Although I am unable to clearly see that in the paper, after considering the information in it more carefully, I think you are right on this point too.
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Here’s an idea: Rather than worry about what the paper says, go download the program and check for yourself!
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I just noticed that this thread is now the most-viewed thread on Peaceful Science (at 18.5k views), beating out the 5 1/2 year old Heliocentric Certainty Against a Bottleneck of Two? (17.5k).
Yeah, but consider it as views per post, and it doesn’t look so good.
True – but the longer each post has been up, the more views/post it would generate. Likewise, ‘Comment’ threads show up to non-members, so would attract more views than ‘Side Comments’ would.
Admit it, you only posted to get even more views, right?
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No. 
I’ve actually been watching its rise to the top of the ‘most viewed’ leaderboard for some time. I am merely amused that the ‘garbage heap’ thread is the most viewed on the forum. I think is says something, somewhat less than complimentary, about human nature. 
That’s very common on every internet forum I’ve ever followed. ATBC might have the longest running junk thread of them all.
The strong claim is I have not seen any attempt to reconcile the assumption of these sequences being retroviruses or endogenous retroviruses that are randomly written in the germ line. If endogenous retroviruses being randomly inserted in the germ line of animals turns out to be a rare event then the current scientific explanation is wrong.
What I mean by rare is the number that are deleterious which makes your claim more challenging if deleterious endogenous retroviruses are not rare.
Sure this is how it is working but when the established results are not solidly tested the claims that are made rely on untested results. You are relying on the assumption of methodological naturalism to draw many of the conclusions that the theory is built on.
You are back to assertions that ignore that we can see the Designers capability by studying biology. The designer is limited by the laws of nature that He established.
There are sequences similarities and differences. This is observed and very similar to human designs.
Biology is best understood when one infers design vs blind unguided processes. This is a claim that is backed up by the complex systems we observe when studying biology. The insistence on blind and unguided processes is due to the limitations of methodological naturalism. Insisting on this limitation is giving us a false view of reality.
You aren’t looking.
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Have you entertained that multiple different life forms have been seeded on earth?
When you invoke “literal magic” to the alternative you are making a parsimony claim. Common descent is simpler than separate creation. This is what Darwins original claim was based on.
There does not exist any population genetics model that can show how animals with different genes and chromosome counts can be reproductively related. See do all deer share a common ancestor. Do all deer share a common ancestor?
Do you discount the possibility a creator is behind the diversity of life?
Ok this is a possibility however remote it is.
Another possibility is you lack imagination for God or a creator and limit your possibilities when looking at the data.
You are becoming the poster child for scientism.
It’s “multiple different life forms”, not “multiple difference life forms”. And yes. I have. So far, the evidence in support of that idea seems insufficient to warrant accepting it.
Again, your grammar is embarassing. It is not I who is invoking literal magic, but you, and not to an alternative, but as one.
Is it? How so? Please, explain.
Please, provide a citation substantiating that Darwin made any original claim based on an appeal to parsimony. Otherwise I am left to conclude you are lying again.
Nobody has made a demonstration that “a creator is behind the diversity of life” (what ever that means) is a possibility. So, no, I do not discount it. I cannot. Because there seems not to be a possibility there to discount.
Can you outline the evidence for and against that has driven you to this conclusion?
Did I make a literal magic claim? You are invoking this claim when you cannot imagine how it happened through natural means.
Reproduction is easier to understand than the ultimate origin if different animals.
Darwin predicts that different species and genera will undergo different selective pressures, and that adaptations and extinctions will be varied too across different lineages. The overall picture delivered by the paleontological record supports the explicative nucleus of common descent and natural selection. Darwin, moreover, openly rejects the hypothesis of independent creations, in that it would require many non-parsimonious assumptions.
So your asserting that no one has made a demonstration that a creator is behind the diversity of life. May I respectfully suggest that you are filtering data that suggests there is a creator behind the diversity of life.
