What’s With NASGOF2 and House Ferret?

NASGOF2IsComing

If you’ve been watching my Twitter account, you’ve undoubtedly seen my parody of Game of Thrones over the last week: NASGOF2 is Coming/NASEM. And if you’re a Game of Thrones fan who works in or around gain-of-function/dual-use research of concern, then you likely giggled and nodded and probably planned to if not be at today’s meeting, at least watch it live on the internets.

If you’re a dual use person who isn’t familiar with Game of Thrones, I can’t help you–I don’t watch the show, either. All I know are the memes from the first season’s “Winter is Coming” advertisements, and I happen to both have Photoshop and be married to a fan of the show who is also one of the dual use experts. So when he offered his suggestion (instead of what I was working on), I jumped.

What was this remarkably funny suggestion? The profile of a ferret, because ferrets are what started this all.[note]Ron Fouchier and Yoshi Kawaoka published a series of experiments passing H5N1 through ferrets, ultimately making it very, very transmissable and very, very deadly. While DURC/GOF studies have been going on for a long time–Ramshaw’s mousepox is probably the most famous–this whole brouhaha can really be traced back to 2011/2012. You can read the start of it here.[/note] And because we’re talking the flu, naturally, the ferret is licking it’s sniffly nose (a detail I added and I’m grateful at least one person noticed and laughed about–oddly, not the husband).

So today, the ferrets have come home to do whatever the ferret equivalence of “roost” is, and the summary of a lot of hard work, arguing, publications, and general debate will be presented in front of a divided group of people. And me. I’ll be there with my gifs and giggles, rolling my eyes at the entire process and wondering if it’d help if I just made everyone read All I Really Need to Know I Learned in Kindergarten.


The Arrogance of Mitch McConnell and Friends– Or, Flaws in Assuming You Know God’s Will

Maybe it’s all part of a great big ineffable plan. All of it. You, me, him, everything. Some great big test to see if what you’ve built all works properly, eh? You start thinking: it can’t be a great cosmic game of chess, it has to be just very complicated Solitaire. And don’t bother to answer. If we could understand, we wouldn’t be us. Because it’s all — all — ”
INEFFABLE, said the figure feeding the ducks.

-Terry Pratchet and Neil Gaiman, Good Omens

 

As you probably know, I’m religious–Tibetan Buddhist, to be precise–so I do understand the idea of following religious moral rules even if that puts you sort of outside lockstep with modern society. I tend to view religion as a separate (complimentary) sphere to say, science. And while we do things differently across the international religious dateline, I know that a lot of Christian-variations feel the same way.

Part of the reason I know this is because I was raised Catholic.

And that’s why the arrogance of modern Christians is often breathtaking and baffling to me, that they think they know God’s will to the point they’re willing to legislate it. I mean, the last I looked, there were at least six different variations on what you could argue was God’s effort at the clearest commands, the 10 Commandments, which between Exodus and Deuteronomy actually come out to more like 17 Commandments.

But somehow they absolutely 100% know God’s word on fetal tissue used in research.

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When I was a kid, and Mom was still trying her best to raise me as a Good Catholic, I had a book called something like Why Does God Allow Bad Things to Happen. It was not, as I recall, Catholic-specific, but non-denominationally broad and probably bought as a form of self-defense.[note]Some personality traits are apparently set from an early age, and “why why why, but why, ok how?” was apparently present early on.[/note]

BankRobberThe book was full of examples of bad things God allowed to happen, and asked questions like “if God doesn’t want you to rob a bank, why doesn’t he just put a giant bag over the bank every night to keep everyone out?” and it was illustrated with something like a Ziploc dropped over a cartoon bank, and a cartoon robber trying to figure out how to get past it.

The answer was always a variation on a two themes: free will and the ineffable nature of God. In short, God wants us to have choices and for those choices to be made with the guidance of his wisdom for the circumstances of our lives, and we can’t actually know what God wants from us, or anyone else, because that Plan is ineffable–literally unable to be known by mortal minds–so we just do the best with the circumstances in front of us and trust that God will trust us, too.

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It seems to me the height of conceit and arrogance to assume a mortal human could understand the will of God, let alone be able to perfectly apply that will to modern life. If you believe, after all, that God can speak to you, where the N of you is Very Quite Large, then why couldn’t God simply reach into the mind of everyone and speak to all at once? Why are some people the special folks God speaks to–not really a question in Catholicism, which has its hierarchy of chatting, but a big, big issue in Protestantism, which holds that everyone has equal access to God.

