Evolution Research - Evomech Forum Posts

[evomech] New theory of environmental inheritance ('05 Press Release)

2006-08-11T15:09:00.000+01:00

New research has provided evidence for 'environmental inheritance', a radical theory of transgenerational genetic adaptation proposed by Professor Marcus Pembrey of the Institute of Child Health, UCL in the mid 1990's

The latest evidence challenges accepted thinking on genetic inheritance, suggesting that historic events can contribute to some common modern illnesses.

The research, published by the Children of the 90s study based at the University of Bristol in collaboration with Umea University, Sweden, could have far-reaching implications for our understanding of modern health epidemics - such as obesity or cardiovascular disease.

Conventionally scientists believe that how we develop as adults depends on two factors - the genes (DNA) we inherit from our parents, and the environmental influences, such as diet, lifestyle, exposure to pollution from conception onwards.

Professor Marcus Pembrey, who is also head of Genetics at Children of the 90s, says that over the long term, the process of Darwinian evolution by random errors in DNA followed by natural selection ensures that the human race adapts to changes in our environment. But it takes very many generations.

Now there is evidence for another mechanism which no-one had considered... some of the father's own experiences in his childhood are captured in some way by his sperm, so affecting the genes that he bequeaths to his descendants.

Also see:

'Cardiovascular and diabetes mortality determined by nutrition'

John Latter / Jorolat

Model of an Internal Evolutionary Mechanism (based on an extension to homeostasis) linking Adaptive Mutations to the Baldwin Effect:
http://members.aol.com/jorolat/index.html

Evolution Research Blog:
http://evomech.blogspot.com/

technorati tags: research, theory, adaptation, marcus+pembrey, obesity, cardiovascular, disease, genes, dna, parents, diet, lifestyle, pollution, genetics, darwinian, evolution, natural+selection, environment, mechanism, sperm

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[evomech] UF scientists discover evolutionary origin of fins, limbs

2006-07-27T16:20:00.000+01:00

Gainesville, Florida: - Performance on the dance floor may notalways show it, but people are rarely born with two left feet. We havegenes that instruct our arms and legs to grow in the right places andpoint in the right directions. They also provide for the spaces betweenour fingers and toes and every other formative detail of our limbs.

Evolutionarilyspeaking, the genetic instructions used to construct and position ourlimbs were being perfected more than half a billion years ago infishes, not along the sides of the body where the fins that precededhuman arms and legs sprouted, but at the midline that runs along thebackbone and belly.

This midline - think of the dorsal, tail andanal fins of a fish - is where the genetic template to produce finsoriginated, about 100 million years before paired fins evolved andabout 200 million years before paired fins evolved into limbs,according to University of Florida genetics researchers. The findings,published online today in the journal Nature, also provide insight intothe evolutionary history of genes involved in human birth defects.[evolution, origin]

[The Nature paper is currently available here but the link won't work for long because it's an advance publication - email if you have any problems.]

technorati tags: florida, genes, limbs, fishes, fins, body, midline, template, nature, evolution, history, origin

John Latter / Jorolat

Model of an Internal Evolutionary Mechanism (based on an extension to homeostasis) linking Adaptive Mutations to the Baldwin Effect:
http://members.aol.com/jorolat/index.html

Evolution Research Blog:
http://evomech3.blogspot.com/

[evomech] [Update] Re: The Spandrels of San Marco and the Panglossian Paradigm

2006-07-19T21:50:00.000+01:00

--- In evomech@yahoogroups.com, "John Latter" <jorolat@...> wrote:
>
>
> --- In evomech@yahoogroups.com, "jorolat" jorolat@a... wrote:
> >
> > [Gould & Lewontin, Royal Society of London, '78]
> >
> > Abstract:
> >
> > "An adaptationist programme has dominated evolutionary thought in
> > england and the United States during the past forty years. It is
> > based on faith in the power of natural selection as an optimizing
> > agent. It proceeds by breaking an organism into unitary "traits" and
> > proposing an adaptive story for each considered separately. Trade-
> > offs among competing selective demands exert the only brake upon
> > perfection; nonoptimality is thereby rendered as a result of
> > adaptation as well. We criticize this approach and attempt to
> > reassert a competing notion (long popular in continental Europe) that
> > organisms must be analyzed as integrated wholes, with baupläne so
> > constrained by phyletic heritage, pathways of development, and
> > general architecture that the constraints themselves become more
> > interesting and more important in delimiting pathways of change than
> > the selective force that may mediate change when it occurs. We fault
> > the adaptationist programme for its failure to distinguish current
> > utility from reasons for origin (male tyrannosaurs may have used
> > their diminutive front legs to titillate female partners, but this
> > will not explain why they got so small); for its unwillingness to
> > consider alternatives to adaptive stories; for its reliance upon
> > plausibility alone as a criterion for accepting speculative tales;
> > and for its failure to consider adequately such competing themes as
> > random fixation of alleles, production of nonadaptive structures by
> > developmental correlation with selected features (allometry,
> > pleiotropy, material compensation, mechanically forced correlation),
> > the separability of adaptation and selection, multiple adaptive
> > peaks, and current utility as an epiphenomenon of nonadaptive
> > structures. We support Darwin's own pluralistic approach to
> > identifying the agents of evolutionary change."
> >
> > Full text at:
> >
> > http://www.aaas.org/spp/dser/evolution/science/spandrel.htm
> >
> > [Bookmarked]
> >
> > Jorolat
>
> Now available at:
>
> http://www.aaas.org/spp/dser/evolution/history/spandrel.shtml
>
> John
> -- Model of an Internal Evolutionary Mechanism (based on an extension to homeostasis) linking Adaptive Mutations to the Baldwin Effect:
> http://members.aol.com/jorolat/index.html Evolution: Where Darwin meets Lamarck? Discussion Forum:
> http://groups.yahoo.com/group/evomech/
>

Now available at:

http://www.aaas.org/spp/dser/03_Areas/evolution/perspectives/Gould_Lewontin_1979.shtml

Wish they would stop moving it! :)

John Latter / Jorolat

technorati tags: gould, lewontin, spandrels, san+marco, paradigm

[evomech] Re: Origin of Instincts

2006-06-15T07:53:00.000+01:00

--- In evomech@yahoogroups.com, "alexbertoglio" <alexbertoglio@...> wrote:
>
> I have searched the internet, talkorigins, Baldwinian explanations,
> and the post archive here and been unable to find a good explanation
> of how instincts (not reflexes) originate.
>
> My dad is reading the book "Improbable" by Adam Fawer, and apparently
> it makes a case for a "shared consciousness" to explain instincts that
> are not coded for in DNA. I have tried to explain the Baldwinian
> effect to him but I cannot explain how exactly the DNA itself passes
> instincts.
>
> According to the book, Biologists have been unable to explain how
> babies have the instinct (or skills) to walk, without ever seeing
> walking in action.
>
> I plan on reading "Improbable" to find out exactly what it says, but
> can anyone explain how instincts are formed?
>
> And can anyone explain why the concept of "shared consciousness" is
> used in this regard? I havn't read the book yet, but apparently the
> point is that some things that don't pass by DNA are instead contained
> in everyone, in some meta-physical sense. I don't buy it, but maybe
> someone with more education in meta-physics can explain it better.
>

Hi Alex,

Perhaps someone more knowledgeable than I could give you anexplanation in terms of conventional theory but I doubt one exists.

Personally, I'm interested in the possibility of an homeostaicinternal evolutionary mechanism. The phenomena of instinct issupportive of this proposal but a coherent explanation from thisperspective is a bit further down the line at the moment.

I'm slightly intrigued by what 'shared conciousness' may mean althoughI'm not particularly interested in anything that can't be tested.

John Latter / Jorolat

technorati tags: internal, evolutionary, mechanism, metaphysics, dna, improbable, instinct, consciousness

[evomech] Origin of Instincts

2006-06-14T07:38:00.000+01:00

I have searched the internet, talkorigins, Baldwinian explanations,
and the post archive here and been unable to find a good explanation
of how instincts (not reflexes) originate.

My dad is reading the book "Improbable" by Adam Fawer, and apparently
it makes a case for a "shared consciousness" to explain instincts that
are not coded for in DNA. I have tried to explain the Baldwinian
effect to him but I cannot explain how exactly the DNA itself passes
instincts.

According to the book, Biologists have been unable to explain how
babies have the instinct (or skills) to walk, without ever seeing
walking in action.

I plan on reading "Improbable" to find out exactly what it says, but
can anyone explain how instincts are formed?

And can anyone explain why the concept of "shared consciousness" is
used in this regard? I havn't read the book yet, but apparently the
point is that some things that don't pass by DNA are instead contained
in everyone, in some meta-physical sense. I don't buy it, but maybe
someone with more education in meta-physics can explain it better.

[evomech] Self-Organization, Emergence and the Architecture of Complexity

2006-03-20T07:57:00.000Z

Heylighen F. (1989): "Self-Organization, Emergence and the Architecture of Complexity", in:
Proceedings of the 1st European Conference on System Science, (AFCET, Paris), p. 23-32.

Abstract:

It is argued that the problems of emergence and the architecture of complexity can be solved by analysing the self-organizing evolution of complex systems. A generalized, distributed variation selection model is proposed, in which internal and external aspects of selection and variation are contrasted. "Relational closure" is introduced as an internal selection criterion. A possible application of the theory in the form of a pattern directed computer system for supporting complex problem-solving is sketched.

Full text at:

http://pespmc1.vub.ac.be/Papers/SelfArchCom.pdf

John Latter

Evolution: Research Blog | Website | Blog Mad | Webring

technorati tags: self-organization, complexity, evolution

Re: [evomech] Re: Darwin on trial (online book)

2006-03-20T05:24:00.000Z

On 19/03/2006 johnhewitt22 wrote:
> Dear All,
>
> I have never seen this book, by Phillip E. Johnson, but I have to say
> that, at a cursory reading, it seems rather good.
>
> Perhaps we could have an update on the author. Who is he? What is the
> backgound of the e-book?
>
> Sincerely
>
> John Hewitt

Hi John,

The last I heard of Johnson he was an IDist law professor at Berkeley. Here are a couple of links:

"Welcome. This page presents Professor Johnson's works, primarily
in the area of origins. On this page, you will also find his speaking schedule."
http://www.origins.org/pjohnson/pjohnson.html

"Articles by Phillip Johnson"
http://www.arn.org/authors/johnson_articles.html

I first came across Johnson in my search for more information about Grasse:

"MY STARTING POINT is a book review that Theodosius Dobzhansky published in 1975, critiquing Pierre Grasse's The Evolution of Life.{1} Grasse, an eminent French zoologist, believed in something that he called "evolution." So did Dobzhansky, but when Dobzhansky used that term he meant neo-Darwinism, evolution propelled by random mutation and guided by natural selection. Grasse used the same term to refer to something very different, a poorly understood process of transformation in which one general category (like reptiles) gave rise to another (like mammals), guided by mysterious "internal factors" that seemed to compel many individual lines of descent to converge at a new form of life."

From "Darwin's Rules of Reasoning" at:
http://www.leaderu.com/orgs/fte/darwinism/chapter1.html

Hope this helps!

John Latter

--

Evolution: Research Blog | Website | Blog Mad | Webring

technorati tags: internal+factors, natural+selection, random+mutations, grasse, johnson, berkeley, dna, dobzhansky, evolution

[evomech] Re: Darwin on trial (online book)

2006-03-19T11:53:00.000Z

Dear All,

I have never seen this book, by Phillip E. Johnson, but I have to say
that, at a cursory reading, it seems rather good.

Perhaps we could have an update on the author. Who is he? What is the
backgound of the e-book?

Sincerely

John Hewitt

[evomech] Regulating General Mutation Rates: Examination of the Hypermutable State Model for Cairnsian Adaptive Mutation

2006-03-19T07:47:00.000Z

Genetics, Vol. 163, 1483-1496, April 2003, Copyright 2003
Regulating General Mutation Rates: Examination of the Hypermutable State Model for Cairnsian Adaptive Mutation
John R. Rotha, Eric Kofoid, Frederick P. Roth, Otto G. Bergc, Jon Segera, and Dan I. Andersson

Abstract:

In the lac adaptive mutation system of Cairns, selected mutant colonies but not unselected mutant types appear to arise from a nongrowing population of Escherichia coli. The general mutagenesis suffered by the selected mutants has been interpreted as support for the idea that E. coli possesses an evolved (and therefore beneficial) mechanism that increases the mutation rate in response to stress (the hypermutable state model, HSM). This mechanism is proposed to allow faster genetic adaptation to stressful conditions and to explain why mutations appear directed to useful sites. Analysis of the HSM reveals that it requires implausibly intense mutagenesis (105 times the unselected rate) and even then cannot account for the behavior of the Cairns system. The assumptions of the HSM predict that selected revertants will carry an average of eight deleterious null mutations and thus seem unlikely to be successful in long-term evolution. The experimentally observed 35-fold increase in the level of general mutagenesis cannot account for even one Lac+ revertant from a mutagenized subpopulation of 105 cells (the number proposed to enter the hypermutable state). We conclude that temporary general mutagenesis during stress is unlikely to provide a long-term selective advantage in this or any similar genetic system.

