Claims of Peer Review for Intelligent Design examined … and debunked 75


One of the many variations of modern creationism (the folks that claim ‘god did it’ is the right answer) is called “Intelligent Design”. There they attempt to refute evolution via the promotion of scientific evidence for an intelligent designer, and also attempt to make it more palatable by omitting all religious terms from what is essentially a religious claim. Well, if they wish to take a scientific approach, then this becomes quite interesting because this is a measurable claim, all we need to do is to take a look and see if they have published any credible peer-reviewed articles within any recognised scientific journals.

Does this matter? Sadly yes it does, a good percentage of the public do still seriously doubt the reality of evolution as a well-established scientific fact, they have been successfully conned by some supposedly credible claims, so it is indeed appropriate to throw a spotlight upon the intelligent design community and reveal that their aura of credibility is simply an illusion.

Almost two years ago, I went through the list of Peer-reviewed articles posted up by the Discovery Institute, a well-financed US-based group that promotes Intelligent Design. What did I find? … (Oh come on, you can guess) … yes, that’s right, exactly nothing, they did not have anything credible, not one jot.

They have since then revised their list and greatly extended it, so the time is now right for a return visit to this bastion of creationist “peer-reviewed” fodder.

The title remains the same, “PEER-REVIEWED & PEER-EDITED SCIENTIFIC PUBLICATIONS SUPPORTING THE THEORY OF INTELLIGENT DESIGN (ANNOTATED)“. My approach will be the same as last time – basically apply an initial filter to remove the junk, then take a look at what remains. But first, there is an observation to be made about some initial commentary they have added. They now make this claim …

Despite ID’s publication record, we note parenthetically that recognition in peer-reviewed literature is not an absolute requirement to demonstrate an idea’s scientific merit. Darwin’s own theory of evolution was first published in a book for a general and scientific audience — his Origin of Species — not in a peer-reviewed paper.

Seriously!! … Origin of Species, published in 1859, was not published in a peer-review journal, so that justifies adding books to their list. Do they not know that the Peer review process has only been a touchstone of the modern scientific method since the middle of the 20th century. No, the bottom line here is simple, books are out, anybody can publish anything (Harry Potter is evidence that Magic is real … right?), if they wish to refute evolution and propose an alternative, then they need to engage with the scientific community with real data, and publish it within a credible and appropriate scientific journal.

The Filter

OK, on to my initial filter:

  • There are articles from a Journal called BIO-ComplexityThis is not a credible peer-review journal, instead it is a creationist journal issued by the Biologic Institute. They in turn are funded by the Discovery Institute … yes, it is their own pet journal and has exactly zero credibility within the scientific community, we can ignore all that.
  • There are also articles from Life : Yet another journal that has no scientific credibility and is treated as something to laugh at, we can ignore that as well.
  • The International Journal of Design & Nature and Ecodynamics : This is a fringe publication of the featherweight Wessex Institute of Technology, in other words it is also not a real scientific journal, but is simply a vanity journal that publishes papers written by its own editors. McIntosh, the author of a listed paper, is on their Editorial Board, and one of their other editors is the young earth creationist Stuart Burgess
  • Papers published as part of the proceedings of a conference are not recognised peer-reviewed journals, we can ignore these.
  • Chapters within books are not peer-reviewed journals, so they can also be tossed.
  • Peer-Edited and Editor-Reviewed articles are not peer-reviewed articles … finding these tossed in to inflate the list really is scraping the bottom of the barrel.
  • Articles in Philosophy journals … er no, we can ignore these, if you want to make claims regarding biology, you publish in a biology journal, and you also need real data.
  • Anything by David Abel, all his papers consist entirely of non-evidentially supported, non-laboratory confirmed, pure fabrication (I let a couple through this filter so that you can see what I’m on about). About 17% of the list is by him and can happily be ignored.
    • Least you pause on the thought of a named individual being a filter, it is simply a short-cut to eliminate papers that are long-winded assertions that contain no data at all — no experiments, no measurements, and no observations  … nada. Should he write a paper that contains some analysis of actual data, then this filter does not apply.
    • So who exactly is this guy? He is David Abel, Department of ProtoBioCybernetics/ProtoBioSemiotics, Director, The Gene Emergence Project, The Origin-of-Life. Science Foundation, Inc., 113 Hedgewood Dr. Greenbelt, MD 20770-1610 USA, at least that is the title on his papers. Wow, sounds impressive … but google that address and you discover it is an ordinary residential house. Yes, the entire foundation is in his garage, and he is the sole representative. Somebody checked him out, this impressive sounding title and organization is a sham and is not real. The claimed title is completely fraudulent.
    • But why does he get published? … well because Abel is making an argument, of sorts, and is backing it up with a reasonable amount of scholarship and some fancy sounding mathy stuff. On the surface it looks credible, so you need to read it all several times to work out that the assertions being made are not actually credible. Rarely do you find bullshit so tortuously Byzantine as the stuff churned out by him, which I guess is by intention.

What do we have left after filtering?

Well, lets take a look at the remains.

Joseph A. Kuhn, “Dissecting Darwinism,” Baylor University Medical Center Proceedings, Vol. 25(1): 41-47 (2012).

  • This is a medical journal, a rather odd place to attempt to refute evolution.
  • The article itself is poorly written, dreadful, and full of scientific errors. It’s an embarrassment to the author, to the journal, and to the field of medicine as a whole. In essence we have a medical doctor claiming evolution is bunk and repeats the usual debunked Discovery Institute claims.
  • Is it credible? Nope, a Professor in the Department of Ecology and Evolution at the University of Chicago, explains why it is not. – Fail

Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations, and ‘The First Rule of Adaptive Evolution,’” The Quarterly Review of Biology, Vol. 85(4):1-27 (December 2010). 

  •  Jerry Coyne has a good summary, he writes “this paper gives ID advocates no reason to crow that a peer-reviewed paper supporting intelligent design has finally appeared in the scientific literature.  The paper says absolutely nothing—zilch—that supports any contention of ID “theory.” – Fail

Wolf-Ekkehard Lönnig, “Mutagenesis in Physalis pubescens L. ssp. floridana: Some further research on Dollo’s Law and the Law of Recurrent Variation,”Floriculture and Ornamental Biotechnology, 1-21 (2010). 

  • Published where? Yes, that is indeed a very obscure journal.
  • An Australian science communicator and biology student, explains here why this is just another daft paper that is not credible. – Fail.

William A. Dembski and Robert J. Marks II, “The Search for a Search: Measuring the Information Cost of Higher Level Search,” Journal of Advanced Computational Intelligence and Intelligent Informatics, Vol. 14 (5):475-486 (2010).

David L. Abel, “Constraints vs Controls,” The Open Cybernetics and Systemics Journal, Vol. 4:14-27 (January 20, 2010).

  • Yes indeed a paper by Mr Abel, and sure enough, no actual data, no experiments, no measurements, and  no observations
  • The first eight references in it are him simply citing other similar papers he has written.
  • And what about the journal? It is an obscure IT journal that handles articles that relate to human computer interaction. – Fail

William A. Dembski and Robert J. Marks II, “Conservation of Information in Search: Measuring the Cost of Success,” IEEE Transactions on Systems, Man, and Cybernetics-Part A: Systems and Humans, Vol. 39(5):1051-1061 (September, 2009).

  • What do others have to say about this, do they find it credible as an ID paper? Nope, see reviews here, and here, and here.
  • Dembski has, for years, been pushing an argument based on some work called the No Free Lunch (NFL) theorems. The NFL theorems prove that average over all possible search landscapes, no search algorithm can outperform a random walk. The NFL theorems are true and correct – they’re valid math, and they’re even useful in the right setting. In fact, if you really think about it, they’re actually quite obvious. Dembski has been trying to apply the NFL theorems to evolution: his basic argument is that evolution (as a search) can’t possibly produce anything without being guided by a supernatural designer – because if there wasn’t some sort of cheating going on in the evolutionary search, according to NFL, evolution shouldn’t work any better than random walk – meaning that it’s as likely for humans to evolve as it is for them to spring fully formed out of the ether. This doesn’t work for a very simple reason: evolution doesn’t have to work in all possible landscapes. Dembski always sidesteps that issue.
  • So yes, this is an appropriate publication in its context, and the maths is OK, but claims that it supports ID when applied to Evolution are not in this paper. Nor can that claim be substantiated by any data from either here or anywhere else
  • Status as a paper that supports ID – Fail.

Richard v. Sternberg, “DNA Codes and Information: Formal Structures and Relational Causes,” Acta Biotheoretica, Vol. 56(3):205-232 (September, 2008).

  • Sternberg’s paper is a theoretical one in which he takes a structuralist approach and proposes “that a variety of structural realism can assist us in rethinking the concepts of DNA codes and information apart from semantic criteria
  • Little problem … no empirical data, so as a paper that actually support ID in our reality – Fail

Douglas D. Axe, Brendan W. Dixon, Philip Lu, “Stylus: A System for Evolutionary Experimentation Based on a Protein/Proteome Model with Non-Arbitrary Functional Constraints,” PLoS One, Vol. 3(6):e2246 (June 2008).

  • This paper describes a computer program (Stylus) that was used for the study of protein evolution using Chinese characters
  • The paper does not offer any support for ID. Indeed, Konrad Sheffler (the PloS editor for the manuscript) explicitly notes that he “did not detect any such [ideological] bias [towards ID] in this manuscript; nor do the results support intelligent design in any way.”
  • As he also points out, “there is still no substitute for empirical data” when examining biological processes – Fail

Michael Sherman, “Universal Genome in the Origin of Metazoa: Thoughts About Evolution,” Cell Cycle, Vol. 6(15):1873-1877 (August 1, 2007).

  • This a paper that makes some dodgy claims from ignorance that evolution can’t explain the Cambrian explosion or the evolution of body plans. It is then followed by an alternative hypothesis which explains nothing that can’t be explained by evolutionary biology, and simply relies on gaps in our knowledge to create doubt. (rebuttal here) – Fail

Kirk K. Durston, David K. Y. Chiu, David L. Abel, Jack T. Trevors, “Measuring the functional sequence complexity of proteins,” Theoretical Biology and Medical Modelling, Vol. 4:47 (2007).

  • Ah yes a “ground breaking” paper that is cited many times, but mostly by the authors (Especially Mr Abel), and has failed to be of interest to anybody else.
  • There’s no reference to ID theory anywhere in this paper, nor is there any reference to the terminology used in ID. The paper does not actually support ID in any way at all, it simply describes a method to measure the functional sequence complexity. – Fail

Felipe Houat de Brito, Artur Noura Teixeira, Otávio Noura Teixeira, Roberto C. L. Oliveira, “A Fuzzy Intelligent Controller for Genetic Algorithm Parameters,” in Advances in Natural Computation (Licheng Jiao, Lipo Wang, Xinbo Gao, Jing Liu, Feng Wu, eds, Springer-Verlag, 2006); Felipe Houat de Brito, Artur Noura Teixeira, Otávio Noura Teixeira, Roberto C. L. Oliveira, “A Fuzzy Approach to Control Genetic Algorithm Parameters,” SADIO Electronic Journal of Informatics and Operations Research, Vol. 7(1):12-23 (2007).

  • “Advances in Natural Computation” are the proceedings of a computer science conference and is not a peer-reviewed journal – Fail
  • “SADIO Electronic Journal of Informatics and Operations Research” – An Argentinian Computer Science journal that is not actually peer-reviewed – Fail

Wolf-Ekkehard Lönnig, Kurt Stüber, Heinz Saedler, Jeong Hee Kim, “Biodiversity and Dollo’s Law: To What Extent can the Phenotypic Differences between Misopates orontium and Antirrhinum majus be Bridged by Mutagenesis,”Bioremediation, Biodiversity and Bioavailability, Vol. 1(1):1-30 (2007).

  • Ah yes, Dollo opus by Mr Lönnig and his former boss at the Max-Planck-Institute for Plant Breeding, plus others. This of course is the same chap who is on the editorial board of BIO-Complexity, the Discovery Institute’s pet journal.
  • This paper has not exactly caused much interest, it has been cited exactly four times … by Lönnig himself, and nobody else.
  • The term “Intelligent Design” is deployed exactly once in this paper – at page 18 about half way through.
  • It is all rather weird really, they explain that they tried to use mutagenesis experiments to cause some related plants to revert to a more “primitive” forms, but failed to do so, and thus suggest that this confirms Dollo’s law. They then proceed to use this as an excuse to plug a bunch of pro-ID people into the paper for no reason at all other than to promote their ideas, but none of it is justified in any way by their failed experiments – Fail

Wolf-Ekkehard Lönnig, “Mutations: The Law of Recurrent Variation,” Floriculture, Ornamental and Plant Biotechnology, Vol. 1:601-607 (2006).

  • This was from an invited paper to a book on commercial flower growing.
  • This so-called “law” seems to exist only in the imagination of Lönnig. No one else has ever referenced, or ‘applied’ it, and it has been cited exactly 4 times by (oh I’m sure you can guess) Mr Lönnig himself and nobody else.
  • It boils down to the (apparent) limit of induced mutation within plants to alter phenotype (esp. outward appearance) before the chemicals, or radiation used kills the organism. This is hardly big news. Particularly in plants, more new species are the product of  polypoid hybrids then any point mutations alone.
  • Includes references to Behe (his long discredited Irreducible complexity), and also Dembski (no free lunch of course) – yes, he is indeed rather desperately plugging in all the ID stars.
  • Does this paper actually support Intelligent Design in any way at all? Nope, it is just another of Lönnig’s failed experiments being used  as an excuse to promote ID thinking without any justification at all.  – Fail

Øyvind Albert Voie, “Biological function and the genetic code are interdependent,”Chaos, Solitons and Fractals, Vol. 28:1000–1004 (2006). – 

  • It’s a paper in a maths journal; what we have here is an attempt to take Gödel’s theorem and try to apply it to something other than formal axiomatic systems … oh that’s such a bad idea. This is a journal for fractals, so it is no shock that the reviewers had the wool pulled over their eyes. If they were familiar with Gödel and information theory it would not have been published. Here is a link to an appropriate Subject matter expert who attempts to digest this and ends up spitting it out.
  • So in summary, it is not just a paper out of context, it is a bad paper that does not hold together – Fail

Kirk Durston and David K. Y. Chiu, “A Functional Entropy Model for Biological Sequences,” Dynamics of Continuous, Discrete & Impulsive Systems: Series B Supplement (2005).

  • And here we have a paper that is filled with unsupported assertions and unnecessary verbosity (this is very much becoming a theme with many of these paper). What it completely lacks is any evidence for any of the claims. If you disagree, then you might want  to read the discussion with Durston on Jeff Shallit’s blog here – Fail

David L. Abel and Jack T. Trevors, “Three subsets of sequence complexity and their relevance to biopolymeric information,” Theoretical Biology and Medical Modeling, Vol. 2(29):1-15 (August 11, 2005).

  • Yes, another Abel paper consisting entirely of non-evidentially supported, non-laboratory confirmed, pure fabrication as usual. – Fail

John A. Davison, “A Prescribed Evolutionary Hypothesis,” Rivista di Biologia/Biology Forum, Vol. 98: 155-166 (2005). – 

  • This is a non-peer reviewed proprietary journal. The article was only published here after the DI sponsored it – no regular journal would have it.
  • However, it was recognised, and did indeed win an award; it was voted “crankiest” on crank.net – Fail.

Douglas D. Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology, Vol. 341:1295–1315 (2004).

  • Yet another article that does not support Intelligent design theory. That fact was established during the Kitzmiller v. Dover Area School District, you can read the testimony here that proves this.
  • If that is not enough, then here is a detailed analysis of the paper. – Fail

Michael Behe and David W. Snoke, “Simulating evolution by gene duplication of protein features that require multiple amino acid residues,” Protein Science, Vol. 13 (2004).

  • This article was indeed peer-reviewed according to the normal procedures. The conclusions, however, were rapidly and voluminously disputed by others in the field, and the controversy was addressed by the editors. It argues against one common genetic mechanism of evolution. It says nothing at all in support of design. It’s assumptions and conclusion have been rebutted (M. Lynch 2005). – Fail

Stephen C. Meyer, “The origin of biological information and the higher taxonomic categories,” Proceedings of the Biological Society of Washington, Vol. 117(2):213-239 (2004)

  • All we actually have here is a very bad attempt to reorganize already existing information. This article was not peer-reviewed according to the standards of the Biological Society of Washington, but rather slipped into the journal by an editor without proper review.
  • The publisher later withdrew the article, but that well-known fact does not appear to deter the DI from claiming it – Fail.

Frank J. Tipler, “Intelligent Life in Cosmology,” International Journal of Astrobiology, Vol. 2(2): 141-148 (2003).

  • Nothing resembling an actual scientific hypothesis or theory is presented by this paper and it contains exactly zero evidence.
  • It does however give a great example of a truly weird bit of wishful thinking, and yes he is a kook, but then most creationists are, so I guess he fits right in. – Fail

David K.Y. Chiu and Thomas W.H. Lui, “Integrated Use of Multiple Interdependent Patterns for Biomolecular Sequence Analysis,” International Journal of Fuzzy Systems, Vol. 4(3):766-775 (September 2002).

  • Chiu and Lui do mention complex specified information in passing, but go on to develop another method of pattern analysis.
  • This paper does not actually support ID – Fail

Michael J. Denton, Craig J. Marshall, and Michael Legge, “The Protein Folds as Platonic Forms: New Support for the pre-Darwinian Conception of Evolution by Natural Law,” Journal of Theoretical Biology, Vol. 219: 325-342 (2002).

  • Here we find that Denton and Marshall and Legge et al. deal with non-Darwinian evolutionary processes, but they do not support intelligent design. In fact, Denton et al. explicitly refers to natural law. – Fail

Wolf-Ekkehard Lönnig and Heinz Saedler, “Chromosome Rearrangement and Transposable Elements,” Annual Review of Genetics, Vol. 36:389–410 (2002).

  • Annual Review of Genetics does not publish new research results; it publishes review articles, which summarize the current state of thinking on some topic. Although the thrust of the article is in opposition to the modern evolutionary picture, nowhere does it mention “design”. It references Behe and Dembski only in a couple long lists of references indicating a variety of different options. Neither author is singled out. This article does not support ID – Fail

Douglas D. Axe, “Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors,” Journal of Molecular Biology, Vol. 301:585-595 (2000).

  • Axe finds that changing 20 percent of the external amino acids in a couple of proteins causes them to lose their original function, even though individual amino acid changes did not. There was no investigation of change of function. Axe’s paper is not even a challenge to Darwinian evolution, much less support for intelligent design. Axe himself has said at the time that he has not attempted to make an argument for design in any of his publications (Forrest and Gross 2004, 42). – Fail.

