COVID-19: the big picture

Today Switzerland became the country with the highest rate of confirmed cases of corona virus per million population. Well, that is if you ignore some micro-populations such as the Vatican City, San Marino, Andorra and Faeroe Islands. Why?  It is landlocked with Italy, France and Germany around it. It did not close the border between Ticino and Italy for cross-border workers and many live in Italy were the virus spread rapidly. Also, it was the height of the ski season and alpine resorts were crowded with skiers from all over Europe, Britain and beyond. Here is a graph I did yesterday comparing confirmed cases per million population  for the thirty leading countries (excluding small countries with population less than one million. Data are from worldometers.com at 13.11 GMT on March 24. A this point Switzerland had not yet overtaken Italy.

The true number of cases will be much higher for most countries, depending on level of testing and availability/access to testing. And data for countries is being updated daily but at different times of day for various countries. The numbers on worldometers.com are quite similar to those on theJohns Hopkins website but seem to be updated slightly earlier and so are usually a little higher.

There is also a nice new site http://91-divoc.com/pages/covid-visualization/ that plots time trends in cases and deaths, total numbers and rates per million population. The time axis is days since 100+ cases/deaths or days since 1 case/death per million population. I’ve included screenshots below of cases/million and deaths/million with Switzerland highlighted. The dotted straight line on the log scale represents a daily growth rate of 1.35 (35% more cases than day before). That corresponds to a doubling time of 2.31 days. Fortunately, most curves are showing some flattening after the first 10 days. Australia has a curve that corresponds to a daily growth rate of 1.2. That difference is huge. At a daily growth rate of 1.35, the first case becomes 3.2 million after 50 days, whereas at 1.2 it becomes 9,100.

The USA is on day 20 since 100 confirmed cases (or day 18 since 1 case/million) and is following the 1.35x line very closely so far. Unlike most other countries this far into the epidemic, it is not yet showing signs of slowing down. US total confirmed cases will likely overtake those of Italy and China by tomorrow or day after.

If you hover over a point on one of the country curves in the graphs on this site, you get growth rates for last day, week, 16 days. You can convert growth rate g (eg. 1.35) to doubling time in days by calculating log(2)/log(g) and the increase in total cases over d days as g to the power d.  Of course, these growth rates cannot continue unchanged. Either people will change their behaviour to socially isolate and more, if the bodies start piling up as happened in Italy, or the level of herd immunity will rise to the extent that the number of new infections caused by an infected person will drop lower. And that latter scenario will come with lots of deaths as well, particularly when health systems become overwhelmed.

Here in Geneva, we are on day 10 of social isolation. Staying home unless necessary to   work, or buy food, or other essential activities. No gathering of more than 5 people. Borders are now closed to all except cross-border workers and essential trips. Most border crossings are completely shut, and the three that are open are checking papers for every person and there are waits of hours to get across. All shops, gyms, restaurants, entertainment, ski resorts closed with the exception of food stores, petrol and pharmacies. Hairdressers are closed, unlike in Australia where they are considered essential for morale. I am also on day 7 of doing Wim Hof breathing. Who knows, it might even pep up my immune system.

Becoming Human Part 1

Our understanding of the evolution of us modern humans has changed dramatically in the last few years as ancient genomes are decoded and we discover that humans, Neanderthals and Denisovans interbred, and also in the remote past interbred with previously unknown “superarchaic” human groups.  Scientists are also discovering new species of extinct hominids, and no doubt will continue to shed further light on our origins. Just to try to sort out the big picture in my own mind and to put these various discoveries in context, I’ve tried to summarize what we think we know, or at least what the evidence available to date suggests. This will no doubt continue to change.

This is the first of two posts and summarizes the evolution of pre-human species from the first monkeys around 35 million years ago (Mya) to the appearance of the first human species around 2 Mya. A following post will summarize the evolution of humans from the appearance of the first human species Homo habilis 2 Mya to the appearance of anatomically modern Homo sapiens sapiens around 250 thousand years ago and  mitochondrial Eve, who lived around 178,000 years ago.

The evolution of mammals and the monkeys

Although the earliest true mammals evolved during the late Triassic period towards the end of the age of the dinosaurs, they remained small and relatively inconspicuous until around 65 Mya, the time of the disappearance of the dinosaurs. The first modern monkeys evolved in Africa or Asia around 35 Mya and around 23 Mya they split into two lines: the Old World Monkeys (which led to many species including baboons, macaques and colobus monkeys) and the Hominoids (which led to gibbons, orangutangs, apes and humans).

