Building Trees Sequentially
by Bradford'High Rates Or Low Rates Say It All': The Shaky Ground Of Molecular Systematics is authored by Robert Deyes and appears at The ID Report. The first paragraph:
Writing over a decade ago, UCLA biologists Laura Maley and Charles Marshall noted how genetic sequence comparisons carried out between different animal phyletic groups can lead to significantly different interpretations of evolutionary relationships depending on which species is chosen to represent each group (Ref 1). Such a finding should raise concern amongst protagonists of molecular systematics who today use sequence data to determine evolutionary relationships. Yale University's Gavin Naylor showed just how inaccurate such comparisons could be in the context of the vertebrate evolutionary tree (Ref 2). Mitochondrial DNA sequence analyses of 19 different taxa generated an astounding result- frogs and fish were clustered in the same clade as chickens even though "strong morphological and fossil evidence" did not show these as being in any way related by a common ancestor (Ref 2). The same mitochondrial DNA sequences placed echinoderms- which include starfish and sea urchins- in closer proximity to the vertebrates than amphioxus even though, being a chordate, we would expect amphioxus to be closer (Ref 2). That is, if we give the evolutionary tree any credibility.
This is not the first time I have come across this critique. The choice of species or the nature of the sequences being compared can affect an analysis. Deyes goes on to discuss rhodopsin before throwing this red hot pepper in the pot:
So it is that within this context we can understand evolutionary biologist Leo Goodstadt's assertion that "genomes are lab books of giant evolutionary experiments" as meaning evolution through undirected, natural causes (Ref 7). Such an assertion is stymied by the fact that not only do we not have any evidence for a common natural ancestor for all vertebrates but we do not have any evidence that natural causes can bring about gross-level evolutionary diversity be it through natural selection on gene fusions and gene duplications, the appearance of pseudogenes, frame shift mutations or any other genetic mechanisms that were identified at the conference (Ref 7).
This flies in the face of the often repeated claim that robust predictability is a basic feature of MET. We've seen that in comments at Telic Thoughts. And there is this concluding paragraph:
The take-home message from such a conflict is that in addition to critically scrutinizing current theories on how mammals and archosaurs supposedly coexisted we should also be carefully examining what we do and do not know about the vertebrate sequence. We seem so intent on placing all of life within an assumed evolutionary framework that, even when genetic differences are inconsistent with supposed taxonomic proximity, we explain away these differences simply on the basis of different rates of evolution. Indeed Goodstadt finished his list of bold claims by asserting that "high or low rates [of genetic change] say it all" (Ref 7). With such sweeping generalizations, who can refute anything?
Or what independent data would confirm the high/low rate claim?
October 11th, 2008 at 9:40 am
Oh my! So now we're rejecting Common Descent.
The Maley and Marshall 1998 article is The Coming of Age of Molecular Systematics. With that title, it's hard to believe that it undermines Molecular Phylogenetics. But let's take a look.
They call for more data and more precise hypothesis-testing. Imagine that. Let's take a look at Deyes' use of his second cite.
That article, from way back in 1997, is titled, Morphologists Learn to Live With Molecular Upstarts. Again, it's hard to see how that would lead one to reject molecular evidence of Phylogenetics. It seems to suggest just the opposite. But let's take a look.
Hey, maybe this molecular stuff is a bunch of hooey.
Okay. Maybe not.
You don't suppose scientists don't account for different rates of evolution. From the first cite.
So rates do matter. High rates lead to higher rates of homoplasy. Some genes evolve faster than others. So constructing a molecular phylogeny may require a fuller understanding of the data.
I wonder what those molecular upstarts have been up to since those halcyon days of yore.
Comment by Zachriel — October 11, 2008 @ 9:40 am
October 12th, 2008 at 6:43 am
Bradford
I know Mike Gene happily accepts common descent. Do you reject it?
Comment by The Pixie Again — October 12, 2008 @ 6:43 am
October 12th, 2008 at 8:34 am
I don't reject scientific evidence for it and as for happily- that is contingent on an acceptance of Mike's front loading concept. There is bias evident in my previous statement and I acknowledge having it. It's something we should all do and if done would make discussions less hostile. I do find however that the evidence for life itself (the origin of unicellular organisms) is consistent with a sudden creative act and if you wish to brand me a creationist for thinking this go ahead. I'm more than willing to discuss the physical reasons for this. Of course I think God would be traced as the ultimate causal source in any physical scenario.
Comment by Bradford — October 12, 2008 @ 8:34 am
October 12th, 2008 at 10:17 am
The clue here, genius, is that its "uncommon" descent. The type Pixie and Zachriel believe is the common one accepted by all chance worshipers.
