Weekly Meanderings 8 February 2020
Greetings from Israel! Kris and I are with a group of Northern DMin students (and others) as we explore the world of the Bible.
When the first Neanderthal genome was sequenced, using DNA collected from ancient bones, it was accompanied by the discovery that modern humans in Asia, Europe and America inherited approximately 2% of their DNA from Neanderthals — proving humans and Neanderthals had interbred after humans left Africa. Since that study, new methods have continued to catalogue Neanderthal ancestry in non-African populations, seeking to better understand human history and the effects of Neanderthal DNA on human health and disease. A comparable catalogue of Neanderthal ancestry in African populations, however, has remained an acknowledged blind spot for the field due to technical constraints and the assumption that Neanderthals and ancestral African populations were geographically isolated from each other.
In a paper published in the journal Cell, a team of Princeton researchers detailed a new computational method for detecting Neanderthal ancestry in the human genome. Their method, called IBDmix, enabled them for the first time to search for Neanderthal ancestry in African populations as well as non-African ones. The project was led by Joshua Akey, a professor in Princeton’s Lewis-Sigler Institute for Integrative Genomics (LSI).
“This is the first time we can detect the actual signal of Neanderthal ancestry in Africans,” said co-first author Lu Chen, a postdoctoral research associate in LSI. “And it surprisingly showed a higher level than we previously thought,” she said.
The method the Princeton researchers developed, IBDmix, draws its name from the genetic principle “identity by descent” (IBD), in which a section of DNA in two individuals is identical because those individuals once shared a common ancestor. The length of the IBD segment depends on how long ago those individuals shared a common ancestor. For example, siblings share long IBD segments because their shared ancestor (a parent) is only one generation removed. Alternatively, fourth cousins share shorter IBD segments because their shared ancestor (a third-great grandparent) is several generations removed.
The Princeton team leveraged the principle of IBD to identify Neanderthal DNA in the human genome by distinguishing sequences that look similar to Neanderthals because we once shared a common ancestor in the very distant past (~500,000 years ago), from those that look similar because we interbred in the more recent present (~50,000 years ago). Previous methods relied on “reference populations” to aid the distinction of shared ancestry from recent interbreeding, usually African populations believed to carry little or no Neanderthal DNA. However, this reliance could bias estimates of Neanderthal ancestry depending on which reference population was used. The Princeton researchers termed IBDmix a “reference free method” because it does not use an African reference population. Instead, IBDmix uses characteristics of the Neanderthal sequence itself, like the frequency of mutations or the length of the IBD segments, to distinguish shared ancestry from recent interbreeding. The researchers were therefore able to identify Neanderthal ancestry in Africans for the first time and make new estimates of Neanderthal ancestry in non-Africans, which showed Europeans and Asians to have more equal levels than previously described.
Orthodox women studying Talmud:
Among devout Orthodox Jews, the intense study of Talmud is no longer just a man's world. Women are increasingly delving into this central religious work, and American expats in Israel are at the forefront of the trend.
They're following a custom called Daf Yomi, Hebrew for "daily page," which involves reading a page a day of this centuries-old, multivolume collection of rabbinic teachings, debates and interpretations of Judaism. It takes about seven years and five months to read all 2,711 pages.
In early January, as Orthodox Jewish men held gatherings to mark the end of the cycle, called Siyum HaShas, Orthodox women in Israel held their own large-scale Talmud celebration for the first time. Some 3,000 women of all ages cheered in a Jerusalem convention center, according to the event's organizers, Hadran.
"I never thought I would live to see this day," said Tamar Stern, a Chicago native, sitting in the second-to-last row at the celebration. She attended Orthodox Jewish schools in the 1960s and 1970s, never allowed to learn Talmud with the boys.
IN SEPTEMBER 2009, over 3,000 bee enthusiasts from around the world descended on the city of Montpellier in southern France for Apimondia — a festive beekeeper conference filled with scientific lectures, hobbyist demonstrations, and commercial beekeepers hawking honey. But that year, a cloud loomed over the event: bee colonies across the globe were collapsing, and billions of bees were dying.
Bee declines have been observed throughout recorded history, but the sudden, persistent and abnormally high annual hive losses had gotten so bad that the U.S. Department of Agriculture had commissioned two of the world’s most well-known entomologists — Dennis vanEngelsdorp, a chief apiary inspector in Pennsylvania, then studying at Penn State University, and Jeffrey Pettis, then working as a government scientist — to study the mysterious decline. They posited that there must be an underlying factor weakening bees’ immune systems. …
The evidence was mounting. Shortly after vanEngelsdorp and Pettis revealed their findings, a number of French researchers produced a nearly identical study, feeding minute amounts of the same pesticide to bees, along with a control group. The study produced results that echoed what the Americans had found.
Drifting clouds of neonicotinoid dust from planting operations caused a series of massive bee die-offs in northern Italy and the Baden-Württemberg region of Germany. Studies have shown neonicotinoids impaired bees’ ability to navigate and forage for food, weakened bee colonies, and made them prone to infestation by parasitic mites.
In 2013, the European Union called for a temporary suspension of the most commonly used neonicotinoid-based products on flowering plants, citing the danger posed to bees — an effort that resulted in a permanent ban in 2018.
In the U.S., however, industry dug in, seeking not only to discredit the research but to cast pesticide companies as a solution to the problem. Lobbying documents and emails, many of which were obtained through open records requests, show a sophisticated effort over the last decade by the pesticide industry to obstruct any effort to restrict the use of neonicotinoids. Bayer and Syngenta, the largest manufacturers of neonics, and Monsanto, one of the leading producers of seeds pretreated with neonics, cultivated ties with prominent academics, including vanEngelsdorp, and other scientists who had once called for a greater focus on the threat posed by pesticides.
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