Archive for the ‘Evolution’ Category

A comment on the conservation of the Galapagos turtle

November 25, 2015

A reader commented on the About page about an old post where comments are closed.

Galapagos conservation project prevents the evolution of ninja turtles

Archie G Says:

Hello, I wanted to comment on a post but couldn’t find where to do it, so I’ll just do it here. About the Galapagos conservation project. I know your post was intended to be humurous but it think it is important to make this clear anyway: it was not a way to protect a charismatic species above an “ugly” species. Even if rats were there before Darwin arrived, they were an introduced european species (Rattus rattus) that had limited the perpetuation of Galapagos turtles since its introduction to the Island. The rats ate 100% of the hatchlings that had no predators before. It is not “specism”, rodents are not bad, but introduced species in general damage ecosystems, whether they are a pretty animal or not. Conservation is not a matter of some animalistic fan group, it takes years of research and effort to understand its mechanics.

But I beg to differ.

(The Galapagos turtle is itself an invasive species and how it got there is not known. And it is interesting to consider all the humans who were “introduced” to Australia and the New World as invasive species who – for the conservation of the indigenous peoples – should now be rooted out).

“Conservationists” are effectively making value judgements which are unjustified. When “general damage to an ecosystem” is quoted, a judgement has already been made as to which ecosystem is “good” and which is “bad”. But all these judgements always penalise the successful species and protect the unfit species. 

I think the Galapagos turtles are fantastically “charismatic” too, but they are fundamentally an unfit species. In evolutionary terms they are ripe for extinction. So are tigers. But they are being “saved” for the aesthetic sensibilities and the entertainment of humans – not for finding or creating an adapted neo-tiger or neo-turtle species which can find a real place in the world, rather than for surviving in a zoo. Protected reserves – as some of the Galapagos islands are – are little more than large zoos and their purpose is just for the entertainment and edification of humans.

“Conservation” as it is practiced today seeks to maintain a past, or an unviable status quo. Such “conservation” is flawed. In the name of “conservation”, reserves and zoos are used to create big cats for “canned hunting”. By default, a “huntable lion”, no good for anything other than being hunted, is now being bred. Far better to help a species to adapt to real, possible futures. Far better if species were helped (by genetic engineering perhaps) to adjust to the new realities and find a new place. What’s the point of saving a species, that is unfit for a current habitat, and freezing it in this unsuccessful form for a habitat which is no longer viable?

As the dominant species on this planet, humans will never allow some other species to become so successful as to be a threat. There is no moral reason they should. And species which cannot adapt to the dominant species are unfit and deserve to become extinct. After all, 99% of all species that have ever lived are now extinct.

Related:

Genetic adaptation – not stagnating conservation – is the way to help threatened species

Ancient Chinese teeth confirm many and older Out of Africa events

October 15, 2015

Over at 6,000 generations I post about the new paper about the 47 human teeth found in Fuyan Cave, Daoxian, China which are between 80,000 and 120,000 years old.

The 47 human teeth found in Fuyan Cave, Daoxian, China. photo S. XING AND X-J. WU via DiscoveryNews

There were clearly many Out of Africa or Africarabia events starting from 130,000 years ago both before and after the Toba explosion.

80,000-120,000 year old modern humans in S China confirm many and older Out of Africa events

The single Out of Africa event for modern humans is clearly far too simplistic. It is also clear that there were many back to Africa movements as well. Humans expanded sometimes because their old habitats were no longer viable. But, it seems, humans also explored and expanded into new territories from regions of plenty and where they maintained some contact with where they had come from. Probably, just because they could.

Evolutionary story of the giraffe’s long neck does not convince

October 8, 2015

A new paper from the New York Institute of Technology reports on fossil studies of the giraffe’s neck vertebrae which show that (press release):

…. the evolution likely occurred in several stages as one of the animal’s neck vertebrae stretched first toward the head and then toward the tail a few million years later. The study’s authors say the research shows, for the first time, the specifics of the evolutionary transformation in extinct species within the giraffe family. ..

