Wednesday, July 11, 2012

'Darwin predicted nested hierarchies'!

Aristotle's taxonomy of marine life, circa 350 B.C.


Commentor oleg, in reply to my observation that natural selection reduces to 'survivors survive':

Darwin's theory isn't a tautology. It posits that different species had a common ancestor in the past. More specifically, it predicts that clades form a nested hierarchy. That of course can be, and has been, tested by several independent means, so it is at the very least falsifiable in principle.

Try to argue with that.


Ok. I'll try to argue with that.

It's true that Darwin's theory isn't a tautology. Darwin posited universal common ancestry, which is a testable hypothesis (although difficult to test). And heritable variation isn't a tautology. Living things vary and pass on some of the variations to their offspring. That's banal, but not a tautology.


Natural selection is a tautology. Individuals that are relatively more reproductively successful than other individuals will pass on more of their traits to the next generation. But individuals who pass on more of their traits to the next generation are..... relatively more reproductively successful. That's merely a restatement of "individuals who pass on more of their traits to the next generation".

Individuals that are relatively more reproductively successful are... relatively more reproductively successful.

Survivors survive, colloquially.

Tautology.

Actually, Darwinists, always loathe to use precision, understand the tautology problem.

So they fudge. They use "natural selection" with one of three meanings, according to the polemics of the moment:

1) Survival of survivors ('Natural selection is survival of the fittest.' Who are the fittest? The survivors!)
2) Acausal statistical observation ("In fact, evolution can be precisely defined as any change in the frequency of alleles within a gene pool from one generation to the next.")
3) Causal mechanism (a "Blind Watchmaker"; "evolution is like a two-cycle engine")

Each of the three definitions of natural selection is an atheist fail. Tautology is banal. Acausal statistical observation is feckless and merely descriptive-- it lacks agency, and by definition causes nothing. Causal mechanism necessarily involves a propensity towards an end (i.e. that which is caused), which is teleological, and which presupposes Him Whom We Shall Not Name.

You understand why atheists are loathe to use precision.


oleg, again:

[Darwin's theory] posits that different species had a common ancestor in the past.

Yep. It does. And it may be true. But the evidence for universal common ancestry is inconclusive. The similarities/differences in organisms over time may be due to common ancestry, or common design, or both. One can group automobiles in phyletic trees (descending from Model T, with 'species' like Chevy and Mustang, etc) in a manner quite similar to the way one can construct a tree of life. But automobiles are designed. Their 'common ancestry' is common design, not descent with modification by variation and natural selection.

oleg again:

More specifically, [Darwin's theory] predicts that clades form a nested hierarchy. That of course can be, and has been, tested by several independent means, so it is at the very least falsifiable in principle.

A clade is a group consisting of a type, represented by a single branch on a phyletic tree, and all of it's related types that are distal to and connected to that branch. In biology, it refers to a species and all of its descendants, as depicted in a tree.

A nested set is an inclusion hierarchy, consisting of the common single "branch" and each distal branch extending from it.

A nested hierarchy is a tree of nested sets. Russian matryoshka dolls are a nested heirarchy. So is the classification of shapes: an isosceles triangle is a subset of triangle is a subset of polygon is a subset of shape.

Thus a clade is a type of nested hierarchy, as a matter of definition.

Darwin didn't 'predict' that clades form a nested hierarchy. The dictionary predicted it.

Nor did Darwin 'predict' a nested hierarchy in biology. The first scientist to propose a classification system of living things that incorporated nested hierarchies was Aristotle. He proposed the first scheme of biological classification-- the Tree of Being. Most of biology from 300 B.C. to the modern era-- for 2000 years-- was based on Aristotle's exploration of the hierarchy of nature.

The system of nested hierarchy used widely today is the Linnaean system of taxonomy, which uses Aristotle's categories of genus and species and consists of numerous nested hierarchies. Linnaeus published his system of taxonomy incorporating nested hierarchies in 1735. 

Darwin was born in 1809.

So Darwin didn't predict that "clades form a nested hierarchy", for two reasons:

1) A clade is a nested hierarchy, as a matter of definition. 
2) The categorization of living things into nested hierarchies is 2000 years old, and the modern system of taxonomy incorporating nested hierarchies was developed a century before Darwin's birth. 

But Darwin did "predict" this: the system of nested hierarchies observed in taxonomy is the result of universal common ancestry by the mechanism of natural selection. Darwin denied common design. In other words, Darwin made an inference from a taxonomy that was already in existence long before his birth.

Darwin did not "predict" the system of taxonomy based on nested hierarchies. He offered an explanation for it. An atheist explanation for it.


There is a compulsion among Darwinists, demonstrated nicely by oleg's assertion, to attribute wildly fantastic accomplishments to Darwin. 'We wouldn't know the relationships between living things without Darwin' and 'Darwin predicted nested hierarchies', and 'Darwin's theory is indispensable to medical science' and 'Darwin's theory predicted DNA and the genetic code', and 'Darwin was the first to propose universal common ancestry (many others, including Immanuel Kant, had proposed it long before Darwin), and "nothing in biology makes sense except in light of evolution", yada, yada.

