Evolution & Viruses

[LiveFreeOrDie]

I made a post in the "germ theory" thread that was slightly OT, but I think rather persuasive in favor of evolution. I'll re-post it here for discussion.

Viruses provide an interesting source for more evidence in favor of evolution.

In certain cases, viruses can insert their own genetic material into the host's genome. (HIV is an example of a virus that is very adept at this). If the insertion happens in the reproductive cells, there is a chance that the viral DNA can then get passed on to the organism's descendants.

Scientists refer to these as endogenous retroviruses, or ERVs. The human genome is in fact full of them. Where evolution comes into play is when scientists examine the similarities in ERVs between species. If two species are closely related by common descent, then theory predicts that they should share similar ERVs as well. As expected, evolution passes this test with flying colors.

The following paper illustrates one experiment where the ERV relationships were tested:

http://www.pnas.org/cgi/content/full/96/18/10254

 

[chickenman]

good one. The phylogenetic trees using maximum likelihood and maximum parsimony analysis of ERV's agree almost perfectly with accepted trees.

i'll be very impressed if anyone can reconcile this with intelligent/common design

wanna have a go npeterly?

 

[LouisBooth]

So anyone who gets a viral infection is a different species? Hmm..So in other words you're saying members of "trees" all get the same DNA, therefore if they get the same virus DNA then that helps evolution? So we get the same diseases and that proves it? Are certain speices more likely to have the same deficiencies when it comes to fighting viruses? I don't see this proving it at all... If I have 4 bikes ... 1 uni 1 bi and 3 tri..they will all have simlar ways they get "broke". Simliar ways they defend against infection, ie viruses..some will be immune to certain things, others will not.

 

[chickenman]

no louis

Endogenous retrovirus loci provide no less than three sources of phylogenetic signal, which can be used in complementary fashion to obtain much more information than simple distance estimates of homologous sequences. First, the distribution of provirus- containing loci among taxa dates the insertion. Given the size of vertebrate genomes (>1 × 109 bp) and the random nature of retroviral integration (22, 23), multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (24). Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place (14). Furthermore, integrated proviruses are extremely stable: there is no mechanism for removing proviruses precisely from the genome, without leaving behind a solo LTR or deleting chromosomal DNA. The distribution of an ERV among related species also reflects the age of the provirus: older loci are found among widely divergent species, whereas younger proviruses are limited to more closely related species. In theory, the species distribution of a set of known integration sites can be used to construct phylogenetic trees in a manner similar to restriction fragment length polymorphism (RFLP) analysis.

Second, as with other sequence-based phylogenetic analyses, mutations in a provirus that have accumulated since the divergence of the species provide an estimate of the genetic distance between the species. Because, for any given provirus, it is highly unlikely that there will be selection for or against any specific sequence, it is safe to assume that the rate of accumulation of mutations approximates the rate of their occurrence, with appropriate corrections for reversion. Analysis of closely related proviruses integrated at different sites should also reveal regional differences in mutation rates.

the problem that this poses for intelligent design is that the sequences support common ancestry, but they can't support common design unless you say that god designed his creations with viral DNA in their genomes, or you believe in incredible coincidences.

I wish I still had access to biomanager (anybody used that site/program? its fantastic for bioinformatics), i'd love to do some phylogenetic trees of my own

 

[LouisBooth]

"you believe in incredible coincidences."

Just to address this..doesn't evolution support this notion?

again, I refer you to what I said...it still seems to apply...

 

[chickenman]

no evolution requires no incredible coincidences at all. perhaps abiogenesis might, but not evolution.

I think you should read the article, there are several reasons why the phylogenetic results are not just because ; "members of "trees" all get the same DNA, therefore if they get the same virus DNA then that helps evolution? "

if your explanation was the correct one, there is absolutely no reason for the viral DNA to occur in the same locations in different species, there is also no reason for their sequences to be such that phylogentic analysis yields an accurate tree- so again we have to come back to "incredible coincidences"

 

[LouisBooth]

"no evolution requires no incredible coincidences at all. "

I disagree. Pretty much all systems in the human body (just for example) are innerdependant and thus have to develop all at once. This is the same thing I see when I took biochem. all the processes are innerdependant and thus have to evolove all at once. Evolution screams increadible coincidences.

