Endogenous Retroviral Insertions: a Falsification of Separate Origin of Species

[WinAce]

Taken from here (http://www.talkorigins.org/faqs/comdesc/section4.html#retroviruses):

Retroviral infections can occasionally infect a germ line cell. The resulting offspring will have bits and pieces of the virus stuck in every cell in its body. We've observed this very rare process in the lab, and the odds of getting two independent infections to leave the same bit of viral DNA at the same exact locus are astronomically unlikely.

Like pseudogenes, the viral fragments can piggyback on the success of an individual and become established in the species. The chances of any particular viral fragment, even if inserted identically in two seperate cases, becoming established in two seperate populations (a rare event in and of itself) makes this not just improbable, but more or less impossible without divine intervention ;)

Any offshoot species will have the same unlikely and easily identifiable ERV, enabling us to construct accurate phylogenies from an independent line of evidence.

http://www.talkorigins.org/faqs/comdesc/images/retrovirus.gif

Exhibit A; human endogenous retrovirii insertions in identical chromosomal locations in various primates. Notice just how well the standard evolutionary phylogeny (humans and chimps closest, then orangutans and gorillas, then gibbons, then old world monkeys, then new world monkeys) is represented by this line of evidence.

ERVs have also been used to reconstruct the relationships between dogs, jackals, wolves and foxes; various breeds of domestic cat and wild cat; and even to establish the shared ancestry of cows and whales. (In the last case, two independent viral infections accounting for the evidence is impossible - whales and cows do not even share the same environment, much less are exposed to the same diseases!)

Needless to say, this offers numerous falsification avenues for evolution. Any ERV shared between organisms farther on the phylogenetic relationship than humans and apes must *also* be found in both. For example, ERVs found in New World Monkeys and chimps MUST be present in humans (aside from a few very rare cases where they've been deleted, but we can tell when a deletion has occured) or evolution is falsified.

An ERV in dogs and humans but not chimps would put the theory on its deathbed; so would a phylogeny reconstructed from these viral fragments if it differed significantly from the accepted phylogeny based on morphological, fossil, pseudogene, anatomical, and other evidence. This is the strongest support for evolution I've ever come across; a truly powerful and damning smoking gun.

Hypotheses proposed by creationists to account for this are inadequate: one entails independent insertion by the same virus affecting different species.

The fact that ERVs, when analyzed, yield evolutionary phylogenies consistent with the ones based on morphological, fossil and other evidence (as opposed to, say, viral infection patterns instead) rules out the independent insertion hypothesis as unlikely. The fact that species that don't even share the same environment, much less diseases (like cows and whales) share unique ERVs falsifies it completely.

Another attempted explanation is that the ERVs found in our genome are actually designed elements originally placed there. Needless to say, this hypothesis is as ludicrous as assertions that dinosaur bones don't actually come from dinosaurs but were intentionally placed there. .

Science generally doesn't deal with Omphalos hypotheses for good reason, because when you deny reality in one area, you might as well say goblins created your mind on a supercomputer 5 minutes ago and this world isn't real.

People who assert this for ERVs have the burden of proof in demonstrating where shared ancestry ends and intentional design begins. Are the various breeds of domestic cat different kinds? (They share ERVs that have been used to reconstruct their phylogenies). Are the various felines related, or seperately created? (Lions, panthers, tigers and domestic cats share ERVs). In other words, where do the divinely faked ERVs end and the real ones begin?

Finally, ERV insertion is a well-documented event, leaving very specific and unlikely patterns. No other process except viral infection has been documented that can create them.

A customary red herring involved in any discussion of molecular evidence for evolution is cries of "but they have a FUNCTION!". While that may well be true, function (or lack of it) is generally not the criterion by which things are considered evidence for evolution.

In summary, the facts are that:

(A) viral infection generally results in a dead cell. Occassionally, fragments of the virus remain but the cell survives.
(B) infection of a germ line cell is even more rare.
(C) no two viral insertions are exactly alike.
(D) viral fragments insert at fairly random locations.
(E) that unlikely viral fragment-carrying germ line cell needs to be the particular egg or sperm cell that gets fertilized and survives to adulthood.
(F) It then needs to to piggyback on the success of an individual and get established in the population via sheer luck.

The combined odds of this happening in two independent "kinds" are probably orders of magnitude larger than those strawmen abiogenesis calculations creationists love to trot out. This leads to the obvious conclusion:

Independent origin of ERVs (and hence, independent origin of species, a.k.a. creationism) is scientifically falsified.

[DivineOb]

You mentioned this in your article and I'm repeating it here because I want a specific answer from a creationist to this exact point.

Humans and chimps share retroviral insertions which are not shared by, say, orangutan. Since chimps and orangutan are the same 'kind', chimps must have been originally created lacking these insertions (otherwise they'd be present in orangutans too). So, these insertions must have occured at some point since the flood, after chimps forked off of the main 'monkey kind'.

If this is the case, and these insertions could have all taken place since the flood, then why did it happen for chimps (I believe seven times to give them the same insertions as humans) but fail to happen for orangutans even once? Why did it fail to happen for the other species in the 'monkey kind' even once? If the odds of these seven insertions happening really is nontrivial, then we should *certainly* expect that one of these seven insertions could have taken place in *any* other species of animal for which we could compare the genetic locations.

The obvious response to this is to insist that chimps are a different 'kind'. But this angle still forces the creationist to increase by one by the number of kinds on the ark, and this argument can be repeated for any two species which differ in a retroviral insertion but which "obviously" belong to the same 'kind'. It would be more forceful for different species (other than humans) actually, where half of the 'kind' has insertions not shared by the other half of the 'kind'.

[WinAce]

Very good point! I'll have to remember that one.

[TheFiveSolas]

This is old news. Ashby Camp dealt with this issue two years ago.

See the following link (specifically Predictions 19-21).
http://www.trueorigin.org/theobald1e.asp

[WinAce]

Since you linked to a rationalization that I specifically targeted and debunked in the OP, should I take that as an admission you have no idea of what you're arguing about? :teeth:

[DivineOb]

No I'm perfectly happy to accept the analysis of that link, since it contains the following sentence

"Of course, if ERV sequences have a function, then God may have had a functional reason for initially placing them at the same chromosomal location in separately created species."

Which indicates that a 'kind' is actually a 'species'... even Hovind would agree that if Noah had to take two of each species onto the Ark then it couldn't possibly have been large enough.

This is not to mention that the linked article misunderstands what a scientific prediction is, and I don't see how it really addresses the point I specifically raised other than by increasing the number of 'kinds' to too high of a level.

[TheFiveSolas]

DivineOb wrote:


This is not to mention that the linked article misunderstands what a scientific prediction is, and I don't see how it really addresses the point I specifically raised other than by increasing the number of 'kinds' to too high of a level.


The article I linked to was a rebuttal to a list of "Evolutionary Predictions" made by Dr. Douglas Theobald on talkorigins. So, if there was a misunderstanding as to what constitutes a scientific prediction it was Theobald. However, I think you merely misunderstood the pupose of the article in question.

[WinAce]

Awww, what the heck. That article by Camp is so incompetent and thus typical of creationist drivel that I can't help but comment on it.


It is not a prediction of the hypothesis of universal common ancestry or the more specific hypothesis of Neo-Darwinism that the same ERVs will exist in the same chromosomal location in two or more species.

That's quite the statement, given that the TO link references several scientific papers using evolution to predict the same ERVs in various chromosomal locations...


Evolution does not even predict the existence of ERVs, much less that they will be found at the same location in two or more species.

And Relativity doesn't predict you can use telescopes to see if light gets bent by stars. Both it and evolution, however, make highly specific and successful predictions when mixed with what we know of genetics.


After all, evolutionary theory was considered robust prior to the discovery of ERVs.

And relativity was considered robust before light was indeed bent as predicted. Your point is?


This is but another example of taking an observation, claiming it as a prediction of evolution, and then using the fact the observation fits the prediction as evidence for the truth of evolution.

Well, this is just flatly incorrect. There are numerous ways ERVs would falsify evolution that are likely to occur if it isn't correct. The fact that none do is an indication it's correct, especially when they occur in the only pattern evolution can accomodate (that of double-nested hierarchies that reinforce phylogenies based on totally different criteria).


Moreover, ERVs are inadequate in principle to support Dr. Theobald’s claim of universal common ancestry, because they are not shared by all groups of organisms.

So? The fact that they establish shared ancestry between such species as apes and humans, cows and whales and various others is enough to falsify separate origin of species, a.k.a. creationism.


The claim here is that common ancestry is the only viable explanation for “finding [ERVs] in identical chromosomal positions of two different species.” It is based on the premise that ERVs are (and always have been) nonfunctional products of retroviral infection that have, for the most part, inserted randomly into the genome of the host organism. The presumed nonfunctionality of ERVs is thought to eliminate the explanation of design (because a Designer could have no purpose in placing nonfunctional sequences at the same locus in separate species).

Ah, I see you didn't bother to read my OP, just as I expected. You merely used argumentum ad linkum without bothering to summarize the relevant points or even seeing if it wasn't already debunked. Tell me, TheFiveSolas, do you think you're adequately defending the cause of creationism with such behaviour?

Camp goes into a rant about how "...it is an unprovable theological assertion that God would not place the same nonfunctional sequences at the same locus in separate species". Does that logic work with dinosaurs? "It is an unprovable theological assertion that God wouldn't place what appear to us to be dinosaur bones in the ground"; "it is an unprovable theological assertion that God would not make all our tests indicate the earth is round when it's actually flat". I didn't think so. Of course, nowhere in my OP (or the TalkOrigins article Camp 'critiqued') was it said that "ERVs are evidence of evolution because they're nonfunctional", so he was attacking a strawman in the first place.

Finally, he says "The suggestion that the hypothesis of common ancestry would be falsified by the discovery of the same ERV at the same locus in two species that are not believed to have shared a recent common ancestor is incorrect. ERVs simply would join the list of alleged markers for evolution that exhibit homoplasy." I would be interested in seeing you expand on that statement to tell us how evolution could explain, say, the vitamin C gene broken in identical ways in humans and Old World monkeys, but broken in a different way in chimps and orangutans.

But that's a moot point anyway - ERVs would reproduce viral infection patterns or otherwise contradict evolution if they weren't the result of shared ancestry anyway.

Now, let's see an actual response next time. OK?

[DivineOb]

Today @ 11:16 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=74941#post74941)
TheFiveSolas:

DivineOb wrote:


The article I linked to was a rebuttal to a list of "Evolutionary Predictions" made by Dr. Douglas Theobald on talkorigins. So, if there was a misunderstanding as to what constitutes a scientific prediction it was Theobald. However, I think you merely misunderstood the pupose of the article in question.

I've seen the article previously, so I am already familiar with it. The section on ERV says that since darwinism doesn't predict the existence of ERV, it makes no predictions regarding them. This is false, and a misunderstanding of what a scientific prediction is.

Just so you can be sure I'm not distorting what he says, the author writes

"Since this is the concept of “shared errors” applied to endogenous retroviruses (and since retroviruses are a type of transposon), much of the two preceding responses is applicable. It is not a prediction of the hypothesis of universal common ancestry or the more specific hypothesis of Neo-Darwinism that the same ERVs will exist in the same chromosomal location in two or more species. Evolution does not even predict the existence of ERVs, much less that they will be found at the same location in two or more species. After all, evolutionary theory was considered robust prior to the discovery of ERVs. This is but another example of taking an observation, claiming it as a prediction of evolution, and then using the fact the observation fits the prediction as evidence for the truth of evolution."

If this is really his view, he misunderstands the concept of a scientific prediction.

