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Can ERVs be explained without common descent? - 4/23/2008 5:55:50 AM
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Agahnim
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I mentioned something about Endogenous Retroviruses in another thread, but I wanted to ask about it in more detail here. I’m most interested in hearing Dan James’s opinion about this, since he’s stated that he doesn’t intend to cling to ideas if science contradicts them. But if anyone else here who doesn’t accept humans’ relationship to other animals has something to say about this, they’re welcome to do so, as long as they actually address what’s said by this essay rather than just making an argument that’s already refuted in it.
I should also mention that for the most part, I didn’t write this essay myself. It was written in 2004 by an online friend of mine named R. Allan Glenn, aka WinAce, who offered his permission for the people who knew him online to redistribute it. WinAce died of Cystic Fibrosis in 2005, but I’m currently adapting his essay to appear in a book of which I’m the editor. This is the adapted version of his essay, which contains a few minor modifications from the original version for the sake of appearing in print rather than online.
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ERVs, a startling line of evidence from genetics (not fossils) provides additional, overwhelming support for human/chimp common ancestry, one that establishes it beyond a shadow of a doubt. Much like stellar parallax could be considered 'proof' of heliocentricism, so too do unique fingerprints of ancient retroviral infection demonstrate relatedness if found in the genome of two different organisms.
1. Background
Viral infections. We all know and hate them. From the common cold to the common cold sore, they're annoying little buggers. The virus particle invades a cell, injects its proprietary genome, hijacks the cellular machinery and turns it into a virus-making factory. Upon successful completion of this process, the cell begins releasing fresh copies of the virus, often by bursting and dying.
Occasionally, however, something goes wrong in the integration process. When this occurs, the cell can survive, but selected portions of the viral DNA remain in its genome. These vary from infection to infection, not just from virus to virus.
In effect, the cell becomes permanently scarred and carries the unique, identifiable fingerprint of its assailant. (1) Since the markers are now in the genome, they become hereditary--hence, any descendant of the afflicted cell will contain the same exact viral fingerprint(s) at the same exact spot in its DNA.
Viral infections are, of course, not limited to the mucous membranes, blood stream and lungs. Under certain conditions, they can also infect a germ line (egg or sperm) cell. The odds of this cell now surviving to adulthood are astronomically low; not only does it have to survive a viral infection, but be one of the extremely lucky few that ever make it to merge with their counterpart and form a viable zygote.
However, this does occur. When it does, the resulting offspring has the unique viral fingerprint embedded in every cell in its body, what is known as an "endogenous retroviral insertion", henceforth referred to as an ERV. (2)
ERVs can be easily identified by their extreme similarity to known retroviruses. They even contain vestiges of gag, env and pol genes that code for viral surface proteins. An explanation of GEP protein coats, and information on their presence in ERVs, can be found at the following page: http://www.microbiologybytes.com/virology/Retroviruses.html
We've directly observed creation of new, identifiable ERVs by viral integration into cells in vitro, as well, so this process is as well-documented (if not more) as fossil formation. When it occurs in ordinary cells, it can cripple vital genes, subsequently causing cancer. High-risk papillomaviruses have been indicted as one of the leading causes of cervical tumors, for example. (3)
Like any genes, the viral elements can then piggyback on the success of an individual and become established in the entire species. In small populations, this can easily occur via genetic drift (random establishment of selectively neutral or deleterious alleles). In larger ones, natural selection can work to establish the few ERVs that yield a benefit to their host. For a more detailed explanation of what genetic drift is, see the explanation of it at Talk.Origins http://www.talkorigins.org/faqs/genetic-drift.html , or at Wikipedia. http://en.wikipedia.org/wiki/Genetic_drift
Each step in the process is not very common, and has unique aspects that are extremely unlikely to be reproduced in two independent cases of ERV creation. Hence, when they all occur, the organisms possessing the ERV are marked with a molecular fossil that will prove indispensable in tracing their origin.
2. Evolutionary Implications of ERVs
In a nutshell, this can serve as a "paternity test" of sorts: if you find the same endogenous retroviral insertion in two different organisms, the only viable explanation is that they inherited same from a common ancestor that, itself, possessed it. Offshoot species will have the same unlikely and easily identifiable ERVs, enabling us to construct accurate phylogenies from an independent line of evidence.
[image]http://www.talkorigins.org/faqs/comdesc/images/retrovirus.gif[/image]
Human endogenous retroviral insertions in identical chromosomal locations in various primates. Notice just how well the standard evolutionary phylogeny, derived from fossil and anatomical evidence (humans and chimps closest, then orangutans and gorillas, then gibbons, then old world monkeys, then new world monkeys) is corroborated by this uniquely independent line of evidence. (4)
As a side note, ERVs have also been used to reconstruct the relationships between dogs, jackals, wolves and foxes, among other species of domestic animal.
Needless to say, this offers a quick and easy way to experimentally test if any two similar organisms are unrelated. If they are, they won't share any ERVs. If you find the same one at the same place in their genomes, however, the hypothesis they originated independently is effectively falsified.
