Biological Dark Matter

[λngelღмander]

It's a little understood phenomena that a select few species exhibit: parts of certain animals genomes (including our own) that code for long strings of RNA that seem to have no functionality.

 

There is scant literature about it, I found this article and the wikipedia page, but there is just so little to read. I thought it was very interesting, to say the least, and I wanted to discuss it.

 

 

These coding pieces of DNA don't even all link back to the same common ancestor; there are thousands of them but only about 100 are shared by all of the animals that we have found to have them. That raises the question, do they all really come from the same place? Is it possible that biological dark matter developed independently in different species?

 

There is credible evidence to suggest that these genes actually did do something once, since a lot of them are shared by placental mammals, furthermore, one was found to limit placenta size.

 

 

 

That doesn't explain why it is so plentiful. A portion of the genetic material found in our blood - as well as almost half of the genetic material found in our gut - is biological dark matter. It does not belong to any one specific domain of life (in other words, it's not an animal, plant, or fungus), and our bodies actually produce this genetic material, which is strange because it seems to have no purpose but to waste our resources. 

 

 

 

 

It's almost eerie, isn't it? Thinking about these kinds of things, there is so much we just don't know about ourselves.

[rico]

interesting concept, although could you clarify exactly why the terminology is "dark matter"? is it simply because of the fact that this and dark matter are the origins of life and matter, respectively, or is there something else I'm missing?

[λngelღмander]

interesting concept, although could you clarify exactly why the terminology is "dark matter"? is it simply because of the fact that this and dark matter are the origins of life and matter, respectively, or is there something else I'm missing?

No, they call it dark matter probably because of how difficult it is to explain, if you read the articles you'll understand where it's coming from. I didn't coin the term.

[rico]

regardless, super intriguing and thought-provoking. where we come from makes up who we are (i learned that in a coors light commercial). i'm always interested in finding out more about the roots of our existence such as to learn about my biological identity and why it is the way it is now.

[Professional Map Painter]

Like the human appendix, it's probably code that was useful once but isn't now. Human foetuses still go through a "fish" stage despite no longer being an aquatic life form - http://www.bbc.co.uk/news/health-13278255.

[λngelღмander]

Like the human appendix, it's probably code that was useful once but isn't now. Human foetuses still go through a "fish" stage despite no longer being an aquatic life form - http://www.bbc.co.uk/news/health-13278255.

This was what I thought at first, but think about it. These pieces of DNA do code for something, but the things they code for literally have no purpose, and they can't because all they are are RNA chains, not proteins or anything, just strings.

 

They, with that one exception mentioned earlier, can't really ever have had a use, because random lifeless organic matter serves no purpose. It's one of the leading pieces of evidence in the theory that the earth has developed two independent forms of life.

 

 

All animals we have so far identified, we think trace back to a SINGLE common ancestor, that spark of organic matter when lightning struck in just the right way, that sort of thing. But there is a theory that life developed twice, independently, and this theory is called shadow life. It basically says that there could be another type of life out there on earth, living unbeknownst to us, and it functions using a completely different type of genome, made out of different materials, like arsenic instead of phosphorus.

 

Could the RNA uselessly coded for by our genomes be residue of a mesh between us and another type of life?

[Tasty Salamanders]

I think you are confusing two different things as a single thing, our bodies don't produce this "biological dark matter" it is simply found in us but doesn't appear to eukaryotic (i.e. our own DNA or the DNA of fungi and parasites like worms) or prokaryotic (i.e. bacteria that live on or within us). It seems to suggest that there is another branch of unidentified life and that this unidentified life can be found to be living in humans.

 

However this...
 

There is credible evidence to suggest that these genes actually did do something once, since a lot of them are shared by placental mammals, furthermore, one was found to limit placenta size.

... is something completely different called Junk DNA, it is a completely different thing and isn't related to "biological dark matter" in the slightest.

[etn]

2spooky4me.

[λngelღмander]

I think you are confusing two different things as a single thing, our bodies don't produce this "biological dark matter" it is simply found in us but doesn't appear to eukaryotic (i.e. our own DNA or the DNA of fungi and parasites like worms) or prokaryotic (i.e. bacteria that live on or within us). It seems to suggest that there is another branch of unidentified life and that this unidentified life can be found to be living in humans.

 

However this...

 

... is something completely different called Junk DNA, it is a completely different thing and isn't related to "biological dark matter" in the slightest.

No, our bodies do produce the biological dark matter, parts of the HUMAN genome actually code for long strings of RNA that don't do anything, and they can be found inside our guts and blood. 

 

And I'm not talking about introns, non coding DNA, I'm actually talking about parts of the genome that DO code for things, just things that don't do anything.

 

 

The parts of our genome that produce this biological dark matter are not introns, because they do code for something, whereas the introns do not code for anything at all, no matter how useless.