[TheFiveSolas]

Winace wrote:


Since you linked to a rationalization that I specifically targeted and debunked in the OP, should I take that as an admission you have no idea of what you're arguing about?


Apparently you are referring to the following in your original post:


Hypotheses proposed by creationists to account for this are inadequate: one entails independent insertion by the same virus affecting different species.

and:


Another attempted explanation is that the ERVs found in our genome are actually designed elements originally placed there.


However, with reference to your first attempt at "hand-waving", Camp points out the following:


In that regard, it is interesting that, in addition to evincing certain functions, some ERVs (and other transposons) also exhibit an insertion bias. Perhaps this is another remnant of a more finely tuned system. Sverdlov writes:

But although this concept of retrovirus selectivity is currently prevailing, practically all genomic regions were reported to be used as primary integration targets, however, with different preferences. There were identified ‘hot spots’ containing integration sites used up to 280 times more frequently than predicted mathematically. A recent study of the de novo retroviral integration demonstrated also preference for scaffold- or matrix-attachment regions (S/MARs) flanked by DNA with high bending potential. The S/MARs are thought to be important functional sequences of the genome that anchor chromatin loops to the nuclear matrix subdividing the genome into functional domains. They often neighbor regulatory elements involved in gene expression and DNA replication.

A cautious generalization from these findings could be that although TEs can integrate into many sites and may prefer non-coding regions, the de novo integration is frequently targeted at the sites in the vicinity of functionally important elements like transcriptions start points or origins of replication. (Sverdlov, 3.)


With regards to your second attempt at "hand-waving" Camp writes:


Again, it is an unprovable theological assertion that God would not place the same nonfunctional sequences at the same locus in separate species. He may have a purpose for doing so that is beyond our present understanding. The objection that placing nonfunctional sequences at the same locus in separate species would make God guilty of deception is ill founded. God cannot be charged fairly with deception when we choose to draw conclusions from data that contradict what he has revealed in Scripture (see Gibson’s comments in the discussion of Prediction 19).

In any event, not all ERVs are nonfunctional. Some are transcriptionally active, and studies have revealed ERV protein expression in humans. (Sverdlov, 1.) We simply do not know all that ERVs (or other transposons) may be doing in an organism or what roles they may have played in the past.

[DivineOb]

Today @ 11:28 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=74951#post74951)
TheFiveSolas:
With regards to your second attempt at "hand-waving" Camp writes:


Now, *I* did already deal with that. If you take that route, you're going to have to greatly increase the number of 'kinds' on the Ark. Look at the picture in the OP -- since 5 insertions are shown there (and assuming the leftmost point is the demarcation of the 'monkey kind'), you now have to take at least 5 pairs of monkeys on the Ark, instead of just one pair for the 'monkey kind'. I'm sure similar patterns will be exhibited among other 'kinds'. This will increase the number of animals you'd have to take on the Ark too much.

[TheFiveSolas]

DivineOb wrote:


Now, *I* did already deal with that.


I don't know if Ashby Camp was using the term "species" as a synonym to biblical "kind", if so I agree, and thus no problem with number of animals on the ark. In other words, I think he was being sloppy in his terminology at that point.

[Socrates]

Winace:Awww, what the heck. That article by Camp is so incompetent and thus typical of creationist drivel that I can't help but comment on it.As if the scientifically ignorant rabbit-brained Winace would have the foggiest idea.

[DivineOb]

Today @ 11:42 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=74966#post74966)
TheFiveSolas:

DivineOb wrote:


I don't know if Ashby Camp was using the term "species" as a synonym to biblical "kind", if so I agree, and thus no problem with number of animals on the ark. In other words, I think he was being sloppy in his terminology at that point.

He has no choice in the matter. He wrote "Of course, if ERV sequences have a function, then God may have had a functional reason for initially placing them at the same chromosomal location in separately created species."

This hypothesis assumes that these insertions did not occur "naturally" following the flood / fall. Thus, the only way we'd see a creature with a particular insertion would be if they survived the flood. The only way a (land dwelling) creature can survive the flood is if they are brought on the ark. Even if he is using species differently from kind (which doesn't really make sense anyway, since Genesis specifically speaks of creating 'kinds'), he still has to take those different species on the ark anyway for the different retroviral insertions to be exhibited in the different species we see today.

Edit: I'd like to have Rufus or someone else who is actually formally trained in genetics to comment on the above, because I can think of some off-the-wall scenarios in which the number of animals necessary to take on the Ark can be reduced possibly (but I have no idea if these scenarios are at all feasible). It would still be larger than the number of created 'kinds', however. I expect it might result in a factor of two decrease in the number of 'pairs' necessary to take on the Ark.

[tgamble]

I love Socrates

[tgamble]

I love Socrates

[TheFiveSolas]

tgamble wrote:


According to an antiscience bigot lawyer.


And you have painted yourself as a bigoted anti-Christian.

By the way, Camp has rebutted Theobald's attempted rebuttal here:
http://www.trueorigin.org/ca_ac_01.asp

[tgamble]

Today @ 12:07 AM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=74986#post74986)
TheFiveSolas:

tgamble wrote:

And you have painted yourself as a bigoted anti-Christian.


Only if you assume disagreement makes me one which is just silly.


By the way, Camp has rebutted Theobald's attempted rebuttal here:
http://www.trueorigin.org/ca_ac_01.asp
[/QUOTE]

Let me know when he presents actual evidence. Evidence that convinces actual scientists that years of research are wrong. Good luck!

P.S. Theobald has responded to his rebuttal.

[WinAce]

One, that some ERVs can have an insertion bias is totally irrelevant.

For one thing, an "insertion bias" would only affect my point D. The other five combined make independent insertion a falsified hypothesis. Let's list them again:

(A) viral infection generally results in a dead cell. Occasionally, fragments of the virus remain but the cell survives.
(B) infection of a germ line cell is even more rare.
(C) no two viral insertions are exactly alike.
(D) viral fragments insert at fairly random locations.
(E) that unlikely viral fragment-carrying germ line cell needs to be the particular egg or sperm cell that gets fertilized and survives to adulthood.
(F) It then needs to to piggyback on the success of an individual and get established in the population via sheer luck.

Those factors are all necessary together to get an ERV, and they combined make independent insertion all but impossible. You're grasping at straws, and it's showing. :teeth:

Moreover, ERVs have been observed as deposited by viral infections, so independent insertion will produce viral infection patterns instead of double-nested evolutionary phylogenies consistent with those derived from other evidence. Independent insertion also can't account for species that don't share the same environment having the same insertions.

Finally, "these places get inserted to 280 times more often" is not really much help to independent insertion when you have millions of spots to choose from, anymore than Homer Simpson's gleeful statement that his chances of winning the lottery were "100 million... to FIFTY!" after he blew his paycheck on lottery tickets.

As for the second point, READ MY DARN POST. Neither I nor the 29+ Evidences FAQ even mention lack of functionality as evidence for evolution.

As a side note, Socrates must be rolling in his grave to have a modern namesake like the one on Tweb.

Now, please explain these facts via the creationist paradigm paradigm:

1. Astronomically unlikely identical viral insertions are found in humans and chimps.
2. The phylogeny produced from ERV insertions matches the one from morphological, fossil and other evidence.
3. Evolution predicts an insertion found in New World monkeys and humans will also be shared in orangutans, chimps, gorillas and Old World monkeys. None have been found that contradict this prediction.
4. Humans and pigs share many of the same viral diseases that don't affect apes, yet have no common ERVs that apes don't have.

Bonus question: If you think ERVs are a valid way of determining the phylogeny of various breeds of domestic cat, please explain at which point they become inaccurate for determining hominid phylogeny.

[tgamble]

I love Socrates

[DivineOb]

Theres another error I realized in the rebuttal. An error which I think belies the fact that the author believes common descent to be true(!).

He says something to the effect of "well, the evolutionists just looked for some trend, and then pretended that trend was a prediction of evolution." But, here is the problem. If these retroviral insertion trends are the result of anything *but* common descent, what possible reason would any scientist have for expecting the trend to continue? If these insertions are as a result of the whim of the creator, or as a result of a very high chance of random insertion, then no one would have any reason to believe that the trend would continue.

I don't know I guess that is obvious, but I think that if the author of that piece really did think Common Descent was just made up, he might consider spending his time looking for retroviral counterexamples, if he really thinks we have no reason to expect them to be found according to the predictions of common descent.

[RufusAtticus]

I've asked this before of creationists, but have not gotten an answer.

Creationist explain the biological word using a combination of two events: creation and the fall. If a shared biological feature is due to common design than it was produced in creation. If a shared biological feature is due to common descent, then it was produced as a result of the fall.

So, shared endogenous retroviruses and shared pseudogenes are the result of _______________?
Common Design Flaws (Creation)
Common Descent (Fall)

[QED]

I notice that Camp does everything he can to suggest that ERV's are actually not fragmentary remains of retroviral insertions, but rather native DNA that was designed for a specific function. I notice even more that he stops well short of actually claiming that this is the case. Reason?

He knows better. He does not want to make his "rebuttal" so easy a mark for refutation that he is likely to have to take it off-line.

Essentially, he takes two disparate approaches:

1) ERV's may have some sort of function ("you draw your own conclusions, because I'm not going to say it out loud") or
2) Shared ERV's are the result of insertion biases.

The first is virtually irrelevant unless the actual claim is that ERVs are designed elements native to their host genomes. I do not think that this is a defensible argument, and I think that professional YECers recognize this, and shy away from the making the argument. I think they can't resist throwing these points out for those who don't know better.

I do not think the second is a defensible claim either, and Theobald in his 29+ Evidences has done a good job showing why. In this thread, WinAce and others have done a good job refuting this claim, too. If insertion bias were the key, we should be able to find an ERV common to new world monkeys and humans, but missing from chimps - or some other such falsification.

So, really, we are left with Rufus' dilemma, slightly amended:

Shared endogenous retroviruses are a result of ___________ ?

1) Common design? (indefensible)
2) Insertion bias? (indefensible)
3) Common descent?

[Dee Dee Warren]

Moderator Note - There have been numerous warnings issued about improving the tone here and not posting items which basically have no substance and serve no other purpose than to mock and insult. There also have been numerous warnings to tone done the rhetoric a bit and provide more substance with any rhetoric that is used. This has not happened so more extreme measures are now going to be taken. Gamble you keep repeatedly posting items that are simply heckling mockery and argument by links. Your posts are now placed in "moderate" status for two weeks and will be reviewed by a moderator before they are posted on the forum. Objectionable posts will be deleted. I do not want to hear "Socrates" does it too." That is no excuse, and in my judgment I have not found his posts to be of the same level and consistent lack of substantive arguments.

Everyone, tone it down. Add some substance with the rhetoric. This whole biology section is not going to disrupted by the bad behaviour of a few.

Socrates, your post was above was edited because it had no substantive merely an insult directed at Winace. Please refrain from such posts.

[Dee Dee Warren]

And I thank everyone who has been posting items with substance even with expressed strong disagreement. Thank you.

[Bald Ape]

TFS,

It isn't my intent to attempt to overwhelm you with responses here, so feel free to not respond to the following thought experiment if you are occupied with responding to others...

Anyway, what really catches my attention about ERV's is the following. Let's say Bill and Bob capture three new species of butterflies in the rain forest, (new in that they have never before even been seen by human eyes). They take them into their lab, extract some DNA, and begin analyzing. Bob is analyzing A and B, Bill is sequencing C. Bob finds 2 distinct ERV sequences in A, call them S1 and S2. When he looks at the same loci in butterfly B, he sees S1, but notices that S2 is missing. He taps Bill on the shoulder, asking him to look for S1 and S2. Bill looks for S1, and notices it is missing.