Full text at:

http://www.genetics.org/cgi/content/full/163/4/1483

John Latter

technorati tags: adaptive, cairns, mechanism, e.coli

Evolution: Research Blog | Website | Blog Mad | Webring

[evomech] Darwin on trial (online book)

2006-03-18T07:24:00.000Z

LIBRARY OF THE FUTURE (R) Series Third Edition Ver. 4.3

1991 DARWIN ON TRIAL by Phillip E. Johnson
(C) Copyright 1991, Phillip E. Johnson
Used with permission of Phillip E. Johnson and Regnery Gateway Publishing Co.
Electronically Enhanced Text
(c) Copyright 1993 World Library, Inc.

CONTENTS:

Chapter One: The Legal Setting

Chapter Two: Natural Selection As a Tautology As a Scientific Hypothesis As a Deductive Argument As a Philosophical Necessity

Chapter Three: Mutations Great and Small

Chapter Four: The Fossil Problem

Chapter Five: The Fact of Evolution

Chapter Six: The Vertebrate Sequence Fish to Amphibians Amphibians to Reptiles Reptiles to Mammals Reptile to Bird From Apes to Humans

Chapter Seven: The Molecular Evidence

Chapter Eight: Prebiological Evolution

Chapter Nine: The Rules of Science

Chapter Ten: Darwinist Religion

Chapter Eleven: Darwinist Education

Chapter Twelve: Science and Pseudoscience Research Notes

Full text at:

http://www.geocities.com/kubyimm2/darwin-on-trial-phillip-johnson.txt

John Latter

--

Evolution: Research Blog | Website | Blog Mad | Webring

technorati tags: research, evolution, reptiles, amphibians, mammals, apes, science, johnson

[evomech] At Berkeley: Intelligently Designed Molecular Evolution (Research

2006-03-17T07:56:00.000Z

BERKELEY, CA - Evolutionary paths to new therapeutic drugs, as well as a wide assortment of other enzyme products, have been created through, of all things, intelligent design. A team of researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California at Berkeley have developed a technique in which the evolution of an important class of proteins is steered towards a desired outcome.

"We've taken enzymes that are promiscuous, meaning they have the capacity to evolve along many different functional lines, and trained them to become specialists," said chemical engineer Jay Keasling, who led this study.

Full text at:

http://www.lbl.gov/Science-Articles/Archive/PBD-molecular-evolution.html

John Latter

--

Model of an Internal Evolutionary Mechanism:

http://members.aol.com/jorolat/index.html

technorati tags: intelligent+design, evolution, berkeley, study

[evomech] Function and the Evolution of Phenotypic Stability: Connecting Pattern to Process

2006-03-16T07:27:00.000Z

American Zoologist: Vol. 41, No. 3, pp. 552 - 563.
Function and the Evolution of Phenotypic Stability: Connecting Pattern to Process
Kurt Schwenk and Gunter P. Wagner

Abstract:

Phenotypes manifest a balance between the inherited tendency to remain the same (phenotypic stability) and the tendency to change in response to current environmental conditions (adaptation). This paper explores the role of functional integration and functional trade-offs in generating phenotypic stability by limiting the responses of individual characters to environmental selection. Evolutionarily stable configurations (ESCs) are systems of functionally interacting characters within which characters are 'judged' by their contribution to system-level functionality. This 'internal' component of selection differs from traditional 'external' selection in that it travels with the organism wherever it goes and is maintained across a wide range of environments. External selection, in contrast, is by definition environment-dependent. The temporal and geographic constancy of internal selection therefore acts to maintain phenotypic stability even as environments change. Functional trade-offs occur when one character participates in more than one function, but can only be optimized for one. Participation of certain ('keystone') characters in a trade-off potentially causes stabilization of an entire system owing to a cascade of functional dependencies on that character. Phylogenetic character analysis is an essential part of elucidating these processes, but patterns cannot be used as prima facie evidence of particular processes.

Full text at: http://icb.oxfordjournals.org/cgi/content/full/41/3/552

John Latter

--

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

technorati tags: environmental, systems, adaptation, selection, patterns, phenotypes

[evomech] From Epigenesis to Epigenetics: The Case of C. H. Waddington

2006-03-15T07:48:00.000Z

Annals of the New York Academy of Sciences 981:61-81 (2002)
2002 New York Academy of Sciences
From Epigenesis to Epigenetics
The Case of C. H. Waddington
Linda Van Speybroeck

Abstract:

One continuous thread in this volume is the name of Conrad H. Waddington (1905-1975), the developmental biologist known as the inventor of the term epigenetics. After some biographical notes on his life, this article explores the meaning of the Waddingtonian equation and the context wherein it was developed. This equation holds that epigenesis + genetics = epigenetics, and refers in retrospect to the debate on epigenesis versus preformationism in neoclassical embryology. Whereas Waddington actualized this debate by linking epigenesis to developmental biology and preformation to genetics, thereby stressing the importance of genetic action in causal embryology, today's epigenetics more and more offers the possibility to enfeeble biological thinking in terms of genes only, as it expands the gene-centric view in biology by introducing a flexible and pragmatically oriented hierarchy of crucial genomic contexts that go beyond the organism.

Full text at:

http://www.uv.mx/evargas/CienciaSagrada/TextosFundamentales/Speybroeck.pdf

John Latter

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

technorati tags: waddington, epigenetics, epigenesis, genetics, embryology, biology

[evomech] The Return of Hopeful Monsters (Stephen Jay Gould)

2006-03-14T08:37:00.000Z

"The Return of Hopeful Monsters" Natural History magazine 86 (June 1976): 24, 30.

Big Brother, the tyrant of George Orwell's 1984, directed his daily Two Minutes Hate against Emmanuel Goldstein, enemy of the people. When I studied evolutionary biology in graduate school during the mid-1960s, official rebuke and derision focused upon Richard Goldschmidt, a famous geneticist who, we were told, had gone astray. Although 1984 creeps up on us, I trust that the world will not be in Big Brother's grip by then. I do, however, predict that during this decade Goldschmidt will be largely vindicated in the world of evolutionary biology.

Goldschmidt, a Jewish refugee from Hitler's decimation of German science, spent the remainder of his career at Berkeley, where he died in 1958. His views on evolution ran afoul of the great neo-Darwinian synthesis forged during the 1930s and 1940s and continuing today as a reigning, if insecure, orthodoxy. Contemporary neo-Darwinism is often called the "synthetic theory of evolution" because it united the theories of population genetics with the classical observations of morphology, systematics, embryology, biogeography, and paleontology.

The core of this synthetic theory restates the two most characteristic assertions of Darwin himself: first, that evolution is a two-stage process (random variation as raw material, natural selection as a directing force); secondly, that evolutionary change is generally slow, steady, gradual, and continuous.

Full text at:

http://www.evolutionary.tripod.com/gould_nh_86_22-30.html

John Latter

--

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

technorati tags: gould, natural+selection, george+orwell, 1984, biology, berkeley, evolution

[evomech] Major transitions in animal evolution: A developmental genetic perspective

2006-03-13T07:53:00.000Z

American Zoologist, 1998, by Holland, Peter W H

Synopsis

Several phases of animal evolution have undergone radical change in developmental mechanisms. I refer to these as major transitions in animal evolution. The six most important transitions in the lineage leading to humans are proposed to be: the origin of multicellularity, the origin of two-germ layers and radial symmetry, the origin of three-germ layers and bilateral symmetry, dorsoventral axis inversion, the origin of vertebrates, the origin of gnathostomes. Here I discuss the genetic changes that may have underlain these transitions. The last two transitions were accompanied by, and possibly facilitated by, large increases in gene number. This probably occurred by tetraploidy, with some of the duplicate genes being subsequently lost. The origin of three germ-layers, bilateral symmetry and a through gut also probably involved gene duplication; in this case, duplication of an ancestral ProtoHox gene cluster to yield two paralogous homeobox gene clusters, Hox and ParaHox, with roles in patterning different germ layers along the anteroposterior body axis. This event may provide a partial genetic explanation for the Cambrian explosion.

Full text at:

http://www.looksmartscience.com/p/articles/mi_qa3746/is_199812/ai_n8819584

John Latter

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

technorati tags: cambrian, explosion, evolution, vertebrates, gene

[evomech] Natural selection and its limits: Where ecology meets evolution (Pigliucci)

2006-03-12T08:04:00.000Z

Pigliucci, M. (2004) Natural selection and its limits: Where ecology meets evolution. In: Casagrandi, R. & Melià, P. (Eds.) Ecologia. Atti del XIII Congresso Nazionale della Società Italiana di Ecologia (Como, 8-10 settembre 2003). Aracne, Roma, p. 29-34.

Abstract:

Natural selection [Darwin 1859] is perhaps the most important component of evolutionary theory, since it is the only known process that can bring about the adaptation of living organisms to their environments [Gould 2002]. And yet, its study is conceptually and methodologically complex, and much attention needs to be paid to a variety of phenomena that can limit the efficacy of selection [Antonovics 1976; Pigliucci and Kaplan 2000]. In this essay, I will use examples of recent work carried out in my laboratory to illustrate basic research on natural selection as conducted using a variety of approaches, including field work, laboratory experiments, and molecular genetics. I also discuss the application of this array of tools to questions pertinent to conservation biology, and in particular to the all-important problem of what makes invasive species so good at creating the sort of problems they are infamous for [Lee 2002].

Full text at:

http://www.xiiicongresso.societaitalianaecologia.org/articles/Pigliucci.pdf

John Latter

--

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

technorati tags: natural+selection, ecology, evolution, darwin, gould, research, genetics, complex

[evomech] Separation of Man and Ape Down to Gene Expression (PR + Article)

2006-03-11T06:21:00.000Z

Contents:

1) Separation of Man and Ape Down to Gene Expression

Humans and chimpanzees have in common more than 98 percent of DNA and 99 percent of genes. Yet, in looks and behavior we are very different from them. For more than 30 years--well before either the human or chimpanzee genome had been sequenced--scientists have speculated that this might be due to the way that the common genes express themselves rather than differences in the genes themselves. A new comparison published in Nature seems to prove that theory.

Full text at:

http://www.sciam.com/article.cfm?chanID=sa003&articleID=0005FB4D-6102-140F-A10283414B7F0000

2) Expression profiling in primates reveals a rapid evolution of human transcription factors

[Gilad et al, Nature, March '06]

Although it has been hypothesized for thirty years that many human adaptations are likely to be due to changes in gene regulation1, almost nothing is known about the modes of natural selection acting on regulation in primates. Here we identify a set of genes for which expression is evolving under natural selection. We use a new multi-species complementary DNA array to compare steady-state messenger RNA levels in liver tissues within and between humans, chimpanzees, orangutans and rhesus macaques. Using estimates from a linear mixed model, we identify a set of genes for which expression levels have remained constant across the entire phylogeny (approx70 million years), and are therefore likely to be under stabilizing selection. Among the top candidates are five genes with expression levels that have previously been shown to be altered in liver carcinoma. We also find a number of genes with similar expression levels among non-human primates but significantly elevated or reduced expression in the human lineage, features that point to the action of directional selection. Among the gene set with a human-specific increase in expression, there is an excess of transcription factors; the same is not true for genes with increased expression in chimpanzee.

Full text at:

http://www.nature.com/nature/journal/v440/n7081/full/nature04559.html

PDF:

http://www.nature.com/nature/journal/v440/n7081/pdf/nature04559.pdf

[Evolution] Contact me if you have any problems.

John Latter

--

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

technorati tags: natural+selection, dna, human, chimpanzee, evolution, nature, genes, rna

[evomech] Epigenetic vs. Genetic, a story of the evolution of the germline

2006-03-10T08:17:00.000Z

[Lachmann & Sella, SFI Working Paper]

Abstract:

Differentiation of multicellular organisms is controlled by epigenetic markers transmitted through cell division. Many of the systems that encode these markers exist also in unicellulars, but in unicellulars these systems do not control differentiation. Thus during the evolution of multicellularity, epigenetic inheritance systems were exapted for their current use in differentiation. During this transition there must have been stages at which epigenetic information passed between generations to an even larger extent than it does now. We show that this can lead to the evolution of cells that do not contribute to the progeny of the organism, and thus to a germline-soma distinction. This hints that an intrinsic instability during a transition from unicellulars to multicellulars may be the reason wide spread of the evolution of germ line.

Full text at:

http://www.santafe.edu/sfi/publications/Working-Papers/03-02-012.pdf

John Latter

--

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

technorati tags: epigenetic, germ, line, inheritance, evolution

Please Note: If you are reading this in a Blog then replying directly to this message (as opposed to making a 'blog comment') requires membership of the 'Evolution: Where Darwin meets Lamarck?' Egroup at: http://groups.yahoo.com/group/evomech/

[evomech] Re: Complexity in Biological Signaling Systems (Science)

2006-03-09T08:11:00.000Z

--- In evomech@yahoogroups.com, "John Latter" <jorolat@...> wrote:
>
> [Weng, Bhalla, & Iyengar , Science, Apr '99]
>
>
> Introduction:
>
> "Biological signaling pathways interact with one another to form
> complex networks. Complexity arises from the large number of
> components, many with isoforms that have partially overlapping
> functions; from the connections among components; and from the
> spatial relationship between components. The origins of the complex
> behavior of signaling networks and analytical approaches to deal with
> the emergent complexity are discussed here."
>
> Full text (PDF file) at:
>
> http://www.csc.liv.ac.uk/~m1pk/Projects/bhalla%202.pdf
> (begins halfway down the first page)
>
>
> Jorolat

Now available at:

http://www.ncbs.res.in/~faculty/upi_file/upi_papers/weng_bhalla_iyengar_Science1999.pdf

John Latter

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

technorati tags: complex, behavior, complexity

[evomech] The inheritance of features (Biology and Philosophy)

2006-03-08T07:31:00.000Z

Mameli, Biology and Philosophy (2005) 20:365–399

Abstract:

Since the discovery of the double helical structure of DNA, the standard account of the inheritance of features has been in terms of DNA-copying and DNA-transmission. This theory is just a version of the old theory according to which the inheritance of features is explained by the transfer at conception of some developmentally privileged material from parents to offspring. This paper does the following things: (1) it explains what the inheritance of features is; (2) it explains how the DNA-centric theory emerged; (3) it clarifies the relation between the DNA-centric theory and the 'unfolding' theory of development; (4) it argues that (given what we now know about developmental processes and genetic activity) the DNA-centric theory should be abandoned in favour of a pluralistic (but not holistic) theory of the inheritance of features. According to this pluralistic theory, the reliable reoccurrence of phenotypes must be explained by appealing not only to processes responsible for the reliable reoccurrence of genetic developmental factors but also to processes responsible for the reliable reoccurrence (or persistence) of nongenetic environmental factors.

