Friday, August 2, 2013

Bell’s Number, the Interactome, and a Peek at a Monumental Problem for Evolution

Oh my

If you ever wondered how the biological world could have arisen from random events and a few simple natural laws then you might be interested in a recent paper introducing some basic, fundamental problems confronting evolutionary theory. For whereas man-made machines may have a great number of components, such machines are specifically designed to limit the number of interactions. The components only interact with a small number of other components and a matrix describing these interactions would be very sparse. Not so for many biological systems. The paper shows that the magnitude of the interactome—the sum total of all interactions in systems such as the nervous system—is on the order of Bell’s number, which scales faster than exponentially. Indeed, for n discrete components, the logarithm of Bell’s number is n[log(n) – 1].

This means that even if we believe, with Moore, that compute power doubles every 18 months or so, it nonetheless will be impossible to analyze even a single synapse for another few millennia. And the visual cortex of a mouse? That will take about 10 million years to analyze.

But what if even Moore was pessimistic? Or what if only a tiny fraction of the interactions actually need to be characterized, say 0.001%? Such luck would not appreciably change the answer.

Technological advances and modeling simplifications do little in the face of the curse of dimensionality and researchers now use the term “complexity brake” to describe the resistance of biological systems to computer analysis. In fact, this brake is only going to become worse, for the more we learn about biological systems, the more complexity we discover:

Improved technologies for observing and probing biological systems has only led to discoveries of further levels of complexity that need to be dealt with. This process has not yet run its course. We are far away from understanding cell biology, genomes, or brains, and turning this understanding into practical knowledge. The complexity break is very apparent in the figure (shown above).

All of this not only means that the analysis of such biological systems is impossible, it also means that the evolution of such biological systems is impossible, or at least scientifically unlikely. For the problems in analyzing these systems also apply to evolving these systems.

Not only is there a large number of interactions but, unlike a bottle filled with a gas which can be characterized by averages and distributions, in biological systems the specific, individual interactions matter.

It would be serendipity on steroids to say that evolution, with its limited experimental powers, designed and created a few basic components which then, as luck would have it, combined in such a way to produce far greater complexity and emergent behaviors.

And that, here in the twenty first century, is increasingly what evolutionary theory is all about: serendipity.

93 comments:

  1. " in biological systems the specific, individual interactions matter."

    Let me beat Thorton to the punch. If the individual interactions are more numerous than the grains of sand on the shore or the number of stars in the sky -- and each one MATTERS, then God did it!

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    1. You've added nothing to the discussion but your own ego.

      Delete
  2. To recap...

    P01. Belief in scientifically impossible theories are religious
    P02. Evolutionarily theory is a scientifically impossible theory
    C01. Belief in Evolutionarily theory is religious

    There are several problems with this, but I'll focus on just one.

    P02. Evolutionarily theory is a scientifically impossible theory

    Actually traveling though space faster than the speed of light is scientifically impossible. This is because it is explicitly prohibited by the laws of physics.

    In what way is evolution scientifically prohibited? This post does nothing to clear this up.

    CH: Not only is there a large number of interactions but, unlike a bottle filled with a gas which can be characterized by averages and distributions, in biological systems the specific, individual interactions matter.

    Matter in what way? At best, you'e indicated that a reductionist theory of how biological organisms work is currently impossible, not that evolution itself is scientifically impossible. And an exhaustive explanation for anything is impossible, in practice. Furthermore, you're assuming that we will not learn anything significantly new, such as how to build working quantum computers with more than a few qbits in the next 50 years.

    CH: It would be serendipity on steroids to say that evolution, with its limited experimental powers, designed and created a few basic components which then, as luck would have it, combined in such a way to produce far greater complexity and emergent behaviors.

    Incredulity != scientifically impossible.

    Again, the underlying theory behind Darwinism is that biological complexity arrises though genetic variation, that is random in respect to any particular problem to solve, and natural selection. It's an emergent process. T

    hat evolution should a reductionist theory is not scientific.

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  3. So, cornelius, since every last detail of billions of years of evolution hasn't been figured out yet, evolution is impossible and evolutionary theory is definitely wrong and evolutionary scientists might as well quit their jobs and become street corner preachers?

    And what exactly do you mean by "analyzing" biological systems? Do you mean that the origin, interaction, and function of every subatomic particle in the universe must be analyzed and completely explained before evolutionary theory or any other scientific theory can be determined to be right or wrong?

    If that's what you mean, then how can you know that evolution doesn't occur and that evolutionary theory is wrong unless you have analyzed and completely explained the origin, interaction, and function of every subatomic particle in the universe?

