Biology friending meme?

[sciatrix]

It occurs to me that I have an awful lot of subscribers and friends who have varying interests and expertises in biology, psychology, and all sorts of related topics and ideas. 'Related' being read broadly here--if it touches on natural or social sciences and you want to share, please do.

Therefore, I thought I'd spin up a biology friending meme. What kind of background in the subject do you have? What things do you find interesting?

Comments

[felinejumper]

Ooooooh, yes please, I would love to have more thoughtful science & science-adjacent in my life/reading page.

Background wise, I flirt with molecular neuroscience & synthetic biology; on the more technical level, I am/have been interested in flexible signalling pathways & molecular influences on human experience (because I am a terrible reductionist even though I try not to be). I am also sort've in developmental biology -- or, rather, at the somewhat-newish confluence of synthetic biology applied to developmental biology, which is my current science/history research/writing project.

I reallllllllllllllyyyy like & am fascinated by how science is made of people, and am sort've...tentatively...making my way into history of science & science studies from research proper with questions about: the way people use science to define themselves & communities, how "scientists" function as this monolithic voice of authority ++ when that breaks down, and how that interacts with the legal system ([epi]genetic testing, psychological diagnoses vs biological, parentage, embodiment of social constructions into epigenetic mechanisms). Do I post about any of that? Not that often, but I have Big Ambitions about it all!

[sciatrix]

reductionism is the only way we can begin to unravel the great knots of understanding, though!

Synthetic biology and developmental biology--are we talking optogenetics here or...? Flexibility and context are my watchwords, intellectually speaking, although my own work focuses a little bit more into the periphery and how hormonal signaling works to let individuals integrate their internal and social contexts.

I would read all of these things! In particular, the embodiment of social constructions into epigenetic mechanisms topic--god, I feel like many biologists don't really appreciate how easily that can be done; that one I would volunteer to help co-write with you if you wanted, because it is such a fascinating topic.

On the other hand, what if you just posted a PARAGRAPH about these things and then we had an exceedingly nerdy discussion in the comments?

[siderea]

Oh, hey! This is me encouraging posting about those things! *encourage* *encourage*

What is synthetic biology?

[felinejumper]

hauls enormous soapbox out, clambers on An embarrassment of question riches!

Synthetic biology is, to sciatrix's question, definitely optogenetics-y! I think of it as using biological mechanisms for engineering ends. That might be to produce chemicals we make anyway more efficiently—Ginkgo Bioworks is a company that bioengineers yeast to produce specific chemicals (they also have an insanely cool laboratory space and do extremely nifty automation things).

There's also genetic circuits, wherein you use proteins and RNA to turn a cell into a logical circuit of on/off switches. The circuits are nominally-independent¹ of each other, so the cell is a tiny modular human-designed computer, but with all the super specific amazing things evolution has given us. So like —if we figure out the system that birds use on a cellular level to detect/navigate via magnetic fields², we could then lift those genes powered it and put them into our cells/organism of choice, and have, I dunno, slime mold that always pointed north. Or you can use them as detector: IF there's high levels of lead, THEN produce green protein, or IF you sense [x toxin in the gut], THEN do [something] to let us know.

The applications I'm MOST excited about though, and comparatively the least leery of, is using biology to report on itself. Because the cost & difficulty of synthesizing, sequencing, and modifying DNA has gone waaayyy down (source), DNA can act as a non-invasive, long term, and organism- or cell-comprehensive information storage mechanism. A favorite example of this idea does come out of the Boyden lab, actually, and it's this proposal for a "molecular ticker tape" for recording neural signalling. Here's the problem: we want to record as much information from as many neurons as possible about when they talk to each other. Ideally, we would know when every neuron was firing, and how much, and what other neurons they were synapsing to, and at the single cell level. Most methods rely on jamming some glass needles in there and recording from a group of 100 neurons at a time (temporally accurate, but non-comprehensive and not single cell) or fMRI-like things (temporally slow, also non-comprehensive and not single cell i have such a chip on my shoulder about fMRIs jeeez) or recording from a single cell in a dish. All really cool; all obviously limited in time and throughput. BUT WHAT IF.

WHAT IF. What if instead, you had a mouse where in each neuron of that mouse there was a very specific and engineered DNA polymerase. Mostly, this polymerase just chugs along, synthesizing some known and inert sequence. But then, the neuron gets activated and there's a massive ion flux where the voltage inside the cell goes from -70 mV to +40 mV, and our special polymerase's synthesis error rate is sensitive to ion changes (i.e. more positive ions, more errors!). And what you end up with³ is: DNA produced over the entirety of the cell's lifetime, that theoretically records every time that cell has fired. And you have that in every single one of the 71 million cells of the mouse, so you haven't been bottlenecked by your sample, and it isn't limited by "wow putting a rig on a mouse is a PAIN", and it isn't limited by even needing to pick a specific time: you have the whole record from birth to death. It's. So Cool. SO COOL. So00ooo00ooo cool.

And um. That's. Some information about synthetic biology! I am most familiar with the Boston biotech scene (hi, neighbor!) and also this is of course my particular lens, which is very much "relevant to my [former] lab or people in it" rather than "a review paper of the field."

<sup>1. I mean, though, ARE THEY REALLY probably not because nothing operates independently anywhoooo
2. Although, even saying this, I do think magnetic sensors are really cool, but I quail at the idea of reducing the extremely complex navigation system of a pigeon to "it's got magnetoparticles all balled up on one side that's it." I basically don't like genetic circuits conceptually because I think biology-as-is is...way better at making things than we are
3. if you solve like 100000000 technical issues with implementation shh we're talking concepts here!</sup>

[siderea]

AHA!

if you solve like 100000000 technical issues with implementation shh we're talking concepts here!

Well, yes, my first thought was, "How very clever. So having made these recordings of every neuron's entire lifetime in the brain of a mouse... how do you extract them from those neurons and read them back? For that matter, how do you keep track of which recording came from which neuron? And how do you capture how each neuron related physically to all the other neurons, i.e. fine morphology?"

But details, details. :)