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Your Genes: More Virus than Human - Comments

Chris Boccia's Avatar Comment 1 by Chris Boccia

I love information. Always learning.

Tue, 21 Jun 2011 05:49:47 UTC | #641079

dreamer-71's Avatar Comment 2 by dreamer-71

Just by chance, I just finished listening earlier today to Carl Zimmer's speech "Viral Time" on this subject to the Long Now Foundation. Interesting stuff. You can d/l the podcast from iTunes or from here: http://longnow.org/seminars/02011/jun/07/viral-time/ (A little over 1.5 hours long, but worth the listen.)

Tue, 21 Jun 2011 06:25:38 UTC | #641087

Michael Austin's Avatar Comment 3 by Michael Austin

Certainly we would just find some new way of giving birth, considering the infinitely high selection pressure for this trait.

Tue, 21 Jun 2011 06:31:56 UTC | #641088

justinesaracen's Avatar Comment 4 by justinesaracen

Jeez, you just can't tell your friends from your foes any more.

It used to be so simple, at least in my naive uneducated mind. The healthy human body was something basically 'clean' and it got sick when a bacteria or a virus entered it. But now we discover that not only are we choc-a-block full of bacteria, but viruses lurk about in our very make-up. It's hard to get one's mind around that.

What is health, then? And how did we get it? Is it just the brief moment when the gyroscope of competing microscopic entities are temporarily in balance?

Full disclosure here: I'm home with the flu and trying to figure out what I did wrong so that I got this.

Tue, 21 Jun 2011 07:44:03 UTC | #641098

Stefan Udrea's Avatar Comment 5 by Stefan Udrea

Since when it's 8% more than 92 % ?!

Tue, 21 Jun 2011 07:53:15 UTC | #641103

hemidemisemigod's Avatar Comment 6 by hemidemisemigod

Comment 4 by esuther :

Jeez, you just can't tell your friends from your foes any more.

It used to be so simple, at least in my naive uneducated mind. The healthy human body was something basically 'clean' and it got sick when a bacteria or a virus entered it. But now we discover that not only are we choc-a-block full of bacteria, but viruses lurk about in our very make-up. It's hard to get one's mind around that.

There's a hypothesis that some viruses may have evolved from bits of DNA from larger organisms. So that a virus might evolve from the DNA of one animal and end up infecting another different animal species in such a way that ends up with its DNA being incorporated and passed on to future generations.

Tue, 21 Jun 2011 08:39:54 UTC | #641117

Krasny's Avatar Comment 7 by Krasny

"We are viruses that have learned how to wear socks"

It seems the urban philosopher Denis Leary was right after all.

Tue, 21 Jun 2011 09:20:00 UTC | #641139

Ignorant Amos's Avatar Comment 8 by Ignorant Amos

Comment 5 by Stefan Udrea

Since when it's 8% more than 92 % ?!

Listen to it again.....1.2% of our genome is protein coding genes, about 20,000. In comparison, viruses have about 100,000 elements or 8-9%.....don't forget about all the redundancy from history we pack, there's your 90% excess baggage.... crudely explained I know, an "expert" here will refine.

Tue, 21 Jun 2011 12:06:23 UTC | #641186

Mathias B's Avatar Comment 9 by Mathias B

Does this fall under lateral gene transfer? How does it affect the tree of life analogy?

Tue, 21 Jun 2011 12:08:15 UTC | #641187

Stefan Udrea's Avatar Comment 10 by Stefan Udrea

Comment 8 by Ignorant Amos :

Comment 5 by Stefan Udrea

Since when it's 8% more than 92 % ?!

Listen to it again.....1.2% of our genome is protein coding genes, about 20,000. In comparison, viruses have about 100,000 elements or 8-9%.....don't forget about all the redundancy from history we pack, there's your 90% excess baggage.... crudely explained I know, an "expert" here will refine.

Ah, I see ; thanks.

