ERVs and evolutionary predictions

Conversation Side Conversation
1

Ok, after some lighthearted posts recently I thought I would post a more intellectually orientated
I am in the middle of a text debate with a mate about ERVs. Something I know has been covered on this board a few times already but I would appreciate some thoughts on
He keeps going back to the notion that a common designer fits the data, so I have tried to list out some of the things that the design hypothesis would need to show and why the common ancestor view fits the data better.
Two questions:

  1. is the list below accurate or have I bodged it?
  2. using the format below of “science has shown x but the design hypothesis needs to explain the data another way and there needs to be evidence for that” what else would you add?
    Clearly I am not a scientist and could be completely misunderstanding it all, so be gentle with my fragile ego :wink:

“Here is what you have to believe for ERVs to be explainable on the design hypothesis
If you accept that these are real viruses that weren’t part of the original genome

  1. despite all known retroviruses inserting basically randomly in the genome, god made the ones we see -that are common across animals insert in the same place in the different animals that share these. Can you provide evidence for this, if not then why should I prefer creationism above the evolutionary model that does explain these patterns
  2. Despite all known mutations in ERVS that we are still being created today being essentially random, God also made these mutational patterns in the animals that share them. Can you provide evidence for this, if not then why should I prefer creationism above the evolutionary model that does explain these patterns
  3. For a young earth timescale God would also need to increase the mutation rate far beyond what we observe today and then stopped these mutation rates so that we only see what is expected today. We even have known divergence dates of populations and reproductive isolation of humans in the last 4 thousan years (post flood) and can see the mutation rate between them and their ancestral population. This doesn’t support the rates in young earth creation. Can you provide evidence for your view, if not then why should I prefer creationism above the evolutionary model that does explain these patterns.
  4. Why do you look at ERVs that have have inserted in that location and have those mutations but have a good function and say that they are designed like that, but the look at ones that have negative function and say that these are corrupted from their original good purposes? On what basis do you make this determination and why can you not make the argument the other way, that an original virus that once harmed humans was endogenised and subsequently gained function. How do you determine between these scenarios?

If you say that these were never real viruses but were coded into the human genome
a) why do they have the distinct signal of the use of reverse transcriptase - something that we only see viruses using, and those to insert their genome into a hosts dna?
b) why do many of them have the full components of a real virus and can be made to become active viruses?
c) how can you distinguish between ERVs that we see being created today and aren’t shared by all humans let alone other animals and those that God originally created? Can you provide a test that could be applied
d) why are some of them so corrupted that they literally have no function? All their genes are mutated beyond repair and can’t express any RNA and their LTRs are so heavily methelated that they can’t act as promoters or regulators. How can you test the hypothesis that this is due to some original good function now going bad due to the fall or some such? How can you test this? If you can’t then why should be go with the designer hypothesis and not evolution which explains this well?

In addition to the above, can you show any mechanism the designer used and explain how we can see that is a designer at work rather than evolution? It is fine to claim design but easy to claim and then never back that up

Happy to pick a point and stick on it. But yes, God could have done all this. Is it testable and is it the best explanation - heck no. I don’t need to disprove creationism though to show that evolution is a valid hypothesis, I just need to ensure that my hypothesis fits the data and is not disproved”

2

Hi Matt,

As someone who has done a fair amount of work on (mouse) ERVs, they are obviously great evidence, but I don’t see a good basis for choosing them as a way to convince someone–IMO there’s too much extra stuff to learn.

That being said, I recommend staying on specifics. Don’t throw all 4 points at someone at once, start with #1. 4 is better than 3.

For #2, avoid the vague term “mutational patterns.” Refer to specific mutations.

1 Like
3

Thanks John.