Atheists have a bizarre propensity to attribute herculean accomplishments to their idols. 

Darwin's explanation for nested hierarchies-- universal common ancestry by natural selection-- remains unproven. There is evidence for and against universal common ancestry. And even if universal common ancestry is true, it can be explained as readily by common design as it can be explained by natural selection. 

Actually, design-- teleology from the perspective of a Thomist-- is a much better explanation for life than natural selection.

Teleology has explanatory power, and it isn't a tautology. 


68 comments:

  1. Darwin's explanation for nested hierarchies-- universal common ancestry by natural selection-- remains unproven.

    It is generally very hard to convince a nutcase of anything, especially a religious nutcase.

    --NA

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    1. Ad hominem baloney detector on here!

      Delete
  2. Causal mechanism necessarily involves a propensity towards an end (i.e. that which is caused), which is teleological, and which presupposes Him Whom We Shall Not Name.

    Oh, any observation of a causal mechanism proves Jeebus. Got it.

    You still don't understand evolutionary theory by a long shot and apparently you have no intention of learning. Your caricature is a bit like saying that neurosurgery is cracking open skulls with a blunt ax and then randomly cutting out a piece of brain with a rusty knife. But less accurate.

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  3. Excellent post Dr. Egnor. Bravo!

    Here is the Darwinist mantra: When you cannot attack the argument, go ad hominem boy!

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  4. @anon,
    It is generally very hard to convince a nutcase of anything...

    I see that Dr. Egnor's post did not convince you. Is this why you have such a low opinion of yourself?

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  5. When someone who actually understands evolution says something like “Darwin predicted nested hierarchies”, they don’t necessarily mean that Darwin uttered those exact word, or that he was the first to have the notion. In this case “Darwin” is simply shorthand for “evolutionary theory as first described by Darwin”.

    The nested hierarchies of evolutionary theory support common ancestry far better than they support common design. In the case of design, there would be no reason to be surprised if you found feathers on a frog or a placenta in a fish any more than if you found electric widows in both a Toyota and a Mercedes.

    -KW

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  6. So, what do we have here? :) Right off the bat, a couple of major concessions:

    It's true that Darwin's theory isn't a tautology.

    Yep. [Darwin's theory] does [posit that different species had a common ancestor in the past]. And it may be true. But the evidence for universal common ancestry is inconclusive.

    The first one is undeniably a reversal from Egnor's previous assertions. Here is the most recent one, from last week: Darwin's theory is a banal tautology and a non-sequitor [sic]. And a few more here, here, and here.

    The second concession is also important because it affirms my main point: Darwin's theory makes a falsifiable prediction, which is what scientific theories do. Common ancestry can be disproven. There are currently debates among mainstream biologists about the structure of the tree near the root (and it may not be a tree there at all, what with the horizontal flow of genes).

    Egnor quibbles with some portions of my argument. I will address those quibbles in a separate comment. Here I just want to savor the moment and thank him for being a good sport.

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    1. ...it may not be a tree there at all...

      So would that falsify Darwin's theory? What about the world swarmed with living creatures before the Cambrian? What about all the other icons of evolution that proved to be false or fraudulent?

      No problem you say?

      Oh, I see. You're playing with play doe...

      Delete
    2. Pépé, it cracks me up when you write, time and again, "play doe." You probably mean something else entirely. (Click on the link!)

      Would finding creatures living before Cambrian falsify Darwin's theory? I am not sure why it would. You don't say why, so I will let you make an argument first.

      On the other hand, finding that the tree of life doesn't work in the roots does indeed show that Darwin's theory does not apply to the earliest stages of life. Whether it means that Darwin's theory has to be discarded, that is not necessarily the case.

      FInding that a scientific theory fails in a certain limit does not always mean that the theory gets discarded. I have asked you a number of times in the past what you think of other scientific theories that failed.

      A prime example would be classical mechanics. We know that it fails at high speeds (close to te speed of light) and at short distances (where quantum effects become important). But did we discard this theory? No, we just learned that it should not be applied in those limits. It still works very well at low speeds and large enough distances and we use it every day.

      So it is with Darwin's model of the tree of life. It fails when we go to the earliest life and we understand why it fails: horizontal gene transfer plays a prominent role, so genes are not carried primarily from ancestors to descendants. But higher up, the tree structure works very well. A nested hierarchy of clades works for all multicellular organisms.

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    3. Peepee's puny brain farts:

      So would that falsify Darwin's theory? What about the world swarmed with living creatures before the Cambrian?

      There were plenty of macroscopic living creatures before the Cambrian.

      How does that falsify Darwin's theory?

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    4. @oleg,

      I see you have difficulty reading between the lines. Play doe (street money) was meant as a pun since advocating Darwinism is a must to get grants!