The split of gibbons and then gorillas from hominines

The split of the Hominoid superfamily (apes) into the Hylobatids (gibbons) and Hominids (great apes) families occurred in the early Miocene, roughly 20 to 16 million years ago. Recent research suggests that the last common ancestor of gibbons and apes — including humans — was much smaller than previously thought, about the size of a gibbon [1]. Mark Grabowski and co-authors compared body size data from modern primates, including humans, to those estimated from a wide range of fossil hominins and primates. They found that the common ancestor of apes and gibbons was likely small, probably weighing about 5.5 kg (12 pounds), which goes against previous suggestions of a chimpanzee-sized, chimpanzee-like ancestor. Our last common ancestor with the gibbons was very likely gibbon-like, a small and nimble tree-dweller.

The last common ancestor of the hominoids was likely a small tree-dwelling and gibbon-like primate.

Among living primates, humans are most closely related to bonobos and chimpanzees and gorillas. The following diagram shows evolution of the hominoid family and the dates at which the major hominoid genera split off from the lines that eventually became humans. The gibbons and then the orangutans were the first groups to split from the line leading to the hominins, including humans—followed by gorillas around 10 Mya, and, ultimately, by the chimpanzees (genus Pan).

With the sequencing of both the human and chimpanzee genome, as of 2012 estimates of the similarity between their DNA sequences range between 95% and 99%. By estimating the frequency of mutations and thus the time required for the number of divergent mutations to accumulate between two lineages, the approximate date for the split between lineages can be calculated.

The split between chimpanzees and humans

The split between hominin and chimpanzee lineages is placed by some between 4 to 8 million years ago, that is, during the Late Miocene. Speciation appears to have been unusually drawn out. Initial divergence occurred sometime between 7 to 13 million years ago, but ongoing hybridization blurred the separation and delayed complete separation during several millions of years. Patterson et al in 2006 [2] dated the final divergence at 5 to 6 million years ago.

Model of the speciation of Hominini and Gorillini over the past 10 million years; the hybridization process within Hominini is indicated as ongoing during roughly 8 to 6 Mya. Credit Wikipedia.

Species close to the last common ancestor of gorillas, chimpanzees and humans may be represented by Nakalipithecus fossils for an ape species that lived in Kenya around 10 Mya  and Ouranopithecus found in Greece and dated to 9 — 8 Mya.

Human evolution began in Africa around 7 million years ago when a now extinct ancestral ape population split and gave rise to the chimpanzee and bonobo family trees, and the hominin or human family tree due to climatic and geological activity pertaining to the formation of the Great Rift Valley in East Africa. The word “human” encompasses many upright walking bipedal apes, not just Homo sapiens (which is the only member left on the hominin family tree). This means that “human” can apply to any species that evolved on the hominin family after the split from the now extinct common ape ancestor we shared with chimpanzees and bonobos around 7 million years ago in Africa.

The evidence suggests that there was a quite long-drawn-out speciation process rather than a clean split between two lineages. The above diagram shows the speciation process lasting from 8 Mya to 5.5 Mya and others have argued that it may have lasted up to 4 million years. Different chromosomes appear to have split at different times, possibly over as much as a 4 million year period. While it has been generally assumed that the last common ancestor of humans and chimpanzees was chimpanzee-like, Sayers et al [3] have argued that many of the behavioural and anatomical characteristics of humans may have evolved in the common ancestral species and that the characteristics of chimanzees evolved subsequent to the split. They also argue that the social and sexual behaviour of humans is closer to that of bonobos than chimpanzees, and that chimpanzee behaviours are what diverged most.

The Australopithecines

Following the split, the human branch evolved into many Australopithecine genera and species, and there is much debate and ongoing revision of the classification of Australopithecine fossil remains into separate species. Most of them lived in Africa, many at the same time, over the period from around 7 Mya to 1 Mya. As shown in the diagram above, there were many evolutionary offshoots that went extinct. There were many species that belonged to various genuses such as Sahelanthropus, Ardipithecus, Australopithecus, Paranthropus, Kenyanthropus, and our own genus, Homo. Most of the African fossils have been found within and near the Great Rift in east Africa, in countries such as Ethiopia, Kenya, and Tanzania. But others have also been discovered in countries such as Chad, South Africa, Zambia, and Morocco.

