Monday, May 7, 2012

Here’s Why Homoplasy (And Other Contradictions) Isn’t a Problem For Evolution

Evolution and common descent expect the species to fall into a tree-like pattern. Species on the same branch should be similar, whether one is looking at their visible features or the microscopic cellular and molecular features. On the other hand, species on very distant branches should be different, again whether one is looking at their visible features or the microscopic cellular and molecular features. And while this expected pattern has some flexibility that is allowed, the observed pattern reveals far more significant contradictions. Allied species that look like they belong to the same branch reveal profound differences upon closer inspection. And different species that look like they belong to distant branches reveal profound similarities. One might think evolutionists would go easy on their truth claims about evolution being overwhelmingly supported by the evidence and a compelling fact. But they don’t, not in the light of these contradictions or in the light of the many other contradictions. Here is a recent paper that shows exactly how evolutionists respond to these evolutionary tree contradictions. First for some background:

Understanding the diversification of phenotypes through time—“descent with modification”—has been the focus of evolutionary biology for 150 years.

And next for the statement that reveals how evolutionists handle contradictions. They don’t consider the possibility that evolution may not be a fact. Rather, they search for evolutionary explanations:

If, contrary to expectations, similarity evolves in unrelated taxa, researchers are guided to uncover the genetic and developmental mechanisms responsible. 

And while that might seem reasonable, one problem is that while the search is on there is no acknowledgment that evolutionary theory has problems. Evolution racks up problem after problem, and still no such acknowledgment. For those problems are interpreted as research problems which deal with the theory of evolution and have no influence on the fact of evolution. Such research is taken as a sign of good science at work.

So while there is nothing wrong with doing research, the years pass by with no acknowledgment of the actual state of the science. This brings us to the second problem, which is that evolution is sufficiently malleable that it always seems to have at least some sort of explanation, albeit unlikely, to service the contradictions. To wit, the paper continues:

Similar phenotypes may be retained from common ancestry (homology), but a phylogenetic context may instead reveal that they are independently derived, due to convergence or parallel evolution, or less likely, that they experienced reversal. 

In this case, the contradictions can be explained by various combinations of common ancestry, convergence, parallel evolution and reversal, to name a few. They could have included unique selection scenarios, accelerated evolution, and other mechanisms to account for those profound differences found amongst otherwise allied species.

In any case, one way or the other the contradictions will be explained by some mechanisms, no matter how speculative or unlikely. And the whole exercise will be cast as an investigation of how evolution really works.

Such examples of homoplasy present opportunities to discover the foundations of morphological traits. A common underlying mechanism may exist, and components may have been redeployed in a way that produces the “same” phenotype. New, robust phylogenetic hypotheses and molecular, genomic, and developmental techniques enable integrated exploration of the mechanisms by which similarity arises.

Components may have been redeployed? Evolutionists will try hard to explain the findings, but don’t expect an objective, theory-neutral, scientific evaluation of their idea.

36 comments:

  1. Cornelius Hunter

    No Ian, you are simply providing yet another great example of how evolution harms science. It's dogma has gone viral and doesn't allow the scientific facts to get out.


    What scientific facts weren't allowed to get out CH? Please be specific.

    If these mystery scientific facts weren't allowed to get out, how did you learn about them?

    You made the claim CH. Why are you now avoiding the issue?

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    1. Thorton:

      You're (and Ian's) skepticism of directed mutations is not unusual. Evolutionists have strongly resisted this since it was a fundamental tenet of evolution for so long that mutations must be random. As one scientist explained: “The really heretical thing to say is that the environment could be pushing the epigenetic information in a direction that is beneficial … that raises the hackles.”

      There is the science, and then there is the dogma. If you're interested in the former there's plenty of material on epigenetics and directed mutations. Here's one example:

      http://jb.asm.org/content/182/11/2993.full

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    2. Here's another recent review article:

      http://www.ncbi.nlm.nih.gov/pubmed/19606595

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    3. Cornelius Hunter

      No Ian, you are simply providing yet another great example of how evolution harms science. It's dogma has gone viral and doesn't allow the scientific facts to get out.


