Let's assume that you mean activation patterns at the level of single cells. Aside from the ethical issues which make it virtually impossible to obtain the full set of data, there is also the fact that the exact timing of expression is one of the major ways in which development produces variability in phenotype and so can vary wildly between individuals. The closest we have right now might be HUBMAP [0] or HCA [1], but I don't think that those had as objectives covering multiple developmental timepoints.
There are various types of triggers for gene activation, some genes turn on/off all the time (housekeeping), some follow the circadian rythm, some are immediate response, some are specific to specific phases of cell division, some are persistently on all the time, etc ,etc. Not sure what type of chart you're looking for.
Thanks. Those modal categories of activations are a great start for organizing a visualization. I wonder what sort of patterns would show up. For example, what role does placement in a specific chromosome have (if at all!) in determining whether the gene is periodic, reactive, systemic, or developmental , etc.
> Not sure what type of chart you're looking for.
Just geek curiosity.
As others have said, a complete dataset for that is basically impossible. You would have to monitor every cell type in an individual from the moment of conception until death. Maybe in a couple hundred years we’ll have nanotech robots that could do that, and our overall morals and ideas of what constitutes ethical research will have changed enough that we allow the creation of such humans with these robots inside them.
Of course it is, and you could say the same with regard to mammalian brains in general. However the divergence starts very early in development (seven weeks) so is very big and very significant. By the time a human is born the brain is very different from a monkey's.
I mean it does add like a millisecond of unnecessary delay that wouldn't be there if it took the most efficient route. It's not much, but it does add up!
Separation of functions/concerns is not great, for starters.
The testes are dangerously exposed, the plumbing is convoluted and failure-prone (and doesn’t recover well from mechanical insults).
The prostate, which serves no function outside of reproduction, lies inline with the urethra and quite consistently loses flexibility and becomes enlarged with age, causing all sorts of structural issues impacting basic urological function.
Female reproductive vs urinary anatomy is largely physiologically distinct (proximity and UTI risk notwithstanding). Though plenty of room for improvement there too — starting with endometrial tissue being far too prolific. Fun fact: endometrial tissue can migrate to the brain and cause haemorrhaging in severe cases of endometriosis.
Plenty of room for improvement across the board, I’d say!
Hey, $DEITY did its absolute best with the constraints and the requirements. But hey, can't please everyone apparently. Be happy you can relieve yourself well past the intended warranty period. The parts were designed to be easily _aftermarket_ replaceable with sufficient advances in technology, retaining the fundamental design without changes.
Mother nature hates weak things that die (that's why they get eliminated), so if we can make it to interplanetary species before killing ourselves, that would be a pretty huge sign of success. At least on mother natures benchmark.
> The most successful at communicating their view that they are the most successful
To who? Other humans?
It's seagull mating season where I am, and I don't speak seagull, but I'm pretty sure one of the things they're trying to convey to their fellow seagulls is that they're extremely successful.
Can't argue with it either. They're very much alive, which is the best you can be in this particular competition.
So, the most successful at arrogance? In other words, the least successful at humility? Ironically, since humble and human share a common root. Just playing devil's advocate here, but what you propose is not a good metric to maximize.
Corn, albeit not an animal has been pretty successful in terms of number of individuals. Their bi-pedal underlings have cleared swathes of land and take meticulous care of their well-being so they can bask in the sun undisturbed.
I fail to see that, it's simply one of all other random mutations, it's just that this one has a big downstream effect of enabling other more complex mutations
Arguably much less successful since jellyfish have been around 700+ million years ands it’s not clear if humans will make it even the next couple thousand.
But the jury is still out on that one
You're positing the existence of a far more advanced lifeform than merely a clever monkey with pretensions, which then somehow created said monkeys. That's like saying that it's easy to become a millionaire, just start with a billion dollars.
That's not an explanation, you just replaced a problem with another harder one.
> HAR1A is active in the developing human brain between the 7th and 18th gestational weeks.
Anyone know of a resource that layouts the temporal activation patterns for all the genes for the life cycle of a human being?
Let's assume that you mean activation patterns at the level of single cells. Aside from the ethical issues which make it virtually impossible to obtain the full set of data, there is also the fact that the exact timing of expression is one of the major ways in which development produces variability in phenotype and so can vary wildly between individuals. The closest we have right now might be HUBMAP [0] or HCA [1], but I don't think that those had as objectives covering multiple developmental timepoints.
0. https://portal.hubmapconsortium.org/ 1. https://data.humancellatlas.org/
My group published a cell atlas of the developing human brain in 2023, giving gene expression in single cells from postconception week 5 to 13. It’s on github: https://github.com/linnarsson-lab/developing-human-brain
The NIH BRAIN initiative is working on the next generation of that, covering more timepoints and better spatial data.
Very cool work!
Thanks!
There are various types of triggers for gene activation, some genes turn on/off all the time (housekeeping), some follow the circadian rythm, some are immediate response, some are specific to specific phases of cell division, some are persistently on all the time, etc ,etc. Not sure what type of chart you're looking for.
Thanks. Those modal categories of activations are a great start for organizing a visualization. I wonder what sort of patterns would show up. For example, what role does placement in a specific chromosome have (if at all!) in determining whether the gene is periodic, reactive, systemic, or developmental , etc.
> Not sure what type of chart you're looking for. Just geek curiosity.
> some follow the circadian rythm
Oh no…
As someone who has an highly irregular sleeping pattern, do you know of any or where I can find more info on this?
This can't be done reliably but you may want to look at Tabula Sapiens which doe some of what you'd like. It's not an obvious problem in lots of ways.
Thanks. Suprised no one has made a visualization (even if it has gaps).
> It's not an obvious problem in lots of ways.
Care to expand on this?
