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« Unconditional Election and Favoritism (Video) | Main | "24" Moral Equivalency »

May 18, 2010

Comments

Cool

Please address the ERV issue:

http://www.youtube.com/watch?v=De-OkzTUDVA

Greg,

I also think you should address why it matters in the first place.

As Dr. William Craig said:

"The theory of evolution is irrelevant to the truth of the Christian faith. Genesis 1 permits all manner of interpretations, and Christians are not necessarily committed to Special Creationism."

http://www.youtube.com/watch?v=fHQsaiMcPLc

So if it just doesn't matter either way, why do you guys spend so much time debating it?

I mean, I think Dr. Craig is nuts for being he can harmonize the Origin of the Species, and the Bible.

But, whatev.

I think it's healthy for every Christian to ask themselves:

"If irrevocable proof of evolution was found tomorrow, would you really stop believing?"

nah

ToNy,

Thanks for that verse of WLC. Hadn't heard that one. I wonder if he would include the common descent of chimps and us among those GEN-1 Compliant interpretations.

RonH

Personally, I think Christianity could be true even if the whole book of Genesis were made up. If we evolved, that would require us to make some theological adjustments, but it wouldn't amount to an argument that Christianity is false.

Sam,

Don't you think Jesus said something at some point affirming Genesis?

I don't know. Something like "the Scripture cannot be broken".

RonH

RonH, yes I think Jesus said that. But if he didn't, Christianity could still be true.

Sam,

What we have here... is a failure to communicate.

What if Genesis were made up AND Jesus did say, "the Scripture cannot be broken"?

RonH

Tony, what did you think of the conversation Daron and Ron just had about ERVs? I was wondering where you were for that one.

RonH, if these statements are true, then Christianity is true, regardless of what else might be the case:

1. There is a God.
2. God created the universe.
3. God imposes a moral law on us.
4. We break the moral law.
5. Jesus is the messiah.
6. Jesus died for sins.
7. Jesus was raised from the dead.

If all of these are true, then I say Christianity is true. If just one of them is false, then Christianity is false. So the only way your two statements can entail that Christianity is false is if you can somehow argue from them to the negation of one of the above statements. I'll leave that to you because otherwise I'd just be guessing at what your argument is. Tell me how you think these two statements:

*Genesis is made up.
*Jesus said that scripture cannot be broken.

...entail the negation of at least one of my seven points, and I'll see if I can respond.

Sam,

I really have no dog in this fight. I should have let someone else take this up with you. I'd rather.

But this is how it looks to me: Jesus is supposed to be God. God can neither make a mistake nor lie. If Genesis was made up it seems to me that Jesus was mistaken and probably more than once.

Is your view common?

RonH

Does anybody else have a huge problem with non scientists making public presentations on topics where what they are saying is in stark contrast to the established scientific consensus and millions of peer-reviewed articles?

Surely Greg must recgonise he is not qualified to talk about the science involved, as it requires a certain level of expertise and first hand engagement with the data. Would Greg ever consider giving people medical advice that contradicts established medical science?

Adam writes,
"the established scientific consensus and millions of peer-reviewed articles?"

The consensus is hardly established and there are not millions of peer-reviewed articles. Peer review is highly over rated any ways and is limited to a specific elite who drink the kool aid of the self-appointed scientific priesthood who believe they are infallible. Suggest any "heresy" and you get yourself removed from the community.

Adam continues,
"Surely Greg must recgonise he is not qualified to talk about the science involved, as it requires a certain level of expertise and first hand engagement with the data."

By certain levels of expertise and first hand engagement with the data, do you mean all those scientists pontificating about how the world began when all of them accept deep time and none of them were even there?

Adam,
Oh yeah. I do.

A shipowner was about to send to sea an emigrant-ship. He knew that she was old, and not overwell built at the first; that she had seen many seas and climes, and often had needed repairs. Doubts had been suggested to him that possibly she was not seaworthy. These doubts preyed upon his mind, and made him unhappy; he thought that perhaps he ought to have her thoroughly overhauled and refitted, even though this should put him at great expense. Before the ship sailed, however, he succeeded in overcoming these melancholy reflections. He said to himself that she had gone safely through so many voyages and weathered so many storms that it was idle to suppose she would not come safely home from this trip also. He would put his trust in Providence, which could hardly fail to protect all these unhappy families that were leaving their fatherland to seek for better times elsewhere. He would dismiss from his mind all ungenerous suspicions about the honesty of builders and contractors. In such ways he acquired a sincere and comfortable conviction that his vessel was thoroughly safe and seaworthy; he watched her departure with a light heart, and benevolent wishes for the success of the exiles in their strange new home that was to be; and he got his insurance-money when she went down in mid-ocean and told no tales.
-W. K. Clifford
RonH

RonH,

Is your view common?

