ababaian

9 ms·

1.
by ababaian 11mo ago
University of Toronto | Postdoc: Synthetic + Molecular Biology on Microplastics | ONSITE Toronto, ON We’re engineering enzymes to degrade microplastics using AI + high-throughput molecular biology. Join the Laboratory for RNA-Based Lifeform
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by ababaian 2y ago
The Laboratory for RNA-Based Lifeforms | University of Toronto | Full-Time | ONSITE | RNAlab.ca Howdy, The Laboratory of RNA-Based Lifeforms based out of UofT is looking for post-doctoral fellows, independent researchers, and/or a clou
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by ababaian 2y ago
Not sure I understand. Obelisks seems an inert descriptor to me, it has no connotation in the field so it's appropriately a blank slate.
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by ababaian 2y ago
How would they exist/maintain themselves without it's DNA counterpart?
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by ababaian 2y ago
Vanya thought that when you run them through the RNA folding software, it would give you these unusual straight rods which reminded him of Cleopatra's Needle (Obelisk, https://en.wikipedia.org/wiki/Cleopatra%27s_Ne
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by ababaian 2y ago
Absolutely, reading Selfish Gene in high school set me on the path to this type of exploration. Genes, in the pure abstract sense, are the unit by which we interrogate understand evolutionary change. There's a large grey area about the
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by ababaian 2y ago
I like to view it that we're all RNA-based lifeforms. Operationally: DNA, RNA, or other are just a vehicles which hold our information. This podcast RadioLab with Carl Zimmer (11m) I think captures the essence of the idea near perfectl
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by ababaian 2y ago
That's exactly what they are though, some piece of garbage RNA cells are producing. A lot of things meet that definition if you think about it.
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by ababaian 2y ago
It's not OT at all. It depends on what you mean exactly by LLM, but we use them all the time. ESMFold2 was an LLM [ https://www.science.org/doi/10.1126/science.ade2574 ] and was instrumental in advancing deep p
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by ababaian 2y ago
The classic phylogenetic classes are a fantastic model, but https://en.wikipedia.org/wiki/All_models_are_wrong :) Phylogeny is the study by which things relate to one another. There is a divergence point at which point
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by ababaian 2y ago
These are two distinct questions. Are Obelisks part of the self? If you think of the "host" as being made up by it's DNA, then these are not part of that set, since they are not found in DNA copies. Or is an organism it'
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by ababaian 2y ago
We certainly have the data, too much so actually. I should correct the statement to say, we have insufficiently developed _applied_ information theory. We know how to quantify homology, it just has not been applied to sufficient depth to th
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by ababaian 2y ago
What have Obelisks ever done to you? Our first reaction shouldn't be to kill everything we don't understand :'( Good pragmatic question though. It's not clear if any drugs up- or down-regulate Obelisk genome copy, you co
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by ababaian 2y ago
If you want the real mind-trip, try to think about how little we know about detecting "life" that is not based on nucleic acids.
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by ababaian 2y ago
Not that I know of, although this doesn't mean it isn't happening, it's something which has to be investigated in detail.
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by ababaian 2y ago
I understood as much. My point is that it's not clear to me that it will be a biologist, and not a statistician/mathematician, or developer/data-scientist that will be the one to sufficiently find the solution. There are lite
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by ababaian 2y ago
There's literally no experts on the subject.
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by ababaian 2y ago
I should certainly hope so.
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by ababaian 2y ago
Don't be a dick. It's totally normal to be skeptical and doubtful of some over-the-top claims. The onus is squarely on the person presenting the information to justify it. Your points about replication are accurate, but let's
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by ababaian 2y ago
Everyday I get to do this kind of research, I'm grateful to be the one doing it.
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by ababaian 2y ago
I think this is the journalist playing at the idea that we don't have a universally accepted definitions of "life", "virus", "viroids", "mobile genetic elements", "plasmids", or the oth
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by ababaian 2y ago
To the limits of where our understanding of how "entities" are connected to one another (homology). Yes, there's nothing like them. You could make an argument they are "viroid-like" and there's a deeper evoluti
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by ababaian 2y ago
The most limiting is our own imaginations. For the nuts and bolts: a class of really engaged and brilliant students at UofT recently documented the tools and methodology to go about characterizing Obelisks [ https://github.com&#x2
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by ababaian 2y ago
I hold no prejudice against the 'soft sciences', or for literature, or for music, or for athletics or for any other human pursuit which demands merit. I am genuinely curious as to how best to present the evidence. What would you l
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by ababaian 2y ago
What's your definition of replication?
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by ababaian 2y ago
It's possible, yes. But right now there is no evidence for Obelisks being linked to any disease, not even a phenotype in the cells carrying them. Keep in mind also that these elements likely interact with bacterial cells, so effects on
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by ababaian 2y ago
No clear ideas. But I would not be surprised if a dozen labs have jumped at the chance of trying to figure it out. So wait a year and ask again. Edit: Or better yet, try and figure it out for yourself. The tools to do this analysis are avai
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by ababaian 2y ago
There are preprints for all the papers [ https://www.biorxiv.org/content/10.1101/2024.01.20.576352v1 ], they're operationally the same. How were they not noticed before? Well that's how science works. Some
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by ababaian 2y ago
Aren't we all?
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by ababaian 2y ago
Sure, in a redutionistic sense. In the same light "Hepatitis Delta Virus" is an RNA plasmid, yet it causes liver cancer in humans. I err on the side that the simplicity of the genetic system should not deceive us into thinking it&

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