The minute you start hearing God tell you things, you’re removing yourself from that equal access situation and insisting God has spoken to you and only you in mysterious ways.

What especially boggles me is this: say Marco Rubio continues his NO ABORTION EVER rhetoric, and continues to insist that this is because he knows God’s will. What’s to stop someone else from coming up and saying “sorry, but God spoke to me and said that abortion is okay, because it’s one of his tools for teaching–people learn different lessons from abortion, and hey, it’s also how he gets necessary donated tissues to researchers who will cure all kinds of diseases in His name!”

Now you have belief in God’s word being spoken to you in two separate people, with two separate belief systems, and…there’s no way to balance out who is right or not, short of God actually speaking to the entire world at once.

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Of course, none of this is really about religion. If it were, Mitch McConnell and his Republican cronies wouldn’t have voted to lift a moratorium on the use of donated fetal tissue from voluntary abortions in 1993. Yet many of the GOP members who voted for that medical research are now speaking out against Planned Parenthood, and it’s not because they’ve gotten more religious in the last 23 years. It’s because we’re gearing up to what is going to be a very contentious election cycle for the GOP, and as usual, politicians are pandering to the extreme members of their base–the ones who vote in primary elections–in an effort to secure money and, ultimately, nominations.

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DrinkThisMuchIn his sign-off from The Daily Show last night, Jon Stewart said “the best defense against bullshit is vigilance. So if you smell something, say something.” You have to decide what your own olfactory tolerance is, but at least for me, when people begin talking about the voice telling them to control the actions of everyone around them, I think a lot less God, a lot more charm and kool-aid.[note]Which, as my pal Laurie points out, was actually Flavor-Aid. Isn’t it weird how the name-brand became the cultural trope, and not the fact? There’s probably something incredibly meaningful and relevant in that.[/note]

If nothing else, ask yourself this: when the federal funds Planned Parenthood receives do not go towards abortion, what do Mitch McConnell, Ted Cruz, Rand Paul, and the rest of the GOP politicians gain from defunding Planned Parenthood?


June: National Ship Live Anthrax Month!

ff_anthrax_fbi4_fOkay, I know we’re a bit ahead of June, but we’re within shipping for June, right? And at this point, a rather concerning pattern of “shipping live anthrax” is developing.

Yep! It’s that time again! Er, yet another mishap involving a lab sending a viable select agent to someone who shouldn’t have it. Er, someones. In this case, an unknown number of private commercial labs in nine states. NINE! And that would be alarming in and of itself, without that whole one year ago gift that keeps on giving. Or the previous Oakland Children’s Hospital incident in 2004.

Well. I guess in defense of the CDC, who owns the previous mishaps, this was a Department of Defense lab “mishap.”

Skeptical Scully

Very seriously, it appears there’s an issue here beyond “oh oops, culture of carelessness” – we have three clear and separate incidents of live anthrax being shipped out to people who should not have live anthrax:

    2004 – Oakland Children’s Hospital (should have received inactivated anthrax from the CDC; never did figure out what they were doing with anthrax)
    2014 – Three in-house CDC labs (should have received inactivated anthrax)
    2015 – Unknown number of private, commercial labs (should have received inactivated anthrax for “field-based testing to identify biological threats in the environment”)

Can we perhaps maybe finally agree that we have a massive problem with research laboratories, select agents, and oh, I dunno, what’s the word I want? Culture? Accountability?

Oh right!

Safety.


Last night, after I was entirely too tired to edit this post, it came out that not only were multiple labs in nine U.S. states–California, Delaware, Maryland, New Jersey, New York, Tennessee, Texas, Virginia and Wisconsin–and South Korea. Osan Air Base, which is an American military base, but still. A statement from the base says up to 22 people in a training laboratory were exposed: Five active duty Air Force members, 10 active duty Army members, three civilian officials and four contractors, all of whom are now receiving prophylactic treatment. -KH, 28 May 2015

Everyone Likes to Fundraise When it Involves Penguins, Right?

As many of you know, Dr. Jacquelyn Gill been the target of some serious online abuse this past week, all for just saying “hey, that shirt’s not cool to wear to a global, history-making science event.” And yet, in addition to her normal job and troll patrol, she started up the Twitter hashtag #scishirt so that men & women could show folks what scientists wear to work every day – and create a better image for aspiring young scientists to see.

OLYMPUS DIGITAL CAMERASo, how about we turn it around and help out some of Jacquelyn’s younger scientists as a thank you? Dulcinea Groff and Kit Hamley are fundraising half their budget for a trip to the Falkland Islands to study climate change. See those cute penguins to the right? If we want to keep them around, we need more information about how their home is being affected by climate change – work few people are doing.

