• Intelligent Design Gets Peer-Review… Sort Of

    In a previous thread, I asked for publications that support Intelligent Design.  Of all the ones listed, only one actually seemed to provide supporting evidence for ID.  The others were interesting ideas, but mainly dealt with how evolution can’t have done x (produce complex folding proteins or whatever).

    But the paper I want to talk about today was different.  The title suggested, in no uncertain terms, what to expect.

    EVIDENCE OF DESIGN IN BIRD FEATHERS AND AVIAN RESPIRATION

    Pretty powerful stuff.  You can download it here (though you must register, it is free).

    Before I talk about the paper itself, I’d like to mention a few things.

    First, and perhaps second most obvious, is this disclaimer by the editors of the journal.

    Editor’s Note: This paper presents a different paradigm than the traditional view. It is, in the view of the Journal, an exploratory paper that does not give a complete justification for the alternative view. The reader should not assume that the Journal or the reviewers agree with the conclusions of the paper. It is a valuable contribution that challenges the conventional vision that systems can design and organise themselves. The Journal hopes that the paper will promote the exchange of ideas in this important topic. Comments are invited in the form of ‘Letters to the Editor’.

    That phrase “does not give a complete justification for the alternative view” is going to be the highlight of our discussion here.  I do find it very interesting that this journal feels that they have to publish this paper, but include this disclaimer.

    If the paper in question is good science, then why does it need a disclaimer?  If the paper is not good science, then why was it published?  After reading the paper, I think the journal made a mistake in publishing this paper.  It’s not good science.  But we’ll get to that.

    The most obvious thing and second note I’ll bring up is that there is a single author, one A.C. McIntosh, of the Energy and Resources Institute, University of Leeds.  Yep, he’s not a biologist or a paleontologist.  While that certainly doesn’t mean he can’t write about, or even be an expert, in a subject.  I think that we should seriously consider the author’s experience here.

    For example, I have been studying and writing about evolution for three decades.  Part of my undergraduate degree is in Earth Science, where I took a lot of historical geology and paleo courses.  I still don’t consider myself an expert on the subject.  Not compared to Dawkins and Gould and the like.  But this gentleman has spent a career in engineering AND is publishing in the field of evolution.  I think any discussion should include his experience… or lack thereof.

    Now that all of that is out of the way, let’s talk about the paper itself.

    Let me sum up the entire paper in one sentence: I can’t imagine how feathers and avian lungs were formed, therefore they were designed.

    That’s the entire paper.  That’s all.

    OK, let’s talk about specifics.

    First, I have a major issue with the Bibliography.  It is stunningly incomplete.  The author of this paper has ignored dozens of highly relevant papers that are directly related to the subject.  That’s a major problem that would almost automatically cause the paper to be rejected by any science journal.  Below, I’ve included a few articles that the author somehow missed concerning the evolution of bird feathers.

    Second, this article does not provide any actual evidence.  There are no experiments, not even models or simulations.  There isn’t anything that could be used to compare or even differentiate between evolution and design.  This is a major flaw when one uses the word “evidence” in the title.  There isn’t any evidence.  A hint to the author, repeating the same phrases over and over does not make them true.

    The introduction of the paper is a classic intelligent design opening.

    However, such thinking fails to realise that functional systems, in order to operate as working machines, must have all the required parts in place in order to be effective. If one part is missing, then the whole system is useless. The inference of design is the most natural step when presented with evidence such as in this paper, that is evidence concerning avian feathers and respiration.

    The inference of design is NOT a natural step.  To have ‘design’ one must have a ‘designer’.  To ignore this simple point refutes almost everything that the ID camp has ever said.  There is no evidence for a designer.

    The inference of design is NOT the only other option and it is not the default option if one thinks that evolution cannot produce a particular product.  Those are the assumptions that this paper is trying to show.  Basically, this paper is one huge logical fallacy of assuming the point trying to be proven.

    Let’s be clear, to scientists, people who actually do this kind of work, there is a hypothesis (for example “A is the result of X”).  The opposite is called the null hypothesis and it doesn’t get the attention it deserves, especially in science classes.  The null hypothesis is not “if A is not the result of X, then design”.  The null hypothesis is “A is NOT the result of X”.  That’s all.

    An experiment or set of observations that do not support the hypothesis do not automatically support another hypothesis (that of design).  This is a mistake called the “false dichotomy”.

    An example, let’s say you have a vitamin pill with a bunch of things in it.  One of the ingredients is green tea extract.  Another is ginseng extract.  If one does an experiment to show that green tea is the cause of weight loss and the evidence suggests that green tea is NOT the cause of weight loss.  That does not mean that ginseng IS the cause of weight loss.

    Only positive evidence can support a hypothesis.  Intelligent Design has zero positive evidence.  And this article sure doesn’t contain any.

