Tag: Oxford University

New ideas about our relationship with dogs.

What a delight to read this latest scientific news.

There’s so much ‘doom and gloom’ to be seen on the news services across the world that a genuine discovery that enlarges the mind is always a treat. Now make that a discovery about our dogs. Better still, let the BBC do it for you.

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How did dogs become our best friends? New evidence

By Helen Briggs BBC News, 19 July 2017

Dogs most probably evolved from wolves at a single location about 20,000 to 40,000 years ago, a study suggests.

Previously, it had been thought that dogs were tamed from two populations of wolves living thousands of miles apart.

Researchers studied DNA from three dogs found at archaeological sites in Germany and Ireland that were between 4,700 and 7,000 years old.

The ancient canines share ancestry with modern European dogs.

By looking at the rates of change to the DNA from the oldest specimen, scientists were able to place the timing of the domestication of dogs to between 20,000 and 40,000 years ago.

Krishna Veeramah of Stony Brook University in New York is a researcher on the study.

He said the process of dog domestication began when a population of wolves moved to the outskirts of hunter-gatherer camps to scavenge for leftovers.

”Those wolves that were tamer and less aggressive would have been more successful at this,” he explained.

“While the humans did not initially gain any kind of benefit from this process, over time they would have developed some kind of symbiotic relationship with these animals, eventually evolving into the dogs we see today.”

DNA was obtained from the skull of an ancient dog.

The story of how dogs came to be tamed from wolves is complex and hotly debated.

Scientists believe dogs started moving around the world, perhaps with their human companions, about 20,000 years ago.

By 7,000 years ago, they were pretty much everywhere, although they were not the kind of dogs that we would consider pets.

”They would likely have resembled dogs we today call village dogs, which are free-breeding that did not live in specific people’s houses and have a similar look to them across the world,” said Dr Veeramah.

The dogs were later bred for their skills as hunters, herders or gundogs, eventually creating hundreds of modern breeds.

The research, published in Nature Communications, suggests even the dog breeds and village dogs found in the Americas and Pacific Islands are almost completely derived from recent European dog stock.

This is probably due to prolific dog breeding in Victorian times.

The dog skull inside an ancient burial chamber.

”In this regard, it appears therefore that our 7,000-year, Neolithic-old dog from Europe is virtually an ancestor to most modern breed dogs found throughout the world,” said Dr Veeramah.

”This ancestral relationship may even stretch back to the oldest dog fossil we know of, which is approximately 14,000 years old from Germany.”

Previous evidence suggested that the first domestic dogs appeared on opposite sides of the Eurasian continent more than 12,000 years ago.

Later, the eastern dogs moved with migrating humans and bred with those from the west, according to this theory.

Dr Greger Larson of the University of Oxford said it was great to see more ancient dog genomes being published.

“There is a fascinating story here and we’re only just scraping the surface,” he said.

“The more we get the more we might have a shot at finally unravelling the story of how we became such good friends over such a long time.”

Follow Helen on Twitter.

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Once read, it was but a moment to do a web search for Dr Veeramah and bring up the news of his research on the Stony Brook Newsroom.

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Study Reveals Origin of Modern Dog Has a Single Geographic Origin

Reported in Nature Communications, the finding counters previous research that suggested two domestication events led to the modern dog

Stony Brook, NY; Stony Brook University: Department of Ecology and Evolution Assistant Professor Krishna Veeramah. His research will be published in Nature and his study reveals origin of modern dog has a single geographic origin.

STONY BROOK, N.Y., July 18, 2017 – By analyzing the DNA of two prehistoric dogs from Germany, an international research team led by Krishna R. Veeramah, PhD, Assistant Professor of Ecology & Evolution in the College of Arts & Sciences at Stony Brook University, has determined that their genomes were the probable ancestors of modern European dogs. The finding, to be published in Nature Communications, suggests a single domestication event of modern dogs from a population of gray wolves that occurred between 20,000 and 40,000 years ago.