Now we get to the crux of the matter. Bob, an evolutionist, is able to say, based on the theory of common descent, that he is certain that S2 will not be present in butterfly C. Bill, a creationist who does not know the mind or will of the Creator, cannot make any such prediction.

Camp's rebuttal, in a nutshell, is that regardless of whether S2 is present or absent, the creationist will have a handy ad hoc explanation - but the whole point is that such a position is utterly useless in the realm of science.

Above, Bob is using the theory of evolution as a tool to predict the outcome of a future measurement (namely, whether or not S2 will be detected). Can you put your finger on what gives Bob the advantage over Bill?

[Socratism]

Your example is flawed because there is no such thing as the lock step belief system of creationists.

A creationist such as myself does not deny that mutations occur and that some creatures have descended from ancestors, e.g. the butterflies in this case.

The objection to "evolution" is the extrapolation back to a single hypothetical primitive protocell.

It is ironic that many creationists like myself hypothesize changes like your example to be occurring even faster than the typical evolutionist would assume. The reason is that there were not that many basic types preserved on the Ark and the time since then has been very short so that rapid diversification and change is a key prediction of a proper theory of creation.

The idea that creation implies no change is obviously a "straw man".

[Bald Ape]

But Socratism,

What if I changed my example from butterflies A, B, and C to humans, chimps, and gorillas? Does your explanation change, or would you agree that humans, chimps, and gorillas are simply the same kind?

If I see an ERV in a human, but notice it is missing in a chimp - how do I KNOW, with an absolute level of certainty, that it will be missing in the gorilla (and I do...)?

[Bald Ape]

Socratism:
A creationist such as myself does not deny that mutations occur and that some creatures have descended from ancestors, e.g. the butterflies in this case.

Here, you are admitting that ERV's do serve as evidence of a common ancestor between humans and apes. Feel free to retract this statement and provide a response for the butterfly hypothetical that doesn't contradict scripture.

[Socratism]

Today @ 11:24 AM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=75448#post75448)
Bald Ape:


Here, you are admitting that ERV's do serve as evidence of a common ancestor between humans and apes. Feel free to retract this statement and provide a response for the butterfly hypothetical that doesn't contradict scripture.

One has to interpret evidence and it is obvious that many would interpret these things in a descent context.

Frankly it would be more logical in most cases to interpret the evidence that the primates descended from humans than the other way around, because it is far easier to lose advanced capabilities through mutation than to gain them.

There is an interesting hint in both scripture and ancient Atlantean myth that pre-flood mankind was perhaps more advanced than many believe and may have been engaging in unwise genetic experimentation (much as is beginning to happen today).

Perhaps this was one of the reasons that the world had to be destroyed and restarted from scratch.

[Bald Ape]

Hmmm, apes evolving from humans... an interesting hypothesis. If apes did evolve from humans, however, we would predict ERV's in chimps and monkeys, but not in humans. This isn't the case (it's the other way around). But you're so close to seeing the light! You no longer seem to feel that apes and humans must be different kinds! Progress!

Now, the same logic that got you to admit that can be extended slightly - monkeys and gorillas are same kind, gorillas and chimps, chimps and humans but that means, just maybe, monkeys and humans have a common ancestry. But it doesn't stop at monkeys! Now we can add lemurs, howlers, tamarins, capuchins! All within the human/ape/monkey/primate kind! All supported by ERV evidence! Isn't this incredible!

[tgamble]

Today @ 03:24 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=75414#post75414)
Socratism:
It is ironic that many creationists like myself hypothesize changes like your example to be occurring even faster than the typical evolutionist would assume. The reason is that there were not that many basic types preserved on the Ark and the time since then has been very short so that rapid diversification and change is a key prediction of a proper theory of creation.

But it fails when tested. In any case, you also deny that new information can be generated and all changes are minor variation. When you start claiming that an entire ORDER was on the ark and then evolved into its member genus and species all without creating anything new, it sounds ridiculous.

They mock Gould and PE and they mock the hopeful monster hypothesis yet unidsputably, both are essential when you have 4000 years to evolve thousands of genus and species out of the basic "kinds" on the ark.

Remember, Noah didn't take fungi or plants or Algae on the ark so you have to assume that in just a few thousand years, a few seeds that may have survived the flood (unlikely in itself) evolved into all plant life (including non seedbearing plants) Algae and fungi. All without new information. Do your seriously believe this and at the same time deny that major change is possible?!

Oh, and don't forget that many plants have abilities that other plants don't have. They must have evolved!


The idea that creation implies no change is obviously a "straw man".

Not really. Nobody claims that creationists deny ANY change, but creationists emphesize that evolution is limited to minor variation. ie. breeds of dogs. Nothing new is ever created they say.

The limits of the change depend on which creationist you're talking to. Some insist that speciation has never been observed and change is limited to change within a species. Others go the other way and claim that "kind" can be an entire order.

The fact that members of an order can't reproduce after their "kind" is ignored. They insist that the many genus and species evolved from two members of the order in just a few thousand years! They also claim that this is "minor" variation and not macroevolution and nothing new is produced.


One has to interpret evidence and it is obvious that many would interpret these things in a descent context.

What does that mean? How would you explain it? Why would you dispute it when you claim that common descent of two species is possible? Perhaps because the same reasoning can be applied to larger groups?


Frankly it would be more logical in most cases to interpret the evidence that the primates descended from humans than the other way around, because it is far easier to lose advanced capabilities through mutation than to gain them.

Humans are primates.

I've asked many creationists why harmful mutations are consistent with intelligent design but so far, I've gotten no answer.


There is an interesting hint in both scripture and ancient Atlantean myth that pre-flood mankind was perhaps more advanced than many believe and may have been engaging in unwise genetic experimentation (much as is beginning to happen today).

There is no evidence that "preflood man" has any meaning since the global flood never happened.

There is also no evidence that man had any knowlege of genetics before Mendal. Perhaps that's why the bible tells the tale of trying to breed striped animals by having them mate near striped plants and pretending that it would work!


Perhaps this was one of the reasons that the world had to be destroyed and restarted from scratch.

but there's no evidence that this ever happened!

[Dee Dee Warren]

Much better Gamble, thank you.

[Vorkosigan]

Creationist explain the biological word using a combination of two events: creation and the fall. If a shared biological feature is due to common design than it was produced in creation. If a shared biological feature is due to common descent, then it was produced as a result of the fall.

So, shared endogenous retroviruses and shared pseudogenes are the result of _______________?
Common Design Flaws (Creation)
Common Descent (Fall)


Rufus' question awaits an answer.

Vorkosigan

[RufusAtticus]

It's been waiting a while. I suspect that it still has a ways to go.

[WinAce]

http://www.feebleminds-gifs.com/tumbleweed.gif

[WinAce]

http://users.rcn.com/rostmd/winace/pics/chirping_cricket.gif

[Bald Ape]

TFS,

A day or two ago, in a different thread, I had mentioned that I hoped you would be responding to WA's most recent (substantive) post in this thread. Specifically, you pointed out that some (not all) ERV's might have insertional bias. WA rebutted that such a bias would be inconsequential to the big picture. I'd like to take a minute to further expound on why I agree.

In a nutshell, the argument you are trying to refute is that it is astronomically improbable that the same virus gene sequence could have been inserted, independently, into the exact same position in the DNA of two different organisms. Your counterargument, in its strongest context, is that because some of the areas of an organism's DNA are more prone to viral insertion than others, it is quite plausible that by chance alone, ERV's would be inserted at the exact same site. I plan to show why your argument fails.

The article you quoted, originally cited by Camp, lists (as the most extreme example of insertional bias) a hot spot which is 280 times more likely to be inserted to than mathematically predicted. That is, the absolute hottest of hot spots is 280 times more likely to be inserted to when compared to a random choice of two nucleotides from the DNA.

Aren't relative figures nice? Let's try some absolutes. We're looking at ERV insertions between any two of the 3 billion nucleotides in human DNA. Without insertional bias, there is a 1 in three billion chance of picking the same insertion point twice. According to Camp, therefore, at even the hottest of hot spots, there is less than a one in ten million chance that this same site will get inserted to twice, independently.

This means that, at best, a virus will need to insert itself into the DNA of two different species hundreds of thousands of times before a single match is statistically likely to occur. So your theory that the matching occurs due to chance, even given the insertional bias, would predict that each matching ERV between two species would exist at thousands of points in the DNA of both species, just to give the one matching location. This is obviously not what is observed.

In fact, we see not just one ERV, but several ERV's defying these odds in the human/chimp comparison alone: each ERV appears in the DNA of the two different species exactly once (not thousands of times), at exactly the same location.

Keep in mind that WA was entirely correct in his response (which you have yet to respond to). Insertional bias has ABSOLUTELY NO impact on the other 5 points he raised (and repeated). To refresh your memory, points A, B, C, E, and F are not impacted by insertional bias at all - and it only serves to reduce D to a best case probability of one in ten million per ERV.

(A) viral infection generally results in a dead cell. Occasionally, fragments of the virus remain but the cell survives.
(B) infection of a germ line cell is even more rare.
(C) no two viral insertions are exactly alike.
(D) viral fragments insert at fairly random locations.
(E) that unlikely viral fragment-carrying germ line cell needs to be the particular egg or sperm cell that gets fertilized and survives to adulthood.
(F) It then needs to to piggyback on the success of an individual and get established in the population via sheer luck.


So even after you've made D "only" an anomoly of one in ten million, A, B, C, E, and F each lower the likelihood of the "independent insertion" hypothesis by many additional orders of magnitude. This doesn't include the unspoken G, which says "A,B,C,D,E,and F must miraculously occur by chance not once, but for every 'independently inserted' ERV between two species". In other words, G says: take the chances of A through F occuring, and then square that to explain two ERV's, cube it to explain 3, take it to the fourth power to explain 4, etc, etc...

Basically, the whole point is that any attempt to explain away ERV insertions as coincidence alone fails. The 'independent insertion coincidence' explanation is absurd. If we can agree on this point, we can start looking at Camp's other ad hoc explanations for ERV's (and there shortcomings).

Also, you accused WA of "hand waving" when he presented this. "Hand waving" is generally a term used to refer to people who are trying to distract you from seeing the obvious. I think it is quite evident that WA simply presented an argument comprised of six specific points, so I'm not clear how that could be considered hand waving to begin with. Ironically, it is also evident that you did all you could to distract the reader from the overall thrust of WA's argument by grandstanding a point that had an utterly inconsequential impact on WA's argument. I respectfully submit (that is, without personal insult) that if anyone's arguments in this thread qualify as "hand waving", they would be yours.

[Bubba]

I'm still waiting for a substantive creationist response to Rufus question.

Bubba:smile:

[Socrates]

Blubba demands immediate responses to arcane questions by evolutionists or else creationists should give up and go home. But when creationists ask for remotely plausible scenarios for chemical evolution or explaining biological motors, they are told "we must look harder because a designer is not science". Heads, the evolutionists win; tails, the creationists lose.

If creationists raise an insoluble problem, they are falsely accused of a "god of the gaps" argument, but there are plenty of "evolution of the gaps" style arguments.

And to put these arguments in perspective, at the time of the Scopes trial, creationists apparently had no good answer to Piltdown Man, about 80 alleged vestigial organs, or embryonic recapitulation. Even earlier, Christians apparently had no answer to liberal archaeologists who thought that the Hittites were a biblical myth. Now, anyone would be laughed at for raising this sort of "evidence". So the moral of the story is, the history of science is full of theories being junked when more evidence comes in.

[Woman]

Soc:

So the moral of the story is, the history of science is full of theories being junked when more evidence comes in.

