human origin

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#199 Nov 19, 2013

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#200 Jan 14, 2014
2014 Jan 1;6:208-24.

Emergence of biological organization through thermodynamic inversion.

Kompanichenko V.

Abstract

Biological organization arises under thermodynamic inversion in prebiotic systems that provide the prevalence of free energy and information contribution over the entropy contribution. The inversion might occur under specific far-from-equilibrium conditions in prebiotic systems oscillating around the bifurcation point. At the inversion moment,(physical) information characteristic of non-biological systems acquires the new features: functionality, purposefulness, and control over the life processes, which transform it into biological information. Random sequences of amino acids and nucleotides, spontaneously synthesized in the prebiotic microsystem, in the primary living unit (probiont) re-assemble into functional sequences, involved into bioinformation circulation through nucleoprotein interaction, resulted in the genetic code emergence. According to the proposed concept, oscillating three-dimensional prebiotic microsystems transformed into probionts in the changeable hydrothermal medium of the early Earth. The inversion concept states that spontaneous (accidental, random) transformations in prebiotic systems cannot produce life; it is only non-spontaneous (perspective, purposeful) transformations, which are the result of thermodynamic inversion, that lead to the negentropy conversion of prebiotic systems into initial living units.

PMID: 24389154
http://www.ncbi.nlm.nih.gov/pubmed/24389154

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#201 Jan 14, 2014
Another look at the samples of Nguna Island and Erika Hagelberg's research (1999) on presumed recombination of mtDNA.

(Hypothesis was that they carry Denisovan DNA just as the individual found in northern Europe and not some exotic recombination as Erika suggests)

2010
The Seven Daughters of Eve: The Science That Reveals Our Genetic Ancestry
Bryan Sykes
http://books.google.nl/books...

Any samples to duplicate the results were never coming forward.
Though requested.
So the method and research was not verifiable.
( In neither direction. Not as far as recombination is concerned or as it being Denisovan.)

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#202 Jan 14, 2014
In august 2000 Erika conceded that her sequences were wrong.

And that would be it if not for some discussion on the correctness of the molecular clock. How slow or fast do mutations occur.

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#203 Jan 14, 2014
More on rebuttal of Cavalli-Sforza's critizism on pg 184 of the Robert Sykes book.
As in mtDNA just being one gene in the total gene-package: might statistical fluctuations make it unrepresentative for the human genetic legacy as a whole.

Farmers did not replace hunter-gatherers in Europe.
Some people can claim a mtDNA lineage going back 9000 years.
The paternal gene.(If the male chromosome Y is carried by the sperm the child will be male, if it carries X the child will be female. Women have nothing to do with this.)
The chromosome is way larger then mtDNA and at the tips has some gene-shuffling occuring with female DNA (10%)
So this is were the idea of recombination stems from.
But the other 90% are used.

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#204 Jan 14, 2014
A Compendium of Human Mitochondrial DNA Control Region: Development of an
International Standard Forensic Database
Kevin W. P. Miller, Bruce Budowle
Federal Bureau of Investigation, Washington DC, USA
http://class.csueastbay.edu/anthropologymuseu...

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#206 Jan 14, 2014
A nice paper on methods as well as usefullness of genetic research:

http://otago.ourarchive.ac.nz/bitstream/handl...

Investigations into the history and possible causes of genetic predisposition to metabolic disorders in Pacific populations
Anna Louise Gosling
A thesis submitted
for the fulfilment of
the requirements for the degree of
Master of Science
University of Otago
2011

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#207 Jan 14, 2014
http://www.topix.com/forum/news/evolution/TVS...
Ancient Denisovans ...and the melanesia link.

Bringing it forward given the above thesis.

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#208 Jan 14, 2014
Forgetting is so annoying.
I baguely recall there being an issue of renaming certain haplo-groups.
Was it M, M1and M2 (which formed a theory on some groups being somewhere at some time in a certain order, but different again from what the ranking suggests) in A, Bb or something like that.
Given that renaming usually means also adding some new insight.
I forgot the context. And recall leaving it with the notion of a revisit and needing to see the paper on it. As well as needing more insight into the first theory and what the changes exactly affected as to the ranking.
Redo from start and hope i bump into it

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#209 Jan 14, 2014
Note to self:

Oceania had long been isolated from diseases of dense populations. While tinea, ring-worm and yaws were widely endured, the small-scale nature of most populations, and the great distances between them, protected most islands from influenza, leprosy, measles, mumps, smallpox, tuberculosis, cholera, plague, typhoid, whooping cough and venereal diseases (Denoon, 1995). This suite of diseases will henceforth be referred to as “Western diseases”, except when one disease is talked about in isolation to the rest. Most of these diseases require population mass before they can become endemic; population mass on the scale required to keep these diseases in circulation during the thousand odd years that these communities were under isolation, was something that most Pacific Islands lack - measles, for instance, requires an interacting population of at least 300,000, which is really the upper limit of what population any single archipelago or island group could sustain. Thus, these diseases became alien to Pacific Islanders, leaving them immunologically naïve (with regards to Western diseases)

