On Mountains, Mountain Climbing, and COVID-19

Memorial to climbers who have died on Mount Everest at the Pheriche Aid Post (h/t akunamatata via flikr; CC BY-ND 2.0)

The language of mountains and mountain climbing is all over the COVID-19 coverage, from the talk of “reaching the peak” of infections to the euphoria of those who proclaim that in various areas, we are “hitting the plateau.” But as a mountain-climbing friend once told me “Climbing the mountain is the easy part — it’s the descent that’ll kill you.”

This is not just a cliche, or a (non-)urban legend, but backed up by the experience of those who know the mountains best:

Kami Rita Sherpa knows Mount Everest better than anyone else: He’s summited the world’s tallest peak 24 times, more than any person in history. . . .

Sherpa said problems arise not from those lines [of climbers waiting at altitude to pass along single-file sections of the climb], but when people accidentally push past what their body can support. Some research suggests that Everest climbers can develop a kind of “summit fever,” racing to the top to prove they can, even when their bodies are showing signs of giving out.

“At that altitude, it takes everything to put one foot in front of the other,” Everest climber and exercise psychologist Shaunna Burke recently told Business Insider. “If you haven’t judged how much gas you have left in the tank, then you can’t make it down. That’s why some climbers sit down and don’t get back up.”

Sherpa echoed this.

“When returning, their body is out of energy, and many people die due to this cause,” he said.

It’s not just one or two climbers’ opinion, either. In 2006, Paul Firth and his colleagues published “Mortality on Mount Everest, 1921-2006: descriptive study” in the British Medical Journal, which looked at every documented death on Mount Everest and sought to understand what commonalities might be found among the fatalities. They first distinguished between deaths below 8000 meters as climbers and their guides traversed areas prone to avalanches, crevasses, and other features of the mountain, and the deaths that took place above 8000 meters, where the mountain is generally more stable but fatigue and altitude sickness are the greatest dangers. On the lower part of the mountain, guides were more likely to be the ones who died, which the authors surmise is because the guides make multiple trips up and down the climbing route, setting ropes and bringing supplies up to the higher camp, before they guide the climbers along the route they found and made more safe. When it came to the deaths above 8000 meters, however, things reversed, and they noticed some shocking numbers:

Table 3 presents data on the mountaineers who died after reaching 8000 m. Fifty three (56%) died during the descent, 16 (17%) after turning back below the summit, and nine (10%) during the ascent. The stage of the summit bid was unknown for 12 mountaineers (13%), and four (5%) died before leaving the final camp.

Look at those top three figures again: 10% died while making the push for the summit, and 73% died while descending. For every death going up, there were 7 going down.

Maybe these climbers who died on the way back down pushed too hard going up, and had nothing left for the descent. Maybe they became disoriented because of lack of oxygen and quit thinking clearly. Maybe they were so excited at having made it to the top that they got sloppy as they turned around and headed down the mountain.

Whatever the cause, the study was clear: descending from the peak is more deadly that making the climb up. As our veteran climber cited above put it:

Burke said that although all climbers want to reach the summit, that objective alone can be a problematic.

“The summit is only halfway,” she said. “Your ultimate goal should be to make it back to camp alive.”

I look at the images of the folks protesting the “stay-at-home” orders issued to fight the COVID-19 epidemic, and their cheers of things like “We made it! We stopped the disease! Now let’s open things up again and get back to work!” I read the tweets to “liberate” this or that state, cheering on those who think the task is done. Then I think of the mountain climbers cheering at having reached the top of the mountain, who don’t realize how dangerous things can be on the way back down. That’s what worries me about all the talk of opening back up right now.

Yes, some places may have reached the peak of new infections, the peak of ICU bed usage, and the peak number of intubated patients. But here’s the thing: we are still on the mountain. Getting to the top is great, but the goal is to make it back to camp alive.

I don’t want to minimize the accomplishment of the climb, whether speaking of those who scale mountains or those who have been struggling to keep ahead of the increasing numbers of those hit by COVID-19. But relatively speaking, climbing the mountain is the easy part. It’s the descent that’s much more likely to kill. Face it, people: This journey has a long way to go, with plenty of opportunities for negligence and for misplaced cheering which will give life to a virus that deals out death.

This is no time for getting complacent or sloppy. Stay home, stay safe, save lives.

Research Misinfo/Disinfo: Check Experts’ Homework

[Check the byline, thanks. /~Rayne]

This is the first of two posts about research information and the disease COVID-19. I want to point out upfront I’m not a scientist/medical professional/public health expert. However I spend a lot of time reading fine print.

One thing I should set straight here is that we tend to use COVID-19 to refer to the disease and to the virus which causes it. This isn’t really accurate; I’ll be referring to SARS-CoV-2 as the virus underlying the disease called COVID-19 in this post.

~ ~ ~

Family members shared with me a link they received from a health care professional we know and trust. This professional told my family a Stanford researcher said “heat and sunshine will help to diminish the virus that causes COVID-19.”

You can imagine my family members’ concern because they’re in Florida where it’s quite warm already and yet COVID-19 cases continue to mount.

This situation provides a good example of how experts misunderstand and/or misuse research information and how lay people can be further misled or confused.

Direct link to video: https://youtu.be/xUGwGgV7r5Y

Note the researcher Dr. Lin’s background, Associate Professor in Neurology and Bioengineering at Stanford. He’s degreed in biochemistry and neurobiology, did postdoctoral work in fluorescent protein engineering. Sharp guy, great CV, but he isn’t a virologist or an epidemiologist.