"Junked" or modified - isn't that the beauty of science? That it refines itself based on new evidence? A pity that Biblical inerrants won't do the same. Also, we're not talking history of science in general here, but rather the theory of evolution which is gathering evidence at an almost exponential rate as the mystery of DNA opens to us.

This evidence, as presented here, to the best of my understanding, seems irrefutable.

[Socrates]

Soc:


So the moral of the story is, the history of science is full of theories being junked when more evidence comes in.

Woman:"Junked" or modified - isn't that the beauty of science?Sure it is -- and it's also its limitation. The examples I've presented show the folly of churchians reinterpreting God's infallible Word by the theories of fallible human beings. Galileo is another example -- the church of his day made the mistake of listening to the establishment Aristotelian scientists and tying the Bible to Ptolemaic cosmology. That it refines itself based on new evidence? A pity that Biblical inerrants won't do the same. Of course not -- the Bible is the written Word of God, and was affirmed as such by Jesus Christ. Makes far more sense to trust that than fallible science. Even some of the advanced chemistry I was taught at uni relatively recently has had to be junked.

And I've provided many examples of evolutionists who won't abandon materialism.Also, we're not talking history of science in general here, but rather the theory of evolution which is gathering evidence at an almost exponential rate as the mystery of DNA opens to us.More elephant hurling. Rather, the complexity of DNA as an information storage retrieval system is gathering evidence for a brilliant Designer at an almost exponential rate -- see AiG's current front page article www.answersingenesis.org/docs2003/0425dna.asp This evidence, as presented here, to the best of my understanding, seems irrefutable.First, so did Piltdown Man, non-existence of the Hittites, 80+ vestigial organs, the Ostraea-to-Gryphaea transitional series and embryonic recapitulation.

Second, AiG HAS answered a lot of "junk DNA" type questions at www.answersingenesis.org/home/area/faq/vestigialorgans.asp#junk

[AdvocatDiaboli]

It still seems that no creationist has answered WinAce's and RA's points. I must confess that I was totally ignorant about ERVs, but now I've learned another new thing about biology and geology. Thanks guys!

[WinAce]

Yesterday @ 11:03 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=79140#post79140)
Socrates:

Blubba demands immediate responses to arcane questions by evolutionists or else creationists should give up and go home.

Well, it does get kinda embarrasing for your side when 5 days have passed without so much as an attempt at a rebuttal that wasn't preliminarily destroyed in the initial post.


But when creationists ask for remotely plausible scenarios for chemical evolution or explaining biological motors, they are told "we must look harder because a designer is not science". Heads, the evolutionists win; tails, the creationists lose.

I sooo need to learn such masterful use of the...

http://users.rcn.com/rostmd/winace/pics/red_herring.jpg

Of course, diverting attention from your failure to answer doesn't really amount to a hill of beans, much less a valid argument. Nevertheless, I've started this thread (http://www.theologyweb.com/forum/showthread.php?s=&threadid=3643) for all the juicy discussions of Biblical mud-to-you evolution vs. scientific theories. :smile:


If creationists raise an insoluble problem, they are falsely accused of a "god of the gaps" argument, but there are plenty of "evolution of the gaps" style arguments.

And there are probably as-yet-unsolved unknowns (in fact, alot of them) in Relativity and Quantum Mechanics. But, for some reason, those "problems" almost always end up as additional questions of how exactly the mechanisms work, not evidence contrary to the theories' predictions that needs to be rationalized away.

Compare that with creationism, which is contradicted by pretty much every branch of study there is (linguistics, plate tectonics, genetics, paleontology, cosmology, astronomy, chemistry, etc.) numerous falsifications of which are available and remain unaddressed right here on this forum.


And to put these arguments in perspective, at the time of the Scopes trial, creationists apparently had no good answer to Piltdown Man,

Of course they did. "By definition, no evidence ... can be valid if it contradicts the scriptural record" is an answer. It's not a good answer, or one that makes creationists look like more than the 21st century equivalent of the 19th century flat-earthers, but it's an answer nevertheless.

Of course, Piltdown Man was never really important to evolution anyway, was mentioned as anomalous (http://www.antievolution.org/topics/law/scopes/scopes.html) at the Scopes trial, and hasn't been used as evidence for around 50 years. Furthermore, the fact that it was a fraud doesn't take away the other, legitimate fossils we have, anymore than the Fen-fen diet drug debacle a few years back was an indictment against antibiotics.

Your evasion is duly noted, however.


about 80 alleged vestigial organs,

Like these (http://www.theologyweb.com/forum/showthread.php?s=&threadid=3642)?


or embryonic recapitulation.

Which has been modified to embryonic homology (http://www.theologyweb.com/forum/showthread.php?s=&threadid=3644) and still requires bizarre ad hoc rationalizations from creationists to this day.


Even earlier, Christians apparently had no answer to liberal archaeologists who thought that the Hittites were a biblical myth.

Names and references of these "liberal archaelogists" can be posted here (http://www.theologyweb.com/forum/showthread.php?s=&threadid=3646), without trying to hijack a thread that you can't address and desperately need to fall off the first page.


Now, anyone would be laughed at for raising this sort of "evidence".

Actually, anyone who links to AiG should be laughed at, but that's a different subject.


So the moral of the story is, the history of science is full of theories being junked when more evidence comes in.

Technically, theories almost never get junked - they get replaced with modified ones that explain all the previous data and new facts that the old theory couldn't. Newtonian mechanics is still valid for the most part, but Relativity explains additional observations. The perfectly spherical earth is technically incorrect, but the round earth is "correct enough" for everyday use.

When you get as much supporting data as evolution or QM, you're not gonna be falsified anytime soon.

I checked your AiG article, but it made comments that I and others already refuted previously. Please do bother reading the links you post and if any arguments there are applicable, just cut and paste them (with an appropriate explanation of how they're relevant) instead.

So, let's have a refutation of my post #19 (http://www.theologyweb.com/forum/showthread.php?postid=74997#post74997) and Bubba's #38 (http://www.theologyweb.com/forum/showthread.php?postid=78648#post78648). No rush, anytime in the next million years will do. Of course, by then, creationists might evolve into 'evolutionists' :ahem:

[RufusAtticus]

We're still waiting for the answer. If creationists' ideas are supposed to be a viable explaination for origins, why is it that this question still stands unanswered? Come one people it's multiple choice. A or B, which one is it?

So, shared endogenous retroviruses and shared pseudogenes are the result of _______________?
Common Design Flaws (Creation)
Common Descent Flaws (Fall)

[Warcraft3]

This evidence is indeed difficult to explain within a creationist framework. I have found this evidence to be some of the most convincing I have seen in favour of evolution. This evidence is one of several factors which has led me to consider theistic evolution (Ive been consiering it as a possibility for about a year now) as a possible viewpoint. So yes this is indeed powerful evidence.




Russ

:em7:

[RufusAtticus]

Russ,

I'm glad that you like it. Let me take this time to point out another interesting genetic feature of humans that signals common descent with the other great apes.

Humans have 23 pairs of chromosomes. Chimps, Gorillas, and Orangutans have 24. If we are related by common descent then either in our lineage two chromosomes have fused to form one, or in the other lineages a single chromosome has split into two. Now when comparing the banding between humans and these organisms, it was discovered that the second largest human chromosome, #2, has analogues in Chimps, Gorillas, and Orangutans like so.
http://www.gate.net/~rwms/hum_ape_chrom_2.gif.
Now the rules of parisonomy would argue that it is more likely to have one chromosomal fusion than three chromosmal fissions.

Thus we can hypothesize that the differences in chromosomal number and the homologies detected are due to a pair of moderately sized chromosomes fusing end to end during our lineage, but after we separated from the chimps, gorillas, and organutans. Now linear chromosomes have special sequences on their ends that protect them from them from shortening during replication. These sequences are known as telomeres. If human chromosome 2 was caused by an end-to-end fusion of two other chromosomes, then we should expect to find telomeres located somewhere in the middle of it.

And guess what. That is exactly what Ijdo and collegues found and reported in 1991.

Ijdo JW et al. (1991) "Origin of Human Chromosome 2: An Ancestral Telomere-Telomere Fusion" PNAS, Vol 88, 9051-9055.

Abstract:
We have identified two allelic genomic cosmids from human chromosome 2, c8.1 and c29B, each containing two inverted arrays of the vertebrate telomeric repeat in a head-to-head arrangement, 5'(TTAGGG)n-(CCCTAA)m3'. Sequences flanking this telomeric repeat are characteristic of present-day human pretelomeres. BAL-31 nuclease experiments with yeast artificial chromosome clones of human telomeres and fluorescence in situ hybridization reveal that sequences flanking these inverted repeats hybridize both to band 2q13 and to different, but overlapping, subsets of human chromosome ends. We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomere-telomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2.

A link to a PDF of the paper. (http://www.pnas.org/cgi/reprint/88/20/9051)

Here is a complete alignment of human and chimp karyotypes.
http://webpages.charter.net/rufusatticus/YunisFig2.GIF

[WinAce]

Bumpity.

[AdvocatDiaboli]

How do we know that ERVs are from virus infection? Is there a specific piece od DNA which indicates a infection in the past?

[Woman]

Rufus,

Thank you for taking the time to post that information. I'm sure I'm not the only one who appreciates it. It's just amazing to me.

BTW, I started a thread to discuss human brain evolution and was hoping you could contribute. Any chance?

W.

[QED]

Today @ 09:25 AM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=82864#post82864)
AdvocatDiaboli:

How do we know that ERVs are from virus infection? Is there a specific piece od DNA which indicates a infection in the past?

Check out this layman's article:
http://www-micro.msb.le.ac.uk/3035/Retroviruses.html

The short answer is that retroviral gemones are very distinctive and unique, and can readily be identified in the host genome as such.

[Socrates]

Nature 423 (May 1, 2003): 26 - 28

Molecular biology: Complicity of gene and pseudogene
JEANNIE T. LEE

Jeannie T. Lee is at the Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, and the Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA.


'Pseudogenes' are produced from functional genes during evolution, and are thought to be simply molecular fossils. The unexpected discovery of a biological function for one pseudogene challenges that popular belief.

Pseudogenes are defective copies of functional genes that have accumulated to an impressive number during mammalian evolution. Dysfunctional in the sense that they cannot be used as a template for producing a protein, pseudogenes are in fact nearly as abundant as functional genes. Why have mammals allowed their accumulation on so large a scale? One proposed answer is that, although pseudogenes are often cast as evolutionary relics and a nuisance to genomic analysis, the processes by which they arise are needed to create whole gene families, such as those involved in immunity and smell. But are pseudogenes themselves merely by-products of this process? Or do the apparent evolutionary pressures to retain them hint at some hidden biological function? For one particular pseudogene, the latter seems to be
true: elsewhere in this issue (page 91), Hirotsune and colleagues report the unprecedented finding that the Makorin 1-p1 pseudogene performs a specific biological task.

[snip]

Whatever the underlying mechanism, the work of Hirotsune et al. is provocative for revealing the first biological function of any pseudogene. It challenges the popular belief that pseudogenes are simply molecular fossils < the evidence of Mother Nature's experiments gone awry. Indeed, it suggests that evolutionary forces can work in both directions. The forward direction is driven by pressures to create new genes from existing ones, an imperfect process that often generates defective copies of the original. But these defective copies need not be evolutionary dead ends, because pressures in the reverse direction could modify them for specific tasks. In the case of Makorin1 and Makorin1-p1, the result of bidirectional selection is that one gene cannot exist without the other < an example of functional complicity between a perfected product of evolution and its derivative castaway. Might the pseudogene copies of other functional genes be similarly useful?