Due to the nature of the branching tree of life, ERVs shared between distantly-related organisms will have made their initial appearance in their common ancestor. Hence, they would have also been present as further, closer organisms split off from the lineage; if you find an ERV common to humans and monkeys, the ancestor of chimps must have had the insertion as well. Similarly, ERVs found in New World Monkeys and chimps will usually be present in humans. ERVs found in humans and gorillas should be found in chimps. And so on. This provides an additional way to test evolutionary predictions.
It should be noted that there are rare but observable genetic phenomena that can remove ERVs from the genome. However, we can almost always tell when this has occured, such as identifying the characteristic fingerprint of a deletion mutation right before the ERV 'should have' been found.
Nevertheless, the more basic question of 'are there shared ERVs between these species at all?' is a much more stringent, rock-solid test of evolution than the specific phylogenetic relationships individual insertions indicate, which can be erroneous on occasion.
When analyzed as a statistical whole, ERV insertion patterns will also recapitulate phylogenies drawn from independent data like the fossil record and comparative anatomy. This is a remarkable confirmation, and totally at odds with the predictions made by the hypothesis of independent origin of species.
As you can see by now, this is the strongest support for evolution I've ever come across; a truly powerful and damning smoking gun.
3. Attempted creationist rebuttals and their drawbacks
Hypotheses proposed by creationists to account for this are woefully inadequate, although there are several worth analyzing.
3.1: Independent Insertion
This one entails independent insertion by the same virus affecting different species. Creationist Ashby Camp, writing at TrueOrigins, quoted a scientific article referring to "insertion hotspots" that were the target of viral integration much more often than other spots in the genome. (5) Although this is superficially a valid criticism to be hurled at the ERV argument, it quickly fails.
The very "hottest" spot Camp could dig up in the scientific literature was one that was 280 times more likely to be involved in a viral integration than we could expect from chance alone. It could be pointed out that this was a virus that doesn't exist in nature, but was specifically designed to facilitate gene therapy by targeting a specific part of the genome and replacing a crippled gene with a functional copy.
But let's ignore that for now, and assume Camp did not misrepresent relevant research. Just how large is this in the big picture? The human genome is 3 billion or so nucleotides long. (6) The chance, then, of randomly inserting into the same section of the genome is 1 in 3 billion.
Now let's assume there are hot spots an unprecedented 1,000 times more likely to be attacked by a virus than the unique, genetically engineered one Mr. Camp was able to dig up. Divide 3 billion by 280,000, and you find the chance of an independent insertion is one in around 10714; this is an unlikely enough figure to be negligible, and it was derived from estimates orders of magnitude more liberal than the data would allow!
Additionally, this doesn't address any of the other factors involved. It doesn't explain why the same viral fingerprint would be left behind, how it would affect the one germ line cell out of millions that advances to zygote status, how that single individual would enjoy reproductive success sufficient to establish his ERVs in the population, etc.
For the reasons listed above, it's astronomically improbable. Not only would the same exact retroviral insertion have to occur independently at the same exact locus of a uniquely lucky sperm or egg cell that survived to adulthood, and achieved enough success to establish the insertion in their respective populations, but this impossible set of coincidences would have to occur for 3, 4, even a dozen species at the same time, and for every single ERV shared between them to boot!
As you can see, the improbabilities keep stacking and increasing by additional orders of magnitude as more factors are introduced.
The additional fact that ERVs, when analyzed, yield evolutionary patterns that reinforce the phylogenies derived from morphological, fossil and other evidence rules out the independent insertion hypothesis completely. If independent insertion was somehow the explanation for shared viral insertions, we would expect to see numerous, extensive groups of ERVs common to chickens and humans, pigs and humans, and other creatures that share many of the same pathogens; ERVs that weren't present, on the other hand, in geographically isolated creatures closer to us in morphology and genetics, such as the apes.
3.2: ERVs are not remnants of ancient viral infection
Another attempted explanation is that the ERVs found in our genome are actually original, designed artifacts instead of viral infection fingerprints.
To be frank, this hypothesis, even on the surface, appears 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 there is no reasonable way to verify or falsify them; they throw explanatory and predictive power, much less parsimony, entirely out the window.
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, independently created organisms? (They share ERVs that have been used to reconstruct their phylogenies). Are the various felines in general related, or separately created? (Lions, panthers, tigers and domestic cats share ERVs).
In other words, where do the divinely faked ERVs end and the real ones, which we can observe being incorporated into the genome in vitro, begin? 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.
Why, then, should any reasonably intelligent person consider accepting rationalizations that are unfalsifiable, unevidenced, predict no unique observations the mainstream explanation doesn't and even require numerous additional assumptions that the obvious answer doesn't?
Nevertheless, let us examine two sub-hypotheses that fall under this main heading.
3.2.1: ERVs are an important part of the immune system
Based on the fact that a few ERVs have apparently been shown to lessen the chances of some types of viral infection, some creationists have asserted that ERVs are actually an anti-viral vector native to the genome, with their similarities to actual retroviruses being coincidental and not the product of intentional deception. But this explanation also fails when all the data is considered.
In the first place, their anti-viral effects are no larger than those of some free-living viruses, so this is not an argument against their being parasitic in the past. Human herpesvirus 6 has recently been shown to suppress HIV, (7) for example. At most, it would provide a miniscule selection advantage for the individual carrying a particular ERV, which could help it piggyback across the population and help slightly improve the odds for one step of the process (out of many) occurring independently.
