Friday, January 10, 2014

Clergy discuss the relationship between science and religion

The Clergy Letter Project is sponsoring the 9th annual "Evolution Weekend" on February 7-0 2014. This is a weekend where clergy talk to their congregations about science and evolution. Here's how they describe the event ...
Evolution Weekend is an opportunity for serious discussion and reflection on the relationship between religion and science. An ongoing goal has been to elevate the quality of the discussion on this critical topic, and to show that religion and science are not adversaries. Rather, they look at the natural world from quite different perspectives and ask, and answer, different questions.
Maybe it's just me, but I thought that "serious discussion and reflection" means that all aspects of the conflict between science and religion would be considered. This includes the possibility that the conflict is very real and cannot be accommodated.

I was wrong. If you are a member of the Clergy Letter Project your mind is already made up.
Because religion and science use different methodologies to understand the world, and because religion and science ask very different questions, there is no reason to view them in conflict. One important facet of Evolution Weekend 2014, therefore, is to explore the questions each ask and to examine the different ways of knowing embodied in each.
There's not going to be any serious discussion about different ways of knowing and which ones are successful.

One of the most important lessons of science is that life evolved from simple primitive organisms over a period of at least three billion years. The history of life can be fully explained by natural causes without any need for miracles or divine intervention. We have learned that the evolution of life on this insignificant planet, in an ordinary galaxy, in a vast universe, has no purpose or goal.

There aren't many religions that can accommodate those facts.


[Hat Tip: Panda's Thumb]

202 comments :

  1. Larry said:

    "The history of life can be fully explained by natural causes without any need for miracles or divine intervention. ...There aren't many religions that can accommodate those facts."

    Consider this fact, Larry: In one of the atoms in one of the bacteria in your gut, one electron is orbiting a nucleus in accordance with an partial differential equation that describes the quantum state of the electron as it changes with time (Schrodinger's equation).

    Could you explain to me the atheist "accomodation" for directedness in each atom of each living thing in accordance with high-level mathematics?

    Or did shit happen and survivors survive?

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    1. Brave Sir Robin arrives, after so recently writing a post about me at ENV-- a blog that permits no comments!

      Brave, brave, brave Sir Robin! He ran away and chickened out.

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    2. Hey Smegnor,

      Could you explain to me the atheist "accomodation" for directedness in each atom of each living thing in accordance with high-level mathematics?

      No. You understand long division, much less Schrodinger's equation.

      Could you please explain to me the theist "accomodation" for directedness in each atom of each living thing in accordance with high-level mathematics, and how that is "explained" by an irrational, supernatural, baby-murdering war deity, who cannot be defined mathematically?

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    3. Diogenes:

      I cross-posted at my own blog. Comment away.

      Delete
    4. Allow me to answer on behalf of mregnor: A certain variation of thomist philosophical gibberish which effectively means there are no forces or laws of physics or nature, that all and everything that happens anywhere in any way is the direct will of god and his "ordering" power over "creation".

      Or also known as "Goddidit". Made up shit about made up shit, which gives mregnor comfort. And wet dreams about what he gets to tell other people about how they should live their (sex)lives.

      Case closed.

      Delete
  2. "Because religion and science use different methodologies to understand the world. . . ."

    Yes, however, religion's methodologies are woo.

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  3. I would be very interested in understanding the "methodology" and "different way of knowing" used by religion to generate reliable knowledge. Can anyone explain it? Does it involve the technique of exproctodiction?

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    1. exproctodiction

      I'm stealing that. Harshman would know-- expert in comparative anatomy...

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    2. Method used by religion to generate reliable knowledge: infer that nature is created by a rational God, in whose Image we are created, which permits us to comprehend His design, and Who wants us to understand His creation.

      In other words, use the method used by all of the great scientists of the Scientific Enlightenment-- Copernicus, Galileo, Newton, Kepler, etc etc.

      The Scientific Enlightenment was a Christian project, ace. The scientific method was invented by Roger Bacon OFM (a Franciscan friar) in the 13th century. All scientific teaching and research through the Scientific Enlightenment was conducted at Christian universities.

      How about listing the atheists who participated in the rise of science. Care to describe the scientific advances in atheist states over the past 200 years (there have been 20 or so atheist nations-- revolutionary France, the Soviet Union, Communist China, Khmer Rouge Cambodia, North Korea, the Soviet-occupied nations of Eastern Europe).

      There's Christian science and there's atheist science. Compare and contrast.

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    3. Haha oh man, do you guys ever come up with something new? This revisionist bullshit has been debunked so many times you really ought to play another tune at this stage. It's even become so stale only the really fundamentalist and conservative religious believers buy into this crap anymore. Seriously? How do you nutbags come up with this shit? Stuck in your rightwing echo-chamber it's like an evolving autocatalytic network of conservative religious propaganda that just spews out what is essentially same unnuanced noise you all want to hear, but in ever newer and more ridiculous, martyr-syndrome infested ways. The fear and loathing of the materialistsoviocommunisticfeministdarwinistoatheistic superbadguy is spontaneously catalyzing ever more grotesque, fevered and halluscinatory historical revisionist bullshit about the horrors of gatling-gun-rate late-term-teen-pregnancy-abortionfactory eugenicist atheonazis. Fears and strawmen that play on fears and strawmen, spawning ever more volitional ignorance, fear, loathing and strawmanning.

      For starters: The scientific method was practiced all the way back in ancient greece. Science wasn't invented in the 13th century, what actually happened leading up to and during the enlightenment was that most alternative methodologies simply got outcompeted because they didn't yield useful results to the extend the scientific method did. Which, you have to admit, is weird if supernaturalism is true.

      Obvious conclusion is obvious.

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    4. The ten countries with the largest percentage of Christians (and at least 10 million of them) are:

      Greece
      Ecuador
      Venezuela
      Colombia
      Zambia
      Romania
      Guatemala
      Poland
      the Congo
      Mexico

      The contribution of Greece to the development of science and civilisation had its climax in pre-Christian times. As for the rest... Proud as I am of my own country, I'd gladly swap a few percent of Christianity for a few Nobel prizes in science.

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    5. And mregnor defines "exproctodiction" by example. Nice.

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    6. Method used by religion to generate reliable knowledge: infer that nature is created by a rational God, in whose Image we are created, which permits us to comprehend His design, and Who wants us to understand His creation.

      I was going to reply to the above comment, then realized that letting his comment stand on its own is quite sufficient. Sigh.

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    7. infer. verb. deduce or conclude (information) from evidence and reasoning rather than from explicit statements.

      Can someone give Egnor a dictionary?

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    8. @Konrad: In his world, conclusions are predetermined. We all know that, but it's nice of Egnor to illustrate it with an example.

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    9. mregnor:

      Method used by religion to generate reliable knowledge: infer that nature is created by a rational God, in whose Image we are created, which permits us to comprehend His design, and Who wants us to understand His creation.

      Exactly so. Which explains how Christian scientists were able to read the Bible, then go out and find overwhelming evidence that all life was created <10,000 years ago, that the Sun revolves around the Earth, that the Earth suffered a global flood resulting in all terrestrial animals going through a severe population bottleneck at the same time a few thousand years ago, and so on.

      Right Egnor?

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  4. If I didn't know Quest is away in the middle of nowhere and no access to internet, I would say mregnor sounds a bit like him.

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    1. If I didn't know Quest is away in the middle of nowhere and no access to internet,

      I wouldn't bet on it.

      I would say mregnor sounds a bit like him.

      He's not the only one.

      Anyway, most of us know quite well who Dr. Egnor is. He's a very famous IDiot:

      http://americanloons.blogspot.ca/2010/12/119-michael-egnor.html

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  5. Religion is a different way of knowing, perfectly expressed by this Jesus and Mo cartoon. "That's what gives religion it's edge!"

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    1. Religion has an edge alright...no shortage of people willing to shovel money its way.

      Its a well-known fact that almost all scientists participate in a liberal conspiracy to hide the facts that evolution is untrue and that the earth is not warming. If we could only turn this conspiracy toward telling "the people" that what they really hope is true is actually true, scientific research would never experience funding problems again.

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  6. Diogens, You are not a stupid guy. I can tell it. IF you are not J. Coyne, I doubt THAT now but agency says its possible I would like to talk to you. You are a really smart guy in your stuff. I'm not going to convert you; you know it and I know it. So? What are we goingto talk about

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  7. The history of life can be fully explained by natural causes without any need for miracles or divine intervention.

    Can it? Can someone explain it?

    Can science explain how univers could have come into being?
    Can science explain how life could have originated?
    Can science demonstrate mathematically what the process of unguided evolution can do?
    Can science demonstrate experimentally how life could have evolved by known mechanisms?

    Evolutionary biochemist Franklin Harold wrote, “We must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.”

    James Tour:
    "Although most scientists leave few stones unturned in their quest to discern mechanisms before wholeheartedly accepting them, when it comes to the often gross extrapolations between observations and conclusions on macroevolution, scientists, it seems to me, permit unhealthy leeway. When hearing such extrapolations in the academy, when will we cry out, “The emperor has no clothes!”?"

    Furthermore, when I, a non-conformist, ask proponents for clarification, they get flustered in public and confessional in private wherein they sheepishly confess that they really don’t understand either. Well, that is all I am saying: I do not understand. But I am saying it publicly as opposed to privately. Does anyone understand the chemical details behind macroevolution? If so, I would like to sit with that person and be taught, so I invite them to meet with me. Lunch will be my treat. Until then, I will maintain that no chemist understands, hence we are collectively bewildered.

    It is totally unacceptable scientists of this caliber not to understand when science claims "evolution is a fact". What are those facts that prove that is a fact? Evolution by undirected processes.

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    1. The emphasis in my statement is on the fact that we have no need for miracles in order to understand the history of life. That does not mean that we have complete and absolute proof of every single step, including the origin of life. It means that we have reasonable scientific explanations that are fully consistent with everything we now about science.

      If you know of something that is so completely mysterious that we are forced to invoke divine intervention then please share it with us.

      Does anyone understand the chemical details behind macroevolution? If so, I would like to sit with that person and be taught, so I invite them to meet with me. Lunch will be my treat. Until then, I will maintain that no chemist understands, hence we are collectively bewildered.

      What you mean to say is that YOU don't understand evolution so you are assuming that professional scientists who spend their life studying evolutionary biology must also be as bewildered as you are.

      It is totally unacceptable scientists of this caliber not to understand when science claims "evolution is a fact".

      It is totally unacceptable for anyone with a brain to engage in this debate without understanding what scientists mean when they say evolution is a fact. [Evolution Is a Fact] [Evolution Is a Fact and a Theory]


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    2. Can it? Can someone explain it?
      Yes.

      Can science explain how univers could have come into being?
      We don't know that it did. But maybe we can't explain it, so what? Making up mythology(goddidit) to satisfy a desire for answers isn't an "explanation".

      Can science explain how life could have originated?
      We don't know that at the moment, that does not entail we should give up and declare "goddidit". As with many unknowns in science, the default answer isn't "goddunnit" until the day science demonstrates it. The default answer is "we don't know".

      Can science demonstrate mathematically what the process of unguided evolution can do?
      Yes. The scientific litterature is rich with mathematical models of evolution. I suggest you spend a little time on google scholar or pubmed, or go and ask actual biologists and mathematicians who are experts in the subject.

      Can science demonstrate experimentally how life could have evolved by known mechanisms?
      Yes. All the mechanisms of evolution used to explain the patterns of biodiversity, comparative genetics and the fossil record, are observed facts.

      All your silly quotemines can be publicly checked and most are available on the talkorigins archive of creationist quotemines. Quotemining is inherently dishonest and the perpetrators of quotemining should ask themselves the question: If my fundamentalist religious doctrine is really true, why do I have to lie, misrepresent other peoples opinions, take their statements out of context without supplying a full context or even a reference, and ignore and cover up the facts, to support it?

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    3. Can science explain how universe could have come into being?

      The best explanation as we sit here today is that the universe came into existence as a result of an instability in the quantum vacuum.

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    4. Can science demonstrate mathematically what the process of unguided evolution can do?

      There is an entire branch of applied mathematics called evolutionary/genetic algorithms that is applied to certain types of non-linear optimization problems. The number of technical papers on this subject runs into the thousands.

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    5. Colnago80,

      Genetic algorithms does not mimic the way natural selection works since they are goal oriented. GAs are good at iterating algorithms until they converge to pre-set criteria and making the locally optimal choice at each stage with the hope of finding a global optimum i.e. not really the mindless process without goal that evolution is made out to be.

      Dawkins have popularized the idea of "climbing mount improbable" by small incremental steps. In “The Evolutionary Accessibility of New Enzymes Functions” BIO-Complexity Vol 2011, Ann Gauger and Douglas Axe examined the members of a large enzyme superfamily, the PLP-dependent transferases, to find a pair with distinct reaction chemistries and high structural similarity and then set out to convert one of these enzymes to perform the metabolic function of the other. The result from the study shows that no gradual pathway of incremental improvements that can be selected for exists even between two structurally similar enzymes and therefore co-opting one to perform the function of the other by means of evolution is highly unlikely in the timeframe available.

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    6. Colonago80 wrote: "The best explanation as we sit here today is that the universe came into existence as a result of an instability in the quantum vacuum."

      In order to believe that the universe created itself from nothing you must believe that the fundamental forces exists independent of matter. How else would quantum vacuum fluctuation lead to the Big Bang?

      Delete
    7. “The Evolutionary Accessibility of New Enzymes Functions”

      Andy, that "study" is a pathetic example of cargo cult science. It may look like real science to an untrained eye only.

      Delete
    8. Genetic algorithms does not mimic the way natural selection works since they are goal oriented.
      Yes they do. Genetic algorithms "fit" a mutating "organism" to an "environment" over successive "generations". That's exactly what happens in evolution by natural selection. You can easily include a process similar to drift too with random sampling.

      This is a typical, malinformed ID talking point, to try to argue that GA aren't good evidence or give good insight into how evolution works, by trying to claim that GA somehow "smuggle in goals/information". That is analogous to claiming that gravity smuggles in goals when natural selection changes organisms fins into legs to walk on. Or that the intrinsic hydrodynamic drag in an aquatic environment "smuggles in" the "goal" of making fish and whales torpedoshaped.

      GA's don't smuggle anything in and don't work towards any particular goal any more than the processes of nature ensures the overarching "goal" of organisms are reproductive success.

      That typical ID talking-point crap has been debunked so many times you should be ashamed of bringing it up.

