Evolution Research - Main Blog

Body Size, Performance and Fitness in Galapagos Marine Iguanas

2007-01-16T11:20:00.000Z

Integrative and Comparative Biology 2003 43(3):376-386; doi:10.1093/icb/43.3.376

Complex organismal traits such as body size are influenced by innumerable selective pressures, making the prediction of evolutionary trajectories for those traits difficult. A potentially powerful way to predict fitness in natural systems is to study the composite response of individuals in terms of performance measures, such as foraging or reproductive performance. Once key performance measures are identified in this top-down approach, we can determine the underlying physiological mechanisms and gain predictive power over long-term evolutionary processes. Here we use marine iguanas as a model system where body size differs by more than one order of magnitude between island populations. We identified foraging efficiency as the main performance measure that constrains body size. Mechanistically, foraging performance is determined by food pasture height and the thermal environment, influencing intake and digestion. Stress hormones may be a flexible way of influencing an individual's response to low-food situations that may be caused by high population density, famines, or anthropogenic disturbances like oil spills. Reproductive performance, on the other hand, increases with body size and is mediated by higher survival of larger hatchlings from larger females and increased mating success of larger males. Reproductive performance of males may be adjusted via plastic hormonal feedback mechanisms that allow individuals to assess their social rank annually within the current population size structure. When integrated, these data suggest that reproductive performance favors increased body size (influenced by reproductive hormones), with an overall limit imposed by foraging performance (influenced by stress hormones). Based on our mechanistic understanding of individual performances we predicted an evolutionary increase in maximum body size caused by global warming trends. We support this prediction using specimens collected during 1905. We also show in a common-garden experiment that body size may have a genetic component in iguanids. This 'performance paradigm' allows predictions about adaptive evolution in natural populations. [Galapagos Islands]

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Recent post: Why are lions not as big as elephants?

Technorati: integrative, comparative, biology, complex, organismal, traits, body, size, evolutionary, fitness, natural, systems, performance, foraging, reproductive, marine, iguanas, island, stress, hormones, global warming, trends, specimens, genetic, adaptive, evolution, galapagos, islands, lions, elephants

Balancing Robustness and Evolvability

2006-12-13T23:04:00.000Z

From PloS Biology:

Balancing Robustness and Evolvability

Richard E. Lenski et al.

One of the most important features of biology is the ability of organisms to persist in the face of changing conditions. Consider the remarkable fact that every organism alive today is the product of billions of generations in which its progenitors, without fail, managed to produce progeny that survived to reproduce. To achieve this consistency, organisms must have a balance between robustness and evolvability, that is, between resisting and allowing change in their own internal states [1 - 3]. Moreover, they must achieve this balance on multiple time scales, including physiological responses to changes over an individual life and evolutionary responses, in which a population of genomes continually updates its encoded information about past environments and how future generations should respond given that record.

Examples of robust biological systems are found at many scales, from biochemical to ecological. At each scale, robustness may reflect the properties of individual elements or, alternatively, the dynamic feedbacks between interacting elements. The expression of some metabolic function, for example, may be robust in the face of temperature change, because an enzyme maintains its shape and specificity across a range of temperatures or because an interconnected network of reactions sustains the supply of product, even when some enzyme fails. A genome may be robust because it encodes proofreading and repair systems that reduce replication errors or because it is organized such that many mutations have little effect on its phenotype. An ecosystem might be robust if it resists the extinction of some keystone species or, if extinction does occur, because surviving species can compensate over physiological, demographic, or evolutionary time scales.

One important question is whether there exists a single unifying mathematical framework that can encompass such diverse examples of biological robustness. Might new insights come from such a conceptual unification, or will future understanding require detailed analyses of specific cases? Across the different scales, recurring mechanisms for achieving robustness - including redundancy of component parts and negative feedbacks - might serve as organizing principles. Yet, similarities in mechanism could mask important differences in the evolutionary origins of those mechanisms. At the level of genes in genomes or of cells in multicellular organisms, it is reasonable to suggest that redundancy evolved by natural selection to maintain some functional capacity in the face of perturbation [4]. But whereas species redundancy could also be critical for robustness of ecosystem functions, differences in redundancy might be an emergent property rather than an ecosystem-level adaptation, because selection generally acts at lower levels (but see [5] for another view).

Continued at "Balancing Robustness and Evolvability" [A modified version of this post (with background info) will be posted to the "General Evolution News" category]

Technorati: balancing, robustness, evolvability, biology, organisms, conditions, generations, progeny, genome, repair, systems, framework, genes, evolutionary, origins, multicellular, demographic, physiological, ecosytem, redundancy, richard, e, lenski, adaptation, phenotype, natural selection, emergent, property, level, keystone, species, extinction

Genomic Imprinting in Mammals: Emerging Themes and Established Theories

2006-11-26T19:46:00.000Z

[This post also appears in the General Evolution News category]

An open access/free review paper from PLoS Genetics:

Genomic Imprinting in Mammals: Emerging Themes and Established Theories

Andrew J. Wood, Rebecca J. Oakey

The epigenetic events that occur during the development of the mammalian embryo are essential for correct gene expression and cell-lineage determination. Imprinted genes are expressed from only one parental allele due to differential epigenetic marks that are established during gametogenesis. Several theories have been proposed to explain the role that genomic imprinting has played over the course of mammalian evolution, but at present it is not clear if a single hypothesis can fully account for the diversity of roles that imprinted genes play. In this review, we discuss efforts to define the extent of imprinting in the mouse genome, and suggest that different imprinted loci may have been wrought by distinct evolutionary forces. We focus on a group of small imprinted domains, which consist of paternally expressed genes embedded within introns of multiexonic transcripts, to discuss the evolution of imprinting at these loci.

Introduction

The process of sexual reproduction dictates that mammals inherit two copies of every gene, one from the mother and one from the father. At most loci, both alleles are actively transcribed and functionally equivalent. Imprinted genes represent an exception to this rule, as the transcriptional activity of each allele is determined by the gender of the parental germ line to which it was most recently exposed. This parental legacy is initiated by epigenetic modifications such as DNA methylation, which is established in the parental germ line and maintained throughout somatic development in the offspring. Individual germ-line marks can control the allele-specific silencing or activation of multiple neighbouring genes, which leads in many instances to clusters of imprinted transcripts. Such loci represent an attractive paradigm for the study of epigenetic transcriptional regulation, as both the active and silent allele are present in the same cell nucleus, and therefore potentially exposed to the same trans-acting regulatory factors. Epigenetic abnormalities at imprinted loci have been observed in cloned mammals [1], and their disruption has been reported in a number of human developmental disorders and cancers [2].

Defining the Extent of Imprinting

Since the identification of the first autosomal imprinted genes in the early 1990s [3–5], much speculation has surrounded the question of how many exist. Attempts to count the exact number have been complicated by difficulties in defining exactly what constitutes a gene, as in several cases multiple functional components are derived from a single core of genetic information [6]. A recent census identified 96 imprinted functional components (54 maternally expressed, 42 paternally expressed) arising from 71 transcriptional units [7], and the relevant literature is summarised on the Harwell and University of Otago online databases [8,9].

A number of different approaches have been employed to define the extent of imprinting in the mouse genome. Mouse stocks carrying translocation chromosomes were used to define chromosomal regions that show parent-of-origin effects on phenotype when uniparentally inherited, and at least 13 distinct regions on eight chromosomes have been identified by this approach (C. V. Beechey, personal communication; [8]). The phenotypes range from early embryonic lethality to postnatal effects on growth and development, and are likely to result from the misexpression of imprinted genes situated within the uniparentally duplicated region [10]. The subsequent identification of imprinted genes on chromosomes without obvious uniparental effects [11-13] suggests that imprinting may be more widespread than initially thought, and not limited to genes that are vital for development. This conclusion is supported by the involvement of imprinted genes in behavioural traits in the mouse [14,15].

Continued at "Genomic Imprinting in Mammals: Emerging Themes and Established Theories"
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Featured Book: "Chromatin and Gene Regulation: Mechanisms in Epigenetics" by Bryan M. Turner (Amazon Astore UK | US)

Books on Epigenetics from the Science and Evolution Bookshop: UK | US

Technorati: open access, plos, genetics, imprinting, mammals, epigenetic, embryo, cell, marks, genomic, evolutionary, forces, domains, genes, evolution, dna, methylation, genetic, genome, mouse, chromosomes, epigenetics, science, regions

Epigenetics: Mother's Diet during Pregnancy can affect Grandchildren

2006-11-14T20:24:00.000Z

[This post also appears in the General Evolution News category]

Oakland, California: A new study by scientists at Children's Hospital Oakland Research Institute (CHORI) is the first to show that a mother's diet during pregnancy influences the health of her grandchildren by changing the behavior of a specific gene. The study was conducted using mice of an unique strain called 'viable yellow agouti' also known as A-vy in scientific terms. These mice possesss a gene that influences the color of their coats as well as their tendency to become obese and develop diabetes and cancer. The new research shows that the diet consumed by a pregnant Avy mouse affects the health of not only her pups, but also their pups - her grandchildren.

The study will be published in the November issue of the Proceedings of the National Academy of Sciences (PNAS) and was conducted by CHORI Scientist David Martin, M.D., and Assistant Scientist Kenneth Beckman, Ph.D., in collaboration with Drs. Jennifer Cropley and Catherine Suter from the Victor Chang Heart Institute in Sydney, Australia. In their experiments, the scientists fed some Avy mice a standard lab diet based on common foods consumed by humans. Other mice were fed this same diet supplemented with common nutritional supplements including folate, choline, betaine, vitamin B12, zinc and methionine.

The supplements were fed to the mice for a week during mid-pregnancy. The offspring were examined for their coat color, and female offspring were themselves mated again (without a supplemented diet) to produce a third generation of 'grandchildren.' The results showed that the supplements changed the behavior of the agouti gene in the first generation of pups, shifting their coats towards a brown color, and had the same effect on pups born in the next generation to mice that were not exposed to the supplemented diet.

Continued at "Epigenetics: Mother's Diet during Pregnancy can affect Grandchildren" [Evolution, Science]
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Based on the PNAS paper "Germ-line epigenetic modification of the murine A-vy allele by nutritional supplementation" (Abstract)

See "Cardiovascular and diabetes mortality determined by nutrition" (very relevant - don't be misled by the title!)

And "New theory of environmental inheritance ('05 Press Release)"

And "Epigenetics: Parentage has effects outside the genome"

Books on Epigenetics from the Science and Evolution Bookshop: UK | US

Epigenetic books from the Science and Evolution Bookshop: UK | US

Technorati: california, oakland, children, hospital, research, institute, chori, mother, diet, pregnancy, health, grandchildren, behavior, gene, mice, agouti, color, obese, diabetes, cancer, pups, mouse, pnas, academy, sciences, national, heart, sydney, australia, epigenetics, evolution, science, epigenetic, genome, enviromental, inheritance

Response to Comment on 'Gene Regulatory Networks and the Evolution of Animal Body Plans' (Science)

2006-09-18T17:04:00.000+01:00

The journal Science 11 August 2006:
Vol. 313. no. 5788, p. 761
DOI: 10.1126/science.1126765

Douglas H. Erwin and Eric H. Davidson

Contrary to Coyne's assertions, our paper did not advocate a macromutational innovation of phyla but considered the consequences of the introduction of developmental constraints for the evolution of gene regulatory networks based on recent empirical studies of gene regulatory networks.