“It’s interesting to note that that the lengthening was not consistent,” said Nikos Solounias, a giraffe anatomy expert and paleontologist at NYIT College of Osteopathic Medicine. “First, only the front portion of the C3 vertebra lengthened in one group of species. The second stage was the elongation of the back portion of the C3 neck vertebra. The modern giraffe is the only species that underwent both stages, which is why it has a remarkably long neck.”

…. “We also found that the most primitive giraffe already started off with a slightly elongated neck,” said Danowitz. “The lengthening started before the giraffe family was even created 16 million years ago.” ….

….. the cranial end of the vertebra stretched initially around 7 million years ago in the species known as Samotherium, an extinct relative of today’s modern giraffe. That was followed by a second stage of elongation on the back or caudal portion around one million years ago. The C3 vertebra of today’s giraffe is nine times longer than its width — about as long as an adult human’s humerus bone, which stretches from the shoulder to the elbow.

Clearly one evolutionary pathway has given us the modern giraffe with its ridiculously long neck, but there was also a pathway which led to the shortening of the neck

As the modern day giraffe’s neck was getting longer, the neck of another member of the giraffe family was shortening. The okapi, found in central Africa, is the only other living member of the giraffe family. Yet, rather than evolving a long neck, Danowitz said this species is one of four with a “secondarily shortened neck,” placing it on a different evolutionary pathway.

But I find the story that the elongation of the giraffes neck was due to natural selection, as a consequence of a survival advantage for longer necked individuals in time of drought, somewhat unsatisfactory. The idea that it was sexual selection at play (a longer neck providing the males with better fighting ability) is even more unsatisfactory.

Let us suppose that a prolonged drought led to all middle size shrubs dying out or at least becoming unavailable to ancestral giraffes through competition. It would have had to have been a very selective drought that allowed only grasses and very low shrubs to survive along with the leaves of taller bushes and trees. We need to remember also that for such a natural selection to work, all the shorter necked giraffes needed to die out and thus be de-selected. It is not impossible that the shorter necked animals were just crowded out by more efficient herbivores which led to the longer necks opening up a niche not available to the other herbivores. But I find the arguments for the extinction of shorter necked giraffes while other herbivores prospered somewhat unconvincing.

The evolutionary pathway to the longer neck is still a mystery.

Why not longer legs? I like this homage to Gary Larson by evolution-outreach.com

Brian Switek reviewed the various theories a few years ago and pointed out

… significant neck elongation began around 14 million years ago during the Late Miocene — after the lineage to which the relatively short-necked okapi split off — and by about 5 million years ago giraffes of modern proportions had evolved. ……..  it appears that the elongation of giraffe necks occurred during a global pattern of aridification in which grasslands replaced forests.

For the moment, the question of “How did the giraffe get its long neck?” must be answered with “We do not yet know”

Switek wrote that five years ago – but it still applies.

We still don’t know.

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.

There was no biodiversity to begin with

September 15, 2015

I was listening to some conservationists on the radio discussing the rate of loss of species and how this was a catastrophe in the making for biodiversity. It was an unsatisfactory talk mainly because they all made what I thought were quite unjustified assumptions. It was more about political advocacy rather than any attempt to argue based on evidence.

The “politically correct” view is that biodiversity (measured as the number of species in existence) is a “good thing” and that more species is “good” and fewer species is “bad”. Saving endangered species is also a “good” thing. That species are becoming extinct at an alarming rate means catastrophically that a 6th mass extinction is nigh. But I find this viewpoint lacking in substance. We have more species existing today than ever before. Probably too many. Mass extinctions have helped “clean out” the rubbish that evolution throws up. Extinction rates may be high but that is hardly surprising when the number of species is so high. A 6th mass extinction may, in fact, be necessary. More species and more biodiversity is not always a good thing.

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 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.

