Archive for the ‘Biology’ Category

India was not completely isolated as it moved from Gondwanaland to Asia

January 15, 2017

India – from Gondwanaland to Asia (after Wikipedia)

About 135 million years ago India and Mandagascar broke away from Gondwanaland and started shifting North North East. Around 88 million years ago, India and Madagascar split and the movement of the Indian tectonic plate speeded up. It crashed into Asia from about 30 million years ago to around 10 million years ago (though the movement still continues today). It had been thought that India was biologically isolated from about 71 million years ago until about 30 million years ago when some species hopping occurred from Africa and Asia.

This period was also extraordinarily rich in the evolutionary history of the mammals. It was the time when snakes and ants first appeared. There was a mass extinction event about 66 million years ago. The dinosaurs disappeared and became birds. Birds proliferated and so did large flightless birds. The diversity of mammals exploded, perhaps just because of the space left by the disappearance of the large, unsuccessful dinosaurs. The first pigs and deer developed. The grasses arrived. Carnivorous mammals appeared as their prey increased. The first primates made an entrance. But whatever was evolving on the Indian land-mass was evolving largely in isolation from that taking place in the areas that were to become Africa and Eurasia. But there are tantalising indications that on its journey the Indian land-mass may have been connected for short periods by a land bridge to the Horn of Africa or to what is now Arabia.

However a new paper suggests that some biological movement – perhaps across island chains – was taking place as early as 54 million years ago.

Frauke Stebner, Ryszard Szadziewski, Hukam Singh, Simon Gunkel, Jes Rust. Biting Midges (Diptera: Ceratopogonidae) from Cambay Amber Indicate that the Eocene Fauna of the Indian Subcontinent Was Not Isolated. PLOS ONE, 2017; 12 (1): e0169144 DOI: 10.1371/journal.pone.0169144

Bonn University Press Release: 

India gradually drifted away from Africa and Madagascar towards the north and collided with the Eurasian plate. Scientists assumed for a long time that the subcontinent was largely isolated during its long journey through the ocean and unique species of plants and animals were therefore able to develop on it. However, paleontologists at the University of Bonn are now showing using tiny midges encased in amber that there must have been a connection between the apparently cut off India and Europe and Asia around 54 million years ago that enabled the creatures to move around. The surprising results are now presented in the journal PLOS ONE.

India harbours many unique species of flora and fauna that only occur in this form on the subcontinent. The prerequisite for such a unique development of species is that no exchange takes place with other regions. For a long time, scientists assumed that India was isolated in this way due to continental drift. The supercontinent Gondwana, which included South America, Africa, Antarctica, Australia, Madagascar and India, broke up over the course of geological history. What is now India also began moving towards the north east around 130 million years ago. It was common belief among researchers that, before it collided with the Eurasian plate, India was largely isolated for at least 30 million years during its migration.

However, according to current findings by paleontologists at the University of Bonn, the Indian subcontinent may not have been as isolated on its journey as we have thought. “Certain midges that occurred in India at this time display great similarity to examples of a similar age from Europe and Asia,” says lead author Frauke Stebner from the working group of Prof. Jes Rust at the Steinmann Institute at the University of Bonn. These findings are a strong indicator that an exchange did occur between the supposedly isolated India, Europe and Asia.

Mining for amber in the Indian coal seams

The scientist from the University of Bonn mined for amber in seams of coal near the Indian city of Surat. Small midges, among other things, were encased in tree resin 54 million years ago and preserved as fossils. The tiny insects, which are often not even a millimeter large, are “biting midges”. Their descendants can still be found today in Germany in meadows and forests – where the little beasts attack you in swarms and suck your blood.

The paleontologist investigated a total of 38 biting midges encased in amber and compared them with examples of a similar age from Europe and China. Scientists from the University of Gdańsk (Poland) and Lucknow (India) were also involved in this. It has been possible to assign a total of 34 of these insect fossils to genera that are already known. “There was significant conformity with biting midges in amber from the Baltic and Fushun in north-east China,” reports Stebner.

Chains of islands presumably created a link to India

How the insects were able to spread between drifting India and Eurasia has not yet been clarified fully. “Nevertheless, it also seems to have been possible for birds and various groups of mammals to cross the ocean between Europe and India at the time,” the paleontologist refers to studies by other scientists. However, it has now been possible for the first time, with the aid of biting midge fossils, to also demonstrate an exchange between India and Asia in this period.

Stebner assumes that a chain of islands that existed at that time between India, Europe and Asia could have helped the biting midges to spread. As if from stepping stone to stepping stone, the insects could have gradually moved forward along the islands. “Some of the biting midges found in Indian amber were presumably not especially good long-distance flyers,” smiles the paleontologist from the University of Bonn. It was therefore probably not so easy to reach the subcontinent or move from there during the migration of India.

Right click to download: Gedanohelea gerdesorum in 54 million-year-old Cambay amber from India:

Gedanohelea gerdesorum in 54 million-year-old Cambay amber from India: (c) Photo: Working group Prof. Ryszard Szadziewski/University of Gdańsk (Poland)



Political correctness is based on fear and a lack of values

January 5, 2016

Offense is ultimately in the minds of those who take offense.

A female (but far from androgynous) MP in the UK wants passports and driving licences to exclude the gender of the holder. “Gender – neutral” is apparently the politically correct term. I suppose a photograph which could be taken as an unflattering or gender-defining image could also be banned.

