Physical anthropologist claims (again) that Homo floresiensis was cretin Homo sapiens

This hypothesis has been proposed before by the same team and then rejected. However I feel obliged to mention it as I'm sure that some readers will find it interesting and also because, if real, it would mean that LB1 is not an Homo erectus (maybe a cretin H. erectus?) nor a new species but a marginal representative of our own expansion in Eurasia and beyond.

However I am skeptic, specially because Oxnard fails to compare with Homo erectus.

Cretinism is a severe chronic medical condition caused by low iodine intake. Iodine is mostly ingested with drinking water and also from sea salt, but not refined table salt (unless enriched).

Judge yourself anyhow:

Charles Oxnard et al. Post-Cranial Skeletons of Hypothyroid Cretins Show a Similar Anatomical Mosaic as Homo floresiensis. PLoS ONE 2010. Open access.

Late human evolution maps

Kambiz Kamrani at Anthropology.net mentions this site of a colleague and also his own dedicated page on human fossils. Both are very interesting and, using their data, I made some maps in order to better understand the chronology of recent human evolution in the range between 1.3 million years ago (oldest estimate for Neanderthal-Sapiens divergence, cf. Aida Gómez) and 60,000 years ago, when the expansion of these two species towards Asia was surely already in action.

As Asian fossils, excepted West Asia, are not relevant for my purpose (they are all Homo erectus senso lato with no transition happening there at all) I have used a base map that only includes the Western parts of the Old World.

Note: I used median ages but, when these overlapped too much with two of my arbitrary time frames, I placed them in the two relevant maps (check for safety but they are likely to be the same specimen.


1. 1.3 million years to 800,000 years ago:


While most of the findings are Homo erectus (purple dots), the likely first known individuals in the H. sapiens and H. neanderthalensis lines appear already, at the end of the period, at Atapuerca (H. antecessor) and Saldanha Bay (H. rhodesiensis).


2. 800-600,000 years ago:


We can appreciate in this period an expansion of H. rhodesiensis to the Horn of Africa and transition to H. heidelbergensis at Atapuerca (c. 600,000 years ago according to fossilized.org).


3. 600-400,000 years ago:

The expansion of Homo heidelbergensis becomes apparent in this period. Restricted to Europe however. Notice how in spite of these changes there are still many specimens categorized as H. erectus around the Mediterranean.


4. 400-200,000 years ago:


While it looks a dull map on first sight, most significant here is the existence of a fossil that may be transition between H. rhodesiensis and H. sapiens. This one is Lake Eyasi, in Tanzania (red-orange hue, not easy to appreciate possibly), dated to c. 240,000 years ago.


5. 200-60,000 years ago:



Whoa! Everything goes a lot faster now: Neanderthals and Sapiens everywhere! Well, each in their specialized area: Sapiens in and around the tropics, Neanderthals in the fresh regions of the North. Even the map caption becomes small as the earliest Neanderthal and Sapiens fossils (controversial chronology) show up in Central and East Asia respectively. I reflected this with a mere two color-coded arrows.

The oldest uncontroversial fossil of H. sapiens is Omo II (c. 195 Ka ago), followed by Herto (Idaltu) and Jebel Irhoud, in Morocco (both c. 160 Ka ago).

Bonobo mtDNA... and some human implications.

Researchers from the University of Bonn have published a new paper on Bonobo mitochondrial genetics:

Gabor Zsurka et al., Distinct patterns of mitochondrial genome diversity in bonobos (Pan paniscus) and humans. BMC Evolutionary Biology. Open access.

Background

We have analyzed the complete mitochondrial genomes of 22 Pan paniscus (bonobo, pygmy chimpanzee) individuals to assess the detailed mitochondrial DNA (mtDNA) phylogeny of this close relative of Homo sapiens.

Results

We identified three major clades among bonobos that separated approximately 540,000 years ago, as suggested by Bayesian analysis. Incidentally, we discovered that the current reference sequence for bonobo likely is a hybrid of the mitochondrial genomes of two distant individuals. When comparing spectra of polymorphic mtDNA sites in bonobos and humans, we observed two major differences: (i) Of all 31 bonobo mtDNA homoplasies, i.e. nucleotide changes that occurred independently on separate branches of the phylogenetic tree, 13 were not homoplasic in humans. This indicates that at least a part of the unstable sites of the mitochondrial genome is species-specific and difficult to be explained on the basis of a mutational hotspot concept. (ii) A comparison of the ratios of non-synonymous to synonymous changes (dN/dS) among polymorphic positions in bonobos and in 4902 Homo sapiens mitochondrial genomes revealed a remarkable difference in the strength of purifying selection in the mitochondrial genes of the F0F1-ATPase complex. While in bonobos this complex showed a similar low value as complexes I and IV, human haplogroups displayed 2.2 to 7.6 times increased dN/dS ratios when compared to bonobos.

