Uncommon or Common Descent?

What I like about Theobald is that he atleast tries to define what he means by common ancestry and then tries to verify it. I appreciate that.
I have also come across some papers criticising Theobald’s paper. Esp with respect to his null hypothesis and an inherent bias in his test itself.
What I was curious about was how @swamidass defines common ancestry. Different people seem to define the idea differently as far as I am able to find out. And that leaves me wondering whether common ancestry is one theory… or a word to describe many different ideas/hypothesis.

I don’t see why anyone would call such a group of organisms common anything…
Is it a semantics issue?

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I know of at least two. Universal common ancestry and common ancestry that does not claim common ancestry for all living organisms. No one has a reasonable explanation for the transition from prokaryotic cells to eukaryotic cells so that stops universal common descent at the base of the tree.

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How does the second option work? Can you point me to any literature on this?

As I understand, there are theories that the first eukaryote cell was formed by the combination of a eubacteria and a archaebacteria… Though it isn’t how common descent is explained classically, doesn’t it count as some kind of descent?
Can you explain what you are saying. It definitely sounds interesting.

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The original Theobald paper you cited was not supporting universal common descent but showing evidence of common descent among multicellular organisms. His 2010 paper was an attempt to support UCD.

[quote]As I understand, there are theories that the first eukaryote cell was formed by the combination of a eubacteria and a archaebacteria… Though it how common descent is explained classically, doesn’t it count as some kind of descent?
Can you explain what you are saying. It definitely sounds interesting.[/quote]

There are theories such as endosymbiosis that try to explain this transition however in reality they explain very little. What they don’t explain are very large innovations not present in prokaryotic cells.
-the spliceosome which is made up of 200 large proteins and the introns it splices out of MRNA.
-alternative splicing
-the nuclear pore complex manages the journey in and out of the nucleus
-the ubiquitin system which manages variable celled division that is mission critical for multicellular organisms
-chromosome structure that manages large amounts of DNA.

I could argue that this transition is a bigger miracle then the origin of life if you look at the additional functional information it requires.

In context, it is a theological statement.

What is going on is that he is imprecisely stating the evidence such that greatly confuses the conversation. Not all features fall into nested clades, because some features evolve rapidly (e.g. color of hair); these are phylogenetically uninformative features. Moreover, even features that evolve slowly, we still expect violations of nested clades by a whole host of well understood mechanisms.

The overall pattern is nested clades for higher level animals (like mammals), but that does not mean there are no exceptions. Mathematical modeling of common descent also predicts there will be violations of nested trees. This an observation correctly made by the young earth creationist Walter Remine, so it is hardly a rescue mechanism for evolution. It is just a brute fact of the theory.

Nope. That is not the case. Incomplete sorting, convergent evolution, and the birthday paradox are all mechanisms that will break the pattern of a tree.

Exactly right.

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@colewd and @EricMH thanks for your patience. I’m sorry I was delayed.

It is correct that these are log units, but the interpretation is incorrect. We are supposed to compute percentages in log space, not as you are doing here. One reason is that even small errors in the dataset (especially if the dataset is large) will artificially increase the error (the magnitude of the Bayes factor) by a linear factor. Just increasing the size of a noisy database will increase the error. There is a lot more here, but at the end I’ll show how @Winston_Ewert responded on the main thread.

I’m unfamiliar with that rule. @Winston_Ewert provides no reference. A google search for “6.6 bits” reveals nothing relevant. He might have mispoken there.

Any how, the general question came up in the main thread…

It appears that @Winston_Ewert agrees with me here.

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No I’m not suggesting that. But it does happen. A lot in plants. So wouldn’t that cause a little conflict in the trees? And I think the point about the human diversity data is, and correct me if I’m wrong here @swamidass, that here is an example of common descent that doesn’t form a perfect tree. Why? Because of various mechanisms. So I think that shows common descent doesn’t predict perfect trees because there are mechanisms, and @swamidass just listed some above me, that are explainable and actually predicted that can cause some conflict.

So, I went back to his original table and computed the percentage for all the lines. The situation improves a bit.

Data Dependency Graph Tree Difference Percent
UniRef-50 6,193,801 6,308,988 111,823 1.8%
OrthoDB 9,214,606 9,730,055 515,450 5.3%
Ensembl 875,350 962,274 86,924 9.0%
TreeFam 1,362,985 1,403,952 40,967 2.9%
Hogenom 884,815 1,022,243 137,428 13.4%
EggNOG 1,497,174 1,579,650 82,476 5.2%
Pfam 1,173,599 1,251,841 78,244 6.3%
OMA 3,265,608 3,451,745 184,777 5.4%
HomoloGene 106,010 116,080 10,064 8.7%

Okay, so it looks like there is a large range between different databases. That is good in one sense for @Winston_Ewert, because if he can justify some of the higher numbers he has an improved case. However, the variance raises questions too. It might be that this number is primarily determined by the intrinsic error of each database. It is hard to know from the table alone. I’ll look forward to see how he responds.

