Thursday, March 31, 2022

Reference Human Genome Almost Complete


Work remains to finalize the reference genome (the Y chromosome still needs to be finished) but researchers are close to finally sequencing every last nucleotide of human DNA.

Ever since the launch of the Human Genome Project more than 30 years ago, genetic sequencing technologies and data-processing pipelines have been getting faster, cheaper and more precise, allowing researchers to sample, sequence and compare more genomes with every passing year.

But huge chunks of DNA – amounting to around 8 percent of the human genome – were still missing from the most recent reference sequence that scientists use as a template to assemble newly-sequenced DNA samples.

Now, scientists have pieced together those parts of the human genome which have long been 'unsequenceable' to assemble the most complete reference genome to date, sharing their findings in a collection of six papers, published in the journal Science.

Read more here and here.

Wednesday, March 23, 2022

Our African Ancestors


All living humans share a common point of origin in eastern Africa. Every person living today is descended from hunter-gatherers in Africa thousands of years ago. On our genetic profiles this appears as mtDNA Macro-haplogroup L, also known as Mitochondrial Eve/Eva. This should not be confused with the biblical Eve who lived no earlier than 7200 years ago.

Overview of the main divisions of haplogroup L.

About 300,000 years ago, people in Africa made new kinds of stone tools and began transporting raw materials up to 250 miles (400 kilometers), likely through trade networks. By 140,000-120,000 years ago, people wore animal skins and pierced marine shell beads.

A new genetic study indicates "The presence of eastern African ancestry as far south as Zambia, and southern African ancestry as far north as Kenya, indicates that people were moving long distances and having children with people located far away from where they were born. The only way this population structure could have emerged is if people were moving long distances over many millennia."

After a period of extensive population movements during which peoples from different regions intermarried, a change took place. Marriage partners were chosen from nearby.

The researchers used their study of Ancient DNA (aDNA) to create "the largest genetic dataset so far for studying the population history of ancient African foragers – people who hunted, gathered or fished. We used it to explore population structures that existed prior to the sweeping changes of the past few thousand years."

The DNA sampling was not uniform and not all of the individuals lived contemporaneously. However, "on average individuals from the same or nearby sites proved to be more closely related than predicted solely on the basis of the broad regional genetic structure, but this relatedness extends only over short distances, particularly within Malawi and Zambia."

This study focuses on population movements within Africa. It does not refer to the movements out of Africa. Stone tools dating to 1.5 million years have been found in Saudi Arabia near the Red Sea. 

The oldest stone tool to be found in Turkey reveals that humans passed through the gateway from Asia to Europe approximately 1.2 million years ago. The worked quartzite flake was found in ancient deposits of the river Gediz in western Turkey.

A trove of hand axes dating to 500,000 years ago was found in central Israel at Jaljulya

Thomas Strasser and Eleni Panagopoulou found stone tools on the southwestern shore of Crete, near Plakias. These date to between 200,000 and 100,000 years. 

A young male was buried 100,000 years ago in Qafzeh Cave in Lower Galilee.

Evidence of human habitation 100,000 years ago in the area of Bethlehem is attested along the north side of Wadi Khareitun where there are three caves: Iraq al-Ahmar, Umm Qal’a, and Umm Qatafa. These caves were homes in a wooded landscape overlooking a river. At Umm Qatafa archaeologists have found the earliest evidence of the domestic use of fire in Palestine.

Saturday, March 19, 2022

1921 Fossil Fuel Prediction and the Alligator Pear


A woman with a Chrysler vehicle, circa 1920s.
(Gamma-Keystone via Getty Images)

This 1921 Science News report predicts modifications to combustion engines that will reduce gasoline consumption. The article was written by E. H. Leslie, Associate Professor of Chemical Engineering at the University of Michigan. He mentions the production of "synthetic gasoline" and the future increased dependence of the United States on imported petroleum products.

H. the production of "synthetic gasoline" and the future increased dependence of the United States on imported petroleum products.