    This is hilarious

    However there has never been a recorded observation of this happening experimentally in the laboratory (where the precursor information or machinery is not already present in embryonic form). Though it is true that a design action is also not observed in the laboratory, nevertheless the inference to original design and intelligence is a perfectly valid alternative from direct analogy to designs within the man-made world.

    This is so contradictory.  Evolution has never been observed to make this change in the lab, so evolution is refuted.  Design has never been observed to make this change in the lab either, but we think it valid.

    Seriously?  This is the quality of work that gets published?  Hell, I could publish my blog posts, many of them are way better than this.

    This really shows the author’s inherent biases.  After ignoring a number of important journal articles that directly address the evolution of feathers, he then shows that no science is acceptable, but his ‘design inference’ is perfect.

    Later in the introduction, the author does another odd thing.  He briefly mentions “specified functional complexity”.  Not odd in and of itself, but he doesn’t define it.  He doesn’t talk about it.  He doesn’t even provide a reference to it.  Yet, he then says that SFC has never been experimentally observed.

    How does he know?  It’s obvious that the hasn’t read the literature.  He probably hasn’t kept up in all the recent research.  He hasn’t even defined what SFC is in the paper, how it is measured, or provided a reference so that readers will know what he’s talking about.  He just assumes we’ll take him for his word.  That’s not how science is done.

    Then we get into the ‘thermodynamics’ issue.  I love it creationists do this.  They often complain that thermodynamics prevents an increase in complexity and other silly notions.  Of course, if this was true, then no organism could grow or develop.  It’s stupid.  Even the “answers in genesis” website says not to use that easily refuted argument anymore.

    Thermodynamics concerns itself solely with the flow of heat within various systems.  All the talk of order, disorder, complexity, breaking things down, etc are all wrong.  The flow of heat that can do work is all thermodynamics is concerned with.  Everything else is analogies that are pushed beyond their useful limits.  Someone remind me to write a post on that.

    I’ll note that the two references that the author makes to support his claim here are both creationists… indeed one of them is the author himself.

    Consequently, to try and assert that natural systems can only ever have come about by a pre-existing natural system without intelligence is an unproven assumption, and must immediately be recognised as such.

    Of course, one should also recognize that the requirement for intelligence to be involved is also an unproven assumption and should be immediately recognized as such.  Again, we see the author’s bias against science and for his own beliefs.

    Science can study the effect on the natural world of systems of pre-existing material, but it cannot preclude the possibility of intelligence extraneous to that very matter and energy being involved in its formation.

    That’s correct.  But in all the hundreds of years that scientists have been looking for some intelligence ‘extraneous’ to the universe, nothing has been found.

    How can science even measure this?  Well, anything that affects the material universe will leave marks, even if it is beyond the material universe.  We can’t see electromagnetic radiation, yet we can clearly see the effects (heated food from microwaves, sunburns on a cloudy day from UV, radar mapping of air traffic, radio communication, etc).  Things that are invisible, but affect the world will leave a trace.  This has never been observed.

    Next we have four pages about the description of feathers. That’s all it is, a description of feathers.  I hate to include large chunks of text, but I have to here.

    King and McLelland [9] and Burgess [10] have shown that there is multifunctioning and multi- optimisation in feather construction. There are the features which are immediately apparent such as aerodynamic loading and the material construction of rachis and barbs to sustain this. However, there are also more subtle features such as the arrangement of hooks and barbules primarily for keeping the feather together, such that they prevent air from going through them during the downstroke but allowing some air to pass through in the upstroke, thus maximising the efficiency of energy use in wing flap. The keratin itself has an extremely high specific strength, and the shape of the filament cross sections used in rachis construction moves from near circular near the root to a curved and ribbed rectangular shape away from the root for structural efficiency under bending and potentially buckling loads. The evidence is consistent with the design thesis both from the fossils found of flight in the past, and in the multifunctional nature of wings today.

    This is a ridiculous statement.  The evidence that is being used here is simply a description of the feathers.  It’s not evidence to support design and more than it’s evidence to support evolution.

    Here’s the issue.  Scientific evidence is used to differentiate between two possibilities, the hypothesis and the null hypothesis.  A description of something doesn’t say anything about how it came into existence.

    Let me help the creationists here.  This is what we expect to see in a scientific investigation

    If an intelligent agent was the cause of A, then we would expect to see X, Y, and Z.  This is because X is a result of intelligence because of reasons 1, 2, and 3.  Y is the result of intelligence because of 4, 5, and 6.  Z is the result of intelligence because of 7, 8, and 9.  X, Y, and Z are features that are not expected in evolution because of 9, 10, 11, 12, 13, 14, and 15.  Therefore, when we look at feature A, we see some stuff that indicates design because it matches reasons 2, 5,  and 6 … but not features 9 and 13.