Most of Coyne's concerns (1) are restatements of long-standing debates over the nature of evolutionary change (2). The comment offers no new data or interpretations but rather comments on issues, such as the nature of phyla, that have a lengthy and disputed history in evolutionary biology and which were not the subject of our paper. Specifically, Coyne seems to reject the role of regulatory genes in evolution. This is refuted by experimental studies of Drosophila, butterflies, echinoderms, fish, amniotes, and other organisms. Therefore, Coyne's conflict is not with our review as much as with developmental biology and its implications for evolutionary process. [Response]
--
See Comment on "Gene Regulatory Networks and the Evolution of Animal Body Plans"

and the original

Gene Regulatory Networks and the Evolution of Animal Body Plans

technorati tags: journal, science, innovation, phyla, developmental, constraints, evolution, gene, regulatory, networks, nature, evolutionary, change, new, data, history, biology, genes, experimental, drosophila, butterflies, fish, organisms, process, response, comment

On Making the Right Choice: The Deliberation-Without-Attention Effect

2006-08-27T17:39:00.000+01:00

Journal: Science 17 February 2006:

Vol. 311. no. 5763, pp. 1005 - 1007

DOI: 10.1126/science.1121629

Reports

On Making the Right Choice: The Deliberation-Without-Attention Effect

Ap Dijksterhuis,* Maarten W. Bos, Loran F. Nordgren, Rick B. van Baaren

Contrary to conventional wisdom, it is not always advantageous to engage in thorough conscious deliberation before choosing. On the basis of recent insights into the characteristics of conscious and unconscious thought, we tested the hypothesis that simple choices (such as between different towels or different sets of oven mitts) indeed produce better results after conscious thought, but that choices in complex matters (such as between different houses or different cars) should be left to unconscious thought. Named the "deliberation-without-attention" hypothesis, it was confirmed in four studies on consumer choice, both in the laboratory as well as among actual shoppers, that purchases of complex products were viewed more favorably when decisions had been made in the absence of attentive deliberation.

Department of Psychology, University of Amsterdam, Roetersstraat 15, 1018 WB, Amsterdam, the Netherlands.
--
The General Evo News category carries an entry from the Guardian (UK) about the above paper - "Trust your instincts: The conscious mind isn't much use in making hard decisions"

technorati tags: journal, science, deliberation, doi, attention, effect, wisdom, conventional, conscious, unconscious, thought, hypothesis, choices, laboratory, complex, department, psychology, university, amsterdam, instints, trust, mind, decisions

Inherited epigenetic variation - revisiting soft inheritance

2006-08-23T08:31:00.000+01:00

Perspective: Nature Reviews Genetics 7, 395-401 (May 2006) | doi:10.1038/nrg1834

Opinion: Inherited epigenetic variation - revisiting soft inheritance

Eric J. Richards

Phenotypic variation is traditionally parsed into components that are directed by genetic and environmental variation. The line between these two components is blurred by inherited epigenetic variation, which is potentially sensitive to environmental inputs. Chromatin and DNA methylation-based mechanisms mediate a semi-independent epigenetic inheritance system at the interface between genetic control and the environment. Should the existence of inherited epigenetic variation alter our thinking about evolutionary change?

[Associated Washington University of St. Louis news release]

technorati tags: nature, reviews, genetics, inherited, epigenetic, variation, inheritance, soft, phenotypic, chromatin, dna, environment, evolutionary, washington, st.+louis

Comment on "Gene Regulatory Networks and the Evolution of Animal Body Plans"

2006-08-11T06:52:00.000+01:00

Davidson and Erwin (Science Reviews, 10 February 2006, p. 796) argued that known microevolutionary processes cannot explain the evolution of large differences in development that characterize phyla. Instead, they proposed that phyla arise from novel evolutionary processes involving large mutations acting on conserved core pathways of development. I question some of their assumptions and show that natural selection adequately explains the origin of new phyla.

(Jerry A. Coyne, Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA)

See: Gene Regulatory Networks and the Evolution of Animal Body Plans

technorati tags: science, evolution, phyla, novel, evolutionary, processes, mutations, development, natural+selection, origin, ecology, chicago, university

Cardiovascular and diabetes mortality determined by nutrition

2006-07-31T09:18:00.000+01:00

A non-pdf version can be found here

Abstract:

Overfeeding and overeating in families are traditions that are often transferred from generation to generation. Irrespective of these family traditions, food availability might lead to overfeeding, in its turn leading to metabolic adaptations. Apart from selection, could these adaptations to the social environment have transgenerational effects? This study will attempt to answer the following question: Can overeating during a child's slow growth period (SGP), before their prepubertal peak in growth velocity influence descendants' risk of death from cardiovascular disease and diabetes? Data were collected by following three cohorts born in 1890, 1905 and 1920 in Overkalix parish in northern Sweden up until death or 1995. The parents' or grandparents' access to food during their SGP was determined by referring to historical data on harvests and food prices, records of local community meetings and general historical facts. If food was not readily available during the father's slow growth period, then cardiovascular disease mortality of the proband was low. Diabetes mortality increased if the paternal grandfather was exposed to a surfeit of food during his slow growth period. (Odds Ratio 4.1, 95% confidence interval 1.33-12.93, P=0.01). Selection bias seemed to be unlikely. A nutrition-linked mechanism through the male line seems to have influenced the risk for cardiovascular and diabetes mellitus mortality. [evolution]

See New theory of environmental inheritance ('05 Press Release)

technorati tags: overfeeding, overeating, generation, family, food, selection, metabolic, adaptations, child, death, descendants, cardiovascular, disease, diabetes, sweden, parents, grandparents, mortality, mechanism, evolution

New theory of environmental inheritance ('05 Press Release)

2006-07-28T08:23:00.000+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.

[NB Although this is only a press release I've got at least one relevant technical paper which I'll be posting soon - when I find it!]

14th December 2005

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

Evolution: Bacterial Mutation in Stationary Phase

2006-07-25T10:54:00.000+01:00

[After clicking on the above link, click on "Full Text"]

Evolution: Bacterial Mutation in Stationary Phase

Paul Sniegowski, Current Biology, March '04

Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA

Abstract:

A recent study indicates that the genomic mutation rate of the gut bacterium Escherichia coli is substantially higher in nongrowing than growing cultures. These findings are important in the light of the ongoing controversy over the generality and robustness of stationary phase mutagenesis and its evolutionary implications.

Article Outline begins:

The genomic mutation rate is a fundamental evolutionary parameter of any population, determining the rate of influx of new deleterious and beneficial alleles. Because most mutations are likely to be harmful to fitness, DNA repair and proofreading systems have probably evolved so as to minimize rates of mutation. Even the microbial extremophiles that normally inhabit harsh and potentially mutagenic environments seem to have low genomic mutation rates, suggesting that selection almost always puts a premium on the faithful maintenance and transmission of genetic information. Nonetheless, geneticists have long known that some environmental extremes can elevate mutation rates; indeed, this is the basis for the use of DNA damaging agents to induce mutations for study.

[email if the link stops working]

technorati tags: e.+coli, controversy, stationary, phase, mutagenesis, evolutionary, population, bacterium, alleles, dna, extremophiles, selection, mutations

The Changing Concept of Epigenetics (New York Academy of Sciences)

2006-07-23T09:38:00.000+01:00

The Changing Concept of Epigenetics

Annals of the New York Academy of Sciences, 981: 82-96. (2002)

Eva Jablonka and Marion J. Lamb

Cohn Institute for the History and Philosophy of Science and Ideas, Tel Aviv University, Tel Aviv 69978, Israel

ABSTRACT: We discuss the changing use of epigenetics, a term coined by Conrad Waddington in the 1940s, and how the epigenetic approach to development differs from the genetic approach. Originally, epigenetics referred to the study of the way genes and their products bring the phenotype into being. Today, it is primarily concerned with the mechanisms through which cells become committed to a particular form or function and through which that functional or structural state is then transmitted in cell lineages. We argue that modern epigenetics is important not only because it has practical significance for medicine, agriculture, and species conservation, but also because it has implications for the way in which we should view heredity and evolution. In particular, recognizing that there are epigenetic inheritance systems through which non-DNA variations can be transmitted in cell and organismal lineages broadens the concept of heredity and challenges the widely accepted gene-centered neo-Darwinian version of Darwinism.

technorati tags: epigenetics, new+york, academy, jablonka, lamb, cohn, institute, genetic, genes, phenotype, cells, medicine, agriculture, heredity, evolution, inheritance, dna, darwinian, darwinism, tel+aviv

Epigenetic germline inheritance

2006-07-20T09:16:00.000+01:00

Our increased knowledge of epigenetic reprogramming supports the idea that epigenetic marks are not always completely cleared between generations. Incomplete erasure at genes associated with a measurable phenotype can result in unusual patterns of inheritance from one generation to the next. It is also becoming clear that the establishment of epigenetic marks during development can be influenced by environmental factors. In combination, these two processes could provide a mechanism for a rapid form of adaptive evolution.

Current Opinion in Genetics and Development
Chong S, Whitelaw E
School of Molecular and Microbial Biosciences, Biochemistry Building-G08, University of Sydney, New South Wales 2006, Australia.

technorati tags: epigenetic, genes, phenotype, inheritance, genetics, development, evolution, university, sydney, australia

Color blindness and contrast perception in cuttlefish (Sepia officinalis) determined by a visual sensorimotor assay

2006-07-19T07:12:00.000+01:00

Full paper at above link

Abstract:

We tested color perception based upon a robust behavioral response in which cuttlefish (Sepia officinalis) respond to visual stimuli (a black and white checkerboard) with a quantifiable, neurally controlled motor response (a body pattern).

In the first experiment, we created 16 checkerboard substrates in which 16 grey shades (from white to black) were paired with one green shade (matched to the maximum absorption wavelength of S. officinalis' sole visual pigment, 492 nm), assuming that one of the grey shades would give a similar achromatic signal to the tested green.

In the second experiment, we created a checkerboard using one blue and one yellow shade whose intensities were matched to the cuttlefish's visual system.

In both assays it was tested whether cuttlefish would show disruptive coloration on these checkerboards, indicating their ability to distinguish checkers based solely on wavelength (i.e., color).

Here, we show clearly that cuttlefish must be color blind, as they showed non-disruptive coloration on the checkerboards whose color intensities were matched to the Sepia visual system, suggesting that the substrates appeared to their eyes as uniform backgrounds.

Furthermore, we show that cuttlefish are able to perceive objects in their background that differ in contrast by approximately 15%. This study adds support to previous reports that S. officinalis is color blind, yet the question of how cuttlefish achieve "color-blind camouflage" in chromatically rich environments still remains. [colour]

technorati tags: cuttlefish, color, colour, experiment, checkerboard, blind, camouflage, visual

The Killer Rat-Kangaroo's Tooth

2006-03-23T09:53:00.000Z

"Natural selection didn't come up with the best design; it just made the best of what was available.

The 'hand' of the Giant Panda (Ailuropoda melanoleuca) has six 'digits'. In processing its staple diet of bamboo, the Giant Panda drags the stalks between its sixth 'digit' and its paw to strip off the leaves. This sixth 'digit' or 'thumb' is a curious device. It is not, as one might expect, simply an additional finger of the type sometimes produced through congenital defect. In fact, the Panda's 'thumb' is not a real digit at all, but a greatly enlarged and specialised wrist bone called the radial sesamoid that lacks much of the flexibility of true digits. Why, one might wonder, did the Panda evolve a 'thumb' out of a wrist bone when it already had a 'real' thumb?

Evolution can be a fickle and opportunistic process. Often the end result can appear surprisingly imperfect, even 'sloppy'. The bottom line is that, at any juncture in its evolution, a species is constrained by accidents of history. When 'fashioning' new adaptations, natural selection can only work with what it's got. Because the real thumb (the first digit) of the Giant Panda was already modified and in use for another task (for walking on), evolution could only work with what was available, in this case, a radial sesamoid bone. It is this very fact of imperfection that underpins the reality of natural selection."

A pdf version is available here

technorati tags: natural+selection, giant+panda, panda, evolution, thumb

From symmetry to asymmetry: Phylogenetic patterns of asymmetry variation

2006-03-22T18:13:00.000Z

[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.
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Books on Symmetry from the Science and Evolution Bookshop: UK | US

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

The Genetics of Hearing and Balance in Zebrafish

2006-03-19T17:29:00.000Z

Annual Review of Genetics
Vol. 39: 9-22 (Volume publication date December 2005)

The Genetics of Hearing and Balance in Zebrafish

Teresa Nicolson

Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, Oregon 97239

Abstract:

The zebrafish is an excellent model system for studying the molecular basis of inner ear development and function. The eggs develop ex utero and the ear is transparent for the first few weeks of life. Forward genetic screens and antisense technology have helped to elucidate the signaling pathways and molecules required for inner ear development and function. This review addresses the most recent advances in our understanding of how the ear forms and discusses the molecules in hair cells that are essential for sensing sound and movement in the zebrafish.