Comment by computerist — October 12, 2008 @ 10:17 am
October 12th, 2008 at 10:47 am
Does Uncommon Descent not result in discernable phylogenetic trees?
Comment by Zachriel — October 12, 2008 @ 10:47 am
October 13th, 2008 at 7:30 am
Bradford
Geat politician answer there. A simple yes or no might have been clearer. The bias in the OP suggests that you reject common descent; is that the bias you admit to having?
computerist
Why do you call me genuius (I assume you are refering to me)? Is it meant ironically? Do you find your arguments are well served by sarcastic insults?
What are you talking about? Are you getting confused about what blog you are posting on?
I have never met a chance worshipper - not even on the internet - so I could not say. The common descent I was referring to was the theory accepted by virtually all biologists, whether theists or atheists (so I guess the chance worshippers too).
Comment by The Pixie Again — October 13, 2008 @ 7:30 am
October 13th, 2008 at 9:34 am
How's this for clarity? There is evidence for common descent. That does not detract from the author's methodology critique.
You're showing your bias. I don't censor the selection of blog links based on conclusions of the authors particularly when they point out issues of interest. If I had to agree before linking I would not have linked to Newman's piece which makes a lot of interesting points.
Comment by Bradford — October 13, 2008 @ 9:34 am
October 13th, 2008 at 10:30 am
Bradford
Anytime anyone asks me a question and my answer is not clear, please do ask for clarification.
I was refering to the comments you made, that seem to suggest you think the article lessens the support for common descent.
So let me try a direct question: Do you think the article in the OP weakens the case for common descent?
Here is another: Do you reject common descent?
Comment by The Pixie Again — October 13, 2008 @ 10:30 am
October 13th, 2008 at 10:51 am
That's one interpretation and it is consistent with your concerns. The article discussed matters that are important apart from common descent. Deyes:
What is your concern when you read this- that sequence comparisons be made as accurately as possible or that CD is being undermined? Are you so insecure in your thinking that if I do link to an article that would deny CD outright that this in itself would be inappropriate? Why not instead focus your comments on the specifics of the blog entry?
Asked and answered. BTW, when commenters ignore specific issues that bear on the science of evolution and instead focus on a pledge of allegiance a non-scientific ideology is the motivation.
Comment by Bradford — October 13, 2008 @ 10:51 am
October 13th, 2008 at 11:34 am
Bradford
My concern is that you are talking out of both sides of your mouth, supporting common descent when you want to distance yourself from creationism and so appear more scientific, and rejecting common descent when you want to distance yourself from Darwinism. The wording in the OP seemed to be trying to sow seeds of doubt, without actually saying you reject common descent (in particular, "This flies in the face of the often repeated claim that robust predictability is a basic feature of MET.", and so I asked the question. Your first reply to me left me none the wiser - which is what one would expect if I am right about your dual position on the issue.
I am only guessing, here, but my hypothesis does fits the facts well. I invite you to prove me wrong by stating clearly where you stand. My guess is that you will not (or do people here think Bradford has been clear; anyone want to tell me what Bradford believes on common descent).
I found nothing concerning in the article itself, only in your presenting of it. So the tree of life cannot be determined with absolute certainty - that is no surprise to me.
Comment by The Pixie Again — October 13, 2008 @ 11:34 am
October 13th, 2008 at 1:31 pm
You're confused. You brought the term common descent into the discussion. I don't distance myself from creationists. If you read my initial response carefully you would note that an abrupt appearance of unicellular organisms is consistent with creation. As for science, I'm the one writing about scientific papers and comments by scientists about scientific issues and critics like you are for the most part ignoring these things in favor of making me the issue instead.
MET refers to mainstream evolutionary theory. The authors critiques could indicate a need to acknowledge the contingency of the tree rather than the need to panick about an all out attack on CD.
Comment by Bradford — October 13, 2008 @ 1:31 pm
October 13th, 2008 at 5:27 pm
Bradford, what aspect of MET do you think the paper challenges, if not common descent?
Comment by The Pixie Again — October 13, 2008 @ 5:27 pm
October 13th, 2008 at 5:57 pm
Pixie:
Prediction accuracy.
Comment by Bradford — October 13, 2008 @ 5:57 pm
October 14th, 2008 at 3:52 am
Oh, okay then. And what does the article about prediction accuracy? Can you tell us what prediction is at question here? What does the article tell us about that prediction? I ask because the obvious prediction I see that is at issue here is one that follows from common descent, and you seem to think otherwise. Or have I misunderstod you?
Comment by The Pixie Again — October 14, 2008 @ 3:52 am
October 14th, 2008 at 7:23 am
Reusing a quote:
The argument is that the choice of species can determine the conceptualization of the tree. The accurate prediction of descent relationships is at issue.