Reconstruction of Lucy, Moersgaard Museum, Denmark

The genus Australopithecus evolved in eastern Africa around 4 million years ago before spreading throughout the continent and eventually becoming extinct 2 million years ago. There were a number of species, including Australopithecus afarensis. Fossilized bones of a female of this species were discovered in Ethiopia in 1974, dated to 3.2 Mya and became famous as “Lucy”. Lucy walked upright, weighed around 29 kg and 1.1 m tall, and looked somewhat like a chimpanzee. She is thought to be a young mature female around 12 years old. Lucy lived around the same time as the earliest known stone tools dating to around 3.3 to 3.4 million years old. These were discovered near Lake Turkana in Kenya and were likely made by Australopithecus afarensis.

The brain size of Lucy and other Australopithecus afarensis was in the range of around 375 to 500 cc, similar to that of modern chimpanzees. Around 2.8 Mya [4], the first species of a new genus Homo with around double that brain size evolved in Africa from an Australopithecine species, quite likely Australopithecus afarensis. The evolution of Homo will be summarized in a following post.

References

[1] Mark Grabowski, William L. Jungers. Evidence of a chimpanzee-sized ancestor of humans but a gibbon-sized ancestor of apes. Nature Communications, 2017; 8 (1) DOI: 10.1038/s41467-017-00997-4

[2] Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D (June 2006). Genetic evidence for complex speciation of humans and chimpanzees. Nature. 441 (7097): 1103–8. doi:10.1038/nature04789

[3] Sayers, Ken; Raghanti, Mary Ann; Lovejoy, C. Owen (October 2012). Human Evolution and the Chimpanzee Referential Doctrine. Annual Review of Anthropology. 41: 119–138. doi:10.1146/annurev-anthro-092611-145815.

[4] Ghosh, Pallab (March 4, 2015). “‘First human’ discovered in Ethiopia”. BBC News. London.

James Mathers and the plague outbreak of 1900

The coronavirus epidemic has now spread to most parts of the world, and Switzerland is in the top 12 countries for confirmed cases, which may not reflect the reality of cases in countries with little or no testing.  This time of social distancing and self-quarantine brought to mind my great-grandfather who lived through an epidemic of bubonic plague in Sydney in 1900, the first and largest plague outbreak in Australia. In this post, I take a look at this outbreak and his experience of it through the window of the detailed journal that he kept at the time.

My great-grandfather James Mathers was born in 1852 and migrated from Scotland to Australia in 1897 with his family, including my four year old grandfather William Melrose Mathers. Some months after their arrival, he started working as a Christian missionary for the Sydney City Mission, having previously undertaken similar urban mission work in Scotland.  For 14 years until his death in 1911, he worked in the Millers Point and Rocks areas of Sydney, areas now either side of the Sydney Harbour Bridge.

James Mathers and residents of the Rocks, circa 1900

In 1901, Miller’s Point and the Rocks had a population of around 112,000, nearly a quarter of the City’s population and its population density was near the highest in the metropolitan area. The Rocks in particular, was a slum area with very high population density (one quarter of Sydney’s population lived there in 1901) and high rates of poverty. The population contained an above-average proportion of non-British immigrants, especially the Chinese, clustered near lower George Street, in Queen and Little Essex Streets. There were 134 men to every 100 women, and three times the average Sydney proportion of bachelors.

In 1900, bubonic plague broke out in the Rocks less than three years after James Mathers started his mission work there. As part of his employment, he kept a detailed daily journal to give an account of his activities for his Mission supervisors but they also provide a personal impression of conditions in Miller’s Point and The Rocks. The sixteen volumes of the Mathers journals span the period July 1897 to February 1911 and collectively weigh about 10 kilos. They were passed down through the family to my mother some years ago. She later gave them to the Mitchell Library in Sydney, where they now held and one of the volumes can also be read online.

James Mathers visiting a family in the Rocks, circa 1900.

