Dirty secret of Evolutionary theory?

[SkepticalOne]

Let me preface this by saying that I am not trying to argue for a creationist interpretation of the data, regardless of my beliefs. But I have some concerns over what seems to be a generally un-discussed problem with evolutionary theory as it pertains to phylogenetics and the fossil record.

Paleontologists construct phylogenetic trees depicting sister taxa branching off from nodes that denote an unidentified common ancestor. I understand that the fossil record is such that it is essentially impossible to claim with certainty that taxon A is the direct ancestor of taxon B, but I don’t understand the justification for using a sister taxon as a stand-in for that unidentified node. For example, Tiktaalik is presented as a transitional form between fish and tetrapods but the Polish tracks prove that it is not ancestral to tetrapods. Paleontologists claim that we can look at Tiktaalik’s morphology to get an idea of what the unidentified common ancestor linking Tiktaalik’s lineage with the tetrapod lineage looked like, but how is this claim supported? What evidence is there that sister taxa can furnish useful information about an unidentified relative? What is the use of looking at Tiktaalik’s purportedly transitional morphology and basing inferences on it when the node for which it is being used as a proxy is not known to exist? Is it just to be assumed that there is an ancestor based on the preconception of common ancestry? I bring these questions here in hopes that they can be addressed properly as I have been unable to find an answer elsewhere.

[psiloiordinary]

This was from Paul by email;

The expression "transitional form" is a slippery one.

Tiktaalik is transitional in the sense that it possesses some, but not all, of the features found in all tetrapods but not in their lobefish ancestors. Crudely, it has radius, ulna, and wrist bones, and what may to my non-expert eye be digits (an expert would look at the anatomy in much more detail, of course, correlating numerous points and ridges) but with only one bone per digit, unlike the jointed digits found in Acanthostega.

Inference; the LAST COMMON ANCESTOR (LCA) of Tiktaalik and tetrapods was later than the LCA of lobefish and tetrapods, but earlier than the LCA of Acanthostega and tetrapods. This, and no more than this, is what is meant by saying that Tiktaalik is intermediate between lobefish and tetrapods, but that Acanthostega is closer to tetrapods than Tiktaalik is.

The Polish footprints show, either that there were in the mid-Devonian two completely separate lines of descent leading to tetrapods (extremely unlikely), or that Tiktaalik is at least 20 million (if I recall the numbers correctly) years more recent than its LCA with tetrapods. And why not? There are ways in which a modern frog is intermediate between lobefish and amniotes (notably, it has limbs, but needs to lay eggs in water), although it is IIRC around 350 million years more recent than its LCA with amniotes including you and me.

The confusion arises because we think of evolution as a ladder, whereas it is really a bush. "Transitional" is defined in terms of features, but is often misunderstood to imply ancestry or at least sequence; hence your perceptive question. Creationists, of course, are unable or more probably unwilling to escape the confusion.

There is another trap lurking, BTW. The temptation is to think of the frog as less evolved than us. WRONG. We and the frog have been evolving for exactly the same length of time since our LCA.

I hope this helps.

Paul S. Braterman,
Professor Emeritus, University of North Texas
Honorary Senior Research Fellow in Chemistry, University of Glasgow

[SkepticalOne]

This was from Paul by email;

The expression "transitional form" is a slippery one.

Tiktaalik is transitional in the sense that it possesses some, but not all, of the features found in all tetrapods but not in their lobefish ancestors. Crudely, it has radius, ulna, and wrist bones, and what may to my non-expert eye be digits (an expert would look at the anatomy in much more detail, of course, correlating numerous points and ridges) but with only one bone per digit, unlike the jointed digits found in Acanthostega.

Inference; the LAST COMMON ANCESTOR (LCA) of Tiktaalik and tetrapods was later than the LCA of lobefish and tetrapods, but earlier than the LCA of Acanthostega and tetrapods. This, and no more than this, is what is meant by saying that Tiktaalik is intermediate between lobefish and tetrapods, but that Acanthostega is closer to tetrapods than Tiktaalik is.