Tue, 21 Jun 2011 12:30:31 UTC | #641195

ai1888's Avatar Comment 11 by ai1888

Comment 8 by Ignorant Amos :

Comment 5 by Stefan Udrea

Since when it's 8% more than 92 % ?!

Listen to it again.....1.2% of our genome is protein coding genes, about 20,000. In comparison, viruses have about 100,000 elements or 8-9%.....don't forget about all the redundancy from history we pack, there's your 90% excess baggage.... crudely explained I know, an "expert" here will refine.

Excess baggage? Not at all. The redundant portions of the genome are now being found out as very important regulatory segments, which play roles in transcription regulation and epigenetics. In no way is 90% of our genome excess baggage.

Tue, 21 Jun 2011 12:39:22 UTC | #641197

DavidMcC's Avatar Comment 12 by DavidMcC

Comment 6 by hemidemisemigod :

There's a hypothesis that some viruses may have evolved from bits of DNA from larger organisms. So that a virus might evolve from the DNA of one animal and end up infecting another different animal species in such a way that ends up with its DNA being incorporated and passed on to future generations.

Do you have a reference to that by any chance, h'd's'god?

Tue, 21 Jun 2011 12:42:43 UTC | #641200

Nunbeliever's Avatar Comment 13 by Nunbeliever

Fascinating. Just fascinating!

Tue, 21 Jun 2011 12:45:32 UTC | #641202

DavidMcC's Avatar Comment 14 by DavidMcC

Apparently, he's talking about HERV-W-type retroviruses in human placental syncytiotrophoblasts expressing highly fusogenic env-type glycoproteins

You learn something new every day! :)

Tue, 21 Jun 2011 13:01:37 UTC | #641211

Schrodinger's Cat's Avatar Comment 15 by Schrodinger's Cat

Is this an example of the extended phenotype, or the reverse of it.......where external genes affect the environment of an organism to an extent that allows them to then become part of the genetic material ?

Tue, 21 Jun 2011 15:14:40 UTC | #641284

hemidemisemigod's Avatar Comment 16 by hemidemisemigod

Comment 12 by DavidMcC :

Comment 6 by hemidemisemigod :

There's a hypothesis that some viruses may have evolved from bits of DNA from larger organisms. So that a virus might evolve from the DNA of one animal and end up infecting another different animal species in such a way that ends up with its DNA being incorporated and passed on to future generations.

Do you have a reference to that by any chance, h'd's'god?

Yes, here at Wiki

Tue, 21 Jun 2011 15:22:24 UTC | #641289

ridelo's Avatar Comment 17 by ridelo

I have a question: I liked this video so much that I wanted to make subtitles in Dutch for it. Therefore I first had to transcribe it in English (making English subtitles, that is). But there are a few passages that were unclear for me or where I'm unsure I understood. Is here somebody here willing to correct my mistakes? Here is the link to the transcribed video.

Tue, 21 Jun 2011 15:25:57 UTC | #641290

Luke_B's Avatar Comment 18 by Luke_B

Sorry for being off topic but I couldn't let Krasney's comment pass without pointing out that he stole that off Bill Hicks (who described us 'a virus with shoes').

Sorry but needed to be said.

Tue, 21 Jun 2011 16:01:44 UTC | #641306

Tyler Durden's Avatar Comment 19 by Tyler Durden

Comment 15 by Schrodinger's Cat :

Is this an example of the extended phenotype, or the reverse of it.......where external genes affect the environment of an organism to an extent that allows them to then become part of the genetic material ?

This sounds like (imho) an example of the extended phenotype where viruses are able to influence the cellular chemistry of the host "at an intimate level... (and) exert considerable power over host phenotypes." - page 226.

As Richard also says in TEP (1982):

"The extended phenotype reaches out of the body in whose cells the genes lie, reaches out to the living tissues of other organisms." - page 220

This could be the process descibed in Comment 16 by hemidemisemigod regarding DNA/viruses, which natural selection has favoured.