Solomon Victor and Vijaya M. Nayak, “Evolutionary anticipation of the human heart,” Annals of the Royal College of Surgeons of England, Vol. 82:297-302 (2000).

  • Quick summary, “Gosh this is really complicated, I have no idea how it could have happened naturally, so God must have done it“, and so this is what happens when you stray outside your area of expertise – Fail

Solomon Victor, Vljaya M. Nayek, and Raveen Rajasingh, “Evolution of the Ventricles,” Texas Heart Institute Journal, Vol. 26:168-175 (1999). 

  • Yes, it is just an earlier draft of their appeal to ignorance – Fail

Stanley L. Jaki, “Teaching of Transcendence in Physics,” American Journal of Physics, Vol. 55(10):884-888 (October 1987).

  • A rather daft paper that gives guidance on how to teach “God did it”, but does not offer any actual evidence – Fail.

William G. Pollard, “Rumors of transcendence in physics,” American Journal of Physics, Vol. 52 (10) (October 1984).

  • Another daft and rather old paper that claims that because our mathematical laws of nature explain the world, it is a miracle — er no, it can’t be otherwise. The laws of nature describe the world we know and that world is a reflection of our thinking and our language. – Fail

… and that is it, the entire list, every possible vague reference that they could  dig up from a trawl through all the scientific literature going back over almost thirty years, and we end up with nothing credible, not one jot, nada … zilch … exactly zero. You see, the reason that 99.9% of biologists reject creationism is not because they are biased or brainwashed, but because there is no credible evidence.

In stark contrast to the output of scientific creationism, hundreds of papers are published each month by authors that find that evolution explains their results. One would think that, if intelligent design had any scientific merit, then there would be a significant number of papers published each month presenting evidence of supernatural intervention by an intelligent designer. Surely the many religious scientists, in particular, wouldn’t fail to publish results that support intelligent design.

Conclusion
The complete lack of any credible scientific evidence tells you all you really need to know. Is there any scientific foundation for Intelligent Design? The quick one word summary is “No“.

With no credible evidence on the table, any and all creationist claims need not be addressed, but instead should simply be dismissed. If they wish to ever assert a claim that is not dismissed, then they need to first go do some science that backs it up.


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75 thoughts on “Claims of Peer Review for Intelligent Design examined … and debunked

  • Scientific Christian

    There are many thousands of errors in this article, such as the aforementioned failures (such as the nonsense critique of Joseph Kuhn), but let’s focus on this rather strange bit in your ‘filters’:

    “There are articles from a Journal called BIO-Complexity : This is not a credible peer-review journal, instead it is a creationist journal issued by the Biologic Institute. They in turn are funded by the Discovery Institute … yes, it is their own pet journal and has exactly zero credibility within the scientific community, we can ignore all that.”

    Rather short-sighted, don’t ya think? For one, it’s obviously not a ‘creationist’ journal — nowhere does it advocate for young earth creationism or whatnot. Do you define creationism as ‘against evolution’? If so, then we have some classical circular reasoning going on, where an examination of peer review against evolution is not considered because said peer reviewed paper is against evolution.

    Is Biologic Institute funded by Discovery Institute? Not exactly any evidence for this notion, so that claim can be obviously tossed out. Although, in 2006, it did receive $261,000 from indirect public support — technically, this money ~could~ have come from Discovery, but no particular reason to force it. In 2007 and 2008, Biologic Institute received $464,000 and $280,000 from public support, showing that the primary funding of the organization is, no matter how you try to slice the numbers, not from Discovery Institute. There are also only a few members in Biologic Institute that are also part of Discovery, and thus calling it Discovery’s own pet journal is error-ridden in the extreme. Sources for the funding figures I mentioned of Biologic Institute can be found here:
    https://ncse.com/library-resource/latest-intelligent-design-journal

    What about it having “exactly zero credibility within the scientific community”? Biologist Gunter Wagner at Yale University who was asked to join Biologic Institute (and refused) outlines the concerns of scientists here with BIO-Complexity:

    “Publishing on this subject in mainstream journals is also better for … the credibility of the eventual answer to this question, as well as for the integrity of the scientific process in general. There are too many reasons for scientists to distrust a journal with a substantial ID influence, regardless of whether this particular enterprise is biased or not. … In the current situation any project of this sort will have a hard time to earn the trust of the scientific community.”

    So, it looks as if the problems with some scientists and BIO-Complexity is not that it’s published material is garbage and unscientific, scientists are simply concerned that the editorial board might be biased towards intelligent design in the first place, and thus some scientists (not all, quite a number of scientists are actually part of the organization) would not like to actually make themselves a part of the thing. So, the scientific community says their problem is potential bias, and Dave takes this as a marker for “exactly zero credibility” as if it were a Ken Ham speech. The opinion of the scientific community on BIO-Complexity does not seem to be accurately reflected by Dave.

    So, since 2008 and after many years pass by, many years after Wanger and the aforementioned facts in this comment, how has BIO-Complexity faired as a scientific journal? Pretty well, actually. The papers published in the journal are indexed in researchgate.net — something that is pretty good. Previous journals that attempted a format for testing intelligent design got nowhere near that far. Secondly, the journal is run by Douglas Axe. Is Axe not a good scientist? He’s a PhD from a rather very, very, very reputable university. Doesn’t this make a difference? What about citations to papers published by BIO-Complexity then? A good way to determine the view of the scientific community on BIO-Complexity is to see which papers and which journals cite papers published to BIO-Complexity. Indeed, this may be the best indicator. Let’s focus on Axe’s publications to the journal.

    The most cited paper I could find by Axe published to BIO-Complexity is titled ‘Lignin–Designed Randomness’ (note: the paper had multiple authors, not just Axe). It has 27 citations. That’s quite a bit, aye? If you take a look at those 27 papers that cite it on Google Scholar… You’ll see most of them are valid, scientific papers, published to valid, reputable scientific journals. Why are scientific papers in scientific journals citing a creationist resource? Oh wait–they don’t, because BIO-Complexity is exactly ~not~ that, a creationist resource. Other papers published to BIO-Complexity (quite a number, actually) also have good numbers of citations, such as 19, 24, etc. Papers published to BIO-Complexity are in fact valid, scientific papers, and have been cited numerous times by the scientific community. After spending time to examine your claims and accusations, they have been found to be in overwhelming error. In order to get rid of all the factual errors on this blog post would require me to write a multi-volume series, which is not happening — perhaps you will take into consideration the scope of the error that can be present on this article after I have found so many errors in less than a single paragraph of your post.

    • Dave Post author

      Perhaps I’m wrong. OK, let’s google the journal name and see what we find.

      From RationalWiki …(http://rationalwiki.org/wiki/BIO-Complexity) …

      BIO-Complexity is an open access journal published by the weirdly named Biologic Institute, a lame front for creation science. The journal “aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life”.[1] Good luck with that!

      The National Center for Science Education are also quite clearly not impressed … (https://ncse.com/library-resource/latest-intelligent-design-journal). If you are a fan of the journal, then you better not click that link, because you will not like what you find.

      OK, you might argue that they are all biased. Let’s see what they claim themselves within their own about page … “http://bio-complexity.org/ojs/index.php/main/about/editorialPolicies#purposeAndScope” …

      BIO-Complexity is a peer-reviewed scientific journal with a unique goal. It aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life.

      Biologic Institute, a 501(c)(3) public charity in the United States, supports the operation of BIO-Complexity.

      Who are the players here?

      The editorial team are all well-known creationists …

      Douglas Axe, Michael Behe, Stuart Burgess, etc…

      Their About page claims …(http://www.biologicinstitute.org/about) …

      Scientists affiliated with Biologic Institute are working from the idea that life appears to have been designed

      And there they also openly clarify exactly how they are principally funded …

      Q: Where do you get your funding?

      A: Most of our funding has been in the form of grants from Discovery Institute, a larger non-profit with an experienced fund-raising team. We also receive direct donations from individuals.

      Conclusion. Dismissing all of this is wholly appropriate, this is religion pretending to be science, and is clearly bankrolled by the Discovery Institute.

      You claimed … // it’s obviously not a ‘creationist’ journal //

      Sorry, but they rather obviously are exactly that. There is nothing subtle here, they tell you explicitly that within their own website.

      You also claimed … // Is Biologic Institute funded by Discovery Institute? Not exactly any evidence for this notion //

      Except perhaps their own website telling you that this is how they are funded.

      • Scientific Christian

        You seem to have made one good point, all the others being nonsensical. Let’s skew through your problems.

        The first thing you try is citing RationalWiki. LOL. You do realize RationalWiki is a hyper-atheistic wiki, right? Or is this news to you? Citing RationalWiki as a valid source on the journal BIO-Complexity is like citing Conservapedia as a reliable source on evolution.

        As for the NCSE website, you’ll realize I’ve not only read it, but literally cited it in my previous post. My quote from Wagner came from it. That doesn’t seem to have been processed by you, has it?

        Finally, let’s move to your ‘creationism’ statements. Indeed, we have a clear case of circular reasoning here. What is your definition of creationism? Is it simply ‘not believing in evolution and instead intelligent design’? If so, which it seems to be, then you’re obviously guilty of circular reasoning. Your post claims to examine the peer-review from intelligent design, and then dismisses BIO-Complexity specifically because it is an intelligent design journal. Whoops. Can’t have it both ways.

        The only correct point you seem to have made is that it’s funding comes from Discovery, which is also a negligible point. Where the money ones from is an almost useless question, the relevant question here is what does the scientific community think of the journal?

        As we’ve seen, the papers from BIO-Complexity are indexed by researchgate, a number of papers from BIO-Complexity have more than even 20 citations, coming from other reputable journals and scientific papers, and that the publishers to BIO-Complexity are themselves also scientists with completely valid credentials. Why doesn’t your page ever discuss the citations to papers from this journal? Why does it hurr durr they are funded by Discovery Institute’ as a means to dismiss them? Why are you dismissing them based off of their persons rather than their scientific credibility?

        • Dave Post author

          // all the others being nonsensical //
          This should probably not come as a shock, but I don’t agree.

          // RationalWiki //
          You don’t like RationalWiki and your primary reason for not liking them is that they don’t promote religious beliefs. The hint is perhaps in their name.

          You feel that RationalWiki is on par with Conservapedia. Personally I find one to be factual and the other to be fiction, so I’d not accept the comparison as valid.

          Regarding NCSE, yes I appreciate that you did quote it. The point was that they do not support the stance you are taking, so it was rather odd to point at them.

          // circular reasoning //
          You appear to be taking the stance that intelligent design is not religious creationism, is that correct, is this your stance?

          That perhaps is the core of our disagreement here, everything else flows from this.

          // Your post claims to examine the peer-review from intelligent design, and then dismisses BIO-Complexity specifically because it is an intelligent design journal.//
          No, the point of the post is to review papers from reputable sources that appear on the DI list (as it was then) that are supposed to provide evidence of ID. BIO-Complexity is not a reputable source. The observation that it gets indexed and the articles get cited does not change that. I confess that I’ve not checked to see who exactly is citing it and why, when time permits I’ll check it out. Moving on, neither does the observation that the people who write such papers have degrees.

          // Why are you dismissing them based off of their persons rather than their scientific credibility? //
          The names are well-known creationists and they do indeed have a reputation. They might indeed be a positive one in the eyes of other creationists, but they do not have scientific credibility within the wider community.

          To illustrate that point, Mr Behe’s own department at his university has a webpage where they clearly distance themselves from him. If he is going to establish some credibility, then he needs to start with his own university.

          For reference that department webpage reads …

          The department faculty, then, are unequivocal in their support of evolutionary theory, which has its roots in the seminal work of Charles Darwin and has been supported by findings accumulated over 140 years. The sole dissenter from this position, Prof. Michael Behe, is a well-known proponent of “intelligent design.” While we respect Prof. Behe’s right to express his views, they are his alone and are in no way endorsed by the department. It is our collective position that intelligent design has no basis in science, has not been tested experimentally, and should not be regarded as scientific.

          The publication of a paper within a peer-reviewed journal is not about declaring “truth” that is then unassailable and beyond criticism, but is instead part of a conversation with the wider community. Who exactly is BIO-Complexity having a conversation with?

          Perhaps one of the definitive golden moments for ID to be able to formally establish itself was the Kitzmiller v. Dover Area School District trial which I would speculate you are probably familiar with (I may of course be wrong about that). The verdict of that case was that intelligent design is not scientific but rather is a religious belief, and so that is not simply an opinion, it is a legal fact.

          You are personally religious, I get that point. You most probably strongly feel that ID is scientific, I get that point as well. The real challenge you face here is not to simply persuade me, but to persuade the entire life-science community.

          • Scientific Christian

            “You don’t like RationalWiki and your primary reason for not liking them is that they don’t promote religious beliefs. The hint is perhaps in their name.
            You feel that RationalWiki is on par with Conservapedia. Personally I find one to be factual and the other to be fiction, so I’d not accept the comparison as valid.
            Regarding NCSE, yes I appreciate that you did quote it. The point was that they do not support the stance you are taking, so it was rather odd to point at them.”

            LOL. No, I do not dislike IrrationalWiki because they “don’t promote religious beliefs”, it’s because their content is pseudononsensical insanity, useless, meaningless, etc, etc, etc. The very guidelines of IrrationalWiki state that the website is ran by a ‘skeptic’ viewpoint, making it on par with Conservapedia, which is run by a conservative viewpoint. IrrationalWiki promotes the madness of Jesus mythicism, view the Gospel accounts as mythical in genre, and a bunch of other complete nonsense that is rejected unanimously by historians and scientists unlike. Conclusion: Un-credible source.

            NCSE gives the information that I quoted it gave, which is quite enough. In short, NCSE does not conclude that BIO-Complexity is a pseudoscientific journal that publishes material on a creationist agenda, contrary to the message of your post.

            “You appear to be taking the stance that intelligent design is not religious creationism, is that correct, is this your stance?
            That perhaps is the core of our disagreement here, everything else flows from this.”

            A number of the advocates of intelligent design are indeed obviously religious, however I find it that they are defending the theory of intelligent design on a scientific basis rather than a religious one. I’ve never found any paper or publication by them that cites God or the Bible to support their claims.

            “No, the point of the post is to review papers from reputable sources that appear on the DI list (as it was then) that are supposed to provide evidence of ID. BIO-Complexity is not a reputable source. The observation that it gets indexed and the articles get cited does not change that. I confess that I’ve not checked to see who exactly is citing it and why, when time permits I’ll check it out. Moving on, neither does the observation that the people who write such papers have degrees. ”

            Not only do they have degrees, but a number of them are or were professors at highly reputable institutions. For example, Michael Behe is a professor of biochemistry at Lehigh University. No small feat. And, as noted, papers published to BIO-Complexity are in fact cited in many academic journals, as you admit to not having checked. You say BIO-Complexity is not a “reputable source”, but of course your article goes much, much further than that — you call it a creationist journal with zero credibility in the academic community. We’ve seen this is shown to be false because of the sources that index its papers, the academics that have cited it, and the academics that publish it. Are you willing to correct your statements?

            I also know about the statement Lehigh University issued against Behe’s advocation of intelligent design, but that’s almost too obvious. If a major university is not going to outright fire one of their members for denying evolution, they’re going to at least do something otherwise they might get a bit of that ‘scientific’ curb-kicking from other evolution-oriented institutions.

            Kitzmiller v. Dover was conducted by a judge, not a scientist, and quite an enormous amount has happened since 2005, much very good for ID in the scientific community. For example, in 2015, another serious scientist switched from the side of evolution to ID, and even ended up converting to Roman Catholicism because of it (I’m not Catholic, though). The books of Stephen Meyer and Douglas Axe on this issue were almost all published after 2005. The situation certainly has been improving for ID as an actual scientific hypothesis.

            As for me needing to convince the entire life-science community, that’s not my job at all — I’m just here to tell you that your criticisms of BIO-Complexity are illegitimate.

            • Dave Post author

              Rational Wiki

              // No, I do not dislike IrrationalWiki because they “don’t promote religious beliefs”, //

              But to make your case you then proceed to cite religious examples. That tends to confirm my point and not actually work as a rebuttal.

              Friendly tip: examples of “pseudononsensical insanity, useless, meaningless“, would perhaps consist of bigfoot claims, anti-vax claims, quack medicine, or perhaps a claim that Relativity is a myth. That would nicely nail it for you.

              But … all this is a tad off topic.

              NCSE Stance on BIO-Complexity

              // NCSE does not conclude that BIO-Complexity is a pseudoscientific journal that publishes material on a creationist agenda //

              If you check the webpage once again you will discover that their article is filed under …

              Anti-evolution (general)
              Creationism (general)

              And concludes that BIO-Complexity simply mimics a real peer-reviewed journal. You can continue to deny it if you wish, but rather obviously they are indeed telling you that it is a pseudoscientific journal.

              Citations

              // you call it a creationist journal with zero credibility in the academic community. We’ve seen this is shown to be false because of the sources that index its papers, the academics that have cited it, and the academics that publish it. Are you willing to correct your statements? //

              Let’s test this.

              The specific paper you cite as an example within your first comment was ‘Lignin–Designed Randomness‘. The basis for your claim is that this has been cited, so let’s take a look and see what is actually going on here.

              First the paper itself. The Abstract sums up the basic hypothesis being presented … “The peculiar proper- ties of lignin therefore make perfect sense when seen as part of a coherent design for the entire ecosystem of our planet.“. Yep, very much a classic ID argument.

              According to google scholar there are 27 citations for this paper, so let’s start to explore these and see what we find. Will we find 27 other papers building upon this ID hypothesis?

              Taking them in the order presented by google scholar …

              The first citation supposedly comes from “Anaerobic retting of banana and arecanut wastes in a plug flow digester for recovery of fiber, biogas and compost“. – This does not actually cite the Lignin–Designed Randomness at all as best as I can tell. I can email you a full copy if you would also like to also check it. Mistakes can happen in the CrossRef citation metadata, this appears to be an instance of that.

              Let’s try the next, “Cyclic and spirocyclic polyacetal ethers from lignin-based aromatics“. This does have a citation, but it simply cites it to verify this statement “lignin is the second most abundant natural polymer” … the word “Natural” is rather at odds with the “Design” claim being asserted in the paper it cites. Clearly this paper is not actually citing the central hypothesis of the original paper at all.

