Introducing Jeffb

Conversation
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Oh, dear. Big problems. Yes, you can build a tree with any data, but unless the data actually have phylogenetic structure you won’t get a tree that’s better than any other tree; there are statistical tests for that.

Well of course. Nothing can possibly exclude design. The question is whether design (by which you mean separate creation) is necessary to explain the data. If what we see is what we expect from common descent, there’s no reason to propose separate creation.

I’m not sure you know what “neo-Darwinism” means, as you’ve misused it here. It has nothing to do with the TOL. Most of the challenges are at the very root of the tree, among bacteria. Once you get to eukaryotes and especially animals, there’s much less difficulty and the picture of pretty clear.

Pardon me for saying so, but that’s insane. Since we don’t know everything, we therefore know nothing? I see this as nothing more than an excuse to avoid looking at the data.

Now, here’s where you need to be more precise. What creation model? Why would we expect that model, whatever it is, to produce the data we see?

That scenario, unfortunately, makes no sense at all. You can’t construct any coherent model to explain the fossil record that way.

Aren’t those all more or less the same thing? But that’s incoherent if you suppose that most geological formations are the result of a single year’s event. No stasis, no explosions, not even a meaning to “sudden”.

This is not a common occurrence. Where did you get that idea?

But there are thousands of transitional fossils, and I’d say they’re all rock solid.

What does that mean?

I invite you to try explaining the record, then. Don’t see it.

Sure. But some are better than others. Separate creation and a global flood 4500 years ago are very, very imperfect. Basically, you are saying that if science doesn’t go your way, you are going to ignore it until it does. You will have a very long wait.

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Well… I just started a TODO list, and put this on one there. Man I went away for just a few hours and came back to 15 posts! Is it always like this, or was it because I ‘kicked the hornets nest’?
So… be patient, I hope to eventually… I think I’m good for about one reply a day…

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I would suggest you start with your claim that you can create a nested hierarchy out of items from your kitchen. Actually try do this, and then listen to the responses from the people who do this sort of thing every day as their jobs.

If you approach this with an open and curious mind, you will learn a lot. Otherwise, it at least promises to be entertaining for many of us.

Welcome to the group, BTW!

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Shouldn’t he try cars and trucks first? That always works.

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I had to go through my notes that I had collected and re-read some of them. I’ll post all those at the very bottom.

Regarding the construction of nested hierarchies, yes, I’m familiar with the fact that statistics are involved. It’s not just arbitrary. The point you seem to be making is that graphs that are created seem in some way compelling to you. Given that, my kitchen’s data might not be very compelling, but a lot of that could be the smaller sample size of objects I’m working with. More data, better graphs. And there’s a LOT of life on earth to work with in creating your trees. Our (creationists) conclusion is from that data: There’s a lot of life on earth, and there’s a lot of similarities in this life that God created. Your ‘strongly fitting data’ speaks of the abundance of life God created.

As I read back on your post, I get the impression that you’re saying “Why would God make a lot of similar life that we can organize into a tree?” Two responses: 1) Your decision to organize it into a tree doesn’t negate God as the author. And 2) This sounds like an “If I were God” argument. Because “you wouldn’t have done it that way”.

I know you say the data sounds compelling. But as I mentioned, phylogenies are good evidence, except when they’re not. There are enough exceptions to the rules (some are listed in the posts below), to make us creationists not look at phylogenies as very compelling. I believe the orphan genes and taxonomically restricted trees are problematic.

Here’s some of my notes on TOL I found:

“Probably no phylogenetic cladogram, no matter how it is constructed, can be totally ‘proved’ or ‘falsified.’” - W.H. Wagner Jr., “Origin and Philosophy of the Groundplan-divergence Method of Cladistics” in Cladistic Theory and Methodology , ed. Thomas Duncan and Tod F. Stuessy (New York: Van Nostrand Reinhold Company, 1985), 166.

Evolutionary Biology in 2016: “Cladograms lack the causal details of the different hypotheses implied by those diagrams to make testing feasible, and falsification has been shown to be problematic for historical sciences.” Kirk Fitzhugh, “Phylogenetic Hypotheses: Neither Testable Nor Falsifiable” Evolutionary Biology 43, no. 2 (2016) 257-266,

“I do not think that claims made by cladists themselves can always be taken at face value.” David L. Hull “Cladistics Theory: Hypotheses That Blur and Grow” in Cladistics ed Thomas Duncan and Tod F. Stuessy (New York: Columbia Univeristy Press, 1984), 16

(here a few paragraphs I saved)

As more DNA evidence has accumulated, the problem has gotten worse. In 2012, four evolutionary biologists reported that “incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive.” And inconsistencies among phylogenetic trees aren’t even the most serious problem. It turns out that many organisms contain DNA sequences that are not found in any other group. These have been named “orphan genes,” and they have been found in yeast, fruit flies, mice, and humans. A 2015 article in Nature reported hundreds of orphan genes restricted to squids and octopuses.

