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Dude
SFN Die Hard
USA
6891 Posts |
 Posted - 10/12/2004 : 09:10:54 [Permalink]
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quote:
(although where in that definition was reverse transcriptase?)
A retrovirus contains RNA (rather than DNA) and the enzyme reverse transcriptase. This enzyme is, essentially, what makes a retrovirus a retrovirus. It takes the viral RNA and synthesizes in into DNA. Then the new DNA is inserted into the DNA of the host cell.
A couple of googled pages that have a nice basic explanation.
http://en.wikipedia.org/wiki/Reverse_transcriptase
http://en.wikipedia.org/wiki/Reverse_transcription
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/R/Retroviruses.html |
Ignorance is preferable to error; and he is less remote from the truth who believes nothing, than he who believes what is wrong.
-- Thomas Jefferson
"god :: the last refuge of a man with no answers and no argument." - G. Carlin
Hope, n.
The handmaiden of desperation; the opiate of despair; the illegible signpost on the road to perdition. ~~ da filth |
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Peptide
Skeptic Friend
USA
69 Posts |
Posted - 10/12/2004 : 13:01:06 [Permalink]
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Below is my first rough draft (there will be grammatical mistakes, but ignore those for now). I will include references and some technical info here and there, but this is close to the final product. I didn't mention the transfer of RNA to DNA since all that really matters is the randomness of insertion. Feel free to make suggestions. It is a bit long, but I think this was necessary to get the argument across.
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Certain types of viruses are able to insert their DNA or RNA into the host DNA. These types of viruses are called retroviruses. By doing so, they are able to take over the machinery of the host cell to make more virus particles. Retrovirus DNA is made up of various genes including an integrase which inserts the viral DNA into the host genome, an envelope gene which makes the outer protein coat of the virus, and various other genes necessary for reproducing viral particles. Also, on each end of the virus are sections called LTRs, or long tandem repeats. These are long stretches of a repeated sequence of DNA. All retroviruses have these characteristics.
A retrovirus has a particular mode of insertion. Different viruses tend to insert into different parts of the host genome. HIV, for instance, prefers to insert into areas with active host genes. These sites, called integration sites, are abundant within the host genome for each virus, numbering anywhere from 500 to 2,000 integration sites per host genome. Also, each integration site is usually between 100,000 to 250,000 DNA letters long (letters being the A, G, T, and C of the genetic code). Taking the low number of 500 and the lower size of 100,000, this limits retrovirus insertion to about 50 million bases in the genome. This would mean that we could expect that one letter of DNA would be used twice every 50 million insertions. This number becomes important later on in this section, so remember it.
An analogy that helps me to visualize this process is an unabridged dictionary. Let's pretend that each letter of the dictionary (the A's, B's, etc.) represent a different chromosome. Let's also pretend that each letter in the dictionary represents a letter in the DNA sequence of the host genome. Now, close your eyes and flip through the pages. Randomly stop on a page, keeping your eyes shut, put your finger down on the page. Open your eyes and record the page number and the letter that you put your finger on. Next, pass the dictionary to someone else and have them repeat the procedure. What are the chances that you would both put your finger on the same letter on the same page? I would think this event is highly unlikely, almost like winning the lottery.
However, not all insertions go well for retroviruses. During rare events only part of the viral genome is inserted which prevents an infection of the cell. What results is a cell that is not killed by the virus and a partial viral sequence permanently implanted into the host genome of that cell. If this rare event happens in an egg or sperm, it is possible that that egg or sperm could be involved in the production of an offspring. As you can imagine, the odds of sperm or egg used in reproduction with a partial viral genome are quite low, but given enough time it does happen. What results is an organism with a partial viral sequence, also called an endogenous retrovirus (ERV), present in every cell of their body including half of their eggs or sperm. Think of it as a scar left in the genome that is passed on to the next generation when it occurs in an egg or sperm.
Now we have a sequence that is part of the genome and is passed on from generation to generation. After numerous generations we look for ERV's in people's genome. What we find is that certain people share the same insertion at the same spot in the DNA sequence, that is at the same letter of DNA. How do we explain this? The most obvious reason is that they share a common ancestor. Why don |
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BigPapaSmurf
SFN Die Hard
3192 Posts |
Posted - 10/12/2004 : 13:14:10 [Permalink]
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"On the flip side, the theory of evolution and common ancestory could be falsified by ERV's."
I would remove this line altogether, The following statements clarify this and it wont allow them to grasp a one sentence quote to thwart your carefully planned statement.
Other than that I think you did a splendid job and I cant wait to read the final draft...