Maria Miller (Getty)

Maria Miller (Getty)

Passports and driving licences should not state if the holder is male or female to avoid causing issues for transgender people, a former Tory cabinet minister has said. Maria Miller, the former culture secretary and chair of the new women and equalities committee, said the Government should “strip back” talking about gender unless it was necessary.

Even the Washington Post actually finds something half-good to say about Donald Trump

Why Trump may be winning the war on ‘political correctness’
Cathy Cuthbertson once worked at what might be thought of as a command post of political correctness — the campus of a prestigious liberal arts college in Ohio.
“You know, I couldn’t say ‘Merry Christmas.’ And when we wrote things, we couldn’t even say ‘he’ or ‘she,’ because we had transgender. People of color. I mean, we had to watch every word that came out of our mouth, because we were afraid of offending someone, but nobody’s afraid of offending me,” the former administrator said. ……. One thing is clear: Trump is channeling a very mainstream frustration.In an October poll by Fairleigh Dickinson University, 68 percent agreed with the proposition that “a big problem this country has is being politically correct.” It was a sentiment felt strongly across the political spectrum, by 62 percent of Democrats, 68 percent of independents and 81 percent of Republicans. Among whites, 72 percent said they felt that way, but so did 61 percent of nonwhites.

“People feel tremendous cultural condescension directed at them,” and that their values are being “smirked at, laughed at” by the political and media elite, said GOP strategist Steve Schmidt.

In Stockholm, the Managing Director of the Kulturhuset City Theatre overruled his Cultural Director to ban the title of a work by an artist (Makode Linde) called “The Return of the Negro King”. 
The gender axis of the human species may be a continuum but it is bimodal. Gender is part of an individual’s identity – like it or not.
Bimodal gender Blackless et al

Bimodal gender Blackless et al

I find nothing wrong in using “negro” as an adjective or in stating that women are attractive (mostly). No doubt that is sexist. “Mongolian” and “Eskimo” and “Chinese” or “Indian” are descriptive. The word gora (pink) is used in Hindi to describe white people and is primarily descriptive. Tall people remain tall and pink people remain pink whether the adjective is politically correct or not. Adjectives describe. As long as the description is not false, offense can only be taken in the minds of those offended. I am not supposed to express my convictions that while most religions can be twisted to give support to the use of violence, Islam today does that better than most. Feminism is (or should be) about combating the unfairness of prejudice not about denying femininity. Gender difference exists and cannot be legislated away. “Affirmative action” and “reservations” try to use unfair practices to try and compensate for some other unfair practice. (In actuality they only entrench either the original unfair practice or the compensating one). It is not correct to admit that intelligence is affected by genes (race) but it is perfectly acceptable to state that running the 100m is.

Political correctness is colourless, sexless, emotionless and without values. Not referring to race and gender and religion may avoid thin-skinned and frightened people from taking offense, but it does not remove the realities of race and gender and religion. The point of having values is to use them to make judgements. Political correctness is mindless. It is censure. It displays fear not courage.


Genetic mutations among the Inuit demonstrate the reality of “race”

September 23, 2015

It is politically correct to claim that “race” is just an artificial social construct. But of course “race” is real. It is about ancestry and about genetic differences that are quite real. It is about the groupings of peoples exhibiting the same genetic variations. Genetic studies are increasingly confirming the genetic differences that are distinguishable among the many ethnic groups of humans. Genetic groupings exist and are real but they are dynamic, not static. The genetic groupings (colloquially “race”) were different 1,000 generations ago and they will be different again in the future.

A new study shows that

“the Inuit and their Siberian ancestors have special mutations in genes involved in fat metabolism. The mutations help them partly counteract the effects of a diet high in marine mammal fat, mostly from seals and whales that eat fish with high levels of omega-3 polyunsaturated fatty acids.

Those genetic mutations, found in nearly 100 percent of the Inuit, are found in a mere 2 percent of Europeans and 15 percent of Han Chinese, which means that these groups would synthesize omega-3 polyunsaturated fatty acids differently from the Inuit. ….

The mutations seem to be at least 20,000 years old, and may have helped many groups of humans adapt to high-meat, high-fat, hunter-gatherer diets from large land and marine mammals high in certain types of omega-3 and omega-6 fatty acids, ……. They may have arisen among the original Siberians, who have lived in the Arctic for more than 20,000 years and arrived in Greenland when Inuit settled there about 1,000 years ago.”

Matteo Fumagalli et al,  Greenlandic Inuit show genetic signatures of diet and climate adaptation. Science, 18 September 2015 DOI:10.1126/science.aab2319

NewsBerkeley: ……. “The original focus on fish oil and omega-3s came from studies of Inuit. On their traditional diet, rich in fat from marine mammals, Inuit seemed quite healthy with a low incidence of cardiovascular disease, so fish oil must be protective,” said project leader Rasmus Nielsen, a UC Berkeley professor of integrative biology. “We’ve now found that they have unique genetic adaptations to this diet, so you cannot extrapolate from them to other populations. A diet that is healthy for the Inuit may not necessarily be good for the rest of us.”

These genetic mutations in the Inuit have more widespread effects. They lower “bad” LDL cholesterol and fasting insulin levels, presumably protecting against cardiovascular disease and diabetes. They also have a significant effect on height, because growth is in part regulated by a person’s fatty acid profile. The researchers found that the mutations causing shorter height in the Inuit are also associated with shorter height in Europeans.

