remarking on the unremarkable
The goal of this Shiny app is to help use our intuitions about how our graphs typically look to estimate the effect size, and thus the required sample size. It s embedded below, but better viewed here: https://samjlord.shinyapps.io/visualsamplesizecalculator Warning: this is still in beta, and I need to confirm that all the calculations are indeed correct. [ ]
The basics of the scientific method—hypothesize, test, revise—rely on prediction. By forming a hypothesis only after seeing the data, we fail to severely test our ideas. I encourage cell biologists to preregister their study designs and statistical analyses. I also provide practical tutorials for making this a reality. Preregistration will Bolster Cell Biology Preregistration has [ ]
This is hilarious: https://arxiv.org/abs/2503.24254
My proposal for funding academic research science: instead of funding grants, just award financial prizes for good papers. Implementation Award half the prize upon publication (or preprint); award the second half upon an independent replication of the results, 25% to the original authors and 25% to the replicators. (If a good-faith replication attempt fails, the [ ]
Let me preface this post with the admission that I m likely wrong about my concerns about eLife s new model. I was actually opposed to preprints when I first heard about them in 2006! The Journal eLife and Mike Eisen announced it s new model for publishing papers: Very interesting and bold move. The goal is to [ ]
One of the worst feelings as a scientist is to realize that you performed n-1 of the controls you needed to really answer the question you re trying to solve. My #1 top recommendation when starting a new set of experiments is to write down a step-by-step plan. Include what controls you plan to do and [ ]
UPDATE: EMBO Reports article here and a write-up in Nature here. As I ve posted before and many others have noted, there is a serious problem with lack of adequate replication in many fields of science. The current peer review process is a dreadful combination of being both very fallible and also a huge hurdle to [ ]
2008 Tsien (predicted 2008) 2010 Suzuki Heck (predicted among others in 2010) 2012 Kobilka (among my 6 predictions in 2012) 2013 Higgs (among my 2 predictions in 2013) 2014 Moerner (among my 3 predictions in 2013); Betzig Hell (predicted among others in 2010) 2018 Allison (predicted in 2018) 2019 Goodenough (predicted 2019) 2020 [ ]
Medicine: Adenovirus vector vaccines Medicine (alternate): A second Nobel Prize for Ivermectin ;) Chemistry: Katalin Karikó, Drew Weissman, Ugur Sahin, Özlem Türeci, Robert Malone, for developing mRNA liposome vaccine technology. Peace: Mike Pence, for following his oath of office and standing up to pressure and physical threats to carry out his Constitutional duties [ ]
CRISPR: Jennifer Doudna, Emmanuelle Charpentier, Francisco Mojica, Virginijus Siksnys EDIT: Announcement. (This year, I’m only predicting the chemistry prize.)