The Polish footprints show, either that there were in the mid-Devonian two completely separate lines of descent leading to tetrapods (extremely unlikely), or that Tiktaalik is at least 20 million (if I recall the numbers correctly) years more recent than its LCA with tetrapods. And why not? There are ways in which a modern frog is intermediate between lobefish and amniotes (notably, it has limbs, but needs to lay eggs in water), although it is IIRC around 350 million years more recent than its LCA with amniotes including you and me.

The confusion arises because we think of evolution as a ladder, whereas it is really a bush. "Transitional" is defined in terms of features, but is often misunderstood to imply ancestry or at least sequence; hence your perceptive question. Creationists, of course, are unable or more probably unwilling to escape the confusion.

There is another trap lurking, BTW. The temptation is to think of the frog as less evolved than us. WRONG. We and the frog have been evolving for exactly the same length of time since our LCA.

I hope this helps.

Paul S. Braterman,
Professor Emeritus, University of North Texas
Honorary Senior Research Fellow in Chemistry, University of Glasgow

These are crucial distinctions indeed. Most creationists do seem unwilling to understand that being related and being ancestral aren't necessarily the same thing. I understand that, but your response doesn't quite address the question I was asking. What I would like clarified is the justification for using a sister taxon such as Tiktaalik to make inferences about a common ancestor that is predicted to exist but is unknown. What evidence do we have that a sister taxon furnishes useful information about that common ancestor? Especially in cases where the sister taxon being used as a proxy is a so-called late-surviving relic like Tiktaalik rather than being especially close in a temporal sense to the unknown common ancestor.

[SkepticalOne]

I have to admit that this is disappointing. Based on what I knew of this community I had expected that a question regarding such a fundamental assumption in paleontology and evolutionary biology would be quickly addressed. So far there has been only a single well-intentioned but not quote germane response. I know from observation that the Free for All board has more traffic. Would reposting my question there elicit more of a response?

[Brian Jordan]

I'll move the thread for you. There are plenty of people on FFI who are familiar with the "were you there?" argument. For which your question seems to be a proxy.

[Brian Jordan]

Mod Note: topic moved from Science.

[a_haworthroberts]

I think SkepticalOne raises a valid question. I don't know the answer. My only thought is that the broad topic of nested hierarchies, involving already known species, may be of relevance.

[Christine Janis]

Hi Guys

Ashley just alerted me to this topic from SkepticalOne ---- have been busy for a while.

“I have some concerns over what seems to be a generally undiscussed problem with evolutionary theory as it pertains to phylogenetics and the fossil record.”

Before I make a more detailed reply, I’ll note two things up front.

1. SkepticalOne is conflating phylogenies with family trees.

2. Whatever the Polish footprints are or are not, any new early tetrapod would not affect the phylogenetic position of Tiktaalik, nor the interpretations derived from it about the common ancestor of fish and tetrapods, because it would lie above Tiktaalik in the phylogeny.

OK, back to a more general discussion.

“Paleontologists construct phylogenetic trees depicting sister taxa branching off from nodes that denote an unidentified common ancestor.”

This focus on the notion of a “common ancestor” belies the error of mistaking a phylogeny for tree. A phylogeny shows the hierarchical nesting of taxa based on acquired derived characters. The nodes denote the places where such characters are acquired. In theory, one can use the accumulation of characters at any particular note to denote the hypothetical common ancestor at that point, but that is not the purpose of the phylogeny. A phylogeny of recent dog breeds would show a similar pattern, despite the fact that we might know what the ancestral breed was.

“I understand that the fossil record is such that it is essentially impossible to claim with certainty that taxon A is the direct ancestor of taxon B, but I don’t understand the justification for using a sister taxon as a stand-in for that unidentified node.”

That is not what a phylogeny is used for. See the above explanation.