      CH, you completely ignored the request to back up your claim that evolution doesn't allow scientific facts to get out.

      You didn't say which facts, and you didn't say how you found out about them.

      If you want to admit you were just making it up as more baseless anti-science propaganda then do so. After all, it wouldn't be the first time you got caught posting deliberate falsehoods.

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    4. Cornelius Hunter

      Here's another recent review article:


      If those articles are suppose to be the "scientific facts that evolution didn't allow to get out", how is it then that they're published in widely read publicly available science journals?

      You didn't think your latest ridiculous anti-science assertion through very well, did you?

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  2. Cornelius Hunter

    Evolutionists will try hard to explain the findings, but don’t expect an objective, theory-neutral, scientific evaluation of their idea.


    At least evolutionists are trying hard to produce explanations that fit the data. Critics of ToE don't have the intestinal fortitude to even offer, let alone test, any alternative explanations.

    How much respect should we give those throwing rocks from the sidelines, deathly afraid to even get in the game?

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    1. How much respect should we give those throwing rocks from the sidelines, deathly afraid to even get in the game?

      Why would anybody be afraid to attack your pseudoscience? There is one prediction of intelligent design that falsifies the TOE: Complex identical DNA sequences will be found in distantly related organisms that cannot be accounted for by common descent or convergence through random mutations.

      You're afraid of this, Thorton. Admit it. What speculative, unobservable (or pseudocientific) mechanism will you come up with to explain this?

      So why is the horizontal sharing of genetic information a prediction of intelligent design? Simple: it is a way for the designers to avoid reinventing the wheel. It is called object or design reuse. It happens all the time in human intelligent designs, as any experienced software engineer/designer figure out sooner or later.

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    2. velikovskys:

      So the designer is human?

      Not necessarily. The designers (I believe there were many) have something that humans have: intelligence. In fact, given enough time, there is no reason to suppose that human knowledge and technology will not advance to the point where we, too, can design lifeforms as sophisticated and complex as the ones we now observe on earth.

      We, too, are gods. But that's a different topic for a different forum.

      PS. veli, you're clever but you ain't as clever as you think you are.

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    3. So I have been told many times, but that is another story as well.

      So if reuse is an indication, of design,must that design be caused by an intelligent being? Spider certainly create designs, not the smartest creature. It the spider was designed to design, couldn't evolution been designed to design?

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    4. Aw, come on, veli. You can do better than that. Spiders, really? Humans are not programmed to design anything in particular. Spiders, on the other hand, are pre-programmed to build a certain type of web or cocoon. The real designer is whoever created the spider's web-building program and coded it in their genes.

      Besides, evolution is not a tangible mechanism that anybody can point to. It's an abstract idea in the minds of a minority of religious folks. It takes intelligence to design and everything that this entails: the ability to predict, to plan, to learn from mistakes, to have goals, to have an affinity for beauty, etc. Wake up.

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    5. Sorry to be disappointing..

      Just to be clear the designers create the genome which creates the brain which has the ability to weave webs as well as the " urge". Since different species have different capabilities ,is each species individually designed?

      Isn't intelligence also an abstract idea like evolution? Several different things combined under a general concept? Design as well seems to be a placeholder for several concepts.

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  3. This is another good thread on theme of why its counter intuitive , in a evolutionary state of mind, to find like forms/functions in very unrelated biology and in like creatures close to each other in evolutionary lineage conclusions one does NOT find like forms/functions as one should.

    A striking hint that creatures are not related or if related are not stuck to evolutionary mechanisms.
    It is as one would expect if there was a creator with a old program that allows biological adaptation as needed.

    Yes they must invoke, convergent , parallel, and reversal evolution to explain what should not be seen if evolution old school was true.

    Is this the reversal thing Darwin talked about in his second book and including his idea retarded people were more hairy because they reversed back more to a ape persona.??

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  4. As to this comment:

    'Similar phenotypes may be retained from common ancestry (homology), but a phylogenetic context may instead reveal that they are independently derived, due to convergence or parallel evolution, or less likely, that they experienced reversal.'

    But what about when phenotypes (body plans) are found to be different but the phylogenetic context (genetic comparison) reveals similarity?

