Gene Tree Incongruence

But only in the most stereotypically pseudoscientific way. At no point do you actually engage on the evidence.

You have neither mentioned nor discussed a single datum, so I have to doubt your alleged finding.

@Cornelius_Hunter

You are deciding how to interpret Genesis based on This?!:

"You could read this paper which unexpectedly finds that transcription factor binding is not conserved between mice and men: “we found that the binding profiles of OCT4 and NANOG are markedly different, with only approximately 5% of the regions being homologously occupied.”

You need to come up for air!

I’m not sure how Genesis got into this. I’ve been talking about the science.

@Cornelius_Hunter… but to what end?

Aren’t you trying to prove that Evolution without God can’t happen?

So… here in BioLogos … we think God is involved. Lots of different opinions about HOW God is involved… but I think God has worked out the bugs in that molecular issue you are describing, right?

So that means you and I are on the same team, yes?

George

Well evolutionists talk a lot about theology. I used to be an atheist and I was an evolutionist. Then I was saved and became a Christian. I remained an evolutionist as I had no reason to doubt it. But then I got interested in evolution on a lark–I happened to hear what evolutionists were saying about it, and the claims they were making seemed strange. I wasn’t against evolution, but rather was neutral. It was OK with me if it was true, but it was also OK with me if it was false. I didn’t have any baggage on the topic. I found that many evolutionists do have baggage on the topic. There is a lot of religious talk, and evolution must be true for non scientific reasons.

Because, for me, it was OK if evolution was false, I was free to explore the science objectively. As a scientific theory, evolution is terrible. It lacks explanatory mechanisms, its fundamental predictions are all falsified, it is incredibly complicated, and it is religiously motivated. Evolutionary thought has a long history that goes way back. You could resurrect arguments from two millennia ago, between the Epicureans and Stoics, and they literally would fit right into today’s discourse. People have sought naturalistic origins for thousands of years, probably for as long as there have been people. There is nothing new in modern evolutionary thought. The idea that the world, especially the biological world with its millions of species, evolved is simply not scientific.

So… Let me get this straight. Do you mean to imply that almost all members of the scientific community worldwide (including loads and loads of Christians) are involved in some sort of religiously naturalistic conspiracy? And you are the “objective” observer engaging in “true” science to debunk the myth?

If that’s your conviction, there’s not much to be gained from this conversation. In the Netherlands we would say you’ve been hit by a windmill.

[credit: Stuff Dutch People Like]

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This is an uncharitable response as there are many scientists who have serious doubts about ToE as it is promulgated these days. I am a scientist, and on the rare occasion when we waste our time discussing ToE, we scientists express opinions that are not dissimilar to those given by @Cornelius_Hunter. It is not to say that we think of a conspiracy, but rather the primitive and inadequate theory that makes such extravagant claims re scientific verification, and the obvious (some may say blindingly obvious) ideological baggage that has always accompanied this inadequate paradigm of biologists.

I have no problems with expressions of criticism of evolutionary theory (or some popular versions of it), purely based on its claims or assumptions.

The craziness problem starts when it is insinuated (as Cornelius does) that the scientists who accept common descent are doing so purely (or primarily) because they are driven by a certain ideological agenda. Now that’s uncharitable towards the thousands of biologists (with very diverse belief systems) who have devoted their lives to this field of scientific inquiry. It is also an unjust accusation of many of our fellow brothers and sisters in Christ who are biologists.

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Perhaps I should read all of the comments to see what may have been insinuated - my response is directed to the notion (or implied assumption) that all scientists accept the ToE as it stands, and thus anyone else must be odd or whatever. The comments I have read leave me with the impression that Cornelius has done a lot of work and developed his outlook with effort and interest. I would add that the range of opinions offered to ToE (be it as support or as criticism) points to an (obvious to me at least) failing if taken as an established paradigm.

It does lead to a great deal of discussion and debate - which I think is part of the wider interest in biology as the science that deals with life on our planet.

Hi George. There’s only one comment you would need to read. My response was triggered by the most recent message of Cornelius. I’ll highlight some quotes for you:

These are just a few examples of unjust insinuations made towards those who work within the evolutionary paradigm. Unfortunately, such assertions are very common in young-earth / intelligent design circles. My intention was to point out that the implications of such claims are just too extreme to be even slightly tenable (e.g., it would imply some kind of worldwide ideological conspiracy with cooperation from many Christians).

That’s a non sequitur. For example, we’re also still having lots of discussions on the age of the earth among Christians, but that does not mean that the old-universe / old-earth paradigm is failing in any way. The big picture is there already, the details are under revision. Most of the friction seems to be due to certain theological and exegetical “paradigms” that are being thwarted by the increasingly well-established science of common descent and the old age of the earth.

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.
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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.