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Rainyjim - I was asking what evidence you are using to come to the conclusion that the virus was engineered. Up to now you have not noted anything other than Dr Cottrell's views so it seemed to be based on that. So I'll ask again - based on your analysis of the GenBank sequences, what evidence is there for it being engineered in a lab?
Could 2019-nCov be engineered - sure, of course, but there actually needs to be some evidence to back up this claim (evidence that isn't almost instantly retracted or supported by the numerical importance of Event 201, Agenda 21, and 2/1 all having the same digits). It's hard to explain how equally non-nonsensical this evidence sounds to my ears as for layman it is all equally valid jargon gobbledygook.
Not that it matters, and it's all been said before, but my background is in Molecular Bio, BioChem, and Bioinformatics, over a decade in big pharma working on small molecule drug discovery. GSK projects has the side benefit of getting to go to the UK on occasion, whereas Merck visits put you in Jersey or Thousand Oaks for Amgen. I have friends who still work in the industry at these companies and also at Genentech/Rosche and Pfizer. But none of that really matters if we're actually discussing the virus.
So about that evidence...
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Again, information concerning “wacky” conspiracy theories is readily available for people who open their minds up.
https://www.justice.gov/opa/pr/harvard-u...na-related
Check the timeline.
Justice.gov. I’m sure this is all nonsense and conspiracy too. The dates, wuhan connection, dept of defense (dod) all fiction right?
https://www.darpa.mil/news-events/2018-01-04
DARPA will hold a Proposers Day on January 30, 2018, in Arlington, Virginia, to provide more information about PREEMPT and to answer questions from potential proposers. For details of the event, including registration requirements, visit: https://go.usa.gov/xnyzB. A full program description will be made available in a forthcoming Broad Agency Announcement.
DARPA, no connection with dod or us military right? Well here you go!
https://beta.sam.gov/search?keywords=Darpa&sort=-relevance&index=opp&is_active=true&page=1
Notice ID
DARPA-SN-20-17
Related Notice
Department/Ind. Agency
DEPARTMENT OF DEFENSE
Sub-tier
DEFENSE ADVANCED RESEARCH PROJECTS AGENCY (DARPA)
Office
DEF ADVANCED RESEARCH PROJECTS AGCY
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Big pharma rep huh ironyak? Ahhh, makes sense now! Lmao
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https://www.justice.gov/opa/pr/harvard-u...na-related
Justice.gov. I’m sure this is all nonsense and conspiracy too. The dates, wuhan connection, dept of defense (dod) all fiction right?
No, not fiction, it's a case against individuals engaged in research espionage. However unless you have evidence that the 21 (!?!?!?!) vials of biological material are somehow related to nCov, it could literally be anything. Again, given the millions of possible explanations of what's in those vials, why must it be nCov related?
I'm not sure what the DARPA PREEMPT links are supposed to imply. Care just to say it outright?
As for Honolulu, there was only one non-daily direct flight to China before so probably isn't going to make a huge difference in visitations from China. I'd probably be more worried about how the outbreak does in Japan (or god forbid South America which it could expand largely unchecked)
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islandlvng - Big pharma rep huh ironyak? Ahhh, makes sense now! Lmao
Ah no, I left the industry when I moved here, due in part to the conflicts I saw between doing good science and good business. You'd be amazed at how drugs and their testing are designed around how best to market them, in addition to any actual efficacy in treating a disease.
If I was repping for pharma wouldn't I want to drive up the fear and hysteria so me and my cronies could sell a cure? I'm sure all these companies are digging through the pipelines to find a drug they can get the market to believe can save the world - just keeping buying on the fear and hype! Can make a million if enough people die.
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So the reason I asked your background was two-fold: 1. I was curious why you are so sure of yourself in this matter and 2. So I know what jargon I can use when conversing with you.
This is an awkward format and venue for conveying this kind of information so please bare with my formatting.
1. I went to NCBI and downloaded all 55 of the 2019-nCov genomes and ran a multiple sequence alignment using the Clustal Omega tool to make a consensus sequence.
