Why Aren't the Twin Locations of >100k+ ERV's (human vs. chimp) Discussed More?


#168

How does not knowing how the virus stopped infecting humans contradict common descent? On top of that, there are several possible mechanisms, such as the evolution of immunity within the human lineage.


#169

That assumes a constant rate of ERV acquisition which is definitely not what happens in real life. Infectious agents tend to come in waves with high susceptibility when the pathogen first enters into the population. Susceptibility is reduced over time as the host population evolves immunity to the pathogen. This produces waves of ERV acquisition, as is seen with PtERV1 insertions in the chimp and gorilla genomes.


(Matthew Pevarnik) #170

I think your questions is a fair one though will a mildly strawmanish interpolation. To begin, as @T_aquaticus already mentioned, there are many reasons why the ERV fixation rate would not be constant over time. In fact, here is a good reason as to why the rate should be decreasing:

If we look at the oldest identified ERV (this might be even older but here is a fine age for a different sort of calculation):

This has a minimum age of 104-110 million years and for sure is shared between many mammals. Let’s say ERV accumulation began in the mammalian line around then. To get to 200,000 shared ERVs this is an average insertion every 500 years or so. As noted by @Cornelius_Hunter above and the pop-sci article I just shared, humans have several mechanisms that help prevent the further fixation of ERVs, including previous ERVs! Thus the rate of fixation should decrease over time and thus the average rate for fixation in our lineage (after splitting with chimpanzees) is quite a bit longer than previous rates (to get 200,000 shared ERVs).

For your argument to be valid, you would have to demonstrate that it is reasonable to infer (as all the evidence we have points otherwise) that the rate has been constant for the past 100,000,000 years at the very least.


(Cornelius_Hunter) #171

Seriously, this again? What exactly is it about evolutionists and the evidence? Here is what the paper says about the lack of endemic infectious retroviruses:


(Matthew Pevarnik) #172

Cornelius,

I’ve asked you multiple times to elaborate on this topic- there are some 200,000 shared ERVs. Some 300 unique to the chimpanzee line and some 100 unique to the human line. Which ERVs were purged or what did the authors then mean by purged in light of these facts.


(T J Runyon) #173

People like you are why I’ve lost so much interest in the origins conversation. You are so pretentious, pompous, and just rude. Please practice some humility. I’m trying to learn something from these two threads but I can’t because of your behavior. Just stop.


(Cornelius_Hunter) #174

Always interesting to be interrogated by an evolutionist about his theory. It’s your theory, not mine. There is no scientific evidence of any purging. This is all driven by your theory. It is based on the idea that the entire biological world arose spontaneously (by law and chance, or the equivalent thereof), and that a rudimentary primate morphed into a human because of a few percent of the DNA changing. I’m sorry, but there is no scientific evidence that this is possible. That is not bluster, it is the science.

But assuming that is true, you need to figure something out about the missing endemic infectious retroviruses, in the other hominids, but not in the human lineage. They must have been inherited according to your theory. And they then must have gone away (hence “purged”). And yet today we have SFVs and SIVs. This makes no sense. A whole bunch of endemic infectious retroviruses, in the other hominids, must have been purged. Don’t shoot the messenger.


(Cornelius_Hunter) #175

We report, you decide.


(Matthew Pevarnik) #176

You continually make sweeping broad claims and statements that make sense in your mind, but don’t actually follow from what we are looking at. Here are a few broad statements that you made just now for example that have nothing to do with the question at hand:

All together, it makes me question where you actually do understand evolution in the first place as I have never read any actual biologist phrase things these ways. The Biological world arose spontaneously? Are you speaking of questions of abiogenesis or what do you mean here? A primate morphed into a human? Have you been watching x-men to learn about evolutionary biology? In which case yeah, I’d have to agree that there is no scientific evidence that any creature ever arose spontaneously and a primate woke up after being bitten by a radioactive spider.

Let’s clear something up here. Silly me. I thought you were trying to argue that the vast number of ERVs that we’ve been discussing that do indicate very strong signals for common descent were part of this problem. What’s the problem with an endemic retrovirus being purged now and what does this have anything to do with common descent? Why is it so hard to believe that a population/group that got isolated effectively removed a virus from the population?

