Gene Tree Incongruence

You are fond of saying that “religion drives science and it matters.” You wrote a book on this!

So tell us, how does religion drive your science? We know that it matters. So, let’s talk about it.

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Strange you should mention that because I do have a fuzzy recollection that, but I got so mad I hit it right back.

Science is not a democracy. As much as we would like it to be, the truth is not up to the consensus. Of course expert opinion is important, and needs to be considered. But it is also wrong quite often. One would need to be ignorant of the history of science to think otherwise.

The reasons why scientists accept theories are many and complex, with the empirical evidence being just one of many factors. Even more so with a theory with as many implications as evolution. So no, I’m certainly not saying that all scientists who accept common descent are doing so for an ideological agenda. I have not talked to all of them. I have not even talked with a fraction of them.

Nor did I ever imply any such thing. What you are doing is engaging in a strawman argument. When I became interested in evolution, my first step, and it was a long, time-consuming step, was to collect all the arguments for evolution. I wanted to understand why it was known to be a fact. I wanted to get that argument in front of me, in all its strength. I wanted the strongest data, evidences, and arguments for evolution. I wasn’t exactly sure how we knew evolution was known to be a fact, and my curiosity was growing. I have always wanted the strongest arguments, and always wanted to avoid the strawman trap. If it was a fact, then great, I’m on-board. I read the literature, and I talked with the experts.

Now these evidences and arguments can be complicated. You will often see a fairly general, or vague, claim made. So you need to follow up, looking at the references, the data, and so forth, to reconstruct the claim. So it took some time. But what I discovered is that there are no scientific supports for this claim. There are a great many supports, and it certainly is true that evolution is a fact. But that claim needs to be understood in the context of the premises and assumptions the support it. What I found is that it always comes down to the underlying metaphysics. Evolution is a fact, but not a scientific fact.

Well not from my perspective. But I have found that when religion is involved, it is very difficult to change ones mind.

Strange that you would find that to be “unjust” since you yourself, earlier in this thread, made just such an assertion. You wrote:

That is what I refer to as the “Greater God” argument. It traces all the way back to the 17th and 18th centuries. It was a powerful argument and foundation for a strictly naturalistic origins narrative and was popular with Lutherans and Anglicans (Darwin’s grandfather Erasmus also used it!).

As the OTHER George on this thread… I have to challenge the view by Cornelius that hundreds of millions of years is not enough time to create the speciation we see.

A) Where DID all the species come from, Cornelius? Did the 1+ million terrestrial species come out of the ark?

B) If not… did God make MORE species after the flood?

Right on cue, following Casper’s incredulousness that there is religion involved.

Unlike the arguments for the fact of evolution, which entail religious premises, my religious beliefs do not dictate evolution being true or false. Historically Christians have occupied a wide spectrum, ranging from just about exclusively secondary causation to just about exclusively primary causation, and pretty much everything in between. I accept that spectrum, taking a tolerant view, rather than a dogmatic view that dictates some point in that spectrum. One reason for this is that I was raised in a tolerant home (hat tip to parents). I have no fundamentalist baggage. I’m not fighting any past wars. For me, evolution can be true. But, importantly, it also can be false. So I look at the science.

@Cornelius_Hunter

But will you answer my questions?

“A) Where DID all the species come from, Cornelius? Did the 1+ million terrestrial species come out of the ark?”

“B) If not… did God make MORE species after the flood?”

Convergence is rampant, but far less common than divergence. So why is this evidence against common descent? The remarkably similar vision systems – are they remarkably similar at the molecular level? Or do they show the kind of molecular divergence we would expect if they were in fact the result of convergent evolution? [quote=“Cornelius_Hunter, post:27, topic:9420”]
Then there are divergences, incredibly different structures in allied species. Like convergence, divergence is rampant in biology.
[/quote]
This is so vague as to be meaningless. What incredibly different structures are you talking about? Why is divergence not to be expected under common descent?

Significantly different, but similar to a much greater degree than they are different. This is again understandable if common descent is true. It can’t be explained under your model, because apparently you don’t have one.

I don’t believe you answered my previous question: where have you published your calculations supporting this conclusion? Just pointing at anomalies and repeating your conviction isn’t science.

Okay, let’s see the rampant incongruence…

That doesn’t say anything about incongruence being rampant; it says it’s serious. The only incongruences that I can see mentioned in the article are ones between deep mammalian branches. Continuing…

That doesn’t say anything about rampant incongruence either. So where did the rampant incongruence come from?

