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 Post subject: from current journals as of 2017 07 02
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Archaeology July-August 2017
Looking beyond the hillforts
We had thread mentioning Iron Age Hill Forts before. Up until recently, these were interpreted as centers of tribal resistance to the Roman invasion, and burials found in them were assumed to be the remains of Britons slain by legionnaires, presumably after fierce resistance. More recent studies suggest that the hillforts were abandoned over 100 years before the Roman conquest, and that the inhabitants moved to villages on lower ground. The particular pair of sites studied here are Maiden Castle and nearby Duropolis (the original name is unknown but the tribal group in the part of Britain was the Durotriges). Duropolis was discovered in 2015, and preserves the outlines of 200-300 “round houses” and numerous “storage pits”. (it’s not clear that the pits were actually used for storage; some of them seem unnecessarily deep – but that’s the best guess). There are also 27 human burials, plus numerous animal burials, interpreted as sacrifices. Some of the animal burials are bizarre; the Durotriges seemed to assemble hybrid animal corpses from parts – half a cow and half a horse, for example.
Set in stone
“Bannerstones” are one of those things originally interpreted as “ritual objects”, since nobody could figure out what they were. They’re Native American artifacts made from ground and polished stone and vaguely resembling a double-bitted axe. They were clearly not used for chopping, though; the best early archaeologists could come up with was that they were mounted on poles as “banners” – perhaps to indicate the position of a commander, or maybe just “ritual”. In the 1930s, a University of Kentucky archaeologist found some bannerstones between an antler hook and an antler handle, deduced that there had been a wooden shaft between the antler objects and through the hole in the bannerstone, and concluded that the whole thing was the remains of an atlatl. That solved part of the problem; since it didn’t explain why the bannerstone was part of the atlatl. One theory was the stone acted as a weight to give more power to the throw, but modern atlatl users found the opposite was the case; they could throw a spear significantly further without a bannerstone on their atlatl. The theory expressed in this article is the bannerstones allowed an atlatl user to hold a atlatl “cocked” – i.e., in the throwing position – longer, and experiments seem to confirm that. I’ve read another theory that isn’t mentioned here – the bannerstones were sound suppressors. That seems to be confirmed experimentally too; atlatls with bannerstones attached make less noise than ones without, possibly allowing the user to reload and try again if the game wasn’t spooked by the first shot.

Science 16 June 2017
News in depth
In a major shift, cancer drugs go “tissue-agnostic”
Previously, the FDA had only approved cancer drugs for tumors in specific tissue – lung, breast, colon, etc. However, this year it approved a drug that instead targets tumors with a specific mutation, regardless of the tissue the tumors appear in. The first trial, with 55 patients with 17 different kinds of advanced cancer bearing the mutation, saw 43 have their tumors shrink by 30% or more and 7 have their tumors disappear completely. An oncologist commented “I’ve done a lot of studies but I’ve never seen a drug this active with as little side effects”. It’s noted that the specific mutation targeted only appears in about 1% of solid tumors, but there are others that could be targeted and drugs for them are under development.
Features
Chimps in waiting
Since chimps were declared an endangered species, all chimps used for research in the US are supposed to be retired to sanctuaries. The process is going much slower than expected; the article notes lots of blame; research labs have “dragged their feet” on releasing animals, sanctuaries aren’t expanding fast enough to take them, and the government, despite forcing the issue, had no plan to make it work. There are five major labs holding 577 chimps, of which two are federally owned; there are eight chimp sanctuaries holding 470 chimps; one is federally owned (the bulk of the sanctuary chimps are in two facilities; the federally owned Chimp Haven, with 202, and the privately owned Save the Chimps, with 220. It’s estimated it costs $16K to $20K per year per chimp to house them.
Policy forum
Linking job loss, inequality, mental health, and education
The article claims that economic theory predicts job loss to globalization and technology will increase upward mobility; supposedly working-class youth will be unable to follow in their parent’s footsteps to jobs at now-closed factories and instead pursue education and join the knowledge economy. That doesn’t sound right but I can’t claim much knowledge on that aspect of economics. At any rate, the authors find that instead of this prediction, job loss worsens adolescent mental health, decreases their college performance, and increases income inequality in poor youth. Sound like a straw man but I don’t know.