How can a phylogenetic tree be based on DNA evidence when some sequences have no match? One way is simply to ignore the orphan genes. In 2016 three evolutionary biologists were able to construct a phylogenetic tree of insects only by ignoring 40 percent of the DNA sequences in fruit flies and 80 percent of the sequences in water fleas. Rather than strongly supporting the idea that all living things share a common ancestor, the DNA evidence has to be trimmed and crammed into the idea.

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No, that’s not it. It’s not the number of species or their similarities that counts. It’s that those similarities are organized in a very particular pattern, that nested hierarchy you keep hearing about. Nested hierarchy naturally and inevitably proceeds from common descent with branching, but it doesn’t naturally or inevitably proceed from anyone else. If it’s the result of separate creation, God is carefully simulating descent, and why would he?

It’s not a decision; that’s what you don’t understand. It’s inherent in the data. God, could of course do anything. But why do it in a way that makes it look like descent? What are the odds?

Then you haven’t looked at the evidence.

I will refrain from commenting on your quote-mines except to note that it’s bad form but all too typical. You should be ashamed, especially since I’m betting you found those somewhere and haven’t actually read the articles they’re from.

Why, by using the sequences that do have matches, obviously. You can also use presence/absence data for sequences that don’t have matches. This is a conundrum only if you think that genes can neither be added or deleted in evolution, and we have good evidence that both can happen. This has been discussed heavily on this very site.

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John, I replied with more on another post, so be sure to read that one. But I will try to address a few of these comments.

Point 1: As I was typing “neo-Darwinism” in that post I thought: “Someone’s going to comment on the fact that I used that phrase”. But, I decided to leave it. I’d like to expound on why I used that, but I’ve got way more things to address. BTW, you can’t say it has nothing to do with the TOL
Point 2: Yes, you are correct that there are a number of challenges at the very root of this tree. There’s a significant variety of biochemical and molecular systems that are quite different from the very start (Eukaryotic release factor proteins, bacteria release factor proteins for example). To me: that’s very problematic, and just adds to the reason that I don’t see the TOL being very strong evidence.

Valid. It does appear like an excuse. We have discovered so much in the area of genetics over the years. But at the same time, I’m making that statement because I’m seeing such a break-through in genetic research, lately. We’re being able to track things at the molecular level far better now. It makes want to say: “Yes, good data… let’s see what else we discover”. For example, we may start finding way more orphaned genes. Or for instance those cellular systems at the root of the tree could get even more problematic with time.

It overlaps in the sense that we fit that data into the fact that God created an abundance of life, much of which looks similar. The concept of a tree of common descent is unique to evolution, but the data is not unique to evolution.

No, those aren’t the same. Definitely not the first from the other two. Interesting that you asked, because as I was typing the third (sudden appearance), I thought some might see those two similar. The ‘explosions’ are groups, the cambrian as the classic, but also things like mammals. Sudden appearance deals with individual species. And btw I should have added: sudden appearance of fully formed species.

Regarding related those to the flood: Statis makes perfect sense within the flood. As for “sudden”: that just means the first time a mammal (for example) was buried. The first ones look similar to the last, and don’t have “lineage” predecessors leading up to them, because they all existed at the time of the flood. Not sure how better to explain that one, but it should be pretty straightforward.

Ok I’m going to have to stop there, I’m sorry John, it’s getting late, got work tomorrow. Plus I see you’ve already posted more questions. There’s no way I keep up with your posts John.

I may just have to sum this up: You asked about phylogenies and fossils. My answer is that too creationists: those two are not very strong arguments. Basically, we have a decent answer to those two. Although they seem compelling, they’re not enough to get us to think ocean worms can turn into eagles.

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Mammals didn’t just “suddenly appear”. They have a long and fairly detailed fossil record of having evolved from synapsid ancestors. I can post lots of scientific papers you won’t read or you can look at the good overview on Wiki

Evolution of Mammals

The evolution of mammals has passed through many stages since the first appearance of their synapsid ancestors in the Pennsylvanian sub-period of the late Carboniferous period. By the mid-Triassic, there were many synapsid species that looked like mammals. The lineage leading to today’s mammals split up in the Jurassic; synapsids from this period include Dryolestes, more closely related to extant placentals and marsupials than to monotremes, as well as Ambondro, more closely related to monotremes.[1] Later on, the eutherian and metatherian lineages separated; the metatherians are the animals more closely related to the marsupials, while the eutherians are those more closely related to the placentals. Since Juramaia, the earliest known eutherian, lived 160 million years ago in the Jurassic, this divergence must have occurred in the same period.