Dogs were the first animal to be domesticated by humans. The oldest dog fossils that can be clearly distinguished from wolves are from the region of what is now Germany from around 15,000 years ago. However, the archeological record is ambiguous, with claims of ancient domesticated dog bones as far east as Siberia. Recent analysis of genetic data from modern dogs adds to mystery, with some scientists suggesting many areas of Europe, Central Asia, South Asia and the Middle East as possible origins of dog domestication.

(L to R) Shyamalika Gopalan, PhD Candidate, Dean Bobo, Bioinformatics Scientist, and Krishna Veermah, Assistant Professor of Ecology & Evolution. (F) Four-legged friend, Joci

In 2016, research by scientists using emerging paleogenomics techniques proved effective for sequencing the genome of a 5,000-year-old ancient dog from Ireland. The results of the study led the research team to suggest dogs were domesticated not once but twice. The team from Oxford University also hypothesized that an indigenous dog population domesticated in Europe was replaced by incoming migrants domesticated independently in East Asia sometime during the Neolithic era.

“Contrary to the results of this previous analysis, we found that our ancient dogs from the same time period were very similar to modern European dogs, including the majority of breed dogs people keep as pets,” explained Dr. Veeramah. “This suggests that there was no mass Neolithic replacement that occurred on the continent and that there was likely only a single domestication event for the dogs observed in the fossil record from the Stone Age and that we also see and live with today.”

In the paper, titled “Ancient European dog genomes reveal continuity since the Early Neolithic,” Veeramah and colleagues used the older 7,000 year old dog to narrow the timing of dog domestication to the 20,000 to 40,000 years ago range.

They also found evidence of the younger 5,000 year old dog to be a mixture of European dogs and something that resembles current central Asian/Indian dogs. This finding may reflect that people moving into Europe from the Asian Steppes at the beginning of the Bronze Age brought their own dogs with them.

“We also reanalyzed the ancient Irish dog genome alongside our German dog genomes and believe we found a number of technical errors in the previous analysis that likely led those scientists to incorrectly make the conclusion of a dual domestication event,” added Veeramah.

Overall, he emphasized, their new genomic analysis of ancient dogs will help scientists better understand the process of dog evolution, even if the exact geographic origin of domestication remains a mystery. He expects further sequencing of the ancient genomes from Eurasia will help to eventually solve the issue.

The study and findings are a collaboration between scientists at Stony Brook University; the University of Michigan, Johannes Gutenberg-University, Germany; University of Bamberg, Germany; Trinity College, Ireland; and the Department of Monumental Heritage in Germany.

The research was supported in part by the National Institutes of Health.

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 About Stony Brook University
Stony Brook University is going beyond the expectations of what today’s public universities can accomplish. Since its founding in 1957, this young university has grown to become one of only four University Center campuses in the State University of New York (SUNY) system with more than 25,700 students, 2,500 faculty members, and 18 NCAA Division I athletic programs. Our faculty have earned numerous prestigious awards, including the Nobel Prize, Pulitzer Prize, Indianapolis Prize for animal conservation, Abel Prize and the inaugural Breakthrough Prize in Mathematics. The University offers students an elite education with an outstanding return on investment: U.S. News & World Report ranks Stony Brook among the top 40 public universities in the nation. Its membership in the Association of American Universities (AAU) places Stony Brook among the top 62 research institutions in North America. As part of the management team of Brookhaven National Laboratory, the University joins a prestigious group of universities that have a role in running federal R&D labs. Stony Brook University is a driving force in the region’s economy, generating nearly 60,000 jobs and an annual economic impact of $4.65 billion. Our state, country and world demand ambitious ideas, imaginative solutions and exceptional leadership to forge a better future for all. The students, alumni, researchers and faculty of Stony Brook University are prepared to meet this challenge.

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Even better than the University providing the link to the above, it also gave me the good Doctor’s email address. I shall reach out to him and see if there is more that I can share with you!

Growing old!!

Are there options?  Are there decisions to be made?

Of the two certainties in life, one of them is pretty stark: death!  (The other certainty is taxes, by the way!)

So one could legitimately argue that if death is ‘non-negotiable’ then it’s not even worth spending a moment dwelling on it.  And certainly not worth the time and effort in writing about it!

But, of course, this misses a very big point.  That is that doing all we can to improve our quality of life, especially in the Autumn of our lives, is very important.