I should probably clarify my own position a little. I don't think Genesis is made up. My original point was that even if Genesis is made up, Christianity could still be true. So we are talking purely hypothetical here.

But no, I don't think my view that Christianity could survive the complete loss of Genesis is very common. I do think getting rid of Genesis would require us to make some theological adjustments, but none that would undermine any of those seven points.

There are several ways a person who rejected Genesis might respond to your argument.

1. Jesus didn't say "scripture can't be broken." The gospel writers simply misquoted him.

2. Jesus isn't God. The Arians are the true Christians, and the Trinitarians and Modalists are heretics.

3. Genesis was never intended to be a historical narrative. It's a work of fiction, just like Job, meant to convey truths other than a literal interpretation would suggest.

4. Jesus wasn't referring to Genesis when he said, "scripture cannot be broken."

5. Jesus wasn't referring to his own belief that scripture cannot be broken. He was assuming his opponents' view for the sake of argument.

I'm sure you could think of others yourself. Like I said, a person who rejected Genesis would have to make some theological adjustments elsewhere. But it would not mean that Christianity is false as long as those seven points remain intact. Your argument didn't lead to a negation of any of them.

Amy,

didnt see it

looks pretty good

I wish i knew who he was so i could get more info. I have looked long and hard for a retort to the ERV argument.

But Amy, answer the question:

If evolution was true, would you stop being a Christian?

Does it really matter?

Really?

If evolution was true, would you stop being a Christian?

No. Christian's would be forced to reevaluate the intended meaning behind the Genesis text, but the resurrection event would remain - and the core of Christianity is built upon the truth of the resurrection.

Now...if the resurrection event didn't happen, would I stop being a Christian? You betcha.

"Surely Greg must recgonise he is not qualified to talk about the science involved"

But he surely IS qualified to talk about the philosophy of science and metaphysics that usually shows in these issues.

"No. Christian's would be forced to reevaluate the intended meaning behind the Genesis text, but the resurrection event would remain - and the core of Christianity is built upon the truth of the resurrection."

The core of Christianity is built upon the fact that a real man sinned and plunged the human race into judgment and condemnation for which Christ died for that sin (Romans 5, 1 Corinthians 15). If Genesis isn't real, or has to be re-evaluated in light of scientific evidence that then suggests it does not mean what it says, then the work of Christ is meaningless. You cannot have a resurrected savior without first having a fallen man. As far as I can tell, I do not sin because some mythological individual in a metaphor made a mistake.

ToNy,

"I have looked long and hard for a retort to the ERV argument."

What is the proper conclusion to reach when you search long and hard for a retort to an argument, but are enable to find one?

Eric notes,

"What is the proper conclusion to reach when you search long and hard for a retort to an argument, but are enable to find one?"

Does no one here even bother to Google? Try here:

http://creation.com/images/pdfs/tj/j22_3/j22_3_16.pdf

http://creation.com/images/pdfs/tj/j23_1/j23_1_99-106.pdf

http://creation.com/images/pdfs/tj/j23_1/j23_1_107-114.pdf

And these are just three articles out of many you can find.

And before you blow them off as being a bunch of hill billy YEC, it would be much wiser for you to actually read through their arguments and interact with how they interpret the data and why.

eric,

well i havent done a search in several months. the argument is indeed _fairly_ new.

Fred,

looks like a cool website thanks!

Fred it sounds like if evolution is true, you're saying you would stop being Christian, yes?

Fred,

After looking briefly at the docs, one quick point of contention in this debate is the question of whether or not some ERV's have a 'function'.

I'd submit that this is merely a curious side-issue.

The real question is that of 'common ancestry'/'common infection' -- Regardless of the current utility of the ERV itself - millions of years down the road.

An accidentally acquired scar can indeed have a function.

For example, in the Robert Burriss study, human male facial scars increased a female's desire to engage in short-term mating goals with the subject.

So having a cool scar gets you more sex, and hence, serves a very important function.

The fact that a scar has a function, says nothing about how it got there. Or if it was designed by an intelligent being or not.

Fred,

It may be interesting stuff, so I will probably continue to read through the articles you cited, but less than 20 seconds into the first one I can tell that the author (Shaun Doyle, in this case) is not competent in this area.

"However, the term ‘endogenous retrovirus’ is a bit of a misnomer. There are numerous instances where small transposable elements thought to be endogenous retroviruses have been found to have functions, which invalidates the ‘random retrovirus insertion’ claim."

This is a non sequitur, and tells us that the author doesn't understand the issue. There is no conflict between "random insertion" and something having a function. Neither of these things are relevant to the name "endogenous retrovirus".