Also, with regard to the 'central theorem' of the extended phenotype:

"An animal's behaviour tends to maximize the survival of the genes 'for' that behaviour, whether or not those genes happen to be in the body of the particular animal performing it." - page 233

Tue, 21 Jun 2011 17:44:52 UTC | #641346

MilitantNonStampCollector's Avatar Comment 20 by MilitantNonStampCollector

Comment 7 by Krasny :

"We are viruses that have learned how to wear socks" It seems the urban philosopher Denis Leary was right after all.


Probably his only original contribution to comedy, seeing as he ripped off Bill Hicks so much.

Tue, 21 Jun 2011 18:03:22 UTC | #641357

MilitantNonStampCollector's Avatar Comment 21 by MilitantNonStampCollector

Could somebody explain how we are more virus than human? I know there are lots and lots of junk bits and leftover dead genes etc, but more virus than human?

Tue, 21 Jun 2011 18:09:10 UTC | #641359

lackofgravitas's Avatar Comment 22 by lackofgravitas

Genes coding for protein transcription keep us alive, doing the day-to-day stuff of life. They keep us alive. They are the genes that code how a collection of cells becomes a foetus, in what order those cells differentiate, how the foetus develops. Quite fundamental stuff. Yet we have more genes in our DNA that have a common source, but isn't originally part of our ancestral mammalian DNA. We have more viral genes than protein transcription genes.

I think it's acceptable, but would argue that 90% is junk. More likely that 90% has an unknown potential. As mentioned earlier, some of the 'junk genes' are involved in gene regulation. Evolution, as a process, tends to conserve beneficial traits, so I think we can assume there will be very little 'junk' once the whole genome is 'figured out'.

As a slight aside, I'd also recommend The Long Now Foundation as something for all of us to familiarise ourselves with. Forward thinking doesn't even begin to cover what they are doing.

Declaration of COI: I'm a member.

Tue, 21 Jun 2011 18:53:45 UTC | #641375

Schrodinger's Cat's Avatar Comment 23 by Schrodinger's Cat

Comment 22 by lackofgravitas

As a slight aside, I'd also recommend The Long Now Foundation as something for all of us to familiarise ourselves with. Forward thinking doesn't even begin to cover what they are doing.

I came across them quite by accident a few months ago when looking for Brian Eno ( one of the founders of The Long Now Foundation ) music on Utube.

Mr Eno is extremely errudite and explains the foundation of the project...

http://www.youtube.com/watch?v=9y3H1fuxXE8

The video at the head of this thread is actually an extension of material one can find here.....

http://longnow.org/seminars/02011/jun/07/viral-time/

Tue, 21 Jun 2011 20:18:52 UTC | #641412

DavidMcC's Avatar Comment 24 by DavidMcC

Comment 16 by hemidemisemigod :

Comment 12 by DavidMcC :

Comment 6 by hemidemisemigod :

There's a hypothesis that some viruses may have evolved from bits of DNA from larger organisms. So that a virus might evolve from the DNA of one animal and end up infecting another different animal species in such a way that ends up with its DNA being incorporated and passed on to future generations. Do you have a reference to that by any chance, h'd's'god?

Yes, here at Wiki

I think you are misinterpreting the Wiki article, h'd's'god. The DNA recombination doesn't create a brand new virus from itself, probably becasue viruses are too complicated to be fully formed by such a chance event.

Wed, 22 Jun 2011 12:43:39 UTC | #641660

DavidMcC's Avatar Comment 25 by DavidMcC

... The evolving species is the host, IMO.