A possible explanation is that the endogenous retrovirus, which is only marginally deleterious, uses up the spaces on the cellular exterior HIV would normally dock with. This would be a textbook example of an evolutionary, jury-rigged defense mechanism, equivalent to hiring polite burglars to slowly work on your doors and windows so the violent ones couldn't get in.
Additionally, virtually all ERVs have no such immunity-boosting function; indeed, many more are actually implicated as the cause of some tumors (8); just like certain free-living viral infections including Epstein-Barr, I might add.
Moreover, you again have the problem that ERVs are distributed across the genomes of species in a pattern that mimicks common descent, not the expected pattern of functionally-oriented resistance to shared viral pathogens. I can safely predict that chickens and humans won't have any common anti-viral ERV that apes won't, despite the fact they share many of the same infections apes generally aren't afflicted by.
3.2.2: Viruses evolved from ERVs, not the other way around
Some have asserted that ERVs were actually designed elements that exogenous retroviruses came from, perhaps after the Fall. This is advocated by creationist Dr. Ian Macreadie of Answers In Genesis, who states "I actually don’t believe God created viruses as separate entities, I believe they were a part of the DNA in cells". (9)
A few things are to be noted. As the Museum Victoria webpage demonstrates, this is a modern reinvention of an ancient, proto-scientific view aimed at explaining the existence of regular, plain vanilla, non-molecular fossils:
"... they were owing to the actions of so-called 'plastic forces' or 'formative virtues' in the Earth... 'Plastic forces' were believed to be unspecified forces within the Earth that were continually striving to produce organic bodies. The notion that fossils were formed by these 'plastic forces', first put forward by the Arab scholar Avicenna (980-1037 AD), was an outgrowth of the Aristotelian idea of spontaneous generation. Fossils were individuals that had 'failed' at spontaneous generation, or else the 'vital essence' of living things had penetrated rocks and formed objects there which resembled living things." (10)
We now know much more about the world, and recognize that fossils are the remnants of organisms, not their ancestors. Can we similarly argue that ERVs can't be the parents of ordinary viruses?
As it turns out, the answer is a resounding "Yes!" This creationist hypothesis is unambiguously falsified by looking at the data.
Many ERVs are merely fragments of code, which nevertheless include readily vestiges of identifiable viral surface coat proteins, which are quite obvious and expected for an exogenous retrovirus that needs to float around independently, but utterly baffling for one that resides within a cell. In other words, they lack key components that allow real viruses to reproduce. (As a side note, this is often, in the first place, a relic of a botched infection, one of the things that lets the cell survive in the first place.)
If a sentence out of Shakespeare is inserted into an essay, one can ascertain the direction of literary borrowing from comparison of the works alone, even without the knowledge that the former wrote earlier. This is the same with ERVs and other out-of-place genetic fragments. They simply look like fragments out of the whole work, so to speak, deposited there by free-living ancestors, not the opposite.
To expand even further and bring in the heavy artillery, many viruses have complex, multipart mechanisms for subverting host immune defenses and injecting their DNA thru the cell membrane that their fragmentary, cell-bound counterparts lack.
[image]http://www.purdue.edu/PER/images/020212.spot_rossmann_T4.jpeg[/image]
The bacteriophage T4 virus has a head, tail, baseplate and a dozen tail fibers. The baseplate serves as a "nerve center" of the virus. When the tail fibers attach to E. coli, the baseplate transmits a message to the tail, which contracts like a muscle, bringing the internal pinlike tube in contact with the outer membrane of the E. coli cell. As the tube punctures the outer and inner membranes, the virus' DNA is injected into the host cell. (11)
Needless to say, asserting that such things could evolve from mere cellular genome fragments is a stretch, especially so if one simultaneously denies the ability of evolutionary mechanisms to generate such staggering complexity.
Finally, 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, as demonstrated by the case I made above.
4. Conclusion
In summary, the facts are that:
(A) A retrovirus infects a cell and, depending on how virulent it is, can kill it. Occasionally, fragments of the virus remain but the cell survives.
(B) No two viral insertions are exactly alike; a botched integration can leave behind a tiny fragment of its DNA, large stretch of the genome, selected portions, and other variants.
(C) Viral fragments insert at fairly random locations, and have literally millions of them to choose from.
(D) Infection of a germ line cell is quite rare.
(E) That particular germ line cell with the unique viral fingerprint can, sometimes, be the lucky egg or sperm cell that gets fertilized.
(F) The individual's genes, including the ERV, can get established in the entire population of a species. This can occur through random genetic drift if it's neutral or deleterious; natural selection, on the other hand, would work to establish the very few advantageous retroviral elements in our genome.
The combined odds of each of these events happening in two independently originated species are a statistical non-event. In sheer unlikelihood, they would likely dwarf even the incorrectly calculated anti-abiogenesis calculations some creationists are fond of. And the odds become even less remote, by additional orders of magnitude, as more and more species are considered.