Reports
Satellites reveal contrasting responses of regional climate to the widespread greening of Earth
The rule of thumb for climate change is nothing good can happen from it. The authors note that the Earth is experiencing “greening”, which they measure using Leaf Area Index – the ration of leaf area to ground area. Satellite measures show (1) LAI is increasing (2) that this contributes to warming in boreal zones, due to decreased albedo (3) and that it contributes to cooling in equatorial zones, due to increased evapotranspiration. The authors note the effect is underestimated in climate models, since these focus on forest cover rather than LAI; the authors don’t state it outright but the implication is shrubs work just as well as trees. Maps show a decadal increase in LAI, very pronounced in Europe, the eastern US, the Sahel, and western Siberia; and corresponding increases and decreases in temperature. It's noted that “…the net effect of vegetation changes on climate systems is not established…” You all know I was always pretty skeptical of “climate changes”, especially some of the extreme “predictions”; it now seems that the money being funneled into climate studies is actually getting some interesting science done, some of which bears out dire predictions and some of which is contrary.

Science 9 June 2017
Editorial
The dishonest HONEST Act
HONEST stands for Honest and Open New EPA Science Treatment; the act has passed the House and is in the Senate. It prohibits the EPA from using scientific studies to make an “agency decision” unless raw data, computer code, and “virtually everything used by scientists to conduct the study” are made publicly available online. The editorial authors throw a hissy fit, claiming that this will “reduce the amount of science used in decision making, undermine the credibility and application of scientific evidence, weaken the scientific enterprise, and imperil public and environmental health.” Well, we know what the problem is; the FOIA has been used by nutbar woowoos and Greendeath to cherry-pick data from published studies and claim everything from space alien bodies in Area 51 to fluoride toothpaste causing brain damage. I sympathize with scientists who have to put up with this but you can’t demand transparency in government without being transparent yourself. Interestingly enough, Science’s own editorial policy requires that raw data and computer codes be available to Science readers: http://www.sciencemag.org/authors/scien ... l-policies.
News in brief
Vaccine tragedy in South Sudan
Antivaccine woowoos will doubtless chortle over the deaths of 15 children in South Sudan after an attempt to stem a measles outbreak. The vaccine must be kept refrigerated, mixed with a sterile solution, discarded after 6 hours, and injected with sterile needles; apparently none of this happened and the children died of “sepsis and toxicity”.
News in depth
Oldest members of our species discovered in Morocco
This made the MSM. The original find came from a Moroccan cave in 1961 but languished in a museum because there was no way to date it. A German team returned to the site in 2004, hoping to find datable sedimentary layers that could be related to the original skull. That not only did that (with thermoluminescence) found that but new fossils, including more partial skulls, jaws, teeth and other bones from at last five individuals, plus fossils of various extinct animals with known date ranges that mesh. The average age is 314Kya. They would then be the oldest Homo sapiens by at least 100ky. The catch is as we’ve discussed before is the definition of exactly what constitutes Homo sapiens is rather cloudy – as evolutionary theory predicts it should be. Paleoanthropologists have generally tiptoed around this by using the term “anatomically modern humans” instead of Homo sapiens to allow for some slack, but this article and the MSM articles are sticking with Homo sapiens.
Circular DNA throws biologists for a loop
Cellular DNA is supposed to be in chromosomes and mitochondria. However, biologists have been finding little loops of DNA – around 300 base pairs long on the average - in a variety of cells from plants and animals. (The article notes some bacteria have circular chromosomes, which are not the same thing). The DNA loops seem to be especially common in tumors; it’s theorized that when a cell divides, the circular DNA loops are not apportioned evenly to the daughter cells like chromosomal DNA is; perhaps if the DNA loops contain oncogenes and a lot of them “pile up” in a cell line they can trigger cancer.
