and sometimes I refrain from replying simply because the schedule at that moment in time is too demanding.

My overall impression of your posts is that you do have something to say. On the other hand I do feel a certain degree of reservation. It's purely a subjective viewpoint of course, but perhaps an analogy will convey the point I want to make:

Leonardo painted the Mona Lisa sometime in the early 1500's (er, I think). Imagine if Lamarck, instead of being interested in the natural world, had come along in at the beginning of the 18th century, dusted the painting off, and then wrote about the techniques Leonardo had used in the creation of his masterpiece.

Imagine if Darwin had an interest in art too. Fifty years later, with advances in science providing relatively more advanced methods of restoration, he might have uncovered information that Lamarck hadn't been able to access.

If this had been the case, then like many others, I can imagine reading about what they had to say and then going to Paris to find out for myself!.

This is not so easy to do in the field of evolution (although I would dearly like to be able to carry experiments!) and as a result of 'cultural conditioning' this appears to have led to some people believing that evolutionary theory defines the subject under scrutiny rather than merely reflects it. Cart before the horse?

Similarly, if any 'engineering/system principles' are found in the natural world it doesn't mean a) there's an engineer or b) that they define how evolution may occur. This may seem at odds with my own interest in the possibility of an internal evolutionary mechanism - I tried to explain this in this:

http://groups.yahoo.com/group/evomech/message/416

and the subsequent replies I posted on that thread.

Finally - and I'm trying to be helpful here rather than 'nagging' - you began this post with

>In response to comments on another thread".

People will be visiting evomech all the time. If they were to read this latest post of yours, would they then want to search for the other thread whose location/identity they don't know? I feel it would have been in your own interest if you had found this other thread, clicked on 'reply', and then posted - it would provide continuity and who knows what future response there might be!

John

Model of an Internal Evolutionary Mechanism:
http://members.aol.com/jorolat/index.html


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[evomech] Pit-Loops

In response to comments on another thread, here is another attempt
to explain pit-loops.

I kind of thought the pit-loop concept would be easy to visualize at
least for people like yourself that understands systems design. Most
likely I am not explaining the concept very well.

Start with something like a neuron or a gene that needs to be
activated or inhibited. The process or program that activates the
neuron or gene can be described in terms of feedback loops or for
complex processes as a set of feedback loops. Any computer program
can be expressed as a set of input-output relationships, and any
input –output relationship can be characterized as a feedback loop.

If the feedback loops are dynamic, programmable or self programming,
and if the feedback loops serve a purpose or function, then the
feedback loops fit my definition for pit-loops. Pit-loops are thus
little more than an effective gimmick for reverse engineering the
programs that control the development and operations of cells and
complex organisms. If you analyze cells and organisms in terms of
pit-loops, you quickly learn that evolution of living systems must
involve the evolution or modification of pit-loops, not changes in
genes.

I clearly don't have all the answers to what are all the pit-loops
ultimately responsible for reprogramming other pit-loops, but
following the results of pit-loop analysis might eventually lead to
resolving the issue.

Again, undoubtedly a most of the problem is that I am not expressing
the concept clearly.

Warren

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Sunday, February 12, 2006

 

[evomech] Robustness of cellular functions (Cell)

[Stelling et al., Cell, Sept '04]

Abstract:

Robustness, the ability to maintain performance in the face of perturbations and uncertainty, is a long-recognized key property of living systems. Owing to intimate links to cellular complexity, however, its molecular and cellular basis has only recently begun to be understood. Theoretical approaches to complex engineered systems can provide guidelines for investigating cellular robustness because biology and engineering employ a common set of basic mechanisms in different combinations. Robustness may be a key to understanding cellular complexity, elucidating design principles, and fostering closer interactions between experimentation and theory.

Full text at:

http://www.cds.caltech.edu/~doyle/CmplxNets/Cell.pdf

John

Model of an Internal Evolutionary Mechanism
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[evomech] Re: Richard Dawkins - The Root of All Evil? (Audio Interview)

"...In this interview with DJ Grothe, he [Dawkins] discusses hisnewest work, a two-part documentary series for British televisionentitled The Root of All Evil?, in which he challenges what he calls 'the process of non-thinking called faith'..."

I've got a funny feeling it might help to include a link to the radio show:

http://www.pointofinquiry.org/?p=36

That'll teach me to post before breakfast!

John

Model of an Internal Evolutionary Mechanism
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[evomech] Richard Dawkins - The Root of All Evil? (Audio Interview)

['Point of Inquiry' Radio Show, 10th Feb '06]

"...In this interview with DJ Grothe, he [Dawkins] discusses his newest work, a two-part documentary series for British television entitled The Root of All Evil?, in which he challenges what he calls 'the process of non-thinking called faith'..."

While disagreeing with Dawkins' perception of how evolutionary changes occur I do feel he has something to say regarding 'faith'. Not least because belief in a theory can have similar origins to belief in a God - I'm reminded of this every time someone says "Evolution does this.." or "Natural Selection does that.."!

And for anyone arguing alternative or new explanations contrary to perceived wisdom it can be useful to understand the nature of the resistance encountered:

"If you know the enemy and know yourself, you need not fear the result of a hundred battles.
If you know yourself but not the enemy, for every victory gained you will also suffer a defeat.
If you know neither the enemy nor yourself, you will succumb in every battle."

(The Art of War, Chapter 3:14, Sun Tzu Wu, 536-496 BC)

Some of the issues Dawkins raises also have a particular topical relevance:

Evolution: The Horse Whisperer, Richard Dawkins, and Danish Cartoons

John

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