    How is this different than what creationists say now?  Right now, the creationists say “X has never been seen to be caused by evolution, therefore design”.

    It’s a subtle, but extremely critical difference.  Science allows the differentiation between causes.  Intelligent Design doesn’t, because anything can be caused by some nebulous intelligence and, as shown above, there is no science that would convince the creationists, while design is not required to have the same level or detail.

    Laudable indeed have been the attempts to find the evolutionary engine to provide specific function, but the attempt is not impressive, since the array of simpler structures is difficult to imagine, let alone find in the fossil record.

    In other words, “It hasn’t been found and I can’t imagine how it happened, therefore design”.

    It is that vital network of barbules which is necessarily a function of the encoded information (software) in the genes. Functional information is vital to such systems

    This a claim that is not supported in any way.  It is not referenced.  It is just a statement that is assumed to be true.  Saying things over and over doesn’t make them true.  Claims like this must be supported.

    There is another long section about ‘functional information’ in which the author mentions a bunch of actual models, then says to ignore them because they don’t talk about ‘functional information’.

    That is, the natural tendency is for the linkages needed for those coding systems (e.g. nucleotide bonds) to decay, and not to be sustained without prior information within the system. Thermodynamically, the very material on which the coded information sits is acting against the natural law which, were it not for the information in the system, would have it fall apart.

    That is a huge claim… with absolutely no support.  Again, thermodynamics has no impact on information or even decay over time.  That’s not what thermodynamics is.

    Basically, at this point, the author is just making things up.  It sure sounds sciency, but it has absolutely no relation to the way things actually are in the real world.  This has always been the Achilles heal of ID arguments.

    People can say lots of things.  They can talk about specified functional complexity and how things always decay over time.  But the simple fact is that this is not what happens in the real world.

    In theory, there is no difference between theory and practice.  In practice, there is.  We have observed complex structures appearing in cells in the lab.  We have observed morphological changes in organisms that provide benefits.  I’ve provided links to them in my ‘debunking the weaknesses of evolution’ series.

    A literature search will show that the statements of creationists about what can and can’t happen are almost universally not true.  Further, and more importantly, there is no evidence that they can bring to support their own claims.

    I’d like to point out that the author does something really odd.  Look at this claim:

    Furthermore, feathers have been found encased within amber (hardened resin), as shown in Fig. 6. The amber, by traditional dating mechanisms, is estimated to be 25 million years old, and yet the full barb system can be seen in some samples, indicating no difference in essence to modern feathers.

    The caption in figure 6 is this

    Pennaceous feather caught in Dominican amber (hardened resin) supposed to be 25 million years old by classical dating schemes. (This specimen from the Dominican Republic was originally for sale via the web. They usually sell for at least $2000.)

    Seriously?  This is a pretty impressive claim and not a single source for it.

    I’ll just point out that according to the Foth, 2011 article below a feather with a full barb system was found 125 million years ago.  Over five times further back in time than the claim in the creationist article.  I’ll freely admit that the Foth article was published after the creationist article, but surely there’s research that shows full barb feathers between 125 and 25 mya.  Alternately, it could just a sloppy mistake by the writer and he really meant 125 mya.  I don’t know… and without references, there’s no way to tell.

    In a real scientific paper, every claim is either supported with experimental or observational or a reference to another paper with experimental or observation support.  This paper is just sloppy.

    The avian lung part of the paper is the same.  Descriptions followed by the claim that it can’t happen via natural methods, followed by ‘it must be designed’.

    I’ll add that the author appears to misunderstand the concept of transitional fossils and homology.

    I’ll put the entire conclusion of the paper here and dissect it.

    In this paper, we have considered two examples of design in birds which defy explanation by gradual changes since to function at all, all the parts necessary for function must be there to begin with.

    They only defy the authors explanation by gradual change since he ignores a significant amount of research on the topic.

    As examples of irreducible complexity, they show that natural systems have intricate machinery which does not arise in a ‘bottom up’ approach, whereby some natural selective method of gaining small-scale changes could give the intermediary creature some advantage.

    The first bit here is assuming the conclusion.  He’s trying to show this, but using them as examples of what he’s trying to show.  I discussed the idea of how an irreducible structure (and provided examples) can be evolved here.

    This will not work since, first, there is no advantage unless all the parts of the new machine are available together and, second, in the case of the avian lung the intermediary creature would not be able to breathe, and there is little selective advantage if the creature is no longer alive.

    This a common misunderstanding of evolution, actually there are two.

    The first is that every change MUST be beneficial to the organism.  As we have seen before, most mutations are actually neutral.  There are also what I call ‘potentiating mutations’ that may be positive, neutral, or negative, but provide a precursor for another mutation that conveys a significant advantage (see Darwinian Evolution on a Chip for an example.

