Viruses intentionally choose how they infect


(Martin R) #81

They are more recent insertions … how is that? i thought these insertions are like millions of years old…


(Steve Schaffner) #82

Millions of years ago is recent. Hundreds of millions of years is old.


(Martin R) #83

we share ERVs with other primates, is that correct?

how old is the oldest known shared ERV sequence which still can be recognized in the human genome? If you can say…


(Martin R) #84

so there is still the possibility that viruses were designed… would you agree?


(Steve Schaffner) #85

Yes.
The oldest reported ERV (as of 2013) was estimated to have a minimum age of 100 million years.


(Martin R) #86

if i would design a virus in front of you, would that be acceptable as a proof that viruses have been designed?

(i predict your answer: no, because it still could have emerged by chance, but we scientists can’t show how)


(Martin R) #87

ok, so this one belongs to the ‘old’ category…

“The longer an ERV is in a genome the more mutations it accumulates and the more it can recombine with sequences around it. After many years it may not be easily recongized as an ERV.”

so are you saying, that you were able to recognize 100,000,000 years old ERV sequence?
How many such old ERV sequences are in the human genome which can be recognized after 100,000,000 years ? If you can tell… i apologize for silly questions…


(Steve Schaffner) #88

Not me, but researchers claimed to do so. They estimate that the maximum age they could do this for would be 150,000,000 years.

Not a silly question, but not one I know the answer to.


(Martin R) #89

if you don’t know the answer, perhaps i should start a new thread. I will wait a little, perhaps someone else replies…

Because, this is very interesting…

The other guy (T_aquaticus) wrote:

“The longer an ERV is in a genome the more mutations it accumulates and the more it can recombine with sequences around it. After many years it may not be easily recongized as an ERV”

and now i learned that 100,000,000 years old ERV sequence(s) can be still recognized.
So i am confused.

It reminds me on an article on so called ultraconserved DNA elements.

Wikipedia:

“An ultra-conserved element (UCE) is a region of DNA that is identical in at least two different species.[1] One of the first studies of UCEs showed that certain human DNA sequences of length 200 nucleotides or greater were entirely conserved (identical nucleic acid sequence) in human, rats, and mice”

“Perfect conservation of these long stretches of DNA is thought to imply evolutionary importance as these regions appear to have experienced strong negative (purifying) selection for 300-400 million years”

“481 ultra-conserved elements have been identified in the human genome.[1][2] A database collecting genomic information about ultra-conserved elements (UCbase) that share 100% identity among human, mouse and rat …”

“Currently, there is no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.” i can imagine…


(Mitchell W McKain) #90

When asked if a virus is alive, I always say yes. Then I explain that life is a highly quantitative thing and that compared to us the life of a virus is infinitesmal. All the learning and adaptability is not in the individual viruses but only in the species as a whole. That is why the question of the op sounds a bit absurd to me, going way too far in the direction that I am usually defending.

I don’t believe in design (when it comes to life), but I do not believe things like purpose and intention require design. For me the whole point of evolution and abiogenesis is that these things as well as creativity and intelligence are emergent from the operation of natural law. But design is where I draw the line, for that is the difference between living things and machines. So in answer to the above questions about a virus which is designed I would say it is an examble of a biochemical machine whereas a virus which has evolved is an example of life – not a whole lot of life there, almost none, but life nevertheless.


(Martin R) #91

are there any ERV sequences not shared by all humans ? If you can tell…


(Steve Schaffner) #92

What are you confused about? What @T_aquaticus wrote is correct: mutations eventually wipe out the evidence of ERVs. Based on the paper I referenced, “eventually” means “after roughly 150 million years.” (Technical note: this applies only to full-length ERVs; most ERVs only retain one of their long terminal repeat region, and will be detectable for a shorter period.)


(Martin R) #93

to be honest, the more i know the more i am confused…

The other guy (T_aquaticus) used a scientific term “after many years” we won’t be able to recognize ERVs insertions in our genomes.

so i have asked, what does “after many years” mean. He replied, it is like 100 million of years.

Then i said, alright, what is the oldest known ERV, … he said, it is like 100 million of years old…

and then i said, ok, so why we can still recognize it?

So first he said “after many years”, then after “100,000,000 of years” and now YOU said “after 150,000,000 of years” where do you guys get these numbers?

By the way, how lucky we are that we live in the time period where ERVs are still recognizable … would you agree?


(Martin R) #94

additional question, why it is still there? Oldest ERV sequence 100,000,000 years old. When i got this right, it is a parasitic insertion, so why it is still there? If you can speculate…


(Steve Schaffner) #95

I still don’t know what you’re confused about.

Okay, so the idea is that roughly 100 million years is how far back we can recognize ERVs.

Because it still looks like an ERV.

“About 150 million years” and “maximum of 150 million years” are giving you the same answer. My number comes from this paper.


(Steve Schaffner) #96

Either because it does nothing – it’s a dead parasite – or part of it turned out to be useful. DNA gets passed on until something happens to it.


(Steve Schaffner) #97

Yes. Particular ERV insertions of the lineage called HERV-K(HML2) are present in some but not all humans.


(Martin R) #98

alright, now i am no longer confused. So it does not take ‘many years’ nor ‘100,000,000 years’ but 150,000,000 years… and then, ERVs won’t be recognizable… as i said before, how lucky we are we live in the era we can recognize 200,000 ERVs insertions…


(Martin R) #99

anyway, it is a funny thing… 3rd party parasitic organisms insert 200,000 times in the genome and nothing gets broken … 200,000 insertions… all the organisms still intact… and, of course, natural selection loves those 200,000 insertions too…


(Steve Schaffner) #100

No. It does indeed take many years, because 150 million years is many years. It also takes roughly 100 million years, because 150 million years is roughly 100 million years. All three statements are true, but with different degrees of precision.

In what era wouldn’t we have been able to recognize 200,000 ERVs?