------------------------------------------------------------------------
Nature © Macmillan Publishers Ltd 2003

[QED]

Nice post, Socrates.

[Warcraft3]

Today @ 08:10 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=83561#post83561)
Socrates:

Nature 423 (May 1, 2003): 26 - 28

Molecular biology: Complicity of gene and pseudogene
JEANNIE T. LEE

Jeannie T. Lee is at the Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, and the Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA.


'Pseudogenes' are produced from functional genes during evolution, and are thought to be simply molecular fossils. The unexpected discovery of a biological function for one pseudogene challenges that popular belief.

Pseudogenes are defective copies of functional genes that have accumulated to an impressive number during mammalian evolution. Dysfunctional in the sense that they cannot be used as a template for producing a protein, pseudogenes are in fact nearly as abundant as functional genes. Why have mammals allowed their accumulation on so large a scale? One proposed answer is that, although pseudogenes are often cast as evolutionary relics and a nuisance to genomic analysis, the processes by which they arise are needed to create whole gene families, such as those involved in immunity and smell. But are pseudogenes themselves merely by-products of this process? Or do the apparent evolutionary pressures to retain them hint at some hidden biological function? For one particular pseudogene, the latter seems to be
true: elsewhere in this issue (page 91), Hirotsune and colleagues report the unprecedented finding that the Makorin 1-p1 pseudogene performs a specific biological task.

[snip]

Whatever the underlying mechanism, the work of Hirotsune et al. is provocative for revealing the first biological function of any pseudogene. It challenges the popular belief that pseudogenes are simply molecular fossils &lt; the evidence of Mother Nature's experiments gone awry. Indeed, it suggests that evolutionary forces can work in both directions. The forward direction is driven by pressures to create new genes from existing ones, an imperfect process that often generates defective copies of the original. But these defective copies need not be evolutionary dead ends, because pressures in the reverse direction could modify them for specific tasks. In the case of Makorin1 and Makorin1-p1, the result of bidirectional selection is that one gene cannot exist without the other &lt; an example of functional complicity between a perfected product of evolution and its derivative castaway. Might the pseudogene copies of other functional genes be similarly useful?

------------------------------------------------------------------------
Nature © Macmillan Publishers Ltd 2003



Interesting.........



Russ

[Bald Ape]

Very nice post Socrates. So it seems some 'pseudogenes' may in fact serve as a "drawing board" of sorts, allowing organisms to generate, test, and adapt new information and functionality without loss of existing information or risk to existing functionality. Very cool!

A small criticism: this would be very interesting as a new thread, but I have to wonder: why did you put it here? To be even more blunt, please site a single post in this entire thread where somebody claimed the evidence for common descent supplied by endogenous retroviruses was even related to (much less relied on) the notion that no pseudogenes are ever useful to any organisms that carry them.

I have to be honest - it really looks like this article is an effort on your part to distract from (not address) the argument at hand. This is a fairly common logical fallacy known as a "red herring" (an old reference to a practice whereby escaping convicts tried to distract guard dogs by tossing them a piece of fish meat). Such fallacies actually reflect poorly on you, draw attention to your inability to address the actual points raised by Winace, myself, and others; and thus ultimately strengthen the case that has been presented.

Please take this as just a small piece of constructive criticism - hopefully it will come of use to you at some future time.

[Socrates]

The Alopecic Simian whinges about the post. Well, first of all, it was brand new research, and SOME people might have appreciated being informed about it :poke:. Second, it is RELATED to the general "junk DNA" argument. Third, it seems to support the geneticist Dr Charles Wood's idea of Altruistic Genetic Elements (AGEs) having an important role in post-Flood diversity.

[Woman]

Alopecic Simian

I hope BA sees the humor in that...

[Bald Ape]

Socrates,

Fair enough - and I should add that I most certainly am amongst the SOME people who like to stay informed on these matters. A closer read of my post will show that I wasn't complining THAT you posted the article, I was merely criticizing WHERE you posted the article. But what I left out of my post, which I just realized, was a word of gratitude for posting the article at all. Thanks!


Woman:
I hope BA sees the humor in that...But of course - in fact, I joked around about it the very first (http://www.theologyweb.com/forum/showthread.php?s=&postid=43743&highlight=simian#post43743) time Socrates used the phrase.

[Socrates]

:smile: That's true BA, I remember. You're welcome. :hrm:

[TheFiveSolas]

An interesting quote:



"Extensive data on genetic divergence among 24 inbred strains of mice provide an opportunity to examine the concordance of gene trees and species trees, especially whether structured subsamples of loci give congruent estimates of phylogenetic relationships. Phylogenetic analyses of 144 separate loci reproduce almost exactly the known genealogical relationships among these 24 strains. Partitioning these loci into structured subsets representing loci coding for proteins, the immune system and endogenous viruses give incongruent phylogenetic results. The gene tree based on protein loci provides an accurate picture of the genealogical relationships among strains; however, gene trees based upon immune and viral data show significant deviations from known genealogical affinities "

W. R. Atchley and W. M. Fitch. Gene trees and the origins of inbred strains of mice. Science 254 (5031):554-558, 1991.

[AdvocatDiaboli]

Yesterday @ 06:39 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=85403#post85403)
TheFiveSolas:

An interesting quote:

"gene trees based upon immune and viral data show significant deviations from known genealogical affinities "



Maybe because immune and viral data are "created" through exposure to wide variety of diseases?
I.e. once species have split from each other, they are exposed to diseases which affect only the other species, leaving the other without the traces of immune and viral genes.

Sounds pretty good, despite the fact that I don't know what I'm saying.:shrug:

[RufusAtticus]

Having just finished reading the Hirotsune et al. (2003) paper. I want to point out their summary of their work.


With these studies, we have uncovered a mechanism of gene regulation of a coding gene, Makorin1, by a transcribed non-coding pseudogene Makorin1-p1. Makorin1-p1 must function as an RNA, as it cannot code for a protein. Protection from mRNA decay of Makorin1 by Makorin1-p1 was easily reproduced by expression constructs in several cell lines and in transgenic mice, suggesting that this type of regulation may be a general phenomenon. Although the precise enzymatic mechanism is unknown, one possibility is that a trans-acting RNA-destabilizing factor—which is able to bind to the 5' UTR of Makorin1 and Makorin1-p1 transcripts—is in limiting amounts or temporally and spatially regulated. Expression of the Makorin1-p1 transcript may titrate out this factor, thus increasing wild-type Makorin1 mRNA stability in a developmentally regulated and tissue-specific manner.

One should note that they were not investigating a single-copy pseudogene like the onese being discussed in this thread (GULO or urate-oxidase pseudogenes), and in fact such pseudogenes cannot have the function seen by them.

Ref: Hirotsune et al. (2003) An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423 (May 1): pp91-96

[Theoriste]

For anyone who's interested, I've created a page showing the alignment of one such endogenous retrovirus on a chimpanzee genomic clone, onto the human genome. Enjoy.

http://www.umich.edu/~lilyth/erv/

[Theoriste]

05-02-2003 @ 06:39 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=85403#post85403)
TheFiveSolas:

An interesting quote:



For the record, that was in 1991, over ten years before the release of the mouse genome. Not to say their results were wrong, but trying to do a phylogenetic analysis on identical genomic elements without knowing that they are indeed identical genomic elements might be problematic.

[Theoriste]

05-01-2003 @ 01:10 AM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=83561#post83561)
Socrates:

Nature 423 (May 1, 2003): 26 - 28

Molecular biology: Complicity of gene and pseudogene
JEANNIE T. LEE

Jeannie T. Lee is at the Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, and the Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA.


'Pseudogenes' are produced from functional genes during evolution, and are thought to be simply molecular fossils. The unexpected discovery of a biological function for one pseudogene challenges that popular belief.

Pseudogenes are defective copies of functional genes that have accumulated to an impressive number during mammalian evolution. Dysfunctional in the sense that they cannot be used as a template for producing a protein, pseudogenes are in fact nearly as abundant as functional genes. Why have mammals allowed their accumulation on so large a scale? One proposed answer is that, although pseudogenes are often cast as evolutionary relics and a nuisance to genomic analysis, the processes by which they arise are needed to create whole gene families, such as those involved in immunity and smell. But are pseudogenes themselves merely by-products of this process? Or do the apparent evolutionary pressures to retain them hint at some hidden biological function? For one particular pseudogene, the latter seems to be
true: elsewhere in this issue (page 91), Hirotsune and colleagues report the unprecedented finding that the Makorin 1-p1 pseudogene performs a specific biological task.

[snip]

Whatever the underlying mechanism, the work of Hirotsune et al. is provocative for revealing the first biological function of any pseudogene. It challenges the popular belief that pseudogenes are simply molecular fossils &lt; the evidence of Mother Nature's experiments gone awry. Indeed, it suggests that evolutionary forces can work in both directions. The forward direction is driven by pressures to create new genes from existing ones, an imperfect process that often generates defective copies of the original. But these defective copies need not be evolutionary dead ends, because pressures in the reverse direction could modify them for specific tasks. In the case of Makorin1 and Makorin1-p1, the result of bidirectional selection is that one gene cannot exist without the other &lt; an example of functional complicity between a perfected product of evolution and its derivative castaway. Might the pseudogene copies of other functional genes be similarly useful?

------------------------------------------------------------------------
Nature © Macmillan Publishers Ltd 2003


This gene is a copy of another gene, which was thought to be a pseudogene. However, it is not a pseudogene as it has function.

The problem with the classification of pseudogenes is that it's used as a blanket statement for any genic region which does not produce protein. It includes the highly disabled and decaying-away non-expressing genes, as well as the more conserved expressing pseudogenes. It's much like calling all four-legged creatures who resemble a horse, "HORSE" and ignoring the details of what differentiates a horse from a donkey from a zebra.

Those who want to try to use this as an example of "junk DNA having some function" shoud tread carefully and examine what a pseudogene "really" is. And let me clarify why, for those not in the know.

The classification of a pseudogene that I give to my students, is that "a pseudogene is a region of the genome that has recognizable gene structure, yet its products have been unattached from the function of the living organism so that it is does not subject the system to selection on mutation."

The classification, used loosely by many people of a pseudogene, is any gene which does not produce a functional product. If something was classified as a pseudogene and then is later found to have a functional product, then, of course, it's no longer a pseudogene.

Now, there is a difference in how pseudogenes behave. Some pseudogenes still express, in that their products enter the cellular milleiu. Expressed pseudogenes are the results of protein-gene copies that have been disabled from protein expression but are not disabled from RNA expression yet. They do not make protein, but they do make RNA. The typical event progression is DNA->mRNA->protein, and the pseudogenes thus classified stops at the mRNA level.

As in the published paper cited above, RNA expression and control may be a very good reason why some pseudogenes are expressed, and has been suggested as a mechanism before. This is no shocking news, as we already know of examples of RNA of a gene interfering with the production of its protein.

However, for an RNA-controlling gene to regulate its own protein-coding-gene copy, it has to maintain a high level of homology to its protein-coding-gene copy because the mechanism for RNA regulation is usually by hybridizaton (copy to copy pairing), otherwise the regulation (by hybridization) won't work. So highly divergent pseudogenes are less likely to play that kind of role as published above.

I predict hat we will find many more of these examples of regulation, but not all expressed pseudogenes will be found to have a function. That's an easy prediction to make, as several pseudogenes have tight resemblence to their original gene copies.

