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And, then there's the whole epigenetic interaction with the germ line. Even the genetics appearing to be 100% identical will still result in widely different outcomes if it's read from and implemented differently because of all the other factors involved. 
The Cosmopolitan Fictioneer
Is it biologically possible for a multicellular animal to naturally produce a virus — or a virus-like pathogen — rather than being a natural host for such a pathogen?
edited 3rd May '16 6:59:02 AM by MarqFJA
Fiat iustitia, et pereat mundus.
Technically, that's what hosts actually do. The virus co-opts host cells and turns them into virus-making cells... therefore other organisms make every virus. *shrugs*
Some viruses aren't that unhelpful, either: just as some parasites can boost your immune system in some ways (to protect their interest in you), long-term viral squatters can hand out such benefits along with the disadvantages. :/
edited 3rd May '16 8:10:55 AM by Euodiachloris
The Cosmopolitan Fictioneer
Zika was probably one. Unfortunately, it's shifted from a population which had adapted to it as it adapted to them and the other bacteria, parasites and viruses that were about.
Not-so-friendly when in a different place, with different people, with a different species of mosquito to adjust to interacting with. -_-
If memory serves, the human placenta uses certain endogenous retroviruses (that is, retroviruses that are part of germline DNA) to glue its cells together - the HERV-W 7q21.2 virus specifically.
As far as "originating", we don't know. Evolutionary history often is essentially educated guessing. As for "assimilating", they exist: See polydnaviruses for example.
"For a successful technology, reality must take precedence over public relations, for Nature cannot be fooled." - Richard Feynman
The Cosmopolitan Fictioneer
Indeed a significant part of the human genome is made of such viral elements
... though they appear to be completely inert, due to being fragments of the original viral codes. And near the tail of the section is an easily missable part that confirms you do remember right, regarding placental formation.
Also, I did not know that those infamously parasitic wasp species actually relied on an endogenous virus (which is completely symbiotic with them!) for their horrific life cycle. Now there's prime fuel for inventive sci-fi horror.
... How did microbiologists figure out that those parts of the human and wasp genomes were of viral origin, though? What makes such ancient viral gene clusters stand out among the rest of the genome?
edited 3rd May '16 2:56:12 PM by MarqFJA
Fiat iustitia, et pereat mundus.
Their structure is very similar to other existent viruses, that's why.
"For a successful technology, reality must take precedence over public relations, for Nature cannot be fooled." - Richard Feynman
The Cosmopolitan Fictioneer
... You may have to elaborate on that, because I have no idea there's such a thing as "structural differences" on the level of the genetic code that would, say, distinguish viral code from non-viral code (especially without knowing what kind of virus you're looking for).
edited 4th May '16 1:31:41 AM by MarqFJA
Fiat iustitia, et pereat mundus.
Well, The problem is working out how retroviruses happened in the first place. Because it's more than possible that the vast majority have spontaneously come about because of random transcription bloopers within cells, rather than starting out from random protein generation outside cells. :/
Another way of looking at it is: wanna pass your DNA, but can't be bothered with the usual methods of asexual or sexual reproduction? Make a mistake to create a rogue protein package to annoy everybody in the vicinity and roll the dice!
Professional Writer & Amateur Scholar
I think this is relevant, biology and all?
Oh God, is there any way parasitic worms can't be creepy?
I'm a (socialist) professional writer serializing a WWII alternate history webnovel.
Oh, is that a nematomorph worm? These things have a habit of altering the behaviour of their hosts.
"For a successful technology, reality must take precedence over public relations, for Nature cannot be fooled." - Richard Feynman
Professional Writer & Amateur Scholar
So apparently that thing eats around inside of spider in a way that will keep it alive for as long as possible.
Very rational...and very wicked.
I'm a (socialist) professional writer serializing a WWII alternate history webnovel.
