Life should be classified not as a tree but as a dependency graph, says researcher

_{Denyse O'Leary

July 19, 2018

Evolution, Intelligent Design, Tree of life}

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Winston Ewert, one of the authors of Introduction to Evolutionary Informatics has a new paper at BIO-Complexity:

Abstract: The hierarchical classification of life has been claimed as compelling evidence for universal common ancestry. However, research has uncovered much data which is not congruent with the hierarchical pattern. Nevertheless, biological data resembles a nested hierarchy sufficiently well to require an explanation. While many defenders of intelligent design dispute common descent, no alternative account of the approximate nested hierarchy pattern has been widely adopted. We present the dependency graph hypothesis as an alternative explanation, based on the technique used by software developers to reuse code among different software projects. This hypothesis postulates that different biological species share modules related by a dependency graph. We evaluate several predictions made by this model about both biological and synthetic data, finding them to be fulfilled. (open access) More.

A friend offers a super-short summary:

1) Modularization is a well-established design methodology
2) Things that are developed with modularization can look as if they have a tree-like structure
3) A bayesian methodology can be used to differentiate between modularized and tree structures
4) For instances where the origins are known, the bayesian methodology correctly separates trees and modularizations
5) According to the methodology, genomes are organized more module-like than tree-like

Watch for Ewert’s work at Mind Matters Today as well, in links from here.

See also: Podcast: Winston Ewert on computer simulation of evolution (AVIDA) that sneaks in information

Dr. Ewertanswers some questions

Open Mike: Cornell OBI Conference Chapter Six – Ewert et all on the Tierra evolution program – Summary

Open Mike: Cornell OBI Conference—Chapter Three, Dembski, Ewert, and Marks on the true cost of a successful search

Also: Bill Dembski on the Evolutionary Informatics Lab – the one a Baylor dean tried to shut down

Evolutionary informatics has come a long way since a Baylor dean tried to shut down the lab

Introduction to Evolutionary Informatics: Media to get you started

Who thinks Introduction to Evolutionary Informatics should be on your summer reading list?