    Kangaroo genes close to humans
    Excerpt: Australia's kangaroos are genetically similar to humans,,, "There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order," ,,,"We thought they'd be completely scrambled, but they're not. There is great chunks of the human genome which is sitting right there in the kangaroo genome,"
    http://www.reuters.com/article/science%20News/idUSTRE4AH1P020081118

    But then again when the neo-Darwinists have not even demonstrated that their mechanism can work, but they 'know' that theory is true anyway, then that relieves them of the pesky problem of having to actually prove anything true with their 'theory',,,

    Response to John Wise - October 2010
    Excerpt: But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. A technique called "saturation mutagenesis"1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism.
    http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html

    further note:

    Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010
    Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator.
    http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies

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    1. bornagain77:

      [T]he neo-Darwinists have not even demonstrated that their mechanism can work…


      To that end, has anyone written a paper that defines the problem? That is, what do scientists need to know in order to demonstrate that evolution does work? And what do scientists know so far?

      As an engineer, I tend to view the problems evolution has to solve as similar to the problems an engineer has to solve. Any engineering project has to have a plan that specifies the parts needed to build the object in question and a process that brings the parts to the assembly point at the proper time.

      How are the three P’s, as they might be called, manifested in an organism during an evolutionary transition?

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    2. Maybe evolution doesn't work that way..it may be a fallacy to overlay an engineering solution.EL is very knowledgable on GAs,perhaps she might have a constructive insight

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    3. Doublee

      To that end, has anyone written a paper that defines the problem? That is, what do scientists need to know in order to demonstrate that evolution does work? And what do scientists know so far?


      Yes. Several *million* papers illustrating not only the mechanisms but the evidence for the mechanisms in action are readily available. There are whole museums and working laboratories full of them. There are whole college undergrad and grad level programs that teach them.

      As an engineer, I tend to view the problems evolution has to solve as similar to the problems an engineer has to solve. Any engineering project has to have a plan that specifies the parts needed to build the object in question and a process that brings the parts to the assembly point at the proper time.

      That's still the crux of your misunderstanding. Evolution does not work like a human engineering process. There is no pre-defined problem to solve, no end product to meet a pre-specified goal, no list of materials, no assembly timeline.

      The only goal is "make more copies of yourself". Doesn't matter if the copies aren't identical, or what they're made from, or what the end product ends up looking like, or what forces produce them. As long as you are good enough to reproduce in your current environment, you stay in the game.

      How are the three P’s, as they might be called, manifested in an organism during an evolutionary transition?

      They're not. As long as you keep anthropomorphizing a naturally occurring physical process you'll never understand it.

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    4. Thorton claims

      "Evolution does not work like a human engineering process." That's true! In fact evolution doesn't work period as to generating functional complexity/information over and above what is already present!

      And yet despite this fatal empirical shortcoming for verification of Darwinian processes, we find this in cells:

      Bacterial Flagellum - A Sheer Wonder Of Intelligent Design - video
      http://www.metacafe.com/watch/3994630

      The ATP Synthase Enzyme - exquisite motor necessary for first life - video
      http://www.youtube.com/watch?v=W3KxU63gcF4

      Powering the Cell: Mitochondria - video
      http://www.youtube.com/watch?v=RrS2uROUjK4

      Molecular Machine - Nuclear Pore Complex - Stephen C. Meyer - video
      http://www.metacafe.com/watch/4261990

      Kinesin Linear Motor - Video
      http://www.youtube.com/watch?v=kOeJwQ0OXc4

      Ribosome Translation High Quality - video
      http://pubs.acs.org/cen/multimedia/85/ribosome/translation_bacterial.html

      Myosin - video
      http://www.youtube.com/watch?v=j8F5GGPACkQ

      The Virus - Assembly Of A Molecular "Lunar Landing" Machine - video
      http://www.metacafe.com/watch/4023122

      The following article has a list of 40 (yes, 40) irreducibly complex molecular machines in the cell:

      Molecular Machines in the Cell -
      http://www.discovery.org/a/14791

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    5. Systems biology: Untangling the protein web – July 2009
      Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. “Combine all this and you can start to think that maybe some of the information flow can be captured,” he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. “The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent,” he says. “The simple pathway models are a gross oversimplification of what is actually happening.”
      http://www.nature.com/nature/journal/v460/n7253/full/460415a.html

      Map Of Major Metabolic Pathways In A Cell – Diagram
      http://www.sigmaaldrich.com/img/assets/4202/MetabolicPathways_6_17_04_.pdf

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    6. Thorton:

      As long as you keep anthropomorphizing a naturally occurring physical process you'll never understand it.