At 6:45 in the video he refers to the outside of the virus as a “plasma membrane” — that’s just another less frequently-used term referring to a cell membrane. Virologists are more specific when discussing the coronavirus which causes COVID-19; it’s an RNA virus with a lipid membrane, attacked readily by soap though he does mention detergents.

When talking about sunshine or UV effects he discusses coronaviruses as a class, not SARS-CoV-2 specifically; he actually uses the word “estimate” with regard to timing.

Here is the first PubMed study Dr. Lin referred to in his video:

Photochem Photobiol. 2007 Sep-Oct;83(5):1278-82.
Inactivation of influenza virus by solar radiation.
Sagripanti JL, Lytle CD.
https://www.ncbi.nlm.nih.gov/pubmed/17880524

Emphasis mine. It’s not a study about *any* coronaviruses at all.

This is the second PubMed doc he cited:

J Virol. 2005 Nov;79(22):14244-52.
Predicted inactivation of viruses of relevance to biodefense by solar radiation.
Lytle CD, Sagripanti JL.
https://www.ncbi.nlm.nih.gov/pubmed/16254359

This study doesn’t even mention coronaviruses and was published *before* the MERS outbreak — another SARS-like variant of coronavirus which was first identified in 2012 in the Middle East, which I’ll point out is both sunny and hot compared to the northern U.S.

When Dr. Lin discussed temperature he referred to this study on the specific corona virus which causes the disease SARS:

Adv Virol. 2011;2011:734690. doi: 10.1155/2011/734690. Epub 2011 Oct 1.
The Effects of Temperature and Relative Humidity on the Viability of the SARS Coronavirus.
Chan KH, Peiris JS, Lam SY, Poon LL, Yuen KY, Seto WH.
https://www.ncbi.nlm.nih.gov/pubmed/22312351

Emphasis mine. Note this is a study of the virus which causes SARS, not the viruses which cause influenza or COVID-19. This is the abstract:

The main route of transmission of SARS CoV infection is presumed to be respiratory droplets. However the virus is also detectable in other body fluids and excreta. The stability of the virus at different temperatures and relative humidity on smooth surfaces were studied. The dried virus on smooth surfaces retained its viability for over 5 days at temperatures of 22-25°C and relative humidity of 40-50%, that is, typical air-conditioned environments. However, virus viability was rapidly lost (>3 log(10)) at higher temperatures and higher relative humidity (e.g., 38°C, and relative humidity of >95%). The better stability of SARS coronavirus at low temperature and low humidity environment may facilitate its transmission in community in subtropical area (such as Hong Kong) during the spring and in air-conditioned environments. It may also explain why some Asian countries in tropical area (such as Malaysia, Indonesia or Thailand) with high temperature and high relative humidity environment did not have major community outbreaks of SARS.

38C = 100F degrees.

People avoid being tightly clustered in confined spaces at that temperature. Note especially the first sentence about inhaled droplets. It’s not just that the virus may lose viability in a shorter period of time which reduces cases but the proximity of humans during the time the virus is active. Temperature alone is not a factor in reducing transmission rates.

The second study about temperature he cited:

Biomed Environ Sci. 2003 Sep;16(3):246-55.
Stability of SARS coronavirus in human specimens and environment and its sensitivity to heating and UV irradiation.
Duan SM, Zhao XS, Wen RF, Huang JJ, Pi GH, Zhang SX, Han J, Bi SL, Ruan L, Dong XP; SARS Research Team.
https://www.ncbi.nlm.nih.gov/pubmed/14631830

Emphasis mine — this is yet another study of the virus which causes SARS. This is a fairly early study dated 2003; the SARS outbreak began in 2002 with the first epidemic ending in June 2003. Here’s the results in the abstract:

RESULTS:
The results showed that SARS coronavirus in the testing condition could survive in serum, 1:20 diluted sputum and feces for at least 96 h, whereas it could remain alive in urine for at least 72 h with a low level of infectivity. The survival abilities on the surfaces of eight different materials and in water were quite comparable, revealing reduction of infectivity after 72 to 96 h exposure. Viruses stayed stable at 4 degrees C, at room temperature (20 degrees C) and at 37 degrees C for at least 2 h without remarkable change in the infectious ability in cells, but were converted to be non-infectious after 90-, 60- and 30-min exposure at 56 degrees C, at 67 degrees C and at 75 degrees C, respectively. Irradiation of UV for 60 min on the virus in culture medium resulted in the destruction of viral infectivity at an undetectable level.

37C = 98.6F (This made me laugh – it’s the temperature used for many years as a baseline for the average healthy human.)

Sure, heat deactivates the SARS coronavirus at temperatures fatal to humans, but it’s active at least a couple hours at temperatures in which humans live.

The last study cited was:

Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1
March 17, 2020
DOI: 10.1056/NEJMc2004973
https://www.nejm.org/doi/full/10.1056/NEJMc2004973
https://www.ncbi.nlm.nih.gov/pubmed/32182409

I’ve referred to this several times in comments with regard to hang time of the aerosolized virus. This study is a pre-print, not peer reviewed I should point out. It’s worth reading this study in particular because it’s about SARS-CoV-2 not SARS-CoV-1 and the findings have been misreported or misused a number of times in the media.

