Closure on the Obokata/STAP affair

I’ve been following the story of stimulus-triggered acquisition of pluripotency (STAP) cells with considerable interest, and there’s a good reason for that: from the very beginning, it contradicted how I’d always thought about cell states, and if it were true, I’d have to rethink a lot of things, which was vexing. But on the other hand, empirical results always trump mental models, so if the results held up, there was no question but that I’d have to go through that uncomfortable process of reorganizing my preconceptions. It would be OK, though, because there’d be a great prize at the end.

Well, it turns out that I don’t have to reboot my brain after all, because now that all the flailing about is over, STAP is a product of sloppiness and fakery, and is dead.

So here’s the controversy, and why I found it vexatious. We want to be able to specify cell states; in particular, we’d love to be able to take any cell from the human body, tickle it with a few specific signals, and see it throw away all of its historical constraints and become a different cell type altogether. In particular, the Holy Grail is to find the right combination of switches to cause any cell to become a pluripotent stem cell — the kind of cell we can then induce to become any other cell type we might need.

We know this can’t be impossible, and is probably even fairly simple, because we know that cells can do this already (well, to some degree; your body accomplishes this task by setting aside reserve populations of stem cells. It’s also likely that some cell types are so tightly locked in by the process of differentiation that their state is not reversible). The idea is that we just need to find the right combination of signals/genes — the right kind of key — and we can unlock the cell, and make it open to additional inductions that will allow us to manipulate it.

We have some idea of the shape of the key. Yamanaka identified four genes, Oct4, Sox2, cMyc, and Klf4, that when activated, switched cells into a pluripotent state, making induced pluripotent stem cells, or iPS cells. It works. The handicap right now is that we only have a kind of brute force method of switching those genes on, and two of them are oncogenic, so it’s as if we’ve got a rather clumsy key that opens the lock, but also damages it in unfortunate ways. The resolution to that problem, though, was learning how to finesse the genes — we need to figure out how to more delicately switch on the necessary genes by a way other than bluntly transfecting cells with copies of the genes that are always on.

Then along came Haruko Obokata, an investigator in Japan who announced that she could induce stem cells with simple, generic stress, such as by exposing them to acid or physically pushing on the cells. It was like saying she didn’t need a specific key, all you needed to do was shake the lock really hard, and it would spontaneously pop open. What, really? That just seems too simple. It would be phenomenally awesome if true, but it seemed unlikely. But then, I remember this one lab I worked in where all the publicly popular drugs, like ketamine, were kept locked in a drawer to which only the PI had a key…but the countertop wasn’t secured to the bench, so if you knew about it, you could just lift the top and get easy access. It was a backdoor to the goodies that was so stupid you couldn’t believe it existed, but it did.

Could it be that cells similarly had a stupid weakness that could be so easily exploited? The short answer is no; read the whole article by David Cyranoski.

But the paper1 that set out the fundamental technique was soon shot full of holes. There was plagiarized text in the article. Figures showed signs of manipulation, and some images were identical or nearly identical to those used later in the same paper and elsewhere to represent different experiments. More damning were genetic analyses that strongly suggested the cells were not what they were purported to be. And although deriving STAP cells was advertised as simple and straightforward, no one has yet been able to repeat the experiment.

Within the space of six months, Obokata was found guilty of misconduct by her institution; well-respected scientists, including RIKEN head Ryoji Noyori, bowed their heads in apology; and both papers were retracted. In the end, the evidence for STAP cells seemed so flimsy that observers began to ask where were the extra precautions and the ‘extraordinary proof’ that had been promised post-Hwang.

It sure would have been nice to have a simple technique for generating stem cells, but I have to confess to being a bit relieved. There’s the vindication of prior thinking and the value of incrementally improving our stem cell protocols, of course, but also, I’d personally rather that it weren’t trivial to switch my cells to a de-differentiated pluripotent state — that’s a recipe for easy cancer generation, too. It is somehow reassuring to think that evolution has shaped multi-cellular organisms to be somewhat resistant to spontaneously going all stem-celly under stress.


