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We know the city where HIV first emerged

bbc.com

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Re: We know the city where HIV first emerged

#31

Post by masklinn »

bad_user wrote: post #30
nonbel wrote: post #23

Earlier quoted context omitted.

They get that date by assuming humans didn't bring it to the island though, they don't do anything to rule that out: >"Barring the possibility that humans introduced multiple species-specific SIV lineages to the wild monkey populations of Bioko, the mainland and island SIVdrl variants must have been evolving independently since Bioko became isolated ~10,000 yr B.P., and perhaps longer given the high levels of genetic…

On the other hand SIV isn't killing the monkeys or apes it infected, which makes likely a long coevolution.

Chimps and gorillas do get AIDS from SIV. IIRC they're relatively recent infections (though older than human HIV) and SIVgor actually descends from SIVcpz. Rhesus Macaques also get AIDS from SIV (SIV was originally discovered in AIDS-suffering macaques)

Re: We know the city where HIV first emerged

#32

Post by wlesieutre »

nonbel wrote: post #4

Simian AIDS was discovered after human AIDS. How do they know the jump didn't occur in reverse? Here is the first report of simian AIDS: "Examination of the species-specific annual mortality rates of macaques at the center during the previous 4 yr showed a significant increase in deaths in 1980 and 1981" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC393899/ Also, it is convenient they do not share the mcmc traces. Base…

Radiolab has an episode that covers some of this. It's a pretty good listen: http://www.radiolab.org/story/169879-patient-zero/

As far as any circular reasoning, they're just reiterating the claim in a different way. It's saying "Based on X data, we deduce Y. Y would explain why X happened."

Direct download if you don't want the Flash audio player: http://50.31.154.42/radiolab/radiolab111411.mp3?downloadId=5...

Re: We know the city where HIV first emerged

#33

Post by hodwik »

nonbel wrote: post #23
bad_user wrote: post #18

Earlier quoted context omitted.

Wikipedia links to an article stating that SIV has been present in monkeys and apes for at least 32000 years: http://www.nytimes.com/2010/09/17/health/17aids.html?_r=2&sr...

They get that date by assuming humans didn't bring it to the island though, they don't do anything to rule that out: >"Barring the possibility that humans introduced multiple species-specific SIV lineages to the wild monkey populations of Bioko, the mainland and island SIVdrl variants must have been evolving independently since Bioko became isolated ~10,000 yr B.P., and perhaps longer given the high levels of genetic…

>" longer given the high levels of genetic diversity seen within local SIV populations."

That is them ruling out that it came from humans.

Re: We know the city where HIV first emerged

#34

Post by fabulist »

caoilte wrote: post #28
hawkice wrote: post #3

Belgian control of the Congo was rife with pretty extreme abuse -- the obvious, often horrifying consequences of conquest. But the influx of ambitious businesspeople and capital which they claim started the wider outbreak of HIV, is a curious case. Often people will hand-wring about vague cultural factors, but this seems like one of the most concrete major international disasters caused by rapid gentrification and in…

_rapid gentrification_ of Congo whuhh??? Just 'caus it had a CIA sponsored coup, doesn't mean things got any better.

This would be the first time I've seen someone suggest gentrification makes things better.

Re: We know the city where HIV first emerged

#36

Post by adevine »

splouk wrote: post #35
nikatwork wrote: post #19

It's a morbid irony that HIV emerged from "Leopoldville" considering the other atrocities unleashed on Africa by Leopold II.

https://en.wikipedia.org/wiki/Leopold_II_of_Belgium If anyone else is curious like I was.

Wow, on the order of 10 million dead - half the population. That's Hitler-level genocide right there.

Re: We know the city where HIV first emerged

#37

Post by univalent »

anton_gogolev wrote: post #16
achille wrote: post #5

There's an excellent Radiolab Podcast that covers the same study, I'd highly recommend listening to it: * http://www.radiolab.org/story/169879-patient-zero/

There's also an updated version which briefly covers recent Ebola outbreak: http://www.radiolab.org/story/patient-zero-updated/

Thanks! I didn't know about the updated one. The original is one of my favorite episodes.

Re: We know the city where HIV first emerged

#38

Post by nikatwork »

adevine wrote: post #36
splouk wrote: post #35

Earlier quoted context omitted.

https://en.wikipedia.org/wiki/Leopold_II_of_Belgium If anyone else is curious like I was.

Wow, on the order of 10 million dead - half the population. That's Hitler-level genocide right there.

Workers who were short of the quotas might have their hands severed. Leopold II is a forgotten monster. Arguably it birthed the international human rights movement.

Re: We know the city where HIV first emerged

#39

Post by jgh »

jonchang wrote: post #27
nonbel wrote: post #26

Earlier quoted context omitted.

>"making MCMC quite difficult" They thinned 250 million steps to 500, then it sounds like they dropped the first 50-100 on top of that post-hoc (the 10-30% burn in gives an impression of manual tinkering). Obviously this is going to bring up questions regarding convergence, so reviewers should have asked for the diagnostic charts. This would probably have been better suited to ABC: https://en.wikipedia.org/wiki/Appro…

BEAST (which I assumed they used) is not very fast. 250 million generations on BEAST with the number of parameters they estimated and the size of their dataset would likely take about 2-4 weeks to run. Assuming they ran all 3 chains in parallel this is still a really long time to wait for an analysis. (edit: just checked, looks like they used 700+ sequences, so this is closer to 1-3 months of compute time) The standa…

Disclaimer: I don't know anything about this stuff.

Would they be able to run these MCMC chains in a way that perhaps progressively renders results at greater and greater accuracy? Then they could get some initial "low resolution" results and they wouldn't necessarily have to wait for weeks, but the full data will eventually be available.

Re: We know the city where HIV first emerged

#40

Post by douglasisshiny »

univalent wrote: post #37
anton_gogolev wrote: post #16

Earlier quoted context omitted.

There's also an updated version which briefly covers recent Ebola outbreak: http://www.radiolab.org/story/patient-zero-updated/

Thanks! I didn't know about the updated one. The original is one of my favorite episodes.

Same here, although the description of chimps hunting was a bit disturbing.
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