Wikipedia:Reference desk/Archives/Science/2020 April 23

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April 23

Could Covid-19 have spread at multiple points from animals to humans?

If it is true that most of the early cases came from a single wildlife market, then one or more of the animals could have been infected prior to being shipped to the market. This would imply that the farmers or others handling the same animal(s) earlier could also have presumably been able to catch the virus.

So why are the earlier cases that were not linked directly to the market assumed to be evidence against zoonotic transmission at the market, rather than as evidence that there might have been an "animal super-spreader" of some kind, or simply that the same animal infected a handful of people handling it, and then was subsequently delivered to the market and spread the virus around at that market?

2600:8806:3400:3DB:793B:C7CF:650:5F5A (talk) 02:31, 23 April 2020 (UTC)Nightvid

My understanding is that the earlier cases and growing evidence against zoonotic transmission occurring at the meat market is because the genetic analysis indicates the possibility that the transfer occurred hundreds of miles away from Wuhan. I'm not sure what you mean by an "animal super-spreader." While it is possible that a single animal or group of animals transferred the virus to more than one person, I'm not sure that's relevant to the issue of the meat market. Basically, the genetic analysis shows 3 main subtypes, each splitting from the previous, i.e. subtype A is the root subtype emerging at or immediately after the zoonotic transfer. At some point, subtype B split off from subtype A, and then substype C split off from subtype B. The viral isolates from Wuhan are subtype B, which indicates that the zoonotic transfer event may not have occurred in Wuhan. Subtype A has been found in Guangdong province, which is 500 miles away from Wuhan, as well as in North America. What this seems to suggest is that the zoonotic transfer event could have happened earlier than we thought, and in southern China, and spread from there. At some point, subtype B mutated off of subtype A, and early on in its spread to Wuhan, mutated into subtype B, which dominated that outbreak. Independently, someone also carried subtype A to North America, which dominated the North American outbreak. Subtype C, at some point, mutated from subtype B, and is what was the type in the outbreak in Europe, as well as other areas of East Asia, but is otherwise largely absent from China.

So, it isn't just that earlier outbreaks occurred, and thus we don't think one animal could have caused both the earlier outbreaks and then the later one in Wuhan (and the wet meat market). Rather, the genetic analysis indicates that the outbreak in Wuhan was a product of human-to-human transmission already occurring, as it was a daughter type to that of the earlier zoonotic transfer event outside of Wuhan. --OuroborosCobra (talk) 02:50, 23 April 2020 (UTC)

Separate from your main point/reply to the question but this bioRxiv preprint suggests the subtype prevalent in New York is closer to the Italian one than the more common "endogenous" US one although they're relying on a marker to identify the subtypes [1] Nil Einne (talk) 18:25, 23 April 2020 (UTC)

As we can read here: "The gene for the spike protein in SARS-CoV-2 has an insertion of 12 genetic letters: ccucggcgggca. This mutation may help the spikes bind tightly to human cells — a crucial step in its evolution from a virus that infected bats and other species." This means that before this mutation arose, there would have had to be infections with the virus with humans that then didn't cause an epidemic. The virus may not have been able to cause much of a disease in humans. But one can estimate what the probability of the insertion of the code "ccucggcgggca" and then deduce if this is so low that it would have had to happen in smaller steps. If so, then that would imply that virus was moving back and forth from the animal host to humans a long time before it had the capability of causing an epidemic in humans. Count Iblis (talk) 10:18, 24 April 2020 (UTC)

Cats vs. dogs cleanliness

I am looking for non-biased scientific information about the cleanliness of cats vs. dogs. I do not want any information from religious sources. For example, Islam does see cats as ritually cleaner than dogs. However, I want to find secular information about cats vs. dogs studied by scientists. Where can I find information about the cleanliness and diseases of these animals online? Thank you. WJetChao (talk) 09:39, 23 April 2020 (UTC)

Cat Cleanliness vs. Dogs. DroneB (talk) 11:01, 23 April 2020 (UTC)

• Cleanliness is not a scientific term, therefore your question cannot be answered using scientific sources, as you wanted. You'll have to define cleanliness. Fgf10 (talk) 12:35, 23 April 2020 (UTC)

  Can't we measure their respective distances to godliness?

