SOP: Sadly Opaque Protocol

Heard in a recent(ish) meeting to define a tumour xenografting SOP to be used by three different labs:

PI 1 (Xenografting Expert): “The first thing you need to do when you get a new tumour is to determine if it’s actually a human tumour, or just a spontaneous mouse tumour”

PI 2 (Aspiring Xenografting Expert): “How?”

PI 1: “Oh, you just look down the microscope”

PI 2: “What stain do you use?”

PI 1: “No stain, you just look at it”

PI 2: “But how can you tell if it’s a mouse tumour?”

PI 1: “Because it looks like a mouse tumour”



PI 2: “Do you wait until you can detect a palpable mass, or do you re-graft after a set number of months?”

PI 1: “Palpable mass. Unless the mice are ready before that”

PI 2: “How can you tell if they’re ready?”

PI 1 (with a grin): “Well, they just look ready. I really can’t explain it any better than that”


I guess some of the Dark Arts just aren’t compatible with standardization, or with shortcuts to expertise…

About Cath@VWXYNot?

"one of the sillier science bloggers [...] I thought I should give a warning to the more staid members of the community." - Bob O'Hara, December 2010
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12 Responses to SOP: Sadly Opaque Protocol

  1. chall says:

    “It just looks ready” ….. oh so true!

    It’s really the smallest things that are the hardest to define when writing those SOPs … enough to drive me crazy sometimes (I had a discussion about “when an egg isn’t right” …. yeah…. “you’ll know when you see one. surely”)

  2. Bob O'H says:

    Pornography’s like that too.

    That’s what I’ve been told, anyway.

  3. Cath@VWXYNot? says:

    Chall, how’s that working out?!

    I remember that at the beginning of my PhD I had a hard time telling by sight if cells were transformed with the virus I was working on, but it didn’t take long to be able to just have a quick glance down the scope for a yes-no answer. It just takes time and practice!

    Bob, what, you know it when you see it? I’d say that’s almost certainly true, although obviously I have no personal experience whatsoever.

    p.s. thanks in advance for the fun Google hits!

    • chall says:

      well, I had to define some of it but then ended up putting in a foot note “for qualified personnel” etc…. ^^ It’s about that thing that “it should be obvious for everyone” but i tried to say it’s for anyone who has trained on it….difference…

    • Bob O'H says:

      Alas rel=nofollow means Google won’t see this. You need “porn” as a tag. Or perhaps “Jeffrey Archer”.

  4. ricardipus says:

    Back in the dim and distant past, a friend of mine who worked in an honest-to-goodness photograph developing shop told me the advice his boss had given him about mixing developer – which went something like this:

    “Mix it until it’s piss yellow”.

    Art, meet science.

    • Speaking physiologically, the shade of yellow-ness of your piss varies considerablydepending on how ‘water-loaded’ you are, and thus as a function of how much fluid you have been slurping down recently. Tricky for photography.

      I actually miss old-style developer-and-fix darkroom B&W photography. But I suppose I never had to work in a darkroom much, as opposed to messing about in one for fun.

      • ricardipus says:

        Is it terribly geeky to admit that I thought exactly the same thing when he told me that?

        In other words, it doesn’t matter much, just develop until it feels right. Kind of like my favourite recipe instruction: “cook until done”.

        • Cath@VWXYNot? says:

          If that was terribly geeky, then I’m a terrible geek!

          (Actually, I suspect it would be a universal response. I shall canvas some non-geeks later).

  5. For stuff like all those

    “the cells round up slightly when transformed and that’s how you can tell”

    – instructions, and other sort of opaque protocol stuff like

    “a something or other was used in a not obvious way to fashion a makeshift this-or-that”

    – I have always thought that video was the way to go, mainly because it mimics slightly the standard way you get taught stuff – watch someone else do it. Consequently the online Journal of Visualised Experiments seems like a great idea, though not sure how well they are doing.

  6. Mermaid says:

    Sadly Opaque Protocol – I have printed that out and have it on my bulletin board. I sadly now review many of these and I think your title is perfectly descriptive of too many of these documents.

    Similar instructions are common when trying to learn an old family recipe from my mom (who learned it from my dad’s mom), which really can’t be written down. “Add flour until it feels right” is a favourite, as is “Mix until it looks the right level of combined”. I am sure with practice I will know what it all means, but in the meantime the failed batches are depressing.

  7. Cath@VWXYNot? says:

    Video would definitely make scientific AND culinary protocols much more transparent! Mermaid, maybe you need to film your mom following her recipe!

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