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NNadir

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Current location: New Jersey
Member since: 2002
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Climate-driven risks to the climate mitigation potential of forests

The paper I'll discuss in this post is this one: Climate-driven risks to the climate mitigation potential of forests (William R. L. Anderegg,*, Anna T. Trugman, Grayson Badgley, Christa M. Anderson, Ann Bartuska, Philippe Ciais, Danny Cullenward, Christopher B. Field, Jeremy Freeman, Scott J. Goetz, Jeffrey A. Hicke0, Deborah Huntzinger, Robert B. Jackson, John Nickerson, Stephen Pacala, James T. Randerson, Science, 368, 1327 (2020))

One of the authors, Stephen Pacala, of Princeton University - where the esprit de corps centers around the belief that so called "renewable energy" will save the day, even though there is no evidence, beyond pure speculation that it will - was the co-author of the once (and possibly still) famous Socolow and Pacala "Wedgie Paper" of 2004, which talked all about how existing technologies, as of 2004, could be utilized to stop climate change dead in its tracks:

Stabilization Wedges: Solving the Climate Problem for the Next 50 Years with Current Technologies (Socolow and Pacala, Science 13 Aug 2004:Vol. 305, Issue 5686, pp. 968-972)

One of the "Stabilization Wedges" (#5) was this one: 5. (Substitute) Gas baseload power for coal baseload power.

If you want to be amused, you can head on over to our beloved E&E forum here, or head over to Daily Kos, and read all about how "coal is dead." The rumor - let's call it what it is, "the big lie" - is that this result, the "death" of coal, is because of the zillion percent growth of so called renewable energy.

This year, as part of my subscription to Science they sent me an AAAS tee shirt with the suddenly controversial slogan on it "Facts are facts." This identity statement seems to have taken on a political context, which is why, when going to my physical therapy sessions where another patient wears her "Blue Lives Matter" tee shirt, I wear the shirt with the AAAS identity statement, which has become, um, political. On the left we think we embrace this identity statement and are thus somehow above and immune from embracing happy faced lies.

Of course, in the United States, our environmentalism is traditionally provincial. We think we can save the world by driving one of Elon Musk's cobalt laced cars.

But sorry, facts, are indeed facts. This is true for us on the left as well as it is for them on the right.

In this century, the use of coal grew by 63.22 exajoules to 159.98 exajoules up to and through 2018. This made coal the fastest growing source of energy in this century.

From 2017 to 2018, the increase in the use of coal amounted to 2.97 exajoules, compared to, in the same time frame, from 2017 to 2018, for solar, wind, geothermal and tidal energy combined an increase of 1.63 exajoules, slightly more than half the rate at which coal energy consumption grew.

2018 Edition of the World Energy Outlook Table 1.1 Page 38 (I have converted MTOE in the original table to the SI unit exajoules in this text.)

2019 Edition of the World Energy Outlook Table 1.1 Page 38] (I have converted MTOE in the original table to the SI unit exajoules in this text.)

In the week of August 13, 2004, when the famous "Wedgie" paper was published, (the week beginning August 8, 2004) the concentration of the dangerous fossil fuel waste carbon dioxide in the planetary atmosphere was 376.43. For the most recent week, pending tomorrow's result as of June 20, 2020, for the week beginning June 7, 2020, the concentration of the dangerous fossil fuel waste carbon dioxide was 416.34 ppm. This year, the running average annual increase over the last decade is 2.4 ppm/year, the highest figure ever recorded. In 2004, it was about 1.9 ppm/year.

Facts are facts. Facts matter.

Just because we in the United States are substituting gas for coal doesn't mean the world is. We like to have these silly big rock and roll concerts that are benefits for some thing or another, and all get together and sing "We Are The World," as if we were. But we are not the world. We are a province, more so than ever, under the dictatorship of the stupid. We are irrelevant, because the lives of poor people matter, and poor people fuel themselves with, um, coal, and biomass, and they (and we) die by the millions from air pollution while Princeton Professors mutter that "Nuclear Power is too dangerous." (Love you on talk Radio Michael Oppenheimer. You certainly don't remember me calling into a radio show on which you were a guest, where you talked about nuclear dangers. I'd guess it was about six or seven years ago, or about 40 or 50 million air pollution related deaths ago. I wonder how many people died from nuclear accidents in that time.)

Anyway...

Anyway...

To turn to the matter at hand: Even intellectual Lilliputians like the Orange Racist in the White House have climate solutions, and one of those he muttered, so I've heard, is the "Trillion Tree Initiative."

The minute I heard it, I muttered to myself, "Whence is the land and the water for this enterprise to come?"

Is it true that "trees are the answer?"

This review paper takes a look at the issue of how much forests can matter in addressing climate. (For perspective, the unit Pg (Petagram) is equal to 1 billion metric tons of carbon dioxide. Humanity adds, through combustion, about 35 to 36 billion metric tons of carbon dioxide to the atmosphere each year, and another 8 to 10 billion tons each year from land use changes.)

From the introduction:

Terrestrial ecosystems currently absorb ~30% of human carbon emissions each year (1), and forests account for the vast majority of this uptake [an estimated 8.8 Pg CO2e year−1 of a total land carbon uptake of 9.5 Pg CO2e year−1 over 2000–2007, where CO2e denotes CO2 equivalents (2, 3)]. A broad body of literature has focused for decades on the role of forests in the climate system (4–6), and forest-based natural climate solutions (F-NCSs) have experienced growing interest in recent years as a potentially major contributor to meeting Paris Agreement carbon targets (7–10). Forest-based strategies might provide up to 7 Pg CO2e of climate mitigation per year by 2030 at a carbon price of $100 per Mg CO2e, which is by far the largest potential category of natural climate solutions (NCSs) (7). Furthermore, many of these forest-based strategies are likely to have substantial cobenefits for biodiversity, ecosystem services, and conservation (9, 11).

Carbon policy that includes F-NCSs is building around the world (Fig. 1). For example, California has recognized 133 Tg CO2e in benefits from forest carbon offset projects in the United States between 2013 and 2019, with these credits making up a meaningful share of the compliance with the state’s cap-and-trade program (12). National and subnational government policies to reduce emissions have included forest projects, with policies in Japan, Australia, New Zealand, and British Columbia, Canada (Fig. 1). Additionally, many F-NCS projects have occurred under the framework of the United Nations’ Reducing Emissions from Deforestation and Degradation (REDD+) (13, 14) and under local and national emissions reduction goals...


