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Author Topic:   Did viruses precede other life?
SUnderwood
Inactive Member


Message 16 of 32 (145688)
09-29-2004 2:10 PM
Reply to: Message 14 by extremophile
09-28-2004 10:52 PM


Re: horizontal gene transfer
Look, for God sake if you don't understand what I'm saying read the damned website! The major issue here is your "belief" that micro-evolution by genetic allel mutation actually provides real beneficial change to the genetic structure. IT DOESN'T! Genetic faults are VERY RARE!! Yes, you see organisms with problems, (i.e. sickle cell) but consider how many hundreds of billions of cells YOU are made out of, and each person is made out of, if so-called micro-evolution had any MAJOR effect on the genetic code, it would be obvious! Cells within us would have different genetic code!
Get out of the dogmatic BOX! Read the website, at least read the Whats New section to see the gradual build up of evidence. You are an intelligent person, i can see that, but don't let yourself be trapped. The only way out is to read. You've said yourself before you haven't read much about it. Read about it and come back.
I have to say its very interesting talk to you because you make me think.
quote:
Doesn't seems to me that this genetic macro evolution by HGT would have a different effect phenotypically than normal mechanisms of genetic-microevolution
HGT transfers WHOLE WORKING GENES! WHOLE PROTEINS! Whole TOOLS that the cell can use. Micro-evolution provides single allel mutations, that will invariably destroy protein effectiveness (i.e. sickle cell) and the probably the organism, if it ever gets past gestation.
quote:
since the activation of a H-acquired gene would depends of a regular mutation, which could "hit" any non-expressed gene that came to existance by mutation too
1st u've made an assumption that muation occurs only on non-expressed portions of the genome. Thats wrong. When it does happen it will happen more likely to expressed "working" regions.
However, you've made me think a little. I would reply this:
Again, random mutation is VERY RARE! The repair mechanism of cells are extremely efficient. You will notice that genetisists say there are regulator regions which change more frequently. Those areas of the genomes which ARE frequently altered via "mutation" seem to be under directed alteration by the genome itself. As yet I haven't come across a piece of research that documents the genetic alteration of a genome by "self-mutation" (except for the rearrangement of genes in general) but I think thats because no-one is looking for it.
quote:
I don't understand much of this
Look, please, following this link and read just this one page.
Interesting links on it are
* More about photosynthesis by gene transfer
* Gene transfer among eukaryotes
* Halobacteria can repair badly damaged DNA
* More animal genes came from bacteria
* Microbes have stolen some of our genes!
And more.
What'sNEW in Cosmic Ancestry. by Brig Klyce
Panspermia is a beautiful theory. And if you're interesting in quantum physics and organic systems, its even more amazing theory than the pure genetics side can "see".
Sean

This message is a reply to:
 Message 14 by extremophile, posted 09-28-2004 10:52 PM extremophile has replied

Replies to this message:
 Message 18 by crashfrog, posted 09-29-2004 2:25 PM SUnderwood has replied
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SUnderwood
Inactive Member


Message 17 of 32 (145691)
09-29-2004 2:24 PM
Reply to: Message 13 by Ooook!
07-02-2004 5:43 AM


