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.

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.