Seals and walruses were part of the traditional diet of the Inuit, as seen in this illustration of a native village on Canada’s Baffin Island, from the book Arctic Researches and Life Among the Esquimaux (1865) by Charles Francis Hall.

“The mutations we found in the Inuit have profound physiological effects, changing the whole profile of fatty acids in the body, plus it reduces their height by 2 centimeters: nearly an inch,” said Ida Moltke, a University of Copenhagen associate professor of bioinformatics who is joint first author on the study. “Height is controlled by many genes, but this mutation has one of the strongest effects on height ever found by geneticists.”

Nielsen noted that this is some of the clearest evidence to date that human populations are actually adapted to particular diets; that is, they differ in the way they physiologically respond to diets. Just as genome sequencing can lead to personalized medicine tailored to an individual’s specific set of genes, so too may a person’s genome dictate a personalized diet. 

Nielsen and his colleagues at UC Berkeley and in Greenland and Denmark came to their conclusions after analyzing the genomes of 191 Greenlanders with a low admixture of European genes (less than 5 percent) and comparing them to the genomes of 60 Europeans and 44 Han Chinese. They looked for mutations occurring in a large percentage of Inuit individuals but in few or no other groups, which indicates that the mutation spread throughout the Inuit because it was somehow useful to their survival while not essential in other groups.

One cluster of mutations — in genes that code for enzymes that desaturate carbon-carbon bonds in fatty acids — stood out strongly, said Anders Albrechtsen, an associate professor of bioinformatics at the University of Copenhagen and a joint project leader. Fatty acids are the fat in our diet, and occur in saturated, polyunsaturated and unsaturated forms, depending on whether the molecules’ carbon atoms are linked together with no, some or all double bonds. Saturated fats are considered bad because they raise levels of cholesterol in the blood and lower the “good” high-density lipoproteins (HDL), all of which leads to plaque formation and clogged arteries. Diets rich in polyunsaturated and unsaturated fats are linked to lower heart disease. Desaturase enzymes convert dietary fatty acids into fatty acids stored and metabolized by the body.

The mutations common in the Inuit, once known as Eskimos, decrease the production of both omega-3 and omega-6 polyunsaturated fatty acids, presumably to account for the high amount of these fatty acids coming from the diet. Changing production of one fatty acid affects all fatty acids, however, since they regulate one another in a complex way, Albrechtsen said.

Thus, while it’s not clear which specific gene or genes within the cluster is responsible for the alteration in fatty acid metabolism, he said that “when you change the genes that are involved in fatty acid synthesis, you change the whole conversation among fatty acids, and that has a lot of downstream effects.” …… The researchers discovered another common mutation in a gene that is involved in the differentiation of brown, subcutaneous fat cells and brite fat cells, the latter of which generate heat. This may also have helped the Inuit adapt to a cold environment.

Race is real but it is dynamic. The genetically distinguishable race of Inuits goes back about 1,000+ generations. And some other genetic groupings of humans will be observable 1,000 generations on. But those groupings (races) will still be there. As I observed some time ago

We have no difficulty in accepting that different populations (effectively different races in colloquial usage) have differences of physical characteristics due to their genetic ancestry. There is no great outrage now that recent studies point to some genetic differences that Tibetans have which may give them an advantage in absorbing oxygen at high altitudes. Similarly there are no screams when other genetic studies suggest that East Africans (Kenyans and Ethiopians in the main) have some genes – or combination of genes – which give them better endurance and therefore – given good nourishment – lead to better performance as long distance runners. West Africans, or those of West African descent, it seems may have some genetic advantages which make them the fastest sprinters over short distances. African genes also seem to give a lower fat content in body mass – which is genetic – and may be one explanation why their performance as swimmers is less than exceptional. That Indians are more prone to Type 2 diabetes than other “races” is not indignantly opposed but just taken for the observation it is. Indian-Americans (3 generations) are already exhibiting lower rates than their Indian ancestry would indicate. Japanese have very low rates of heart disease but already (in less than 6 generations) Japanese-Hawaiians have heart disease rates that are 2 -3 times higher.

It is illogical to assume that these genetic variations between different geographic populations ( colloquially “races”) have only manifested themselves as physical variations. It is highly probable and probably inevitable that these genetic developments will also have affected the brain, its functioning and behaviour. And intelligence.

If it is acceptable – and not racist – to observe that there are genetic differences in physical characteristics between the “races” of today, then it is just as acceptable and no more racist to observe that there are genetic differences of intelligence between the “races” of today.

The taboo against even discussing genetic groupings (race) and physical and mental characteristics (intelligence) and behaviour is illogical.

Earth has too many failed species and 30% need to go extinct

May 1, 2015

There is a biodiversity myth that “more species” is better than “fewer species”. Even when the species are failed or useless species. The myth counts the 5 mass extinctions of the past as “bad events”, even though many current species (including humans) could not have evolved without the mass extinctions creating the space for new species. Every mass extinction has provided a cleansing (though not always effective) process for removing the failures of evolution.