Hi ooook
Here is some evidenace from What'sNEW in Cosmic Ancestry. by Brig Klyce
Gene transfer among eukaryotes Two independent studies show that there have been horizontal gene transfers between parasites and their vertebrate or plant hosts. "The huge significance of horizontal gene transfer for the evolution of prokaryotes has been known for a long time, as has the large contribution that intracellular endosymbiont ancestors of mitochondria and chloroplasts have made to eukaryotic genomes.... Studies such as these show that ongoing horizontal gene transfer from a range of parasites and endosymbionts might be more important for eukaryotic evolution than we previously realized just how important remains to be seen."
Nick Campbell, "Genome Evolution: Give and take" [article], p 638-639 v 5, Nature Reviews Genetics, Sep 2004.
Nature - Not Found
More about photosynthesis by gene transfer. In 2002, geneticists Raymond, Zhaxybayeva et al. used whole genome comparisons to conclude that photosynthesis in five groups of prokaryotes was acquired by gene transfer. In 2003, biologists at the University of Warwick found photosynthesis genes in a virus, S-PM2. Now, a team of biologists from Boston and San Diego "report the presence of genes central to oxygenic photosynthesis in the genomes of three phages from two [other] viral families...." The abstract of their writeup mildly concludes, "These gene transfers are likely to play a role in the fitness landscape of hosts and phages in the surface oceans." We note that evidence supporting gene transfer as the source for new genetic programs continues to accumulate. Meanwhile, evidence supporting a darwinian mechanism as the source for new genetic programs is lacking.
Debbie Lindell et al., "Transfer of photosynthesis genes to and from Prochlorococcus viruses" [abstract], p 11013-11018 v 101, Proc. Natl. Acad. Sci. USA, 27 July 2004.
Just a moment...
More animal genes came from bacteria. According to a report coming in the July 2004 issue of Trends in Genetics, genes for enzymes involved in the manufacture of important chemical messengers were transferred from bacteria to animals, perhaps half a billion years ago. The genes are essential for animal functions including learning, memory, mental alertness, sleep patterns, and allergic responses. NIH's website reports:
"For the study, the researchers conducted a comprehensive search of the National Library of Medicine's genetic databases. They identified a group of genes needed to make some enzymes involved in the manufacture of the chemical messengers that cells use to communicate. The genes are present in bacteria and in vertebrate animals, but with a few exceptions, not in plants, or other complex living organisms. The search was prompted by the group's earlier observation that [another] enzyme ...was present in animals, bacteria, and yeast, but in no other living organisms.
"It is not known how the genes were transferred, but [one member of the research team, David] Klein, theorizes that one form of transfer took place during the reproductive cycle, with the genes having been incorporated into either sperm or egg cells or incorporated shortly after fertilization. It's possible that the transfer could also represent a form of infection where genetic material is transferred into these reproductive cells and thereby into the entire genome of the recipient."
According to our reasoning, wholly new genetic programs must be acquired by gene transfer. The new report from NIH adds to the growing list of apparent examples of this process. Examples documenting the darwinian creation of new genetic programs remain few in number and very weak. [Thanks, Newshub.]
Genes Promoting Nerve, Other Cell Communications May Have Come From Bacteria, National Institutes of Health (NIH), 1 June 2004.
Request Rejected
Genes Promoting Nerve, Other Cell Communications May Have Come From Bacteria, ScienceDaily.com, 3 June 2004.
http://www.sciencedaily.com/...ases/2004/06/040603063920.htm
Viruses old as life? When virologists analyzed a hyperthermophilic virus from an archaeal host living in a Yellowstone hot spring, they found "astounding" conformational relationships linking it to known viruses of bacteria and animals. They conclude, "some viruses may have a common ancestor that precedes the division into three domains of life > 3 billion years ago."
George Rice et al., "The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life" [abstract], Proc. Natl. Acad. Sci. USA online, 3 May 2004.
http://www.pnas.org/cgi/content/abstract/0401773101v1
Organelles transfer genes, wholesale, to eukaryotes, an international team of biologists based in Australia reports. This mechanism is yet another way for gene transfer to install genetic programs into eukaryotic species. Among the team's findings
"Genome sequences reveal that a deluge of DNA from organelles has constantly been bombarding the nucleus since the origin of organelles.... at frequencies that were previously unimaginable.
"Phylogenetic analyses and genome comparisons show that influx of organellar DNA to the nucleus has had a marked quantitative impact on the gene content of eukaryotic chromosomes.
"Translocated genes might be expressed to provide products that are targeted to all parts of the cell.
"This mechanism of natural variation is unique to eukaryotic cells and was an important force in the genesis of eukaryotic genomes."
Jeremy N. Timmis, Michael A. Ayliffe, Chun Y. Huang and William Martin, "Endosymbiotic Gene Transfer: Organelle Genomes Forge Eukaryotic Chromosomes" [abstract], p 123-135 v 5 n 2, Nature Reviews Genetics, Feb 2004.
Nature - Not Found

This message is a reply to:
 Message 13 by Ooook!, posted 07-02-2004 5:43 AM Ooook! has replied

Replies to this message:
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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 18 of 32 (145692)
09-29-2004 2:25 PM
Reply to: Message 16 by SUnderwood
09-29-2004 2:10 PM


Yes, you see organisms with problems, (i.e. sickle cell) but consider how many hundreds of billions of cells YOU are made out of, and each person is made out of, if so-called micro-evolution had any MAJOR effect on the genetic code, it would be obvious! Cells within us would have different genetic code!
What the fuck?
Exactly what sort of selection pressure do you think my individual cells experience?