An endangered species is one whose population is low and dangerously in decline. If numbers of individuals of a species are that low, then that species has already become irrelevant in its contribution to the functioning of the biosphere. It may well be a matter of regret, just as there is always regret when a language becomes extinct from disuse. But apart from providing entertainment value for humans, the saving of a few members of a doomed species provides no real benefit for the functioning of the biosphere. I would be very sorry to see tigers becoming extinct, but the reality is that their numbers are so low that they play no significant part in the sustenance of the biosphere. The role of a predator species is primarily to control the population of its prey. From a biodiversity point of view they are already irrelevant. Saving the tiger has nothing to do with maintaining a healthy biodiversity and everything to do with human entertainment (including that of the conservationists) and “feeling good”.

(I am of the opinion that helping an endangered species to survive can be desirable but then “conservation” should be based on helping that species to adapt genetically rather than to freeze it into an artificial habitat – zoos and reserves – to which it is not suited).

At one time there was just a single species that all life derives from – perhaps even just one living cell. (And even for creationists, all the diversity of humankind has derived from a single mating pair – and the raging incest that that implies). There was no biodiversity to begin with. Genetic variation with each generation and genetic mutations then caused new species to come into being, first to fill up the spaces that the prevailing environment allowed and then to adapt to changing environments. If each generation of the first species had bred true there would, of course, be no biodiversity. Genetic variation and empty space in the environment led to growth of species. Overcrowding of a given space or drastic environment change cause the decline and extinction of species. The prevailing level of “biodiversity” at any time is not then some target to be achieved, but just the current balance between the birth and death of species.

It seems almost self-evident to me that, for any given environment there must be an optimum number of species, with particular combinations of characteristics, which allow the ecosystem or biosphere to be in a self-sustaining equilibrium (not growing or declining but self-sustaining). This optimum will vary depending upon the characteristics and interactions between the particular species existing and the available space in the prevailing environment. Then, having fewer than the optimum number of species in that environment would mean that all the complex interdependent, interactions between species that seem to be necessary for sustaining each of the participating species would not be fully developed. I say “seem” because it is not certain that all interdependencies are necessarily of benefit to individual species. “It is the entire ecosystem which benefits” I hear some say, but even that is more an assumption than a conclusion.

But what would happen in such a situation?  If the interactions are truly necessary, then some of these sub-optimal number of species should logically be on the way to stagnation or to extinction. But it is not certain that some new equilibrium will not be reached. One species too few for a given environmental space will only lead to the space being occupied by an existing or a new species. One species too many for a given space will lead to the extinction of a redundant species or of a number of species existing under genetic stress, until genetic variation reduced the stress. The interactions between species in any environment are not planned in advance. They are just those that happen to prevail and survive because they succeed in the environmental space available. Too few species will give an increase of species until overcrowding reduces the number of species. A rapid change of environment and a reduction of the space available must give a decrease in the number of species making up the optimum for a self-sustaining biosphere.

Generally species of plant life have increased in the wake of human habitations.

For example, more than 4,000 plant species introduced into North America during the past 400 years grow naturally here and now constitute nearly 20 percent of the continent’s vascular plant biodiversity.

But then we try to eradicate “invasive” species even though that represents a decrease in biodiversity. Clearly some biodiversity “is not good”. We hunt down successful species as pests when they reach and thrive in new or empty environmental spaces. We protect and support unsuccessful (failed) species in the name of conservation and biodiversity. We have no qualms in trying to eradicate insects, microbes and bacteria which cause human disease even if biodiversity is consequently reduced. From the perspective of the biodiversity of the genetic pool, losing a species of some unknown bacteria may be just as significant as the extinction of the elephant.