The alarmist brigade are publicising a paper which claims that 1 in 6 species will go extinct due to global warming. (I note that the paper refers to global warming but all the publicity quotes “climate change”. What if the climate change was a global cooling?) The paper published in Science is a nonsense speculation and the abstract begins “Current predictions of extinction risks from climate change vary widely depending on the specific assumptions and geographic and taxonomic focus of each study.” He then goes on to selectively review the literature and chooses just those papers which support his conclusion. The author, Mark Urban, really has no value to add to anything about the climate and has just used the most “politically correct” opinion which ensures his funding and his publication. He uses “politically correct” assumptions to come to – surprise, surprise! – “politically correct” conclusions. He is a biologist but his “suggestions” about species and species extinction are equally valueless. He concludes that if global temperatures rises by 4ºC then up to 1 in 6 existing species will go extinct.

There are two things wrong with this example of bad science:

  1. Both the magnitude of global warming and the effect of warming are assumed (by the author and the papers he chooses to cite). The argument is circular.
  2. He assumes that the extinction of 1 in 6 species is a “bad thing”, even though there are more species now than ever before.

The sheer number of species in existence today is an indicator of how inefficient the process of evolution is. There are more failed species struggling along today and which need to go extinct, than ever before. It is my thesis that there is an optimum number of interconnected species to suit any given conditions. Evolution does not go for the optimum and because of the ineffectiveness of the process produces a great deal of “rubbish”. It is my contention that the Earth desperately needs another mass extinction to clean out the accumulated and accumulating muck of the “rubbish” of failed species.

Evolution fails in over 99% of its attempts to create species that can survive. The 1%  of species that do and have survived may seem to be perfectly tailored for the prevailing conditions but that is putting the cart before the horse. Evolution has no direction and does not seek excellence. It only throws up a plethora of species where just 1% of those species happen to suit the prevailing conditions.

The “conservation” movement and its blind worship of “biodiversity” borders on the stupid. Failed and useless species are given as much weight (sometimes more weight) than successful and useful species. Failing species are protected and successful species are persecuted. Useful species are hunted and useless species are coddled.

The fossil record shows that biodiversity in the world has been increasing dramatically for 200 million years and is likely to continue. The two mass extinctions in that period (at 201 million and 66 million years ago) slowed the trend only temporarily. Genera are the next taxonomic level up from species and are easier to detect in fossils. The Phanerozoic is the 540-million-year period in which animal life has proliferated. Chart created by and courtesy of University of Chicago paleontologists J. John Sepkoski, Jr. and David M. Raup.

The 3rd and 5th mass extinctions probably reduced the then existing number of species by about 50%. More than 30% of the species alive today (plant and animal) could be considered failed species – where a “failed species” is one which cannot cope with current change, or provides no benefit to any other species, or is in an evolutionary cul-de-sac. These species need to be allowed to go extinct or – when they are harmful to human or other life – to be terminated.

Hearing came before ears existed (as sight must have come before eyes)

February 12, 2015

Of course all our senses lie in the brain and not in the sensors receiving the input from our surroundings. So while our ears, eyes, skin and taste-buds detect certain physical characteristics and convert them into electrical signals, it is our brains which interpret the electrical signals they receive as being sound or colour or taste or heat. Our sense organs are merely transducers, converting some physical characteristic into an electrical signal. So how did the brain evolve and develop the interpretation “software” for these signals before the sensors had even been developed?

Two new papers show that Lungfish and salamanders can hear, despite not having an outer ear or tympanic middle ear. 

  1. C. B. Christensen, H. Lauridsen, J. Christensen-Dalsgaard, M. Pedersen, P. T. Madsen. Better than fish on land? Hearing across metamorphosis in salamanders. Proceedings of the Royal Society B: Biological Sciences, 2015; 282 (1802): 20141943 DOI: 10.1098/rspb.2014.1943
  2. K. Knight. Lungfish hear air-borne sound. Journal of Experimental Biology, 2015; 218 (3): 329 DOI: 10.1242/%u200Bjeb.119487

Aarhus University Press Release:

Lungfish and salamander ears are good models for different stages of ear development in these early terrestrial vertebrates. Two new studies published in the renowned journals Proceedings of the Royal Society B and The Journal of Experimental Biology show that lungfish and salamanders can hear, despite not having an outer ear or tympanic middle ear. The study therefore indicates that the early terrestrial vertebrates were also able to hear prior to developing the tympanic middle ear. …….

……. However, available palaeontological data indicate that the tympanic middle ear most likely evolved in the Triassic period, approximately 100 million years after the transition of the vertebrates from an aquatic to a terrestrial habitat during the Early Carboniferous. The vertebrates could therefore have been deaf for the first 100 million years on land. ….. 

…… They studied the hearing of lungfish and salamanders by measuring auditory nerve signals and neural signals in the brainstem as a function of sound stimulation at different frequencies and at different levels. Surprisingly, the measurements showed that not only the terrestrial adult salamanders, but also the fully aquatic juvenile salamanders – and even the lungfish, which are completely maladapted to aerial hearing – were able to detect airborne sound despite not having a tympanic middle ear. By studying the animals’ sense of vibration, the researchers were able to demonstrate that both lungfish and salamanders detect sound by sensing the vibrations induced by sound waves. …..

My experience in the engineering world suggests that there must be a connection  – a feedback loop – between the “software” interpreting the signals in a brain and the development of the transducers generating the signals. For example, rotating equipment (turbines, compressors or pumps) are routinely plastered with pressure and temperature and stress (really just pressure) sensors. But the 4 – 20 mA signals they generate have to be interpreted by software in a brain. Over the last 40 years I have observed that simple interpretation software has led to improved (more focused and more accurate) sensors which has in turn given even more sophisticated software.