              On on to the next, “Occurrence of lignin degradation genotypes and phenotypes among prokaryotes“. Once again, just one reference as follows … “Natural lignin, a complex heteropolymer, contains phenolic and non-phenolic aromatic residues organized in clusters of different molecular weights (Leisola et al. 2012).“. Once again, this is not a reference to the central ID claim in the original paper.

              Let’s try again. The next is “Biological pretreatment of Eucalyptus grandis sawdust with white-rot fungi: study of degradation patterns and saccharification kinetics“. The one and only citation is … quote … “The degradation of lignin by white-rot fungi has some special particularities. The lignin is not degraded during fungal growth but only after nutrient depletion triggers secondary metabolism [21].“.

              The pattern is clear, nobody is citing this for the core ID hypothesis, just fringe basic references to backup basic lignin characteristics.

              Keep going and you find a similar pattern. Nobody is citing the central “designed” assertion at all, they are not building upon that in any way. Clearly some researchers are simply googling snippets and sticking in citations that look and feel right to bulk up their papers. It happens. To be honest the arrival of I4OC this month (citation metadata) will most probably change that, and clean up a lot of that.

              It all looks sciency … citations … but this is an illusion. Nobody finds any reason or value in citing the actual ID hypothesis.

              All this however perhaps avoids the rather obvious (to some) elephant in the room.

              The fundamental flaw in the mix here is that the Intelligent Design hypothesis itself is not actually science at all. If you are going to formulate a hypothesis then it needs to be both testable and also falsifiable. If you can’t test it or falsify it, then it is not a scientific hypothesis. The core assertion is one where there is a meta-assertion that can be summed up as follows “I have no idea how X could have happened naturally, therefore Design”.

              Seriously now, how exactly do you test and falsify that?

              The entire self-described remit of BIO-Complexity is ID, and that means that they quite literally self-certify as pseudoscientific. The credentials of anybody involved, and the apparent abundance of citations that do not actually reference any ID ideas at all, does not change that reality.

              There are perhaps two other rather important points to add.

              1) ID is a fringe religious idea and not at all mainstream. The vast majority of people who have a belief are generally quite content to accept the prevailing scientific evolutionary biological consensus and are not ID proponents.

              2) The modality itself is actually quite ancient. Sitting between our ears is a pattern matching machine that does of course offer us distinct survival advantages but will also yield false positives. Our ancestors in the not too distant past gazed upon the sun, moon, and stars, and also observed weather patterns. Unable to grasp that all of this was natural, they attributed it to supernatural entities. ID is simply the modern variation of this psychological pareidolia.

              I must also be pragmatic and recognise that in the end you will remain unconvinced and will persist in the assertion that BIO-Complexity is wonderfully sciency stuff. And if that is the case, then so be it. It is like this because you are perhaps too deeply invested in it all emotionally … but then again, there is still the distinct possibility that you just might prove me to be quite wrong about that.

              • Scientific Christian

                “But to make your case you then proceed to cite religious examples. That tends to confirm my point and not actually work as a rebuttal.”

                Perhaps you suffer from hallucinations, LOL. I clearly pointed out that the reason RationalWiki is a failure is not because of religion, it’s because they are a worthless information sourcing site. I cited the James Ossuary to prove that — something that is non-religious, of course (although you seem to love misconstruing facts). The James Ossuary is an ossuary that dates upwards to 70 AD, and says “James, the son of Joseph, father of Jesus”. Now, because RationalWiki has no clue that this is an authentic tablet (or cannot come to terms with it), they attempt to simply pretend it away as a forgery.

                So, this is not religion, you quack. This is the simple fact that RationalWiki is a site filled with inaccuracies and biased information, primarily because the editors have no understanding of putting their presuppositions past them when documenting something.

                “If you check the webpage once again you will discover that their article is filed under …
                Anti-evolution (general)
                Creationism (general)
                And concludes that BIO-Complexity simply mimics a real peer-reviewed journal. ”

                Quackboy Dave continues pretending reality into some sort of configuration to finally make himself feel better. First of all, according to NCSE themselves, the NCSE is the “National organization devoted to defending the teaching of evolution in public schools, and keeping creationism out.” Therefore, an evolutionist lobbying organization putting a title under ‘anti-evolution’ is meaningless, and secondly, putting BIO-Complexity under ‘anti-evolution’ (which is correct) does *not* mean they invoke it as a pseudoscientific journal — if you actually read the article, it is completely the opposite, and of course says nothing about them ‘mimicing’ actual peer-reviewed journals. We’ve already seen that BIO-Complexity is an actual peer-reviewed journal, and its credibility is up for debate here. As we’ve seen, its articles are indexed by academic sources and its papers are cited by many other scientific journals and papers. In other words, case-closed.

                Anyways, you try to combat the actual citations of the paper on Lignin, so let’s see your attempt. You say that the first paper doesn’t actually cite the paper at all. I can confirm this is correct.

                However, we enter a problem with your ‘explanations’ when we get to the second paper:

                “Let’s try the next, “Cyclic and spirocyclic polyacetal ethers from lignin-based aromatics“. This does have a citation, but it simply cites it to verify this statement “lignin is the second most abundant natural polymer” … the word “Natural” is rather at odds with the “Design” claim being asserted in the paper it cites. Clearly this paper is not actually citing the central hypothesis of the original paper at all.”

                This is of course, a clear nonsensical excuse. When a paper cites another paper, they will never necessarily cite the main thesis of the paper — the purpose of citing your sources is to find reliable sources that can verify your claims. Therefore, the authors of this second paper found a paper published to BIO-Complexity arguing for ID reliable enough to be considered a source for one of their claims, and the editors of ‘Polymer Chemistry’ (publishers of this paper) decided that the paper was good and the sources were good enough to publish into their journals. Indeed, this discussion has nothing to do with citing the thesis of ID, this has to do with the reliability of BIO-Complexity, and in fact there is no way to get around this here.

                You go on to make the same ridiculous error a number of times — I will give you the benefit of the doubt by simply presuming you didn’t understand how citations really work before now, instead of just assuming you’re stupid.

                But of course, the term ‘stupid’ certainly does apply when you continue your response to explain why these papers cited such sources:

                “Clearly some researchers are simply googling snippets and sticking in citations that look and feel right to bulk up their papers.”

                Indeed, your explanation as to why seriously credentialed researchers are publishing papers with a title that literally says ‘Lignin-designed randomness’ is that these highly qualified researchers are actually morons who do their research similar to the manner of a high school student, and that the editors of these journals (like Polymer Chemistry) are complete blithering morons at their job and totally missed the reference to an ID paper. Fantastic job. Perhaps we can see exactly what’s happening here, your presuppositions have strangled you and now you’re trying to somehow come to terms with scientists actually finding BIO-Complexity a credible journal. Your main argument against this seems to be the blog-claims of an evolutionist lobbying organization (NCSE).

                Funnily enough, based on all of this, your conclusion is as follows:

                “I must also be pragmatic and recognise that in the end you will remain unconvinced and will persist in the assertion that BIO-Complexity is wonderfully sciency stuff. And if that is the case, then so be it. It is like this because you are perhaps too deeply invested in it all emotionally … but then again, there is still the distinct possibility that you just might prove me to be quite wrong about that.”

                You clearly need to get your head out of your arse, the obvious conclusion when we see a journal being cited by numerous other journals and scientific papers and academic researchers is that such a journal is not “pseudoscientific”, the conclusion is that the journal is reliable, reliable enough to be discussed, whether or not its claims are true or not. If this reality that I have put forth to you is based on ’emotion’, perhaps it is emotion that you need to start figuring out.

                • Dave Post author

                  RationalWiki

                  I do confess that I was rather astonished to read your latest attempt to make the case that RationalWiki is not rational and that you don’t have a religious bias in play involved citing yet another religious claim. (About here is where I quite literally did a face-palm)

                  Your latest assertion is that they “pretend” that “The James Ossuary” is a forgery. That however is not a factual claim, no pretence is required. The item, a religious artefact, is controversial with many labelling it a forgery, and others claiming it is proof. This is essentially yet another example of a religious bias.

                  You have had several passes at this and keep coming up with religious examples. Unless you have a specific non-religious example, then we are done as far as RationalWiki is concerned. All you are doing is to continuously provide evidence that verifies my observation.

                  One further thought. If we completely ignore RationalWiki and went to Wikipedia itself then you would find that Intelligent Design is labelled pseudoscience. I get that you do not agree, so you don’t need to explain that. What I am curious about is to see how you feel about Wikipedia. Is that, from your viewpoint, also a godless conspiracy that touts unreliable pseudoscience?

                  NCSE

                  // putting BIO-Complexity under ‘anti-evolution’ (which is correct) does *not* mean they invoke it as a pseudoscientific journal — if you actually read the article, it is completely the opposite … says nothing about them ‘mimicing’ actual peer-reviewed journals//

                  This is a testable claim, so I’ll quote the article for you without the need to even comment on it …

                  “It seems safe to predict that it will be difficult for BIO-Complexity to attain its ostensible goal of serving as “the leading forum for testing the scientific merit of the claim that intelligent design … is a credible explanation for life.” But was that really the point? Unable to convince the scientific establishment of the merits of their views, creationists have long been engaged in the project of constructing a counter establishment, which mimics — or perhaps the mot juste is “apes” — not only peer-reviewed journals but also professional societies, textbook publishers, media organizations, natural history museums, and graduate programs at accredited universities.”

                  Science vs Pseudoscience

                  Back in my previous comment I rather clearly asked you exactly how the ID hypothesis could be tested and falsified. You have not addressed that rather key question at all. That silence confirms that it is indeed not a scientific hypothesis at all.

                  Given that BIO-Complexity clearly states that their focus is ID, then rather obviously it is pseudoscientific. The observation that others cite fringe information, and not the actual ID hypothesis, does not change that. You can indeed mix apple pie with cow pie, but it will not in any way make the apple pie taste better, nor will it render the cow pie into a viable supper.

                  Your only argument is that it is all sciency because it is being cited, but as has already been clearly demonstrated, it is not ID that is being cited. Having citations is not science, nor is it even evidence that a scientific methodology is being practised. That requires the development of a testable and falsifiable hypothesis. It is quite frankly bizarre to cite the existence of citations as “evidence” that a scientific methodology is being practised.

                  If indeed you feel citations are a meaningful measure, then what happens if you lookup the Impact factor for Bio-Complexity?

                  The answer is that you discover that it has no impact factor at all.

                  One last thought

                  Looking back over your last comment …

                  // Perhaps you suffer from hallucinations, LOL. …., you quack …. Quackboy Dave continues pretending reality into some sort of configuration to finally make himself feel better. … you’re stupid. … You clearly need to get your head out of your arse … //

                  Friendly Tip: You might wish to seriously ponder over the strategy you have adopted when striving to win hearts and minds. Call me a tad picky if you wish, but there appears to be a wee bit of scope for improvement.

                • Scientific Christian

                  “I do confess that I was rather astonished to read your latest attempt to make the case that RationalWiki is not rational and that you don’t have a religious bias in play involved citing yet another religious claim. (About here is where I quite literally did a face-palm)
                  Your latest assertion is that they “pretend” that “The James Ossuary” is a forgery. That however is not a factual claim, no pretence is required. The item, a religious artefact, is controversial with many labelling it a forgery, and others claiming it is proof. This is essentially yet another example of a religious bias.”

                  ROTFL. It should be common sense that RationalWiki is irrational, and now that your attempt to contest this will sadly diminish away at your credibility.

                  The James Ossuary seems to only be ‘controversial’ amongst internet atheists. Almost every study conducted by the top epigraphers in the scholarly community have deemed it authentic. In fact, I have found a rather very good report that sums up all the authenticity tests that have been conducted on it:
                  http://normangeisler.com/wp-content/uploads/2015/04/The-James-Ossuary-Dr.-Joseph-Holden.pdf

                  Indeed, this ‘doubt’ seems to be non-existent in the scholarly community. Controversy has been closed quite a while ago. If you actually take a look at the edit history and talk page of the James ossuary article, you’ll realize that I (korvexman) repeatedly attempted to mention *any* of these studies by *any* of these studies by the worlds leading experts in the actual James Ossuary page, and my edits were un-done almost every single time.

                  The James Ossuary of course, is not a ‘religious example’ — it is a historical one. As we’ve seen, RationalWiki is quite literally an atheist version of Wikipedia, and the editors attempt to re-write history to make it fit with their atheistic presuppositions. The atheist mass-bias on IrrationalWiki has caused them to corrupt countless of their pages on science and history, as shown. And even if this was a religious example — it would not matter, this is an excuse made up by yourself to try to invalidate the failure of RationalWiki to conduct adequate research. You try this again:

                  “You have had several passes at this and keep coming up with religious examples. Unless you have a specific non-religious example, then we are done as far as RationalWiki is concerned”

                  An astonishing failure when it comes to logic — an error is on error, whether or not it is religious. Indeed, your terribly inadequate logic seems to dictate that as long as the RationalWiki editors are biased by their irreligious motives, their inaccuracies do not count. LOL. In fact, the entire point here seems to be that RationalWiki is a worthless source on BIO-Complexity *specifically because* of its religious bias, LOL.

                  Anyways, I’m a former editor of RationalWiki, Wikipedia, and another Wiki as well — one thing in common with these Wikis is that all (or at least most) have pages that specifically state they are unreliable sources. For example, Wikipedia;
                  https://en.wikipedia.org/wiki/Wikipedia:Academic_use

                  That should completely close any thoughts of citing these works, indeed. Especially garbage like RationalWiki. Wikipedia has its own streamline of fantasies.

                  Back to NCSE:

                  As we’ve seen in my previous reply, NCSE defines themselves specifically in the following way;
                  “National organization devoted to defending the teaching of evolution in public schools, and keeping creationism out.”

                  A by-definition evolutionist talking-piece is a rather useless source when it comes to assessing BIO-Complexity; nevertheless, your quote from NCSE failed to show even NCSE accuses BIO-Complexity of ‘mimicking’ scientific journals — it merely states that creationists themselves have a history of trying to do this, and NCSE simply warns that the same could become of BIO-Complexity if it advances in a non-specialist way like its predecessors.

                  Impact factor:
                  This one is rather a useless ranting by you — the page does not say “zero impact factor” — it says “no data” — BIO-Complexity is obviously way too miniature and new of a journal to have any data inputted on it. With only 20-30 publications as of yet, it’s obvious that no one has actually tabulated anything on it as of yet. Imagining an impact factor of 0 for this journal, when one can do the calculations on their own with the assistance of Google Scholar is rather funny. As I noted earlier, to know if BIO-Complexity is a pseudjournal, you simply search up if the papers are being cited, especially if so multiple times. Some of the BIO-Complexity papers have 20-30 citations — which is not only pretty good, its quite above average. Therefore, this discussion can be considered closed.

                • Dave Post author

                  // this discussion can be considered closed //

                  After numerous comments, you have finally written something that I do agree with.

                  So let’s sum things up then.

                  It is indeed tempting to wade into the detail of your latest comment and perhaps make the observation that the latest “evidence” for your non-religious example of a Wiki-bias is an article from Christian apologist’s website. However, what is truly fascinating is the revelation that the real reason you don’t like it is because they rolled back your attempts to edit. The talk page for the religious artefact is indeed an interesting read, and there we can observe your comments as Korvexman, and the other editors carefully explaining the problem to you.

                  However, none of that is in any way relevant. Nor for that matter is the primary argument that you advance – that BIO-Complexity is a credible science journal because it has been cited.

                  What perhaps cuts directly to the heart of it all is this. I’ve asked you several times to explain exactly how the ID hypothesis can be tested and falsified. The continuous lack of any answer and a complete failure to even attempt to address this rather key point does indeed end the discussion.

                  If indeed the ID hypothesis cannot actually be tested and falsified, then it is not science, but rather is pseudoscience. Until that point is addressed in a credible manner then it truly is indeed the end of our discussion.

                • Scientific Christian

                  Another comment by you, and of course another laughable slew of errors. It’s rather hard to get through all of it, but let’s try once again. Perhaps your first and most important problem;

                  “It is indeed tempting to wade into the detail of your latest comment and perhaps make the observation that the latest “evidence” for your non-religious example of a Wiki-bias is an article from Christian apologist’s website.”

                  The logic you attempt to exercise is rather nonsensical to say the very least. Indeed, this “Christian apologist website” seems to have been a link to a PDF written by a well respected historian of the New Testament that does *nothing more* then record all the testimony and academic analyses that have been conducted on the James Ossuary. Geisler literally creates a chart and shows the testimony of all the scholars and rigorous testing of the James Ossuary, and… All the renowned scholars who examined the artifact (Andre Lemaire, Ada Yardeni, etc) concluded it was authentic. Unfortunately for yourself, accusations of ‘Christian apologists’ don’t degrade the credibility of any argument. Indeed, the entire thing seems to be an Ad Hominem Fallacy on your part — it seems to be a nice magic trick to wave away the countless academic papers and scholars that have entirely affirmed that the ossuary is authentic.

                  And again, you try to round up all your thoughts on IrrationalWiki to this one article, because it looks as if it’s the only one in which you are able to at least attempt trying to defend the jokers who edit that website. The countless errors on its religious content are hard to count. Trying to read its page on Christianity without barfing is a true challenge — and thus of course, its claims against BIO-Complexity are obviously useless.

                  “What perhaps cuts directly to the heart of it all is this. I’ve asked you several times to explain exactly how the ID hypothesis can be tested and falsified. The continuous lack of any answer and a complete failure to even attempt to address this rather key point does indeed end the discussion.”

                  What the hell are you talking about? It’s not anywhere in my memory when you attempted to ask this question before. I will answer it quite easily, but it’s most important to first and foremostly note that this is an obvious red-herring, LOL. Indeed, the question has nothing to do with the veracity of BIO-Complexity, which is what is actually in question. As we’ve seen, the journal has been cited numerous times in numerous papers, that really ends the debate on this issue.

                  As for ID being ‘testable’, a completely different subject then the one at hand, this has been addressed countless times before. A quick google search into resources published by the ID scientists will give lengthy explanations; http://www.discovery.org/a/584

                  And again, this is a completely different question then the veracity of BIO-Complexity. It has been shown that journals and scientists are very comfortable citing BIO-Complexity. Interestingly, we’ve seen you try to explain this away earlier by claiming that scientists do their research with quick google-searches, LOL.

                • Dave Post author

                  // It’s rather hard to get through all of it //

                  You are under no obligation to reply.

                  OK, so there are perhaps a couple of observations to make here.

