Did We Have "Reptilian" Ancestors?


(Bill Cole) #101

If you say that common descent only confirms similarities then I certainly agree based on that definition that there is good evidence.

Sal’s flower plus Ewerts dependency graph.

I used to think they were the same until you told me that common descent only explains similarities. If you make a claim of common ancestry then you need to explain the differences.

Joshua is a scientist developing an argument for potential the existence of a genealogical Adam and claiming science cannot rule it out.

Claiming science cannot rule something out is a scientific claim as science has a chance to challenge and falsify that specific claim with data.

(Timothy Horton) #102

I notice you’re studiously avoiding the manatee ancestral fossil with hind legs and feet. Why is that?

(John Harshman) #103

Sorry, word salad again.

Neither of which you understand.

There is no difference. Common descent (= common ancestry) explains the pattern of similarities and differences among species. If species X and Y share a character to the exclusion of species Z, that tells us that species X and Y share a common ancestor in which that character appeared, not shared with species Z. (It’s more complicated than that, but you should start with the simple stuff.)

On this we disagree.

(John Mercer) #104

Behe no longer does studies. He writes books.

(Mikkel R.) #105

Yes, so they evolved from ancestors with four limbs which have clear homologous attributes to terrestrial and semi-aquatic mammals? Why should that be the case if they don’t share common descent with terrestrial mammals? Why should such an intermediate stage exist in the whale ancestral past? God just mysteriously felt like creating transitional whale attributes?

(Bill Cole) #106

They are both fairly straight forward. You accept gene loss as an explanation and I am skeptical especially with the incidence in the dependency diagram where genes are shared uniquely in humans and rats that do not occur in mice and chimps.

Neither of us know what happened in the past so your explanation cannot be made with certainty.

Your conclusions are based on universal common descent as a working hypothesis.

Does common descent explain echolocation emerging in bats and whales and flight occurring in birds and bats?

You previously had claimed that common descent did not explain the origin of novelty. Are you backing off that claim as novelty is a difference that needs to be explained.

(John Harshman) #107

And yet you don’t understand them.

Why does that make you skeptical?

That’s a version of the creationist canard “Were you there?”, for which you should be mightily ashamed. We can be quite sure of a great many things that happened in the past, so long as they left evidence to be found in the present.

No, common descent within the group being investigated is a conclusion, which is to say it’s a hypothesis that has been tested by the data.

No. But it explains the quite different structures and adaptations that are shown by those organisms for the purpose.

True. What it explains is the pattern of distribution of those novelties among taxa. How many more times does this have to be said?

Once more, you have to distinguish between the explanation for the origin of a feature and the explanation for the taxonomic distribution of that feature. It’s my forlorn hope that if I tell you that often enough you will come to understand it.

(Herculean Skeptic) #108

Curious as I was reading this thread to know how it is that one would assume that these legs protruding from the body were left over from a predecessor and not something from some new, evolutionary next step instead??

(John Harshman) #109

Simply put, parsimony. Whales are phylogenetically embedded deep within Tetrapoda, and all of their ancestors up until fairly recently (40 million years or so) had rear legs. Further, there are fossils showing the progressive reduction in size of legs in early whales. To assume that legs were lost and then regained in a similar form is unparsimonious.

(Bill Cole) #110

Because I see no explanation for this to occur from ancestry alone that seems probable. Perhaps you do.

So you pull out the evolutionist “all the overwhelming evidence canard” to battle the creationist canard. Your level of certainty is not warranted and only due to your commitment to the paradigm.

You have yet to support this claim by clearly describing an objective test that would reject the hypothesis in one case and accept it in another.

(Bill Cole) #111

Based on the working assumption that all Tetrapoda share a common ancestor.

(Herculean Skeptic) #112

Thanks, that’s interesting. If parsimony rules, when would we expect (or how would we determine) that an incomplete appendage was some new feature that was under development rather than an old feature fading away. (I’m certainly using the wrong technical terms, so please extend a little grace here.) It would seem that if one were to go back in time, they would find an ancestor that had to go through a similar process of growing legs or fins, for instance.

Finally, are there any species alive now about which scientists are able to point out new features that are developing (as per my initial question?)

(John Harshman) #113

It’s unclear what you mean by “from ancestry alone”. Do you mean that you think gene loss doesn’t happen? Does it mean that the same gene can’t be lost in two different species independently? Does it mean that you think it can’t happen as often as required by phylogeny?

How would you know? You’ve never looked at the evidence, despite my having sent you to it many times.

That’s true with most statistical tests. You can either reject the null hypothesis or fail to reject it. You can’t accept the null hypothesis. In this case you can consider “no tree” as the null hypothesis, and in the cases at hand we can with high confidence reject it in favor of the particular tree supported by the data. Now go back and look at the papers to find the statistical tests performed in them.