Full text at:

http://www.phil.cam.ac.uk/~gmm32/MAMELI_INHERITANCE_2005.pdf

John Latter

--

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

technorati tags: dna, inheritance, features, theory, phenotypes

[evomech] [News] Stowers Scientists Demonstrate Mechanism of Vertebral Formation

2006-03-07T09:03:00.000Z

Kansas City, Mo. (March 6, 2006) - Jacqueline Kim Dale, Ph.D., formerly a Senior Research Associate at the Stowers Institute for Medical Research, and Olivier Pourquie, Ph.D., Stowers Institute Investigator and an investigator with the Howard Hughes Medical Institute, have demonstrated that the long-studied family of transcription factors called Snail is expressed in a cyclic fashion during the formation of the vertebral precursors in the mouse and chick embryo.

The findings, which were published in the March 7 issue of Developmental Cell, indicate that the genes governing many cellular properties are downstream of the segmentation clock, the mechanism that controls the formation of the vertebral column.

Full text at:

http://www.stowers-institute.org/WhatsNew/pr2006/PR030606.asp

John Latter

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

technorati tags: research, embryo, genes, mechanism

[evomech] Evolution as context-driven actualization of potential: Toward an interdisciplinary theory of change of state

2006-03-06T09:45:00.000Z

Gabora, L. & Aerts, D. (2005). Evolution as context-driven actualization of potential: Toward an interdisciplinary theory of change of state. Interdisciplinary Science Reviews, 30(1), 69-88.

Abstract:

It is increasingly evident that there is more to biological evolution than natural selection; moreover, the concept of evolution is not limited to biology. We propose an integrative framework for characterizing how entities evolve, in which evolution is viewed as a process of context-driven actualization of potential (CAP). Processes of change differ according to the degree of nondeterminism, and the degree to which they are sensitive to, internalize, and depend upon a particular context. The approach enables us to embed phenomena across disciplines into a broad conceptual framework. We give examples of insights into physics, biology, culture and cognition that derive from this unifying framework.

Full text at:

http://www.vub.ac.be/CLEA/liane/papers/cap.htm

John Latter

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

technorati tags: evolution, natural+selection, biology, physics, culture

[evomech] In the News: More info on "'Jurassic Beaver' find stuns experts"

2006-03-05T09:11:00.000Z

Anyone who read the recent 'Jurassic Beaver' find stuns experts news report might be interested in the following:

Perspective:

Early Mammalian Evolutionary Experiments
Thomas Martin*

Mammals of the Mesozoic era (248 to 65 million years ago) generally are considered to be primitive, shrew-like creatures living in the shadow of the dinosaurs (1). Only after the extinction of the dinosaurs at the end of the Cretaceous era (144 to 65 million years ago) did they have a chance to explore a greater variety of ecological niches. During the adaptive radiation that began about 65 million years ago, mammals were able to invade all kinds of terrestrial environments, even the aquatic and aerial realms. Pushing back the mammalian conquest of the waters by more than 100 million years, Ji et al. (2) report on page 1123 of this issue a Middle Jurassic, 164-million-year-old skeleton with a beaverlike tail and seal-like teeth perfectly adapted for an aquatic lifestyle.

and

Research Article the above Perspective refers to:

A Swimming Mammaliaform from the Middle Jurassic and Ecomorphological Diversification of Early Mammals
Qiang Ji,1,3 Zhe-Xi Luo,2,1* Chong-Xi Yuan,3 Alan R. Tabrum2

A docodontan mammaliaform from the Middle Jurassic of China possesses swimming and burrowing skeletal adaptations and some dental features for aquatic feeding. It is the most primitive taxon in the mammalian lineage known to have fur and has a broad, flattened, partly scaly tail analogous to that of modern beavers. We infer that docodontans were semiaquatic, convergent to the modern platypus and many Cenozoic placentals. This fossil demonstrates that some mammaliaforms, or proximal relatives to modern mammals, developed diverse locomotory and feeding adaptations and were ecomorphologically different from the majority of generalized small terrestrial Mesozoic mammalian insectivores.

The links work OK but email me if you have any problems (I made a typo on the research article url and got "We've redesigned our Web site, and some Carnegie Museum of Natural History pages have gone the way of the dinosaurs."!)

John Latter

technorati tags: jurassic, carnegie, beaver, museum, insectivores, natural+history, fossil, dinosaurs

[evomech] From symmetry to asymmetry: Phylogenetic patterns of asymmetry variation

2006-03-04T14:02:00.000Z

[A. Richard Palmer, PNAS, Dec '96]

From symmetry to asymmetry: Phylogenetic patterns of asymmetry variation in animals and their evolutionary significance

Abstract:

Phylogenetic analyses of asymmetry variation offer a powerful tool for exploring the interplay between ontogeny and evolution because (i) conspicuous asymmetries exist in many higher metazoans with widely varying modes of development, (ii) patterns of bilateral variation within species may identify genetically and environmentally triggered asymmetries, and (iii) asymmetries arising at different times during development may be more sensitive to internal cytoplasmic inhomogeneities compared to external environmental stimuli. Using four broadly comparable asymmetry states (symmetry, antisymmetry, dextral, and sinistral), and two stages at which asymmetry appears developmentally (larval and postlarval), I evaluated relations between ontogenetic and phylogenetic patterns of asymmetry variation. Among 140 inferred phylogenetic transitions between asymmetry states, recorded from 11 classes in five phyla, directional asymmetry (dextral or sinistral) evolved directly from symmetrical ancestors proportionally more frequently among larval asymmetries. In contrast, antisymmetry, either as an end state or as a transitional stage preceding directional asymmetry, was confined primarily to postlarval asymmetries. The ontogenetic origin of asymmetry thus significantly influences its subsequent evolution. Furthermore, because antisymmetry typically signals an environmentally triggered asymmetry, the phylogenetic transition from antisymmetry to directional asymmetry suggests that many cases of laterally fixed asymmetries evolved via genetic assimilation.

Full text at:

http://www.pnas.org/cgi/content/full/93/25/14279

John Latter

--

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

technorati tags: asymmetry, variation, ontogeny, evolution, development, symmetry, larval, phyla, directional, origin, genetic+assimilation

[evomech] Re: Antisymmetry (Chapter 16 of 'Variation')

2006-03-03T10:00:00.000Z

--- In evomech@yahoogroups.com, "John Latter" <jorolat@...> wrote:
>
> [A. Richard Palmer. "Antisymmetry." In Variation, Editors B Hallgrimmson and BK Hall. Elsevier (2005): 359-397]
>
> Introduction:
>
> The notion of antisymmetry likely strikes most people as bizarre. How can any
> variation exist that is "anti-" something else? To dismiss antisymmetry as mere
> intellectual catnip of academic snoots would seem easy. To dismiss it too hastily
> would be a big mistake.
>
> Antisymmetry is a peculiar kind of variation whose evolutionary significance is
> surprisingly unappreciated, no doubt in part because the term seems odd and foreboding. However, the phenomenon, with its particularly apt moniker, is actually
> widespread and offers the promise of valuable insights into a century-old debate
> about the interplay between development and evolution.

Now available at:

http://www.bms.bc.ca/library/Palmer'05%20CH16-Antisym-proofs-ed-4.pdf

John Latter

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

technorati tags: antisymmetry, variation, development, evolution

Re: [evomech] Limbs in whales and limblessness in other vertebrates: mechanisms of evolutionary and developmental transformation and loss.

2006-03-03T03:06:00.000Z

From: "John Latter" <jorolat@gmail.com>
> Subject: [evomech] Limbs in whales and limblessness in other
> vertebrates: mechanisms of evolutionary and developmental
> transformation and loss. [Bejder & Hall, Evolution &
> Development, '02]
> text; http://whitelab.biology.dal.ca/lb/Bejder%20and%20Hall.pdf

> We address the developmental and evolutionary mechanisms
> underlying fore- and hindlimb development and progressive
> hindlimb reduction and skeletal loss...

There's nothing in the article about the evolutionary origin of
limbs.
That little point is glossed over in this discussion of
development
and of the evolutionary reduction of limbs.

> Limblessness in most snakes is also associated with adoption
>of a new (burrowing) lifestyle...

Were early snakes tunnelers? Or does this new burowing include
merely burrowing through surface debis? Just wondering.

> An evolutionary change in Hox gene expression--as occurs
> in snakes--or in Hox gene regulation--as occurs in some limbless
> mutants--is unlikely to have initiated loss of the hindlimbs in
> cetaceans. Selective pressures acting on a wide range of
> developmental processes and adult traits other than the
> limbs are likely to have driven the loss of hindlimbs in whales.

Are they suggesting that a change occurring via Hox genes or
their regulation can occur more quickly? Selective pressure may
drive the loss of a feature, but how do we know whether or not
Hox genes are involved?

Cliff

technorati tags: whales, limbs, vertebrates, loss

[evomech] Limbs in whales and limblessness in other vertebrates: mechanisms of evolutionary and developmental transformation and loss

2006-03-02T08:41:00.000Z

[Bejder & Hall, Evolution & Development, '02]

Summary:

We address the developmental and evolutionary mechanisms underlying fore- and hindlimb development and progressive hindlimb reduction and skeletal loss in whales and evaluate whether the genetic, developmental, and evolutionary mechanisms thought to be responsible for limb loss in snakes "explain" loss of the hindlimbs in whales. Limb loss and concurrent morphological and physiological changes associated with the transition from land to water are discussed within the context of the current whale phylogeny. Emphasis is placed on fore- and hindlimb development, how the forelimbs transformed into flippers, and how the hindlimbs regressed, leaving either no elements or vestigial skeletal elements. Hindlimbs likely began to regress only after the ancestors of whales entered the aquatic environment: Hindlimb function was co-opted by the undulatory vertical axial locomotion made possible by the newly evolved caudal flukes. Loss of the hindlimbs was associated with elongation of the body during the transition from land to water. Limblessness in most snakes is also associated with adoption of a new (burrowing) lifestyle and was driven by developmental changes associated with elongation of the body. Parallels between adaptation to burrowing or to the aquatic environment reflect structural and functional changes associated with the switch to axial locomotion. Because they are more fully studied and to determine whether hindlimb loss in lineages that are not closely related could result from similar genetically controlled developmental pathways, we discuss developmental (cellular and genetic) processes that may have driven limb loss in snakes and leg-less lizards and compare these processes to the loss of hindlimbs in whales. In neither group does ontogenetic or phylogenetic limb reduction result from failure to initiate limb development. In both groups limb loss results from arrested development at the limb bud stage, as a result of inability to maintain necessary inductive tissue interactions and enhanced cell death over that seen in limbed tetrapods. An evolutionary change in Hox gene expression--as occurs in snakes--or in Hox gene regulation--as occurs in some limbless mutants--is unlikely to have initiated loss of the hindlimbs in cetaceans. Selective pressures acting on a wide range of developmental processes and adult traits other than the limbs are likely to have driven the loss of hindlimbs in whales.

Full text at;

http://whitelab.biology.dal.ca/lb/Bejder%20and%20Hall.pdf

John Latter

--

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

technorati tags: evolutionary, mechanisms, genetic, developmental, whales, hindlimb, limb, loss, forelimbs, adaption, hox, snakes, gene, evolution, tetrapods

[evomech] Conrad Hal Waddington: the last Renaissance biologist? (Nature)

2006-03-01T08:39:00.000Z

[Slack, Nature, Nov '02]

Perspective (Timeline):

Conrad Hal Waddington was a leading embryologist and geneticist from the 1930s to the 1950s. He is remembered mainly for his concepts of the 'epigenetic landscape' and 'genetic assimilation'. This article reviews his life and work, and enquires to what extent his ideas are relevant tools for understanding the biological problems of today.

Full text at:

http://wwworm.biology.uh.edu/evodevo/lecture3/slack02.pdf

John Latter

--

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

technorati tags: genetic+assimilation, waddington, epigenetic, landscape, nature

[evomech] The morphogenesis of evolutionary developmental biology (Int. J, Dev. Biol.)