      O.K., so you don’t like my engineering analogy. Let me try to ask my question in another way.

      During reproduction every zygote eventually matures into a fully functioning organism. Cells divide at certain times and assume new functions. Along the way the cells start arranging themselves into wings, feet, hearts, lungs, etc. at the right time and the right place.

      There is information – if I may use that word – in the zygote that directs or somehow controls this entire process. I have briefly looked at some of the material bornagain77 provided and I am amazed at the incredible complexity of the inter-cell signaling and feedback loops.

      Now a random mutation occurs that somehow alters that above process such that a slightly different organism is going to be built. That mutation has to affect something in the nature of the information in the zygote so that during the maturation process the change is effected at the right place and the right time.

      What does the random mutation change? My understanding that a random mutation creates a different protein is surely inadequate. The new protein is certainly a part that is placed somewhere during the process of embryo development according to some plan.

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  5. It is as one would expect if there was a creator with a old program that allows biological adaptation as needed.

    But there's a rule that has been linked to people's professional identity as scientists that they can only imagine what a Creator wouldn't do and not what one might do.

    In fact, apparently one can imagine pretty much anything about the past and even include multiple universes in the present while imagining what a Creator wouldn't do. But if you imagine what a Creator would actually do then you cannot be a scientist. That's the rule. It safeguards us from people passing off their ignorance as knowledge, don't you know. Lol...

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  6. Gould wrote a lengthy book trying to define the "structure of evolutionary theory" out of all the babble that has emerged from the type of occult societies that the Darwin's were involved with. But in the end, its structure or endpoint is probably pretty simple: "The God of the Jews didn't do anything."

    That's pretty much it. You can see almost anything in the Rorschach tests typical to evolution (e.g. imagining things about skeletons, etc.) but you can't see that. So even if you think that the God of the Jews may have done something or other you have to play pretend and imagine that it's not the case if you want to keep your professional identity.

    After all, that is allowed by laws emerging from the bowels of nature by happenstance... naturally. It's similar to the structure or end of the law and logic in other forms of paganism. There it is summarized as: "Do what thou wilt." In contrast, "Thy will, not my will be done." just won't do! So imagine what you will...

    I would imagine that if it had been said by the Jews that God or gods emerged from the earth then all "out of chaos, order" evolutionary creation myths would probably have to be structured to say that the gods or life descended from the heavens by rule. And if you didn't imagine things in that way then you'd lose your professional identity as a scientist, etc.

    Meanwhile, stupid and ignorant biologists stare at their test tubes and imagine that they have developed all of their creation myths in a vacuum based on experimental knowledge of some sort. But if that is the process that they were actually engaged in then why did occult societies develop rules for them about how they must always imagine things toward an endpoint? Wouldn't the endpoint of "God didn't do this." have emerged, naturally! In any event, it seems that the only consistency in ivory towers of babble that the "hidden hand" built is that God didn't do anything. And more specifically, it was the God of the Jews that didn't do anything. So saying or imagining that God did do something is the great heresy these days and the reason for censorship, etc.

    But imagine if the occult societies that gave biologists the ridiculous structure of their creation myths get around to revealing that a Great alien Architect sits atop their pyramid $chemes? I'd imagine that at that point people will probably be "allowed" to imagine that's the case without their professional identities and their careers being destroyed and so on. I would also imagine that the structure of these old evolutionary myths originally given by illuminated to the stupid at the base of the $cheme may have almost reached the limit of their usefulness. And as far as mythologies of progress go, imagine if historians look back and wonder how anyone was ever stupid enough to believe that they were on a path to knowledge and sight based on "rules" about explaining everything in terms of ignorant and blind mechanisms.