 

[chickenman]

well I've done a fair bit of metabolic biochemistry and I don't remember any systems that required every enzyme present at the one time to provide a selective advantage

 

[LouisBooth]

For the system to work, yes, they have to be present or the system breaks down and doesn't work, and stops working.

 

[chickenman]

perhaps the entire system doesn't function, but evolution only requires a selective advantage at each step in the evolution of a system (it may not even require that, depending on how much neutral selection has contributed). The individual enzymes in many pathways on their own provide a selective advantage

 

[Christian Soldier]

"no evolution requires no incredible coincidences at all."

An amoeba swimming through the alleged "primordial ooze" and evolving by "natural selection" into an untold number of different organisms over billions of years, until it finally ends up as a man---doesn't require any "incredible coincidences at all."?

Suuuuuuuuuure!

 

[Jerry Smith]

This is the same thing I see when I took biochem. all the processes are innerdependant and thus have to evolove all at once.

I think the conclusion is faulty. There are plenty of complex and interdepnendent systems, but one need not conclude that they evolved all at once. Matter of fact, it would be absurd to think they evolved all at once.

 

[Jerry Smith]

An amoeba swimming through the alleged "primordial ooze" and evolving by "natural selection" into an untold number of different organisms over billions of years, until it finally ends up as a man---doesn't require any "incredible coincidences at all."?

Suuuuuuuuuure!

The evolution of straw men, on the other hand, apparently requires a lot of incredulity.

 

[Christian Soldier]

"The evolution of straw men, on the other hand, apparently requires a lot of incredulity."

Please explain how my previous statement classifies as a straw man argument. As usual, you make a meaningless "neh neh neh" post that says or proves nothing.

If evolutionists don't believe that humans evolved from single cell organisms, please explain exactly what we evolved from, and how.

 

[Jerry Smith]

Originally posted by Christian Soldier
"The evolution of straw men, on the other hand, apparently requires a lot of incredulity."

Please explain how my previous statement classifies as a straw man argument. As usual, you make a meaningless "neh neh neh" post that says or proves nothing.

If evolutionists don't believe that humans evolved from single cell organisms, please explain exactly what we evolved from, and how.

All dogs are hairy.

Buttons is hairy.

Therefore, buttons is a dog. (Nope - she's a cat. I do however, like the dogs better - if that helps.)

Human's didn't evolve from amoeba - despite the fact that amoeba are single celled, and the common ancestor of all living things is thought to have been single celled.

Furthermore, the single celled ancestor is not thought to have been an individual, but instead a population. Nor is thought to have swum in an "ooze" though it may have swum in murky water, replete with organic chemicals which it used for nourishment.

Lastly, this population evolved by a combination of "mutation" (if quotation marks are required when natural processes are involved), "natural selection", "genetic drift" and quite likely lateral gene flow, with results over three billion years that include all life today.

It would have been quite a coincidence if human life, and no other primate, mammal, vertebrate, invertebrate or animal life had been the result. Matter of fact, it would have been large enough a coincidence that it would then be necessary to think it "infeasible." (whoops! quotations around something that isn't an observed natural process...)

 

[chickenman]

creationists conveniently forget the whole "natural selection" thing when it suits them

 

[Christian Soldier]

"creationists conveniently forget the whole "natural selection" thing when it suits them"

No, we haven't forgotten natural selection. Here is a statement from one of the great philosophers of science, on natural selection:

"There is a difficulty with Darwinism....It is far from clear what we should consider a possible refutation of the theory of natural selection. If, more especially, we accept that statistical definition of fitness which defines fitness by actual survival, then the survival of the fittest becomes tautological and irrefutable."

Karl Popper, "Science: Problems, Aims, Responsibilities," Proceedings, Federation of American Society of Experimental Biology

 

[Christian Soldier]

"Human's didn't evolve from amoeba - despite the fact that amoeba are single celled, and the common ancestor of all living things is thought to have been single celled."

Name the evolutionists who were there at the time and observed the alleged "fact" that we didn't evolve from an amoeba, but another single-cell organism. We are "thought" to be the ancestor of an unknown single-cell organism? In other words, you don't know what we evolved from, but you're sure it wasn't an amoeba.

