Alternatives to Modern Evolutionary Theory

i think that most people will disagree with this option. dont you think?

true. but we cant do that for almost all of them (if not all of them), since its suppose to happen millions of years ago. see the problem? you need to believe that these are indeed viral insertions. we cant prove this notion. and by the way; what kind of evidence will falsify your claim about ervs? what if we will find an erv that is shared between say gorila and chimp but not human?

I don’t see how what most people think is a reliable guide to truth. For most of human history, the majority of people have believed falsehoods. We do science to discover what is true, not opinion polls.

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They exist in the modern age where we can empirically measure them.

We have an observed and empirically measurable mechanism that produces ERV’s, no belief needed. We can observe retroviruses producing new insertions. Do we have the same for your supposed designer? No. So which one requires belief?

What would falsify common descent is a lack of a statistically significant phylogenetic signal in the ERV data. As with nearly all scientific tests and natural processes, there is noise. Things like incomplete lineage sorting can produce ERV insertions that violate the expected tree. However, ERV’s that don’t match the predicted outcome, the noise, should be swamped by the ERV’s that do match the predicted outcome, the signal. We test for noise and signal using statistics.

An analogy would be the link between lung cancer and smoking. Many studies have shown that smoking increases your risk of getting lung cancer. However, there are people who smoke who never get lung cancer and there are people who never smoke and get lung cancer. Does this falsify the link between the two? No. When we apply statistics we find that smokers have a much higher rate of lung cancer than non-smokers. This is the signal that sticks out above the noise. This is how hypothesis testing works in science.

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but you cant do that for an old erv (say a million years old). so basically we have no empirical evidence for almost any erv.

again: we have the opposite too. we can see that a retrovirus can be created from host parts. so even without any designer in the picture we just need to assume that these are indeed viral insnertions and not the opposite.

so how many shared ervs we should find to falsify the theory? say that gorila shared more ervs with a chimp then with human. do you think that such a situation will falsify evolution? if so why?

and you should also explain this interesting finding:

https://jvi.asm.org/content/77/7/3893

That’s where we do an inference to the best explanation. They are found in sequences increasingly similar to retroviral sequences at all stages of degradation, they are distributed in nesting hiearchical patterns, and the mutations that have accumulated in them are highly significantly consilient with trees from countless other independent lines of investigation. The only explanation that makes sense of this totality of facts is that they really are retroviral insertions that have accumulated over geological time and been passed on into different lineages.

you need to believe that these are indeed viral insertions. we cant prove this notion.

We don’t need to PROVE it. Once again, we are dealing with a case of some explanations making more sense than others. I believe I already explained this at length in this post:

Common descent is a much better explanation for the patterns in how ERVs are distributed in different species, and the patterns in their sequences, than any competing explanation.

and by the way; what kind of evidence will falsify your claim about ervs?

Anti-hierarchical structure in their distribution and sequences.

what if we will find an erv that is shared between say gorila and chimp but not human?

There probably are such ERV insertions shared between gorilla and chimp due to incomplete lineage sorting. But for reasons that should become clear if you read and understand the article I linked, the mere existence of a shared ERV insertion between Chimp and Gorilla, but not humans, will not be a problem for evolution.

So we can see a modern virus insert a sequence all but identical to ERVs, and we can subsequently monitor how such an observed viral insertion can accumulate mutations over time, and be passed on in tree patterns in splitting lines of descent.

So when we find ERVs in living species and we find that they fall immediately into tree patterns with splitting lines of descent, and accumulate mutations as we go further back in time, how are we NOT to simply infer that they really are progressively older ERV insertions shared due to common descent?

What other explanation, based on a straightforward mechanism which we can also see operate in the present, explains their existence, nature, and distribution in known life?

Let me guess “The invisible magic man decided to produce them in exactly the pattern expected by common descent because he’s a bit of a trickster and likes to test our faith”? Why would you even TRY to convince yourself that God would deliberately PLANT the evidence for common descent?

God, planting evidence to trick investigators since 6000 AD? C’mon.

Also, but very rarely, ERVs can be exactly excised, leaving flanking sequences intact. Or two insertions can happen in exactly the same place. But lineage sorting is much more common.

@scd

You seem impervious to instruction. This has been explained any number of times:

If ERVs (or any unique genetic string) follows a random pattern of transmission… so that the pattern is inconsistent with common descent from mutual ancestors… but shows a mostly random appearance of thousands of ERVs all across animal classes and orders…

… THAT is how you disprove Common Descent.