This message is a reply to:
 Message 16 by SUnderwood, posted 09-29-2004 2:10 PM SUnderwood has replied

Replies to this message:
 Message 19 by SUnderwood, posted 09-29-2004 2:31 PM crashfrog has replied

  
SUnderwood
Inactive Member


Message 19 of 32 (145694)
09-29-2004 2:31 PM
Reply to: Message 18 by crashfrog
09-29-2004 2:25 PM


Read a little more. I'm saying that genetic allel mutation occur very rarely.

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 Message 18 by crashfrog, posted 09-29-2004 2:25 PM crashfrog has replied

Replies to this message:
 Message 20 by crashfrog, posted 09-29-2004 2:50 PM SUnderwood has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 20 of 32 (145701)
09-29-2004 2:50 PM
Reply to: Message 19 by SUnderwood
09-29-2004 2:31 PM


I'm saying that genetic allel mutation occur very rarely.
Over the lifetime of an organism, yes, that's true.
Over the lifetime of a population, mutations are copious.

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 Message 19 by SUnderwood, posted 09-29-2004 2:31 PM SUnderwood has replied

Replies to this message:
 Message 21 by SUnderwood, posted 09-29-2004 2:57 PM crashfrog has replied

  
SUnderwood
Inactive Member


Message 21 of 32 (145707)
09-29-2004 2:57 PM
Reply to: Message 20 by crashfrog
09-29-2004 2:50 PM


No, allel mutation is not cupious. A lot of mixing occurs due to fertilisation, but mutation of allels does not occur often. Don't get the two confused.
And you can't talk about over the lifetime of a population. thats doesn't make sense. Of a species, well, yes, mutation of allels does occur quite often over millions of years or so, and most die because of it, so are a hinderance to evolution (or a benefit, as that mutation was deleted and not passed on).
This message has been edited by SUnderwood, 09-29-2004 02:04 PM

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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 22 of 32 (145709)
09-29-2004 3:04 PM
Reply to: Message 21 by SUnderwood
09-29-2004 2:57 PM


No, allel mutation is not cupious. A lot of mixing occurs due to fertilisation, but mutation of allels does not occur often.
Over the lifetime of a population, it does occur often. According to Molecular Evolution: A Phylogenetic Approach (Page, Colmes; Blackwell Science, 1998), a graduate level genetics text, the average number of synonymous substitutions in mammalian nuclear DNA is about 3.5e-9 per base, per year.
There's a lot of bases, and a lot of mammals. 3 or 4 per billion bases every year is a lot of mutations to a population.
And you can't talk about over the lifetime of a population. thats doesn't make sense.
In fact, viewing it from the perspective of populations is the only way that evolution makes sense. Populations grow and divide; it makes perfect sense to talk about the "lifetime" of a population.
This message has been edited by crashfrog, 09-29-2004 02:06 PM

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Rei
Member (Idle past 7013 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 23 of 32 (145719)
09-29-2004 3:24 PM
Reply to: Message 22 by crashfrog
09-29-2004 3:04 PM


Not to mention how significant one BP mutation can be. It's always interesting when people trace back the presence of a mutation - say, a human tail, or an XY female - to its genetic cause. Often there's only a few BP mutation that was ultimately the reason for the change.

"Illuminant light,
illuminate me."

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SUnderwood
Inactive Member


Message 24 of 32 (145736)
09-29-2004 4:13 PM
Reply to: Message 22 by crashfrog
09-29-2004 3:04 PM


I take your point. Synonymous substitutions is more frequent than I had thought. But codon substitutions is still deleterious. The paper to which you refer is interesting in its conclusions, that amino acid substitution is deleterious, whilst nucleotide subsitution (depending on its synonymity) is not, necesarily. My apologies, I have mixed up the codons and allels. Thank you very much for the reference.
The paper referenced does howver provides support to the argument, that evolution, at the protein level, is a rare event, and that nucleotide mutation (and so codon change) is usually damaging. HGT, then, is still a major source of genetic information.
BTW, did u read the list of references which I posted?