      Your comparison with classical mechanics is an analogy logical fallacy. Classical mechanics is not an historical science and can be easily tested whereas evolution must work with old crumbling bones and fruit flies that refuse to speciate even when forced to mutate ad infinitum.

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    5. @troy, the ad hominem champion

      What about creatures with a body plan, as found in the Cambrian?

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    6. Peepster: What about creatures with a body plan, as found in the Cambrian?

      And? Do you have a point?

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    7. "Play doe (street money)"

      A doe is a female deer. Do is a note on the major musical scale. Dough is what bread and other similar baked good are before they are baked. Dough is also a slang term for money. Play-doh is a trademarked name for a clay-like children's product.

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    8. Peepee:

      What about creatures with a body plan, as found in the Cambrian?

      I just linked to a paper describing creatures with "body plans."

      Let me guess, the word "plan" in "body plan" implies an intelligent planner, right?

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    9. That would be dough, not doe. Urban dictionary is written by internet users who are not always up to snuff on spelling.

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    10. Peepster: Doe: check definition number 5!

      As said before, dough is a slang term for money. It is derived from the slang us of the word "bread" for money, which is in itself derived from the slang term for someone who earns money as a "bread-winner".

      Doe is a homonym for dough, but it is not the same word, and using it to mean "money" is incorrect even as a slang term. Further, "play-doh" is a specific item, and unrelated to either.

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    11. @abomynous,

      Je t'emmerde!

      (just google it)

      Delete
    12. Peepster: That's fine. If you want to continue to make yourself look stupid by talking about "play-doe", that's your business.

      Delete
  7. Pépé: Egnor's tedious repetition of old, tired, discredited arguments are like a catechism: good for convincing the faithful (like yourself), but unconvincing to everyone else.
    -- NA

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    1. Discredited? Unconvincing? By whom and how? Egnor is so logical and exact it scares Darwinists.

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    2. Let me rephrase that:

      Darwinists' tedious repetition of old, tired, discredited arguments are like a catechism: good for convincing the faithful (like yourself), but unconvincing to everyone else.

      Now that's a lot better fit!

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    3. Peepster: I see that you're still pooping in your pants and announcing it as a great accomplishment.

      Delete
    4. Engorge and his ilk, with their design / teleology arguments make NO predictions. All they do is criticize.

      They could for instance, predict that we will find design elements shared outside the nested hierarchies so wildly observed, such as feathers on a mammal, or mammary glands on an amphibian.

      The fact is that any predictions they could make for intelligent design are so ludicrous that even their own well funded institution don’t bother trying. They are simply driving a wedge between religion and science to protect religion from the truth.

      -KW

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    5. Anonymous: I see that you're still pooping in your pants and announcing it as a great accomplishment.

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    6. @KW,
      ...make NO predictions...

      ID predicted that junk DNA was not junk. Darwinists then said that they always new that! They need their Play Doe...

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    7. ID predicted that junk DNA was not junk.

      Actually, no, it didn't. But keep lying to yourself. It will keep your cognitive dissonance to a minimum.

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    8. “Junk DNA” is a colloquial term of little relevance. I doubt very much that anyone ever predicted that the presence of “junk DNA” is irrelevant to the functioning of a genome. Even when there are obviously broken copies of protein coding genes, the spacing of genes in the chromosome caused by the presence of the broken gene can, and often does, have an effect on the surrounding genes. The spacing and location of genes matter, so even the presence of entirely random sequences in the DNA can have an effect.

      A prediction based on an incorrect interpretation of a couuoquial term isn’t much of a prediction at all.

      -KW

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    9. @KW,
      "The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.“ The Selfish Gene, Richard Dawkins

      We are finding functions for all these useless parasites, as ID predicted. But you are free to try to maneuver around this fact as much as you want....

      I can list a few more of ID's predictions if you want, or better, just look them up on page 496 of S. Meyer's Signature in the cell.

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    10. "We are finding functions for all these useless parasites, as ID predicted."

      No you're not. You're just making up shit or repeating comforting lies you've been fed by charlitains like Meyers.