and

Evolutionary Informatics takes off

Comments

Joshua Swamidass:
Also, there is unfortunate confusion about evolution here. Common descent does not predict that data will fall perfectly in nested clades. Common descent does not produce DNA that falls into a tree. This is well known by experts, but “popularizers” have been wrong. So Ewert’s might be understood to dispatch a cartoon version of evolution. This has nothing to do with evolution as understood in mainstream science.
Given that a clade is, by definition, monophyletic, common descent most certainly does predict "perfectly nested" clades. The data does not match the prediction. So what do we do? We ignore the data, or say it doesn't matter, or add epicycles to the theory.Mung_{July 30, 2018
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Don't be a scoffer.Mung_{July 29, 2018
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The nonsensical answer to my question was "Evo devo- using the same genes differently". This has been the rallying cry for those advocating Common Decent for at least a coupe decades and nothing has come of it. But this is their view and they will not have it challenged. I had my account suspended for the weekend for scoffing at the notion that evo-devo offered a testable mechanism for Common Descent and offering Drs Denton and Sermonti for my support.ET_{July 29, 2018
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Actually, Dr. Swamidass is attempting to sweep the impact away with some math equivocation. He divides the D. Graph v Tree log Bayes factor by the Tree v Null factor to claim the D. Graph is only 1.7% better than a Tree. However, the log Bayes factor means the D. Graph is 2^111,823 times better than a tree. Big difference.EricMH_{July 26, 2018
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I see. This is why in Dr. Swamidass' thread I stated the evidence he provides seems to best support the dependency graph model, and he may be equivocating between common descent by birth and common descent of genetic material. If a unborn baby has a portion of its genome genetically engineered while in the womb, then it will be a descendant of its parents by birth, but not genetically. The big problem for me is the discussion is not boiled down to easy to understand terms, but makes use of technical language. When I look into the meaning of the words it isn't clear to me why the concepts are considered to be evidence for evolutionary common descent. So, to use the terms to dismiss Dr. Ewert's result is confusing to me. At any rate, my take away is that Dr. Ewert is correct and Dr. Swamidass agrees with him: a tree model is a bad model of what's happening in biological history. There is some kind of dependency injection going on. Whether that is de novo creation of many individual kinds using a genetic library, or directed evolution, or unrelated segments accidentally deposited by viruses, or some combination, or something else, external dependencies are entering the genetic code somehow. Therefore, genetic common descent is dead. If I'm misunderstanding somehow, let me know.EricMH_{July 25, 2018
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EricMH "A small percentage of a very large graph is still a very large number. A more useful metric would be graph edit distance, and some kind of empirical data whether that edit distance can be accounted for by known non-intelligent evolutionary operations." Yep - "still a vary large number." And your point about distance is interesting as well. Looking at it from another way besides pure information and statistics. Many discoveries recently in molecular biology, DNA, and Epigenetics, are overwhelming blind evolution. The communication and location systems involved within molecular systems allowing for different domain retrieval and editing of DNA, Splicing and post-translation modifications swamps the appeal to "non-intelligent evolutionary operations" as you state.DATCG_{July 25, 2018
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EricMH @42,
So, this means it could easily be attributed to missing data or the atypical evolutionary operations of gene transfer or convergence.
"Convergence" = the magic pixie dust of Darwinist imho. I'm with ET @40 in that "we don't know" yet. Now, if by Design and Common Descent, there should still be a mechanism at play to show how life unfolded and are "convergent" as this should be discoverable as reverse engineering of life continues. While complex, if by Design and not by blind events, engineers and scientist should eventually be able to discover mechanisms of convergent technology. As "convergence" tends to pop up all over the place. Naturally Design and not blind chance is more amenable to this reality of what we see as Common Design. Swamidass has passed this off before. I'm not against Convergence as a form of factually what we see in the fossil record or in molecular mechanisms. Only against it as a blind, unguided series of events. And I think as the Epigenome grows in function, it will confirm and make harder any appeal to blind, unguided mutations contributing to "convergent" evolution. Edit: one of two outcomes? In the future as research grows in depth and knowledge, they will ... 1) they will discover mechanisms of Convergence by Design 2) or, the spaces between will never be solved as Design can often take leaps of knowledge increases utilizing them across disparate technology. And in classifications of the fossil record as well as in molecular biology at the nano-level Simply appealing to "convergence did it" by a blind series of events is not a robust answer.DATCG_{July 25, 2018
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ET @38, Yep, yet both sources are deemed credible though by Darwinist and others in the case of BioLogos. And Swamidass was part of BioLogos in the past, thus my reason for posting it. But I realize like the ID community they can have different opinions on subjects.DATCG_{July 25, 2018