That’s why a recent item on the BBC News website jumped off the page at me.  It was an article called: Health kick ‘reverses cell ageing’ written by Michelle Roberts, Health editor, BBC News online.  Here is how the article opened:

Going on a health kick reverses ageing at the cellular level, researchers say.

The University of California team says it has found the first evidence a strict regime of exercise, diet and meditation can have such an effect.

But experts say although the study in Lancet Oncology is intriguing, it is too early to draw any firm conclusions.

The study looked at just 35 men with prostate cancer. Those who changed their lifestyle had demonstrably younger cells in genetic terms.

“Reverses ageing”!  How on earth can that work?

The researchers saw visible cellular changes in the group of 10 men who switched to a vegetarian diet and stuck to a recommended timetable of exercise and stress-busting meditation and yoga.

The changes related to protective caps at the end of our chromosomes, called telomeres.

Their role is to safeguard the end of the chromosome and to prevent the loss of genetic information during cell division.

As we age and our cells divide, our telomeres get shorter – their structural integrity weakens, which can tell cells to stop dividing and die.

Researchers have been questioning whether this process might be inevitable or something that could be halted or even reversed.

The latest work by Prof Dean Ornish and colleagues suggests telomeres can be lengthened, given the right encouragement.

Now if you, like me, are noticing some of the rather frustrating aspects of ageing, then this one piece of science research could turn out to be invaluable.  But best not to get too carried away just now, as the BBC article underlines:

Prof Ornish said: “The implications of this relatively small pilot study may go beyond men with prostate cancer. If validated by large-scale randomised controlled trials, these comprehensive lifestyle changes may significantly reduce the risk of a wide variety of diseases and premature mortality.

“Our genes, and our telomeres, are a predisposition, but they are not necessarily our fate.”

Dr Lyn Cox, a biochemistry expert at Oxford University in the UK, said it was not possible to draw any conclusions from the research, but added: “Overall, though, the findings of this paper that changes in lifestyle can have a positive effect on markers of ageing support the calls for adoption of and adherence to healthier lifestyles.”

Dr Tom Vulliamy, senior lecturer in Molecular Biology at Queen Mary University of London, said: “It is really important to highlight that this is a small pilot study.

Nevertheless, here’s how the article ends:

But past work has shown that people who lead a sedentary lifestyle can experience accelerated cellular ageing in the form of more rapid shortening of their telomeres.

All of which rather embarrassingly reminds me that back on the 6th August, in a post called The habit of doing nothing, I set out Leo Babauta’s  ‘How To Meditate‘ guide.  Then, frankly, ignored it!  So to me and all you other readers who would like to chill out like your dog, here’s that guide again.

How to Do It Daily

There are lots and lots of ways to meditate. But our concern is not to find a perfect form of meditation — it’s to form the daily habit of meditation. And so our method will be as simple as possible.

1. Commit to just 2 minutes a day. Start simply if you want the habit to stick. You can do it for 5 minutes if you feel good about it, but all you’re committing to is 2 minutes each day.

2. Pick a time and trigger. Not an exact time of day, but a general time, like morning when you wake up, or during your lunch hour. The trigger should be something you already do regularly, like drink your first cup of coffee, brush your teeth, have lunch, or arrive home from work.

3. Find a quiet spot. Sometimes early morning is best, before others in your house might be awake and making lots of noise. Others might find a spot in a park or on the beach or some other soothing setting. It really doesn’t matter where — as long as you can sit without being bothered for a few minutes. A few people walking by your park bench is fine.

4. Sit comfortably. Don’t fuss too much about how you sit, what you wear, what you sit on, etc. I personally like to sit on a pillow on the floor, with my back leaning against a wall, because I’m very inflexible. Others who can sit cross-legged comfortably might do that instead. Still others can sit on a chair or couch if sitting on the floor is uncomfortable. Zen practitioners often use a zafu, a round cushion filled with kapok or buckwheat. Don’t go out and buy one if you don’t already have one. Any cushion or pillow will do, and some people can sit on a bare floor comfortably.

