evomech : Messages : 545-574 of 604

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

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

technorati tags: research, embryo, genes, mechanism

#573

From: John Latter <jorolat@...>
Date: Mon Mar 6, 2006 9:44 am
Subject: Evolution as context-driven actualization of potential: Toward an interdisciplinary theory of change of state

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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

#572

From: John Latter <jorolat@...>
Date: Sun Mar 5, 2006 9:10 am
Subject: In the News: More info on "'Jurassic Beaver' find stuns experts"

jorolat

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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

#571

From: John Latter <jorolat@...>
Date: Sat Mar 4, 2006 2:01 pm
Subject: From symmetry to asymmetry: Phylogenetic patterns of asymmetry variation in animals and their evolutionary significance

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[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

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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

#570

From: "John Latter" <jorolat@...>
Date: Fri Mar 3, 2006 9:59 am
Subject: Re: Antisymmetry (Chapter 16 of 'Variation')

jorolat

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--- 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

#569

From: "Cliff Lundberg" <cliff_lundberg@...>
Date: Fri Mar 3, 2006 3:05 am
Subject: Re: Limbs in whales and limblessness in other vertebrates: mechanisms of evolutionary and developmental transformation and loss.

cliff0000000

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From: "John Latter" <jorolat@...>
> 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

#568

From: John Latter <jorolat@...>
Date: Thu Mar 2, 2006 8:40 am
Subject: Limbs in whales and limblessness in other vertebrates: mechanisms of evolutionary and developmental transformation and loss.

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[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

#567

From: John Latter <jorolat@...>
Date: Wed Mar 1, 2006 8:38 am
Subject: Conrad Hal Waddington: the last Renaissance biologist? (Nature)

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[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

#566

From: John Latter <jorolat@...>
Date: Tue Feb 28, 2006 8:33 am
Subject: The morphogenesis of evolutionary developmental biology (Int. J, Dev. Biol.)

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[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

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

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

#565

From: "John Latter" <jorolat@...>
Date: Mon Feb 27, 2006 9:44 am
Subject: Re: Symmetry Breaking and the Evolution of Development (Science)

jorolat

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--- 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 leftward�the nodal cascade�varies 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

#564

From: John Latter <jorolat@...>
Date: Sun Feb 26, 2006 8:44 am
Subject: Putting Genes in Perspective (Book Review)

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[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

#563

From: John Latter <jorolat@...>
Date: Sat Feb 25, 2006 8:49 am
Subject: Genetic assimilation of an acquired character (Classic Paper)

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Genetic assimilation of an acquired character

[Waddington, Evolution 7, 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

#562

From: "John Latter" <jorolat@...>
Date: Fri Feb 24, 2006 8:27 am
Subject: Dollo's law and the re-evolution of shell coiling (Royal Society of London)

jorolat

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

Abstract:

Gastropods have lost the quintessential snail feature, the coiledshell, numerous times in evolution. In many cases these animals havedeveloped a limpet morphology with a cap-shaped shell and a large foot.Limpets thrive in marginal habitats such as hydrothermal vents, thehigh-energy rocky intertidal areas and fresh water, but they areconsidered to be evolutionary dead-ends, unable to re-evolve a coiledshell and therefore unable to give rise to the diversity seen amongcoiled snails. The re-evolution of a coiled shell, or any complexcharacter, is considered unlikely or impossible (Dollo's law) becausethe loss of the character is followed by the loss of the geneticarchitecture and developmental mechanisms that underlie that character.Here, we quantify the level of coiling in calyptraeids, a family ofmostly uncoiled limpets, and show that coiled shells have re-evolved atleast once within this family. These results are the firstdemonstration, to our knowledge, of the re-evolution of coiling in agastropod, and show that the developmental features underlying coilinghave not been lost during 20-100 Myr of uncoiled evolutionary history.This is the first example of the re-evolution of a complex charactervia a change in developmental timing (heterochrony) rather than achange 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

#561

From: "John Latter" <jorolat@...>
Date: Thu Feb 23, 2006 9:17 am
Subject: Re: Birds that make teeth (Press Release + Summary)

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>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

#560

From: John Latter <jorolat@...>
Date: Wed Feb 22, 2006 9:47 am
Subject: Birds that make teeth (Press Release + Summary)

jorolat

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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

#559

From: John Latter <jorolat@...>
Date: Tue Feb 21, 2006 9:25 am
Subject: Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism

jorolat

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[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

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Model of an Internal Evolutionary Mechanism:
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technorati tags: vertebrate, morphological, evolution, genetic, trait, analysis, mexican, cave, tetra, cavefish, albinism, convergence, molecular, species, ecological, environment, assay, john+latter

#558

From: "John Latter" <jorolat@...>
Date: Mon Feb 20, 2006 9:28 am
Subject: Research points to new theory driving evolutionary changes ('04 PR + Article)

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

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 speciesfound in the fossil record. They also help explain the variability inappearance 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 differentcomponents of evolution, one that goes against the central dogma thatcurrently explains how certain aspects of evolution take place," said Dr. Harold "Skip" Garner.