  "Cleanliness" might not be a scientific term, but its a concept that could be defined in such a way that it could be scientifically investigated. I don't have any answers, but I don't think the question should be dismissed like that. Iapetus (talk) 08:45, 24 April 2020 (UTC)

There's no doubt it could be. But it hasn't been by the OP so far, so my statement about this particular question is completely correct. Fgf10 (talk) 15:09, 24 April 2020 (UTC)

• It doesn't take a rocket scientist to observe that cats tend to be more fastidious than dogs. That doesn't necessarily mean you want them walking on your dinner table, though. ←Baseball Bugs ^{What's up, Doc?} carrots→ 13:30, 23 April 2020 (UTC)
• Having had both cats and dogs, one very observable difference is that cats groom their coats, while dogs don't. Also, dogs like a playful rough-and-tumble with other dogs – which they make clear by inviting their playmates by vocalizing “rough! rough!”. This may get them pretty dirty. Adult cats may fight each other, but then it is not a play fight. If they have gotten dirty, most dogs will not mind getting a good wash, but many cats will resist vehemently. All this is strictly anecdotal and non-scientific. One could define a cleanliness measure by determining how much dirt can be collected from an animal's body, but how to define the population from which samples are taken? Should feral cats and dogs be included? Is it reasonable to compare dogs that go outside with cats that are kept indoors? And should the measure be absolute (in which case a St. Bernard will prove more dirty than a chihuahua) or relative to the animal‘s surface area? And are we really interested in just dirt? What about the shedding of hair? And so on. I doubt a scientist would undertake such a study in the face of such issues, unless there was an urgent need for an answer to some question – in which case the reason for the urgency would probably determine the operationalization of the concept.  --Lambiam 15:00, 23 April 2020 (UTC)

It has long intrigued me that we regard the cat behaviour of licking themselves all over as a sign of cleanliness. That wouldn't be the case if I did it. Probably more likely to be seen a sign of extreme weirdness and yuckiness. HiLo48 (talk) 18:53, 23 April 2020 (UTC)

We see it that way because it is actually part of their grooming/cleanliness practice, and if they don't do it, they don't get clean. Similarly, we wouldn't think of it as super clean to pick parasites out of each others hair, but certainly a lot of other primates would view that as part of keeping clean. For cats, part of why their tongue has evolved those backwards facing barbs is for the purpose of use in cleaning themselves. If you licked yourself that way, you don't have backwards barbs on your tongue, so you wouldn't effectively clean anything. --OuroborosCobra (talk) 18:57, 23 April 2020 (UTC)

CNBC reports air pollution drops by 180%

On April 23, an article on pollution during coronavirus situation said fine particle pollution in Manila went down by 180%. This might be an error. Or could it be theresult of calculating percent change as 100*(new amount-old amount)/(new amount), instead of 100*(new amt- old amount)/(old amt)? If that’s what it is, is this calculation standard, or becoming more common? Is it a more useful way to measure things?Rich (talk) 18:30, 23 April 2020 (UTC)

This teacher of Mathematics says it's utter nonsense. HiLo48 (talk) 18:36, 23 April 2020 (UTC)

Can you link to the article in question so we can look it over ourselves? --Jayron32 18:52, 23 April 2020 (UTC)

Here are two news articles giving the 180% figure: [2], [3]. The last one references a press release by the Environmental Pollution Studies Laboratory of the Institute of Environmental Science & Meteorology at the University of the Philippines.  --Lambiam 19:15, 23 April 2020 (UTC)

Let's for a moment assume they did mean 100*(new amount-old amount)/(new amount). Let us calculate. Put for brevity x for the old amount and y for the new amount. Then we get

180      =   100 (y − x) / y

180 y   =   100 y − 100 x

  80 y   =             − 100 x

       y   =            − 1.25 x.

Negative air pollution! Probably from burning negative oil. This article reports a decrease from the typical Thursday peak value of 38 μg/m³ to 7.1 μg/m³, which is a decrease by 81%. Probably, 180% was a typo for a rounded 80%.  --Lambiam 19:10, 23 April 2020 (UTC)

Yes but people typically will say there is a “50% off sale”, meaning the 50% is negative. So if -180%=100(y-x)/y, then -1.8=(y-x)/y, so -1.8y=y-x, so -2.8y=-x, so y=x/2.8. Since x was old amt and y is new amt that means if the old fine particulate was 38ug/m^3, then the new fine particulate is

amount is about 14ug/m^3, which i admit doesnt match the 7ug you found, but might have been correct on a different day.Rich (talk) 08:44, 24 April 2020 (UTC)

A quick review of the main page of www.cnbc.com (in the United States) shows this article: Photos show impact of temporary air pollution drops across the world from coronavirus lockdown. In that article, they make the more precisely-stated claim:

"In Philippines’ capital city, fine particulate matter — the world’s deadliest air pollutant — dropped by 180% since quarantine measures were imposed in Metro Manila on March 16, according to the Environmental Pollution Studies Laboratory of The Institute of Environmental Science and Meteorology."

