Evolution Research - Main Blog

New deadline for Yahoo Groups data request

2020-01-11T08:51:00.000+00:00

Hi Yahoo Member,

In recent weeks, we communicated the latest changes to Yahoo Groups and explained how to request a download of any content you've previously posted to the platform. Some Groups users asked us for more time, and in response to these requests, we have decided to extend the deadline. Groups users now have until Friday, January 31, 2020 at 11:59pm PST to submit a request for their data.

We have now taken down all user content from the Yahoo Groups website. However, we will continue to accept users' requests for their data until January 31, 2020, and will ensure these have been fulfilled prior to deleting the data.

For additional support, users can email YahooGroupsEscalations@verizonmedia.com and our team will troubleshoot any issues.

Best,
The Yahoo Groups team

Next Steps: The Evolution of Yahoo Groups (Final Notification)

2019-12-11T05:58:00.001+00:00

Dear Group Moderators and Members,

Last month we notified you of the changes coming to Yahoo Groups that better align with user habits, and today we are providing an update to guide you through the next steps of the transition. Yahoo Groups is not going away - but we are making adjustments to ultimately serve you better. We are amazed at the vibrant community you've created through Yahoo Groups and we want to make sure you feel supported as we introduce these changes.

The following changes were made since our last communication:

   •   Users can now only join a Yahoo Group through an invite or group request approval by the Group Moderator.
   •   New Groups can't be public. They can only be private (not listed in Groups directory, membership by invitation only) or restricted (listed in Groups directory, membership requests must be approved by a Group Moderator).
   •   Members must share all content via email, and can no longer upload or host new content on the Yahoo Groups website itself.

The following changes will be made on December 14, 2019:

   •   Public groups will no longer exist. All existing public Groups will become restricted Groups that require Group Moderator approval to join.
   •   Any content that was previously uploaded via the website will be removed.

If you would like to keep any of the content you've posted or stored within your Yahoo Group, please download it by December 14 by accessing the Groups Download Manager at this link. Once you provide your preferred email address, we will send you a confirmation of your download request and notify you once the download is complete.

You will receive a link to a downloadable zip file via email for each of your Groups organized into a separate folder. Download time varies depending on the amount of information and file size.

If your download request is made by 11:59pm PST on Saturday, December 14, 2019, your content will not be deleted until your download is complete. We are unable to accommodate any download requests made after this deadline.

This is the final reminder to download your content. You can find additional information about the upcoming changes here.

We have worked extensively with our customer support team to develop recommendations for tools that can help you with any download issues. See help article here.

We have watched the evolution of Yahoo Groups with awe, as we grew to a community of millions with over 10 million Groups. Every day, we witness the power of community and shared passions, and our mission is to provide a platform for the strong connections people make with each other around their interests.

We thank you for being part of the Yahoo Groups community and look forward to continuing to provide ways for you to connect with one another about your shared interests and passions.

Sincerely,
The Groups Team

Yahoo Groups - Upcoming Product Changes to Yahoo Groups

2019-11-08T16:19:00.001+00:00

Dear Group Moderators and Members,

Thank you for your commitment to Yahoo and for helping us define the power of digital communities. Eighteen years ago, we combined the functionality of a site called eGroups.com with a precursor community platform called Yahoo Clubs to launch Yahoo Groups. Since then, you and millions of others have helped prove our hypothesis, by creating and joining more than 10 Million groups.

A lot has changed about the Internet since 2001, including the ways most people now use Yahoo Groups. Today, most Yahoo Groups activity happens in your email inbox, not on the bulletin boards where Yahoo Groups started in the pre-smartphone age. Increasingly, people want content and connections coming directly to them, and this is why we continue to invest in Yahoo Mail -- including the recent launch of a new Yahoo Mail app that is currently the highest-rated email app in the App Store and Google Play.

So, as our users' habits have evolved, we have begun the process of evolving our approach to help active Yahoo Groups thrive and migrate to our email platform. To help you plan for these changes, below is the schedule of how this transition will happen.

Beginning October 28, 2019:

Users will be able to join a Yahoo Group only through an invite from the Group Moderator or by submitting a request to join a Group, which requires approval by the Group Moderator.
Since we are moving Group communication from posting on message boards to email distribution, uploading and hosting of new content will also be disabled on the Yahoo Groups website.

Beginning December 14, 2019:

All Groups will be made private and any content that was previously uploaded via the website will be removed. We believe privacy is critical and made this decision to better align with our overall principles.
If you would like to keep any of the content you've posted or stored in the past within your Yahoo Group, please download it by December 14 by accessing this link.

As these dates get closer, we will send follow-up reminders. More information about the upcoming changes can be found here.

While this evolution of Yahoo Groups is inspired by how we see the platform being used today, we know change can be difficult. Here are a few important facts as we make this transition:

1. Yahoo Groups is not going away - We know that our users are deeply passionate about connecting around shared interests, and we are evolving Groups to better align with how you use it today.

2. New groups can still be formed - Users can continue to connect with others around their common bonds and interests. From animal rescues to sporting and activity groups, civic organizations to local PTAs, members of our Yahoo Groups will remain connected and able to share their activities and interests. All of the content that you have shared previously on the website, can continue to be shared via email.

We know that Yahoo Groups is an important online extension of your real-life group of friends, interests and communities, and we are committed to supporting communities that rely on Yahoo Groups. Thanks for coming along with us this far. We look forward to seeing where the technology -- and you -- take us in the decades to come.

Sincerely,
The Groups Team

Body Size, Performance and Fitness in Galapagos Marine Iguanas

2007-01-16T11:20:00.000+00:00

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

Martin Wikelski and L. Michael Romero

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

2006-12-13T23:04:00.000+00:00

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

2006-11-26T19:46:00.000+00:00

[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

2006-11-14T20:24:00.000+00:00

[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

2006-03-23T09:53:00.000+00:00

"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

2006-03-22T18:13:00.000+00:00

[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

2006-03-19T17:29:00.000+00:00

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)

2006-03-18T14:26:00.000+00:00

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)

2006-03-17T09:09:00.000+00:00

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

2006-03-16T08:11:00.000+00:00

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

2006-03-15T12:03:00.000+00:00

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)

2006-03-14T14:51:00.000+00:00

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