[This item has been included because a post on the lateral line and the proposed internal evolutionary mechanism will eventually appear in the Personal Posts category of this weblog]

technorati tags: lateral+line, zebrafish, genetics, ear, weblog

Re: The evolution of adaptations (Waddington) (MB)

2006-03-18T14:26:00.000Z

On tuesday Waddington's "The Evolution of adaptations" (link goes to the paper itself) appeared on the Main Blog and since then 3 commentaries have been added to the Personal Posts category:

Re: The evolution of adaptations (Waddington) (1)

The reigning modern view is that, in nature, the direction of mutational change is entirely at random, and that adaptation results solely from the natural selection of mutations which happen to give rise to individuals with suitable characteristics. I want to argue that this theory is an extremist one

Brief comments on the intellectual strategy used to reduce an initially 'incredible' possibility (derived from the above quote) to a far more 'credible' one.

Re: The evolution of adaptations (Waddington) (2)

Describes how ostrich callosities could have become hereditary from the perspective of the proposed internal evolutionary mechanism.

Re: The evolution of adaptations (Waddington) (3)

Waddington only refers to the callosities found "fore and aft" on the underside of the body.

The ostrich also has callosities on the ankle and the proposed mechanism shows why these have 'persisted' even though they "are of no use" (further indicating the proposed mechanism has no connection with such outmoded concepts as "The Law of Use and Disuse).

John Latter

technorati tags: internal+evolutionary+mechanism, waddington, ostrich, nature, random, theory, strategy

The Imaginary Lamarck (The Textbook Letter)

2006-03-17T09:09:00.000Z

A Look at Bogus "History" in Schoolbooks

Michael T. Ghiselin

Jean-Baptiste de Lamarck (1744-1829) takes a prominent place in many biology textbooks and life-science textbooks, which depict him as the author of a "theory" of evolution based upon the inheritance of acquired characteristics. Lamarck's views, these books say, should be rejected in favor of the theory of evolution by natural selection, propounded by Charles Darwin (1809-1882), because only Darwin's theory is compatible with the findings of 20th-century genetics.

The Lamarck presented in schoolbooks, however, is a fiction -- an imaginary figure who has been fashioned from hearsay and wrong guesses, and who has been replicated in countless books by successive teams of plagiarists. This figure shares very little, except his name, with the Lamarck of history. Textbook-writers have imbued the fictitious Lamarck with an importance that the real Lamarck never had, and they have credited him with ideas that the real Lamarck did not hold. They also have invented a myth in which those ideas are compared falsely with Darwin's ideas, to produce a bogus dichotomy.

Textbooks typically introduce Lamarck with a flourish, as in this passage from Prentice Hall's Biology: The Study of Life:

One of the first theories of evolution was presented by the French biologist Jean Baptiste de Lamarck in 1809. From his studies of animals, Lamarck became convinced that species were not constant. Instead, he believed that they evolved from preexisting species. . . . According to Lamarck's theory, evolution involved two principles. He called his first principle the law of use and disuse. . . . The second part of Lamarck's theory was the inheritance of acquired characteristics. Lamarck assumed that the characteristics an organism developed through use and disuse could be passed on to its offspring.

Much the same material appears in Holt's Biology Today:

In 1809 a French biologist named Jean Baptiste de Lamarck presented an explanation of the origin of species in his work Zoological Philosophy. Lamarck developed a theory of evolution based on his belief in two biological processes:
1) The use and disuse of organs. According to Lamarck, organisms respond to changes in their environment by developing new organs or changing the structure and function of old organs. . . .

2) Inheritance of acquired traits. Lamarck believed that acquired characteristics were passed on to the organism's offspring....

Such claims give many false or misleading impressions, starting with the implication that Lamarck's views were original.

technorati tags: lamarck, biology, inheritance, darwin, traits, genetics, evolution

Darwinism Design and Purpose: A European Perspective

2006-03-16T08:11:00.000Z

Paper Title: Darwinism Design and Purpose: A European Perspective
Author: Jean Staune
Institutional Affiliation: General Secretary, Université Interdiciplinare de Paris
(This paper was prepared for "Science and Religion: Global Perspectives" June 4-8,
2005, in Philedelphia, PA, USA , a program of the Metanexus Institute

Abstract:

In the USA 'Issues in Biology and Religion' usually implies a debate between neo- Darwinians and Creationists or, more recently, the Intelligent Design movement. In Europe, however, the situation is somewhat different since no one really believes in creationism anymore and Intelligent Design is unheard of. Consequently the debate is completely different. It is a debate between evolutionists. The first debate is between 'Classical Darwinians' and scientists like Christian de Duve (Belgian Nobel Laureate for Medicine) or Simon Conway Morris (UK Paleontologist based at Cambridge) and is about the reproducibility of evolution. Presenting an alternative view from Gould for whom contingence rules supreme in the processes of evolution, de Duve and Conway Morris postulate that if you 'run' evolution again on a planet with more-or-less the same conditions as you find on Earth the result will be more-or-less the same. More specifically it will lead to intelligent beings that resemble us. They accept that there are no other forces that act on evolution than Darwinian mechanisms (random mutations and natural selection) but they show evidence that chance is channeled by the laws of nature. If you play dice for a very long time you can be sure that a very special result will certainly occur.

The second debate is between classical neo-Darwinians and non-Darwinians i.e. scientists that claim that Darwinian mechanisms are not the main forces driving evolution. There are in France, Italy and England two main schools of thinking in this area. One believes that there is a goal in the process of evolution and so randomness is just apparent, not real, in the mechanism of evolution. At a much deeper level evolution is more or less predictable because it has a purpose. The other supports the idea of self-organization, autopoeisis and emergence. For them these concepts are just as important, if not more important than Darwinian concepts in our understanding of evolution. In our first part we will describe these debates and the main scientists whose positions differ from the classical non-Darwinian one, but who are, WITHOUT EXCEPTION, evolutionists. It is of special interest for an American audience because it will show how the debate is much wider in this field than the narrow controversies between Darwinians on one hand and 'crazy creationists' or the proponents of Intelligent Design on the other.

It could be very surprising and interesting for an American audience to discover that there are non-Darwinian scientists who claim they support evolution more strongly than Darwinians! The reason is epistemological: Teilhard supporters who form the majority of non-Darwinian scientists in Europe, claim that the existence of purpose and directionality is better evidence for the reality of evolution than any demonstration using Darwinian concepts.

To conclude we will ask a question of a scientific and epistemological nature, namely: is there a way of applying, in evolutionary biology, the concepts that have appeared in other areas or research and which show the limitations of our capacity to understand reality e.g. Heisenberg's uncertainty principle or Godel's theorem of incompleteness? If so then what concept of evolution can this lead us to?

technorati tags: natural+selection, random+mutations, intelligent+design, biology, religion, gould, darwinian, research, heisenberg

Evolution Of Morphological Integration: Developmental Accommodation Of Stress-induced Variation

2006-03-15T12:03:00.000Z

Contents:

1) Press Release

Stress is a major factor in evolution, but for stress-induced modifications to have evolutionary importance they have to be inherited and persist in a sufficient number of individuals within a population. This requires an organism to survive stress and reproduce at least once; thus stress-induced variation has to be accommodated by an organism without much reduction in its functionality. How is such accommodation accomplished?

In an article in the September issue of The American Naturalist, Alexander V. Badyaev (University of Arizona) and colleagues show that complexity and cohesiveness of foraging structures of shrews enables accommodation of stress-induced developmental abnormalities in individual components of morphological complexes. Such developmental compensation and accommodation not only allow shrews growing under stressful environments to maintain locally adaptive foraging morphology, but also provide a mechanism for stress-induced evolutionary change.

Full text here

2) Article

[Badyaev et al, The American Naturalist, Sept '05]

Abstract:

Extreme environmental change during growth often results in an increase in developmental abnormalities in the morphology of an organism. The evolutionary significance of such stress-induced variation depends on the recurrence of a stressor and on the degree to which developmental errors can be accommodated by an organism's ontogeny without significant loss of function. We subjected populations of four species of soricid shrews to an extreme environment during growth and measured changes in the patterns of integration and accommodation of stress-induced developmental errors in a complex of mandibular traits. Adults that grew under an extreme environment had lower integration of morphological variation among mandibular traits and highly elevated fluctuating asymmetry in these traits, compared to individuals that grew under the control conditions. However, traits differed strongly in the magnitude of response to a stressor--traits within attachments of the same muscle (functionally integrated traits) had lower response and changed their integration less than other traits. Cohesiveness in functionally integrated complexes of traits under stress was maintained by close covariation of their developmental variation. Such developmental accommodation of stress-induced variation might enable the individual's functioning and persistence under extreme environmental conditions and thus provides a link between individual adaptation to stress and the evolution of stress resistance.

Full text at:

http://eebweb.arizona.edu/faculty/badyaev/papers/73.pdf

technorati tags: american+naturalist, population, stress, complexity, traits, evolution, environmental, shrews

The evolution of adaptations (Waddington)

2006-03-14T14:51:00.000Z

Endeavour 134-139 (July 1953)
The evolution of adaptations
C. H. WADDINGTON

Current biological belief regards evolution as being primarily the result of the natural selection of random mutations, useful adaptations gradually spreading throughout a race. Professor Waddington regards this as an 'extreme view, and in this article puts forward a hypothesis to explain how acquired characteristics may become hereditarily fixed by a process of genetic assimilation not invoking the generally discredited theory of direct inheritance.

It is abundantly found in the living world that the structure of an animal or plant is very precisely adapted to the functions which it has to perform. The nature of the processes by which this situation has been brought about during evolution provides one of the major problems for biological theory. The hypothesis of the inheritance of acquired characters suggested that in some way or other the effects of functioning become themselves inherited. It has usually been interpreted to mean that the reaction between the organism and its surroundings has, as one of its results, an effect on the germ-plasm such that new hereditary changes occur, of a kind which determines the development in later generations of individuals suited to these particular conditions of life. Although this idea has recently been revived in a rather nebulous form in the Soviet Union, it has been so completely rejected by the rest of the scientific world that it is hardly considered to be worthy of discussion in most of the important recent works on evolution. The reigning modern view is that, in nature, the direction of mutational change is entirely at random, and that adaptation results solely from the natural selection of mutations which happen to give rise to individuals with suitable characteristics. I want to argue that this theory is an extremist one, and that, in essaying to account for adaptation, it neglects to call to its aid the doctrines emerging in other fields of modern biology which can quite properly be combined with the conclusions of genetics in the strict sense. In the discussion which follows, attention will be confined to animals, but there is no reason to doubt that similar arguments could be advanced in the botanical field.

It will be advisable first to glance briefly at the phenomena which are usually referred to under the heading of adaptation, since they are of several different kinds which must be distinguished from one another.

technorati tags: random+mutations, genetic+assimilation, natural+selection, soviet+union, nature, evolution, waddington

Common objections to 'Internal Evolutionary Mechanisms' (2)

2006-03-14T14:38:00.000Z

5) Internal Mechanisms are 'directional' (objections 1 to 4 are here)

The mathematical model currently used is very basic so an explanation of why the proposed homeostatic internal evolutionary mechanism isn't 'directional' has initially been posted to the Personal Posts category:

"An Internal Evolutionary Mechanism and 'Direction in Evolution': Preliminary Notes"

John Latter

technorati tags: internal, evolutionary, mechanism

The fall and rise of Dr. Pangloss: Adaptationism and the Spandrels Paper 20 years later

2006-03-13T10:20:00.000Z

[Pigliucci & Kaplan, Trends in Ecology and Evolution, '00]

"Twenty years have passed since Gould and Lewontin published their critique of 'the adaptationist program' - the tendency of some evolutionary biologists to assume, rather than demonstrate, the operation of natural selection. After the 'Spandrels paper', evolutionists were more careful about producing just-so stories based on selection, and paid more attention to a panoply of other processes. Then came reactions against the excesses of the anti-adaptationist movement, which ranged from a complete dismissal of Gould and Lewontin's contribution to a positive call to overcome the problems. We now have an excellent opportunity for finally affirming a more balanced and pluralistic approach to the study of evolutionary biology."

