Archive | July, 2012

What does the genetic evidence say?

29 Jul

A summary of the main points relating to the use of mitochondrial (and nuclear) DNA that I found very useful is given here in this link: http://www.digplanet.com/wiki/Mitochondrial_Eve. I will quote the relevant sections here for consideration: ‘By analysing descendants’ DNA, parts of ancestral genomes are estimated by scientists. The variation of mitochondrial DNA between different people can be used to estimate the time back to a common ancestor, such as Mitochondrial Eve. This works because, along any particular line of descent, mitochondrial DNA accumulates mutations at the rate of approximately one every 3,500 years. A certain number of these new variants will survive into modern times and be identifiable as distinct lineages. At the same time some branches, including even very old ones, co me to an end, when the last family in a distinct branch has no daughters.

Mitochondrial Eve is the most recent common matrilineal ancestor for all modern humans. Whenever one of the two most ancient branch lines dies out, the most recent common ancestor (MRCA) will move to a more recent female ancestor, always the most recent mother to have more than one daughter with living maternal line descendants alive today. The number of mutations that can be found distinguishing modern people is determined by two criteria: firstly and most obviously, the time back to her, but secondly and less obviously by the varying rates at which new branches have come into existence and old branches have become extinct. By looking at the number of mutations which have been accumulated in different branches of this family tree, and looking at which geographical regions have the widest range of least related branches, the region where Eve lived can be proposed.

The date when Mitochondrial Eve lived is estimated by determining the MRCA of a sample of mtDNA lineages. In 1980, Brown first proposed that modern humans possessed a mitochondrial common ancestor that may have lived as recently as 180,000 years ago. In 1987, Cann et al. suggested that mitochondrial Eve may have lived between 140-280 thousand years ago.’

My comments on the implications of the Eve hypothesis: The Eve hypothesis, which rules out all forms of multiregional hypotheses that date all current humanity to a common ancestral population of around 2 million years ago (thus excluding the suggestion of this blog that Han Chinese in particular descended from the East Asian Homo erectus that migrated there from Africa 1.5 million years ago), needs to be discussed in light of the following concerns that I have:

(1) We need to examine how it was determined that mtDNA only accumulates mutations at the rate of 1 every 3,500 years, so that the methodology needs to be analysed on the basis of this assumption upon which the rest of the calculations are made. Jokodo response: ”http://www.sciencedirect.com/science/article/pii/S0002929709001633 – short answer, they use colonisation events which can be dated from the archeological record, as well interspecific differences, as an anchor.”

(2) We need to know that the methodology ensures that the sample size for analysis represents the relevant global human populations.

(3) How do we know what branches emerged and became extinct in the past 1.5 million years to work out the ‘rates at which new branches have come into existence and old branches have become extinct’?

(4) We need an answer for why two different estimates of mitochondrial Eve were obtained by Brown and Cann et al, and why the latter generated a big range. I have modified this sentence on Jokodo’s response that they are both providing broadly the same estimate, which are ‘an order of magnitude off from what we need‘. This is strange because of Jokodo’s response of the empirical fact being that ‘genetic evidence strongly indicates that modern humans have emerged largely or entirely from a single ancestral population no longer than 100,000 years ago‘. This is between half to a third of figures that I cited above and Jokodo has not made any attempt to reconcile his figure with these estimates of an earlier divergence point. He merely queries my 1.5 million years ago figure.

(5) We need an answer for why the mitochondrial Eve results do not tally with the patrilineal ancestor as determined to be the Y-chormosomal Adam. Jokodo responds: ‘They’re not expected to align with each other. Why should they?’ I would like to ask him back: how could an Adam population have lived at a different time to an Eve population to be able to generate the humanity we see today?

In summary, is it not the case that in reality there is continuous divergent and convergent mutations that take place over long periods of time even in mtDNA thus giving such variable estimates and an unrepresentative picture of the total dispersal and extinction of humankind worldwide over 1.5 million years? Do not ‘colonisation events based on archaelogical’ and ‘interspecific differences’ alluded to by Jokodo constrict the time period over which humans existed in a biased way? If mutations in mitochondrial DNA cannot be predicted with the degree of certainty assumed by the researchers cited, can the conclusions of Eve-hypothesis that nothing now remains in humankind of human populations that preceded the species that is to be regarded as the Eve-generation worldwide, still be regarded as reliable?

What I find also of interest in the debate is that humans share as much as 95% or more of the DNA-sequence with its nearest evolutionary relative, the chimpanzees: http://www.ncbi.nlm.nih.gov/pubmed/12368483?dopt=Abstract. That leaves at most only 5 per cent of DNA-variation to account for all the phenotypic differences that is apparent between these two species of primates: so much gene-based differences contained in so little actual DNA does not seem plausible to me. Jokodo responds: ‘on what are you basing this? How did you quantify the differences?’ My reply: observations of the biological capacities of chimpanzees and humans. Humans are not a 5 per cent more improved species than chimpanzees but about 25 per cent more improved, would not Jokodo agree?

