
Mysterious ‘Jumping Gene’ That Appears 500k Times in Human DNA - curtis
https://www.theatlantic.com/science/archive/2018/06/line1-jumping-gene/563354/?single_page=true
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PaulAJ
The parasite theory is that transposons are rather like early computer viruses
that replicated by embedding themselves in other executables: they exist only
to make copies of themselves in their host genome. This theory is not
incompatible with these results. Evolution is not a rational design process.
Once a transposon starts replicating it is quite possible for the host genome
to evolve to incorporate the transposon in its regular mechanisms.

To continue the computer analogy, imagine that some mad programmer decided to
practice software reuse by calling a routine embedded in a virus. Now when you
clean the viral infection from your computer the mad programmer's app no
longer works. But that doesn't mean that the virus isn't continuing to
replicate and cause other harm.

Aside: this is yet another counter-example to the Intelligent Design "theory";
no sane engineer would have done it like that.

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Erlich_Bachman
Aren't most intelligent designs actually done by sane engineers filled with
quirks like this? Spaghetti code at places, leaky abstractions, hard-coded
things, replicating old bugs to make the program compatible with bad OSes or
other old software, etc. etc. This could just as easily be an artifact of the
complexity of reality, not an argument for- or against "intelligent design".
There might be reasons do doubt intelligent design hypothesis, but this one
does not seem like one of them. (Also why would it need to be a "sane"
engineer? It could have just as easily be a bad junior engineer, that does not
produce "perfect" code - just code that works.)

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Retric
Wait what? Are you arguing that 'god(s)' where and or might be incompetent?

Anyway, I don't think ID requires that every mutation was designed, rather
that an intelegent agent made at least one adjustment to an ongoing process.
The problem is it's not a falsifiable theory because it makes no specific
testable predictions.

~~~
Erlich_Bachman
> Wait what? Are you arguing that 'god(s)' where and or might be incompetent?

I get the humor in your question. Yet I would like to comment for the people
who might be more seriously interested in this question, that the most
enlightened view seems to be that 'god(s)' are not incompetent, but are simply
not done yet, they haven't completed the design. That the design itself is not
a finished final product, but rather a continuous form of development. If
there is such a development, it would be quite logical that one could take any
future (or just further in terms of advancement) iteration of some thing (like
human genome), compare it to a previous version and make a claim that it's
"inferior" or "incompetent". But this is just an assessment of a logical mind.
It could just as easily be called an iteration which is perfectly designed for
it's time and place and has an irreplaceable role in the grand scheme of
things.

> The problem is it's not a falsifiable theory because it makes no specific
> testable predictions.

I so wish that more people would understand this. I was trying to point into
exactly this by the original comment, saying basically that no scientific
truth can be an argument for or against any spiritual claim, that they simply
belong to the different areas of knowledge. People who are proficient in
either areas of knowledge, are often ignorant to this incompatibility, trying
to prove each other wrong. The solution is to recognize the proper way to fuse
the two areas, not choose one of them and pretend that it's enough.

~~~
mgamache
> saying basically that no scientific truth can be an argument for or against
> any spiritual claim.

This is an agument for "NOMA" or Non Overlapping Magisteria. While this is
true in the abstract pure Deist standpoint, it's not true for most religions
or supernatural belief systems. All Abrahamic regions (for example) make
specific claims about the nature of reality that is in direct conflict with
science.

~~~
labster
The degree to which practitioners of Abrahamic religions believe best guess
scientific claims from thousands of years ago varies, of course.

~~~
d0lph
And also, in some scenarios people mock the bible for calling a whale a fish
in the story of Jonah, when a whale is a mammal. However the people of the
time did not distinguish animals like we do. We only started classifying
animals like that in the 1800s.

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Viliam1234
I suppose before the 1800s whales were also able to swallow humans. /s

~~~
thedailymail
A sperm whale could theoretically swallow an adult human, but it is very
doubtful that this has ever actually happened.

[http://www.whalefacts.org/can-whales-swallow-
people/](http://www.whalefacts.org/can-whales-swallow-people/)

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lkrubner
If you are interested in this, you might also be interested in "promoter
genes" which tend to be destructive to the organism they are part of, but
which are also very good at promoting themselves, so they survive in the
genome despite being harmful. A good book on the subject:

Genes in Conflict: The Biology of Selfish Genetic Elements

[https://www.amazon.com/Genes-Conflict-Biology-Selfish-
Elemen...](https://www.amazon.com/Genes-Conflict-Biology-Selfish-
Elements/dp/0674027221/ref=sr_1_1?s=books&ie=UTF8&qid=1529667609&sr=1-1&keywords=genes+in+conflict&dpID=51LvhyS38vL&preST=_SY291_BO1,204,203,200_QL40_&dpSrc=srch)

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dfsegoat
Indeed. It is this sort of "worm-like" or "near-virus" -like behavior of these
genes (transposons, promoters, etc) that made me decide to split the
difference between comp sci and molecular biology (bioinformatics) as an
undergrad.

Nevermind the mitochondria - the powerhouse of our cells - which is basically
believed to be a bacterial companion that our single celled ancestors
integrated so tightly with - that it became part of our genome [1].

1 - [https://www.nature.com/scitable/topicpage/the-origin-of-
mito...](https://www.nature.com/scitable/topicpage/the-origin-of-
mitochondria-14232356)

~~~
mallomarmeasle
Mitochondria are indeed thought to have arisen from incorporation of free-
living organisms, but interestingly they mostly retain their own replicating
DNA that is not incorporated into our genome [1]. 1-
[https://en.wikipedia.org/wiki/Mitochondrial_DNA](https://en.wikipedia.org/wiki/Mitochondrial_DNA)

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wintorez
What if it's just a semicolon?

~~~
regularfry
Please, please be a parenthesis...

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madaxe_again
A few years ago I read Nick Lane’s _The vital Question_ , which explored “junk
DNA” extensively, in the context of abiogenesis.

The analogy I particularly liked was that they are little turing machines, and
the very original stuff of life - indiscriminate, self-replicating, and
therefore part of the bootstrap for everything that came after.

Also, more on LiNE.
[https://en.m.wikipedia.org/wiki/Retrotransposon#LINEs](https://en.m.wikipedia.org/wiki/Retrotransposon#LINEs)

~~~
otherme123
They're not self-auto-replicating. They need the host cell machinery to do so,
thus they can not be the original stuff of life.

They are a very specialized DNA chunks that retains the absolute bare minimal
needs to trick a host to replicate them. They are parasites.

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chiefalchemist
> "Geneticists tend to pay attention when LINE1 inserts itself in a bad place,
> causing cancer or genetic disorders like hemophilia."

But it's not always doing bad, correct? The point being, these random
insertions are not only part of the process, they are key. Without deviation
these is no evolving.

~~~
ufo
Transposons are waaay more likely to break things than to evolve them in a
positive direction

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rubatuga
Well that’s with any mutation :)

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ufo
While I understand the joke this isn't actually true :) A substitution
mutation might not have any effect or might just result in switching an
aminoacid for a similar one (due to how the genetic code works). On the other
hand, a large insertion will likely mess up the gene much more than that.

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stevebmark
Does so called "junk DNA" consist entirely of this "LINE1" DNA, or does junk
DNA cover other genes as well?

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Gatsky
Not just LINE1. Currently only about 6% of human DNA has ascribed function.

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zellyn
Clearly, it's Core Wars :-)

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ivanstame
They are goto statements :)