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    9. “The Evolutionary Accessibility of New Enzymes Functions” Axe et al.
      They don't actually test the evolutionary hypothesis in this pseudo-scientific paper, they test a strawman of their own dreams.

      They change one extant enzyme directly into another but very distantly related one, mutation by mutation, and find that introducing mutations from one of them directly into the other breaks enzyme function.

      This is not what evolution postulates happened, instead they should be using Ancestral Sequence Reconstruction, to resurrect common ancestral states, and test them for function. They didn't do that, they test a strawman.

      Here's a nice little picture I made to show what they did wrong and why their work is irrelevant: http://i.imgur.com/od3V0wt.jpg

      They should have used Ancestral sequence reconstruction, but didn't.

      See, this is what the higher-ups in the ID movement do. Present false information to the uninformed, who are all too keen to believe in their crap and don't bother checking with actual evolutionary biologists.

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    10. More on Ancestral sequence reconstruction:
      RESURRECTING ANCIENT GENES: EXPERIMENTAL NALYSIS OF EXTINCT MOLECULES

      Ancestral Sequence Reconstruction: methods and applications

      You won't find creationists or ID proponents doing ASR in their "tests", EVER. They only test and argue against strawmen, they ignore modern phylogenetic methods where at all possible. They sell lies to the gullible and they know it.

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    11. @Andy Wilberforce:

      Possibly a more concise explanation of why Axe's "study" is such a farce:

      Suppose you encountered someone who claimed to be a distant cousin of yours. How would you test his claim? One method would be to sequence both of your genomes and then compare them to the genome of a person you would share as an ancestor.

      However, the method Axe would use, if he follows the example of his paper, would be this: He would see if one of the person's children is an identical clone to yourself. If that isn't the case, he would conclude there is no way the two of you could be related.

      And you wonder why they're called IDiots?

      It should be pointed out that, unlike most IDiots, Axe is actually a qualified and apparently competent biochemist. So how could he make such an obvious, schoolboy error? Is it possible he knows it is an error, and his only goal is to dupe people like yourself into believing he actually has scientific evidence for the existence of God? Does someone who is trying to play you for a fool deserve your respect, Andy?

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    12. Rumraket, I hate referring to Wikipedia, but it's so accessible that sometimes the temptation is just too strong. This is one of those rare occasions...
      This is what it says about GAs "In the computer science field of artificial intelligence, a genetic algorithm (GA) is a search heuristic that mimics the process of natural selection, if natural selection was goal-oriented."
      And yes, I read it before I posted. We use GAs at work for our design, so I have a pretty good idea what they can and cannot do, but it doesn't hurt to check how they are used in different fields.

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    13. Andy, an anonymous user revised the Wikipedia entry just the other day by inserting the phrase "if natural selection was goal-oriented". The addition is slightly ungrammatical, which is the hallmark of many IDiots, and since the same person also tried to vandalise the entry "Natural selection" on 10th January, his IDiocy is beyond doubt. Was it you, Andy? Or is it just a miraculos coincidence?

      http://en.wikipedia.org/w/index.php?title=Genetic_algorithm&diff=590066936&oldid=589887792

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    14. LOOOOL. Good catch Piotr. How UTTERLY pathetic Andy.

      If your fundamentalist creationist doctrine is really true, why do you have to LIE to support it? Aren't you propagandizing on behalf of a religious belief that explicitly prohibits lying by divine command?

      Delete
    15. The edit was done by IP 24.62.24.89:

      Owned by Comcast Cable Communications Holdings, Inc RW2-NORTHEAST-1 (NET-24-60-0-0-1) 24.60.0.0 - 24.63.255.255
      Comcast Cable Communications Holdings, Inc NEW-ENGLAND-5 (NET-24-62-0-0-1) 24.62.0.0 - 24.63.255.255

      Here are some recent Wikipedia changes made by that IP:

      12:57, 10 January 2014 (diff | hist) . . (+118)‎ . . Natural selection ‎
      12:54, 10 January 2014 (diff | hist) . . (+40)‎ . . Genetic algorithm ‎

      Is that you Andy ?

      IP locator shows that this IP is located somewhere in the northeastern US area (Connecticut/Massachusetts) area.

      I'm sure Larry could confirm what IP Andy posts from ...

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    16. @Rumraket: Obviously ASR would be a lot less wrong than direct interpolation, but in most cases it still wouldn't be reliable enough - even for the ASR sequences one doesn't necessarily expect them to be biologically viable, there's just too much uncertainty in the reconstruction. So even if they did it that way one still couldn't conclude anything from the study.

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    17. Well if they decide to do ASR directly on two(or actuall three, because they'd need at least 3 to be able to do ASR) such distantly related proteins I agree, But that in itself would be a flawed way to do the study, they'd need many, many different versions of the protein distributed through a significant fraction of life.

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    18. By the way, the attempt to edit the article on "Natural selection" was so inept that ClueBot-NG, Wikipedia's anti-vandal algorithm, detected it and undid the change automatically. AI scores a point against ID.

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    19. In the Natural Selection edit on Wikipedia, the following was added:

      "What Darwin called natural selection is actually a process of elimination." Ernst Mayr page 117* "What Evolution Is".

      I think a better quote from Ernst Mayr might have been:

      Elimination does not have the "purpose" or the "teleological goal" of producing adaptation; rather, adaptation is a by-product of the process of elimination.

      What do you think Andy ?

      * On page 144 of the Phoenix paperback edition.

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    20. Hey, isn't Joe Gallien a Massachusetts man? Just the day before the vandal attack (9 Jan) he was making a lot of the very same quote from Mayr on his blog. LOL, the plot thickens. Andy, are you Joe's sockpuppet or only a close collaborator?

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    21. I'm sure the Wikipedia "editor" was Joe G himself. I have even found out what makes him think genetic algorithms are goal-oriented: he believes the Dawkins Weasel is "a perfect example" of a genetic algorithm!

      http://intelligentreasoning.blogspot.com/2014/01/genetic-algorithms-vs-darwinian.html

      http://intelligentreasoning.blogspot.com/2014/01/evotards-proudly-ignorant-of-genetic.html

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    22. Well that was a hoot.

      If Andy is not the perpetrator it will give him a chance to play the injured innocent drama queen and if he is he can take comfort in the fact that it would not be possible to have a lower opinion of him than the one he has worked so hard at earning.

      Good work Andy and keep on lying for baby Jebus.

      One thing I have noticed in the Joe Galliens, mregnors, LouiseGs and other bottom feeding creotards and IDiots that infest the intertubes is that they seem to have cornered the market on vicious and stupid, all rolled up into one smug, narcissistic and self entitled package.

      Which leads me to believe that Andy is not a sockpuppet for Joe G, while he is certainly qualified on the stupid part he appears to be a gentle soul at heart.

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    23. Well, Rasmussen has totally eviscerated Wilberforce's nonsensical claims about evolutionary/genetic algorithms so I need not respond to his comment.

      However, relative to his comment on the quantum vacuum, it shows total ignorance of the subject matter. The quantum vacuum consists of virtual particles, e.g. protons, neutrons, electrons, and their anti-particles etc. that come into existence for very brief time intervals and then mutually annihilate each other. However, occasionally, the number of particles exceeds the number of anti-particles due to CP violation and the excess particles are what form the universe. If one takes the strings hypothesis seriously, this has happened multiple times, each occasion producing another universe, vis the multiverse hypothesis.

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    24. Colnago80, the question was not the reason for the quantum vacuum fluctuation, rather why it would lead up to the Big Bang. Let's see what Hawking has to say on the subject. : "Because there is a law such as gravity, the universe can and will create itself from nothing. Spontaneous creation is the reason there is something rather than nothing, why the universe exists, why we exist."

      Rumraket, since you have to set the criteria for the fitness evaluation you are effectively introducing teleology into the equation. Adaptedness in nature is thought to be a posteriori result rather than the priori goal-seeking used in GAs.

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    25. Umm, Andy? I think there are other, more serious questions for you to be addressing at the moment, dude. (See above.)

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    26. Konrad & Rumraket,
      a quote from Ann Gauger concerning your comments above: "The problem with these (protein evolution) scenarios is that they require proteins to be remarkably tolerant of sequence rearrangements and insertions, or remarkably easy to shift to new functions, or remarkably different at the dawn of life from what they are now"

      - See more at: http://www.evolutionnews.org/2013/08/protein_evoluti075091.html#sthash.6xTjeQmG.dpuf

      These requirements clearly are mutually exclusive. A more personal reflection is that much of the argumentation seem to be aimed at shielding the prevailing hypotheses from testing and evaluation. This is not unique to protein evolution, I have had exactly the same kind of response when discussing e.g. paleontology.

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    27. Andy, can you explain that remarkable coincidence -- the Wikipedia text being faked just in time to provide you with a "reference"?

      Delete
    28. Andy, you are dodging a pretty important question. It's dishonest and it's a huge waste of our time to be tracing IP addresses of Wikipedia edits. This is not arguing in good faith. IMHO this kind of "Edit the Wikipedia page, then cite the page I just edited" is grounds for banning.

      Piotr and Oberski have presented remarkable evidence that Joe "Security Clearance" Gallien was the one responsible for the edits to the Wikipedia page. I am persuaded that it was Joe G who edited the Wikipedia page.

      A very short time after that, you just happen to cite that Wikipedia page.

      Blind chance or intelligent design?

      I doubt Andy is Joe Gallien, because Gallien cannot resist the urge to engage in threats of violence and name-calling, and you can. But why the coincidence?

      Why would you want to associate yourself with Joe G? He was actually fired from a job for threatening people. There are other examples of physical threats from Joe G.

      In a recent UD comment he suggested a Final Solution for evolutionists:

      Joe G: "If this is true, that he [Mark Armitage] was fired for writing that paper and questioning evolutionism, then it is time for a war- a bloody war at that because this crap has to stop and obvioulsy the only way to stop it is to rid the world of all the cry-baby loser materialists." [Joe G threatens extermination at UD, August 6, 2013]

      Do you want to cover for him? Are you carrying water for him?

      Delete
    29. BTW great detective work, Piotr, Oberski.

      Delete
    30. Andy Wilberforce wrote: Konrad & Rumraket,
      a quote from Ann Gauger concerning your comments above: "The problem with these (protein evolution) scenarios is that they require proteins to be remarkably tolerant of sequence rearrangements and insertions, or remarkably easy to shift to new functions, or remarkably different at the dawn of life from what they are now"

      This is nothing more than an attempt to sidestep the criticism. Why did they pick two of the most distantly related proteins within a certain superfamily and then try to introduce mutations directly from one into the other, when this is NOT what biology tells us happened.

      Why would they test a strawman of the position they are attempting to criticize? I'm asking you, Andy, whether you can explain it, instead of just copy-pasting commentary that does not address this question.

      The evolutionary postulate, the one we extract from doing phylogentics sequence and structural alignmentsm is that the two proteins in question each evolved from a common ancestor. Which means the route to both of them through mutations is radically different from the one Axe and Gauger introduced in their research.

      Again, they took one protein and then introduced mutations in this protein directly from the other, very distantly related protein, instead of collecting large amounts of sequence and structure data from many independent species of organisms, and trying to reconstruct these two protein's independent evolutionary histories from a common ancestor. Then that had been done, they could have tried to resurrect ancestral versions and tested those instead, to see if they worked.

      But they didn't do that, Andy. Isn't that weird?

      Andy Wilberforce wrote: These requirements clearly are mutually exclusive. A more personal reflection is that much of the argumentation seem to be aimed at shielding the prevailing hypotheses from testing and evaluation.
      This is diametrically opposite to fact. It is Axe and Gauger who are not actually testing the evolutionary postulate, but a scenario of their own fantasies making.

      The evolutionary postulate, using the methodology of reconstructing ancestral states, have actually been tested many many times. That's exactly why the methodology of Ancestral Sequence Reconstruction was invented in the first place, to see if we can reconstruct evolutionary history and determine functional ancestral states.

      Here's a study using ancestral sequence reconstruction on a set of carbohydrate metabolizing enzymes that document AND TEST their evolutionary history: Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication.

      This is how such studies are done, but Axe and Gauger elected not to do this kind of work. How come?

      I emplore you to read this paper through Andy, and think about what they did and why they did it, and then contrast it to what Axe and Gauger did in their paper.

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    31. Sorry for the typing errors, should have proofread it before I posted. Should still be readable.

      Delete
    32. Diogenes, I wasn't going to dignify those ludicrous conspiracy accusations with a response, but since you ask so politely...
      No I'm not Joe Gallien, I'm not in cahoots with Joe Gallien and I never even heard of him before yesterday. All I can say is that he's right about Genetic Algorithms not mimicking Natural Selection since when you set the criteria for the fitness evaluation you are effectively introducing teleology into the equation. Adaptedness in nature is thought to be a posteriori result rather than the priori goal-seeking used in GAs.

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    33. Andy, I'm VERY glad you are not Joe G -- glad for your sake, because Joe G is a very unpleasant individual. I wonder, though, how Joe G can be right about something he so profoundly misunderstands (see his blog). The accusations above may seem ludicrous to you, but try to look at them from our side: you find a convenient quote in a Wikipedia article and -- who would have thought? -- it turns out to have been inserted there by a notorious creationist troll just two days earlier. What would you have thougfht?

      Criteria for fitness evaluation are not teleological. They constrain the evolutionary process, but do not impose a predetermined direction on it. That's why solutions reached by genetic algorithms are often unexpected and unlike anything a typical engineer would come up with.

      Delete
    34. Piotr wrote: "Criteria for fitness evaluation are not teleological. They constrain the evolutionary process, but do not impose a predetermined direction on it. That's why solutions reached by genetic algorithms are often unexpected and unlike anything a typical engineer would come up with."

      Not true, not the way we use them. If you have an example of this, then I would like to see it.

      Delete
    35. Piotr, it is admittedly a remarkable coincidence, but as we both know those happen every day :-) Here is a response that I wrote to Steve in October last year when the Genetic Algorithms were last discussed. As you can see it's similar and places my response before Joe Gallien's.

      "Andy WilberforceThursday, October 03, 2013 3:44:00 PM
      Steve, the automated design systems that you describe are very good at iterating algorithms until they converge to pre-set criteria, i.e. not really the mindless process without goal that evolution is made out to be.
      Dawkins have popularized the idea of "climbing mount improbable" by small incremental steps. Douglas Axe has shown that for e.g. two functional folds of protein no such gradual pathway of incremental improvements exists."