Finally, and as discussed earlier, whilst the real science should be based on an examination of the origins of actual genes in the human DNA (believed to range between 20,000 – 25,000) I am also not convinced that such an analysis will also yield direct modelling evidence of the origins of all current humans in terms of the first Homo ancestor, although it will establish real differences between populations across the world that science should endeavour to analyse. How can such studies inform us whether the Homo erectus of East Asia from 1.5 million years ago left any descendents that we can see today especially in China? If there were rates at which genes develop it might have some merit, but the reality is that there is no predicting the rates at which mutations take place in the genome and within genes. We therefore do not know how different genes develop through the apparently random process of DNA-mutations over time.

Jokodo’s conclusion: ‘It’s entirely conceivable (though very unlikely) that the argumentation for interpreting the data as evidence for a recent common origin is flawed, but you’re not giving us any reason to believe that this is so.’ Jokodo has not stated why he thinks it is very unlikely, has he?

Edited: 09.18 am, 31 July 2012 to incorporate Jokodo’s comments.

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Species and Speciation in Human Evolution

28 Jul

The classification of the biosphere according to species, genus, family, order, class, phylum and kingdom, that is based on shared characteristics, has value in our understanding of the relationships between different organisms to determine long-term evolutionary lineages. Without such a taxonomic classification scientists historically would not have been able to arrive at any reasonable proposition for the Darwinian theory of evolution and its subsequent development into the paleontological tree of life. However, the compartmentalisation of a fluid and dynamic evolutionary process in these terms does not provide us with the processes at work at the finer level of evolutionary detail, and this appears to have particular significance for our modelling of how modern humans came about from apes as an apparently single species of Homo sapiens sapiens, according to conventional wisdom.

At the heart of the matter concerns what constitutes a distinct species. The classical theory of evolution depends on establishing the mutational, natural selection and genetic drift mechanisms for the emergence of distinct populations of animals in Nature based on a definition of species that talks of reproductive compatibility in the main.  This does not get us very far in our quest to ascertain which organisms emerged from a common ancestor. In my view the intractable problem of speciation in evolutionary biology may be addressed as follows: should populations be defined as distinct species specifically in relation to the degree of speciation that will prevent the reproductional fusion of gametes for embryogenesis to a viable foetus, or should speciation be defined in terms of phenotypic parameters that takes into account morphological, physiological, biochemical and behavioural separations to the point that incompatiblity between representative samples of male and female from being able to engage in sexual intercourse can be established whether or not mating between fertile and healthy individuals can demonstrably result in a successful offspring that, in turn, was able to pass on its own genes to another generation. For the consideration of human evolution I take the latter view that is testable but the ethics of the science preclude its implementation.

Further, I consider all extant and extinct Homo phenotypes from Homo ergaster onwards as consituting ‘human beings’ on the basis that they all had a highly evolved ‘mind’ that governed intelligence and culture, as distinct from Homo habilis and its predecessors that were a lot more ape-like and instinctive rather then deliberative. This means that they were all able to produce successful offsprings with each other but chose not to do so when they came into contact. Thus, the terms Homo erectus, Homo georgicus, Homo neanderthalensis, Homo heidelbergensis, Homo floresiensis, etc should only be used for the purposes of describing particular fosssil finds in terms of geography and age on the assumption that they did not differ from each other to any significant degree in the non-intelligence and non-cultural parameters. They would have differed on the other parameters but not to the point that they would have ruled out mating.

So the question that arises is whether there is any value to describing any of the Homo ergaster-derived variants as its subspecies according to some type of classification that may be formulated based on the above considerations of the phenotype. My view is apart from the differences highlighted in this  blog that gives sufficient reason to consider that the Han Chinese descended from Homo ergaster via Homo erectus and not via Homo sapiens, a major source of variation in human populations is that which comes under the subject of differences in the ‘workings of the mind’ which governs human behaviour to a very high level in comparison with other animals. This has implications for our definition of what constitutes relative docility between different human groups, for example, and why religion of various descriptions are adopted by different people. Science will attribute both intelligence and culture to an underlying genetic natural cause. However, the study of the mind itself in terms of brain tissue formation, the transmission of neurotranmitters, memory storage,  thought production, consciousness/awareness, foresight, visions, imaginations and the relationship each of these to physical ‘genes’ in the DNA is in its absolute infancy. Indeed, as psychology and psychiatry it may be regarded as unscientific and not what we know today as modern medicine.  The obvious racial differences are superficial and do not address the intelligence and cultural dimension of human differences. We do not currently have the scientific tools required for a thorough investigation of these topics. Although neuroscience has made a great deal of progress in recent decades thoughts and consciousness have not been amenable to scientific probing, without which differences in culture and intelligence cannot be understood to determine human subspeciation.

As mentioned earlier human species and speciation also brings us to ethical issues for identifying what constitutes legitimate and worthwhile topics for scientific scrutiny. In this regard an aspect of the ethics of the type of science that one needs to bring under consideration was also alluded to by ‘Someone’ (as reproduced in my 23 July post), and I do acknowledge and appreciate his/her contribution to the discussion in this blog.