    In other words, if you expect proof at that level of detail before you'll accept that evolution occurs and that evolutionary theory is at least generally right, then you can't legitimately claim that evolution doesn't occur and that evolutionary theory is definitely wrong unless you've analyzed and completely explained that same level of detail.

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    1. "And what exactly do you mean by "analyzing" biological systems? Do you mean that the origin, interaction, and function of every subatomic particle in the universe must be analyzed and completely explained before evolutionary theory or any other scientific theory can be determined to be right or wrong?"




      I would be impressed if it could be scientifically demonstrated that nde is capable of producing a bacterial flagellum!

      Delete
  4. CH: The paper shows that the magnitude of the interactome—the sum total of all interactions in systems such as the nervous system—is on the order of Bell’s number, which scales faster than exponentially. Indeed, for n discrete components, the logarithm of Bell’s number is n[log(n) – 1].

    Given that organisms make copies of themselves, which includes the instructions of how to build these very complex feature sets, a proposed designer would need to posses the knowledge that all of those interactions would result in a specific, desired outcome, rather than some other specific, non-desired outcome.

    Why doesn't observations of this complexity indicates a designer would be highly complex and therefore unlikely?

    IOW, it seems you're reached a concussion on these observations based on specific assumptions about designers, such as that they are not complex, etc.

    Again, we cannot extrapolate observations without putting them into some kind of explanatory theory.

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    1. This comment has been removed by the author.

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    2. Scott:"Given that organisms make copies of themselves, which includes the instructions of how to build these very complex feature sets, a proposed designer would need to posses the knowledge that all of those interactions would result in a specific, desired outcome, rather than some other specific, non-desired outcome."

      So, to make more progress, you have to open your mind about how you think about God. This article gives new understanding to the majesty of the Creator. He cannot be fully comprehended by us little guys and gals.

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    3. Scott: Why doesn't observations of this complexity indicates a designer would be highly complex and therefore unlikely?

      Scott: IOW, it seems you're reached a concussion on these observations based on specific assumptions about designers, such as that they are not complex, etc.

      Marcus: So, to make more progress, you have to open your mind about how you think about God. This article gives new understanding to the majesty of the Creator. He cannot be fully comprehended by us little guys and gals.

      My mind is open, Marcus. This includes realizing assumptions that the designer is simple, complex or inexplicable are not "out there" for us to observe. Rather, they are conjectured ideas which people use to extrapolate observations.

      So, it would seem that, if anyone's mind isn't open, it's yours, not mine.

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    4. Scott: So, it would seem that, if anyone's mind isn't open, it's yours, not mine.

      J: Your problem, Scott is that since you deny having ever experienced a natural-caused observation or memory that you could use in an explananation (since, God forbid, that would make you a foundationalist of a sort), anyone can criticize anyone else's wild guess as to whether or which "observations" have ever occurred on the mere grounds of degree of speculativeness. Science is literally indistinguishable from absolute blind speculation by your approach.

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    5. Jeff: Your problem, Scott is that since you deny having ever experienced a natural-caused observation or memory

      I've adopted the idea that I've experienced actual memories.

      If my memories are not my actually memories, then what are they? Someone else's actual memories? But even that assumes that there are *some* actual memories. What other explanation for them do you have?

      What would they be other than some reflection of reality? What would simulations of a tree be based on if not actual tree or something similar to it? I can dreams of using a phone in San Francisco because I've both experience using a phone and being in San Francisco. And I can dream of using a phone in France because I've experienced it to some degree by watching several television series hat are based there. If not, then what else would those dreams be based on?

      Furthermore, who or what would replace memories of everything I've ever experienced with a false memories? What purpose would it serve? What would they gain? How would they do it?

      "Theory X might be false" isn't a valid criticism because it's applicable to all theories.

      IOW, we adopt the idea that there are at least some actual memories because it has best withstood criticism.

      Jeff: Science is literally indistinguishable from absolute blind speculation by your approach.

      Knowledge grows though conjecture and criticism, not just conjecture. You keep forgetting the criticism part.

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    6. Scott: I've adopted the idea that I've experienced actual memories.

      J: "Adopted" is past tense. You can't even know you've ever completed a sentence in your head if you don't ACTUALLY remember. That's why literally EVERYTHING you say is SHEER blind faith non-sense. Call it "knowledge" if you wish. But then what ISN'T knowledge?

      Scott: "Theory X might be false" isn't a valid criticism because it's applicable to all theories.

      J: Right, because the mere fact that you conjecture that there has actually been a criticism that was also "good" proves both are true. Unbelievable!