The rate of growth of the human species has meant that other species have not been able to adapt fast enough – genetically – to their loss of habitat or the increase of competition. The environmental space available to them has drastically reduced. But that is reality. Creating artificially unsustainable habitats will not change that. The optimum level of biodiversity for the environmental space today is different to that of 100 years ago. Biodiversity cannot be considered independently of the environmental space available. Conservationism which seeks to maintain the wrong level of biodiversity for the available space seems to me to be both futile and stupid. Especially when conservationism has no idea what the “optimum” level of biodiversity is and whether the current level lies above or below the optimum level.

 

Natural selection is about “good enough”, but artificial selection could be about excellence

September 11, 2015

“Natural” selection is brainless.

I am always irritated by the assumption that natural selection and its resultant evolution is a “good thing”. After grinding my teeth for a while I tend to switch off when a “scientist” starts assigning values of goodness or badness to something that just is. So this comes as a reaction to an idiot scientist I just heard on radio, gushing about how wonderful evolution is.

Natural selection has no direction. In fact it is unintended selection. It just allows for the survival and the reproduction of the “just good enough” individuals (not of the best individuals). “Evolution” is then just the resulting changes in species, where some individuals have had the genetic variation (errors or abnormalities) to be able to survive in a changed environment (habitat and/or competing species). Paradoxically, species which display a wide genetic variation in individuals (large errors), have a greater chance of surviving change. Of course, many abnormal individuals fail to survive, which is the price paid for the survival of the species. In that sense, “natural selection” sacrifices individuals for the sake of the species. The unplanned, unintended “selection” occurs primarily by the deselection of the unfit individuals. You could say it was unethical, since the end (species survival), justifies the means (deselection of unfit individuals). There is no compassion for deselected individuals in natural selection.

Excellence of a particular attribute is never selected for. Survivors are those just good enough, to live long enough, to reproduce. Evolution by this “natural selection” clearly works, but it is not intentional, is not very efficient and can only cope with slow, small changes to the environment. Rapid or large changes cannot be matched by the available genetic variation. When the genetic variation (errors) among individuals does not throw up some which can survive some external change, species go extinct. It is the selection not by a pro-active choice but by whatever is left surviving after a multitude of trials of the errors.

It is said that 99% of all species that ever existed are now extinct. It follows, then – by that measure – that evolution has a pretty dismal 1% success rate. A process with 99% of the production being rejected. It is hardly six-sigma. It also follows that many of the species alive today are not quite suitable, are intended for rejection and must go extinct. (I have always thought that this embarrassing level of inefficiency is in itself a powerful denial of any “intelligent design”).

The “wondrous evolution” of the eye, for example, is not all that wondrous considering the length of time involved (3.8 billion years from light sensitive algae to the human eye), and the mamillions of generations of trial by error. (A mamillion is the mother of all millions and is one million raised to the one millionth power). The eye is no doubt wonderful, but as a sensor of electro-magnetic radiation, it is only just “good enough”. It could have been much “better”, if excellence of the sensor was a purpose. The long, slow process by which the human eye has evolved is pretty unimpressive as a process, even if the result is not that bad. Natural selection does not even have survival as a purpose. It just throws up a multitude of possibilities and survival of some lucky few is the result. It is this shotgun approach of natural selection which is so inefficient – but to its credit, I have to admit it is a low-cost process which has been sufficiently effective to keep the selfish genes alive.

My contention is that an “artificial selection” approach, which had purpose, intelligence and direction, could have produced a superior eye and in much less time. Having direction means that excellence of an attribute could explicitly be sought. “Artificial selection” would be the precisely targeted, rifle-shot, giving a better eye with every generation, compared to  the “something should hit the barn sometime” approach of natural selection’s shot-gun, where a better eye was only one of many possibilities for the coming generations.

