index.scroll
Changed around line 216: Thankfully, many people are experimenting with better ways for sharing science.
- Scientific essays are intriguing because they are free to be everything papers are not: opinionated, informal, and dare I say, fun to read. Instead of every sentence being assembled by committee to avoid a reviewer’s wrath, essays offer an opportunity for unfettered scientific expression. We even already have a platform for distributing them: Twitter! Over the past few years, Twitter is where I’ve discovered my favorite scientific essays, some of which I’ll link here, here, and here. It doesn’t escape my attention that none of these were written by scientists in academia. While I’d love for this to change overnight, I realize that academics don’t have many tangible incentives to write. So for now, here’s my more concrete suggestion: PhD students should write part of their dissertation as a scientific essay.
+ Scientific essays are intriguing because they are free to be everything papers are not: opinionated, informal, and dare I say, fun to read. Instead of every sentence being assembled by committee to avoid a reviewer’s wrath, essays offer an opportunity for unfettered scientific expression. We even already have a platform for distributing them: Twitter! Over the past few years, Twitter is where I’ve discovered my favorite scientific essays, some of which I’ll link here, here, and here. It doesn’t escape my attention that none of these were written by scientists in academia. While I’d love for this to change overnight, I realize that academics don’t have many tangible incentives to write. So for now, here’s my more concrete suggestion: *PhD students should write part of their dissertation as a scientific essay*.
header.scroll
Changed around line 8: theme tufte
- container 800
+ container 800px
header.scroll
Changed around line 1
- importOnly
- buildHtml
- buildTxt
-
- metaTags
- theme tufte
-
- homeButton
- viewSourceButton
-
- container
- printTitle
- printDate
+ importOnly
+ buildHtml
+ buildTxt
+
+ metaTags
+ theme tufte
+
+ homeButton
+ viewSourceButton
+
+ container 800
+ printTitle
+ printDate
index.scroll
Changed around line 212: Here’s what I came up with: the ideal purpose of sharing science is to stimula
+ https://www.arcadia.science/ Arcadia
+ https://research.arcadiascience.com/reimagining-scientific-publishing open notebooks on PubPeer
+
+ http://jck.bio/learning-representations-of-life/ here
+ match 0
+ https://ldeming.posthaven.com/sequencing-is-the-new-microscope here
+ match 1
+ https://jsomers.net/i-should-have-loved-biology/ here
+ match 2
index.scroll
Changed around line 203: Happy exploring,
- Postscript: why write this?
+ # Postscript: why write this?
+
index.scroll
Changed around line 196: While live imaging followed by fixed in situ measurements might reveal how past
- Why should we care about the future? I recently watched a video speculating on when the last human would live. The main premise was that if we manage to avoid cataclysmic events that wipe out all of humanity (a big if, but stay with me), humans will conservatively survive for at least a million years. And if we solve global warming and space travel and other future issues, we may survive many, many orders of magnitude beyond that. But given that we’ve existed for only 200 thousand years, it’s exceedingly likely we live right at the start of human history rather than towards the end. On the cosmic scale of human civilization, we are still discovering the foundational technologies.
+ Why should we care about the future? I recently watched a video speculating on when the last human would live. The main premise was that if we manage to avoid cataclysmic events that wipe out all of humanity (a big if, but stay with me), humans will conservatively survive for at least a million years. And if we solve global warming and space travel and other future issues, we may survive many, many orders of magnitude beyond that. But given that we’ve existed for only 200 thousand years, it’s exceedingly likely we live right at the start of human history rather than towards the end. *On the cosmic scale of human civilization, we are still discovering the foundational technologies*.
index.scroll
Changed around line 197: While live imaging followed by fixed in situ measurements might reveal how past
+ https://youtu.be/LEENEFaVUzU when the last human would live
index.scroll
Changed around line 192: multimodal.png
- Early days
+ # Early days
+
index.scroll
Changed around line 192: multimodal.png
+ Early days
+ By synthesizing the very best of microscopy and sequencing, the in situ technologies of the future will let us perceive biology at unprecedented resolution. And the new discoveries they enable will propel us to create even more advanced technologies that make the future a brighter place.
