Are Random mutations and Common Descent fundamentally intertwined processes?

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I have decided to hold off on updating my theory to find out whether random mutations automatically precludes Universal descent. I know natural selection is not necessarily synonymous with common descent but I thought it was different when it comes to the randomness of mutations.

I argued before that you cannot separate random mutations from common descent, Then, I pointed out that a biologist named Gert Korthof suggested the same thing in his book Why Intelligent Design Fails :

"Common descent of life means that all life on Earth is physically, historically, and genetically connected. Common descent of life means that life is one unbroken chain of ancestors and descendants. Common descent of life means that every organism inherited all its genes from the previous generation (with slight modifications). And that includes irreducibly complex systems. Every supernatural intervention is a violation of common descent, because it means that a new irreducibly complex system in the first individual showing it was not inherited from its parents. It would be unjustified to say, ‘I inherited all my chromosomes from my parents, except an irreducibly complex system on chromosome X, which has a supernatural origin.’

Common Descent: It’s All or Nothing (updated chapter) (wasdarwinw

However, in my discussions with @John_Harshman, he disagreed with him and made some comments arguing otherwise. This has prompted me to finally end the previous topic since it is a big reason why the common design model is supposed to be potentially useful and ,thus, continuing the conversation on the topic seemed pointless. More importantly, it has got me wondering whether this was more his opinion than fact.

I’ve done research on it and I found this article that seems to suggest Gert is right:

"do non-random mutations affect phylogenetic analysis? …

…This paper advances a new hypothesis to understand alignment of mutations in homologous DNA sequences of separated species as the result of a common mechanism operating in similar genomes, and provides the first biological evidence that the location where a mutation will occur and the type of mutation (transition or transversion) are largely predetermined. The consequence is that we may not be able to discriminate between common descent and this common mechanism."

(PDF) Shared mutations: Common descent or common mechanism? (researchgate.net)

Remarkably, there does not seem to be a lot of information or discussion on the subject outside this article.

So my question to all the biologists here is… Do you agree with @John_Harshman over Gert? If so, would you say there is a consensus on the matter that agrees with John?

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That article is by creationist Pieter Borger from a creationist “journal”. It’s not a legitimate scientific paper. You sure can pick 'em.

That’s because it’s a loony subject for which there is no real evidence and against which there is vast amounts. For one thing, we would not expect this alleged process to produce nested hierarchical data.

Seriously, you call that doing research? Just stop.

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Can you point out articles that support your contentions then or at least articles that discuss it?

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I’m afraid you have convinced me that it’s futile to engage with you. You don’t really read what anyone says. You’re not willing to.

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That’s not true, I have actually read alot of articles from @Michael_Okoko. Not all, of course, but the ones that were highly relevant to the topic. I don’t remember you ever providing any sources that support you assertions and there were many instances where you have steered away from the topic at hand.

It’s ok though. I identified why there is a disconnect in our conversation and I am waiting for other users to be the final arbiter

BTW, just because creationist journals are considered illegitimate scientific journals does not mean every paper they publish is automatically illegitimate just like not every journal that is considered to be legit always publishes legit papers.

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Do you and your siblings/cousins share a common ancestor? Do you think you each carry random mutations?

That’s false. Common descent would still be true for groups of species even if all species did not share a universal common ancestor. Even Darwin was open to the possibility that life could have separate ancestors.

Universal common descent is a conclusion based on the evidence, not a requirement of the theory of evolution. It just so happens that UCD is where the evidence led.

If non-random mutations were widespread then it would make the phylogenetic signal disappear. But the phylogenetic signal has not disappeared. It’s there. Therefore, the type of non-random mutations that your citation is discussing would have to be very limited and only apply in special cases.

What you need to remember is that we have reality to contend with. In reality, there is a strong phylogenetic signal. The tree-like structure in the genetic data is there. We also have observations of mutations happening in real time. These observations don’t go away.

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Then your memory is very bad.

True, but that’s the way to bet, and the one you cited is a clear example. He can’t even manage to spell “Futuyma”. It’s just a bunch of verbiage designed to impress people like you. If you disagree, stop just quoting assertions and present the evidence that favors his claim.

You should also explain why the paper’s conclusion actually supports your own claim, which is apparently that in order for common descent to be true, mutations must be random. Borger never addresses that claim at all, so once again you have quoted an irrelevant source that you don’t understand.

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Borrowing from Churchill . . . peer review is the worst possible method for publishing papers, except for all the others. Peer review is fallible, but its a step up from absolutely no peer review. By “peer” I mean people who do research and publish in the field that the author is writing about. The paper you cited is really no different than a blog post pretending to be a scientific paper.

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“Automatically,” no. In practice, yes.

But in any event, you should understand that if you intend to convince serious-minded people of a proposition, citing creationist materials is a complete non-starter. All creationist movements have failed completely in obtaining even the slightest bit of intellectual credibility. If you’re going to do right what they’ve done wrong, you need to discard all existing creationist work and start fresh.

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Here, let me pull a random paragraph from the primary source.

How many elementary errors of fact can you find in this?

  1. “When unstable atoms drop”??
  2. Beta radiation is characterized as “energy waves”.
  3. Alpha radiation is called “a hydrogen particle”.
  4. Mutation “destroys the information”.
  5. The assumption that in order to be random, mutation must have an equal probability of occurrence at all sites.

I really think I could have chosen any paragraph at all. Why, right in the next paragraph I find monazite referred to as an element. Sure, the majority of the errors don’t affect the main point, but they do demonstrate the author’s ignorance of the subjects he’s talking about. And the main point is equally in error.

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That’s probably the most relevant mistake. The randomness of mutations was established before the structure of DNA was known, so it was never about each base having the same chance of being mutated.

