
A Quarter of Cow DNA Came from Reptiles - sohkamyung
https://www.theatlantic.com/science/archive/2017/10/how-a-quarter-of-the-cow-genome-came-from-reptiles/542868/?single_page=true
======
eggie
It remains difficult to observe genome variation in transposon content. The
situation is improving as we get longer single-molecule reads, as these let us
reach through these sequences into bits of DNA that let us anchor the position
of transposons against genomes which we've already sequenced.

I think some people may have the idea that we can observe whole genomes
easily, but consider the case of repeats like transposons. Half of the human
genome is made up of these, but we still have trouble seeing when and where
they are active. A new insertion of a big piece of DNA can be much more
phenotypically effective than a little SNP, and yet our observational methods
make the latter much easier to see than the first. It seems that structural
variation in genomes is a likely place to find at least a partial solution to
the missing heritability problem posed by the GWAS community.

[https://en.wikipedia.org/wiki/Missing_heritability_problem](https://en.wikipedia.org/wiki/Missing_heritability_problem)

~~~
throwanem
> I think some people may have the idea that we can observe whole genomes
> easily

I think a lot of people do. Certainly I did, before I spent a year working in
a genomics institute and had the opportunity for close observation of the
massive uncertainty produced by short reads, and the concomitant complexity of
the methods required to develop useful information from them.

At that time, long reads were just beginning to look reasonably attainable
with new approached from Pacific Biosciences and other challengers to
Illumina's market share; I'd be curious to know whether there's been any major
movement in the half decade or so since I returned to industry.

~~~
eggie
The biggest development in single-molecule sequencing (aside from the steady
improvement in PacBio's methods) is the arrival of the Oxford Nanopore devices
on the market. These are also pretty rough around the edges, but they suggest
a future in which labs have direct access to long-read, low-cost sequencing.
Also, techniques like that from 10X genomics allow large-scale haplotype
resolution, which is another missing component of a true "whole genome"
sequence (humans and many other creatures have more than one different genome
copy).

------
pbhjpbhj
Given this shows how easily DNA is acquired from an external source; how do we
know certain sequences come from common ancestry rather than by other means?

~~~
api
We've known about horizontal gene transfer for a long time. We do seem to be
learning that it's more common than we thought, making species boundaries much
more fuzzy and fluid than previously believed.

Common ancestry is probably best understood in aggregate. When we look at
genetics in aggregate we see a lot of common sequences that are highly
conserved across all of nature.

Edit: also shows why most anti-GMO hysteria is nonsense. Everything is
"transgenic." Species are fuzzy.

~~~
pygy_
Monsanto's practices with GMO are problematic, and need to be denounced and
made illegal (terminator genes, glyphosate resistant crops, etc...).

GMO _per se_ are IMO a net good, we're increasing biodiversity.

Also, they are crucial in medicine. Insulin and other peptide-derived
treatments are synthesized by GMO bacteria and yeasts (see "recombinant DNA").

~~~
mitochondrion
>we're increasing biodiversity

Are you sure? Farmers used to have their own subtly different strains of crops
at the individual, village, town, and country levels in a kind of expanding
concentric ring pattern. Now, at least for cash crops, it's just a few
varieties all "manufactured" by one central power.

~~~
pygy_
It is artificial biodiversity. Without the current legal framework (where
seeds/genes can be patented), farmers could hybridize GMO with their own crops
to add interesting traits to their own strains.

The current uniformity predates GMOs, it stems from F1 hybrids that are
effectively clones, and the legislation that makes it practically illegal to
sell or plant non-patented seeds.

~~~
mitochondrion
>The current uniformity predates GMOs, it stems from F1 hybrids that are
effectively clones, and the legislation that makes it practically illegal to
sell or plant non-patented seeds.

Granted.

But in the grand scheme of things, this is as equally an astonishingly new
situation as is mechanized agriculture. A hundred years ago, most people lived
and worked on farms; now it's like 1% or something like that.

I know that Monsanto's shareholders need to make rivers of dosh, boatloads of
cash, money hand over fist, but I don't understand how in practice they've
managed to get a vice-grip on everybody's family jewels.

------
grandalf
Can someone explain a bit more about "horizontal transfer"?

It would seem that a gene is simply a symbol in relation to the DNA it is a
part of, and so there is no reason to believe that a particular gene would
mean the same thing in two different species DNA.

The context for the meaning of the gene would seemingly be completely
accidental. But then if a horizontal transfer resulted (by chance) in
something with selection value, it would be likely to remain in the
population.

Do horizontally transferred genes typically do something novel? Or do they
interact with other (distantly, vertically shared) genes in their resulting
expressions?

Is my description of a gene in the context of DNA being a "symbol" accurate?
Or is there a more accurate programming metaphor. I would hesitate to liken it
to a subroutine, but I am curious if it might be more analogous to a type
class or something like that.

~~~
thaumasiotes
"Gene" is often used as a technical term to refer to a stretch of DNA that
produces a protein. If it's being used that way here (no opinion), then in a
pretty raw sense it would mean exactly the same thing in two different
species. Specifically, it would mean that both species produced e.g. lactase.

The overwhelming majority of DNA is not "genes" in this sense, which confuses
a ton of people.

~~~
grandalf
> Gene" is often used as a technical term to refer to a stretch of DNA that
> produces a protein.

How does something like _pleiotropy_ happen if a gene simply codes for a
protein? Is the thing that is pleiotropic actually the protein?

~~~
thaumasiotes
Well, in the first place, I think my original comment was pretty clear that
the word "gene" is used in multiple senses. For example, the words
_immediately following_ your quote are "if it's being used that way here...".

In the much less important second place, it shouldn't be hard to imagine that
two different phenotypical processes might both be cued by the presence of the
same chemical.

------
redeemedfadi
Or, like any good programmer, when God was coding animal DNA:

#include <BovB.h>

~~~
eternalban
God would not use an imperative language.

p.s.

Look, imperative is most of what I've done and ~understand. I am not making it
out to be inferior, rather questioning fitness for the job. Time and Place
peekaboo thinking just seems pedastrian for a transcendent entity devising a
world. (That's even an inside joke in Genesis with God looking for Adam.)
Short scripting of little bits, sure, but blueprints and stuff, no way.

But, yes, this is just an opinion.

~~~
oblio
let light = true

?

~~~
rvense
(call-with-two-lights world)

------
c517402
And yet, it doesn't taste like chicken. :)

~~~
once_inc
Do you know what it really reminds me of? Tasty Wheat. Did you ever eat Tasty
Wheat?

------
stefantalpalaru
The bovine DNA has around 22,000 genes:
[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200/)

The claim that 5,500 of those are in common with reptiles is unsubstantiated.
The claim that they came directly from reptiles and not from a common ancestor
is absurd.