In this essay, we've seen that ERVs are, indeed, remnants of ancient viral infection. We've also seen that no explanation except inheritance from a common ancestor can reasonably account for the occurrence of the same viral insertion in two different organisms or species. This, in turn, leads to the inescapable, iron-clad, demonstrated-beyond-a-reasonable-doubt conclusion:
Independent origin of ERVs (and hence, independent origin of species, a.k.a. creationism) is scientifically falsified.
Works cited
1: Park, Jinseu. "Integration & Transcription." Virology Lab. Accessed 24 Feb. 2004 <http://www.hallym.ac.kr/~jinpark/int.html>.
2: “Retroviruses.” MicrobiologyBytes. 11 Sept. 2007. Accessed 24 Feb. 2004 <http://www.microbiologybytes.com/virology/Retroviruses.html>.
3: Ziegert C., Wentzensen N., Vinokurova S., Kisseljov F., Einenkel J., Hoeckel M., von Knebel Doeberitz M. (2003) “A comprehensive analysis of HPV integration loci in anogenital lesions combining transcript and genome-based amplification techniques.” Oncogene 24: 3977-84.
4: Lebedev, Y. B., Belonovitch, O. S., Zybrova, N. V, Khil, P. P., Kurdyukov, S. G., Vinogradova, T. V., Hunsmann, G., and Sverdlov, E. D. (2000) "Differences in HERV-K LTR insertions in orthologous loci of humans and great apes." Gene 247: 265-277.
5: Camp, Ashby. “Molecular Evidence.” TrueOrigin. 2001. Accessed 24 Feb. 2004 <http://www.trueorigin.org/theobald1e.asp>.
6: “Bioinformatics.” Swiss Institute of Bioinformatics. Accessed 24 Feb. 2004 <http://www.isb-sib.ch/institute/bioinformatics.htm>.
7: Bock, Robert. “Harmless Virus Prevents HIV Variant From Spreading In Human Tissue Blocks.” National Institutes of Health. 31 Oct 2001. Accessed 24 Feb. 2004.
<http://www.nih.gov/news/pr/oct2001/nichd-31.htm>.
8: Cotterill, Simon. “Viruses and Cancer.” Cancer Index. 11 Jan. 2003. Accessed 24 Feb. 2004. <http://www.cancerindex.org/clinks4v.htm>.
9: Wieland Carl, Batten Don. “Creation in the Research Lab.” Answers in Genesis. March 1999. Accessed 24 Feb. 2004
<http://www.answersingenesis.org/creation/v21/i2/research.asp>.
10: “Early views on the nature of fossils.” Museum Victoria. Accessed 24 Feb. 2004
<http://museumvictoria.com.au/dinosaurs/sci-views.html>.
11: Purdue University. Accessed 24 Feb. 2004 <http://www2.itap.purdue.edu/periodicals/020212.spot_rossmann_T4.html>.
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Before someone accuses me of plagiarism or being unable to write things for myself, keep in mind that I’m adapting this essay for my book with the permission of the author, giving him proper credit for it, and am also writing two essays for this book myself. The reason I’m posting this essay here is because it’s relevant to something discussed in another thread, and there don’t seem to be any other threads here providing a detailed description of this line of evidence for common descent. What do the people here have to say about this?
EDIT: I forgot, images in posts don't show up at this board. Just copy and paste the URLs, I guess. The first image, showing which groups of primates have which ERVs, is definitely worth paying attention to.
< Message edited by Agahnim -- 4/23/2008 7:41:37 AM >
_____________________________
"I like your Christ. I do not like your Christians. Your Christians are so unlike your Christ." --Mahatma Gandhi
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RE: Can ERVs be explained without common descent? - 4/23/2008 10:50:06 AM
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Jhud
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Well, I have never understood the 'evolutionary' part of the ERV argument as ERVs are said to be the product of external entities rapidly modifying the genomes of organisms; that isn't of course an evolutionary process in the Neo-Darwinian sense of the word.
But as far as the main thesis of the OP, I think for the IDist the question is, "Does the ERV serve a purpose in the development of life?", and I think that yes, like the trend with presumed 'junk DNA', we are finding that it may serve a very important purpose in that regard.
_____________________________
Jack
“I mean to live my life an obedient man, but obedient to God, subservient to the wisdom of my ancestors; never to the authority of political truths arrived at yesterday at the voting booth”
William F. Buckley Jr. 1925-200
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RE: Can ERVs be explained without common descent? - 4/23/2008 2:01:26 PM
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Agahnim
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quote:
Well, I have never understood the 'evolutionary' part of the ERV argument as ERVs are said to be the product of external entities rapidly modifying the genomes of organisms; that isn't of course an evolutionary process in the Neo-Darwinian sense of the word.
I know ERV’s aren’t evidence for “evolution” as defined by a specific mechanism; we already discussed this. What the essay means by them being evidence for evolution is that they’re evidence for common ancestry of humans and chimps, which is one aspect of the theory of evolution that’s generally rejected by creationists. This is why was asking specifically how people who reject common descent would explain this line of evidence.