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    7. Scott: I've adopted the idea that I've experienced actual memories.

      Jeff: "Adopted" is past tense. You can't even know you've ever completed a sentence in your head if you don't ACTUALLY remember. That's why literally EVERYTHING you say is SHEER blind faith non-sense.

      And what's was your criteria for determining which beliefs are basic, such as memories? Oh, that's right. You still haven't provided on.

      Why do you think that might be, Jeff?

      Delete
  5. Scott: Furthermore, you're assuming that we will not learn anything significantly new, such as how to build working quantum computers with more than a few qbits in the next 50 years.

    Moore's law is specific to classical computing, not quantum.

    From the wikipedia entry on Shor's Algorithm

    On a quantum computer, to factor an integer N, Shor's algorithm runs in polynomial time (the time taken is polynomial in log N, which is the size of the input).[1] Specifically it takes time O((log N)3), demonstrating that the integer factorization problem can be efficiently solved on a quantum computer and is thus in the complexity class BQP. This is substantially faster than the most efficient known classical factoring algorithm, the general number field sieve, which works in sub-exponential time — about O(e1.9 (log N)1/3 (log log N)2/3).[2] The efficiency of Shor's algorithm is due to the efficiency of the quantum Fourier transform, and modular exponentiation by squarings.

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  6. This post contains two spectacular logical failures. (1) The author seems to assume that if we cannot faithfully model a system on a computer then we cannot understand it. (2) From there he jumps to a conclusion that such a system could not have formed through natural means.

    Take any physical system with N particles. The number of physical states grows exponentially with N. A simple magnet has 2^N possible states. An attempt to simulate all these states on a computer fails when N exceeds 40. Does that mean we do not understand how magnets work? Hardly. Instead of trying to simulate all states of the system, we have found ways to zoom in on a small subspace of states that actually matter. Such numerical approaches, combined with analytical methods, have provided a good deal of understanding about magnets.

    Needless to say, magnets themselves have no trouble going through the vast space of states. They don't need any help from an intelligent designer to form or to reach a ground state.

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    1. "Needless to say, magnets themselves have no trouble going through the vast space of states. They don't need any help from an intelligent designer to form or to reach a ground state."

      And what is the origin of electromagnetic force? or gravity? or strong nuclear force? or weak nuclear force? Anyone?

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    2. awstar,

      Are you suggesting that we cannot understand how magnets work without knowing the origin of the weak force? This is pretty bizarre. With an attitude like that, science is impossible.

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    3. Ginnungagap, the Yawning Void?

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    4. Awstar,

      Problem solving isn't magic.

      To make progress, we specifically devise tests that would conflict with at least one competing theory, but not others.

      However, "We lack an exhaustive explanation for X" is a bad criticism because it is equally applicable to all theories. As such, it's unclear how you can use it in a critical way.

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    5. Living systems are like magnets. That is spectacular.

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    6. I never said they are. However your arguments are not specific to living systems. They apply equally well (or shall I say badly?) to magnets.

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    7. "Are you suggesting that we cannot understand how magnets work without knowing the origin of the weak force? This is pretty bizarre. With an attitude like that, science is impossible."


      Says Oleg, who continues to attempt to rival E Liddle in who can obfuscate some relatively straight forward issues more than the other. It is truly mind boggling to try and follow the rabbit trails that some nde proponents create in these discussions.

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    8. oleg, you said: "They don't need any help from an intelligent designer to form or to reach a ground state."

      I was just pointing out to you that the help to form or to reach a ground state came from the one who created electromagnetic force to begin with, along with the atoms and molecules and such to effect the force. In other words, your statement is in error.

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    9. CH: Living systems are like magnets. That is spectacular.

      So, what are you saying, Cornelius? Living things are just "too weird", therefore conventional logic doesn't apply to them?

      But that's just yet anther example of a general purpose strategy to deny anything.

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  7. CH:

    All of this not only means that the analysis of such biological systems is impossible, it also means that the evolution of such biological systems is impossible, or at least scientifically unlikely. For the problems in analyzing these systems also apply to evolving these systems.

    Every day a study that contradicts Darwinism.

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    1. PaV Lino

      Every day a study that contradicts Darwinism.


      Every day a willfully ignorant Creationist stupidly claiming that a scientific study contradicts Darwinism.

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    2. "Every day a willfully ignorant Creationist stupidly claiming that a scientific study contradicts Darwinism."


      Every day a willfully ignorant nde philosopher stupidly claiming that speculation based on uncountable, {many even unknowable} assumptions, scientifically confirms nde.