And so it must have also been with our senses. Primitive brains must have interpreted some “sound waves” picked up incidentally as “sound”. Some feedback loop must have then provided the impetus for the evolution of a “sound detector”. The improved sensor would then have increased the sophistication of the interpretation in the brain and given rise to further development of the sensors. Today our ears detect pressure waves of frequency between 20 and 20,000 Hz and convert them into electrical nerve signals interpreted by the brain as sound. Evolution is really not about pro-active selection of advantageous characteristics but of deselection of those not fit enough to aid survival. Evolution has nothing to do with the selection of the “best” or even of the “fittest” characteristics but is all about deselection of those having an insufficient fit. Of course in a competitive environment between individuals, those with “advantageous characteristics” would surely have helped in the culling – directly or indirectly – of the less fit. But that begs the question as to why we cannot hear ultrasound? Was the ability to hear ultrasound of no survival benefit? Was it too much for the “software”? Or was the audible range just a compromise between range on the one hand and intricacy of the sensor on the other?

There must have been a similar start to the development of sight. The incidental or accidental detection of certain frequencies of electromagnetic radiation must have led to a feedback loop between the interpretation software in the brain and the development of suitable sensors. And now our eyes detect electromagnetic radiation of frequency between 430 and 790 terraherz (TH) and convert them into electric signals which are sent to the brain for interpretation. We find benefit in cameras which can “see” uv and infrared light. But it is not an ability that has evolved in our eyes.

I begin to think that in considering evolution we must distinguish between external forces which direct the death of unfit species (environmental changes mainly) and the internal forces within the individuals of a species which leads to “deficient” individuals being “deselected”. And the feedback loop between the brain and our sensory organs – which is no doubt still operating – is probably one such internal force.

To put it crudely, our ears and our eyes are as good as they are because those individuals who had worse ears or eyes could not survive to reproduction. And our ears and eyes are not any better than they are because being any better does not contribute to any increased survival and reproduction.

The shameful vilification of James Watson

December 12, 2014

In a recent post about the Nobel ceremony I observed that James Watson who had sold his Nobel medal had it returned to him by the purchaser. Apart from his recognition along with Crick and Wilkins for their DNA work, he has been and still is one of the most important evolutionary biologists of our time. But he has become persona non grata now with the self-appointed guardians of public morality and the prevailing “political correctness” which disallows “intelligence” – however it may be defined – from being in any way dependent upon the genetic variations between different human populations. His vilification and downfall was a rapid business in 2007, even though, everything Watson got in trouble for saying was entirely correct” as Gene Expression pointed out in October 2007:

It’s difficult to name many more important living figures in 20th century biology than James Watson. He ushered in the current age of molecular biology with his achievements in 1953, he built up one of the world’s greatest biological research facilities from damn near scratch, and he is a former head of the Human Genome Project.
Given such an august curriculum vitae, you would think that this man perhaps understands just a few things about genetics. But given only the condescending media coverage, you’d think this eminent geneticist was somehow “out of his depth” on this one.
In his interview with the Times on Oct. 14th, we learned that:

… [Watson] is “inherently gloomy about the prospect of Africa” because “all our social policies are based on the fact that their intelligence is the same as ours – whereas all the testing says not really”, and I know that this “hot potato” is going to be difficult to address.

These thoughts were a continuation of an important theme in his book Avoid Boring People:

… there is no firm reason to anticipate that the intellectual capacities of peoples geographically separated in their evolution should prove to have evolved identically. Our wanting to reserve equal powers of reason as some universal heritage of humanity will not be enough to make it so.

Although Watson’s book had already been out for a month with these more euphemistic, but still obvious, comments on race and intelligence, no one expressed any outrage. In fact the reviews were reverential and universally positive.
The explicit reference to intelligence and people of African heritage in his interview was clearly a violation of a much more formidable taboo. Still I am not aware of there being much noise about it until Oct. 17th when the Independent caused an immediate stir by calling attention to the remarks: Africans are less intelligent than Westerners says DNA pioneer.
There’s no point in rehashing the rapid sequence of events in detail: several of Watson’s sold-out speaking engagements were cancelled, many critical articles appeared in the British press, trailed by the American press a few days later, hundreds of blogs were fuming with negative commentary, including ones by the editors of Scientific American and Wired Magazine, a number of associations issued statements condemning his words, and soon he was suspended from his chancellorship at Cold Spring Harbor. Watson cancelled his already ruined book tour and flew home to tend to the destruction. It was too late; the eminent biologist retired in disgrace on Oct. 26th. 
One thing, though, was conspicuously missing from this whole irritating denouement: any semblance of factual refutation. There is good reason for this: everything Watson got in trouble for saying was entirely correct!

Gene Expression goes on to show that the data support what James Watson said.

Unfortunately our esteemed band of sputtering media scientists forgot to provide, in all of these instances, any of their allegedly voluminous citations to the contrary. Allow me, then, to take a different position, with the added benefit of evidence: ………

………. 65 psychometric intelligence study citations for sub-Saharan Africa, collected in IQ & Global Inequality, Race Differences in Intelligence, and IQ & the Wealth of Nations. The citations cover 47% of SS African countries or 78% of the people by national population numbers. The studies vary in quality, sample size, and representativeness, but broadly agree in their findings. Representative studies of the school age population with large sample sizes do not exhibit higher scores, much less scores that approach anything like European norms. …..

