Archive pages

Better late than never. Now you can more easily browse through all that matters on Genetics and Prehistory (and similar) that was posted in Leherensuge in its three years of existence: I created two archive pages that are accessible from the top of the blog (tab bar). 

These two archives were originally posted at the new blog For what they were... we are but their location had become hard to find even for myself. I believe this is a much better location. 

Also, on occasion of the formal year change, I wrote a yearly review of 2010 anthropology and prehistory stuff that mostly revisits Leherensuge posts.

Remember please (some seem not to have noticed yet) that Leherensuge was discontinued on October 1st 2010 and replaced by two more sectorial blogs:

• For what they were... we are (anthropology, genetics, prehistory...)
• For what we are... they will be (the real thing: politics and such)

Hope that this change has been for the best.

The 'Homer Simpson gene' found

No kidding. A gene that makes mice dumber than they can potentially be and which also exists in humans (mice are very close relatives of us). Naturally the researchers have nicknamed it the "Homer Simpson gene".

The gene is techically known as RGS14 and is part of the CA2 region. Mice with the RGS14 gene knocked down (marvels of genetic engineering) surprisingly were much faster and effective than their normal cousins navigating mazes and overcoming obstacles. In other words: they were mice geniuses of sorts.

Naturally this finding begs a question:

why would we, or mice, have a gene that makes us less smart -- a Homer Simpson gene?

Good question. Scientists still do not know. I wonder if they should knock out that gene in themselves before the next research. Ok, sure, now I am kidding... or maybe not.

Why do we have a gene that makes us, it seems, dumber than we could potentially be. What advantages does stupidity confer?

Or does its absence cause some other kind of problems? Researchers speculate on some possible related issues (epileptic seizures, altered social behavior) but so far have not been able to find any clear correlation: the Homer Simpson gene makes you dumb and its absence does not seem to confer any disadvantage whatsoever.

So what's going on? Why hasn't this gene be selected against? Nobody knows... yet.

Source: Science Daily.

Ref. Sarah Emerson Lee et al., RGS14 is a natural suppressor of both synaptic plasticity in CA2 neurons and hippocampal-based learning and memory. PNAS 2010. Pay per view depending on where and when.

Louse TMRCA provides estimate for human clothing

Research on age estimates for the evolutionary divergence of head and body lice suggest that clothing was already in use when humans left Africa.

Melissa A. Topus, Origin of clothing lice indicates early clothing use by anatomically modern humans in Africa. Molecular Biology and Evolution, 2010. Open access.

The following graphic synthesizes the paper very well:

However it must be said that there are other alternative dates jumping around in the paper. For example the 95% CI estimate for head/clothes louse divergence is 29-691 Ka ago, the mean is 229 Ka and the mode just 83 Ka. So 170 Ka is just a reasonable good hunch, considering always their methods.

Also a much older date is suggested by a single author for hair loss: 3 million years ago. This however would have forced Homo erectus in Asia to make their own clothing, of which we have no evidence so far. Interestingly, the 1.2 Ka figure would allow our Neanderthal cousins to be hairy, a rather convenient biological equipment in Ice Age Europe, provided that the long chronology for Neanderthal-Sapiens divergence is correct (Gómez defends 1.3 million years, a date with strong, and growing, archaeological support).

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.

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.

Hybridation pros and cons

An issue that has arisen more than once in discussions as of late, specially in relation with the recently discovered Neanderthal admixture in Eurasian Homo sapiens, is that of hybrid vigor or lack of it thereof. This is addressed at a new paper in PLoS Biology:

Ulises Rosas et al., Cryptic Variation between Species and the Basis of Hybrid Performance. PLoS Biology 2010. Open access.

Author summary:

A major conundrum in biology is why hybrids between species display two opposing features. On the one hand, hybrids are often more vigorous or productive than their parents, a phenomenon called hybrid vigor or hybrid superiority. On the other hand they often show reduced vigour and fertility, known as hybrid inferiority. Various theories have been proposed to account for these two aspects of hybrid performance, yet we still lack a coherent account of how these conflicting characteristics arise. To address this issue, we looked at the role that variation in gene expression between parental species may play. By measuring this variation and its effect on phenotype, we show that expression for specific genes may be free to vary during evolution within particular bounds. Although such variation may have little phenotypic effect when each locus is considered individually, the collective effect of variation across multiple genes may become highly significant. Using arguments from theoretical population genetics we show how these effects might lead to both hybrid superiority and inferiority, providing fresh insights into the age-old problem of hybrid performance.

A news article synthesizing the findings can be found at Science Daily:

The results show that hybrids might be expected to exhibit increased performance in basic traits such as growth. However, they also show that in the longer term, other traits such as those involved in sexual reproduction might be expected to perform less well, accounting for reduced fertility of hybrids.