                  Observation 1 – Wiki

                  The long justification regarding a specific religious artefact that you keep banging on about is utterly irrelevant. Initially I thought you had a specific religious bias, but clearly I was wrong. What is now rather clear, as your previously explained, is that you simply feel bitter about having your attempts to edit rolled back.

                  Observation 2 – Addressing the question “Is ID Science?”.

                  // What the hell are you talking about? It’s not anywhere in my memory when you attempted to ask this question before //

                  Except within this previous comment, and then this comment, and finally again within this comment.

                  This perhaps illustrates the problem here, you don’t fact check. All you had to do was scan the previous comments, and then simply explain that you had missed it … twice.

                  // it’s most important to first and foremostly note that this is an obvious red-herring //

                  Rather understandably you need to take this stance, because the observation blows away your entire claim. This is foundational. If ID is not science, then rather obviously BIO-Complexity, a self-professed ID journal, is not a science journal.

                  // As we’ve seen, the journal has been cited numerous times in numerous papers, that really ends the debate on this issue.//
                  If you truly believe that “debate” is over, then why do you keep replying.

                  What we have clearly seen is that nobody is citing any ID hypothesis. The claim that it has been cited means it is a “science” journal is about as credible as claiming that simply putting on a white lab coat makes you a scientist.

                  Can you put your finger on just one single case of an article within a credible science journal actually citing any ID Hypothesis. I’ve already laid out exactly what is going on.

                  // this has been addressed countless times before //

                  If that is true then it should be no problem to actually answer, but apparently it turns out that this is indeed a bit of a problem.

                  You had no idea how to answer it so you simply googled the question and posted a link to an archaic discovery institute page from 2001 that claims to answer it. Unfortunately that DI page does not in any meaningful way actually provide an answer at all.

                  Easy questions
                  These are, from your viewpoint easy questions, so let’s see what happens.

                  1) In your own words, how exactly do you test and falsify the ID hypothesis, how is it not simply an appeal to ignorance, a stance that claims “I have no clue how this could have happened naturally, therefore design”?.

                  2) Who outside the ID community actually thinks that the ID hypothesis is science, can you name anybody at all?

                  3) Can you even specify just one contribution that the ID hypothesis has made to our understanding of reality that is generally recognised as such?

                  Further Thoughts

                  Will this conversation progress?

                  Nope.

                  No doubt if you continued, then the “but citations hence case closed” arm waving would pop up yet again, and while it might indeed satisfy you, it does not convince me for the reasons I have already covered.

                  You have stated your position and explained why you adhere to that position. I’ve explained to you why it does not convince, not just me, but anybody and everybody outside of the ID community.

                  You are wholly convinced that I am wrong, and I am wholly convinced that you are wrong. Clearly how we both work out what is and is not actually true is where we truly disagree – everything else is a symptom of that.

                • Scientific Christian

                  Your mind seems to be rolling on in fiction for some time. Let’s try to streak through all of it.

                  Your second rant is about fact-checking it seems;

                  “This perhaps illustrates the problem here, you don’t fact check. All you had to do was scan the previous comments, and then simply explain that you had missed it … twice.”

                  In a second, we’re going to see the hypocrisy in this. But, for the record, after seeing you claim that you had repeatedly asked this question, I did in fact go back through your previous comments and find it. And thus, I answered the question in my previous response.

                  Secondly, it’s rather too ironic to see someone with your caliber of research insisting on the importance of fact-checking. We’ve already seen that your brain didn’t even conceive of actually taking a look at how other scholars use BIO-Complexity papers (citations) before claiming that the scholars don’t use it. This is rather funny.

                  As for the James Ossuary again, an important note can be made is that I directed you to a website that culminates all the research by different scholars on this artifact, and unsurprisingly, virtually all critical analyses on the James Ossuary revealed it to be authentic (it has a natural accumulation of patina, the Aramaic script is the same as well-known Aramaic script of the first century AD, etc). You responded by, not actually taking a look at the research by Ada Yardeni, Andre Lemaire of others, but whined that the site I sent you that gathered together all the studies on the James Ossuary was ‘religious’. This is rather interesting, it seems that you consider the religion someone participates in more relevant to their position then the actual information they use to defend their position.

                  Secondly, another observation I noted was that when I used a ‘religious’ source, this was found as problematic by you as it may entertain ‘bias’, however the fact that RationalWiki is an atheistic encyclopedia seems to have never come across your mind when it comes to establishing bias. Very interesting.

                  Anyways, you go again and claim that no one is citing any “ID hypothesis”. Again, you attempt to disingenuously get past the actual discussion here, and that is the discussion of the veracity of BIO-Complexity, and whether or not it is a valid journal, and indeed, any look at my original comments here, and my further comments that took apart your weakly formulated responses, will reveal that the exact point of discussion here is whether BIO-Complexity is a valid journal, and has nothing to do with ID.

                  So, is BIO-Complexity a valid journal? Again, the citations have proven this. The purpose of citations is irrelevant, as we’ve already seen it proven that countless scholars and countless other journals seem to be just fine for retrieving their information from BIO-Complexity research. If scholars consider BIO-Complexity a valid research source to cite and publish with, then the discussion is over, BIO-Complexity is a valid journal.

                  And unfortunately, there goes the rest of your case. There’s so much utter nonsense on your overall post that I was forced to address a single point.

                  “Who outside the ID community actually thinks that the ID hypothesis is science, can you name anybody at all?”

                  Err.. Perhaps the scholars who are citing ID papers? LOL.

                  “In your own words, how exactly do you test and falsify the ID hypothesis, how is it not simply an appeal to ignorance, a stance that claims “I have no clue how this could have happened naturally, therefore design”?

                  The enter question can be dismissed as it simply misrepresents ID, because nowhere in any ID publication, ID book, or statements of any ID scholars have stated “I have no idea how this biological process works, therefore it must be due to design”. It’s evident then, that the entire thing is a strawman. The only way for me to address such a question is if it was re-formulated and fixed to avoid these intentional lies you put forth in your previous comment.

                  One last interesting thing:

                  “I’ve explained to you why it does not convince, not just me, but anybody and everybody outside of the ID community.”

                  And what exactly brought you to the conclusion that every single member outside of the ID community shares your response to ID arguments? This seems to be a rather too-hasty generalization that has nothing to verify it.

                • Dave Post author

                  // Your mind seems to be rolling on in fiction for some time. //

                  … says the guy who believes that “magic” is the right answer.

                  // I answered the question in my previous response. //

                  You might indeed truly believe you did, but in this reality you did not.

                  // Secondly, it’s rather too ironic to see someone with your caliber of research insisting on the importance of fact-checking. We’ve already seen that your brain didn’t even conceive of actually taking a look at how other scholars use BIO-Complexity papers (citations) before claiming that the scholars don’t use it. This is rather funny. //

                  I can simply refer you back to where exactly that was done … in detail, it would appear that once again your complete and utter lack of fact checking takes precedence yet again..

                  // As for the James Ossuary again, //

                  Seriously … again!

                  You keep harping back to this religious artefact. It borders on an obsession. We get it, you tried to edit the RationalWiki page, got bounced, feel sore about that, and so have a desperate need to prove you are right. This is quite frankly deeply insecure?

                  // So, is BIO-Complexity a valid journal? Again, the citations have proven this. //

                  As predicted, the citation arm waving pops up once again.

                  // The purpose of citations is irrelevant, //

                  Seriously!

                  // “Who outside the ID community actually thinks that the ID hypothesis is science, can you name anybody at all?”

                  Err.. Perhaps the scholars who are citing ID papers? LOL. //

                  This is testable and verifiable. Cite just one that is actually citing the ID Hypothesis

                  Prediction: you don’t have any examples.

                  // And what exactly brought you to the conclusion that every single member outside of the ID community shares your response to ID arguments? This seems to be a rather too-hasty generalization that has nothing to verify it. //

                  A simple rebuttal is to cite just one example … apparently you can’t, why is that the case?

                  So basically you failed to actually address any of the questions in any meaningful way. As a brief reminder, here they are again …

                  1) In your own words, how exactly do you test and falsify the ID hypothesis, how is it not simply an appeal to ignorance, a stance that claims “I have no clue how this could have happened naturally, therefore design”?.

                  2) Who outside the ID community actually thinks that the ID hypothesis is science, can you name anybody at all?

                  3) Can you even specify just one contribution that the ID hypothesis has made to our understanding of reality that is generally recognised as such?

                  … and to add to the above …

                  4) What would it take to convince you that you are wrong?

                  Prediction: Past experience is an indicator of future behaviour you won’t write an honest meaningful answer.

                • Scientific Christian

                  “// Your mind seems to be rolling on in fiction for some time. //
                  … says the guy who believes that “magic” is the right answer.”

                  LOL. Anyhow, even magic would seem to be more logical than the frenzy nonsense that I can find on your favorite source, RationalWiki , LOL.

                  “I can simply refer you back to where exactly that was done … in detail, it would appear that once again your complete and utter lack of fact checking takes precedence yet again..”

                  You go again and re-quote yourself posting the same red herring. Indeed, you try and try again to claim that the citations aren’t specifically for design, but as I have had to repeat again and yet again, we’re not talking about design, we’re talking about the reliability of BIO-Complexity. BIO-Complexity being cited makes it a reliable scientific source for information and citation, according to the many scholars and scientific journals that have published papers with reference to BIO-Complexity. The fact that the papers (at least the ones we’ve examined) don’t cite BIO-Complexity for the specifics of intelligent design is irrelevant, because that’s not even the discussion, LOL.

                  “You keep harping back to this religious artefact. It borders on an obsession. We get it, you tried to edit the RationalWiki page, got bounced, feel sore about that, and so have a desperate need to prove you are right. This is quite frankly deeply insecure?”

                  LOL! It looks as if you’re trying to slant a failure to conduct research as an insecurity all of a sudden. As we’ve seen earlier, quite literally all academics in the field that have published studies on the James Ossuary have accepted it as a simple factual ancient artifact. However, any attempt to include any of these studies immediately triggers and instantaneous deletion by the skeptics on RationalWiki. Doesn’t it at least intrigue you that your source of information is hell-bent on disincluding all information that contradicts it?

                  “// “Who outside the ID community actually thinks that the ID hypothesis is science, can you name anybody at all?”
                  Err.. Perhaps the scholars who are citing ID papers? LOL. //
                  This is testable and verifiable. Cite just one that is actually citing the ID Hypothesis”

                  Irrelevant. All the scientists who cited these ID papers knew full well they were citing ID papers, regardless of whether or not the purpose of citation was for ID science itself. That means these scientists don’t view ID in the way you do. Therefore, your claim that all scientists outside of ID not considering ID as valid is blatantly false. It is disingenuous to claim that everyone on ID shares your interpretation. As for the testability of ID, I’ve already sent you a resource from the ID scientists themselves that explains a lot of these predictions for you. Here’s another link you can look at:
                  http://www.ideacenter.org/content1156.html

                  As for the same 4 questions that I’ve already answered before, that you are intent on continuing to repeat again and again;

                  1) See link above
                  2) See comments above, every author who was willing to cite an ID paper from an ID journal
                  3) Sure I can. At least we have a new question here. Perhaps you are familiar with the experiments of Lenski on citrate, where e. coli were able to, after some tens of thousands of generations, metabolize citrate. This was hailed as speciation or something, but then some scientists, including at least one professional ID scientist I know of (Scott Minnich) conducted experiments on these e. coli and published them to the Journal of Bacteriology analyzing the findings of Lenski, here’s the paper;
                  http://jb.asm.org/content/198/7/1022.short

                  Minnich and his peers conducted experiments and were able to cause a specific mutation to occur in the e. coli to metabolize citrate, they completely re-did Lenski’s experiments 46 times over, and sometimes were able to cause the e. coli to gain the mutation to metabolize citrate in as little as 12 generations. These findings put away the idea of speciation here, and advanced our knowledge of e. coli and these mutations first analyzed by Lenski’s famous experiments. The paper was published (as I noted earlier) into the prominent Journal of Bacteriology just last year in 2016, and has already been cited and discussed several times at that. For example, shortly after this publication by Minnich and his peers, another paper was published to the Journal of Bacteriology by the American Society for Microbiology, noting that Lenski’s conclusions about his experiments require “reinterpretation”. Here’s that paper:
                  https://www.researchgate.net/profile/Sophie_Maisnier-Patin/publication/298786808_Reinterpreting_Long-Term_Evolution_Experiments_Is_Delayed_Adaptation_an_Example_of_Historical_Contingency_or_a_Consequence_of_Intermittent_Selection/links/56eb33d108aec6b500169e19.pdf

                  4) What would it take to convince me that I am wrong? I’m not 100% on the side of ID anyways, because I think that in the evolutionary record — there is particularly *one* really good argument for macro-evolution, and that is the hominid fossils. Nothing else is particularly convincing or really well argued. However, to convince me I’m wrong, perhaps someone could show me a really, really good transitional fossil. Past ‘transitional’ fossils that have turned out to be unconvincing include archaeopteryx, which turned out to be a secondarily flightless bird, and a few other ones that have seen been put away. Like, a *really* good transitional fossil. Undeniable, unarguable. The vast majority I’ve seen are quite debatable. I’d also need some pretty good answers to the Cambrian Explosion as well, most of which that I’ve read in the peer-reviewed literature are either clear nonsense or fanciful exaggerations (or have simply been addressed by the ID proponents).

                • Dave Post author

                  In opening this comment I think I should clarify one point. I’m staying focused on the specific questions and will not be commenting any further on either RationalWiki or the specifics of the religious artefact within this thread.

                  Should this be taken as an acceptance of your stance on either?

                  Basically no. Instead I simply accept that you hold a specific position on both that you have clearly articulated. Since neither is the primary topic of immediate interest, I’m content to let that slide. Perhaps at some point I should write a posting on the James Ossuary and we can then debate it all in that context.

                  OK, so on to the questions. Let’s look at each in turn.

                  1) In your own words, how exactly do you test and falsify the ID hypothesis, how is it not simply an appeal to ignorance, a stance that claims “I have no clue how this could have happened naturally, therefore design”?.

                  // 1) See link above //

                  The ever so subtle clue was contained within the term “In your own words”, but let’s take a look at the link anyway. The 4 examples given of a successful prediction include things such as “irreducible complexity”. So let’s take that first one (a similar observation can be applied to the others).

                  The idea of “irreducible complexity” will of course be familiar, and will also perhaps forever be associated with Mr Behe because it came up in the 2005 trial. The rather clear rebuttal to all that was in the final ruling …(Page 79)

                  Professor Behe conceded that the proposed test could not approximate real world conditions and even if it could, Professor Minnich admitted that it would merely be a test of evolution, not design. (22:107-10 (Behe); 2:15 (Miller); 38:82 (Minnich)). We therefore find that Professor Behe’s claim for irreducible complexity has been refuted in peer-reviewed research papers and has been rejected by the scientific community at large. (17:45-46 (Padian); 3:99 (Miller)). Additionally, even if irreducible complexity had not been rejected, it still does not support ID as it is merely a test for evolution, not design. (2:15, 2:35-40 (Miller); 28:63-66 (Fuller)).

                  If time permits you to do so, it is also worth reading what follows after the above.

                  So there are a couple of points here …

                  – “irreducible complexity” is quite literally an appeal to ignorance.
                  – How can anybody realistically test and verify it and completely eliminate the more probable explanation?
                  – The null hypothesis should prevail when faced with something that can’t be explained (although for the record, as best as I am aware, there are no current claims of irreducible complexity that do not have a better explanation.

                  Let’s suppose that somebody did come up with an example that could not be explained … yet. Should the default be “design”? How can you possibly test that and reach that conclusion by eliminating the far more reasonable “I don’t know” placeholder?

                  In summary, I’m honestly not finding the link to contain a satisfactory answer.

                  2) Who outside the ID community actually thinks that the ID hypothesis is science, can you name anybody at all?

                  The essence of your response here is that various researchers outside the ID community have cited references. There is a problem with this position …
                  – None of those researchers I checked are citing any variation of the ID hypothesis, and you do now acknowledge that, so for that reason alone it does not actually address the question.
                  – You make the observation that // All the scientists who cited these ID papers knew full well they were citing ID papers //. I’m not convinced this is the case and short of polling each and every one, you have no way of actually knowing that. Remember that you yourself were not initially aware that BioComplexity declared themselves to be an ID journal.

                  An interesting comparison is perhaps “Signature in The Cell”. The first four chapters are fine, all good solid basic foundational stuff. Chapter 5 is where the book takes a left-hand turn into the ID universe. I have no problem with the first 4 chapters, but for rather obvious reasons I do take issue with the book.

                  The point here is this – The reason for publishing work within any peer-reviewed journal is to engage the wider community in a conversation and so we build upon what has come before and lay a foundation for what comes next. Given that the specific remit of BioComplexity is ID, then if nobody is citing the ID hypothesis, who exactly are they having a conversation with, and who is utilising their published work on ID to advance our understanding?

                  Once again, I’m quite honestly not finding this to be an answer.

                  3) Can you even specify just one contribution that the ID hypothesis has made to our understanding of reality that is generally recognised as such?

                  The example you cite is of course interesting, but has rather confused me.
                  – We have Richard Lenski’s grand experiment, and that continues to this day.
                  – We have a paper written by Scott Minnich that writes up the details of a replication of it.
                  – We have another paper that suggests a reinterpretation

                  None of it in any way relates to the ID hypothesis except we can perhaps make the observation that Scott Minnich happens to be on the DI board and is a well-known ID proponent who became famous for being part of the Dover trial in 2005.

                  As a point of related interest Richard Lenski wrote up a few notes on his blog regarding Mr Minnich’s paper

                  There he wrote …

                  Let’s begin by saying that it’s great to see other groups working on interesting systems and problems like the evolution of citrate utilization in E. coli.

                  Moreover, the actual science that was done and reported looks fine and interesting, though we have a few quibbles with some details that we will overlook for now. By and large, the work confirms many of the findings that were reported in our papers cited above:

                  … (lists details of agreement) …

                  The problem, then, is not with the experiments and data. Rather, the problem is that the results are wrapped in interpretations that are, in our view, flawed and fallacious.

                  … (Proceeds to explain what the problem is in detail) …

                  So yes, Mr Minnich’s paper, confirmed Mr Lenski’s on-going work, and that is indeed a valuable piece of independent work, but no, none of this is an example of the ID hypothesis contributing to anything at all. That aside, the interpretation is questionable.

                  To perhaps claim that because Mr Minnich is a supporter of the ID hypothesis, hence ID contributed to our understanding is about as credible as suggesting Catholicism did something similar because Georges Lemaître, a Catholic Priest, contributed to our understanding of cosmology in the 1920s.

