Although, there are some hits against HIV, there are also equally matching hits against bacteriophages; viruses that only target bacterias, they are completely unrelated to any viruses that target humans and animals.
Furthermore, the E value is around 170, that means that matches are statistically completely insignificant, meaning they happened by chance only. Such a high E value corresponds to a p-value of very, very close to 1 (https://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html).
These guys that published such a paper are either completely clueless or nefarious in trying to stir up conspiracy theories.
Both inserts 1 and 2 also match to Streptococcus phage, but a bacteriophage would of course not be such a bold claim as HIV matches are.
Also, be aware that because of the scientific interest in HIV, there are hundreds of HIV strains sequenced, a virus known for its mutation rate (especially in these two proteins gp120 and gag, as they are under pressure to mutate in order to evade the immunesystem). So in such a large library of protein sequences one is bound to find a match of a short 6 letter (amino acid) sequence. That's why E values exist to make a statement about the statistical significance.
I just did the experiment with my first name that is coincidentally 6 letters long, and lo and behold: a match to HIV env protein!
Has my first name now been designed by a bioweapons facility?
No, of course not. Your parents were designed by a bioweapons facility, so that they would choose that name.
And the fact that there's no known CoV with any of these inserts is quite intriguing.
In your opinion, do you think this kind of subterfuge could have been picked up by Dr. Eric Feigl-Ding or someone with a similar calibre, before broadcasting this preprint for wider consumption? Thanks.
But in the spirit of open-mindedness, what do I need to be convinced this is even interesting? First I want to see where on gp120 these inserts align to. Are they receptor/carbohydrate binding regions? Where do they map to on the coronavirus? These structures are known, so I don't know why this isn't in this manuscript.
If somehow this is engineered, I am honestly impressed that someone could take features from one protein and estimate how to engineer those same features in another protein altogether, with little homology. It's like engineering a monkey tail onto an elephant and somehow getting the elephant to swing through the trees.
1. A group of scientist have submitted a manuscript for review with a number of exceptionally (and uncharacteristically) bold claims.
2. A huge amount of scrutiny and additional reproducibility will necessarily need to be conducted before conclusions of this nature can be drawn.
3. This manuscript hasn't even passed the normal muster... a biorxiv post isn't much different than a Medium post. Claims like these require many eyes.
EDIT: My sentiment echoed by someone who know more than I https://twitter.com/DrEricDing/status/1223325141364592640?s=...
A great outcome would be if reputable scientists see this on HN or Twitter or learn about it through colleagues, and subsequently refute it or dismiss it as bad science.
Isn't it a waste of those eyes' time if it turns out to be false? When there are plenty of confirmed things they could be reading?
I just upvoted your comment at https://news.ycombinator.com/item?id=22206393.
It shouldn't be surprising that this new virus that is related to SARS can also be treated by HIV antiviral drugs.
Edit: by trust, I don’t mean blindly believe, but mean one should consider his comments seriously.
Don't trust anyone, just weigh their claims and their background. In this case, I have yet to see people with serious credentials in genomics make this claim (outside of the original scientists who published the paper relating it to HIV - IIT is impressive, but I don't really know how to assess their credentials writ large)
He graduated from The Johns Hopkins University with Honors in Public Health and Phi Beta Kappa. He then completed his dual doctorate in epidemiology and doctorate in nutrition, as the youngest graduate to complete his dual program at age 23 from Harvard SPH. Teaching at Harvard for over 15 years, he has advised and mentored 2 dozen students, and lectured in more than a dozen graduate and undergraduate courses, for which he received the Derek Bok Distinction in Teaching Award from Harvard College.
He's also calling for confirmation before everyone goes nuts:
It would seem that there were doubts around the content in the Wikipedia entry.
From 2K followers to 64K+ followers in less than 7 days!
"Information indicates that the People’s Republic of China (China) engaged during the reporting period in biological activities with potential dual-use applications, which raises concerns regarding its compliance with the BWC. In addition, the United States does not have sufficient information to determine whether China eliminated its assessed biological warfare (BW) program, as required under Article II of the Convention."
(That's followed by some more details, which you can read about in .)
Given this ongoing scrutiny, it would be very surprising if a smoking gun that the PRC has in fact been developing bioweapons were just swept under the rug.
Even if this is not, you just cannot trust them. They leak sars in their Beijing lab
“ In fact, the SARS virus had ‘escaped’ multiple times from a lab in Beijing, according to the Nature article.”
Good viruses kill after a few days of showing few (if any) symptoms so that they can maximise their spread.