Evolution of sperm

There is a fascinating new paper dealing with the origin and evolution of sperm production in animals.

Chirag Shah, M. J. W. VanGompel et al. Widespread Presence of Human BOULE Homologs among Animals and Conservation of Their Ancient Reproductive Function. PLoS Genetics 2010. Open access.


Author Summary

While sexual reproduction is widespread among animals, it remains enigmatic to what extent sexual reproduction is conserved and when sex-specific gametogenesis (spermatogenesis and oogenesis) originated in animals. Here we demonstrate the presence of the reproductive-specific protein Boule throughout bilaterally-symmetric animals (Bilateria) and the conservation of its male reproductive function in mice. Examination of Boule evolution in insect and mammalian lineages, representing the Protostome and Deuterostome clades of bilateral animals, failed to detect any evidence for accelerated evolution. Instead, purifying selection is the major force behind Boule evolution. Further investigation of Boule homologs among Deuterostome species revealed reproduction-specific expression, with a strong prevalence of testis-biased expression. We further determined the function of a deuterostomian Boule homolog by inactivating Boule in mice (a representative mammal, a class of Deuterostomes). Like its counterpart in Drosophila (a representative of the opposing Protostome clade), mouse Boule is also required only for male reproduction. Loss of mouse Boule prevents sperm production, resulting in a global arrest of spermatogenesis in remarkable similarity to that of Drosophila boule mutants. Our findings are consistent with a common origin for male gametogenesis among metazoans and reveal the high conservation of a reproduction-specific protein among bilaterian animals.


The authors argue that no positive selection is apparent in the Boule gene but only purifying selection.

... the low Ka/Ks [non-synonymous/synonymous mutation] ratio suggests that purifying selection was responsible for the strong functional constraint on the entire protein, making Boule an exception to the rapid evolution commonly seen in reproductive genes.

In other words: it is a key component of the reproductive system in males across animal species that cannot be easily altered without causing the collapse of the system.

They also tested for gene expression of the Boule gene in male and female reproductive systems across the Bilaterian taxon (animals with front and back sides), finding that this gene is only manifest in the male reproductive system, unlike DAZL, which manifests in both genders among the species it does exist (most vertebrates).

Another finding is that animals (mice in the experiment) with mutant Boule gene are perfectly normal except that they are infertile. They even have a normal mating behavior. The only apparent difference is in the testes, which are somewhat smaller. Similar effects were found in fruit flies.

However, inside the testes, the effect of the mutant Boule gene is dramatic, totally impeding spermatogenesis.


Further references:

• BOLL (Boule) gene at HUGO database (located in chromosome 2)
• DAZL gene at HUGO database (located in chromosome 3)
• DAZ1 (DAZ) gene at HUGO database (located in chromosome Y)
• DAZL gene at Wikipedia
• DAZ1 (DAZ) gene at Wikipedia
• Article at Science News

Inbreeding and fitness in mysid shrimps

There is an interesting new paper on a subject that often drives much discussion in this blog at least: how bad is inbreeding. The answer of course depends on several issues such as the intensity of inbreeding (not a mere true/false dichotomy) and the environmental pressure.

This paper deals with these matters in an experimental set with Americamysis bahia, a species of mysid shrimps.

Jeffrey E. Markert et al.,Population genetic diversity and fitness in multiple environments. BMC Evolutionary Biology, 2010. Open access.

The authors created a number of extremely inbred populations by

1. Taking a single pregnant female (presumably impregnated by a single male, as is typical in this species) from the main population (AMX) and removing it when the brood was released

2. Taking then one impregnated female from one of the resulting populations and another from a different one and placing them in the same tank until the brood was released.

3. Taking then one single impregnated female from the population resulting from step 2.

Overall it means that the hyper-inbred brood at the start of the experiment, described as 1X, had went through a narrow 2-4-2 bottleneck, being the equivalent to having 2.4 founders.

Populations of the type 2X, 6X and 8X were generated by mixing the respective number of 1X inbred populations, so they represent lesser degrees of inbreeding each.

By the end of the experiment, after 40 weeks, these were some of the results (more tables, graphs and explanations in the paper):



Figure 1 - Population fitness, estimated with Median Population Size (A), Last Census size (B), and Reproductive Index (C) [not shown here].
Paired box plots define the median and middle two quantiles in stressful (left) and permissive environments (right). Lower case letters unite groups that are not statistically distinguishable using post-hoc tests (Tukey’s HSD) at α = 0.05.

We can see that extremely inbred populations performed badly, specially in stressful environments (low salinity) but that not so extremely inbred ones performed reasonably well, specially in permissive (normal) environments.