However, many more pseudogenes are NOT expressed. The RNA products of these pseudogenes DO NOT enter the cellular millieu and have no evidence of being expressed at all. So instead of stopping at the mRNA level, they never even make it there.
These pseudogenes, as just spots on the DNA where a gene copy -- or fragments of a gene -- had deposited, CAN be considered "junk DNA" in the human genome and have no expression products we can detect. In fact, I've hopefully gone looking for evidence that several were expressing, on intellectual property grounds, but no luck. There are more patches of hopeful-looking pseudogenes on the human genome than there are expression products.

This recently published "pseudogene", which was mistakenly classed as a pseudogene just based on the fact that it doesn't produce a protein product, was show to have some function. Since RNA regulation study is only a few years old , we may find many *expressed* pseudogenes have RNA regulatory functions. These expressed pseudogenes will likely be renamed to something like "RNA-regulatory genes".

A problem is that many on-the-bench wetlab researchers classify "pseudogenes" incorrectly as any apparent protein-coding gene that doesn't make a protein, since proteins are what most wetlab molbio bench researchers are immediately interested in. Until someone starts using the term "RNA-regulatory gene" in any kind of regular sense, be very careful about the difference between expressed pseudogenes with no apparent function, expressed pseudogenes with apparent function, and pseudogenes with no expression nor apparent function.

However, in all of this, even the non-expressed pseudogenes are only a small fraction of "junk DNA". For instance, the fish, FUGU, has a much smaller quantity of junk DNA than humans or some plants, or some animals, or even some fish...but it seems to get along just fine as a complex vertebrate.

[Bald Ape]

Theoriste,

Great link, and great site! Nothing supports the theory of common descent of humans and chimpanzees like raw data with inescapable inferences.

An aside: from your link, it appears that you might have access to chimpanzee genomic data. In a related thread on this board, Socratism and I are looking at DNA and amino acid sequences for Cytochrome C. I found an abundance of amino acid sequences for the protien in various organisms, but my search for nucleotide sequences came up relatively dry.

The chimp CytC nucleotide sequence (as well as the CytC nucleotide sequence of any other mammal), would be very helpful in our discussion. (Especially a marsupial sequence, or echidna).

Any help you could give would be most appreciated (if you have any sequences, you can post them here, on the CytC thread, or PM them to me).

Thanks in advance,

Bald Ape

[Socrates]

Dr Ian Macreadie is a highly regarded Australian researcher in the fields of molecular biology and microbiology. Author of more than 60 research papers, he is a Principal Research Scientist at the Biomolecular Research Institute of Australia’s Commonwealth Scientific and Industrial Research Organisation (CSIRO), and national secretary of the Australian Society for Biochemistry and Molecular Biology.

In 1997 he was part of a team which won the CSIRO’s top prize, the Chairman’s Medal. In 1995 he won the Australian Society for Microbiology’s top award, for outstanding contributions to research. He is also adjunct professor of the Royal Melbourne Institute of Technology.

In an interview www.answersingenesis.org/docs/3985.asp he said:


‘I actually don’t believe God created viruses as separate entities, I believe they were a part of the DNA in cells. Some evolutionists put viruses down as a predecessor of cells, but that doesn’t work, because they need to have the machinery of cells to reproduce. I actually see viruses as genetic garbage, having escaped from cells way back, as a result of mutation, environmental damage — part of the Curse on creation [Genesis 3]. I would predict from that theory that we should find pieces of “virus” DNA in the human genome (DNA). And that’s starting to be found.’

This might not apply to all viruses, because some appear to be created entities with a benign pre-Fall role -- see www.trueorigin.org/virus.asp

[Jimmy Higgins]

Today @ 09:13 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=90584#post90584)
Socrates:
This might not apply to all viruses, because some appear to be created entities with a benign pre-Fall role -- see. God create this stuff to make yogurt?! :teeth:

[Bald Ape]

I would predict from that theory that we should find pieces of “virus” DNA in the human genome...

So virus pieces resulted from the Fall. No problem with that. Why do we find the exact same virus pieces at the exact same place in both chimpanzees and humans, but not gorillas, if they are the result of the Fall?

You have been reading the thread, haven't you Socrates?

[WinAce]

05-07-2003 @ 09:13 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=90584#post90584)
Socrates:

Dr Ian Macreadie is a highly regarded Australian researcher in the fields of molecular biology and microbiology. ...
In 1997 he was part of a team which won the CSIRO’s top prize, the Chairman’s Medal. ...

In an interview www.answersingenesis.org/docs/3985.asp he said:

‘I actually don’t believe God created viruses as separate entities, I believe they were a part of the DNA in cells. ... I would predict from that theory that we should find pieces of “virus” DNA in the human genome (DNA). And that’s starting to be found.’

So your hypothesis for ERVs is that they're the original, and the virii we know now split off from them later.

Somewhat unparsimonious - we've observed virii depositing ERVs, but we've never observed a new, functional virus evolving from a fragment of several nucleotides. (Would that be evolution of the hopeful monster variety?)

Already, your defense amounts to the equivalent of "those aren't really dinosaur fossils, but designed elements that were later magically turned into dinosaurs".

And I would predict from that hypothesis that the endogenous retroviral fragments we find in our genomes (at least the original ones) will be much larger than mere fragments or modern virii. After all, a chapter will generally be larger than the sentence ripped out of it, will it not? :smile:

Well, looks like our little hypothesis is toasted. We don't find complete virii larger than their free-living fragments in the genome, but the exact opposite: parasitic fragments of virii much smaller than their free-living counterparts.

Since the origin of virii isn't the topic of this, I won't even go into how a benign virus (an oxymoron if there ever was one) can acquire irreducibly complex mechanisms for subverting the immune system and killing the host, all without gaining new information.

[WinAce]

It appears the creationists have ditched the usual strategy, that of assorted red herrings, in favor of Plan B - ignoring the facts and hoping they'll go away.

http://users.rcn.com/rostmd/winace/pics/chirping_cricket.gif

[SLPx]

05-08-2003 @ 02:13 AM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=90584#post90584)
Socrates:

Dr Ian Macreadie is a highly regarded Australian researcher in the fields of molecular biology and microbiology. Author of more than 60 research papers, he is a Principal Research Scientist at the Biomolecular Research Institute of Australia’s Commonwealth Scientific and Industrial Research Organisation (CSIRO), and national secretary of the Australian Society for Biochemistry and Molecular Biology.

In 1997 he was part of a team which won the CSIRO’s top prize, the Chairman’s Medal. In 1995 he won the Australian Society for Microbiology’s top award, for outstanding contributions to research. He is also adjunct professor of the Royal Melbourne Institute of Technology....

Argumentum ad verucundiam.

[Korihor]

I found one argument by OEC Fuz Rana of Reasons to Believe in a Creation Update webcast last year. You can listen to it here:

Creation Update webcast - 06/04/02 (http://www.reasons.org/resources/multimedia/rtbradio/cu_archives/cu20020604.ram)

Fast forward to about 1 hour, 35 min. into the program.

Rana's main argument was that some endogenous retroviruses had a function, like chromosome repair and defenses against harmful mutations. However, I don't see how that's incompatible with common ancestry.

Rana took a step further and argued that ERV's in the genome may not be ERV's at all, but some form of created material. He also speculates that in creating Adam and Eve, God used previous creations as templates (chimp spare parts, I guess), thus genes (and ERV's) are passed on but not through common ancestry.

In my opinion, that's at least a plausible interpretation of ERV's, but it just seems to throw parsimony out the window. Common ancestry just explains it better a lot more simply without resorting to invoking ad hoc supernatural tinkering. His claim that ERV's may not be ERV's is not very credible either. For example, if it's not an ERV, the why the heck is there a gene in it to code for the protein that coats the envelope for a virus?

[WinAce]

Today @ 10:44 AM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=102155#post102155)
Korihor:

Rana took a step further and argued that ERV's in the genome may not be ERV's at all, but some form of created material. He also speculates that in creating Adam and Eve, God used previous creations as templates (chimp spare parts, I guess), thus genes (and ERV's) are passed on but not through common ancestry.

In my opinion, that's at least a plausible interpretation of ERV's, but it just seems to throw parsimony out the window.

Oh yeah. Next he'll be saying that dinosaur bones aren't really fossils, but designed elements that God planted because he used templates from other planets that did have fossils.

[WinAce]

Bumpity.

[Bald Ape]

So, about those chunks of viral protein DNA (you know, those annoying ones which code for viral proteins, and are found stuck at the exact same place in all human DNA and in all chimp DNA, but are completely absent in all other animals on the planet)...

If chimps are not distant cousins of humans, then how can these viral insertions exist at the exact same place?

[WinAce]

*Cough* *Cough*

I hope this topic and the lack of substantive replies will be a lesson to everyone here that (A) creationists can't deal with the evidence and (B) they like ignoring it and hoping it'll go away.

[WinAce]

In another thread (http://www.theologyweb.com/forum/showthread.php?postid=122707#post122707), our very own inimitable Socrates wrote:


Except that you have confused history and science. In reality, evolution from goo to you via the zoo is NOT a claim about science but history. And it's a historical interpretation of the data under a belief system that excludes a priori miraculous acts by God.

Since endogenous retroviral insertions and other data are simply "interpreted differently" by those godless atheists, Hindus, Christians, Jews, Muslims and others who accept evolution, let's see how they can be interpreted under the "theory" of independent creationism.

Oh look! I think I saw a flying pig!

[QED]

Except that you have confused history and science. In reality, evolution from goo to you via the zoo is NOT a claim about science but history. And it's a historical interpretation of the data under a belief system that excludes a priori miraculous acts by God.

Wait!!! You took that quote out of context! You left out:

... you can believe this because I said so, and I am pretty darn close to never wrong....

Never mind that it sounds like I just made this up, or that I have demonstrated a lack of even a basic understanding of the relevant issues....

And don't forget to ignore the reams of evidence for common descent that make would make my view untenable if you paid them any attention. Trust me, they are just "interpretations". Remember: "I said so!"

If you are going to quote someone, you should include the full context of the quote, so that others can see the meaning behind it.

Oh, wait... It seems that the original was also missing those important disclaimers! Gork!

[Bald Ape]

Since I recently referenced it, I thought I'd bump this thread back to the top, and again open the floor to anyone who'd like to attempt to account for the existence of shared human ERV insertions in a YEC worldview. Are they a part of God's perfect creation? Are they an affliction of the post-Fall era?

Surely a falsely accused suspect would offer some plausible explanation of how his fingerprints came to be on the murder weapon... surely he'd not take the 5th, and expect the jury to just ignore that particular piece of evidence.

[CobraA1]

Huh? OK, let me try to understand this . . .

-There seems to be some retroviral insertions in the DNA of some animals. A "retroviral insertion" is insertion of DNA by a virus, right?

Ok, first we've got to establish all of our facts here.

-First of all, how do we tell the difference between DNA shared because of natural evolution (or, in the case of creationism, common design), and DNA shared because of retroviral insertion?

-Also, you seem to claim that two species geting the same insertion a the same position is rare - I'd like to see some statistics, just to make sure that part of the claim is OK.

[The Barbarian]

Because we observe that such insertions are random, you can figure out the probability of an insertion in any particular spot by calculating

P = 1/(number of possible insertion sites)
A rather small number.

The probability of getting two in the same place would be P^2
A much, much smaller number.

Of course, if there were more insertions, the probability of at least two in the same place, given N insertions is higher, but that's not common, either.

[Roy]

Today @ 02:01 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=144176#post144176)
The Barbarian:

Because we observe that such insertions are random, you can figure out the probability of an insertion in any particular spot by calculating

P = 1/(number of possible insertion sites)
A rather small number.

The probability of getting two in the same place would be P^2
A much, much smaller number.

uh oh - math failure alert. The probability of getting two viral insertions in the same place is p, not p2, since the location of the first insertion has no constraints. The probability of getting two viral insertions at a specified point is p2.