An Australian historian, Malcolm Prentis has summarized the journal observations of James Mathers on the 1900 plague [1] and I gratefully acknowledge drawing on his research for this post. Sydney experienced outbreaks of bubonic plague in 1900, 1902, 1907 and 1921-22. The 1900 outbreak was by far the worst. Between 19 January and 9 August 1900, 103 residents of Sydney died of bubonic plague. Another 200 contracted the disease and survived. The 1900 outbreak is thought to have originated in South China in the 1890s and reached Sydney from New Caledonia, carried by the fleas on ship-borne rats. The bubonic plague, or ‘Black Death’ as it became known during the pandemic of the 17th century, is one of the most deadly diseases to which humans have ever been exposed. The disease is caused by the bacterium Yersina pestis (Y pestis), which is carried by rat fleas.

James Mathers knew the family of the first victim well and made the following entry in his journal for 25 January 1900:

“Great excitement prevails all over my district just now through a reported case of Bubonic Plague, the sufferer being Arthur Payne 10 Ferry Lane, & who along with his family has been removed to the quarantine station, for further examination.

“Visiting in that part of the district and hearing of the man’s illness I went to the door. I was met by Mrs Payne whom I know well, and whose mother, Mrs Holms, attends my meetings regularly. I asked her if I could see her husband, but she refused my request for 2 reasons, 1st, because it was suspected bubonic plague, and 2nd, because he was suffering severely with his heart & did not like to be spoken to on such a subject, as he was a peculiar man, but a good man she said.

“I asked her if he was saved & she could not answer the question. I was very anxious to deal with the poor fellow about his soul, not knowing how soon he may pass from off this stage of action with an unsaved soul, but for some wise end I was prevented from seeing him.

“The authorities removed the family immediately I left, also all those who had been in the house from Friday. The Lord knew best, if I had got an entrance to the house I would have been in Quarantine along with the rest & the Lord preferred me in my district. Praise be his name, he doeth all things well.

“Oh: that people were just as much excited about the plague of sin in the soul, as they are about the supposed Bubonic Plague in Sydney, we would have a real revival in our midst. I believe it is coming, that God is going to pour upon us a great blessing, & that not very far in the distance.”

A number of accounts I’ve seen state that Arthur Payne was the first person to die from the plague, but in fact he survived, and the first fatality was Captain Thomas Dudley. About a month later, Dudley, who also worked at the wharves in the Rocks, began showing symptoms. He had noted scores of dead rats in his neighbourhood and said he had been pulling dead vermin from his toilet before falling ill. Dudley became the city’s first plague fatality and his death set off a wave of panic. Fun fact: 16 years earlier, Dudley had been convicted of murder for the purpose of cannibalism  [2].

Buildings and Tents, North Head Quarantine Station, c.1900. Courtesy National Archives of Australia

There was a wave of public panic in inner Sydney as the plague, which arrived on fleas brought ashore by ships’ rats, began to thrive during the warm wet autumn. Those who could afford to fled the city, real estate agents were inundated with calls for suburban properties and there were stories of residents fleeing to the Blue Mountains. Fear bred hostility and the newspapers were full of lurid stories about the “Black Death”. People were marched off in the middle of the night to be quarantined and the names of those infected or deceased were published daily.The authorities made North Head’s quarantine station the city’s first line of defence, designed to delay and destroy the “deadly foes threatening to storm the great metropolis.” In all, more than 1700 people were sent to the station, of whom only 303 were cases. There were 103 deaths, and the dead were interred with quick lime to hurry their decomposition.

While there was a tendency to blame the Chinese residents of the Rocks area, much of the blame for the outbreak of plague was assigned by the press to the government and City Council, for lack of  enforcement of existing public  health and housing laws and regulations.

Within a few months of Captain Dudley’s death, the plague had spread along transport routes across the city and quarantine areas were established from Millers Point west to Chippendale and Glebe, as far east as Paddington and Manly in the north. Squadrons of ratcatchers were formed and in the next few months, tens of thousands of vermin were killed and burned in a special rat incinerator with some councils paying six pence a head, making the pestilence very profitable.

Rat catchers with a pile of dead vermin in Sydney in 1900. Rats were fetching up to six pence a head during the outbreak. Picture: State Library of NSW

Other references to the plague in the journals are rare over the next few months. A couple of entries in March note that Mission meetings were well attended despite the plague. He also notes increased difficulty in visiting Chinese opium dens and brothels in Queen Street: “but for the love of God the task would have been too much for me, more especially at a time when the plague is in my district” (20 March 1900). He also noted the problems caused by the quarantining, particularly the loss of work due to the closing of the wharves.