“For example, Tiktaalik is presented as a transitional form between fish and tetrapods but the Polish tracks prove that it is not ancestral to tetrapods”

Many issues here. (i). Tiktaalik is placed where it is on the phylogeny because possesses morphology intermediate between the fish Panderichthyes and the tetrapod Acanthostega. This is a different issue from whether or not it is ancestral to Acanthostega. Extant monotremes possess a morphology intermediate between that of cynodont therapsids and therian mammals (marsupials and placentals): they are clearly not ancestral to therians as they are alive today, some 150 million years after the first known therian).
(ii). The Polish tracks are interesting, but at best only inform us about the timing of tetrapod evolution. Tiktaalik is known from a moment in time --- we cannot tell when that lineage first began or ended from the current resolution of the fossil record. Additionally, many paleontologists have doubts about the validity/relevance of those footprints (as I understand from conversations at meetings).

“Paleontologists claim that we can look at Tiktaalik’s morphology to get an idea of what the unidentified common ancestor linking Tiktaalik’s lineage with the tetrapod lineage looked like, but how is this claim supported?”

Because paleontologists don’t decide a priori where to place Tiktaalik on the tetrapod lineage. It is placed there by virtue of its morphology. For example: Tiktaalik, unlike any other known fish (that is, a vertebrate that possesses fin rays rather than digits), lacks a bony operculum. As tetrapods lack a bony operculum, this leads us to the conclusion that the common ancestor of tetrapods and Tiktaalik lacked an operculum (assuming that this loss is not convergent between Tiktaalik and tetrapods, but given the weight of evidence of other similarities there is no reason to consider this assumption to be unreasonable).

“What evidence is there that sister taxa can furnish useful information about an unidentified relative?”

Because of how they are defined. See above.

“What is the use of looking at Tiktaalik’s purportedly transitional morphology and basing inferences on it when the node for which it is being used as a proxy is not known to exist?”

The node is a point on a cladogram. It exists as part of a generated pattern from the similarities in morphologies. The morphology of Tiktaalik is what has generated that node in the first place. To ask how its morphology supports the node is a completely circular question.

“Is it just to be assumed that there is an ancestor based on the preconception of common ancestry?”

The entire point of a phylogeny is that it is a representation of a pattern of a nested hierarchy of characters, from which processes of evolution can be deduced/inferred. Common ancestry is not a preconception on which phylogenies are based: common ancestry is a deduction based on the phylogenetic pattern that is generated by the nested hierarchies of morphological characters (which in phylogenies of extant taxa are backed up by many different types of molecular/genomic characters).

“Let me preface this by saying that I am not trying to argue for a creationist interpretation of the data,”

I’m dubious about this disclaimer

Christine Janis
Professor of Biology, Brown University
Fellow of the Paleontological Society
(if Paul Braterman is going to list his qualifications to answer, then so shall I).

[Michael]

Christine
It is often important to know how qualified someone is, as that shows where they are competent

This issue attacts those who think they know, especially among creationists.

However most who post here are frank about their knowledge and admit to limitations

M ichael

[Brian Jordan]

Christine Janis
Professor of Biology, Brown University
Fellow of the Paleontological Society
(if Paul Braterman is going to list his qualifications to answer, then so shall I).

Just for the record, Paul didn't post his qualifications on the forum. What was posted (by Psi) was a copy of an email, from before SO joined the forum, which contained Paul's email sig. An email containing an answer to SO's question that evidently didn't satisfy him, btw.

[SkepticalOne]

Excellent. This is what I was after, Christina. You would perhaps be surprised at how unsuccessful I was at finding an answer like that through various Google searches. I think I understand what you're saying, but I want to clarify a bit. Let us leave out the phylogenies for a moment as they represent a specific scientific tool designed for a specific purpose as you said.