Roy

[Bald Ape]

Cobra,

See post #19 and #38 in this thread for more extensive treatments of probability. As for your first question, this article (http://jvi.asm.org/cgi/content/full/72/7/5955?view=full&pmid=9621058) may be enlightening...
The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences.

(from the article, emphasis added)


HERVs (see Table 2) have been discovered as a result of
different experimental approaches. Screening human genomic
libraries under low-stringency conditions with probes derived
from animal retroviruses has allowed the isolation and characterization
of multiple, albeit defective, proviruses, representing
different families [e.g., HERV-E (17), HERV-R (13),
HTDVyHERV-K (21)]. Other approaches relied on the use of
oligonucleotides with homology to viral primer binding sites
(HERV-P; ref. 20). Furthermore, HERV families were detected
by chance during analyses of human gene loci [HERV-H (11),
ERV-9 (14), HERV-I (18)]. Table 2 summarizes some of the
characteristics of these HERV families.
HERVs have been classified according to their homologies
to animal retroviruses (reviewed in ref. 23). Class I families
have sequence similarities to mammalian type C retroviruses.
Three families sharing substantial homologies not only in the
well-conserved pol region but also in the gag and env genes
have been grouped into a superfamily, the ERI family. Their
closest infectious relatives are murine leukemia virus (MuLV)
and baboon endogenous virus (BaEV). Other HERV families,
such as ERV-9, HERV-I, and especially HERV-H, are more
distantly related.

Source:
Proc Natl Acad Sci U S A. 1996 May 28;93(11):5177-84.

[Elisha]

I haven't ever posted anything of much value at this place. I'm just the "observer-guy" who loves to read and keep up with debates. <big time JP Holding fan :D>

I'm hoping Dee Dee will understand the reasoning in this post and not edit it :)

I'm curious as to why Socrates is ignoring observable facts, which does put a bad stain on Christianity (kinda like Kent Hovind). This isn't a personal attack against you Socrates, because I do respect you very much and I do admire your devotion. The problem comes when you've been presented obvious facts and you toss them aside as mere blah.

Today, when I woke up, I woke up a hardcore anti-evolutionist (kinda like yourself), but WinAce did present this case before me and I readily admitted that it is observable proof for evolution. One simple question - How and why deny it? There's a difference between being honest and lying to yourself and the world << just pointing that fact out.

I'd just like to see you open up your mind a bit. I'm incredibly impressed by your intelligence, so it makes me sad to see such an intelligent guy perform such unreasonable actions. Once again, I'm just being honest with you :) No beef at all.


In Christ,


Tim

[Socratism]

There seems to be a whole lot of assuming going on here.

Although these assumptions may appear today to be reasonable, the whole history of cellular investigation seems to be one big "surprise" after another.

[The Barbarian]

uh oh - math failure alert. The probability of getting two viral insertions in the same place is p, not p2, since the location of the first insertion has no constraints. The probability of getting two viral insertions at a specified point is p2.


That's why I said "any particular spot". If you specify it beforehand, it's p^2

It's like asking what's the probability of getting 2 heads in a row.

It's 0.5X0.5 or 0.25. The probability of getting heads after you've gotten heads the first time, is still 0.5, however.

[The Barbarian]

There seems to be a whole lot of assuming going on here.

Although these assumptions may appear today to be reasonable, the whole history of cellular investigation seems to be one big "surprise" after another.

Even if you retreat to "well, someday, some evidence might overturn what the evidence says today", that still doesn't support your argument.

And considering the mass of evidence for scientific theories today, it would seem that something rather striking would have to happen to overturn it all.

In short, Socrates, there is a very small likelihood of a "magic bullet" that will kill evolution. Science doesn't work that way.

[Socratism]

One can not appeal to "the mass of scientific evidence for theories" in an attempt to shore up evolution, because most scientific theories have nothing to do with evolution.

The history of these things as far as evolution is concerned is that the favorite "evidence" for one generation is found to have been misunderstood and/or flawed and so soon forgotten, but is replaced by the latest "new thing", which in turn is found to be flawed and so forgoten, etc, etc, ad nauseum.

At the same time there is a steamroller effect of information which is slowly squeezing the "goo to the zoo" concept with steady progress in understanding and appreciating the marvellous complexity of cellular life as well as multicellular mechanisms and interconnections. At some point this will overcome the massive propaganda which supports evolution, just as the free flow of information eventually led to the demise of communism in the Soviet Union.

Only a closed state that tightly controls the information that people hear can sustain a failed paradigm, and even that is only temporary in the long range scheme of things.

Thus I am optimistic that the truth will eventually prevail.

[chickenman]

Only a closed state that tightly controls the information that people hear can sustain a failed paradigm

the documentation of the science that leads to the acceptance of evolution is available to everyone. Theres no conspiracy to conceal the truth here socratism

[Elisha]

Socratism,

Thanks for taking the time to reply. It's nice to see that you didn't interpret me as being a jerk, because I wasn't meaning to be.

You typed,


There seems to be a whole lot of assuming going on here.

Although these assumptions may appear today to be reasonable, the whole history of cellular investigation seems to be one big "surprise" after another.

With all due respect, this is equivalent to a flat-earther saying to a round-earther:

"Although these assumptions may appear today to be reasonable, the whole history of man seems to be filled with one big 'surprise' after another"

It just seems quite circular, indeed, do you not agree?

If WinAce presents before me a ball that I can safely conclude is there, an anti-baller can say:

"Although these assumptions may appear today to be reasonable, the whole history of "ball'ism" seems to be filled with one big 'surpise' after another"


Simply put, it's arguing in circles, as you well know. It's also untenable, which falls for William Craig's "untenable, therefore, irrational" argument.

P1: If a statement is untenable, it is irrational to hold.
P2: Your statement is untenable.
C: Therefore, it's irrational to hold.



I'll pause here and welcome a response from you.

[Socratism]

Today @ 05:08 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=213997#post213997)
chickenman:
the documentation of the science that leads to the acceptance of evolution is available to everyone. Theres no conspiracy to conceal the truth here socratism

If by conspiracy you mean that people are deliberately trying to deceive the public then I would certainly agree with you that there is no conspiracy.

If you mean that that the average person is exposed to the creation argument on an equal footing with the evolution argument then you are most certainly mistaken.

Of course most educators would say that there is nothing wrong with the lop sided information coverage because evolution is the true answer anyway.

[Socratism]

Today @ 05:30 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=214007#post214007)
Elisha:

Socratism,

Thanks for taking the time to reply. It's nice to see that you didn't interpret me as being a jerk, because I wasn't meaning to be.

You typed,

[]

With all due respect, this is equivalent to a flat-earther saying to a round-earther:

&quot;Although these assumptions may appear today to be reasonable, the whole history of man seems to be filled with one big 'surprise' after another&quot;

It just seems quite circular, indeed, do you not agree?

If WinAce presents before me a ball that I can safely conclude is there, an anti-baller can say:

&quot;Although these assumptions may appear today to be reasonable, the whole history of &quot;ball'ism&quot; seems to be filled with one big 'surpise' after another&quot;


Simply put, it's arguing in circles, as you well know. It's also untenable, which falls for William Craig's &quot;untenable, therefore, irrational&quot; argument.

P1: If a statement is untenable, it is irrational to hold.
P2: Your statement is untenable.
C: Therefore, it's irrational to hold.

I'll pause here and welcome a response from you.

With all due respect you had me fooled by your earlier post in thinking you were interested in discussing these subjects in a serious way.

Your above posting caused me to change my mind about that, for you attempted (very ineptly) an argument by ridicule.

[The Barbarian]

One can not appeal to "the mass of scientific evidence for theories" in an attempt to shore up evolution, because most scientific theories have nothing to do with evolution.

Well, it was physicists who first figured out the age of the earth, not evolutionists, so we have to toss physics.

And geologists have found that the evidence in the rocks can be understood only in terms of billions of years, so geology has to go.

And since astronomers have observed phenomena that cannot be reconciled with YE creationism, astronomy has to go. (apparently, heliocentrism is O.K.; there's been a change in position since Luther correctly asserted that a literal reading of Scripture ruled out a moving Earth)

And genetics has to go; all that evidence for evolution is inconsistent with creationism. So does molecular biology, and chemistry (probability arguments of creationists depend on chemistry being a random process)

Well, they still have meteorology and metallurgy, I think. :teeth:


The history of these things as far as evolution is concerned is that the favorite "evidence" for one generation is found to have been misunderstood and/or flawed and so soon forgotten, but is replaced by the latest "new thing", which in turn is found to be flawed and so forgoten, etc, etc, ad nauseum.

I don't think so. I'm reading Louis Agassiz, the great Swiss-American biologist, and the last anti-Darwinian of any stature. He pretty much uses the same arguments against much of the same evidence as today. He admits, BTW, that if the evolution of a new species were documented, that would change things for him.


At the same time there is a steamroller effect of information which is slowly squeezing the "goo to the zoo" concept with steady progress in understanding and appreciating the marvellous complexity of cellular life as well as multicellular mechanisms and interconnections.

Indeed. And the rise of evo-devo and molecular biology has increasingly demonstrated how such things have evolved. Behe, in his first book, asserted that there were no such articles, but even the journals of his professon are full of them.


At some point this will overcome the massive propaganda which supports evolution, just as the free flow of information eventually led to the demise of communism in the Soviet Union.

For the most part, the ire of creationists is aroused by the fact that there is a free flow of information. If you want to see what it's about, you have only to go to a library, and read the research.

On the other hand, you will see that the ICR, for example, strictly controls information and access to anything under their control. A loyalty statement to creationism is required to even apply to their graduate school; when they had a discussion board, they banned all but YE creationists. No, they banned all but their particular brand of YE creationists; the well-regarded and honest Optional of the old OCW board was banned, even though he was YE.

It's fitting then, that the ID people have given up on research and science, and have focused on political action to get by force of law what they could not get by evidence.


Only a closed state that tightly controls the information that people hear can sustain a failed paradigm, and even that is only temporary in the long range scheme of things.

As long as the libraries are still open to the public, you're out of luck.


Thus I am optimistic that the truth will eventually prevail.

It sounds more like you're worried that it will continue to prevail.

[Elisha]

Socratism,

You accuse me of using an argument of ridicule, yet you don't point out where. You don't challenge any of the facts I presented, so I'll stick to questions:


1. If a flat-earther used your defense (with all honesty, they very well can use it), would it be tenable and rational?

2. Is it a scientific answer? If so, how.

3. Is it arguing in circles? If not, how not.


Also, note that I haven't ridiculed you. If anything, I've shown you great respect (that you deserve) - however, I have also been honest at the same time. Why look at just the latter without the former?

[Roy]

Yesterday @ 05:57 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=213765#post213765)
The Barbarian:




That's why I said &quot;any particular spot&quot;. If you specify it beforehand, it's p^2

Yes, but why would you?

Roy (MSc Mathematics)

[The Barbarian]

You're right, there is no need to specify them both.

[Elisha]

A fellow Christian posted this from her science teacher:

Anyone care to explain this to me? lol I've read it repeatedly, but (2) and (3) are above me.

"(1) Similarity in genetics does not necessarily point to common ancestry. There are many examples of similarities in species that no evolutionist believes has common ancestors. The squid and human have incredibly similar eyes. However, no one thinks that they each inherited the eye from a common ancestor. Evolutionists say that they each evolved their eyes separately, and they just happen to look similar. That's what they call "convergent evolution." The person who posted this message wants ERVs to imply common ancestry, so he ignores the fact that when similar structures are found in wildly divergent creatures, evolutionists say that it is NOT common ancestry.

