A big chunk of the oft-quoted ‘reproducibility crisis’ is due to people not doing experiments the same way it was done in the first place. It turns out that if you actually do the experiment the way it was done in the first place, it reproduces. Case-and-point. - ThreadSky

hitenmadhani.bsky.social • 5 days ago

A big chunk of the oft-quoted ‘reproducibility crisis’ is due to people not doing experiments the same way it was done in the first place. It turns out that if you actually do the experiment the way it was done in the first place, it reproduces. Case-and-point.

Reposted from Coleen Murphy

Highlighting this new paper NOT by my lab, but by Andres Vidal-Gadea's lab: doi.org/10.7554/eLif...
#Celegans - more to say on this later 🧪

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navinpokala.bsky.social•5 days ago

Of course, sometimes the irreproducibility is coming from inside the lab! #calcium

hitenmadhani.bsky.social•4 days ago

😱

navinpokala.bsky.social•4 days ago

Yup. Ringer’s lazy assistant kept giving him tap water as distilled. When assistant went on vacation, Ringer had to make his own (bona fide) distilled water … and things didn’t work anymore. Testament to Ringer’s rigor that he figured out it was the calcium.

rossbiology.bsky.social•5 days ago

Well, yes, if methods are perfectly described and if identical reagents made available, then - excepting stochasticity - experiments should reproduce. How should we go about addressing the "ifs?"

c0nc0rdance.bsky.social•5 days ago

There are some methodological variables that are unintentional/hard to eliminate & rigorous science does require replication without an expectation of perfect agreement.

merz.bsky.social•5 days ago

It is not always obvious what actually *is* a methodological variable, until well after the early publications. The discovery that AlF can form a transition state analog with GDP is a case in point. And that discovery in turn led to huge advances.
½

merz.bsky.social•5 days ago

The uncontrolled variable: in vitro reactions were run in competing labs using either disposable plastic tubes, or re-usable glass ones, giving opposite results. The glass tubes (containing Fl) were washed with Alconox detergernt (Al).
2/2

https://pubmed.ncbi.nlm.nih.gov/9382787/

merz.bsky.social•5 days ago

Addendum: commercial preps of nucleotide triphosphate also frequently contained Al as a contaminating ion, further complicating efforts to disentangle what was happening. None of this was obvious, a priori.

merz.bsky.social•5 days ago

I think it was @stroupe.net who first told me about this.

stroupe.net•5 days ago

Certainly commercial nucleotide products are pretty messy. I distinctly remember a paper noting that their "raw" GDP contained a substance "chromatographically indistinguishable from GTP"...

mcduncanlab.bsky.social•5 days ago

We had a methodological variable when we moved from UNC to UM. Suddenly, starving cells for glucose did not induce cell surface clearing.

The difference turned out to be amino acid solubility in our stock solutions.

mcduncanlab.bsky.social•5 days ago

At NC (and also UCLA), the amino acid stock solutions always had a precipitate. In hindsight, it sounds crazy that was what we were using for AA's, but that was how AA's looked when I was a postdoc, why would I change it as a new PI.

mcduncanlab.bsky.social•5 days ago

At UM, the AA stock solutions didn't precipitate, so the cells were being grown in much higher AA than at UNC. I think this induced some GCN pathway that interferes with whatever signaling induces endocytosis in glucose starvation.

mcduncanlab.bsky.social•5 days ago

It took a while to figure it out, in part, because we'd moved our AA stock bottles with us from UNC, so it was only as people started using new AA stock that the problem emerged.

Thankfully, we had collaborators who had it working, and we were able to compare media formulations and switch over.

ctmurphy1.bsky.social•5 days ago

Following directions is hard

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