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Ferociousfeind t1_isfvph0 wrote

It's generally not a very scientific number at all. There are multiple types of mutations that can occur, and they're not all readily comparable. If a certain section of 24 nucleotide pairs get duplicated in one mutation event, is that 1 change, 24, or hundreds to thousands (by offsetting everything after the duplication)?

What this number really means is "human DNA is remarkably similar, human to human" and that's about as far as it goes.

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Tractorcito22 t1_ishdyjn wrote

> remarkably

Is it remarkable though? I would imagine most species' DNA is unremarkably similar to the same species DNA? Are humans more remarkable?

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Sincerly_ t1_isi5c28 wrote

Yes, we are compared to other animals, and the reason we think this is because tens of thousands of years ago there was a super volcano eruption that made our population around 10,000 or less. So we are not as genetically diverse as other animals are

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Mylaur t1_isioah7 wrote

What?... So we would have been even more genetically diverse huh.

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pihwlook t1_isjmc6t wrote

Why did this event not also constrict other species?

Because they had time to diverge before it, and our divergence came after it?

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Sincerly_ t1_isk48bd wrote

It did affect certain animals of course, but we were ran to near extinction. But most of the animals we see today don’t seem like there genetic diversity was affected that much. And yeah, most likely they diverged way before that, even before the super volcano we have had times where we have had extremely low population.

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DuskyDay t1_isjejxw wrote

From what I've read, other species have generally much higher variance.

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Ffdmatt t1_isgfk3v wrote

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.

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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.

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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).

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Splatulance t1_isiapmr wrote

Some dna isn't transcribed but has a significant impact on transcription/expression. Transcription is like the publicly exposed API

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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).

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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."

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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.

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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.

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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.

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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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Kevin_Uxbridge t1_ish01ze wrote

So similar that it bespeaks of an interesting population history, recent bottlenecking and rapid expansion.

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reginald_burke t1_ishxsag wrote

Don’t we have good definitions for this, such as the Levenshtein edit distance? For your example, Levenshtein would say 24 edits (via 24 additions).

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Ferociousfeind t1_isib75n wrote

Single mutations can also involve the copying or deletion of large chunks of DNA. Levenshtein would be 23 edits off, because only one event was involved in adding a single 24-segment DNA piece. This is a simple thing to calculate, but it misses some of the behavior of mutation, and so misses a bit of the picture. The more true-to-life version is more complex, more nuanced, a bit more up to interpretation, and less capable of giving a single concrete percentage.

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light24bulbs t1_isi9wop wrote

Truly that's just a count of the number of differing base pairs, which makes complete sense. This isn't that complicated. I'm sure you could argue it isn't the most RELEVANT figure that a geneticist would be concerned with, but, I think it's fair to say that's what they would take it to mean. I'd love to know if I'm wrong about that.

It's binary data, run a diff and give me the count. Since we are talking about the number 24, if there's 24 base pairs out of the total different, it's just total / 24 = variance ratio.

Likewise, the average is simply: take any two people, could the number of base pairs differing in each or present in one and not the other. Do that many times between different people, that's the average.

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JackOCat t1_isic5l1 wrote

What no one explains that often is that it isn't really differences in our proteins that make us different from each other (they do a bit of course). What really differentiates humans is all the differences in the timing genes that control our development. The fluctuations there have huge effects on how we look and function at our macro level.

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