This is the difference between epidemic and pandemic viral contagions.
We don't know yet if this virus has any long-term consequences. HIV would seem harmless if we estimated its effects after 1 month.
But I don't think bioweapons need to be deadly. If you can make a virus that kills 2% of people but shuts down global trade with your main economic competitor for example - that's quite useful (if you don't care for morality of course).
I'm not persuaded it's human-created, but it's a possibility.
The mortality rate will rapidly increase as it spreads to areas where it can overwhelm the local infrastructure. Not every country is capable of creating hospitals in 6 days like China, and China has a lot of experience responding to these crises since the Sars days.
We are only a month in, it's too early to really count mortality.
Further, do you assume that other members cannot read the preprint warning and decide for themselves? This strikes me as some sort of bizarre way to patronize the entire community.
Also, there are thousands of researchers studying this new virus. If this turns out to be an important finding, I can wait until it is validated. At this point, this paper looks poor quality, and it was a waste of time for me to click on it and read it.
Any relevant work on nCoV will be unreviewed at this point.
If it's true then the cause is an entirely different question.
> In Submissions
> Please don't do things to make titles stand out, like using uppercase or exclamation points, or saying how great an article is. It's implicit in submitting something that you think it's important.
Ignoring the odd word-choice, this ties in to the conspiracy theory that this was a Wuhan biolab containment leak.
I have been writing it off as a crackpot conspiracy until now, depending on peer review.
And what is the probability that this is not just a third type of major coronavirus, but in fact a secret bioweapon?
Knowing how commonly there are arguments about mixed up samples in the biolabs friends work in, I know where I would place my bets.
If both virus infect a cell simultaneously, there is a small possibility that something like this happens. I think it's so small that is not possible to do it in a laboratory even on purpose, and definitively not by accident but IANAB.
It is easier with other virus. For example mixing variants of flu, because they have (IIRC) 8 strands of DNA. There are avian, swine, human, others flu, and each of them has many subvariants. If some animal get infected with two variants at the same time, a cell may have a double infection and the viral offspring may have a mix.
But the mix is a mix of the strands of DNA, like 3 swine flu + 5 human flu. This is usual, but you must consider that there are millions and millions of animals in the wild and farms. It's more difficult to do it in a small lab, but IANAB.
The main difference is that the article claim that the usual coronavirus and the HIV parts are in a single strain, not a bunch of strains packed together.
China is not very reliable in gdp (one top guy told us to look at the electricity and we look at pollution). It is very hard to get stat.
So far touch wood no one died outside of China. The death rate should not be high unless the alternative saying hiv death rate after 1 month is 0%.
The conspiracy theory in a proper sense is accidentally leaked for an experiment, like sars virus leaked (later and during study) by Beijing level 3 lab.
"For non-scientists, if you see something posted from a site called BioRxiv, have some skepticism. It could be a fantastic paper! (I've used it!)--but. The site is for preprints, which means they haven't undergone peer review yet."
If this is an engineered virus, why as a race do we keep doing these things to ourselves? Do we _really_ think that weapons of mass destruction won't be turned on us? Is our hubris so high that we think no one else can replicate what we built?
Our military has to study this ...
But officially one has to study this as dual use as one has to prepare the natural evolution of say SARS to another strain. Can’t be sitting duck, let evolution run its course (2% death rate is not high but times 1.4 billion it is 28m people). Hence there is a case to study it, even change it. But then ...
Just like we should fight hiv. But then someone in china use human to experiment on it.
It is not there is no case. There are. Just stupidity of human ...
How do we know someone else hasn't already built what we've built? They don't exactly post these things on Facebook...
....which is why we have to build it too.
But, that is what the paper is saying. Extraordinary claims, extraordinary evidence is what I think. I feel the evidence here is quite small, but I'm not a bio-data-scientist.
That said: What are the priors on a "natural" virus erupting in the only city in China with a level 4 biohazard facility?
Just wanted to clarify the language here.
> Our analysis of the spike glycoprotein of 2019-nCoV revealed several interesting findings: First, we identified 4 unique inserts in the 2019-nCoV spike glycoprotein that are not present in any other coronavirus reported till date. To our surprise, all the 4 inserts in the 2019-nCoV mapped to short segments of amino acids in the HIV-1 gp120 and Gag among all annotated virus proteins in the NCBI database. This uncanny similarity of novel inserts in the 2019- nCoV spike protein to HIV-1 gp120 and Gag is unlikely to be fortuitous. Further, 3D modelling suggests that atleast 3 of the unique inserts which are non-contiguous in the primary protein sequence of the 2019-nCoV spike glycoprotein converge to constitute the key components of the receptor binding site. Of note, all the 4 inserts have pI values of around 10 that may facilitate virus-host interactions. Taken together, our findings suggest unconventional evolution of 2019-nCoV that warrants further investigation. Our work highlights novel evolutionary aspects of the 2019-nCoV and has implications on the pathogenesis and diagnosis of this virus.