EDIT: I should also point out that if your definition of evolution excludes genetic modifications resulting from viruses, your definition of what constitutes an “evolutionary process” is a lot narrower than the definition used by most biologists. Most mainstream biologists already accept that viral infections are one of the things that can modify the genomes of animals, and consider this part of the process of evolution. This is one of the ways that the theory of evolution has changed since Darwin’s time. It’s important to recognize the distinction between Darwin’s primitive version of the theory, and what the theory of evolution currently says.
quote:
But as far as the main thesis of the OP, I think for the IDist the question is, "Does the ERV serve a purpose in the development of life?", and I think that yes, like the trend with presumed 'junk DNA', we are finding that it may serve a very important purpose in that regard.
What purpose do you think they serve? The essay acknowledges that they occasionally provide an advantage to the organisms that have them, but also explains why that doesn’t change the fact that their origin can’t be explained by anything other than a viral infection in a shared ancestor. Or are you saying that they serve a purpose which could explain why two unrelated animals have the exact same viral fingerprints in the exact same places?
quote:
I also talk about ERV's here and why it's actually a problem for evolution.
This is why I said people who reject common descent are welcome to comment on this, as long as they actually address what’s said by this essay rather than just making an argument that’s already refuted in it. I was actually thinking specifically of your posts in the other threads on this topic when I included that qualification.
< Message edited by Agahnim -- 4/23/2008 2:13:02 PM >
_____________________________
"I like your Christ. I do not like your Christians. Your Christians are so unlike your Christ." --Mahatma Gandhi
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RE: Can ERVs be explained without common descent? - 4/23/2008 2:19:54 PM
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Bettawrekonize
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quote:
ORIGINAL: Agahnim
This is why I said people who reject common descent are welcome to comment on this, as long as they actually address what’s said by this essay rather than just making an argument that’s already refuted in it. I was actually thinking specifically of your posts in the other threads on this topic when I included that qualification.
I don't see how this essay refutes any of my arguments.
quote:
In small populations, this can easily occur via genetic drift (random establishment of selectively neutral or deleterious alleles).
I don't see any reason it would be easy for a "random establishment" to cause an ERV fingerprint to constantly spread across an entire population and to reach the germ line of each member if there is no selective pressure for it (especially if you are talking about multiple different small populations being infected during different times by multiple ERV's. It just so happens that, in so many instances, each germ line gets infected or each member somehow acquires this ERV code). You are also assuming a small population. If not everyone share so many common ERV's, evolution would be just as happy to accommodate that evidence too because evolutionists can then argue that it spread across some members of the population and not others. We would expect to have many ERV's that survive among some members and not others, just like is the case with many other traits (ie: brown eyes, black hair, etc...). So either way, evolution would not be falsified. Talkorigins (and other sources) gives some examples of possible evolutionary pathways that allegedly may lead to the current set of evidence. However, there are many other possible pathways that might lead to a total different set of evidence. One can always speculate some evolutionary pathway to explain just about any combination of evidence. That which can explain anything explains nothing and hence predicts nothing.
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In larger ones, natural selection can work to establish the few ERVs that yield a benefit to their host.
If an ERV code is favored by natural selection, then it is useful, meaning that it would make sense for an intelligent designer to include it. Your post has also been addressed in many other ways, if anyone is interested in clicking the link and reading.
< Message edited by Bettawrekonize -- 4/23/2008 2:36:37 PM >
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RE: Can ERVs be explained without common descent? - 4/23/2008 2:31:32 PM
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Agahnim
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Betta, don’t assume that just because I replied to your first post, I’m assuming that anything you say here is worth addressing. I just wanted to point out, for anyone else reading this thread, that all of your arguments about this (including the one you just posted) are already addressed by the essay itself.
_____________________________
"I like your Christ. I do not like your Christians. Your Christians are so unlike your Christ." --Mahatma Gandhi
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RE: Can ERVs be explained without common descent? - 4/23/2008 2:31:59 PM
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Jhud
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quote:
I know ERV’s aren’t evidence for “evolution” as defined by a specific mechanism; we already discussed this. What the essay means by them being evidence for evolution is that they’re evidence for common ancestry of humans and chimps, which is one aspect of the theory of evolution that’s generally rejected by creationists. This is why was asking specifically how people who reject common descent would explain this line of evidence.
quote:
What purpose do you think they serve? The essay acknowledges that they occasionally provide an advantage to the organisms that have them, but also explains why that doesn’t change the fact that their origin can’t be explained by anything other than a viral infection in a shared ancestor. Or are you saying that they serve a purpose which could explain why two unrelated animals have the exact same viral fingerprints in the exact same places?
We all actually had this discussion awhile back, and one of the things I brought up was the recent research that indicated that ancient retroviruses played a role in modifying the p53 "master gene regulator" which regulates gene expression, which in turn plays a part in producing the significant physical differences between great apes and humans.
So even if one were to concede common descent, the sum total of it is that we have an external organism rapidly infusing novel genetic information into the mammalian geneome which then has the effect of rearranging the genome, creating a complex regulatory network, and regulating the changes in gene expression which effect massive morphological changes in the organism.
Whatever that is, it ain't what Darwin imagined.
< Message edited by Jhud -- 4/23/2008 3:03:03 PM >
_____________________________
Jack
“I mean to live my life an obedient man, but obedient to God, subservient to the wisdom of my ancestors; never to the authority of political truths arrived at yesterday at the voting booth”
William F. Buckley Jr. 1925-200
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RE: Can ERVs be explained without common descent? - 4/23/2008 2:36:25 PM
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Bettawrekonize
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quote:
ORIGINAL: Jhud
So even if one were to concede common descent, the sum total of it is that we have an external organism rapidly infusing novel genetic information into the mammalian geneome which then has the effect of rearranging the genome, creating a complex regulatory network, and regulating the changes in gene expression which effect massive morphological changes in the organism.