"If the ‘junk DNA’ is not junk, then it puts a big spanner in the work of molecular taxonomists, who assumed that ‘junk DNA’ was free to mutate at random, unconstrained by the requirements of functionality. "

This is not a general assumption of molecular systematists (the term "molecular taxonomists" is incorrect in this context). Phylogeny reconstruction in general does not assume that DNA has no function. Many of the best phylogenetic trees currently available are made specifically from protein-encoding genes, which everyone agrees are functional.

"Evolutionists have used shared mistakes in ‘junk DNA’ as ‘proof’ that humans and chimps have a common ancestor".
This article appears to be intended as a scholarly article. It has a reference section, and even references a couple legitimate scientific publications. So where is the reference for this statement?

It is labeled as "Perspectives" at the top of the page, so maybe I can cut them a little slack for not carefully referencing everything (and even for including a reference to a Casey Luskin blog post), but I can't excuse the lack of understanding that is apparent.

I look forward to reading the other articles you posted. It's always possible that someone has a good argument in there.

Eric,
"Fred it sounds like if evolution is true, you're saying you would stop being Christian, yes?"

Evolutionary constructs are only good on small scales. It shows natural selection, speciation, adaptation to changes in environment, etc. What it fails to do is demonstrate large scale changes that changes an entire organism into a newer organism with increased information, ie, a shared common ancestor that produced chimps and humans.

So to answer your question, no. Where evolution is actually observed is with helping a species adapt to an environmental change. In that context it is viable. That has no conflict with biblical Christianity.

Where it does have a conflict with biblical Christianity is insisting humanity has a common ancestor with soul less hominds. ERVs and pseudogenes and the like are really uncompelling for me as evidence of shared, common ancestry. I would expect such things in a world created by a single creator who has created life to share in the same biosphere, environments, eat similar food, etc.

"but less than 20 seconds into the first one I can tell that the author (Shaun Doyle, in this case) is not competent in this area."

Really? I suggest you email him and share with him your criticisms. http://creation.com/shaun-doyle
Emails can be sent through the contact page.

And like I noted, those were just three articles. I can send you 20 more written by other individuals that may meet your expectations of competence if you insist. Or just search the site yourself. If you genuinely want a perspective from an opposing side, its there if you will work a bit. But please don't go away from this comment board under the impression no non-Darwinian has interacted with or responded to the ERV arguments.

Hi Tony.
Do read the discussion I had with Eric (not RonH, as it turns out) on ERVs. There are two pages and the evidence refutes the very claim you are expressing concern about. The issue is, indeed, about common inheritance/common 'infection'. And ortholgous ERVs at orthologous sites do not prove common inheritance ( with the caveat that I am using the same semantics as they appear in the literature .. even though the word "orthologous" itself indicates common inheritance).

Fred,

Read the first one. The points eric and ToNy made - they beat me to it - have been made in detail many times and are available to you and the folks at creation.com.

The ERV evidence for the common ancestry of chimps and us never relied on ERV's being 100% junk - even if some biologists erroneously assumed that ERV DNA must be junk.

It makes no difference if some of the ERV DNA is functional to you and/or Nim Chimpsky. Don't be surprised that we can make a protein using a some DNA or a modified version of some DNA that a virus once used to make a protein.

What matters is 1) whether it really is an ERV sequence, 2) whether it is in the same locus across species, and 3) whether it bears other expected marks of having been inherited.

RonH

Fred,

I plan to read more articles from the Journal of Creation, including the ones you posted. Not being familiar with the journal, I browsed the site to find their Instructions for Authors. This is a good place to start when trying to get a feel for a journal. In the Instructions for Authors at the Journal of Creation, it states:

"All our editors adhere to the Creation Ministries International (CMI) Statement of Faith and most papers will be designed to support this."

In other words, the journal is not about scientific discovery, or a quest for knowledge. It is about propaganda in support of a predetermined conclusion. While this doesn't mean that what they say is necessarily wrong, it is a very different approach from that of a scientific journal, and the Journal of Creation should not be confused with a peer reviewed scientific publication.

Fred,

You cannot have a resurrected savior without first having a fallen man.

Explain to me how "evolution is true" in the scientific sense means that man is not a fallen, spiritual being. You can only conclude that if you import theology.

Eric writes,
"In other words, the journal is not about scientific discovery, or a quest for knowledge."

That statement demonstrates you certainly are, as you state, unfamiliar with the organization. I take it you probably have this opinion with all the various groups who hold to a biblical model of creation, like ICR?

Creation Ministries are exactly that, a ministry that does have the agenda to promote the understanding of biblical creationism. You write as if there is something nefarious about them.

Eric continues,
"It is about propaganda in support of a predetermined conclusion."

I have to chuckle. And every evolutionary organization like NCSE, and publications like Nature, Science, etc., are NOT about propaganda in support of a predetermined conclusion? Please. Usually the ones who say they are unbiased and have no predetermined conclusions are the ones with the biggest bias with truck loads of predetermined conclusions with lots of propaganda in tow.

