Posted by jbotz 6 hours ago
In any case, what would you expect from such a platform? That would help with recomendations.
I think the best place to discuss most things nowadays is the real world, but it takes time to build connections in the real world. HN is still a place of real productive discussions but not without a lot of moderation and even so it's still barely functional.
This is always a problem when one tries to view biology through an engineering lens. The functions we see today emerged well after the genes themselves started on the path that allowed them to support these specific functions in us. Nor are the genes restricted to exactly identical functions even when their sequence is identical. The context of each cell matters.
Rather than beginning from external function and going down to find energy, replication and cancer/escape from multicellularity as factors affecting these organ’s behavior, it’s a lot better to go cell up, where metabolism, DNA replication, waste clearance, and cell to cell communication and cell-microenvironment sensing are all constantly having to be balanced.
The functions we see from ensembles of cells are composed of these cell level behaviors multiplexing.
And when we look at the eukaryotic cell, we don’t just see linear DNA. We also see mitochondria. Our mitochondria reproduce and proliferate in all cells, depending on energy requirements. The process also produces a lot of reactive oxygen species which need to be kept tamped down to prevent damage.
And the mitochondrial endosymbiotic event also potentially explains why we have linear DNA in a separate compartment. From first eukaryotic common ancestor (FECA) to the last eukaryotic common ancestor (LECA), you had two genomes inside one cell, and by the time we got to LECA a bunch of DNA from the alphaproteobacter that became mitochondria migrated to the core genome, leaving the mitochondrial genome to remain circular.
The exact time and reason for linearization of DNA is (as yet) lost to deep time. But we can see a path from two circular genomes to one linear one circular and construct a fairly believable hypothesis to why you got linearization: as cell type increased, you needed more transcript copies, and access to different transcripts at different times at different rates. A linear genome is much better able to accommodate these requirements. And this has resulted in prokaryotes also partially or fully linearizing some of their genomic material when the need arises (Cyanobacteria, the first autotrophs, have some strains with linear ends, and Lyme disease and streptococcus also break from full circularity).
This linearization is also critical for mitosis and meiosis.
As far as the exact causal chain, we are, at the moment, groping in the blind, since the FECA->LECA transition occurred some 2 billion years ago, and we don’t have candidate fossils. They are reconstructed from genomic puzzle pieces, which is why we have these holes.
In that transition timetable, it is possible commitments were made that shape everything we see today.
Beyond doubt, those commitments had to thread everything a single cell has to thread.
And then came multicellularity, which had its own tradeoffs.
Teleology doesn’t help because none of these early commitments were being made with the specifics of our current lifestyle in mind, or even that complex beings like us could exist.
Evolution is a blind watchmaker. Ignore that and you’ll end up with nice sounding ideas that may not quite fit what we see.
Basically every flavor compound in an herb or spice we eat is a poison directed at insects, microbes, or other creatures. (much less every medicinal or psychoactive compound found in nature)
This is common in evolutionary algorithms anyway so it's notable we don't see it in nature, at least not in the form of extended lifespan perhaps measured by average lifetime heart beats. It's easy to imagine a world where nature might want to keep the alpha lion around longer than the others so it can have more offspring, for example.
There is, if there were no advantage a whole lot more species would die immediately after reproduction like the octopus.
Many simpler organisms are vaguely immortal.
>It's easy to imagine a world where nature might want to keep the alpha lion around longer than the others so it can have more offspring, for example.
The utility of genetic diversity puts a lot of pressure against this.
We can expect evolution to do the right thing for the genes. Not for us.
That's it. That's the entire thing. Plus some nuance about things that self-replicate faster than other things...
It occurs at all levels. Amyloid protein in Alzheimer's patients is self-replicating. So are cells. So are individual parts of cells. Sometimes things replicate by being parts of a larger thing that replicates, sometimes they don't. It's all one big chaotic tangled mess with no particular purpose or design. Human cells evolve, so do humans, so do human societies. So do rocks.
And amyloid protein doesn't self-replicate. An instance of the misfolded form causes other folded proteins of the same type to transition to the misfolded form. It's a form of catalysis, not self-replication.
I greatly resent having to be a biological organism and subject to all the poor engineering and design decisions that entails.
And then this:
Brains. After you reach adulthood, neurons don’t divide. If some of your neurons die—which happens every day—then they’re gone. If you get a brain injury, the other neurons will try to “learn around” the injury, but the neurons themselves are never replaced.
Loss of neurons isn't disastrous as long as it's not too many. Babies are born with several times more neurons than children have, and spend a few months letting all the useless ones die. Apparently it's better to start with a random tangle and prune it to shape (like cutting a box hedge) than to make a hedge grow in a box shape to begin with.
And IIRC brains can grow more neurons under some circumstances (certain drugs?) - they just normally don't.
https://www.sciencedirect.com/science/article/pii/S193459092...
It may seem odd to demote correctness in that way, but it doesn't mean we value incorrectness. Correctness is good, just not at the top of the hierarchy. Curiosity (specifically, intellectual curiosity) is what we're optimizing for: https://hn.algolia.com/?dateRange=all&page=0&prefix=true&sor....
We value the freedom to meander curiously. Some paths turn out to be wrong [1], but that is how new things are learned, and it's a good way to spend time. People are allowed to be wrong on HN as part of figuring out what's true [2]. Truth is crucial, but one ought not to squeeze the throat of speculation so tightly that wrong things aren't allowed to be spoken, or fun to be had.
[1] not saying the OP is right or wrong - I have no idea - but the article looks like the fun kind of meandering that has a place here.
Edit: https://www.etymonline.com/search?q=meander - "from Greek Maiandros, name of a river in Caria noted for its winding course". Is there a better website than etymonline?
[2] https://hn.algolia.com/?dateRange=all&page=0&prefix=false&qu...