Conclusions

Some variants of mitochondrially encoded subunits of the ATPase complex in humans very likely decrease the efficiency of energy conversion leading to production of extra heat. Thus, we hypothesize that the species-specific release of evolutionary Background We have analyzed the complete mitochondrial genomes of 22 Pan paniscus (bonobo, pygmy chimpanzee) individuals to assess the detailed mitochondrial DNA (mtDNA) phylogeny of this close relative of Homo sapiens.

Pan genus mtDNA phylogeny (fig. 1)
PanTrog = Pan troglodytes (chimpanzee), PP = Pan paniscus (bonobo)

It is very apparent that bonobos have three major mtDNA haplogroups, named A, B and C.

Unlike humans (or at a lesser extent common chimpanzees), bonobos live in a well defined area of the SW Congo basin, limited by rivers, and have therefore never experienced a expansion since they became separated from their chimpanzee cousins. This makes them a good reference to better understand how demographic expansion affected our genetics, specifically our mtDNA.


Chronology

The authors say that the most recent common ancestor (MRCA) of all bonobos (by mtDNA) lived some 540,000 years ago (430-670 Ka. with 95% confidence interval).

If the graph above has a scale (and I understand it does) and assuming this estimate is correct, then the divergence of both Pan species happened c. 2.1 million years ago (1.7-2.6 Ma at 95% CI) - using simple linear maths.

Notice that Caswell 2008 already suggested a possible divergence age of 1.5-2.0 Ma in order to make it coincident with the formation of the Congo basin as we know it, a geological phenomenon that was surely itself the cause of the chimp-bonobo divergence. In my own words back then:

That the chimpanzee-bonobo split should be move backwards in time to at least 1.29 million years ago. And, that if the human-chimp divergence age is actually older (8 million years instead of 7), then this event would be coincident with the formation of the Congo river (1.5-2 Myrs BP), that many people belive is at the origin of bonobo speciation.

So I think we can confirm that the Pan paniscus speciation event happened most likely some 2 million years ago, when some undifferentiated Pan became isolated from the rest in the SW Congo basin on purely geological reasons.

It is also said that:

The maximal nucleotide difference between bonobo groups is, however, 1.5 times higher than in humans, and thus somewhat closer to the distance between modern humans and the extinct Neandertal.

While this affirmation is unspecific on the details, it seems to weight against the shortest claimed divergence ages for the two big-headed human species.


Bonobo reference sequence is a mix

The authors find that the bonobo reference sequence (GeneBank) seems to be not a genuine one but a mix of two rather unrelated ones. Hence they propose deprecating the extant reference and use the closest one of theirs, PP23, as new reference.


Purifying selection

The authors find strong support for purifying selection in both bonobos and humans. However some of this funtional constraint seems to have been lifted for some groups when humans spread around the world, specially to colder locations. Therefore they suspect it related to the metabolic determinants of high tropical temperatures. However some of this constraint may have been already lifted still in Africa as the branch leading to humans evolved hairlessness and sweat.

For ATPase, the nonsynonymous/synonymous (dN/ds) ratio is lowest among the Khoisan (haplogroups L0 and L1 essentially) and highest in haplogroup A. However other Siberian/Native American haplogroups (C and D) do not show anything so extreme, so rather than thinking in terms of positive selection, the authors argue that it is loss of evolutionary constraint what we see here:

Therefore, we conclude, in agreement with others [16], that the observed increase of dN/dS values for the mitochondrial ATPase genes in humans cannot be interpreted in favor of positive selection at colder climate conditions, but rather is the result of the release of strong evolutionary constraints during population expansion and migration of modern humans.

Another interesting finding is surely that one of the three bonobo haplogroups displays a mutation at locus 8344A>G, which is strongly implicated in MERRF syndrome (a mildly incapacitating degenerative disease) in humans. However they suspect that a nearby bonobo-specific mutation, present in all bonobo mtDNA, may be acting to prevent this effect in bonobos.

Signs of positive selection favoring disease risk genes

It is very much counterintuitive but that is what Stanford University researchers conclude after looking at the evidence.

Erik Corona et al., Extreme Evolutionary Disparities Seen in Positive Selection across Seven Complex Diseases. PLoS ONE 2010. Open access.