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#210 Jan 14, 2014
cont.
For instance, Neel’s suggestion that cycles of feast and famine influenced hunter-gatherer populations does not stand up to ethnographic and ethnohistoric observations which indicate that hunter-gatherer populations seldom experience shortages – in fact, agricultural populations are more likely to experience regular and severe food shortages due to their reliance on a limited number of plant crops (Allen and Cheer, 1996; Benyshek and Watson, 2006; Prentice, 2005). The central concept remains the same, whether or not a past hunter-gathering or agrarian lifestyle is seen as responsible for the selection of the genes that contribute to the modern disease state. This core idea has been expanded to include other disorders, under the umbrella of “evolutionary medicine”, where a mismatch between so-called “Stone Age” genes and recently adopted lifestyles are thought to contribute to degenerative diseases in modern populations (Elton, 2008).

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#211 Jan 14, 2014
genotype and phenotypical behaviour connected:

The underlying concept is that foetal nutrient conserving adaptations in response to intrauterine under nutrition are overwhelmed by nutrient abundance postnatally and manifests in adult metabolic diseases (Hales and Barker, 2001).
This hypothesis takes some of the emphasis off genes, but simultaneously, it does not assume that genes do not have contributing roles to the development to the diseases of the MetS. Interestingly, a recent study of small for gestational age babies in a cohort based in Auckland found that some of the candidate genes for T2D and obesity occur more frequently in babies born small for gestational age (SGA) than those born average sized (Morgan et al., 2010). In the same cohort, it was found that maternal diet during pregnancy (Mitchell et al., 2004), as well as other environmental factors (Thompson et al., 2001) also contribute significantly to the SGA phenotype.

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#212 Jan 14, 2014
re. Sykes

It was reported that there was a significant drop in the amount of aDNA recovered from samples which were processed using standard drill speeds (ca. 1000 RPM) compared to the use of low drill speeds (eg. 100 RPM). There was a decrease in yield up to 30 times, which is likely to be related to heat damage (Adler et al., 2010). Other laboratory protocols have also been adapted in order to optimise the recovery of aDNA (Knapp and Hofreiter, 2010).

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#213 Jan 14, 2014
Next Generation Sequencing

Whole genomes (or parts thereof) have been sequenced from Neanderthals (Green et al., 2010), an archaic hominin from Denisova Cave, Siberia (Reich et al., 2010) and a Palaeo-Eskimo from Greenland (Rasmussen et al., 2010). Entire mitochondrial genomes from the Bronze-Age “Tyrolean iceman”(Ermini et al., 2008), an early modern human from Kostenki, Russia (Krause et al., 2010a), another Denisovan hominin sample (Krause et al., 2010b) and multiple Neanderthals (Briggs et al., 2009) have been sequenced and published, mostly within the past year. These studies constitute large amounts of raw data, on which in depth analysis is yet to be undertaken. These data are allowing glimpses into the past, showing genetic interactions between populations and human variation.

Given that we are now in 2014 at least some analyses should be open access by now.

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#214 Jan 14, 2014
Analyses of the Neanderthal genome have identified a surprising genetic relationship between Neanderthals and the modern human genomes that were used as a basis of comparison; the Neanderthals were more closely related to the three Eurasian genomes (French, Chinese and Papuan) than they are to the two African genomes (San and Yoruba). It appears that admixture between the Neanderthals and non-African anatomically modern humans contributed between one and four percent of the diversity seen in non-Africans (Green et al., 2010). The gene flow appears to be exclusively from the Neanderthals to modern humans, as there is no evidence of modern human genes in the Neanderthal genome (Green et al., 2010).
Similarly, analyses of the mitochondrial genome sequenced from the archaic hominin from Denisova, suggest that it shared 4-6 % of its genetic material to the genomes of modern day Melanesians (Reich et al., 2010), despite the archaic hominin and modern humans last shared an ancestor 1.04 million years ago (Hodgson and Disotell, 2010). This suggests that the previous models of expansion out of Africa, where relatively simple population replacement models have been suggested, need to be drastically reconsidered.

For instance, comparisons of mtDNA recovered from skeletal remains of early European hunter-gatherers with Neolithic farmers, as well as modern European populations have been undertaken in order to test a population replacement model (Bramanti et al., 2009; Haak et al., 2010). The data show discontinuity of population, with the probable movement of people into the area from the Near East during the Neolithic (Haak et al., 2010).

(It's not like everyone was included. Think of Lord Barths 9000 y.o. specimen of aDNA incorporated in his butler. Sykes Or maybe the question should be when methods were introduced to farm and at what stage the neolithic starts in various arts of Europe. And where the replaced went to. Best to read Tinekes blog)

http://otago.ourarchive.ac.nz/bitstream/handl...
Still reading Goslings informative thesis.

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#215 Jan 14, 2014
http://dienekes.blogspot.nl/2010/11/near-east...