Do we have permission to use this after the debate? (for thwarting others on other sites) |
"...things I have neither seen nor experienced nor heard tell of from anybody else; things, what is more, that do not in fact exist and could not ever exist at all. So my readers must not believe a word I say." -Lucian on his book True History
"...They accept such things on faith alone, without any evidence. So if a fraudulent and cunning person who knows how to take advantage of a situation comes among them, he can make himself rich in a short time." -Lucian critical of early Christians c.166 AD From his book, De Morte Peregrini |
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Dr. Mabuse
Septic Fiend
Sweden
9688 Posts |
Posted - 10/12/2004 : 13:22:58 [Permalink]
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| Excellent post! |
Dr. Mabuse - "When the going gets tough, the tough get Duct-tape..."
Dr. Mabuse whisper.mp3
"Equivocation is not just a job, for a creationist it's a way of life..." Dr. Mabuse
Support American Troops in Iraq:
Send them unarmed civilians for target practice..
Collateralmurder. |
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Ricky
SFN Die Hard
USA
4907 Posts |
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Dude
SFN Die Hard
USA
6891 Posts |
Posted - 10/12/2004 : 14:49:16 [Permalink]
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Nicely written!
And I agree with BPS and Ricky.... perhaps a slight rewording of that sentence. |
Ignorance is preferable to error; and he is less remote from the truth who believes nothing, than he who believes what is wrong.
-- Thomas Jefferson
"god :: the last refuge of a man with no answers and no argument." - G. Carlin
Hope, n.
The handmaiden of desperation; the opiate of despair; the illegible signpost on the road to perdition. ~~ da filth |
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Peptide
Skeptic Friend
USA
69 Posts |
Posted - 10/12/2004 : 14:58:16 [Permalink]
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Sorry for taking up space, but this is close to final. Includes references and figures. I would like to spend more time on it, but I have two more arguments to write by Thursday. This site has different url codes than skeptictimes so the references may look a little screwy. Everyone has my permission to use this article with credit given to "Peptide at www.skepticfriends.org". On a side note, Wednesday night I have bowling league so I won't make it to the online meeting. Let me know what you guys discussed.
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Certain types of viruses are able to insert their DNA or RNA into the host DNA. These types of viruses are called retroviruses. By doing so, they are able to take over the machinery of the host cell to make more virus particles. Retrovirus DNA is made up of various genes including an integrase which inserts the viral DNA into the host genome, an envelope gene which makes the outer protein coat of the virus, and various other genes necessary for reproducing viral particles. Also, on each end of the virus are sections called LTRs, or long tandem repeats. These are long stretches of a repeated sequence of DNA. All retroviruses have these characteristics.
A retrovirus has a particular mode of insertion. Different viruses tend to insert into different parts of the host genome. HIV, for instance, prefers to insert into areas with active host genes. These sites, called integration sites, are abundant within the host genome for each virus, numbering anywhere from 500 to 2,000 integration sites per host genome. Also, each integration site is usually between 100,000 to 250,000 DNA letters long (letters being the A, G, T, and C of the genetic code)([url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15314653]Reference[/url]). Taking the low number of 500 and the lower size of 100,000, this limits retrovirus insertion to about 50 million bases in the genome. This would mean that we could expect that one letter of DNA would be used twice every 50 million insertions. [url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=509299&action=stream&blobtype=jpg&blobname=pbio.0020234.g001.jpg]This figure[/url] shows 3,000 insertions by three different retroviruses. As you can see, the retroviral insertions are spread over all of the chromosomes in a random pattern. Not one nucleotide is used twice. There has never been a retrovirus that has been shown to insert at the same letter in the host genome even 0.001% of the time.
An analogy that helps me to visualize this process is an unabridged dictionary. Let's pretend that each letter of the dictionary (the A's, B's, etc.) represent a different chromosome. Let's also pretend that each letter in the dictionary represents a letter in the DNA sequence of the host genome. Now, close your eyes and flip through the pages. Randomly stop on a page, keeping your eyes shut, put your finger down on the page. Open your eyes and record the page number and the letter that you put your finger on. Next, pass the dictionary to someone else and have them repeat the procedure. What are the chances that you would both put your finger on the same letter on the same page? I would think this event is highly unlikely, almost like winning the lottery.
However, not all insertions go well for retroviruses. During rare events only part of the viral genome is inserted which prevents an infection of the cell. What results is a cell that is not killed by the virus and a partial viral sequence permanently implanted into the host genome of that cell. If this rare event happens in an egg or sperm, it is possible that that egg or sperm could be involved in the production of an offspring. As you can imagine, the odds of sperm or egg used in reproduction with a partial viral genome are quite low, but given enough time it does happen. What results is an organism with a partial viral sequence, called an endogenous retrovirus (ERV |
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Peptide
Skeptic Friend
USA
69 Posts |
Posted - 10/12/2004 : 15:05:16 [Permalink]
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Arrrrg, still didn't like the paragraph on falsification. Here is the new one.