One of his colleagues in the Mission, Mr J.H. Mills, was quarantined with his whole family at North Head. Mills’ eldest son died, much distress among the Mission workers. Mathers’ wrote in his journal on 28 March:

“It caused a deep feeling of sympathy towards our bro. I never was in a more earnest prayer meeting. Every one poured out his & her heart on behalf of Mr Mills & his family. May the Lord restore them all to health again, & Bless & sanctify it to us all, is my earnest prayer.”

Although the Chinese were a popular scapegoat for the plague, nowhere in his journals does my great-grandfather reveal any prejudice or assign any blame to the Chinese  whom  he  continued  to visit  throughout 1900. One Chinese dwelling he described as “exemplary clean”. He noted the tiny bound feet of the Chinese lady living there, who showed him proudly over the house and listened with attention to his message, “at least appreciating the name of Jesus” (2 February 1900).

The 1902 plague barely affected the Rocks area, in contrast with the 1900 plague. By 1902 its transmission was understood and there was much less panic; also the quarantine policy was applied more humanely and rationally. Mathers makes no reference whatsoever in his journals to the 1902 plague. Even “rat Wednesday” on 5 March when residents of Sydney joined in a great festival of rodent extermination, is merely noted in his journal as a “public holiday”.

Overall, James Mathers was remarkably relaxed and fearless of his personal safety during the 1900 plague. He did not really change any of his usual activities. He was compassionate about others’ tragedies and annoyed by the problems caused to others by the quarantining of much of his district. Malcolm Prentis makes particular note that there was no reflection in his journal on the plague as divine vengeance, unlike an address of Rev. William Macky of Scots Church in May 1900. Prentis speculates that Mathers thought the victims of the plague in inner Sydney were no more in need of punishment that the politicians whose negligence had allowed unhealthy conditions to persist.

Slum shanty dwellings in the Rocks, circa 1900.

Historically, the three major outbreaks of bubonic plague have been among the greatest disasters to strike humans in historical times. The 5th century plague in the time of Justinian killed around one quarter of the population of the eastern Mediterranean and that of the 14th century around one third of the population of Europe. In 20th century Australia, however, there were relatively few deaths due to a coordinated response from health authorities and government. In all the outbreaks from 1900 to 1922, there were a total of 1371 reported cases and 535 deaths.

The colonial and city governments instituted a three-pronged approach to controlling the disease in Australia: transporting infected individuals and anyone they may have had contact with to the quarantine station at North Head; intensive cleaning and, in some cases, demolition of sections of the inner city and dock area; and a rat extermination program. Initially the quarantine period was 10 days but this was eventually reduced to five. In the first nine months of 1900, 1759 people were quarantined. Of these only 263 were confirmed cases.

In February 1900 cleaning of infected neighbourhoods began under the direction of the newly formed Plague Department. Between March and July 1900, the Rocks and waterfront areas were barricaded off and residents armed with lime, carbolic acid and sulfuric acid, enlisted to cleanse, disinfect and even burn and demolish their own houses in infected areas. In March the city council began organising teams to exterminate the rat population. The government paid two pence per rat delivered to an incinerator on Bathurst Street.  Eventually, more than 108,000 rats were killed by government employees, although the number killed by private individuals using poison provided by the authorities may have exceeded that number.

Areas of The Rocks were barricaded off and its slums were demolished. Picture: State Library of NSW

The 1900 plague paved the way for substantial urban renewal, of waterfront precincts such as The Rocks and Millers Point, where a century of unregulated building had created shanty towns ripe for disease. The NSW Government took back ownership of virtually the entire headland from Circular Quay to Darling Harbour and demolished hundreds of slum houses and businesses in what are now prime real estate precincts such as George St, Sussex St, Kent St and Martin Place.

The pathogen that caused plague had been discovered by the French and Japanese epidemiologists Alexander Yersin and Kitasato Shibasaburo during the Hong Kong epidemic in 1894, and another French epidemiologist, Paul-Louis Simond, then proved during the 1896 plague outbreak in Bombay that fleas could act as vectors for transmission between rats. However, this theory was not widely accepted by the medical community until the chief of the New South Wales Board of Health, John Ashburton Thompson, isolated the Y pestis bacterium in fleas on dead rats captured in Sydney in 1900. Apart from spurring the rat extermination program and slum cleaning, Ashburton Thompson’s experiments were instrumental in changing public health methods around the world to combat bubonic plague.