Rely on that last study the most because it’s about SARS-CoV-2, not SARS-CoV-1. It confirms that like the virus which causes SARS that SARS-CoV-2 can hang in the air as aerosol, and in this case the study showed it was viable for 3 hours:

SARS-CoV-2 remained viable in aerosols throughout the duration of our experiment (3 hours), with a reduction in infectious titer from 103.5 to 102.7 TCID50 per liter of air. This reduction was similar to that observed with SARS-CoV-1, from 104.3 to 103.5 TCID50 per milliliter (Figure 1A).

A friend sent me a link to this new pre-print study, not peer reviewed yet, published Friday March 27:

Stability of SARS-CoV-2 in different environmental conditions
Alex W.H. Chin, Julie T.S. Chu, Mahen R.A. Perera, Kenrie P.Y. Hui, Hui-Ling Yen, Michael C.W.
Chan, Malik Peiris, Leo L.M. Poon
https://www.medrxiv.org/content/10.1101/2020.03.15.20036673v2.full.pdf

This work confirms the viability of SARS-CoV-2 virus drops with increases in temperature and over time, but do note the data table provided in the study.

What the March 17 and March 27 studies say is that SARS-CoV-2 does weaken and become inactive with heat and over time.

What these and the other studies above do NOT say is that “heat and sunshine will diminish the virus.” There haven’t been any studies about SARS-CoV-2 viability over time with exposure to UV that I’m aware of . And while heat does speed the inactivation of SARS-CoV-2, the virus is still active for 2-3 hours in aerosolized form.

Like exhalation from infected humans, whether symptomatic or not.

It’s critically important that the public understands this virus SARS-CoV-2 is different from its relative, SARS-CoV-1. We can see this difference in both the ease with which it spreads and its much lower case fatality rate. Using studies of SARS and SARS-CoV-1 to extrapolate what SARS-CoV-2 will do has limits because of these key differences.

The same goes for anyone claiming SARS-CoV-2 is just another flu bug, that COVID-19 is just another influenza. It’s definitely not — anecdotal evidence of dead Americans by the truckloads tell you this is not just another flu. This difference is so obvious you should reject any such claims as propaganda. And any researcher making claims about SARS-CoV-2’s viability under certain conditions based on influenza viruses isn’t helping the public.

It’s as unhelpful as telling people erroneously that “heat and sunshine will help to diminish the virus that causes COVID-19.”

~ ~ ~

The bottom line: STAY HOME because aerosolized virus from asymptomatic and pre-symptomatic carriers in closed spaces has resulted in a significant number of confirmed cases versus fomite transmission — virus left on surfaces — though fomite transmission is still possible.

I’ll point to the story the Los Angeles Times published this week — sharing The Daily Beast’s summary because the LAT article is behind a paywall:

The Los Angeles Times reports that 45 out of 60 Skagit Valley Chorale who gathered at the Mount Vernon Presbyterian Church have tested positive. Three have been hospitalized and two have died.
https://www.thedailybeast.com/coronavirus-strikes-45-of-60-people-who-went-to-mount-vernon-washington-choir-practice

These people were careful; they observed social distancing techniques and heightened hygiene. But aerosolized virus got them, and it can get to others even when the weather is warm.

~ ~ ~

Next: the lack of solid research behind a particular off-label therapy.

Craig Simpson [CC BY 2.0])">CC by 2.0

Straddling the COVID-19 Barbed Wire Fence in Kansas

Pro Tip: Don’t sit on this fence. (photo h/t to Craig Simpson [CC BY 2.0])

The Democratic governor of Kansas, Laura Kelly, has put her finger in the eye of conservatives in Kansas by issuing a state-wide stay-at-home order yesterday in the face of the growing COVID-19 epidemic. Out in the western part of the state, the wingnuts have already been saying “this is an urban problem – we’re just fine – we don’t have any Chinese people here – why did she close all our schools?” and now they’ll scream just a little harder.

Note, however, that Kelly does not have the last word on this. When she issued her initial state of emergency declaration at the end of February, it lasted for 30 days. To extend it, the GOP-dominated legislature had to consent . . . which they did, but not without a fight. From the AP’s John Hanna in Topeka:

The [KS] Senate voted 39-0 and the House 115-0 to approve a resolution to extend the state of emergency until May 1 and to allow legislative leaders to extend it further every 30 days. Kelly declared a state of emergency last week, and without the resolution, it would have expired March 27.

But the resolution also requires legislative leaders to review all of Kelly’s executive orders and allows them to overturn many of them within days. It also prohibits Kelly from having guns and ammunition seized or blocking their sale.

The unanimity of those two votes is almost unheard of these days in Topeka, and it was a sign that the GOP was willing to go along with closing the schools for the rest of the year and take other measures as the COVID-19 outbreak began to surface across the state. But they sure didn’t like it, and wanted to make damn sure that they could shut down an out of control governor (in other words, a Democrat) when they did something they considered outrageous. The guns and ammo provision is another sign of how fearful the rightwing is of folks coming for their weaponry.
That was ten days ago. As soon as Kelly’s Stay-At-Home order came out yesterday, so did the folks on the right, waving around that provision that provides for a veto those orders. Again from John Hanna:

Conservatives in the Republican-controlled Legislature said Kelly overreached this month when she ordered public schools closed for the rest of the semester and complained that the state’s economy was being damaged too much. Legislative leaders have the power to revoke her orders related to the coronavirus pandemic.