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As to the falsification of evolution, if you were able to find a sequence shared by gorillas and humans that was not found in chimps then the theory of evolution would be in serious doubt. Additionally, find an ERV only shared by orangutans and humans and not chimps or gorillas, you would again cast serious doubt on the theory of evolution. However, these potential falsifications have never been observed. Only recently has the human genome been decoded, and even more recently the chimp genome. Soon, the gorilla genome will be complete, so even more ERV's may show up. As more genomes are completed this test can be continually applied as new ERV's are discovered in other primate and ape species, not to mention other non-primate species. Therefore, ERV's are a fine example of a repeatable and falsifiable data set that can be used to test the theory of evolution. |
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H. Humbert
SFN Die Hard
USA
4574 Posts |
Posted - 10/12/2004 : 15:07:47 [Permalink]
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Excellent post, Peptide. But I would suggesting concluding your argument with the statement, "I pwned you."
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"A man is his own easiest dupe, for what he wishes to be true he generally believes to be true." --Demosthenes
"The first principle is that you must not fool yourself - and you are the easiest person to fool." --Richard P. Feynman
"Face facts with dignity." --found inside a fortune cookie |
| Edited by - H. Humbert on 10/12/2004 15:08:07 |
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H. Humbert
SFN Die Hard
USA
4574 Posts |
Posted - 10/12/2004 : 15:12:43 [Permalink]
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quote:
Originally posted by Peptide
Therefore, ERV's are a fine example of a repeatable and falsifiable data set that can be used to test the theory of evolution.
While I agree it is important to point out that this data could potentially falsify Evolutionary theory (and thus quelch the creationist argument that Evolution is untestible), I still think the point should end with a positive statement that the data in fact supports evolution.
Perhaps, "...that can be used to test the theory of evolution. Thus far all data supports the pattern of evolution through common descent."
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"A man is his own easiest dupe, for what he wishes to be true he generally believes to be true." --Demosthenes
"The first principle is that you must not fool yourself - and you are the easiest person to fool." --Richard P. Feynman
"Face facts with dignity." --found inside a fortune cookie |
| Edited by - H. Humbert on 10/12/2004 15:18:04 |
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Ricky
SFN Die Hard
USA
4907 Posts |
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Siberia
SFN Addict
Brazil
2322 Posts |
Posted - 10/12/2004 : 15:19:06 [Permalink]
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... if they read it at all. Which I doubt.
But either case, that's a wonderful post for us resident skeptics to learn a couple new things :) |
"Why are you afraid of something you're not even sure exists?"
- The Kovenant, Via Negativa
"People who don't like their beliefs being laughed at shouldn't have such funny beliefs."
-- unknown
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Peptide
Skeptic Friend
USA
69 Posts |
Posted - 10/12/2004 : 15:36:41 [Permalink]
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quote:
Originally posted by H. Humbert
quote:
Originally posted by Peptide
Therefore, ERV's are a fine example of a repeatable and falsifiable data set that can be used to test the theory of evolution.
While I agree it is important to point out that this data could potentially falsify Evolutionary theory (and thus quelch the creationist argument that Evolution is untestible), I still think the point should end with a positive statement that the data in fact supports evolution.
Perhaps, "...that can be used to test the theory of evolution. Thus far all data supports the pattern of evolution through common descent."
Every one of my three arguments will include potential falsifications. I think this is important in a debate like this one. Hopefully, jimi will also include potential falsifications, but I'm not holding my breath.
I like your rewording, I will include it. |
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Dave W.
Info Junkie
USA
26022 Posts |
Posted - 10/12/2004 : 17:54:13 [Permalink]
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tkster is now giving jimi eight days, compared to Peptide's seven. Someone should ask tkster why jimi needs any extra time, since jimi's first post should contain no response to Peptide. Jimi is, in effect, getting two weeks to write his introductory post, versus Peptide's single week. Don't forget, tkster said it himself:Neither Introduction are for rebuttals so any "rebuttal" will be removed. And he also said:There will be no more... getting upset when you break your own rules... Well, whatever that means. I'm sure if tkster breaks his own rule by allowing jimi to rebut some or all of Peptide's introduction, tkster isn't going to get upset about it.
[Shakes head in pity for the youth of today.] |
- Dave W. (Private Msg, EMail)
Evidently, I rock!
Why not question something for a change?
Visit Dave's Psoriasis Info, too. |
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Ricky
SFN Die Hard
USA
4907 Posts |
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