Whatever that is, it ain't what Darwin imagined.
Arguments we have brought up against this beg the question, where did this retrovirus get this code? How did this code develop? You have to realize that, when a random mutation happens in a virus, it's very unlikely that the virus will infect a germ line (heck, the virus may not even infect a cell). Most viruses that do acquire a beneficial mutation to the organism it infects won't infect the germ line which means it probably won't benefit the descendants of the organism it infects which means its code probably won't have a survival advantage over other virus code. Eventually, one of its descendants may get lucky and infect a germ line, but for the most part, the virus code is not subject to natural selection (in terms of giving an organism and its descendants a survival advantage) nearly as much as code that already exists within an organism (and its germ line). In effect, one would be arguing that this code was produced by far more random mutation and far less natural selection than Darwin proposed. It also assumes that the germ line somehow produces a virus with the code for this beneficial mutation that the virus acquired and that the other virus continues to infect germ lines and gain beneficial mutations. The other option is to assume that a virus independently created this code entirely via random mutation and spread it to a germ line. If you assume that these benefits were produced via infecting non - germ line cells, it would be very unlikely it would provide any physical advantages to an organism (and have those advantages spread to the germ line) since the physical characteristics of the organism have probably already been mostly developed by the time the organism gets infected (ie: a virus infection is unlikely to transform your arm into a leg). So there won't be much selective pressure to produce physical differences within the organisms it infects by infecting non - germ line cells. This whole hypothesis is problematic, there are just so many problems with it it's hard to even make sense of it. We have gone over this in much more detail on other threads (as Jhud points out), but I can't find the exact posts at the moment.
< Message edited by Bettawrekonize -- 4/23/2008 3:39:13 PM >
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RE: Can ERVs be explained without common descent? - 4/23/2008 2:44:26 PM
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Agahnim
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quote:
We all actually had this discussion awhile back, and one of the things I brought up was the recent research that indicated that ancient retroviruses played a role in modifying the p53 "master gene regulator" which regulates gene expression, which in turn plays a part in producing the significant physical differences between great apes and humans.
So even if one were to concede common descent, the sum total of it is that we have an external organism rapidly infusing novel genetic information into the mammalian geneome which then has the effect of rearranging the genome, creating a complex regulatory network, and regulating the changes in gene expression which effect massive morphological changes in the organism.
Whatever that is, it ain't what Darwin imagined.
Your link isn’t working, but I’m not sure it matters anyway, since I don’t really disagree with the what you’re saying. The only problem I have is with what I think you’re inferring from it.
You’re definitely right that Darwin had no idea what sorts of factors lead to the hereditary changes on which natural selection acts. In his time DNA hadn’t been discovered yet, so he didn’t know what mutations were, and he certainly didn’t know anything about ERVs. But you seem to think the fact that Darwin was wrong about certain things is a problem for the current theory of evolution, which is considerably different from the theory that Darwin came up with. Is it a problem for atomic theory that Neils Bohr was wrong about electrons orbiting the nucleus like little planets, now that atomic theory is based on Schrödinger’s model of the atom instead?
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"I like your Christ. I do not like your Christians. Your Christians are so unlike your Christ." --Mahatma Gandhi
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RE: Can ERVs be explained without common descent? - 4/23/2008 3:05:21 PM
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Jhud
Posts: 6781
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You’re definitely right that Darwin had no idea what sorts of factors lead to the hereditary changes on which natural selection acts. In his time DNA hadn’t been discovered yet, so he didn’t know what mutations were, and he certainly didn’t know anything about ERVs. But you seem to think the fact that Darwin was wrong about certain things is a problem for the current theory of evolution, which is considerably different from the theory that Darwin came up with. Is it a problem for atomic theory that Neils Bohr was wrong about electrons orbiting the nucleus like little planets, now that atomic theory is based on Schrödinger’s model of the atom instead?
The core of what Darwin (and modern Neo-Darwinsts) said was that gradually accumulated beneficial and incremental changes produced the large complex and interdependent changes that we see today.
The article (which is fixed now, thanks) indicates these were rapid changes which infused a large amount of information into the genome which effected different expressions of information already present.
Those are two different processes.
_____________________________
Jack
“I mean to live my life an obedient man, but obedient to God, subservient to the wisdom of my ancestors; never to the authority of political truths arrived at yesterday at the voting booth”
William F. Buckley Jr. 1925-200
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RE: Can ERVs be explained without common descent? - 4/23/2008 3:28:08 PM
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Agahnim
Posts: 161
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The core of what Darwin (and modern Neo-Darwinsts) said was that gradually accumulated beneficial and incremental changes produced the large complex and interdependent changes that we see today.
The article (which is fixed now, thanks) indicates these were rapid changes which infused a large amount of information into the genome which effected different expressions of information already present.
Those are two different processes.