      Delete
  8. Mike,

    I think what it boils down to is quite simple really.
    Most people like to chew gum AND walk, some people prefer the simplicity of chewing OR walking.
    For some science and faith are hand in glove. For others they focus on one. In extreme cases they decry the validity of the other. These minorities have always been VERY loud compared to the vast majority of 'chewer & walkers'.
    There are folks who loath any sort of scientific inquiry, as they see it as overcomplicating matters and irrelevant, due to their very strong faith in God. They, as a result are suspicious of and hostile to science in general.For brevity's sake I will coin them theocratic due to their desire to enforce their beliefs on society as a whole.
    Then there is their opposite numbers, who feel empirical inquiry such as the scientific method is only complicated and somehow nullified by faith in God; that such faith is irrelevance 'superstition'. They are suspicious of and hostile to any sort of religious beliefs or broad faith in God or purpose. For brevity's sake I will call them technocratic due to their desire to direct society to their ends.
    These latter groups include many Atheists and even some Agnostics, while the former includes immaterialist types and 'fundamentalists'.
    Neither of the two extremes care to compliment the other in any way, and both attack the middle ground with frequency. The other 'side' (which includes the moderates) is described as idiotic or fantastical.
    They both tend to think themselves more intelligent than those of a more moderate approach, and this is exuded in the form of the arrogance and dismissive language that is often used in their polemics. Unfortunately both groups seem to be bent on political power and societal influence, and the historic record is replete with examples of their extreme influence on cultures even to this day. Ironically, both these groups also employ the very technologies and philosophies of their opposites to push their ideas. Witness the anti-science people blogging and doing TV interviews, and the anti-religious extreme employing ideas that are teleological and clearly goal oriented.

    I saw glaring evidence of this illusory divide the other day while reading a back and forth on a news article about a certain Dr Salam, who has been vilified by the Pakistani government for his Ahmadi beliefs (a 'heretical' form of Islam) even though he was a major player in the whole Higgs-Boson affair and a brilliant physicist in general who won many accolades.
    The comments raged against each other. One side blaming 'religion' and 'faith in nonsense' for all the worlds evils, the other blaming scientific study for all the worlds evils. - all in defence of Dr Salam.
    A few of us pointed out the obvious error that Dr Salam was both a scientist and a man of profound faith. We were savaged by both sides in this cartoon style debate between obviously literate adults.
    I see this kind of clash between extremes all the time on the web and in the media. Indeed their is an entire market of books, films, and websites that support one 'side' or the other.
    In reference to your excellent post, I would say Charles Darwin started off near the middle ground and fell victim to the simpleness of the 'walk only' movement. I guess the gum had lost all flavour for him, if he had ever really enjoyed chewing it at all.
    Shame.
    Personally I like to do both.

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    1. Very good comment crusadeRex.

      I think Darwin was a very good scientist because he offered ways to falsify his theory but Neo-Darwinists will have none of that. If he was alive today Darwin would surely side with Wallace and acknowledge that life needs intelligence to flourish.

      The reason I think he stopped enjoying chewing gum is the loss of his daughter that devastated him.

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    2. I think Darwin was a very good scientist because he offered ways to falsify his theory but Neo-Darwinists will have none of that.

      Actually, quite the opposite. "Neo-Darwinists" are fine with the possibility of falsifying the theory. The problem for you is that nothing has falsified it ye. Even more galling is the realization that if it ever is falsified, it will be done by actual scientists working in the field, who will replace it with something other than Egnor's Thomist drivel, and the "luminaries" at places like the Discovery Institute will be a little remembered joke of a footnote.

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    3. crus,

      Since you mentioned Abdus Salam as a man who can "walk and chew gum at the same time," I'd like to see the relevance of his faith to his science. Now, I have nothing against walking and chewing gum. My question is whether one activity requires the other.

      My feeling is that it doesn't. These activities are entirely independent. One can be an impressive scientist and a religious person or an impressive scientist and an atheist. In fact, Salam's example is quite pertinent. He was a devout Muslim. Steven Weinberg, a second among the three recipients of the 1979 Nobel Prize in physics, is a staunch atheist. They worked on the same theory and had achieved greatness. So they could walk the walk. Chewing gum was entirely optional.

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    4. Oleg,

      "I'd like to see the relevance of his faith to his science."
      The relevance is in the fact that it is possible to be both a chewer and a walker. One does not have to make the choice in order to be reasonable or to achieve greatness in ones field. In fact they can compliment each other quite nicely. The argument from the extremes is that science and faith are mutually exclusive. That is just not the truth.
      Whether it is an anti-religious atheist telling me I am a superstitious idiot, or a religious fanatic telling me I do not know god because I value scientific endeavour - It's just not true.

      "Chewing gum was entirely optional."
      Sure it was. I agree. Weinberg was not hindered by his atheism, and Salam was not hindered by his faith.

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    5. Pépé,
      Thanks, mate. I appreciate the feedback.

      "If he was alive today Darwin would surely side with Wallace and acknowledge that life needs intelligence to flourish."
      I tend to agree with you here, Pépé. In light of various discoveries and historical events, I think he probably would too.

      "The reason I think he stopped enjoying chewing gum is the loss of his daughter that devastated him."
      Yes, I have often wondered about that too. If so, it is completely understandable too.
      Such a loss is a horrible burden and can have the effect of shattering a man's faith in God, purpose, and all things sacred. It leaves one wondering 'why', and often the conclusion reached in such dark times is that there is no 'why' at all.

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  9. Teleology has explanatory power

    Teleology is an assertion, not an explanation.

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    1. Teleology is a cause. Aristotle's Four Causes include teleology.In fact, he described teleology as the "cause of causes"-- that which directs change.

      As a cause, teleology has agency.