5. Start with just 2 minutes. This is really important. Most people will think they can meditate for 15-30 minutes, and they can. But this is not a test of how strong you are at staying in meditation — we are trying to form a longer-lasting habit. And to do that, we want to start with just a two minutes. You’ll find it much easier to start this way, and forming a habit with a small start like this is a method much more likely to succeed. You can expand to 5-7 minutes if you can do it for 7 straight days, then 10 minutes if you can do it for 14 straight days, then 15 minutes if you can stick to it for 21 straight days, and 20 if you can do a full month.

6. Focus on your breath. As you breathe in, follow your breath in through your nostrils, then into your throat, then into your lungs and belly. Sit straight, keep your eyes open but looking at the ground and with a soft focus. If you want to close your eyes, that’s fine. As you breathe out, follow your breath out back into the world. If it helps, count … one breath in, two breath out, three breath in, four breath out … when you get to 10, start over. If you lose track, start over. If you find your mind wandering (and you will), just pay attention to your mind wandering, then bring it gently back to your breath. Repeat this process for the few minutes you meditate. You won’t be very good at it at first, most likely, but you’ll get better with practice.

And that’s it. It’s a very simple practice, but you want to do it for 2 minutes, every day, after the same trigger each day. Do this for a month and you’ll have a daily meditation habit.

Yet again, dogs offer us a great example.

For here’s a photograph of Pharaoh that I took just a few moments ago showing him deep in meditation behind my chair!

Demonstrating the art of doing nothing!
Demonstrating the art of doing nothing!

A mathematical approach to the demise of the Neanderthals.

Pure mathematics is, in its way, the poetry of logical ideas. Albert Einstein.

I have never been proficient at mathematics. But that doesn’t mean that I am not fascinated by the field of maths.

Hold that in your thoughts as I mention the name of blogger: Patrice Ayme.  It’s a non-de-plume but so what!  What blows me away, to use the vernacular, is the depth of thought expressed through the keyboard of Mr. Ayme (even the gender is an assumption).  The sub-heading on the home page of his blog is “Intelligence at the core of humanism“.  Just run your eye down the list of Recent Posts to the right-hand side of the home page to get a feel for the topics covered in the last few months.  Impressive is an understatement!

Anyway, five days ago Patrice published a post proposing how the Neanderthals were outbred, under the title of Math Extinguished Neanderthals.  It fascinated me and Patrice was gracious in allowing me permission to republish it on Learning from Dogs.

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Math Extinguished Neanderthals

HOW NEANDERTHALS WERE OUTBRED:

Zillions of theories about the “disappearance” of Neanderthals. The latest one, from Oxford University, claims that Neanderthals’ big, beautiful eyes, and their big muscles caused their demise. They were too busy looking at things, and flexing their muscles. The idea is that significantly larger eyes would have crowded the Neanderthal brain out, making them relatively stupid. In particular it made them incapable of having social groups as large as those of Homo Sapiens Sapiens.

Big Eyes Do Not Kill

Big Eyes Do Not Kill

Sapiens girl on the left, Neanderthal girl on the right (reconstitution published in Science Magazine a few years ago).

I have long argued that the strength of democracy came from having many brains working in parallel. There is little doubt that larger social groups bring a higher cultural intelligence, hence higher individual intelligence. So I agree about that bit of logic. Yet, ironically, to reach the conclusion that Neanderthals’ social group were less numerous, the simple fact that Neanderthals were bigger, is enough. There is no need for hazardous demeaning allegations about Neanderthals’ brains.

That big eyes made Neanderthals stupid contradicts some facts that were thought to be established:

1) Sapiens Neanderthalis’ brains were significantly larger to start with. See Wikipedia.

2) Many very clever Homo Sapiens Sapiens have small brains. Famously Anatole France, an intellectual, had only a 1,000 cubic centimeters brain. Homo Floresiensis, the “hobbit” species living on the island of Flores, Indonesia, until it was wiped out recently, was extremely intellectually capable, although it had really small (and completely different) brains.

3) In the Middle East, Neanderthals and Sapiens went back and forth through the same large caves over 50,000 years. So whatever happened, it was not in evidence for 50,000 years.

