A Quarter of Cow DNA Came from Reptiles
theatlantic.com
theatlantic.com
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.
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.
By and large, we can. Yes there are minute aspects which lack perfect resolution, but we are well into the sub-1000 dollar whole-genome age.
Particularly in humans, can get a highly accurate reading of your variation across your entire genome, including insertions and deletions which are even easier to spot.
Of course there is cryptic variation, but it is only in really obscure genetic diseases and complex phenotypes that we start to run into trouble. Both of which can be addressed by simply sequencing a deeper population of individuals.
Insertions and deletions are usually harder to spot with the short reads that make up the data that you'll get back from your typical "sub-1000 dollar whole genome". The reason is simple. There are vastly more possible insertions and deletions that SNPs, and these all must be considered by algorithms in order to detect them. Worse, as the length of the insertion or deletion increases to a reasonable fraction of the length of your reads, it becomes impossible to hope to resolve the event without considering an untenable space of possible indels and opening yourself to spurious matching.
Those cheap genomes have a serious blind spot--- they don't easily yield information about the large scale variation in structure (indels, copy number, inversions, translocations) that are apparently very important to evolution. I believe the field has blinded itself to the importance of large variation simply because it is hard to observe. Recent papers based on long read data have started to respond to this assumption in a serious way (https://www.biorxiv.org/content/early/2016/09/24/076562).
> Yes there are minute aspects which lack perfect resolution
In the context of humans there is ample evidence that the things we are missing with short reads are not minute, but are rather an enormous elephant in the room, see https://biosci-batzerlab.biology.lsu.edu/Publications/Sudman... and http://science.sciencemag.org/content/349/6253/aab3761. They report that some genomic regions are expanding by up to 50-fold between individuals. Some whole human populations feature quarter-megabase duplications not present in other groups. The scope of the studies are actually very narrow, with hundreds of individuals being considered. I would be surprised if this is anything less than the tip of the iceberg, and incredibly surprised if this turns out to be a minute detail.
Iontorrent has very short reads (250bp) but I think they have 1kb working at least in the lab.
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.
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").
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.
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.
As for glyphosate resistant crops, beyond the currently insufficient science (lots of invalid studies!), I can't see any reason to denounce it or make it illegal).
As a layman, the story I've seen up to now is roughly "these sequences are the same, therefore there is a common ancestry"; but this information shows that argument doesn't work on a wide scale across species in this simplistic form -- so either the basis of common ancestry being inferred from similar DNA is not scientific (or is falsified) or we have results that show whence the particular sequences came from (ie there's a more nuanced result)?
In short that answer is unsatisfyingly vague.
Technologies are just tools. It's all in how they are used.
Also, the reason why a person does or does not do such a thing is rather of less importance than what that thing is that he does or does not do. For example, if pigs carry disease, and your religion proscribes you from eating pigs because "God says so", your life is preserved whether or not you or anyone else have any conception of germ theory whatever.
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.
The overwhelming majority of DNA is not "genes" in this sense, which confuses a ton of people.
How does something like pleiotropy happen if a gene simply codes for a protein? Is the thing that is pleiotropic actually the protein?
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.
Most genes code for proteins, so in a programming sense, the genome would be a directory and the genes files. Obviously, the raw order and position of files on disk doesn't matter if you just want to run them.
But it seems that there is also information in the genome which is position dependent, which is more of what you alluded, that moving stuff around would break things.
#include <BovB.h>
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.
?
#ifndef __BOV_B_H__
#define __BOV_B_H__
#endif
The entire problem is that he left an extra underline at the end of the #define, and 3 underlines look exactly like 2.
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.