      Considered under secondary causation (nature), teleology in nature is an impersonal cause.

      Considered under primary causation, teleology is agency by God.

      Teleology is by no means an assertion. It is an inference drawn from logic and nature.

      Rudimentary logic, and obvious nature, I should say.

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    2. No. It is an assertion, as you just demonstrated. You asserted that teleology has agency, and that it is that which directs change. Nothing in your chain of assertions is in any way explicative, all you have are unbacked assertions.

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    3. No. Teleology is a cause. It can be primary i.e. God or secondary i.e. nature.

      You don't know shit about teleology, do you Abomynus?

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    4. Peepster: Teleology is an unsupported assertion that claims to be a cause. It is a false comfort to think of teleology is a cause, primarily for the reason as explained as long ago as Bacon that a teleological cause is going to be beyond any human ability to assess.

      In short, teleology is a fairy tale told by adults to make themselves feel better, but it has no explanatory power at all.

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  10. Michael,

    'Actually, design -teleology from the perspective of a Thomistic - is a much better explanation for life than natural selection. Teleology has explanatory power, and it isn't a tautology'.

    Well, actually explanation isn't the aim of scientific theories. Being consistent with all the data that the real world throws at us is the aim that scientists aim to achieve with their scientific theories.

    'A theory that explains everything, explains nothing' is a good maxim.

    In 1857, 2 years before 'On the Origin of Species', Henry Gosse published 'Omphalos', as an attempt to reconcile the Bible and the flood of new scientific discoveries coming from all parts of the world, including new species and the evident great age of the Earth.

    So he hypothesised, in a way similar to that used by painters depicting Adam and Eve with navels (omphalos is Greek for umbilicus), God created the Earth 6,000 years ago with an apparent history it didn't have. With all the fossils. With the Earth's apparent great age.

    Explains everything, and nothing, ever, will be inconsistent with the theory. Theologigians of the time hated it, rightly, as making God into a deceiver, and that's supposed to be in the job description of Satan.

    Intelligent Design is in the same position as 'Omphalos'. It explains everything, and explains nothing. God did something, somewhere, somewhen, for completely unknown reasons and by completely unknown mechanisms.

    It's not just bad science, as your fellow co-religionist Ken Miller notes, but also bad religion, because it makes God not just a serial creator but also a serial INCOMPETENT creator, allowing species to periodically go extinct, and replacing them with other species that are often very similar.

    Actually 'teleology' is the tautology in this argument. If a species changes then it has a target it's trying to reach. It's changed, therefore the target has been reached. If its still alive, then it's a good target. If its gone extinct, then it was a bad target.

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    1. @bachfiend,
      Well, actually explanation isn't the aim of scientific theories...

      Well that is news to me!

      Being consistent with all the data that the real world throws at us is the aim that scientists aim to achieve with their scientific theories.

      So you are not a Darwinist any more?

      'A theory that explains everything, explains nothing' is a good maxim.

      Got ya!

      As for the rest of your comment, it's like Dr. Egnor says: yada yada yafa!

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    2. bach,

      Your critique of intelligent design has some merit. I see life from the perspective of teleology and a Thomist view.

      But the ID folks, regardless of philosophical merit or lack thereof, have real scientific merit.

      Intelligent design is discernible in nature. They propose that it is a better scientific explanation than unintelligent processes. They have a point.

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    3. I would like to see a program that prints METHINKSITISLIKEAWEASEL without a fitness routine!

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    4. Michael,

      ... (continued). Darwin proposed the only mechanism, natural selection, that potentially causes speciation. It isn't a tautology, as your idiotic summary of it as 'survivors survive' tries to make it.

      Individuals never survive, they all die. Individuals don't evolve. Species evolve (strictly speaking, separate isolated interbreeding populations evolve). If you'd written 'surviving species survive' then you would have got the gist of evolutionary biology.

      Darwin's other insight was that evolution was slow and gradual. Predictably, you'll want to bring up Punctuated Equilibrium, but if you go back to your thread on Maxwell, you'll find my answer. It isn't a problem for Darwin's theory.

      Common ancestry isn't based on similar morphology, but also on similar genetics. Humans have the FOXP2 protein differing in just two amino acids from our closest relative, the chimp, which differs from the mouse in a further amino acid, and Homo neanderthalis is identical with humans. Drosophila melanogaster (a fruit fly) has the same gene with a different function in foregut development). In humans, mutations in FOXP2 cause facial dyspraxia making speech difficult.

      Nature has performed your experiments on common ancestry. Oceanic islands, undisturbed by humans, tend to have few mammals (save bats and seals), snakes and amphibians, although they're perfectly suited for them, as shown by the way they overrun islands if humans are foolish enough to introduce them.

      Pre-human islands, such as the Galapagos Islands, New Zealand and the Hawaiian Islands, had ecologies dominated by birds, which consisted of a large number of species filling every niche available.