So Tiktaalik's morphology makes it appear transitional (regardless of whether it is ancestral) between fish and tetrapods. The incompleteness of the fossil record makes it very unlikely that Tiktaalik is actually on the direct line to tetrapods so it is being used to represent the animal that actually is our direct ancestor. You are saying that Tiktaalik's mosaic morphology indicates its relationship to fish and tetrapods and if it is related in this way then it implies the existence of the ancestral animal that must have looked similar. Do I have that right?

Also, Christina, while I appreciate the detailed response, I think you should not be so quick to judge the motives of those posting here unless they reveal them. I wanted a scientific answer to a question about science, not to try to express any metaphysical position.

[Roger Stanyard]

Excellent. This is what I was after, Christina. You would perhaps be surprised at how unsuccessful I was at finding an answer like that through various Google searches. I think I understand what you're saying, but I want to clarify a bit. Let us leave out the phylogenies for a moment as they represent a specific scientific tool designed for a specific purpose as you said.

So Tiktaalik's morphology makes it appear transitional (regardless of whether it is ancestral) between fish and tetrapods. The incompleteness of the fossil record makes it very unlikely that Tiktaalik is actually on the direct line to tetrapods so it is being used to represent the animal that actually is our direct ancestor. You are saying that Tiktaalik's mosaic morphology indicates its relationship to fish and tetrapods and if it is related in this way then it implies the existence of the ancestral animal that must have looked similar. Do I have that right?

Also, Christina, while I appreciate the detailed response, I think you should not be so quick to judge the motives of those posting here unless they reveal them. I wanted a scientific answer to a question about science, not to try to express any metaphysical position.

I'm confused as to what you are saying. Given that creationists don't believe that evolution leads from one species to anoth, precisely what is your explanation of the position of Tiktalik either in the fossil record or the nested hierarchy of species. I'm not interested in what holes you think you have found in evolutionary biology. I'd like, instead, for you to provide your creationist position.

[Peter Henderson]

I'm not interested in what holes you think you have found in evolutionary biology. I'd like, instead, for you to provide your creationist position.

Yep, indeed Roger.

I'd like to know Skepticalone's science background, and if he's actually qualified in biology or not, or is he simply repeating a creationist claim while not even understanding the science ?

For example, how old does he think the Earth is and why ?

[a_haworthroberts]

IF SkepticalOne is saying he does not wish to argue for a creationist position, which I gather might be what he is saying when using the word 'metaphysical', then I personally think it is rather poor debating for three of you to suggest that he is not telling the truth in his comments (though I would agree that the phrase 'dirty secret' is fairly emotive).

[Christine Janis]

So Tiktaalik's morphology makes it appear transitional (regardless of whether it is ancestral) between fish and tetrapods. The incompleteness of the fossil record makes it very unlikely that Tiktaalik is actually on the direct line to tetrapods so it is being used to represent the animal that actually is our direct ancestor. You are saying that Tiktaalik's mosaic morphology indicates its relationship to fish and tetrapods and if it is related in this way then it implies the existence of the ancestral animal that must have looked similar. Do I have that right?

Not exactly. Tiktaalik is not being used to represent any particular ancestor. It places itself into the known phylogeny (or, rather, people using its anatomical characters find that it fits in that position). Tiktaalik likely has its own specialties. Indeed, its "bendable elbow" is likely convergent with that of later tetrapods, as it is not present in the earliest known tetrapod, Acanthostega.

What Tiktaalik shows us is the ordering of character change. For example, without Tiktaalik we would not know that the operculum was lost before digits were obtained. The same as, without the example of modern monotremes, we would not know that lactation was developed before breasts had nipples.

Also, Christina, while I appreciate the detailed response, I think you should not be so quick to judge the motives of those posting here unless they reveal them. I wanted a scientific answer to a question about science, not to try to express any metaphysical position.

Firstly, if you were indeed paying attention to my post, then you would know that my name is "Christine", not "Christina". Secondly, anyone who uses the term "dirty little secret" in a heading about an issue of evolutionary biology still has my reservations.