I'm sorry, excuse me if I don't agree that California's 133 Tg (1 Teragram = 1 million tons) is meaningful. It's like announcing that spitting a lot will solve a drought.

The authors rapidly note that climatic changes might compromise this climate wedgie, in fact by doing something completely unusual in discussions of climate mitigation, looking at what is actually happening rather than what we predicted would happen. To wit:

Fundamental questions remain, however, about the fate of carbon stored in forests in a rapidly changing climate, particularly the extent to which climate change and climate-driven changes in disturbance regimes might compromise forest permanence (17–19). Climate-induced tree mortality events have been widely observed across the globe over the past few decades (20, 21). In addition to direct climate impacts on trees like drought events, additional disturbance agents including wildfire and insect outbreaks are sensitive to climate and have major carbon cycle consequences for forests (22–25). The biomass dynamics of an estimated 44% of forests globally are strongly sensitive to stand-replacing disturbance (including harvest) (Fig. 2) (26). Further, climate-driven tree mortality and disturbances are nonstationary (they change with time) and are projected to increase with climate change (25). Finally, due in part to the large uncertainties about climate impacts, CO2 fertilization, and disturbances in forests (27), Earth system model projections over the 21st century indicate that terrestrial ecosystems could sequester as much as 36.7 Pg CO2e year^(−1) or release as much as 22 Pg CO2e year^(−1) by 2100 for a high-emissions scenario (28).


Well, they do lapse into that famous word could at the end. That word has been thrown around my whole adult life about the environment. For example, I don't know how many times I've read about "studies" that "show" that "wind power could power the world by" (fill in a year that the current membership of Greenpeace will all be dead here).

If I heard one, I've heard many thousands, and I pretty much hear one at least once a week.

What could prevent forests from the terrestrial ecosystems that "could sequester as much as 36.7 Pg CO2e year^(−1)" from doing so?

The authors list possible threats to climate mitigation owing to, um, climate changes. Some Examples:


Fire

Fires in forests are perhaps the most well-quantified global disturbance and permanence risk. Between 1997 and 2016, an average of ~500 million ha of land burned each year, most of which is outside of forest ecosystems (36). Although burned area is declining in grasslands and savannas, burned area is increasing in many tropical, temperate, and boreal forest ecosystems (36). Fire in forests emits ~1.8 Pg CO2e year−1 (37, 38). Fire accounts for ~12% of stand-replacing disturbances in forest ecosystems annually (26) and is particularly important in key forest regions like the western United States, Australia, Mediterranean-type climates, and boreal forests in North America and Asia (39, 40). Climate-driven changes in fire regimes can affect permanence both through changes in burned area and through changes in fire behavior (i.e., fire temperature or scorch height) that influence tree mortality...


...and...

...Drought

Globally, droughts represent a major and widespread permanence risk, underscored by the explosion of research relating to drought-induced tree mortality that has been done in the past decade (21, 52). Drought events have major impacts on forest carbon cycling through declines in productivity and carbon losses through mortality (20, 27). Major climate extremes explain up to 78% of the variation in global gross primary productivity in the past 30 years, and severe droughts made up ~60 to 90% of the largest extremes (53). As an example, the severe 2011–2015 drought in California killed more than an estimated 140 million trees and drove the full carbon balance of the state’s ecosystems to be a net source of −600 Tg CO2e from 2001 to 2015, which is equivalent to ~10% of the state’s greenhouse gas emissions over that period (54). A 2011 drought in Texas killed 9.5% of tree cover across the state...


...and...

...Biotic agents

Biotic disturbance agents, including insects and pathogens, cause substantial tree mortality globally. For example, bark beetles, which feed on tree phloem and introduce fungi that interrupt tree water transport, have killed billions of trees across millions of hectares of land in temperate and boreal coniferous forests in the past two decades (68–70) and have converted large regions of the Canadian boreal forest from a sink to a source over the course of a decade (34). Defoliators feed on leaves and can kill trees after multiple years of severe damage. Widespread tree mortality has occurred from defoliators in both coniferous and broad-leaved forests in temperate and boreal regions (24, 71). In addition to these native biotic agents, non-native invasive biotic disturbance agents are responsible for killing many trees globally. Prominent examples include Phytophthora-induced sudden oak death and the emerald ash borer in the United States and the red turpentine beetle in China (72)...


...and...

...Other disturbances

Other disturbances—particularly storms and wind-driven events, snow and ice events, and lightning—can also influence forest ecosystem carbon cycling (25, 83). These disturbance events can matter for local- to regional-scale carbon cycling in some areas but are thought to have relatively minor-to-modest global effects (25, 53). Hurricanes damage coastal forests and can have pronounced impacts on carbon budgets. For example, Hurricane Katrina damaged 320 million large trees that contained 385 Tg CO2e (83), and tropical cyclones had a net effect of a modest carbon source in the 20th century across U.S. forests (33)...


...and so on...

A few pictures from the text:



The caption:

Fig. 2 Sensitivity of global forest biomass dynamics to stand-replacing disturbance (excluding human land use changes) captured by disturbance return interval (years).

Warm colors indicate areas where biomass dynamics are highly sensitive to the frequency of stand-replacing disturbance and cool colors indicate areas that are relatively less sensitive. Redrawn from (26).


From the provinces, the only country that matters.



The caption:

Fig. 4 Climate change has already increased fire risk in ecosystems.

(A and B) Integrated 100-year fire risk of moderate- or high-severity fire from the Monitoring Trends in Burn Severity (MTBS) dataset based on fire occurrences in years 1984–2000 aggregated to ecoregions (A) and for fire occurrences in years 2001–2017 aggregated to ecoregions (B). Fire risk was computed as follows. First, within each ecoregion and year, a pixel-wise burn probability was computed as the fraction of pixels in that ecoregion labeled as moderate or severe fire, and these probabilities were then averaged in each time period. To project an integrated 100-year risk, we computed the probability of any pixel experiencing at least one fire under a binomial distribution with 100 trials and success probability given by the pixel-wise annual risk described above. This is a simple analysis that does not account for spatial or temporal autocorrelation or attempt to model any drivers of fire risk. Raw data obtained from www.mtbs.gov/direct-download, and Python code to create figures is available at https://github.com/carbonplan/forest-climate-risks.