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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 25 of 32 (145742)
09-29-2004 4:37 PM
Reply to: Message 24 by SUnderwood
09-29-2004 4:13 PM


But codon substitutions is still deleterious.
Not universally, and remember, "deleterious" is generally only meaningful in reference to environment. For instance, is a mutation conferring longer, thicker fur advantageous or deleterious?
It depends on if you live in the arctic circle or the Sahara desert.
BTW, did u read the list of references which I posted?
No - I'm not certain I have the background to engage you on your main point. I simply wanted to clear up some of your misconceptions.

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extremophile
Member (Idle past 5595 days)
Posts: 53
Joined: 08-23-2003


Message 26 of 32 (145831)
09-29-2004 10:23 PM
Reply to: Message 16 by SUnderwood
09-29-2004 2:10 PM


Re: horizontal gene transfer
quote:
Look, for God sake if you don't understand what I'm saying read the damned website! The major issue here is your "belief" that micro-evolution by genetic allel mutation actually provides real beneficial change to the genetic structure. IT DOESN'T! Genetic faults are VERY RARE!! Yes, you see organisms with problems, (i.e. sickle cell) but consider how many hundreds of billions of cells YOU are made out of, and each person is made out of, if so-called micro-evolution had any MAJOR effect on the genetic code, it would be obvious! Cells within us would have different genetic code!
Get out of the dogmatic BOX! Read the website, at least read the Whats New section to see the gradual build up of evidence. You are an intelligent person, i can see that, but don't let yourself be trapped. The only way out is to read. You've said yourself before you haven't read much about it. Read about it and come back.
ave to say its very interesting talk to you because you make me think.
Thanks. I do not consider myself a dogmatic person (although hardly someone dogmatic would admit it easily), there's a lot of things that I don't understand, and there's the way I understand things. And, in the way I understand things (that might be wrong, of course) this thing of HGT driving evolution didn't seems to make much sense. I'll keep with this further on the message, now I just want to say that there's a considerable time since I'm planning to read this site, among lots of other stuff (such as things about directed - or not - mutations). I didn't read it yet due to lack of time, not because dogmatic refusal or something. Actually, even if I was "against" this idea (but in this case I'm more curious than against), it would paradoxically increase my interest about that... it happened with creationism and some other alternatives ways of evolution that I've briefly heard (although I couldn't find much things on these yet).
quote:
HGT transfers WHOLE WORKING GENES! WHOLE PROTEINS! Whole TOOLS that the cell can use. Micro-evolution provides single allel mutations, that will invariably destroy protein effectiveness (i.e. sickle cell) and the probably the organism, if it ever gets past gestation.
...but, genes really work this way? Like man-made program sub-routines? Don't they generally depends on the "context" of the genome?The site provides examples of possible traits/sequences acquired this way?
... I don't want to bomb you with all the questions that came to my mind, but, anyway, just one more for this part of the post... what about phylogeny? How much the standard phylogenetic tree would be affected by this theory, or it stays the way it is? Seems to me that if HGT is more frequent and relevant than commonly thought, then many shared characters could not be due to common descent, but due to HGT. But yet I guess that the phylogenetic tree would retain the same basic look of a tree, with the addition of a tangled web of thin "veins" linking many branches... but... I have no idea yet of what could be those H-shared traits....
quote:
1st u've made an assumption that muation occurs only on non-expressed portions of the genome. Thats wrong. When it does happen it will happen more likely to expressed "working" regions.
No, I didn't, I was just making an analogy the most equivalent possible to the example that you gave, where a mutation activates unexpressed genes that were H-acquired, but instead of unexpressed genes H-acquired it could just be a "normal" sequence, that were deactivated for some reason.
And, for the second case, there's, I think, the advantage of the sequence reactivated being a former activated sequence of the same lineage of organisms, so, that wouldn't be a completely odd, alien, sequence suddenly activated, which I think that doesn't differ much of mutationism/saltationism. I think that it would be a problem because the RA Fisher's analogy of the focus adjustment; the more radical a change in an organism is, the more unlikely is to fit in the actual environment, since the fitness of the parent organism obviously is due to its present phenotype. I don't discard totally "hopeful monsters", but I don't think they are the main cause of drastic changes in evolution... but I don't even know if that would be the case with H-inheritance....
That's all for while, I got to go.... but I'll read the next post and the recomended page, and hopefully, more on the site.... but, just one more question... how exactly this stuff of HGT connects with panspermia? Suddenly I realized that we didn't talked of panspermia properly, but only about stuff that can exist independently, and, maybe be some sort of support for that (yet I couldn't wonder much far how would that be)
sorry if I left some part unanswered (I probably did), I'll check that later....

