Side Comments on The Dependency Graph of Life

Comments

(S. Joshua Swamidass) #1

Continuing the discussion from Winston Ewert: The Dependency Graph of Life:

Side comments unrelated to the scientific conversation should be continued here. Do not be offended if your comments have been moved here. Peace.


Winston Ewert: The Dependency Graph of Life
(Guy Coe) #2

It would seem that his aim is not so much designed to reject common descent, but to improve the predictive paradigm therefrom, by positing an additional factor he calls “common design.”
To wit, from his concluding remarks:

Our hope is that this research is a large step forward in developing common design not as a critique of common descent, but as a research program which produces
testable models and increases our understanding of the biological world.

If this isn’t mere double-speak, it may be an actual innovation?


Winston Ewert: The Dependency Graph of Life
(Guy Coe) #3

May I say that it’s this kind of exchange that makes me enjoy being a Christian? Two good men who obviously love God and want to do the best science they can to glorify Him. Though from different sides of an aisle, they both sit in the same sanctuary/cathedral, willingly offering mutual assistance. Godspeed to you both!


(Guy Coe) #4

I’ll make that three good men. May God increase your fellowship.


(T J Runyon) #5

I second this. I was aware of @Winston_Ewert but have never spoken to him. Very gracious. These conversations are enjoyable when you have people like Winston and @Agauger, who sent me a lovely message checking up on my health, on the other side of the aisle.


(S. Joshua Swamidass) #6

I agree. I’m also glad @Cornelius_Hunter joined, and hope he is willing to engage on his own thread, or even back on the main one, with some helpful information.


(Guy Coe) #7

A very real privilege, and please do return and contribute in whatever way you feel led to. We are all learning from one another here.


Winston Ewert: The Dependency Graph of Life
(Guy Coe) #8

So, this is more than a “rose by any other name” kind of argument? Will try to peruse it myself. Thanks, Josh, and Dr. Ewert!


Winston Ewert: The Dependency Graph of Life
(S. Joshua Swamidass) #9

Someone at DI should tell @Cornelius_Hunter to back off. He is not helping @Winston_Ewert.

This is legitimate enough that it should not be pushed as polemics. Let the honest scientists outside ID take a look and assess. It will take some time. I will be fair. This is a legitimate proposal, even if it ultimately does not pan out.

@cwhenderson, what do you think of it?


(S. Joshua Swamidass) #10

As I said, they have NOT actually engaged the strong evidence for common descent.

They are engaging one type of weaker evidence, nested clades. They may (though I have not verified) have a plausible advance, but I have several key scientific questions. If Ewert want’s a fair hearing, he will get it here. I do, however, have some questions. I do have a critique. I’m not sure he made his case yet.


(S. Joshua Swamidass) #11

Related news on the original article are here. Two from ENV and one from Uncommon Descent. Of note, @Winston_Ewert’s paper and conversation with us was professional and with appropriate cautiousness. I’m not sure the news stories are helping them. The contrast is strong.

https://evolutionnews.org/2018/07/bio-complexity-presents-a-better-model-than-common-ancestry-for-explaining-the-pattern-of-nature/

https://evolutionnews.org/2018/07/new-paper-by-winston-ewert-demonstrates-superiority-of-design-model/


(S. Joshua Swamidass) #12

@Winston_Ewert I was thinking about this a bit, and I think it is in error. Data in a perfect nested clades will fit a tree. Data not in perfect nested clades (I’m nearly certain) will usually be a better fit in a directed graph. The Birthday Paradox means that random inactivations will reliably create violations of nested clades, which will then fit better in a directed graph.

It is possible I am wrong, and I’m close to 80% sure I’m not. I’d have to think for a while to see the type of control experiments you could run to settle this…


(S. Joshua Swamidass) #13

Entertaning quote about this from @AMWolfe.

I think overall what I see is that Dr. Ewert has offered the tentative beginnings of a research program, and he has admirably entered the ring to test it, and you have lifted up his arm and declared him the undisputed winner by KO before the fight has even really begun.
https://discourse.biologos.org/t/new-paper-demonstrates-superiority-of-design-model/39018/131?u=swamidass

The “you” here is @Cornelius_Hunter. Unfortunately, also, he is equivocating a perfect tree for common descent, forgetting all the lessons ReMine has to offer.


Uncommon or Common Descent?
(S. Joshua Swamidass) #14

@bob_o_hara, I saw your comment on Uncommon Descent. Welcome to Peaceful Science. You can continue the conversation here, or even start a new thread. Peace.