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Swamidass states the Bayes factor difference between the tree and dependency graph is a small percentage of the tree's Bayes factor. So, this means it could easily be attributed to missing data or the atypical evolutionary operations of gene transfer or convergence. I'm not sure how correct he is. 1.7% is a small percentage, but it is unclear what that translates to in difference between trees and graphs. A small percentage of a very large graph is still a very large number. A more useful metric would be graph edit distance, and some kind of empirical data whether that edit distance can be accounted for by known non-intelligent evolutionary operations.EricMH_{July 25, 2018
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Oh well, Dr Joshua balked and failed to show that what I said was falseET_{July 25, 2018
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I have been told by Dr. Joshua Swamidass that the following is false: What Common Descent requires is a mechanism capable of explaining the anatomical and physiological differences observed between two allegedly related species such as chimps and humans. Right now we don’t have that. So right now the best we can do is say “we don’t know”. That is the only honest scientific answer to the question. He, a real scientist, will explain how/ why that is false later. Does anyone disagree with the first sentence? What Common Descent requires is a mechanism capable of explaining the anatomical and physiological differences observed between two allegedly related species such as chimps and humans. Maybe it's the next one that I mess up: Right now we don’t have that. Real scientists Dr. Michael Denton tells us that DNA does not determine the final form of what develops. Real scientist, geneticist Giuseppe Sermonti agrees. Survival of the fittest- the fittest clown fish is still a clown fish- doesn't seem to help with the issue of producing different body plans. So we will see what I said that is allegedly false.ET_{July 24, 2018
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Well, we know our theory is true so what we need is not more accurate stories but more effective propaganda. It doesn't matter if the more effective propaganda is inaccurate, because we know our theory is true anyway. And around we go again ...ScuzzaMan_{July 24, 2018
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DATGC- Both of your sources make the common mistake made by those who don't understand nested hierarchies. They think that because a nested hierarchy, like Linnaean Classification, can be depicted as a branching tree then all branching trees can placed into a nested hierarchy. That isn't so. Also they lose sight of the fact that with nested hierarchies each level consists of and contains the lower levels. With the UCB site each level is an alleged ancestral populations. These do not consist or nor contain their descendent populations. See The use of hierarchies as organizational models in systematics and a summary of the principles of hierarchy theory:
Nested and non-nested hierarchies:ted hierarchies involve levels which consist of, and contain, lower levels. Non-nested hierarchies are more general in that the requirement of containment of lower levels is relaxed. For example, an army consists of a collection of soldiers and is made up of them. Thus an army is a nested hierarchy. On the other hand, the general at the top of a military command does not consist of his soldiers and so the military command is a non-nested hierarchy with regard to the soldiers in the army. Pecking orders and a food chains are also non-nested hierarchies.
ET_{July 24, 2018
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Mung @31, Excellent rebuttal to Swamidass's snob-foolery. His strawman argument against Ewert... "Also, there is unfortunate confusion about evolution here. Common descent does not predict that data will fall perfectly in nested clades." No, there's no confusion here. And Ewert did not say this in his paper, "perfectly in nested clades." He merely pointed to usual position of Darwinist or like your friend Venema at BioLogos. Another Example: Berkeley University... Lines of evidence: The science of evolution :
Nested hierarchies Common ancestry is conspicuous. Evolution predicts that living things will be related to one another in what scientists refer to as nested hierarchies — rather like nested boxes. Groups of related organisms share suites of similar characteristics and the number of shared traits increases with relatedness. This is indeed what we observe in the living world and in the fossil record and these relationships can be illustrated as shown below.
https://evolution.berkeley.edu/evolibrary/article/lines_16 The animated "Nested Clade" GIF at Berkeley page... https://evolution.berkeley.edu/evolibrary/images/lines/nested_clade_animated.gif Maybe Swamidass will write Berkeley and inform them of their "confusion" Many posters and commenter's here know the revolutionary times and changes taking place over the last several decades in Darwin's Evolutionism and by Darwinist supporters. It's not news to us what is happening in the field.DATCG_{July 23, 2018
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Swamidas sets up a pedantic strawman argument against Ewert, insults readers and commenters here, but fails to remember his own associates from BioLogos, 2015... Dennis Venema... "The shared mutations make a precise pattern that is exactly the pattern we expect if indeed these species share common ancestral populations that progressively divided into four lineages—a pattern known as a nested hierarchy." Link: Common Ancestry, Nested Hierarchies, and Parsimony Expert or Cartoon?DATCG_{July 23, 2018
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ET