2006-02-28T08:34:00.000Z

[Gilbert, Int. J. Dev. Biol. 47: 467-477 (2003)]

Abstract:

The early studies of evolutionary developmental biology (Evo-Devo) come from several sources. Tributaries flowing into Evo-Devo came from such disciplines as embryology, developmental genetics, evolutionary biology, ecology, paleontology, systematics, medical embryology and mathematical modeling. This essay will trace one of the major pathways, that from evolutionary embryology to Evo-Devo and it will show the interactions of this pathway with two other sources of Evo-Devo: ecological developmental biology and medical developmental biology. Together, these three fields are forming a more inclusive evolutionary developmental biology that is revitalizing and providing answers to old and important questions involving the formation of biodiversity on Earth. The phenotype of Evo-Devo is limited by internal constraints on what could be known given the methods and equipment of the time and it has been framed by external factors that include both academic and global politics. [Evolution]

Full text at:

http://www.ijdb.ehu.es/web/contents.php?vol=47&issue=7-8&doi=14756322

John Latter

--

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

technorati tags: evo-devo, biology, ecology, genetics, paleontology, systematics, biodiversity, evolution

[evomech] Re: Symmetry Breaking and the Evolution of Development (Science)

2006-02-27T09:44:00.000Z

--- In evomech@yahoogroups.com, "John Latter" <jorolat@...> wrote:
>
> [Palmer, Science, Oct '04]
>
> Abstract:
>
> " Because of its simplicity, the binary-switch nature of left-right asymmetry permits meaningful comparisons among many different organisms. Phylogenetic analyses of asymmetry variation, inheritance, and molecular mechanisms reveal unexpected insights into how development evolves. First, directional asymmetry, an evolutionary novelty, arose from nonheritable origins almost as often as from mutations, implying that genetic assimilation ("phenotype precedes genotype") is a common mode of evolution. Second, the molecular pathway directing hearts leftwardthe nodal cascadevaries considerably among vertebrates (homology of form does not require homology of development) and was possibly co-opted from a preexisting asymmetrical chordate organ system. Finally, declining frequencies of spontaneous asymmetry reversal throughout vertebrate evolution suggest that heart development has become more canalized."
>
> Copies of the full article can be obtained either by emailing Rich direct or from myself here
>

This paper is now available at:

http://www.biology.duke.edu/nijhout/PDFs/Palmer04.pdf

John Latter

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

technorati tags: symmetry, evolution, inheritance, novelty, genetic+assimilation, phenotype, genotype, asymmetry, vetebrate

[evomech] Putting Genes in Perspective (Book Review)

2006-02-26T08:44:00.000Z

[Pfennig, American Scientist Book Review, Jan '04]

Developmental Plasticity and Evolution. Mary Jane West-Eberhard.

An unfortunate outgrowth of the modern revolution in genetics is the widespread belief that the genes of an individual organism determine its appearance, physiology and behavior. The genome does not, of course, completely determine how an organism is constructed: The environment is an essential partner. Nowhere is this point more clearly illustrated than by the principle of developmental plasticity—the tendency for genetically identical organisms to differ in response to various environmental stimuli, or for individuals to vary over time as the result of changing conditions in their surroundings...

... In Developmental Plasticity and Evolution, Mary Jane West-Eberhard, an evolutionary biologist at the Smithsonian Tropical Research Institute and a member of the National Academy of Sciences, undertakes to explain how developmental plasticity fits within a genetic theory of evolution. She believes (with considerable justification) that evolutionary and developmental biologists have failed to incorporate developmental plasticity into their framework for understanding the living world.

Full text at:

http://www.americanscientist.org/template/BookReviewTypeDetail/assetid/29782

Amazon.com link:

http://www.amazon.com/gp/product/0195122356/qid=1140942822/103-2980949-5514221

John Latter

--

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

technorati tags: plasticity, evolution, book+review, genetics, theory, developmental, genes

[evomech] Genetic assimilation of an acquired character (Classic Paper)

2006-02-25T08:54:00.000Z

Genetic assimilation of an acquired character

[Waddington, Evolution, Jun '53]

Introduction

Under the influence of natural selection development tends to become canalized so that more or less normal organs and tissues are produced even in the face of slight abnormalities of the genotype or of the external environment (Waddington, 1940).

It has been suggested that if an animal is subjected to unusual circumstances to which it can react in an adaptive manner, the development of the adaptive character might itself become so far canalised that it continued to appear even when the conditions returned to the previous norm (Waddington, 1942). This mechanism would provide a means by which an "acquired character" in the conventional sense could be "assimilated" by the genotype, and eventually appear comparitively independent of any specific environmental influence.

Schmalhausen (1947) has independently suggested a very similar process, which he has discussed at some length under the name "stabilising selection"; a phrase which, however, he uses in a number of different senses, as Simpson (1947) has pointed out.

Full text at:

http://wwworm.biology.uh.edu/evodevo/lecture3/waddington53.pdf

John Latter

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

technorati tags: natural+selection, evolution, waddington, mechanism, genetic+assimilation, genotype, environment

[evomech] Dollo's law and the re-evolution of shell coiling (Royal Society of London)

2006-02-24T08:27:00.000Z

[Collin & Cipriani, Proceedings of the Royal Society of London B , Dec '03]

Abstract:

Gastropods have lost the quintessential snail feature, the coiled shell, numerous times in evolution. In many cases these animals have developed a limpet morphology with a cap-shaped shell and a large foot. Limpets thrive in marginal habitats such as hydrothermal vents, the high-energy rocky intertidal areas and fresh water, but they are considered to be evolutionary dead-ends, unable to re-evolve a coiled shell and therefore unable to give rise to the diversity seen among coiled snails. The re-evolution of a coiled shell, or any complex character, is considered unlikely or impossible (Dollo's law) because the loss of the character is followed by the loss of the genetic architecture and developmental mechanisms that underlie that character. Here, we quantify the level of coiling in calyptraeids, a family of mostly uncoiled limpets, and show that coiled shells have re-evolved at least once within this family. These results are the first demonstration, to our knowledge, of the re-evolution of coiling in a gastropod, and show that the developmental features underlying coiling have not been lost during 20-100 Myr of uncoiled evolutionary history.This is the first example of the re-evolution of a complex character via a change in developmental timing (heterochrony) rather than a change in location of gene expression (heterotopy).

Full text at:

http://striweb.si.edu/publications/PDFs/Collin_Dollo's%20Law%20Print%20version.pdf

John Latter

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

technorati tags: dollo's+law, royal+society, london, gastropods, limpets, shell, re-evolution, evolution, hydrothermal+vents, diversity, genetic, developmental, history, complex, character

[evomech] Re: Birds that make teeth (Press Release + Summary)

2006-02-23T09:17:00.000Z

>http://www.current-biology.com/content/article/abstract?uid=PIIS0960982206000649
>I'll post when I have more info on obtaining the full paper.

One of the authors (John F. Fallon) sent me a copy yesterday. His email address is at the link above or contact me here

John Latter

--

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

[evomech] Birds that make teeth (Press Release + Summary)

2006-02-22T09:47:00.000Z

Contents:

1) Birds that make teeth (Press Release)

Gone does not necessarily mean forgotten, especially in biology. A recent finding by researchers at the University of Wisconsin, Madison, and colleagues from the University of Manchester have found new evidence that the ability to form previously lost organs--in this case, teeth--can be maintained millions of years after the last known ancestor possessed them.

Birds do not have teeth. However, their ancestors did--about 70 - 80 million years ago. The evolutionary loss of teeth corresponded to the formation of the beak that is present in all living birds. Nonetheless, it has been known that if mouse tooth-forming tissue is in contact with bird jaw tissue, the bird tissue is able to follow the instructions given by the mouse tissue and participate in making teeth, and that these teeth look very much like those of mammals. However, Drs. Matthew Harris and John F. Fallon and colleagues have found that modern birds retain the ability to make teeth even without instruction from their tooth-bearing cousins.

Full text at:

http://www.eurekalert.org/pub_releases/2006-02/cp-btm021506.php

2) The Development of Archosaurian First-Generation Teeth in a Chicken Mutant

[Harris et al., Current Biology, Feb '06]

Summary:

Modern birds do not have teeth. Rather, they develop a specialized keratinized structure, called the rhamphotheca, that covers the mandible, maxillae, and premaxillae. Although recombination studies have shown that the avian epidermis can respond to tooth-inductive cues from mouse or lizard oral mesenchyme and participate in tooth formation 1; 2, attempts to initiate tooth development de novo in birds have failed. Here, we describe the formation of teeth in the talpid2 chicken mutant, including the developmental processes and early molecular changes associated with the formation of teeth. Additionally, we show recapitulation of the early events seen in talpid2 after in vivo activation of Î²-catenin in wild-type embryos. We compare the formation of teeth in the talpid2 mutant with that in the alligator and show the formation of decidedly archosaurian (crocodilian) first-generation teeth in an avian embryo. The formation of teeth in the mutant is coupled with alterations in the specification of the oral/aboral boundary of the jaw. We propose an epigenetic model of the developmental modification of dentition in avian evolution; in this model, changes in the relative position of a lateral signaling center over competent odontogenic mesenchyme led to loss of teeth in avians while maintaining tooth developmental potential.

Summary available at:

http://www.current-biology.com/content/article/abstract?uid=PIIS0960982206000649

I'll post when I have more info on obtaining the full paper.

John Latter

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

(Evolution)

technorati tags: birds, mandible, epidermis, mouse, lizard, tooth+formation, teeth, chicken, evolution, developmental, molecular, embryo, alligator, formation, epigenetic, jaw, recapitulation, biology, university, wisconsin, madison, manchester, organs, ancestor, mutant, avian

Please Note: If you are reading this in a Blog then replying directly to this message (as opposed to making a 'blog comment') requires membership of the 'Evolution: Where Darwin meets Lamarck?' Egroup at:
http://groups.yahoo.com/group/evomech/

[evomech] Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism

2006-02-21T09:26:00.000Z

Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism
[Jeffery et al., Nature Genetics, Dec '05]

Letter:

The genetic basis of vertebrate morphological evolution has traditionally been very difficult to examine in naturally occurring populations. Here we describe the generation of a genome-wide linkage map to allow quantitative trait analysis of evolutionarily derived morphologies in the Mexican cave tetra, a species that has, in a series of independent caves, repeatedly evolved specialized characteristics adapted to a unique and well-studied ecological environment. We focused on the trait of albinism and discovered that it is linked to Oca2, a known pigmentation gene, in two cave populations. We found different deletions in Oca2 in each population and, using a cell-based assay, showed that both cause loss of function of the corresponding protein, OCA2. Thus, the two cave populations evolved albinism independently, through similar mutational events.

Full text at:

http://www.nature.com/ng/journal/v38/n1/full/ng1700.html

PDF version:

http://www-biology.ucsd.edu/labs/hoekstra/EvoDevo%20pdfs/Tabin2005.pdf

(NB I thought I had already posted this but it didn't show up in a search of the group's archives)

John Latter

--

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

technorati tags: vertebrate, morphological, evolution, genetic, trait, analysis, mexican, cave, tetra, cavefish, albinism, convergence, molecular, species, ecological, environment

[evomech] Research points to new theory driving evolutionary changes ('04 PR + Article)

2006-02-20T09:29:00.000Z

Contents:

1) Research points to new theory driving evolutionary changes (Press Release)

DALLAS - Dec. 13, 2004 - Researchers at UT Southwestern Medical Center at Dallas have used canine DNA to identify a genetic mutation mechanism they believe is responsible for rapid evolutionary changes in the physical appearance of many species.

The findings, based on data gathered from hundreds of museum specimens of dogs and from blood samples of volunteered live dogs, offer a new explanation for the sudden, rapid rise of new species found in the fossil record. They also help explain the variability in appearance among individual members of a species, such as the length of the nose in different breeds of domestic dogs.

"We're offering an explanation for a lot of different components of evolution, one that goes against the central dogma that currently explains how certain aspects of evolution take place," said Dr. Harold "Skip" Garner.

Full article at:

http://www8.utsouthwestern.edu/utsw/cda/dept37389/files/198556.html

2) Molecular origins of rapid and continuous morphological evolution

[Garner & Fondon, PNAS, Dec '04]

Abstract:

Mutations in cis-regulatory sequences have been implicated asbeing the predominant source of variation in morphologicalevolution.We offer a hypothesis that gene-associated tandem repeat expansionsand contractions are a major source of phenotypic variationin evolution. Here, we describe a comparative genomic studyof repetitive elements in developmental genes of 92 breeds ofdogs. We find evidence for selection for divergence at codingrepeat loci in the form of both elevated purity and extensivelength polymorphism among different breeds. Variations in thenumber of repeats in the coding regions of the Alx-4 (aristaless-like4) and Runx-2 (runt-related transcription factor 2) genes werequantitatively associated with significant differences in limband skull morphology. We identified similar repeat length variationin the coding repeats ofRunx-2, Twist, and Dlx-2 in severalother species. The high frequency and incremental effects ofrepeat length mutations provide molecular explanations for swift,yet topologically conservative morphological evolution.

Full text at:

http://www.pnas.org/cgi/content/full/101/52/18058

PDF version:

http://www.pnas.org/cgi/reprint/101/52/18058

John Latter

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

technorati tags: new+theory, evolution, dallas, dogs, new+species, fossil+record, pnas, central+dogma, cis-regulatory, morphological, polymorphism, genes

[evomech] Unintelligent Design: A monstrous discovery suggests that viruses..

2006-02-19T08:31:00.000Z

[Siebert, Discover Magazine, Mar '06]

A monstrous discovery suggests that viruses, long regarded as lowly evolutionary latecomers, may have been the precursors of all life on Earth

Extracts:

Few things on Earth are spookier than viruses. The very name virus, from the Latin word for "poisonous slime," speaks to our lowly regard for them...

