Saturday, February 11, 2006

 

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

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

Warren

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


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

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

Abstract:

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

Full text at:

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

John

Evolution: Where Darwin meets Lamarck? Discussion Forum:
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[evomech] Biology inspires perceptive machines (PhysOrg]

[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:
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Friday, February 10, 2006

 

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

Contents:

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

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

Full text at:

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

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

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

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

Full text at:

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

John

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

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

[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



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Thursday, February 09, 2006

 

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

Contents:

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

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

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

Full text at:

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

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

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

Full text at:

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

PDF versions:

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

John

Model of an Internal Evolutionary Mechanism

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


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Wednesday, February 08, 2006

 

[evomech] Define of Evolution 2

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

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

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

Warren


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

[McElheny, The Scientist, Feb '06]

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

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

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

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

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

Full text at:

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

John

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



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Tuesday, February 07, 2006

 

[evomech] A New Definiition of Biological Evolution

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

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

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

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

Warren

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

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

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

Cliff
www.zainar.com/evblog.html


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

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

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

Abstract:

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

Full text at:

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

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

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Monday, February 06, 2006

 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

John

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


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





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

Contents:

1)
Molecular Evolution (News Item)

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

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

Full text at:

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

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

[Pevzner & Tesler, PNAS, June '03]

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

Full text at:

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

John

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


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

[Alon, Science, Sept '03]

Viewpoint

Abstract:

This viewpoint comments on recent advances in understanding the design principles of biological networks. It highlights the surprising discovery of "good-engineering" principles in biochemical circuitry that evolved by random tinkering.

Full text at:

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

John


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


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

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

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

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

Cliff



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Sunday, February 05, 2006

 

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

On 05/02/2006 Cliff Lundberg wrote:
> No doubt a lot of details are being learned about ontogeny
> and its regulation, but something's lacking in the general
> concept,
> namely, what it is that is being regulated.


I feel some consideration should also be given to exactly 'what' is doing the regulating! For example, in the press release from:

Researchers evolve a complex genetic trait in the laboratory
http://groups.yahoo.com/group/evomech/message/511

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

Which part of the brain? its nature, characteristics? OMG - now I'll have to look up 'regulatory hierarchies' or something.. :)

John

What's being regulated
> is the expression of a primordial form, a form that has many
> parts, any of which may or may not be expressed. A form that's the
> basis for an arthropod, or a vertebrate, or some other segmented
> animal. Only something like this fits with those complex and
> characteristic types emerging gradually in development, yet
> suddenly in the fossil record. The basic forms are real,
> yet archetypal, and their origins as trains of identical segments
> were rapid processes of duplication. In a context where all
> changes are reductions and distortions, the progenitor is
> an archetype, underlying and explaining anatomy.
>
> Cliff
> www.zainar.com/evblog.html

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


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

No doubt a lot of details are being learned about ontogeny
and its regulation, but something's lacking in the general
concept, namely, what it is that is being regulated. What's being regulated
is the expression of a primordial form, a form that has many
parts, any of which may or may not be expressed. A form that's the
basis for an arthropod, or a vertebrate, or some other segmented
animal. Only something like this fits with those complex and
characteristic types emerging gradually in development, yet
suddenly in the fossil record. The basic forms are real,
yet archetypal, and their origins as trains of identical segments
were rapid processes of duplication. In a context where all
changes are reductions and distortions, the progenitor is
an archetype, underlying and explaining anatomy.

Cliff
www.zainar.com/evblog.html

----- Original Message -----
From: "John Latter" <jorolat@gmail.com>
To: <evomech@yahoogroups.com>
Sent: Sunday, February 05, 2006 12:27 AM
Subject: [evomech] The control of body size in insects (Dev Biol)


[Nijhout, Developmental Biology, Sept '03]

Abstract:

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

Full text at:

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

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

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

and a '98 paper:

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

John

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


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

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

[Nijhout, Developmental Biology, Sept '03]

Abstract:

Control mechanisms that regulate body size and tissue size have beensought at both the cellular and organismal level. Cell-level studieshave revealed much about the control of cell growth and cell division,and how these processes are regulated by nutrition. Insulin signalingis the key mediator between nutrition and the growth of internalorgans, such as imaginal disks, and is required for the normalproportional growth of the body and its various parts. Theinsulin-related peptides of insects do not appear to control growth 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


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

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

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

John

Palash Bhattacharya wrote:

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

Palash

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

Thank you for your kindness Palash :)

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

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

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

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

John


Palash Bhattacharya wrote:

>Here is a copy of the paper.

>Palash,

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



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