      Delete
    36. What do you use them for, then? To get a predetermined result? Would you care to share an example?

      There are some classical examples of totally baffling solutions that work, though it's hard to figure out why:

      http://www.damninteresting.com/on-the-origin-of-circuits/

      Delete
    37. Piotr, you do not predetermine the results of course, but you set up acceptance criteria used in the local and global fitness evaluation. The problems are typically complex with interdependent factors with opposed optima, i.e. it will be a design with balanced trade-offs. We then use the result as a first shot to come up with a working conceptual design and apply old fashion engineering work to refine it.
      Wiki used "the traveling salesman" problem as an example, which is a much more straight forward and could be solved by a pretty basic iteration algorithm.

      Delete
    38. OK, but I gave you an example of a solution which could not be found using standard engineering methods. Adrian Thompson's sound discriminator "discovered" an unorthodox solution not used by human designers (and hard to understand) -- a subtle interaction between unconnected logic cells via magnetic flux effects. The fitness of evolving circuits was measured on the basis of how well they passed discrimination tests -- no structural solutions were "front-loaded" in the experiment. Humans usually think in terms of functional modules, and have some model of their expected behaviour -- that is where teleology may creep in, but it was absent in the case I'm talking about.

      Delete
    39. Genetic algorithm's still mimic natural selection, because the constraints of the selection operation are analogous to the environmental selection leading to adaptations in nature. We're back to the consistent result of "torpedo shapes" of bodies of organisms that live in water, because they're all subject to hydrodynamic drag. While on the grander scale, evolution as a whole doesn't have goals, natural selection consistently biases outcomes towards those of less energy consumption(it takes energy to power cellular processes, and it takes energy to get to more energy), which is why the snouts of fish are pointy and their bodies are long and slim, and why birds have low body weight to volume ratios and so on and so forth.

      In fact, some intelligent design theorists like William Dembski has used this to go to far as to argue that nature itself(it's laws and so on) has "built in" goals for natural selection to find. Things here is, though, if someone wants to go down that route, you have to concede that Genetic Algorithms DO work like natural selection (the outcomes of GA are constrained by the fitness landscape of the simulation, just like the outcome of natural selection operating in specific natural environments constrains workable solutions to a small subset, like the bodyshapes of fish and whales and so on... ). While Dembski never did concede this explicitly, when the above was pointed out to him by, among others, Joseph Felsenstein, Wesley Elsberry and Jeffrey Shallit in various criticisms of his work, he sort of abandoned that whole line of argument in his public writings.

      I'm surprised to see Andy Wilberforce doesn't even keep up with the "developments" within the ID community.

      Delete
    40. Piotr, do you have anything that's published in an actual engineering publication?

      Delete
    41. Andy, on the voice recognition circuit Piotr mentioned:

      Davidson, Clive. "Creatures from primordial silicon." New Scientist, vol.156, no.2108, p.30-35 (November 15, 1997). Available online at http://www.newscientist.com/hottopics/ai/primordial.jsp.

      Describeed at TalkOrigins: http://www.talkorigins.org/faqs/genalg/genalg.html.

      Note this circuit is irreducibly complex by Behe's definition, but Behe says that only purposeful intelligent design can produce irreducibly complex structures.

      IDers responds that the scientists must have cheated by "smuggling in" information to predetermine the design. But this design involves wireless communication between logic gates that have no wired connection to anything else. No human designer would have designed such a thing-- we're prejudiced, but evolution isn't. How could scientists "smuggle in" information about a design no sane human would have proposed?

      The "smuggling information" argument is sour grapes. We won. The end.

      Delete
    42. Thompson, A., P. Layzell, and R.S. Zebulum. 1999. Explorations in design space: unconventional electronics design through artificial evolution. IEEE Transactions on Evolutionary Computation 3: 167-196.

      Delete
    43. Andy's argument is as follows:

      the automated design systems that you describe are very good at iterating algorithms until they converge to pre-set criteria, i.e. not really the mindless process without goal that evolution is made out to be.

      Here Andy is ignoring the fact that the "pre-set criteria" are always functional, not structural. The output of the algorithm is a novel structure which no human could have anticipated nor designed. Evolution has been observed to arrive at structures no human could or would design, so no scientist did or could have "smuggled in" information about structures no human could devise or anticipate.

      It is precisely this which established the analogy between NS and genetic algorithms. NS imposes functional, but not structural constraints. The output structure is often like nothing a human engineer would design.

      Andy, do you deny that NS imposes functional constraints?

      Do you deny that the pronghorn antelope is constrained by NS to outrun the cheetah? How is that not a "pre-set criteria" imposed by nature?

      Do you deny that e.g. Galapagos finches are constrained by NS to adapt to changing food sources? How is that not a "pre-set criteria" imposed by nature?

      Do you deny that e.g. African people are constrained by NS to have some level of resistance to malaria?

      Do you deny that peppered moths are constrained by NS to have coloration that matches their environment?

      If you agree NS imposes functional constraints, how are these different from what you call "pre-set criteria", what scientists do with GA's? My point is that the criteria in nature and in GA's are functional; the output is structural.

      Moreover, many GA's have no structural constraints and can in principle produce billions or trillions of possible solutions. Schneider's ev program, for example, can produce trillions of unique possible solutions. The functional constraint is that the "protein coding" part of the digital genome must fit the "protein binding" part of the digital genome, but since both start out randomized, there are trillions of possible solutions. Schneider can let the program run all night while he's asleep and make 10,000 independent solutions.

      The "billions of solutions" argument applies to many GA's. There is no way a scientist can "smuggle in" the information for all those independent solutions. Just let the program run while you're asleep.

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    44. Diogenes wrote: "If you agree NS imposes functional constraints, how are these different from what you call "pre-set criteria"
      I do agree about NS introducing constraints, but as I wrote earlier adaptedness in nature is thought to be a posteriori result rather than the priori goal-seeking used in GAs.

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    45. Andy: I do agree about NS introducing constraints, but as I wrote earlier adaptedness in nature is thought to be a posteriori result

      NS introduces functional constraints. The a posteriori result is structural.

      Now compare this to your description of GA's: you're shifting goalposts.

      rather than the priori goal-seeking used in GAs.

      What "a priori goal" in GA's are your referring to? In GA's, there is no a priori structural goal, and in practice, in many cases, no human engineer can anticipate the structural output. The only thing a priori in GA's are the functional constraints. Thus the analogy is established.

      You're trying to make a distinction without a difference, and I note that you do not use the words "structural" or "functional" in your description of GA's. Why avoid those words?

      Delete
    46. Diogenes wrote: " In GA's, there is no a priori structural goal, and in practice, in many cases, no human engineer can anticipate the structural output. The only thing a priori in GA's are the functional constraints. Thus the analogy is established."
      With all due respect Diogenes, that is just BS talk. You are yet to produce evidence that any such engineering work is used in product development. I know how we use them, it also agrees with the example that JimV posted. Do you think big corporations are charity organizations handing out fat salaries to engineers that could easily be replaced by algorithms?

      Delete
    47. Clarification, it should be: "any such un-guided engineering work"

      Delete
    48. "You are yet to produce evidence that any such engineering work is used in product development."

      They were being used in GE Energy Services when I left in 2003. GE sometimes trumpets their latest turbine designs, but does not often disclose the methods used to develop them. As my old boss Frank Ryan once told a turbine conference, when asked why our Services Shops charged thousands to run our nozzle area-check program, instead of publishing the code, "We spent millions of dollars to develop that program, and GE is in business to make a buck." I thought you said that GA's were used in your company also?

      " I know how we use them, it also agrees with the example that JimV posted."

      Yes, you did say that, in the very next line. In the example I cited, a major selling point what that the flow path design found was an unusual configuration which was more efficient than the design that the Aircraft Engine department had already developed.

      "Do you think big corporations are charity organizations handing out fat salaries to engineers that could easily be replaced by algorithms?"

      When I started at GE in 1968, the Schenectady plant employed 28,000 workers and the Steam Turbine-Generator departments had about 3000 engineers (many of them internally classified as technicians and specialists, but doing engineering work). When I left in 2003, the plant had about 4000 employees, five other ST-G plants had been shut down entirely (Lynn, MA; Fitchburg, MA, Charleston, SC, Durham, NC; and Portsmouth, ME) and the ST-G engineering department (consolidated from all the previous plants) had about 400 people doing engineering work.

      I was one of the better-compensated engineers there, but at no time did I consider my salary "fat".

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    49. Re: clarification as to "unguided".

      I take it this means a computer able to read technical reports for itself to get necessary materials data and loadings, or perform independent experiments to get such data, and decide for itself how to balance cost vs. efficiency vs. reliability. This is similar to creationists saying, until you show me a fish evolving into a cat I won't believe that evolution is possible.

      As I have said, as far as I know no current super computer matches the computing power of our nanotech brains with their 86 billion neurons, nor do computers have the ability to access decades of technical reports from past years which are stored on microfiche, nor to scan mylar quarter-scale layouts of turbine sections which are over a yard high and about 18 feet long.

      But computers are getting more powerful and getting access electronically to more and more data. Meanwhile, human design engineers with their nanotech brains depend heavily on formulas and procedures which evolved over hundreds (in some cases thousands) of years, and when something new that doesn't fit past experience is encountered, use random guesses and trial and error to develop new devices and procedures; and it seems feasible and likely to me that among the procedures which evolution has programmed our neurons with are ... genetic algorithms.

      I think more than enough evidence and reasons have been given on this side topic, and will try to stop commenting so the experts can resume discussing their science. I submit that it you want to get the discussion back on track you could comply with the original post and tell us how you think brains work - by magic?

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    50. Jim, with unguided I simply mean that a designer has not set the structural model (the parametric representation of the item studied), the search envelope and the acceptance criteria (i.e. the fitness evaluation based on functional requirements).

      It's interesting that you write "I take it this means a computer able to read technical reports for itself to get necessary materials data and loadings, or perform independent experiments to get such data, and decide for itself how to balance cost vs. efficiency vs. reliability" and "nor do computers have the ability to access decades of technical reports from past years which are stored on microfiche" yet you do not seem to see the implication of someone feeding this information in to the program.

      Delete
    51. Jim, with unguided I simply mean that a designer has not set the structural model (the parametric representation of the item studied), the search envelope and the acceptance criteria (i.e. the fitness evaluation based on functional requirements).

      Andy, those programs and circuits don't live in the wild. Functional requirements play the same role as the environment in real evolution. You can't model natural selection without modelling selective pressures. In an artificial "world" of course they have to be provided by the human designer. The point made above is that the fitness criteria are purely functional (e.g. how well the sound discriminator can distinguish high and low tones, or two different vocal commands) and very similar to what we find in nature (this particular case is a highly simplified analogue of the evolution of hearing). The designer does not tell the system what kind of structural solution is expected. Actually, the optimal solutions found by a genetic algorithm may completely baffle an engineer -- just because the search for them is not directed. Thompson had little idea how exactly his simple circuit worked, how it managed to compensate for the absence of a clock, or why the unconnected part was essential for its functioning.

      Delete
    52. Piotr, first if you insist on referring to your "primordial circuit" story then at least have the common decency to refer me to a reputable publication, so that I can make a fair evaluation of it.
      Second, you miss the point that you also need a the parametric representation of the item studied, that provides the structural information. If you look at e.g. the ST5 spacecraft antenna that NASA developed, it is clear that they used a model consisting of 6 bars connected by 5 nodes with 360 degree rotational freedom in the horizontal and vertical plane. It's clear that the parametic model sets the limits of the outcome even if you have 3.6*10E10 possible solutions, when changing all rotational angles by 1 degree increments through the whole search envelope.
      The bold claim is that the solution is something that an engineer would never envision. Well, the theory is actually not any rocket science. You simply want to achieve an antenna where one section does not fall in the shadow of another.
      Third, I still maintain that the functional requirements in GAs are a pre-set goals. I natural selection you do not have any fixed goal.

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    53. 3,6*10E25 possible solutions, of course...

      Delete
    54. Piotr, first if you insist on referring to your "primordial circuit" story

      "Primordial circuit"? What are you talking about?

      then at least have the common decency to refer me to a reputable publication, so that I can make a fair evaluation of it.

      I have actually referred you to a paper in a reputable journal where Thompson et al. describe their experiment in detail.

      Delete
    55. You referred to damninteresting.com/on-the-origin-of-circuits/ and Diogenes to The New Scientist...I haven't seen any link to the publication above.

      Delete
    56. That's a paper publication, but never mind. The explanation that I wrote for the ST5 spacecraft antenna that NASA developed (above) and the fuel-efficient aircraft turbine engines developed by GE and posted by Jim V should be sufficient demonstration that:
      1. structural model (the parametric representation of the item studied)
      2. the search envelope
      3. the acceptance criteria (i.e. the fitness evaluation based on functional requirements
      are needed to set up a Genetic Algorithem. This is then used in combination with conventional engineering methods.

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    57. Humans could in principle find the same solutions that GA's find (and by the same method of sophisticated trial and error) although it would take them longer (and/or more of them). The point is that GA's can find good solutions, just as natural selection finds solutions to the problem of survival and reproduction in hostile environments. If GA's couldn't find solutions then Mr. Wilberforce would have an argument.

      What the engineers who specific the parameters are doing is defining the fitness landscape which is to be searched. In the case of natural selection, the fitness landscape is the environment. Natural selection itself has often been modeled with computer programs, and of course the modeler has to specify an environment under which the natural selection will take place - food resources, predator characteristics, etc..Saying that a GA has to specify its own fitness landscape in order to be unguided in its search is like saying natural selection chooses the environment which it adapts creatures to.

      Delete
    58. Jim, I would say that if you want to make a comparison between GAs and a conception of evolution, then the closest would be created "kinds" (i.e. the parametric model) as a starting point and evolution with a direction ( because of the teleology introduced in the fitness evaluation).

      Delete
    59. Re: ilikai1820rentalFriday, January 17, 2014 1:50:00 AM

      I don't have a problem with that. Obviously, the closer you can start a random search to the place where a good solution lies, the easier and shorter the search will be. So of course engineers try to restrict the search landscape to where they think it will bear the most fruit (although they could be wrong). The point is that random searches work. And I have already previously stated that I consider that natural selection can be said to have a goal, which is to adapt a population to survive in an environment (although it is not a conscious goal, nor does it have a predetermined solution). And of course its most successful solution by far is not Homo sapiens but bacteria.