                  I’m honestly not finding that this example addresses the question.

                  4) What would it take to convince you that you are wrong?

                  The answer to this is the one truly impressed me. What you articulate is a willingness to follow evidence and that is of course to be applauded, but also is perhaps the best possible answer to this, or any variation of this question. I believe you have indeed fully addressed it.

                  In summary, you are rather frustrated that the first three questions keep popping up. While my repetition of them is not designed to frustrate you, I do understand that it can indeed be the case. The reality is that the answers given don’t actually address the questions in a way that convinces me, and while you might indeed firmly assert they do, I promise you that they really don’t.

                  I understand your position and you have articulated it well, the problem is that I just don’t adhere to the same position for the reasons I’ve laid out.

                • Scientific Christian

                  “In opening this comment I think I should clarify one point. I’m staying focused on the specific questions and will not be commenting any further on either RationalWiki or the specifics of the religious artefact within this thread.
                  Should this be taken as an acceptance of your stance on either?”

                  Fine, do away with RationalWiki. Just remember that — the only reason it came up, is because you tried to cite this atheistic wiki to back up your accusations against BIO-Complexity.

                  “Perhaps at some point I should write a posting on the James Ossuary and we can then debate it all in that context.”

                  Sure, I’d be up for that. However, I don’t follow your blog, so you’d have to bring it to my attention.

                  Anyways, it looks like our conversation is going to go specifically to the 4 points you primarily brought up.

                  1) I sent you a link regarding predictions of intelligent design, and you contested one of the four examples in the link, irreducible complexity by quoting a trial that occurred 12 years ago. Now, I don’t want to exactly dive into irreducible complexity here, because this will enter an extremely drawn out conversation on the flagellum or something — so perhaps a more simple prediction I’m aware of will suffice. If we wanted to discuss irreducible complexity, that warrants an entire conversation for its own.

                  Here are two predictions, that you ask of “in your own words” of the intelligent design scientists that I’m aware of and think are pretty good;

                  1a) The prediction that the non-coding regions of DNA are actually meaningful and not junk

                  Perhaps just two decades ago, scientists mostly considered and called the non-coding regions of DNA “junk DNA”, but as far as I’m concerned, intelligent design scientists as early as the 80’s have been predicting otherwise. Then, the international research project of ENCODE commenced (2003-2012), and catastrophically damaged such a supposed paradigm. Although the ‘extent’ of which function was found in DNA by ENCODE is attacked by some scientists here and there (they dispute ENCODE’s definition of ‘function’, claiming that just because some parts of DNA are transcripted, that doesn’t necessarily equate to function), there is without a doubt that ENCODE broke open the chambers of science to reanalzying the function of DNA.

                  Before ENCODE, scientists altogether ignored the ‘functionless’ regions of DNA, but after ENCODE, research has perhaps exploded. The website http://www.lncrnablog.com/ records most (if not all) of the most recent research papers finding functions in lncrna’s from 2013 onwards. Since 2013 alone, excluding all ENCODE papers, about 400 papers have been published finding more and more function in the non-coding regions of DNA, and this research continues to explode. It will likely be propelled now, because starting in 2017, the ENCODE research project is reactivating. This was predicted decades ago, only and only by ID scientists.

                  1b) The prediction of overwhelming specified information and complexity in DNA. The overwhelming amounts of more and more information that has been discovered in DNA since the ID scientists predicted it should be self-explanatory to almost anyone who has a grasp on the field of biology. I’d also recommend reading this ID article: https://www.evolutionnews.org/2017/04/genetic-code-complexity-just-tripled/

                  I think that should be enough to show that ID scientists, based on their view of design in biology, have in fact made predictions. You should not off-handedly dismiss this.

                  2) Again, back to scientists taking ID seriously. I pointed out that many scientists have cited ID papers, and many serious journals have published papers that have ID papers in their bibliographies. I noted that these scientists were full aware that they were citing papers that specifically are arguing for ID. You said you are… “not convinced” they knew this.

                  This is rather an enormously problematic claim of yours. Are you seriously willing to tell me that scientists *do not* read the papers they are citing? This idea is as incorrect as it is presumptuous against people who have devoted their lifetimes to this field. The BIO-Complexity paper we discussed in specific was titled ‘Lignin – Designed Randomness’. Do you not think… That such a title would at least raise the eyebrows of some of the scientists citing these papers whom you claim actually think ID is pseudoscience? For example, one of the papers that cites this one (https://link.springer.com/article/10.1007/s00253-014-6142-4) is very, very well-researched. Were the researchers utterly oblivious to the fact that one of their references has a title that includes ‘Designed Randomness’, published into the journal BIO-Complexity, and one of the authors being Douglas Axe?

                  This seems simply… Unwarranted. You try to make it as if no scientist or journal could seriously ever publish or cite such a paper, you think it is not even possible, but the data speaks specifically otherwise. Unfortunately, you will have to concede this point.

                  3) Now, we go into the actual contributions of ID scientists. Regarding the work of Scott Minnichs (and some of his collaborators) published just in 2016, you make a few notes;

                  -this research actually confirms Lenski’s experiments
                  -Lenski wrote something on his blog where he doesn’t agree exactly with the paper (important to note that Lenski only disagreed with the interpretation, not the data)
                  -Just because an ID scientist has contributed to science, that does not mean ID itself has contributed

                  Firstly, before the work of Minnich and his colleagues, many scientists believed that Lenski’s experiments revealed speciation or whatnot, a serious example of what could eventually become macro-evolution, etc, etc, and many of the scientists who are outspoken against ID (like PZ Meyers) have actually quoted this work.

                  However, Minnichs work revealed that there was in fact no speciation, and through direct selection, the research was able to cause the E. coli to metabolize citrate in as little as 12 generations.

                  Lenski’s experiments initially showed that after tens of thousands of generations, ‘evolution’ can slowly work and allow through natural selection (or whatnot) for an organism (like E. coli) to do something it wasn’t able. It took Lenski something like 40,000 generations to get this ‘rare feat’, but the research of the ID scientists replicated this in as little as 12. This was not as rare, impressive, or anything whatnot, and does not represent speciation as some have previously speculated.

                  For more, read this:
                  https://www.evolutionnews.org/2016/05/richard_lenski/

                  Now, I do find that this *is* a contribution from ID, because Minnichs only went to do this research because he found that evolution didn’t necessarily need to be the explainer of Lenski’s results, as his convictions had put this up to ID. Without ID, Minnichs would not have engaged in this work.

                  4) I think perhaps this is the best part of our conversation. You indeed state that you believe I have “fully addressed” it here, and I think we can come to a rather strong agreement, despite our different views on the life in this world, on this specific issue.

                  It’s not everyday where on the internet an evolution VS ID debate can be so respectful. I feel good that this part of the conversation can be considered ‘resolved’ — we should now focus on only the first 3 points.

  • Jimmy

    Sorry Christine, not only did Casey get the discovery right, he previewed the exact discovery diagram comparison between Tiktaalik and actual wrists by the person who discovered Tiktaalik in his response. You should probably also have tried to read my full discussion with Dave, Tiktaalik is not a transitional fossil to tetrapods. I’ve proven that tetrapods predate Tiktaalik and all other supposed transitional fossils to tetrapods by tens of millions of years.

    • Dave Post author

      Sorry Jimmy, but you have not actually “proven” anything. Your argument is simply an updated variation of “If we evolved from Monkeys, then why are there still Monkeys”. Tiktaalik is basically one more example of transition, nobody is claiming that it is “the” one and only transition.

      The scope of our entire discussion revolved around this …
      – Your stance was that the posting is “pathetic and ambiguously silly responses to a body of peer-reviewed literature”
      – My stance was that none of this “body of peer-reviewed literature” is credible.

      To explore that, we drilled down into the first paper by Mr Kuhn. In the context of that paper
      – Your stance is that (if I may paraphrase) it is super stuff and that My Coyne fails to address it
      – Mine is (as outlined within a previous comment) that is contains 3 basic arguments, none of which are credible or reputable arguments and that was the point being made by Mr Coyne.

      What you might assert regarding the three arguments is irrelevant to this, the scope is not what you or other creationists might or might not feel is viable and why, but rather is specifically the content of Mr Kuhn’s paper.

      Has anybody anywhere (apart from other creationists) found any of it to be credible? If not, then it is indeed a fail.

      That is basically the essence of it all.

      Yes, I have disengaged, and have no burning desire to rush in and correct each and every point raised. People believe things for many different reasons, sometimes they simply do not have the right information, but often there is something else going on.

      Seriously now, does it not cause you some pause to realise that there is a rather strong correlation between ID and religious belief, and none at all amongst the prevailing evidence-based scientific consensus where you will find a vast diversity of religious belief with some of the most deeply religious adopting the stance of “Well, that is how God did it”.

      We might indeed proceed to quibble about the colour of the leaves as part of a discussion about the reality of the existence of a season that follows Summer. “Look, this leaf is the wrong colour, hence Autumn does not exist” really does not cut it.

      You believe certain things … I get that. You feel that TS3 is an appropriate rebuttal for IR (I don’t), but in the end it is not me you need to convince, rather it is the entire life-science community.

      • Jimmy

        Please read this comment in full before replying (I wont be making “arguments and responses” here on the specific points. In my previous comment, I spent a great deal of time making various corrections to your comment, however it is annoying to see that you didn’t bother to read one line of it, rather continue postulating the “ID=creationism/religious belief” nonsense that ID scientists have spent a great deal of time replying to, and have tried their best to keep religion out of their theories, so much as not even calling the ’cause’ of life not God, rather just an ‘Intelligent Designer’ (which as you can see, greatly differs from guys like the ones who post to Answers in Genesis and guys like Kent Hovind and Ken Ham). ID has defined the word design in an EXTREMELY religiously neutral manner; “the intentional assembling of parts”. Nothing creationist-ish about that.

        However, at the end of your comment, your position boils down to “you wont convince me if you cant convince the rest of the scientists”, which, annoyingly enough, when it comes to the people at Discovery Institute, is what all the evolutionists say, “convince the others to convince me”. However — there IS major growing dissent on Evolution. A scientist in EES wrote the following to Nature:

        “The number of biologists calling for change in how evolution is conceptualized is growing rapidly. Strong support comes from allied disciplines, particularly developmental biology, but also genomics, epigenetics, ecology and social science. We contend that evolutionary biology needs revision if it is to benefit fully from these other disciplines. The data supporting our position gets stronger every day. Yet the mere mention of the EES often evokes an emotional, even hostile, reaction among evolutionary biologists. Too often, vital discussions descend into acrimony, with accusations of muddle or misrepresentation. Perhaps haunted by the spectre of intelligent design, evolutionary biologists wish to show a united front to those hostile to science. Some might fear that they will receive less funding and recognition if outsiders — such as physiologists or developmental biologists — flood into their field.”

        Here is the nature paper where this was written in: http://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080

        Darwinian Evolution has, quite frankly, failed. In Stephen Meyer’s book, Darwins Doubt, he capitalizes on almost 10 substitute evolutionary models that have sprung up extremely recently to cover the holes for evolution. I know you didn’t read my last comment — to note, if you read it, you’ll find where I show from discoveries, that tetrapods Tiktaalik by tens of millions of years (or was it 18 mil?), and all other “transitional” fossils to tetrapods. That is EXTRAORDINARILY problematic for evolutionary theory. Mutations and natural selection have failed to explain the origins of information, the Cambrian Explosion, the discovery of Junk DNA being virtually entirely functional has devastated virtually all the most respected evolutionary models, a whale fossil was discovered that predates virtually ALL its ‘ancestors’, dating at 49,000,000 years old (thus predating indohyus, ambulocetus, rodhocetus, dorudon, basilosaurus, you know the ones I’m talking about, all of them excluding pakicetus, a fully-terrestrial land-mammal)… I could go on for hours. As noted in Nature, dissent is exploding, classical Darwinian evolution is dying. The 20th century was very good for evolution, but in the last two decades, it has been undergoing apocalyptic death. Now that you know the community IS being convinced of these problems, will YOU?

      • Glen

        There is certainly a strong correlation between ID and religious belief, if God did actually do it, then science will eventually point in that direction, which is what we are beginning to see. But there is also a strong correlation between materialists, their belief in evolution and stubbornness to accept any scientific research that points towards a different theory which challenges their world view. As the Nature article Jimmy referenced, we see mostly hostile reception towards anyone who challenges the status quo.

        • Dave Post author

          Hi Glen

          You write … // if God did actually do it, then science will eventually point in that direction, which is what we are beginning to see //

          I do agree that in the long run truth will prevail, but I’m not convinced we are beginning to see that god did it. I’d like to suggest that it is the other way around. It has perhaps been the universal stance that a god did it, and it is only in our recent history that we have begun to realise that this might not be true.

          // there is also a strong correlation between materialists, their belief in evolution //

          As a counter observation, I’d like to point out that there are many many (perhaps the vast majority) of life-scientists, who are religious, and yet they also happily accept the prevailing consensus, not because it is either mandatory or a belief, but because that is where all the evidence points. The majority stance that most religious people take is generally “evolution is how god did it”, creationism is a minority belief.

          // As the Nature article Jimmy referenced, we see mostly hostile reception towards anyone who challenges the status quo.//

          The Nature article was not really a challenge to evolution at all, there are a few points to note about it …
          – It was written 2 years ago, it is not new
          – It is structured into two sections with champions for each side making their points.
          – Of interest is the ‘Yes’ camp that argues for a rethink
          – There is nothing in it that suggests tossing out evolution. It does not in any way suggest that ID is credible, not even a hint, so observing Jimmy use this to support his ID stance is quite frankly astonishing and perhaps a tad silly.

          When he quotes it as saying “The number of biologists calling for change in how evolution is conceptualized is growing rapidly. …” and makes a choice to omit the previous paragraph which puts that in context by saying “We believe that the EES will shed new light on how evolution works.” … well that omission is itself a bit of a revelation.

          I can add that if a revolution in thinking was really called for, then there would be no debate, it would simply happen. The wording is dramatic and is perhaps driven by deeply felt emotions coming from individuals who are passionate about their work. To be a bit more specific, the yes camp argues that “developmental bias” is a more “succinct” hypothesis than convergent evolution. They also propose that an adaptive change in an organism is caused by phenotypes alone, with the genetic change lagging well behind. They also appear to be arguing for non-genetic forms of evolution. All interesting, and none of it really challenging the fundamental idea itself. Then right under it all is the rebuttal.

          As for Jimmy’s GishGallop, when time permits I might write a rebuttal for all of it and create a new posting. The degree of detail it all calls for goes way beyond a simple comment stream. I can however make one prediction, regardless of the robustness of the rebuttal, he will maintain his stance, not because it is true, but rather due to his deep emotional investment in the idea itself.

  • Jimmy

    It’s hilarious to see such pathetic and ambiguously silly responses to a body of peer-reviewed literature. Indeed, trying to find the smallest thing conceivable that you can pick at, and concluding with a “Fail”, when the only fail is the article. Indeed, a two lines response to published peer review is not a response at all.

    If the publishers of these papers saw this nonsense, they would have a good laugh, and then point out the massive contradictions, inconsistencies, errors, and erroneous “fail” accusations.

    • Dave Post author

      Why not pick the best strongest most robust paper and then explain why it is not a “fail”. If your comment is correct then it should be easy.

      • Jimmy

        I wonder if you understood the purpose of my comment at all, LOL. The fact is, as I explained, peer reviewed papers for a fact simply cannot be dismissed by two or three lines of ambiguous text. As I pointed out, if you simply contacted the authors, presented your ridiculous quick-liners, they would have a good laugh and certainly defend their work from such fatuous accusations.

        If I did exactly what you did, and applied it to evolutionary peer review, I would be able to peel of thousands in a matter of hours. With such knowledge, this methodology can be dismissed as nonsensical. Let’s take your first response for example. It amounts to “this is all garbage because this guy says so”. The fact is, ANY anti-evolution peer-review is sure to get, and simply citing attacks is not quite an intelligently designed argument, LOL.

        • Dave Post author

          Jimmy, to be brutally frank, you don’t appear to grasp what the peer-review process is all about. It is essentially a conversation within the scientific community. None of those papers are gaining any traction basically because they are not making a reasonable evidence-based case. It is all driven by an already existing religious inspired conclusion.

          So yes, they can and are dismissed because they are not making credible arguments that withstand any analysis. To pick out the example you cite, you claim that this basis for the rejection of the first one amounts to “this is all garbage because this guy says so”. That is not a factual claim but is instead a distortion. I’m not claiming, here is a guy who says so, I’m pointing you are a link by a subject matter expect who takes it apart point by point and explains exactly why Mr Kuhn is not making a credible argument.

          It is wholly appropriate for Mr Kuhn to publish, but it is also wholly appropriate for Jerry Coyne to examine it in detail and pull it apart. That is a conversation, Mr Kuhn’s paper does not stand in isolation, but instead is part of a conversation. If the conversation is to continue then Mr Kuhn can of course expand upon the rebuttals presented by Mr Coyne, but as best as I can determine, he has opted to not do so, and so that rebuttal stands as the end of that.

          So far the number of peer-reviewed papers presenting a reasonable evidence-based argument that gains traction and moves our overall understanding forward amounts to zero.

          You are of course free to criticise the prevailing body of scientific research, or if you prefer specific individual papers and that is fine.

          • Jimmy

            Nice try, the reason these do not gain traction is not because they do not make adequate claims, rather it is in fact due to the overwhelming bias. When Stephen Meyer published a peer-reviewed paper against Evolution, the editor of the journal was quite literally put on a witch hunt. He was even INTERROGATED on his religious beliefs.

            As for the response by, I believe you said his name was “Jerry Coyne”, I actually ended up reading both the peer-reviewed paper by Joseph and the response by Jerry. I was simply appauled by just how amazingly weak it was. Now, before I address its three points, I shall point out the fact that is did not come close to addressing all the points made by Joseph, rather it ambiguously responded to very little material in the paper on each point. Thus, on this basis alone, I can entirely dismiss it as a refutation of Joseph’s paper, but we can go further in showing just how ridiculous this response is.

            1. All Jerry addressed here was the DNA-Protein problem Joseph brought up, and claimed that the “co-evolutionary scenario” and RNA solution can bring this up. Indeed, that is all he said, extremely ambiguous to say the least, but I probably know why — if he was any more specific on these “solutions” to the DNA-Protein problem he mentioned, his viewers would laugh at this nonsense. The co-evolutionary scenario, which is if I’m not mistaken, the idea that DNA-Protein used to be the same thing but magically evolved apart, is extremely unrealistic, unscientific, and has not shown in the slightest degree to be feasible in any manner, whatsoever. This can HARDLY be posited as a solution. As for RNA, Joseph DOES address this.