So, of course, I have my own theory. That’s what philosophy is all about: trying to guess what really matters most, and how that most significant data logically articulate. Then scientists, politicians and writers can swoop, figure out the details, and attribute themselves the glory.

What could have happened by around 28,000 years ago that caused the demise of Neanderthals? At the time, the last fierce glaciation was gaining ground. (It reached its maximum 25,000 years ago.) Some have argued, absurdly, that the Neanderthals could not take it. That’s beyond silly, as Neanderthals had evolved, from half a million years ago, precisely to handle extreme cold.

Neanderthals were stocky, powerful, and they had thrived through hundreds thousands years of glaciation, mostly on a meat diet, hunting big game. But they also knew how to cook plants, and eat them.

50,000 years ago, Neanderthals exterminated Cave Bears, a huge animal who lived in caves, prime real estate Neanderthals craved for. Could the disappearance of Cave Bears be logically linked to the disappearance of Neanderthals? Yes. That’s a consequence of my theory. More advanced technology played a direct role.

How did Neanderthals kill Cave Bears? With technology. We do not know exactly what weapons Neanderthals had at their disposal. However, technology had improved, and kept improving. Recently it was found that Sapiens Sapiens (Homo SS; I hope one gets the joke) in Africa had invented bows and arrows 80,000 Before Present (BP).  (About 60,000 years earlier than previously thought!) Before bows and arrows, the propeller had been invented, and was used in Europe. The propeller took advantage of angular momentum to send a sort of mini lance further and stronger than by hand.

Why did the Neanderthals and Denisovans (another human species from Central Eurasia) lose their edge? Advancing technology is the obvious answer. When technology of clothing and weapons was sufficiently advanced, the physiological advantage that the Neanderthals genetically had, disappeared. Homo Sapiens Sapiens could thrive just as well through winter.

At that point, Homo Sapiens Sapiens from Africa could be as successful as the Neanderthals through the freezing wastelands of Europe. OK.

But the Homo SS outbred the Neanderthals, so they became genetically more successful. How do I explain that?

Simple. However, the explanation involves the exponential function, the same function found all over, and that the mathematician Rudin called “the most important function in mathematics”. The exponential also explains the plutocratic phenomenon, and that is why it’s so dangerous. The exponential always rules extinction events, that’s why one day a species is all over, like the American Pigeon, or the Tasmanian Tiger, and the next day, it’s gone.

So visualize this. Neanderthals were bigger than Homo SS, just like the Polar Bear is bigger than the Black Bear. Bigness is an adaptation to cold. Southern Europe’s Brown Bears are smaller than those found in Kamchatka, or Alaska (also known as Grizzlies: the Grizzly is an emigrated European Brown Bear!) Bigger makes warmer inside. That’s why the most massive animal that ever was, the Blue Rorqual, at up to 180 tons, is nearly twice the mass of the largest dinosaur (it’s not just that it’s floating, but also that water is cooler than Jurassic air, I hold).

To simplify, let’s use a bit of exaggeration (that’s reasoning by exaggeration, one of my preferred tactic of thought; the one humor exploits, and why joking helps thinking). Let’s assume Neanderthals were twice more massive than Homo SS.

Now let’s consider an habitat where Homo SS and Neanderthal bands roamed. They will tend not to mix, for obvious racist reasons. The racial hatred between Neanderthals and Homo SS has got to have been colossal. People who look too different are not even sexually attracted to each other (and where Neanderthals and Homo SS were in contact in the Middle East, for 50,000 years, there is no evolution of an interbred species, an indirect proof that there was no love lost there!)

The density of human mass is going to be roughly the same all over, because that density depends only upon the resources available (mostly meat on the hoof, and fur in burrows in glaciating conditions).

Thus, there would have been apartheid. But the Homo SS would have been twice more numerous, where they reigned (from my assumption of twice the mass). So now graft on this a catastrophe; a drought, a flood, a very tough winter, a volcanic super disaster, whatever. The climate was highly variable, starting about 40,000 years ago, just when Homo SS appeared. Some have stupidly argued that Neanderthals were too stupid to adapt to this changing circumstances. Like this paralyzing stupidity struck them just when Homo SS were around. My explanation is more subtle.