References

[1] Malcolm D.Prentis. Christian responses to plague in Sydney 1900: James Mathers of Miller’s Point. Studying Australian Christianity in international perspective 1997.

[2] Dudley He had been employed to sail a yacht from Britain to Sydney and when it sank in a storm, he and three other crew took to a life boat without food. On the 20th day he and the mate killed the cabin boy and the three surviving crew ate him, and then were rescued four days later by a passing ship. He was charged with murder and tried. Although the jury found him and the mate guilty of murder, the judge took into account that they thought there was no prospect of rescue or survival otherwise, and sentenced them to only six months imprisonment. https://trove.nla.gov.au/newspaper/article/241262248

 

Is freedom increasing or decreasing?

Last week, Freedom House released its 2020 annual report on global freedom. The report documents trends in every region of the world of declining political and civil freedom: “In every region of the world, democracy is under attack by populist leaders and groups that reject pluralism and demand unchecked power to advance the particular interests of their supporters, usually at the expense of minorities and other perceived foes.”

The report compiles a freedom index for countries based on an average of two indices for political rights and civil liberties, composed of numerical ratings and descriptive texts for each country. The 2020 index adds to a time series for countries that extends back to 1972.  I’m interested to see to what extent the time series upholds the view of Stephen Pinker that there has been sustained long-term improvement in both political rights and human rights globally and this will continue (Enlightenment Now, Chapters 13 and 14).

The graph below shows time trends for the number of countries falling into three broad categories of the freedom index, labelled as Free (green shades), Partly free (orange shades) and Not free (purple shades). The graph includes 185 countries. 11 very small countries with populations less than 90,000 in 2015 are not included.

Trends in numbers of countries by broad freedom category

The report’s methodology is derived in large measure from the Universal Declaration of Human Rights, adopted by the UN General Assembly in 1948. The index is based on the premise that these standards apply to all countries and territories, and operates from the assumption that freedom for all people is best achieved in liberal democratic societies. The Freedom Index is an average of the scores for Political Rights and Civil Liberties and ranges from 1 (Free) to 7 (Not free). Three broad categories are defined as follows, and I’ve broken each into two subcategories for displaying trends in graphs here.

     Freedom Index       Category                Upper subgroup     Lower subgroup

            1.0 to 2.5            Free                         1.0                              1.5 – 2.5

            3.0 to 5.0            Partly Free            3.0 – 3.5                   4.0  – 5.0

            5.5 to 7.0            Not Free                 5.5 – 6.0                  6.5 – 7.0

The graph above shows numbers of countries by these three categories (and also distinguishing two levels within each category defined as show in the third column above. The following graph shows the proportion of the global population in each category, by weighting each country score by its total population.

Trends in proportions of global population by freedom category

Over the last 14 years, 25 of the 41 established democracies have experienced declines in their freedom indices. This can be see in the diminishing width of the green zone from around 2006. Though there is a long-term trend of increasing global freedom until around 2005-2010, this trend has ceased and there are declining levels of freedom in the last decade. Comparing changes in the freedom index between 2015 and 2020, the gap between setbacks and gains widened compared with 2018, as individuals in 44 countries experienced deterioration in their political rights and civil liberties while those in just 24 experienced improvements. The negative pattern affected all regime types, but the impact was more visible near the top and the bottom of the freedom scale.

At the bottom of the scale, large countries like Russia and China are intensifying their suppression of domestic dissent and at the top of the scale many freely elected leaders are also taking steps to reduce existing human or political rughts. The Global Freedom Report notes that “such leaders—including the chief executives of the United States and India, the world’s two largest democracies—are increasingly willing to break down institutional safeguards and disregard the rights of critics and minorities as they pursue their populist agendas.”- The Freedom House Report goes into more detail about the trends and changes for individual countries in each region.