Gradualism isn’t really the “core” of evolution anymore. I recommend doing a Google search on “punctuated equilibrium”. The idea that evolution happens rapidly and in small bursts has been part of the theory for around thirty years now.
I often get the impression that when you attack what you call “evolution”, you’re attacking what the theory of evolution was around 100 years ago. If you want to attack that theory, go right ahead, but keep in mind that you’ll be in agreement with most modern biologists that the theory of evolution as it existed before DNA was discovered is wrong. If you equate that theory with the current theory of evolution, though, you’re attacking a strawman.
Looking at the article you linked to, it looks like the theory of evolution may be undergoing another change. This quote from the article in particular stuck out to me:
Moreover, the team has proposed a new mechanism for evolutionary change. Conventional wisdom says that evolution is driven by small changes--point mutations--to the genetic code. If a change is beneficial, the mutation is passed onto future generations.
Now it appears that another level of evolution occurs that is not driven by point mutations. Instead, retroviruses insert DNA sequences and rearrange the genome, which leads to changes in gene regulation and expression. If such a change in gene regulation is beneficial, it is passed onto future generations.
I don’t have a problem with the theory of evolution being modified on the basis of a new discovery like this. It’s the same thing that happens to any other scientific theory when new data about it is discovered, as in the example I mentioned of atomic theory. The important thing is just that we not throw out more of the theory than is falsified by this new discovery, just as when Schrödinger created his new version of atomic theory he didn’t reject the idea that atoms exist, with protons and neutrons in the nucleus, surrounded by several distinct orbital levels of electrons.
_____________________________
"I like your Christ. I do not like your Christians. Your Christians are so unlike your Christ." --Mahatma Gandhi
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RE: Can ERVs be explained without common descent? - 4/23/2008 3:49:31 PM
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Bettawrekonize
Posts: 1078
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ORIGINAL: Agahnim
Gradualism isn’t really the “core” of evolution anymore. I recommend doing a Google search on “punctuated equilibrium”. The idea that evolution happens rapidly and in small bursts has been part of the theory for around thirty years now.
We are familiar with punctuated equilibrium, we have been debating it on these forums many times long before you ever showed up. The problem here is lack of observable mechanism. In the case of punctuated equilibrium, the evidence does not support evolution so they speculate some unobserved mechanism to explain why the evidence is not what it should be if evolution is true. Of course, this requires faith and is not scientific. Darwin (evolution) predicts gradualism, it turns out to be false, so now they change the alleged evolutionary prediction to punctuated equilibrium. So if the evidence is non - stasis (as evolution predicts) it's gradualism. If it's stasis, it's punctuated equilibrium. Either way, evolution is unfalsifiable. Now, if you can show me that punctuated equilibrium can produce new limbs, appendages, organs, and body plans (as it claims to) and the DNA thereof (ie: if you can demonstrate the mechanism works), then I'll accept it. Until then, it merely demonstrates the unfalsifiable nature of evolution.
You shouldn't talk to us like we've never seen these arguments before or we aren't familiar with punctuated equilibrium. Jhud, for example, has his masters in biology from ISU. Drmark, from my understanding, has his bachelors in biology and he's a medical doctor who specializes in infectious diseases and the immune system. While I may have no credentials in biology, I have been reading up on these arguments for years, so I'm pretty familiar with what punctuated equilibrium claims. Many other senior ID advocates and creationists (who haven't posted here in a while) are also well versed in biology. Heck, DanJames is pretty new here and he seems familiar with biology. You shouldn't come here and act like the only reason that we reject evolution is because you perceive we are ignorant on the subject. Jhud is clearly more versed in biology than you, please don't come here telling us to look up stuff we have been debating over long before you ever showed up here. We know what punctuated equilibrium is, thank you very much, we don't need you to tell us to look it up. Sorry if I sounded rude, it just gets annoying when people keep portraying this stereotype that critics of evolution are ignorant and that's why they reject it.
< Message edited by Bettawrekonize -- 4/23/2008 4:51:34 PM >
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RE: Can ERVs be explained without common descent? - 4/23/2008 4:29:18 PM
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Jhud
Posts: 6781
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From: Lake Wobegon
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I don’t have a problem with the theory of evolution being modified on the basis of a new discovery like this. It’s the same thing that happens to any other scientific theory when new data about it is discovered, as in the example I mentioned of atomic theory. The important thing is just that we not throw out more of the theory than is falsified by this new discovery, just as when Schrödinger created his new version of atomic theory he didn’t reject the idea that atoms exist, with protons and neutrons in the nucleus, surrounded by several distinct orbital levels of electrons.
I think the problem I have is it really waters down the notion of evolution so far that it becomes a very broad, often moving target. It's morphed (evolved?) so much that it really no longer represents the concept most casual evolutionists claim to defend.
Berlinski talked about this in Expelled; it's really an amorphous amalgam of ideas rather than a robust and testable theory.
_____________________________
Jack
“I mean to live my life an obedient man, but obedient to God, subservient to the wisdom of my ancestors; never to the authority of political truths arrived at yesterday at the voting booth”
William F. Buckley Jr. 1925-200
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RE: Can ERVs be explained without common descent? - 4/23/2008 4:32:17 PM
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Jhud
Posts: 6781
Joined: 4/11/2005
From: Lake Wobegon
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We Jhud, for example, has his masters in biology from ISU.