After a catastrophe in said habitat, say one of these numerous habitat in Europe isolated by glacial mountain ranges, or seas and lakes, most of the human population would be wiped out, Homo SS, just as Neanderthals. There would tend to be always a small remaining population, because the greatest limit on man is man himself: as a population gets wiped out, resources rebound, and life of the survivors tend to get much easier (that’s what happened in Europe after the Black Death of 1348 CE; if nothing else, survivors could ask for higher salaries from their plutocratic masters, and they did).

So say 90% of the population of the habitat was wiped out. As suddenly resources are now not limited, the human population will rebound exponentially. The equation is: N(t) = N(0) exp(Rt). “R” is the “Malthusian” parameter, the rate of growth. Now it’s going to require twice the resources to feed a Neanderthal to sexual maturation (under our outrageously simplifying assumption that Neanderthals are twice the mass). Thus one may assume that R(Homo SS)/R(Neanderthal) is 2. The end result is that the quotient:

Number Homo SS/ Number Neanderthal = A exp(2t). (Where A is the ratio of the populations H SS/Neanderthal after the catastrophe.)

Thus the population of H SS would exponentially grow relative to that of the Neanderthals, resulting in a quick extinction. And in no way this is happening because Homo SS were superior. Just because they were more gracile.

Hence the mystery of the evolution of contemporary man is smoothly explained. Just a bit of math. QED.

Europeans & Asians: Not Just African

Europeans & Asians: Not Just African

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Patrice Ayme

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Note 1: what of the mentally deliquescent and racist article in the Proceedings of the Royal Society? First, they sank so low as to“using orbit size as a proxy, that Neanderthals had larger visual systems than contemporary AMH [Anatomically Modern Humans]“. That’s about as intelligent as saying that, because special forces use night vision goggles, they have got to have bigger visual systems.

The main woman author also found the same physiological feature, bigger eyes, in the past, about people presently living at high latitude. She contentedly asserted that, because light levels are lower in the north, people living in the north (40,000 years at least for Homo SS) have bigger eyes. Amusingly, she did not draw, in that case the conclusion that Norwegians and the English are therefore more stupid. Somehow, though, in her lack of smarts, she applies that controversial reasoning to Neanderthals. Does she have giant eyes?

Seriously the Oxford study rests on a central fact that contradicts one of established facts about Neanderthals. Indeed it claims Neanderthals’ brains were not any larger than Homo SS.

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Note 2; what catastrophes am I talking about? Well the climate fluctuated wildly, to start with. Second, A Campanian ignimbritevolcanic super-eruption around 40,000 years ago, followed by a second one a few thousand years later, certainly crashed Neanderthal populations (based on logic, and evidence fromMezmaiskaya cave in the Caucasus. Mitochondrial DNA analysis of a specimen there is C14 dated 29,000 years BP, one of the latest living pure Neanderthals). After such a catastrophe, the exponential rebounds of populations would have advantaged Homo SS, as explained above.

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Note 3: OK, I exaggerated with the mass ratio. (Mathematicians often do this, considering an exaggerated case to understand the mean, through the tails.) But the real mass ratio would be aggravated because, Neanderthal was built in such a way, relative to gracile Homo SS, that they consumed more calories per day (some paleontologists have come up with 300). So there is no doubt that the effect above will play a role, even if the mass ratios were not as bad. Notice the mechanism above would tend to extinguish the Neanderthal traits that were most characteristic of the subspecies.

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Note 4: A preferred trick of Neanderthals’ haters is to exhibitArchaic Neanderthals‘skulls, and compare them to those of modern men. The skull of an Archaic Neanderthal of 400,000 years ago should not be compared to a modern human, less than 40,000 year old! All the more since Neanderthals’ brain size augmented faster than the brain size of Homo Sapiens Sapiens.

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Note 5: Part of the mechanism above generalizes for other species in competition. It provides with a disappearance mechanism after ecological turbulence, according to species’ ecological footprint.

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So hope that others shared my pleasure at reading the essay.

Going to close with another quotation from Mr. Albert Einstein: “As far as the laws of mathematics refer to reality, they are not certain, and as far as they are certain, they do not refer to reality.”