Link for others:
https://www.science.org/doi/10.1126/science.abl4896
https://maayanlab.cloud/Harmonizome/dataset/Tabula+Sapiens+G...
I think people who aren’t already experts in this aren’t the right ones to try. For experts, the technical questions are very evident.
You may also like GTEX and the Human Protein Atlas (which also has gene expression data)
As others have said, a complete dataset for that is basically impossible. You would have to monitor every cell type in an individual from the moment of conception until death. Maybe in a couple hundred years we’ll have nanotech robots that could do that, and our overall morals and ideas of what constitutes ethical research will have changed enough that we allow the creation of such humans with these robots inside them.
Interesting. So, the human brain is the scaled-up monkey brain with significant architectural changes.
What did you think it was before you read this brief Wikipedia article?
Of course it is, and you could say the same with regard to mammalian brains in general. However the divergence starts very early in development (seven weeks) so is very big and very significant. By the time a human is born the brain is very different from a monkey's.
What was the alternative?
We didn’t have any. The project manager set it at 3 story points.
Scaling-up without significant architectural changes.
Or significant architectural changes without scaling up.
Or a single magic mutation.
And if we ran an experiment where we gave it to some apes…
Let’s observe their reactions to a big slab of obsidian.
huh, I always assumed they were metal-clad objects with something inside
wikipedia tells me they are machines, but not what they're made of
Like birds, let's say? There have been some articles on HN about how crows can be so intelligent with such a small (absolute size) brain.
Evolution would design the alternative to be something slightly less capable than the minimum. /s
Really, the likelihood is that these mutations must have had an impact that far outweighs their space in the genome.
That’s how all our close competition got murdered by Homo Sapiens. Just significant difference in mental abilities.
There has to be a car analogy for this.
Which is why we think we're the center of the universe.
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Implies intelligent design
I think its rather some mutations that produced more reelin and created the most successful animal in earth's history
I'd really rather liked it if that supposedly "intelligent" designer took a bit more time at designing the urogenital tract of human males.
I'd like it if the vagus nerve didn't do a loop around my neck for no particular reason. (Giraffes would probably like that even more)
Is that a big concern? I've been pretty happy with my vagus nerve functionality until now... although I have not given it much thought to be fair.
I'm going to stick my neck out and say no.
I mean it does add like a millisecond of unnecessary delay that wouldn't be there if it took the most efficient route. It's not much, but it does add up!
mine seems ok what version are you on
Y'all get firmware updates?!
I hope we don't vibe-evoluate....
It's actually worse, but with robust unit tests.
What's wrong with it?
Separation of functions/concerns is not great, for starters.
The testes are dangerously exposed, the plumbing is convoluted and failure-prone (and doesn’t recover well from mechanical insults).
The prostate, which serves no function outside of reproduction, lies inline with the urethra and quite consistently loses flexibility and becomes enlarged with age, causing all sorts of structural issues impacting basic urological function.
Female reproductive vs urinary anatomy is largely physiologically distinct (proximity and UTI risk notwithstanding). Though plenty of room for improvement there too — starting with endometrial tissue being far too prolific. Fun fact: endometrial tissue can migrate to the brain and cause haemorrhaging in severe cases of endometriosis.
Plenty of room for improvement across the board, I’d say!
Hey, $DEITY did its absolute best with the constraints and the requirements. But hey, can't please everyone apparently. Be happy you can relieve yourself well past the intended warranty period. The parts were designed to be easily _aftermarket_ replaceable with sufficient advances in technology, retaining the fundamental design without changes.
The most successful animal by what metric?
Tetris high scores, obviously
Mother nature hates weak things that die (that's why they get eliminated), so if we can make it to interplanetary species before killing ourselves, that would be a pretty huge sign of success. At least on mother natures benchmark.
Some of us don't spend days looking for food, don't die of cold, and survive the flu...
aaand we have Quake and Comand&Conquer - Red Alert
> aaand we have Quake and Comand&Conquer - Red Alert
Agreed, it would seem that evolutionary biology peaked in the late 90s then
As related in the documentary _The Matrix_.
The most successful at communicating their view that they are the most successful. Whether they are or not. But that means they are. By that metric.
Has another animal proposed they are more successful by a different metric?
Crickets?
> The most successful at communicating their view that they are the most successful
To who? Other humans?
It's seagull mating season where I am, and I don't speak seagull, but I'm pretty sure one of the things they're trying to convey to their fellow seagulls is that they're extremely successful.
Can't argue with it either. They're very much alive, which is the best you can be in this particular competition.
You sound like you’ve never been disdainfully stared at by a cat..
Really interesting article though. I’m very hopeful AI can help work out how all these things interact.
So, the most successful at arrogance? In other words, the least successful at humility? Ironically, since humble and human share a common root. Just playing devil's advocate here, but what you propose is not a good metric to maximize.
Corn, albeit not an animal has been pretty successful in terms of number of individuals. Their bi-pedal underlings have cleared swathes of land and take meticulous care of their well-being so they can bask in the sun undisturbed.
Until they are cut down and bombarded with micro waves by the very same bi-pedal underlings.
I fail to see that, it's simply one of all other random mutations, it's just that this one has a big downstream effect of enabling other more complex mutations
Merely implies a very good fitness function.
Yes. Though according this fitness function we're not necessarily more successful than a jellyfish or a tapeworm.
Arguably much less successful since jellyfish have been around 700+ million years ands it’s not clear if humans will make it even the next couple thousand. But the jury is still out on that one
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So Steely Dan documented this first?
You're positing the existence of a far more advanced lifeform than merely a clever monkey with pretensions, which then somehow created said monkeys. That's like saying that it's easy to become a millionaire, just start with a billion dollars.
That's not an explanation, you just replaced a problem with another harder one.
Intelligent mutations? How does that work?