Eric concludes,
"and the Journal of Creation should not be confused with a peer reviewed scientific publication."

It is a peer-reviewed, scientific publication, you just dismiss it because they fall outside boundaries of the authorities you think are the best experts.

A couple of thoughts you may want to take away with you: First, like I stated above, peer review is over-rated and the "community" only allows their cherry picked elite to participate in peer review. Hence, creationists and ID proponents are automatically excluded from the process because of their beliefs. This is documented fact, not envious hear say from disgruntled anti-Darwinians who don't have the intellect to participate. Heck, Ben Stein made a movie about it.

Second: Many ID and creationists publish in peer reviewed publications under a false pen name just so they can get their ideas out in the peer reviewed market. Many are successful at it because they get their material published a lot.

SteveK writes,
"You can only conclude that if you import theology."

Steve, I readily admit I import my theology onto everything. Something every man does in this world.

RonH writes
"The ERV evidence for the common ancestry of chimps and us..."

Ron, evidence has to be interpreted. It doesn't just hang out their in the air self authenticating on its own. Those who interpret the evidence do so from a set of presuppositions, such as the unquestioned idea of "common ancestry." You are, in the words of the other commenter, SteveK, importing your theology onto the evidence.

Fred,

Steve, I readily admit I import my theology onto everything. Something every man does in this world.

Agreed. I just found your conclusion to be a complete non-sequitur.

If evolution is true in the scientific sense, it does not follow that the salient spiritual points described in the Genesis text aren't historical facts of reality.

Specifically, because evolution is true, it doesn't follow that man wasn't created by God as a spiritual being, is fallen and is in need of saving grace. The core of Christian reality remains fully intact.

Fred,

I think you have taken undue offense from my comments. I have stated facts, which you haven't refuted. You seem to be upset by what you see as the implications of these facts. A proper scientific endeavor does not begin with a conclusion and set about finding evidence to support that conclusion. That is backwards. Surely, many scientists frequently make this mistake as well, but that doesn't make it any more correct.

"I have to chuckle. And every evolutionary organization like NCSE, and publications like Nature, Science, etc., are NOT about propaganda in support of a predetermined conclusion? "

NCSE is a propaganda organization. I think they are a propaganda organization with the truth on their side, but that doesn't change the fact that they are a propaganda organization. I would not cite an NCSE article in a scientific paper. Nature and Science are legitimate scientific publications. They have editorial positions on certain topics, but it is not the case that "most papers will be designed to support this.". The editorial positions do not dictate the content of the research that is published in the articles.

"It is a peer-reviewed, scientific publication, you just dismiss it because they fall outside boundaries of the authorities you think are the best experts"

This is mistaken on three points:
1) It's not a peer reviewed scientific publication. It is a propaganda publication with some of the traits of peer reviewed scientific publications.

2) I didn't dismiss it. I specifically said "this doesn't mean what they say is necessarily wrong". I explicitly rejected the dismissal of their content simply because it is not actually a peer reviewed scientific publication. Propaganda is not necessarily false.

3) To the extent that I cautioned against giving too much weight to the Journal of Creation, I did not do so " because they fall outside boundaries of the authorities you think are the best experts". I clearly did so because the journal is a propaganda vehicle. I provided the evidence for this conclusion in the form of a quote from the journal's Instructions to Authors. Their primary purpose is to publish articles supporting their position. There's nothing wrong with that, but it means they are a propaganda publication and not a scientific journal.

"This is documented fact, not envious hear say from disgruntled anti-Darwinians who don't have the intellect to participate. Heck, Ben Stein made a movie about it."

Surely you recognize this film as unadulterated propaganda. Have you looked into any of the responses to the claims made in the film? The film is largely "envious hear say from disgruntled anti-Darwinians who don't have the intellect* to participate".

*There's a big difference between "having the intellect to participate", and actually applying that intellect properly. Very smart people can be wrong, and I would not characterize ID proponents primarily a lacking the intellect. I think it's more a question of application of intellect to properly understanding the issue. I don't think Ben Stein is a stupid man, but someone who says "science leads you to killing people" is not the person I would rely on to present an unbiased assessment of the situation.

Fred,

If Genesis isn't real, or has to be re-evaluated in light of scientific evidence that then suggests it does not mean what it says, then the work of Christ is meaningless. You cannot have a resurrected savior without first having a fallen man.

I don't see why we need Genesis to be historically accurate before Christ's work is meaningful. We have only to look around us and at ourselves to tell that man is sinful.

Eric,

Their primary purpose is to publish articles supporting their position. There's nothing wrong with that, but it means they are a propaganda publication and not a scientific journal.

From what I've heard, there aren't any "peer reviewed scientific journals" that will publish anything by people advocation intelligent design. They will only publish articles that are consistent with evolution. If that's true, then would you say they are just propoganda publications and not really peer reviewed journals? If not, what's the difference?