Don't worry, be happy.

They'll be destroying our coastal shelf here in New Jersey with a big brand new array of steel towers - with steel being made from burning coal to heat coal to make coke - for wind turbines that in 20 years the people who are children and babies now will have to take down and dump at their expense, in a world with far fewer resources.

...that could be a generational justice issue...could it not?

There are people who call themselves "environmentalists" cheering loudly for this. I miss the days of John Muir, when "environmentalists" tried to prevent wilderness from becoming industrial parks.

That's what we think will save the world.

We couldn't be more clueless.

I wish all involved a happy fathers day tomorrow. I'm personally looking forward to it, even though deep down, I know I have no right to look young people in the eye.

'I can't even enjoy this.' #BlackBirdersWeek organizer shares her struggles as a black scientist.

A news item from the careers section of Science:

‘I can't even enjoy this.’ #BlackBirdersWeek organizer shares her struggles as a black scientist.



This week, black scientists and recreational birders flocked to Twitter for #BlackBirdersWeek. “Nature is my favorite place to be, & I’ve been fortunate enough [to] use my PhD to travel & be #BlackInNature across the world,” tweeted a graduate student.

The first-of-its-kind event was organized in response to an incident that transpired in New York’s Central Park last week. Christian Cooper—a black man who works as a writer and editor and is an avid birdwatcher—encountered a white woman who was walking her dog while he was birding. When he asked her to leash her dog, she called the police, telling them that an African American man was threatening her. A video of the encounter went viral—unleashing a torrent of discussion about racism and the dangers black people face when they are simply enjoying, or working in, outdoor spaces.

For black scientists in field disciplines such as ecology and geology, Cooper’s experience was a familiar one. Many are sent to remote places to conduct fieldwork—and that can land them in uncomfortable, and potentially dangerous, situations, says Corina Newsome, a master’s student at Georgia Southern University who studies seaside sparrows in coastal marshes. “I’m in these remote, expansive natural areas, and in the South no less, and so my family is … always scared for my safety.”

She and others organized #BlackBirdersWeek to highlight the stories of black people in the outdoors...

...Q: How did you all come up with the idea for #BlackBirdersWeek?

A: The idea came from a group that I’m a part of, which includes probably 100 black people who enjoy the outdoors—either as scientists or outdoor enthusiasts. When the incident happened with Christian in Central Park, one of the members who's actually an economist—she's in mathematics—messaged to say that we need to do something to celebrate black birding. It took off from there; it came together in literally 48 hours. We designed events to highlight the experience of black people, the existence of black people, the work of black people, and to open dialogue.

We were motivated to do that because the incident in Central Park was something that all of us, at some point and in some shape or form, have experienced. But it's never been recognized on such a level...


There are more "Karens" - far more - than those of whom we've heard.

Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period

The paper to which I'll refer is this one: Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period. (Stephen M. Kissler1*, Christine Tedijanto2*, Edward Goldstein2, Yonatan H. Grad1†‡, Marc Lipsitch, Science Vol. 368, Issue 6493, pp. 860-868 May 22, 2020)

The paper is about a month old. I didn't get around to checking it out until this morning. I'm logged in, but it should be open sourced as all Covid papers are. It's an interesting study of the possible long term behavior of the virus should vaccination efforts fail.

Since it's probably open sourced, there's no need for me to discuss much of it, so I'll just offer some excerpts and post a few pictures at which interested persons can look.

From the introductory text:

The ongoing severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) pandemic has caused nearly 500,000 detected cases of coronavirus disease 2019 (COVID-19) illness and claimed >20,000 lives worldwide as of 26 March 2020 (1). Experience from China, Italy, and the United States demonstrates that COVID-19 can overwhelm even the healthcare capacities of well-resourced nations (2–4). With no pharmaceutical treatments available, interventions have focused on contact tracing, quarantine, and social distancing. The required intensity, duration, and urgency of these responses will depend both on how the initial pandemic wave unfolds and on the subsequent transmission dynamics of SARS-CoV-2. During this initial pandemic wave, many countries have adopted social distancing measures and some, like China, are gradually lifting them after achieving adequate control of transmission. However, to mitigate the possibility of resurgences of infection, prolonged or intermittent periods of social distancing may be required. After the initial pandemic wave, SARS-CoV-2 might follow its closest genetic relative, SARS-CoV-1, and be eradicated by intensive public health measures after causing a brief but intense pandemic (5). Increasingly, public health authorities consider this scenario unlikely (6). Alternatively, the transmission of SARS-CoV-2 could resemble that of pandemic influenza by circulating seasonally after causing an initial global wave of infection (7)...

...The pandemic and postpandemic transmission dynamics of SARS-CoV-2 will depend on factors including the degree of seasonal variation in transmission, the duration of immunity, and the degree of cross-immunity between SARS-CoV-2 and other coronaviruses, as well as the intensity and timing of control measures. SARS-CoV-2 belongs to the Betacoronavirus genus, which includes the SARS-CoV-1 coronavirus, the Middle East respiratory syndrome (MERS) coronavirus, and two other HCoVs, HCoV-OC43 and HCoV-HKU1. The SARS-CoV-1 and MERS coronaviruses cause severe illness with approximate case fatality rates of 9 and 36%, respectively, but the transmission of both has remained limited (9). HCoV-OC43 and HCoV-HKU1 infections may be asymptomatic or associated with mild to moderate upper respiratory tract illness; these HCoVs are considered the second most common cause of the common cold (9)...


The authors model SARS-COV-2 by studying closely related viruses with which there is long experience.



The caption:

Fig. 1 Effects of depletion of susceptibles and seasonality on Re by strain and season.
Shown are the estimated multiplicative effects of HCoV-HKU1 incidence (red), HCoV-OC43 incidence (blue), and seasonal forcing (gold) on weekly Res of HCoV-HKU1 (top) and HCoV-OC43 (bottom), with 95% confidence intervals. The black dot (with 95% confidence interval) plotted at the start of each season is the estimated coefficient for that strain and season compared with the 2014–2015 HCoV-HKU1 season. The seasonal forcing spline is set to 1 at the first week of the season (no intercept). On the x-axis, the first “week in season” corresponds to epidemiological week 40.