We can be infected by them today, but how about this story from the black death in medieval Europe:
https://www.nature.com/news/2005/050307/full/news050307-15.html

No Cornelius, they are not inherited the same way. Here’s an example from modern human retroviruses:

HTLV-l is endemic in southwestern Japan, the Caribbean basin, southeastern United States, southern Italy, and sub-Saharan Africa. Up to 15 percent of normal blood donors in endemic areas of Japan and the Caribbean basin are positive for antibodies to HTLV-l; in nonendemic areas, fewer than 1 percent are positive. Data for HTLV-2 are incomplete. HTLVs can be transmitted by transfusion of blood from infected donors, by sexual contact, and from mothers to babies via breast milk.

Over time, it is possible though for such retroviruses to become fixed in a population when they infect meiotic cells. Since most ERV of this sort do nothing, they are just simply subject to the typical mutation rate over time and these are the ERVs that we are looking at for CD. This is very different from an endemic retrovirus like HTLV that is passed on via fluid contact. Thus for humans to be ‘purged’ of SFVs, it would be equivalent to the HTLV endemic being effectively eliminated from the population with the only remnants being perhaps some genetic ‘scars’ so to speak.

I’m not terribly grumpy at the moment but must take out my contacts or that could change.


(Chris Falter) #177

As a casual observer, I would hypothesize that the other hominids did not lose sialic acid N-glycolylneuraminic acid, unlike the human lineage. As you yourself quoted:

But there may be better hypotheses. Like I said, I’m just a casual observer.

Chris

P.S. The one thing I don’t understand in this conversation is that you are challenging those who disagree with you to supply a testable hypothesis for the “purge” of endemic viruses, yet the paper you are quoting has already supplied that hypothesis. :man_shrugging:


(Cornelius_Hunter) #178

I do.

Well can you blame evolutionists for not admitting they believe the biological world arose spontaneously?

Natural selection, cladogenesis, anagenesis, drift, sexual selection, etc., are all mechanisms which can come and go as needed. They are not core to the theory. But evolution does hold that naturalistic processes are sufficient to explain the origins of the species, as well as everything else for that matter. IOW, the world arose spontaneously. There were no external inputs, at least that are observable. If you don’t like the scientific terminology, I’ll be happy to use other terms more to your liking. But that won’t change anything about evolutionary thought. And if you want to claim I’m playing word games, you would simply be judging your side, as I’m not the one playing word games. Evolutionists disagree about a great many things, but not that there were no observable external inputs. Naturalistic processes must be sufficient. This goes back long before Darwin, and was increasingly influential in his day. As Desmond and Moore put it, the “lawful” approach was carrying the day. Today, you can float a lot of wild hypotheses about origins, but not external inputs. Those are the ground rules.

Hmmm. Project evolutionary beliefs onto me, and then suggest that I am the one who is projecting.


(Matthew Pevarnik) #179

If you could at least address the ERV portion too that’d be great…

Thanks for clarifying what you meant by spontaneously- and yes indeed it does hold that the natural processes that we know, are learning about and will learn about are sufficient to account for the origins of species. I would never use the word spontaneous in this case as it’s quite vague what ‘without external input’ can actually mean.

As in without the direct supernatural involvement of God, well sure but as a creationist who acknowledges the sufficiency of the natural laws that God is actively sustaining past, present and future- I’m not so sure about the notion of spontaneous as I’d acknowledge the active and constant involvement of an external input.

Do you think so? Or maybe it’s just that one cannot actually detect the supernatural’s involvement in any experiment ever. Let’s say I do some of my Biophysics research. I measure a sigmoidal voltage gating curve after attaching a molecule with a pKa value of 8.2. In my paper, I work tirelessly to figure out what is happening and why actually using this philosophy that ‘natural processes must be sufficient.’ After some more data anyalysis and numerical modeling, I’ve got my answer, ‘I can’t explain this and God is opening and closing my channel.’ I cry foul and persecution when the reviewers challenge my conclusions, saying they are unfounded and unsupported. After all, they are just evolutionists who believe natural processes must be sufficient.