      And then picking on a Creationist in attempts to set up a false dichotomy, thinking that this somehow bolsters the case for adequate scientific grounding of nde.

      Delete
  8. How parts interact in a biological system is a problem that Stephen Meyer addressed in “Darwin’s Doubt.”

    If an automaker modifies a car’s paint color or seat covers, nothing else needs to be altered for the car to operate, because the normal function of the car does not depend on these features. But, if an engineer changes the length of the piston rods in the car’s engine, the engine won’t run. Similarly, animal development is a tightly integrated process in which various proteins and cell structures depend critically on earlier events. As a result, one change early in the development of an animal will require a host of other coordinated changes in separate but functionally interrelated components and entities downstream. This tight functional integration helps explain why mutations in early development inevitably result in embryonic death and why even when mutations expressed somewhat later in development commonly leave organisms crippled.

    In other words for evolution to work it must solve a myriad of engineering problems. I have always wondered how a group of engineers could change a truck into a submarine such that the vehicle would be operable each step of the way. I frankly don’t see how it could be done unless whole subsystems are redesigned at once. Even then, I suspect that what would result is a series of mechanical monstrosities that would consist of so many simultaneous changes that this certainly would not be analogous to what evolution is expected to do.

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    1. A truck into a submarine? You gotta check this out: Whale evolution: The blowhole.

      The fact that the cetacean nose moved, in the course of evolution, from the tip of the rostrum up to the vertex of the head, is among the most perfect of adaptations to aquatic life. In this and many other special adaptations of their morphology and physiology, cetaceans surpass most primarily aquatic animals even though they themselves have developed from land mammals that breathe with lungs, and have only secondarily conquered the aquatic environment. To a certain extent, cetaceans can be considered to be the most successful group of aquatic animals of all time.

      Conclusive paleontological evidence shows the way in which the nasal openings were moved in the course of phylogeny (see Kellogg 1928; Slijper 1962; Gaskin 1976; Oelschlager 1978, 1987, 1990; Moore 1981). That this evolutionary process is repeated in a way during ontogeny became obvious through external observations on embryos and fetuses (Kukenthal 1893). At the earliest embryonic stages the nasal openings are still situated at the rostra tip like those of land mammals; they are gradually shifted more and more towards the vertex of the head at the older stages. At the same time, a long rost rum with narrow jaws develops. Until recently, practically nothing was known about the morphogenetic processes concealed in this metamorphosis, about what cranial structures take part in it, and about the exact way in which the cetacean skull becomes transformed during embryogeny.

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    2. Oleg,

      Conclusive paleontologcial evidence doesn't tell us a thing about all the coordinated changes that must take place simultaneously to cause the blowhole to move.

      You argue against my admittedly corny analogy but have nothing to say about Dr. Meyer's quote.

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    3. Doublee

      You argue against my admittedly corny analogy but have nothing to say about Dr. Meyer's quote.


      Sorry Doublee but science isn't done by analogy. Biological life is a lot more robust and tolerates a much greater range of variation that human designed machines. Just look at the variations in the 7 billion humans on the planet if you need an empirical example.

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    4. Let's first agree that the fossils captured the motion of the blowhole from the nose to the top of the head. Evolutionary theory predicted the existence of intermediate forms, in which the blowhole is in an intermediate position. Such fossils have indeed been found.

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    5. "Let's first agree that the fossils captured the motion of the blowhole from the nose to the top of the head. Evolutionary theory predicted the existence of intermediate forms, in which the blowhole is in an intermediate position. Such fossils have indeed been found."

      The Blowhole.... THE FRIGGIN BLOWHOLE!!!!!!! (slap on the forehead) Why did I not think of that before? That's it. The blowhole. PERFECT.

      THAT EXPLAINS EVERYTHING!!!!!!!

      That perty much describes it all. How could anybody be so stupid as to doubt nde's ability to transform a land animal into a fully aquatic organism. Get that blowhole right AND YOU'VE GOT IT MADE BABEEE!


      And THOSE FOSSILS. HAH, How could anybody for even a second have any doubts that those are REAL REPRESENTATIONS OF TRANSITIONS between the fully land dwelling creation and the fully aquatic animal??? And who could ever doubt that random mutation and natural selection etc. are sufficient to account for all of the changes required to transform a land dwelling animal into a fully aquatic animal? Somewhere in the literature there surely is an adequately demonstrated scientific accounting of the changes needed for the transformations required, oh, and of course demonstration and accounting of selection pressures, on all the levels required, that simply pulled everything into place.