See:

""The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme"

STEPHEN JAY GOULD AND RICHARD C. LEWONTIN

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...

technorati tags: spandrels, biology, natural+selection, evolution, traits, ecology

Mutation and adaptation: the directed mutation controversy in evolutionary perspective

2006-03-12T18:50:00.000Z

[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. [Evolution]

Also available at:

http://myxo.css.msu.edu/lenski/pdf/1995,%20ARES,%20Sniegowski%20&%20Lenski.pdf

technorati tags: evolution, variation, adaptation, mechanism, nonrandom, directed+mutation, adaptive+mutation, darwinian, natural+selection

Phenotypic integration: studying the ecology and evolution of complex phenotypes (Ecology Letters)

2006-03-12T07:53:00.000Z

Ecology Letters
Volume 6 Page 265 - March 2003
doi:10.1046/j.1461-0248.2003.00428.x
Volume 6 Issue 3

Massimo Pigliucci

Abstract:

Phenotypic integration refers to the study of complex patterns of covariation among functionally related traits in a given organism. It has been investigated throughout the 20th century, but has only recently risen to the forefront of evolutionary ecological research. In this essay, I identify the reasons for this late flourishing of studies on integration, and discuss some of the major areas of current endeavour: the interplay of adaptation and constraints, the genetic and molecular bases of integration, the role of phenotypic plasticity, macroevolutionary studies of integration, and statistical and conceptual issues in the study of the evolution of complex phenotypes. I then conclude with a brief discussion of what I see as the major future directions of research on phenotypic integration and how they relate to our more general quest for the understanding of phenotypic evolution within the neo-Darwinian framework. I suggest that studying integration provides a particularly stimulating and truly interdisciplinary convergence of researchers from fields as disparate as molecular genetics, developmental biology, evolutionary ecology, palaeontology and even philosophy of science.

Full text at:

http://www.blackwell-synergy.com/doi/full/10.1046/j.1461-0248.2003.00428

technorati tags: ecology, adaptation, genetics, phenotypic, plasticity, evolution

Expanding evolution: A broader view of inheritance puts pressure on the neo-darwinian synthesis

2006-03-11T20:29:00.000Z

Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life by Eva Jablonka & Marion J. Lamb Bradford Books: 2005. 462 pp (Amazon UK | US).

Book Review by Massimo Pigliucci (Nature Magazine)

Extracts:

There have been rumblings for some time to the effect that the neo-darwinian synthesis of the early twentieth century is incomplete and due for a major revision. In the past decade, several authors have written books to articulate this feeling and to begin the move towards a second synthesis. In the past decade, several authors have written books to articulate this feeling...
...I framed the debate in terms of the integration of development, environment and genetics by articulating the concept of "developmental reaction norms"...
...Jablonka and Lamb provide a framework that includes not one but four sources of inheritance in living organisms: there is the standard genetic one, based on nucleic acids such as DNA and RNA; there are epigenetic inheritance systems, such as (but not limited to) chromatin marking systems and RNA-interference systems for gene silencing; third, there are behavioural inheritance systems, including behaviour- influencing substances (think pheromones) and social learning (both imitative and not); finally, humans have also developed a symbolic inheritance system based on the ability to communicate by manipulating symbols...
...The authors argue that there is more to heredity than genes; that some hereditary variations are non-random in origin; that some acquired information is inherited; and that evolutionary change can result from 'instruction' as well as selection. This may sound rather revolutionary, even preposterously close to lamarckism. But Jablonka and Lamb build on evidence from standard research in evolutionary and molecular biology, and their case should be examined on its merits, rather than being dismissed by a knee-jerk reaction...
...The clamour to revise neo-darwinism is becoming so loud that hopefully most practising evolutionary biologists will begin to pay attention. It has been said that science often makes progress not because people change their minds, but because the old ones die off and the new generation is more open to novel ideas. I therefore recommend this and the other books I mentioned on the future of evolutionary theory to the current crop of graduate students, postdocs and young assistant professors. They'll know what to do.

technorati tags: evolution, neo-darwinian, genetics, dna, rna, epigenetic, inheritance, lamarckism

Embracing Complexity: Organicism for the 21st Century (Developmental Dynamics)

2006-03-11T07:16:00.000Z

[Gilbert & Sarkar, Developmental Dynamics, Sept '00]

Abstract:

Organicism (materialistic holism) has provided the philosophical underpinnings for embryology since the time of Kant. It had influenced the founders of developmental mechanics, and the importance of organicism to embryology was explicitly recognized by such figures as O. Hertwig, H. Spemann, R. Harrison, A. M. Dalq, J. Needham, and C. H. Waddington. Many of the principles of organicism remain in contemporary developmental biology, but they are rarely defined as such. A combination of genetic reductionism and the adoption of holism by unscientific communities has led to the devaluation of organicism as a fruitful heuristic for research. This essay attempts to define organicism, provide a brief history of its importance to experimental embryology, outline some sociologically based reasons for its decline, and document its value in contemporary developmental biology. Based on principles or organicism, developmental biology should become a science of emerging complexity. However, this does mean that some of us will have to learn calculus. [Evolution]

technorati tags: biology, complexity, organicism, evolution, embryology

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

2006-03-10T10:46:00.000Z

[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]

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

A Third Way (Boston Review)

2006-03-09T09:29:00.000Z

[Shapiro, Boston Review, Mar '97]

Introduction:

"The recent reviews in your columns of books by Dennett, Dawkins, and
Behe are testimony to the unflagging interest in controversies about
evolution. Although such purists as Dennett and Dawkins repeatedly
assert that the scientific issues surrounding evolution are basically
solved by conventional neo-Darwinism, the ongoing public fascination
reveals a deeper wisdom. There are far more unresolved questions than
answers about evolutionary processes, and contemporary science
continues to provide us with new conceptual possibilities.

Unfortunately, readers of Boston Review may remain unaware of this
intellectual ferment because the debate about evolution continues to
assume the quality of an abstract and philosophical "dialogue of the
deaf" between Creationists and Darwinists. Although our knowledge of
the molecular details of biological organization is undergoing a
revolutionary expansion, open-minded discussions of the impact of
these discoveries are all too rare. The possibility of a non-
Darwinian, scientific theory of evolution is virtually never
considered. In my comments, then, I propose to sketch some
developments in contemporary life science that suggest shortcomings
in orthodox evolutionary theory and open the door to very different
ways of formulating questions about the evolutionary process. After a
discussion of technical advances in our views about genome
organization and the mechanisms of genetic change, I will focus on a
growing convergence between biology and information science which
offers the potential for scientific investigation of possible
intelligent cellular action in evolution."

technorati tags: shapiro, dawkins, dennett, behe, evolution, biology

Evolutionary Transitions: how do levels of complexity emerge?

2006-03-08T17:30:00.000Z

Heylighen F. (2000): "Evolutionary Transitions: how do levels of complexity emerge?", Complexity 6 (1), p. 53-57-- A joint review of 5 books (by Pettersson, Maynard Smith & Szathmary, Coren, Stewart and Turchin) discussing the evolution of complexity levels.

It is a common observation that complex systems have a nested or hierarchical structure: they consist of subsystems, which themselves consist of subsystems, and so on, until the simplest components we know, elementary particles. It is also generally accepted that the simpler, smaller components appeared before the more complex, composite systems. Thus, evolution tends to produce more complex systems, gradually adding more levels to the hierarchy. For example, elementary particles evolved subsequently into atoms, molecules, cells, multicellular organisms, and societies of organisms. These discrete steps, characterized by the emergence of a higher level of complexity, may be called "evolutionary transitions". The logic behind this sequential complexification appears obvious: you can only build a higher order system from simpler systems after these building blocks have evolved themselves. The issue becomes more complicated when you start looking for the precise mechanisms behind these evolutionary transitions, and try to understand which levels have appeared at what moment, and why.

In recent years, several authors have tried to tackle this issue. As we will see, their approaches are diverse, and their results are concomitantly different. Part of the reason for this incoherence is that these researchers have worked mostly in isolation: they come from different traditions, and their works hardly make reference to each other. This is understandable, since the emergence of hierarchical levels is a pre-eminently multidisciplinary issue, involving at least physics, chemistry, biology and sociology.

technorati tags: complexity, hierarchical, evolution, transitions, biology

Irreducible Complexity Revisited (PCID)

2006-03-08T07:55:00.000Z

[Dembski, PCID, '04]

Abstract:

"Michael Behe's concept of irreducible complexity, and in particular his use of this concept to critique Darwinism, continues to come under heavy fire from the biological community. The problem with Behe, so Darwinists inform us, is that he has created a problem where there is no problem. Far from constituting an obstacle to the Darwinian mechanism of random variation and natural selection, irreducible complexity is thus supposed to be eminently explainable by this same mechanism. But is it really? It's been eight years since Behe introduced irreducible complexity in Darwin's Black Box - a book that continues to sell 15,000 copies per year in English alone (Amazon UK | US). I want in this essay to revisit Behe's concept of irreducible complexity and indicate why the problem he has raised is, if anything, still more vexing for Darwinism than when he first raised it. The first four sections of this essay review and extend material that I've treated elsewhere. The last section contains some novel material."

technorati tags: irreducible+complexity, darwinism, natural+selection, darwin, dembski

As promised in last night's Personal Post (Are Human Beings 'Irreducibly Complex'? A whimsical thought...) here is the caveat:

My perception of the concept [irreducible complexity] is similar to that of Pierre-Paul Grasse who believed 'Internal Factors' were involved in how evolutionary changes occurred - see Grasse, Behe, and "Irreducible Complexity". [John Latter]

University of Chicago study overturns conventional theory in evolution (Jun '05)

2006-03-07T12:25:00.000Z

Contents:

1) Press Release

New data suggest that the accumulation of genetic changes is not solely determined by natural selection. A study by University of Chicago researchers contradicts conventional theory by showing that the percentage of mutations accepted in evolution is also strongly swayed by the speed at which new mutations arrive at a gene: the faster the speed of new mutations, the greater the percentage of those mutations accepted.

"We've discovered a striking phenomenon that challenges a paradigm of molecular evolution that has been around for several decades," said lead author Bruce Lahn, Ph.D., assistant professor of genetics at the University of Chicago and Howard Hughes Medical Institute investigator. "As such, it may cause a significant shift in the field."

Full text at:

http://www.eurekalert.org/pub_releases/2005-06/uocm-uoc060305.php

2) A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate.

[Wyckoff et al, Trends in Genetics, Jul '05]

Under prevailing theories, the nonsynonymous-to-synonymous substitution ratio (i.e. K(a)/K(s)), which measures the fixation probability of nonsynonymous mutations, is correlated with the strength of selection. In this article, we report that K(a)/K(s) is also strongly correlated with the mutation rate as measured by K(s), and that this correlation appears to have a similar magnitude as the correlation between K(a)/K(s) and selective strength. This finding cannot be reconciled with current theories. It suggests that we should re-evaluate the current paradigms of coding-sequence evolution, and that the wide use of K(a)/K(s) as a measure of selective strength needs reassessment.

Full text at:

http://boisei.uchicago.edu/pdfs/tig2005.pdf

technorati tags: natural+selection, evolution, molecular, paradigm, mutations

Re: The proposed Internal Evolutionary Mechanism and 'Cultural Evolution'

2006-03-06T23:35:00.000Z

Todays entry in the Personal Posts category briefly comments on why no attention will be given to "Cultural Evolution" other than that applicable to the third of the current Aims:

3) Address those cultural factors which are applicable to answering the question "If an internal evolutionary mechanism exists, then why hasn't it been found before?"

John Latter

technorati tags: cultural+evolution

The Evolution of Life on the Earth (Gould '94)

2006-03-06T12:09:00.000Z

The Evolution of Life on the Earth: Scientific American Magazine; October 1994; by Gould

Some creators announce their inventions with grand eclat. God proclaimed, "Fiat lux," and then flooded his new universe with brightness. Others bring forth great discoveries in a modest guise, as did Charles Darwin in defining his new mechanism of evolutionary causality in 1859: "I have called this principle, by which each slight variation, if useful, is preserved, by the term Natural Selection."

