Fuzz, Birds, and DNA

When physical appearance contradicts the DNA analysis, which do you believe?

This article was pasted verbatim in an email sent to me by a creationist thinking that it refuted in some way the validity of Archaeopteryx as a transitional form.

Link: www.ridgenet.net/~do_while/sage/v6i2n.htm

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There was an extremely insightful article by Sid Perkins in Science News about the debate over bird evolution recently. Evolutionists are troubled because there are some dinosaurs that “are covered with peculiar structures that some scientists call dino-fuzz. All are geologically younger than Archaeopteryx-some by tens of millions of years.”
It's news to me that "evolutionists" are "troubled" by the proto-feathers on some dinosaurs, and I know several palaeontologists who have worked in the Chinese feathered dinosaurs. Publishing papers in Nature and making a "Dino/Birds" exhibition to be presented at venues all over the world does not indicate any sense of being "troubled".
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This is a problem for them because the dino-fuzz looks like primitive feathers that are just beginning to evolve. But Archaeopteryx already had fully developed, modern feathers tens of millions of years earlier (by their time scale). So, the presumed evolutionary sequence doesn’t fit into their view of chronology.
Complete and utter bunkum, showing that the writer doesn't have a clue about evolutionary biology. "Dino-fuzz" is not something striving to become a feather. It is a structure which helps the dinosaur to adapt to its environment. The chronology is irrelevant. It's equivalent to saying that the existence of egg-laying mammals is a problem for evolution.
FALSE
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In what can charitably be called a contentious debate, the two most strident groups of these paleontologists sometimes--okay, almost always--reach interpretations of the data that are poles apart. They defend their analyses with fundamentalist fervor and fling darts at the opinions of scientists who hold a different view.When these guys get together the feathers can really fly.
Scientists argue over interpretations of data. This is how science works. The arguments will be decided on the basis of the evidence and argument offered.
Irrelevant
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There is more truth in that paragraph than Perkins probably meant to convey. They reach interpretations that are poles apart because they are just interpretations, not proven facts.
Science does not work on the basis of "proven facts". Science does not prove anything. It offers the best interpretation for the evidence. When the evidence is patchy - as is usually the case in palaeontology - there can be different interpretations of the same data.
Irrelevant
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“Interpretations” is just another word for “opinions.”
No it isn't. "Interpretations" are based firmly on the evidence. Opinions go beyond the evidence, and are expressed as such. Scientists frequently offer opinions.
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What is often stated as fact is really just an opinion, which “sometimes--okay, almost always” is opposite to some other equally qualified scientist’s opinion.
Scientists do not state opinions as fact, and any scientist doing so would lose any reputation they have.
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The reason why the scientists “defend their analyses with fundamentalist fervor” is that the opinions are closer to religion than science.
Utter bunkum. Scientists may defend their analyses vigourously, but most will concede that they are wrong when the evidence shows that their position is no longer supportable. Scientists who defend their position "with religious fervour" generally lose what reputation they may have had.
FALSE
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Their analyses are really opinions that are strongly connected with the scientist’s personal belief about the origin and meaning of life. That makes it hard for them to be objective.
The opinions of scientists about interpretation of data have nothing to do with their personal beliefs. Many scientists have strongly held religious convictions, but such beliefs play no part in how that carry out their scientific investigations.
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This is illustrated by a tangent in Perkins’ “Ticklish Debate” article. The tangent is the real reason for including this Evolution in the News column in the same issue as the Whale Tale Two essay. In that essay we noted that whale evolution has been controversial because the DNA analysis did not agree with the traditional fossil interpretation. This is commonly the case. Perkins has provided us with yet another example of this disagreement. Perkins says,
Again, why is this a problem for evolutionary scientists? Scientists disagree over the interpretation of evidence. That is how our knowledge advances.
Irrelevant
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The members of one camp of paleontologists rely on the fossil record and cladistics, the science of determining the evolutionary relationships between organisms by analyzing their shared characteristics. By looking at traits such as general body structure, the number and shape of bones, and the presence of body coverings such as feathers, these scientists can construct family trees.
Quite so.
Irrelevant
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But Perkins doesn’t think this is a reliable way to construct a family tree.
As it happens, I agree with him and think that too much emphasis is placed on the output of character-based cladistic analyses. Disagreements over evidence and how to analyse that evidence are which drives scientific research.
Irrelevant
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Another argument against cladistics based solely on fossils: Looks can be deceiving, as genetic analysis of living animals attests (see box). This kind of disconnect between physical appearances and genetic relationships helps fan the debate over how feathers evolved.
So scientists disagree over how to interpret the evidence. So what?
Irrelevant
