Cracks In The Edifice

The Theory of Evolution has been reigning the academic world for close to a century and a half, but the alleged proofs and demonstrations have been playing a vanishing game. The latest one to do so is what is usually called the “Phylogenetic Tree”.

A theory like Evolution needs multiple proofs and evidences, and thankfully the proponents have been offering a generous number of proofs. This helps both the sides. The proponents get an opportunity to organize their house, while the opponents get an opportunity to examine whether it is a real house or only one made of cards.

Phylogenetic_tree.svg An arrangement of all the known flora and fauna in an organized tree, starting from the simplest known life and culminating in the most advanced one is called a Phylogenetic Tree. Initially they used an intuitive classification based upon perceived similarities, but gradually the work became more sophisticated. Today almost all standard textbooks on biological evolution necessarily contain at least one picture of the Phylogenetic Tree, mainly in support of Evolution.

The first such tree was made by Charles Darwin and his predecessors, and the picture that is shown in most textbooks today was perfected before the 1930s. However, cracks began to appear in the picture soon after that. The Cladists were almost the first to challenge this picture. They refuted the idea of a single tree and substituted multiple trees, each one evolving independently of the other.

Non-evolutionists have always insisted that this tree has no empirical basis and that the whole construction is arbitrary. This arbitrariness was demonstrated repeatedly by the way the tree was rearranged, and also by the absence of established “links” between branches. The question of the non-evolutionist empiricist like me is, “how do you know the branch connects in a certain place when the link that ought to connect is missing”.

The latest issues of Scientific American, New Scientist, and several other scientific magazines accept this observation of non-evolutionists in so many words. Not that they have abandoned the framework of evolution. No, that is not the issue here. The basic issue is that this particular proof, as presented in biology textbooks, is simply not true. Empirical observations have shown — particularly after the arrival of genetic studies — that the tree will not hold together. The presumed edifice will not hold together. [Picture from http://en.wikipedia.org/wiki/Phylogenetic_tree]

The author is a physicist, and has worked in the filed of Quantum-Nuclear physics, particularly on the quark structure of protons, neutrons, and deuterium binding energy.

8 replies
  1. Ian
    Ian says:

    An arrangement of all the known flora and fauna in an organized tree, starting from the simplest known life and culminating in the most advanced one is called a Phylogenetic Tree.

    The increase from simple to advanced is irrelevant – they are listed in chronological order only. There are simple creatures at the end of the tree as well as complex ones.

    The first such tree was made by Charles Darwin and his predecessors, and the picture that is shown in most textbooks today was perfected before the 1930s.

    To claim this tree has ever been “perfected” is to utterly misunderstand both science and evolution. It is constantly being improved, updated, and refined as we learn more. There is a problem with textbooks using out of date images but that has nothing to do with evolution.

    This arbitrariness was demonstrated repeatedly by the way the tree was rearranged, and also by the absence of established “links” between branches.

    This is called learning. You will note that each change generally makes the whole tree fit the evidence better and presents a more realistic picture. This is exactly what we would expect from a vibrant scientific area. The absence of links is not a problem for evolution because we wouldn’t expect all animals to fossilize. However you might note there has not been a single animal found that does not fit into the evolutionary chronology. You don’t find rabbits in the pre-Cambrian.

  2. Dr. Johnson C. Philip
    Dr. Johnson C. Philip says:

    @Ian

    Thank Ian for your response. Mutual interaction can always make us understand the subject better and remove out blind spots.

    Since you have asked several questions, I would make a full post today to answer your questions in a systematic way.

    Thanks for your comments !!

    Johnson C. Philip

  3. Heraclides
    Heraclides says:

    To Ian:

    To claim this tree has ever been “perfected” is to utterly misunderstand both science and evolution.

    I agree, Johnston’s statement is wrong on many levels, although I would append “and phylogenetics” to your reply (as someone who knows the field, it’s clear he doesn’t).

    With regard to “Darwin’s tree”, I presume he refers to the illustration in The Origin of the Species. This presents a tree-like diagram to illustrate his concept. It was an illustration, not evidence. The illustration does not show any species at all, but only illustrates how species could conceptually be related through descent and time according to his thinking. It illustrates the structure of these relationships, not an actual tree of species. If you read the text referring to it in “The Origin” and see the tree for yourself, you will see that it is a generic diagram, not a phylogenetic tree. (e.g. http://en.wikipedia.org/wiki/Tree_of_life_(science) – source chosen for ease of access; better sources are available.)