As of this writing – about 7:45pm ET on Thursday, November 20, Dulcinea and Kit are $300 shy of the halfway point. That $5,000 is their airfare to the Falklands. Can we hit that by midnight? One way to find out,..

Know Your Variants: Kikwit vs Gueckedou

This is an update of an earlier post, Know Your Species: SUDV vs EBOV.

When last we discussed the Democratic Republic of Congo outbreak of Ebola, it was presumed that it was actually an outbreak of the genus Ebolavirus, species Sudan ebolavirus (SUDV), largely because that’s what initial reports indicated. It hasn’t yet been clarified why there were reports of a positive test for SUDV and a positive test for a SUDV/EBOV mix (although I’ve heard speculations about earlier outbreak exposure), but what we do know is that on 2 September, the World Health Organization released the results from their virological analysis, showing that while the Ebola outbreak in the DRC was actually EBOV (Zaire ebolavirus),See Maganga G, Kapetshi J, Berthet N, Ilunga B, et al. Ebola Virus Disease in the Democratic Republic of Congo. NEJM 2014;DOI: 10.1056/NEJMoa1411099. it also was not linked to the on-going epidemic in West Africa.I say “was” because there is currently no known active transmission occurring, and the country is in the cool-down period, waiting for 42 days to pass in order to be declared virus-free.

This brings us back to my last post illustrating Ebola with kittehs.The language of the internet. For a quick refresher, all ebolaviruses are the family Filoviridae and the genus Ebolavirus. There are five different species within that genus: Reston ebolavirus (RESTV); Taï Forest ebolavirus (TAFV); Bundibugyo ebolavirus (BDBV); Sudan ebolavirus (SUDV); Zaire ebolavirus (EBOV).

And then we have a obligatory illustrative cute cat picture, because this is just likeWell, with significantly less cuddles. how cats are members of the same family (Felidae) and the same genus (Felis), but have a variety of different species.

Bv48v2KIQAAFYEE

But what does it mean when we learn that, in fact, it’s the same species of ebolavirus, but different variant? Simply put, it just means being even more specific: variant fits inside species fits inside genus fits inside family.Are you having flashbacks to biology class yet? (Inside order. Viruses stop at that point; for the curious, the family Filoviridae is part of the order Mononegavirales.)

Variants are written out in a specific way that tells you the virus name, the isolation host-suffix, country of sampling, year of sampling, variant designation, and isolate designation. It looks like this:

The current epidemic started with, it is presumed, a Guinea variant Guéckédou,The NEJM article discussing contact tracing back to a December case in Guéckédou. which would be written like this:

    Ebola virus H.sapiens-wt/GIN/2014/Gueckedou-XXXXX

This tells us that it’s an ebolavirus infecting homo sapiens (that’s us humans), wild type (it hasn’t been cultured), that it was sampled in Guinea in 2014, and that the variant is Guéckédou.There is a brief post on Virology Down Under about this, too. (Don’t worry about the isolate. That’s basically an individual code that’s given per sample, hence the name.)

Clearly, at this point, it becomes harder to do a one-to-one correlation between viruses and kitties, because kitties don’t break down into variants and isolates, but work with me a bit here. What cats do break down into is year they were born, litter, and even what they look like. So we do have ways we tell each individual Felis catus apart, even though we recognize them all as belonging to the genus Felis and species catus.

DifferentVariants80Per

In theory, we could roughly write these two cats out like this, utilizing their species, country of origin, year they were born, where they were born, and their name:

    F.catus-wt/USA/2005/Philadelphia-Zeus
    F.catus-ct/USA/2003/Cougar-ToledoYes, Toledo is from a place in Washington called Cougar. Honest.

Just as we can all look at Zeus and Toledo and see that they’re different domestic cats (but still clearly domestic cats, all the same), researchers can look at the virus they isolate from individuals and see that they’re different variants of the same strain. In the case of the outbreak in the DRC, it was a variant most closely related to the 1995 Kikwit Zaire ebolavirus outbreak.

So why does this matter? In an era of ebolanoia, it’s important to understand what it means when there’s an epidemic of Ebola in one area of the world and a new outbreak in another. People are quick to panic and assume that all outbreaks are connected to the epidemic, and equally quick to forget that ebolavirus has been cropping up sporadically for nearly 40 years in other parts of Africa. Knowing how scientists differentiate between strains and variants within viruses is another tool in being an educated and informed media consumer.