Natural selection is an immensely powerful yet beautifully simple theory that has held up remarkably well, under intense and unrelenting scrutiny and testing, for 135 years. In essence, natural selection locates the mechanism of evolutionary change in a "struggle" among organisms for reproductive success, leading to improved fit of populations to changing environments. (Struggle is often a metaphorical description and need not be viewed as overt combat, guns blazing. Tactics for reproductive success include a variety of nonmartial activities such as earlier and more frequent mating or better cooperation with partners in raising offspring.) Natural selection is therefore a principle of local adaptation, not of general advance or progress.

Yet powerful though the principle may be, natural selection is not the only cause of evolutionary change (and may, in many cases, be overshadowed by other forces).

[This article is also available here]

technorati tags: natural+selection, gould, darwin, evolution

The Internal Evolutionary Mechanism: Basic Concept

2006-03-05T21:47:00.000Z

The first of the "Aims" referred to in yesterday's Main Blog post is:

1) To develop the model indicated by the 'anomalies' referred to in Why research an 'Internal Evolutionary Mechanism'? (1) - and hopefully avoid the pitfalls inherent in doing so!

Below is a description of the basic concept (warts and all) as it has appeared on my website since 1998:

The Post-Notochord Model

The diagram opposite shows a dotted area within which all internal and external "inputs" come together and it is here that an internal evolutionary mechanism is proposed to exist. Cannon (1929) formulated the concept of "homeostasis" whereby activity at this level can be described as "self regulating" or "automatic" which are observations of a closed system made from an external standpoint.

The model proposes, when viewed from the inside, any non thinking and non intelligent organism with such a configuration is simply maintaining equilibrium and that this equilibrium extends in another direction - that of evolution.

The dotted area, arbitrarily labeled the A.O.N.E. ("Area of Natural Equilibrium"), is a localized area at the apex (or center) of the internal homeostatic hierarchy [Note 1: The Triune Brain]. The genome in such an organism's germ cells, equally hierarchically integrated, will also have a localized area and this connectivity reflects the continuity of organism-genome-organism.

Changes in the life experiences of an organism as 'experienced' at the level of the AONE - not that of consciousness - may cause single or co-ordinated evolutionary/devolutionary changes to occur if existing thresholds are exceeded, or just as importantly, not met. These 'changes', transmitted to germ cells, would then cascade down (or radiate outwards) from their localized areas into the genome, and in a direction that would begin (or achieve) restoration of equilibrium in the next generation(s).

The following flowchart will be used to demonstrate how an homeostatic mechanism can accounts for various aspects of evolution:

To recap: The fibonacci series begins "0, 1, 1, 2 ,3, 5" and each subsequent number can be formed by adding the two preceeding numbers together, eg 2 + 3 = 5, 3 + 5 = 8, 5 + 8 = 13 (etc.).
If the larger of two sucessive fibonacci numbers is divided by the smaller then a number is obtained which increasingly approximates to the 'golden ratio' or 'golden number': 1.6180339887498948482....
The flowchart opposite will generate the fibonacci series endlessly.
For simplicity it ignores the first zero, and rather than 'seeding' the program and adding succesive fibonacci numbers together, it generates the numbers via testing the ratio of 'x over y' against phi (where phi equals the golden number/ratio).
'y' is the fibonacci number produced, 'x' the incremental count. 'F' is required to test whether the 'x over y' ratio is closer to the golden ratio when x/y is above or below it.
NB I hope the maths are correct - please email any comments (and I would like help/advice in developing this further).

The above two entries have been taken from existing material and will serve as an initial 'baseline'. I'll post ongoing development in the Persoanl Posts category and then here in the Main Blog when I'm happier with how things are going - correspondence over a recently reported phenomena, for example, gives an indication of how a mathematical model could be developed but also demonstrates just how basic the above is!

John Latter

technorati tags: internal+evolutionary+mechanism, evolution, fibonacci, homeostasis, triune+brain

Lamarckian mechanisms in Darwinian evolution

2006-03-05T15:20:00.000Z

[Jablonka, Lamb, Avital, Trends in Ecology & Evolution, May '98]

Opening paragraph:

Lamarckism and Darwinism are traditionally seen as alternative
theories trying to account for evolutionary change. The verdict of
history is that Lamarck got it wrong - evolutionary change does
not occur through the inheritance of acquired characters. Acquired
characters are the outcome of instructive processes, such as those
seen in embryonic induction, transcriptional regulation, and
learning all of which involve highly specific and usually adaptive
responses to factors external to the responding system. The
inheritance of the outcomes of instructive processes is deemed to
be impossible. Adaptive evolutionary change is assumed to be based
on darwinian (or more accurately neo-darwinian) evolution in which
guidance comes exclusively from selective processes. The
production and nature of heritable variation is assumed to be
uninformed by the environment or by previous history. The future
is open-ended, determined solely by the contingencies of life. lt
is neither foretold nor intimated.

technorati tags: ecology, evolution, lamarck, inheritance

Why research an 'Internal Evolutionary Mechanism'?

2006-03-04T22:41:00.000Z

Why research an 'Internal Evolutionary Mechanism'?

Part 1: Background and Perspective: 'Life isn't a rehearsal'

and

Part 2: Aims

have been posted to the Personal Posts category.

John Latter

technorati tags: internal+evolutionary+mechanism

Modularity and sense organs in the blind cavefish, Astyanax mexicanus.

2006-03-03T17:27:00.000Z

Franz-Odendaal TA, Hall BK
Modularity and sense organs in the blind cavefish, Astyanax mexicanus.
Evol Dev. 2006 Jan-Feb;8(1):94-100.

Mexican tetra (Astyanax mexicanus) exist as two morphs: a sighted (surface) form and a blind (cavefish) form. In the cavefish, some modules are lost, such as the eye and pigment modules, whereas others are expanded, such as the taste bud and cranial neuromast modules. We suggest that modularity can be viewed as being nested in a manner similar to Bauplane so that modules express unique sets of genes, cells, and processes. In terms of evolution, we conclude that natural selection can act on any of these hierarchical levels within modules or on all the sensory modules as a whole. We discuss interactions within and between modules with reference to the blind cavefish from both genetic and developmental perspectives. The cavefish represents an illuminating example of module interaction, uncoupling of modules, and module expansion.

Reprints of Modularity and sense organs in the blind cavefish can be requested from Tamara Franz-Odentaal at the email address here

technorati tags: modularity, cavefish, bauplane, genes, cells, modules, eye, pigment, organs

TalkOrigins webpage on Atavisms and Vestigial Structures

2006-03-02T12:05:00.000Z

Retrograde Motion and Evolution, yesterday's post to the Personal Posts category, contained:

If the proposal of an internal evolutionary mechanism is seen as a Copernican expansion upon the Ptolemaic modern synthesis, then in terms of explanatory power alone, obvious areas to zero in on would be any evolutionary equivalents to retrograde motion.

Evolutionary atavisms are among such suitable candidates and have been brought to the fore (for a day or two at least!) by John F. Fallon's kind response to a request for a copy of The Development of Archosaurian First-Generation Teeth in a Chicken Mutant.

Vestigial Organs/Structures are equally interesting - hence the previous post of To See or Not to See: Evolution of Eye Degeneration in Mexican Blind Cavefish and a request in Wanted Papers for Modularity and sense organs in the blind cavefish*).

The TalkOrigins webpage (title link) gives a useful overview of both Atavisms & Vestigial Structures and has the following outline:

1. Anatomical vestigial structures
* Answers to criticisms of vestigial structures
1. Vestiges can have functions
2. Positive evidence demonstrates lack of functionality
3. Negative evidence is scientific when controlled
2. Atavisms
* Living whales with hindlimbs
* Newborn babies with tails
3. Molecular vestigial structures
4. Ontogeny and developmental biology
* Mammalian ear bones and reptile jaws
* Pharyngeal pouches and branchial arches
* Snake and whale embryos and with legs
* Embryonic human tail
* Marsupial eggshell and caruncle
5. Present biogeography
6. Past biogeography
* Marsupials
* Horses
* Apes and humans

John Latter

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

*This paper now appears on the Main Blog (here) and contains details on how to obtain reprints

technorati tags: internal+evolutionary+mechanism, atavisms, vestigial+organs, talkorigins, evolution, structures, whale, hindlimbs, eye, marsupial

The Inapplicability of the Biogenetic Rule to Behavioral Development

2006-03-01T10:37:00.000Z

Medicus, G. (1992) The inapplicability of the biogenetic rule to behavioral development. Human Development, 35, 1-8.

Abstract:

The validity of this rule for behavioral ontogeny has never been proven. Few developmental psychologists or ethologists have committed themselves on the issue. A clear position, based on empirical data, is needed. The present interdisciplinary article offers cogent reasons why the biogenetic rule has no relevance for behavioral ontogeny.The biogenetic rule states that ontogeny repeats phylogeny. The validity of this rule for behavioral ontogeny has never been proven. Few developmental psychologists or ethologists have committed themselves on the issue. A clear position, based on empirical data, is needed. The present interdisciplinary article offers cogent reasons why the biogenetic rule has no relevance for behavioral ontogeny.

technorati tags: biogenetic+rule, ontogeny, developmental, phylogeny

Common objections to 'Internal Evolutionary Mechanisms' (1)

2006-02-28T12:15:00.000Z

Brief notes on four common objections to current or historical proposals of internal evolutionary mechanisms (if you can think of any more then please leave a comment or email me):

1) Internal Evolutionary Mechanisms are 'Mystical'

2) Internal Evolutionary Mechanisms are 'Lamarckian'

3) "Populations Evolve, Individuals Do Not"

4) Weismann's experiment with Rodents

1) Internal Evolutionary Mechanisms are 'Mystical' [Return to Top]

In their paper "The Spandrels of San Marco and the Panglossian Paradigm" Gould and Lewontin briefly described the European concept of Bauplan ('bodyplan') which, in its 'strong' form, speculates:

"But the important steps of evolution, the construction of the Bauplan itself and the transition between Bauplane, must involve some other unknown, and perhaps 'internal,' mechanism."

An internal mechanism cannot be 'mystical' because if one exists then it would be testable. This suggests the concept ought to evoke no greater uncertainty than that which would be appropriate to the words of Einstein: "If we knew what we were doing, we wouldn't call it research, would we?".

2) Internal Evolutionary Mechanisms are 'Lamarckian' [Return to Top]

[The following also appears as "An error in associating Lamarck with 'Adaptive Mutations?"]

In 1640 Galileo Galilei wrote a letter to Fortunio Liceti in which he said:

"If Aristotle were to see the new discoveries recently [made] in the heavens, whose immobility he had asserted, because no alteration had previously been seen in them, he would now without doubt state the contrary." ['Galileo Galilei - Towards a Resolution of 350 Years of Debate', Paul Cardinal Poupard].

The above statement highlights the danger of placing dependence on words frozen in time without taking into account how different those words might be if their author had had access to the discoveries that have since been made.

Lamarck, for example, published his "Zoological Philosophy" in 1809 and is today popularly associated with "the inheritance of acquired characteristics" whereby organisms somehow direct their own evolution. On the basis of Galileo's words, however, it could be argued that had Lamarck been alive in the 1890s, over thirty years after publication of Darwin's "On the Origin of Species", his views would have progressed from the moment in time in which they had been caught.

With access to the discoveries and discussions that occured throughout the 19th Century it is conceivable that Lamarck might even have reached broad agreement with J. Mark Baldwin over the latter's proposal of an indirect factor in evolution, known today as the "Baldwin Effect", and described in the 1896 paper "A New Factor in Evolution" [American Naturalist].

Pure speculation ,of course, but if sufficient to illustrate a general principle (that "words frozen in time should be differentiated from those carved in stone") then the inappropriateness of interpreting new discoveries or proposals in 'Lamarckian terms' is readily apparent.