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Ok. Fair enough.
So what would it take to falsify common descent?
Back at Biologos, I wasted a lot of time with guys who claimed nested heirarchies were proof of “common descent”.
And no one has offered a statement of exactly what they mean by common descent.
Is it just that this idea is better than seperate ancestry (which I understand to be the null hypothesis). Why should a non scientist consider common descent fits the data better than special creation.After all scientists don’t even consider special creation as a possibility (probably because they can’t test for it).
I am an engineer. So I am not surprised that all organisms use similar basic systems. Its the only way to design an eco system. For example, engineers have standards sizes of nuts or bolts which they use in their designs.(The purpose is to make spares easily available).We use the same engine in different models of cars as much as possible. Its not a matter of creativity, its a matter of economy of scale/making spares available easily.
So all life being DNA based would be a requisite of design. Because an ecosystem is being designed as opposed to individual organisms.Even humans and chimps having very similar genetic make up shouldn’t be a problem.

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Ok fair enough.
I recently read a peer reviewed paper where a bunch of scientists were pushing for panspermia… Basically theorising that DNA from space seeded the biosphere with all the innovation required (for example the Cambrian explosion, octopuses and what not).
Their basic contention is that all these organisms appeared suddenly and enough time was not there for them to evolve.
So you have some company there with respect to skepticim of evolution… Though their solution is kinda crazy.
I really don’t see why some versions of special creation cannot be published if stuff like panspermia can be.

Common descent is the hypothesis that a set of distinct species today share ancestors in the distant past. That is it.

From there, it different more specified hypothesis can be offered. For example, we can test if “chimpanzees and humans” share common ancestors; this is the “common descent of man”. We can also assert or wonder if “all life on earth today” shares common ancestors; this is “universal common descent.”

We, here at Peaceful Science, focus in on the common descent of man. No one cares whether bacteria share a common ancestor. A lot of people care whether humans and chimps share a common ancestors. Here, also, the evidence is much much stronger.

Does that help?

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Yeah but that paper has taken a beating and actually has been laughed at. Philosopher of biology Peter Godfrey Smith discusses it here: http://metazoan.net/63-octopuses-not-from-space/

We covered that here too: Octopus not an Alien.

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Oh yeah! Forgot about that thread

What’s the big fuss about it then? I am sure even some YEC guys would affirm that a set of distinct species share ancestors in the past… (of course they wouldn’t agree for UCD, and stop at the point where they define kinds).
And the other contention is regarding how novelty arises. Suppose God used viruses to change how genes are regulated and created new species in some cases. Why should it be called common descent? After all the focus should be on the vehicle of change. Why not viral descent? Or natural genetic engineering? Or unnatural genetic engineering if you happen to be a creationist… the point is, there are mechanisms in which descent becomes trivial to the evolutionary event.
In such cases, would you agree to call it something else?

I am sure some people care.I certainly do.I find theories on bacterial evolution fascinating. I am sure there is a lot we can learn about how unicellular organisms evolve that can inform us about human evolution. The big picture is always important.

I am trying to go through this stuff. What bugs me about the human evolution story is the difference between when civilisation arose and human beings emerged. I find it very difficult to assume that “modern humans” were around for hundreds of thousands of years while civilisation started out only about 20000 years ago.

Yes it does help…

My point is that it was published. So why not the same treatment for special creation or ID. Publish and then discuss/trash etc.
Afterall the arguments are similar. The only difference seems to be philosophical implications connected to the conclusions.

The big fuss has always been about the common descent of man.

That is all independent of common descent.

Sure, but there isn’t durable conflict here. We can certainly talk about bacterial evolution, and we do.

Have you seen the Genealogical Adam yet? This solves the problem.

If common descent becomes compatible with any mechanism … wouldn’t that make the idea itself useless in terms of explaining anything?

I have gone through Genealogical Adam. It doesn’t solve the problem. Unless you are claiming Adam was superior in intelligence or had some other special quality that kickstarted civilisation.In which case, you are arguing against the common descent of modern humans.(atleast with respect to he qualities that make us different from animals).

A lot of that has to due with environmental factors. Ice ages etc. if you are interested in discussing this more I can split it into a new topic

You mean something like the tree of knowledge? Oh wait, he had that…

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