With a little bit of follow-up, we can see the Environment and Pollution Studies Laboratory (the group who originated that "180%" number) are a research group in the Institute of Environmental Science and Meteorology at the University of the Philippines Diliman, the flagship campus of the University of the Philippines System and an organization of national repute.

I am still looking for the official source (e.g. a research paper, pre-print, or press-release) for the statement that CNBC is reporting.

Nimur (talk) 19:14, 23 April 2020 (UTC)

I assume when someone decided to publish those photos, they looked for something which sounded spectacular, but as the dates and ABS-CBN story shows, this is fairly "old news". Based on the ABS-CBN story linked above by Lambian [4]), the lack of any sign of this at [5], I guessed that social media may be where this originated.

Sure enough, scrolling through the history of this Facebook page @UPIESMEPSL, I found [6]. That's actually just a comment of a Facebook post [7] by @RCMakAirtoday. So I had a look at RCMakAirtoday and found this post of theirs on the ABS-CBN story, [8] where someone questioned the 180%. In response, they pointed to this story [9] where we find:

In calculating the percentage reduction, <name removed> said she got the difference between the value recorded during the enhanced community quarantine (ECQ) and the value two weeks before it was imposed.

“Then you divide the result by the value during the ECQ and and multiply it by 100,” she explained.

(20 less 7.1 results in a difference of 12. 19, which is then divided by 7.1. The result of 1.8 is then multiplied by 100, or a reduction by 181.6 percent)

Someone else responded questioning the 180% even with this explanation but there was no further followup. I don't know if there has been more discussion in other media outlets although I had a quick search and couldn't find anything.

BTW, whole looking into this, I found the figure is mentioned in 2020 Luzon enhanced community quarantine#Environmental. So if anyone is interested in getting into a debate over WP:CALC vs figures that are published in secondary sources, they could look into whether this needs to be changed. (Although you could just exclude any percentage figure.)

Nil Einne (talk) 06:54, 24 April 2020 (UTC)

So it's exactly what I wrote below. 89.172.105.179 (talk) 17:27, 24 April 2020 (UTC)

In a formula, the Facebook explanation amounts to 100×(old amount−new amount)/(new amount). What you wrote amounted to 100×(old amount−new amount)/(baseline level), where the baseline level is the oldest of all. The Facebook explanation is precisely the theory in the post that started this thread, except for the sign. If you replay the bit of elementary algebra I posted above, but replace "180" by "−180", you end up with y = 0.357 x, a reduction of about 64%. This still does not mesh with the Facebook explanation, but by itself it makes enough sense that it wouldn't have been questioned. I'm curious what the original press release said.  --Lambiam 18:40, 24 April 2020 (UTC)

No offense meant, but as i indicated in a note underneath your algebra above, a 180% drop can be interpreted as -180%, and my algebra in that note showed that it would make some kind of sense. As the OP, I naturally want people to know I understood the mathematics.Rich (talk) 20:06, 25 April 2020 (UTC)

They could mean that it decreased to an amount where it would have to increase by 180% to regain the original level. Sadly I see non-maths people mix that stuff up all the time even when they should know better. That would be 1/2.8 = 5/14 ~ 0.357 of the original amount (or a 64.3% decrease). Or maybe they mean it dropped by 80% (to 0.2 of the original amount) and the "1" is a typo. 89.172.105.179 (talk) 01:17, 24 April 2020 (UTC)

Perhaps the 180% is measured relative to an earlier and much lower-than-current baseline level, such as that in, say, 1950 (to take a random date). If the average level has tripled since 1950, then a 180% decrease would still leave it at 120% of the 1950 level. I stress this is just a conjecture, but it seems plausible to me that such a method might be used in some scientific context, though it would be a grave and confusing error to use the figure unexplained in a report destined for public consumption. {The poster formerly known as 87.81.230.195} 2.122.178.214 (talk) 06:25, 24 April 2020 (UTC)

If scientists worth their mettle measured a level, found it to be at 120% of a certain reference value and wanted to compare this new level with an earlier level at 300% of the same reference value by calculating the arithmetic difference of the two percentages, they would report a decrease by 180 percentage points. More likely though, if that reference value was so important that it is used as the yardstick, they'd give this unit a name, say PP₁₉₅₀, and report a decrease from 3.0 PP₁₉₅₀ to 1.2 PP₁₉₅₀.  --Lambiam 14:43, 24 April 2020 (UTC)

A drop of 100 percent would take it to 0. What a drop of 180 percent would be is anybody's guess. ←Baseball Bugs ^{What's up, Doc?} carrots→ 21:18, 25 April 2020 (UTC)