….. Thus typical African IQ scores of 70 and below can still be taken as a reliable finding. It is not simply the manufactured data of racialist researchers, or a byproduct of inadequate testing procedures. And, more importantly from the standpoint of the Watson controversy, certainly no reliable body of evidence has shown anything like parity with typical European scores.

The entire episode and shameful treatment meted out to Watson by an unscrupulous and sensationalist media and by politically correct but cowardly members of the scientific community was based, I think, on

  • the intellectual laziness in defining what “race” is, and the sloppy way in which the term is used, and 
  • a fear of confronting the ideological notion that some meaningless, diffuse “equality” of all humans transcends and overrides the real genetic variations due to ancestry

We use the term “race” colloquially and loosely and for convenience. There is no firm scientific definition of what constitutes a “race”. Often it is taken – wrongly – to be just a difference of skin colour. The politically correct brigade claim that race is a “social construct” but this is just nonsense. An “African-American” carries genes from his African ancestry and not any particular social behaviour from his ancestors. But “race” is also a dynamic term and shifts with the generations of man. The races we recognise and classify humans into today, is based on the prevailing groupings of populations that are convenient today. Fifty generations ago the “races” of that time would have been quite different. And fifty generations from now they will be quite different to the “races” we recognise today. The classification is about ancestry and is based on (or should be based on) the separate packages of genetic characteristics (some visible and some not) which are discernible and allow the grouping and classification of populations.

It seems perfectly logical, and is highly probable, that humans, though they may have originated from just a few relatively small populations out of Africarabia, have then over the next 5,000 generations, continued evolving in situ, giving the genetic diversity and the consequent physical diversity that we see today. The geographical populations we observe today are the result both of evolution in situ and a plethora of admixtures as people have migrated and mixed over the last 100,000 years. There were no “African-Americans” 50 generations ago. But already “African-Americans” today are different to “Africans” and both continue to evolve and develop in situ. It is quite unlikely that “African-American” or “Asian-British” or “Turkish-Germans” or “Chinese-Indonesian” will be classifications of race or ethnicity that will be used 50 generations from now. This geographically evolved and still evolving diversity, already shows up as genetic differences not only of skin, eye and hair colour but also as differences in disease resistance, physical characteristics, athletic capabilities, behaviour and surely many more invisible (including mental) characteristics.

We have no difficulty in accepting that different populations (effectively different races in colloquial usage) have differences of physical characteristics due to their genetic ancestry. There is no great outrage now that recent studies point to some genetic differences that Tibetans have which may give them an advantage in absorbing oxygen at high altitudes. Similarly there are no screams when other genetic studies suggest that East Africans (Kenyans and Ethiopians in the main) have some genes – or combination of genes – which give them better endurance and therefore – given good nourishment – lead to better performance as long distance runners. West Africans, or those of West African descent, it seems may have some genetic advantages which make them the fastest sprinters over short distances. African genes also seem to give a lower fat content in body mass – which is genetic – and may be one explanation why their performance as swimmers is less than exceptional. That Indians are more prone to Type 2 diabetes than other “races” is not indignantly opposed but just taken for the observation it is. Indian-Americans (3 generations) are already exhibiting lower rates than their Indian ancestry would indicate. Japanese have very low rates of heart disease but already (in less than 6 generations) Japanese-Hawaiians have heart disease rates that are 2 -3 times higher.

It is illogical to assume that these genetic variations between different geographic populations ( colloquially “races”) have only manifested themselves as physical variations. It is highly probable and probably inevitable that these genetic developments will also have affected the brain, its functioning and behaviour. And intelligence.

“Intelligence” is many things to many people and – by most definitions – more than just an IQ test. The IQ test only really measures the ability to do the test. Nevertheless the IQ test results do seem to correlate well to whatever we may choose to call intelligence. There is without doubt a genetic component to both intelligence and IQ test results. IQ test measurements do show that results are significantly lower – for whatever reason –  among sub-Saharan African populations – on average. If intelligence has a genetic component and the colloquial use of the term “race” refers to an identifiable population exhibiting a certain package of genetic characteristics, then it is quite likely that the different genetic packages lead to some differences of intelligence.

If it is acceptable – and not racist – to observe that there are genetic differences in physical characteristics between the “races” of today, then it is just as acceptable and no more racist to observe that there are genetic differences of intelligence between the “races” of today.

That is all that Watson said.

(What “intelligence” actually is or may be is another story for another day).

Junk DNA is the genome’s hedging instrument

May 19, 2014

I have always been somewhat confused by the manner in which the word “junk” has been attached to the repeating sequences of DNA in our genes which – as far as was known – had no function, and also for high risk securities which offer high returns.

There is a new paper in PLOS Genetics called The Case for Junk DNA (which is a little beyond me) but there is also an eminently readable commentary by Carl Zimmer. My take-aways from Zimmer’s piece are:

  • Genomes are the pattern for life.
  • Genomes contain genes.
  • Genes are made up of DNA.
  • Our DNA is a string of units called bases.
  • Our cells read the bases in a stretch of DNA–a gene–and build a molecule called RNA with a corresponding sequence.
  • The cells then use the RNA as a guide to build a protein.
  • Our bodies contain many different proteins, which give them structure and carry out jobs like digesting food.
  • The human genome contains about 20,000 protein-coding genes.
  • Protein-coding genes only make up about 2 percent of the human genome. 
  • In the 1950’s the non-coding 98% began being called “junk” genes.
  • Functions performed by some of these “junk” gene are constantly being found. The ENCODE project has assigned some bio-chemical function to about 80% of the genome.
  • Having large amounts of truly “junk” DNA is a protection against mutation (by making most mutations of the junk portion of no consequence). Evolution requires “junk”. A junk-free genome would be too vulnerable to mutations to survive (mutational meltdown). This suggests that humans need about 90% junk DNA to avoid mutational meltdown.
  • Junk portions are also important for evolution since protein-coding genes can evolve from these non-coding regions.
  • Much of our genome is made up of viruses, and every now and then, evolution has used those viral genes. 