The caption:

Fig. 2 Transmission model fits for HCoV-OC43 and HCoV-HKU1.
(A) Weekly percent positive laboratory tests multiplied by percent ILI for HCoV-OC43 (blue) and HCoV-HKU1 (red) in the United States between 5 July 2014 and 29 June 2019 (solid lines) with simulated output from the best-fit SEIRS transmission model (dashed lines). (B and C) Weekly Re values estimated using the Wallinga–Teunis method (points) and simulated Re from the best-fit SEIRS transmission model (line) for HCoV-OC43 and HCoV-HKU1. The opacity of each point is determined by the relative percent ILI multiplied by percent positive laboratory tests in that week relative to the maximum percent ILI multiplied by percent positive laboratory tests for that strain across the study period, which reflects uncertainty in the Re estimate; estimates are more certain (darker points) in weeks with higher incidence.


The authors consider several possible scenarios based on the (still unknown) long term dynamics of infection:

We summarized the postpandemic SARS-CoV-2 dynamics into the categories of annual outbreaks, biennial outbreaks, sporadic outbreaks, or virtual elimination (tables S2 to S7). Overall, shorter durations of immunity and smaller degrees of cross-immunity from the other betacoronaviruses were associated with greater total incidence of infection by SARS-CoV-2, and autumn establishments and smaller seasonal fluctuations in transmissibility were associated with larger pandemic peak sizes. Model simulations demonstrated the following key points...

...SARS-CoV-2 can proliferate at any time of year...

...If immunity to SARS-CoV-2 is not permanent, it will likely enter into regular circulation...

...High seasonal variation in transmission leads to smaller peak incidence during the initial pandemic wave but larger recurrent wintertime outbreaks...

...If immunity to SARS-CoV-2 is permanent, the virus could disappear for 5 or more years after causing a major outbreak...

...Low levels of cross-immunity from the other betacoronaviruses against SARS-CoV-2 could make SARS-CoV-2 appear to die out, only to resurge after a few years...


Here's a graphic from one scenario:



The caption:

Fig. 6 Intermittent social distancing scenarios with current and expanded critical care capacity.
SARS-Cov-2 prevalence (black curves) and critical cases (red curves) under intermittent social distancing (shaded blue regions) without seasonal forcing (A and C) and with seasonal forcing (B and D). Distancing yields a 60% reduction in R0. Critical care capacity is depicted by the solid horizontal black bars, and the on/off thresholds for social distancing are depicted by the dashed horizontal lines. (A) and (B) are the scenarios with current critical care capacity in the United States and (C) and (D) are the scenarios with double the current critical care capacity. The maximal wintertime R0 is 2.2 and for the seasonal scenarios the summertime R0 is 1.3 (40% decline). Prevalence is in black and critical care cases are in red. To the right of each main plot (E to H), the proportion immune over time is depicted in green with the herd immunity threshold (horizontal black bar).


There is also scenarios involving herd immunity, etc... For more graphics and information, one should check out the full paper.

Our Republican fellow citizens, those most invested in a cult of personality and hatred, will be working this weekend to advance herd immunity. It appears that some are from out of town in Tulsa, the city with the worst history of post slavery racist violence, for which it was clearly chosen by the racist Steven Miller, the racist "brain" of the brainless administration. Of course, it will kill a lot of innocent people, but that has not troubled Republicans ever going back to 1968 and the "Southern (Race Baiting) Strategy."

Happily however, the worst of them - and among the "worst" are anyone who sets foot in Tulsa to worship the Orange God of Hatred - will have a high probability of doing themselves in, and perhaps their equally stupid friends and family. I have no compassion whatsoever for anyone who includes such people among "friends" and "family."

We do not know, however, the real dynamics or the immunological effects of SARS-CoV-2, and thus, it is quite possible that the Tulsa transmission may further Putin's goal, so expertly realized, of destroying America over the long term.

For the remaining human beings in our country, who have fathers and/or are fathers, I wish you the happiest of Father's days.

It appears that I can't donate blood.

I'm a long time blood donor, going back more decades than I'd care to confess. The Red Cross hounds me all the time, and I don't even have a rare blood type.

But my life was saved when I was a kid by a blood donation, and I've always done by best to give in to the hounding and donate when there is time.

One of the recent emails said, "Free Covid antibody testing, with a blood donation." I said to myself, "I should do that one, what the heck," but I didn't get around to making my appointment. Today I needed a tee shirt and one that came out of the pile was one of those donor, "I saved a life today," tee shirts I use for yard work so reminded, I said to myself, "I'll go down to the computer and sign up."

Apparently the free antibody testing has led to a run appointments. Here in Central New Jersey, there seem to be no appointments available anywhere; they're full.

It's a good thing I guess. The testing and screening is a good thing too, since antibody positive blood has been considered as a possible treatment for severe Covid cases.

Eventually they'll be a shortage again, and I'll head on in when they really need me.

Incest uncovered at the elite prehistoric Newgrange monument in Ireland.

The paper I'll discuss in this post does not have the title of this post, but does have the title of the news item in the current issue of Nature referring to it. The paper is: A dynastic elite in monumental Neolithic society (Lara M. Cassidy, Ros Ó Maoldúin, Thomas Kador, Ann Lynch, Carleton Jones, Peter C. Woodman, Eileen Murphy, Greer Ramsey, Marion Dowd, Alice Noonan, Ciarán Campbell, Eppie R. Jones, Valeria Mattiangeli & Daniel G. Bradley Nature, Nature volume 582, pages 384–388 (2020))

Perhaps there would be less contempt for science such as we see rising in America if we could have more salacious titles like Trump's pal at the National Enquirer, the aptly named David Pecker, creates in his wide appeals to the preternaturally stupid.

Ignorance rules and ignorance kills.

Anyway.