            2. For irreducible complexity, Jerry tells us that Joseph gave us no examples of this — and then immediately contradicts himself by trying to address one of the examples Joseph gave involving the eye, LOL. What’s even better than that, is that Joseph EVEN ADDRESSES the supposed solution that is Jerry gave in that very paper, which is also commonly given by evolutionists to the problem, and so the fact that Jerry failed to address what was right before his eyes shows just how inadequate his comprehension of this paper was — either because he is stupid, but I’ll give him the benefit of the doubt on that one, or that he is just so embarrassingly blinded by his bias and cognitive dissonance.

            3. Jerry claims that Joseph says there are outright “no examples of transitional fossils”, which is funny because I saw no such claim. On the supposedly transitional fossil of Tiktaalik, Jerry tries to attack Joseph for citing Casey Luskin. Now, I don’t know who Casey is, but I’m not going to have a bad impression on him because some biased twat doesn’t like him. Jerry claims that there was more than just the transitional wrist in the fossil of Tiktaalit, like a transitional skull, but what’s funny is tht I ended up reading the citation to Casey. Casey points out and shows, by going right to the peer-reviewed discovery and book published by Shubin on this, that there is in fact nothing transitional about this except for the supposed wrist and the hind fins as a “tetrapod”. The skull has no transitional features like Jerry claims. I also gained respect for Casey, as he utterly dismantled any hope, whatsoever for this being a transitional fish fossil of fish getting to land by utterly refuting a supposed wrist. Funnily enough, Casey points out that a lungfish has more of a “wrist” than Tiktaalik, and coincidentally, it has those SAME HIND FINS! LOL. Interestingly enough, the lungfish hasn’t become some mammal on land yet. Casey shows beyond question that if this is a transition of anything, it is towards a lungfish. Not land breathing tetrapods for goodness sake.

            Jerry has failed to postulate a substantiate response to this very, very good paper (that I saved after reading)… In other words… -Fail

            LOOOOOOOOOOOL

            • Dave Post author

              Hi Jimmy,

              Our comments are getting longer and longer …

              // overwhelming bias //

              So basically your position is that there is some sort of conspiracy or something similar?

              It perhaps unpacks to the observation that ID, or to be more specific, some of those that promote it, have more or less blown their credibility by promoting what is essentially a religious belief that pretends to be scientific.

              OK, back on point. The paper in question by Dr Kuhn, is not one that is rejected exclusively by Jerry Coyne, but in reality is rejected by almost every professional evolutionary biologist on the planet who has read it.

              For example …

              https://afarensis99.wordpress.com/2012/01/22/a-response-to-joseph-kuhns-dissecting-darwinism/

              http://sandwalk.blogspot.co.uk/2012/01/physicians-can-be-idiots.html

              http://stonesnbones.blogspot.co.uk/2012/02/joseph-kuhn-md-part-1.html

              http://stonesnbones.blogspot.co.uk/2012/02/joseph-kuhn-md-part-2.html

              Even Baylor University Medical Center, Dr Kuhn’s own medical centre where he published has a rebuttal for it as well …

              http://www.baylorhealth.edu/Documents/BUMC%20Proceedings/2012%20Vol%2025/No.%201/25_1_Roberts_Commentary.pdf

              and here …

              http://www.baylorhealth.edu/Documents/BUMC%20Proceedings/2012%20Vol%2025/No.%202/25_i2_Dimijian_bapr.pdf

              Clearly Dr Kuhn’s entire hypothesis gravitates around the long discredited idea of “Irreducible complexity”, and so he cherry picks a few things, gets rather mixed up along the way, and then tosses it all out as if it was some amazing revelation.

              I have it here, it really is not a good paper.

              I understand that you define it as a // very, very good paper // and I translate that to simply mean that it confirms your existing religious belief. I would define “good” as a paper that makes a meaningful contribution that extends our understanding and persuades. It most certainly does not do that, and instead contains rather a lot that is clearly wrong. It is understandable because Dr Kung is a medical doctor and is publishing in a medical journal on a topic he is not wholly familiar with.

              Now here is an interesting meta-question to ponder, the real heart of the matter.

              You clearly hold a specific view. If we together picked Dr Kuhn’s paper apart and proceeded to go though it line by line and it became clear to you that it really is nonsense, would that change your mind at all?

              I’m convinced that the honest answer to that would be “no”. This is because in my experience people who reject the prevailing scientific consensus, do so for deeply and sincerely felt emotional religious reasons, and not evidence-based scientific ones.

              There really is a reason why 99.9% of the life-science scientists on the planet today (many of whom are religious) do accept the prevailing consensus.

              • Jimmy

                Correct, it seems our comments are going to get quite lengthy. Would you like to move this conversation to e-mail? All up to you.

                As for the idea of a “conspiracy”, not really. These people are just ridiculously biased, that’s all. The evidence wouldn’t matter to them. I believe this is how you would view Kent Hovind. Now, imagine a Kent Hovind situated for Evolution, except there are thousands of them and they control most of the journals. I really do not think the existence of bias can be debated. If these people were not horrifyingly biased, they would not have literally witch hunted an editor for merely letting Meyer’s paper get published.

                Anyways, it seems to me that you did not contest my utter refutation of Coyne. I like that, perhaps you are not one of those evolutionist zombies who will deny any and everything. You accuse me of accepting this paper because it merely confirms my religious beliefs — this is incorrect, I used to be a Theistic Evolutionist. I will go back to this position if my worldview against evolution becomes incoherent, but I have very good reason as of now.

                As for all these links, certainly I will not be able to reply to all of them at once. Let’s address one at a time, starting from the first one. Now, I will only address the arguments made in response to the three points of Joseph’s paper, because as I go across your first link, it seems that the person replying wants to make paragraph-long responses to virtually every sentence Joseph makes, regardless if they are points he is/isn’t defending in the paper. The last thing before getting into my response, is the fact that this first link, now that I’ve finished going through it, actually does not dispute any of the three points Joseph argues and presents evidence for. What a pity.

                Now, the first and second paragraphs go hand in hand, as the author here quotes ‘transitional’ fossils like Homo Habilis, Homo Erectus, and the Neanderthals. Now, this is quite strange, as the author here (which you call a “professional” evolutionary biologist) does not seem to know that neanderthals are not a transition to humans. Indeed, I’m not aware of any serious biologists who think so, all evolutionary biologists agree we did not come from neanderthals, rather neanderthals were just some evolutionary dead-end. So this one obviously doesn’t show that humans evolved. As for homo habilis, first, I would strongly contest it is part of the “homo” genus, australopithecus is much, much better. It seems that the homo genus has become a dump for every time we find a new monkey in the dirt. Bernard Wood and Mark Collard greatly argue for this in the journal Science.
                http://science.sciencemag.org/content/284/5411/65.long

                The discovery of habilis, as documented by the people who discovered habilis, was extremely messy. Tons of fossils of poor condition were found, these could easily be of multiple hominid species, incorrectly assigned to habilis. What I have to say habilis is that our information lacks serious adequacy to rigorously test it in the scientific field, and thus we cannot determine with certainty that it is an ancestor of us. I don’t have much to say for erectus, as I don’t have one of those sparkling outright refutations for it. For Paranthropus (robustus), if I’m not mistaken, this also is not considered to be in the line to man (like neanderthals), and thus we didn’t come from them either. This is my critique of these examples, but amazingly enough, the guy starts giving more in his next paragraph, like australopithecus sediba. Now, here is a quote I found critiquing this one;

                A. sediba, critics are quick to point out, is everything that H. habilis is not: It’s a small-brained australopith living in southern Africa 2 million years ago — a good 300,000 years after the larger-brained H. habilis first appeared in East Africa. They say A. sediba is the wrong hominin in the wrong place at the wrong time to be our direct ancestor. “It’s just too young to lead to Homo,” says [paleoanthropologist Fred] Spoor.
                (Colin Barras, “The unexpected ape,” New Scientist, Issue 2925: 34-37 (July 13-19, 2013))

                If these ones at 2,000,000 years ago are too young to show any good evidence for this, then robustus, at 3,000,000 years ago is worse. I think I’m talking about these hominids a little too much.

                Continuing, he accuses Joseph of “creationist nonsense” for referencing stone tools that existed millions of years ago, because these are “outright fake”, but to defend Joseph, a quick search found me this;
                http://www.livescience.com/50908-oldest-stone-tools-predate-humans.html

                And to top it off, yet ANOTHER attack on Casey Luskin. These people seriously don’t like Casey. The author did not dispute Casey’s case against Tiktaalik, only laughed at Casey for not looking at the peer-review on this, even though that’s exactly what Casey addressed. Am I the only person in the world who has read Casey’s article on this?

                I’m not quite impressed by these responses. Allow me to add an opinion of mine to this — could it be that these people are trying to challenge Joseph’s paper — not because of its veracity — but perhaps because it contradicts their narrative? Just a thought. Feel free to comment on some of my responses to the author of this first link.

                • Glen

                  Because of a previous comment on this post I’ve been getting email notifications, I haven’t had time to throughly read each comment but I’m assuming it’s on a similar topic as the blog post itself and thought I would contribute an article which I came across last week, it’s on BioMed which is a “quality peer reviewed” biology journal. It’s a lengthy read but it’s basically saying that there isn’t enough time in the Universe for Evolution to do what it claims.

                  The BioMed paper: https://goo.gl/xKUHw8
                  There is a much easier to read summary of the paper here: http://goo.gl/G0mQ9G

                  This peer reviewed paper isn’t “intelligent design” but it does deal with a popular topic within the ID movement – the information in DNA. It’s conclusion is that the claims of Neo-Darwinism evolution aren’t possible given the age of the Universe. Any opposing view, peer reviewed article or whatever it may be needs to be judged on the merits of it’s science not what publication published it or otherwise.

                • Dave Post author

                  Couple of problems there Glen …

                  Key Point – If somebody is going to publish a paper that goes against the prevailing consensus then it needs to be good, really good, but its not, it really is not. It basically takes a very simplistic and unreal model, then plucks out sweeping claims. It has been published since 2015 and has been cited by … well nobody, except for one ID journal.

                  Secondary Point – It did get noticed by somebody and was found to not really be persuasive at all… http://biology.stackexchange.com/questions/40845/do-the-claims-in-this-paper-have-any-degree-of-validity

                  Prediction: This bit of pseudoscience will continue to pop up on various ID sites as some sort of “proof” for years to come.

                  “Not enough time” is an old claim of course, and has been promoted from many a pulpit over the years. This latest paper simply attempts to give it a sciency look and feel. You can of course google the topic “not enough time” or similar and find much ID stuff and also many biologists rolling their eyes at it all with words. If truly curious then a 2010 PNAS paper on the topic can be found here. They also have a go at a mathematical model and find plenty of time – http://www.pnas.org/content/107/52/22454.full

                  (Side note: I’ll reply to Jimmy’s latest looooong comment later)

                • Dave Post author

                  Hi Jimmy,

                  We are seriously at risk of getting very bogged down in details here, so it may be appropriate to step back a bit. I have a few questions that might (or might not) help, but first I do wish to clarify my position.

                  Do I accept your rebuttal of the criticism by Jerry Coyne as valid? No, I honestly don’t, instead I simply widened the scope to point out that in the context of that one paper by Mr Kuhn, the issue is not criticism by one lone voice, but rather is wholesale rejection by the entire community, and that includes the journal that published the paper itself. To be clear, The publication, Proceedings of Baylor, are from Mr Kuhn’s employer, and so even his own employer rejects his stance.

                  To be a tad more specific regarding the comments you raised on Mr Coyne’s criticism … // utter refutation of Coyne // … “utter”, er no. And as an observation regarding a turn of phrase … //evolutionist zombies// … what was it you were saying about bias?

                  Regarding the three key points raised by Mr Coyne that basically address the three sections within Mr Kuhn’s paper …

                  1. Origin of Life … we really do not know. Nobody does. But, if I may paraphrase, all Kuhn is actually doing is playing the “gosh this is all really complex, I have no idea how this could have happened naturally, therefore ID” card, and that is not exactly a compelling argument for most biologists familiar with the topic at hand.

                  2. irreducible complexity is an interesting idea, but it has very much had its day, and no, the eye really is not a viable example.

                  3. transitional fossils … // Jerry claims that Joseph says there are outright “no examples of transitional fossils”, which is funny because I saw no such claim. // Having read it I did, because that is essentially what Mr Kuhn is attempting to assert within the section entitled “TRANSITIONAL SPECIES DATA”. It is basically a claim that there are none.

                  ——

                  We can of course continue to review such details, with various points and counter points, but I would like to suggest that this really will not persuade. It may be appropriate to step back a bit, so putting such details all to one side for the moment. I’d like, if I may, to ask you a couple of hopefully easy questions:

                  – You mentioned that your position was previously “Theistic Evolutionist”, so what category would you place yourself in currently?
                  – As an extension to your answer for the previous question, how did you arrive at that conclusion, what actually convinced you that it was the best possible answer over and above everything else?

          • Jimmy

            Before I address the points you make, I would like to answer the two questions you ask me first.

            As of right now, I am obviously still a Theist (Christian, as you may have guessed), but I do not hold to Evolution, rather Intelligent Design. I do affirm that the Earth is several billions of years old, and I strictly deny the idea that the Bible teaches a 6,000 year old Earth.

            As for the second question, I was initially convinced by realizing all supposed evidence for Evolution was either not viable, or is explained even better in our world by the Design Model. I can give you one example — and that is in respect to the evidence for Evolution from “vestigial traits”. People have said that some traits have lost their original function from Evolution, and because we have traits in our body that are useless, this shows this could only happen from Evolution. Unfortunately, virtually all examples they give of ‘vestigial traits’ have actual purposes in our body, including the coccyx (“tail” bone), palmarus longus (that tendon 14% of people don’t have in one of their arms), appendix, tonsils, pelvis in whales, etc, etc, etc. As medical science progresses, we will continually learning more about these traits and the myth of vestigial traits in our bodies will meet its slow demise.

            You do not accept my refutation of Coyne? That is quite strange, considering there is simply no question to me that Coyne’s “debunking” is entirely invalid, especially considering he completely ignored the bulk of arguments made by Joseph, he defended the eye from being irreducibly complex with an argument that Joseph addressed in that very paper, his claims on Tiktaalik was completely incorrect (of course Coyne wouldn’t have figured this out because he simply is not open enough to even consider Casey’s points), etc, etc, etc. You do however, respond to three of my points, and this is my response to all three points;

            1. It is true that we do not know how it “naturally” happened, I guess, but you are completely, completely incorrect on Joseph’s claims. He is not saying that it is complex, therefore it was created, rather Joseph puts forth evidence to show that it is far too complex to be accounted for by random mutations/natural selection, as such things simply could not produce what we find in our bodies.

            As for life appearing “naturally”, I would completely reject this possibility, based on Cell Theory, which we know to be as much of a fact as Germ Theory or the Theory of Relativity. Cell Theory makes three points;

            1) All living organisms are composed of cells. They may be unicellular or multicellular.
            2) The cell is the basic unit of life.
            3) Cells arise from pre-existing cells.

            http://biology.about.com/od/biologydictionary/g/celltheory.htm

            If cells can only arise from pre-existing cells, then abiotic materials simply could produce cells, and thus the cell had to be automatically created right from the start. It is as simple as that, it must have been designed. The Law of Biogenesis says similar things.

            2. The eye is not a viable example? I have seen many responses to it, including from Coyne and Dawkins, and I would entirely agree if I had not gone through this article of yours, but I did go through it. This led me to read Joseph’s paper, and as far as I am concerned, he has provided a legitimate response. I have no reason to doubt it, and thus I simply will not doubt it unless I am given good reason to. That’s science, baby.

            3. It would seem to me, rather than claiming that the record is quite literally bankrupt of what can possibly be called a ‘transitional fossil’, he is merely challenging the idea that the known “transitional” fossils are actually transitional in the first place, such as Tiktaalik.

            • Glen

              I’d like to add comment on the transitional fossil issue with Neo-Darwinism. We are probably all familiar with Darwin’s tree of life theory, where all living things we see today can be traced back to a common ancestor. Darwin was expecting for us to find in the fossil record gradual and continuous change. But instead what we see is the sudden appearance of new life forms, known as the Cambrian Explosion. So we have Darwin’s theory and then the facts (fossil record) which don’t support his theory. Darwin was even humble enough to admit that the fossil record didn’t support his theory but hoped that it would eventually with further exploration. There’s quite a good lecture Stephen Meyer did on this topic here:

              https://www.youtube.com/watch?v=PbcY9iya40o

              Dave, you’ve talked about the flu virus and how it mutates. The central mechanism of modern Darwinian evolution does a great job of explaining something such as the flu virus mutating and adapting to Antibiotics by the way of natural selection, random variation. Or microevolution within a species as it adapts to it’s environment. However it lacks the power to describe events like the Cambrian Explosion where we see the sudden appearance of new forms of life instead of the gradual and continuous change forming a “tree of life” which dates back hundreds of millions of years.

              Far too often the term “Natural Selection” is used, it’s like some kind of magic that happens which can create new things from very little, it’s not very scientific and certainly not proven. Which takes me all the way back to my very first comment on this post. Evolution theory has some interesting ideas, proven ones even with the Antibiotics example being a good one. But when it comes to dealing with the origin of the vast amount of species we have today Evolution’s account is not scientific fact, it’s pseudoscience.

              • Dave Post author

                Hi Glen, No the Cambrian explosion does not conflict with our modern understanding of evolutionary biology and no it was not a “sudden” appearance. The claim that evolution is a pseudoscience is not a factual claim, however it can be argued quite successfully that the claim that it is, is itself pseudoscience.

                Since you kindly cited Meyer’s clip, let me in turn cite an article that is a rebuttal of Mr Meyer’s stance.

                http://science.sciencemag.org/content/sci/341/6152/1344.1.full.pdf

                • Dave Post author

                  The fundamental problem is that nobody, apart from other Creationists, are finding any of the arguments presented to be credible arguments.

                  It is basically a perfect record. Not one single argument has gained any traction and exactly nothing has been added to the on-going scientific endeavour. One common pattern often observed when criticism is deployed is to ignore the main argument and focus on detail. This is what Mr Meyer does within his rebuttal to Mr Marshall’s criticism.

