Saturday, March 11, 2006

 

[evomech] Separation of Man and Ape Down to Gene Expression (PR + Article)

Contents:

1) Separation of Man and Ape Down to Gene Expression


Humans and chimpanzees have in common more than 98 percent of DNA and 99 percent of genes. Yet, in looks and behavior we are very different from them. For more than 30 years--well before either the human or chimpanzee genome had been sequenced--scientists have speculated that this might be due to the way that the common genes express themselves rather than differences in the genes themselves. A new comparison published in Nature seems to prove that theory.

Full text at:

http://www.sciam.com/article.cfm?chanID=sa003&articleID=0005FB4D-6102-140F-A10283414B7F0000

2) Expression profiling in primates reveals a rapid evolution of human transcription factors

[Gilad et al, Nature, March '06]

Although it has been hypothesized for thirty years that many human adaptations are likely to be due to changes in gene regulation1, almost nothing is known about the modes of natural selection acting on regulation in primates. Here we identify a set of genes for which expression is evolving under natural selection. We use a new multi-species complementary DNA array to compare steady-state messenger RNA levels in liver tissues within and between humans, chimpanzees, orangutans and rhesus macaques. Using estimates from a linear mixed model, we identify a set of genes for which expression levels have remained constant across the entire phylogeny (approx70 million years), and are therefore likely to be under stabilizing selection. Among the top candidates are five genes with expression levels that have previously been shown to be altered in liver carcinoma. We also find a number of genes with similar expression levels among non-human primates but significantly elevated or reduced expression in the human lineage, features that point to the action of directional selection. Among the gene set with a human-specific increase in expression, there is an excess of transcription factors; the same is not true for genes with increased expression in chimpanzee.

Full text at:

http://www.nature.com/nature/journal/v440/n7081/full/nature04559.html

PDF:

http://www.nature.com/nature/journal/v440/n7081/pdf/nature04559.pdf

[Evolution] Contact me if you have any problems.

John Latter
-- 
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Friday, March 10, 2006

 

[evomech] Epigenetic vs. Genetic, a story of the evolution of the germline

[Lachmann & Sella, SFI Working Paper]

Abstract:

Differentiation of multicellular organisms is controlled by epigenetic markers transmitted through cell division. Many of the systems that encode these markers exist also in unicellulars, but in unicellulars these systems do not control differentiation. Thus during the evolution of multicellularity, epigenetic inheritance systems were exapted for their current use in differentiation. During this transition there must have been stages at which epigenetic information passed between generations to an even larger extent than it does now. We show that this can lead to the evolution of cells that do not contribute to the progeny of the organism, and thus to a germline-soma distinction. This hints that an intrinsic instability during a transition from unicellulars to multicellulars may be the reason wide spread of the evolution of germ line.

Full text at:

http://www.santafe.edu/sfi/publications/Working-Papers/03-02-012.pdf

John Latter

-- 
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Thursday, March 09, 2006

 

[evomech] Re: Complexity in Biological Signaling Systems (Science)

--- In evomech@yahoogroups.com, "John Latter" <jorolat@...> wrote:
>
> [Weng, Bhalla, & Iyengar , Science, Apr '99]
>
>
> Introduction:
>
> "Biological signaling pathways interact with one another to form
> complex networks. Complexity arises from the large number of
> components, many with isoforms that have partially overlapping
> functions; from the connections among components; and from the
> spatial relationship between components. The origins of the complex
> behavior of signaling networks and analytical approaches to deal with
> the emergent complexity are discussed here."
>
> Full text (PDF file) at:
>
> http://www.csc.liv.ac.uk/~m1pk/Projects/bhalla%202.pdf
> (begins halfway down the first page)
>
>
> Jorolat

Now available at:

http://www.ncbs.res.in/~faculty/upi_file/upi_papers/weng_bhalla_iyengar_Science1999.pdf

John Latter

Model of an Internal Evolutionary Mechanism:
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Wednesday, March 08, 2006

 

[evomech] The inheritance of features (Biology and Philosophy)

Mameli, Biology and Philosophy (2005) 20:365–399

Abstract:


Since the discovery of the double helical structure of DNA, the standard account of the inheritance of features has been in terms of DNA-copying and DNA-transmission. This theory is just a version of the old theory according to which the inheritance of features is explained by the transfer at conception of some developmentally privileged material from parents to offspring. This paper does the following things: (1) it explains what the inheritance of features is; (2) it explains how the DNA-centric theory emerged; (3) it clarifies the relation between the DNA-centric theory and the 'unfolding' theory of development; (4) it argues that (given what we now know about developmental processes and genetic activity) the DNA-centric theory should be abandoned in favour of a pluralistic (but not holistic) theory of the inheritance of features. According to this pluralistic theory, the reliable reoccurrence of phenotypes must be explained by appealing not only to processes responsible for the reliable reoccurrence of genetic developmental factors but also to processes responsible for the reliable reoccurrence (or persistence) of nongenetic environmental factors.

