Monday, July 26, 2021

Steven Weinberg Has Passed

Physicist Steven Weinberg, who was born in 1933, died on July 23, 2021.
He was arguably the dominant figure in theoretical particle physics during its period of great success from the late sixties to the early eighties. In particular, his 1967 work on unification of the weak and electromagnetic interactions was a huge breakthrough, and remains to this day at the center of the Standard Model, our best understanding of fundamental physics.

Science News has another nice obituary for him.

The Common Cold Is Old

The common cold virus is much older than modern humans. 

The origins of viral pathogens and the age of their association with humans remains largely elusive. To date, there is no direct evidence about the diversity of viral infections in early modern humans pre-dating the Holocene. We recovered two near-complete genomes (5.2X and 0.7X) of human adenovirus C (HAdV-C), as well as low-coverage genomes from four distinct species of human herpesvirus obtained from two 31,630-year-old milk teeth excavated at Yana, in northeastern Siberia. 
Phylogenetic analysis of the two HAdV-C genomes suggests an evolutionary origin around 700,000 years ago consistent with a common evolutionary history with hominin hosts. 
Our findings push back the earliest direct molecular evidence for human viral infections by ∼25,000 years, and demonstrate that viral species causing common childhood viral infections today have been in circulation in humans at least since the Pleistocene.
From Sofie Holtsmark Nielsen, et al., "31,600-year-old human virus genomes support a Pleistocene origin for common childhood infections" bioRxiv (June 28, 2021).

The Testimony Of The Mandarin

Mandarin citrus fruits were first domesticated in the mountainous regions of Southern China, and spread widely from there. 

Hybridization of these mainland Chinese fruits and some wild species native to Japan's Southern Ryukyu Islands accounts for most important modern varieties of them.

Hunan Province of southern China, which is the center of wild mandarin diversity and the genetic source of most well-known mandarins. When the scientists re-analyzed previously published genomic data, they unexpectedly found that wild mandarins of this mountainous region are split into two subspecies.

"We found that one of these mandarin subspecies can produce offspring that are genetically identical to the mother," said Dr. Guohong Albert Wu, a research collaborator at the Lawrence Berkeley National Laboratory in California. "Like many other plants, wild citrus typically reproduces when the pollen of the father combines with the egg of the mother, mixing the genes from both parents in the seed. 
But we found a subspecies of wild mandarins from Mangshan, in southern China, where the seed contains an identical copy of the mother's DNA without any input from a father. So, the seed grows to be a clone of the mother tree."

From Science Daily.

The body text of the source paper explains that:

We find that the complexity of mandarin relationships is considerably simplified by the discovery of three ancestral lineages which, together with pummelo, gave rise to all extant mandarin diversity by hybridization and introgression. One of these groups is a previously unknown wild species currently found in the Ryukyu islands; the other two are previously unrecognized sister subspecies of mainland Asian mandarin. 
Our analysis leads to a comprehensive revision of the origin and diversification of east Asian citrus, including the elucidation of the origins of apomixis in mandarin and its spread to related citrus including oranges, grapefruits and lemons.

The paper and its abstract are:

The origin and dispersal of cultivated and wild mandarin and related citrus are poorly understood. Here, comparative genome analysis of 69 new east Asian genomes and other mainland Asian citrus reveals a previously unrecognized wild sexual species native to the Ryukyu Islands: C. ryukyuensis sp. nov. 
The taxonomic complexity of east Asian mandarins then collapses to a satisfying simplicity, accounting for tachibana, shiikuwasha, and other traditional Ryukyuan mandarin types as homoploid hybrid species formed by combining C. ryukyuensis with various mainland mandarins. These hybrid species reproduce clonally by apomictic seed, a trait shared with oranges, grapefruits, lemons and many cultivated mandarins. 
We trace the origin of apomixis alleles in citrus to mangshanyeju wild mandarins, which played a central role in citrus domestication via adaptive wild introgression. Our results provide a coherent biogeographic framework for understanding the diversity and domestication of mandarin-type citrus through speciation, admixture, and rapid diffusion of apomictic reproduction.
Guohong Albert Wu, et al., "Diversification of mandarin citrus by hybrid speciation and apomixis." 12(1) Nature Communications (July 26, 2021) (open access). 

Friday, July 16, 2021

Medieval Astronomy

The Syriac Text
The reconstructed sky in the place where the Syriac text was written on May 25, 760 at 2:40 a.m.