      So yes, if there had been separately created kinds each with their own DNA as a starting point, evolution would still have inevitably followed. However, the evidence does not support that model.

      To put it another way, humans by trial and error evolved machines from roller logs to wheels to water mills to turbines, and now use GA's (which are directly modeled on natural evolution - it seems strange to speak of comparing them to a concept of evolution as though that were somehow a stretch) to extend that evolution further.

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    60. Jim wrote: "So yes, if there had been separately created kinds each with their own DNA as a starting point, evolution would still have inevitably followed. However, the evidence does not support that model"

      So what about the sudden appearance of most animal phyla during the Cambrian Explosion?

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    61. I am not an expert in paleontology, but my understanding is that: a) animals at about that time were beginning to have bony/shelled structures which leave more fossil remains than soft-bodied worms; and b) evolution can go through surges of accelerated development after very useful pieces of the genetic tool-kit, such as Hox genes, have evolved. An example from human design evolution would be the rapid expansion of electronic devices after first electric power generation, and second transistors, were developed. The alien archaeologists who dig up our remains a million years from now may designate this period, "the Electrican Explosion". However, I doubt if they will conclude from this that all electronic appliances were brought into being as separate kinds instantaneously and without precursors by magic.

      Now I will try very hard not to waste Internet space with my layman's knowledge and leave such questions to the experts - which they have answered here and at Talk Origins and numerous other places long ago and many times.

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    62. So what about the sudden appearance of most animal phyla during the Cambrian Explosion?
      In what alternative reality is a 15 million year period sudden? Sure, on the grand geological timescale we may describe it as an "explosion" in a sort of tongue in cheek way. The appearance of a large number of fossils over a 15 million year period is pretty far from sudden.

      And then there's the fact that from an evolutionary perspective, there ARE simpler antecedents in the ediacaran. Throwing the genetic evidence on top it becomes pretty clear that there was a significant period of evolution between the first hard-body part organisms to fossilize and the eventual 15 million year explosion at the beginning of the cambrian.

      Tell me Andy, do you ever bother actually thinking about these matters, or is it simply enough for you that some IDcreationist somewhere has given his personal apologetic spin on the matter?

      The whole thing about soft body parts being much rarer to find good fossils of explains parts of it. Then theres the fact that simpler antecedents DO exist and go back morphologically almost a 100 million years before the "explosion", explains another part. Then there's the fact that the earliest fossilizations are imprints of softbodied organisms, later are simple works with hard parts (segmented shells), explains yet another part. Then there's the fact that the earliest cambrian organisms are also segmentated shelly organisms, sort of like trilobite precursors. The subsequent "explosion" is a massive diversification (still over tens of millions of years) of these shelled, segmented organisms. We also get a parallel diversification of soft-bodies organisms. Then there's the fact that this makes sense because when there are large diversifications, new niches open up, (such as one organism becoming)food for another), which is a whole subjet unto itself. Then there's the fact that whole period from the end of the Ediacaran to and through the cambrian explosion happens to coincide with significant alterations to the earth's atmosphere and oceans. The rise in planetary oxygen powers large parts of the increase in biomass and diversity, which impacts the chemistry of the ocean, which becomes more calciferous and carbonated, which constitutes a new niche just waiting to be taken advantage of, which cellular life subsequently does in it's eventual origin and evolution of hard body parts. And so on and so forth.

      All of these events are corroborated and supported by paleogeochemistry, fossil chronologies and comparative genetics. There is no evidence that contradicts this, it is fully compatible with evolution.

      There's no simple answer to the cambrian explosion. But there is one. Go to 38:27 in this video and get quick once-over of the "why did all this happen?". Maybe if you dare you can see all of it for some other interesting insights, such as the fact that the cambrian explosion in it's rate of diversification, is no more explosive than any other period of diversification(as in diversifications following large extinction events for example) in life's history.

      Yes yes I know, it's that terrible militantfeminaziatheistevolutionistfundamentalist PZ Myers talking, but however much you despise the man, he at least bothers to explain some of the science.

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    63. Andy,

      So what about the sudden appearance of most animal phyla during the Cambrian Explosion?

      So much error is contained within that one sentence that it's hard even to begin. But I will. First, "sudden" is wrong, since the appearances in question cover around 40 million years, from around 560ma to 520ma, marked by a gradual accumulation of more, larger, and more diverse forms. Second, "appearance" is wrong, or at least misunderstood, since it merely means the first fossil record, not first existence, and the difference can be many millions of years, depending on the vagaries of preservation. Third, "most" is wrong, as around half of all animal phyla have no fossil records whatsoever, and several others are so sparsely represented that they might as well not be (which underscores my second point, by the way). What we actually see are most of the well-skeletonized, readily preservable phyla, plus a couple of windows into some of the soft-bodied ones. The whole is much more gradual, fragmentary, and complicated than you believe.

      Reading Stephen Meyer is bad for your intellectual health. I suggest, as antidote, Erwin & Valentine's book The Cambrian Explosion.

      Delete
    64. I have to note that Andy has still not responded to my comment about Axe and Gauger's test-of-a-strawman-position publication. Mysteriously also published in the journal belonging to the very same institute that employs Axe and Gauger, in which Axe and Gauger are on the editorial board. Why not an independent 3rd party? Regardless, this point is secondary. I've dealt with the actual claims of the paper above but have not recieved and answer, not even an acknowledgement that I have responded to it.

      Delete
    65. That's because, having had his ass served to him on a platter on that subject, in true creationist fashion he has now Gish-galloped on to the Cambrian explosion. Where, yet again, he has been handed his ass on a platter.

      Where will gallop to next? The bacterial flagellum? Darwinists predicted no functional non-coding DNA? Any guesses?

      Delete
    66. John, did you read Erwin & Valentine's book yourself? This is what the write:
      “Although there is truth to some of the objections, they have not diminished the magnitude or importance of the explosion. A long history of metazoan evolution did precede the Cambrian, perhaps by 200 million years or more. This long history was unknown when the explosion faunas were first described but is being gradually revealed by comparative studies of the rates of molecular sequence divergence (so-called molecular clocks), by studies of molecular fossils or biomarkers and by a growing knowledge of the fossil record. The only animals present during most of the preexplosion interval were sponges and architecturally simple organisms built of sheets of tissues. A few tens of millions of years before the explosion, however, small organisms that had body plans designed for locomotion on the seafloor — bilaterian-grade forms — evolved. Their evolution may have been enabled by an increase in oxygen levels that permitted an expansion in metabolic activities, although oxygen levels were still quite low by modern standards (1–10% of present atmospheric levels). A continuing increase in oxygen levels may have permitted the evolution of larger-bodied architectures that arose from varied members of the chiefly worm-like bilaterian fauna. Solutions to some of the biomechanical problems posed by those larger bodies commonly involved the evolution of either tough organic or even mineralized skeletons. It was this round of metazoan evolution that produced the fossils of the Cambrian explosion. Thus, explosion fossils did have a metazoan ancestry stretching back well before the Cambrian into the Neoproterozoic, but the earlier faunas did not consist of numerous, large, complicated body plans.
      “…a great variety and abundance of animal fossils appear in deposits dating from a geologically brief interval between about 530 to 520 Ma, early in the Cambrian period. During this time, nearly all the major living animal groups (phyla) that have skeletons first appeared as fossils (at least one appeared earlier). Surprisingly, a number of those localities have yielded fossils that preserve details of complex organs at the tissue level, such as eyes, guts, and appendages. In addition, several groups that were entirely soft-bodied and thus could be preserved only under unusual circumstances also first appear in those faunas. Because many of those fossils represent complex groups such as vertebrates (the subgroup of the phylum Chordata to which humans belong) and arthropods, it seems likely that all or nearly all the major phylum-level groups of living animals, including many small soft- bodied groups that we do not actually find as fossils, had appeared by the end of the early Cambrian. This geologically abrupt and spectacular record of early animal life is called the Cambrian explosion. The explosion tells us a great deal about ecological and evolutionary history and, even more importantly, about the many processes involved in evolutionary change.”

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    67. Yes, it supports and explains what we said. That's why you should read it in it's entirety, instead of copy-pasting pieces of it here and there you think supports creationism. Which, by the way, I have to note is quite dishonest. If your fundamentalist religious doctrine is really true, why do you have to respresent other people's positions to support it?

      Delete
    68. Well, if Andy has read and understood the criticisms of the Axe and Gauger paper he cited, even if he has no wish to acknowledge the mistake it was to cite it in the first place, as long as he understands why he shouldn't cite it in the future that's fine with me. We all make mistakes and sometimes we don't research things properly and jump to conclusions. I'm sure I've been guilty of the same thing before. I would like to hear from Andy, though, a statement that he will not be referencing their pseudo-research of strawman positions as arguments against evolution in the future. In fact, I would go so far as to say I would highly respect that, because it takes balls to admit to such a mistate and make such a statement.

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    69. John, did you read Erwin & Valentine's book yourself?

      Yes I did. Did you, or did you find those little quotes on some creationist web site? Did you even read those quotes? I would be glad to explain why they say pretty much the same thing I said, if you're interested. It's more obvious if you remove Casey Luskin's gloss, as you did.

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    70. I'm also not seeing what point you think you are making with that quote, Andy.

      Compare it with the account given in section "A" of Nick Matzke's review of Darwin's Doubt in the link below. Are there any contradictions between that and Erwin and Valentine? Pay particular attention to the errors and omissions committed by Meyer that Matzke points out:

      http://pandasthumb.org/archives/2013/06/meyers-hopeless-2.html

      Delete
    71. John wrote: "I would be glad to explain why they say pretty much the same thing I said, if you're interested."

      Well John, I would really be interested in hearing that explanation.

      Delete
    72. Andy, you present your quotes in the wrong order (the first is from page 6, the second from page 5 of the book), and skip the beginning of the page 5 paragraph:

      Some 120 million to 170 million years after the origin of sponges, the
      scrappy fossil record improved with a bang, geologically speaking. Following a prelude of a diverse suite of enigmatic, soft-bodied organisms beginning about 579 Ma, ...


      The same omission is made by Luskin, so you evidently have the quotes from him and have no first-hand familiarity even with the introductory chapter of the book. Can't you read and think for yourself? Do you have to be spoon-fed by the likes of Luskin?

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    73. Piotr, the introduction and first chapter can be found here:

      http://www.roberts-publishers.com/biology/the-cambrian-explosian-and-the-construction-of-animal-biodiversity.html


      I never claimed to have read the whole book, but I read the part that's available for free. It did not seem to contain any radically new information, so I figure that I can use my time better. I do think it's funny though that John referred to it as a source of authority when it actually contradicts the points he was trying to make...

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    74. So it's just a coincidence that you happened to make the exact same omission that Luskin made? These "coincidences" just seem to keep happening, eh, Andy?

      Exactly what part of that passage do you think contradicts what John wrote?

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    75. Funny that you should truncate the first sentence in exactly the same way as Luskin, and that you should parrot his moronic conclusion. I'm sure John will want speak for himself, though.

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    76. Piotr, did you btw finally get how Genetic Algorithms work or do you still think computers do un-guided product development?

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    77. Andy, you made no effort to understand what Thompson's experiment was all about and what it meant. Sorry for giving you a reference to a mere "paper publication", as you put it. Now I see why you don't like complete books either, and have to rely on blurbs and cutouts pre-digested by more eminent IDiots.

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    78. Piotr, I don't want to embarrass you but didn't you write: "The designer does not tell the system what kind of structural solution is expected. Actually, the optimal solutions found by a genetic algorithm may completely baffle an engineer -- just because the search for them is not directed." Do you still believe that?

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    79. Andy Wilberforce wrote: Piotr, did you btw finally get how Genetic Algorithms work or do you still think computers do un-guided product development?
      Andy, did you finally figure out how natural selection works or do you think there are organisms that don't expend energy? Do you think there exists a body of whater somewhere that does not impart hydrodynamic drag on objects submerged therein?

      The solutions GA come up with are shaped by the constraints of the fitness landscape. This is directly analogous to natural selection. All organisms in existence are subject to the laws of physics, they all need to expend energy to survive and reproduce. The environment they live in constrains what is and isn't a good "solution". There is no difference Andy, you've bought into a vapid talking point with a glaring fundamental flaw.

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    80. Rumraket, I think you had one too many Tuborg, you're even harder than usual to understand.

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    81. Rumraket's post makes perfect sense to me. So I don't think he's to blame for your comprehension problems, Andy.

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    82. Do you still believe that?

      Yes, I have reasons to believe that. If it weren't for your aversion to reading, you would be able to learn something about those reasons too. I did my best to help you, but wilful ignorance is hard to cure.

      It may interest you to know that the anonymous Wikipedia user from New England made another attempt to vandalise the article on "Genetic algorithms" again. I hope that problem has been solved effectively now, so you can quote Wikipedia safely.

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    83. Well, he is right about GAs, who ever he is.

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    84. Lutesuit, for starters please explain what this means and what it has to do with anything: "Do you think there exists a body of whater somewhere that does not impart hydrodynamic drag on objects submerged therein?"

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    85. I find it interesting that as soon as Andy's challenged on the Cambrian explosion he retreats to genetic algorithms. And it's also interesting that he just happened to pick the same two quotes from Erwin and Valentine that Casey Luskin did, purely by coincidence.

      Anyway, this was Andy's assertion:

      ...the sudden appearance of most animal phyla during the Cambrian Explosion?

      I said that "sudden" was wrong, "appearance" was misinterpreted, and "most" was wrong. So what do E&V say in the quoted material? Well, they say that many fossils first appear in the record between 530 and 520ma, but they also mention that there was as much as 200 million years of metazoan evolution preceding this, and that bilaterians begin appearing in the fossil record a few tens of millions of years before the explosion.

      And they're also careful to use "appearance" as referring to preservation of fossils, not to the origin of taxa.

      Finally, they say that what appears in the explosion are not most phyla, but "nearly all the major living animal groups (phyla) that have skeletons". That's a couple of major differences from Andy's claim, only one of which I complained about. Now, they do mention the soft-bodied fauna that appear (remember what that means) around the same time. And they also mention that, on the basis of molecular studies, we can suppose that almost all phyla for which we have poor fossil records had also evolved by the end of the Early Cambrian. Notice the part about "poor fossil records", which is also what I said.

      In short, Andy, any disagreement you see here between what I said and what Erwin & Valentine said is just a result of your (and Casey Luskin's) poor reading of carefully chosen snippets.

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    86. John, You are not stupid are you? Why would you believe in s...t that a volcano sped up the Cambrian explosion? Really???? Why?