Full text at:

http://www.phil.cam.ac.uk/~gmm32/MAMELI_INHERITANCE_2005.pdf

John Latter
-- 
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Tuesday, March 07, 2006

 

[evomech] [News] Stowers Scientists Demonstrate Mechanism of Vertebral Formation

Kansas City, Mo. (March 6, 2006) - Jacqueline Kim Dale, Ph.D., formerly a Senior Research Associate at the Stowers Institute for Medical Research, and Olivier Pourquie, Ph.D., Stowers Institute Investigator and an investigator with the Howard Hughes Medical Institute, have demonstrated that the long-studied family of transcription factors called Snail is expressed in a cyclic fashion during the formation of the vertebral precursors in the mouse and chick embryo.

The findings, which were published in the March 7 issue of Developmental Cell, indicate that the genes governing many cellular properties are downstream of the segmentation clock, the mechanism that controls the formation of the vertebral column.

Full text at:

http://www.stowers-institute.org/WhatsNew/pr2006/PR030606.asp

John Latter

Model of an Internal Evolutionary Mechanism:
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Monday, March 06, 2006

 

[evomech] Evolution as context-driven actualization of potential: Toward an interdisciplinary theory of change of state

Gabora, L. & Aerts, D. (2005). Evolution as context-driven actualization of potential: Toward an interdisciplinary theory of change of state. Interdisciplinary Science Reviews, 30(1), 69-88.

Abstract:

It is increasingly evident that there is more to biological evolution than natural selection; moreover, the concept of evolution is not limited to biology. We propose an integrative framework for characterizing how entities evolve, in which evolution is viewed as a process of context-driven actualization of potential (CAP). Processes of change differ according to the degree of nondeterminism, and the degree to which they are sensitive to, internalize, and depend upon a particular context. The approach enables us to embed phenomena across disciplines into a broad conceptual framework. We give examples of insights into physics, biology, culture and cognition that derive from this unifying framework.

Full text at:

http://www.vub.ac.be/CLEA/liane/papers/cap.htm

John Latter


Model of an Internal Evolutionary Mechanism:
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Sunday, March 05, 2006

 

[evomech] In the News: More info on "'Jurassic Beaver' find stuns experts"

Anyone who read the recent 'Jurassic Beaver' find stuns experts news report might be interested in the following:
Perspective:

Early Mammalian Evolutionary Experiments
Thomas Martin*

Mammals of the Mesozoic era (248 to 65 million years ago) generally are considered to be primitive, shrew-like creatures living in the shadow of the dinosaurs (1). Only after the extinction of the dinosaurs at the end of the Cretaceous era (144 to 65 million years ago) did they have a chance to explore a greater variety of ecological niches. During the adaptive radiation that began about 65 million years ago, mammals were able to invade all kinds of terrestrial environments, even the aquatic and aerial realms. Pushing back the mammalian conquest of the waters by more than 100 million years, Ji et al. (2) report on page 1123 of this issue a Middle Jurassic, 164-million-year-old skeleton with a beaverlike tail and seal-like teeth perfectly adapted for an aquatic lifestyle.

and
Research Article the above Perspective refers to:

A Swimming Mammaliaform from the Middle Jurassic and Ecomorphological Diversification of Early Mammals
Qiang Ji,1,3 Zhe-Xi Luo,2,1* Chong-Xi Yuan,3 Alan R. Tabrum2

A docodontan mammaliaform from the Middle Jurassic of China possesses swimming and burrowing skeletal adaptations and some dental features for aquatic feeding. It is the most primitive taxon in the mammalian lineage known to have fur and has a broad, flattened, partly scaly tail analogous to that of modern beavers. We infer that docodontans were semiaquatic, convergent to the modern platypus and many Cenozoic placentals. This fossil demonstrates that some mammaliaforms, or proximal relatives to modern mammals, developed diverse locomotory and feeding adaptations and were ecomorphologically different from the majority of generalized small terrestrial Mesozoic mammalian insectivores.
The links work OK but email me if you have any problems (I made a typo on the research article url and got "We've redesigned our Web site, and some Carnegie Museum of Natural History pages have gone the way of the dinosaurs."!)

John Latter

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