Look, if the incongruence is really rampant, just point out the many cases within, say, higher primates. How many of these microRNAs are shared by humans and New World monkeys but not by gibbons or chimpanzees?

Since you like clarity, let me supply some. I have repeatedly used common descent to carry out research in my field, a field in which you seem to have no expertise at all. I have used the concept of common descent to draw conclusions and make predictions, conclusions and predictions that can be verified in other ways or that were subsequently borne out by independent lines of evidence. I use it because it works. In order to get me to reconsider the basic validity of common descent, you will have to either show me data that contradicts the model (i.e., that is impossible under it), or an alternative model that explains the full range of data better.

You tell me that common descent is wrong. As evidence, you point to a variety of things, all of which can easily be true even if common descent is in fact correct. You present no argument showing that these data are impossible under common descent, nor a calculation of their (im)probability under that model, nor any alternative explanation for all of the myriad data that common descent explains very well, or indeed for anything at all.

I’ve had my understanding of quite a few scientific topics changed when presented with new evidence or arguments. What you’re offering isn’t even in the right ballpark.

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Well, perhaps. That sounds like a difficult comparison to make. In any case, there is a whole lot of both.

Well in normal science (in the Kuhnian sense), it can be very difficult for proponents to view evidence, no matter how contradictory, as problematic. Any Theory A, can explain any Evidence, B. But for objective observers, it is obvious that rampant convergence is not a natural fit for common descent. The whole idea is that you are exploring this astronomical design space, and as the evolutionary tree grows, the different characters are going to be phylogenetically congruent. Converged characters are incongruent. These fundamental assumptions are instantiated into every tree-building algorithm, every textbook explanation. Evolutionists have non dimentional goodness-of-fit metrics, such as the “Consistency Index,” (CI) which tells you how well a set of character data, from a set of species, fits the common descent model. CI goes from 0-1, with 1 meaning a perfect fit. Similarities, in otherwise distant species (i.e., the so-called convergences) reduce the CI value. So while, of course, a proponent can always say “Hey, convergences are no problem, evolution can do that,” the fact is from an objective perspective they don’t fit. Now couple that with the massive divergences, and what we’re looking at is a pattern that simply is not the CD pattern. You can add all the epicycles you want, and you can always explain any evidence, but all that additional theory complexity speaks volumes. The data contradicts the model. This would never survive a model building algorithm, such as AIC or BIC.

Well it is a little bit of both. I think it is true that convergences are often easier to spot at the morphological level, but there are a lot of important molecular convergences as well. For instance, the human and kangaroo genomes are strikingly similar. As one evolutionist explained: “There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order. We thought they’d be completely scrambled, but they’re not.” Another interesting example are the genome architecture features that are sporadically distributed and strikingly similar in distant species. They often occur repeatedly in a variety of otherwise distant species. This phenomenon is called “recurrent evolution.”

Simon Conway Morris is an evolutionist who has realized that convergence is rampant and a serious issue.

Well OK, let me give you some examples. There is the leaproach (Saltoblattella montistabularis). It is a cockroach that is the only cockroach that leaps like a grasshopper (actually better than a grasshopper). So here you have this cockroach, in a cockroach lineage, that suddenly instantiates this leaping functionality. There are myriad examples of such unique, lineage- or species-specific designs in biology. At the molecular level there are the microRNA genes which are different in allied species. Or there are the novel genes, showing up in one species, but with no homologues in otherwise allied species. The examples of divergence are all over.

Now, again, a proponent can always say, “So what, that’s what evolution does. And the CD model obviously does not require no change in allied species.” True enough, but these are huge changes. So instead of the usual RM+NS, we need some creative, fast, mechanisms, to work the magic. The data just isn’t consistent with the theory.

Sure, of course. I completely agree. Incredulousness is not an argument. But what I’m talking about is no secret–it is all over the literature. Let me give you one example. I mentioned CI above. A few years ago a meta study computed the CI for a whole bunch of data sets that had been compiled in previous studies (data set = character data for a set of species). In one figure they showed the CI value plotted as a function of the #species. The CI values were consistently terrible. This was especially evident in the more meaningful studies, with greater #species. Above about 30, almost all the CI values were less then a half! They ranged from about 0.2-0.4. They actually were fairly close to your favored null hypothesis, the randomized data case! So IOW, this meta study incorporated a lot of data, and showed that you are usually closer to a randomized data set than the ideal CD model.

Now of course we’re not expecting a value of 1.0 for the CD model. It doesn’t have to be ideal. But this is nowhere close. The results are closer to random, but not all the way to random. This would fit a design view much better, as species are designed, but must function according to common constraints (same planet, same atmosphere, same chemistry, etc).