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    87. I wrote “So what about the sudden appearance of most animal phyla during the Cambrian Explosion?”
      John wrote “"sudden" is wrong, since the appearances in question cover around 40 million years, from around 560ma to 520ma, marked by a gradual accumulation of more, larger, and more diverse forms. Second, "appearance" is wrong, or at least misunderstood, since it merely means the first fossil record, not first existence”
      What Erwin and Valentine wrote “…a great variety and abundance of animal fossils appear in deposits dating from a geologically brief interval between about 530 to 520 Ma…” “nearly all the major living animal groups (phyla) that have skeletons first appeared as fossils ... In addition, several groups that were entirely soft-bodied and thus could be preserved only under unusual circumstances also first appear in those faunas.” “Because many of those fossils represent complex groups such as vertebrates (the subgroup of the phylum Chordata to which humans belong) and arthropods, it seems likely that all or nearly all the major phylum-level groups of living animals, including many small soft- bodied groups that we do not actually find as fossils, had appeared by the end of the early Cambrian”
      So John do you maintain you statement: “I said that "sudden" was wrong, "appearance" was misinterpreted, and "most" was wrong”

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    88. Why would you believe in s...t that a volcano sped up the Cambrian explosion?

      I truly have no idea what that was supposed to mean.

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    89. Andy,

      DId you even read my reply? Nothing you quote lends support to your claim. There are two meanings of "appeared", and you confuse them. Erwin and Valentine are unfortunately switching back and forth too. For the groups for which we have fossils, "appeared" means "show up in the fossil record". For those for which we don't it means "had come to exist". Note that in the latter case, there is an upper (most recent) bound, the end of the Early Cambrian, but no lower (oldest) bound given. And the fact that a majority of phyla have no fossil record yet are stated as having existed shows that Erwin & Valentine don't take the fossil record with naive literalism.

      The Cambrian explosion is the combination of several factors: a fairly rapid (approximately over 25 million years) increase in skeletonization, a narrow window (around 20 million years, partly overlapping the previously mentioned period) of unusual preservation in soft-bodied faunas, and several potential environmental triggers, including increasing oxygen levels and the invention of macropredation. To a large degree, the first two are taphonomic artifacts that don't represent the actual times of diversification. And this is why molecular dates of the divergence of most phyla, including those with good records, precede by "a few tens of millions of years" their fossil appearance.

      Again, you should read the book, and you should stop using Casey Luskin as your guide to what it says.

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    90. "Piotr, I don't want to embarrass you but didn't you write: "The designer does not tell the system what kind of structural solution is expected. Actually, the optimal solutions found by a genetic algorithm may completely baffle an engineer -- just because the search for them is not directed." Do you still believe that?"

      For what reason would he not believe it? I do. One last try:

      Your argument seems to be, engineers input parameters which define the design space (/fitness space/environment), therefore genetic algorithms are being guided. Our replies are:

      1) Neither evolution by natural selection nor GA's can work without something to work on. The design space set by engineers is exactly analogous to the constraints imposed on natural selection by natural law and natural environment (e.g., hydrodynamic drag on fish). If you want to call this being guided, then you are using a much different meaning for that word than us. To us, a guide is someone or something that directs someone or something to a destination that is known to the guider. This is not the case with either natural evolution or GA's. If engineers knew the design solution before running the GA's there would be no need to run them.

      2) Genetic algorithms, as the name implies, are directly based on how natural evolution works (genes, mutations, recombinations). There are much simpler ways to do random searches, but it turns out this is a very powerful method that produces unexpected results*. Companies like General Electric would not pay engineers fat salaries (or any salaries) to use it otherwise.

      3. The key point about GA's is that they demonstrate that random searches of a design space or fitness environment can and do produce useful results, although in a computer they may take millions of iterations and in nature they may take millions of years.

      * My favorite example is something I read in Scientific American's Tech Notes section when I had a subscription about 15-20 years ago. It stated that NASA had used a GA approach to develop a computer routine to control the steering jets on the space shuttle. The problem to be solved was, given a random direction of drift and state of spin: when and how long should which steering jets be fired to bring the shuttle back into level flight with a desired orientation and direction, with minimum fuel use. According to SA, the result was a single statement in some programming language, multiply-nested, 254 characters long, which the NASA engineers and scientists did not well understand, but which did all (thousands) of trials successfully and used 20% less fuel than the program previously written for the task by a NASA scientist. (Of course the engineers had to program orbital physics, the mass characteristics of the space shuttle, and test cases in order to run the GA - see item 1.)

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    91. John, I wrote “So what about the sudden appearance of most animal phyla during the Cambrian Explosion?

      I think most of us know what appear means, but somehow you got into your mind that I was talking about the fossil record. You also claimed that it was only used that way by E&V.

      You first wrote: "And they're also careful to use "appearance" as referring to preservation of fossils, not to the origin of taxa."

      Now it seams that the coin finally dropped and you try to change you claim writing: "There are two meanings of "appeared", and you confuse them. Erwin and Valentine are unfortunately switching back and forth too."

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    92. Jim, my example above on the ST5 spacecraft antenna that NASA developed is a clear simple examples how GAs are used. Computers are great for iterating algorithms, but they can not do un-guided product development since for starters they lack the capacity for intentionality. I do not think that you seriously believe that you can ask a computer to come up with a solution of optimizing the function of an antenna while minimizing the the number of parts and weight. What you have to do is define: a parametric model of the antenna (the structure), the search envelope (what to vary and how) and the fitness evaluation.

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    93. Andy Wilberforce wrote: Rumraket, I think you had one too many Tuborg, you're even harder than usual to understand.

      I'm not hard to understand, you're trying to avoid dealing with the subject of my posts because you have nothing of worth to say. Instead of engaging in this kind of silly dismissive behavior, if you were rational it would cause you to reconsider the merits of your position seeing how you can't effectively defend it.

      Lutesuit, for starters please explain what this means and what it has to do with anything: "Do you think there exists a body of whater somewhere that does not impart hydrodynamic drag on objects submerged therein?"

      I have already explained that, it's plain english. You're the only one with this all too convenient comprehension problem. Makes it a lot easier to avoid dealing with criticism you don't know how to handle if you can just feign incomprehension.

      Here we go again. Drag:"In fluid dynamics, drag (sometimes called air resistance, a type of friction, or fluid resistance, another type of friction) refers to forces acting opposite to the relative motion of any substance moving in a fluid."

      An object submerged in water will experience drag opposite to the relative direction of motion. Since organisms must expend energy to move, this drag acting on their bodies will increase the cost of moving. But shape is obviously important, if you can change the shape such that you can reduce the amount of drag, you can save energy. How do organisms change their shapes? Mutation. Which mutations are more beneficial? Those that change the shape of the organism such that they reduce drag.

      This is a consistent bias of natural selection acting on organisms that swim and fly. Just like a genetic algorithm that homes in on a small subset of all possible solutions to a given problem. The problem here being reduction of drag (which is why almost all fish, particularly those that swim a lot and travel long distances every day, are sort of torpedo shaped). There might be several different possible solutions, but natural selection, just like the GA, will consistently search for and home in on such solutions.

      So there's no difference between GA's and natural selection.

      This is all plain english, not hard to understand at all and it shows you're simply wrong to claim there's a difference. You bought this stupid talking point from Bill Dembski, didn't bother thinking too much about it, and now you're here propagandizing with his nonsense.

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    94. Andy, if you simply read the book instead of relying on Casey Luskin's glosses, much will become clearer. Or, if you prefer, you can remain smugly ignorant. Failing to address any of my arguments will aid you in that goal.

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    95. "I do not think that you seriously believe that you can ask a computer to come up with a solution of optimizing the function of an antenna while minimizing the the number of parts and weight."

      Nor do I think that you could take a person off the street, give them the exact same task, and expect them to accomplish it. Evolution requires random variation, a selection criterion or criteria, and some form of memory so past efforts can be used as a basis for further improvements. Natural evolution has had billions of years to evolve genetic tool kits, so that bacteria, for example, are adept at adapting themselves to new conditions (e.g., in Lenski's experiment they learned how to perform a new chemical process). Start with the first proto-cell (such as the one the Szostak lab produced and described in Nature recently) and evolution would be billions of years away from producing complex organisms. An untrained human on a desert island would similarly have a difficult task to develop a steam engine. As evolution uses DNA for its memory, human engineers transfer information through generations via written records and verbal instructions, at school and on the job.

      You think engineers are giants because they are standing on the shoulders of thousands of previous generations. The facts are: given the same set of information to work with, GA's have produced solutions as good or better than those of engineers. Your response is to say that without some input information the GA's could not get results, ignoring the fact that without that information the engineers would not get any results either. If that is your notion of a fair argument, it is useless to try to reason with you.

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    96. P.S. As for "intentionality", a computer program gets it from the operating system of the computer, which forces it to run, and engineers get it from their bosses, who will fire them if they refuse a task. (And I have had bosses like you, who took credit for my work because they directed me to do it.) Natural evolution gets it from the fact that populations of organisms which can survive and reproduce can continue to evolve. The others get fired.

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    97. John wrote "Or, if you prefer, you can remain smugly ignorant. Failing to address any of my arguments will aid you in that goal."

      Sorry I guess...but your comment "So much error is contained within that one sentence that it's hard even to begin." To a perfectly valid question and repeated un-called for references to Casey Luskin didn't exactly lead me to believe you were after a serious discussion.

      So John, please remind me which were your serious arguments that you would like me to respond to. And no, I'm not being sarcastic, just genuinely surprised.

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    98. Jim, I don't think we get any further on this issue. I thought your last comment was funny, even if I don't agree with it. For the record I try very hard not to take credit for other peoples work and I'm a strong believer of the intentionality of the individual engineer.

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    99. Ah, tone trolling. Well played, sir. My point is that your question wasn't perfectly valid. Its premises, as I pointed out, were false. And I still think you got your quotes from a DI web site, as they're suspiciously chopped off in just the same spots. Was that really a coincidence?

      What I would like to try would be a serious discussion of the Cambrian explosion: what you think it actually was, and why, and why you think my characterization is wrong. Now, in preparation for that, you should probably learn something about it first by reading some of the scientific literature. Erwin & Valentine would be a good introduction.

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    100. I don't even buy that Andy genuinely thinks it was "funny" (what's funny about it? They were all perfectly reasonable, salient points), he made that up as a rethorical device to use to escape from this discussion.

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    101. John, if you want to continue on that road I suggest that you first show me where on DIs web site those quotes can be found. I may also suggest that you read Erwin and Valentine's book, because it's clear from the comments above that either you haven't or you simply did not understand it.

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    102. How would you know whether John has understood the book, without having read it yourself, Andy?

      BTW, have you ever heard of the Dunning-Kruger effecte?

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    103. Andy wrote: John, if you want to continue on that road I suggest that you first show me where on DIs web site those quotes can be found

      Uhm, googling them yields christian apologetics blog and website upon christian apologetics blog and website, all pro-ID/pro-creationism, all blathering about "Darwin's doubt" and how Nick Matzke and Donald Prothero are super wrong, frothing darwinists who just hates it when someone questions "their religion".

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    104. Well Rumraket, I was going to let it slide since since un-founded accusations are too common to be dealt with here. I told you where I took the quote and you kept insisting it was from Luskin. Now it's time to own up, no cheap excuses. Just admit that it's all fabulations.

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    105. The lady doth protest too much, methinks.

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  8. Re: ... if natural selection was goal-oriented"

    The danger of using Wikipedia is that any creationist can add a modifier such as the above to make technical information conform to their prejudices (and put it back in after someone else removes it). Natural selection is goal-oriented in the same sense as genetic algorithms are. Its goals are survival and reproduction via adaptation of a population to its environment. The difference is not in the goals but in the environment, which is artificial in the case of GA's. (Find a better solution to this problem or we will kill you.)

    To twist this topic back into to my pet idea, the super computers which ran the genetic algorithms which designed the flow-path of the current generation of GE jet engines have much less processing capability than the 86 billion neurons of the human brain, so it seems feasible to me that human intelligence is based on genetic algorithms looking for solutions to problems by random guesses. (We cannot sense directly what is going on in all those neurons since there are no nerves which monitor the brain's operation; just as the CEO of GE does not know what the clerks in the GE mail rooms are doing at any given time.) The problems we direct those neurons to solve are those we associate with our well-being, as a result of our own evolutionary history. Instead of turtles, it is evolution, all the way down.

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    1. Darn typos: "back into to" should be "back into"

      P.S. If I recall correctly, there was testimony about Axe's paper at the Dover/Kitzmiller trial. You can read the trail transcript to see how well it stood up under cross-examination. Clearly it did not impress Judge Jones.

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    2. And again: trail should be trial.

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    3. Actually, the paper by Axe that was discussed at the Kitzmiller trial is a different paper from the Axe and Gauger one, which was only published in 2011. The earlier paper from 2004 was debunked here.

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    4. Re Wilberforce

      All the material that makes up the universe (or at least the one we are in) consists of the excess particles that were created during the instability and CP violation in the quantum vacuum. You are now asking the question as to how these particles resulted in the inflation followed by the big bang. For that, I will refer you to Neil Tyson who explains it in one of his books. I'm not sufficiently knowledgeable in cosmology to respond. There are also articles on various web sites (e.g. Starts With a Bang, Sean Carroll, etc.) that discuss this issue. Google is your friend.

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    5. Colnago, it was a rhetorical question since you had proposed a solution akin to lifting yourself by the bootstraps to the question "Can science explain how universe could have come into being?"

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    6. Re Wilberforce

      Actually, at one time there was a proposal by a UC Berkeley physicist named Geoff Chew to describe strong interaction physics using what was known as the bootstrap hypothesis. Without going into the gory details as my understand of the hypothesis was less then satisfactory, Prof. Chew once admitted to me that the bootstrap hypothesis was not a scientific theory. Of course, since then, a satisfactory explanation of strong interaction physics, namely quantum chromodynamics, has been developed and proposals like the bootstrap hypothesis have been discarded. That's how science progresses, discarding old hypotheses in favor of newer ones that more satisfactorily explain what is observed.

      As for the claim that creating a universe from an instability in the quantum vacuum, this is not a bootstrap hypothesis as I understand what is meant by bootstrap. The quantum vacuum is known to exist because particles interacting with it have observable consequences. Thus, via quantum electrodynamics, one can compute the anomalous magnetic moment of the electron, which computation agrees with observations to 10 significant digits (that's 1 part in 10 billion). As Richard Feynman, the developer of quantum electrodynamics observed,l that's like measuring the distance between the Empire State Building in New York City and City Hall in downtown Los Angeles to the nearest inch.