Fred,

I have been reviewing this thread and wanted to give you some moral support. I whole-heartedly agree with your assessment and position (and I dont think that he is offended when he responded).

You are being a great ambassador!!!!!

Daron and eric,

I just discovered the second page of comments where you two continued the discussion begun by Daron and me on ERV's. I'm impressed by the content and tone.

Daron pointed out that there's an ERV site shared by gorillas and chimps that we don't have. This suggests (human (chimp gorilla)). But we usually say ((human chimp) gorilla). What's up?

eric offered post-split interbreeding between chimps and gorillas as a possible explanation. That's a strong possibility.

I have another possible explanation that wasn't mentioned (unless I missed it): polymorphism in the common ancestor of all three. You two probably both know where I'm going already, but I'll spell it out.

Think about the whole population of the common ancestor species for chimps, gorillas, and humans. Some of these individuals have the ERV insertion; the others do not.

Now let the (will-be) gorillas split from this population. Let some or all of them have the insertion. Eventually, for whatever reason, any without the insertion die out. All subsequent gorillas have the insertion.

Next, let the (will-be) humans split from the (will-be) chimps. Some or all chimps have the insertion. As with the gorillas, for whatever reason, those chimps without the insertion die out. All subsequent chimps have the insertion.

Finally, let some or none in the alternate (will-be) human line have the insertion. If any do have the insertion let them die out. All subsequent humans don't have the insertion.

This provides a simple explanation for the HERV-K provirus insertion that chimps and gorillas have but we lack.

RonH

Sam,

The difference is between "won't publish anything" and "haven't published anything". If it turns out that explicitly ID research is never good enough to pass peer review, then you won't see ID papers published. The lack of published articles that are explicitly supporting ID is consistent with both possibilities (that there is an a priori refusal to publish such work, and that the work is not adequate.)

There are articles in major journals that question long-established notions in biology (and in other areas, but we are dealing with biology here). In some cases, it is known that the editor responsible for accepting the manuscript for publication disagrees with the conclusions. But the work is up to the standards of the journal, and the reviewers are satisfied that it should be published.

I think many people outside of the scientific community would be surprised at the rigors of good peer review. It is a nerve-wracking experience, and most authors can give you horror stories of reviewers they have had that were nearly impossible to satisfy. It is difficult to get a paper published in a high quality journal, and this is proper. There are lower quality journals, with more relaxed standards, but even they will have some standards and will typically reject more articles than they accept. It is too easy for people with a particular idea to think they they are being rejected because of that idea. It is more difficult to accept that you are being rejected because your work just isn't good enough. It's not a perfect system, but I haven't seen the evidence that any particular viewpoint is being inappropriately singled out.

For most journals, the review process is anonymous and confidential. Aside from the editor, the authors, and the reviewers, no one knows why a particular article was rejected. I would be interested to know if some of the articles published in the Journal of Creation were first submitted to a different journal and rejected. If they were, then what were the reasons given for the rejection? If they weren't, why not?

D Ward,

"and I dont think that he is offended when he responded"

Are you telling me that you don't think Fred was offended? If so, I hope you are right. Sometimes it's hard to properly interpret tone in a pure text format.

Anyway, I hope I haven't offended. I make an effort to avoid that, as the topics I like to discuss are often touchy enough without piling on.

Hi RonH,
That answer is not very simple at al, is very ad hoc, and both presumes and relies upon what you are claiming ERVs prove; namely, common descent.
The researchers already suggested what is the crux of your solution, that apes were susceptible to the integration and humans resistant, but without the difficulty of your polymorphism. You are left with the unenviable task of trying to explain why all gorillas and chimps, from the same stock as humans, were so blessed to have the ERV that they survived and others did not, while the exact opposite is true of the humans from the same lineage.
Eric's solution fares no better for the proof of CD because it either demands that either chimps or gorillas are the offspring of the other (not at 3-4 MYA, that's for sure) or merely admits what has already been offered as the solution; namely, that the orthologous entered each population after the split and after the split from humans.
None of your solutions logically saves orthologous ERVs as indicators of common descent but merely offers some way to explain away the data if we already presume common descent.

In other words, to answer Tony, there is no ERV issue.

Eric,

Yes, I was saying that I dont think that Fred was offended when he gave his responses (of course, I am now speaking for him). He was just responding to the questions/critques.

his responses echo the feeling on "our side" in my personal opinion as it relates to peer review, etc.

Hi Eric,
The question is as you state it, whether or not anything about ID is good enough to publish. And when we look at the subject fairly we see that the matter is not resolved based upon that question. Specific ID and Creation scientists have published dozens and many dozens of papers until the implications of their work became apparent. Then they could no longer publish, at least on that topic.
Examples are not hard to find in biology, geology, astronomy, etc.
Ron Gentry is the first Creationist scientist whose name actually comes to mind as I write this.

