Ffdmatt t1_isgfk3v wrote
Reply to comment by Ferociousfeind in When it's said 99.9% of human DNA is the same in all humans, is this referring to only coding DNA or both coding and non-coding DNA combined? by PeanutSalsa
Would it be better to say that we use the same base pieces for the code? We start with the same gene set and build from there. Mutations and differences in combinations are bound to occur (as random distribution helps prepare for change and survival anyway), but after millions of years I'd imagine a ton of the "formulas" end up the same or similar, simply because it's the most optimal combination for the function.
halfhalfnhalf t1_isghm3t wrote
It's not that our cells are optimally designed, it's that they are so intricate that any major deviation from the genome results in a non-viable organism.
Multi-cellular organisms are SO complex that there are extremely tight tolerances on most of their parts. A tiny deviation in one protein can mean the organism won't ever make it past fertilization. Most of those gene combinations were eliminated from the pool eons ago.
The 0.1% or whatever difference between humans is the wiggle room that can result in a viable human.
regular_modern_girl t1_ishp1le wrote
yeah genes are just sequences of codons which each correspond to an amino acid subunit of a protein, certain amino acids have to be in just the right places in a protein’s structure for it to not end up as a useless squiggly mess (useless at best, potentially toxic at worst, just look at the formation of amyloid plaques), and if even one base pair is off in DNA, that changes a given codon to another one (meaning there will be the wrong amino acid, and the whole protein is probably ruined).
I do 3D printing, and kind of think protein synthesis and folding as similar in a certain way; when you’re 3D printing something (on a FDM printer, at least), all it takes is one little crossing of one layer being set down wrong, and before you know it, you have an unrecognizable mass of plastic spaghetti that doesn’t resemble what you were originally trying to print in the slightest, and you have no choice but to toss the whole thing in the recycle bin and start over. The problem is, with misfolded proteins there sometimes isn’t any “starting over” if they’re essential enough to a cell, and there often isn’t an analogue to a recycle bin either (so some misfolded proteins can just keep accumulating until there’s severe disease).
Basically, in both cases all it takes is one small error, and an entire print/protein ceases to be functional.
This is why mutations that lead to disease are generally more common than ones which end up being beneficial (as for an organism to benefit, it basically takes the altered protein actually being better than the original, or good for something else).
Splatulance t1_isiapmr wrote
Some dna isn't transcribed but has a significant impact on transcription/expression. Transcription is like the publicly exposed API
regular_modern_girl t1_islczzm wrote
Yeah I was kind of thinking how errors in promoters could be thought of like issues in the g-code (the programming language that 3D printers, laser cutters, etc. use) leading to certain layers not being printed and stuff like that.
Of course one aspect where this metaphor really breaks down is the time it takes to 3D print something versus a protein to fold into shape; the former takes anywhere from minutes to hours (depending on the size of the print, resolution, etc.), whereas the latter somehow occurs in just fractions of a second (and the mechanics of exactly how it happens so fast is still not entirely clear, which is why we still don’t really have accurate computer models of protein folding, and the field of protein engineering is still fairly nascent. Once we do have a better understanding, synthetic biology will enter a new age in which it will become not only possible to use tools like CRISPR Cas9 to edit genomes by inserting or removing pre-existing genes like we do now, but actually build entirely new genes from scratch, for novel proteins that have never existed in nature. We’ll basically have the most powerful pre-existing system for nano-engineering right at our fingertips).
Georgie_Leech t1_isgggwj wrote
That's just how DNA is though, it doesn't tell us anything about how similar it is across a given population. Like, you wouldn't make the observation that "most books are written transcriptions of language."
Muroid t1_isggua6 wrote
That’s really a better description of all DNA-utilizing life.
Humans are remarkably similar in their genetic code even by that baseline.
Quantum-Carrot t1_isgvs4l wrote
You also have to take into account epigenetics, like DNA methylation and histone modifications.
> I'd imagine a ton of the "formulas" end up the same or similar, simply because it's the most optimal combination for the function.
This happens even between different species. It's called convergent evolution.
regular_modern_girl t1_ishnfh1 wrote
I’ve brought this up several times here, but evolution doesn’t “optimize” things (at least in the way an intelligent being would), it’s a mindless process that stumbles onto “good enough” solutions for keeping organisms alive long enough to reproduce in a given niche. If evolution optimized things, we’d probably have really different anatomy.
adc34 t1_isgl231 wrote
I don't agree with so much in your comment, that I have to reply, sorry. First of all, we don't start with the same gene set. Ok, maybe we did 4 billions years ago, but it's a pure speculation and we don't have any instruments to infer anything valuable from the fact that 'there was a single organism at some point of time from which everything evolved'. I'm pretty sure the whole picture is much-much more complicated. As for humans, I can say with a high confidence that there was not a single human being evolved that become the genesis of all humans. Specification is a complex thing and there's always a period of hybridisations with closely related species. I won't delve into it deeper, but some fishes even rely on other species for their reproduction. This fish is actually really amazing and there's a lot to unpack with its reproduction. Secondly, there's no such thing as random distribution that does something for organism fitness. The species that got an appropriate set of genes (and maybe even more than genes, like some epigenetic markers) survived. The ones who didn't, didn't. That's it. In many organisms there's not a unique set of genes ("formula") that lets it survive in a given environment. Gene regulation is incredibly intricate and has a ton of feedback loops. For example some genes, that are very important are often duplicated, like ribosomal or histone genes, and mutations in them doesn't do much.
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