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    7. Colnago, I do not question the existence of fluctuations in quantum vacuum. My beef is that if you say that you start with nothing, then I think postulating quantum vacuum as being part of it is a stretch (even though it does not violate Heisenberg's uncertainty principle) to then go on to include the fundamental forces needed to get the Big Bang going in "nothing" is a joke. What we can learn from this is that when cosmologists talk about "nothing" they really mean "something". Personally I think it's too much ado about "nothing".

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    8. Andy Wilberforce says,

      My beef is that if you say that you start with nothing, then I think postulating quantum vacuum as being part of it is a stretch ...

      Andy, could you give me a brief summary of your theory on the origin of the universes? What, if anything, existed before the Big Bang and where did all the energy and matter come from, according to your scientific theory?

      Do you envisage that God, Jesus, Holy Spirit, Satan, and a host of angels were just floating around in a void until one them (probably Satan) decided to create all the matter in the universe out of nothing? Were they bored? Did they have eyes? If so, what did they see?

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    9. @JimV: To twist this topic back into to my pet idea, the super computers which ran the genetic algorithms which designed the flow-path of the current generation of GE jet engines have much less processing capability than the 86 billion neurons of the human brain, so it seems feasible to me that human intelligence is based on genetic algorithms looking for solutions to problems by random guesses.

      Do you have a reference for the GE jet engine design?

      Here is a typical creationist saying evolution can't produce airplanes!

      In fact, Mr. [Bill] Nye used to work at Boeing and trust me, we can all thank God he didn’t use evolution techniques to engineer airplanes. Imagine sending a tornado through a yard full of airplane parts and expecting a perfectly good airplane to result. [The evolving creationist argument. Wednesday, October 3, 2012. The Observer (Sarnia, Ontario).]

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    10. @Diogenes, re reference for GE jet engine design.

      Like too much of what I write, it is based on (fallible) personal recollection. The background is:

      When I was working in the GE Energy Services Department as mechanical design/development engineer in Schenectady NY, we sometimes got presentations from the Phd's at the the nearby GE Corporate Research and Development Center in Niskayuna, NY, since under Jack Welch they had to justify their existence by coming up with commercially-relevant stuff and stop doing pure research. The one I am recalling was about their artificial-intelligence design system, called something like "GEnius". The example they gave of its use was a significant improvement to the efficiency of the GE-90 jet engine, with before and after diagrams of the flow path (stages of stationary and rotating vanes) which showed a considerable difference and a solution that a human designer would probably not have considered.

      I left GE in 2003 just as GEnius was beginning to be used in my field (steam turbines). Probably it has evolved since then, or been made extinct by a better competitor. I will try an internet search to see if I can find any press release on the system online. I don't have access to internal GE publications anymore.

      From my point of view, after 35 years of designing turbines, the statement "thank God he didn’t use evolution techniques to engineer airplanes" reveals that the author has little or no design experience. Everything design that I know of evolved.

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    11. Diogenes, re reference for GE jet engine design, part deux:

      Found it:

      http://www.thefreelibrary.com/Natural+selection+for+computers%3A+nature+provides+the+model+for+a...-a08170707

      "Some of the most promising systems are hybrids, combining genetic algorithms with conventional expert systems and traditional optimization methods in a computer-aided design procedure. David J. Powell of the General Electric Corporate Research and Development Center in Schenectady, N.Y., and his colleagues have developed just such a tool for engineers involved in designing mechanical components, from simple cooling fans to fuel-efficient aircraft turbine engines. Powell says the technique improves the quality of engineering designs and, by allowing the investigation of a greater number of potential designs in a shorter time, increases engineers' productivity by at least a factor of 10.

      The hybrid method has already yielded a jet-engine design that GE intends to build and test. "The design system tried things an engineer would never have thought to try," Powell says."

      P.S. Made the usual typos in my first reply, e.g., "everything design that I know of" should be "every design that I know of."

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    12. Re Andy Wilberforce

      The issue of that "nothing' means in physics is a poorly understood concept. Before Einstein's 1905 paper on special relativity nothing was defined as the aether which was a mysterious substance which supported the waves of electromagnetic radiation, much like air supports sound waves. That was superseded by a vacuum, defined as the absence of all mater after that date. With the development of quantum electrodynamics, the quantum vacuum was proposed which consists of virtual electrons, protons, virtual photons, virtual neutrinos, etc. The quantum vacuum has no macroscopic effects that can be measured as, if it affects the motion of planets, moons, and stars, the affects are far too small. It does have microscopic effects as if a physical electron is promoted out of the vacuum, the hole left behind manifests itself as a positron, thence pair production.

      The quantum vacuum is one of those features of quantum mechanics which cause physicists like Lawrence Krauss to state that nobody understands quantum mechanics or Steven Weinberg to state that quantum mechanics is a preposterous theory which, unfortunately, appears to be correct. It's an example of the old saw that the proof of the pudding is in the eating. The pudding of quantum mechanics smells awful but tastes wonderful.

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    13. Colnago, Laurence Krauss has also said that people in general do not understand "nothing" (not in the non-standard English usage meaning, but the cosmological concept). He's certainly right about that. The problem is when cosmologists like Stephen and Laurence bring it in to pop science and people take "nothing" to mean exactly (for lack of a better word) -nothing.
      It may seem petty to argue about, but it's an important philosophical question since origins theories always go back to "matter" or "mind" first. Both Laurence and Stephen, to make life a little easier, assume the existence of both matter (particles from quantum fluctuations) and mind (the fundamental forces) in their origin of the universe theories.

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    14. JimV wrote: "Some of the most promising systems are hybrids, combining genetic algorithms with conventional expert systems and traditional optimization methods in a computer-aided design procedure." This is exactly how we use it in our design (i.e. GAs do not exclude but supplement the traditional engineering work, see my response to Piotr above), and it's any thing but the mindless evolution of technology argued by Rumraket and Piotr. We use our sharpest engineers in to set up the GAs and while it certainly saves time it will never put engineers out of work since mind is an intricate part of the design process.

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    15. A reply to the notion that "nothing" should not include any natural laws, such as gravity or QM is that in that case, "nothing is unstable" (bit of a pun, not original with me, due I think to Dr. Stengler). That is, if there are no rules than there is no rule to prevent rules from forming, until eventually a stable set of rules, such as apparently our universe has, evolve.

      I doubt if we will ever know if that was the case, but the main point is that the "god hypothesis" is even less satisfying, to me and many others who think about it, because it explains nothing. "God did it" is not an explanation, involving as it does an incomprehensible entity (which has no evidence of existence that would be acceptable in a court of law), but rather just an excuse for not having an explanation. I call it "the god ate my homework" excuse.

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    16. Re: "We use our sharpest engineers in to set up the GAs and while it certainly saves time it will never put engineers out of work since mind is an intricate part of the design process."

      It has in fact put a lot of engineers out of work. When I started at GE we used mechanical calculators (and sometimes slide rules) and had a small army of technicians to do calculations (one of those technicians was the best engineer I ever knew). It turns out that a lot of things which some people believed only minds could do can be done by computers.

      The last time I checked, several years ago, the most powerful super computer was only capable of simulating one column of neurons of a rat's brain, but was capable of taking the same inputs and producing similar outputs. More recently, I saw somewhere that a project has been at least proposed to develop a super computer which will attempt to model a human brain, but I think it is many years away. And perhaps the human race will destroy its civilization before then, but it seems feasible in principle to me, based on what we already know. Such as that random searches are a good way of finding solutions, that computers can beat human grand masters at chess and Jeopardy, and that human design work evolves designs, using procedures which themselves evolved, rather than doing anything magical.

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    17. @JimV: Thanks for the reference. It goes in my notes.

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  9. Larry said:

    "If you know of something that is so completely mysterious that we are forced to invoke divine intervention then please share it with us."

    Pick one electron orbiting one nucleus in one of the hydrogen atoms of you nose hairs. How is it that the electron has position, energy, spin etc. constrained according to the mathematics of quantum mechanics?

    The fact that any physical process in nature is directed-- that is, tends to one state of affairs rather than another-- is teleology, which is the nidus of Aquinas' Fifth Way, which is one of many proofs for God's existence.

    Explain the correspondence of the motion of that one electron with the mathematical formulation of quantum mechanics, using naturalistic assumptions.

    Then multiply that problem by the number of all electrons in the universe, and you have some sense of the overwhelming evidence for God.

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    1. Then multiply that problem by the number of all electrons in the universe

      What for? One electron is like any other electron. They are simply indistinguishable. Does theology predict the mass of the electron and explain its position in the lepton family?

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    2. The last gasp of the theists is that a rational universe, *any* rational universe must be the product of a rational designer. The mere existence of 'rationality', they say, must point to a rational force that pre-dates the universe. This little belief is the last vestige of the once great Christian theological structure. The rest of it's gone. It's almost sad.

      As discussed in the 'what do IDiots believe?' thread, this is underpinned by 'teleology', literally looking at the universe ass-backwards and declaring that where we are is the deliberate destination of a 'divine purpose'.

      If we're talking about electrons and unlikeliness, try calculating the energy needed to deliberately steer every particle in the universe from the Big Bang to its precise current position. Then try explaining the mechanism without invoking magic.

      It's silly. I'll should probably wait for mregnor to splutter one of the tired old moves before doing the countermove, though, it's only polite.

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    3. Hm, let's see - OK, how about this: The electron has properties consistent with a viable universe (i.e., a universe capable of existence) because these are electrons in an existing (therefore viable) universe.

      Is this the *only* viable universe, and are these thus the *only* properties the electron can have? Are there viable universes that have electrons with different properties, or particles so different that they can't be called electrons, or nothing corresponding to the concept of particles at all? Don't know, no one does, and until you do, there is zero evidence of fine tuning, thus zero evidence of a fine tuner.

      Ask us a harder one next time, Dr. Egnor.

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    4. judmarc:

      I'm not making a anthropic argument. I didn't claim that only one specific teleology is proof God. I assert that any teleology is proof of God.

      If only one electron in only one of countless universes once tended to one end, and not another, that would prove God.

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    5. "I didn't claim that only one specific teleology is proof God. I assert that any teleology is proof of God. If only one electron in only one of countless universes once tended to one end, and not another, that would prove God."

      As with TOF in the 'What do IDiots believe?' thread, this is the simple tactic of taking a bit of medieval-via-Aristotle theology and welding it to a bit of modern science and pretending that's an argument.

      What does 'if one electron tended to one end' mean? Is it a scientifically testable statement? If so, run the test. It's not hard to find electrons lying around the place.

      If it's an appeal to a quantum miracle, then yeah, bring it on. Show us one. It'll be far more convincing than laughable medical miracles (Cardinal Newman got to be a Saint because a man in hospital for back pain took pain medicine and the pain cleared up in 48 hours. The man credited it to Newman because he was watching an EWTN special on Newman. One that ended 'oh, if only a miracle could be attributed to him, that would be grand'. Oh yes ... and the man who was cured was a Catholic priest. Convinced, yet?). But then, once you've shown us this quantum miracle, perhaps you'd like to repeat some of the modern theology that notes that miracles are discredited now, because why would a burning bush 'prove' God existed?

      You're playing a 'heads I win, tails you lose' game. You're appealing to the fine tuning argument and saying how could a universe that runs so lawfully exist without a God. You're then saying if this God tweaked and tucked away at it and performed miracles that would prove there was a God.

      The argument here is self-refuting, that's the thing. We call things with all the properties of electrons and nothing else 'electrons'. We don't call things with a different set of properties of electrons 'electrons'. If we found a duck with tentacles that didn't fly or quack, we wouldn't have found a duck.

      There are many wrinkles on the philosophy of teleology, but it basically boils down to 'nature has goals'. Which, of course, is pretty meaningless by itself. We're part of nature, we have goals. What is generally meant is that things without consciousness still have purpose. As they don't have consciousness, the purpose must be coming from somewhere else.

      It's massively muddled. Yes. If an archer aims an arrow at a target, the goal is to hit the target. But the teleology crowd believe that God aimed evolution at giraffes. That when we trace the line back, we can see giraffes evolved 'to' eat the tall leaves, and that as the proto-giraffes and the genes don't know that, someone must know, and that's God. Obviously there's a little more bafflegab to it than that, and so brace yourselves for 'you clearly don't understand teleology' and endless waffling about the Four Causes, but that's the simple version.

      Child's play to dismiss this as a laughable idea ... but that's all they've got left.

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    6. Something happens consistently - therefore god.

      Thanks, you have lost your mind.

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    7. Yet if things happened completely randomly and inconstistently, that is if nothing like observable laws of nature existed and matter just happened to end up clumped together into thinking living beings seemingly at random, then that would be claimed as evidence of God.

      The only coherent universe that could possibly exist in the absence of God, i,e. one which operates in accordance with regular, predictable natural laws, just happens to be the one in which we find ourselves. That's an interesting coincidence, isn't it?

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    8. Smegnor is defining the rules so that any conceivable observation is proof of his baby-murdering queer-hating war deity.

      If physical laws are violated, it's a miracle! The only possible "explanation" for math not working is God did it. If physical laws are obeyed, it's math! The only possible "explanation" for math working is that God did it.

      If scientists can't understand a phenomenon, that's proof scientists are stupid, and therefore religious people like Egnor are smart (the only evidence of intelligence he'll ever obtain.) And if scientists can understand a phenomenon, that is not proof that scientists are smart, of course not! because the "only possible explanation" for their math working is a triune God that is just one single deity but three persons: one person a genocidal Middle Eastern war deity, the second person a murdered rabbi who comes back as a zombie bent on revenge, and a third person that is a pigeon but occasionally takes the form of a ghost to impregnate teenage girls. Together, they send babies to hell if they're not of the right religion.

      Here Smegnor is arguing that because particles obey mathematical laws, that must be "teleology" which demonstrates purpose and therefore, proof of God. Of course, particles not obeying mathematical laws is a miracle and also demonstrates purpose and is also proof of God.

      Now let's deconstruct this mother bugger.

      Smegnor: Explain the correspondence of the motion of that one electron with the mathematical formulation of quantum mechanics, using naturalistic assumptions.

      The key word here is "Explain." Whenever you hear some theist ass use the word "explain" in an apologetic sense, the fix is in. They use "explain" to mean one thing for science and a totally different thing for religion.