...Now, with the recent discovery of a truly monstrous virus, scientists are again casting about for how best to characterize these spectral life-forms. The new virus, officially known as Mimivirus (because it mimics a bacterium), is a creature "so bizarre," as The London Telegraph described it, "and unlike anything else seen by scientists . . . that . . . it could qualify for a new domain in the tree of life." Indeed, Mimivirus is so much more genetically complex than all previously known viruses, not to mention a number of bacteria, that it seems to call for a dramatic redrawing of the tree of life...

...Viruses, long thought to be biology's hitchhikers, turn out to have been biology's formative force. This is striking news, especially at a moment when the basic facts of origins and evolution seem to have fallen under a shroud. In the discussions of intelligent design, one hears a yearning for an old-fashioned creation story, in which some singular, inchoate entity stepped in to give rise to complex life-forms - humans in particular. Now the viruses appear to present a creation story of their own: a stirring, topsy-turvy, and decidedly unintelligent design wherein life arose more by reckless accident than original intent...

...The discovery of Mimivirus lends weight to one of the more compelling theories discussed at Les Treilles. Back when the three domains of life were emerging, a large DNA virus very much like Mimi may have made its way inside a bacterium or an archaean and, rather than killing it, harmlessly persisted there. The eukaryotic cell nucleus and large, complex DNA viruses like Mimi share a compelling number of biological traits. They both replicate in the cell cytoplasm, and on doing so, each uses the same machinery within the cytoplasm to form a new membrane around itself. They both have certain enzymes for capping messenger RNA, and they both have linear chromosomes rather than the circular ones typically found in a bacterium. "If this is true," Forterre has said of the viral-nucleus hypothesis, "then we are all basically descended from viruses."...

...We have been looking for our designer in all the wrong places. It seems we owe our existence to viruses, the least of semiliving forms, and about the only thing they have in common with any sort of theological prime mover is their omnipresence and invisibility. Once again, viruses have altered the way that we view them and, by extension, ourselves. As it turns out, they are not the little breakaway shards of our biology - we are, of theirs.

Full text at:

http://www.discover.com/issues/mar-06/cover/?page=1

See also: The Animal Self (New York Times)

John Latter

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

technorati tags: evolution, viruses, discovery, mimivirus, bacteria, telegraph, biology, intelligent+design, rna, creation, dna, traits, cell, forterre, theological, animal+self, new+york+times

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

2006-02-18T14:16:00.000Z

[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

technorati tags: central+tenet, evolutionary+theory, evolution, variation, adaptation, mechanism, nonrandom, phenomena, controversial, directed+mutation, adaptive+mutation, darwinian, natural+selection

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

2006-02-17T08:44:00.000Z

[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

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

technorati tags: evolution, mary-claire+king, human, chimpanzee, dna, genetics, genome, wilson

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

2006-02-16T10:37:00.000Z

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&amp;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

--

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

technorati tags: great+evolution+mystery, evolution, willow-moth, caterpillar, gordon+rattray+taylor, experiments, rats, lamarck, lamarckian, acquired+behavior, internal+evolutionary+mechanism, homeostatic, schroeder, griffiths

[evomech] 'Turned On': A revolution in the field of evolution? (Book Review)

2006-02-16T07:25:00.000Z

[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
http://members.aol.com/jorolat/index.html

technorati tags: evo+devo, popular+science, biology, genomics, proteomics, genetics, genomes, species

Re: [evomech] The main thrust of the group

2006-02-15T15:54:00.000Z

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

--

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

technorati tags: internal+evolutionary+mechanism, evolution

[evomech] The main thrust of the group

2006-02-15T14:11:00.000Z

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

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

2006-02-15T09:21:00.000Z

"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
http://members.aol.com/jorolat/index.html

technorati tags: darwin, vqr, virginia+quarterly+review, niles+eldredge, evolution, intelligent+design, michael+ruse, thomas+eisner, david+quammen, theory+of+evolution, dinosaurs, natural+history, museum

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

2006-02-14T15:07:00.000Z

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:
http://members.aol.com/jorolat/index.html

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

2006-02-14T13:53:00.000Z

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

'Warren'

technorati tags: Gene+Regulatory+Network

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

2006-02-14T09:39:00.000Z

[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
http://members.aol.com/jorolat/index.html

technorati tags: development, animal, body+plan, gene+regulatory+network, hierarchical+organization, morphology, cambrian, phylum, paleontology

[evomech] Viva Lamarck: A Brief History of the Inheritance of Acquired Characteristics

2006-02-14T09:09:00.000Z

[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
http://members.aol.com/jorolat/index.html

technorati tags: inheritance+of+acquired+characteristics, lamarck, weismann, controversy, steele, gorczynski

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

2006-02-13T11:08:00.000Z

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

technorati tags: evolution,, phenotypic+plasticity,, pigliucci,, research,, genetics,, molecular

Please Note: If you are reading this in a Blog then replying directly to this message (as opposed to making a 'blog comment') requires membership of the 'Evolution: Where Darwin meets Lamarck?' Egroup at:
http://groups.yahoo.com/group/evomech/

Re: [evomech] Pit-Loops

2006-02-13T10:47:00.000Z

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

Please Note: If you are reading this in a Blog then replying directly to this message (as opposed to making a 'blog comment') requires membership of the 'Evolution: Where Darwin meets Lamarck?' Egroup at:
http://groups.yahoo.com/group/evomech/

technorati tags: evolution,, phenotypic+plasticity, pigliucci, research, genetics, molecular

[evomech] Pit-Loops

2006-02-13T00:26:00.000Z

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

Please Note: If you are reading this in a Blog then replying directly to this message (as opposed to making a 'blog comment') requires membership of the 'Evolution: Where Darwin meets Lamarck?' Egroup at:
http://groups.yahoo.com/group/evomech/

[evomech] Robustness of cellular functions (Cell)

2006-02-12T10:18:00.000Z

[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
http://members.aol.com/jorolat/index.html

technorati tags: robustness, theory, cellular, cell, complexity, biology, engineering

[evomech] Re: Richard Dawkins - The Root of All Evil? (Audio Interview)

2006-02-12T08:46:00.000Z

"...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
http://members.aol.com/jorolat/index.html

Please Note: If you are reading this in a Blog then replying directly to this message (as opposed to making a 'blog comment') requires membership of the 'Evolution: Where Darwin meets Lamarck?' Egroup at:
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[evomech] Richard Dawkins - The Root of All Evil? (Audio Interview)

2006-02-12T08:22:00.000Z

['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

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

technorati tags: richard+dawkins, evolution, faith, natural+selection, Sun-Tzu-Wu, theory

[evomech] Re: Regulatory gene networks and the properties of the developmental process (PNAS)

2006-02-11T16:25:00.000Z

The proper term for regulatory gene networks would be genetic
control programs. Note that the control programs are not controlled
by genes, are more complex and more influential than the genes they
control. Finally, note that these programs are made up of
progressive, intelligent, teleological feedback loops (pit-loops).

Warren

--- In evomech@yahoogroups.com, "John Latter" <jorolat@...> wrote:
>
> [Davidson et al., PNAS, Feb '03]
>
> Abstract:
>
> Genomic instructions for development are encoded in arrays of
> regulatory DNA. These specify large networks of interactions among genes
> producing...
>
> Full text at:
>
> http://www.pnas.org/cgi/content/full/100/4/1475
> http://www.pnas.org/cgi/content/full/100/4/1475

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[evomech] Regulatory gene networks and the properties of the developmental process (PNAS)

2006-02-11T08:41:00.000Z

[Davidson et al., PNAS, Feb '03]

Abstract:

Genomic instructions for development are encoded in arrays of regulatory DNA. These specify large networks of interactionsamong genes producing transcription factors and signaling components.The architecture of such networks both explains and predicts developmentalphenomenology. Although network analysis is yet in its early stages,some fundamental commonalities are already emerging. Two suchare the use of multigenic feedback loops to ensure the progressivityof developmental regulatory states and the prevalence of repressiveregulatory interactions in spatial control processes. Gene regulatorynetworks make it possible to explain the process of developmentin causal terms and eventually will enable the redesign of developmentalregulatory circuitry to achieve differentoutcomes.

Full text at:

http://www.pnas.org/cgi/content/full/100/4/1475

John

Evolution: Where Darwin meets Lamarck? Discussion Forum:
http://groups.yahoo.com/group/evomech

technorati tags: dna, genetics, regulatory, development, transcription

[evomech] Biology inspires perceptive machines (PhysOrg]

2006-02-11T07:18:00.000Z

[PhysOrg, Feb '06]

Biology inspires perceptive machines

Teaching a machine to sense its environment is one of the most intractable problems of computer science, but one European project is looking to nature for help in cracking the conundrum. It combined streams of sensory data to produce an adaptive, composite impression of surroundings in near real-time.

The team brought together electronic engineers, computer scientists, neuroscientists, physicists, and biologists. It looked at basic neural models for perception and then sought to replicate aspects of these in silicon.

"The objective was to study sensory fusion in biological systems and then translate that knowledge into the creation of intelligent computational machines".

Full text at:

http://www.physorg.com/news10712.html [PhyOrg]
http://istresults.cordis.lu/index.cfm/section/news/tpl/article/BrowsingType/Features/ID/80430 [IST]

John

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

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technorati tags: biology, intelligent+machines, adaptive, computer+science

[evomech] Why Some Animals Have Smaller Eyes: Lifestyle Matters (PR + Article)

2006-02-10T15:15:00.000Z

Contents:

1) Why Some Animals Have Smaller Eyes: Lifestyle Matters (Medical News)

If brain size is proportional to body size in virtually all vertebrate animals, Cornell University biologists reasoned, shouldn't eye size and body size scale the same way? While they failed to find a one-size-fits-all rule for eyes, what they learned about the 300 vertebrates they studied helps to explain how animals evolved precisely the orbs they need for everyday life. The biologists reported their findings in the journal Vision Research (August 2004, "The allometry and scaling of the size of vertebrate eyes").

Full text at:

http://www.medicalnewstoday.com/medicalnews.php?newsid=11824

2) The allometry and scaling of the size of vertebrate eyes

[Howland et al., Vision Research, Aug '04]

We compiled data from the literature and colleagues to examine the relationship between eye axial length and body weight for vertebrates as well as birds, mammals, reptiles, and fishes independently. After fitting the data to logarithmic and semi-logarithmic models, we found that axial length of vertebrate eyes does obey a conventional logarithmic relationship with body weight rather than a semi-logarithmic relationship as Suggested by the results of previous Studies (Handbook of Sensory Physiology, VII/5: The Visual System in Vertebrates, Springer-Verlag, Berlin, 1977; The Allometry of the Vertebrate Eye, Dissertation, University of Chicago, UMI, Ann Arbor, T28274, 1982). The regression slopes and intercepts appear to be characteristic of various animal groups. The axial length of the eye is largest in birds and primates, smaller in other mammals (especially rodents) and reptiles, and widely varying in fishes.

Full text at:

http://www.psych.upenn.edu/courses/psych600-311_Spring2005/homework/Howland_VertebrateEyes_VisRes2004.pdf

John

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

technorati tags: reptiles, mammals

[evomech] Science losing war over evolution (Harvard Gazette)

2006-02-10T08:45:00.000Z

[Powell, Harvard University News Office, Feb '06]

Screening airs evolution versus intelligent design debate

This just in from the front lines of the battle between evolution and intelligent design: evolution is losing.

That's the assessment of Randy Olson, a Harvard-trained evolutionary biologist turned filmmaker who explored the debate in a new film, "Flock of Dodos: The Evolution - Intelligent Design Circus," which was screened Monday (Feb. 6) at the Harvard Museum of Natural History.

Full text at:

http://www.news.harvard.edu/gazette/2006/02.09/13-dodo.html

John

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

[evomech] UCSD Study Shows 'Junk' DNA Has Evolutionary Importance (News + Article)

2006-02-09T08:49:00.000Z

Contents:

1) UCSD Study Shows 'Junk' DNA Has Evolutionary Importance (Press Release)

Genetic material derisively called "junk" DNA because it does not contain the instructions for protein-coding genes and appears to have little or no function is actually critically important to an organism's evolutionary survival, according to a study conducted by a biologist at UCSD.

In the October 20 issue of Nature, Peter Andolfatto, an assistant professor of biology at UCSD, shows that these non-coding regions play an important role in maintaining an organism's genetic integrity. In his study of the genes from the fruit fly Drosophila melanogaster, he discovered that these regions are strongly affected by natural selection, the evolutionary process that preferentially leads to the survival of organisms and genes best adapted to the environment.

Full text at:

http://ucsdnews.ucsd.edu/newsrel/science/mcjunk.asp

2) Adaptive evolution of non-coding DNA in Drosophila (Article)

A large fraction of eukaryotic genomes consists of DNA that is not translated into protein sequence, and little is known about its functional significance. Here I show that several classes of non-coding DNA in Drosophila are evolving considerably slower than synonymous sites, and yet show an excess of between-species divergence relative to polymorphism when compared with synonymous sites. The former is a hallmark of selective constraint, but the latter is a signature of adaptive evolution, resembling general patterns of protein evolution in Drosophila. I estimate that about 40-70% of nucleotides in intergenic regions, untranslated portions of mature mRNAs (UTRs) and most intronic DNA are evolutionarily constrained relative to synonymous sites. However, I also use an extension to the McDonald-Kreitman test to show that a substantial fraction of the nucleotide divergence in these regions was driven to fixation by positive selection (about 20% for most intronic and intergenic DNA, and 60% for UTRs). On the basis of these observations, I suggest that a large fraction of the non-translated genome is functionally important and subject to both purifying selection and adaptive evolution. These results imply that, although positive selection is clearly an important facet of protein evolution, adaptive changes to non-coding DNA might have been considerably more common in the evolution of D. melanogaster.