Here is one reply Behe got from a journal about publishing his work:

9 February 2000

Dear Dr. Behe:

We are sorry to have been delayed in getting back to you about the possibility of organizing a dialogue on the question of purposeful intelligent design. We have explored the notion with a number of individuals and have had extensive discussion among ourselves over a period of time.

The editors have concluded that the journal should not undertake this project. The reasons are varied, but primarily they reduce to our general feeling that it is not possible to develop a meaningful discussion when the fundamental assumptions of the arguments are so different: on the one hand, the concept of intelligent design beyond the laws of nature is based on intuitive, philosophical, or religious grounds, while on the other, the study and explanation of all levels of the living world, including the molecular level, is based on scientific fact and inference.

As you no doubt know, our journal has supported and demonstrated a strong evolutionary position from the very beginning, and believes that evolutionary explanations of all structures and phenomena of life are possible and inevitable. Hence a position such as yours, which opposes this view on other than scientific grounds, cannot be appropriate for our pages.

Although the editors feel that there has already been extensive response to your position from the academic community, we nevertheless encourage further informed discussion in appropriate forums. Our journal cannot provide that forum, but we trust that other opportunities may become available to you.

Yours sincerely,

[The editorial board]


http://www.arn.org/docs/behe/mb_correspondencewithsciencejournals.htm

Notice the metaphysical precommitment expressed by the editor.

When I argue this point with ID critics they always start out by saying that it is not the case that there are rules against publishing ID explicit material but they always end up by admitting that such rules do exist - but that they find the rules appropriate.
This, at least, is the honest response.

One has to look no further than the firestorm around Sternberg to know that suppression is the norm. The post hoc arguments about procedure adn quality are just that. Such stringency and gnat choking is never applied to the thousands of other papers published annually.

RonH,

After reading the paper more closely, I found that the authors suggest what you have outlined as a likely explanation. It's called incomplete lineage sorting, and you gave a good explanation of how it works. I think the incomplete lineage sorting explanation is more likely that the inter-species breeding I had suggested.

Daron,

This kind of scenario is rare, but common enough to be well studied. The idea is that there is a single phylogeny that explains most of the relationships between a set of species. But there are some cases where a single trait (such as a gene, or some other marker) shows a pattern that disagrees with the main phylogeny. There are three general explanations for this kind of phylogenetic incongruence.

1. Noise. In almost every case, there is noise in the data because of random fluctuations or systematic effects. Sometimes the noise will swamp out the signal, and can lead to erroneous results.

2. Incomplete lineage sorting.(See RonH's explanation above). This happens when a lineage splits in two, followed relatively quickly by a second splitting of one of the daughter lineages. The loss of different versions of the marker in different lineages gives the impression of a species tree that is at odds with the correct tree.

3. Horizontal Transfer. This is when some genetic material enters the gene pool in a manner other than parent-child descent. This is rare in animals, but can be mediated by viruses (and perhaps other as-yet-unknown mechanisms).

Hybridization, or inter-species breeding, could be seen as a kind of horizontal transfer (and is sometimes decried that way), but it can also be viewed as a mechanism behind some cases of of incomplete lineage sorting. Basically, it means that the gene pools are not yet completely separated, and some mixing of genes is still possible.

The presence of the same inserted sequence, at the same locus, in two different genomes is very strong evidence of common descent. Taken as a single data point, it may give a misleading impression of the exact pattern of descent, but that doesn't invalidate it as evidence supporting common descent.

Hi Eric,
The researchers did indeed suggest such explanations. What they concluded was that chimps and gorillas most likely integrated the same ERV at the same locus independently and that it had never entered the human lineage.

While this evidence knocks down one more of the claims of the ERV evidence - that it confirms phylogenetic trees otherwise derived - the conflicting pattern is not really the point. What is the point is that ERVs at the same locus do not necessarily indicate common descent. It is a bonus that the phylogenies derived from ERV evidence have to be massaged to match presumed phylogenies. So there go two of the pillars. The third is already conceded - ERVS are not useless remnants of accidental genetic events.

Nothing is left of this "proof" of common descent beyond what was already known - humans and apes are physically similar, and therefore have similar body plans, and therefore have similar parts lists.

The data can be coerced into line with common descent, but it is not proof of it.

Daron,

I'm referring to the paper you cited in the other thread, http://www.ncbi.nlm.nih.gov/pubmed/11378389.

(full version at http://linkinghub.elsevier.com/retrieve/pii/S0960-9822(01)00227-5 for those with access)

The alternative is an allelic segregation model (Figure 2d) in which the provirus formed in the most recent common ancestor of Homo, Pan, and Gorilla just before the three lineages separated.

