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Evolution mechanism: a small difference

March 13, 2006

Genetic Evolution of Scientific Terms

25 July 2007

A. The "scientific" term 'de novo' is scientifically a de novo term:

1) Merriam-Webster Online: de novo = over again, anew <a case tried de novo>

2) First evolutionary step:

http://ghr.nlm.nih.gov/ghr/glossary/denovomutation

No 'de novo gene', but 'de novo mutation' = An alteration in a gene that is present for the first time in one family member as a result of a mutation in a germ cell (egg or sperm) of one of the parents or in the fertilized egg itself.

B. Next step, de novo genes:

1) Cornell Univ, Chronicle Online, July 23, 2007

"Fruit fly gene from out of nowhere may change ideas about how new genes are formed, researchers report"

http://www.news.cornell.edu/stories/July07…olution.kr.html

And early evidence indicates that the new gene is functional (as opposed to being nonfunctional "junk" DNA) and is likely to express a protein involved in late stages of sperm cell development (spermatogenesis). This finding is consistent with work of other scientists who are discovering that many of the most recently formed functional genes in any species also are expressed in male testes and appear related to spermatogenesis.

"This is a de novo — out of nowhere — gene," said Hsiao-Pei Yang, a senior research associate in Cornell's Department of Molecular Biology and Genetics and senior author of a paper published in the July 6 2007 issue…

2) Genetics, April 15, 2007 and Genetics, Vol. 176, 1131-1137, June 2007

http://www.genetics.org/cgi/content/abstract/176/2/1131

"Evidence for de Novo Evolution* of Testis-Expressed Genes in the Drosophila yakuba/Drosophila erecta Clade

The mutational origin and subsequent evolution of de novo genes, which are hypothesized to be genes of recent origin that are not obviously related to ancestral coding sequence, are poorly understood. However, accumulating evidence suggests that such genes may often function in male reproduction. Here we use testis-derived expressed sequence tags (ESTs) from Drosophila yakuba to identify genes that have likely arisen either in D. yakuba or in the D. yakuba/D. erecta ancestor. We found several such genes, which show testis-biased expression and are often X-linked. Comparative data indicate that three of these genes have very short open reading frames, which suggests the possibility that a significant number of testis-biased de novo genes in the D. yakuba/D. erecta clade may be noncoding RNA genes. These data, along with previously published data from D. melanogaster, support the idea that many de novo Drosophila genes function in male reproduction and that a small region of the X chromosome in the melanogaster subgroup may be a hotspot for the evolution of novel testis-biased genes."

* This is an accidental, non-intended correct 'non-scientific' application of the term de novo…

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Feb 11, 2005 Dov, in biologicalEvolution forum

In a recent browsing through an article on human/chimp genomes in Science, Vol 302, Issue 5652, 1876-1877,12 December 2003 I was shocked to read a sentence ( I placed it between > <) in the following abstract written by the Science reporter :

"Human and chimpanzee genomes are thought to be more than 98% identical. What is different between the two, > and how have these differences influenced the evolution of each species? < Clark et al. (p. 1960; see the news story by Pennisi) compared the sequence of more than 7000 genes from the common chimpanzee with their homologs in humans and mouse to identify genes that are under positive or adaptive evolutionary selection. Organizing these genes into pathways and clusters of genes related by function suggests that changes to particular physiological processes, such as hearing, olfaction, and protein catabolism, have occurred along the human lineage since the split from the common ancestor with chimpanzee."

Before proceeding to the text of the article I checked the abstract written by the authors and was relieved at their presentation:

"This…approach revealed an informative set of genes with significantly different patterns of substitution on the human lineage compared with the chimpanzee and mouse lineages. Partitions of genes into inferred biological classes identified accelerated evolution in several functional classes, including olfaction and nuclear transport…suggesting adaptive physiological differences between chimps and humans…"

A small difference…

end.DH

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PS 09-22-2006, Forum Hypo, Non-genetic Inheritance

Turtle : effects on progeny… what goes on during gestation has an impact…

Dov:

Of course, not only during gestation and not only on fetus and not only on humans… on all organisms and at all times…an organism is continuously effected by its surroundings, senses and responds by various feedbacks.

And especially humans, also grown-ups (now put your cup-o-coffee down!):

Wife to husband "you know", she says "when I married you you looked like a young Greek God" says she "now look at you" she says "you look like a Goddamn Greek"!

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PS 10-10-2006, Forum Hypo.

Re non-genetic inheritance and selection:

1) I suggest this link for thoughts of some science philosophers;

http://www.phil.cam.ac.uk/~gmm32/MAMELI_INHERITANCE_2004.pdf

2) Mameli's survey deals with phenomena of various types and cases of non-genetic or apparently non-genetic inheritance and selection. The survey does not deal with the molecular mechanisms of non-genetic inheritance.

In my own opinion this subject is of a very very wide scope and the only way of doing justice to this infinitely complex jungle of a subject is not to examine it from among the trees but to survey it from high above:

A. Each case within this subject involves behaviours of tremendous numbers of in-cells organisms, genes, and of the components and tools within their cells.

B. Humans have only recently started to be able to learn and to learn somethings about genes and genetics. But they have'nt yet gotten used to the idea that a genome is a complex living organism, the communal coop of now interdependent but long-ago independent and most probably yet uncelled living organisms, i.e. genes.

C. Humans also have'nt yet gotten used to the idea that each multicelled life form is a spacestation comprising many spaceships-cells. Thus a human space station comprises circa 10^13 spaceship cells inhabited with our active dynamically living genomes-bases editions plus 10^14 spaceship cells inhabited with genomes of hundreds of varieties of monocelled organisms, bacteria and viruses. Now considering the numbers plus variety of these factors in a space-station it is feasible and expected to find variations between spacestations of a single genotype group and to find several or many possible ways and mechanisms by which functional capabilities or practices may be transferred from a mother space-station to a progeny space-station….

D. Just for a relatively easy thinking exercise consider only two countries/space-stations, each with only circa 10^9 population/spaceships, China and In
dia. Ask yourself to what you would attribute the variety of differences between them…and what are the ways and mechanisms of the phenotypicals survival in each of these two space-stations…then recall how many living inhabitants, genomes, there are in a human space-station organism…

D. We need to bear in mind how minute we are, how only recently we learned to think, how small our total extent of knowledge and comprehension are of the universe, of life and of ourselves.

I think,

Dov

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