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
This is great to see!
Congrats to Ewert and Bio-Complexity on this new research concept and paper. And to JohnnyB as Editor.
For being bold enough to think outside of Darwin’s box 🙂 And thanks to all at Discovery Institute for all the work they do. So glad to see this approach taking form. I know it’s just at the beginning of hashing out concepts, ideas and more details.
I think this is the correct approach for reverse-engineering the Code(s) of Life.
Looking forward to reading through it.
Well said.
Of somewhat related interest is this recent finding:
The preceding study, in over the top fashion, also confirms what Michael Denton had found over 30 years ago in his book “Evolution: A Theory in Crisis”. Specifically, “However, the most striking feature of the matrix is that every identifiable subclass is isolated and distinct. Every sequence can be unambiguously assigned to a particular subclass. No sequence or group of sequences can be designated as intermediate with respect to other groups. All the sequences of each subclass are equally isolated from the members of another group. Transitional or intermediate classes are completely absent from the matrix. 4”
This can’t possibly be an ID paper. I smell a hoax.
1- I doubt that Winston understands what a nested hierarchy entails. Evolutionists don’t.
2- Linnaean taxonomy is a nested hierarchy and it was based on a common design
BA77 @2,
Thanks for those links.
from 1st link…
Highlighting one of your quotes…
“The absence of “in-between” species is something that also perplexed Darwin, he said.”
Essentially nothing has changed? Still no closer to an unguided, blind explanation than when Darwin lived?
Here’s the PDF paper referenced by BA77 @2 …
by Stoeckle M.Y., Program for the Human Environment
The Rockefeller University.
by Thaler D.S., Biozentrum, University of Basel
https://phe.rockefeller.edu/news/wp-content/uploads/2018/05/Stoeckle-Thaler-Final-reduced.pdf
They include an interesting history of COI Barcoding and Skeptic’s viewpoints at beginning of the paper.
I guess a good question is how might this research of COI Barcode information findings confirm or enhance Ewert’s approach of Dependency Graphs vs that of the long-held consensus TOL?
And another intriguing question is, does this study by Thaler and Stoeckle align with Gould’s Punctuated Equilibrium?
If so, then does the hypothesis by Ewert align as better heuristic for research than blind, random, Darwinian gradualism?
Dr. Cornelius Hunter broke down the the numbers in Ewert’s paper and put is in proper perspective:
Common Descent or Design? Which model best explains the genetic data?
Darwin never said that descent with modification predicts any tree or nested hierarchy.
What Darwin said that was his mechanisms could also account for/ explain (away) the observed pattern- the pattern Linnaeus attributed to a Common Design. As Drs Mayr and Simpson said decades ago:
What sort of graph would descent with modification create? Unless you have species materializing out of nothing and converging into a single species, you have a tree. Perhaps a tree with a couple roots if life started in a couple different places.
The core of evolution, whether Darwinian or theistic, is common descent with modification. Common descent necessitates a tree model. Dr. Ewert has decisively refuted the tree model. Therefore, evolution of every flavor is kaput.
I’m please to report a dialogue (and critique) of this paper at: https://discourse.peacefulscience.org/t/winston-ewert-the-dependency-graph-of-life/728
You are welcome to join the conversation. 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.
Joshua Swamidass,
I do not care for your approach towards Winston as someone who is dishonest and needs to gain your trust.
EricMH:
Perhaps an undirected dependency graph.
But let’s be honest. The Darwinian model is that of a tree.
If that has changed it would sure be nice to know when and why.
Perhaps the evidence didn’t fit the model and scientists are having to face the facts.
Mung @ 13 – No, the graph is directed (as time only goes in one direction). But it’s bifurcating, i.e. each node (except the root) has one edge going to it, and 2 leaving it.
@Mung, yes I agree. While the tone is much more cordial than the skeptic zone, it is also condescending. Dr. Ewert’s paper is well argued and he added many qualifications to minimize his claims. He has the necessary credentials and expertise for the methods he used. So, Dr. Ewert’s paper should be received as one would receive any other serious researcher. Not as if Dr. Swamidass is the gatekeeper to the scientific world, and he is allowing Dr. Ewert into the fold.
Mung:
That depends on your definition of “tree”. 😉
If you want to get technical then divergence would expect patterns as diverse as every population would represent a bifurcating node to a chain of being.
Just think how messy the diagram of every population depicted that way- as a bifurcating node.
As a reference in the diagram in the OP the lines of descent contain thousands to millions of populations that need to be made into a bifurcating nodes. Messy. Very. Quickly.
So evos simplify to try to fool the masses and unfortunately it has worked.
Bob O’H to keep the main thread focused on Winston Ewert, we closed it when he left. That is out of respect for him, and we hope he will come back as he advances his effort.
There is a side discussion where we can hash our your point about @sygarte. You might be right. Join us there and explain?
https://discourse.peacefulscience.org/t/side-comments-on-the-dependency-graph-of-life/743
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.
The Darwinian model is that of a tree. This ought to be without any question. Why pretend otherwise?
See the Wikipedia article and the see the drawing by Darwin himself.
https://en.wikipedia.org/wiki/Tree_of_life_(biology)
And then you have books like this:
The Tree of Life
And web sites like these:
http://tolweb.org/tree/
http://www.onezoom.org/
https://itol.embl.de/
Now they want to pretend like the Darwinian model is NOT a tree? Please.
See also:
https://en.wikipedia.org/wiki/Tree_of_life_(biology)#/media/File:Tree_of_life_by_Haeckel.jpg
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 […].”
Bob O’H,
Sorry, I mean an undirected graph model.
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.
Joshua Swamidass:
LoL
First they will need to establish that they are telling the truth in order to gain our trust.
Joshua Swamidass:
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.
@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.
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.
Mung:
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.
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.
Joshua Swamidass:
Did you give a thread to each of the critics who were also hurting Winston’s case? No?
Joshua Swamidass:
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.
More from Joshua Swamidass, this time over at TSZ:
My response:
For the record, Ewert does not propose an alternative to common descent. Read for yourself:
http://bio-complexity.org/ojs/.....O-C.2018.3
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.
I blame it on the pop sci authors.
ET
And those are the lest significant differences.
Human consciousness, rationality, communication/language, innovation … there is a very large gap between chimp and human.
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?
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 :
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.
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:
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 …
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.
Oh well, Dr Joshua balked and failed to show that what I said was false
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.
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.
EricMH @42,
“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.
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.
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.
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.
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.
Don’t be a scoffer.
Joshua Swamidass:
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.