Abstract

Positive selection is known to occur when the environment that an organism inhabits is suddenly altered, as is the case across recent human history. Genome-wide association studies (GWASs) have successfully illuminated disease-associated variation. However, whether human evolution is heading towards or away from disease susceptibility in general remains an open question. The genetic-basis of common complex disease may partially be caused by positive selection events, which simultaneously increased fitness and susceptibility to disease. We analyze seven diseases studied by the Wellcome Trust Case Control Consortium to compare evidence for selection at every locus associated with disease. We take a large set of the most strongly associated SNPs in each GWA study in order to capture more hidden associations at the cost of introducing false positives into our analysis. We then search for signs of positive selection in this inclusive set of SNPs. There are striking differences between the seven studied diseases. We find alleles increasing susceptibility to Type 1 Diabetes (T1D), Rheumatoid Arthritis (RA), and Crohn's Disease CD) underwent recent positive selection. There is more selection in alleles increasing, rather than decreasing, susceptibility to T1D. In the 80 SNPs most associated with T1D (p-value less than 7.01×10⁻⁵) showing strong signs of positive selection, 58 alleles associated with disease susceptibility show signs of positive selection, while only 22 associated with disease protection show signs of positive selection. Alleles increasing susceptibility to RA are under selection as well. In contrast, selection in SNPs associated with CD favors protective alleles. These results inform the current understanding of disease etiology, shed light on potential benefits associated with the genetic-basis of disease, and aid in the efforts to identify causal genetic factors underlying complex disease.

Maybe the best understood case is that of rheumatoid arthritis, which, following the archaeological record, seems to have only manifested in west central Kentucky (USA) some 6500 years ago, slowly extending to other parts of North America (West Ohio some 1000 years ago) and then scattering worldwide after colonization. In contrast the alleles that favor the disease are much older everywhere and seem to work well against tuberculosis (TB). So it would be a clearly favorable allele (protecting against TB) until whatever (not yet known) pathogen or allergenic that triggers RA spread from the Ohio basin.

So now RA susceptibility alleles have become deleterious in those areas where TB is not anymore a problem but, until a few centuries ago, they were only being selected for, because there was no exogenous trigger for RA outside of the Ohio basin and instead they protected from tuberculosis.

A good example of how fitness value is therefore not absolute but contextual.

There are also some indications that T1D susceptibility alleles may be implied in defense against enteroviruses, which cause some pretty bad diseases such as poliomyelitis and meningitis.

Lucy's knives

New evidence in form of unmistakable stone-tools' marks on bone, push back the earliest known systematic use of tools to an species that was surely not still "human" (in the sense of belonging to the genus Homo) but to Australopithecus afarensis or another similar (but unknown) species. This happened some 3.4 million years ago in the central-northern Ethiopian highlands.



Australopithecus afarensis, the species to which the famous fossil Lucy belonged to, is the only hominin species known to have lived in that space-time. However until now it was commonplace to think that they were vegetarians and did not use tools.

It seems now that such ideas were wrong and that Lucy's species, with a brain barely larger than that of a chimpanzee, was already using not just random rocks but sharp ones able to cut meat. Forensic analysis leaves no room to doubt the marks are product of cutting tools and not animal fangs or paws.

This has potentially interesting implications for the evolutionary history of human brain and intelligence, as well as our highly precise hand, both tightly associated to tool use.

More detailed news stories at Science Daily and BBC.

Ref. Shannon P. McPherron et al., Evidence for stone-tool-assisted consumption of animal tissues before 3.39 million years ago at Dikika, Ethiopia. Nature, 2010. Pay per view.

Sex chromosomes complex history in primates

Just a quick mention of what seems to be an important piece of research in the evolution of sex chromosomes in humans and primates in general. The main finding being the existence of a number of evolutionary gene conversions (transference between the X and Y chromosomes, in either direction).

Mineyo Iwase et al. Frequent gene conversion events between the X and Y homologous chromosomal regions in primates. BMC Evolutionary Biology 2010. doi:10.1186/1471-2148-10-225. Open access.


Conclusion

Gene conversion events between the X and Y homologous regions have been suggested, mainly in humans. Here, we found frequent gene conversions in the evolutionary course of primates. An insertion of a LINE element at the proximal end of the region may be a cause for these frequent conversions. This gene conversion in humans may also be one of the genetic causes of Kallmann syndrome.

Homo ergaster had elephant in the menu

Mundo Neandertal[es], citing newspaper Público[es], mentions today that Spanish researchers (a branch of the Atapuerca team) working in Olduvai gorge have found elephant bones with cut marks (sign of human meal) in association with bones of Homo ergaster, the ancestor of our species, dated some 1.3 million years ago.

Femur and radius of H. ergaster found at Olduvai

This quite clearly tells that, at least occasionally, our ancestors did feast on elephant meat. Whether they hunted the huge animal themselves or just found a recently dead one is another story.

Remains of Sivatherium, another large animal, a relative of modern giraffes, have also been found in the same circumstances.