The Cosmopolitan Fictioneer
Pffft, that's nothing compared to the parasitoid wasps that can pretty much zombify the caterpillars they use as hosts for the eggs so that they would end up guarding the pupating larva until it hatches. Faceful of Alien Wing-Wong meets Real Life, yo.
Fiat iustitia, et pereat mundus.
Professional Writer & Amateur Scholar
It is not nothing, because holy shit look at that thing, it's almost as big as the spider itself.
I'm a (socialist) professional writer serializing a WWII alternate history webnovel.
If you think those are creepy, you should hear about Rhizocephalans. They sound like something out of a Lovecraftian nightmare.
First, a female injects themselves into a crab's body, where it then grows all across it's body. Eventually, an abdomen erupts out of the crab's genitals. All the while, the parasite feeds maternal hormones into the host's brain, where it then believes that the parasite is its eggs. This behavior is even seen in males, where they care for the parasite in the same way a mother would care for its eggs, despite never being able to have them.
A male Rhizocephalan then comes and injects its testicles into the female mass and the eggs are fertilized. The host then releases the eggs into the ocean as if it were its own offspring.
The Cosmopolitan Fictioneer
~Euodiachloris: Quite late, but your post here didn't actually answer my inquiry towards Septimus Heap's own post.
On a different note, does anyone know if scientists have figured out any possible benefits to non-pathological polyspermy in those animal species in which polyspermy is a natural aspect of the reproductive cycle (e.g. chickens)?
edited 18th May '16 11:28:40 AM by MarqFJA
Fiat iustitia, et pereat mundus.
Sorry. I was pointing out that on the very basic level, there is little difference between the tRNA and rRNA recoding back into DNA that viral code actually is. The trick is finding and recognising the patterns that code the equivalent of "go it on your own" and working backwards from them. However cut up they get. :/
The Cosmopolitan Fictioneer
... Why would they need to know what viral tRNA or rRNA looks like when they're looking at the chromosomes? Do they have the chromosomal DNA transcripted into RNA form, or something?
And on another different note... Can anyone verify the claims that science has proven the veracity of the Wim Hof Method's responsibility for the namesake's seemingly superhuman powers?
There is generally no such thing as viral tRNA or viral rRNA, except in very large viruses where you can tell simply by looking at the viral genome and noting similarities with cellular tRNA and rRNA.
edited 18th May '16 1:02:41 PM by SeptimusHeap
"For a successful technology, reality must take precedence over public relations, for Nature cannot be fooled." - Richard Feynman
The Cosmopolitan Fictioneer
... OK, that cleared up the confusion on the whole RNA issue.
RE my actual question: So you're saying that the endogenous viral elements in the human genome were identified because there exist actual viruses whose genomes resemble them too closely (through comparisons with their respective RNA equivalents) for the EVEs to not be of viral origin themselves?
Fiat iustitia, et pereat mundus.
Bingo. But... it's also not quite that simple. There's always the really, really insanely low chance of normal cell division glitching and effectively creating a new, ready-for-vaguely-independence virus — instead of going for cancer.
It could be the way viruses actually started in the first placd. Or, one of them.
The Cosmopolitan Fictioneer
Well, on a different note, how plausible would it be for relatively minor tweaks in the human genome to allow the human body to naturally manufacture hair/skin pigments that, while naturally occuring in many animals, are completely unknown as natural colors in humans (e.g. blue, which occurs frequently among birds as well as some mammals, including primate species such as mandrills)?
edited 12th Jun '16 12:31:11 PM by MarqFJA
Fiat iustitia, et pereat mundus.
You know, chimps have an additional chomosome pair (our chromosome number 2 is the result of a fusion). How do we aknowledge that?
Molecular clocks and time of divergence are far better indicators than "98% identical". That degree of similitude across a complete genome is pretty much useless in terms of evolutionary genetics, which is pretty much the field where you'd be comparing genomes. And you'd be looking for inversions, duplications and other interesting stuff, rather than just if sequences match.
DNA can tell us more than just matching sequences.