3) "Populations Evolve, Individuals Do Not" [Return to Top]

From the TalkOrigins page "What is Evolution?":

"Evolution is a process that results in heritable changes in a population spread over many generations."
This is a good working scientific definition of evolution; one that can be used to distinguish between evolution and similar changes that are not evolution. Another common short definition of evolution can be found in many textbooks:
"In fact, evolution can be precisely defined as any change in the frequency of alleles within a gene pool from one generation to the next."
- Helena Curtis and N. Sue Barnes, Biology, 5th ed. 1989 Worth Publishers, p.974
One can quibble about the accuracy of such a definition (and we have often quibbled on these newsgroups) but it also conveys the essence of what evolution really is. When biologists say that they have observed evolution, they mean that they have detected a change in the frequency of genes in a population.

Individuals do not evolve, but if shared circumstances 'triggered' individual internal evolutionary mechanisms in a subset of a population then this could cause similar genetic changes to appear in their progeny. Thereby causing a "change in the frequency of alleles within a gene pool from one generation to the next."

4) Weismann's experiment with Rodents [Return to Top]

Extract from the transcript (click here) of a radio program in which Robyn Williams (ABC: Australian Broadcasting Corporation) talked to Ted Steele (author of "Lamarck's Signature"):

Steele: ...First, in 1885, three years after Darwin's death, a German biologist, August Weismann, responding to the challenge of Darwin's Theory of Pangenesis, erected his now famous 'barrier' between the somatic cells and germ cells. 'Weismann's Barrier' was assumed to protect the germ cells from any type of genetic change within the body.
The bulk of Weismann's experimental refutation focused on testing whether acquired parental mutilations could be inherited.
He is most famous for his work on chopping off the tails of rats shortly after birth. He then showed in breeding experiments extending over many generations, that such tail chopping at birth never produced a tailless offspring.
Critics of this experiment have pointed out that such experiments did not test Lamarck's idea. A short tail caused by chopping is a modification that was not produced by the rat. In contrast, Lamarck believed that only modifications produced by a response of the rat to the environment would be inherited.

Although the criticism is valid the most important point is that Weismann wasn't testing for a specific internal evolutionary mechanism whereby it had been proposed that 'acquired characteristics' could be inherited.

John Latter

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

technorati tags: internal+evolutionary+mechanism, lamarck, darwin, baldwin, weismann, gould, spandrels, einstein, galileo, steele, inheritance, acquired+characteristics, evolution, talkorigins

Stress-induced variation in evolution from behavioural plasticity to genetic assimilation

2006-02-27T08:48:00.000Z

[Badyaev, Proceedings The Royal Society Biological Sciences, May '05]

Stress-induced variation in evolution from behavioural plasticity to genetic assimilation

Abstract:

Extreme environments are closely associated with phenotypic evolution, yet the mechanisms behind this relationship are poorly understood. Several themes and approaches in recent studies significantly further our understanding of the importance that stress-induced variation plays in evolution. First, stressful environments modify (and often reduce) the integration of neuroendocrinological, morphological and behavioural regulatory systems. Second, such reduced integration and subsequent accommodation of stress-induced variation by developmental systems enables organismal `memory' of a stressful event as well as phenotypic and genetic assimilation of the response to a stressor. Third, in complex functional systems, a stress-induced increase in phenotypic and genetic variance is often directional, channelled by existing ontogenetic pathways. This accounts for similarity among individuals in stress-induced changes and thus significantly facilitates the rate of adaptive evolution. Fourth, accumulation of phenotypically neutral genetic variation might be a common property of locally adapted and complex organismal systems, and extreme environments facilitate the phenotypic expression of this variance. Finally, stress-induced effects and stress-resistance strategies often persist for several generations through maternal, ecological and cultural inheritance. These transgenerational effects, along with both the complexity of developmental systems and stressor recurrence, might facilitate genetic assimilation of stress-induced effects. Accumulation of phenotypically neutral genetic variance by developmental systems and phenotypic accommodation of stress-induced effects, together with the inheritance of stress-induced modifications, ensure the evolutionary persistence of stress-response strategies and provide a link between individual adaptability and evolutionary adaptation.

technorati tags: evolution, phenotypic, mechanisms, stress, variation, regulatory, developmental, genetic+assimilation, adaptability, complex, systems

Epigenetic Mechanisms of Character Origination

2006-02-26T10:00:00.000Z

[Newman & Muller/Müller, J. Experimental Zoology, '00]

Abstract:

"The close mapping between genotype and morphological phenotype in
many contemporary metazoans has led to the general notion that the
evolution of organismal form is a direct consequence of evolving
genetic programs. In contrast to this view, we propose that the
present relationship between genes and form is a highly derived
condition, a product of evolution rather than its precondition.
Prior to the biochemical canalization of developmental pathways, and
the stabilization of phenotypes, interaction of multicellular
organisms with their physico-chemical environments dictated a many-to-
many mapping between genomes and forms. These forms would have been
generated by epigenetic mechanisms: initially physical processes
characteristic of condensed, chemically active materials, and later
conditional, inductive interactions among the organism's constituent
tissues. This concept, that epigenetic mechanisms are the generative
agents of morphological character origination, helps to explain
findings that are difficult to reconcile with the standard neo-
Darwinian model, e.g. the burst of body plans in the early Cambrian,
the origins of morphological innovation, homology, and rapid change
of form. Our concept entails a new interpretation of the relationship
between genes and biological form."

technorati tags: epigenetic, genotype, evolution, canalization, mechanisms, body+plans, neo-darwinian

Symmetry Breaking and the Evolution of Development

2006-02-25T23:01:00.000Z

Symmetry Breaking and the Evolution of Development

[Palmer, Science, Oct '04]

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.
-------

Books on Symmetry from the Science and Evolution Bookshop: UK | US

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

Classic Papers on Human Origins from Nature Magazine

2006-02-25T14:59:00.000Z

1) Dart, R. A. Australopithecus africanus:
The Man-Ape of South Africa
Nature 115, 195-199 (1925)
When Dart, an anatomist from South Africa, reported the first 'ape-man', he was derided by the same people who fell for the fraudulent Piltdown Man. But Piltdown was a fake and Dart was vindicated. The modern study of human origins starts here. http://www.nature.com/nature/ancestor/pdf/115195.pdf

2) Leakey, L. S. B.
A new fossil skull from Olduvai
Nature 184, 491-493 (1959)
Fossil-hunter Louis Leakey had been scouring East Africa for clues about human origins in vain for 30 years before he (or rather, his wife) hit the jackpot at Olduvai Gorge in Tanzania. The new player on the fossil scene was lantern-jawed 'Nutcracker man'. http://www.nature.com/nature/ancestor/pdf/184491.pdf

3) Leakey, L. S. B., Tobias, P. V. and Napier, J. R.
A new species of the genus Homo from Olduvai Gorge.
Nature 202, 7-9 (1964) Leakey scores again with fossils associated with primitive tools. He announces Homo habilis - 'handy man' - the first fossil member of our own genus; and with him, the first stirrings of technology. http://www.nature.com/nature/ancestor/pdf/202007.pdf

4) Leakey, R. E. F.
Evidence for an advanced Plio-Pleistocene hominid from East Rudolf, Kenya
Nature 242, 447-450 (1973)
Richard Leakey - son of Louis - describes a skull as iconic as they come, but always known enigmatically as '1470'. Thought to belong to an early form of Homo (now Homo rudolfensis), this specimen is a key fossil in the understanding of human origins. http://www.nature.com/nature/ancestor/pdf/242447.pdf

5) Johanson, D. C. and Taieb, M.
Plio-Pleistocene hominid discoveries in Hadar, Ethiopia
Nature 260, 293-297 (1976)
Donald Johanson pushes the human story back beyond the 3-million-year- mark with a skeleton, later assigned to Australopithecus afarensis. The skeleton is now known as 'Lucy', after Lucy in the Sky with Diamonds, the Beatles' tune popular in the field camp. http://www.nature.com/nature/ancestor/pdf/260293.pdf

6) Leakey, M. D. and Hay, R. L.
Pliocene footprints in the Laetolil Beds at Laetoli, northern Tanzania
Nature 278, 317-323 (1979)
When a volcanic eruption sent a rain of ash over what is now Tanzania, an adult and child, probably both Australopithecus afarensis, set out to watch the show - leaving, as a poignant souvenir, perfect and very modern-looking footprints, preserved in the ashfall. http://www.nature.com/nature/ancestor/pdf/278317.pdf

7) Brown, F., Harris, J., Leakey, R. and Walker, A.
Early Homo erectus skeleton from west Lake Turkana, Kenya
Nature 316, 788-792 (1985)
This report of a young but surprisingly tall young Homo erectus male raises many questions about our own African genesis, and the origins of that very human feature called 'childhood'. http://www.nature.com/nature/ancestor/pdf/316788.pdf

8) Cann, R. L., Stoneking, M. & Wilson, A.
Mitochondrial DNA and human evolution
Nature 325, 31-36 (1987) A molecular bombshell that traces the human story by comparing mitochondrial DNA frrom modern humans. The message is clear - all modern humans have their roots in Africa, and surprisingly recently, between 100,000 and 200,000 years ago. http://www.nature.com/nature/ancestor/pdf/325031.pdf

9) Arsuaga, J.-L., Martínez, I., Gracia, A., Carretero, J.-M. & Carbonell, A.
Three new human skulls from the Sima de los Huesos Middle Pleistocene site in Sierra de Atapuerca, Spain
Nature 362, 534-537 (1993) The 'Pit of Bones' near Burgos in Spain is a treasure-trove of information on the first Europeans. At around 300,000 years old, these skulls may have been close to the ancestry of the classic caveman, Neanderthal Man. http://www.nature.com/nature/ancestor/pdf/362534.pdf

10) White, T. D., Suwa, G. and Asfaw, B.
Australopithecus ramidus, a new species of early hominid from Aramis, Ethiopia
Nature 371, 306-312 (1994) Now known as Ardipithecus ramidus, this extremely primitive creature was the first member of the human family known from beyond 4 million years ago. Still controversial, its affinities with the new finds from Chad have yet to be investigated. http://www.nature.com/nature/ancestor/pdf/371306.pdf

[Evolution]

technorati tags: piltdown+man, human+origins, fossil, olduvai+gorge, louis+leakey, tanzania, richard+leakey, lucy, johanson, footprints, lake+turkana, dna, burgos, neanderthal, chad, evolution

An Error In Associating Lamarck With 'Adaptive Mutations'?

2006-02-24T19:52:00.000Z

An Error In Associating Lamarck With 'Adaptive Mutations'?

Words frozen in time should be differentiated from those carved in stone:

In 1640 Galileo Galilei wrote a letter to Fortunio Liceti in which he said:

Lamarck, for example, published his "Zoological Philosophy" in 1809 and is today popularly associated with "the inheritance of acquired characteristics" whereby organisms somehow direct their own evolution. On the basis of Galileo's words, however, it could be argued that had Lamarck been alive in the 1890s, over thirty years after publication of Darwin's "On the Origin of Species", his views would have progressed from the moment in time in which they had been caught.

Pure speculation of course, but if sufficient to illustrate a general principle (that "words frozen in time should be differentiated from those carved in stone"), then the inappropriateness of interpreting new discoveries or proposals in 'Lamarckian terms' is readily apparent.

John Latter

--

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

technorati tags: galileo, lamarck, zoological, philosophy, origin, species, darwin, baldwin

Birds that make teeth (Press Release + Summary)

2006-02-23T09:30:00.000Z

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

One of the authors (John F. Fallon) sent me a copy of the full paper yesterday. His email address is at the link above. Contact me here if you have any difficulty.

John Latter

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

Books on Evolution from the Science and Evolution Bookshop: UK | US

(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

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

2006-02-22T22:26:00.000Z

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 Latter

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

technorati tags: junk, dna, evolutionary, protein, organism, survival, nature, genes, fruit+fly, natural+selection, adaptive, evolution, genome, environment, eukaryotic

Darwinism's Rules of Reasoning: Phillip Johnson on Pierre Grasse

2006-02-21T21:03:00.000Z

From "Darwinism's Rules of Reasoning" (Chapter 1 of "Darwinism: Science or Philosophy") by Phillip Johnson:

"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. Grasse denied emphatically that mutation and selection have the power to create new complex organs or body plans, explaining that the intra-species variation that results from DNA copying errors is mere fluctuation, which never leads to any important innovation."