Sivatherium reconstruction

The Homo ergaster bones are potentially very informative because, unlike what happens with Neanderthals and their ancestors (H. antecessor and H. heidelbergensis), very little is known of this human branch leading to us. Most of the information we have on how was H. ergaster is derived from a single individual, the 13 years old Turkana boy, who died by the infection caused by a rotten tooth, and who is believed would have reached 1.85 m. of height as adult, reaching 1.60 m. when he died.

However this extrapolation may perfectly be wrong. In my family at least, the height you have at 14 is almost the same you have for life (I have only grown 1 cm. or so since that age and is the same case with most of my relatives and probably many other people).

In any case these new findings should be of great help in understanding a little better the anatomy of the ancestral species.

Human existence: ownership versus community

This is something I woke up chewing on. And I think it's an important understanding of the human condition.

Let's go by parts.


Paleolithic primitive communism

As we know, most of the existence of our species and genus, of humankind, of the very evolution that shaped our being, happened in a hunter-gatherer context that has been called primitive communism because all was (is still in a few cases) shared. Working individually was unproductive and accumulation of wealth impossible. Hence individuals could be only understood within communities and communities were highly dependent on their individual components, whose abilities and knowledge (or potential for them in the case of the young ones) were the most precious assets that could be held, not by any individual but by the community as a whole. The other asset was maybe territory but this was a diffuse collective possession anyhow.

The only individually held property was surely stuff like weapons and tools and decorative objects such as necklaces. And as the economy was totally based on sharing (giving and taking freely as a matter of course) even these minor elements of private property were not important.

Even child care was shared to a great extent, so not even children were from this or that mother (or parents) but belonged fundamentally to the community.

Hence we evolved to have individual adaptative traits that were fit for cooperative work in small tightly knit communities. Communicating powers such as language and gestures, emotions such as love and shame, behaviors such as spontaneous altruism, all evolved for that cooperative purpose. We are natural born communists.


Neolithic and Industrial new orders

Things changed however as the Neolithic Revolution allowed for surplus production, accumulation of some wealth and eventually some specialization in diverse roles like warriors, priests (bureaucrats), specialized artisans and traders. The process was not immediate (early Neolithic sites still show no such distinctions) but took place almost everywhere sooner or later. As result some classes (occasionally converted in hereditary castes), specially warriors and priests, took control over the huge masses of farmers and benefited from their collective surplus in a dynamic that oscillated between symbiosis and parasitism but that really tended to the latter.

For several millennia this "neolithic with aristocratic rule" was the main socio-economic system. Again this changed with the Industrial Revolution, which allowed much more effective economy, generating larger surplus and allowing the development of other classes at the expense of the traditional ones. From the masses of farmers and the less numerous but more qualified artisans, arose the working class, now mostly dedicated to secondary (industrial) and tertiary (transport, services) economy. Farming gradually became a minor, residual, industrialized occupation. From the much smaller group of traders, and absorbing a good deal of the classical upper classes, whose previous accumulation of wealth was recycled into the new system, arose the bourgeoisie. Humankind had arrived to Capitalism.


Individualism

Both processes of "modernization" are different in many aspects but the economical basis and the psycho-social impact on us is largely similar: we are being deprived from our natural economy and social system and for that the natural community must be destroyed and the individual must be created.

This process has been often detected and sometimes denounced as a common activity of missionaries wherever tightly knit (tribal) communities still exist. The preachers, ideological avant-guard of the new "individualist" order, persuade the locals that they are not just members of a tribe and clan but whole individual beings, with individual souls bound to individual destinies even after death.

The process is of course imperfect because it is not so easy to destroy ethnic identities but, overall and in the long run, it tends to succeed, creating amorphous pseudo-communities of individuals with competing individual interests all under the umbrella of a huge apparatus, both political-legal (state and supra-state alliances) and economical (Capitalism).

Unlike in a natural communist society, such as those that can still be found among some surviving hunter-gatherers, individual property becomes central. It can be said, and this was what really got me thinking this morning, that the individual is defined by his/her property (or lack of it). And society largely qualifies you on such grounds.

Thanks to the virtual codification we call money, property does not need anymore to be just real state or material objects such as a ship or a gold hoard, it can be a bank account or deeds of some sort. But in any case it is property what makes the individual and the main measure of his/her value in our twisted reality.

Of course, there's another element that cannot be easily quantified: personal attributes, such as knowledge, skill, creativity, intelligence, sociability, health, beauty, fertility, etc. They can sometimes be monetized but their essence largely escapes the wealth scale. I'd call these traits personality rather than individuality, because they make what we can call the person, as opposed to the individual and his/her supposedly intrinsic egoism. They cannot be accumulated, they cannot be transfered except by altruistic deeds such as biological reproduction (genes) and social reproduction (memes) and while they can sometimes be used to accumulate wealth to some extent they are not really central to this process but pretty much peripheral and pre-Neolithic/pre-Industrial in nature.