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I stayed out of your previous thread, because your earlier threads had persuaded me that you have nothing to offer. Perhaps I should have stayed out of this thread, too.

I think you are misunderstanding Gert Korthof. He is not discussing non-random mutations. He is discussing saltational mutations – mutations that introduce irreducible complexity in a single step.

If I am reading him correctly, he is arguing that we should not use the term “descent” when there is a saltational mutation. But that’s not a scientific argument. That’s a semantic argument. I’m inclined to disagree with Korthof on that semantic point. But it doesn’t much matter. The plain fact is that scientists are not finding any evidence of actual saltational mutations. Whether we should still it “common descent” in that case seems a moot point until there is convincing evidence that such mutations occur.

I think this brings out what so often goes wrong in these debates. Creationists want to argue semantics while scientists want to see actual evidence.

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I am a layman, not a biologist, but I’ll take a shot at this one.

  1. I take common descent of a particular group of organisms to mean that if you followed the lineage of every member of that group back, generation by generation, eventually all would meet at a single organism or population. Depending on what particular group of organisms a person is interested in, a person may investigate the common descent of all humans, all mammals, all animals, etc.

  2. I take universal common descent to mean that if you followed the lineage of every organism (living or dead) back, generation by generation, eventually all would meet at a single organism or population. Including dead organisms would bring extinct lineages into the picture.

    1. As each organism in the lineage is conceived (or born, or spored, or however reproduction occurs), there are some mutations in DNA of the new organism. Mutations are ways in which the DNA sequence of the new organism is not identical to the DNA sequence of its parent (or either parent, in sexual reproduction).
    1. Those mutations are random with respect to the needs of the organism, which is to say that no one has shown that they are, as a whole, more advantageous or more deleterious than would be expected if their nature and location were determined by chance.

I think each of those 4 items reflect the mainstream understanding of things. 4 might be a little iffy.

I think meerkat’s definition of a random mutation may be a mutation that was not caused by or influenced by some interfering intelligence.

Whether common descent and random mutation are intertwined depends on what you mean by intertwined and what you mean by random.

I think that common descent is not intertwined with random mutations by Meerkat’s definition of random. By that I mean that it would be possible to have common descent with no random mutations, and it would be possible to have only random mutations and not have common descent.

For example, if there were some original organism or population of organisms, and when those organisms reproduced through every following generation, all the mutations in the DNA of the descendants were chosen and induced by an interfering intelligence, there would be common descent and no random mutations.

And, if there were originally an “orchard” of organisms or populations of organisms, and when those organisms reproduced through every following generation, none of the mutations in the DNA of the descendants were chosen or induced by an interfering intelligence, there would not be (universal) common descent and there would be only random mutations.

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“Random with respect to fitness” is the best description. There are hotspots where the mutation rate is higher, so it isn’t random with respect to location.

The best analogy I have come up with is the game of craps. In the game you roll two dice and add them together. A 7 is much more common outcome than a 2 or 12, but the game is still random because the dice aren’t influenced by which bet the bettor is making. Putting a hundred bucks on hard 8 (i.e. four and four) doesn’t increase the probability of rolling a hard 8. The dice are blind to the chips on the table in the same way mutations are blind to the needs of the organism.

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Just for reference, Luria and Delbruck used their fluctuation test to evidence random mutations in this 1943 paper:

A good summary can be found here:

In 1943 I don’t think anyone even knew that DNA was a string of bases, and yet they were able to show that mutations were random.

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It isn’t iffy, but it isn’t part of the meaning of common descent. #3 isn’t either, though without mutations there would be no way to figure out common descent, and there would be only one species in the world.

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Yeah, by iffy I meant I was less sure about the accuracy of my description of that principle, not that the underlying principle was any less well supported.

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I forgot to show you guys the empirical basis of Gert’s argument that he presented. Here it is:

"It is true that CD is distinct from the mechanism of natural selection acting on random mutation. But are they independent? No. Maybe they were separate and independent at Darwin’s time, but not today. New scientific discoveries have revealed deep connections between previously unconnected theories. So, Mayr is simply not relevant for Behe’s argument…

…The link between mechanism and CD is much stronger than Behe realizes. Behe, unknowingly, presents evidence for the fact that CD and mechanism are closely interwoven in the chapter “What Darwinism Can Do”. Here are Behe’s proofs for Common Descent:

  • “Both humans and chimps have a broken copy of a gene that in other mammals helps make vitamin C.” (p.71)
  • “More compelling evidence for the shared ancestry of humans and other primates comes from (…) a broken hemoglobin gene.” (p.71)
  • “Although duplicated genes can be used to trace common ancestry” [yeast] (p.74)
    Please note that these examples are all based on random mutation. Behe describes these broken genes as “mutational mistakes”. So, Behe knows that “genetics has supported common descent”.

The nature of the evidence for CD is random mutation. Whatever his claims about the limitations of Darwinism, Behe uses cases of random mutation as evidence for CD. I think the connection between CD and Random Mutation and Natural Selection could be elaborated much more. Probably all DNA evidence for CD is based on random mutation supplemented with neutral evolution, genetic drift and horizontal gene transfer (5)"

This is what he cited as evidence (5):

  1. H. A. Orr (2003) “A minimum on the mean number of steps taken in adaptive walks.” Theor. Biol. 220:241-47.
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No they aren’t. Sure, the pseudogenes and duplications are the result of random mutation, but they would be evidence for common descent even if they weren’t. Gert hasn’t made his case, and you should stop trying to make your own case by quoting the bare assertions of other people.

It happens to be, but the evidence would be equally useful if it weren’t. Try again.

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Why? what’s wrong with relying on experts other than you?