Policy forum
De-extinction, nomenclature, and the law
Legal complications don’t get discussed in all the hype about cloning mammoths or passenger pigeons or whatever else might appeal. As discussed here before, the law – in such things as the Endangered Species Act and restrictions on what species can be held as pets - tends to take a creationist view of species: they are fixed and immutable and you can tell exactly what species a given organism belongs to. The actual situation in nature is, of course, a lot hazier. The article discusses three situations involving extinct species: (1) selective back-breeding, where breeders try to create something that looks like the extinct form (an example is Heck cattle, bred to physically resemble the aurochs, Bos primigenius); (2) Cloning, where preserved somatic cell nuclei from the extinct species is transferred to the germ line of a suitable host species; (3) and genetic engineering, where the genome of the extinct species gets completed by inserting missing information from a surrogate species. It’s noted that under the International Union for the Conservation of Nature taxonomy rules, a back bred species is simply the species used for breeding; i.e., no matter how much it looks like an aurochs it’s still Bos taurus, not Bos primigenius. A cloned species has the mitochondrial genome of the host but the somatic genome of the target; under the IUCN code they are the species that donated the somatic genome; i.e, if you clone a mammoth using an Africa elephant, it’s Mammuthus columbi, not Loxodonta africana. The IUCN code has no provision for a genetically engineered extinct species as yet, and the authors suggest one will need to be formulated. They also not that while the IUCN code is accepted by all biologists, it has no legal standing; legislators and regulators could decide whatever they want rather than following the Code rules.
Review
Regenerating optic pathways from the eye to the brain
It’s conventional wisdom that once the optic nerve is gone it’s gone forever and sight is permanently lost. The optic nerve is made up of retinal ganglion cells, and mammalian RGCs do not regenerate; if damaged they eventually die and are not replaced. Mammalian peripheral nerves do regenerate (“avidly”, according to the article) so they have been attempts to transplant peripheral nerve cells to RGCs; this apparently works in rodent models but the amount of neurosurgery necessary to do it in humans would be prohibitive. Some other things have been tried; the myelin sheath around RGCs seems to secrete a protein that inhibits regeneration but suppressing the protein doesn’t seem to do any good; other proteins released by nerve damage sometimes inhibit regeneration and sometimes enhance it but nobody knows how and why; growth stimulating substances molecules found in embryonic nerve cells can promote nerve growth when used on adults, but the new nerves often grow in the wrong direction or form tumors. Even if RGCs can be regrown, they have to correctly connect to the brain; mouse experiments show that the animals can recovery enough vision to react to “looming overhead stimuli” but not enough to re-acquire depth perception. A promising approach is allogenic transplantation; extracting RGCs from healthy eyes. This appears to have some success in rodent models and the authors note transplanting RGCs from recently dead humans may work for human eyes. Another cause of blindness is retinal failure, and there are a couple approaches here as well. One is implanting an electric array into the eye; light cause electric signals that fire the RGCs. Another is using a virus to deliver light-sensitive proteins to degenerated retinal cells. Mouse models suggest this might restore enough vision to detect motion and recognize high-contrast objects.

Nature 8 June 2017
Editorials
Rescue remedy
The article discusses glucagon rescue for diabetics. I confess I had never heard of this; my understanding was that if a diabetic got dangerously low blood sugar they were supposed to get orange juice or something similar, but glucagon can be given to an unconscious recipient. The catch is it’s difficult to use; it has to be mixed from a powder into a solution and then injected, and the article notes it’s difficult to do in a hurry even for people trained in its use. The article notes several lines of research that might allow shelf-stable glucagon.
World View
We need a science of philanthropy
The article notes grant recipients are heavily scrutinized to make sure they are using money effectively, but givers have no way of knowing what sort of donations will prove effective. Facebook founder Mark Zuckerberg reportedly gave $100M to Newark public schools that ended up having no discernable effect; other recipients have declined grants because the paperwork involved consumed more time and money than the grants provided in the first place. It’s noted there are lots of opportunities for research; are many small grants more or less effective than a few large ones; what’s the best method for evaluating potential recipients; how do you evaluate if a grant was successful?