While Capital, of course, also tries to grab the personalities and include them in their system somehow, these are nearly impossible to capitalize. I cannot sell you shares of my intelligence, you cannot sell me a fraction of your creativity or your beauty. At most you can rent it as a proletarian (work for a salary, as a physical or intellectual prostitute). However continuous rent of such attributes generally causes them to grow dry because these traits have not evolved for mere selfishness and because the alienation involved in the work process typically corrupts the soul, rending it arid and unproductive.

Luckily for Capital there are many souls to be raped for a few crumbs. Not all are for sale but there's always some, many surely, who are desperate enough to be bribed.

But I'm deviating from the main issue a bit. A necessary deviation maybe anyhow.


Conclussion

The key point I meant to expose in this, somewhat self-evident, essay is how we humans, at least most of us (studies seem to demonstrate that there is a natural born parasitic minority but they are a tiny fraction anyhow), have evolved for sharing, for communism, but that the socio-economical reality we are involved in since birth forces us to become individuals, stimulating our selfishness and deprecating our cooperative skills, which are largely laid waste (or at best recycled in a tainted form within the capitalist production system).

After all, what I'm talking here is of alienation. But surely in a wider sense than Marx did: not just alienation of the worker from his/her product but alienation of the person from his/her community.

Now immersed in what surely is the final crisis of Capitalism, we are forced to search for alternatives and our only valid reference is our own human nature, something that cannot really be altered so easily and something that is, at least to a very large extent, cooperative. Of course I'm talking of Communism. Not the so-called "communism" in the Stalinist systems of Russia and China, which are largely nothing but a state-directed bourgeois revolution, with a more advanced theoretical ideology but with similar practices to right-wing pseudo-socialist systems such as fascism, but something else.

Something else that must be deeply democratic at grassroots level, but democratic not only in the political aspect but also in the economical and communicational ones. There are no models, we have to create it from scratch... and that scratch is our human nature.

Folate and not cancer caused dark skin and the ability to tan

It is well known that depigmentation in humans was caused because of the need of vitamin D generation at the skin, but what was not so clear was why pigmentation, dark skin (conventionally called black, though it's actually brown in most cases) first evolved.

Researchers from Pennsylvania State University have now concluded that skin cancer, which is a quite weak selective pressure, is not the main reason for dark skin but the protection of folate (folic acid, vitamin B9) from being destroyed by the ultraviolet radiation.

Much like vitamin D deficiency can cause major problems in newborns, folate deficiency also does, causing neural tube defects, anemia, low birth weight and premature births. Additionally, it also affects, although less severely, adults, causing weakness, depression, weight loss, headaches and behavioral disorders.

Nina G. Jablonski and George Chaplin, Human skin pigmentation as an adaptation to UV radiation. PNAS 2010. Freely accessible (it seems).

Also discussed at Science Daily.

Life in the cold, life under the heat

Gathering here a couple of at least curious news I read recently at Science Daily. They have nothing to do with each other except one thing: they both deal with life at extreme temperatures.


Being human is cool... literally so.

Benjamin Passey and colleagues report that temperatures were hellishly high most of the time in one of the most likely cradles of human evolution: the basin of Lake Turkana, including the last three million years.

This may support the thermal hypothesis of human evolution, that would explain why we don't have any fur and sweat so much (intended for cooling) and also maybe why we walk on only two legs, reducing the direct impact of both the Sun and the overheated soil.

The article does not mention it but I recall reading some time ago that even brain size increase has been attributed tentatively to such heat challenge, as larger brains would prevent fainting under the heat allowing our ancestors to exploit the territory at noon, when predators are enjoying their siestas. That would also explain why we keep "natural hats" of hair on our heads, of all bodily places (and I'd dare hunch it might also explain thinly curled hair, still overwhelmingly dominant among tropical peoples, as a means to secure free circulation of air near it).

Source article.


Where water is a rock... methane fills the rivers. Life in Titan?

This in fact was already known. What is new is that astronomer Chris McKay suspects that the chemistry of Titan could well be indicative of the existence of some form of life on it.

Saturn's satellite Titan, as you probably know, has many similitudes with Earth's environment, just that with a much lower temperature range that does not allow water to melt ever. At such freezing temperatures, methane, an organic compound, takes the role of water switching between liquid and gaseous states in the hazy orange atmosphere of this planetoid, the largest moon of the Solar System.