Full text at:

http://www.euchromatin.com/Andolfatto01.htm

PDF versions:

http://evogen.bio.uci.edu/JC_PDFs/flygenomearticle.pdf
http://eebweb.arizona.edu/Courses/Ecol426_526/Andolfatto_2005.pdf

John

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

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[evomech] Define of Evolution 2

2006-02-08T16:09:00.000Z

Evolution means change. One possible alternative to `biological
evolution is genetic change or genetic change in populations' is
thus `biological evolution is defined as any change in a biological
operating or assembly instruction'. As should be obvious, this
represent a very dramatic proposed change in the definition and
concept of biological evolution. The rationale for proposing such a
dramatic change is reasonably straight forward- the old model or
concept didn't work and the new one will.

With respect to the six points raised in the initial post:

1. What changes?- The proposed definition suggests that
biological evolution involves changes in information processing or
causal (input-output) relationships (rather than changes in genes).
Note that causal relationships are probably a more traditional or
conventional object for scientific analysis than genes.
2. When does it change?- In the proposed definition,
evolutionary change occurs continuously in individual cells. Again,
this time-frame for change is more conventional for scientific
analysis than the once per life-time framework implicit by the
genetic model.
3. What are the processes and mechanisms responsible for
change?- The proposal here is that biological evolution(change) is
the product of multi-tiered processes. At the bottom of basic level,
evolutionary change is produced by actions of a type of feedback
loop called a PIT loop. At a higher level, evolutionary change is
the result of changes in PIT loops or the parameters controlling PIT
loops.
4. How are change processes observed and measured.- There are
well established techniques for measuring the operations of feedback
loops.
5. Who is involved in developing and evaluating definitions?-
There is an existing set of professionals who can model and analyze
complex systems involving feedback loops.
6. How are testable, predictive theories formulated.-
Predictive theories are readily formulated for feedback loop based
systems using what I refer to in another thread as biological or bio-
engineering determinism.

Warren

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[evomech] The Human Genome Project +5 (The Scientist)

2006-02-08T08:24:00.000Z

[McElheny, The Scientist, Feb '06]

Five years after publication of two drafts of the human genome, Maynard Olson of the University of Washington finds himself longing for another "lurch." To be sure, genomic scientists across the world have chalked up many achievements since 2001, but, like many of his colleagues, Olson is feeling more impatient than celebratory.

Progress has included a blizzard of comparisons between the human sequence and many others, including the chicken, the mouse, the rat, the dog, and the chimp. The flourishing of comparative genomics, says Olson, has changed the focus of genomics from a single reference sequence of genes to a rich variety of "functional elements," largely sequences that serve as ignition switches, brakes and accelerators for gene expression. And the focus on single-base changes has widened to an array of evolutionary rearrangements: insertions, deletions, reversals, and duplications. There are new tools: new global databases of all functional elements in genomes (e.g., ENCODE), small molecules for chemical genomics (e.g., PubChem), and a raft of protein structures.

And yet the last five years, in Olson's view, have been "a period of a great grinding of gears, kind of shifting of gears." In the terms of the science historian Thomas Kuhn, it's been "a period of consolidation and more normal science." Others, such as Sydney Brenner of the Salk Institute, the Nobel Prize-winning pioneer of the worm, Caenorhabditis elegans, go further, worrying that the genome sequence and the growing lists of sequences and proteins and protein interactions and functional elements don't get very deep into such core problems of biology as the operations of the cell, of development from egg to adult, or the problem of consciousness. "We've become very geno-centric," says Brenner. "The cell must become the focus."

What vexes many thousands of colleagues around the world most is that genomics hasn't yet moved into the "real world" of medical relevance. Olson led a team that sequenced the principal microbe involved in lung infections in cystic fibrosis patients, Pseudonomas aeruginosa. Referring to changes in cells of both the patient and the infecting organisms, says Olson, "it's clear that mutational cascades are a really critical aspect of disease progression, just as is the case with cancer." To build a genomics "bridge" into this area is going to call for a "very large" amount of sequencing of both patients and microbes to follow the progression of the disease. For this, the faster second-generation sequencing technologies emerging from several startup companies will be essential, Olson thinks, just as it will be for the new National Institutes of Health Cancer Genome Project, on which pilot work has begun. "They're over-promising and are trying to move too quickly, without a strong enough strategic plan," Olson argues. "Nonetheless the scientific idea is right. These policy things usually eventually fall into place as reality exerts itself."

Such issues as cheaper, faster DNA sequencing to get genomic tools into the clinic sooner will define the field for the next five years, and beyond. Echoing Olson, Cold Spring Harbor Laboratory's Lincoln Stein says the last five years have fit Kuhn's definition of 'normal science," although "the number of questions never decreases."

Full text at:

http://www.the-scientist.com/article/display/23065/

John

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

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[evomech] A New Definiition of Biological Evolution

2006-02-07T14:47:00.000Z

As should be obvious, once you reject genetic determinism, you are
also forced to rethink your definition of biological evolution. If
genetic determinism is false, then any definition of evolutionary
change based on genetic change must also be inadequate and
inappropriate. The purpose of this thread is to discuss and
speculate on alternative definitions of biological evolution.

Biological evolution is a change process. At least IMO, a definition
of evolution would need to address the following six types of
questions:

1. What changes?
2. When does it change?
3. What are the processes and mechanism responsible for change?
4. How are changes and change processes observed and measured?
And
5. Who is involved in developing and evaluating definitions?
6. How are testable predictive theories of the change and
change processes formulated?

It should be obvious, that without genetic determinism, RM&NS
Darwinism has no answer for either what changes or what are the
mechanisms of change. What are the possible alternatives?

Warren

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Re: [evomech] The innovation triad: an EvoDevo agenda (Journal of Experimental Zoology)

2006-02-07T11:48:00.000Z

This article's "distinction between ADAPTATION vs NOVELTY" seems
parallel to what I mentioned a few days ago, distinction between
regulation and that which is being regulated, i.e., novelty that came about
through a process different from mere variation.

They suggest various means for generating novelty other than
conventional adaptation: direct environmental effects upon the
development process; symbiosis ala Margulis; colonial organisms;
and other vaguer things like self-organization and 'genetic
modulation' and 'developmental autonomization' of tissues.
But they don't mention my interest, multiplication of the soma
to create a mass of homologous parts. They even mention one
criterion for novelty that by definition excludes homologous
parts.
My model seems to be unthinkable.

Cliff
www.zainar.com/evblog.html

From: "John Latter" <jorolat@gmail.com>
Subject: [evomech] The innovation triad: an EvoDevo agenda
(Journal of Experimental Zoology)
> [Müller & Newman, Journal of Experimental Zoology, MDE 304 '05]
> Abstract:
> This article introduces a special issue on evolutionary
> innovation and morphological novelty, two interrelated themes
> that have received a remarkable increase of attention over the
> past few years. We begin with a discussion of the question of
> whether innovation and novelty represent distinct evolutionary
> problems that require a distinct conceptualization. We argue
> that the mechanisms of innovation and their phenotypic results -
> novelty - can only be properly addressed if they are
> distinguished from the standard evolutionary themes of variation
> and adaptation, and we present arguments for making such a
> distinction. We propose that origination, the first formation of
> biological structures, is another distinct problem of
> morphological evolution, and that together with innovation and
> novelty it constitutes a conceptual complex we call the
> innovation triad. We define a problem agenda of the triad, which
> separates the analysis of the initiating conditions from the
> mechanistic realization of innovation, and we discuss the
> theoretical problems that arise from treating innovation as
> distinct from variation. Further, we categorize the empirical
> approaches that address themes of the innovation triad in
> recognizing four major strands of research: the morphology and
> systematics program, the gene regulation program, the epigenetic
> program, and the theoretical biology program. We provide
> examples of each program, giving priority to contributions in
> the present issue. In conclusion, we observe that the innovation
> triad is one of the defining topics of EvoDevo research and may
> represent its most pertinent contribution to evolutionary
> theory. We point out that an inclusion of developmental systems
> properties into evolutionary theory represents a shift of
> explanatory emphasis from the external factors of natural
> selection to the internal dynamics of developmental systems,
> complementing adaptation with emergence, and contingency with
> inherency
> Full text at:
> http://homepage.univie.ac.at/gerhard.mueller/pdfs/2005InnovTriad.pdf

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[evomech] The innovation triad: an EvoDevo agenda (Journal of Experimental

2006-02-07T09:16:00.000Z

[Müller & Newman, Journal of Experimental Zoology, MDE 304 '05]

Abstract:

This article introduces a special issue on evolutionary innovation and morphological novelty, two interrelated themes that have received a remarkable increase of attention over the past few years. We begin with a discussion of the question of whether innovation and novelty represent distinct evolutionary problems that require a distinct conceptualization. We argue that the mechanisms of innovation and their phenotypic results - novelty - can only be properly addressed if they are distinguished from the standard evolutionary themes of variation and adaptation, and we present arguments for making such a distinction. We propose that origination, the first formation of biological structures, is another distinct problem of morphological evolution, and that together with innovation and novelty it constitutes a conceptual complex we call the innovation triad. We define a problem agenda of the triad, which separates the analysis of the initiating conditions from the mechanistic realization of innovation, and we discuss the theoretical problems that arise from treating innovation as distinct from variation. Further, we categorize the empirical approaches that address themes of the innovation triad in recognizing four major strands of research: the morphology and systematics program, the gene regulation program, the epigenetic program, and the theoretical biology program. We provide examples of each program, giving priority to contributions in the present issue. In conclusion, we observe that the innovation triad is one of the defining topics of EvoDevo research and may represent its most pertinent contribution to evolutionary theory. We point out that an inclusion of developmental systems properties into evolutionary theory represents a shift of explanatory emphasis from the external factors of natural selection to the internal dynamics of developmental systems, complementing adaptation with emergence, and contingency with inherency

Full text at:

http://homepage.univie.ac.at/gerhard.mueller/pdfs/2005InnovTriad.pdf

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

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[evomech] Re: The control of body size in insects (Dev Biol)

2006-02-06T10:50:00.000Z

> Regulation is the important thing, it's what creates
> diverse organisms from a common ancient skeletal pattern,
> which is simple in form and is only known by extrapolation
> from the pattern of reduction and distortion among parts.
> Regulation of the ontogeny of this original form is what
> sculpts organisms.
>
> What is doing the regulating? An unlimited variety of
> opportunistic mechanisms, I would think. I just speak
> for the necessity of recognizing that there is a something
> whose ontogeny is regulated, a something distinct from
> regulation itself.
>
> Cliff

I think I've said before that I have quite a strong interest in the 'psychology' of evolutionary theory.

I might also have said this before too (so stop me if I have!): Man once thought the earth was flat, then that the sun revolved around the earth, but now we know the earth orbits the sun. The point being that Man's perception of a natural reality sometimes has to change while the natural reality itself (obviously) does not.

Similarly, I believe evolution to be a natural process (specifically, that a testable internal mechanism may be involved - but I won't go into that!), unaffected by our intellectual perception of it, but that 'cultural conditioning' inhibits the exploration of this natural process[1].

For example, I'm still trawling the net looking for info about trilobite eyes & the fibonacci series (http://groups.yahoo.com/group/evomech/message/484) and I came across these quotes from Levi-Setti's book 'Trilobites':

"The design of the trilobite's eye could well qualify for a patent disclosure" and "What we would like to hear, to appease our Darwinian upbringing"
(http://www.asa3.org/ASA/PSCF/2000/PSCF12-00Chadwick.html)

Appease our Darwinian upbringing? Usually such appeasement is unconsciously reflected in an author's writing style rather than being so explicitly stated!

In a more general way, however, the effects of 'cultural conditioning ("The only thing that interferes with my learning is my education": Einstein) can be found in the terminology of evolutionary theory. Regulation, for example, implies 'control':

"One of the most important examples of homeostasis is the regulation of body temperature" and "in humans temperature homeostasis is controlled by..."
(http://www.biologymad.com/Homeostasis/Homeostasis.htm - the first return after putting "homeostasis temperature" into Google)

Do organisms 'control' their temperature or do they respond to temperature changes?
(I'm nearly out of time so I better stop waffling - was going to go on to "niche" and "adaptation" etc.)

I know for sure that I've previously expressed my agreement with Gould & Lewontin's "Organisms should be analyzed as integrated wholes" and yet, as a single example, it wasn't until April 2000 that the following appeared:

"Once seen as distinct, yet complementary disciplines, developmental biology and evolutionary studies have recently mergedinto an exciting and fruitful relationship. The official unionoccurred in 1999 when evolutionary developmental biology, or "evo-devo,"was granted its own division in the Society for Integrative andComparative Biology (SICB). It was natural for evolutionary biologistsand developmental biologists to find common ground."
(http://www.pnas.org/cgi/content/full/97/9/4424)

Again, the point being that the natural (integrated) relationship between "developmental biology and evolutionary studies" already existed! So (and I'm really really out of time and have to end on a more abrupt note than I intended) where you see "An unlimited variety of opportunistic mechanisms" doing the "regulating" I tend to see an integrated response with finite limits.