      What a bunch of pompous boneheads!

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    6. "on all the levels required"

      In other words, you expect proof of the 'naturalistic' origin, interaction, and function of every subatomic particle in the universe, going back to the big bang and beyond, that led to the existence of extant whales and every other life form past or present, before you'll accept that evolution occurs.

      Would you please be kind enough to provide some details about how you believe whales and all other life forms came to be? And if you can match or exceed the level of details that you expect from science, that would be even better.

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    7. Oleg: Evolutionary theory predicted the existence of intermediate forms, in which the blowhole is in an intermediate position.

      J: A prediction of a theory is an implication of a theory. So which aspect of evolutionary theory IMPLIES that the blowhole transition you're talking about would have occurred when you say it occurred? Write down for us those propositions entailed in the theory that imply it?

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    8. It goes to the very basics of Darwin's theory, Jeff. Strange that you aren't aware of them.

      Darwin, like many people of his time, observed natural variation in living organisms, which represents small, incremental changes of the phenotype. He posited that these incremental changes, directed by natural selection and accumulated over time, are responsible for the formation of new species.

      So, according to his theory, incremental changes accumulated to become large changes. Thus we should find intermediate forms.

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    9. Twt said:
      "on all the levels required"


      Bpragmatic says

      To reiterate what was said:

      "and of course demonstration and accounting of selection pressures, on all the levels required"



      Twt said:
      "In other words, you expect proof of the 'naturalistic' origin, interaction, and function of every subatomic particle in the universe, going back to the big bang and beyond, that led to the existence of extant whales and every other life form past or present, before you'll accept that evolution occurs."


      Bpragmatic says

      Keep in mind, my assumption is that when someone uses the term "evolution" it refers to the concept of Neo Darwinian Evolution.

      So to answer your question, some might consider "proof" of what you list above as being an unreasonable requirement.

      So how about the nde philosophers take that first baby step towards establishing itself as a real science, and scientifically demonstrate that nde mechanisms are capable of producing, oh, lets say, a bacterial flegellum?


      Twt says

      "Would you please be kind enough to provide some details about how you believe whales and all other life forms came to be?

      Bpragmatic says

      I don't know how it was done or how it happened. Any "belief" I have, I will have to call speculation. Not scientific.


      Twt says
      "And if you can match or exceed the level of details that you expect from science, that would be even better."


      Bpragmatic
      To me, from a scientic pov, I dont believe there are sufficient scientific grounds to conclude anything other than we do not know enough to say anything very meaningful about "how all life forms came to be"

      It sure doesn't stop nde philosophers from claiming sufficient knowledge to stongly imply or even assert speculation as fact in many ways.

      Delete
  9. Cornelius Hunter

    For whereas man-made machines may have a great number of components, such machines are specifically designed to limit the number of interactions. The components only interact with a small number of other components and a matrix describing these interactions would be very sparse. Not so for many biological systems.


    Cornelius logic:

    1. Designed things have a large number of parts but the parts don't interact except with few localized others.

    2. Life has a large number of parts that each do interact with many other parts in many ways.

    3. Therefore life = designed???

    Great own goal there CH, one of your best yet!

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    1. "Cornelius logic:

      1. Designed things have a large number of parts but the parts don't interact except with few localized others.

      2. Life has a large number of parts that each do interact with many other parts in many ways.

      3. Therefore life = designed???

      Great own goal there CH, one of your best yet!"





      What idiotic statements. Thorton can not even scientifically demonstrate that nde can produce a tit on a hedgehog, yet he insists on criticizing valid critiques on his beloved philosohpy, which are the basis of his daily philosophical rants on CH's blog. Just goes to show you the BS funded by tax dollars to support a dying publically funded realm of horseshit wont die by itself. Thinking tax payers have to step up and call bullshit on the crap speculation.

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  10. If there is a lot of connectivity , that means that if you make changes to one part, you might have to make changes to a lot of other parts. So how do you make random changes by a random process, that is, evolution? You have to change a number of parts simultaneously. How do you that without intelligent input?

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    1. You're assuming the features of biological organisms represent intentional goals. However, that is an idea that isn't "out there" for us to observe.

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    2. natschuster the lying homophobic bigot

      If there is a lot of connectivity , that means that if you make changes to one part, you might have to make changes to a lot of other parts.


      Nope. Gene expression doesn't produce a boatload of specific sized parts that then have to fit together like a human machine. Gene expression is more like a set of instructions, i.e. "grow bone A for 20 hrs, connect blood vessels to bone A, connect nerves to bone A." If you change the expression to "grow bone A for 21 hours" you also get the changes to the corresponding blood vessels and nerves too.