    Present-day phylogentic trees represent the result of an algorithm applied to quantitative data. When used with appropriate statistics, they can be used as evidence. Phylogenetic trees were hardly “perfected” in the 1930s. At that time, they were made using only morphological data (i.e. differences in body shape measured in some way) or “higher level” properties (like warm/cold blooded, etc.).Phylogenetics is hardly a discipline that has stopped in the 1930s because it had the “perfect” solution, as even the quickest look at the field would show. As a trivial example, DNA sequence data wasn’t available until decades later, which in time made huge improvements to the field.

    Johnston seems to be (over-)simplifying, or confusing phylogenetics with, the development of the so-called “modern synthesis” of evolution which started around the 1930s. The development of the modern synthesis was not the “perfection” of phylogenetics. (And could hardly be, given that DNA sequence data had yet to incorporated into the trees for several decades.)

    I would add that the mathematics to construct (true) phylogenetic trees wasn’t around until after Darwin’s day.

    (And is still being improved upon today: NZ has some of the leading people in this field.)

    To Johnson:

    To add a few criticisms of my own of the original article (not all of my my criticisms; there are too many faults for me to address):

    The proponents get an opportunity to organize their house, while the opponents get an opportunity to examine whether it is a real house or only one made of cards.

    You have the “opponents” only “objecting”, not doing anything towards presenting a reasonable alternative. If they’re can’t present a reasonable alternative, then they can’t claim there is a better explanation. (In fact, you could say that if they don’t present evidence supporting an alternative, they would have to claim the the theory of evolution is the best available, even if they disagreed with it.)

    This arbitrariness was demonstrated repeatedly by the way the tree was rearranged, and also by the absence of established “links” between branches.

    Your statements here are too vague to know what you mean to be referring to (they could mean a lot of things).

    I would point out, though, that Darwin’s illustration in The Origin says nothing about present-day support for evolution from phylogenetics. Darwin’s tree was an illustration of his concept, not evidence, nor even an actual phylogenetic tree (more below). His illustration is mainly of historic interest now to say anything about present understanding, as the field has moved on too far since.

    I would also add, that new ideas of what the overall “tree of life” looks life, doesn’t take away that evolution occurs, but deals with how.

    but the alleged proofs and demonstrations have been playing a vanishing game.

    To be blunt: what rubbish. As a simple example, a small sample of the papers presented in just one journal are summarised here: http://www.nature.com/nature/newspdf/evolutiongems.pdf

    That evolution occurs is well established, and has plenty of support. The details of how evolution occurs also has plenty of support, but continues to be refined, as happens for any area of science.

    Put another way, there is no controversy that evolution occurs (as your article implies); there are different points of view over the relative contributions of different types of evolutionary processes and the particular ones used in evolving particular species. Discussions over the latter, do not “take away” that evolution occurs.

    the Phylogenetic Tree

    Not “the” phylogenetic tree, but phylogenetic trees. That you misuse the term indicates you don’t understand the field: no-one with a working knowledge of the field writes it like this.

    starting from the simplest known life

    It starts from a representative of the earliest known life form inferred from the phylogenetics.

    Also, a nit-pick: some calculations yield phylogenetic trees that are unrooted, because the type of data used as input (and the algorithm used) cannot infer the earliest branches. In these cases, the trees don’t start at a “earliest form”, but the earliest forms (plural) that can be determined reliably from the data and methodology used.

    The question of the non-evolutionist empiricist like me is, “how do you know the branch connects in a certain place when the link that ought to connect is missing”.

    As someone who understands how phylogenetics works, what this is saying to me is that you don’t understand how phylogenetics works. It is a question that might be needed by those who don’t understand phylogenetics in order to understand it, but it’s not a question that criticises phylogenetics or evolutionary theory.

    The latest issues of Scientific American, New Scientist, and several other scientific magazines accept this observation of non-evolutionists in so many words.

    This is not correct. (Yes, I have read some of these articles.) If you are referring to the cover titles, they are teasers.

    The basic issue is that this particular proof, as presented in biology textbooks, is simply not true.

    This is also incorrect in the sense you are writing (as Ian has already addressed).

    Empirical observations have shown — particularly after the arrival of genetic studies — that the tree will not hold together.

    This turns reality upside-down.

    This is being either being ignorant (not being rude here, just literally “lacking in understanding”) or being intentionally misleading. Given you don’t seem to understand phylogenetics, I will take it to be the former. Present-day phylogenetic trees most often include genetic data. The genetic data certainly supports the notion of evolution by descent and the overall tree of life, and are consistent with trees made using other data. Details do get revised with additional data and new techniques, as you would expect them to, but none of these new developments have compromised evolutionary theory as a whole, nor the overall nature of the trees.

    The presumed edifice will not hold together.

    Not correct either, and “the edifice” is not presumed.