no one is close to linking the genetic differences to the anatomical and physiological differences.
And those are the lest significant differences. Human consciousness, rationality, communication/language, innovation ... there is a very large gap between chimp and human.Silver Asiatic_{July 23, 2018
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I blame it on the pop sci authors.Mung_{July 23, 2018
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Joshua also thinks that there is strong evidence for Common Descent. That is strange because both chimp and human genomes have been sequenced and no one is close to linking the genetic differences to the anatomical and physiological differences.ET_{July 23, 2018
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More from Joshua Swamidass, this time over at TSZ:
For example, see this engagement with Ewert on his alternative to common descent...
My response: For the record, Ewert does not propose an alternative to common descent. Read for yourself: http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2018.3Mung_{July 23, 2018
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Joshua Swamidass:
Also, there is unfortunate confusion about evolution here. Common descent does not predict that data will fall perfectly in nested clades. Common descent does not produce DNA that falls into a tree. This is well known by experts, but “popularizers” have been wrong. So Ewert’s might be understood to dispatch a cartoon version of evolution. This has nothing to do with evolution as understood in mainstream science.
This is disingenuous at best. One of the complaints in the thread about Winston's paper over at Peaceful Science is that he does not use DNA sequences. Instead, he uses gene families. And I may need to understand the paper better, but for one of his controls Winston used an evolution simulator which of course uses common descent, and just guess which model fit it best. Hint: Not the dependency graph.Mung_{July 23, 2018
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Joshua Swamidass:
3. Regarding Cornelius, I gave him his own thread because he was hurting Ewert’s case.
Did you give a thread to each of the critics who were also hurting Winston's case? No?Mung_{July 23, 2018
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Swamidass states that biological information "does not require a communication system". Such statements serve his bureaucratic purposes, but there isn't a chance in hell he can defend such a thing. The key to his success is that he'll never have to. He'll make certain of that.Upright BiPed_{July 22, 2018
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Mung:
The Darwinian model is that of a tree.
And the Ptolemaic model has the Earth as the center of the universe. Both the Ptolemaic and Darwin models have been superseded and replaced by models using modern knowledge based on ancient ideas.ET_{July 22, 2018
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Hello all. Pleasure to see some regular faces around here again. Just answering a few quick questions, and I'm not likely to be back after that. 1. Yes, I did separate from BioLogos. If you google my name and BioLogos, look at my blog/forum, and look at ENV, you'll see the whole story laid out largely correctly. 2. I'm happy to answer any questions at the peaceful science forum, including those about evolution and the nature of Peaceful Science. https://discourse.peacefulscience.org/ Everyone is welcome, including ID advocates and opponents of evolution. We will treat you fairly. 3. Regarding Cornelius, I gave him his own thread because he was hurting Ewert's case. Winston impressed all of us, and we are genuinely excited about his work. We want to see where it goes. He was appropriate reserved, and careful in his contributions. He earned a lot of respect. Cornelius was not helping his case, and I didn't want him interfering with Ewert's respectable effort. One person aptly told Cornelius: "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." 4. As I've said before, comments related to Ewerts you can make here: https://discourse.peacefulscience.org/t/side-comments-on-the-dependency-graph-of-life/743/12, or jump into any thread you like there. See you soon. Until we meet again, thanks for being kind hosts. I am not planning to return to this thread, so please send questions to the forum. Peace.Prof. S. Joshua Swamidass_{July 22, 2018
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@Swamidass What would be super interesting is an explanation of how a non-tree can come from common descent with variation. The only possibilities I can think of are: 1. Incomplete data 2. Converging branches 3. Spontaneous generation of new organisms If 1 is true, then claiming common descent is fitting the data to our model, as nonlin points out. 2 might be true, but not mentioned in any account of evolution I've heard of. Plus, it wouldn't fit the dependency graph model all that great. 3 is much more supported by creationism. A final possibility is horizontal gene transfer, but if it is so much that a dependency graph results, then common descent is not really happening here.EricMH_{July 22, 2018
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Joshua Swamidass:
@Cornelius_Hunter, with all due respect, this is @Winston_Ewert’s thread. We are not interested in your arguments on his behalf here. He can make his own case.
Yet everyone and their briother is invited to point out what's wrong with Ewert's paper. No is allowed to defend it except Winston. Sounds more like Peaceful Bias than Peaceful Science. And hardly the Christian response.Mung_{July 22, 2018
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Joshua Swamidass:
Let the honest scientists outside ID take a look and assess.
LoL First they will need to establish that they are telling the truth in order to gain our trust.Mung_{July 22, 2018