Kansas House Speaker Ron Ryckman, Majority Leader Dan Hawkins and Speaker Pro Tem Blaine Finch, all Republicans, said in a joint statement that the new order “will no doubt impact our families and our businesses. As members of the Legislative Coordinating Council we have a duty to carefully assess this executive order and the reasons for it. Over the coming days we will consult with the Attorney General, health care professionals, the business community, and the state’s emergency management team to make sure we are on the right path.”

Kansas Senate President Susan Wagle, a Wichita Republican, said she was concerned about a “one size fits all” solution.

“I want to assure Kansans, particularly those in rural areas, the legislature is actively working to thoroughly review the Governor’s orders and ensure the specific needs of rural Kansans are addressed,” Wagle said in a statement.

Kansas Congressional Districts

[Note to the folks worried that the state’s economy was being damaged too much: a virus does not care.]

Speaking of those rural areas, let me direct your attention to OB-GYN Roger Marshall, who also serves as the US Representative from KS-01 (the large green area on the map to the right). Marshall is running to replace Pat Roberts in the US Senate, and he is trying to straddle a barbed wire fence on all this. He’s been loud about backing Trump’s “close the borders” stuff, but he’s still enough of a physician that he realizes that science actually matters. He doesn’t like the “big government” approach at all, but he has conspicuously not condemned Kelly for closing the schools. From an story two weeks ago in the Manhattan KS paper “The Mercury”:

Following Gov. Laura Kelly’s recent decision to close K-12 school buildings for the rest of the school year, halt mortgage foreclosures and evictions, and ban gatherings of more than 50 people, Marshall said he would rather people exercise an overabundance of caution at the moment.

“We have to assume that the virus is out in every community,” he said. “I hope there’s not, but we have to assume that. Kids and young adults, they’re super infectors so if one child has the virus, they’re going to transmit it a bunch more often than say an older person who just doesn’t have as many social contacts. Think of senior citizens, for the sake of people with illnesses.

“I hope in a couple of weeks you can say we did too much,” Marshall continued, “but I think right now, it’s so critical that this is the acceleration phase of the spread of this virus. Every virus we prevent spreading today is going to prevent dozens in the future and save many, many Kansas lives.”

Yesterday, Marshall retweeted John Hanna’s story about the Stay-At-Home order to his followers, perhaps trying to signal them that the GOP is watching this. He did not, however, attack or even question Kelly’s judgment for ordering this. To borrow from Sherlock Holmes, this is the dog that did not bark, and the silence is deafening.

And then there’s Marshall’s big opposition in the GOP primary (this was before Kelly’s order was issued yesterday):

U.S. Senate contender Kris Kobach reached for campaign gold amid the coronavirus pandemic by promising to intensify construction of a border wall to defend the country against illegal immigrants from China who may import deadly viruses.

“Over 12,000 Chinese nationals snuck across the border into the United States last year,” Kobach said in a video fundraising appeal delivered Thursday to potential voters in Kansas. “No checks. No visas. No health screening. In times of global pandemic, borders matter.”

The fence in Kansas between science and wingnuttery is made of very sharp barbed wire. Kobach is planted firmly on the Wingnuttery side of that fence, and Marshall does not want to cede all those voters to him by planting his feet firmly on the side of science. But Marshall is is going to find that straddling a barbed wire fence is not comfortable, to say the least.

The KS senate race will be very very interesting this November.

 

[Photo: Paul Rysz via Unsplash]

Three Things: Eclipsed, Killer Robots, Back to the Salt Mines [UPDATED]

I’ve been trying to write all morning but I’ve been interrupted so many times by people looking for information about eclipse viewing I’m just going to post this in progress.

Mostly because I’m also helping my kid rig an eclipse viewer — lots of tape, binder clips and baling wire.

~ 3 ~

As you’ve no doubt heard, much of the U.S. will experience a solar eclipse over the next three hours. It’s already begun on the west coast, just passing totality right now in Oregon; the eclipse started within the last 25 minutes in Michigan. And as you’ve also heard, it is NOT safe to look directly at the sun with the naked eye or sunglasses. A pinhole viewer is quick and safe to make for viewing. See NASA’s instructions here and more eclipse safe viewing info here.

You can also watch NASA’s live stream coverage on Twitch TV.

We are also experiencing one of NASA’s most important services: public education about our planet and science as a whole, of particular value to K-12 educators. We can’t afford to defund this valuable service.

At this point you may imagine me on my deck holding a Rube Goldberg contraption designed to view the early partial eclipse we’ll see in Michigan — only 77% or so coverage.

~ 2 ~

KILLER ROBOTS: There’s been a fair amount of coverage this week touting Elon Musk’s call to ban ‘killer robots’. Except it’s not just Elon Musk, it’s a consortium of more than 100 technology experts which published an open letter asking the United Nations to restrain the development of ‘Lethal Autonomous Weapon Systems’ (LAWS).

I’ve pooh-poohed before the development of new military technology, mostly because DARPA doesn’t seem to be as fast at it as non-military researchers. Exoskeletons are the best example I can think of. But whether DARPA, the military, military contractors, or other non-military entities develop them, AI-enabled LAWS are underway.

More importantly, we are very late to dealing with their potential risks.

Reading about all the Musk-ban-killer-robots pieces, I recalled an essay by computer scientist Bill Joy:

… The 21st-century technologies – genetics, nanotechnology, and robotics (GNR) – are so powerful that they can spawn whole new classes of accidents and abuses. Most dangerously, for the first time, these accidents and abuses are widely within the reach of individuals or small groups. They will not require large facilities or rare raw materials. Knowledge alone will enable the use of them.