Yes. The evidence in favour of the idea that multiple different life forms have been seeded on earth is none. The evidence against the idea that multiple different life forms have been seeded on earth is also none. Sufficient evidence to warrant accepting the idea that multiple different life forms have been seeded on earth is more than none. Therefore, I conclude, the evidence in support of the idea that multiple different life forms have been seeded on earth is insufficient to warrant accepting it.
That’s nice. But you said it was “simpler”, not “easier to understand”. Are they one and the same to you? In that case, why do you repeat yourself? Are they different? In that case, why do you switch topic instead of addressing the question?
The quote you continue with after that passage reiterates your own claim, but does not include, in context or out of it, an actual reference to Darwin’s writings. Perhaps this is my fault, and I should have been more specific when I asked for a citation. I am not looking for some blog article that merely claims what you claim, but for something that actually substantiates the claim itself beyond merely asserting it.
That’s “you’re”, not “your”. Learn your language. And no. Please, also learn to read. I asserted that noone has made a demonstration that “a creator is behind the diversity of life” (what ever that means) is a possibility.
Sure, suggest all you want. In fact, if it is of any concern to you, I hereby grant you explicit permission to openly accuse me of doing that. If you can substantiate an accusation like that, I might walk away humbled, and having learned something new. And if not - well, I don’t think either of our reputations stands to gain or suffer much from that. I’d frankly much rather discuss data, but I understand that’s not traditionally been your purview.
Unlike you, he looks at the data.
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Doesn’t that depend on just how rare it is?
You are unusually bad at expressing yourself. We have good reason to believe that they’re rare. But what does HIV have to do with anything?
For solid testing, read Larry’s book.
What makes you think so?
What evidence do you have for this assumption? And if he’s limited by the laws of nature, how can there be any supernatural intervention?
The gross statement is true, but in detail it isn’t. The nature and pattern of those similarities and differences is quite unlike human design. Nor is there any reason to believe that divine design must resemble human design anyway.
That’s an unsupported assertion, and your attempt at support is loaded with unexpressed and unconsidered assumptions. I also note that you have once again conflated common descent (the subject under discussion) with blind, unguided processes, a separate and independent hypothesis. As you always do.
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Which is precisely never. A claim doesn’t get to be established before passing some rather intense testing. This is science we are talking about here, remember?
Really? How do we study what the designer is incapable of, then? How does the designer idea contribute to our understanding of any aspect of nature? What novel predictions can we derive from it, given that our only means of making assertions about the designer is to claim that it was him all along, no matter what we find? Scientifically speaking, I say this is garbage.
Convenient, that, wouldn’t you say?
No, it’s nothing like human designs. Not proposed by competent engineers, anyway.
An interpretation that yields no predictive capability is no kind of “understanding” at all. Biology is best understood when one infers mechanisms underlying observations and tests them against more data. People who make it their mission to infer religious or anti-religious implications over an actual study of the phenomena themselves traditionally offer no worthwhile contributions to the understanding of said phenomena. That’s not to say that people who infer one or the other don’t or can’t. But time spent philosophizing about such things is time spent not doing anything to advance actual understanding of nature.
A claim about what is the most effective strategy to achieve some goal had better be backed by evidence of that strategy’s effectiveness. The presence, or frequency, or magnitude of complex systems in biology does nothing to indicate that the design inference (or any competing one, for that matter) is a means by which biology is best understood.
Methodological naturalism does not inform inferences about the fundamental nature of things. The only thing it says is that appeals to magic are not helpful in understanding how things actually work. Meanwhile, evolution on a grand scale appears unguided and blind because it appears to operate without what we would recognize as hindsight or foresight, as structures are warped and twisted to fit new needs instead of getting replaced by objectively better suited ones found elsewhere. It looks exactly like no thinking agent capable of inventing designs like that is actually in charge of doing so. And biochemistry appears to be blind and unguided because it is, at its core, governed by electrostatics and thermodynamics, again, entirely devoid of anything we could recognize as deliberate.
That false view being what? Philosophical naturalism? Alright. Prove it. Both of it. The first one, that methodological naturalism gives “us” an impression of philosophical naturalism, should be easy. Next, prove that philosophical naturalism is a false view of what ever it is you mean by “reality”.
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