(2) The similarity actually supports the argument that they are a part of the immune system. In order to provide protection against a pathogen, the body often produces an antibody that is quite similar to a protein produced by the pathogen. This allows the antibody to latch on to the pathogen and disrupt an important pathway. The very fact that what he calls ERVs are similar to the viral genes is strong evidence that they are part of the immune system. Of course, he WANTS the similarity be be evidence of insertion and common descent, but that's only one way to interpret the data. He says that he can safely predict that chickens and humans won't have any of what he calls ERVs that are not also in apes. However, I would predict that as well, since the biochemistry of a chicken is quite different than that of humans and apes. As a result, the immune response of a chicken to the same kind of virus will almost certainly be different than that of an ape or human. Thus, the gene will have to be different as well. The fact that they also lessen the chance of viral infection further points to the fact that they are a part of the immune system. He says that he has a "possible explanation" around this, but once again, it is simply his way of interpreting the data. He claims that design advocates have the burden of proof in determining where common ancestry ends and where design begins. I disagree. The design explanation is clearly better at explaining the wonders that we see around us. Thus, it is the common ancestry people who have the burden of proof. The bottom line is that he WANTS what he calls ERVs to "prove" common ancestry, so he simply rejects other explanations, even when those explanations have strong evidence in their favor.

(3) There is no mechanism by which ERVs become a part of a MULTICELLED creatures REPRODUCTIVE genome. This is, to me, the serious problem. We can easily see how a single cell can pass on an ERV to its descendants. The insertion gets in the genome, and each time the cell goes through mitosis, its daughter and its daughters' daughters, etc. will have the insertion. Indeed, we see this in the lab. However, please remember that in sexual reproduction, in order for any insertion to be passed on to the next generation, it must be in the GAMETES. This is awfully difficult. In humans females, for example, the gametes all exist at birth but are in a "suspended" state of meiosis. They are released only once in the woman's period, usually one at a time. They are not susceptible to viral attacks while suspended. In the human male, the gametes are continually made via meiosis and then die. Thus, for an insertion to be passed from a human (or any mammal) to its offspring, the insertion must occur WITHIN A GAMETE OR A CELL THAT WILL BECOME A GAMETE. This is awfully difficult, as female gametes (eggs) are not susceptible to viral infections while in their "suspended" state. Thus, how does the insertion get in there? In a male, it is a bit more likely, but not by much. A diploid cell that is about to undergo meiosis must be infected by a virus, but the virus must not destroy its ability to undergo meiosis. At the same time, the sperm produced by THAT cell must be the one that fertilzes the egg. This is all incredibly unlikely, since I know of few viruses that specifically attack the diploid cells bound for meiosis! Think about this. A person gets a viral infection (let's say in the lung tissue). An ERV occurs, and the epithelial cells that were infected continue mitosis so that eventually, ALL LUNG CELLS have the ERV. Unless that ERV is in the cells that produce gametes (way down in the reproductive organs), the ERV will die with the person. In the end, this is typical of evolutionary argumentation. We see something happen in a very simplistic way (a single cell passing on an ERV) and then the evolutionists simply assume it can happen in a complex way. There is simply no reason to expect this. Until someone can produce some viable mechanism by which the ERV gets into the cells that produce gametes, there is simply no way for the ERV to be an inherited trait in creatures that sexually reproduce."

Discuss.

[chickenman]

The similarity actually supports the argument that they are a part of the immune system. In order to provide protection against a pathogen, the body often produces an antibody that is quite similar to a protein produced by the pathogen.
No it doesn't


The very fact that what he calls ERVs are similar to the viral genes is strong evidence that they are part of the immune system.
this guy obviously isn't an immunologist, not a geneticist - if the ERV sequences aren't expressed - they can't induce an immune response.
if they are expressed - clonal selection would get rid of the immune cells capable of mounting a response because they'd be self-reactive and cause an auto-immune reaction


The fact that they also lessen the chance of viral infection further points to the fact that they are a part of the immune system.

is that a fact? or is it made-up


here is no mechanism by which ERVs become a part of a MULTICELLED creatures REPRODUCTIVE genome.

apart from the virus infecting the gametogenic cells

1: J Natl Cancer Inst. 1975 May;54(5):1173-6. Related Articles, Links

Vertical transmission of C-type viruses: their presence in baboon follicular oocytes and tubal ova.

Kalter SS, Heberling RL, Smith GC, Panigel M, Kraemer DC, Helmke RJ, Hellman A.

C-type viruses were found in baboon follicular oocytes and tubal ova adjacent to the plasma membrane in the perivitelline space or along the inner margin of the zona pellucida. Their presence support the concept of vertical transmission of C-type viruses.

[The Barbarian]

Squid/Octopus eye:
http://soma.npa.uiuc.edu/courses/bio303/Image192.jpg

Vertibrate eye:
http://www.godandscience.org/images/eye.gif

Some ways that the two eyes are not alike:

The retinas of cephalopods are arranged inside out compared to vertebrates, which have a "blind spot" as a result.
l
There are fewer cell types in the cephalopod retina, and more of the visual processing takes place in brain.

Photosensitive parts of photoreceptors are arranged in rhabdoms like those of insect, not like rods of vertebrate.

[Ediacaran]

09-20-2003 @ 05:54 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=216365#post216365)
Elisha:

A fellow Christian posted this from her science teacher:

1) Similarity in genetics does not necessarily point to common ancestry. There are many examples of similarities in species that no evolutionist believes has common ancestors. The squid and human have incredibly similar eyes. However, no one thinks that they each inherited the eye from a common ancestor. Evolutionists say that they each evolved their eyes separately, and they just happen to look similar. That's what they call &quot;convergent evolution.&quot; The person who posted this message wants ERVs to imply common ancestry, so he ignores the fact that when similar structures are found in wildly divergent creatures, evolutionists say that it is NOT common ancestry.

Actually, the regulatory gene known as pax-6 (aka aniridia in humans, small eye in mice, and eyeless in fruit flies) is due to common ancestry, and results in the development of photoreceptive organs. Of course, there are other factors involved in morphological aspects of the resulting visual organs, so eyes are convergent in some characters (for example, lens crystallins have evolved from many different co-opted proteins in various organisms) and homologous in others (as with the pax-6 homologs). See Chapter 13 of Walter Gehring's Master Control Genes in Development and Evolution: The Homeobox Story. The anonymous creationist science teacher is mistaken, and is misleading students.

Have the creationist ask a competent colleague (i.e., "evolutionist") in the science department how to perform a GenBank sequence search for homologs to pax-6.

Also have the teacher compare the retinal opsins to learn how they evolved through gene duplication and point mutation. For example, our blue opsins evolved from an ancestral rhodopsin, and a long-wavelength opsin that evolved from an ancestral blue opsin subsequently evolved into our red and green opsins. If the teacher wants to dig deeper, the consequences of this evolutionary duplication and the subsequent point mutations account for the higher incidence of red-green colorblindness in male humans compared to females (see Lubert Stryer's Biochemistry textbook for an introduction to the topic). Just another way in which evolution explains biology, and creationism doesn't.

Or, the creationists can use their blind spots to continue to ignore the genetic data.

[Socrates]

09-21-2003 @ 04:02 PM post located here (http://www.theologyweb.com/forum/showthread.php?s=&postid=216684#post216684)
The Barbarian:

Squid/Octopus eye:
http://soma.npa.uiuc.edu/courses/bio303/Image192.jpg

Vertibrate eye:
http://www.godandscience.org/images/eye.gif

Some ways that the two eyes are not alike:

The retinas of cephalopods are arranged inside out compared to vertebrates, which have a &quot;blind spot&quot; as a result.

There are fewer cell types in the cephalopod retina, and more of the visual processing takes place in brain.

Photosensitive parts of photoreceptors are arranged in rhabdoms like those of insect, not like rods of vertebrate.

This is true. It is simplistic to claim that the cephalopods are simply a verted-retina version of the inverted vertebrate eye. As Barbarian says, their retinal structure is completely different, with rhabdomeres dividing it so that it is really "a compound eye with a single lens". They don't see as well as us! Let's face it, when people want to make a metaphor of sharp vision, they say "eyes of a hawk/eagle", despite their inverted retinas, not "eyes of a squid"!

And in case anyone wants to allege that our inverted retina is an examle of bad design, I covered this a few months ago at http://www.theologyweb.com/forum/showthread.php?action=showthread&postid=58473#post58473 citing spectroscopist and ophthalmologist opinions. They count for a lot more than those of the likes of Kenneth Miller and Richard Dawkins, who have no qualifications in optics or ophthalmology. One even said,

The idea that the eye is wired backward comes from a lack of knowledge of eye function and anatomy.

In fact, if our eyes were designed the "superior" way that Miller or Dawko suggest, it would take ages before we recovered from flash-blindness, because our photoreceptors would take so long to regenerate. This by far makes up for the disadvantage of the blind spot, which takes up only 0.25 % of the visual field, and in an area of the retina with a visual acuity of only about 15 % of that at the foveola.

[Stratnerd]

They don't see as well as us!

where did you see this? Does this include humans with poor eyesight or octupi that could have used reading glasses?

anyways, my research does include an aspect of vision so I'd appreciate the reference...

[Athanasius]

I'm no biologist, but couldn't horizontal transfer explain why we find these retroviral insertion points in the same place in similar species? Here's my idea: a retrovirus inserts some subset code. Then a larger set of code containing the subset code (intact, at the very same insertion point) is transfered by various documented transfer mechanisms into similar species.

[Athanasius]

Perhaps horizontal transfer occurred on the Ark (as seems reasonable with so many different species in such close quarters). If some transferred code was copied many times by a virus or bacteria that causes horizontal transfer, each copy would of course contain the very same retroviral insertions. Since some viruses and bacteria attack only similar species, this might explain why species with common design elements have the very same retroviral insertions.

Regarding whales and cows, a possible scenario:

After the flood, cow feces containing viruses or bacteria with code from a previous host, complete with a retroviral insertion, gets washed into a stream and particles of this flow into the ocean. Whales ingest these particles while filter feeding, become infected, and horizontal transfer takes place. The infection spreads throughout the population, resulting in transfer of the code to multiple individuals. Eventually, through breeding, the transferred code spreads throughout the population. The whales then have a copy of a retroviral insertion surrounded by the very same code found in cows!

Again, I'm no creation scientist, just a layman who enjoys science, who only has only been equipped in this area by lay science reading and some college biology courses. So if there is some fatal flaw in this idea, or if I have used some terminology incorrectly, please go easy on me. If this idea is not plausible for some reason unknown to me, since I make no claims to having any expertise in biology, please do not use this as an example of a stupid statement from a creationist! I would, however, like to hear an evaluation of this idea from both evolutionists and creationists who do have some expertise in biology.

[Fedmahn Kassad]

Bumped in memory of WinAce, whose young life tragically ended yesterday morning. He died from complications of cystic fibrosis. He was 20 years old. I am bumping a pair of his posts so that people may be reminded what a brilliant young man he was.

FK

[Jake]

Bumped in memory of WinAce, whose young life tragically ended yesterday morning. He died from complications of cystic fibrosis. He was 20 years old. I am bumping a pair of his posts so that people may be reminded what a brilliant young man he was.

FK

What a shame. He seemed like a very pleasant and incredibly gifted young man.

[rogero]

Bumped in memory of WinAce, whose young life tragically ended yesterday morning. He died from complications of cystic fibrosis. He was 20 years old. I am bumping a pair of his posts so that people may be reminded what a brilliant young man he was.

FK

Thanks for doing this, FK. I got the news from DeeDee's avatar title. I appreciate all you've done in helping raise awareness of WinAce's illness.

R