Thus we have the possibility not just of weapons of mass destruction but of knowledge-enabled mass destruction (KMD), this destructiveness hugely amplified by the power of self-replication.

I think it is no exaggeration to say we are on the cusp of the further perfection of extreme evil, an evil whose possibility spreads well beyond that which weapons of mass destruction bequeathed to the nation-states, on to a surprising and terrible empowerment of extreme individuals.

Nothing about the way I got involved with computers suggested to me that I was going to be facing these kinds of issues. …

He wrote this essay, The Future Doesn’t Need Us, in April 2000. Did we blow him off then because the Dot Com bubble had popped, and/or our heads hadn’t yet been fucked with by post-9/11’s hyper-militarization?

This part of his essay is really critical:

… Kaczynski’s dystopian vision describes unintended consequences, a well-known problem with the design and use of technology, and one that is clearly related to Murphy’s law – “Anything that can go wrong, will.” (Actually, this is Finagle’s law, which in itself shows that Finagle was right.) Our overuse of antibiotics has led to what may be the biggest such problem so far: the emergence of antibiotic-resistant and much more dangerous bacteria. Similar things happened when attempts to eliminate malarial mosquitoes using DDT caused them to acquire DDT resistance; malarial parasites likewise acquired multi-drug-resistant genes.2

The cause of many such surprises seems clear: The systems involved are complex, involving interaction among and feedback between many parts. Any changes to such a system will cascade in ways that are difficult to predict; this is especially true when human actions are involved. …

The Kaczynski he refers to is Ted “Unabomber” Kaczynski, who Joy believes was a criminally insane Luddite. But Kaczynski still had a valid point. Remember StuxNet’s escape into the wild? In spite of the expertise and testing employed to thwart Iran’s nuclear aspirations, they missed something rather simple. In hindsight it might have been predictable but to the experts it clearly wasn’t.

Just as it wasn’t obvious to computer scientists over more than a decade to close every possible port — including printer and server maintenance ports — regardless of operating system so that ransomware couldn’t infect systems. Hello, WannaCry/Petya/NotPetya…

We’ve already seen photos and videos of individuals weaponizing drones — like this now-five-year-old video of an armed quadrotor drone demonstrated by a friendly chap, FPSRussia — the military-industrial complex cannot and should not believe it has a monopoly on AI-enabled LAWS if these individuals have already programmed these devices. And we don’t even know yet how to describe what they are in legal terms let alone how to limit their application, though we’ve received guidance (read: prodding) from technology experts already.

The genie is out of the bottle. We must find a way to coax it back into its confines.

~ 1 ~

SALT MINES: On a lighter note, molten salt may become a cheaper means to reserve energy collected by alternative non-fossil fuel systems. Grist magazine wrote about Alphabet’s X research lab exploring salt as a rechargeable battery as an alternative to the much more expensive current lithium battery systems. Lithium as well as cobalt have challenges not unlike other extractive fuels; they aren’t widely and cheaply available and require both extensive labor and water for processing. Salt — sodium chloride — is far more plentiful and less taxing on the environment when extracted or collected.

One opportunity came to mind as soon as I read the article. Did you know there was a salt mine 1200 feet below the city of Detroit for decades? It’s a source of road salt used on icy roads. It may also be the perfect place for a molten salt battery system; the Grist article said, “Electricity in the system is produced most efficiently when there is a wider temperature difference between the hot and cold vats.” A salt mine underneath Detroit seems like it could fit the bill.

Could Detroit become an Electric Motor City? Fingers crossed.

~ 0 ~

I feel for you folks in states with cloud cover — no good excuse today to take a break outside and slack off beneath the eclipse.

This is an open thread.

Other Priorities: Another Launch Today – Blue Origin Reusable Rocket

Hurry, we’re less than three minutes from launch, all systems go. I’ll add more remarks in a moment.

11:20 a.m. EDT — Wow. What a picture-perfect launch and landing. This is the most excitement out of West Texas since some lousy bird hunter shot his friend in the face a few years back. Today’s mission by Blue Origin, an aerospace company founded by Amazon CEO Jeff Bezos, had several objectives. The reusable rocket’s fourth mission included testing of backup and safety systems intended for future manned flights as well as multiple scientific project payloads. At least one project required the microgravity conditions (video) this mission would realize as the ship approached, reached, and left apogee at 331,501 feet (roughly shy of 63 miles above earth).

I’ve replaced the live feed of the mission with a video summary of the same New Shepherd rocket’s third flight from April this year. Compare and contrast with Elon Musk’s SpaceX’s recent reusable rocket launches; I am completely in awe of SpaceX’s attempts to stick a landing repeatedly on a puny drone raft at sea. (Video embedded here is from SpaceX launch last Wednesday carrying Eutelsat/ABS telecommunications satellites.)

If we have to endure gross inequality and a siphoning plutocracy, this space race is the kind of crazy oligarchs’ spending I love to see. Granted, Bezos is probably checking out future warehousing for Amazon facilities in space, crewed by robots — there’s no rent in space, right? But the opportunities for aerospace development and accessibility to the public have increased greatly with these two companies working fast and hard on this implicit competition. They also offer opportunities for us to save costs on government-funded missions — SpaceX has already won contracts formerly awarded to companies with an oligopolistic hold on launches.