Consider then what “artificial selection” might have achieved – may yet still achieve – for the human form. Surround-sight eyes seeing deep into the uv and ir spectra. Ears able to discern pressure waves from the rumble of elephants and whales and upto the ultrasound of some creatures. Skin with an ability to absorb solar energy. Retractable gills. Cells for photosynthesis. Intelligent, armed, police cells patrolling the body for nasty, criminal cancers. Generalist antibodies. Regenerating cells. Rebooting capabilities for the mind. A brain which could beat a supercomputer at chess. Auto-translation cells between the ear and the brain. A hooded “third eye” to detect the undetectable. A heightened olfactory sense. A shielded “inner ear” to detect gravitation waves. A multi-tasking, retractable tail. Tunable radio receivers in our heads.(And many more desirable attributes I cannot even imagine).

Natural selection is about being just good enough. Artificial selection could be about excellence, an excellence as perceived at the time of selection. Artificial selection would then indeed be the application of intelligence to design. It would not take a million years for an “all seeing eye”.

That would be a Brave New World for a brave new species of homo sapiens superior.

Gene mixing promotes height and intelligence – but is this an evolutionary benefit?

July 2, 2015

A new international study of the genetic make up and physical characteristics of 350,000 people indicates that greater genetic diversity leads to an increase of height and cognitive skills. But – somewhat surprisingly – lower genetic diversity did not lead to any visible increase in complex diseases. Genetic diversity was found to have no effect on blood pressure or cholesterol levels.

But I question the assumption that increased height and faster thinking are of “evolutionary advantage”. Evolutionary advantage must lead to an individual having a greater number of offspring than one without the advantage. Previous work has indicated that both child nourishment and genetics determine height.

And so I wonder what evolutionary advantage height may have in modern society? Does the ability to think faster lead to a greater number of surviving descendants? Richer and “more intelligent” groups tend to have much lower fertility rates than poorer, “less intelligent” groups.

Using the criterion of greatest surviving descendants indicating evolutionary advantage, leads to the conclusion that populations in Africa with the highest population increase rates must also have the greatest evolutionary advantages!

Peter K. Joshi et al. Directional dominance on stature and cognition in diverse human populations. Nature, 2015 DOI: 10.1038/nature14618

Abstract: Homozygosity has long been associated with rare, often devastating, Mendelian disorders, and Darwin was one of the first to recognize that inbreeding reduces evolutionary fitness. However, the effect of the more distant parental relatedness that is common in modern human populations is less well understood. Genomic data now allow us to investigate the effects of homozygosity on traits of public health importance by observing contiguous homozygous segments (runs of homozygosity), which are inferred to be homozygous along their complete length. Given the low levels of genome-wide homozygosity prevalent in most human populations, information is required on very large numbers of people to provide sufficient power. Here we use runs of homozygosity to study 16 health-related quantitative traits in 354,224 individuals from 102 cohorts, and find statistically significant associations between summed runs of homozygosity and four complex traits: height, forced expiratory lung volume in one second, general cognitive ability and educational attainment (P < 1 × 10−300, 2.1 × 10−6, 2.5 × 10−10 and 1.8 × 10−10, respectively).

University of Edinburgh Press Release:

People have evolved to be smarter and taller than their predecessors, a study of populations around the world suggests. Those who are born to parents from diverse genetic backgrounds tend to be taller and have sharper thinking skills than others, the major international study has found. Researchers analysed health and genetic information from more than 100 studies carried out around the world. These included details on more than 350,000 people from urban and rural communities.

The team found that greater genetic diversity is linked to increased height. It is also associated with better cognitive skills, as well as higher levels of education. However, genetic diversity had no effect on factors such as high blood pressure or cholesterol levels, which affect a person’s chances of developing heart disease, diabetes and other complex conditions.

Researchers from the University of Edinburgh examined individuals’ entire genetic make-up.

They pinpointed instances in which people had inherited identical copies of genes from both their mother and their father – an indicator that their ancestors were related. Where few instances of this occur in a person’s genes, it indicates greater genetic diversity in their heritage and the two sides of their family are unlikely to be distantly related. It had been thought that close family ties would raise a person’s risk of complex diseases but the researchers found this not to be the case.

The only traits they found to be affected by genetic diversity are height and the ability to think quickly.