The paper includes a report on the Alligator Pear, otherwise known as the avocado. At the time of the report (July 18, 2921) over 1200 acres of avocados grew in Florida and California. The cost of this fruit was high in the 1920s due to scarcity. The growers have managed to sustain the high prices throughout the subsequent decades.

STEM students will find the Science News Archives helpful for research on historical developments in science.

Wednesday, March 9, 2022

Remembering John Polkinghorne One Year Later


“Science is privileged to investigate a universe that is both rationally transparent and rationally beautiful. Scientists frequently speak of the experience of wonder as the reward for all the weary labour involved in their research.” - John Polkinghorne

John Polkinghorne died on 9 March 2021. He was an English particle physicist, theologian, Anglican priest, and Professor of Mathematical Physics at Cambridge University. He served as the president of Queens' College, Cambridge from 1988 until 1996.

His achievements were recognized in 1974 by his election as a Fellow of the Royal Society. His work concentrated on quantum physics and the theory of elementary particles. He published a large volume of papers and his books ranged from research texts to popular science such as The Particle Play (1979) and The Quantum World (1984).

In 1977, he decided that he had “done [his] bit for physics”, and he resigned from his university position to begin a second career in the Church. He was ordained a priest in 1982. He served as canon theologian of Liverpool Cathedral from 1994 to 2005.

After a number of years as a parish priest he returned to the academic world and made a significant contribution to the field of science and religion, something he continued to do until his death at age 90.

In his 2007 book Quantum Physics and Theology: An Unexpected Kinship (London: SPCK), Polkinghorne articulated five points of comparison between the ways in which science and theology pursue truth: moments of enforced radical revision, a period of unresolved confusion, new synthesis and understanding, continued wrestling with unresolved problems, deeper implications.

Polkinghorne believed that because "we are creatures made in the divine image, then it is entirely understandable that there is an order in the universe that is deeply accessible to our minds." It seems natural then that Dr. Polkinghorne would turn to theology as a way to shine light on reality and the material world. Polkinghorne suggests that the experience of meaning in the practice of science hints at God. Science and theology explore a common reality and therefore, share a common starting point for meaningful dialogue.

In the 2008, Polkinghorne wrote, "There are aspects of our scientific understanding of the universe that become more deeply intelligible to us if they are viewed in a Trinitarian perspective." (Science and the Trinity, p. 61)

He considered himself a "creationist", but he rejected the literalism of American Fundamentalism. In an article published in 2008 in The Times, Polkinghorne wrote:

An irritating feature of modern life is the way in which useful words get hijacked and used for different, and often unacceptable, purposes. An example is “creationist”. As a Christian believer I am, of course, a creationist in the proper sense of the term, for I believe that the mind and the purpose of a divine Creator lie behind the fruitful history and remarkable order of the universe which science explores. But I am certainly not a creationist in that curious North American sense, which implies interpreting Genesis 1 in a flat-footed literal way and supposing that evolution is wrong.

The irony of this notion of creationism is that it not only involves many scientific errors, but is also the result of a bad theological mistake. When we read any kind of deep literature, if we are to give it the respect that it deserves we must make sure we understand the genre of what is written. Mistaking poetry for prose can lead to false conclusions. When Robert Burns tell us his love “is like a red, red rose”, we know that we are not meant to think that his girlfriend has green leaves and prickles. Reading Genesis 1 as if it were a divinely dictated scientific text, intended to save us the trouble of actually doing science, is to make a similar kind of error. We miss the point of the chapter if we do not see that it is actually a piece of deep theological writing whose purpose, through the eight-times reiterated phrase “And God said, ‘Let there be . . .”, is to assert that everything that exists does so because of the will of the Creator. Thus literal creationists actually abuse scripture by the mistaken interpretation that they impose upon it.

Related reading: Remembering John Polkinghorne by Tom C. B. McLeish (University of York, UK); Obituary: The Revd Professor John Polkinghorne