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Prof. S. Joshua Swamidass @10 Good to see your new blog, but are you no longer affiliated with Biologos? If so, why? I am looking forward to debating you as you were one of the few bright minds at Biologos.Nonlin.org_{July 22, 2018
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Bob O'H, Sorry, I mean an undirected graph model.Mung_{July 22, 2018
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Ewert might be right, but why do many ID proponents always complicate matters? The whole tree of life is fake science. It's real simple: http://nonlin.org/nested-hierarchies-tree-of-life/ 1. “Nested hierarchies” or “cladistic analysis” or “consilience of independent phylogenies” is often offered as support for Darwinist evolution. This is the idea that the “tree of life” classification of organisms is somehow objective despite being a creation of very zealous “evolution” advocates. The three basic assumptions of cladistics models are: a) Any group of organisms are related by descent from a common ancestor (UCD - universal common descent); b) There is a bifurcating pattern of cladogenesis; c) Change in characteristics occurs in lineages over time. Although not explicit, UCD (“descent from a common ancestor”) here means by a Darwinian “natural selection mechanism” and not by a process generated by a designer that also happens to make use of biologic reproduction. 2. No assumption can be tested by the model that uses them. That is why they’re called ‘assumptions’ and not ‘conclusions’. Instead, assumptions have to be tested independently through an entirely separated method or be accepted as axioms. An UCD “mechanism” has never been observed or proved elsewhere and is not “self-evidently true”, therefore not a valid axiom. Because UCD is an assumption in “cladistic analysis”, it cannot be logically also a conclusion of any such analysis. Furthermore the conclusions of any “cladistic analysis” will always and trivially be compatible with the UCD assumption in that model. 3. Hypothesis testing requires an alternative (null) hypothesis and a procedure that demonstrates how the data available is compatible with the successful hypothesis and at the same time is statistically incompatible with the alternative hypothesis. In the “cladistic analysis” case, the alternative hypothesis to UCD is “common design”, and of course UCD cannot be an assumption of such an analysis. However this rule is violated twice, first by the use of an assumption also presented as conclusion, and second by the prejudiced rejection of the alternative “common design” hypothesis before analysis. This clearly demonstrates that “cladistic analysis” can never be logically used as proof of UCD. What “cladistic analysis” is instead is ‘curve fitting’ where the cladistics model is best fitted to certain (conveniently selected!) morphologic/biochemical/genetic biologic data points. 4. The ‘designer’ hypothesis cannot fail against the ‘no designer’ (Darwinist evolution) alternative in a biologic comparative analysis as designers have maximum flexibility. This is not surprising as designers are free to incorporate whatever mechanism they want, including intelligent “selection” (human breeders do!) and “common descent” (human breeders do!) if they so desire. 5. The claim that cars and other entities cannot be uniquely and objectively classified (“nested hierarchy”), while organisms can, is false. On one hand, we do know the history of the automobile, so a proper classification must be able to reconstruct their unique “evolution”. Yes, vehicle share parts, so to get to the actual development tree, we must group them differently than organisms since mass production works differently than biologic reproduction. On the other hand, organisms may not be uniquely classified as demonstrated by the numerous revisions and exceptions to the “tree of life”, and in any case, “uniquely classified” is an absolute claim that can never be proven since it is impossible to compare the infinity of possible organism classifications. 6. The claim that the “tree of life” based on anatomy is validated by the match with the tree based on biochemistry fails. Anatomy is not independent of biochemistry. Also, the oldest DNA ever found was 700k years old therefore any match between the independent trees is limited. This is not to say that the fossil record is complete, or that fossils can be positively linked to one another and the living without – once again – presupposing UCD. The claim that “there is no known biological reason, besides common descent, to suppose that similar morphologies must have similar biochemistry” is false as the ‘designer’ hypothesis produces the same result when one designer creates all morphologies, and furthermore “I cannot think of an alternative reason why…” is not a valid argument. 7. A “tree of life” is an artificial human construct as organisms do not come labeled with their position in a cladistics hierarchical structure. To decide the position of a certain organism, the human creators of the “tree” have to decide which morphologic/biochemical/genetic characteristics to include and what weight to attach to each of those measures. This further supports the claim that “cladistic analysis” is ‘curve fitting’ rather than ‘hypothesis testing’ - if a tree must be built, a tree will be built as in this example: “The close relationship between animals and fungi was suggested by Thomas Cavalier-Smith in 1987, […] and was supported by later genetic studies. Early phylogenies placed fungi near the plants and other groups that have mitochondria with flat cristae, but this character varies. More recently, it has been said that holozoa (animals) and holomycota (fungi) are much more closely related to each other than either is to plants […].”Nonlin.org_{July 22, 2018
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