I still want NASA to do all this and more as well; space shouldn’t be the domain of corporations after all. But if NASA has to work with fewer resources thanks to anti-science GOP-led Congress, at least they have a much larger hiring pool of experts to drawn from when they look for aerospace folks to add to their team, thanks to Blue Origin and SpaceX.

Explaining his refusal to serve in the military, that aforementioned sloppy hunter who shot his friend in the face said he had other priorities. It’s amazing in contrast what other rich guys do with their other priorities.

Jeff Bezos had one helluva Father’s Day already. Hope yours is just as exciting.

As Disneyland Measles Outbreak Rages in California, Pakistani Father Arrested After Unvaccinated Son Contracts Polio

There is very interesting news out of Pakistan today that the father of a child who has developed polio has been arrested because he refused to allow his son to be vaccinated:

After a polio case was detected here on Thur­sday, the Kohat administration arrested the father of the affected child because he had refused to get his child vaccinated against polio when vaccinators visited his home. Two health supervisors and a patwari have also been taken into custody for showing negligence in performing their duty.

Three-year-old Moham­mad is the second victim of polio in Dhodha area of Kohat district this year.

Deputy Commissioner of Kohat Riaz Khan Mehsud told Dawn on telephone that he issued orders for arrest after an inquiry revealed that the father of the affected child, Mullah Mohammad Yousuf, had not allowed vaccinators to give polio drops to his son.

But Yousuf is not the only parent who has been arrested:

He said 56 people had so far been arrested this year for refusing to get their children vaccinated against polio.

Also on Thursday, two men were arrested in Kohat for not allowing vaccinators to give polio drops to their children. They were identified as Amir Khan and Hassan Khan.

Islamic extremist groups in Pakistan agitate against polio vaccines, spreading conspiracy theories that the vaccines are Western attempts to kill or dominate Muslims. They even attack health workers and in 2014, those attacks killed more people administering vaccines than the disease itself killed.

But of course, in a civilized country like the United States, there couldn’t be misguided attempts to prevent vaccination despite the solid scientific basis of the public health benefits of vaccines, could there? Sadly, the mass delusion that has led far too many parents to leave their children unvaccinated due to unfounded fears of autism is having the very predictable result of outbreaks of viral diseases previously under control. Here’s the latest on the current outbreak of measles that epidemiologists have traced to Disneyland. Unfortunately, we are learning that because of the reckless behavior of not vaccinating children, even those who have been vaccinated are now developing the disease because of the increased exposure from the outbreak: Read more

Ebola Outbreak Finally Receding in Sierra Leone; CDC Modeling Was Incredibly Accurate

Back in late September, just a week before Ebola panic hit a peak in the US when a patient in Dallas was diagnosed with the disease, the CDC produced a remarkable study in which they modeled the expected number of Ebola cases both with and without intervention. That study received a huge amount of press coverage, primarily because the model predicted that without intervention by public health authorities, as many as 1.4 million people could be infected. By contrast, with a program of isolating infected patients and educating survivors on proper burial techniques, the model showed that the outbreak would be much less widespread. The modeling projected cases through yesterday’s date, January 20.

Less reported in the media at the time was the projected number of cases under the scenario of intervention. The model predicted an actual number of cases between 25,000 and 30,000 by this week and a reported number of cases of nearly 10,000. Here are the two projections placed alongside one another:

CDC modeling of projected number of Ebola cases without (left) and with (right) improved patient isolation and safe burial practices.

CDC modeling of projected number of Ebola cases without (left) and with (right) improved patient isolation and safe burial practices.

The latest data from WHO indicate just over 21,000 cases as of January 11. That is a remarkable achievement by the team that developed the model. The observed actual number of reported cases fell squarely within the range predicted by the model. With the influx of health professionals to the region to provide care for infected patients, it seems likely to me that the correction factor applied in the CDC model to correct from the reported number of cases to the actual number would be very different now, so that the reported number and actual number would be much closer to one another, making the prediction even more accurate.

Last time I posted on progress in stopping the spread of the virus, we saw that the rate of appearance of new cases was dropping rapidly in Liberia but was still accelerating in Sierra Leone. The good news is that the improved practices have finally been implemented sufficiently in Sierra Leone that the rate is now dropping there. Here are the plots of weekly new cases in the two countries from the latest WHO Situation Report:

Weekly number of new cases of Ebola in Liberia (left) and Sierra Leone (right). Control of the virus was achieved about two months later in Sierra Leone than in Liberia.

Weekly number of new cases of Ebola in Liberia (left) and Sierra Leone (right). Control of the virus was achieved about two months later in Sierra Leone than in Liberia.

Although the battle is not yet over, all indications are that the outbreak is well past the worst phase and should end soon. Considering how closely the CDC model predicted the eventual size of the outbreak with the control measures that were implemented, it seems safe to say that the world would have witnessed a truly horrific level of spread of the virus had improved safety measures not been implemented. As of the January 14 WHO Situation Report, a total of 825 health care workers have been infected, with 493 of them dying. Without their sacrifices, many more would have been lost.