Full text at:

http://www.leaderu.com/orgs/fte/darwinism/chapter1.html

[For more on Grasse see: Grasse, Behe, and "Irreducible Complexity"]

technorati tags: darwinism, science, philosophy, dobzhansky, grasse, evolution, neo-Darwinism, transformation, reptiles, mammals, internal+factors, life, mutation, selection, DNA, body+plans, innovation, Phillip+Johnson

Grasse, Behe, and "Irreducible Complexity"

2006-02-21T00:19:00.000Z

Dr Pierre-Paul Grasse (editor of the 28-volume "Traite de Zoologie",
ex-president of the Academie des Sciences, etc.) is considered to
have been one of the most eminent of French zoologists.

I am currently* reading his "Evolution of Living Organisms: Evidence
for a New Theory of Transformation," (Academic Press: New York NY,
1977) with a view to summarizing the reasons why he should feel
that 'internal factors' are involved in evolution.

At the moment, however, I am quite intrigued by the following two
quotes:

"Life is an epiphenomenon arising from a COMPLEX, structural, and
autonomous system forming an object endowed with an IRREDUCIBLE
individuality" (my capitals) [p.172]

and:

"The system has become functional only when all its components
have come together and adjusted themselves to one another. The
Darwinian hypothesis compels us to postulate a preparatory period
during which selection acts upon something that does not,
physiologically speaking, yet exist. Under the necessary conditions
of the postulate, the action can only have been prophetic! Any
explanation ruling out the active intervention of the organism in the
acquisition of regulating systems may be regarded as inadequate.

To take as an evident truth the fact that the control mechanisms
attenuating or neutralizing the actions of the environment (these
are, let it be remembered, complex systems having several coordinated
elements) could have been assembled by successive and lucky strokes
of chance without the slightest need for the organism to play any
role whatsoever, is to sacrifice objective scientific analysis to a
wholly verbal magic trick" (Grasse's italics) [p.152]

I haven't read Michael Behe's "Darwin's Black Box: The Biochemical
Challenge to Evolution" but a TalkOrigins article [1] provides the
following quote:

"By irreducibly complex I mean a single system composed of
several well-matched, interacting parts that contribute to the basic
function, wherein the removal of any one of the parts causes the
system to effectively cease functioning. An irreducibly complex
system cannot be produced directly (that is, by continuously
improving the initial function, which continues to work by the same
mechanism) by slight, successive modifications of a precursor system,
because any precursor to an irreducibly complex system that is
missing a part is by definition nonfunctional. An irreducibly complex
biological system, if there is such a thing, would be a powerful
challenge to Darwinian evolution. (Behe's italics) [p.39]

This article describes irreducible complexity as "essentially a
rehash of the famously flawed watchmaker argument advanced by William
Paley at the start of the 19th century" and comments elsewhere liken
the concept to "The old 'chicken-and-egg' question". Even so, I can't
help wondering if Behe had been inspired by Grasse's words!

From a wider perspective I found it interesting that Grasse
was arguing the case for 'internal factors' while others are using
similar reasoning to argue for external ones..

John Latter

*Grasse, Behe, and "Irreducible Complexity" first appeared here and was written in 2002.

[1] Irreducible Complexity and Michael Behe:
http://www.talkorigins.org/faqs/behe.html

[Grassé]

technorati tags: grasse, grassé, evolution, organisms, new+theory,
transformation, new+york, academic+press, internal+factors,
irreducible+complexity, behe, darwinian, hypothesis, watchmaker,
paley, john+latter

To See or Not to See: Evolution of Eye Degeneration in Mexican Blind Cavefish

2006-02-19T17:13:00.000Z

To See or Not to See: Evolution of Eye Degeneration in Mexican Blind Cavefish [Jeffery et al., Integrative and Comparative Biology Vol 43 #4, '03]

Synopsis:

The evolutionary mechanisms responsible for the loss of eyesin cave animals are still unresolved. Hypotheses invoking naturalselection or neutral mutation have been advanced to explaineye regression. Here we describe comparative molecular and developmentalstudies in the teleost Astyanax mexicanus that shed new lighton this problem. A. mexicanus is a single species consistingof a sighted surface-dwelling form (surface fish) and many blindcave-dwelling forms (cavefish) from different caves. We firstreview the evolutionary relationships of Astyanax cavefish populationsand conclude that eye degeneration may have evolved multipletimes. We then compare the mechanisms of eye degeneration indifferent cavefish populations. We describe the results of experimentsshowing that programmed cell death of the lens plays a key rolein controlling eye degeneration in these cavefish populations.We also show that Pax6 gene expression and fate determinationin the optic primordia are modified similarly in different cavefishpopulations, probably due to hyperactive midline signaling.We discuss the contributions of the comparative developmentalapproach toward resolving the evolutionary mechanisms of eyedegeneration. A new hypothesis is presented in which both naturalselection and neutral mutation are proposed to have roles incavefish eye degeneration.

Full text at:

http://icb.oxfordjournals.org/cgi/content/full/43/4/531

and:

http://icb.oxfordjournals.org/cgi/reprint/43/4/531

A couple of news stories regarding some of Jeffrey's earlier work:

Blind fish reveal eye growth factors (July '00)
http://www.abc.net.au/science/news/stories/s156871.htm

UM Scientists Find Clue to Blindness in Cavefish (Oct '04)
http://www.newsdesk.umd.edu/scitech/release.cfm?ArticleID=978

[apoptosis, teleost, genes, biology]

technorati tags: jeffery, evolution, eye+degeneration, eye+regression, mexican, blind, cavefish, evolutionary+mechanisms, hypothesis, natural+selection, neutral+mutation, molecular, developmental, teleost, astyanax+mexicanus, species, cave-dwelling, apoptosis, pax6, genes, biology

Origination of Organismal Form: The Forgotten Cause In Evolutionary Theory

2006-02-19T12:17:00.000Z

Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology (Gerd B. Müller (Muller) and Stuart Newman)

Chapter 1:

Origination of Organismal Form: The Forgotten Cause In Evolutionary Theory

Evolutionary biology arose from the age-old desire to understand the origin and the diver-sification of organismal forms. During the past 150 years, the question of how these two as-pects of evolution are causally realized has become a field of scientific inquiry, and the standard answer, encapsulated in a central tenet of Darwinism, is by "variation of traits"and "natural selection." The modern version of this tenet holds that the continued modification and inheritance of a basic genetic tool kit for the regulation of developmental processes, directed by mechanisms acting at the population level, has generated the panoply of organismal body plans encountered in nature. This notion is superimposed on a sophisticated, mathematically based population genetics, which became the dominant mode of evolutionary biology in the second half of the twentieth century. As a consequence, much of present-day evolutionary theory is concerned with formal accounts of quantitative variation and diversification. Other major branches of evolutionary biology have concentrated on patterns of evolution, ecological factors, and, increasingly, on the associated molecular changes. Indeed, the concern with the "gene" has overwhelmed all other aspects, and evolutionary biology today has become almost synonymous with evolutionary genetics.

These developments have edged the field farther and farther away from the second initial theme: the origin of organismal form and structure. The question of why and how certain forms appear in organismal evolution addresses not what is being maintained (and quantitatively varied) but rather what is being generated in a qualitative sense. This causal question concerning the specific generative mechanisms that underlie the origin and innovation of phenotypic characters is probably best embodied in the term origination, which will be used in this sense throughout this volume.

Full text of Chapter 1 available at:

http://homepage.univie.ac.at/gerhard.mueller/pdfs/2003Origin.pdf

Amazon.com link:

http://www.amazon.com/gp/product/0262134195/002-9464151-6378437?v=glance&n=283155

technorati tags: gerd, müller, muller, stuart+newman, origin, organisms, form, evolutionary+theory, evolution, biology, darwinism, central+tenet, genetics, variation, ecological, molecular, gene, amazon.com, phenotypic

Lamarck's "ZOOLOGICAL PHILOSOPHY" Part 1

2006-02-18T18:30:00.000Z

TABLE OF CONTENTS:

Foreword

Preliminary Discourse

PART ONE
Considerations of the Natural History of Animals, Their Characteristics, Their Interrelationships, Their Organic Structure, Their Distribution, Their Classification and Their Species

Chapter One
On the Role of Art in the Productions of Nature

Chapter Two
The Importance of Considering Affinities

Chapter Three
Concerning Speciation in Living Things and The Idea We Should Attach to This Word

Chapter Four
General Observations on Animals

Chapter Five
On the Present State of the Distribution and Classification of Animals

Chapter Six
The Degradation and Simplification in Organic Structure from One Extreme to the Other of the Chain of Animal Life, from the Most Complex to the Simplest

Chapter Seven
Concerning the Influence of Circumstances on the Actions and Habits of Animals, and the Influence of the Actions and Habits of these Living Bodies As Causes Which Modify Their Organic Structure and Their Parts

Chapter Eight
Concerning the Natural Order of Animals and the Arrangement Which Must Have Led to Their General Distribution to Make it Conform to the Very Order of Nature

[Lamarckian, Zoological Philosophy]

technorati tags: lamarck, lamarckian, zoological+philosophy, evolution, animals, classification, nature

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

2006-02-17T08:45:00.000Z

[King & Wilson, Science, Apr '75]

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

(No Abstract Available: Related Terms include Mary-Claire King, Wilson, DNA and Genetics, the Genome, Human and Chimpanzee)

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

Info wanted on two intriguing 'Lamarckian' experiments

2006-02-16T10:27:00.000Z

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 on these pages of Amazon.com and Amazon.co.uk

[Related terms: Lamarck and Lamarckian]

John Latter

*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, schroeder, griffiths, john+latter

Confessions of a Darwinist (VQR)

2006-02-15T09:21:00.000Z

Niles Eldredge (Virginia Quarterly Review, VQR)

[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

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

Gene Regulatory Networks and the Evolution of Animal Body Plans

2006-02-14T09:38:00.000Z

[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, evolution

Viva Lamarck: A Brief History of the Inheritance of Acquired Characteristics

2006-02-14T09:04:00.000Z

[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
characteristics. 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, evolution

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

2006-02-13T11:07:00.000Z

[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

"A New Factor In Evolution" by J. Mark Baldwin

2006-02-12T08:57:00.000Z

J. Mark Baldwin's Original Paper (published in 1896) in which be
proposed the concept known today as "The Baldwin Effect":

Abstract:

"In several recent publications I have developed, from different
points of view, some considerations which tend to bring out a certain
influence at work in organic evolution which I venture to call "a new
factor". I give below the list of references [1] to these
publications and shall refer to them by number as this paper
proceeds. The object of the present paper is to gather into one
sketch an outline of the view of the process of development which
these different publications have hinged upon.

The problems involved in a theory of organic development may be
gathered up under three great heads: Ontogeny, Phylogeny, Heredity.
The general consideration, the "factor" which I propose to bring
out, is operative in the first instance, in the field of Ontogeny; I
shall consequently speak first of the problem of Ontogeny, then of
that of Phylogeny, in so far as the topic dealt with makes it
necessary, then of that of Heredity, under the same limitation, and
finally, give some definitions and conclusions."

technorati tags: a+new+factor+in+evolution, j.+mark+baldwin, baldwin+effect, ontogeny, phylogeny, heredity, evolution

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

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

Biology inspires perceptive machines (PhysOrg]

2006-02-11T07:17:00.000Z

[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

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

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

2006-02-10T07:39:00.000Z

[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

technorati tags: evolution, intelligent+design, harvard, dodo, natural+history

[PP] Evolution: The Horse Whisperer, Richard Dawkins, and Danish Cartoons

2006-02-09T12:53:00.000Z

Brief notes from an evolutionary perspective:

In March 2005 'The Guardian' newspaper (UK) printed "The Horse Whisperer is called in to tame children" and said:

"Monty Roberts, the original whisperer who inspired the film and has tamed more than 70,000 wild horses, flew to Britain last week to hold a three-day workshop for Global Education Management Systems (Gems), one of the biggest operators of independent schools in the UK."