    The second is that the transitional step is ‘half a lung’ or ‘half a wing’ and therefore conveys no advantage since half a wing doesn’t allow for flight and half a lung just doesn’t work.  This is fundamentally incorrect.

    In evolution, there is this concept where a system that evolved for one purpose is modified and used for another purpose, like feathers, for example (see Dimond 2011 for example).  Feathers are thought to be insulation for warm blooded dinosaurs and/or used in mating or fighting displays and where only used for flight after the fact.

    As stated in the introduction, the possibility of an intelligent cause is both a valid scientific assumption, and borne out by the evidence itself.

    There isn’t a single piece of evidence in this entire article that suggests an intelligence exists or that anything described in the article could have ONLY appeared via intelligent cause.  Again, saying things again and again without support isn’t evidence.

    This approach suggests that there is a basic design of bird with furcula, keeled sternum, acrocoracoid process, air sac system, counterflow mass exchanger lung and feathers which have hooked and ridged barbules, which is ancestral and quite different to reptile design where these salient features are absent.

    Of course, to REPTILES, I would agree.  But dinosaurs are a highly derived group of reptiles now aren’t they.  And (as shown in the references below and thousands more) it is obvious that the features that exist in birds have evolved, slowly, from theropod dinosaurs.

    Do we have lungs?  No, lungs rarely fossilize.  Do we have feathers?  Yes.  And they show a steady progression from simple tufts to the complex feathers found in modern birds and derived theropod dinosaurs.

    This article is simply crap.  There is no evidence (unlike what the title claims).  There is no good science here.  Critical references are missing.  The author makes basic mistakes about physics and evolution.

    Any conclusions drawn from this article must be rejected as not supported.  Does that mean there is no intelligent designer?  Of course not.  It just means that this article is not support for one.

    But, until we see actual evidence of the kind I describe, we must go with the explanation that actually explains the process of feathers developing in some dinosaurs and evolutionary theory provides that explanation and paleontology provides evidence to support the evolutionary explanation.

    __________________________________________

    A partial list of peer-reviewed research ignored by A.C. McIntosh.  At least three of these articles directly refute claims made in the McIntosh article.  I gave him a buy on papers published in or after 2009.

    Sumida, SS & CA Brochu (2000). “Phylogenetic context for the origin of feathers”American Zoologist 40 (4): 486–503. doi:10.1093/icb/40.4.486.

    Bock, WJ (2000). “Explanatory History of the Origin of Feathers”. Amer. Zool. 40 (4): 478–485.doi:10.1093/icb/40.4.478.

    De Ricqles, A. J., K. Padian, J. R. Horner, E. T. Lamm, and N. Myhrvold (2003). “Osteohistology of confuciusornis sanctus (theropoda: Aves)”. Journal of Vertebrate Paleontology 23: 753–761.

    http://www.ncbi.nlm.nih.gov/pubmed/17784647

    Dimond, C. C.,R. J. Cabin and J. S. Brooks (2011). “Feathers, Dinosaurs, and Behavioral Cues: Defining the Visual Display Hypothesis for the Adaptive Function of Feathers in Non-Avian Theropods”. BIOS 82 (3): 58–63.doi:10.1893/011.082.0302.

    Xu, Xing (2006). “Feathered dinosaurs from China and the evolution of major avian characters”. Integrative Zoology 1 (1): 4–11. doi:10.1111/j.1749-4877.2006.00004.xPMID 21395983.

    Xu, X., H. H. Zhou, and R. O. Prum (2001). “Branched integumental structures in Sinornithosaurus and the origin of feathers”. Nature 410 (6825): 200–204. doi:10.1038/35065589PMID 11242078.

    Foth, C. (2011). “On the identification of feather structures in stem-line representatives of birds: evidence from fossils and actuopalaeontology.” Paläontologische Zeitschrift, (advance publication) doi:10.1007/s12542-011-0111-3

    Category: CreationismEvolutionResearchScienceSkepticism

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    Article by: Smilodon's Retreat

    • Dan Eastwood

      Since the journal is looking for letters inn response, you should edit this down and submit it.

      • SmilodonsRetreat

        The article was published in 2009. Surely they don’t still want them… hmm….

        • Kevin – have you got access to any letters that they might have received?

          • SmilodonsRetreat

            No, the free part of the journal is the papers only. Letters and editorials aren’t available online. I sent them an e-mail about it.

    • Kevin – I have done a little delving:

      http://journals.witpress.com/jdne.asp

      McIntosh is on the fucking editorial board for that journal!

      • SmilodonsRetreat

        Oh that explains a lot.

        But he still got the editor’s note in the beginning. LOL