News in focus
Italy rebuked in olive fiasco
We’ve had threads on the Italian olive disease outbreak before. The European Union has sanctioned Italy over failure to track the spread of Xylella fastidiosa infected trees and failure to observe an agreed-on containment plan. Italian efforts have been hampered by “environmentalists”, who insisted that the disease wasn’t really Xylella fastidiosa; that even if it was it could be treated by “organic” methods rather than cutting down the affected trees; and that the whole thing was a plot by Monsanto or land developers. In one case “environmentalists” chained themselves to trees to keep them from being uprooted; it was sort of a Pyrrhic victory, as the trees were not destroyed – but they and all the ones around them died from the disease. Local governments blocked scientists from even entering the affected area – Nature notes that Italian lab records show virtually no samples were tested for Xylella fastidiosa during 2016 – and Italian prosecutors seized computers and other equipment at the local university on the hypothesis that botanists there had deliberately introduced the disease. The head of the Italian commission that was supposed to supervise destroying affected trees and creating a buffer zone in compliance with EU regulations resigned in disgust, saying he had been blocked at every turn; a new task force has supposedly been created but its composition and mandate has never been publicized. Other countries are concerned the disease may spread from Italy unless there are drastic measures.

Nature 1 June 2017
This Week
Toward Greater Reproducibility
Any life sciences manuscript submitted to Nature will now have to include details of experimental design, including reagents used and analysis methods. Cell-line data must be authenticated.
News in Focus
Mummy DNA unravels ancestry of ancient Egyptians
The conclusion is that ancient Egyptians were more closely related to ancient Middle Easterners than to people from further south in Africa. This might annoy some Afrocentrists, but they just might have reasons to be critical; none of the mummies examined was older than New Kingdom, and they all came from a single Egyptian town, Abusir el-Meleq. There’s a very subtle criticism of Zahi Hawass’ Pharaonic mummy studies; it’s commented that “many scientists are skeptical of purported genetic information acquired from the mummy of King Tutankhamun”.
Comment
Taxonomy anarchy hampers conservation
Rather disturbing. The authors, Australian professor and grad student Stephen Garnett and Les Christidis, complain that there is no clear definition of “species” in biology, and that biologists can “split” or “lump” species “with no consideration of the consequences”. Well, there’s certainly some truth to this. The history of what species are goes back to Linnaeus, who was operating from a Biblical perspective – all the “species” had been specially created, no new species could develop (and no species could go extinct). Paleontology and evolutionary biology gradually changed this perspective, and it eventually became generally acknowledged that each species is the result of a “distinct evolutionary lineage”, as the authors put it. So far, so good. This idea, the “biological species concept”, was proposed by Ernst Mayr in the 1940s; in order to be recognized as a species, a population of organisms should be reproductively isolated – i.e., unable to hybridize – with any other natural population. We’ve had a lot of discussion about this before; there are a lot of difficulties with the BSC; it’s not an operational definition, it doesn’t work for organisms that do not reproduce sexually, it doesn’t work for fossils, it has problems with “ring species”, etc. However, it represents an ideal. Garnett and Christidis, astonishingly, suggest abandoning the BSC for something they call the “phylogenetic species concept” – two populations are distinct species if they differ “physically and genetically”. Well, the PSC is the way biologists actually identify species, with insignificant exceptions; nobody sits around watching – for example – grasshoppers to see if they mate or not; instead you collect them, pin them, check out their physical morphology, find differences, publish somewhere, and voila – a new grasshopper species. But at least, if only in the back of your mind, you acknowledge that your goal is conforming to the BSC. You would use the same methodology under the PSC, but all pretense of actually identifying an evolutionary lineage would be abandoned. The salient advantage of this, according to Garnett and Christidis, is it would greatly enhance conservation efforts; by simply defining a new species you can get it placed on various national and international endangered lists. According to the authors, using the PSC would change one species of endangered central Asian mountain sheep into nine, and nine species of African antelope into 25. They propose bringing this all under the umbrella of the International Union of Biological Sciences, who would establish rules – for example, agreed-on differences in calls to delineate bird “species” (I’m going to start to put “species” in quotes because this definition is so different from what I’m used to); establish agreed subsets of life, such as “amphibians” and “arachnids”; and establish a judicial procedure to be responsible for upholding the rules. The suggest including lawyers, anthropologists, and sociologists on the various committees to ensure that definitions will withstand legal challenge and to “advise on social equity”. This is bizarre; it flies in the face of the most powerful concepts in modern taxonomy, cladistics and evolution, and essentially returns to a Linnean system except the Creator becomes various international committees. The authors are naïve enough to believe – or perhaps cynical enough to propose – that involving lawyers, anthropologists and sociologists in the process will somehow make things better, which is totally at odds with anything I know about lawyers, anthropologists and sociologists.