But what is new and interesting is that scientists expected that natural chemistry in Titan would produce lots of acetylene but Cassini has failed to find any of it so far. The most likely chemistry for life without water at such gelid temperatures would be a metabolism of acetylene by hidrolization (reaction with hydrogen instead oxygen, as usually happens on Earth) and, according to McKay, the available data seems to indicate that this is actually happening on Titan.

Still, Mark Allen, says that all non-biological explanations are not still ruled out. Acetylene might be just degraded by solar radiation for example.

But the aboundance of organic compounds on Titan is so overwhelming that it is difficult to think that life has not evolved upon them at the slightest chance. This last is my opinion.

Source article.

Connection between high creativity and schizophrenia found

It's all about a filter we have in our heads, it seems: the thalamus. What schizophrenics and healthy highly creative people share is low density of dopamine receptors in the thalamus, which act as filter for incoming information. Normal people have many more of such dopamine receptors, filtering a lot of inputs and are hence less sensible but also more stable. Highly creative people and schizophrenics have less and hence filter little, what makes their brains to process much more information for good or bad.

Örjan de Manzano et al., Thinking Outside a Less Intact Box: Thalamic Dopamine D2 Receptor Densities Are Negatively Related to Psychometric Creativity in Healthy Individuals. PLoS ONE 2010. Open access.

Also discussed at Science Daily.

It is interesting because it gives some adaptative meaning to the genetics and epigenetics behind schizophrenia, as being highly creative is surely an adaptative trait.

I wonder if it offers some hope of treating schizophrenia by positivizing this attribute instead of mere chemical straight jackets, that is all psychiatrists can offer now. I've just seen too many lives ruined by this plague and the horribly arrogant and highly inefficient psychiatric handling of it.

It is also interesting because in the latest paper on Neanderthal genetics (Green 2010), they have found that some of the genetic regions exclusive to our species, H. sapiens, are related with mental conditions such as schizophrenia and autism, suggesting that maybe these traits offer also great potential rather than just a handicap (in which case they would have been selected against long ago, I presume).

On some details of the Neanderthal genome draft

Still chewing on the Neanderthal genome draft (Green 2010). Only today I have got some time to dwell on some of its details.


Alleles specific to all Homo sapiens (and not to Neanderthals)

It's interesting not just that some of us carry a small apportion of Neanderthal alleles but also the list of alleles that are exclusive of our species. Green et al. dwell on this matter in the section titled A catalog of features unique to the human genome.

There is a list of 78 alleles (table 2) that are fixated in the derived (non-Chimpanzee) form in the species Homo sapiens exclusively and found in their ancestral state among Neanderthals. Many are not really known their role but others seem to accumulate in certain processes such as skin (sweat...), melanin, smell, vision, sperm motility, hormonal and cellular division regulatory processes. This suggests me that there were some marked biological and appearence differences among the two species in spite of the proximity.

Therefore the inter-species barrier was possibly rather high even if still not total.

The authors emphasize specially five alleles in which more than one SNP is different, suggesting greater differences. These are specially related to skin morphology and regulatory substitutions (specificity).

Also the studied certain regions in clear rapid evolutionary change in the line leading to humans called HARs. The vast majority of these HARs had already evolved before the Neanderthal-Sapiens transition but a few (c. 1.7%) had not yet and belong specifically to Homo sapiens.

These human-specific HARs include genes related to mental functions (associated with mental disorders such as Dow syndrome, schizophrenia and autism) as well as a the RUNX2 (CBFA1) gene that would be related to changes in skull, clavicle and ribcage morphology.


Are Chinese slightly 'more Neanderthal' than other Eurasians?

Less definitely, when working with the comparative data at table 4, I find that the Han Chinese sample (n=2) appears very slightly but maybe significantly "more Neanderthal" than the other Eurasians, including the only Japanese. The Chinese individuals differ from the African sample in Neanderthal alleles by an average factor of 5.05 (4.95 and 5.15), while the non-Han Eurasian average is 4.21 (3.93-4.65), that is: almost a point more. Only one European individual (4.65) really approaches the Han Chinese figures, which differ by almost a whole point (0.92) from the rest.


This, of course, can only be a very preliminary indication but it does seem intriguing and potentially meaningful. The fact that the greatest difference is with the, otherwise very close, Japanese could even point to some greater diversity patterns in East Eurasia in regard to Neanderthal genes in us, and, considering the tiny sample sizes, even in much of the rest of Eurasia.

Neanderthal gene flow found in humans

Finally an aperitif from the so much expected Neanderthal genome. We will still have to wait for the other specimens from several parts of Europe but the three individuals of Vindija (Croatia) have already been sequenced and provide some interesting information.

Richard E. Green et al., A Draft Sequence of the Neanderthal Genome. Science Magazine 2010. Open access.