Scientists have
analyzed ancient historical accounts from Syria, China, the Mediterranean and West Asia (most critically, the detailed accounts in the hand written Syrian Chronicle of Zuqn¯ın, part of which ended up in the Vatican Library and part of which ended up in the British Museum) to confirm that all of these accounts viewed key parts of the appearance of a particular comet in their skies in late May and early June of the year 760 CE.  

The scientists matched these observations with calculations of where the comet 1P/Halley would have been in the sky at that time based upon its current observed trajectory with key dates pinned down to a margin of error of one to two days for particular events.

This 760 CE fly-by was the comet's last return before a close encounter with Earth in 837 CE. The 760 CE perihelion of the comet that was observed is particularly important for extrapolation further back in time. This study provides one of the longest time frames of confirmed continued observations of the same celestial object. This helps to confirm the accuracy and robustness of astronomy's current gravitational calculations of solar system orbits, and to remind us just how long quite accurate scientistic astronomy observations have been collected and recorded by people.

Historical Context

This was near the end of the period known as the "dark ages" in the former western Roman Empire in Europe, during the life of Charlemagne, eight years before he began his reign as the King of the Franks in what is now France, and forty years after the remarkably wet summer of 720 CE in Europe.

Decisive battles on land and at sea with the Byzantine Empire ended the expansion of the Umayyad Caliphate into the territory of the former Roman Empire fourteen years earlier (746 CE). The Eastern Orthodox Christian Byzantine Empire was the last remnant of the Roman Empire, in what is now most of Turkey, Greece and Italy, and would persist in a gradually diminished form over about three more centuries. The West Asian accounts were written by Byzantine subjects.

As the body text of the new paper explains:
The author of the chronicle was probably the stylite monk Joshua; a stylite is an early Byzantine or Syrian Christian ascetic living and preaching on a pillar in the open air, so that many celestial observations can be expected in his work. The author of the Chronicle of Zuqn¯ın may have lived on a pillar for some time. During the time of writing of the Chronicle of Zuqn¯ın [ed. completed in 775/776 CE], the area was outside the border of the Byzantine empire and already under 푐Abbasid rule.
Thus, the Syrian chronicle entries were written by a Christian monk under the jurisdiction of the Islamic Abbasid Caliphate (750-1517 CE) in areas recently reclaimed by the Caliphate after a brief Byzantine expansion into the territory of the Umayyad Caliphate which preceded it. The Abbasid Caliphate had been formed ten years earlier in the Abbasid Revolution and replaced the Umayyad Caliphate (661-750 CE). The Umayyad Caliphate had been led by an ethnically Arab elite that treated even non-Arab Muslim converts as second class citizens, while the Abbasid Caliphate was led by a multi-ethnic, mostly non-Arab, and eastern oriented Abbasid Caliphate that ruled in a more inclusive manner, whose Caliphs claimed to have descended from an uncle of the Prophet Muhammad (who died about four decades before the comet appeared).

The provenance of the Chronicle was somewhat involved. As the body text explains:
The Chronicle of Zuqn¯ın is not known to be copied and disseminated; sometime during the 9th century it was transferred to the Monastery of the Syrians in the Egyptian desert . . .  Shortly after the manuscript was found and bought for the Vatican, it was considered to be written by the ¯ West Syrian patriarch Dionysius I of Tell-Mah. re, so that this chronicle was long known as Chronicle of Dionysius of ¯ Tell-Mah. re. Dionysius did write an otherwise lost world chronicle, but lived later (died AD ca. 845). Since this mistake was noticed, the chronicle has been called the Chronicle of Pseudo-Dionysius of Tell-Mah. re or, better, the Chronicle of Zuqn¯ın, because the text mentions the monastery of Zuqn¯ın as the living place of the author; Zuqn¯ın was located near Amida, now Diyarbakır in Turkey near the border to Syria. 
The Chronicle of Zuqn¯ın is made of four parts: Part I runs from the creation to Emperor Constantine (AD 272-337), Part II from Constantine to Emperor Theodosius II (AD 401-450) plus a copy of the so-called Chronicle of PseudoJoshua the Stylite (AD 497 to 506/7), Part III from Theodosius to Emperor Justinian (AD 481-565), and Part IV to the time of writing, AD 775/776. The Chronicler used a variety of sources, some of them otherwise lost. The author knew that some of his sources did not provide a perfect chronology; for him, it is more important to convey his message (to learn from history) than to give perfect datings. 
The events reported in the text are dated using the Seleucid calendar; the Seleucid Era (SE) started on October 7, BC 312 (= Dios 1). There are several versions of the Seleucid calendar, including the Babylonian (Jewish), Macedonian, and West Syrian (Christian) ones. The author of our chronicle systematically used the latter version for reports during his lifetime – a solar calendar, in which the year ran from Tishri/October 1 to Elul/September 30, applied since at least the fifth century AD.
This was also two years before the city of Baghdad was founded within the Abbasid Caliphate, near the ancient city of Seleucia, which had been the capitol of the Nestorian Christian Church of the East from 410 CE, until it had to be abandoned to the desert sands when the Tigris River that made it possible to live there shifted, a few decades after Baghdad was founded.