So, maybe, maybe not. What's the likelihood of natural occurences resulting in these inserts ? Are these novel evolutionary aspects natural or engineered ?
Can't outright say "It was made in a lab" but can say "Something's new here".
> Because many viruses integrate their own genomes into the genomes of their host cells in order to replicate, mutagenesis caused by viral infections is a fairly common occurrence. Not all integrating viruses cause insertional mutagenesis, however.
This paper does seem to allege that these particular sets of insertions aren't via natural causes, though.
The real question is: how far are we from this becoming real ?
> Due to the presence of gp120 motifs in 2019-nCoV spike glycoprotein at its binding domain, we propose that these motif insertions could have provided an enhanced affinity towards host cell receptors. Further, this structural change might have also increased the range of host cells that 2019-nCoV can infect.
Evidence/article on it here:
Not only that, but just last year there was a case of a Chinese scientist who was banished from a Canadian bio lab level 4 for stealing virus samples, as well as a Harvard Academic found to be taking money from the Chinese gov to help develop the lab in Wuhan.
None of this proves the lab theory, but I do believe that with enough genetic analysis the truth will come out.
Intentional leaking? Sure, I think it's fair to consider that a conspiracy theory. But not accidental.
I agree that anything with intentional leaking is really far into conspiracy theory land, but the idea that it was a leak is not so crazy.
Of course, people usually use the term "conspiratorial" to be synonymous with "untrue" or even "patently absurd."
Recently available data shows that the first few cases happened in November.
The attempted and partially continued cover-up and downplaying of the outbreak does add a significant amount of credence to the theory.
You learn. But so far due to the source is far away from more reliable scientific base (hk in 2003), no one knows. Hence one have to reconstruct.
These might be wrong but investigation is needed. “ For his contemporaries, the ideas presented by Copernicus were not markedly easier to use than the geocentric theory and did not produce more accurate predictions of planetary positions. ”
Let the river flow. Dead water you can step in twice is not good water.
Does this lend support to the theory that the coronavirus was engineered in Wuhan's bioweapons laboratory?
> A lower-end estimate is 18 million and upper estimates find that some 45 million people died.
That's more than virtually all epidemics. Black Death, Spanish flu, and (maybe) HIV exceed it.
Happening by a lucky chance.
It's implying it was inserted on purpose... (Sorry had to look up that meaning.)
Throwing your hands up and saying "God must've done it!" when you don't have an immediate explanation and can't be bothered to do some research into one is the bad science part.
A religious flamewar on top of whatever else we've got here is the last thing this thread needs!
The issue from an HN moderation point of view isn't religion; it's religious flamewar, which is what internet arguments about religion—at least in large public forums—inevitably degrade into. Therefore we don't go there.
Well, if there are atheists who do so, they are in that respect specifically not like Thomas Nagel. While Nagel does endorse certain criticisms of the consensus models made by proponents of intelligent design (in the same breath as noting that those criticism have also been made by people not promoting intelligent design), he explicitly does not endorse the alternative explanation provided by intelligent design (and does also explicitly point to intelligent design as being motivated by religion.) So, it's beyond ludicrous to cite Nagel as not only a supporter of ID but support for the idea that ID is independent of religion.
Nagel’s also a philosopher best known for advancing the perspective that materialist objectivity is a limiting perspective, that is, he is a skeptic of the framework in which science operates. So he's even a worse example to use to make the argument (even if he supported ID, which he doesn't) that ID is within the domain of science.
For reference, here is an article Nagel wrote explaining the core of his book.
"This means that the scientific outlook, if it aspires to a more complete understanding of nature, must expand to include theories capable of explaining the appearance in the universe of mental phenomena and the subjective points of view in which they occur – theories of a different type from any we have seen so far."
That is totally ID in a nutshell. One may then go on to make theological inferences, or not, as Nagel does.
In which case, perhaps he thinks the current paradigm of science as methodological naturalism is lacking. This is the same perspective that ID promotes. If correct, then Nagel and ID are on the side of science.
At any rate, I propose the relationship between ID and religion is not quite as you believe it to be. Happy to discuss the topic further if you are interested.