While the results should not be strictly extrapolable to other species, we can reasonably conclude that a very low number of effective population founders (5 or so) seriously hampers survivability, specially in challenging environments, where essentially means a death sentence. However a not so tiny number of founders (25-30) can do quite well, in particular if the environment is favorable.

Genetic diversity of SE Asian chickens

An interesting read for those curious about the origins of domestic chicken, its genetic diversity within and across breeds and the interactions between domestic and wild animals within the Gallus gallus species at their likely ancestral homeland.

C. Berthouly-Salazar et al. Vietnamese chickens: a gate towards Asian genetic diversity. BMC Genetics. Open access.

Some DNA sequences have mutation rates 10-50 faster than normal

Just a quick note for the reference.

Methylated CpG sequences in DNA (C-G sequences noticed as CpG to make them apart from C-G bonds between the two 'mirror' DNA chains) have a much faster mutation rate than all other DNA. This is because the group, apparently related to the immune system often, is most unstable what yields a mutation rate 10-50 times faster than for the rest of DNA.

This may have implications for the molecular clock hypotheses but I'm not sure in which sense right now.

More information at Science Daily.

Ref. J.C. Walser and A. Furano, The mutational spectrum of non-CpG DNA varies with CpG content. Genome Research 2010. Pay per view.

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).

Atapuerca experts: Neanderthals diverged one million years ago

Atapuerca researchers Aida Gómez and María Martinón have declared to Spanish newspaper Público that the material evidence from fossils clearly tell of a divergence time of c. 1 Ma., what strongly contradicts the short chronology proposed in a section of Green 2010 (but itself contradicted in the paper by another estimate of 850 Ka, more realistic).

Martinón says that the [proto-]Neanderthals who lived some 600,000 years at Atapuerca were already a different species from Homo sapiens. This makes impossible that their last common ancestor lived only 300,000 years ago, as the Neanderthal Genome project proposes. The teeth of other homins from the Gran Dolina of Atapuerca, from 900,000 years ago, already presented traits making them more Neanderthal than Sapiens, adds Gómez.

Source: Público.

Reference research: Aida Gómez Robles et al., Geometric morphometric analysis of the crown morphology of the lower first premolar of hominins, with special attention to Pleistocene Homo. Journal of Human Evolution 2008. Pay per view.

Interfertile seal species retain different gene pools in spite of hybridation

This is probably a paper of interest for all those surprised or otherwise intrigued by the gene flow now detected between H. neanderthalensis and H. sapiens.

Melanie L. Lancaster et al. Two behavioural traits promote fine-scale species segregation and moderate hybridisation in a recovering sympatric fur seal population. BMC Evolutionary Biology 2010. Open access.

The two fur seal species share the same reproductive spot at Macquarie island in New Zealand (and two other sites) and they do engage in fact in rather high interbreeding. However the two species remain neatly separated because of habitat preferences (colder/warmer waters, pebble/boulder beaches) and maybe also proposed fitness costs for the hybrid offspring.

BDNF gene confirmed crucial in stress-caused brain damage

I have mentioned before that environmental stress such as pollution, parental violence, mother-child separation, etc. are in fact behind most mental disorders, from low intelligence to schizophrenia and even Alzheimer syndrome.

While the effect is environmental and hence not really genetic but epigenetic, there is a gene that seems specially associated, known as BDNF (in particular polymorphism Rs6265).

It was already known that:

When normal mice are exposed to chronic stress (simulated by confinement in a wire mesh restraint), there is a significant retraction in the projections, or dendrites, of some of the neurons in the hippocampus, which shrinks in overall volume as well.

Left: healthy neuron, right: stress-damaged one

Now researches from New York have found that genetically altered mice with only one copy of the gene were stress-resistant and had brains apparently healthy even after prolonged stress.

However the research only seems to confirm the crucial role of this gene in stress damage in brain but does not explain why the mice with only one copy of BDNF managed to overcome neuronal stress damage.

Source: Science Daily, SNPedia

Ref. A. Magariños et al., Effect of brain-derived neurotrophic factor haploinsufficiency on stress-induced remodeling of hippocampal neurons. Hippocampus 2010. Pay per view.


Some thoughts on allele distribution:

The best researched SNP in humans within this gene seems to be the already mentioned rs6265, whose likely ancestral variant GG is very dominant among people of recent African ancestry but less so among Eurasians.

Eurasians have greater frequencies of the AA allele (not detected in Africans) and the heterozygous AG allele (only at very low frequencies in Africa), which would seem to have been affected by a marked selective sweep early on in human/hominin history. The AA allele seems to be quite negative for motor learning and favors introversion, however it also seems to provide resistence to depression and to some neurodegenerative diseases such as Parkinson syndrome. This variant is most concentrated in East Asia.

However all Eurasians have some of it and much more commonly the heterozygous AG allele, which has similar influences but not the depression resistance benefit.