Yep, that is fair. I have read book chapters on them and watched videos about them from professionals in the field. Despite that I definitely don’t have more than a surface level understanding and just have to be open to being corrected

I also agree with this. I suggested to him to pick one and we can stick on that but should have followed my own advice from here - just ensure I only introduce one at a time

I have basically given up now. He has just raised again gone an argument that if atheism and evolution are true then Hitler would be moral for “implementing evolution”
I have likened that to throwing people off cliffs as moral given that it is “implementing gravity”
Given that we are not able to agree even on this point anything with more nuance seems pointless

I have enjoyed the reading enough that I will keep up with it. Not worth it in the context of my dialogue with him though

Also thanks for these. I will revise my views accordingly

4

That’s the usual outcome.

Hitler sounds like a creationist here:

The consequence of this racial purity, universally valid in Nature, is not only the sharp outward delimitation of the various races, but their uniform character in themselves. The fox is always a fox, the goose a goose, the tiger a tiger, etc., and the difference can lie at most in the varying measure of force, strength, intelligence, dexterity, endurance, etc., of the individual specimens.

Mein Kampf (Ralph Manheim Translation), p. 285.

5

This fellow is deeply confused and lacking in critical thinking skills. He has never considered what it means for something to be moral, what makes something moral or not. He’s just regurgitating creationist talking points without any thought behind them.

6

You should consider throwing the Euthyphro dilemma at him.

7

My other clue to stop the conversation was when he cited Collins as saying

genetic similarity “alone does not, of course, prove a common ancestor” because a designer could have “used successful design principles over and over again.” (The Language of God, pg. 134.)

I decided to buy the book to check the quotation and of course it says something different when taken in context

The study of genomes leads inexorably to the conclusion that we humans share a common ancestor with other living things. Some of that evidence is shown in Table 5.1, where the similarity between the genomes of ourselves and other organisms is displayed. This evidence alone does not, of course, prove a common ancestor; from a creationist perspective, such similarities could simply demonstrate that God used successful design principles over and over again. As we shall see, however, and as was foreshadowed above by the discussion of “silent” mutations in protein-coding regions, the detailed study of genomes has rendered that interpretation virtually untenable—not only about all other living things, but also about ourselves.

Initially he was the guy who knows more than anyone else alive on genetics (dubious statement at best) but after repeatedly pointing out that he says the creationist view is virtually untenable my friend continued to assert that he is relatively in the middle on the topic and that he doesn’t think the evidence is conclusive one way or the other. Finally, the “virtually untenable” statement was responded to with “but that is just his opinion”. Apparently he is only the guy who knows the most for the bits that are liked

It has been an interesting experience, it has spurred me onto reading again and enjoying learning basic stuff. Just forked out for the fifth edition of Futuyma’s book “evolution” after getting some money unexpectedly. So not a loss overall, just no minds changed on either side of the discussion

4 Likes
8

Matt,

Are you trying to successfully argue for “no designer”? This is a pretty tall order.
But so is the ID argument which insists that God would never use Evolution.

Millions of Americans have already accepted Evolution as part of a divine design.
This should be the default position for Peaceful Science, even though it makes the
Atheist Evolutionists cringe.

9

Why should Peaceful Science have a default position, and if it should why should that be it?

Further, I’ve never been able to get a coherent response to this: how would “Evolution as part of a divine design” differ from evolution as undesigned processes and events? And would it differ in any observable or testable ways?

3 Likes
10

I think that question revolves around whether this is simply a forum for the discussion of issues relating to science, or whether it has a ‘mission’ to win conservative Christian creationists over to acceptance of evolution.

Whilst I can see the attraction of the objective of the latter view, such a mission smells too much like apologetics to me – and I’ve yet to hear of an apologist that seems in any way trustworthy. Apologetics cannot seem to help valuing winning an argument over revealing inconvenient truths.