Another news item, which is in Science , puts it this way:

wenty-five kilometers north of Dublin, a masterpiece of Stone Age engineering rises from the hills: a circular structure 12 meters high, almost the area of a U.S. football field, and made up of more than 200,000 tons of earth and stone. Some of the first farmers to arrive in Ireland erected this monument, called Newgrange, nearly 1000 years before Stonehenge or Egypt's first pyramids were built. Archaeologists have assumed it was a ceremonial site and communal tomb—an expression of an egalitarian society.

Now, DNA from a middle-aged man buried in 3200 B.C.E. at the center of this mighty mound suggests otherwise. His genes indicate he had parents so closely related they must have been brother and sister or parent and child.

Across cultures, incest is almost always taboo—except in inbred royal families. Its genetic traces at Newgrange suggest social hierarchy took hold in Ireland earlier than thought, according to a new study. “Maybe we've been arguing too far that [these people were] egalitarian,” says Jessica Smyth, an archaeologist at University College Dublin who was not part of the team.


Royal families...

It is notable that the First World War, which resumed after a brief interlude as the Second World War, arguably had some of its origins with inbreeding - Czarina Alexandra Feodorovna was both the second and third cousin of her husband, Nicolas II - with the result that their son, Alexis was born a hemophiliac, leading the Czarina to embrace the mystic Rasputin, who greatly influenced the Royal family, this at a time her husband was precipitating the World War. Who knows, a saner environment may have lead to a saner outcome; who knows.

Anyway, from the original paper's introduction:

Previous analyses of ancient genomes have demonstrated common ancestry between the societies of the Atlantic seaboard during the Neolithic7,8,9, while recent modelling of radiocarbon determinations has defined repeat expansions of megalithic architecture from northwest France at a pace that implies more advanced maritime technology than was previously assumed for these regions10. This includes the spread of passage tombs along the Atlantic façade during the fourth millennium BC—a period that also saw the arrival of agriculture in Ireland, alongside other distinct megalithic traditions. These structures reached some of the highest concentrations and diversities known for Europe on the island of Ireland. However, the political systems that underlay these societies remain obscure, as does the genetic input from indigenous Mesolithic hunter-gatherers.

To investigate these issues, we shotgun-sequenced individuals dating to the Irish Mesolithic (n = 2) and Neolithic (n = 42) periods to a median 1.14× coverage (Fig. 1a, Supplementary Tables 1, 2). We imputed 43 of these individuals alongside relevant ancient genomes (Supplementary Table 3), including an additional 20 British and Irish individuals7,9,11. We then merged these individuals with a published dataset of imputed ancient genotypes12 to allow for fine-scale haplotypic inference of population structure13 and estimations of inbreeding. Four key individuals were subsequently sequenced to higher (13–20×) coverage.

We sampled remains from all of the major Irish Neolithic funerary traditions: court tombs, portal tombs, passage tombs, Linkardstown-type burials and natural sites (Fig. 1a, c, Supplementary Information section 1). Within this dataset, the earliest Neolithic human remains from the island—interred at Poulnabrone portal tomb14—are of majority ‘Early_Farmer’ ancestry (as defined by ADMIXTURE modelling15), and show no evidence of inbreeding (Fig. 1a, Extended Data Fig. 1), which implies that, from the very onset, agriculture was accompanied by large-scale maritime colonization...

...Overall, no increase in inbreeding is seen through time in Neolithic Ireland, which indicates that communities maintained sufficient size and communication to avoid matings between relatives of the fifth degree or closer (Fig. 1a). However, we report a single extreme outlier interred within the Newgrange passage tomb—a focal point of the monumental landscape of Brú na Bóinne, a United Nations Educational, Scientific and Cultural Organization world heritage site (Fig. 2a). Incorporating over 200,000 tonnes of earth and stone, this megalithic mound is one of the most spectacular of its kind known from Europe16...

...The exceptional location of these remains is matched by a genomic heritage that—to our knowledge—is unprecedented in ancient genomics. He possessed multiple long runs of homozygosity, each comprising large fractions of individual chromosomes (Fig. 2e, Extended Data Fig. 3a), and totalling to a quarter of the genome (inbreeding coefficient = 0.25). This marks him as the offspring of a first-order incestuous union, which is a near-universal taboo for entwined biological and cultural reasons4. However, given the nature of the interment, his parentage was very likely to have been socially sanctioned...


Some pictures from the full text:



The caption:

a, Timeline of analysed Irish genomes with inbreeding coefficients are shown for those with sufficient coverage. All dates are direct and calibrated, excluding that for individual CAK534 (translucent). The key for the sample sites is given in c. The earliest widespread evidence of Neolithic activity (house horizon) is marked with a black line. The Irish Neolithic ends at about 2500 BC. NA, not applicable. b, Stable isotope values for samples from the Irish and British Neolithic (n = 292). The key for the Irish samples is given in c, and samples included in the ancient DNA analysis are outlined in black. British samples are shown as hollow shapes; black, Scotland; grey, England or Wales; circles, pre-3400 BC; squares, post-3400 BC. An infant with Down syndrome (PN07) is labelled; this individual showed isotope values consistent with a high trophic level. c, Site locations for Irish individuals sampled or included in this study coloured by burial type: yellow, court tomb; blue, portal tomb; green, Linkardstown-type; magenta, passage tomb and related; light pink, natural sites; and light blue, the unclassified Ballynahatty7 megalith. Sites outlined in black were included in ancient DNA analysis. d, ChromoPainter13 principal component (PC) analysis of individuals from the Atlantic seaboard of majority Early_Farmer ancestry (n = 57), generated using a matrix of haplotypic length-sharing. Passage tomb outliers in Fig. 2d are labelled. e, fineSTRUCTURE dendrogram derived from the same matrix as in d with five consistent clusters.