Distribution of the r6265 alleles AA, AG, GG (from SNPedia)
Click here for the population codes

As most of the effects of this genetic variant seem negative (at best we could consider it to be neutral possibly, according to the described effects), I am in principle inclined to blame a founder effect for it. However, if the A allele has similar protective effects as the lack of one copy of the gene in the mice of the experiment (as the depression and neurodegenerative resistance may suggest), it might have been favored by selection in stressful conditions of some sort. This however is not at the moment demonstrated in any way and I mention only as a hypothetical scenario B.

Genetics and biology: rather 'soft' sciences

That's what I gather from: D. Fanelli, “Positive” Results Increase Down the Hierarchy of the Sciences. PLoS ONE 2010. Open access.

It's an interesting research on the reality of the generally accepted hierarchy of the sciences between harder and softer ones. Fanelli measured, among other factors, the number of positive results reported when testing a hypothesis, which broadly are likely to be more the less rigorous a science is.

However applied sciences tend to break this rule, reporting in general more positive results and with little differences for the "hard" and "soft" sciences (see fig. 2).

So, once we remove the applied sciences (labelled as "a") from the above graph, it seems pretty obvious that some biological sciences (immunology, MB and genetics, biology, medicine and pharmacology) seem to have as much procedural bias or even "cheating" as the social sciences.

Vanity, procedural sloopinness and lack of rigor are likely to exist to some extent in these disciplines. The difference is of course one of degree (see fig. 3) but from c. 70% positive results to c. 90% there is a clear difference that probably means almost 25-30% of undeserved complacency for the worst scoring disciplines (the one mendtioned above).

It is also noticeable that highly regarded Psychiatry/Psychology scores a lot worse than the general Social Sciences. While the often criticized Ecology scores very well instead.

In any case one thing is clear: the expression "it's not rocket science" has all validity, as Space Science is the one with the best results.

Major breakthrough in differentiating between form and function coding genes

Researchers from Taiwan and the USA have been able to differentiate between some 900 morphogenes and a similar number of physiogenes (out of more than five thousand tested) in genetically modified mice. In the words of co-researcher Jianzhi Zhang:

We found very large differences." Morphogenes were more likely to carry instructions for transcription -- the step that determines whether a gene should be turned on and how much gene product should be manufactured. Physiogenes were more likely to be blueprints for enzymes, receptors, transporters and ion channels (molecules that control the flow of ions across cell membranes).

The finding also seems to seriously challenge some hypothesis that suggested that genes caused both types of effects simultaneously.

The researchers also compared these genes in tissue from different species and found more differences in morphogenes than physiogenes, what means that form evolves effectively faster than function.

Source: Science Daily.

Ref. Ben Yang-Liao et al., Contrasting genetic paths to morphological and physiological evolution. PNAS 2010. (Pay per view depending on world region, should be open access everywhere in six months).

'Non-coding' DNA actually codes indivdual differences

New research has found that most of the individual differences, some even related to genetic illnesses such as lupus or schizophrenia, do not depends on the 0.25% variation in coding DNA (genes) but on the quite larger (1-4%) diversity in non-coding regions of the genome (sometimes called "junk DNA"), which nevertheless directly influence how key proteins, known as transcription factors, bind to the actual genes.

In the words of co-researcher Michael Snyder:

... the bulk of the differences among individuals are not found in the genes themselves, but in regions we know relatively little about. Now we see that these differences profoundly impact protein binding and gene expression.

More details at Science Daily.

Relevant research papers:
- Maya Kasowski et al., Variation in Transcription Factor Binding Among Humans. Science, 2010. Pay per view.
- Wei Zheng et al., Genetic analysis of variation in transcription factor binding in yeast. Nature, 2010. Pay per view.

Origin of small dogs in West Asia

New genetic research suggests that the alleles causing small size in certain dogs may have evolved early in the process of domestication and be derived from the wolf of West Asia (Canis lupus pallipes), of smaller size and tamer behavior than its more common relative Canis lupus lupus.

Melyssa M. Gray et al., The IGF1 small dog haplotype is derived from Middle Eastern grey wolves. BMC Biology, 2010.

See also the commentary by C.A. Driscoll and B. Macdonald: Top dogs: wolf domestication and wealth. Journal of Biology, 2010, arguing for a true origin of the dog in West Asian Mesolithic and later introgression of large size genes from the common wolf.

Mutation rate is "less than half"

From Science Daily.

Jard C. Roach et al., Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing. Science, 2010. Pay per view.

By comparing the parents' DNA sequences to those of their children, the researchers estimated with a high degree of certainty that each parent passes 30 mutations -- for a total of 60 -- to their offspring.

Scientists long had estimated that each parent passes 75 gene mutations to their children.

That means an effective mutation rate of just 2/5 the usual estimates.