[1] An Error In Associating Lamarck With 'Adaptive Mutations'?
http://members.aol.com/jorolat/laam.html

John

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

--- In evomech@yahoogroups.com, "Cliff Lundberg" wrote:
>
> From: "John Latter" jorolat@...
> Subject: Re: [evomech] The control of body size in insects (Dev
> Biol)
> > On 05/02/2006 Cliff Lundberg wrote:
> >> No doubt a lot of details are being learned about ontogeny
> >> and its regulation, but something's lacking in the general
> >> concept,
> >> namely, what it is that is being regulated.
> >
> > I feel some consideration should also be given to exactly
> > 'what' is doing the regulating! For example, in the press
> > release from:
> > Researchers evolve a complex genetic trait in the laboratory
> > http://groups.yahoo.com/group/evomech/message/511

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[evomech] New theory could have implications for cancer research (PR + Article)

2006-02-06T09:45:00.000Z

Contents:

1) Molecular Evolution (News Item)

Researchers from the University of California, San Diego (UCSD) Jacobs School of Engineering have uncovered evidence that major evolutionary changes are more likely too ccur in approximately 400 'fragile' genomic regions that account for only 5% of the human genome.

The findings, reported in the June 24, 2003, issue of the Proceedings of the National Academy of Sciences USA (PNAS), undercut the widely held view among scientists that evolutionary breakpoints - disruptions in the order of genes on chromosomes - are purely random. Apart from its implications for evolutionary theory, the study could have major implications for medical research related to diseases such as leukemia, which are caused by clinical (rather than evolutionary) chromosomal breakpoints.

Full text at:

http://www.obgyn.net/newsheadlines/headline_medical_news-Molecular_Evolution-20030707-8.asp

2) Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution

[Pevzner & Tesler, PNAS, June '03]

The human and mouse genomic sequences provide evidence for a larger number of rearrangements than previously thought and reveal extensive reuse of breakpoints from the same short fragile regions. Breakpoint clustering in regions implicated in cancer and infertility have been reported in previous studies; we report here on breakpoint clustering in chromosome evolution. This clustering reveals limitations of the widely accepted random breakage theory that has remained unchallenged since the mid-1980s. The genome rearrangement analysis of the human and mouse genomes implies the existence of a large number of very short "hidden" synteny blocks that were invisible in the comparative mapping data and ignored in the random breakage model. These blocks are defined by closely located breakpoints and are often hard to detect. Our results suggest a model of chromosome evolution that postulates that mammalian genomes are mosaics of fragile regions with high propensityfor rearrangements and solid regions with low propensity forrearrangements.

Full text at:

http://www.pnas.org/cgi/content/full/100/13/7672

John

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

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[evomech] Biological Networks: The Tinkerer as an Engineer (Science)

2006-02-06T08:55:00.000Z

[Alon, Science, Sept '03]

Viewpoint

Abstract:

This viewpoint comments on recent advances in understandingthe design principles of biological networks. It highlightsthe surprising discovery of "good-engineering" principles inbiochemical circuitry that evolved by random tinkering.

Full text at:

http://www.weizmann.ac.il/mcb/UriAlon/Papers/Biological%20Networks-%20The%20Tinkerer%20as%20an%20Engineer.pdf

John

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

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Re: [evomech] The control of body size in insects (Dev Biol)

2006-02-06T04:32:00.000Z

From: "John Latter"
Subject: Re: [evomech] The control of body size in insects (Dev
Biol)
> On 05/02/2006 Cliff Lundberg wrote:
>> No doubt a lot of details are being learned about ontogeny
>> and its regulation, but something's lacking in the general
>> concept,
>> namely, what it is that is being regulated.
>
> I feel some consideration should also be given to exactly
> 'what' is doing the regulating! For example, in the press
> release from:
> Researchers evolve a complex genetic trait in the laboratory
> http://groups.yahoo.com/group/evomech/message/511

Regulation is the important thing, it's what creates
diverse organisms from a common ancient skeletal pattern,
which is simple in form and is only known by extrapolation
from the pattern of reduction and distortion among parts.
Regulation of the ontogeny of this original form is what
sculpts organisms.

What is doing the regulating? An unlimited variety of
opportunistic mechanisms, I would think. I just speak
for the necessity of recognizing that there is a something
whose ontogeny is regulated, a something distinct from
regulation itself.

Cliff

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Re: [evomech] The control of body size in insects (Dev Biol)

2006-02-05T15:09:00.000Z

On 05/02/2006 Cliff Lundberg wrote: > No doubt a lot of details are being learned about ontogeny > and its regulation, but something's lacking in the general > concept, > namely, what it is that is being regulated. I feel some consideration should also be given to exactly 'what' is doing the regulating! For example, in the press release from: Researchers evolve a complex genetic trait in the laboratory http://groups.yahoo.com/group/evomech/message/511 Nijhout is quoted as saying "...'It's long been known that polyphenisms are controlled by hormones, with the brain sensing environmental signals and altering the pattern of hormonal secretions,' said Nijhout. 'In turn, these hormonal patterns turn sets of genes on or off to produce different traits. However, we understood only the developmental mechanism, and how it is possible with a single genome in an animal to produce two very different phenotypes,' he said..." Which part of the brain? its nature, characteristics? OMG - now I'll have to look up 'regulatory hierarchies' or something.. :) John What's being regulated > is the expression of a primordial form, a form that has many > parts, any of which may or may not be expressed. A form that's the > basis for an arthropod, or a vertebrate, or some other segmented > animal. Only something like this fits with those complex and > characteristic types emerging gradually in development, yet > suddenly in the fossil record. The basic forms are real, > yet archetypal, and their origins as trains of identical segments > were rapid processes of duplication. In a context where all > changes are reductions and distortions, the progenitor is > an archetype, underlying and explaining anatomy. > > Cliff > www.zainar.com/evblog.html

--

Model of an Internal Evolutionary Mechanism (based on an extension to homeostasis) linking Adaptive Mutations to the Baldwin Effect: http://members.aol.com/jorolat/index.html Please Note: If you are reading this in a Blog then replying directly to this message (as opposed to making a 'blog comment') requires membership of the 'Evolution: Where Darwin meets Lamarck?' Egroup at: http://groups.yahoo.com/group/evomech/

Re: [evomech] The control of body size in insects (Dev Biol)

2006-02-05T14:48:00.000Z

No doubt a lot of details are being learned about ontogeny and its regulation, but something's lacking in the general concept, namely, what it is that is being regulated. What's being regulated is the expression of a primordial form, a form that has many parts, any of which may or may not be expressed. A form that's the basis for an arthropod, or a vertebrate, or some other segmented animal. Only something like this fits with those complex and characteristic types emerging gradually in development, yet suddenly in the fossil record. The basic forms are real, yet archetypal, and their origins as trains of identical segments were rapid processes of duplication. In a context where all changes are reductions and distortions, the progenitor is an archetype, underlying and explaining anatomy. Cliff www.zainar.com/evblog.html ----- Original Message ----- From: "John Latter" <jorolat@gmail.com> To: <evomech@yahoogroups.com> Sent: Sunday, February 05, 2006 12:27 AM Subject: [evomech] The control of body size in insects (Dev Biol) [Nijhout, Developmental Biology, Sept '03] Abstract: Control mechanisms that regulate body size and tissue size have beensought at both the cellular and organismal level. Cell-level studieshave revealed much about the control of cell growth and cell division,and how these processes are regulated by nutrition. Insulin signalingis the key mediator between nutrition and the growth of internalorgans, such as imaginal disks, and is required for the normalproportional growth of the body and its various parts. Theinsulin-related peptides of insects do not appear to control growth by themselves, but act in conjunction with other hormones and signaling molecules, such as ecdysone and IDGFs. Size regulation cannot be understood solely on the basis of the mechanisms that control cell size and cell number. Size regulation requires mechanisms that gather information on a scale appropriate to the tissue or organ being regulated. A new model mechanism, using autocrine signaling, is outlined by which tissue and organ size regulation can be achieved. Body size regulation likewise requires a mechanism that integrates information at an appropriate scale. In insects, this mechanism operates by controlling the secretion of ecdysone, which is the signalthat terminates the growth phase of development. The mechanisms for size assessment and the pathways by which they trigger ecdysone secretion are diverse and can be complex. The ways in which these higher-level regulatory mechanisms interact with cell- and molecular-level mechanisms are beginning to be elucidated. Full text at: http://www.biology.duke.edu/nijhout/images/ControlBodySize.pdf For Nijhout's latest paper (Jan '06) - see: http://groups.yahoo.com/group/evomech/message/511 and a '98 paper: http://groups.yahoo.com/group/evomech/message/81 John Model of an Internal Evolutionary Mechanism http://members.aol.com/jorolat/index.html

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[evomech] The control of body size in insects (Dev Biol)

2006-02-05T08:44:00.000Z

[Nijhout, Developmental Biology, Sept '03]

Abstract:

Control mechanisms that regulate body size and tissue size have beensought at both the cellular and organismal level. Cell-level studieshave revealed much about the control of cell growth and cell division,and how these processes are regulated by nutrition. Insulin signalingis the key mediator between nutrition and the growth of internalorgans, such as imaginal disks, and is required for the normalproportional growth of the body and its various parts. Theinsulin-related peptides of insects do not appear to control growth bythemselves, but act in conjunction with other hormones and signalingmolecules, such as ecdysone and IDGFs. Size regulation cannot beunderstood solely on the basis of the mechanisms that control cell sizeand cell number. Size regulation requires mechanisms that gatherinformation on a scale appropriate to the tissue or organ beingregulated. A new model mechanism, using autocrine signaling, isoutlined by which tissue and organ size regulation can be achieved.Body size regulation likewise requires a mechanism that integratesinformation at an appropriate scale. In insects, this mechanismoperates by controlling the secretion of ecdysone, which is the signalthat terminates the growth phase of development. The mechanisms forsize assessment and the pathways by which they trigger ecdysonesecretion are diverse and can be complex. The ways in which thesehigher-level regulatory mechanisms interact with cell- and molecular-level mechanisms are beginning to be elucidated.

Full text at:

http://www.biology.duke.edu/nijhout/images/ControlBodySize.pdf

For Nijhout's latest paper (Jan '06) - see:

http://groups.yahoo.com/group/evomech/message/511

and a '98 paper:

http://groups.yahoo.com/group/evomech/message/81

John

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

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Re: [evomech] Researchers evolve a complex genetic trait in the laboratory

2006-02-05T05:45:00.000Z

That one arrived OK Palash and it'll make it easier for other members - thank you!

John

Palash Bhattacharya wrote:

Sorry about that John. I am sending the relevant one again just in case..

Palash

From: John Latter
Reply-To: evomech@yahoogroups.com
To: evomech@yahoogroups.com
Subject: Re: [evomech] Researchers evolve a complex genetic trait in the laboratory (News + Article)
Date: Fri, 03 Feb 2006 19:43:14 +0000

Thank you for your kindness Palash :)

Unfortunately, however, the paper you attached is "Evolution of the Gene Network Underlying Wing Polyphenism in Ants" from Science 2002. On the other hand I have heard from Yuichiro Suzuki (who is one of the authors of "Evolution of a Polyphenism by Genetic Accommodation") and anyone who would like a reprint can contact him at the email address given here:

http://www.sciencemag.org/cgi/content/abstract/311/5761/650

(email jorolat@gmail.com if you have any problems)

I guess you must have clicked on the wrong file Palash (and I'm going to read it later anyway!) but I would like to emphasize I do appreciate your help!

John

Palash Bhattacharya wrote:

>Here is a copy of the paper.

>Palash,

Model of an Internal Evolutionary Mechanism (based on an extension to homeostasis) linking Adaptive Mutations to the Baldwin Effect:
http://members.aol.com/jorolat/index.html

[evomech] The Animal Self (New York Times)

2006-02-04T18:44:00.000Z

[Siebert, New York Times, Jan '06]

Extract:

...

Anderson and Mather's resulting 1993 paper in the Journal ofComparative Psychology, entitled "Personalities of Octopuses," was notonly the first-ever documentation of personality in invertebrates. Itwas the first time in anyone's memory that the term "personality" hadbeen applied to a nonhuman in a major psychology journal.

Scientists are not typically disposed to wielding a word like"personality" when talking about animals. Doing so borders on thescientific heresy of anthropomorphism. And yet for a growing number ofresearchers from a broad range of disciplines - psychology,evolutionary biology and ecology, animal behavior and welfare - it isbecoming increasingly difficult to avoid that term when trying todescribe the variety of behaviors that they are now observing in anequally broad and expanding array of creatures, everything fromnonhuman primates to hyenas and numerous species of birds to waterstriders and stickleback fish and, of course, giant Pacific octopuses.

In fact, in the years since Anderson and Mather's original paper, awhole new field of research has emerged known simply as "animalpersonality." Through close and repeated observations of differentspecies in a variety of group settings and circumstances, scientistsare finding that our own behavioral traits exist in varying degrees anddimensions among creatures across all the branches of life's tree...

