201–210 of 232 posts
This is actually kind of a huge deal since it means that all 24 chromosomes have now been fully sequenced. As it says in the abstract, up until now the Y chromosome proved difficult to sequence due to its nature.
You can tell it's the Y chromosome because of the way it is.
Here is the "dumb question" I've always had about recording the human genome. We all have different DNA. So is "the human genome" some kind of "average" DNA, or is it the DNA of whoever they sampled, or is it maybe an overview of what is common for all of us?
I assume it's one person's DNA. The last time there was talk about this in popular media was the DNA of one person.
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What makes the Y chromosome more difficult?
All of the chromosomes have difficult bits in them. The Y chromosome in particular has huge sections that are difficult. By difficult, imagine a jigsaw puzzle. Difficult bits in the jigsaw puzzle are where you have the same sub-image repeated over and over again, or where the same image section is repeatedly scattered over the wider image. Puzzle pieces from these bits are difficult because you can't tell which part…
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If you think like an ML engineer, the genome is a feature vector 3B bases (or 6B binary bits) long that is highly redundant (many sections contain repeats and other regions that are correlated to other regions), and the mapping between that feature vector and an individual's specific properties (their "phenotype", which could be their height at full maturity, or their eye color, or hair properties, or propensity to d…
> If you had a list of all the genomes of all the people in the world, and all their phenotypes (height, eye color, hair type, etc), you could take all their genomes as input variables and treat all their phenotypes as output variables, and make embeddings or other models that mapped from genomes to phenotypes. The result would be a predictive model that could take a human genome, and spit out a prediction of what th…
The model would be highly nonlinear and nonlocal, at the very least.
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All of the chromosomes have difficult bits in them. The Y chromosome in particular has huge sections that are difficult. By difficult, imagine a jigsaw puzzle. Difficult bits in the jigsaw puzzle are where you have the same sub-image repeated over and over again, or where the same image section is repeatedly scattered over the wider image. Puzzle pieces from these bits are difficult because you can't tell which part…
What does "mole" mean in this context?
Here is the "dumb question" I've always had about recording the human genome. We all have different DNA. So is "the human genome" some kind of "average" DNA, or is it the DNA of whoever they sampled, or is it maybe an overview of what is common for all of us?
They are talking about one 'reference genome'. The variation from human-to-human is relatively small (a few million bases out of 3 billion). The reference genome has historically been some kind of average/mosaic of several individuals (this has obvious disadvantages), good enough to put reads in the right place (mostly), and call 'variants' - the differences that make the test genome unique. The latest/greatest end-t…
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Many genes are highly conserved or consistent enough. E.g.: if there's a 1% difference between two people, then it's a bit like two very unique sentences that have a couple of small typos. They're sill recognisable, and it's also still pretty obvious that they're the "same". A gene sequence allows researchers to determine the amino acids that are coded for, and from those, which proteins match which genes. This can b…
But you can only know that by having a large sample of very “stable” (have few genetic irregularities) gene samples compared to a large pool of samples from people with very narrow and pronounced gene irregularities, right? Is this why it’s so hard? This feels more like a healthcare records keeping people and less like an “actually reading the data problem”. I can’t help but feel like some form of single payer health…
No- A "gene" isn't an A/G/C/T- it's a sequence of 1000-1000000 base pairs. Each gene has a well-defined start/stop sequence called a start/stop codon. When people have genetic differences, one (an SNP- single nucleotide polymorph) of the tens of thousands of base pairs in that gene is different. Even for genes that are entirely "missing" in some people, they're really just different in a way that makes them nonfunctional.
Does that make it obvious how sequencing all those genes is useful, even if everyone has different genes? It tells us 99.999% of how proteins are coded, even if individual variation is the other .001%.
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"The media" isn't a uniform entity, but when people refer to it in this context they typically mean the large consolidated media corporations that own major print and television outlets. And those entities have essentially eroded their own credibility to the point that trusting anything they say is foolish. If they say the sky is blue, go out and check. They could do better, but until they do , it makes sense to cast…
The larger news outlets are some of the few remaining places that actually hold their news rooms to some kind of factual standard and facsimile of objective reality. If NYT or the Economist or the BBC tells me the sky is blue, I'm pretty sure it is. If they report on some scientific topic the reporter is not an expert on, I understand that there's probably some signal lost. If they publish something on a contested po…
In large corporations it's effectively already dead, because many of the "trusted" names have already abandoned it, and you can't even tell which ones they are without being inside the newsroom to know if stories there get spiked on behalf of advertisers.
Where you can still get this is the likes of Substack, where you're paying a subscription to someone who doesn't have advertisers.
> The loudest voices that castigate the media, in America at least, tend to be the ones that profit the most from being the sole arbiter of truth for their own audiences.
That's to be expected when it benefits them. But their criticisms would sure have a lot less weight if they weren't accurate.
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This is a complex question. The cocktail soup in a gamete (sperm or egg) and the resulting zygote contains an awful lot of stuff that would be extremely hard to replace. I could imagine that if the receiving civilization was sufficiently advanced and had a model of what those cells contained (beyond the genomic information) they could build some sort of artificial cell that could bootstrap the genome to the point of…
I’m just pondering this, and it’s not clear to me that there is anything intrinsic in the genome itself that explicitly’says’ “this sequence of DNA bases encodes a protein” or even “these three base-pairs equate to this amino acid”. I wonder if that information could ever really be untangled by a civilisation starting entirely from scratch without access to a cell
Coding DNA and non-coding DNA looks very different. Proteins are full of short repetitive sequences that form structural elements like alpha helixes: https://en.wikipedia.org/wiki/Alpha_helix
Once you've identified roughly where the protein-coding genes are it would be trivial to identify 3'/5' as being common to all those regions. You could pretty easily imagine a much more complicated system with different transcription mechanisms and codon categories, but earth genomes are super simple in that respect. Once you have those you just have the (incredibly complex) problem of creating a polymerase and bam, you'll be able to print every single gene in the body.
Without the right balance of promoters/factors/polymerase you probably won't get anything close to a human cell, but you'd be able to at least work closer to what the natural balance should be, and once you get closer to building a correct ribosome etc the cell would start to self-correct.
For those who don't recall: Back in the Dark Ages, there was a race to decode the human genome. The leading competitiors (wealthiest) were Celera Genomics and the Human Genome Project. After some time, Celera (headed by Craig Venter), announced they had done the deed. However, what Celera had actually done was used what they called a "shotgun method", which meant they took small samples here and there, then built a m…