An Amphibious Whale from the Middle Eocene of Peru Reveals Early South Pacific Dispersal of Quadrupedal Cetaceans

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21

I don’t know what you mean by “trivial sense”. You may be investing the term “common descent” with baggage that isn’t actually there.

Yes, and that’s a problem for you. If it isn’t a hypothesis, there’s no way to discuss it in a scientific context.

Depends on what you mean by both those terms. I agree that’s it’s possible for there to be created kinds within which but not between which common descent operates. But that just makes the claim too vague to consider unless you specify what the kinds are.

22

That’s a possibility. But I wasn’t referring to that.
What about those people who consider evolution itself as something used by God to create.
Why would you see creation and common descent as mutually exclusive?

Remember the paper by the guys who’s believe in panspermia? Even that scenario where viruses from space caused the Cambrian explosion is ok for common descent.
Its a big tent explanation that will incorporate any natural explanation
Hence it’s trivial in that sense. Accommodates all kinds of theories, but explains norhing.

23

That’s why I said “Depends on what you mean by both those terms.” Obviously, given that definition, creation and common descent are not mutually exclusive. But that isn’t what you think, so why bring it up? You really resist making your ideas clear.

And you are very confused about common descent and what it does and does not explain. Viruses from space are, essentially, mutations. Common descent doesn’t deal with the source of mutations, which could, if you like, be God as easily as space viruses. Common descent explains the pattern of distribution of similarities and differences among species, and it explains the stratigraphic patterns in the fossil record too, as well as various other patterns. Common descent is compatible with any source of mutations, and the nature of that source is not relevant to common descent.

24

I was trying to find out what you mean. Hence I asked for a clarification before making any assumptions.

I wonder if it falsifiable. What kind of pattern would falsify it?

If de-novo genes exist, would it falsify common descent?

25

Notice how I explained what I meant when asked? You should try that. Or perhaps it turns out that you don’t mean anything.

You are trying to distract me from your inability to articulate any sort of alternative. Typical creationist: it’s all about evolution being wrong, but that’s as far as it goes. It reminds me of the Trump position on health care: get rid of it now, and after the election we’ll come up with a much better replacement. But don’t ask about that now.

No. You’re still confused about the difference between common descent and the source of mutations.

26

Is that necessarily bad? I don’t have a better scientific hypothesis. But, I am not approaching it from a purely scientific stand point. I believe in miracles and allow for the same.
My problem with common descent is that it’s almost an axiom that results from assuming natural causes.
I have already explained why I think so.

So the first concern with an axiom is whether it can be falsified.

27

Absense of significant cladistic structure, and a significant amount of anti-cladistic structure in the data. See this: 29+ Evidences for Macroevolution: Part 1
Scroll down to “potential falsification”.

Absense of cladistic structure would make us unable to infer common descent, and anti-cladistic structure would contradict common descent.

If de-novo genes exist, would it falsify common descent?

No. After all, it could be that de novo genes evolved independently in different species, or that they were inserted by those famed space viruses, or even intelligent designers, into species that nevertheless share common descent.

28

You are very, very confused. Common descent isn’t an axiom. It isn’t even almost an axiom. It’s a conclusion from the data. If you had an alternative we could try to determine whether it fits the data better. But of course you don’t. We thus have nothing to talk about other than the nature of your confusion.

29

Any finding of a striking half-mammal, half-bird intermediate would be highly inconsistent with common descent. Many other examples of prohibited intermediates can be thought of, based on the standard tree

Are you talking about something like this?
Didn’t something like this happen with prokaryotes with the tree getting totally jumbled up?

Is that a falsification?

30

Edit: Yeah.

Didn’t something like this happen with prokaryotes with the tree getting totally jumbled up?

No. There has been a lot of horizontal gene transfer between prokaryotes, but not enough to actually fully erase significant tree-like structure in the data, and it isn’t anti-correlated.

There are certainly many gene families where the position of the roots can’t be resolved, or at least resolved with high certainty, but there are also gene families that clearly exhibit significant levels of tree-like structure, which are universally shared between all known life. Particularly genes encoding components of the translation system.

I think you’re also confusing two related but not identical issues, which is whether there is tree-like structure in the data, and the extent to which different data sets corroborate the same tree.

Some gene families have been changing at higher rates than others, so for some putatively very deep relationships signal that would make us able to infer common descent can be lost in those gene families. Other gene families change more slowly, and so for those more slowly changing gene families, their common relationship can still be clearly identified.

Is that a falsification?

Nope.