GAO Analysis Highlights Lab Samples Excluded in Sloppy FBI Anthrax Investigation

As the last Friday before Christmas, late yesterday afternoon was the most obvious Friday news dump hour of the year, and the government didn’t disappoint. The Government Accountability Office released the results of a twenty-three month long study of the genetic analysis that was used to tie the material found in the anthrax attacks of 2001 to the laboratory of Bruce Ivins, whom the FBI concluded (pdf) was solely responsible for the attacks. The FBI’s conclusion is highly suspect for many reasons. On the science side, it is very unlikely that Ivins could have produced all of the attack material on his own and the detailed chemistry of the attack spores suggests that highly sophisticated materials and techniques unavailable to Ivins likely were used to prepare the attack material. Regarding that second point, note that even William Broad refers indirectly to the chemistry concerns in his New York Times article on the GAO report:

To the regret of independent scientists, the report made no mention of an issue beyond genetics: whether the spores displayed signs of advanced manufacturing. They have pointed to distinctive chemicals found in the dried anthrax spores that they say contradict F.B.I. claims that the germs were unsophisticated.

Evidence of special coatings, they say, suggests that Dr. Ivins had help in obtaining his germ weapons or was innocent.

The GAO study was undertaken, in part, because of questions raised by the National Academies study released in 2011 and with special prompting by Representative Rush Holt, from whose district the letters likely were mailed. The GAO study focused on obtaining a better understanding of the validity of the genetic analysis that was carried out and the statistics underlying the conclusions reached.

For a refresher, a helpful illustration from the GAO report shows the underlying biology of the genetic analysis that was carried out in the Amerithrax investigation. Here we see photos of a typical colony of the Ames strain of Bacilus anthracis on an agar plate and four variant colony types that occurred at low frequency when the attack material was spread out on agar so that colonies arose from single cells of the overall population of bacteria that were present in the attack material:
morphs

DNA sequence analysis was employed to identify the changes that led to these variant colony shapes. The FBI then commissioned private laboratories to develop DNA-based tests (relying on polymerase chain reaction, or PCR, methodology) that could be used to screen the large bank of isolates of the Ames strain that the FBI had accumulated through a subpoena submitted to all 20 laboratories known to have isolates of the Ames strain. Developing these assays represented a new frontier in forensic genetics and it did not prove possible to develop tests for all of the mutations identified in the original DNA sequencing. In the end, four tests were developed by the four different contractors.

The Amerithrax report stated that of the 947 samples included in the final analysis, only eight showed all four of the DNA changes the tests were designed to detect. Seven of those samples came from the laboratory where Ivins worked (U.S. Army Medical Research Institute of Infectious Diseases, or USAMRIID) and one came from Batelle Memorial Institute in Columbus, Ohio. The FBI noted that there was a record of material being transferred from USAMRIID to Battelle, accounting for the sample found there.

The GAO analysis finds a number of significant issues with the FBI’s work: Read more

Ebola Outbreak Receding in Liberia, Still Strong in Sierra Leone

Back in late September, the press had a field day with a mathematical model developed by CDC that estimated that if left unchecked, the Ebola outbreak in West Africa could wind up infecting over 1.4 million people. Almost missed in the hysteria over that high number was the fact that this same model predicted that even with key public health measures (patient isolation, monitoring of at-risk population who had contact with infected people and safe burial practices) falling short of 100% implementation, the outbreak could be brought under control around January of next year.

Word has been leaking out for a while now that the rate of new Ebola infections in Liberia is falling. Reports in the Washington Post on October 29 and November 3 told us as much. A chart in the WHO Situation Report for November 5 drives home just how dramatic the decline in new cases has become:

WHO Ebola Situation Report November 5, 2014

WHO Ebola Situation Report November 5, 2014

As can be seen in the chart, the rate of new infections for the two most recent weeks is less than one fourth the rate at the peak of the outbreak. Unfortunately, the news for Sierra Leone is not as good. While the rate of new infections may be leveling off, it is not yet falling appreciably:

WHO Ebola Situation Report November 5, 2014

WHO Ebola Situation Report November 5, 2014

Digging into the WHO report a bit further, we can find some evidence for how this dramatic drop in new cases has been brought about. We see that 52% of cases are now isolated. The WHO target for December 1 has been set at 70%, with a target of 100% by January 1. When it comes to management of dead bodies, though, the December 1 target has already been surpassed. WHO reports that 87% of the dead are being “managed in a safe and dignified manner” while the targets were set at 70% for December 1 and 100% for January 1. Also, although no benchmarks are reported, WHO states that 95% of registered contacts were reached daily (although in the text of the report, there are suggestions this number may be somewhat overstated).

It should come as no surprise that progress in implementing these basic measures has had a huge impact on bringing down the rate of new infections. It fits perfectly with the CDC mathematical model and it also addresses the known biology of Ebola infections. Patients are most infectious at or near death, so establishing safe burial practices is vitally important. Conversely, identifying infected individuals through daily monitoring of the at-risk population and then isolating infected individuals once symptoms begin means that far fewer people are exposed to people producing large amounts of virus.

Sadly, those who remain exposed are the health care workers who are providing care to those who are infected. Despite shortages of equipment and supplies, WHO and other organizations are doing their best to overcome those shortages and to beef up training to reduce risk to these brave people on the front lines in the work to control the virus. As of this November 5 report, 546 health care workers have been infected, with 310 of them dying. Only four new infections were reported for the week ending November 2, so it is hoped that this rate is also dropping.

Had the alarmists who insisted that this was a new super-strain of Ebola capable of airborne transmission (or even a strain developed in a bioweapons laboratory), it is doubtful that these basic public health measures would have had such a dramatic impact on the rate of new infections. Perhaps those folks can go back to railing about chemtrails or the evils of vaccines, because basic boring science appears to be on the road to controlling the current outbreak before all of mankind succumbs.