      No religious belief nor theologian nor apologist has ever explained any observed phenomenon under supernaturalistic assumptions. They merely redefine the meaning of the verb "to explain", using one definition of "to explain" for the theist (make any shit up!) and a different definition for the scientist (give us indisputable video evidence!).

      In religion, an "explanation" is any fairy tale that alleges a cause for an event. I call these SNAC: supernatural allegation of cause. Examples of SNACs include

      1. Snow White was dead. Why did she come back to life? A prince kissed here.

      2. The prince was a frog. How did he change back? A princess kissed him.

      3. Natural phenomena may be described and predicted by mathematical laws. Why does math work in science? A triune deity consisting of an irrational, despotic, basically insane Semitic war deity, a zombie rabbi, and a pigeon that occasionally takes the form of a ghost created the universe by an means unspecified, except we know it was magic.

      A SNAC is not an "explanation" that flies in science. Scientific explanations require evidence.

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    9. To continue, against Smegnor: Scientific explanations require evidence. There are only two kinds of scientific explanations.

      1. Ordinary claims. A chunk of sandstone with amphibian trace fossils is at the bottom of the Grand Canyon instead of being in the strata of amphibian trace fossil-bearing Coconino sandstone, which is hundreds of feet higher up the canyon. How did it get there? It broke off and slide down by the law of gravity and by analogy to past observed processes of rocks rolling down hills. i.e. Induction by analogy to uniform past experience.

      2. Extraordinary claims backed up by extraordinary evidence. Why do leptons and quarks have rest mass? They are interacting with a neutral spin zero boson with a nonzero expectation value in the vacuum, which should be synthesized, and thus be detectable, if we smash together protons and antiprotons at a resonant energy of 125 GeV. i.e. Theories that make testable predictions which may match observable quantities.

      So to return to Smegnor's question,

      Explain the correspondence of the motion of that one electron with the mathematical formulation of quantum mechanics, using naturalistic assumptions.

      The point is that neither Smegnor, nor any Christian nor Jew nor any theist, can explain anything about the universe under super naturalistic assumptions.

      All he can do is redefine the verb "to explain", replacing it with "make shit up, and say it again and again, until you exhaust your intellectual superiors."

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    10. I'm not making a anthropic argument.

      Neither am I. I'm not talking about a universe in which we exist. I'm talking about a universe that exists, period. Any universe that exists requires constituents. The universe in which we find ourselves has - zut alors! - constituents, including electrons. Duh.

      If you are claiming that the raw fact of at least one universe existing indicates God, I've read books about inflation, the landscape, and other scientific discussion regarding potential explanations, which I must say seem to have stuff like actual evidence and math notably lacking from your argument.

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  10. "Explain the correspondence of the motion of that one electron with the mathematical formulation of quantum mechanics, using naturalistic assumptions. ". Particles do what particles do. Quantum mechanics is a human constructed mathematical model of what they do. The only room for god is in the fevered imagination of religionists.

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    1. As Laplace put it when proving that the Solar System did not require outside intervention to remain stable over long periods of time, when asked by Napoleon what role god might play, he replied, "I have no need of that hypothesis". Similarly, we have no need of a god hypothesis to explain the hydrogen atom.

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  11. For me science is science and religion is religion. I don't get why so many try to call oranges, apples and apples, oranges.

    Science is about the facts, the evidence, the experiments.

    However, for myself there is a basic purpose here -though it be a unitarian one. All life persists to survive and reproduce, yes? If we look at the parts that help us breath we could say the purpose is to aide in respiratory function. The function is the purpose.


    Religion is just another way of saying how people define life which varies and which is the intuitional, the feeling, the experiential. Is it a method? I would not call it so.

    Some people may find higher purpose in this and others may not.

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  12. On a more interesting note: Inter-Species Communications can be found at Iowaprimatelearning.org with the Bonobo Kanzi who can sign and I hoe to work with Bonobos and Orangutans in a few years after a bit more study -I'm convinced they can learn to write.

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  13. On a side note:
    Nature does not need man to exist...yet it persists.

    Religion does.

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  14. We have no need for miracles in order to understand the history of life. - Agreed.

    That does not mean that we have complete and absolute proof of every single step, including the origin of life. It means that we have reasonable scientific explanations that are fully consistent with everything we now about science. -Agreed

    One of the most important lessons of science is that life evolved from simple primitive organisms over a period of at least three billion years. -Agreed

    The history of life can be fully explained by natural causes without any need for miracles or divine intervention. -Agreed

    We have learned that the evolution of life on this insignificant planet, in an ordinary galaxy, in a vast universe -Agreed

    has no purpose or goal. -----Not sure I agree. Nature's purpose is not always Man's ideas of purpose. To me it seems like nature persists to survive and this leads to eventual reproduction. Even the "non-living" -cosmos evolved. But the more complex and ordered things become, the faster their energy leads to entropy yes?

    So nature persists to survive (life) and energy persists to entropy (death).

    There aren't many religions that can accommodate those facts- Not sure I agree, life and death are common themes in religion.

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  15. evolution of a skeptic

    M. Behe: As a Roman Catholic I was always taught that God made life, and how He made it was up to Him. I was taught that the best scientific answer, so far, for how God made life was Darwinian evolution. That made sense to me, so I never gave evolution much of a thought. I was taught in my undergraduate years and graduate studies in biochemistry that all of these fantastically intricate systems that I was learning about were the result of Darwinian evolution. I had a thesis to complete, so I didn't think much about it.

    However, in 1987 or so, I read Evolution: A Theory in Crisis by Michael Denton. It startled me because he said there were huge and unaddressed problems with evolutionary theory. In fact, there was a very good chance the theory was incorrect; it could not really describe how life came to be. When I read [Denton's] book, I got mad; I was upset because I realized much of my world view was not based on science, but rather on people saying, "Well, yes, this is the way it happened. Don't worry about it. Maybe you don't know how it happened, but somebody else does."

    Well, reading Denton's book made me realize that nobody else knew about the problems. And from then on I became increasingly interested in it. I looked in my own field of biochemistry and in the National Academy of Sciences and the Journal of Molecular Biology and places like that for research that might say how these biochemical systems were gradually put together. I rapidly found out that there were no such papers.

    the critics of my book have uniformly agreed that the biochemical systems I describe are enormously complex and currently unexplained, but they differ in their prescriptions. Some of them say, "Well, Darwinism will eventually explain this." Other people say, "Well, we don't know how it will be explained, but we'll come up with something in the near future." My reply is that the something that we can come up with in the near future is intelligent design theory. It is a perfectly legitimate scientific idea and there is no reason to avoid it.

    An analogy I like to draw is to physics: many physicists were unhappy with the idea of a big bang because it seemed to have clear theological implications. Nonetheless, physicists embraced it as a legitimate scientific theory and built on it. I see intelligent design the same way; it may have religious implications but it's a clear scientific theory based solely on observations of biochemical systems that we should embrace and build on.

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    1. "I was upset because I realized much of my world view was not based on science, but rather on people saying, "Well, yes, this is the way it happened. Don't worry about it."

      You start there by seeming to demonstrate a really good understanding of what scientists do, then undercut it by showing you just don't get it at all.

      Yes, 'the scientific method' is basically a mechanism to instill trust. It involves training, dedicated personnel, systems in place to record, test, review and disseminate information. Trust Larry, he's written peer-reviewed textbooks.

      The main reason to do this: so that we can all move on to the next thing. We don't need to endless prove things we already know to be the case.

      The bit you get *totally* wrong is that Larry is saying 'don't worry about it'. He is saying worry about it *all the time*. Attack it with all your might. Pick holes in it. Question it. Try to prove him wrong. Try to prove that what we think of the case isn't. But you do that with science, not by aggressive guessing.

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    2. Jem, the whole post is one long quote from an interview with Michael Behe (with gaps, left ummarked). Unless it's Professor Behe himself disguised as "Unknown" (which is extremely unlikely), the author is simply

      Trollin', trollin', trollin',
      Rawhide!

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    3. "I see intelligent design the same way; it may have religious implications but it's a clear scientific theory"

      It's testable and makes falsifiable claims? Go on, then, name one falsifiable claim that ID makes. Give one example of a situation where ID predicts one thing and evolutionary theory predicts another and we observe what ID predicts.

      ID isn't a coherent system, it's a challenge to an existing system. Which is fine, as it goes - as a non-scientist, it's great to see a creationist argument about, say, the evolution of the eye utterly demolished, because it helps throw the elegance and simplicity of evolutionary theory into sharp contrast with the witch doctor muttering and incantation of the superstitious.

      Go on: give an example of one falsifiable ID proposition.




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    4. "Jem, the whole post is one long quote"

      OK. Thanks. A troll mindlessly quoting an idiot? I think that's as good a definition of religion as I've ever seen.

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    5. @Jem,

      Egnor has attempted to defend his proof of God in Larry's nose hair at his own blog. His blog post is entitled, "God, in Larry Moran's Nose." I'm clobbering him. Perhaps you might like to watch.

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    6. Michael Denton describes his current view in Nature's Destiny (1998). He believes that God created the universe in a way that makes the evolution of intelligent beings (humans) inevitable. Once He set the ball rolling, all other process are completely naturalistic. Denton's God does not meddle with making bacterial flagella and Denton's God is quite happy with modern evolutionary theory.

      Here's what Denton says in the introduction to his book ...

      ... it is important to emphasize at the outset that the argument presented here is entirely consistent with the basic naturalistic assumption of modern science—that the cosmos is a seamless entity which can be comprehended ultimately in its entirety by human reason and in which all phenomena, including life and evolution and origin of man, are ultimately explicable in terms of natural processes.

      The IDiots, including Michael Behe, are not happy with this idea. They want to prove that there's something wrong with evolution.

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    7. Following up on your comments on contingency in another thread, however, Larry: If Denton believes the evolution of intelligent beings was inevitable, does he really understand modern evolutionary theory?

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    8. Too bad Behe never read Nature's Destiny. Could have saved a lot of trouble.

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    9. Denton's position is similar to Ken Miller's position. Miller once thought that the evolution of humans was inevitable but it appears that he has backed off somewhat from this position and now thinks that the evolution of intelligent life was inevitable.

      IMHO, this is, at least, a defensible position that has some data to support it.

      As I have argued over at Panda's Thumb, a necessary (but not sufficient) condition for intelligence is encephalization, defined as an increase in the ration of brain size to body size (for example, in humans, it's about 7 times the average value for mammals; in bottlenose dolphins, it's about 5 times the average of mammals).

      We have two data points in the evolution of life on this planet. The Cretaceous dinosaurs had larger encephalization factors then their Jurassic antecedents. Current mammals have larger encephalization factors then the mammals of 50 million years ago. Thus it would appear that there is evidence that encephalization may have a selection advantage. Note that encephalization is not sufficient as Neanderthals also had an encephalization factor of about 7 and went extinct.

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    10. You have two data points, but you have picked them from among the thousands of available data points. Why choose dinosaurs and mammals out of all the various animal groups? Greater encephalization may be selected for sometimes, for a while, but certainly not all the time. It doesn't even work throughout vertebrates.

      The mammal thing is commonly interpreted as an arms race between mostly carnivoran predators and mostly artiodactyl prey. Not all orders took part in it, certainly.

      I'm unclear about the dinosaurs. Do you have a reference?

      I don't see how this is evidence of inevitability. Two small groups within a single phylum? Even if you add cephalopods, it doesn't amount to inevitability.

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    11. Re John Harshman

      I don't have a handy reference for the dinosaurs but the most encephalized species were the Troodons. Paleontologist Dale Russell has speculated that, had they not gone extinct, they might have evolved into intelligent birdlike creatures. I understand that this is a controversial issue.

      I think that Harshman is missing the point. The point is that the average encephalization of mammals today is larger then the average of mammals of 50 million years ago. It's not just one or two species. Similarly, it is my information that the average encephalization of Cretaceous Dinosaurs was higher then the average encephalization of Jurassic Dinosaurs. Again, we're not talking about just one or two species of dinosaurs.

      As for the reason for the increase in encephalization it doesn't really matter what the reason was. The result is that it did increase for whatever reason.

      By the way, I never said that these two data points "prove" the inevitability of the development of intelligence. It is evidence of a selection advantage for encephalization. My only claim is that Miller's argument of inevitability can't be summarily dismissed. On the other hand, since encephalization is not a sufficient condition for the evolution of intelligence, (sic transit Neanderthals) it doesn't "prove" inevitability. Brain organization is also important and the evidence we have so far is that the organization of Neanderthal brains was rather different then human brains.

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    12. Brain organization is also important and the evidence we have so far is that the organization of Neanderthal brains was rather different then human brains.

      What evidence do you have in mind?

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    13. I'd say you have no evidence for your conclusion of a "selective advantage for encephalization". You may have evidence of an advantage in some places, in some taxa, at some times. But so far it's at most two places, two taxa, two times. And you do know that averages are affected by individual points, right? If just one mammal species increased in encephalization, the average would go up. Now in fact it was many species, but as I've said that many was mostly in two orders (or perhaps lifestyles, as monophyly isn't all that clear) out of all the mammal orders.

      The question of brain organization is separate, certainly.

      And one paleontologist's unsupported speculation about dinosaurs isn't evidence of anything.

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  16. I am not engaging any debate, just looking for answers.

    What I observe is that there are scientists who are skeptic about darwinian evolutionary theory and are working on alternatives. ( why would they do that?)
    There are others who admit they don't know.there are others who admit that are wishfull speculations.
    And there are who claim they know and although the burden of proof is on them they don't provide reasonable arguments to the public. The only argument is from their supposed authority. "We are scientists trust us"

    How do I decide which group is more reliable?

    Did science demonstrate the supposed fact that life evolved by unguided known mechanisms? What are the mechanisms and what are the arguments /evidence of their adequacy to generate all life forms?

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    1. What I observe is that there are scientists who are skeptic about darwinian evolutionary theory and are working on alternatives. ( why would they do that?)

      Leaving aside what you think you mean by "darwinian evolutionary theory", this is true for sufficiently broad meanings of "scientists" and "working". But they have to be pretty broad. Why they do that, if you are referring to IDers, is because of a prior commitment to theism and an emotional need to have god active in earth history.

      I don't know who falls into your other groups. Sounds like a bunch of strawmen to me.