From all of this I come to the layman’s understanding that about 2% of our genome is made up of about 20,000 active protein-coding genes, another 10 – 30% has some active bio-chemical function (such as switching genes on of off), some unknown portion is passive material which could feasibly be activiated and the remainder is the buffer material which both provides protection from rampant mutation and provides a pool resource for future evolution.

Junk bonds are risky investments, but have speculative appeal because they offer much higher yields than safer bonds. Companies that issue junk bonds typically have less-than-stellar credit ratings, and investors demand these higher yields as compensation for the risk of investing in them. A junk bond issued from a company that manages to turn its performance around for the better and has its credit rating upgraded will generally have a substantial price appreciation. 

Now as it becomes  clear that not all sections of non-protein-coding  DNA are entirely useless, I begin to see an analogy between “junk DNA” and “junk bonds”. A high – but manageable – risk but giving high yield on the one hand and a high – but manageable –  genetic redundancy giving high evolutionary appreciation on the other.

Junk DNA is the genome’s hedging instrument.

Vertical species evolution (rather than horizontal evolution for mere survival) is then probably dependent upon achieving some optimum  balance between genome size, coding DNA and junk DNA.

This is my attempt to apply a similar description to junk DNA,

Junk DNA are the genome’s hedge instruments and have evolutionary appeal because they offer a much wider range of evolutionary possibilities. Species that build up massive genomes with very high levels of junk DNA typically lie lower on the evolutionary hierarchy and evolve horizontally rather than vertically. When junk DNA in a species high up on the vertical scale (mammals) achieves a balance with the coding genes and the size of the genome, the species will have its rating upgraded and will generally have a substantial evolutionary appreciation. 

Idiot science: Babies cry at night to prevent Mom from having another child!!

April 28, 2014
David Haig

David Haig

Some so-called “science” is done primarily for headlines – even at Harvard. I wonder if there is a correlation between headlines generated and funding received?

This time the idiot science is from David Haig – a biology Professor at Harvard. His abstract states

All these observations are consistent with a hypothesis that waking at night to suckle is an adaptation of infants to extend their mothers’ lactational amenorrhea, thus delaying the birth of a younger sib and enhancing infant survival.

From Science News:

When a baby cries at night, exhausted parents scramble to figure out why. He’s hungry. Wet. Cold. Lonely. But now, a Harvard scientist offers more sinister explanation: The baby who demands to be breastfed in the middle of the night is preventing his mom from getting pregnant again.

This devious intention makes perfect sense, says evolutionary biologist David Haig, who describes his idea in Evolution, Medicine and Public Health. Another baby means having to share mom and dad, so babies are programmed to do all they can to thwart the meeting of sperm and egg, the theory goes.

Since babies can’t force birth control pills on their mothers, they work with what they’ve got: Nighttime nursing liaisons keep women from other sorts of liaisons that might lead to another child. And beyond libido-killing interruptions and extreme fatigue, frequent night nursing also delays fertility in nursing women. Infant suckling can lead to hormone changes that put the kibosh on ovulation (though not reliably enough to be a fail-safe birth control method, as many gynecologists caution).

Of course, babies don’t have the wherewithal to be interrupting their mothers’ fertility intentionally. It’s just that in our past, babies who cried to be nursed at night had a survival edge, Haig proposes.

The timing of night crying seems particularly damning, Haig says. Breastfed babies seem to ramp up their nighttime demands around 6 months of age and then slowly improve — precisely the time when a baby would want to double down on its birth control efforts. … 

Tenured Professors would seem to have little need for common sense.

What is worse than the idiot science is the fawning article by Laura Sanders in Science News.

Plant and virus life revived after 30,000 years in the Siberian permafrost

March 4, 2014

Two years ago we heard about plants being grown from seeds and pods preserved for 30,000 years in the Siberian permafrost. And now comes the news that a giant virus of that time has also been revived and is still capable of infecting other life.

This would have been about 1,500 generations ago. 30,000 years ago the Neanderthals had just disappeared, mammoths, woolly rhinoceros and long-horned bison roamed in Siberia. Modern humans had reached Europe but had not reached the Americas. It was at the peak of the last glacial and the spread of agriculture was still some 15,000 years in the future.

A prehistoric plant resurrected from frozen tissue. S. Yashina et al. Proc. Natl Acad. Sci. USA

1. Wild flower blooms again after 30,000 years on ice 

During the Ice Age, Earth’s northern reaches were covered by chilly, arid grasslands roamed by mammoths, woolly rhinoceros and long-horned bison. That ecosystem, known by palaeontologists as the mammoth steppe, vanished about 13,000 years ago. It has no modern counterpart.