After the Cretaceous–Paleogene extinction event wiped out the non-avian dinosaurs (birds being the only surviving dinosaurs) and several mammalian groups, placental and marsupial mammals diversified into many new forms and ecological niches throughout the Paleogene and Neogene, by the end of which all modern orders had appeared.

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Are you interested in learning or not?

What in the world would a not fully formed species look like? A crocoduck?

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That seems odd, since I just did that very thing.

Challenges? No. Just bits that aren’t a simple tree. You can’t say anything is different from the very start. Nor does this help your creationist theory, which of course you haven’t articulated, unless you want to say that Eukaryota is a kind.

In other words, as I already said, you ignore the current data because you hope future data will be different. That’s not healthy.

Yes it is, because the data agree with the concept of a tree of common descent, not just “an abundance of life, much of which looks similar”.

It’s much too vague to be straightforward, and it doesn’t fit the data. A flood just doesn’t sort fossils in the way you suppose. Species have definite ranges in the record, not what you expect from a flood, and the aggregate of sepecies falls into a pattern that matches common descent to a tremendous degree, not any conceivable model of flood sorting.
You are exposing your ignorance of paleontology here.

I’m afraid your answers are not decent. They’re superficial and don’t stand up to a close examination. Examine them closely yourself and you might see that.

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Maybe, but maybe not. We won’t know til you try.

So why don’t you?

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That doesn’t explain why there is a twin nested hierarchy.

  1. If life evolved it doesn’t negate God as the author. There are millions of Christians who accept evolution as the way in which God created.

  2. Evolution does explain the twin nested hierarchy. As you have shown, YEC does not. This is why evolution is the better explanation.

There are exceptions to every rule in science. There is noise in every phylogeny, as we would expect. The problem for Creationism is that the twin nested hierarchy is a fact, and YEC needs to deal with it. If they just ignore it then they can’t claim that they are interpreting the same facts.

Inconsistencies are expected. Noise is expected. This doesn’t refute the fact of the twin nested hierarchy.

They are based on the sequences that do match. The sequences that don’t match should be lineage specific, and they are.

Absolutely no one is ignoring orphan genes. First, the vast majority of orphan genes do have matching DNA in other species, but that DNA isn’t transcribed in those other species. Gene and DNA are not synonyms since much of the DNA in your genome is not found in genes. Second, mutations producing new genes is exactly what we would expect to see in evolution. Orphan genes are some of the best evidence for evolution that we have.

Yes, probably due to them not being able to align highly divergent DNA. Why is this a problem?

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@jeffb, do you know what “twin” means in this context? It’s pretty important.

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Let’s see if this helps, Jeff.

Suppose there is a group of people who are convinced that their Holy Book says gravity does not exist.

You provide them with the evidence for the existence of gravity.

Their response: “That does not show that gravity is real. Our god could just be making things move in exactly the way we would expect if this thing you call ‘gravity’ actually existed. Also, we could take things from our kitchen and put them on the ground, just as if they were pulled there by ‘gravity’.”

Are those good arguments, in your opinion?

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I’ve never liked “twin nested hierarchy”. All it really means is that different data sets tend to support the same tree. But there are more than two data sets or sorts of data. The nature of those data sets, whether osteology, DNA sequences, indels, behavior, or whatever, isn’t important. It’s the independent confirmation that’s important.

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I don’t like it either. I would suggest that “superimposable nested hierarchies” is more descriptive and more easily understood.

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Same here. I use it because TalkOrigins used it, and it makes it easier to discuss the topic when there is consistency in the terms being used.

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If Talk.origins jumped off the roof, would you jump too? Terms that create a false idea should be jettisoned.

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You make a good point. If someone knows of a better description that is more widely used I would certainly use it.

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@jeffb, let help you out here. This would be a good excercise to do. The way you’d get started is by:

  1. Get a list of items for which you want to construct a phylogeny, and aim for at least 20 items.
  2. Get a list of “Traits” or “attributes” for these items, being sure that there are some examples of each trait among the items, and aiming for at least 10 attributes.
  3. Make a table which has each item as a row, and lists out the traits for that item in different columns.

Can you do that?

From there, we can see if your data forms a tree or not, and how far away from a tree it is.

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I like consilience of independent phylogenies because it seems to describe all the important aspects of the evidence.
That they are phylogenetic trees, that they corroborate each other, but also that they are independent and don’t systematically affect or bias each other to result in the same trees. Which means that the fact that they nevertheless do corroborate each other implies something else must be biasing them to do so.
There simply is no good explanation for that other than they are biased by real genealogical history. The phylogenies are similar because the characters used to construct them went through the same genealogical history of descent with modification and splitting.

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