2. I blasted the consensus sequence using the Betacoronavirus genus as a filter - it returned BatCoV RaTG13 as most likely.
3. I ran another multiple sequence alignment using the consensus sequence and then BatCoV RaTG13 as the reference sequence.
4. The results were very similar to the Indian paper's alignment using SARS-GZ02 as the reference, i.e. the same insertions the Indian paper mentioned.
5. 3 of the insertions represent key changes in the receptor binding motif of the N-terminal domain.
6. A simple literature search reveals the N-terminal domain in coronaviruses encodes the part of the spike glycoprotein that mediates virus entry into the host.
7. All of the insertions share 100% identity with HIV. How would a Bat virus and HIV come into contact? I'm all for the emerging theories in the field of horizontal gene transfer as a driver of evolution, but I hope we can agree that spontaneous natural recombination between BatCoV RaTG13 and HIV would be unlikely, though not impossible.
So. That's my thought process. I understand its not a proof of artificial engineering. I'll repeat myself again: it’s too soon to say for sure but it looks like 2019-nCov was engineered in a lab.
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Can we assume if engineered in a lab would the virus potentially be more difficult to contain and treat? Or does it depend on how good of a bio-engineering job was performed?
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007, certainly. If that’s the case then the virus went from being harmless to humans to killing hundreds (at least) in the space of a couple months. I’d say that’s more difficult to contain and treat than just infecting bats.
That said, I don’t think you should expect some crazy scenario like a zombie epidemic ; D
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rainyjim - Thanks for taking the time to lay it out. Without seeing the actual sequences you BLASTed I would have to ask:
How long are they? Do they match other organisms 100% as well? What's the E-values involved? For the HIV matches are they all one strain, or do different inserts match different strains of HIV? Any evidence of common lab techniques for gene splicing/insertion?
You'd probably glean some interesting info from here as well - lots of people have run these sequences for themselves. No one seems to be able to justify choosing HIV as the definitive match when hundreds of other organisms match as well or better.
https://www.reddit.com/r/China_Flu/comme...cov_spike/
If you didn't notice, well-informed others also identified RaTG13 as the closest related strain, noting 2019-nCov and it likely had a common ancestor several decades back.
Punatic007 - Can we assume if engineered in a lab would the virus potentially be more difficult to contain and treat?
Not a fan of assuming, but IF it was engineered, it could have been made for a variety of research purposes, which may or may not increase its transmissiblility or lethality. IF it was designed as a bioweapon, it's really not much of one when compared to ebola, smallpox, polio, or many of the viruses mother nature has come up with. (or did she - quick, check the medieval viral genomes for 4 amino acid "HIV" inserts 
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How long are they?
They ranged from 18 to 36 bases
Do they match other organisms 100% as well?
Yes, many viruses were on the first page, at least 25 HIV genomes were all showing 100% identity.
What's the E-values involved?
2e-42 (edited). I'm not sure how valuable this will be to you, but I was using the nucleotide to nucleotide blast fwiw.
For the HIV matches are they all one strain, or do different inserts match different strains of HIV?
All of the inserts matched multiple strains at 100% identity.
Any evidence of common lab techniques for gene splicing/insertion? I don't see scars from any common restriction enzymes (but who knows, its not like I have all of them memorized), TALENs, ZFNs or CRISPR... not that you could find CRISPR scars unless maybe you found a PAM site, but of course you would find a PAM site for at least one CAS protein regardless of editing or not, somewhere nearby.
FWIW, I think focusing on the HIV issue is maybe a false flag of sorts. It doesn't really matter if the insertions were from HIV or any other virus that might have a host range including humans. What matters (IMHO) is if it was actually engineered or not. Don't take this as distancing myself from the HIV idea - i'm just trying to point out there are common motifs shared amongst many viruses that could help mediate viral entry into a human host. So, perhaps these insertions originated from HIV or maybe even another virus entirely - OR of course there is always the possibility this was just a natural recombination.
edited to update the E-value I was typing from memory, the value in bold is correct.
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