1 Like
11

Sadly I cannot make much of a comment on matters of biology, and lately it would seem I rather poorly understand the philosophy of science therein. Nevertheless, and with no promises of effectiveness, here is a point I noticed in the preamble to the question at hand:

OP is trying to argue which, between evolution and design, “better fits” the data. There is a number of ways to interpret this phrase, and with maximal charity many could just assume that it means exactly the criterion one might oneself find paramount in judging how scientific some given idea is. At the risk of becoming uncharitable in so doing I shall not make this assumption, and instead present something that more precisely matches my own sensibilities on such issues, whether they ultimately align with OP’s well or poorly.

Surely, in the most naive sense, “fitting the data” is trivial to achieve better than any scientific description ever could. Suppose, if you will, a god who has full control of every aspect of nature and makes it at every instant behave exactly the way it does. A scientific description may approximate some mechanism arbitrarily closely, but it is trivially easy to just say that god makes it this way, and for no reason we are privy to above and beyond just wanting it so. That our theories map to the data is on this view a reflection of us attempting to model the data in a logically consistent way, but ultimately not of any underlying nature of things, for that is entirely due to god’s whims, which happen to be to make things exactly as they are. An account like that stands in no conflict with any data, of course, and it never can. It is, from the ground up, designed to be unfalsifiable. If it turns out that some measurement the outcome of which we explained as being god’s will is some other value after all, we could either say that god changed the universe, or rendered the measuring results what ever they were in all cases, or makes us conclude things exactly as we do. It certainly accounts for such errors, and in a colloquial sense one may even call them “explained” in this manner. There can be no discrepancy between any data and a model as incorrigible as this. With regards to fitting the data, every scientific model is always going to remain inferior to “god makes us record the data exactly as we do at all times”.

Because such a naive criterion makes devising the perfect model trivial, a case can be made that it is no healthy metric to evaluate the merits of all other models. After all, if a perfect one is so easy to propose, why would we ever waste any time at all to considering anything else? We must therefore either introduce some nuance into what we mean by “fitting the data”, or identify a different criterion that lets us meaningfully grade falsifiable models of nature. In my opinion, whether we consider it nuance or a different metric, the key is predictive power.

Our vulnerability and, ultimately, mortality, is the prime motivator of all our instincts. That’s not to say all other feelings are illusory, but rather that, if we follow the chain of motivations for any given sensibility, we end up with some form of well-being, which in one way or another maps to a well-being of the physiological sort. We are the heirs of beings who succeeded in the struggle for survival, those who evolved to function despite all natural threats to their continuation. Science, being a thing we do, is ultimately one of many means by which we make our lives more stable. In order to outmaneuver threats we must understand their maneuvres in the first place. Understanding how nature works means, under this admittedly crass reduction, knowing what to do in order to survive in it, be it personally or collectively. A given about our condition is that we have memories of the past but none of the future. So in order to make decisions that further our well-being we must find a way to see the future in some way with just the tools at our avail.

This is science. The best scientific description of a phenomenon is not so much one that perfectly fits all previously recorded data – that much, as discussed earlier, can be achieved easily by simply over-fitting – but rather one that consistently ends up fitting data it was not constructed to accomodate. An unfalsifiable model is bad not because it is a poor fit on the data, but because one cannot logically derive dependable predictions from it. It is bad, because it is useless. If we cannot employ it to foresee the future, then it cannot service the advancement of our ultimate goals of mastering the future’s threats and opportunities.

This failure is easy enough to see with the exaggerated manipulator god idea I presented earlier: “What ever observation we shall make in this experiment is going to reflect God’s will for it, just like everything in the past already has” does not tell us what to expect specifically, so we cannot devise strategies to prepare for it. But the common designer account of similarities between various living organisms also falls short of meeting this criterion, for it is an account of all biological features, and as such cannot discriminate between expected and unexpected ones. To account for any specific ones one must begin modeling minutia of the designer’s will.

But at that point one might as well dismiss the designer and model the minutia of natural processes directly, for the bundling of such things into a person-like entity adds nothing to the model’s fitness to predict experimental data. If anything, it over-complicates the model, providing thereby more opportunities to err.