    Imagine that!

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  7. How much respect should we give those throwing rocks from the sidelines, deathly afraid to even get in the game?

    The rules of the game were generally given to stupid and credulous people by members of secret societies who often aren't even taken in by the game that they gave to you to play at. Not to mention that the rules are so transparently and obviously rigged toward the end result of "God didn't do it." that only the truly stupid and ignorant at the base of the scheme mistake games of this sort and the memes they generate as the epistemic equivalent of experimental or empirical scientia/knowledge.

    Indeed, there is no evidence necessary to play the game that has been given to you. False knowledge of an endpoint has already been invoked in mythologies of progress toward it, naturally.

    Seriously, you don't realize that the game is rigged? Actually, you probably don't... so you'd probably agree that the only way to play the game is to imagine what God wouldn't do. Anyone who didn't imagine things in that way should have their funding cut off, their professional identity done away with and so on. Because that's the way the game is played in the shadow of the all seeing eye at the top of the pyramid and given the $tate of things these days.

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  8. None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism.

    Who said anything about observing anything? Given that evolution is the defining characteristic of science, imagining things about the skeletal remains of organisms should be sufficient.

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  9. What is an "objective, theory-neutral, scientific evaluation of [an] idea", Cornelius?

    Can you give me an example?

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  10. This comment has been removed by the author.

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  11. Lizzie,

    Einstein proposed three tests of general relativity, subsequently called the classical tests of general relativity, in 1916:

    1. the perihelion precession of Mercury's orbit
    2. the deflection of light by the Sun
    3. the gravitational redshift of light


    What was that test for evolution?

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    1. Which particular hypothesis of the theory of evolution are you referring to?

      (No, this is not evasion, it is key).

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    2. What was that test for evolution?

      Nothing highlights the abject scientific ignorance of internet Creationists than their demand to see THE test for evolution, or THE single bit of best evidence.

      They just can't grasp that the overarching ToE is an entire body of scientific work composed of hundreds if not thousands of well supporting hypotheses. It wasn't discovered by one person with one experiment. It's the collected body of work by millions of scientists over hundreds of different scientific fields.

      The analogy many use is that ToE is like seeing the big picture in a giant jigsaw puzzle. There is no one piece that gives the entire view, it's the collective and consilient picture that emerges from all the pieces taken in total.

      Sad that internet Creationists choose to remain so willfully ignorant of such elegant and well supported science.

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  12. Nothing like the subject of Homoplasy to make evolutionists quiet or promise to get back to you after looking into it and ... crickets

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    1. Actually, it's a really interesting paper, and the responses you are looking for are actually there, in the paper.

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    2. Liddle:

      Actually, it's a really interesting paper, and the responses you are looking for are actually there, in the paper.

      You mean the usual speculative fiction? No thank you.

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  13. mynym
    Funny and on mark that they do stress these days what a creator would not do and so nature shows no creator.
    Yet what a creator would do first would be above us and second in some ways we just need to expand imagination to see other options.
    A creator with a great program would have like results for like needs regardless of any biological connections.
    Thats what it would look like and convergence in nature would fit this prediction and is surely unlikely in any other prediction especially dealing with such glorious chance of random mutations.
    If they still believe in random mutations as of this moment that I type.

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  14. Crickets... crickets. This has to be the most uncomfortable subject for evolutionists. Darwins argument from the nested hierarchy was so compelling that on that basis alone he would adopt his theory even if it were unsupported by other arguments. From it springs the so called "fact" of evolution.

    Evolutionists can choose to dance with all the old arguments until the cows come home, but the bottom line is that the objective nested hierarchy and tree of life is no longer scientifically valid... and the evolutionist response is... ? I'm not sure if they fully understand or accept the implications of how more genome research is going to further undo their objective nested hiearchy argument. Do they really understand how serious this is?


    Can evolution survive without the objective nested hierachy?

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  15. Translated into Portuguese so as to bring light on evolution...

    http://pos-darwinista.blogspot.com.br/2012/05/eis-porque-homoplasia-e-outras.html

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