      There's two possibilities. Either God decided for unknown reasons to put only birds on oceanic islands (and, strangely, decided to make New Zealand birds similar to Australian ones and Galapagos birds similar to South American ones). Or a small number of birds managed to reach oceanic islands, and then proceeded to evolve in an adaptive radiation to fill all the ecological niches.

      One scenario (evolution) makes predictions. The other doesn't. The God hypothesis just assumes that similarities are common design as a given. Evolution makes testable predictions. Galapagos birds will be more similar, genetically, to the South American equivalents, than to African or Australian ones, and more similar between themselves.

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    5. Michael,

      I was waiting for you to comment on my continuation. However, since no one knows what ID actually is (and Stephen Meyer, an ID proponent, and Paul Nelson, a young earth creationist, managed to cooperate in making an ID science pornography film 'Darwin's Dilemma' on the Cambrian radiation 540 MYA - how's that for cognitive dissonance on the part of Paul Nelson?), your perspective of Thomistic philosophy and teleology fits ID.

      If it doesn't, then you need to expand on your beliefs, giving mechanisms, and explaining how you think the world got to its present state from the beginning 4.55 billion years. Not in detail. Just a very broad outline.

      Incidentally, 'Darwin's Dilemma' used exactly the same analogy of automobile manufacture as an example of common design. Did you get it from that source?

      Also your article on the intelligent design/Discovery Institute website regarding brain tumours, with its mutations and increased 'complexity' (which no one has provided a way of quantifying), as never leading to increased function - cognition etc - is just stupid.

      For a start, almost all brain tumours are glial, the supporting cells, and rarely neuronal. The high grade tumours, save tumours such as medulloblastomas and neuroblastomas, are glial. Glial cells do moderate brain function, but in a structured arrangement of cells. A haphazard arrangement of uncontrolled proliferating tumour cells won't be effectively structured.

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    6. The point about tumors is fairly straightforward.

      A tumor is a great model of a Darwinian process. Billions of cells, Robust variation, rapid division, natural selection like there's no tomorrow (sorry-pun).

      Indeed, surviving tumor cells do survive, at least until the host dies.

      But tumor cells degenerate with time (eg glioblastoma). They don't evolve more elegant glia or neurons. They evolve monsters.

      Random variation and natural selection is a destructive process. It cannot account for the beautiful life we observe.

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    7. bach- your question about my own views on evolution is a good one. I'll try to post on it soon.

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    8. bach,

      [Darwin proposed the only mechanism, natural selection, that potentially causes speciation. It isn't a tautology, as your idiotic summary of it as 'survivors survive' tries to make it.]

      Natural selection isn't a mechanism, unless you consider it teleological.

      Natural selection can mean three things (vide supra)

      1) Survivors survive.
      2) Acasual statistical observation
      3) Casual mechanism.

      1 is tautological, 2 is not a mechanism (but good science), and 3 is, on close inspection, teleological, in which case 'natural selection" is superfluous.

      My own view is that the general scheme of evolution as currently understood is right, more or less. But it is a teleological process-- there are forms to which organisms evolve.

      Convergent evolution is a particularly obvious example of this.

      "random variation and natural selection" misses the important point.

      Teleology is the cause of causes, and the cause of evolution.

      The extent to which one can make the inference to God from teleology is a fair question- not all scholastic philosophers, including devout Christians, agree that teleology gets you to God.

      But teleology is real, and nature cannot be understood without it.

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    9. Teleology is the cause of causes, and the cause of evolution.

      Teleology is the definition of a "just-so" story.

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    10. Michael,

      You're becoming more incoherent. It isn't 'random variation'. It's 'natural variation'. Variation within populations isn't random. It's determined by the genes in the population. Mutations within a gene may or may not have an effect - the mutation within the gene may be neutral or near neutral - but there has to be the gene (or rather the gene variant, the allele). The gene has to be in the population - which isn't random - for a mutation to have an effect.

      And natural selection is a non-teleological mechanism. It's not 'survivors survive', an acausal statistical observation or a causal teleological mechanism. The central point of natural selection is that organisms have many more offspring than can survive without irreparably damaging its environment and starving itself to death.

      Not all of its offspring can or will survive, and some of non-survival is genetic, due to the specific combination of specific genes in the parents. And some of it is just blind bad luck. A young emperor penguin may be fortunate in inheriting the optimal combination of genes from its parents, making it the fastest, strongest, most clever penguin around, but if it chooses by ill luck to dive into the Southern Ocean for the first time in front of the mouth of a hiding hungry leopard seal, then it's gone.

      Nature doesn't care about individuals - there's always others around. It also doesn't care about species, since about 99.9% of species have gone extinct. That might disturb your sense of personal and species worth, thinking that you and humans are special in the eyes of 'God', but you're deluded.

      I suppose CrusadeRex will pop in one of his usual comments about me being a nihilist. I'm not. I'm an optimist. Humans are intelligent social animals, and as such, we're deeply concerned with what happens to other humans, ones we don't even know.