The caption:

a, Front elevation and interior of the Newgrange passage tomb. Photographs by Fáilte Ireland; Photographic Unit, National Monuments Service. b, Plan of chamber, redrawn after ref. 16. Scale bar, 6 m. c, The coefficient of relatedness (pi-HAT) between car004 (an interment from the central monument at Carrowmore)9, and 38 British and Irish Neolithic samples, with the top 5 hits labelled (CAK68 and CAK530 are equal in value). d, Average length of donated haplotypic chunks between all reciprocal pairs of the ‘passage tomb cluster’ (pink; n = 42) and ‘British–Irish cluster’ (grey; n = 1,190) as defined by fineSTRUCTURE in Fig. 1e. The highest values for passage-tomb-cluster pairs are marked along the x axis, with an excess of longer chunks shared between the inferred kin of car004 (CAK533, MB6 and NG10) in c. Darker lines link reciprocal donations. Combined symbols are used for inter-site pairs. e, A sliding window of heterozygosity is plotted for transversions along selected chromosomes of NG10, revealing extreme runs of homozygosity. Scale bar, 50 Mb.




a, Right, the maps show the estimates of shared drift between Irish and British or continental hunter-gatherers (HG) (jittered) from the Mesolithic and Upper Palaeolithic (triangles, Magdalenian culture). Left, the top ten hits with sufficient coverage are cross-compared with one another and with Irish hunter-gatherers in a heat map using the statistic f3(Mbuti; HG1, HG2), in which HG1 and HG2 represent all possible pairs. b, Short and long runs of homozygosity (ROH) spectra in modern and ancient genomes. Hollow shapes indicate direct (rather than imputed) diploid calls. For four Irish samples, both imputed and direct data are presented, showing close agreement. c, Normalized haplotypic length donations from hunter-gatherer populations to Neolithic individuals, arranged by their geographic region (labelled). The top three hunter-gatherer donors are outlined for each individual. Donor hunter-gatherer population colours are as in b; British and northwestern European hunter-gatherers are merged into one donor population (blue).


That the orange racist in the White House has expressed some grotesque - if, we assume, restrained, unnatural interest in his daughter of course doesn't make him royalty, no matter how much he channels Caligula and Nero. We'll have to look for some reason other than inbreeding to account for the intellectual disability of Eric and Don Jr., poor parental genes may be involved, given that their father is an idiot, coupled with poor upbringing in the complete absence of any trace of moral guidance.

Without placing too much emphasis on genetic reductionism, which I oppose, I am happy to think that my own father was quite a different species, at least where moral guidance was involved.

Be this all that it may, it is interesting that we can now sequence long dead individuals to understand something about their societies and social structure. With all due respect to Shakespeare, it does appear that while "The evil men do lives after them, the [evil] is also interred with their bones."

Pretty cool I think.

I wish all fathers out there, the happiest Father's Day. I hope to enjoy my two sons, one remotely, and reflect, with love and affection, on my own father, now long passed but very much alive in my heart.



I would just like to take a moment to applaud Senator Klobuchar.

in removing herself twice from consideration for higher office in response to events, she has demonstrated the kind of patriotism not seen on the right, valuing her country over herself.

I received a legal agreement from a foreign company to evaluate, with the words "repugnant to..."

Did you hear variants of that joke when you were a kid that went like, "I looked up ugly in the dictionary, and I saw your picture..."

Since the language "repugnant to," appeared several times in the agreement, I assumed it was a standard legal language in the country of origin.

To be sure, I googled the phrase "Repugnant to" including the quotation marks."

Guess whose picture showed up...

Quiz: Electrification of the Chemical Industry: What's wrong with this picture?

Here's a news item from the current issue of Science: Electrification of the chemical industry (Barton, Science 12 Jun 2020 Vol. 368, Issue 6496, pp. 1181-1182)

Curbing carbon emissions while maintaining quality of life is a global challenge for manufacturing processes that will require process innovation. One approach is replacing energy from the burning of carbon-based fuels with energy supplied by “green” electrons. This goal can be achieved in some cases by simply replacing heat supplied by combustion with electrical heating (1). In chemical synthesis, it can also more elegantly supply reaction energy through electrochemistry. On page 1228 of this issue, Leow et al. (2) propose an electrochemical route to ethylene oxide (EO) and propylene oxide (PO) that promises cleaner, more efficient, and more selective processing. Ethylene and propylene were epoxidized electrochemically to EO and PO, respectively, at industrially relevant current densities with Faradaic (electron-specific) selectivities ∼70% to the target epoxide (2).

Leow et al. coupled an electrochemical flow cell to homogeneous reactions for an overall reaction, C2H2 + H2O → C2H2O + H2, for EO synthesis (see the figure). Two electrochemical reactions drive this reaction. Chlorine evolution occurs at the anode, 2Cl− → 2e− + Cl2, and hydrogen evolution occurs at the cathode, 2H2O + 2e− → H2 + 2OH−, where e is the charge on the electron. These reactions are not particularly interesting; what is innovative is coupling these two simple reactions with three subsequent, homogeneous chemical reactions. Dissolved chlorine in the anodic solution dissociates into hydrochloric and hypochlorous acid (HCl and HOCl, respectively)...

...Technoeconomic analysis by Leow et al. suggests that this process could scale to produce EO at a cost comparable with current industrial practices with a lower carbon footprint when supplied with renewable energy (2). Such a process would be a carbon-negative path to an important, large-scale commodity chemical. Improvements are still possible, particularly in product selectivity and catalyst selection. Nonetheless, the electrochemical productivity of EO reported in this study is a factor of 10 higher than that of the electrochemical process of Simmrock and Hellemanns (3).


As usual, it sounds wonderful, does it? (By the way there is nothing particularly surprising or innovative in the chemistry here; it should be obvious to a strong undergraduate in a decent chemistry program.)

The full paper, open sourced, is here: Chloride-mediated selective electrosynthesis of ethylene and propylene oxides at high current density (Leow, et al., Science Vol. 368, Issue 6496, pp. 1228-1233)

In the United States, chemical manufacture accounts for 28% of total industrial energy demand (1). At present, this demand is largely met by the consumption of fossil fuels, resulting in substantial carbon dioxide (CO2) emissions (2, 3); a recent report showed that the plastics industry alone releases 1.8 billion metric tons of CO2 per year and that replacing fossil fuels–based production methods with ones powered with renewable energy offers a route to reduce net greenhouse gas emissions associated with plastics manufacture (4).

One attractive strategy involves the development of electrochemical systems that produce the necessary raw materials by using renewable electricity (5–8).


I have added the bold and italics.