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31

Darwin already tackled this issue:

Side branches on the cetacean tree can still carry the transitional states found in the direct lineage.

32

To add to @Rumraket post, horizontal genetic transfer is very rare in eukaryotes so we shouldn’t see the same web-like structure in vertebrates that we see in prokaryotes.

33

To be more precise, approximately 5% of plant speciation is through hybridization, most often of close relatives. Still doesn’t obscure the tree.

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34

So the collapse of the “tree like” structure or various different trees which contradict each other doesn’t amount to a falsification…
If a reticulate tree cannot falsify common descent… then what can?

35

Is it your claim that a reticulate tree falsifies common descent? Or do you carefully avoid making any sort of claim about anything?

36

I don’t think anything can falsify common descent. Because it’s the only possible conclusion once natural causes are assumed.

But if it’s about patterns as you claim. Then prokaryote evolution could be called reticulate descent as much as common descent.
A tree like pattern is distinctly different from a web like pattern.

37

We would expect a noisy phylogenetic signal, so you would have to show how there is not a statistically significant phylogenetic signal.

Numerous and gross violations of the expected phylogeny. Species with mammary glands and feathers is a good example. Finding reticulation in closely related branches is expected, but it should be exceedingly rare in distantly related branches. All of this is couched in the language of statistics.

38

You’re wrong. It can be falsified. All you need to do is to demonstrate a lack of a statistically significant phylogenetic signal.

Just as we would expect since prokaryotes participate in both vertical and horizontal genetic transfer.

39

Actually it depends. How much do they contradict each other? It’s not that simple.

Suppose I have a hypothesis that your room temperature is 20,6783955 degrees C, I then give you two thermometers, and one measures your room temperature at 20,6782391 degrees C, and the other measures 20,6785441 degrees C.

Do they contradict each other? Yes. Do they “fit” my hypothesis? Well, not exactly. Have we falsified my hypothesis? Well, to what level of accuracy? Can we now believe that your room temperature is plausibly fifteen thousand degrees C, or minus 260?

I think we can say that there is a level of disagreement between both the thermometers, and my hypothesis, where we would start to have serious doubts about my hypothesis. But the level of disagreement between the individual measurements and my hypothesis doesn’t (yet) take us there.

Phylogenetic trees to the extent they aren’t identical, can be different from each other, in the sense that they can have incongruencies, which range from total, as in all branches are different, to one mismatching branch. And the relative degree of mismatch of some branches can also go from minor to large. There could be some doubt about whether we are most closely related to chimp or gorilla (say), or it could hypothetically be the case that the data implies we are most closely related to insects .

So it’s really not that simple. If you read the next section of the link I supplied, Prediction 1.3 consilience of independent phylogenies, the nature of the degree of corroboration of common descent is well explained, and compared to other scientific theories and their potential (dis)agreement with observation and measurement.

In science, independent measurements of theoretical values are never exact. When inferring any value (such as a physical constant like the charge of the electron, the mass of the proton, or the speed of light) some error always exists in the measurement, and all independent measurements are incongruent to some extent. Of course, the true value of something is never known for certain in science—all we have are measurements that we hope approximate the true value. Scientifically, then, the important relevant questions are “When comparing two measurements, how much of a discrepancy does it take to be a problem?” and “How close must the measurements be in order to give a strong confirmation?” Scientists answer these questions quantitatively with probability and statistics (Box 1978; Fisher 1990; Wadsworth 1997). To be scientifically rigorous we require statistical significance. Some measurements of a given value match with statistical significance (good), and some do not (bad), even though no measurements match exactly (reality).

(…)

“Biologists seem to seek the ‘The One Tree’ and appear not to be satisfied by a range of options. However, there is no logical difficulty in having a range of trees. There are 34,459,425 possible [unrooted] trees for 11 taxa (Penny et al . 1982), and to reduce this to the order of 10-50 trees is analogous to an accuracy of measurement of approximately one part in 106.” (Penny and Hendy 1986, p. 414)

40

Wouldn’t this only falsify individual trees?

You have reticulation in entire domains of life in bacteria.
The Evolution of the first eukaryote is also reticulate in nature. Photosynthesis too…
Recent studies show the importance of hybridisation in the evolution of some bird species, mosquuties., Etc.
What’s so special about mammary glands and bird feathers?

Fair enough. What’s the cut off below which a phylogenetic signal is not statistically significant.
And how can such methods be used to evaluate the entire tree as opposed to just branches.

Lastly, how did you arrive at the low statistical significance for an organism with both mammary glands and feathers?
Is there some calculation?