      So how do you make random changes by a random process, that is, evolution? You have to change a number of parts simultaneously.

      No, you don't as explained above.

      How do you that without intelligent input?

      Through random genetic variations filtered by selection.

      Tell us bigot: if a 6' man and a 5' woman have a 5'6" child, did the child need millions of separate mutations to get every one of his parameters to grow his 5'6" body?

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    3. "Tell us bigot: if a 6' man and a 5' woman have a 5'6" child, did the child need millions of separate mutations to get every one of his parameters to grow his 5'6" body?"

      What a STUPID comment.

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    4. Scott: You're assuming the features of biological organisms represent intentional goals. However, that is an idea that isn't "out there" for us to observe.

      J: My intentions aren't there for you to observe either. Only analogy gets us to an inference of other intentions of other minds. But by your view, you don't even know if you yourself ever intention. You have to choose to believe that seeing's how you can't even remember anything.

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    5. Jeff,

      My point to Nat was that we cannot extrapolate observations without first putting them into some kind of explanatory framework. This includes the conclusion that "You have to change a number of parts simultaneously."

      A number of parts would need to be changed simultaneously if the functionality in question was pre-selected from the start and didn't have some other unintended functionality in a number of intermediate steps. But, like all ideas, that isn't something "out there" that we can extrapolate from observations.

      jeff: But by your view...

      Apparently, you can't remember anything either since, as I've already explained, you're the one that is a Foundationalist, not me.

      Tell me again, Jeff, what did you say your criteria was for determine which beliefs are basic? Oh, that's right. Despite asking you directly, several times, you haven't.

      Why do you think that might be?

      It wouldn't have anything to do with such a criteria representing a form of criticism, and that you adopted the idea that has best stood up to such criticism, would it?

      Delete
  11. natschuster August 2, 2013 at 4:18 PM

    If there is a lot of connectivity , that means that if you make changes to one part, you might have to make changes to a lot of other parts. So how do you make random changes by a random process, that is, evolution? You have to change a number of parts simultaneously. How do you that without intelligent input?


    I know you don't like the idea but evolution isn't trying to design anything, not better eyes, not bigger brains, not anything.

    In evolutionary terms, we are no more the crowning glory of creation than the amoeba or beetles. For the moment, we happen to be quite successful but a lot could happen to change that. Which is one reason why religion is so popular, of course. It offers those guarantees of personal survival, in one form or another, which science can't.

    Mutations occur in the genome for a number of reasons but they are random with respect to the fitness of the host organism. Most of them have no observable effect on the organism. A large minority are definitely harmful. A much smaller number are beneficial. Which is which is decided by the environment in which the organism is trying to survive.

    Over time, the harmful ones will be slowly filtered out natural selection. The beneficial ones will tend to survive and flourish. The rest will just come along for the ride.

    The interconnectedness of biological organisms is an advantage. The knock-on effects of mutations are felt down the line around more quickly. It contributes to adaptability and survival. It's a feature not a bug.

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  12. It's good to see some rigor in a field with too many mathematical illiterates. Now there remains only one statistic that is needed. What is the accepted scientific practical definition of zero. Experiments will never yield a calculation of zero to an infinite number of decimal places. So Dr. CH what is the standard? And how does the probability of evolution compare to this value. I think the probability of evolution has already been shown to be zero. But it would be nice to have a scientifically rigorous calculation.

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  13. This is one point of the question, other point is the lack of good theories to measure complexity in living sistems. How many complexity units are there in an active site on an enzyme?
    This answer should be based in the complementarity between the substrate-enzyme, the dynamics of the reaction, the whole structure, the kinect law of the reactions, activation mechanisms, coenzime binding,....
    This theory would help to understand that the complexity is higher than estimated by the most optimistic study.

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  14. Guys:

    You have a protein that has to bind to a another protein. Then that protein has to connect to another protein, and so on. That just some of the oonnectivity found in organisms. They have to have specially designed binding sites and such. If you change the first protein, you might have to change the second one,the chain,and so on. How od you that in a gradualistic, that is, Darwinian way?

    And the human skull sit son the spine in a way that is different that the way it is in apes. This is so we can walk upright. Put upright walking also requires other changes to the entire human anatomy. This is another example of connectivity. How did all this happen?

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  15. natschuster the lying homophobic bigot

    And the human skull sit son the spine in a way that is different that the way it is in apes. This is so we can walk upright. Put upright walking also requires other changes to the entire human anatomy. This is another example of connectivity. How did all this happen?