November 09, 2010Near Eastern origin of European Neolithic farmers
(Last Update Nov 10)

I first became aware of this research in an ISBA4 abstract, and now it seems that a full article has been published in PLoS Biology.

Today, a fascinating new paper has appeared which completes the picture by studying for the first time both mtDNA and Y-chromosomes from a Central European Linearbandkeramik site, Derenburg Meerenstieg II in Germany.

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#216 Jan 14, 2014
One of the discoveries of GWAS is that most of the disease-associated variants identified have small effects and explain little of disease heritability and thus, are not suitable for immediate risk prediction and clinical use (Rosenberg et al., 2010; Witte, 2010). This observation has caused some to question the value of investing vast amounts of money in detecting variants which may or may not be linked to the development of disease (Goldstein, 2009; Rosenberg et al., 2010). As of October 2010, 702 human GWAS papers have been published on 421 traits. The majority of these had medical relevance (Stranger et al., 2011). Given that fundamental questions like why identified variants have low associated risks and account for so little of the heritability of disease, have not been addressed, one can see why some medical geneticists are disillusioned with this form of study. It could be that rare variants which are not captured by currant GWAS, or that structural variants, which are poorly captured by current studies, are responsible for more of the risk and heritability of disease (Manolio, 2010).
The study of rare variants has been improved by the development of next generation sequencing (NGS), which has impacted GWAS just as it has aDNA studies; the complementary application of GWA scans and whole-genome sequencing looks to be a more effective way at detecting rare or low frequency SNPs which may contribute to the development of disease (Holm et al., 2011). However, few of such studies have yet emerged. This has not stopped commentators lauding such studies as ‘next generation association studies’(Zeggini, 2011).

See former chapters with technical details and the mention that one run on a particular sequencer can cost upto US$ 9000.
Various overlapping runs would have to be made.

The other critique is that studies sofar only looked at Europeans.

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#217 Jan 14, 2014
Teouma is located on the island of Efate, which is in the Republic of Vanuatu. It is a high island with 899.5 square kilometres of land area. The island is volcanic and limestone (raised reef) in origin. Much of the island is fringed by a reef, which harbours a wide variety of marine life. This has been an important part of subsistence on the island from the time the Lapita people first arrived, until modern times (Bedford et al., 2006). The climate on the island is tropical, which means that there is little seasonality affecting the growing of crops.
The site itself is located about 800 metres from the sea on the edge of an upraised former beach terrace and reef about 8 metres above current sea level and is set amongst a decaying coconut plantation. It is on the northeast side of Teouma Bay, adjacent to a tributary of the Teouma River (Bedford et al., 2006). At the time of Lapita settlement, the site would have been located on a low promontory bounded by the sea on its western side, the small stream on its northern side and uplifted limestone cliffs extending several hundred metres to the east and south east. Subsequent to the Lapita occupation, uplift and massive infilling of the shallow end of the Bay with alluvial deposits transported down the Teouma River over a 3000 year period has effectively shifted the site to its current, higher inland location (Buckley, 2007.

As to the global warming threat, they are prominently in the news for, it can be said that the mayor factor of water rising is actually of the Island sinking, rather the plate subsiding.(uplift and tilting.)
Bit of a controversial place. As in supporting whaling just to get money for an electric plant.

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#218 Jan 14, 2014
Over 55 species of bird are represented in the middens recovered from Wairau Bar, including vast quantities of moa (Scofield et al., 2003). Large amounts of dog bone were also present, which indicates that dogs were an important food source (Scofield et al., 2003); it is possible that they were being farmed for consumption (J. Spinks, pers. com). Fish species, shellfish and marine mammals including elephant seals, sea lions and fur seals were also represented in the samples. Interestingly the fish species present in the midden are limited to only a few species (J. Spinks, pers. com.)

The first time i come across the non-modern explicite idea of dogs farmed for consumption.(Archaic site from ca. 1450-1288 CE)
Women breastfeedingdogs are known from pre-historic europe and eurazia. Usually in the context of hunting partner and mens best friend c.q protector.
But it sure makes sense.

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#219 Jan 14, 2014
Given the entire process (it seems you can throw any and everything at DNA) i was amazed anything at all was found.
Well not the hoped for result, but nevertheless.
So revert to looking at modern DNA:

Studies focussed on the New Zealand Maori and Cook Islander population so far have not detected a significant association signal. This differs from SLC2A9, which is a strong risk factor for gout in both Maori and Pacific Island people (Hollis-Moffatt et al., 2009).

This is interesting given that the current orthodox archaeological view is that the populations of Eastern Polynesia are descended from subsets of people moving out from Western Polynesia. One might expect, therefore, that an allele that is found to be significantly associated with disease in a Western Polynesian population should similarly be associated with disease in Eastern Polynesian populations. This is clearly not the case. This could suggest that the association of rs2231142 is an artefact of population structure and genetic drift; if the populations of Eastern Polynesian Pacific Islands are derived from migratory events that create bottlenecks, altered genetic structure can be expected in the founding populations.

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