I’ll delete that part how about that- I misunderstood what you meant by spontaneous.


#180

i actually talking about retrovirus that got its genes from the host. have you heard about the escape theory?


(Matthew Pevarnik) #181

How do theories on the origin of viruses relate to this thread at all especially with regards to the strong evidence that ERVs provide for common descent?


#182

If escape theory is true then this occurred well before animals evolved and well before the ERVs scientists are looking at invaded the genomes we are looking at. Escape theory can’t explain the ERVs shared by primates.

"The first viruses probably originated in a world of cells already harbouring ribosomes (ribocells), but well before the Last Universal Common Ancestor of modern cells (LUCA). Several viral lineages originated independently by transformation of ribocells into virocells (cells producing virions). Viral genomes originated from ancestral chromosomes of ribocells and virions from micro-compartments, nucleoprotein complexes or membrane vesicles present in ancient ribocells. "
Forterre and Krupovic (2012)


(Chris) #183

On the other hand you would have to demonstrate that it is reasonable to infer (from the numbers you’ve given) at least a 40 fold decrease in the rate at which they accumulate. I don’t think this is reasonable without additional evidence.


(Chris) #184

Is this correct? Only 16 of 200,000 are in identical locations?


(Chris Falter) #185

Hi Chris,

It’s the opposite. The word “not” should be in the sentence for it to read accurately.

Grace and peace,
Chris Falter


(Chris Falter) #186

That’s a fair point. But there is a hypothesis available to be tested: the other hominids did not lose sialic acid N-glycolylneuraminic acid, unlike the human lineage.

Presumably someone is gathering evidence about this plausible hypothesis, and will be presenting it in a peer-reviewed journal.

Best,
Chris Falter


(Stephen Matheson) #187

Are you claiming that we don’t have a mechanism for the loss of a genetic element from a lineage? Because that’s so far from true that it couldn’t have been written by a person with basic knowledge of genetics.

It’s interesting that they put ‘purged’ in scare quotes. I think I know why. (BTW, for others trying to follow this thread, the quote comes from a comprehensive review article, by top experts in the field, on “Explaining human uniqueness: genome interactions with environment, behaviour and culture.”)

In Box 3, the authors are considering the hypothesis that ERVs of a specific type were present in a lineage preceding humans but were then removed. They are trying to explain why humans don’t have these ERVs but related lineages do. Cornelius Hunter gets this much right: that there are ERVs in humans, indeed a whole particular class of them, that are missing from our relatives, and this is the kind of observation that requires a specific explanation. He quotes the authors writing that “there seems to have been an episode in which the ancestral human lineage was somehow ‘purged’ of these endemic viruses.” Then he claims we have no mechanism for this.

The word ‘purging’ should have been a big clue to the first mechanism that would be considered. It’s a mechanism so basic that it dates to Darwin: natural selection. Specifically this would probably be a case of purifying selection, but definitely negative selection. The authors are using ‘purging’ in scare quotes because that term is used to signify purifying selection and I suspect they didn’t want to be so specific. They are simply saying that one possibility is that this class of ERVs was present in ancestral genomes, but then were subjected to negative selection.

If we postulate strong negative selection against some kind of genetic element, then all we need is some mechanism(s) to generate versions of the genome that lack those genetic elements. And that’s easy. To explain the absence of those elements, the mechanisms are called deletions, and they’re ubiquitous, and no one with basic knowledge of genetics is unaware of them.

But the authors do not seem to prefer that hypothesis. Instead they propose the testable hypothesis that these particular infectious ERVs could not get access to humans because humans jettisoned a required element for viral spread. That’s a simple, straightforward, testable hypothesis that does not involve purging of mutations or insertions.

In either case, the mechanisms we would consider are well known, based on established biology. This doesn’t mean that we always know what happened in a very interesting case like this. It does mean that readers should always – ALWAYS – be suspicious of apologetic claims about things we “don’t have a mechanism for.” Such claims tend to be purged, quickly, from scholarly discourse.