This message is a reply to:
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Ooook!
Member (Idle past 5815 days)
Posts: 340
From: London, UK
Joined: 09-29-2003


Message 27 of 32 (145931)
09-30-2004 8:44 AM
Reply to: Message 17 by SUnderwood
09-29-2004 2:24 PM


Hello SUnderwood,
Good to see this topic up and running again.
A few points:
As you can see from my previous posts to Razd I don't think it's unreasonable to think that HGT drove early evolution (ie before the split into the three distinct domains): the 'bushiness' of the 'tree' of life () at this stage is testament to the amount of genes whizzing from organism to organism. I also don't dispute the evidence that suggests there being a transfer of genes from symbionts to the nucleus of hosts. But I have a few reservations about making the bold claims you seem to be making.
  1. Although I accept that there does seem to be transfer of genes from parasite to hosts (and presumably visa versa), the extent to which this happens and its' evolutionary significance is unclear. To quote from one of your cited papers:
    quote:
    just how important remains to be seen
  2. It is clear that transfer of genes from the protobacterial progenitors of mitochondria and chloroplasts was central to the evolution of a separate Eukaryotic 'identity'. However, extrapolating this to suggest that it supports a role for HGT in 'macro' events further down the line is an error. I simply don't think that the evidence is there.
  3. Once past the promiscuous beginnings of life, genetic phylogenies tend to demonstarte a very vertical pattern of gene transference. If you have any evidence for large scale HGT I honestly would be interested to see it.
  4. The evidence to date is that the best candidate mechanism for generating change (on a large or a small scale) is gene duplication and changes in gene expression patterns. While viruses and other transposable elements do have a role in such duplication events the effect is very much vertical - gene duplications run in families.
To sum up: an interesting idea, but nothing to shout about (yet)
Cheers
Edit: Got my laterals and verticals mixed up - which can be quite painful I can tell you!
This message has been edited by Ooook!, 09-30-2004 10:35 AM

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Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 28 of 32 (147523)
10-05-2004 1:05 PM
Reply to: Message 25 by crashfrog
09-29-2004 4:37 PM


Ah, the carnivore in me, druuuls...
It is not time for me- but WHEN IS an ANGLE not the pectoral fin handle- when it is snapping the turtle soup--
You would have had to think of the SAMPLE outside the code but within your posting discourse for one to have thought yous two confused the shape of the organism for a different environment. but then we get the the artic compared with the sahara here. Oh how I wish panbiogeography was better used.
I put my record in - NO I DONT THINK VIRUSES "PRECEDED" other life. just like I think virus as AIDS is a more sociological than anthropological. I do know that cartoons were made of algebraists however.

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Lex_Luthor
Inactive Member


Message 29 of 32 (313954)
05-20-2006 4:32 PM


A virus could not precede life for the simple reason that a virus requires a host to survive.
Edited by Lex_Luthor, : No reason given.

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Chiroptera
Inactive Member


Message 30 of 32 (313961)
05-20-2006 5:12 PM
Reply to: Message 29 by Lex_Luthor
05-20-2006 4:32 PM


Hiya, Lex.
It is true that a virus needs a host. However, that host need not have been something that we would consider to be "life" -- the original hosts of viruses (virii?) may have been precursors that were far simpler than what we would be comfortable with assigning to the category of "living".
Here is an link to an article to which I have already posted that suggests that viruses may have been an important contributor to what eventually became "life".

"We must respect the other fellow's religion, but only in the same sense and to the extent that we respect his theory that his wife is beautiful and his children smart."
-- H. L. Mencken (quoted on Panda's Thumb)

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