Full text at:

http://www.gan.ca/animal+news.en.html?neid=72

PDF version:

http://www.udel.edu/anthro/ackerman/animal.pdf

Charles Siebert also appeared on the radio show "Animal Personality" along with Sam Gosling, Psychologist and founder of the Animal Personality Institute at the University of Texas, and Terry Curtis, Vetinary Behaviorist with the University of Florida College of Vetinary Medicine:

http://www.onpointradio.org/shows/2006/01/20060123_b_main.asp

John

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

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[evomech] Proximodistal patterning of the limb: insights from evolutionary morphology (ED)

2006-02-04T06:57:00.000Z

[Richardson et al., Evolution & Development, Jan '04]

Summary:

There is an active debate about how skeletal elements are encoded along the proximodistal (PD) axis of the developing limb. Our aim here is to see whether consideration of the evolutionary morphology of the limb can contribute to our understanding of patterning mechanisms. Of special interest in this context are animals showing reiterated skeletal elements along the PD axis (e.g., dolphins and plesiosaurs with hyperphalangy). We build on previous hypotheses to propose a two-step model of PD patterning in which specification of broad domains in the early limb bud is distinct from subsequent processes that divides an initial anlage into a segmental pattern to yield individual skeletal elements. This model overcomes a major evolutionary problem with the progress zone model, which has not previously been noted: pleiotropy. Parallels with other developmental systems are briefly discussed.

(IA) Full text at:

http://www.mk-richardson.com/PDFs/Richardson%20Jeffery%20Tabin%20evo%20devo.pdf

John

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

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Re: [evomech] Researchers evolve a complex genetic trait in the laboratory

2006-02-04T05:45:00.000Z

That one arrived OK Palash and it'll make it easier for other members - thank you!

John

Palash Bhattacharya wrote:

Sorry about that John. I am sending the relevant one again just in case..

Palash

From: John Latter <jorolat@gmail.com>
Reply-To: evomech@yahoogroups.com
To: evomech@yahoogroups.com
Subject: Re: [evomech] Researchers evolve a complex genetic trait in the laboratory (News + Article)
Date: Fri, 03 Feb 2006 19:43:14 +0000

Thank you for your kindness Palash :)

Unfortunately, however, the paper you attached is "Evolution of the Gene Network Underlying Wing Polyphenism in Ants" from Science 2002. On the other hand I have heard from Yuichiro Suzuki (who is one of the authors of "Evolution of a Polyphenism by Genetic Accommodation") and anyone who would like a reprint can contact him at the email address given here:

http://www.sciencemag.org/cgi/content/abstract/311/5761/650

(email jorolat@gmail.com if you have any problems)

I guess you must have clicked on the wrong file Palash (and I'm going to read it later anyway!) but I would like to emphasize I do appreciate your help!

John

Palash Bhattacharya wrote:

Here is a copy of the paper.

Model of an Internal Evolutionary Mechanism (based on an extension to homeostasis) linking Adaptive Mutations to the Baldwin Effect:
http://members.aol.com/jorolat/index.html

Please Note: If you are reading this in a Blog then replying directly to this message (as opposed to making a 'blog comment') requires membership of the 'Evolution: Where Darwin meets Lamarck?' Egroup at:
http://groups.yahoo.com/group/evomech/

Re: [evomech] Researchers evolve a complex genetic trait in the laboratory

2006-02-03T20:08:00.000Z

Thank you for your kindness Palash :)

Unfortunately, however, the paper you attached is "Evolution of the Gene Network Underlying Wing Polyphenism in Ants" from Science 2002. On the other hand I have heard from Yuichiro Suzuki (who is one of the authors of "Evolution of a Polyphenism by Genetic Accommodation") and anyone who would like a reprint can contact him at the email address given here:

http://www.sciencemag.org/cgi/content/abstract/311/5761/650

(email jorolat@gmail.com if you have any problems)

I guess you must have clicked on the wrong file Palash (and I'm going to read it later anyway!) but I would like to emphasize I do appreciate your help!

John

Palash Bhattacharya wrote:

Here is a copy of the paper.

Palash

--

Model of an Internal Evolutionary Mechanism (based on an extension to homeostasis) linking Adaptive Mutations to the Baldwin Effect:
http://members.aol.com/jorolat/index.html

Please Note: If you are reading this in a Blog then replying directly to this message (as opposed to making a 'blog comment') requires membership of the 'Evolution: Where Darwin meets Lamarck?' Egroup at: http://groups.yahoo.com/group/evomech/

[evomech] Rediscovering Darwin After a Darwinian Century (Evo Anth)

2006-02-03T15:40:00.000Z

[Weiss & Buchanan, Evolutionary Anthropology, Sept '00]

Research Article - No abstract is available so I've included some of the highlighted text:

Anthropological geneticists would uniformly count themselves as Darwinians, but our work has been largely restricted to the evolution of genes chosen as markers for reconstructing temporal and geographic history, often intentionally stripped of any other biological content, relying on chance (genetic drift) as the calibrating phenomenon. The rest of biological anthropology has mainly been concerned with the Darwinian evolution of human and primate traits (phenotypes), relying on deterministic adaptation as the calibrating phenomenon...

...Initially, the idea of genes based on the modern synthesis was classically Darwinian: natural selection screened genetic variation and favored the best-adapted. Beginning in the 1950s, advances in genotyping methodology revealed much more variation than had been anticipated...

...To the extent that genetics is at the root of biology, our understanding will be fundamentally incomplete if we do not know how genes affect the assembly, variation, and evolution of a trait...

...Thinking of traits and genes in terms of interaction may be more difficult than thinking of genes as separable components of an engineered structure but, whether we like it or not, may be the biological reality...

...Has our nearly centuryold love affair with genes, driven by the theoretical focus on their presumed biological primacy, led to an exaggerated reductionism in our attempt to understand phenotypes and their evolution?...

Full text at:

http://www.anthro.psu.edu/weiss_lab/papers/WeissBuchanan.pdf

John

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

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[evomech] Researchers evolve a complex genetic trait in the laboratory (News + Article)

2006-02-03T09:31:00.000Z

Contents:

1) Researchers evolve a complex genetic trait in the laboratory (Press Release)

Duke University biologists have evolved a complex trait in the laboratory -- using the pressure of selection to induce tobacco hornworms to evolve the dual trait of turning black or green depending on the temperature during their development. The biologists have also demonstrated the basic hormonal mechanism underlying the evolution of such dual traits.

Their experiments, they said, offer important insight into how complex traits involving many genes can abruptly "blossom" in an organism's evolution...

..."It's long been known that polyphenisms are controlled by hormones, with the brain sensing environmental signals and altering the pattern of hormonal secretions," said Nijhout. "In turn, these hormonal patterns turn sets of genes on or off to produce different traits. However, we understood only the developmental mechanism, and how it is possible with a single genome in an animal to produce two very different phenotypes," he said...

..."Homeostatic mechanisms tend to stabilize a phenotype such as color and, therefore, allow the accumulation of underlying, covert mutations just as an electrical capacitor acts to accumulate charge. And eventually, these mutations could 'break out' of that constraint to produce a sudden phenotypic change; and one way for them to break out is for a mutation to happen -- for example, one that alters a hormonal level -- releasing all this variation.

Full text at:

http://www.eurekalert.org/pub_releases/2006-02/du-rea012706.php

2) Evolution of a Polyphenism by Genetic Accommodation (Science)

[Suzuki & Nijhout, Science, Feb '06]

Abstract:

Polyphenisms are adaptations in which a genome is associatedwith discrete alternative phenotypes in different environments.Little is known about the mechanism by which polyphenisms originate.We show that a mutation in the juvenile hormone-regulatory pathwayin Manduca sexta enables heat stress to reveal a hidden reactionnorm of larval coloration. Selection for increased color changein response to heat stress resulted in the evolution of a larvalcolor polyphenism and a corresponding change in hormonal titersthrough genetic accommodation. Evidently, mechanisms that regulatedevelopmental hormones can mask genetic variation and act asevolutionary capacitors, facilitating the origin of novel adaptivephenotypes.

http://www.sciencemag.org/cgi/content/abstract/311/5761/650

This is very interesting stuff from my point of view but as usual I don't have a subsciption to Science ('sigh') - I'll let you know if I can get hold of a copy!

John

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

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Re: [evomech] Re: Peer Review and Genetic Determinism

2006-02-03T07:17:00.000Z

From: "warrenbergerson" <warrenbergerson@msn.com> Subject: [evomech] Re: Peer Review and Genetic Determinism > Do you accept the published assertion that the concensus among > geneticists is that genetic determinism is false? Is there a biological question here? I don't care about consensuses. A minority view might be more interesting. Cliff

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[evomech] Re: Peer Review and Genetic Determinism

2006-02-02T13:49:00.000Z

Do you accept the published assertion that the concensus among geneticists is that genetic determinism is false? --- In evomech@yahoogroups.com, "Cliff Lundberg" <cliff_lundberg@...> wrote: > > From: "warrenbergerson" <warrenbergerson@...> > > > For anyone interested in understanding the inherent unsoundness > > of > > peer reviewers, the peer review process, and the peer review > > literature, it is interesting to go back and look at the really > > awful logic and techniques used by peer reviewers and Internet > > experts support the genetic determinism assumption and to > > suppress > > arguments and evidence contradicting the assumption. > > I'd rather spend the time learning about where or how genetic > determinism is wrong. Is it just a matter of how far one goes with > it in explaining evolution? > > We don't hear much about peer reviews. There must be > very few interesting insights expressed in this medium. > > Cliff >

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[evomech] Evolution as Fact and Theory (Discover Magazine)

2006-02-02T10:26:00.000Z

[Gould, Discover Magazine, May '81 ]

Essay:

Kirtley Mather, who died last year at age ninety, was a pillar of both science and Christian religion in America and one of my dearest friends. The difference of a half-century in our ages evaporated before our common interests. The most curious thing we shared was a battle we each fought at the same age. For Kirtley had gone to Tennessee with Clarence Darrow to testify for evolution at the Scopes trial of 1925. When I think that we are enmeshed again in the same struggle for one of the best documented, most compelling and exciting concepts in all of science, I don't know whether to laugh or cry.

According to idealized principles of scientific discourse, the arousal of dormant issues should reflect fresh data that give renewed life to abandoned notions. Those outside the current debate may therefore be excused for suspecting that creationists have come up with something new, or that evolutionists have generated some serious internal trouble. But nothing has changed; the creationists have presented not a single new fact or argument. Darrow and Bryan were at least more entertaining than we lesser antagonists today. The rise of creationism is politics, pure and simple; it represents one issue (and by no means the major concern) of the resurgent evangelical right. Arguments that seemed kooky just a decade ago have reentered the mainstream.

The basic attack of modern creationists falls apart on two general counts before we even reach the supposed factual details of their assault against evolution. First, they play upon a vernacular misunderstanding of the word "theory" to convey the false impression that we evolutionists are covering up the rotten core of our edifice. Second, they misuse a popular philosophy of science to argue that they are behaving scientifically in attacking evolution. Yet the same philosophy demonstrates that their own belief is not science, and that "scientific creationism" is a meaningless and self-contradictory phrase, an example of what Orwell called "newspeak."

In the American vernacular, "theory" often means "imperfect fact" part of a hierarchy of confidence running downhill from fact to theory to hypothesis to guess. Thus creationists can (and do) argue: evolution is "only" a theory, and intense debate now rages about many aspects of the theory. If evolution is less than a fact, and scientists can't even make up their minds about the theory, then what confidence can we have in it? Indeed, President Reagan echoed this argument before an evangelical group in Dallas when he said (in what I devoutly hope was campaign rhetoric): "Well, it is a theory. It is a scientific theory only, and it has in recent years been challenged in the world of science that is, not believed in the scientific community to be as infallible as it once was."

Well, evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts do not go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's, but apples did not suspend themselves in mid-air, pending the outcome. And humans evolved from apelike ancestors whether they did so by Darwin's proposed mechanism or by some other, yet to be discovered.

Full text at:

http://www.stephenjaygould.org/ctrl/gould_fact-and-theory.html

and

http://www.georgealozano.com/teach/evolution/papers/Gould1980.pdf

John

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

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[evomech] Dinner at Baby's: Werewolves, dinosaur jaws, hen's teeth,

2006-02-02T08:48:00.000Z

[Weiss & Sholtis, Evolutionary Anthropology, Nov '03]

Occasionally traits arise that appear to be atavistic throwbacks to the remote past. How can this make evolutionary sense?

As we get older we have a tendency to become nostalgic and think back on old times. We've recently seen a surge of nostalgia for the 1950s; among the remarkable comebacks are the new old diners, like Baby's here in State College (Figure 1). These new-old wonders proffer burgers and shakes like they used to be in the good old days. The decades of change in the competitive fast-food industry seem not to matter at all. The old taste is back! Even Patsy Cline and Elvis are still singing the same songs in the background.

There is a similar phenomenon in biology. Nobody accepts Ernst Haeckel's famous recapitulation argument that, as embryos, we literally go through the adult stages of our ancestors. Nonetheless, many seem to think the evolutionary past can rise again.
Can it?

Full text at:

http://nitrogen.la.psu.edu/weiss_lab/CQ/CQ11_DinnerAtBabys.pdf

John

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

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Re: [evomech] Peer Review and Genetic Determinism

2006-02-02T02:52:00.000Z

From: "warrenbergerson" <warrenbergerson@msn.com> > For anyone interested in understanding the inherent unsoundness > of > peer reviewers, the peer review process, and the peer review > literature, it is interesting to go back and look at the really > awful logic and techniques used by peer reviewers and Internet > experts support the genetic determinism assumption and to > suppress > arguments and evidence contradicting the assumption. I'd rather spend the time learning about where or how genetic determinism is wrong. Is it just a matter of how far one goes with it in explaining evolution? We don't hear much about peer reviews. There must be very few interesting insights expressed in this medium. Cliff

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