Thanks for setting up a dialogue, but it would help if you didn’t then close it! The discussion started by @sygarte on Table 4 contains several mis-understandings of what Bayes Factors are. FWIW, when I saw Table 4 my reaction was that the values are barely plausible: some are several orders of magnitude larger than any other (log-)Bayes Factor I’ve seen.

I’d be curious why you object to my explanation.

Do you disagree?


(S. Joshua Swamidass) #15

3 posts were merged into an existing topic: Uncommon Descent questions Common Descent


(S. Joshua Swamidass) #16

New article from ENV references our comments:

https://evolutionnews.org/2018/07/response-to-a-critic-but-what-about-undirected-graphs/


#17

Another side question…

Is time considered in the dependency graph work?

The idea of common descent isn’t merely about a grouping pattern but includes a temporal component as well. Single-celled organisms preceded multicellular life. Invertebrates appeared before vertebrates. Therapsids and Synapsids preceded mammals, & etc. A priori, from a design viewpoint, the temporal appearance of various groups did not have to occur this way.

And, compared to other factors, the time since apparent divergence correlates reasonable well with sequence variation. If one interprets the “dependency graph pattern” as arising from a designer, how does that mesh with the temporal patterns and relationships that are also in the data?


(Jon Garvey) #18

Without second guessing Ewert’s own way of thinking about this, it would appear that he’s talking about the re-use of modules to modify existing forms (whether those forms are the physical manifestations or some kind of informational blueprint, as in the old Owen or Agassiz shemes, is another matter).

In other words there is some kind of chronological ordering presupposed in it.

The same could be true in other design views based on less fashionable philosophies. For example, on the principle of plenitude held by Linnaeus, every form that could be created would be created. It’s easy to imagine that a rational God might, in a creation-extinction over time model based on plenitude, create the variations sequentially rather than randomly. Hence you might get a sequence of similar moths, but probably not a Precambrian rabbit. This is particularly apt as an explanation for nested clades, because logically people tend to start with a global category and then branch out to fill its sub-classes in increasing detail, rather than starting bottom up.

Come to think of it, the fact that taxonomic groups appear to start with major groups and diversify fits that rather better than the idea of one major group slowly evolving into another major group randomly, which isn’t a common pattern in life. No doubt evolutoionary theory has a fix for this, but at the instinctive level top-down tree taxonomy fits design better than RV&NS. And it at that instinctive level of what design ought to look like that your point was made.

The overall patterns of increasing complexity might also be explained, on design, in the same way that evolutionary theory sometimes does - early organisms terra-formed the earth (and in design models were created for that): plants prepared the land for land creatures, etc.

I can see faults in all those ideas, but am also aware that (a) I’ve drawn them out of thin air as possible explanations and (b) any model has faults when nobody’s spent a lot of time refining it.


#19

Yes, he is talking about reuse of modules. I’m wondering about how such reuse left temporal signatures. To me, this suggests a pattern of largely incremental modification over time rather than special creation of groups or species, ie. Common descent.

This applies as well to Ewert’s work as well by comparing the patterns to human software implementation. I’m wondering how the temporal patterns we see will integrate with this model. Ultimately it’s not what design ought to look like but what the data tells us it must look like. It’s going to likely be design implemented via modification with descent over time without massive horizontal transfer, at least among many ‘higher’ eukaryotes.

Aside: If we take software design as a guide, not only do we see module reuse but also massive horizontal transfer between individual programs. This is not common in many branches of life, again suggesting small modification with descent rather than ad hoc or de novo modes of creation.


(Dan Eastwood) #20

My first comment here, and I haven’t quite figured out the comment threading yet …

I have a technical issue with how Ewert is calculating the Bayes Factors. He is maximizing the probability for the Dependency Graph, but taking a fixed value for the Tree Graph (assumed to be maximum). Even with penalties for added complexity I would expect this to bias towards the DG.
I think he should be maximizing both the numerator and denominator, adding/subtracting nodes as appropriate to the DG and TG hypotheses, excluding the common “tree” nodes between models, and testing the remaining “dependency” nodes.

However, all this seems to be reinventing the wheel. There are existing Bayesian phylogenetic methods which are well developed and accepted (See Theobald 2010). If ID is to become an acceptable scientific concept, then proponents should approach the problem using acceptable scientific methods. By trying to tackle an unpopular idea with unproven methods published a (shall we say?) fringe journal, Ewert is setting himself up for failure.

Reference
Theobald, D. L. (2010). A formal test of the theory of universal common ancestry. Nature, 465(7295), 219.