Govern land as a global commons
Yet another proposal, like the above, by an academic who has no apparent grasp of political and economic reality. This time, Felix Creutzig, a professor of Land Use, Infrastructures and Transport at the Mercator Institute on Global Commons and Climate Change at Berlin Technical University proposes that access to land and its products is an inalienable human right, and that therefore land and its products should be redistributed so everybody has a fair share. He notes “this will be harder than governing Antarctica and meeting treaties on climate change”. I withhold further comment.
News and Views
The self-cleaning ability of prehistoric air
Isotopic evidence of multiple controls on atmospheric oxidants over climate transitions
It’s noted that the atmosphere has a “self-cleaning” capability that prevents pollutants and greenhouse gases from reaching catastrophic levels; that this capacity is based on oxidation; that the principal oxidant in the troposphere is hydroxyl radical (OH); that OH concentration cannot be measured directly since it has such a short lifetime; that Δ¹⁷O(NO₃⁻) data that can be collected from ice cores is a proxy for troposphere oxidation capacity; that this isn’t behaving the way it’s predicted to during global warming and cooling episodes; and that “the new results highlight once again how little we understand about the complexity of chemistry-climate feedbacks…”. Well, OK then. Note and full paper.

Science 31 March 2017
News in brief
Neutrino lab dealt serious blow
We had a thread discussing the proposed Indian Neutrino Observatory. Apparently the project is on hold again, this time because the National Green Tribunal directed the preparation of new environmental permits. I sort of feel any country that has a government entity named the Nation Green Tribunal deserves whatever happens to it.
Measles surge in Europe
Italy reported 1010 cases in the first four months of 2017; there were 866 cases in all of 2016. In Romania, 3446 cases have been reported since 20160101; there have been 17 deaths, mostly immunocompromised children.
News in depth
The perhaps unfortunately named DONG Energy of Denmark has developed the REnescience system which accepts unsorted household waste, processes it in rotating steel cylinders, and produces three output streams: “bioliquid”, which is feed to anaerobic digesters for conversion to methane which in turn is burned for power production; metals and glass, which are recycled; and everything else, which is incinerated for power production. The first REnescience plant went into operation in Norwich, England, this year. Environmentalists oppose the system, noting being able to dispose of unsorted waste discourages households from reducing their overall waste streams.
News Features
Deadly chemistry
Underground labs in China are busy cranking out fentanyl derivatives. Up until 2015, fentanyl was unregulated in China; although the Chinese DEA proscribed it that year, it’s fairly easy for anyone with a modest lab and a modest knowledge of chemistry to tweak the molecule to something different and thus avoid detection. The article notes one fentanyl derivative, carfentanil, began showing up in the US and Canada last year; this was originally developed as a veterinary tranquilizer. For elephants. The drug is so potent – about 10000 times stronger than morphine, according to the article – that police officers have been sickened by dust kicked up from the floor during drug busts. Cincinnati police are now forbidden to test drugs at a crime scene and are carrying naloxone autoinjectors. Science notes a web search discloses a number of Chinese sites selling fentanyl derivatives by direct mail as “research chemicals”, one site was selling 50 grams of carfentanill for US$361; I can’t find an LD50 for carfentanil – and probably lit up a whole bunch of DEA search engine trackers by trying – but the Science article provides a picture of a vial with a few grains clinging to the side and says it’s a lethal dose.