What they call an "allelic segregation model" is what I was calling "Incomplete lineage sorting". The authors of this paper propose that this is the best explanation for this particular provirus.

The evidence from ERVs goes well beyond "humans and apes are physically similar, and therefore have similar body plans, and therefore have similar parts lists."

I believe that this article may clear things up.

Article name:
"Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans" in PLOS Biology.

http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0030110;jsessionid=EFD9BC3BE263605D959843AFB2468FE5

The diffences between the ERVs shared by humans and chimps and the ERVs shared by chimps and apes and not humans is that the chimp-gorilla only ERVs are almost all inserted a different locations in the respective genomes. That suggests that they are not inherited from a common ancestor.

By the contrast, the number of shared ERV in chimps and humans that are found in the same loci is too great to be explained as being the result of independent infections. Based on what is observed with chimp-gorilla only ERVs, if chimps and humans picked up their ERVs by independent infection, we'd expect to see the same non-orthologous insertion pattern that we see with chimp-gorilla only ERVs. However, the orthology pattern in chimps and humans is quite different from the orthology pattern in chimps and gorillas.

This is not to say that it's impossible for a given ERV to independently insert at the same locus in chimps and humans, but the chimp-gorilla story gives us a chance to see what the orthology pattern would look like if ALL ERVs are acquired by independent infection. Given the chimp-gorilla pattern, it would seem that the hypothesis that chimps and humans picked up ALL of their ERVs by independent infection is disproved. On the other hand, the evidence does support the conclusion that chimp-human ERVs are there due to common ancestry, and it's difficult to see what alternative explanations are left.

It's not really a matter of "proof". Rather, ERVs offered an opportunity to test the hypothesis of common ancestry. If there was no common ancestry, the data could have easily contradicted the hypothesis. However, the data support the hypothesis.

Daron,

You are left with the unenviable task of trying to explain why all gorillas and chimps, from the same stock as humans, were so blessed to have the ERV that they survived and others did not, while the exact opposite is true of the humans from the same lineage.

If I understand you correctly there is no such unenviable task.

The chimps and gorillas both descend from a subset of the CA with the insertion. The humans descend from a subset of the CA without.*

It has to happen this way some of the time - there is no law that tells speciation, "Hold off while I fix every allele in the CA." So the (will-be) chimps and gorillas don't have to 'survive' something that kills off the (will-be) humans. No blessings are required.

Furthermore, it is not a matter of 'explaining away' data. The theory predicts this kind of scenario will occur.

The only question is: How often?.

The longer it takes for an allele to become fixed the more likely that a speciation takes place while it is not fixed. How long does it take for an allele to be fixed? It depends on selection pressure and population size. (A small population can fix an allele in a short time without selection pressure.)

There might be ways to get some numbers here. But I have no idea how.

Likely to be off the air for a few days. Daughter graduating. How sweet it is!

RonH

* This is one of the ways it could go under my original description which was meant to capture all the possibilities (and likely didn't).

Henry,
sounds interesting
had trouble with the link
thisworks
RonH

Hi Eric
I get you, Eric. You are talking about the HERV-K which exists at orthologous sites in Gorillas and Chimps but never integrated in humans.

We identified a human endogenous retrovirus K (HERV-K) provirus that is present at the orthologous position in the gorilla and chimpanzee genomes, but not in the human genome. Humans contain an intact preintegration site at this locus.

I was talking about the PTERV-1 that exists in Gorillas and Chimps but never integrated in humans. In this more recent paper the integration in Gorillas and Chimps is seen to be independent and contemporary, 3-4 million years ago, and many million years after the split. Thus, allele fixing would have no bearing on the matter.

Our data support a model where ancestral chimpanzee and gorilla species were infected independently and contemporaneously by an exogenous source of gammaretrovirus 3–4 million years ago. While similar infections with a related retrovirus appear commonplace among the Old World monkeys, contemporary human and orangutan populations show no molecular vestiges of this infection (see Figure 2).

Here's another paper I looked at that contends with anomalous HERV K data (sorry for the formatting)

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

[When the expected topology is not seen]:
Alternatively, the topology of the tree in Fig. 2 B may indicate that the HERV-K18 provirus of gorillas and the HERV-K18 provirus of humans􏰀chimpanzees are not true orthologues. There are at least two mechanisms to explain this possibility:

(i) The proviruses are derived from two independent integration events (xenology). This possibility would require two nearly identical viruses (differing by no more than 11 substitutions within the LTRs) to integrate into precisely the same nucleotide position in two different lineages—a highly unlikely possibility. A similarly unlikely variation on this possibility is independent integrations into very similar cellular target sequences.

(ii) In one of the two lineages, HERV-K18 was largely replaced by recombination with a separate (but nearly identical) provirus. Such recombination would have been restricted to sequences within the provirus, as the flanking cellular sequences are identical in both lineages. It should be noted that there are hundreds of HERV-K LTR sequences within the primate genome (31–34).