[Lmf]

as we speak, scientists are coming up with ideas as to why organisms age and whatnot. dark matter could or may not contribute. who knows. 

[Hyperqube]

I have to agree with Tasty
 
The wikipage

Biological dark matter is uncategorized genetic material found in humans and throughout Earth that does not fall under the three existing domains of life: bacteria, archaea and eukaryotes. Its presence suggests that a possible fourth domain of life may yet to be discovered.

 
We, as human being, are eukaryots (as our cells have a nucleus).
 




And from there we go  Metazoa, - Chordata, -  Mammalia, -  Primates, - Haplorhini, -  Hominidae, - Homo - H. sapiens

And yes - inside humans, one can find non-human DNA: for example, the bacteria that live in one's gut, digesting food (which would be a bacteria, not a eukaryot)
 
-----------------
 
The second article talks about
 

The "classical" role for a gene is to produce proteins, which are essential for the functioning of cells. However, our genomes also encode genes that produce long non-coding RNAs, whose functions are more mysterious.
 

That's something else completely different. our genome resides in a cell that has a membrane - our genome is that of an eukaryot. That it creates RNA that might or might not be usefull, is fun and all, but that's not the same as a different species (in the same sense that

• human sperm (50% DNA) isn't a different specie as a human (100% DNA),
• a female (XX) is a different species of a male (XY),
• a male bee (X) different from a female bee (XX)

that's not a fourth domain of life - as proposed by the wikipedia article

 

 

one is inconsistant

[λngelღмander]

snip

I don't think it's a new domain of life, not really, but I do believe that it has to mean something. At some point or another, these useless RNA coding genes became part of our DNA, and they trace back to a few other animals, and this is very interesting.

 

I know that viruses are capable of editing the genome, is it possible that an early virus added itself to our genome, and all it ever did was code for random pieces of DNA? That would be an unflattering realization, that this entire mystery is really just some primordial bacteria. Either way, there's a mystery, and it's not due to any resident bacteria, as the article claims that it is a genuine part of our genome (if it is to be believed.

[Hyperqube]

> I don't think it's a new domain of life,

 

but that's the point: what wikipedia calls bio dark matter, does

 

Biological dark matter is uncategorized genetic material found in humans and throughout Earth that does not fall under the three existing domains of life: bacteria, archaea and eukaryotes. Its presence suggests that a possible fourth domain of life may yet to be discovered.

 

> I know that viruses are capable of editing the genome, is it possible that

> an early virus added itself to our genome, and all it ever did was code for

> random pieces of DNA?

 

While AFAIK,it would make sense, I don't think so: we know of such virusses. In fact, IIRC part of the genetic evidence of that humans and apes have a common ancestor is just that.

[λngelღмander]

> I don't think it's a new domain of life,

 

but that's the point: what wikipedia calls bio dark matter, does

 

Biological dark matter is uncategorized genetic material found in humans and throughout Earth that does not fall under the three existing domains of life: bacteria, archaea and eukaryotes. Its presence suggests that a possible fourth domain of life may yet to be discovered.

 

> I know that viruses are capable of editing the genome, is it possible that

> an early virus added itself to our genome, and all it ever did was code for

> random pieces of DNA?

 

While AFAIK,it would make sense, I don't think so: we know of such virusses. In fact, IIRC part of the genetic evidence of that humans and apes have a common ancestor is just that.

I'm not sure that this means there is a completely new form of life out there that we don't know about. To try to define useless RNA as life would mean really defining life itself again...

 

 

So what is life? Is it sentience, or the ability to reproduce? The ability to feel emotion? Or simply being made of organic matter?

 

I think it's evidence of something, not that I know what that something is, and we just have to figure it out. 

[Hyperqube]

> So what is life? Is it sentience, or the ability to reproduce? The ability to feel emotion? Or simply being made of organic matter?

well, while there's no clear cut definition of when something is alive - bacteria are considered alive, and virusses, while borderline, aren't. so a few awnsers can be given

• ability to reproduce - no
• emotion - no
• organic material - no.
• sentience... perhaps. depends on how one defines sentience

 

 

 

> I'm not sure that this means there is a completely new form of life out there that we don't know about. To try to define useless RNA as life would mean really defining life itself again...

 

you're mixing the two up:

• the wikipedia's BDM  - the posibility of a completely new form of life -
  is generic material found inside a human, not of a human.
• The phys's BDM - the presumably useless RNA - is of a human -
  are the parts of our genetic code that apparently contain the blueprint for RNA instead of enzymes and stuff.

the 'completely new lifeform' wikipedia talks about would be like archaea: to the leymen it would be just the same as other single celled organisms, but instead biologist would point out that for this and that reason they don't fit any of the currently existing categories.