
The nightmarishly complex wheat genome finally yields to scientists - LinuxBender
https://arstechnica.com/science/2018/08/give-us-this-day-our-daily-bread-wheat-genome/
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cabaalis
I've been seeing "Genome of X has been fully sequenced" articles over the
course of some years. Can someone who understands it explain to a layman like
myself how exactly this benefits us?

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toasterlovin
I think the best big picture explanation of why this is important is this: our
ability to feed and care for humanity is dependent on biology. Genomes are the
source code for biology. Reading the source code is the first step to
understanding the source code. Understanding the source code will allow us to
build better expressions of biology (those being both ourselves and the
animals and plants we depend on).

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aluren
I hope you won't take it personally because you're far from the only one to
say it (and I would have refrained from posting if I hadn't seen people taking
this further in this thread), but I really wish people stopped using the "DNA
is the source code of your body" analogy. It is used way more than what's it's
actually worth, even though I can see how that analogy can be seductive. The
structure of a program's source code is nothing like the way DNA encodes and
propagates information. Even if you add a bunch of adjectives such as 'self-
modifying', 'full of GOTOs', 'nondeterministic', 'live monkeypatched', and
thus twist the picture many people have of the way source code translates into
execution, it would still be misleading. We are a product of _both_ our genome
and environment, at the same time, all the time. Not one then the other. Or,
if you will, the source code is its own executable. It doesn't make sense
because the analogy doesn't either.

And that's not even taking into account non-DNA things that encode and
propagate information, such as microbiota or anything linked to epigenetics.

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toasterlovin
It’s actually a great analogy. Analogies aren’t supposed to be exact
representations; they are supposed to allow you to quickly communicate a
decent approximation of what something is by relying on preexisting
understanding of how another thing works. The source code analogy does that
well.

And, by the way, running programs are also the result of their source code and
the environment in which they execute. It’s just that the environments which
computer programs run in are very homogenous and predictable. But flip some
bits in memory or have a user thrash the UI and you’ll see that a running
program interacts with its environment in much the same way as a biological
organism.

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aluren
I never said it was a bad analogy, I even used a rather positive word
('seductive'). It _is_ overrated, though, and it does stop making sense sooner
than many people think. What I'm really saying is that relying on this analogy
to understand how DNA works in relation to organism development, function,
etc. won't get you past a very cursory understanding of it. It may be enough
for many people but:

-I like to think that HN is filled with people who take interest in many things, especially science-related subjects, and would hope that many of them on this site would like to know more than an analogy-based understanding of genomics

-For better or for worse, the recent bloom and advances in genetics and biology in general have taken over the modern world and been hailed (probably with reason) by all kinds of circles, from the media to governments or the tech world, as a promising new era that's going to revolutionize our understanding of life, disease, what it means to be human, cognition, what have you. It does feel pretty cool as an insider to know that you're working in the 'hot new thing' but a side effect of that is, I have seen people develop a pretty bizarre fascination with DNA, whether it be their own or other people's. And it's not something that can be pinpointed to entirely rational reasons. I don't want to go off tangents any further, but let's say it can't hurt to occasionnally remind people what DNA is and what it isn't, what it's like and what it's definitely not like. I dislike pedants as much as the next person but seeing so many (presumably very educated) people take that analogy in the same thread made me think that the reminder wasn't that out of place.

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rubatuga
I disagree, DNA is pretty much the source code. any differential DNA
expression are due to histone modification, proteins, or RNA (and rarely CpG
DNA modification in humans) so DNA in the purest form is indeed the source
code.

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aluren
Source code for what, though? How about pre-natal influences in the womb, does
this mean the womb is a sort of compiler? What about the structure of DNA
itself, known to influence gene expression levels? What about the microbiota,
which is arguably more 'you' than your own body in terms of raw cell count?
What about the phages found in the microbiota (the phageome)? Why are they not
part of the so-called source code?

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rubatuga
Source code/machine code, I am just interchanging but in this analogy they are
equivalent. Pre-natal influences change the epigenetics, i.e. "on" the genome.
The structure of DNA is almost completely determined by histones, which are
proteins that DNA wrap around, so once again, not the DNA. Microbiota affect
the environment of the cells, meaning it is an input to the cell, not the
source code. Any phages affecting the microbiota will affect the input to the
cell. These factors aren't considered source code simply because it only
affects the execution of the cell's source code.

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Alex3917
> For example, about 26 genes are differentially active in wheat varieties
> with solid stems and those with hollow stems

If it has a solid stem, wouldn’t it no longer be in the grass family by
definition?

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grey413
Nope. Phylogenetic families are based on the degree of shared ancestry, not
the presence or absence of any given trait.

I mean, don't get me wrong, you CAN develop phylogenetic trees based on
traits. That's how Linnaeus and all subsequent taxonomists did it before they
could just look directly at DNA. But it takes a lot of traits, and has been
preempted by DNA based methods anyway.

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Alex3917
> Phylogenetic families are based on the degree of shared ancestry, not the
> presence or absence of any given trait.

What about the rhyme “Sedges have edges, rushes are round, and grasses are
hollow right down to the ground?” You’re telling me scientists are now saying
that DNA testing is more accurate than just using the rhyme?

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ufo
It is not about DNA vs phenotypes. The issue is that biologists are more
interested in building an universal classification, a single tree of life for
all species, than they are in building single-phenotype-based classifications
that dont nest particularly well.

For example, if you looked at just the ability to fly, you would group birds
and bats on a same group. But that would be wrong because bats are clearly
more closely related to flightless mammals than they are to birds. This
becomes obvious if you account for more characteristics of the animal
(presence of fur, bone shape, pregnancy, etc) or if you examine the DNA.

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avip
Israeli press gives lots of credit to Bioinformatics company NRGene.

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a_bonobo
Yes, NRGene is an Israeli company, so that would make sense.

NRGene has a proprietary algorithm that uses a large amount of Illumina
sequences to build a pretty good genome assembly. This technology has been
used in a few organisms with large genomes, as it has been used in v1.0 of
this assembly.

However there have been previous, less high quality wheat genome assemblies
based on Bacterial Artificial Chromosomes (BACs), and that information has
made its way into this assembly too, along with long-distance information from
HiC and genetic maps and Bionano technology.

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avip
Yep I’m not qualified to tell facts from PR on this one (which is why I made
that comment)

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skookumchuck
It's necessary to sequence all these so presumably they can be recreated
if/when they go extinct.

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panic
Is it possible to recreate a wheat plant from just its genome?

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bohadi
A decent analogy might be:

is it possible to recreate a running program from just it's source?

(lacking a compiler, development and production environments, and perhaps user
inputs)

so my feeling is, not really, to an approximation

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skookumchuck
Sure it's possible. (I've recreated programs from source despite lacking the
compiler, etc., originally used on it. The trick is to adapt something else to
the task.) The source contains instructions on how it works, and those
instructions can be used elsewhere.