"Furthermore, the single celled ancestor is not thought to have been an individual, but instead a population. Nor is thought to have swum in an "ooze" though it may have swum in murky water, replete with organic chemicals which it used for nourishment."

Where did this "population" come from? One day they just popped into existence out of nowhere?

"Lastly, this population evolved by a combination of "mutation" (if quotation marks are required when natural processes are involved), "natural selection", "genetic drift" and quite likely lateral gene flow, with results over three billion years that include all life today."

Still need the names of those who observed these alleged processes and events.

"It would have been quite a coincidence if human life, and no other primate, mammal, vertebrate, invertebrate or animal life had been the result. Matter of fact, it would have been large enough a coincidence that it would then be necessary to think it "infeasible." (whoops! quotations around something that isn't an observed natural process...)"

Virtually everything you mentioned is pure speculation that cannot be established as scientific fact.

 

[Jerry Smith]

Originally posted by Christian Soldier
"creationists conveniently forget the whole "natural selection" thing when it suits them"

No, we haven't forgotten natural selection. Here is a statement from one of the great philosophers of science, on natural selection:

"There is a difficulty with Darwinism....It is far from clear what we should consider a possible refutation of the theory of natural selection. If, more especially, we accept that statistical definition of fitness which defines fitness by actual survival, then the survival of the fittest becomes tautological and irrefutable."

Karl Popper, "Science: Problems, Aims, Responsibilities," Proceedings, Federation of American Society of Experimental Biology

Would you care to disucuss with us what Popper's profession was? Would you mind telling us whether he continued to hold this view after being exposed to a better analysis of what constituted the methods of evolution?

Would you like to read why natural selection is not a tautology and why  "survival of the fittest" is a crude term that is employed exclusively by non-scientists, including creationists?

http://www.talkorigins.org/faqs/evolphil/tautology.html

 

[Jerry Smith]

Originally posted by Christian Soldier
"Human's didn't evolve from amoeba - despite the fact that amoeba are single celled, and the common ancestor of all living things is thought to have been single celled."

Name the evolutionists who were there at the time and observed the alleged "fact" that we didn't evolve from an amoeba, but another single-cell organism. We are "thought" to be the ancestor of an unknown single-cell organism? In other words, you don't know what we evolved from, but you're sure it wasn't an amoeba.

Lets just say that the theory isn't compatible with an ameobic common ancestor, and leave it at that. After all the theory is very strong, has been supported by bus-loads of evidence, and has proven reliable where its conclusions can be checked.  

"Furthermore, the single celled ancestor is not thought to have been an individual, but instead a population. Nor is thought to have swum in an "ooze" though it may have swum in murky water, replete with organic chemicals which it used for nourishment."

Where did this "population" come from? One day they just popped into existence out of nowhere?

Maybe. Maybe God created them. The theory of evolution doesn't say. One hypothesis was that they were a result of an intricate process of abiogenesis, but there is no conclusive evidence that this is the case.

"Lastly, this population evolved by a combination of "mutation" (if quotation marks are required when natural processes are involved), "natural selection", "genetic drift" and quite likely lateral gene flow, with results over three billion years that include all life today."

Still need the names of those who observed these alleged processes and events.

Just crack open the Journal of Evolutionary Biology, and you will find numerous names. Since there are far too many to list, I will just go with the most famous. Charles Darwin.  

"It would have been quite a coincidence if human life, and no other primate, mammal, vertebrate, invertebrate or animal life had been the result. Matter of fact, it would have been large enough a coincidence that it would then be necessary to think it "infeasible." (whoops! quotations around something that isn't an observed natural process...)"

Virtually everything you mentioned is pure speculation that cannot be established as scientific fact.

If you ever actually get curious about the subject, & you only have limited time & energy to give to the project of learning about it, you will find some of the very simple reasons that we are able to know what we know at the http://www.talkorigins.org website. I particularly recommend:

http://www.talkorigins.org/faqs/evolution-fact.html 

http://www.talkorigins.org/faqs/comdesc/

http://www.talkorigins.org/faqs/faq-speciation.html

http://www.talkorigins.org/faqs/molgen/

And of course the classic:

http://www.talkorigins.org/faqs/faq-transitional.html

As long as you are just out to disparage the science no matter what, I won't attempt to have a substantial conversation with you. For a while, at least, I will try to correct any errors that I find in the posts on this board (including my own).