Yet one of its plants has reportedly been resurrected by a team of scientists who tapped a treasure trove of fruits and seeds, buried some 30,000 years ago by ground squirrels and preserved in the permafrost 

The plant would be by far the most ancient ever revived; the previous record holder was a date palm grown from seeds roughly 2,000 years old. ….. . took samples of placental tissue from S. stenophylla fruits. The plant placenta — an example of which is the white matter inside a bell pepper — gives rise to and holds the seeds. The tissue produced shoots when it was cultivated in vitro, and the scientists used these to propagate more plants. They are the oldest living multicellular organisms on Earth, the team says.

The plants have already blossomed to produce fertile seeds, which were grown into a second generation of fertile plants. During propagation, the ancient form of the wild flower produced more buds but was slower to put out roots than modern S. stenophylla, which is found along the banks of the Kolyma. This suggests that the original has a distinct phenotype, adapted to the extreme environment of the Ice Age.

(S. Yashina et al. Proc. Natl Acad. Sci. USA; 2012).

2. Giant virus resurrected from 30,000-year-old ice

In what seems like a plot straight out of a low-budget science-fiction film, scientists have revived a giant virus that was buried in Siberian ice for 30,000 years — and it is still infectious. Its targets, fortunately, are amoebae… The newly thawed virus is the biggest one ever found. At 1.5 micrometres long, it is comparable in size to a small bacterium. Evolutionary biologists Jean-Michel Claverie and Chantal Abergel, the husband-and-wife team at Aix-Marseille University in France who led the work, named it Pithovirus sibericum, inspired by the Greek word ‘pithos’ for the large container used by the ancient Greeks to store wine and food. “We’re French, so we had to put wine in the story,” says Claverie. The results are published in Proceedings of the National Academy of Sciences.

Legendre, M. et al. Proc. Natl Acad. Sci. USA

Under a microscope, Pithovirus appears as a thick-walled oval with an opening at one end, much like the Pandoraviruses. But despite their similar shapes, Abergel notes that “they are totally different viruses”. …. Pithovirus has a ‘cork’ with a honeycomb structure capping its opening (see electron-microscope image). It copies itself by building replication ‘factories’ in its host’s cytoplasm, rather than by taking over the nucleus, as most viruses do. Only one-third of its proteins bear any similarity to those of other viruses. And, to the team’s surprise, its genome is much smaller than those of the Pandoraviruses, despite its larger size. ….

While “cloning” of ancient and extinct species is not really possible, it is not too fanciful to imagine that ancient DNA and modern hosts could give rise to creatures having characteristics beneficial during an ice age. And perhaps that could be of some interest when this interglacial ends – as it must – and we do enter into another glacial period.

Cold resistant, woolly cattle and well trained sabre-tooth tigers to mange the wandering herds perhaps. Maybe we might then even want some extra Neanderthal DNA injected into us!! Finally a use for biodiversity!

New Denisovan genome indicates inter-breeding with another, unknown, archaic human

November 19, 2013

The period some 30,000 – 50,000 years ago is getting positively crowded with different branches of humans. The direct ancestors of modern humans lived and interbred not only with Neanderthals and Denisovans but also apparently with still another, as yet unknown, branch of humans.

NatureNew genome sequences from two extinct human relatives suggest that these ‘archaic’ groups bred with humans and with each other more extensively than was previously known.

The ancient genomes, one from a Neanderthal and one from a different archaic human group, the Denisovans, were presented on 18 November at a meeting at the Royal Society in London. They suggest that interbreeding went on between the members of several ancient human-like groups living in Europe and Asia more than 30,000 years ago, including an as-yet unknown human ancestor from Asia. ..

… All humans whose ancestry originates outside of Africa owe about 2% of their genome to Neanderthals; and certain populations living in Oceania, such as Papua New Guineans and Australian Aboriginals, got about 4% of their DNA from interbreeding between their ancestors and Denisovans, who are named after the cave in Siberia’s Altai Mountains where they were discovered. The cave contains remains deposited there between 30,000 and 50,000 years ago. 

Those conclusions however were based on low-quality genome sequences, riddled with errors and full of gaps, David Reich, an evolutionary geneticist at Harvard Medical School in Boston, Massachusetts said at the meeting. His team, in collaboration with Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have now produced much more complete versions of the Denisovan and Neanderthal genomes — matching the quality of contemporary human genomes. The high-quality Denisovan genome data and new Neanderthal genome both come from bones recovered from Denisova Cave.

The new Denisovan genome indicates that this enigmatic population got around: Reich said at the meeting that they interbred with Neanderthals and with the ancestors of human populations that now live in China and other parts of East Asia, in addition to Oceanic populations, as his team previously reported. Most surprisingly, Reich said, the new genomes indicate that Denisovans interbred with another extinct population of archaic humans that lived in Asia more than 30,000 years ago, which is neither human nor Neanderthal.

It would seem that when the world was still in the grip of an ice age 30,000 – 50,000 years ago, the reality of human history was not so far away from Tolkien’s Middle Earth.  Ancient history but it was only 1,500 – 2,500 generations ago. Middle Earth was where men could breed with elves and hobbits were an off-shoot of men. The Druedain were also off-shoots of men and some – if not all – orcs were deliberately bred from elves while all trolls and dragons were artificially bred.

From the J.R.R. Tolkien Encyclopedia: Scholarship and Critical Assessment

from The biology of Middle eart - Tolkien Encyclopedia

from The biology of Middle Earth – JRR Tolkien Encyclopedia

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