      Convergent evolution doesn't indicate teleology. All it's means that non-related species develop similar structures as a result of different problems in their environment. Bat wings and bird wings are convergent on flight, but they probably arose via different routes. Birds probably arose via small feathered theropods jumping and flapping their forelimbs attempting to catch flying insects. Bats probably arose from small basal rodent-like mammals falling part gliding from trees.

      There's no teleological target of flight being a very good idea in the far distant future. The dodo on Mauritius in the 17th century couldn't suddenly decide that it would be a very good idea to regain active flight with the approach of bored English and Dutch sailors looking for 'sport'.

      You're just wrong. Natural variation and natural selection do generate beauty in nature (although beauty is in the eyes of the beholder - is a spider beautiful? Many people don't. I personally think they are, and I love to study jumping spiders close up, if I'm fortunate enough to have one run across my hand - and to look into its 8 eyes with my two, and to wonder what it sees).

      You still haven't refuted the point that your beliefs fall in the ID spectrum, which includes everything from Paul Nelson's YEC to Michael Behe's acceptance of virtually all evolutionary biology, save some things, such as the bacterial flagellum and chloroquine resistance in malaria parasites (so God can kill humans more efficiently?)

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    11. Bach,

      "I suppose CrusadeRex will pop in one of his usual comments about me being a nihilist. I'm not. I'm an optimist. Humans are intelligent social animals, and as such, we're deeply concerned with what happens to other humans, ones we don't even know."

      Why should I bother when you make such an excellent case all by yourself over weeks and weeks of commentary?
      I am glad you have embraced some sort of ideology that permits compassion and caring as reasonable emotions. No need for me to refute that, whatever you call it. If my critiques, or those of others have reinforced this in your mind - this is a good thing.
      Baby steps.

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  11. Let's look at the quibbles Egnor has with my comment.

    Egnor: Darwin didn't predict that "clades form a nested hierarchy", for two reasons: 1) A clade is a nested hierarchy, as a matter of definition.

    Darwin of course didn't use the term clade—it was only invented in 1958. Darwin's original formulation of the tree-of-life hypothesis is too long to cite, but it can be found here. It is not a trivially true statement. Different species could, in principle, have independent origins.

    Today's formulation is not a trivially true statement, either. Although clades form a hierarchy by definition, the nontrivial part of the formulation is that (groups of) organisms form clades. It's just another way of saying that there is a tree of life.

    Egnor: 2) The categorization of living things into nested hierarchies is 2000 years old, and the modern system of taxonomy incorporating nested hierarchies was developed a century before Darwin's birth. Darwin did not "predict" the system of taxonomy based on nested hierarchies. He offered an explanation for it. An atheist explanation for it.

    This point is simply wrong. Darwin's tree of life was not merely a just-so explanation of an older taxonomic system, say, Linnaean. He proposed an entirely new way to classify taxa. One that could be potentially wrong and thus open to falsification. That set it apart from all of the previous taxonomic systems, from Aristotelean to Linnaean. Let me explain.

    All of the previous taxonomic systems were based on subjective choices of their authors. They grouped plants and animals by certain characteristics suitably chosen by the authors. Aristotle's classification is different from Linnaeus's, but neither is wrong in any objective sense. They subjectively draw the lines and then placed organisms within that scheme. The only type of error they could make would be to misclassify an organism within their own personal scheme. The artificial nature of this classification is responsible for the existence of wastebasket taxa—organisms that didn't fit anywhere else.

    Thanks to Darwin, we now have an entirely different, objective (at least in principle) approach to taxonomy. There are no organized groups as in previous taxonomies: no kingdoms, phyla, or classes. Just a tree of species. Whenever two species diverge from each other, the tree branches out. The resulting tree has none of the neatness of the Linnaean taxonomy; in fact, it is a big mess (and that figure is just a tiny portion of it). The advantage of the new scheme, however, is that it gives an objective way to determine the degree of relatedness between taxa, for the simple reason that it is based on ancestral relations!

    The objectivity comes at a price: it is not an easy task to figure out ancestral relationships between species, not in the least because the ancestors are dead. Fortunately, there are ways to obtain that information indirectly, e.g. through genetic analysis.

    It's true that Linnaean taxonomy agrees, to a considerable extent, with modern phylogenies. Particularly when it comes to relatively closely related taxa. That means that the subjective choices made by Linnaeus were sensible. But it never occurred to him that birds were relatives of reptiles and both groups were related to mammals. He placed all three in separate classes.

    So no, Darwin didn't just put some gloss on Linnaean taxonomy. He changed the way biologists classify taxa entirely.

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    Replies
    1. oleg:

      There's no question that Darwin based his tree on putative common ancestry, unlike trees based on morphology.

      But most inferences to common ancestry are based on morphology (and now on genetics), which inherently form the basis for phyletic hierarchies without the need for invocation of common ancestry.