                • Glen

                  You can turn that argument around though; no one other than materialists find Neo-Darwinism findings credible. Neither theory has all the answers and scientists need to continue their work. I think that if Neo-Darwinism was conclusive and had all the answers then there would be no debate, likewise with ID. There are too many gaps in evolution, such as the origin of life, the origin of information and the fossil record as I’ve pointed out previously. There’s also plenty of traction and interest in other theories, the latest by Tom Wolfe: http://www.nytimes.com/2016/08/31/books/tom-wolfes-kingdom-of-speech-takes-aim-at-darwin-and-chomsky.html

                • Dave Post author

                  Hi Glen,

                  // You can turn that argument around though; no one other than materialists find Neo-Darwinism findings credible. //

                  The term “no one other” within the sentence above includes 99.99% of the subject matter experts, the life-science scientists, and perhaps almost every university and college on the planet. The word that perhaps best describes the things beyond the material is fantasy.

                  // Neither theory has all the answers and scientists need to continue their work. //

                  ID is not actually a scientific theory, but is more accurately termed a religious hypothesis.

                  // I think that if Neo-Darwinism was conclusive and had all the answers then there would be no debate, likewise with ID. //

                  There is no actual debate.

                  // There are too many gaps in evolution, such as the origin of life, the origin of information and the fossil record as I’ve pointed out previously. //

                  The default when something is not known is “I don’t know” and not “magic”. Natural selection is all about the diversity of life, not the origin.

                  // There’s also plenty of traction and interest in other theories, the latest by Tom Wolfe: http://www.nytimes.com/2016/08/31/books/tom-wolfes-kingdom-of-speech-takes-aim-at-darwin-and-chomsky.html //

                  Tom Wolfe is not a life-science scientist. Somebody who is, read his book and is truly unimpressed – https://www.washingtonpost.com/opinions/his-white-suit-unsullied-by-research-tom-wolfe-tries-to-take-down-charles-darwin/2016/08/31/8ee6d4ee-4936-11e6-90a8-fb84201e0645_story.html?utm_term=.bc17afc8d867

                  Within the life-science community, there is no traction for ID. Amongst the general public, perhaps, but remember the fact that there is also a lot of public interest in alien abductions and astrology lends no credibility to either position. That is perhaps because we don’t actually get to vote on what is and is not real.

            • Dave Post author

              Hi Jimmy,

              // there is simply no question to me that Coyne’s “debunking” is entirely invalid //

              And from my viewpoint, in all honestly, I find it to be wholly valid.

              So back to the point I made, that basically the essence of the claim being made in Point 1 is this …

              “gosh this is all really complex, I have no idea how this could have happened naturally, therefore ID”

              To which you replied …

              // He is not saying that it is complex, therefore it was created, //

              But then expanded and explained …

              //rather Joseph puts forth evidence to show that it is far too complex to be accounted for by random mutations/natural selection, as such things simply could not produce what we find in our bodies. //

              And then rather oddly, you proceed to make exactly the same claim yourself …

              // As for life appearing “naturally”, I would completely reject this possibility, based on Cell Theory, which we know to be as much of a fact as Germ Theory or the Theory of Relativity. Cell Theory makes three points; //

              Do you not see the problem with a claim that is in essence, exactly as I described it …
              “this is really complex”
              “I have no idea how it could have happened naturally hence I reject that as a possibility”
              “Therefore a god must have done it”

              Can you try to grasp why this plea to not knowing something is not an argument that tends to convince skeptics such as myself.

              I suspect we will not agree on this, and if that is to be the case, then so be it.

              I would like to thank you for answering my questions, I do appreciate that, and I would like to add the observation that it is good to see that there are some things that we do agree upon. For example we do both agree regarding the age of the earth as advocated by geological science is fundamentally correct.

              • Jimmy

                Something that is troubling me is that you continue to latch on to Coyne’s claims, however I have pointed out numerous problems that you are not seeming to try to recognize. Before I respond to your accusations that makes it seem as if I contradicted myself, I will number out the problems I shown in Coyne’s response.

                1. Probably the biggest point is, yet again, Coyne simply did not address the bulk of Joseph’s argument in all three of the point in Joseph’s paper. Thus, to say it debunked the entire thing when in reality it only addresses a minority of the points is, on its face, nonsensical.

                2. Coyne issued an “explanation” for the irreducible complexity of the eye, that Jodeph in the very paper that Coyne was responding to, had already shown problems with this explanation

                3. Coyne gets the discovery on Tiktaalik entirely wrong, and he would have realized this if he merely read Casey’s points

                4. To try to solve the DNA-Protein problem, Coyne (extremely) ambiguously mentions the “co-evolutionary scenario”, which is the idea that DNA and Protein were once the same thing, and they magically separated. This hypothesis is unscientific, unrealistic, and has absolutely zero scientific validation. He also accused Kuhn of not engaging with the RNA explanation, even though he did (dare I say this qualifies as a misrepresentation of Joseph)

                Considering these incredible problems and errors that are simply all over Coyne’s response, I would simply like to ask you which part of his argument you were actually convinced by, taking into account seeing my points on it. This is an enigma to me as of now.

                Now, on to my supposed contradiction. First, I explain Joseph is simply not saying “this is complex therefore design”, I correctly pointed out he said that it is too complex to be explained by mutations and natural delection. However, your problem seems to be when I added in my view on it. You clearly just recognize that my points against life from non-life are not actually in Joseph’s paper, simply because I said it in my last comment, does not mean it is part of Joseph’s paper.

                Furthermore, this is an errorful analogy, as I did not invoke creation because of “oh my just wow this is so complex”, my argument was based on the implication of Cell Theory and the Law of Biogenesis.

                2 more quick things to add:

                1. Are you a biologist?
                2. I actually found Joseph’s response to these critics… But what was most funny is that… It was on CASEY LUSKIN’S WEBSITE, LOL. This entire thing is certainly hilarious as I go through the discourse on Joseph. Anyways, I went through the entire thing, and I found it highly impressive, and so I’ll ask you to check it out for yourself.

                http://www.evolutionnews.org/2012/05/darwin-doubting059241.html

                • Dave Post author

                  So here you go then Jimmy, a reply. Some of us do have a life and tend not to spend our entire life on the Internet.

                  // you continue to latch on to Coyne’s claims //

                  You keep dismissing them as if it was a done deal, I quite sincerely do not find that to be the case.

                  // I have pointed out numerous problems that you are not seeming to try to recognize. //

                  Because they are not actually problems at all.

                  // I will number out the problems I shown in Coyne’s response. //

                  OK, let’s take it step by step

                  // 1. Probably the biggest point is, yet again, Coyne simply did not address the bulk of Joseph’s argument in all three of the point in Joseph’s paper. Thus, to say it debunked the entire thing when in reality it only addresses a minority of the points is, on its face, nonsensical. //

                  Mr Kuhn lays out 3 arguments within his paper and Mr Coyne highlights all three. It is true that he does not dissect each and every line of detail, but you are missing the big picture here, the three primary arguments are not actually credible arguments at all. Nothing Mr Kuhn writes changes that in any meaningful way.

                  Section 1 (CHEMICAL ORIGIN OF LIFE) … the “Gosh it is all really complex” section that is a plea to ignorance. As I already pointed out, nobody really knows.
                  Section 2 (IRREDUCIBLE COMPLEXITY OF CELLULAR SYSTEMS) … not science but pseudoscience, and well documented as such … https://en.wikipedia.org/wiki/Irreducible_complexity
                  Section 3 (TRANSITIONAL SPECIES DATA) … there are lots of examples … https://en.wikipedia.org/wiki/List_of_transitional_fossils

                  Mr Coyne simply highlights that these three non-viable arguments are all that the paper contains, there is no need to go any further because these are not (in the eyes of the wider community) credible. If for example a paper on astrology popped up that seriously advocated that the movement of the planets influenced human lives, then simply highlighting that this is all it actually says is sufficient, there would be no need to dig into a claimed correlation between the interactions of Venus and Mars with real human lives.

                  I get that you are all excited by Mr Kuhn’s paper and truly think it is super stuff, but it really is just those three tired old arguments that have not convinced anybody.

                  // 2. Coyne issued an “explanation” for the irreducible complexity of the eye, that Jodeph in the very paper that Coyne was responding to, had already shown problems with this explanation //

                  The evolution of the eye is a topic that has been extensively studied and is well documented by many. As for Mr Coyne not addressing Mr Kuhn’s “irreducible complexity” argument about the need for a pre-existing complex system for even the most primitive form of an eye to function, you did get that he is mocking him for attempting to support an absurd bit of pseudoscientific nonsense.

                  My Kuhn also claims “many other mathematical and logistical weaknesses to the Nilsson example of eye evolution have been uncovered”, and cites Berlinski as a rebuttal to Nilsson … but Nilsson has in turn robustly rebutted Mr Berlinski’s criticism. http://www.talkreason.org/articles/blurred.cfm#lund

                  // 3. Coyne gets the discovery on Tiktaalik entirely wrong, and he would have realized this if he merely read Casey’s points //

                  Actually no, it is both Mr Kuhn and Mr Luskin who do that. The claim that everything is based upon the discovery of just one wrist bone is not factual.

                  Since Mr Kuhn cites Mr Luskin as an authority, it is worth asking who he is and if he actually is a credible source?

                  No, he is not, people appears to spend rather a lot of time laughing at Mr Luskin …

                  http://pandasthumb.org/archives/2010/01/casey-luskin-em.html

                  http://stifledmind.blogspot.co.uk/2008/07/luskins-wrist-rant-leave-it-to-experts.html

                  .. and in fact Mr Luskin is very embarrassingly wrong …

                  http://blogs.discovermagazine.com/loom/2008/07/14/746/#.V7muImWdvOw

                  So no, he is really not a reliable source for anything (except perhaps law because that is his area, he is a Lawyer, not a biologist).

                  // 4. To try to solve the DNA-Protein problem, Coyne (extremely) ambiguously mentions the “co-evolutionary scenario”, which is the idea that DNA and Protein were once the same thing, and they magically separated. This hypothesis is unscientific, unrealistic, and has absolutely zero scientific validation. //

                  He does not “try to solve it”, he simply pointed out that it was not mentioned at all.

                  As an aside, you might indeed claim it is “unscientific, unrealistic, and has absolutely zero scientific validation”, but that does not make it so.

                  http://www.ncbi.nlm.nih.gov/books/NBK6360/

                  However, as I previously pointed out, right now nobody actually knows how life originated … yet.

                  // He also accused Kuhn of not engaging with the RNA explanation, even though he did (dare I say this qualifies as a misrepresentation of Joseph) //

                  His precise phrase was “The co-evolutionary scenario, and involvement of RNA in this, isn’t mentioned” … so is it, and if so, then exactly where is that? Dare I say that you are actually misrepresenting Mr Coyne.

                  // I did not invoke creation because of “oh my just wow this is so complex”, my argument was based on the implication of Cell Theory and the Law of Biogenesis. //

                  Now you are simply playing with words … what you claim as “the implication of Cell Theory and the Law of Biogenesis” really does translate to “Gosh, this is all very complex, so I simply cannot see any possible solution except for creation as an explanation” … right?

                  So, apart from those who already embrace one of the vast diversity of different Creationist beliefs that are essentially rooted within some variation of religious belief, who exactly is being persuaded by Mr Kung’s paper?

                  The point is not that I don’t, nor is it that Mr Coyne does not … the key observation is that apart from those that already believe (it has just one citation from a creationist), nobody does, not even the medical journal that it was published within (as previously highlighted, they had a rebuttal)

                  Given the observation that nobody is being persuaded by this paper, why do you think that is the case?

                  In anticipation that you will claim that some bias is at play, I will perhaps point out that you are in essence arguing for what is a fringe position that is inspired by a religious belief (and that is the real bias in play here). If the ID stance being adopted was indeed correct, then the implication is that the vast majority of life-science scientists, many of whom are themselves religious, are being both foolish, deluded, and unthinking … is that really your position?

                  You appear to have an almost evangelistic need to convince others that your position is correct and went as far as chasing me twice for a reply to your comment. My thoughts and your thoughts on the topic are in reality irrelevant. This is because the scientific methodology will prevail. What is true will remain true even if we both dismissed fact as myth, and embraced myth as fact.

                  You sincerely believe specific things that conflict with the evidence-based prevailing consensus … I get that, and that is fine.

                  You sincerely believe you have evidence on your side and that the prevailing consensus does not … I get that, and that is also fine if that is what you wish.

                  However, wishing it to be so and sincerely believing it to be so, will not make it so. Remember, it is not me that you need to convince, it is the entire life-science community consisting of millions of highly educated scientists. Good luck with that.

                • Jimmy

                  —I apologize in advance for the long response — you just made a LOOOT of points

                  //Some of us do have a life and tend not to spend our entire life on the Internet.//

                  I didn’t mean to say you have no life dude.

                  Let’s get right into your response now. Now, my statement was not just that Coyne didn’t address every detail, my point was that on all three of Joseph’s points, he addressed the minor detail rather than the main argument. Coyne did not address even nearly half of Joseph’s points.

                  Again, for the first point, as I explained, it is very clearly not “gosh this is really complex”, what Joseph is actually arguing for that the biodiversity and origins of life simply cannot be accounted for by mutations and natural selection. For the second point, you call Irreducible Complexity as ‘pseudoscience’, and to demonstrate this, you cite a source that is renowned across the world for its credibility, Wikipedia. I’ve already been through this link before, and it invalid. Let us analyze its response to both the complexity of the eye and the bacterial flagellum.

                  For the eye, it does exactly what Coyne tried. Provide an explanation for the evolution of the eye that Joseph rebutted in his very paper. Joseph already addresses this. As for the bacterial flagellum, it merely propagates Kenneth Miller’s pseudoscience of the TS3 (Type 3 Secretory System) being a precursor to the Bacterial Flagellum. The fact is, the TS3 is both completely dissimilar to the bacterial flagellum, not only in function, but the basal (base) of the Bacterial Flagellum also is different from the TS3, regardless of the nonsense Kenneth tells us. A 2011 paper, by Schraidt and Marlovits, in Science Magazine, found that the OM ring of a TS3 is comprised of a C-terminal region of secretins, with a 15-fold symmetry. The bacterial flagellum, on the other hand, has OM rings that are comprised of completely different proteins, lipoprotein FlgH, as well as containing an L (lipopolysaccharide) ring in the OM. The L ring is associated with a periplasmic P ring, which is composed of 26 copies of Flgl. Together, the L and P rings form a stiff structure that serves as a bushing for the rotating rod of the flagellar. The TS3 has nothing similar to the above, nor does it have a proton-drive motor which is capable of spinning the filament (90% of the flagellum’s mass) at over 40,000rpm. 

                  Here’s the paper I was talking about:
                  http://www.ncbi.nlm.nih.gov/pubmed/21385715

                  There are also other facts that entirely dismiss such a notion is even possible. One is that the bacterial flagellum actually predates the TS3, and so being a precursor is out of the picture. In a lecture, Scott Minnich completely disavows any possibility for this to be a serious precursor, as well as establishes the Irreducible Complexity for the bacterial flagellum in a number of ways, such as proving if you mutate any gene of the FihD protein of the bacterial flagellum, it loses complete motility. Here is the lecture, I highly recommend it.

                  https://www.youtube.com/watch?v=MvZniAnYJrQ

                  Now, you say Nilsson offers a response to Berlinski — but Berlinski has a response to this response and many other attempted responses to his claims.
                  http://www.discovery.org/a/1509

                  You say that Tiktaalik is not only the wrist — however, it seems we have a misunderstanding here. The only feature is the wrist, the rest of the claims are of homology, which is scattered across our biological world and used by the evolutionists, even Darwin himself, as evidence for common ancestry. However, as Jonathan Wells points out, people before Darwin had recognized this ‘homology’, however they did not attribute it to a common ancestor, rather a common designer. So, which one is it? Well, the truth is, it could be either one, but any claims of homology cannot be used for one side against the other, as they work perfectly well with both.

                  Now, you give three links to show Casey Luskin is “embarrassingly” wrong about Tiktaalik. I disagree. The entire first link simply adds up to “no Casey, we don’t say Tiktaalik is our direct ancestor, rather just cousin to our ancestors”. Err, whether that’s true or not, it doesn’t respond to a THING Casey made in his actual arguments. The other two links basically say “no Casey, the Tiktaalik wrist is similar to ours (homology) as it is a transition between fish to us”, and again, not addressing his argument that it isn’t transitional in the first place. Casey shows that modern day zebrafish have wrists more similar to us than Tiktaalik does. I think this point that Casey made is really where Tiktaalik just falls apart here. You also say he is just a lawyer and not a biologist, but he actually has an M.S. in Earth Sciences from the University of California.
                  http://www.discovery.org/p/188

                  You also disagree with me that the co-evolutionary scenario, as Coyne puts it, is not simply entirely scientifically invalid, and cite a paper to show this, but your paper does not argue for this scenario (just read the summary bro), it simply shows, and I quote, data has “revealed that several of these enzymatic activities have been invented independently more than once, indicating that the transition from RNA to DNA genomes was more complex than previously thought”. In other words, it shows that the origins of life is more complex than previously assumed. The summary goes on to call the entire thing “puzzling”. It reviews many hypotheses but I do not think it mentions the co-evolutionary scenario, nor validates it. It mostly tries to show that viruses could have been very important in the grand idea of these origins. Again, the co-evolutionary scenario, if anything we’ve discussed yet, is pure pseudoscience. It’s also suicide for anyone who wants to claim that life can come from non-life, as now you must also explain how some mechanism that played the role of both DNA protein immediately came from non-life before splitting off, which is ten thousand times more problematic than how it’s already looking for those guys.

                  You say the following:

                  “Now you are simply playing with words … what you claim as “the implication of Cell Theory and the Law of Biogenesis” really does translate to “Gosh, this is all very complex, so I simply cannot see any possible solution except for creation as an explanation” … right?”

                  Not right. This has nothing to do with complexity. Unless I’m missing some super secret rule of Cell Theory or the Law of Biogenesis, they outright rule out the production of cells from not only anything abiotic, but also anything other than cells in the first place on a naturalistic basis. You also say that my position states life-scientists are foolish, deluded, and unthinking. No, they’ve just been tricked by the evolutionists to pursue a false hope of life from non-life. Many intelligent people who are not foolish, deluded, and unthinking, chase false hopes. Newton spent decades trying to invent alchemy. He was definitely not foolish, unthinking, or deluded. Someone just tricked him into following a false hope.

                • Dave Post author

                  Hi Jimmy,

                  Tempting as it might be to continue with a point-by-point discussion, I think I’d like to try and unstack things a bit.