3 Likes
12

Briefly popping back on the forum to show my ignorance :slight_smile:

Hi George. No, I wasn’t trying to argue there is no designer. Rather that the evidence for evolution seems to fit the evidence better here. Essentially, why should I prefer the design inference over a naturalistic one when many of the data items have a straightforward natural explanation. Also some points such as the reverse transcriptase point don’t seem to me to have a reason on a design view
@Gisteron I will try to ponder what you have said and respond at some point. Thanks for contributing

Most of the arguments I have given above come from this book Human Evolution: Genes, Genealogies and Phylogenies

1 Like
13

To @John_Harshman (and other Atheistic participants):

The fact you even offer these questions (below) shows us how disconnected you are from the current situation.

Let’s start with a reality check within the English speaking world: the great majority of those raised in a Christian context accept the merits that Evolutionary theory has the most evidence and explanatory power regarding the study of nature.

When he/she asks if such a view REQUIRES a complete rejection of Chritianity, the answer comes back “No!”.

If we here can agree with this basic premise, then we are left with this conclusion: toxic political and policy concerns are more often triggered by “evolution-deniers” than by Christians who acccept evolutionary principles.

Armed with this conclusion, it becomes obvious that helping Christians “defend” the science is just as important as trying to convince Creationists to accept Evolutionary theories as a possible working model for their faith.

Nowhere in this analysis is the idea that Christian faith itself is somehow more important to reject than I.D.

John:
Your question “… how would “Evolution as part of a divine design” differ from evolution as undesigned processes and events?” can best be answered “there would be
NO difference”. This fact should not compel atheists to accept Christianity. But we DO NEED Christians to feel compelled to reject evolutionary denialism.

The reasons are self evident!

14

Hi Matt
The evidence of different animals having the same ERV in the same location is compelling evidence for common descent if what we are observing is indeed an ERV caused by a random insertion.

The difficult problem I see here is answering is how a random, location specific, ERV insertion can become fixed in a population?

https://doi.org/10.1016/j.virs.2022.01.019

15

You are making some odd assumptions, though exactly what isn’t clear.

Sure, no problem there. But that’s not what you were talking about.

That’s nice, and I think we would all agree that it’s true. But that doesn’t entail the statement we’re supposedly arguing about, nor does it seem to have anything to do with making the atheists cringe.

What we’re supposedly arguing about is whether the default position of PS should be “accept evolution as part of a divine design”. Perhaps this is so vague as to mean nothing whatsoever except that God exists and at some point did something, which is what you may suppose. But since there is apparently no possible way to test the assertion, there seems no reason to articulate it. Anyone is free to accept or deny it. The important point is that there’s no requirement to deny it. But making it a default position adds nothing.

16

Why is that difficult? In almost all cases, the answer would be “drift”. Are you claiming that fixation by drift is not possible? Or is this perhaps you being the Texas sharpshooter again?

17

A post was merged into an existing topic: The Argument Clinic

18

What’s required for that isn’t “model parameters”. It’s the resemblance between the observed sequences and the sequence expected of an ERV.

Good question. Have you looked for data? I havenm’t.

I would suggest that the answer to both questions would be “rarely”.

Still, the answer would seem obvious, given that most ERV insertions are in junk DNA.

What’s the probability that a designer would put the same sequence in separately created species, and what’s the probability that the sequence would look just like an ERV?

1 Like
19

Come back when you can also show that there is any difficult problem.

It is not difficult to just claim, based on nothing but unfounded personal intuitions, that something is a difficult problem, without stating any reasoning as to why a given observation should not be expected, or why candidate explanations are unlikely to account for it.

TL;DR: Maths or dwot.

2 Likes
20

Briefly but not to the extent required. We have several people here that can do searches to try to show feasibility. The problem is that there is little curiosity when we assume like sequences are caused by random insertion of retro viruses.

Do you consider HIV a rare type of retrovirus?

I think your a little ahead of yourself here.

It is very likely a designer would re use sequences vs re inventing the wheel for no reason.