Uncommon or Common Descent?

(Intelligent Design Deist) #70

Yes. Dr Spetner introduced “built-in response to environmental cues” as one possible design evolutionary mechanism- that was back in 1997.

I envisage the designer using real genetic algorithms for protein coding genes, overlapping genes and alternative splicing.

(Mark M Moore) #71

I see some gray areas on that- particularly if we live in a universe fit for beings like us. Even if we want to do God’s will, even if their are mechanisms for us to do it, we can’t seem to pull it off without His further intervention.

(Jon Garvey) #72

At the same time, since even human design, in its strict sense, is not mechanical (we never include the “nechanism of thought” in considering human design), the ID proposition is also strictly speaking orthogonal to mechanism.

That’s why, given an assumption of design in the living species we see, ie that they originated as a plan in the mind of God, say, then the instantiation of design could have occurred by any number of mechanisms. As Asa Gray said when discussion the mechanism even of Darwinian evolution, “It leaves the design question entirely as it was before”.

That’s analogous to the human situation, too: I compose a tune (non-mechanically, in my mind), and I can hum it, play it on a tuba, write it in manuscript so some other tuba player can play it, code it for a synthesizer etc.

In biology, only one set of mechanisms was involved - ie science can help show how God put the design into life. But the design itself remains outside that, unless one conceives of a God designing by trial and error using prototypoes. Evolution, of course, can be interpreted in such a way, but it’s not inevitable; and as Gray showed, if the darwinian mechanism covered the facts, then it would leave the design question open.

Of course, we now know it doesn’t cover the facts, because of the predominance of neutral evolution and all the rest - making “mechanism” even less tractable.

(George) #73


This is a red herring.

It doesn’t matter how many types of factors are involved in common descent… it is only necessary that each new generation can be satisfactorily analysed to confirm or deny descent.

(Ashwin S) #74

Hi Dr @swamidass,
I found this comment of yours very interesting. Yet we have people like Dr Theobald at talk origins essentially saying the opposite.

He claims that nested clades is a prediction and proof of common descent. So what’s going on here?

You stated that common descent is a design princliple. Is that a theological conviction or a scientific statement? Scientists don’t usually refer to common descent that way. There seems to be a fundamental difference between how you define common descent and how scientists like Dr Theobald do. Can you share your definition?

(T J Runyon) #75

Notice how @swamidass said PERFECT trees.

(Ashwin S) #76

I noticed that. However, a pattern of gradual change in which new species are formed by bifurcation from an existing species should lead to perfect nested clades…
I am interested in knowing what kind of common descent leads to the observed pattern. And if this is a prediction of evolution or an observation which can be explained by various mechanisms of change.
And of course whether Dr Swamidass agrees with Dr Theobald’s definition of common descent and the claims and arguments in the link posted.
Do you feel that’s an unfair question?

(T J Runyon) #77

No it shouldn’t . @swamidass made a compelling point in another thread, and I’m ashamed I never thought of it as a control and a rebuttal to the conflicting tree arguments, since I’m aware of the data he mentioned because of my archaeogenetic studies.

“I can produce strong evidence that human diversity does not follow a tree, even though we all agree it arises from a process of common descent. That is de facto evidence that common descent does not produce DNA that fits a tree perfectly.”

This is a great point. Everyone agrees that the diversity we see among humans is a result of common descent. But this data doesn’t form a perfect tree.

(T J Runyon) #78

Here is one study he linked to.

(Ashwin S) #79

That proves my point.
Common descent in human beings is a kind of hybridisation.
We are a product of a male and female with unique and distinct genomes cross fertilising. This will obviously produce a pattern that is different from a scenario in which a new species arises from an existing species over time through gradual changes.

Are you suggesting that hybridisation has a big role in speciation?
Edit: You must realise this is very different from the scenario people like Theobald talk about…

(Paul A Nelson) #80

Theobald’s (2010) definition of “common descent” is actually highly counterintuitive:

"…UCA [universal common ancestry] does not demand that the last universal common ancestor was a single organism, in accord with the traditional evolutionary view that common ancestors of species are groups, not individuals. Rather, the last universal common ancestor may have comprised a population of organisms with different genotypes that lived in different places at different times."

(emphasis added)

From here: https://www.nature.com/articles/nature09014

(Ashwin S) #81

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?

(Bill Cole) #82

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.

(Ashwin S) #83

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.

(Bill Cole) #84

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.

(S. Joshua Swamidass) #85

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.

(S. Joshua Swamidass) #86

@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.

(T J Runyon) #87

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.

(S. Joshua Swamidass) #88

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.

(Ashwin S) #89

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.