Last edited: 10.49 am, 29 July 2012.

Has the hypothesis suggested in this blog been reported earlier?

26 Jul

I examined the link provided by Jokodo (http://159.226.149.45/compgenegroup/paper/subing%20NatureReview.pdf)

and found that it is not the Model D that he suggested to me for my hypothesis, if we go by the conclusions reported by the authors, as follows: ”Conclusions: On the basis of the genetic evidence generated so far, particularly from Y-chromosome data, modern humans in East Asia have a recent common origin in Africa. It is suggested that the first entry of modern humans into the southern part of East Asia occurred about 18,000–60,000 years ago, and was followed by a northward migration that coincided with the receding glaciers in that area”.

DNA-sequence analysis as a guide to origins

24 Jul

Now that Jokodo has shown himself to be totally exhausted [and let me make it explicitly clear that having just trashed two of his submissions (‘just google it and come back when you know enough to criticise specific assumptions….’; & ‘I am seeing someone who spouts ill-defined claims…’ ) I do not wish to hear any more from him in this blogsite so he should consider himself banned] we can turn to a serious consideration of the basis upon which alternative theories of the origins of man from apes are determined. The flaw in these theories concerns the use of ‘known’ or ‘predicted’ mutation rates in the genome to establish the relationships between different groups of current populations in terms of their common ancestor.

Since I posted the above paragraph, Jokodo would not be deterred and had to have his say as shown in the comments section of this post. I therefore restored his two trashed submissions in order that there is continuity in these proceedings. He has not replied to the final question that I asked, so I presume that he is now fully exhausted.

Edited: 7.21 pm, 25 July 2012.

Jokodo was not finished. He came back with another comment (No 7) which I replied to with a further question (N0 8).

Edited: 10.07 pm, 25 July 2012.

Genetic convergence?

23 Jul

It is unfortunate that Jokodo had to leave us at the point of the crucial question of genetic convergence theories in the consideration of how modern humans came about. Are there any further inputs on this from the wider scientific community, especially from ‘Someone’ whose second contribution to the debate I had put on hold, but is now reproduced here?:

Submitted   on 2012/07/17 at 6:22   amI   expect there are thousands of mixed-race couples, if mixed-race couples had a   dramatically increased chance of infertility, that would be testable. But   because they weren’t forcibly mated in a lab, you can’t conclude anything   from that? According to that criteria, we couldn’t find out if cigarettes   cause cancer, because we didn’t force anyone to smoke.According   to this:
http://en.wikipedia.org/wiki/Interracial_marriage

A study   of mitochondrial DNA found, “1.34% of West Eurasian female admixture in Hong   Kong Cantonese population” Hong Kong has a population of 7 million, so that   would require tens of thousands of cross-bred people to reach that level.

In the   U.S. according to this:
http://www.washingtonpost.com/wp-srv/national/daily/dec98/melt29.htm
“36 percent of young Asian Pacific American men born in the United States   marry white women, and 45 percent of U.S.-born Asian Pacific American women   took white husbands”

So   you’re proposing that with these thousands and thousands of examples, nobody   has noticed if they have a higher rate of fertility problems.

And   then you propose we need to “examine records of their relative susceptibilities   to diseases like malaria …” How are you going to do that? Are you going to   put them in a lab and expose them to malaria over and over? Doesn’t that   raise even worse ethical questions? Oh wait, apparently now you think it’s   okay to “examine records.”

But we   already know a disproportionate number of black Africans have a genetic   resistance to malaria, thanks to a sickle-cell gene. You’re the only one who   thinks that’s enough to call them another species.

Are the officials of Freethought and Rationalism Discussion Board following this blog-thread?

22 Jul

When one of their leading posters, Jokodo, (who incidentally returned to Freethought and Rationalism Discussion Board (FRDB) following a period of ‘Self Ban’ (so important he regards that Forum), has been making such time-consuming technical contributions to the debate in this blogsite, do the officials of FRDB still feel vindicated at throwing my threads into ~Elsewhere~ and finally ‘The Trash‘? I would in particular like to appeal against their decision not to lift the life-ban on me that prevents me from returning to the forum where I had made many good friends in the FRDB Community.

So Jokodo: would you please point this out to Saramago and Sabine Grant so that I may have a chance of returning to the Forum to continue with these discussions there in order that other learned FRDB posters eg Duke Leto, G O R T, skepticalbip, and Keith&Co may join in? – please.

Foundational principles of the aetiology of genes

20 Jul

An outline of the genetics governing the foundational principles of the aetiology of genes will assist the study of the various models of how humans beings arrived and separated into the different groups in particular regions of the world. The science underlying the mechanism of gene development will be elucidated in this post in order to assess how favourably the hypothesis presented in this blog compares with other serious competing hypotheses that are currently under consideration.

Please note that there will be no new posts by me in this blogsite until a consensus view on this topic has been reached. All future comments on all posts submitted to this blogsite will be edited by me to ensure that this objective is maintained.