 

“Mad Professor” Ehrlich cries wolf again

June 20, 2015

Paul Ehrlich will probably be remembered as being the professor who has been more wrong, more often than any other.

To be proved spectacularly wrong , time after time, is apparently a prime qualification for “mad professors” to remain employed. Paul Ehrlich is the perfect example of what is wrong with the tenure system. Of course it helps if your predictions are about catastrophes to come which inevitably garner headlines – no matter how stupid the predictions are. He is at it again making doomsday predictions. This time the doom approaching is because humans have already started the 6th mass extinction which may include the disappearance of the human species. (Actually the earth has too many species and a drastic cull of species is needed).

It is worth recalling all the sensational, headline grabbing but wonderfully wrong predictions that Ehrlich has made:

  • 1968, “The battle to feed all of humanity is over. In the 1970s hundreds of millions of people will starve to death in spite of any crash programs embarked upon now. At this late date nothing can prevent a substantial increase in the world death rate …”
  • 1968, “India couldn’t possibly feed two hundred million more people by 1980.”
  • 1969, “By 1985 enough millions will have died to reduce the earth’s population to some acceptable level, like 1.5 billion people.”
  • 1969, He predicted that by the end of the century the population of the US would be under 20 million, and our life expectancy would be around 40 years – due not to starvation, but to pesticides.
  • 1970, “In ten years all important animal life in the sea will be extinct. Large areas of coastline will have to be evacuated because of the stench of dead fish.”
  • 1970, “When you reach a point where you realize further efforts will be futile, you may as well look after yourself and your friends and enjoy what little time you have left. That point for me is 1972.”
  • 1970s, “The train of events leading to the dissolution of India as a viable nation is already in motion.”  He proposed a number of radical solutions to the overpopulation crisis; dumping sterilizing agents into water supplies, allowing only selected people the privilege of reproduction, and performing mass “triage” of nations, between those who don’t need help (North America, Australia, parts of Europe), those who can be saved, and those who are beyond help – India, Sub-Saharan Africa, and much of Asia, which he predicted would be hell on earth by the 1980’s
  • 1971, “By the year 2000 the United Kingdom will be simply a small group of impoverished islands, inhabited by some 70 million hungry people. …… I would take even money that England will not exist in the year 2000.”

For 4 decades he has made predictions about catastrophes due to famine, depletion of resources, disease, poisoning by pesticides, global warming and climate disruption. Every one of his predictions about the future has been, or is being, proved wrong. Sometimes he gets his history right, but his ability to look forward, even over short times, is hopelessly flawed.

Now he is at it again about the 6th mass extinction that has “already started”. But we actually have more species today than we have probably ever had. The detritus of failed and failing species needs to be cleaned out.

Gerardo Ceballos, Paul R. Ehrlich, Anthony D. Barnosky, Andrés García, Robert M. Pringle and Todd M. Palmer. Accelerated modern human–induced species losses: Entering the sixth mass extinction. Science Advances, 2015 DOI: 10.1126/sciadv.1400253

Abstract: ...  We assess, using extremely conservative assumptions, whether human activities are causing a mass extinction. First, we use a recent estimate of a background rate of 2 mammal extinctions per 10,000 species per 100 years (that is, 2 E/MSY), which is twice as high as widely used previous estimates. We then compare this rate with the current rate of mammal and vertebrate extinctions. The latter is conservatively low because listing a species as extinct requires meeting stringent criteria. Even under our assumptions, which would tend to minimize evidence of an incipient mass extinction, the average rate of vertebrate species loss over the last century is up to 114 times higher than the background rate. Under the 2 E/MSY background rate, the number of species that have gone extinct in the last century would have taken, depending on the vertebrate taxon, between 800 and 10,000 years to disappear. These estimates reveal an exceptionally rapid loss of biodiversity over the last few centuries, indicating that a sixth mass extinction is already under way.