I appreciate the boost Betta, but I don't have a masters in biology, just an undergraduate degree. I don't think I ever indicated otherwise, but I just want to maintain my integrity on this.
_____________________________
Jack
“I mean to live my life an obedient man, but obedient to God, subservient to the wisdom of my ancestors; never to the authority of political truths arrived at yesterday at the voting booth”
William F. Buckley Jr. 1925-200
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RE: Can ERVs be explained without common descent? - 4/23/2008 4:40:01 PM
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Bettawrekonize
Posts: 1078
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ORIGINAL: Jhud
I appreciate the boost Betta, but I don't have a masters in biology, just an undergraduate degree. I don't think I ever indicated otherwise, but I just want to maintain my integrity on this.
I'm sorry, I thought I remember reading that you did somewhere. I apologize, my memory isn't perfect.
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RE: Can ERVs be explained without common descent? - 4/23/2008 10:25:31 PM
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Agahnim
Posts: 161
Joined: 2/27/2008
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I think the problem I have is it really waters down the notion of evolution so far that it becomes a very broad, often moving target. It's morphed (evolved?) so much that it really no longer represents the concept most casual evolutionists claim to defend.
Well, so much the worse for “casual evolutionists”, then. I consider a lot of the people at Christian Forums who call themselves “evolutionists” to be just as unscientific as the creationists there. Rather than attacking a strawman of the theory, they defend a strawman, which is just as bad in my opinion.
I have a thread there from a few months ago in which I was trying to call people’s attention to this, if you’re interested in reading it: http://christianforums.com/t6651409 . My dissatisfaction with the arguments evolutionists were using there is part of the reason why I registered at this forum.
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Berlinski talked about this in Expelled; it's really an amorphous amalgam of ideas rather than a robust and testable theory.
How is evolution different than any other scientific theory in this respect? Going with the atomic theory example again, the model of the atom used by that theory has gone through at least five different versions: Dalton’s, Thomson’s, Rutherford’s, Bohr’s and Schrödinger’s. Every time experimental results have contradicted one of these models, atomic theory as a whole wasn’t considered completely falsified; scientists just came up with a new model that took these results into account. Atomic theory is certainly a “moving target” also, but I’m not aware of anyone arguing that because of this we shouldn’t assume that atoms exist.
This pattern of continuously modifying a theory as new discoveries are made is just how science works in general. Why is this a problem for evolution but not any other theory?
_____________________________
"I like your Christ. I do not like your Christians. Your Christians are so unlike your Christ." --Mahatma Gandhi
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RE: Can ERVs be explained without common descent? - 4/23/2008 10:38:52 PM
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Bettawrekonize
Posts: 1078
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ORIGINAL: Agahnim
How is evolution different than any other scientific theory in this respect? Going with the atomic theory example again, the model of the atom used by that theory has gone through at least five different versions: Dalton’s, Thomson’s, Rutherford’s, Bohr’s and Schrödinger’s. Every time experimental results have contradicted one of these models, atomic theory as a whole wasn’t considered completely falsified; scientists just came up with a new model that took these results into account. Atomic theory is certainly a “moving target” also, but I’m not aware of anyone arguing that because of this we shouldn’t assume that atoms exist.
You're confusing operational science with origins science.
Atomic theory is a model about how things work here and now. It tries to explain how atoms work and we can observe it here and now. Evolutionists claim that evolution was the mechanism by which new limbs, organs, body plans, appendages, etc... (or the DNA that codes for them) emerged. However, unlike atomic theory, we are not able to observe this. So evolutionists must resort to faith based speculation, and not science, to justify their beliefs. Evolution is not equivalent to atomic theory. You have no evidence that evolution would ever produce new limbs, organs, body plans, appendages, (or the DNA that codes for them) etc... The only thing you assert is, "they exist, so evolution must have produced them." Of course, this requires faith. I can just as easily equate creationism with atomic theory. "We exist, therefore God must have created us." Just because you choose to equate them does not make it so. There is no reason to believe evolution is falsifiable. When Darwin was wrong about predictions, it didn't falsify UCD. Instead, evolutionists simply change what would allegedly falsify UCD. There is no reason for me to believe they won't continue to do so if the current model gets falsified (they did it in the past). There is no reason to believe UCD is falsifiable. You can assert, "but if we find such and such animal below such and such layer, it would falsify UCD" even though Darwin may have never predicted any such thing. There is no reason for me to believe that it would falsify UCD. Darwin was wrong about many predictions and it didn't falsify UCD. Likewise, if your new alleged prediction were wrong, I have good reason to believe the secular community would simply move the goal posts again (because they did it in the past). I see no reason to believe otherwise (because they assert it is so?). They can just come up with some new criterion that would falsify their new model (like they did in the past, claiming that finding certain animals below certain layers would falsify it when Darwin never said any such thing), and if that gets falsified, they can make up some new criterion again. Why should I believe otherwise? They did it in the past, why should I believe they won't do it again?
< Message edited by Bettawrekonize -- 4/23/2008 11:12:41 PM >
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RE: Can ERVs be explained without common descent? - 4/23/2008 11:14:52 PM
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Agahnim
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