In China, this comet's appearance coincided with the unsuccessful seven year long An Lushan Rebellion against the Tang Dynasty. This rebellion ended with a pair of stunning betrays, first when An Lushan, the leader of the rebellion, was killed by one of his own eunuchs in 757, and then when his successor as leader of the rebellion, Shi Siming, was killed by his own son in 763, which ended the rebellion.

Citizen Science In Astronomy

The actual goal of this project, to find gravitational lensing evidence of a small dark matter halo from a database with tens of thousands of observations, is pretty ordinary as astrophysics goes, and it doesn't yet have any definitive results. Still, it is a worthwhile project that adds incrementally to what we know in a well focused way to expand the margins of our existing knowledge.

It illustrates the reality that the many modern telescopes in multiple frequencies that are now being used can collect a vast amounts of information. But this has made a lot of questions in astrophysics and astronomy "big data" problems.

With a smaller database, a single skilled research could personally review each one. This painstaking pouring over of data by a single highly trained scientist with the PhD in the relevant subfield of astronomy is how this kind of research got started. But it is impossible for a single astronomer to conduct the necessary fairly detailed analysis of each observation required for this kind of study, for such a large collection of data, in a reasonable amount of time. But timely analysis is necessary because the amount of data to review gets larger every month. 

The firehose of incoming data is only getting stronger. For example, a new European Space Agency project targeted for the year 2045 will collect information on 10 to 12 billion new sources of light in the sky that are too faint to discern now.

The citizen science methodology used in this study is remarkable and exciting. It presents an alternative to statistical, machine learning, and supercomputing approaches to sorting through masses of data. Unlike these automated alternatives, this citizen science approach doesn't sacrifice the human judgment element of the process present when a single scientist analyzes a large, but tractable body of data. 

In this case, twenty people, about a quarter of whom were scientists, about quarter of whom were graduate students, and about half of whom were undergraduates, mostly at the University of Crete, worked together to tackle the large dataset to identify 40 strong candidates out of 13,828 (many of which have multiple images at different wave lengths that had to be considered) including two particularly promising needles in the haystack.

It is a kind of project I am familiar with from my day job as an attorney, where, for example, I've had to mobilize similar numbers of people with similar skill levels, to review an entire room full of banker's boxes of not very well organized hard copy business records to locate a handful of key documents in complex securities fraud litigation.

The way this project managed to mobilize so many people to volunteer their time for this somewhat esoteric goal, hearteningly democratized this scientific endeavor and made this task possible to complete.

The paper and its abstract are as follows:

Dark Matter (DM) halos with masses below 108 M, which would help to discriminate between DM models, may be detected through their gravitational effect on distant sources. The same applies to primordial black holes, considered as an alternative scenario to DM particle models. However, there is still no evidence for the existence of such objects. 
With the aim of finding compact objects in the mass range  106 -- 109M, we search for strong gravitational lenses on milli (mas)-arcseconds scales (< 150 mas). For our search, we used the Astrogeo VLBI FITS image database -- the largest publicly available database, containing multi-frequency VLBI data of 13828 individual sources. 
We used the citizen science approach to visually inspect all sources in all available frequencies in search for images with multiple compact components on mas-scales. At the final stage, sources were excluded based on the surface brightness preservation criterion. We obtained a sample of 40 sources that passed all steps and therefore are judged to be milli-arcsecond lens candidates. 
These sources are currently followed-up with on-going European VLBI Network (EVN) observations at 5 and 22 GHz. Based on spectral index measurements, we suggest that two of our candidates have a higher probability to be associated with gravitational lenses.

C. Casadio, et al., "SMILE: Search for MIlli Lenses" arXiv: 2017.06896 (July 14, 2021) (accepted for publication).