Abstract

Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.

Related materials (all open access) can be found at Special Feature: The Neanderthal Genome, also at Science Magazine.

The authors estimate that this gene flow is quantified in 1-4% of the Eurasian genome and this is the same for West Eurasians, East Asians or Papuans but not for the Yoruba nor the San. This means that, most likely, there was gene flow between the two species soon after the Out of Africa migration.

More later maybe. This is just a quick heads up.

Molecular clock speculation obscuring the real Jurassic origin of primates

Again reality and reason clash frontally with the molecular clock hypothesis (or at least the most common interpretations of it).

If we'd have to follow the molecular clock speculations, so fashionable these days, we'd have to have sailor monkeys, which would have crossed oceans to get into America already in the Eocene, when the Atlantic Ocean was already huge. Such a colossal feat is plainly impossible, even for humans before just some centuries ago, but the fanatics of the molecular clock religion have argued for transoceanic rafting and hypothetical "island hopping" en masse.

Non-human primate range.

Common Sense shakes its head in disbelief, Folly laughs delighted at the naivety of even some of the supposedly most brilliant human minds.

Luckily Reason still has good cards to play in this surrealistic meta-game of honest facts versus trickster blind faith. The card that Reason plays now reads:

Michael Heads, Evolution and biogeography of primates: a new model based on molecular phylogenetics, vicariance and plate tectonics. Zoologica Scripta 2010.

Abstract:

The ages of the oldest fossils suggest an origin for primates in the Paleocene (∼56 Ma). Fossil-calibrated molecular clock dates give Cretaceous dates (∼80–116 Ma). Both these estimates are minimum dates although they are often 'transmogrified' and treated as maximum or absolute dates. Oldest fossils can underestimate ages by tens of millions of years and instead of calibrating the time-course of evolution with a scanty fossil record, the geographical boundaries of the main molecular clades of primates are calibrated here with radiometrically dated tectonic events. This indicates that primates originated when a globally widespread ancestor (early Archonta) differentiated into a northern group (Plesiadapiformes, extinct), a southern group (Primates), and two south-east Asian groups (Dermoptera and Scandentia). The division occurred with the breakup of Pangea in the Early Jurassic and the opening of the central Atlantic (∼185 Ma). Within primates, the strepsirrhines and haplorhines diverged with volcanism and buckling on the Lebombo Monocline, a volcanic rifted margin in south-east Africa (Early Jurassic, ∼180 Ma). Within strepsirrhines, lorises and galagos (Africa and Asia) and lemurs (Madagascar) diverged with the formation of the Mozambique Channel (Middle Jurassic, ∼160 Ma). Within haplorhines, Old World monkeys and New World monkeys diverged with the opening of the Atlantic (Early Cretaceous, ∼130 Ma). The main aspects of primate distribution are interpreted as the result of plate tectonics, phylogeny and vicariance, with some subsequent range expansion leading to secondary overlap. Long-distance, trans-oceanic dispersal events are not necessary. The primate ancestral complex was already widespread globally when sea-floor spreading, strike-slip rifting and orogeny fractured and deformed distributions through the Jurassic and Cretaceous, leading to the origin of the modern clades. The model suggests that the topology of the phylogenetic tree reflects a sequence of differentiation in a widespread ancestor rather than a series of dispersal events.

The paper is behind paywall but you can read a synthesis at Science Daily.

The molecular clock, if it still makes any sense at all, is certainly much slower. Primates migrated to South America in the Jurassic, when it was still part of Gondwanaland.

Does testosterone increase generosity instead of selfishness?

An interesting experiment has been done on women. A group of female volunteers received an injection of testosterone, the male hormone, associated with aggression in rodents, while, as usual, a control group received a placebo.

Among the women who did not know what was all about, those under testosterone behaved more generously than the control group (offering an average of 50 cents more in the test's deals). However those women who were told that had been injected testosterone, whether true or not, behaved more aggressively and offering up to 1 dollar less in their bargains.

These results contradict an earlier experiment in which young men did behave stereotypically macho under the effects the hormone. This other test did not consider bias though.

Source: New Scientist (I could not find the original paper, though I know it's been published in Nature).

Inefficient selection behind complexity

In the pure Darwinian scenario of draconian selection that can exist for instance among microorganisms, which are numerous enough for drift and randomness not to be a factor, and among whom competence is maximized like in the ideal free market of liberal economists, all accidental extra copies of genes (paralogs) are eventually erased because they are inefficient.