In the meantime, we are at about two weeks into the three week incubation period both for anyone “exposed” by Craig Spencer or for Kaci Hickox (or anyone she “exposed”) to show symptoms. No reports of transmission so far, and the odds of any cases showing up are dropping very rapidly from the already very low levels where they started.

Glaring Front Page Error by David Sanger, New York Times as Iran Nuclear Negotiations Near Deadline

See the update below, as of about 2:45 pm, the Times has changed the wording of the erroneous paragraph without adding a note of the correction. Oops. I got off on the wrong paragraph when I checked back. See the comment from Tony Papert below.

For someone who has written on a range of technical issues for many years, the error committed last night by David Sanger could not be worse nor come at a worse time for the important events he is attempting to cover. In an article put up last night on the New York Times website and apparently carried on page A1 of today’s print edition, Sanger and the Times have garbled a key point at the heart of the negotiations between Iran and the P5+1 group of nations as they near the critical November 24 deadline for achieving a full agreement on the heels of last year’s interim agreement.

The article ostensibly was to announce a major breakthrough in the negotiations, although Gareth Porter had worked out the details of the progress last week. Here is what Porter deduced:

The key to the new approach is Iran’s willingness to send both its existing stockpile of low enriched uranium (LEU) as well as newly enriched uranium to Russia for conversion into fuel for power plants for an agreed period of years.

In the first official indication of the new turn in the negotiations, Iranian Foreign Ministry spokesperson Marzieh Afkham acknowledged in a briefing for the Iranian press Oct. 22 that new proposals combining a limit on centrifuges and the transfer of Iran’s LEU stockpile to Russia were under discussion in the nuclear negotiations.

The briefing was translated by BBC’s monitoring service but not reported in the Western press.

Undersecretary of State Wendy Sherman, who heads the U.S. delegation to the talks, has not referred publicly to the compromise approach, but she appeared to be hinting at it when she said on Oct. 25 that the two sides had “made impressive progress on issues that originally seemed intractable.”

As Porter goes on to explain, such an arrangement would allow Iran to maintain a large number of centrifuges continuing to enrich uranium, but because there would be no stockpile of low enriched uranium (LEU), the “breakout time” (time required to highly enrich enough uranium for a nuclear weapon) would remain at about a year. By having Russia convert the LEU to fuel rods for Iran’s nuclear power plant, that LEU would be removed from any easy pathway to a weapon. This would provide Iran the “win” of maintaining its present level of around 10,000 operational centrifuges but give the P5+1 its goal of a longer breakout time. The key here is that unlike a proposal in 2005 where Russia would take over enrichment for Iran, this new proposal would allow Iran to continue its enrichment program while shipping virtually all of of its LEU to Russia for conversion to fuel rods.

Sanger appears to start off on the right track with his article:

Iran has tentatively agreed to ship much of its huge stockpile of uranium to Russia if it reaches a broader nuclear deal with the West, according to officials and diplomats involved in the negotiations, potentially a major breakthrough in talks that have until now been deadlocked.

Under the proposed agreement, the Russians would convert the uranium into specialized fuel rods for the Bushehr nuclear power plant, Iran’s only commercial reactor. Once the uranium is converted into fuel rods, it is extremely difficult to use them to make a nuclear weapon. That could go a long way toward alleviating Western concerns about Iran’s stockpile, though the agreement would not cut off every pathway that Tehran could take to obtain a nuclear weapon.

But about halfway through the article, Sanger displays a shocking ignorance of the real points of recent negotiations and somehow comes to the conclusion that Russia would be taking over enrichment for Iran rather than converting LEU into fuel rods:

For Russia, the incentives for a deal are both financial and political. It would be paid handsomely for enriching Iran’s uranium, continuing the monopoly it has in providing the Iranians with a commercial reactor, and putting it in a good position to build the new nuclear power reactors that Iran has said it intends to construct in the future. And it also places President Vladimir V. Putin at the center of negotiations that may well determine the future of the Middle East, a position he is eager to occupy.

Somehow, Sanger and his New York Times editors and fact-checkers are stuck in 2005, suggesting that Iran would negotiate away its entire enrichment program. Such a drastic move would never be contemplated by Iran today and we are left to wonder whether this language found its way into the Times article through mere incompetence or more nefarious motives meant to disrupt any possible deal by providing false information to hardliners in Iran.

At the time of this writing (just before 9 am on November 4), the Times still has not added any correction or clarification to the article, despite the error being pointed out on Twitter just after 10:30 pm last night (be sure to read the ensuing Twitter conversation where Laura Rozen and Cheryl Rofer work out the nature of the error).

Update: And now, around 2:45 in the afternoon, I see that the Times has changed the erroneous paragraph. So far, I don’t see a note that a correction has been made. Here is the edited paragraph:

Russia’s calculus is also complex. It stands to gain financially from the deal, but it also has an incentive to see the nuclear standoff between Iran and the rest of the world continue, because an embargo keeps Iranian oil off the market. With oil prices falling, a flood of exports from Iran could further depress prices.

Will they ever get around to adding a note? I’ll keep an eye out. Well dang, this is embarrassing. I went to the wrong paragraph when I looked back. The article is still unchanged. Thanks to Tony Papert in comments for catching my bone-headedness.

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