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see? when it fit with evolution you say that its evidence for evolution and when it doesnt fit we just call it “incomplete lineage sorting”. but it just an ad hoc explanation.

not realy:

" First, we examined the distribution of shared sites between species. We found that the distribution is inconsistent with the generally accepted phylogeny of catarrhine primates"

and:

“If these sites were truly orthologous and, thus, ancestral in the human/ape ancestor, it would require that at least six of these sites were deleted in the human lineage. Moreover, the same exact six sites would also have had to have been deleted in the orangutan lineage if the generally accepted phylogeny is correct.”

so when it doesnt fit it doesnt fit.

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@scd

Comprehension should be tested… and you have missed the point of the article. Just reading its title should give you a clue!

Here’s a key part if the abstract!:

" Phylogenetic analysis of the endogenous retrovirus reveals that the gorilla and chimpanzee elements share a monophyletic origin with a subset of the Old World monkey retroviral elements, but that the average sequence divergence exceeds neutral expectation for a strictly nuclear inherited DNA molecule. Within the chimpanzee, there is a significant integration bias against genes, with only 14 of these insertions mapping within intronic regions."

“Six out of ten of these genes, for which there are expression data, show significant differences in transcript expression between human and chimpanzee.”

[The Actual Conclusion] < @Scd,note!

"Our data are consistent with a retroviral infection that bombarded the genomes of chimpanzees and gorillas independently and concurrently, 3–4 million years ago [that did not include the bombardment of the human branch!-G.B.]

We speculate on the potential impact of such recent events on the evolution of humans and great apes."

No, incomplete lineage sorting is an unavoidable consequence of population dynamics playing themselves out in time and space. It is not ad-hoc. When you say that it really just reveals you didn’t read, or understand, the article I linked. You should be able to work out in your head how incomplete lineage sorting actually must necessarily follow from population mechanics working themselves out in time and space.

At any given moment there is non-uniform spatial distribution of alleles in the human population. Statistically speaking, people who are geographically closer together, are also more likely to be more closely related. That means if some chance event isolates a geographically restricted subsection of the population, it will NOT contain a perfectly mixed sample of all alleles present in the human population.

That means incomplete lineage sorting is unavoidable, even if creationism is true. Even if the human species was specially created, then within the human species there will be incomplete lineage sorting happening when different groups travel around the world and decide to settle new areas, islands, or what have you. And a creationist researcher wanting to try to work out how the different human lineages and genealogies have played themselves out over time, would have to explain the distributions of genes within the human population as a consequence of human migration patterns and genetic mutations resulting in incomplete lineage sorting.

Again, it is an unavoidable consequence of population dynamics, of how alleles move through populations over generations.

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The claim was not that ALL retroviral insertions were inherited by common descent. They can happen subsequently to speciation, independently in different lineages. After all, you can get a virus infection this very moment which can insert in your genome.

The claim is that SOME retroviral insertions are only rationally explained by common descent, not that ALL of them are.

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actually in this specific case the paper say nothing about ils. they just says that the accepted phylogeny can be wrong.

so when they fit to the suppose hierarchy they are evidence for a common descent, and when they arent they are still evidence for a common descent?.

@scd

This is getting monotonous.

All you have to do is show a genetic pattern that :

A] genes only found in fish are also in birds… but not in amphibians…

B] genes only found in birds are also in primates, but no other mammals…

C] genes only found in worms are also in giraffes, but nowhere else.

THIS is the kind of evidence you need to invalidate a scientific framework as successful and as comprehensive as Common Descent.

You cant disprove Common Descent based on one or two odd exceptions.

You need multiple and broad patterns of genetic findings that contradict the heart of Common Descent.

If it existed, we would have heard about it by now.

@colewd,

If you dont write ANY text… its difficult to use the quote tool.

Your article is fun… but it doesnt meet the criteria i set forth.

I said to find genes that are ONLY in fish and in humans… then you can legitimately ask: how did the fish genes get to humans by common descent?

I believe this article talks about genes common across a broad spectrum of animals!

The criteria you set forth ends the discussion. There is evidence that a slightly lesser criteria which is genes disappearing and re appearing in later lineages is true. 70 plus genes that are in Zebra Fish are not in birds and some mammals. This is not supportive of the universal common descent idea.

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It has been explained seemingly countless times to you that this is not what is occurring. Somehow you still persist in misunderstanding.

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On what basis do you know what caused this pattern?

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