      Darwinists infer common ancestry primarily from morphological and genetic hierarchies. It is circular reasoning to then assert that the hierarchies thus generated transcend morphology and genetics.

      Again, what Darwin offered that was somewhat original was the assertion that hierarchy was the consequence of common descent, not common form/design, and that such evolution was the consequence of RM + NS.

      You overstate his actual contributions.

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    2. Egnor: Again, what Darwin offered that was somewhat original was the assertion that hierarchy was the consequence of common descent, not common form/design, and that such evolution was the consequence of RM + NS.

      Hah, another concession!

      It is in fact this hypothesis that justifies the reliance on morphology and genetics to build phylogenies. Evolution through heritable variation means continuous changes are responsible for the branchings of the tree. Thus closely related taxa have much in common both in the phenotype and in the genotype. This is why we infer that the smaller the changes, the more closely related the two taxons are. Darwin's theory requires that continuity. And that's precisely what paleontologists are constantly looking for: transitional forms between taxa, both extant and extinct. And finding them.

      Egnor: Darwinists infer common ancestry primarily from morphological and genetic hierarchies. It is circular reasoning to then assert that the hierarchies thus generated transcend morphology and genetics.

      It's not circular reasoning, it's how scientific theories are tested. (How many times do we need to go through them?) There is no scientific theory that is not circular in this sense. It's not a logical proof. You make predictions on the basis of your theory and test them empirically. That part—empirical testing—is what makes science non-circular. And you somehow keep missing that. Darwin's theory could be disproven by empirical findings, not by pure logic as you are trying to.

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    3. Oleg,

      Too right. As Victor Stenger noted in his latest book 'the Folly of Faith', a scientific theory is a model of reality, not reality itself. All we can say is that the model is consistent with all the data that the real world throws at us. Models can be disproved by brute ugly facts, one will do.

      Michael's approach explains everything and explains nothing. Everything can be made to be consistent with his worldview, and nothing will conflict with it, ever. And he makes the unsupported unproven assertion that there's an invisible God who cares deeply about humans

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  12. Egnor: Random variation and natural selection is a destructive process.

    It is destructive in the sense that organisms die. They die sooner or later. However, some—those that are better fit to the environment—tend to leave more offspring than their less fit counterparts. Fitness can thus improve as time goes on.

    Egnor: It cannot account for the beautiful life we observe.

    Why not? You have made no argument here, just an assertion.

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    Replies
    1. Cancer is random mutation and natural selection on crack.

      It is purely destructive.

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    2. One problem with this little theory: variation produced by cancer is not heritable.

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    3. Michael,

      No. Cancer isn't random mutation and natural selection. Tumors arise, if they arise as a result of mutations, as a result of mutations within non-random genes, tumor suppressing genes (turning them off) or tumor enhancing genes (up regulating the genes). These genes have other more important functions within development, and tumors are just a byproduct.

      The type of tumor can often be predicted, just by knowing the genetic abnormality, without looking at the tumor under the microscope. The genetic abnormality is that specific and non random.

      Tumors often progress and accumulate increasing numbers of mutations, becoming more bizarre. It's easy to get distracted and to regard the bizarre giant tumor cells within the tumor as being the bad actors within the tumor and the survivors in a process of 'natural selection' within the tumors, but usually they're lethally damaged, can't divide (explaining their bizarre form) and are destined to die. And to ignore the background of more normal appearing tumor cells with the specific non random mutations which are going to kill the patient.

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    4. [One problem with this little theory: variation produced by cancer is not heritable.]

      Of course it is heritable-- by the daughter cells following mitosis. In the cancer analogy, the cells are the individuals, and evolution occurs on the population of cells-- on the tumor.

      The improvements/deterioration are in the individual cells. As I noted, the cells invariably become more dysfunctional.

      I can't believe you are so clueless about biology that you didn't understand the analogy.

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    5. OK, maybe I'm clueless (IANAB), or maybe you did not convey your analogy sufficiently well.

      But let's take this analogy and see whether it makes sense. Let's see if there is selection pressure. Would cancers cell get any advantage (and thus procreate faster) if they turned into neurons?

      And furthermore, even if some small advantage were conveyed, the cells die along with the organism. Cells in the next organism will have to start from scratch. This cancer model of evolution lacks cumulative selection (something I have already pointed out).

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  13. Michael,

    And I can't believe that your are so clueless about oncology that you make the analogy.

    Daughter tumor cells don't inherit anything from the original tumor cells. They are clones of the original tumor cells. If they acquire mutations, then they generally harm themselves rather than the host.

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  14. Late to the party-

    Darwin's tree was groups subordinate to groups. Nested hierarchies require groups within groups.

    Cladograms are semi-nested. Phylogenetic trees are non-nested. Only Linnean classification is a nested hierarchy.

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  15. What could possibly be the difference between "within" and "subordinate to"? Is it like, "giraffes are subordinate to lions because lions are the king of the jungle?"

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