Saturday, March 18, 2006

 

[evomech] Darwin on trial (online book)

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

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Friday, March 17, 2006

 

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

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

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Thursday, March 16, 2006

 

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

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

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Wednesday, March 15, 2006

 

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

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:
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Tuesday, March 14, 2006

 

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

"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

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Monday, March 13, 2006

 

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

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:
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Sunday, March 12, 2006

 

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

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

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Model of an Internal Evolutionary Mechanism:
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