In the following graphs, I have plotted trends in the proportions of regional populations falling into each of the freedom categories. Because large populations dominate, and crossing one of the freedom thresholds will shift that entire population to another area, these graphs are more spikey than if I had plotted numbers of countries rather than people. For example, the large discontinuity in the purple sub-areas for East Asia and Pacific from 1977 to 1988 reflects the freedom score for China decreasing from 6.5 to 6 in that period. Similarly, the graph for North America shows the decrease in freedom from 2016 onwards in the USA with the index increasing one step from 1 to 1.5.

Finally, I also calculated a population-weighted average freedom score for regions and the world, shown in the following graph.  This also highlights the recent declines in freedom in most regions in recent years, but perhaps in a more comparative way than the regional plots above (where the population proportions relate only to the categories relevant to each region).

Is Pinker right that freedom is increasing and will continue to increase?  Maybe, he is taking a longer view than the last decade, and in the big picture there has been an overall increase in global freedom. But the reversal is worrying and may continue if populist responses continue to attack political and human rights, and humans increasingly turn away from evidence-based approaches to global issues such as pandemics, refugees, overpopulation, and the climate crisis.

My maternal ancestors – from Eve via ice age Europe to Victorian England

In an early post on this blog, I summarized my maternal-line ancestors and where and when they lived. In the last 6 years, there have been substantial revisions to estimates of the dates associated with these mitochondrial DNA (mtDNA) haplogroup founders, and revisions to the mtDNA haplogroup tree (deep-maternal-ancestry-and-mtdna) and this post provides an update. I am a member of mtDNA haplogroup U5, which is one of nine native European haplogroups stemming from haplogroup U which most likely arose in the Near East, and spread into Europe in a very early expansion. The presence of haplogroup U5 in Europe pre-dates the last ice age and the expansion of agriculture in Europe. Today, about 11% of modern Europeans are the direct maternal descendants of the founder U5 woman. They are particularly well represented in western Britain and Scandinavia. My more recent maternal ancestors were part of the population that tracked the retreat of ice sheets from Europe at the end of the last ice age and re-colonized Britain about 12,000 years ago.

The mtDNA sequence at the root of each haplogroup arose from one or more mutations in the mtDNA of just one woman, and the age of the associated haplogroup gives the time in the past when this specific woman lived. To emphasise that the maternal clan founders were real individuals, I have used the names given to them by Sykes [1] and Oppenheimer [2] and given my own names to the more recent subgroup founders. The Table below summarizes these founders, dates and locations and is followed by brief biographies. The haplogroups are identified by the labels used in Build 17 of the ISOGG mtDNA tree which can be accessed at http://phylotree.org/ [3]. Dates in the table below have been updated using most recent available dating estimates as described in my previous post deep-maternal-ancestry-and-mtdna.

The migration path out of Africa into Europe of the “grandmothers” linking mitochondrial Eve through to Ursula (U5) is shown on a map in my previous post deep-maternal-ancestry-and-mtdna. The subsequent migration from Europe to Britain is shown in the map below.

Figure 1. Migration path of my maternal ancestors from Ursula (U5) to Viviane (410 CE). A map of the earlier migration from mitochondrial Eve to U5 is included in an earlier post.

Updated biographies of my maternal haplogroup great* grandmothers follow below.

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Skiing in the French Alps

I have just spent a week skiing in the French Alps with my younger son. We stayed in a chalet above the village of Les Gets in Les Portes du Soleil ski doman (the Gates of the Sun). Normally the snow is down to the village, but this February is the warmest I have experienced since I have lived in Geneva and the snow did not extend much lower than our chalet. Fortunately it snowed quite a bit after we arrived, and there was plenty of fresh powder for skiing. And enough to ski back to our chalet at the end of the day.

View from our chalet

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Our Asgardian ancestors

I grew up reading northern European myths and legends, including tales of Odin, Thor, and the other gods of Asgard. I was largely unaware of the Marvel comics appropriation of Thor and other Asgardians as superheros until the Marvel cinematic universe started to hit the big screens in the last 12 years.

Loki, Thor and Odin (from the Marvel Cinematic Universe)

I have only recently come across the growing evidence that an Asgardian was one of our ancestors, way back near the beginning of the evolution of life, when the first eukaryotic cell appeared. Eukaryotes are organisms whose cells contain membrane-wrapped internal structures, such as a nucleus, unlike prokaryotes (Bacteria and Archaea), which have no membrane-bound internal structures.

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