Policy forum
Looking backward to move regulations forward
The authors make the astonishing proposal that it might be a good idea to look at the aftereffects of regulations to determine if they actually worked and how much they actually cost. It’s noted that the EPA does Regulatory Impact Analysis, which is supposed to estimate how much a regulation will cost and how much benefit will accrue, but there are no requirements to follow up after the regulation is promulgated and see if observation meets predictions. The authors cite two examples, the EPA Cluster Rule, which was intended to reduce hazardous air and water emissions from pulp and paper mills; and the NOx Budget Trading Program, which was supposed to reduce summertime emissions from power generating units and industrial boilers. With the Cluster Rule, after-regulation analysis suggested mixed results. Since not all plants were regulated, the unregulated ones provided a control group. With the Cluster Rule, the EPAs estimate for chloroform reduction was met almost exactly; however, the other regulated pollutants (benzene, carbon tetrachloride and methylene chloride) only decreased by half the estimated value, and there was no reduction at all in PM10 particulates. Employment declined by 6-7% in facilities subjected to both air and water regulations but there was no employment reduction in plants subject to air regulations only. The authors claim the EPA seriously underestimated the capital costs of compliance but do not comment if that contributed to employment reductions. For the NOx rule, the authors conclude success, with a 6-7% reduction in ozone production and a corresponding mortality reduction of 2500 deaths. The authors suggest a number of things the EPA could do to improve retrospective estimates: collect better data on compliance costs; collect better emission data; implement regulations to provide a control group, and institute a formal process for retrospective analysis. Although the authors comment on data collection for the study, they don’t explain the differences; the Cluster Rule data came from the Toxic Release Inventory. The TRI is self-reported, and based almost entirely on estimates. I only had to do one TRI report and it was years ago, but the process was rather strange; despite the use of “inventory” in the title, nothing was actually measured. Instead the TRI forms I had to fill out instructed me to count the number of pipe fittings and valves involved and apply an EPA provided value for the amount of material released by each. (I stress this was a long time ago and the rules may have changed). The NOx rule, and the other hand, depended on actual measurements; the regulated targets were required to have continuous emissions monitoring equipment that measured how much they were emitting.
Harnessing legal complexity
The authors treat US law and regulations as a Complex Adaptive System, subject to study by complexity science. This is interesting in an abstract way, but the authors don’t cite any concrete examples of how it might work, other than complaining that “agencies, courts, and other components of the legal system have reacted in unexpected ways that can frustrate adaptive management”.

Archaeology March-April 2017
The First American Revolution
After the Pueblo revolt of 1680, many of the natives prepared defensive fortifications on mesa tops anticipating the Spanish return. Archaeological work at these sites was difficult “until the 1990s”, which may be optimistic. The article discusses defensive works at Zuni (Dowa Yalanne); Cochiti (Hanat Kotyiti); Jemez (Patokwa, Boletsakwa, and Astialakwa); and San Ildefonso (Black Mesa). Dowa Yalanne was never besieged by the Spanish; Hanat Kotyiti and Astialakwa were taken and burned, confirmed by archaeology. Black Mesa was excavated by San Ildefonso archaeologist Joseph Aguilar, who argues, contrary to Spanish records, that it was a temporary battlefield camp; that the San Ildefonso women and children were sent elsewhere; and that the Spanish didn’t capture it but the defenders came down of their own accord after prolonged negotiations. Aguilar cites oral tradition in support; in fact, the building remains at the top of Black Mesa do not correspond to Spanish general Diego de Vargas’ description of the site so perhaps the oral tradition is correct. Although the Spanish reoccupied the lost parts of New Mexico, Aguilar notes that there were changes; native religious practices were quietly tolerated and the encomienda andrepartimiento systems, that made the natives essentially serfs, were abandoned.


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