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Perkins believes looks are deceiving because looks say one thing and DNA says another. How does he know that the DNA is right, and the looks are wrong? The answer, of course, is that looks are deceiving when things don’t look like he thinks they should.
So scientists disagree over how to interpret the evidence. So what?
Irrelevant
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Looks really don’t matter, unless they confirm what he already believes to be true.
I'm struggling to understand what the author means here. Is he suggesting that character-based analyses are ignored if they don't support DNA-based analyses? If so, perhaps he could support this assertion with evidence of such behaviour.
Unsupported assertion
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If the DNA analysis didn’t agree with what he believed, no doubt he would say the DNA analysis is deceiving. Many other scientists might say that any analysis that says flamingos and grebes are closely related must be incorrect, and therefore deceiving
So scientists disagree over how to interpret the evidence. So what?
Irrelevant
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Perkins argued against physical appearance as an indication of common ancestry with an example placed in a prominent box in his article. Here is the text from that box. (The box also contained two pictures. One of a western grebe, and the other of a flamingo, showing that the two birds are about as different as two birds can be.)
And ...?
Irrelevant
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Consider that a family tree based on DNA similarities can be much different from one drawn according to body characteristics preserved in fossils (SN: 11/25/00, p. 346). Markers in the DNA of modern animals, for example, link African creatures as diverse as elephants, elephant shrews, and aardvarks to a common ancestor (SN: 1/6/01, p.4).
Quite so. Different evidence can support different hypotheses. This is how science works
Irrelevant
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Similar DNA analyses suggest that the flamingo’s closest relatives could be grebes--medium-size diving birds with stocky bodies, slender necks, and small heads. These and other skeletal characteristics have led most evolutionary biologists to group grebes with loons, another diving bird, says S. Blair Hedges of Pennsylvania State University in State College. But two completely different types of genetic testing indicate that the leggy flamingo and the squatty grebe may in fact be long-lost cousins.
Wow! Scientists find out that new methods give different and possibly more reliable results! I'm struggling to follow the argument here.
Irrelevant
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The fossil record for flamingos goes back at least 50 million years, and none of their body characteristics suggest that they’re related to grebes,” says Hedges, who reported the DNA tree in the July 7 Proceedings of the Royal Society of London B. That DNA links flamingos and grebes “was a big surprise,” he says. 5
As I said, wow! Why is this so significant? Birds in particular are a taxon in which there is very strong morphological convergence between distantly related branches.
Irrelevant
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Given the number of terrible bird and feather puns in that article, we were expecting him to say, “That DNA links flamingos and grebes is loony.” He probably didn’t say that because he believes the DNA analysis rather than physical appearance, so the physical appearance, not the DNA evidence, is loony to him.
No, it's not "loony to him". The DNA analysis showed that it's not necessarily a reliable guide to analysing evolutionary relationships.
Unsupported assertion
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We are just asking evolutionists to be consistent.
No you're not. You're asking "evolutionists" to ignore evidence, ignore new methods of analysis, and stick to their assertions regardless of what the evidence shows. In other words, you want them to behave like creationists.
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We will not allow evolutionists to claim that physical similarity is reliable evidence whenever it supports their argument, and then claim that physical similarity is irrelevant whenever it contradicts their argument.
Evolutionary scientists do not need the permission of a creationist whose writing shows that he has little knowledge of science to claim whatever they want! Furthermore, this misrepresents the dispute in palaontological circles over the validity of character-based analyses.
Misrepresentation
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Either physical appearance provides reliable evidence of common ancestry or it doesn’t.
It's not an either/or situation. When dealing with fossil taxa DNA evidence is not available, so any analysis has to be on the basis of morphological characters. The hope is that DNA evidence from extant taxa, and a greater understanding of the way in which evolutionary processes are controlled by gene expression will lead to a better understanding of which anatomical characters are significant in analysing evolutionary relationships.
Misrepresentation
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Of course, there should not be an argument between molecular biologists and paleontologists to begin with. If evolution were true, then a family tree based on DNA similarities should NOT be much different from one drawn according to body characteristics.
Once again, complete nonsense. Biomechanical factors play a strong role in constraining evolutionary processes, leading to strong similarities in morphology. This can make phylogenetic analysis difficult. The algorythms used to make such analyses take into account the impact of homoplasy on the outcome.
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But, if creatures were independently created, and physical similarities in appearance are simply accidents of design, or fanciful whims of the designer, then one would not expect the DNA analysis to agree with relationships based on physical appearance.
Where there are discrepancies between DNA and character-based analyses, scientists try to understand why these differences exist, and in doing so gain a better understanding of homplasy and gene expression. To ascribe such differences to the fanciful whims of a supernatural creator is in scientific terms completely useless.
Unsupported assertion