Further into the article Monty is quoted as saying:

"It takes a leap of faith because here's a cowboy with ways of working with horses, then he starts talking about children,' he said. 'It's a difficult leap for some people, but not for me.

'I am not for a moment suggesting that animals and humans are the same but, psychologically speaking, their behavioural patterns have more similarities than they have differences."

Why are there more "similarities than differences" - and how does Monty know this?

Monty Roberts has repeatedly spoken of the violence he was subjected to as a child and how his father employed the same brutality against horses. So far so good, but that's only the beginning of the answer - after all, people are people and horses, of course, are horses:

"The neurologist Paul MacLean has proposed that our skull holds not one brain, but three, each representing a distinct evolutionary stratum that has formed upon the older layer before it, like an archaeological site. He calls it the "triune brain." MacLean, now the director of the Laboratory of Brain Evolution and Behaviour in Poolesville, Maryland, says that three brains operate like "three interconnected biological computers, [each] with its own special intelligence, its own subjectivity, its own sense of time and space and its own memory". He refers to these three brains as the neocortex or neo-mammalian brain, the limbic or paleo-mammalian system, and the reptilian brain, the brainstem and cerebellum (see above diagram). Each of the three brains is connected by nerves to the other two, but each seems to operate as its own brain system with distinct capacities."
(From The Triune Brain)

As a rule of thumb, the disruption to internal integrity known as psychological trauma (not to be confused with the popular conception of trauma - see Note 1) gives every appearance of occurring somewhere within the limbic system. An indication of how trauma has been part of Man's heritage since 'before there were words' and the probable basis of Monty's non-intellectual empathy with other animals who have sustained a similar injury.

Like the background radiation from the 'Big Bang', psychological trauma pervades every aspect of human society and its characteristic signature can be found in many cultural institutions - and for the purpose of these notes, specifically Religion.

Scotland's Sunday Herald recently said:

CONTROVERSIAL scientist Richard Dawkins will assert tomorrow evening that religion is a 'virus' that amounts to child abuse.

The new two-part series, to be shown on Channel 4 (UK), will compare Moses to Hitler and claim that God is racist. It will also argue that religion is a 'backward belief system' responsible for terrorism.

The controversial films, which were produced by IWC creative director Alan Clements and written by Dawkins, are a polemic against faith and a stout defence of science.

and:

More controversially, he states 'sectarian religious schools' have been 'deeply damaging to generations of children. 'It's time to question the abuse of childhood innocence with superstitious ideas of hellfire and damnation ,' he says. 'Isn't it weird the way we automatically label a tiny child with its parents' religion?'

While disagreeing with Dawkin's perception of how evolutionary changes occur, and aware of the fact that a 'deeply' held belief in aetheism/science can be the other side of the coin to fear of believing in a God of psychological origin (rather than any 'other kind' - if such exist), the above observations hold an uncomfortable truth.

From Channel 4's own page on the program:

In addition, though religions preach morality, peace and hope, in fact, says Dawkins, they bring intolerance, violence and destruction.

Again from a psychological perspective: 'morality' is needed to compensate for the ongoing presence of maladjustment to a compounded trauma within individuals so that they can then co-exist as a group, 'peace' means suppression and internal 'soothing' of the wound (hence the 'sing-song' voice often employed during church services), and 'hope' promises a future free from internal reactions with one's own wound (often caused by other people outwardly expressing the presence of theirs). Unfortunately the hope proferred can only be realized in some kind of 'afterlife'.

In short, and at best, Religion can be seen as an archaic form of therapy. At worst, the surface veneer may easily be broken down and lead to events like those which promped the writing of these notes: people have died over the publication of cartoons!

It is very telling that no God does its own killing...

There is more at issue with Islam here than with the cartoons published in Jyllands-Posten or with the principle of 'freedom of speech'. I for one feel an obligation to those people, who in the Society I live in, once suffered during the process of separating Church from State - the ugliness of the current pedophile scandal in the Roman Catholic Church is but an echo of how much worse things once were.

Finally, and in a related vein, an item from today's Daily Telegraph (UK):

Church offers apology for its role in slavery

Two hundred years after Anglican reformers helped to abolish the slave trade, the Church of England has apologised for profiting from it.

Last night the General Synod acknowledged complicity in the trade after hearing that the Church had run a slave plantation in the West Indies and that individual bishops had owned hundreds of slaves.

It voted unanimously to apologise to the descendents of the slaves after an emotional debate in which the Archbishop of Canterbury, Dr Rowan Williams, urged the Church to share the "shame and sinfulness of our predecessors".

John Latter

Note 1:
Trauma in other Species
Creating Trauma in Infants
Trauma - A Simple Internal Model
[back to text]

Technorati tags: horse+whisperer, evolution, richard+dawkins, monty+roberts, danish+cartoons, religion, trauma, triune, brain, abuse, child, god, society, roman+catholic+church, morality, peace, hope, Islam, freedom+of+speech, rowan williams, slavery, archbishop, synod, religion, Jyllands-Posten, john+latter, jorolat

A 21st Century View of evolution

2006-02-09T09:06:00.000Z

ABSTRACT

Physicists question whether there are "universals" in biology. One reason is that the prevailing theory of biological evolution postulates a random walk to each new adaptation. In the last 50 years, molecular genetics has revealed features of DNA sequence organization, protein structure and cellular processes of genetic change that suggest evolution by natural genetic engineering. Genomes are hierarchically organized as systems assembled from DNA modules, which themselves generally constitute systems at lower levels. Each genome is formatted and integrated by sequence elements that do not code for proteins. These formatting elements constitute codons in multiple genetic codes for distinct functions such as transcription, replication, DNA compaction and genome distribution to daughter cells. Consequently, the genome has a computational system architecture. Proteins are systems composed of functionally distinct domains connected in polypeptide chains. Whole-genome sequencing indicates that rearrangement of genetic modules plus duplication and reuse of existing genomic systems are fundamental events in evolution. Studies of genetic change show that cells possess mobile genetic elements and other natural genetic engineering activities to carry out the necessary DNA reorganizations. Natural genetic engineering functions are sensitive to biological inputs, and their non-random operations help explain how novel system architectures can arise in evolution.

Technorati tags: genome system architecture, signal transduction, cellular computation, natural genetic engineering, mobile genetic elements,dna, biology, evolution, shapiro

The Spandrels of San Marco and the Panglossian Paradigm

2006-02-08T09:17:00.000Z

"The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme"

STEPHEN JAY GOULD AND RICHARD C. LEWONTIN

REPUBLISHED FROM THE ORIGINAL WITH THE KIND PERMISSION OF THE ROYAL SOCIETY OF LONDON: GOULD, S. J. AND LEWONTIN, R. C., 'THE SPANDRELS OF SAN MARCO AND THE PANGLOSSIAN PARADIGM: A CRITIQUE OF THE ADAPTATIONIST PROGRAMME,' PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON, SERIES B, VOL. 205, NO. 1161 (1979), PP. 581-598.

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 baupl�ne 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."

Technorati tags: spandrels, gould, lewontin, evolution, adaptationist, natural+selection, trait, allometry, pleiotropy, developmental, nonadaptive, epiphenomenon

The innovation triad: an EvoDevo agenda (Journal of Experimental Zoology)

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

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

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

A Model of an Internal Evolutionary Mechanism

2006-02-05T11:39:00.000Z

Evolution, The Evolutionary Mechanism, Psychology

The above link will take you to my main website where you'll find articles on Psychology, Social Psychology, various evolutionary topics, archives (such as Lamark's "Zoological Philosophy") and sundry other stuff.

If you want to go directly to the "Model of an Internal Evolutionary Mechanism (based on an extension to homeostasis) linking Adaptive Mutations to the Baldwin Effect" page then click here.

The model is derived from 'anomalies' found below the level at which psychological trauma occurs: this is different to the popular conception of trauma - see Trauma: A Simple Internal Model

It has been several years since the pages were published on the web and it wasn't until about 6 weeks ago that I suddenly found I now have time to take up the reins again! At the moment, I'm busily researching a rewrite of the proposal (although the core concept will obviously be unchanged) and I thought that creating a blog would make the process more enjoyable - providing anyone reads it of course... :)

In addition to occasional personal posts this blog also contains auto-added entries (all with 'evomech' in the title) from the Evolution: Where Darwin meets Lamarck? discussion forum.

Don't be deterred if the papers from the forum look too technical (a lot of them make my eyes boggle), there's plenty of other stuff in the message archives - just pick and choose the bits you like!

Researching the possibility of an internal mechanism - particularly when its non-intellect based and therefore testable - necessarily raises the question "If an internal mechanism exists, then why hasn't it been found before?".

The subjective answer is because of 'cultural conditioning'. Consequently, the posts I make to evomech are a combination of topics containing the 'homeostatic signature' that I'm looking for and those in which the exploration of natural realities appears to be in conflict with cultural conditioning - to illustrate the basic problem see An Error In Associating Lamarck With 'Adaptive Mutations'?

Any feedback would be welcome, you can add a blog comment to this post, visit the main web site's Guestbook, or email direct

I'm out of time for now but one final (deletes "plea for help") point: As an independent researcher my resources are very limited and I often have difficulty in obtaining papers (for example, see Wanted: 'Obscure' 1889 Paper on Trilobite Eyes & The Fibonacci Series) - if you can help then please do!

John Latter

technorati tags: evolution, lamarck, internal evolutionary mechanism, psychology, trauma, adaptive mutations, baldwin effect, homeostasis, trilobite, john+latter, jorolat

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

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

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

2006-02-04T06:57:00.000Z

[Richardson et al., Evolution and 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: here

John Latter / Jorolat

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

technorati tags: Internal+Evolutionary+Mechanism, john+latter, jorolat, proximodistal, evolution, development, axis, developing, limb, evolutionary, morphology, animals, dolphins, plesiosaurs, hypotheses, domains, bud, processes, model, pleiotropy

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

Researchers evolve a complex genetic trait in the laboratory

2006-02-03T08:10:00.000Z

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').

John

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

Wanted: 'Obscure' 1889 Paper on Trilobite Eyes & The Fibonacci Series

2006-02-02T20:02:00.000Z

Can anyone help me find the 'obscure' paper by JM Clarke that Niles Eldredge refers to on page 64 of "Time Frames"? A scan of the page is available here:

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

In fact I would be grateful for any information regarding the appearance of the fibonacci series in the lens arrangement of trilobite eyes!

If you know the citation (or better still, have a copy) then please email me or post here.

NB This isn't the paper I'm looking for:

CLARKE, J. M. 1889. The structure and development of the visual area in the trilobite Phacops rana Green. Journal of Morphology, 2:253270.)

Finally, I emailed Niles Eldredge and he said "I've lost touch with it [the paper]--journal such as American Naturalist..". I don't have a subsciption to Jstor but someone did a search of American Naturalist on my behalf but couldn't find anything ('sigh').

John

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

technorati tags: trilobite, trilobite+eyes, time+frames, niles+eldredge, fibonacci, fibonacci+series, american+naturalist, jm+clarke, john+latter, jorolat

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 sciencethat 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

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

Evolution: Where Darwin meets Lamarck? Discussion Forum

2006-02-01T11:22:00.000Z

'Evolution - Where Darwin meets Lamarck?' places an emphasis on concepts and discoveries consistent with the possible existence of testable internal evolutionary mechanisms and alternative (non-creationist) explanations for 'problem areas' of conventional evolutionary theory.

In their paper "The Spandrels of San Marco and the Panglossian Paradigm" Gould and Lewontin briefly described the European concept of Bauplan ('bodyplan') which, in its 'strong' form, speculates:

"But the important steps of evolution, the construction of the Bauplan itself and the transition between Baupläne, must involve some other unknown, and perhaps 'internal,' mechanism."

An internal mechanism cannot be 'mystical' simply because, if one exists, then it would be testable. This suggests the concept ought to evoke no greater uncertainty than appropriate to the words of Einstein:

"If we knew what we were doing, we wouldn't call it research, would we?".

technorati tags: Baupläne, bauplan, darwin, lamarck, forum, paradigm, john+latter, jorolat