Based on the masses of data showing that all Tetrapoda share a common ancestor. Again, have you ever looked?

(John Harshman) #114

That’s a technical question, hard to answer except with pictures of trees and complex character coding. But if the ancestor had legs, and they resemble in detail the new appendage we find on that occasional whale, to suppose that it’s a completely new feature would require that all those details arose coincidentally rather than being retained, unexpressed, from an ancestor. Too many coincidences are unparsimonious.

There’s rarely anything in the history of life that’s a completely new feature. Most new features arise from changes to old features. And how would you recognize an incipient new feature to distinguish it from a minor variation? How can you tell if a new feature is going to develop any further? This really isn’t something that could be recognized except in retrospect. I could show you plenty of new features in retrospect, but I don’t know how to show you one that’s happening now.

(Herculean Skeptic) #115

A post was split to a new topic: Greg On The Odds of Macroevolution and Vegas

(Herculean Skeptic) #116

Thanks for your response… I know that the example being discussed here was the whale, but I meant the question to be less specific, so feel free to answer it in general if this is not a good example. I often hear of specific items of interest (functions) being referred to as vestigial, but I never hear of these kinds of things being discussed in terms of being newly evolved functions.

That make sense, so you look back at the predecessor to see if it possesses a similar feature or function, if so it can be said that it was likely to have inherited the function or feature from that earlier species?

We all know that, assuming common descent, that every function or feature was once new. How did parsimony come into play earlier on then? It seems to me that as we look further back in time, we see species develop from much simpler species from which a library of functions and features were not available to contribute to the newer species.

It seems as though novel features came about, initially at least, in an environment where there were there was very little prior work from which to draw (changes to old features, as you have described), and further that parsimony did not seem to come in to play as it does now.

I realize that my questions and scenarios are gross oversimplifications, but I would imagine that scientists in your position must wrestle with these questions also, if they don’t already have good answers for them. I welcome other scientists to chime in, also. This is one of the ‘stumbling block’ areas for me as I try to wrap my brain around how evolution can explain the breadth of species that existed over time.

(John Harshman) #117

So you’re looking for something that looks the same as a vestigial organ but is instead newly evolved? I don’t think new functions begin as vestigial organs.

Roughly, though of course we can never say that this predecessor is an ancestor. We reconstruct ancestral states based on the phylogenetic tree.

It’s surprising how rarely anything truly new happens. Of course it does sometimes, but even then it’s hard to recognize it as new. Lungs, for example, likely began as just a section of the pharynx with a few more capillaries than usual, then as a depression in the pharynx that increased the vascularized area, then as an outpocketing. Enough little changes, and you have a new organ. But where’s the new bit? It’s just a combination of pharynx and capillaries. Do we then have to go back to the origin of the pharynx and of capillaries? But they come from prior parts too. There’s so rarely anything that’s fundamentally new in evolution.

Not sure what that means.

(Timothy Horton) #118

In addition genetic studies show all extant cetaceans (and sirenians and pinnepeds) have the functional but unexpressed Tbx4 genes for hind limbs in ther genomes. Atavisms occur when an occasional mutation reactivates all or part of the leg forming genes.

Sequence Variation in the Tbx4 Gene in Marine Mammals

(Timothy Horton) #119

Look over there Bill! It’s a shiny thing!!

(Herculean Skeptic) #120

Thanks again, John. I didn’t mean that exactly. I was referring back to the example in this thread. There was a whale that have vestigial hind limbs. Those limbs were referred to as being leftovers, so to speak, from the predecessor. These “hind limbs” were said to be remnants from a four-legged land animal from which the whale evolved. So, my question was regarding why, when we see something like the remnant of a hind limb that is not used by a whale, it is assumed to be a remnant from the past rather than something developing for the future.

The reason for asking this question is because of the next point that I make… namely, that if you go back far enough in time, you will find very simple animals. From that point forward, all of the functions or features that we see in the more complex animals are, in essence, new.

So, if we say that very early, very simple animals had “tissue” and “skeleton” for instance, then I guess you have the ingredients that you need for “tissue” to become “trachea” and then “lungs.” But, while one can look back in retrospect to see that lungs were merely tissue, once, the entire process still seems to go against the rule of parsimony. It seems that all of the function that did evolve over time should not have been expected to have done so.

This is interesting. So in the whale example above, there seems to be naturally occuring hind limbs, but they are not fully developed and are described as vestigial. These “limblets” seem to be normal (I know nothing about whales, but the thread above seems to indicate such.) So what is the difference between the vestigial limblets shown above and an animal where an atavism occurs? Are you saying that a fully formed limb, rather than a limblet (sorry, my silly term) would be there? Would it be a whale with a true hind leg, flesh and all? Is there a picture of anything like this that can be seen?