Under the usual definition of percentage drop, a drop of 100% would indeed bring it to zero. But under the following different definition, it would not: If percent drop in price for an item on sale meant 100*(new price-old price)/(new price), then a 100% drop would cut the price in half(which is what is normally called a 50% drop in price). Now suppose a business suit normally sells for $100.00. If the suit went on sale for $35.70, then under the new definition the price dropped by 180%, instead of 64.3%, since 100*(35.70-100)/35.70 = -180%. Note that 1.8*35.70+35.70 would bring the price back to $100.00. Rich (talk) 07:57, 26 April 2020 (UTC)

Is there any solid evidence of what CNBC actually meant, as opposed to trying to "figure it out"? ←Baseball Bugs ^{What's up, Doc?} carrots→ 12:25, 26 April 2020 (UTC)

??? I don't see any reason to think CNBC meant anything. They just followed what was reported. The way the number was derived is discussed above based on the Philippine Daily Inquirer source linked above who communicated with the researcher who came up with the number. Nil Einne (talk) 04:31, 27 April 2020 (UTC)

Which of the links specifically explains what the 180 is about? ←Baseball Bugs ^{What's up, Doc?} carrots→ 16:25, 27 April 2020 (UTC)

Deducing vegetation types

Hello. I am wondering if it is possible to deduce what kind of vegetation would exist in a given place that currently does not exist, for lack of habitat. I'm specifically referring to deducing what type of vegetation the Southern Hemisphere would have that would be analogous to the boreal forest/taiga and the temperate broadleaf deciduous forests of the Northern Hemisphere. If we look at a map of the world and maps of what kind vegetation types exist in different parts of the world, we can see that for the most part, all vegetation types that exist in the Northern Hemisphere have analogous types in the Southern Hemisphere as well. The specific flora may not be the same, but their adaptations, their form, their composition, will be very similar. This is true with two major exceptions, which I listed above.

So what I'm asking is, what would a Southern Hemisphere taiga and temperate deciduous forest look like? The reason that these ecosystems don't exist in the Southern Hemisphere is because of a lack of land at the right latitudes. So the north has extensive areas of taiga and deciduous forest because land exists for it in northern and eastern North America, in Russia, Siberia, Europe, and East Asia. No such land exists at the right latitudes in the south.

The reason I ask this is because I think it might be possible to deduce. The evergreen oaks of California have relatives in eastern North America that are evergreen and deciduous. The spruces, hemlocks, cedars, of the Pacific Northwest have relatives all over North America and Europe and Asia as well. So plants and trees of the same genus and families can certainly adapt to different climate types, as they have in the Northern Hemisphere. Can we make the same deduction that flora like Eucalyptus, Nothofagus, Podocarpus, can adapt to a humid continental climate and a subarctic climate like the Northern Hemisphere taiga and deciduous forests have? I know it's a stretch of the imagination, but I believe it might be possible. I just wonder if there are more educated views than mine on this topic. Thank you for your help.2600:1702:4000:5D40:C817:71F5:DF5A:F287 (talk) 19:22, 23 April 2020 (UTC)

Temperate deciduous forest exist in the Southern Hemisphere, it notes so in the lead section of that article. The closest Southern Hemisphere equivalent to taiga appears to be Magellanic subpolar forests, which aren't really taiga. As you note, there simply is no land in the Southern Hemisphere taiga belt, between the subpolar forests of Tierra del Fuego and the tundra of Antarctica is basically the Southern Ocean, where larch and spruce trees may find a wee bit hard to take hold. The closest to tiaga-like trees I can find in the southern hemisphere might be the Araucaria araucana, an alpine pine tree that grows in cold, dry areas of the Andes. --Jayron32 19:33, 23 April 2020 (UTC)

In the eucalyptus genus in Australia there is Eucalyptus pauciflora, commonly known as snow gum, thereby indicating where it grows. Rather than being at higher latitudes, it grows at higher altitudes, above 700 metres and up to a little over 2,000 metres (7,000 feet). It's known to survive temperatures down to −23 °C (−9 °F) and year-round frosts. It is, of course, evergreen, but can survive the loss of all its leaves and the death of all parts of the tree above ground (typically from fire) by re-sprouting from lignotubers. Given that there are over 700 species of eucalypt, and most seem to have evolved in quite recent geological times, the genus may well have been (and might still be) capable of creating a species to survive in even bleaker conditions, if such places existed. HiLo48 (talk) 00:07, 24 April 2020 (UTC)

The snow gum is the most common eucalypt grown in the UK, but there are about 35 others that can cope with the British weather. Not sure that they can reproduce themselves without human assistance though. Alansplodge (talk) 17:10, 27 April 2020 (UTC)