“So where did the rampant incongruence come from?” The “incongruence” came from phylogenies, inferred from microRNA genes, being significantly different from the traditional tree. The “rampant” came from this being the case for not one, or a few but, err, thousands of microRNA genes.

Well OK, your view is that massive convergence, divergence, incongruence, recurrence, gain / loss, etc., all fit comfortably within common descent. As you asked above “So why is this [rampant convergence] evidence against common descent?” Likewise for divergence. So there really isn’t anything that could possibly rule out your theory. It can pretty much accommodate anything we find, no matter how much at odds it is with the model. The one exception is if the data were purely random, as you have indicated. The fact the data aren’t random gives you confidence common descent is true. So all these contradictions really aren’t really a problem for you.

The fact that you have use the common descent model successfully is great, but congratulations, you’re now up there with the flat earth (yes, the flat earth is commonly used today for problems, with great success), geocentrism, etc.

So, this is a very Darwinian argument.

Ever since Darwin this has been a favorite argument. It is a shifting of the burden of proof. How could I show that something is impossible under common descent when, apparently, the only thing that is considered impossible is a purely random data set. Otherwise common descent is true. And now I’m supposed to prove to your satisfaction it is impossible? Even though essentially identical vision systems in fish and mammals, different genes in allied species, incongruent characters, etc., all do not so much as put a dent in the theory.

I can show you big changes between allied species, but not a problem, common descent says nothing about tempo. I can show you dramatic convergences, but not a problem, common descent says nothing about designs repeating in distant lineages. I can show you recurring designs, but not a problem, common descent says nothing about multiple, isolated repeats. I can show you divergences, but not a problem, common descent says nothing about new species rapidly developing new structures. I can show you massive incongruencies, but not a problem, common descent says nothing about the pattern. I can show you incredible designs like biosonar allowing tracking better than an F16, but not a problem, common descent says nothing about complexity. I can show you codes, epigenetics, lineage specific designs, etc, etc. The list goes on and on. This makes no sense, but not a problem, common descent says nothing–it simply is true. The one thing common descent says is that it is true. This is tennis balls on tanks. I’m chucking tennis balls and you’re rumbling along inside a tank, saying I’ve got nothing on you. Evolution is impervious to the data.

Hi Casper,

My comment re discussions and criticisms is meant for scientific discussions and debates - I have not managed to get my head around the culture wars between TE/ID/YEC/OEC etc and so will not make any comments on such. If you were to examine arguments based on PoS related to evolution, I think you will find a wide range of opinions that are consistent with a theory under considerable debate. If you can point to another area of the natural sciences that has engendered such a range of views, I would be interested to read such debates.

It is unfortunate that some evolutionary biologists will quote QM as a similar example of debates - I cannot accept such an outlook and I have made previous comments to show why such an outlook adds to a notion that extremist claims are often made for ToE.

Your statement on theological “paradigms” is difficult for me - I accept orthodox theology and this includes many discussions of creation by God from nothing. My guess is you may refer to synthesis of portions of novel theology with some scientific theories, and if so, I cannot comment - perhaps you may clarify what you mean.

Not to distract from @glipsnort, but can you tell us what you think happened? You are not a YEC, so what model do you think fits the data?

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@Cornelius_Hunter

I’m hoping you can provide your personal answers to questions “A” and “B”.

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Hi George

It is indeed wise to stay out of the culture wars as much as possible. The best way to do that in my opinion is to avoid making sweeping generalizations about the motivations of people we don’t know personally. That’s what got me so worked up about @Cornelius_Hunter’s rhetoric, because he is doing that nonstop. A considerable part of his reasoning is based on assumptions he makes about other people’s motivations.

If you can point me to any debates in peer-reviewed academic journals that call into question the notion of common descent of modern-day species, I would be extremely interested in reading such debates. Because, AFAIK, there is no such discussion. There are current discussions that center on the adequacy of known evolutionary mechanisms to describe how exactly things happened. But universal common descent has been established so strongly that practically no leeway is left. If you can point me to any peer-reviewed sources that suggest otherwise, I would be very thankful for that.

Do you think orthodox theology is compatible with common descent?

Despite re-asking these two questions at least 2 other times … he never offered an answer. A telling gap in his array of answers.

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Orthodox theology has not, in my experience and understanding, had a problem with considering the merits of science or scientific paradigms. Evolution has had debates that parallel debates outside orthodoxy (minus the creationists YEC and whatever variations there are), and we can easily find opinion that range from acceptance to deep skepticism. I had given a few blogs and web sites as examples in the past and am disinclined to repeat these.