                  Basically, our discussion has revolved around Mr Kuhn’s paper. From your viewpoint his position stands un-challenged, and mine is that Mr Coyne’s commentary is a sufficient rebuttal.

                  His paper contains 3 arguments, which for ease of reference are …
                  – CHEMICAL ORIGIN OF LIFE
                  – IRREDUCIBLE COMPLEXITY OF CELLULAR SYSTEMS
                  – TRANSITIONAL SPECIES DATA

                  Mr Coyne addresses all 3, not via a rebuttal of each in detail, but by explaining that these are basically the arguments presented.

                  They are not new arguments and Mr Kuhn does not add any actual research, but instead simply expands upon each using arguments that have been made by others. The key point is that none of these arguments carry any credibility within the life-science community in general. You will know that to be the case, and while you might take the stance that they are wrong, that is very much the reality of it.

                  Let’s take each in turn …

                  Origin of Life

                  As previously outlined, the origin of life is currently an unknown, so to argue against it is to argue against the various unverified hypothesises that are being examined by some.

                  Irreducible complexity

                  During the Kitzmiller et al v. Dover trial in 2005 Mr Behe had a golden opportunity to present the case for this and lay out all the evidence. He did try, but had all his evidence demolished. He did also try the “bacterial flagellum” argument, and found that it did not withstand a rebuttal. It would appear that it is not simply an opinion that Irreducible Complexity is a pseudoscience, the trial established it to be a legal fact. Barbara Forrest’s paper makes a good case for that description. You can verify that in Section V here … http://www.centerforinquiry.net/uploads/attachments/intelligent-design.pdf

                  Transitional Fossils

                  Tiktaalik is just one of many many examples, there really is no shortage here. If it turned out that everything we know about Tiktaalik was wrong (that is not a position I hold, but let’s pretend that is the case for a moment), would that in any way undermine evolutionary biology? Not really, it is not a decisive make-or-break item. Anyway, since that is what we have been discussing, I note that what Mr Kuhn writes is this …

                  “The 2004 transitional species between water- and land-based creatures (Tiktaalik roseae) was based on a recovered bone fragment representing the wrist structure that would be necessary for moving on land (36) (Figure ​(Figure22). Even though this species has been disparaged by scientific circles, …”

                  [I’m not convinced this is correct, but we need not quibble about this]

                  “… it is important to realize that any transition from a water-based organism to an air-breathing land-based organism would also require thousands of simultaneous mutations in the basic physiology of the eyes, nose, alimentary system, lungs, muscles, and bones.”

                  In other words, his real arguments here is that an evolutionary transition from water to air is way too complex to have evolved.

                  That perhaps is in many respects a repeat of much of what he writes, and is also the theme you presented for cell biology. The meta-argument decomposes down to “Its way too complex to have evolved, therefore creation”. You do not agree that this is your argument, but it really is just that.

                  Given the consistent re-appareance of the above meta-argument it may be appropriate to illustrate that often an apparent biological impossibility is not actually impossible at all. Protein Folding is a great example of this …
                  – As I’m sure you are aware, Proteins have two states, folded in which it performs a biological function, and unfolded where it might not do specific biological things, but can do other useful things
                  – There is only one folded state, but rather a lot of unfolded states … if we take a 66 amino acid protein where each bond can have say 36 combinations, then with a 66 amino acid protein that yields a huge number, at least 20 to the power of 100 possible combinations
                  – If it explored say 1 trillion combinations per second, it should take well over the lifetime of the entire universe to hit the right combination

                  The reality we live in is one where typical proteins of the above size will find their folded state in 1/1000th of a second. Every cell in your body is doing exactly this (no miracle required).

                  The point is this, often an apparently biological impossibility is in reality what is actually happening.

                  Finally, is is perhaps appropriate to briefly discuss the observation you made …

                  // No, they’ve just been tricked by the evolutionists to pursue a false hope //

                  In one respect we do actually agree upon something rather important. Human bias can and does potentially skew a truly objective understanding. The classical example that illustrates this is of course the importance of the prevailing norm for the deployment of double-blinding during clinical trails. Without that in place human bias will potentially corrupt the results.

                  Now with that thought in mind, clearly we both would maintain the position that there is a bias in play.
                  – Your would perhaps maintain (I speculate) that a lack of belief is the root cause of the bias
                  – I do maintain that the existence of a specific religious belief, one that often involves a considerable degree of temporal and emotional investment, will quite naturally lead to a rather obvious bias towards creationism

                  One interesting question to ponder over is how do we truly eliminate such a bias, how do we know that we have not been gripped by (for example) confirmation bias or one of the many other common cognitive biases.

                  If indeed we consider the hypothesis that evolutionary biology is fundamentally flawed and wrong, then we can make predictions and test this. There should be things way beyond any and all subjective arguments that appeal to specific things being possibly implausible, and instead observe very concise measurable objective things such as the rather obvious, for example …

                  – The now famous observation that the discovery of “fossil rabbits in the Precambrian” or similar would falsify it. In other words, if evolutionary biology is indeed wrong, then we can safely predict that we should find fossils in the wrong strata … but we don’t.
                  – We can also predict that should not find genetic variation in one species … ah but we do.
                  – The previously discussed flagellum argument of irreducible complexity should hold tight … except a stepwise adaptive process is plausible
                  – How about a total discordance between phylogenies based on morphology and DNA. For example, suppose we sequenced a whale genome and found it was related to fish and not mammals. That would seriously fracture a rather foundational aspect, but that also does not happen.

                  These are all big ticket items that would or should show up if our current understanding of evolutionary biology was seriously flawed. The bottom line here is that they don’t.

                  To be honest, I’m not convinced our dialog can really progress any further. Each of us perhaps does have a clear understanding of the stance being taken by the other, and also why that is the case, so what more is there to add?

                • Jimmy

                  Unstack things? Very well, can’t hurt.

                  You first tell me that what Joseph presents is not new research, however I have found a number of things in Joseph’s paper that is definitely something I have not seen anywhere else, such as involving the irreducible complexity of the eye, I have never seen the response presented to the evolutionists case of the major parts being able to evolve in intermediate steps, but this cannot work because of all the changes that must also occur on a smaller scale which are out of question in order for the bigger structure to work. Without its foundations, a building cannot stand.

                  Origin of life, as I am not using it as of now to defend the Intelligent Design Hypothesis (although I did show you what my case for it was involving Cell Theory, however you stopped responding to that it may seem), I and Joseph will definitely use it to debunk evolution, by pointing out there exists no possible evolutionary mechanism to bring about such changes, and the idea of it randomly coming together in a soup is impossible by the statistical odds as Doug Axe’s calculations show, which are not questioned by the evolutionists, like Richard Dawkins.

                  Although I definitely do not like what happened in the Dove VS Kitzmiller trial, those arguments made against Behe have now been addressed. In my previous comment, you’ll see that the idea that the TS3 (Type 3 Secretory System) existing as a precursor to the bacterial flagellum has been entirely debunked, as further peer-reviewed research (not submitted by ID) has, as well as Scott Minnich’s work, crushed such a scenario.

                  Finally, transitional fossils. I do know that you evolutionists claim that there are indeed many examples, and I can in fact cite the research of evolutionists own work on this subject to demolish entire rows of them at once, but we are just discussing Tiktaalik here. Now, for one, Casey has shown that even modern day zebrafish have more ‘transitional’ features than Tiktaalik does, and it’s not becoming anything. Now, there’s two more things here, and when you hear them, I definitely believe you could not possibly continue denying the in-authenticity of Tiktaalik — indeed it shall become entirely impossible.

                  First of all, it is thought, if I am not mistaken, that this tetrapod transition happened 379,000,000 years ago. Now, Tiktaalik is dated as 375,000,000 years old…
                  http://tiktaalik.uchicago.edu/meetTik.html

                  So it all seemed nice and in place. However, research published in nature actually found that this transition must have been pushed back a complete 18,000,000 years to 397,000,000 years ago in light of new evidence of when this could have even possibly taken place.
                  -Niedzwiedzki, G. et al. 2010. Tetrapod trackways from the early Middle Devonian period of Poland. Nature. 463 (7277): 43-48

                  But what really buries Tiktaalik right in the dirt is the following facts… Tetrapods predate Tiktaalik… By around 20,000,000 years. Indeed, new tracks in Poland found of tetrapods date about 20,000,000 years before Tiktaalik, which was originally thought to have become a tetrapod or something, meaning that if Tiktaalik is really a transitional fossil, it MUST predate tetrapods, however it is does not. Here is the paper:
                  -(Philippe Janvier & Gaël Clément, “Muddy tetrapod origins,” Nature Vol. 463:40-41 (January 7, 2010).)

                  Nature records how these footprints wreak havoc on tetrapod evolution. There can be no denying this, tetrapods come before Tiktaalik, no evolution has occurred here, Coyne is wrong about Tiktaalik and Joseph is right.

                  Now, you respond to Doug Axe’s arguments, showing how it is inconceivably improbable that proteins will fold a certain way. Now, this argument is clearly just… Incorrect. I can immediately point out two major problems. One, the folding of proteins is anything but random. Number two… The information for the protein to fold is already there. It can easily be done without an appeal to probabilities. A computer can do numerous commands, but it does one. Now, what is the probability that it would have done that one command? Well… 100%. Why? Because the information in the computer is already there, it couldn’t have possibly failed unless there is a malfunction (mutation) in the information.

                  Now, we’re nearing the end here. I do agree of course that bias exists *COUGH COUGH JERRY COYNE COUGH*, and it is true that Evolution makes correct predictions, however as does Intelligent Design, such as predictions made by ID scientists on the destruction of Junk DNA. Now, you claim one of the predictions of evolution is that a step-wise account can be given for the bacterial flagellum. Again, read my previous comment, the mere possibility of this notion has been entirely disavowed. It was also shown that the flagellum predates the TS3 anyways, so this is obviously incorrect.

                  At the end you ask — what more is there to add? Well, perhaps I’ve given you some new pieces of information to… Weaken, at least, your stances of evolution, such as the fact that tetrapods are now known to predate all supposedly transitionary fossils to their existence, and thus the mere idea of tetrapod evolution is non-existent in the record. What does that mean? By the way, take a look at this diagram of whale evolution:

                  http://evolution.berkeley.edu/evolibrary/article/evograms_03

                  We have now found whale bones that are 49,000,000 years old, in other words, whales lived alongside ambulocetus. Whale evolution has entirely collapsed as a scientific concept because of this fact. It never happened. What does this do to evolution, do you exactly think?

                • Christine Janis

                  “Coyne gets the discovery on Tiktaalik entirely wrong, and he would have realized this if he merely read Casey’s points”

                  Coyne’s office is down the hall from Neil Shubin’s. He’s probably seen the original material. Luskin can’t even get the published description right.

  • Glen

    “Evolution as a well-established scientific fact.” I thought it was still a theory? In which case, I’ve missed some key discoveries. So my first question would be; what is the scientific explanation for the missing fossils and how do they fit with neo-Darwinism?

    • Dave Post author

      I’d highly recommend googling the term “Scientific Theory” … here let me google that for you … (From the Wikipedia Page, the 1st para) …

      A scientific theory is a well-substantiated explanation of some aspect of the natural world that is acquired through the scientific method and repeatedly tested and confirmed through observation and experimentation.[1][2] Scientific theories are the most reliable, rigorous, and comprehensive form of scientific knowledge.[3]

      • Glen

        Hi Dave, this is the issue I’m facing as so far it appears evolution can’t be tested or observed and there is little to no “well-substantiated” evidence for it. Therefore it isn’t scientific fact, it’s still a theory or pseudoscience.

        However, since it’s been 150 or so years since Darwin first penned his theory we might have some “well-substantiated explanation of some aspect of the natural world” that can help support his theory. I think the fossil record is a good place to start.

        Darwin assumed that the missing fossils would eventually be unearthed. By “missing” I mean transformational fossils which would show each gradual step in the evolutionary process of each species leading back to the original single cell organisms he claims all life started from. But so far they haven’t been found. I’m trying to get answers to this basic question first because it’s key to neo-Darwinism. Without the fossil’s Darwin’s theory falls apart.

        • Dave Post author

          It may be appropriate to find out if we use the same words to describe different things, so with that thought in mind, what do you think that the theory of evolution is? If asked to describe it in a few words, how would you do so?

            • Dave Post author

              OK good start.So to break it down to very simple terms … we have variation and we have natural selection.
              – You are not a clone of your parents, that is variation
              – If you have brothers and sisters, then when compared to each other you will appreciate that some do better than others within the context in which you find yourselves … that is natural selection

              I suspect you have also personally experienced evolution in the sense that the flu virus mutates, hence the need to get regular flu shots. The flu shot might or might not work, it depends … if the variation of flu has mutated beyond the ability of the vaccine to handle they it will not work Each season we play catch-up. Perhaps another example is the deployment of Antibiotics. We are basically in deep trouble here because bacteria have evolved antibiotic resistant strains and our ability to deploy antibiotics that are as effective as they once were is a growing issue of extreme concern.

              When it comes to evolution, there is a prevailing consensus and so generally the only people who challenge it tend to do so for religious reasons. Often the basis is one where you start with a conclusion and then work backwards looking for anything that can confirm that conclusion (science tends to work the other way around).

              If curious to delve into the topic in more detail, then I can recommend simply googling “Evidence for evolution”. The Berkley 101 site is good and covers it all quite well. Another alternative is the book “Why evolution is true”.

              Best Regards,

              Dave

              • Jimmy

                Are you going to be replying to my comment anytime soon? If you missed it, I will copy and paste it for you.

                Something that is troubling me is that you continue to latch on to Coyne’s claims, however I have pointed out numerous problems that you are not seeming to try to recognize. Before I respond to your accusations that makes it seem as if I contradicted myself, I will number out the problems I shown in Coyne’s response.

                1. Probably the biggest point is, yet again, Coyne simply did not address the bulk of Joseph’s argument in all three of the point in Joseph’s paper. Thus, to say it debunked the entire thing when in reality it only addresses a minority of the points is, on its face, nonsensical.

                2. Coyne issued an “explanation” for the irreducible complexity of the eye, that Jodeph in the very paper that Coyne was responding to, had already shown problems with this explanation

                3. Coyne gets the discovery on Tiktaalik entirely wrong, and he would have realized this if he merely read Casey’s points

                4. To try to solve the DNA-Protein problem, Coyne (extremely) ambiguously mentions the “co-evolutionary scenario”, which is the idea that DNA and Protein were once the same thing, and they magically separated. This hypothesis is unscientific, unrealistic, and has absolutely zero scientific validation. He also accused Kuhn of not engaging with the RNA explanation, even though he did (dare I say this qualifies as a misrepresentation of Joseph)

                Considering these incredible problems and errors that are simply all over Coyne’s response, I would simply like to ask you which part of his argument you were actually convinced by, taking into account seeing my points on it. This is an enigma to me as of now.

                Now, on to my supposed contradiction. First, I explain Joseph is simply not saying “this is complex therefore design”, I correctly pointed out he said that it is too complex to be explained by mutations and natural delection. However, your problem seems to be when I added in my view on it. You clearly just recognize that my points against life from non-life are not actually in Joseph’s paper, simply because I said it in my last comment, does not mean it is part of Joseph’s paper.

                Furthermore, this is an errorful analogy, as I did not invoke creation because of “oh my just wow this is so complex”, my argument was based on the implication of Cell Theory and the Law of Biogenesis.

                2 more quick things to add:

                1. Are you a biologist?
                2. I actually found Joseph’s response to these critics… But what was most funny is that… It was on CASEY LUSKIN’S WEBSITE, LOL. This entire thing is certainly hilarious as I go through the discourse on Joseph. Anyways, I went through the entire thing, and I found it highly impressive, and so I’ll ask you to check it out for yourself.

                http://www.evolutionnews.org/2012/05/darwin-doubting059241.html

  • Hoax Busters Call

    “Peer review: a flawed process at the heart of science and journals”…

    “That is why Robbie Fox, the great 20th century editor of the Lancet, who was no admirer of peer review, wondered whether anybody would notice if he were to swap the piles marked `publish’ and `reject’. He also joked that the Lancet had a system of throwing a pile of papers down the stairs and publishing those that reached the bottom. When I was editor of the BMJ I was challenged by two of the cleverest researchers in Britain to publish an issue of the journal comprised only of papers that had failed peer review and see if anybody noticed. I wrote back `How do you know I haven’t already done it?”

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1420798/

    LOL!

  • herrmann

    Do they not know that the Peer review process has only been a touchstone of the modern scientific method since the middle of the 20th century.

    Peer Review History

    The first recorded editorial pre-publication peer-review process was at the Royal Society of London in 1665 by the founding editor of Philosophical Transactions of the Royal Society, Henry Oldenburg.[9][10][11] In the 20th century, peer review became common for science funding allocations. This process appears to have developed independently from that of editorial peer review.[12] See a competing understanding of the history of peer review using a scientific approach in Gaudet [13], that builds on historical research by Gould [14], Biagioli [15], Spier [16], and Rip [17]. Using a scientific approach means carefully tending to what is under investigation, here peer review, and not only looking at superficial or self-evident commonalities among inquisition, censorship, and journal peer review.

    The first peer-reviewed publication might have been the Medical Essays and Observations published by the Royal Society of Edinburgh in 1731. The present-day peer-review system evolved from this 18th-century process.[18]

    still you guys are a bunch of lying assholes ! periode!

  • Alicia LeMarie

    For years evolutionists have been screaming for Peer Reviewed Literature whenever researchers with alternative interpretations presented their conclusions. Now that many papers have come forth, evolutionists are screaming that “they don’t count”. How outrageous and ridiculous! Really, it’s sad.

    • Dave Gamble Post author

      Feel free to pick the one you feel is the very best example of a peer-reviewed paper that supports intelligent design using actual data and explain why it is not a fail and is actually credible.

      • Nick Singh

        Sadly people in the US have not accepted the bullshit pseudoscience of evolution???? you know, this theory has plenty of holes. for you to call this nonsense science just shows how devilishly dishonest you people are. let the damn science work it out. no need to jump to conclusions.

        • Dave Gamble Post author

          I do have to ask Nick, given the observation that the OP article examines all the claims to peer-reviewed evidence and ends up with nothing left, then where exactly are these “plenty of holes”?

          Can you even point to one single published peer-reviewed paper in a credible science journal that identifies these holes – if they existed that there should at least be one, but there is none at all, so why is that the case?

  • Joel Stapley

    thorough? yes. accurate? no.

    there is no evidence for evolution. no fossil records or examples of any kind to explain the macro evolution that those who hold the religious view of evolutionism suggest exist.