    A 6' man and a 5' woman had a 5'6" child. Think of all those changes to make all the 5'6" parts fit just right - skeleton, muscles, nerves, blood vessels, etc. How did all this happen bigot? Is it MAGIC???

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  16. I'm not sure what your point is. The genome has built in mechanisms to allow for variability. But a change in the genome itself, that is evolution, that causes a significant change in anatomy has to make a number of changes simultaneously, or there might be connectivity problems. I understand that the mutation, for example, that cause giantism in humans causes all kinds of problems because things don't quite fit. Large dogs have problems, too. Connectivity problems, again. Dachshunds develop hip problems because of their short legs. It looks like you can anly change things so far, without running inot connectivity problems.

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    1. natschuster the lying homophobic bigot

      I'm not sure what your point is.


      You avoided the question bigot. Get that hateful prejudiced little brain revved up and try again:

      A 6' man and a 5' woman had a 5'6" child. Think of all those changes to make all the 5'6" parts fit just right - skeleton, muscles, nerves, blood vessels, etc. How did all this happen bigot? Is it MAGIC???

      Delete
    2. natschuster August 3, 2013 at 7:38 PM

      I'm not sure what your point is.... It looks like you can anly change things so far, without running inot connectivity problems.


      The point is that biological organisms are not as rigid and fault-intolerant as human-designed machines.

      Yes, a mutation that suddenly caused major changes in the dimensions of an organ in an animal could be detrimental. That's expected in evolution. There are many more ways for something to go wrong than to go right, that's why far more mutations are harmful than beneficial.

      But consider this.

      Suppose some weird phenomenon suddenly caused an aircraft's wings to get bigger by 0.5%. All the connections would be out of alignment and the wings would break off. Not a good thing, especially if the aircraft is in flight.

      Now suppose a mutation in a bird caused it to grow wings that are 0.5% bigger than its contemporaries. Connective tissues, skin, nerves, tendons etc would be able to stretch enough to cope with the change. Perhaps it would feel a bit uncomfortable to begin with but animals soon adapt to small changes. More to the point, perhaps the extra wing area enables the bird to fly a bit higher or a bit further than the others. Under certain circumstances that might be a useful advantage, maybe even the difference between life and death on a very long flight over water, say.

      I know that the foregoing is just an illustration but I would hope that, as a special needs teacher, you try to understand the arguments for evolution even if you disagree with them for religious or other reasons.

      Scientists don't make this stuff up just for reasons of prestige or power. Yes, a few have been caught doing that or fudging data. they've fallen below that standards of their profession just as there are priests and pastors who've fallen short of the ideals of their calling. We're all human and make mistakes. But the vast majority of scientists, like the vast majority of the clergy, are decent people who do the best they can by their lights.

      In spite of what CH argues, The theory of evolution is not gospel but it is the best working explanation we have at this time for how life changes and diversifies over time. If anyone has any better idea then bring it on. Science can use all the help it can get.

      Delete
  17. Are you sue you read my post?


    "The genome has built in mechanisms to allow for variability."

    Now, how about addressing my problems? Start with protein evolution. Then move on from there to the evolution of our upright posture.

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    1. natschuster the lying homophobic bigot

      Are you sue you read my post?


      Bigot, you ignored the question again,

      "A 6' man and a 5' woman had a 5'6" child. Think of all those changes to make all the 5'6" parts fit just right - skeleton, muscles, nerves, blood vessels, etc. How did all this happen bigot? Is it MAGIC???"

      I know you're dead set on being a trolling ass but answering the question answers your question. So quit stalling bigot.

      Delete
  18. I think I understand what you are asking now. No, it isn't magic when a 6" man and 5' woman have a 5'6" child. Organisms can tolerate some variation. How does this answer my question point about proteins? Or giantism? Or big dogs?

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    1. natschuster the lying homophobic bigot

      I think I understand what you are asking now. No, it isn't magic when a 6" man and 5' woman have a 5'6" child. Organisms can tolerate some variation.


      You're still evading the question bigot.

      "A 6' man and a 5' woman had a 5'6" child. Think of all those changes to make all the 5'6" parts fit just right - skeleton, muscles, nerves, blood vessels, etc. How did all this happen?"

      What mechanisms caused all the 5'6" parts to fit together so well?

      Delete
  19. Well, I suppose ti has something to do with genetics. Now what does this have to do with the fact that dachhunds develop hip problem because things don't fit toghether all that well?

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    1. natschuster the lying homophobic bigot

      Well, I suppose ti has something to do with genetics.