Key components of the scientific process are: controls, avoiding bias, and replication. Most scientists are great at controls, but without the other two, we re simply not doing science. The lack independent samples (and thus improper inflation of n) and the failure to blind experiments are too common. The implications of these mistakes, especially when combined [ ]
Check out our newest preprint at arXiv: If your P value looks too good to be true, it probably is: Communicating reproducibility and variability in cell biology Lord, S. J.; Velle, K. B.; Mullins, R. D.; Fritz-Laylin, L. K. arXiv 2019, 1911.03509. https://arxiv.org/abs/1911.03509 UPDATE: Now published in JCB: https://doi.org/10.1083/jcb.202001064 I ve noticed a promising trend away from bar [ ]
OK, it s Nobel season again, and time for my annual blog post. (Quite literally this year, unfortunately.) Chemistry: Lithium-ion batteries (John Goodenough) EDIT: Yay! Finally! Medicine: DNA fingerprinting and blotting (Edwin Southern, Alec Jefferys, George Stark, Harry Towbin) Physics: Two-photon microscopy (Watt Webb, Winfried Denk, Jim Strickler) Last year, I correctly predicted Jim Allison.…
It s approaching Nobel season again, and here are my predictions: Chemistry: Cytoskeletal motor proteins (Ron Vale, Mike Sheetz, Jim Spudich) Medicine: T-cell and cancer immunotherapy (Jim Allison, Stephen Rosenberg, Philippa Marrack) Physics: Dark matter (Sandra Faber, Margaret Geller, Jerry Ostriker, Helen Quinn) I know I ve made this prediction before, but I think it s high time that the…
A few years ago, I compared different immersion oils. I concluded that Nikon A was the best for routine fluorescence because: (A) it had low autofluorescence, (B) it didn t smell, (C) it was low viscosity, and (D) the small plastic dropper bottles allowed for easy and clean application. Unfortunately, my two favorites, Nikon A and [ ]
I thought I d pass along one of my favorite tips: I have several of these Belkin Conserve Switch power strips in lab. I use them to turn on a scope and all its peripherals with a flip of one single switch! You can set one switch to power multiple strips. It s so much better than flipping [ ]
It s approaching Nobel season again, and here are my predictions: Chemistry: CRISPR (Doudna, Charpentier, Zhang) [awarded in 2020] Medicine: Unfolded protein response (Walter, Mori) Physics: Gravitational waves (Kip Thorne, Rainer Weiss, Ronald Drever, or maybe Barry Barish and the entire LIGO collaboration) Last year, I think the detection gravitational waves happened a little too late to…
Technical Instruments loaned me a Photometrics Prime95B back-thinned CMOS camera. I had demoed this camera before, but I was able to put it on our scope this time. Our spinning disk confocal has two camera ports, so I installed a tube lens that made the effective pixel size on the Prime95B approximately the same as [ ]
I bought a $500 camera from Point Grey that has the Sony IMX249 chip. It is a fairly large field of view with intermediate sized pixels (5.86 um), so it has a great dynamic range. The great thing is that it has low dark/read noise of 7-14 electrons per frame and a very high quantum efficiency of 80%. [ ]
I learned during my PhD that you should always have plastic sheeting in lab, because it might just save your equipment when/if a water leak happens. It saved one of our scopes recently, although I wasn t fast enough to prevent some water damage on an expensive camera. :( For less than $5, you can get some [ ]
UPDATE: Turns out the Simpsons were right once again Time for my 2016 Nobel Prize predictions: Chemistry: Lithium-ion batteries (John Goodenough, Stanley Whittingham, Akira Yoshino) [awarded in 2019] Medicine: T-cell receptor (James Allison [awarded in 2018], Ellis Reinherz, Philippa Marrack) Physics: Gravitational waves (Kip Thorne [awarded in 2017], Rainer Weiss [awarded in 2017], Ronald Drever,…
Electrically tunable lenses (ETLs) are polymeric or fluid-filled lenses that have a focal length that changes with an applied current. They have shown some great potential for microscopy, especially in fast, simple z-sweeps. The above figure shows the ~120 um range of focal depths an ETL installed between the camera and a 40x objective (from reference 1). Note [ ]
A while ago, I installed a very simple filter for the air vent in our scope room. It barely did anything, honestly. The filter is nothing more than a very loose mesh of fibers. So I ve bumped up to a 20x20x1 inch MERV13 pleated air filter with a paperboard frame. It fits perfectly between the vent and [ ]
(See my second post on this camera here.) Photometrics has released the Prime 95B, the first scientific CMOS camera with a back-thinned sensor. This means that the sensor is significantly more sensitive than the front-illuminated versions of other CMOS scientific cameras. So the Prime 95B has a 95% quantum efficiency, whereas other scientific CMOS cameras [ ]
We got a chance to try out a cool new label-free microscope from NanoLive: the 3D Cell Explorer. It works on a holographic tomography, by rotating a laser beam around the top of the sample and records many transmitted-light images. It then uses software to reconstruct the image with phase and even 3D information. The [ ]