I am of course, a critic of so called "renewable energy," but I hold the possibly naive notion that some things are so absurd that they should be obvious. To me, this one has a hole so large that one can drive a zepplin sufficient to hold the carbon dioxide that drove that atmospheric concentration of CO2 up by 45.34 ppm since May 28, 2000 and now right through it. (I note, with bitter and tragic schadenfreude, that since May, 28, 2000, almost exactly 20 years ago, we've all been cheering wildly for so called "renewable energy," for the whole period, claiming that so called "renewable energy" is a positive good that cannot be questioned.)

I'm curious whether there is anyone with enough of a knowledge of Chemical Engineering to see what that hole is.

I'd guess there isn't any such person who will read this, but if someone wants to surprise me, I'm open to hearing it. (Hint: Consider what types of processes are the most economic for producing high volume chemical commodities.)

Have a pleasant evening.

Root of the Tree: The Significance, Evolution, and Origins of the Ribosome.

The paper having the title of this post is here: Root of the Tree: The Significance, Evolution, and Origins of the Ribosome (Jessica C. Bowman, Anton S. Petrov, Moran Frenkel-Pinter, Petar I. Penev, and Loren Dean Williams, Chem. Rev. 2020, 120, 11, 4848–4878)

I go through a number of scientific papers in the course of a day, but seldom am I inspired to read any in their entirety. I just go to the "good parts" and most often leave unimportant details out. (I'm the same with books; but recently, in the age of Covid and the cloture of libraries, I find myself reading some books cover to cover.) I almost never read a journal issue cover to cover, but I may find myself inspired to read one now. The current issue of Chemical Reviews is devoted largely to Scientific Reviews of the origin of life, a subject that has fascinated me ever since my high school biology teacher described the Miller Urey experiment. I didn't know doodley squat about chirality then, but nevertheless, the interest in the prebiotic origins - and for that matter the abiotic origin of chirality - have fascinated me during my long life. What better time is there to muse on the origins of life as one's own life winds down. I hope I find and have the time to read this issue in its entirety.

This particular paper is really striking, inasmuch as it touches on the key structure at the interface of the two main classes of molecules that have been the subject of speculation as the originating molecules, peptides/proteins/amino acids and nucleic acids: The ribosome.

This is a very long paper, and I can only excerpt a tiny portion, but if one finds a way to these papers, and one is interested in this mysterious topic, "why and how life?," one may find some fascinating discussion.

All cells contain ribosomes, the cellular structures that translate DNA/RNA into the proteins that basically run life's machinery. (Thomas Cech and others found that RNA can also catalyze molecular transitions.)

The partnership between RNA and protein dominates biology. The durability of this ancient partnership is documented in the universal tree of life (TOL), which is the lineage of the translation system. Woese and Fo1,2) sketched out a universal TOL revealing the blueprint of the common origins and biochemical interrelatedness of all living systems. This TOL contains three primary branches, which are the bacterial, archaeal, and eukaryotic superkingdoms of life. More recent determinations of the TOL, using concatenated sequences of ribosomal proteins (rProteins), increased the resolution and accuracy of the tree.(3,4) TOLs now incorporate reconstructed genomes of unculturable organisms from a variety of environments.(5,6) In the most recent TOLs, eukarya branches from within archaea.(6,7) The last universal common ancestor of life (LUCA) lies at the first branch point of the TOL. Extant biology is the crown. The origin of life occurred within the root of the TOL. As a system to organize and frame vast amounts of information, the TOL is on par with the Periodic Table.

The ribosome, made from RNA and protein, is responsible for synthesizing all protein in living systems. The ribosome is composed of a small ribosomal subunit (SSU) that decodes mRNA and a large ribosomal subunit (LSU) that catalyzes peptidyl transfer. To make a protein, the ribosome initiates, interprets an mRNA codon (decodes), transfers an amino acid from a tRNA to a nascent peptide, translocates, repeats the last three of these steps over and over again, and ultimately terminates synthesis at an mRNA stop codon.(8−12) In Bacteria, new peptide bonds are formed at a rate of ∼20 amino acid additions per second. The functional core of the SSU is the decoding center (DCC) and the functional core of the LSU is the peptidyl transferase center (PTC). The distribution of ribosomal functions within rRNA secondary structures is shown in Figure 1. Aminoacyl-tRNA synthetases (aaRSs) enforce the genetic code by joining amino acids to their cognate tRNAs...

...2.1. Universality of the Ribosome

Genes encoding the translation machinery dominate the universal gene set of life (UGSL),(13−15) which is the set of protein-encoding genes that are shared as orthologues throughout the TOL and are found in essentially every living system. Koonin’s version of the UGSL contains around 65 genes.(14) Fifty-three of these are directly involved in translation, including 34 genes for rProteins (Figure 2) and genes for aaRSs and translation factors. The Pace(13) and Doolittle(15) versions of the UGSL are very similar to that of Koonin. The USGL is larger and even more translation-centric if it is expanded to include nontranslated genes such as those encoding rRNAs and tRNAs. A few constituents of the USGL are involved in transcription and even fewer in replication. There are no genes for metabolism, membrane biosynthesis or proton pumps in the UGSL.

The universality of translation across living systems extends beyond sequence homology to three-dimensional structures. Ribosomal and other translational components are universal in three-dimensions for all living systems (Figures 3, 4, and 5).(17−20) The extreme structural conservation of the DCC and the PTC(21−23) is illustrated in Figure 3. All ribosomes, from large bacterial to even larger archaeal ribosomes to gigantic mammalian ribosomes, are built upon the same basal structure, which we call the universal common core. The universal common core has a mass of nearly 2 million Daltons.(18,19)...


The point of the review is the understanding that this structure, the ribosome, is rather universal and is thus an essential point to consider in the origins of life.

Now I'll share some "science porn" with the captions...



The caption:
Figure 1. Functional regions of rRNA. (a) Information mapped onto the E. coli SSU rRNA secondary structure. CPK indicates the central pseudoknot; FPK is the functional pseudoknot. (b) Information mapped onto the E. coli LSU rRNA secondary structure. A plurality of LSU rRNA is assigned to the exit tunnel (cyan), indicating that it performs a principal function of the LSU. The second shell of the exit tunnel provides buttressing for the first shell of the exit tunnel. Regions of multiple function, for example, rRNA that contributes to both the A-site and the PTC, are striped with two colors. Strand termini and select helices are indicated. Domains are indicated on the SSU rRNA. Domains are not indicated on the LSU rRNA where they have no physical significance. Interactions with ribosomal proteins are not included.