You focus on common descent may indicate your personal preference - my background includes secular education that included classes which taught the “missing link” and other erroneous views (I still remember pictures in class showing cave men fighting saber tooth tigers with fire, and the mighty Rex in the background; we were taught such rubbish - I guess that also reveals my age :blush:) so I would be a “hard man” to convince, especially since evolutionist students would debate their position against my scepticism with vigour. But in terms of peer-reviewed journals, I tend to read review of subjects and am especially interested in philosophy of science treatments of scientific theories, including evolution. My thinking is that if the foundations of a theory are weak, the rest of the edifice is inadequate, and of course, the opposite (strong foundations lead to a strong edifice). I have provided two PoS treatments in past comments, one from an avowed evolutionist/materialist, and another of imo more balanced treatment. Both of these treatments identified inadequacies in ToE, but of course, the materialist believes it without question, and looks forward to a time when ToE is the ultimate theory.

On common descent, my impression is that genetic similarity is the grounds for such confidence. Yet (I think it was Wagner, but there are others, if memory serves) debates include definition of species, inferences from fossils, various trees and branches, cause me to think the great confidence may evaporate. The key to settle this debate to me, is to show a link between genetic similarity and the end product (phenotype). Just for discussion, if chimps and human are 98% similar genetically, then it is up to proponents of CD to show how the 2% difference leads to human beings. This is not a trivial statement - that 2% must account for the great difference between chimps and humans. So much emphasis is placed on the similarity, that people ignore the elephant in the room - humans are very different to chimps, just as elephants differ from fish, or from eagles etc etc. What is it that supports the theory? Comparative analysis, or a direct correlation between each species and the genetic aspect that defines each species? These are questions that have not been answered.

I have made a longer response that planned, but the ramble should be sufficient to address your concerns about orthodox theology and my skepticism regarding the current version of ToE.

Cheers.

The confidence in the idea of common descent ultimately rests in Geology and Physics. As in the biography of Dr. Karl Giberson, once you see the overwhelming evidence for Earth’s age being in the billions of years… suddenly all the minutia about cellular structure and operations becomes a side-show.

If the Earth is billions of years old, and the Bible doesn’t allow for that… all of a sudden you are faced with millions of species (just terrestrial species!) since the days of Noah and his ark.

How did they get here? If they didn’t come from common ancestors of “types” or “kinds” … then you have to hypothesize that God specially created all these millions … some time after the Ark hit dry ground.

Where are the Intelligent Design supporters for That Idea?

The humorous aspects of such belief is simply great - people have undertaken modelling of planet earth formed from plasma ejected from the sun, and followed its cooling into a solid planet. Calculation using physics and chemistry lead to an unambiguous conclusion - as this imagined earth “forms” over many millions of years, the resulting composition cannot sustain, or form, life as we know it. This is beyond debate - the result is purely from a scientific outlook is (no biblical insertions or interpretations): such a model is dead wrong :weary: Yet many evolutionists simply invent new ways of circumventing sound science.

It is not minutia or a side-show. It is a conclusion that simply shows the idiotic model is dead wrong. Not from biblical discussions, in case this is not clear. It is from science ONLY! Wrong, not correct, bad model — perhaps this is clear to some :rage:.

To the “First George” [ @GJDS ], from the “2nd George” [ @gbrooks9 ] - -

I really can’t fathom what you mean. When I compare what you say about how wrong geologists and physicists are … and compare it to the idea that God created the Earth in 6 days … and then Flooded the Earth for a year … right in the middle of the first 10 Egyptian dynasties - - magically leaving no trace of interruption to the Egyptian culture and physical finds… I just can’t imagine how you can expect me or anyone else to favor your scenario.

And I haven’t even opened up a biology book or considered the mysteries of ribosomes. . . . or read about the millions of terrestrial species that we have since Noah’s Ark.

That’s how easy Geology and Physics makes the general topic…

I believe we are looking for an explanation for where all these genetically different versions of kinds came from. I have yet to hear a peep out of any Evangelical on the topic. But I’m sure someone has come up with a brilliant notion or two…

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I agree with your basic statement, yet disagree with your use of “Evangelical” in this context. That term covers a lot of territory, and includes many in the EC tent, including myself. There is a lot of debate about what makes an evangelical, especially with the events of the recent political season. Perhaps a new term will arise, but for now most of us evangelicals are stuck with this one, with all its baggage.

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