[[When an ERV is in early divergent species but not in more recently diverged one]]:
The HERV-K(C4) LTR sequences (Fig. 2C) give the predicted topology; however, as noted prev iously (15, 16), the provirus was missing altogether from gorilla and chimpanzee DNA, in which only an unoccupied integration site was detectable. HERV-K(C4) is found in some ape and OWM species, proving that integration occurred in a common ancestor of apes and OWMs (15, 16). The provirus is located within the human C4B gene, which arose by duplication before the separation of the apes and OWMs. The absence of HERV-K(C4) from some species is most likely caused by frequent homogenization of the C4-CYP21 locus (35), resulting in conversion back to the unoccupied integration site. Both alleles of the C4 locus (with and without the HERV-K(C4) provirus) have been identified within more than one species, suggesting that such conversions have occurred multiple times during primate evolution (35).

Once again, we have CD-consistent fixes applied when the evidence is problematic rather than supporting of CD.

Hi Henry,
I do like that article. I cited it to Eric (and Ron) on the previous thread.
Henry:

The diffences between the ERVs shared by humans and chimps and the ERVs shared by chimps and apes and not humans is that the chimp-gorilla only ERVs are almost all inserted a different locations in the respective genomes. That suggests that they are not inherited from a common ancestor.
But some are shared at common sites (up to 4%). And the researchers in this paper admit that ERVs will cluster in the same locations and that they will be subject to selection to those areas.
Cite:
This apparent independent clustering of retroviral insertions at similar locations may be a consequence of preferential integration bias or the effect of selection pressure against gene regions, limiting the number of effective sites that are tolerated for fixation.

They had to work fairly hard, it appears, to demonstrate that many apparently ortholgous sites were not, in fact, ortholgous. One of the lines of evidence they used was that if they were orthologous they would be arguing against the normal topology.
One other solution to the problem posed and that they suggested was this one:
Cite:
An alternative explanation may be that the primate phylogeny is grossly incorrect, as has been proposed by a minority of anthropologists [29].


Much of your narrative is interesting but does not derive at all from this paper.
Henry:

By the contrast, the number of shared ERV in chimps and humans that are found in the same loci is too great to be explained as being the result of independent infections.
This is one question I've had and have been a little unfortunate in not finding the information.
Do you know exactly how many are found at the same loci, among the tens (or is it hundreds now?) of thousands of ERVs we share with chimps? And do you know if as much effort was put into establishing that they are precisely the same loci as was put into dispelling this notion in the above example where orthologous loci would not support CD?

Since it seems that we have been confusing multiple papers within a single discussion, I think it is helpful to deal with only one paper per comment. I would suggest that others do the same, or at the very least be very clear about what paper you are discussing at any given point.

In this comment, I am discussing the paper "Constructing primate phylogenies from ancient retrovirus sequences", which was quoted at length in Daron's previous comment.

This paper uses ERV sequences to construct phylogenies of primates. The species involved are human, chimpanzee, bonobo, gorilla, orangutang, gibbon, rhesus macaque, cynomolgus macaque, baboon, marmoset, spider monkey,and African Green Monkey (AGM). However, the primary goal of this study is not to establish or to test the current primate phylogeny. The goal is to see how good ERV sequences are as phylogenetic markers. (The sequences themselves, not the locus of integration). How do I know this is the goal of the study? Because that's what the authors say, in exactly the places where a good paper tells you the primary goal of the study. It's in the abstract, and it's at the end of the Introduction.

From the Abstract:

"Moreover, tree topology is highly sensitive to conversion events, allowing for easy detection of sequences involved in recombination as well as correction for such events. "

This means, that if there are problems with the trees, this tells them something is wrong with using that particular ERV sequence as a marker - because the tree is taken as already well established:

"the specific use of HERVs in this study allows comparison of trees to a well established phylogenetic standard, that of the Old World primates"

From the Introduction:

"The evolution of primates has been the subject of intense study for well over a century, providing a well established phylogenetic consensus with which to compare and evaluate the performance of ERVs as phylogenetic markers."

So it is backwards to say any disagreement between trees means the standard primate tree is wrong. Rather, it means that the particular marker that generated that tree is not reliable. The fact that most of the trees completely agree with the standard tree is taken to validate the use of those ERV sequences as phylogenetic markers. It does provide additional support for that standard tree, but that is not the goal of this study.

This study is trying to establish that ERV sequences are useful markers for phylogenetic reconstruction. This is important, because these sequences are present in many species and are similar enough to allow them to be identified in many species. In order to determine how good they are, you need to use them to derive a tree for a set of species for which you already know the correct tree. Because the primate tree is so well established, this is the tree the authors chose for their "known tree".

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