But among a much smaller population, like humans, Darwinian evolution works inefficiently and these troublesome extra copies of genes do in fact persist. In principle paralogs are problematic and can cause degenerative diseases like Alzheimer because they produce less efficient proteins. But what Ariel Fernández and Jianping Chen of the University of Texas have found is that these paralogs also drive complexity, that it is the accumulation of these errors by drift what in fact generates complexity, that complexity can only arise when selective evolution becomes weak and drift (chaos) rules instead.

After all every order is just a subset of pure Chaos, right?

Source: Science Daily.
Original paper: Human capacitance to dosage imbalance: Coping with inefficient selection. Genome Research 2009 (paywall).
.

Proteins that control genes

An interesting breakthrough in how the human genome actually works: many proteins are in fact controlling what genes do.

Of course, these proteins are ultimately a encoded by some genes, so the DNA code would still be the ultimate arbiter, but now it seems that the key may not be in the gene alone but also in those proteins that control its behavior, which in turn are generated by other "master genes".

This complex interaction beyond the simple "DNA rules" axiom may explain how humans, allegedly much more complex that other organisms like plants, have not more genes than them.

Source: Science Daily.
The original paper seems to be this one (paywall).
.

Kenyan tool discovery could push Homo age back to two million years

Just a quick mention of these interesting findings. The tools found by Thomas Plummer's team in Kenya are the oldest Olduwayan style tools found in what used to be a savannah habitat (there are older ones but belong to jungle ecosystem). For this reason the researchers are quite confident that they do belong to members of the genus Homo. The oldest dates considered at the moment were of some 1.8 million years.

Thomas W. Plummer et al., Oldest Evidence of Toolmaking Hominins in a Grassland-Dominated Ecosystem. PLoS ONE, 2009 (free access like all PLoS materials).
.

Ardipithecus, chimps, bonobos and christians

Martín Cagliari has uploaded at his most interesting blog Mundo Neandertal, the full documentary of Discovery Channel on the Ardipithecus Ramidus. A must view (while the blog is in Spanish, the film is still only available in English).

I was watching it yesterday and is most educative, specially for the amateur with just a side interest in ancient hominins, as is my case. But, as always they have to outline a theory, a Christian-sounding one, of course.

So I was not too persuaded that the two most surprising features of aunt Ardi and her kin, the grasping but bipedal feet and the very short and blunt canines responded too well to the theory suggested at Discovery Channel. They argue that this means two things: bipedalism in forest area (this last ratified by botanical and zoological research of the sediments - excellent job with that too) and lack of the kind of male competition we see among chimps for group dominance and hence reproductive advantage (they talk about controlling females but it's in fact more as I describe it here, as chimps are polyamorous, even if in a hierarchical manner).

So far sounds good. But the hypothesis launched is that these new bipedal males with low aggresivity responded to a new kind of bond (couple) sort of reproductive economy, in which the males could go farther looking for "quality food" (whatever that means) and carry it on their backs sounded kind of implausible and too moralist to be real. I was not persuaded.

As it happens often checking with your pillow helps to clarify thoughts and when I woke up I came with fresh ideas: they had been all the time ignoring bonobos!

Bonobos have relatively large canines but are much more bipedal than chimps, ability that they use to carry things around or just to walk, either on ground or on branches (someone pointed out recently too that even gibbons, the most distant ape, are sort of arboreal bipedal animals, that arboreal bipedalism is not that rare among our kin). Bonobo males also do not compete for the females (so their canines may well be somewhat redundant) but that is not because they live in couples and males have any enhanced role looking for food in far away places but because they are even more polyamorous than chimpanzees but females tend to lead the groups up to a point.

And when you look at Ardi after considering the bonobos, she looks very much like one in fact, right? In fact it is then when she stops looking like some sort of ape-ish chimera and starts making sense. At least for me.

Bonobos are more closely related to chimpanzees than to us but they share with us some traits that chimpanzees do not: they have a clear sense of empathy and compassion and the females are sexually available all the time, not just when ovulating. This allows them to have much more cohesive and horizontal societies, where males do not need anymore to compete for females' favors.

As I said before, they are also more bipedal than regular chimpanzees. They look like a much better comparison than regular chimpanzees for our evolution, at least in many aspects.

So my hypothesis is that Ardi and her kin were to some extent like bonobos in the social aspect. What do you think?
.

And still another critical role for vitamin D

As I said yesterday, it's been known for decades that it's critical in bone formation, recently was found that it is also critical in neural development and yesterday I read that it is also important in disease prevention and recovery.

And now I read that it has yet another function: it allows macrophages to ignore cholesterol, what prevents these vital defense cells from becoming "foam cells", a central element of atherosclerosis, the degenerative disease that clots blood vessels.

So, well, there are loads of reasons for depigmentation north of the tropics, where winters exist and cause a serious decrease of the natural intake of this crucial vitamin.
.