But there are still more species around than ever before. And a lot of them need to go extinct to make way for others that are more suited. No previous mass extinction has been any threat to life on earth though it has each time cleared the decks of species not fit or worthy to continue.

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.

But the one good thing about Paul Ehrlich’s predictions is that it provides a clear identification of an area not to worry too much about.

A jawbone with a Neanderthal for a great-great-grandmother

May 30, 2015

That humans today have genes from Neanderthals, Denisovans and some other ancient cousin species seems to be quite clear from the genetic evidence (though I am always quite amazed at the wondrous ability to extract DNA from ancient bones). In fact, it seems that the mainstream of AMH had various breeding encounters with these other species at many different times and (presumably) at many geographic locations. These encounters could not have been rare isolated events suggesting that there was more than a little promiscuity in the pleistocene.

Gene flow in the late pleistocene (Kay Prüfer et al)

It has been thought that most of the Neanderthal/AMH interactions must have taken place in the Middle East or central Asia, but new work indicates that these interactions took place in Europe as well. DNA analysis of a jawbone from a Romanian cave from about 40,000 years ago had a Neanderthal for a great-great- grandparent.

I take this grandparent to be a Neanderthal grandmother who was abducted by some marauding group of promiscuous humans only because the ensuing child survived to give rise to us and it is the human environment which has continued. The picture I have is that our Neanderthal genes today are due mostly to the Neanderthal females who were “impressed” into service by an aggressive and expanding human population. There may well have been Neanderthal male – human female offspring but they would more likely have been brought up in a Neanderthal environment, which – along with them -has not survived.

Ewen Callaway reports in Nature News:

Early European may have had Neanderthal great-great-grandparent

One of Europe’s earliest known humans had a close Neanderthal ancestor: perhaps as close as a great-great-grandparent.

The finding, announced on 8 May at the Biology of Genomes meeting in Cold Spring Harbor, New York, questions the idea that humans and Neanderthals interbred only in the Middle East, more than 50,000 years ago.

Qiaomei Fu, a palaeogenomicist at Harvard Medical School in Boston, Massachusetts, told the meeting how she and her colleagues had sequenced DNA from a 40,000-year-old jawbone that represents some of the earliest modern-human remains in Europe. They estimate that 5–11% of the bone’s genome is Neanderthal, including large chunks of several chromosomes. (The genetic analysis also shows that the individual was a man). By analysing how lengths of DNA inherited from any one ancestor shorten with each generation, the team estimated that the man had a Neanderthal ancestor in the previous 4–6 generations. (The researchers declined to comment on the work because it has not yet been published in a journal).

……. All humans who trace their ancestry beyond sub-Saharan Africa carry a sliver of Neanderthal DNA — around 1–4% of their genomes. Researchers have long thought it most likely that early humans exiting Africa interbred with resident Neanderthals somewhere in the Middle East around 50,000—60,000 years ago, before travelling on to Asia, Europe and the rest of the world.

That possibility has gained support in the past year. Last year, a team that included Fu used the genome of a 45,000-year-old human from Siberia to date his Neanderthal ancestors to between 50,000 and 60,000 years ago (when modern humans were probably starting to leave Africa)2. Another reported finding the 55,000-year-old partial skull of a human in an Israeli cave not far from sites at which Neanderthals lived around the same time3.

But radiocarbon dating of remains from sites across the continent suggests that humans and Neanderthals lived together in Europe for up to 5,000 years in some areas — plenty of time for them to have met and interbred there, too.

But the AMH / Neanderthal co-existence was not a short-lived thing.

Encounters between AMH and Neanderthals probably took place at different times in different places to leave the genetic signal of some 3% Neanderthal genes in non-African AMH. Early encounters would have taken place in central Asia (perhaps 50,000 years ago) with later encounters in Europe (c. 30,000 years ago). Now new methods of radiocarbon dating at archaeological sites is providing evidence which indicates that Neanderthals and AMH overlapped for many hundreds of generations.

 

 

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.


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