    Since you have asked several questions

    Ian didn’t ask questions, he made statements. Turning statements into questions can read as self-justifying turning them around. Wouldn’t it be fairer to treat them as he wrote them, as statements?

    To readers in general:

    The original poster is a physicist, not a specialist in phylogenetics: you would do much better with at least a biologist presenting this. Furthermore, as a practical matter, and with all respect, it is clear to me that the author of this article knows little about the field as actually practised. Common sense suggests that if you want an explanation of a field of science, to ask the people that work in it. The fair thing to do would be to let people in their respective fields represent themselves, not have outsiders in opposition to them “paint a picture” of them.

    I would add that choosing an apologist to do these things (as seems to invariably be done here) is a form of confirmation bias. It hardly adds to critical thinking, never mind questioning your own beliefs to test if they are correct.

  4. schizo
    schizo says:

    Oh! Of course there are cracks in the edifice!!!

    Darwinism or the theory of evolution (not interchangeable) is not a building made of únbreakable material finished and perfected in the 19th century or whenever (though I admit, Darwin-believers and evolution-fanatics do make it sound like that, and so do the opposite camp).

    Science is almost always a work in progress, so the edifice was faulty, HURRAH!! thats another victory for science. Now we build a new, better one.

    So do the holes in the phylogenetic tree take away any credibility from the theory of evolution as a whole? perhaps, if one starts of by assuming that there was something wrong with the theory of evolution. But scientifically speaking, Not at all.

    Thats what matters. Chances are in future a lot of what was thought was evidence or support for evolution will be found wrong or incomplete, does that mean that the theory of evolution is beginning to founder and come apart? far from it, whats happening and what might in the future is a restructuring of beliefs and precepts and an expansion of the theory to a better more and more refined one.

    ciao

    schizo

  5. Johnson
    Johnson says:

    @schizo

    Thanks schizo for your comment. Thanks for being straightforward in your presentation.

    Darwinism or the theory of evolution (not interchangeable) is not a building made of únbreakable material finished and perfected in the 19th century or whenever

    As long as someone accepts that I have no disagreement with that person.

    Science is almost always a work in progress, so the edifice was faulty, HURRAH!! thats another victory for science. Now we build a new, better one.

    As long as someone accepts that I have no disagreement with that person.

    So do the holes in the phylogenetic tree take away any credibility from the theory of evolution as a whole?

    My article is not about evolution as a whole, but only about Darwinism/Evolution as it is taught in school/college textbooks.

    Evolution as a whole is a “theoretical framework”. Theoretical framework is part of not only physical and biological science, but also of the other branches of learning such as history and economics. As long as a person is willing to accept the empirical problems faced by a theoretical framework, I have no disagreement.

    The disagreement comes in when people refuse to accept the current empirical problems and claim infallibility for the framework/theory. A concept of science cannot be claimed as infallible unless it is demonstrated empirically that it is so. This has so far not happened to evolution. I have not disagreement with you if you accept that.

    Thats what matters. Chances are in future a lot of what was thought was evidence or support for evolution will be found wrong or incomplete, does that mean that the theory of evolution is beginning to founder and come apart?

    Not necessarily. But it definitely will show that the theoretical framework is not yet an established law of science. That will also show that it is not time for the adherents of the theory to claim that finally the theory has rigorous support of empirical observations.

    whats happening and what might in the future is a restructuring of beliefs and precepts and an expansion of the theory to a better more and more refined one.

    Amen! Let that happen. But as long as that does not happen, do not claim infallibility for the theory. Also, do not claim that the theory has a rigorous empirical foundation.

    Well done schizo ! I hope that this interaction will help you to see my arguments a bit more clearly.

    My basic claim is that “evolution/Darwinism is not rigorously established with the support of empirical evidences. Those who made such claim for the past 150 or so many years built up a false edifice and that edifice is cracking”.

    Let a million scientists arise and continue work on the theoretical framework and give it a thorough empirical basis. Let them revise the theory in that process if need be. But do not claim “work completed” or QED before you actually complete the work!!!

    The fact that we we are father-son and that you are basically an agnostic has already been discussed in the anti-creationist blogs. They seem very happy that one from my family does not agree with me. But let not this fact deter you from openly confronting me with your objections.

    All what I expect from you is straightforward and honest comments, not the smokescreen kind of posts where much is posted with little said.

    with love

    Johnson C. Philip

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  1. […] these lines has been gifted us by  Christian apologist creationists (Thinking Matters). This is an article “Cracks in the Edifice” by Dr. Johnson C. Philip telling us that Darwin’s […]

  2. […] am thankful to Ian who posted a lengthy response to my post Cracks In The Edifice. I am basically an empiricist because of my scientific training, and questions at the empirical […]

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