Wed, 22 Jun 2011 13:03:20 UTC | #641666

DavidMcC's Avatar Comment 26 by DavidMcC

More on HERV-W: onlinelibrary

Beneficial Functions of HERVs ... Of even greater significance is the fact that the placentas of primates, including humans,52 produce retrovirus particles.53–55 Originally observed by electron microscopy and later supported by the demonstration that the trophoblast specific human growth factor pleiotrophin (PTN) is under the control of a HERV LTR,56 these results prompted studies of HERV expression in placentas. In syncytiotrophoblasts, but not in cytotrophoblasts, high levels of HERV-W and HERV-FRD envelope proteins are demonstrable, named syncytin-1 and syncytin-2, respectively,57–59 and additional HERV env proteins were subsequently detected in syncytiotrophoblasts.58, 60 Retrovirus envelope proteins are anchored in the lipid bilayer membrane of both viral particles and cell surface membranes and initiate the fusion of viral and cellular membranes during the infection process. In cases where the cell surface viral envelope protein can interact with its receptor on adjacent cells, they have also been shown to cause fusion of infected and uninfected cells. Thus, the cell–cell fusogenic activity mediated by HERV Env proteins probably contributes to the physiological placenta morphogenesis by mediating fusion of cytotrophoblasts to syncytiotrophoblasts.61

Placentas are, from the viewpoint of the mother, allogeneic organs and the reasons for maternal tolerance are still only poorly understood. The fetal multinucleated villous syncytiotrophoblast layer acts as the fetal-maternal interface and is responsible, among other functions, for trophic and hormonal exchange. At this boundary, immunological tolerance has to be effective to prevent allogeneic rejection of the fetus. It is therefore not at all surprising that the already known immunosuppressive property of retroviral Env proteins could also be demonstrated for syncytin-2 and other HERV Env proteins, although not for syncytin-1.61 HERVs may therefore be instrumental in safe-guarding placenta morphogenesis, physiology and fetal–maternal tolerance. ...

Wed, 22 Jun 2011 13:21:58 UTC | #641675

DavidMcC's Avatar Comment 27 by DavidMcC

Comment 9 by Mathias B :

Does this fall under lateral gene transfer? How does it affect the tree of life analogy?

I don't think so, Mathias, because the virus isn't acting as an agent to transfer genes from one cellular species to another. All it is is a mechanism that effectively causes evolution of cellular species. Like a very complicated mutation that isn't random, because it contains working genes. It is more like a large DNA duplication event, except that it isn't actually a duplicate of the host DNA.

Wed, 22 Jun 2011 13:59:47 UTC | #641691

Mathias B's Avatar Comment 28 by Mathias B

The topic reminded me of a short story I once read... it's still online at http://www.davidbrin.com/givingplague.htm

Wed, 22 Jun 2011 17:04:18 UTC | #641772

DavidMcC's Avatar Comment 29 by DavidMcC

Comment 22 by lackofgravitas :

Genes coding for protein transcription keep us alive, doing the day-to-day stuff of life. They keep us alive. They are the genes that code how a collection of cells becomes a foetus, in what order those cells differentiate, how the foetus develops. Quite fundamental stuff. Yet we have more genes in our DNA that have a common source, but isn't originally part of our ancestral mammalian DNA. We have more viral genes than protein transcription genes. I think it's acceptable, but would argue that 90% is junk. More likely that 90% has an unknown potential. As mentioned earlier, some of the 'junk genes' are involved in gene regulation. Evolution, as a process, tends to conserve beneficial traits, so I think we can assume there will be very little 'junk' once the whole genome is 'figured out'.

As a slight aside, I'd also recommend The Long Now Foundation as something for all of us to familiarise ourselves with. Forward thinking doesn't even begin to cover what they are doing. Declaration of COI: I'm a member.

The 90% is mainly what you could call "packaging", which plays a vital role in the regulation of gene transcription, as Stefan said. The packaging (known as chromatin) has to be "silent", and prevents uncontrolled gene expression, something that is much less of an issue in bacterial cells, but is vital when most of the genes in a given cell have to remain permanently silent, because they code for the wrong protein(s).

Fri, 24 Jun 2011 08:01:36 UTC | #842154

T F Rhoden's Avatar Comment 30 by T F Rhoden

good stuff!

Fri, 24 Jun 2011 13:07:40 UTC | #842240