The caption:
Figure 2. The Tree of Life mapped with universal and superkingdom-specific ribosomal proteins. The line width of the TOL is weighted by the total number of rProteins in a given superkingdom. Universal rProteins are listed in white text in the black region at the bottom. Bacteria-specific rProteins are in the blue region on the right, and Archaea-specific rProteins are in the lime-green region in the center. Eukarya-specific rProteins are in the red region on the left. All Archaea-specific rProteins are found in Eukarya, and thus, no rProteins are unique to Archaea. This rProtein nomenclature is consistent with the TOL; rProteins in Eukarya that are of archaeal ancestry are labeled as archaeal. This rProtein naming scheme, by incorporating evolutionary relationships into rProtein names, is intended to facilitate understanding of the evolution of the translation system. Adapted with permission from ref (16), where a dictionary of various rProtein naming schemes can be found.




The caption:
Figure 4. The universal common core of rRNA mapped onto the secondary and three-dimensional structures of rRNAs of a bacterium and an archaeon. The SSU (left) contains the 16S rRNA and the LSU (right) contains the 23S and 5S rRNAs. Red (SSU) and blue (LSU) indicate common core rRNA. Black or gray indicate rRNA that is not part of the common core and is variable in structure or absent from some species. (a) The rRNA of the bacterium E. coli. (b) The rRNA of the archaeon P. furiosus. Some sites of insertion of microexpansion segments are indicated by dashed lines in the archaeon secondary structure. Each three-dimensional structure is viewed from the solvent exposed surface of the assembled ribosome, with the subunit interface directed into the page. E. coli, PDB 4V9D, and P. furiosus, PDB 4V6U. Adapted with permission from ref (19).




The caption:
Figure 5. The universal common core mapped onto the secondary and three-dimensional structures of rRNAs of the eukaryote S. cerevisiae. The SSU (left) contains the 18S rRNA, and the LSU (right) contains the 26S, 5.8S, and 5S rRNAs. Red (SSU) and blue (LSU) indicate common core rRNA, as in the previous figure. Some sites of insertion of expansion segments are indicated by dashed lines. S. cerevisiae: PDB 4V88. Adapted with permission from ref (19).


And where bugs like us fit in to this key:




The caption:
Figure 11. Secondary structures of ES7 mapped onto the canonical eukaryotic TOL. Colors indicate the extent of conservation of ES7 rRNA. Blue is Helix 25, part of the universal common core. Green rRNA is universal to all eukaryotes except those with reduced genomes. Yellow is universal to metazoans. Red is tentacle rRNA. Tentacles reach extreme lengths in birds and mammals.


And how all this life might have arisen from simplicity:



The caption:
Figure 17. The coevolution of LSU rRNA, SSU rRNA, tRNA, and proteins. Six phases of the accretion model lead to the LUCA ribosome. In phase 1, RNAs form stem-loops and minihelices that begin to accrete. In phase 2, the PTC is formed and catalyzes condensation in the absence of coding. The SSU may have a single-stranded RNA binding function. In phase 3, the subunits gain mass. At the end of phase 3, the interface is acquired and the subunits associate, mediated by the expansion of tRNA from a minihelix to the modern L-shape. LSU and SSU evolution is independent and uncorrelated during phases 1–3. In phase 4, evolution of the subunits is correlated. The ribosome is a noncoding diffusive ribozyme in which proto-mRNA and the SSU act as positioning cofactors. In phase 5, the ribosome expands to an energy-driven, translocating, decoding machine. In phase 6, the ribosome matures, marking completion of the common core with a proteinized surface (the proteins are omitted for clarity). The colors of the rRNA and rProtein phases are the same as in Figures 13c,d, and 15. mRNA is shown in light green. The A-site tRNA is magenta, the P-site tRNA is cyan, and the E-site tRNA is dark green. Adapted with permission from ref (114).


A little beauty on a beautiful day.

I wish you a pleasant, safe, and healthy afternoon.


Vaccines that use human fetal cells draw fire

In case, at this late date, you had any doubt that the right wing is far more interested in fertilized eggs than it is in living breathing humans, adults and children, there's this news item from this week's issue of Science: Vaccines that use human fetal cells draw fire. (Meredith Wadman, Science, June 12, 2020, Vol. 368, Issue 6496, pp. 1170-1171) It appears to be open sourced.

Some excerpts:

Senior Catholic leaders in the United States and Canada, along with other antiabortion groups, are raising ethical objections to promising COVID-19 vaccine candidates that are manufactured using cells derived from human fetuses electively aborted decades ago. They have not sought to block government funding for the vaccines, which include two candidate vaccines that the Trump administration plans to support with an investment of up to $1.7 billion, as well as a third candidate made by a Chinese company in collaboration with Canada's National Research Council (NRC). But they are urging funders and policymakers to ensure that companies develop other vaccines that do not rely on human fetal cell lines and, in the United States, asking the government to “incentivize” firms to make only vaccines that don't rely on fetal cells...

...Now, research groups around the world are working to develop more than 130 candidate vaccines against COVID-19, according to the World Health Organization. At least six of those candidates use one of two human fetal cell lines: HEK-293, a kidney cell line widely used in research and industry that comes from a fetus aborted in about 1972; and PER. C6, a proprietary cell line owned by Janssen, a subsidiary of Johnson & Johnson, developed from retinal cells from an 18-week-old fetus aborted in 1985. Both cell lines were developed in the lab of molecular biologist Alex van der Eb at Leiden University.

Two of the six vaccines have entered human trials (see table, below). Five are made by using human fetal cells as “factories” to make adenoviruses that carry genes from SARS-CoV-2, the virus that causes COVID-19...


It's OK, though, to put babies in cages after they're born. There has been no announcement as to whether it will prove "ethical" to use cell lines from babies in cages after they die. Probably, the same people carrying on about the fetal cells from 1972 couldn't care less about those babies, because they were already born, and lost protection from the self declared "ethics" mavens, the minute they took air into their lungs.

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