      The reason we think evolution is unguided is that nobody has been able to find a mechanism of guidance or a pattern that suggests guidance. The mechanisms of evolution are fairly well known and can mostly be subsumed under the categories of selection and drift. As evidence of their adequacy, we can point to a couple of things. First, the differences among species genomes are precisely the sorts of things that arise from random mutation. Second, we have never observed any other mechanisms operating, either in the wild, in the lab, or in historical data. And you would think that if there were something else going on we might have some evidence of its operation.

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    2. I am not engaging any debate, just looking for answers ...

      How do I decide which group is more reliable?


      In order to decide who you should trust, you have to learn how to think critically and to recognize critical thinking in others.

      Then you have to practice it by engaging in debate and testing your skills against worthy opponents. Try it. It takes a few years but it's worth the effort.

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    3. Re unknown

      In the first place, Prof. Moran is not a "Darwinist" as he makes clear. He considers that random genetic drift plays a greater role in evolution then the supporters of natural selection, like Richard Dawkins and Jerry Coyne admit.

      In the second place, the evidence for common descent is extensive. For starters, the presence of ERVs at the same locations in mammalian genomes is only explainable if they had common ancestors. As Ken Miller says, "I'm a theist but I don't believe that god is a trickster who has placed ERVs in these locations to fool us." For humans in particular, the fact that humans and the great apes all have a broken gene for the production of vitamin C, almost alone among the mammals, is strong evidence for common descent. Further, there is the presence of 4 telomeres and two centromeres in human chromosome 2, which have been identified with chromosomes 12 and 13 in chimpanzees. This explains why apes have 24 pairs of chromosomes and humans 23. Chromosomes 12 and 13 fused together sometime after the split between the ape line and the hominid line. See attached link to a portion of a presentation by Ken Miller.

      http://goo.gl/SDSkV7

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    4. Yes and while on the subject of trying to decide who's right about a certain scientific theory, you have to learn the science being debated, in addition to critical thinking.

      This kind of appeal to "someone questions X, therefore the matter isn't settled" is a fallacy. There are people who question logic itself.

      Questions have right and wrong answers, someone is right in the evolution-creationism "debate". Quick hint: Almost the entirety of the opposition to evolution comes from deeply religious people. While this in istelf does not conclude the matter, alarm bells should be going off in any thinking person. Read the science, learn critical thinking. The matter actually IS settled. The lone fringe-nut standing on the sidelines screaming "2+2=5" doesn't constitute a genuine scientific controversy that puts the whole matter up for grabs.

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  17. I am not questioning common descent. I don't think common descent proves the mechanisms.

    I would like to know what are the evidence that random mutations and natural selection or whatever are adequate?
    I thought that scientists confidence is based on some experimental demonstration. I imagine for instance to get X from Y you need these mutations and is reasonable to happen in n years, but I think it's not the case.

    When I read something on the topic I always get the feeling that all they have is not much. Not even bacteria (for instance can science show how bacterial flagella evolved?) If you follow an ID vs evolution debate the argument always goes like this: just because there are problems with the darwinian theory doesn't mean that ID is true. Of course it doesn't , but why the darwinists can't defend the theory if it's settled that the random processes are adequate?

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    1. You might want to peruse this early post from Larry. It concerns the genetic differences between humans and chimpanzees, and whether the available time between us and our common ancestor is sufficient to have produced these differences:

      http://sandwalk.blogspot.ca/2012/01/whats-difference-between-human-and.html

      (Because, let's be honest: This is the one example of common ancestry you creationists are most upset about)

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  18. John Harshman:
    "The reason we think evolution is unguided is that nobody has been able to find a mechanism of guidance or a pattern that suggests guidance."

    Isn't that similar to the argument from ignorance IDsts are charged? We cannot find a guided mechanism so it's unguided. If God did it I can easily imagine that the mechanisms are not detectable. But the result can be detected if it's caused by intelligence or not.

    Doesn't irreducible complexity show that guidance or design is required?

    Jem said:
    "It's testable and makes falsifiable claims? Go on, then, name one falsifiable claim that ID makes."

    Didn't some claim that have falsified irreducible complexity? Is it falsifiable or not?

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    1. Isn't that similar to the argument from ignorance IDsts are charged? We cannot find a guided mechanism so it's unguided. If God did it I can easily imagine that the mechanisms are not detectable. But the result can be detected if it's caused by intelligence or not.

      So it's undetectable and detectable at the same time?

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    2. Isn't that similar to the argument from ignorance IDsts are charged?

      No. The ID argument is that we don't know how something happened, therefore God. My argument is that we know of those mechanisms but no other mechanisms, and those mechanisms operate in ways that would produce the data we see, so it's a good, if tentative conclusion that those mechanisms are responsible, not others. "I had no need of that hypothesis." Now of course that doesn't mean we have detailed, step by step explanations for every single thing that happened in evolution. But everything we do have such explanations for uses the standard mechanisms.

      Doesn't irreducible complexity show that guidance or design is required?

      No, it doesn't. There are many ways in which irreducible complexity can evolve naturally. You may want to look up "scaffolding", for example.

      Is it falsifiable or not?

      Do you mean to ask whether we can tell if something is irreducibly complex? Well, of course we can as long as both the system and each of its parts are well defined. In practice, that can be difficult. But all that would be required in such cases would be to remove each of the parts, one at a time, and show that in each case the system no longer functions. However, that says nothing about evolution, since there is no requirement that evolution works by sequential addition of invariant parts.

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  19. Re unknown

    Irreducible complexity has not been disproved as a general proposition. However, it has been shown that the blood clotting cascade, the bacterium flagellum, and the immune system are not irreducibly complex. In fact, the IDiots have yet to point to a biological system that can be shown to be irreducibly complex. A good discussion for the layman (in this case for federal judge John Jones III) can be found in Ken Miller's testimony in the Dover Trial which can be found in several locations on the web. Google is your friend. In particular, he shows that the bacterial flagellum could have evolved from the type three secretory system. Again, Miller gives a good layman's description in his Dover testimony.

    As for whether natural selection is robust enough to account for the evolution of life as it currently exists, the owner of this web site is one of the folks who doesn't accept this. It is his position that random genetic drift and other mechanisms also are important. This is an active controversy in the evolutionary biological community as Richard Dawkins and Jerry Coyne are biologists who strongly favor natural selection as the overwhelming mechanism driving evolution.

    As someone whose degree is in physics, there is nothing at all unusual about such a scientific difference of opinion. For a long time, many physicists thought that quantum field theory was not applicable to strong interaction physics. However, development of the quark model and quantum chromodynamics have put that controversy to rest.

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    1. I think there are examples of irreducible complexity. The enzymes of the citric acid cycle are a good example and so are the various photosystem complexes.

      However, I think we have excellent explanations for how these systems evolved. Thus, it's simply not true that irreducible complexity cannot be explained by evolution.

      That's why some IDiots are redefining irreducible complexity so that now it only applies to those systems where we don't (yet) have a very good understanding of how they evolved.

      Pretty clever, eh? It's sophisticated theology, otherwise known as the gods of the gaps.

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  20. Andy Wilberforce asks,

    So what about the sudden appearance of most animal phyla during the Cambrian Explosion?

    I'll leave to others to address your misunderstanding.

    I'd like to find out what YOU think happened? Nobody, including Stephen Meyer, has explained the "goddidit" model. Did your god(s) get tired of playing with bacteria, plants. algae, fungi, and protozoa after several billion years and decide to make something a bit different around 500 million years ago?

    Why did it take them tens of millions of years to come up with species that they allowed to go extinct after few million years? Why did they "design" the new species so that the sequences of their genes resembled all the species that had existed up 'till then? Why were they so fond of arthropods and so skimpy about making chordates?

    Why did the gods only make sea creatures? Didn't they know how to make animals that could live on the land and breathe air? Why did they make different animals in China from the ones in Canada?

    Which gods made Hallucigenia? Why?

    Were the gods drunk when they designed Anomalocaris? Why are there no animals that look like that today?

    You don't have to have precise answers to all these questions but if you could flesh out your theory a little bit I'd sure appreciate it.

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    1. Larry, I think that if you thought about creation more along the lines of terraforming/planetary engineering instead of magic then many of your questions would be answered. An example of what I mean by terraforming is the process leading to an atmosphere rich in oxygen by means of photosynthesis. This in turn permits an expansion in metabolic activities necessary for complex life forms. This is a teleological approach where earth’s history leads up to the world as we know it today, not by magic or chance, but because of the directed forethought of a Supreme Being.

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    2. So your planetary engineering just looks like natural processes where one thing impacts and results in another? Why believe this kind of engineering takes place in the first place then, how would you distinguish situations where it's just a natural process that leads to these events, from situations where they're being directed to a supreme being?

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    3. Imagine that you could visit 100 different planets that were teaming with life. Each one of them has a history that's unique and none of them are similar. Would you interpret each of them as examples of design by your god(s) or would you start to doubt your explanation?

      The history of life on Earth is a unique event. It's amusing to look back on it from our perspective and assume that it all had to happen exactly the way it did because it was directed by your favorite imaginary being. That's a post hoc fairy tale that's completely devoid of any explanatory power. Those sorts of vacuous statements only make sense to true believers who have long ago abandoned the concept of critical thinking.

      When I look at the history of life on Earth I see little evidence of design or direction. If I had the power to produce truly humane and intelligent beings using directed evolution, I could have done a much better job.

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    4. The vast majority of lineages go extinct eventually. From time to time, climate changes, asteroid impacts or volcanic mega-eruptions wipe out most of the species. The Designer apparently spent tens of millions of years in the Early Cambrian designing various bilaterian groups only to destroy many of them at the close of the Cambrian, and still more by the end of the Paleozoic. Even birds and mammals were almost completely killed off by the K-Pg event, and the descendants of the survivors kept being decimated later on. It all that was indeed planned in advance, the Designer must have an alternative sadistic personality -- the Bloody Butcher.

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    5. Larry wrote: "That's a post hoc fairy tale that's completely devoid of any explanatory power. Those sorts of vacuous statements only make sense to true believers who have long ago abandoned the concept of critical thinking"

      So, what is the alternative then? Naturalism? Does it provide the explanations needed or are they only credible to the "true believers"?

      In order for Naturalism to be an explanation for our existence it need to provide a theory which makes it not unlikely that a sequence of naturalistic processes starting with the chemistry on the infant earth could lead up to the first self-replicating unit. Naturalism must further be able to provide a reasonable explanation for how this self-replicator can account for the diversity of life, now and as shown in the fossil records, in the timeframes available. Further it needs to show how minds with consciousness and intentionality are not unlikely by-products of this process.

      To me it's clear that Naturalism fails give us answers to certain questions because it is built on the wrong premise.

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    6. The observation is that natural processes has resulted in what we see. There is nothing that motivates or merits positing divine terraformers to "will" these events into motion. One naturally leads to another. The cambrian explosion, which was the subject we were discussing but you're now trying to sidestep and start blathering about the origin of life, is fully explainable as a natural phenomenon.

      Not only that, we have evidence of the sequence of events that lead to it, and it makes sense given what we already know of physics, biology and natural processes.
      To posit unobserved, undetectable, unfalsifiable supernatural terraformers operating in the deep geological past, somehow "willing" these events to manifest consitutes a complication, an additional entity not required to explain the observed data. Your model is uneconomical, it is entirely ad-hoc and cannot be falsified. There's simply no need to posit this kind of entity to cause this sequence of events. Even worse, there's no concievable series of events for which you could not simply fall back on the same ad-hoc rationalization "it's what the divine miraculous terraformer wanted". Which was the point Larry was alluding to with observing 100 different biospheres.

      Whether they were the result of natural processes or your divine homemaker, the simple fact is that the observed will always be the result of some contingent history before it. "Then a meteor hit, which destroyed life on this continent, leading to a change in oxygen levels and blocking out a lot of daylight for decades" and so on and so forth. One natural thing causing and leading to another. It would be the same thing everywhere, whatever had evolved(or not), there would be some long series of events leading up to that result.

      How would you distinguish the works of your designer from not? You couldn't. It doesn't matter what the result is, the same silly after-the-fact rationalization you offer is fits-all. "Yes yes, on this planet the designer wanted the highest form of life to be scotoplanes, that's why X, Y and Z happened to cause it. Yes, the designer wanted this planet to be dead, that's why the local sun died out."

      It would be a lot more impressive if you could predict something instead of going back through history and thinking "this happened, somethign else could have, so the Yahweh-Terraforming Corp must have dunnit".

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    7. Andy Wilberforce asks,

      So, what is the alternative then? Naturalism? Does it provide the explanations needed or are they only credible to the "true believers"?

      For those of us who don't believe in any of the gods, there is no alternative. "Naturalism" (=reality) is the only possibility. Now, that doesn't mean that we have detailed explanations for everything but it does mean that we see no need to invoke extraordinary supernatural explanations for anything we see. The Cambrian explosion, for example, is perfectly compatible with everything we know about nature and although we aren't sure which explanation is correct there are several plausible scenarios.

      In order for Naturalism to be an explanation for our existence it need to provide a theory which makes it not unlikely that a sequence of naturalistic processes starting with the chemistry on the infant earth could lead up to the first self-replicating unit.

      We have the theory. What we don't know is the exact sequence of historical events leading to the origin of life. In this case, the best answer is "I don't know how life originated." Saying "I don't know" is a perfectly reasonable position while awaiting more data [see "Yes," "No," and "I Don't Know"].

      Fact is, you don't know either. You have yet to offer us any theory of the origin of life involving your favorite god(s). If you did, then we could examine it and see if it conforms to all the data we have collected over the past century. Right now it doesn't seem necessary to postulate the existence of some mysterious, omnipotent being in order to explain the origin of life on Earth.

      Besides, it doesn't really solve the problem since we still need a reasonable explanation for the origins of those gods. Do you have one? Who came first, Satan or the God of the Bible? Did one of them make angels or were angels there from the beginning? What about cherubim? Is the Holy Spirit older than God or Jesus? What do your gods look like? Do they look like humans?

      Did they create life on lots of other planets or just on Earth? Why did they pick Earth? Why did they choose evolution—it's very sloppy and inefficient?

      To me it's clear that Naturalism fails give us answers to certain questions because it is built on the wrong premise.

      I hope I've explained that we don't have detailed natural explanations for everything in spite of what you might think. It's okay to say "I don't know."

      But since you seem to demand detailed explanations maybe it's time for you to step up to the plate and give some?

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  21. Which gods made Hallucigenia? Why?

    Were the gods drunk when they designed Anomalocaris? Why are there no animals that look like that today?


    Perhaps God was under the influence of the mushrooms he had just started growing.

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