Full article at:

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-associatedtandem repeat expansionsand contractions are a majorsource of phenotypic variationin evolution. Here, wedescribe a comparative genomic studyof repetitiveelements in developmental genes of 92 breeds ofdogs. Wefind evidence for selection for divergence at codingrepeatloci in the form of both elevated purity and extensivelengthpolymorphism among different breeds. Variations in thenumberof repeats in the coding regions of the Alx-4 (aristaless-like4) and Runx-2 (runt-related transcription factor 2)genes werequantitatively associated with significantdifferences in limband skull morphology. We identifiedsimilar repeat length variationin the coding repeats ofRunx-2, Twist, and Dlx-2 in severalotherspecies. The high frequency and incremental effects ofrepeatlength mutations provide molecular explanations for swift,yettopologically 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

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, morphology, polymorphism, genome, genes

#557

From: John Latter <jorolat@...>
Date: Sun Feb 19, 2006 8:31 am
Subject: Unintelligent Design: A monstrous discovery suggests that viruses.. (Discovery)

jorolat

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[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)
http://groups.yahoo.com/group/evomech/message/518

John

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

#556

From: John Latter <jorolat@...>
Date: Sat Feb 18, 2006 2:13 pm
Subject: Mutation and adaptation: the directed mutation controversy in evolutionary perspective

jorolat

Offline

[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

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

technorati tags: central+tenet
<http://www.technorati.com/tags/central+tenet>, evolutionary+theory
<http://www.technorati.com/tags/evolutionary+theory>, evolution
<http://www.technorati.com/tags/evolution>, variation
<http://www.technorati.com/tags/variation>, adaptation
<http://www.technorati.com/tags/adaptation>, mechanism
<http://www.technorati.com/tags/mechanism>, nonrandom
<http://www.technorati.com/tags/nonrandom>, phenomena
<http://www.technorati.com/tags/phenomena>, controversy
<http://www.technorati.com/tags/controversy>, directed+mutation
<http://www.technorati.com/tags/directed+mutation>, adaptive+mutation
<http://www.technorati.com/tags/adaptive+mutation>, darwinian
<http://www.technorati.com/tags/darwinian>, natural+selection
<http://www.technorati.com/tags/natural+selection>

#555

From: John Latter <jorolat@...>
Date: Fri Feb 17, 2006 8:44 am
Subject: Evolution at two levels in humans and chimpanzees (Classic Paper)

jorolat

Offline

[King & Wilson, Science, Apr '75]

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

(No Abstract)

Scanned PDF file available at:

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

John Latter

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

#554

From: John Latter <jorolat@...>
Date: Thu Feb 16, 2006 10:37 am
Subject: Info wanted on two intriguing 'Lamarckian' experiments

jorolat

Offline

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@...

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

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

and

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

John

*This is an update of evomech message #43:
http://groups.yahoo.com/group/evomech/message/43

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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

#553

From: John Latter <jorolat@...>
Date: Thu Feb 16, 2006 7:25 am
Subject: 'Turned On': A revolution in the field of evolution? (Book Review)

jorolat

Offline

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

[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:

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

#552

From: John Latter <jorolat@...>
Date: Wed Feb 15, 2006 3:07 pm
Subject: Re: The main thrust of the group

jorolat

Offline

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:
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technorati tags: internal+evolutionary+mechanism, evolution

#551

From: "johnhewitt22" <johnhewitt22@...>
Date: Wed Feb 15, 2006 1:30 pm
Subject: The main thrust of the group

johnhewitt22

Offline

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

#550

From: John Latter <jorolat@...>
Date: Wed Feb 15, 2006 9:18 am
Subject: Confessions of a Darwinist (Virginia Quarterly Review)

jorolat

Offline

"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

#549

From: John Latter <jorolat@...>
Date: Tue Feb 14, 2006 3:06 pm
Subject: Re: Re: Gene Regulatory Networks and the Evolution of Animal Body Plans

jorolat

Offline

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.

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#548

From: "warrenbergerson" <warrenbergerson@...>
Date: Tue Feb 14, 2006 1:48 pm
Subject: Re: Gene Regulatory Networks and the Evolution of Animal Body Plans

warrenbergerson

Offline

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

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#547

From: John Latter <jorolat@...>
Date: Tue Feb 14, 2006 9:39 am
Subject: Gene Regulatory Networks and the Evolution of Animal Body Plans

jorolat

Offline

[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@... :

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

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#546

From: John Latter <jorolat@...>
Date: Tue Feb 14, 2006 9:04 am
Subject: Viva Lamarck: A Brief History of the Inheritance of,Acquired Characteristics (Aeon)

jorolat

Offline

[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

#545

From: John Latter <jorolat@...>
Date: Mon Feb 13, 2006 11:07 am
Subject: Evolution of phenotypic plasticity: where are we going now? (TREE)

jorolat

Offline

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

Abstract:

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

Full text at:

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

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