Common descent is a very general term that by itself does not specify which species descended from which and when divergence occurred. You can see a tree and not correctly get the branching if your view is not right.
Comment by Bradford — October 14, 2008 @ 7:23 am
October 14th, 2008 at 7:52 am
If that is all you are arguing then we all agree, and modern evolutionary theory (MET) is not affected one jot.
And you are saying that that prediction relates to modern evolutionary theory, but not to common descent?
Are you claiming that if we get the branching wrong, then that suggests MET is dubious, but it says nothing about common descent? Can you talk me though your logic here, because I really have no clue what you are getting at.
Comment by The Pixie Again — October 14, 2008 @ 7:52 am
October 14th, 2008 at 10:29 am
If the branching is wrong the theory needs adjusting. If the methodology utilized yields an unacceptable pattern of errors a more fundamental adjustment is suggested.
You're the one who introduced the phrase into the thread and you're the one who repeats it as if it were a concern to someone other than you.
Comment by Bradford — October 14, 2008 @ 10:29 am
October 14th, 2008 at 11:36 am
When trying to untangle complicated relationships in the distant past, the details may be difficult to discern. It doesn't mean the Theory of Evolution needs to be revamped.
Yes, and Common Descent may be an inappropriate model for the root of the Tree of Life. However, the objections in the article were misleading.
You linked to and quoted from an article that purports to poke holes in the Theory of Common Descent. From the article:
Comment by Zachriel — October 14, 2008 @ 11:36 am
October 14th, 2008 at 12:40 pm
That's your interpretation. The author made specific points which could be interpreted as aimed the accuracy of current understanding. That's the most straightforward way of viewing it.
Comment by Bradford — October 14, 2008 @ 12:40 pm
October 14th, 2008 at 4:21 pm
Bradford
I am really not getting you. The article is all about teasing out the tree of life, and how reliably that can be done. The tree of life is a part of common descent. If you can refute the tree of life, then you refue common descent. Of course, common descent is in turn a part of evolution, and so if you refute common descent you will also refute modern evolutionary theory (MET). What I cannot understand (and I am starting to wonder if you do) is how you can imagine that refuting the tree of life can refute MET, but leave common descent in tact.
Hence your latest effort is pushing vagueness to new heights with "aimed the accuracy of current understanding", which so desparately tries to avoid saying our understanding of common descent.
We brought it up because we were trying to understand what your point is. When you said "This flies in the face of the often repeated claim that robust predictability is a basic feature of MET." the only robust predictability that relates to the article that I can see is about common descent (and so of MET too, I know). You have certainly not offered any other explanation, and indeed have done your best to avoid giving any straight answers at all.
Comment by The Pixie Again — October 14, 2008 @ 4:21 pm
October 14th, 2008 at 5:13 pm
Are you are saying that robust predictability reduces to common descent? Not very detailed or robust is it? How robust is a tree whose branches are in need of continual untangling?
Comment by Bradford — October 14, 2008 @ 5:13 pm
October 15th, 2008 at 5:05 am
Predictability about the tree of life certainly is about common descent. I do not understand why you might think otherwise.
So are you now arguing against common descent?
Hmm. Perhaps it goes like this. You accept common descent, and so you accept that there is a tree of life, however, you reject the specefic structure that MET currently proposes. Therefore you feel that as this paper questions that specific structure, then thast calls into question MET, but not the general idea of common descent. Is that close?
By the way, do you think humans and monkeys are related? Perhaps if you could answer that (a simple yes or no is, I imagine, out of the question) it would give us some better idea of your position.
Comment by The Pixie Again — October 15, 2008 @ 5:05 am
October 15th, 2008 at 7:57 am
Large flightless birds of the southern continents – African ostriches, Australian emus and cassowaries, South American rheas and the New Zealand kiwi – do not share a common flightless ancestor as once believed.
These types of adjustments occur fairly regularly.
Comment by Bradford — October 15, 2008 @ 7:57 am
October 15th, 2008 at 8:12 am
Of course they do. Notice that the evidence doesn't refute common descent. Just because we find out that Sally Hemings' descendents are unexpectedly related to Thomas Jefferson doesn't mean that we toss out our theory of how babies are born. Indeed, we adjust the family tree and come to a better understanding of these hereditary relationships.
Comment by Zachriel — October 15, 2008 @ 8:12 am
October 15th, 2008 at 8:26 am
Bradford
Do you think that argues for or against common descent?
Do you think that argues for or against the tree of life?
Do you think that argues for or against MET?
Can you explain your reasoning? I am guessing no, by the way, judging by past performance.
Comment by The Pixie Again — October 15, 2008 @ 8:26 am
October 15th, 2008 at 8:52 am
A strawman played up by you and Pixie.
Comment by Bradford — October 15, 2008 @ 8:52 am