  1. originalantigenicsin says

    I really liked the part about problematic image manipulation. I think this issue is often neglected.

  2. firetree says

    Enjoyed your comment. It has taken 3 billions years to tangle up the balls of yarn we call differentiated cells. We refer to the process as evolution and the result as the biota. Saying, that “It is somehow reassuring to think that evolution has shaped multi-cellular organisms to be somewhat resistant to spontaneously going all stem-celly under stress”; is tantamount to saying it is surprising to find that it takes a lot of work to disassemble an adult sized Lego toy elephant and expect to end up with an miniature elephant all curled up in the last lego block. People know apoptosis is not a study in reductionism; the death process says nothing about organization and leaves only building blocks. Perhaps, the reason you and other serious scientists even considered Obakato’s work valid is that they must—that is their (your) profession. In contrast, another scientist you named was Yamanaka, who was looking for a key to a complex lock, and not trying to disassemble the entire lock mechanism.

  3. DonDueed says

    If you could induce arbitrary cells to become stem cells by merely applying pressure, couldn’t you cause an amputated limb to regrow just by pressing on the stump? Or maybe, if you did that, you might grow a new ear there?

    It almost sounds like this Obokata paper was elf-refuting on the face of it.

  4. says

    “It is somehow reassuring to think that evolution has shaped multi-cellular organisms to be somewhat resistant to spontaneously going all stem-celly under stress.”

    On the other hand, that sounds like a really interesting addition to the X-Men.

  5. says

    “…all you needed to do was shake the lock really hard, and it would spontaneously pop open.”

    Something like that works surprisingly often with padlocks.

  6. says

    I find it very hard to understand why an investigator would do such a thing. Obviously people are going to immediately try to replicate this and they will very quickly find out that it doesn’t work. If you know you can’t possibly get away with it, what is the motive? Different situation with obscure findings that aren’t going to attract much attention but will still get you a publication or a grant, but this is just bizarre.

  7. says

    Another illustration of the principle that every good Bayesian knows:

    Never trust an experiment until it has the support of a good theory.

    This often strikes people as contradicting the necessarily empirical basis of science, but it doesn’t – a ‘good theory’ is basically just a summary of prior empirical findings.

  8. ChasCPeterson says

    There’s a certain schadenfreude-like slightly disappointed satisfaction that comes from data-supported retention of one’s existing world-view.

  9. Callinectes says

    If something like this did work, could the triggers be weaponised? Forcing great swathes of a person’s somatic cells to turn pluripotent seems like nasty business.

  10. dannysichel says

    cervantes@9 – think of it like this.

    You’ve got a great theory, one that you’re positive is right. But none of your research corroborates it. So you decide to fudge the results, just a little bit. And people believe it! So you keep going. Because you’re sure that your results are actually correct, you don’t need to go back and fix things, right? Nobody will notice. It’ll be fine. Except you’re STILL not getting the results your theory predicts. So maybe you have to adjust the data a LITTLE bit more. Double down, you know?

    And then once you’ve done that, you might as well fill out the paper with some paragraphs from other places. Nobody will notice, and even if they do, your theory has to be right, so if anyone notices they’ll just let it slide!


  11. musiclover says

    This article was posted in7 July 2014,almost a month ago.
    Now the situation just a little changed.
    1 The flaw was found in “the mice genetic test” itself which has indicated the fatal errors in STAP theory.
    2 Now,Dr Obokata is trying to verify STAP theory in the lab with some surveillance cameras.

    After the verification finished,you may know whether the theory is true or false or partially true(false) .

    *This is comment as one of supporters of her.(not scientific comment.)
    It should be taken into account that Dr Obokata had not been allowed to enter her lab for a couple of month, even though she has claimed her innocence of falsifying the result.
    I understand many people has been irritated about this matter,but I would sincerely like to ask you to be patient a little more to judge herself as a researcher.

    Best regard.