+
+ Why should we care about the future? I recently watched a video speculating on when the last human would live. The main premise was that if we manage to avoid cataclysmic events that wipe out all of humanity (a big if, but stay with me), humans will conservatively survive for at least a million years. And if we solve global warming and space travel and other future issues, we may survive many, many orders of magnitude beyond that. But given that we’ve existed for only 200 thousand years, it’s exceedingly likely we live right at the start of human history rather than towards the end. On the cosmic scale of human civilization, we are still discovering the foundational technologies.
+
+ Happy exploring,
+
+ ZC
+
+ Postscript: why write this?
+ My original plan for my PhD dissertation was to staple all of my papers together. I know many people disagree with this practice, but this has always seemed patronizing to me. If I’ve published actual articles, why should I waste time re-writing them in a form nobody will read? Then some of my collaborators’ experiments failed, and during my newfound free time, I thought a lot about what it really means to share your science.
+
+ Here’s what I came up with: the ideal purpose of sharing science is to stimulate discussion, inspire new ideas, and in the best cases, shift the collective consciousness.
+
+ Though Science Twitter is known for its disagreements, it’s safe to say we all agree on one thing: our current system for sharing science does not live up to our ideals. We could discuss the issues with scientific journals all day, but the problem with actual papers is they are both longer and emptier than we would like. Modern papers are filled with pages and pages of supplementary figures to appease cantankerous reviewers, while devoid of the thought-provoking speculations and musings once found in older literature. Most PhD dissertations, on the other hand, are little more than glorified lab notebooks, written more for obsessive completeness than for readability to fellow scientists.
+
+ Thankfully, many people are experimenting with better ways for sharing science. Preprints let us share our work faster and theoretically open up peer review to the public, but are still largely beholden to the formatting and style whims of the traditional publishing system. Arcadia is piloting open notebooks on PubPeer, but for now, this is more at the institutional level rather than a choice an individual can make. Personally, I believe the long-term solution is not a single approach, but a buffet of options for every circumstance. Here, I’d like to advocate for a format that may appeal more to those in academia: the scientific essay.
+
+ Scientific essays are intriguing because they are free to be everything papers are not: opinionated, informal, and dare I say, fun to read. Instead of every sentence being assembled by committee to avoid a reviewer’s wrath, essays offer an opportunity for unfettered scientific expression. We even already have a platform for distributing them: Twitter! Over the past few years, Twitter is where I’ve discovered my favorite scientific essays, some of which I’ll link here, here, and here. It doesn’t escape my attention that none of these were written by scientists in academia. While I’d love for this to change overnight, I realize that academics don’t have many tangible incentives to write. So for now, here’s my more concrete suggestion: PhD students should write part of their dissertation as a scientific essay.
+
+ In the spirit of being the change I want to see, I have shared my own attempt here. It was certainly harder than I thought it would be! After years of writing papers, it was difficult to deprogram the jargon from my brain and write in a more accessible way. I also worry that people will think I’m boring or stupid or pretentious for believing my thoughts are worth sharing. But in the end, my goal was to write the essay I would’ve wanted to read as a 1st year grad student, and I feel I’ve put forth my best effort.
+
index.scroll
Changed around line 184: Unfortunately for temporal measurements, one technology we won’t see any time
+ https://www.nature.com/articles/s41592-018-0111-2 label-free microscopy
+
+ multimodal.png
+ caption Ounkomol et al. Nature Methods (2018)
+
+ While live imaging followed by fixed in situ measurements might reveal how past behavior affects cell state, we also want to learn how cell state predicts future behavior. Given that we can’t perform live imaging of a cell after fixed measurements, how can we accomplish this? One possibility is to train deep learning models that can foresee the future. Several years ago, Buggenthin and colleagues demonstrated that live imaging can be used to predict a stem cell’s lineage prior to the appearance of known molecular markers. In theory, you could train similar models for any cellular system with a heterogenous response, such as drug resistance or epigenetic reprogramming, and then perform in situ measurements at an early time point to identify which molecular states are most commonly associated with each predicted fate.
+ https://www.nature.com/articles/nmeth.4182 Buggenthin and colleagues