      Then the evolution of proteins and upright posture isn't a problem because it has something to do with genetics.

      There you go bigot, questions answered.

      Delete
  20. But we know from genetics that only limited changes will work. Giantism cause problems in humans. Changing the spine to allow upright posture without changing the skull won't work very well. And changing one protein without changing the other proteins it interacts with will lead to problems. It's like giving a car a bigger steering wheel. You can only make it so big.

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    1. natschuster the lying homophobic bigot

      But we know from genetics that only limited changes will work


      What are the limits and how did you determine them? We know that many changes which require things to fit together aren't a problem because of something to do with genetics.

      Delete
    2. It looks like the limits might be confined to the normal variation within species. Sort of a micro-evolution thing.

      Delete
    3. natschuster the lying homophobic bigot

      It looks like the limits might be confined to the normal variation within species. Sort of a micro-evolution thing.


      Evasive non-answer by the bigot noted.

      Delete
    4. How am I being evasive? You look at the normal variation within a species. Variation beyond that might get you into trouble with things not fitting right.

      How would you address the problem? Sometimes, when you change things too much you get problems. For example, human giants, dachshunds, big dogs, etc. Where do you draw the line?

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    5. natschuster the lying homophobic bigot

      You look at the normal variation within a species.


      Normal variation in a population doesn't equal limits on evolutionary change bigot. You claimed evolution has limits. The only limits I know are the ones due to the laws of physics and the mechanical strength of biological materials. We have mammals from 30mm and 1.5g to almost 30m and 200,000kg. Why aren't those the limits?

      Variation beyond that might get you into trouble with things not fitting right.

      You also told us that "something to do with genetics" makes all the parts fit right.

      Make up your trolling bigot mind.

      Delete
    6. Did you read my post? Okay, maybe I wasn't clear. Genetics can allwo hings to fit together within the normal variation within the species. When try to change an organism beyond that, you get problems because things don't fit. That's why human giants have problems. That's why dachshund have problems. That's why big dogs often have problems. When you have any sort of integrated system like a machine or car or organism, you can only change a component so far without running into problems.

      Delete
    7. I think that engineers call this concept "tolerance." If organism are only elaborate machines following the laws of physics, then they have to follow principles of tolerance.

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    8. natschuster the lying homophobic bigot

      Genetics can allwo hings to fit together within the normal variation within the species When try to change an organism beyond that, you get problems because things don't fit.


      Unsupported assertion. You can't identify any limits so you're just making things up. Lying in other words.

      That's why human giants have problems. That's why dachshund have problems. That's why big dogs often have problems.

      Bullcrap. Show me an example of a human or a dog whose 'parts don't fit'. Where the leg bones were 5' long but the blood vessel, skin, and nerves were only 3' long. Purebred dogs often have genetic problems due to inbreeding and because they weren't subjected to normal natural selection. It has nothing to do with any imaginary "limits'.

      I think that engineers call this concept "tolerance."

      Life forms don't have their individual parts pre-made and then assembled. The parts are all grown in place as a whole organism. You said it was "something to do with genetics", remember?

      However, the large irony of having a disgusting homophobic bigot like you talk about tolerance isn't lost on me.

      Delete
    9. According to this:

      http://en.wikipedia.org/wiki/Dachshund

      Dachshunds develop problems because their skeletons aren't proportioned right. Things don't fit.

      Delete
    10. Large dogs are more likely to get hip dysplasia and deep chested dogs are more likely to get bloat.

      Delete
    11. Aren't the individual parts in organisms controlled by individual genes, like the HOX genes? Chane one gene, change the morphology of that part. Isn't each protein controlled by it's own gene? Change the gene, change that protein, but not necessarily the proteins it needs to interact with.

      Delete
    12. Why does acromegaly in humans cause so many problems? It has nothing to do with things fitting?

      Delete
    13. natschuster the lying homophobic bigot

      Dachshunds develop problems because their skeletons aren't proportioned right. Things don't fit.


      Because of all the inbreeding and artificial selection imposed by humans, not because of any imaginary limits to evolution.

      Aren't the individual parts in organisms controlled by individual genes, like the HOX genes?

      Now we're back to how does a 6' man and 5' woman have a healthy 5'6" child. We already went over that one bigot.

      If you're going to keep lying you're going to need a better memory. Aren't you getting tired of this stupid troll yet?

      Delete
    14. This is from the wikipedia rtciel on dachshunds:

      "The breed is known to have spinal problems, especially intervertebral disk disease (IVDD), due in part to an extremely long spinal column and short rib cage.[39] The risk of injury may be worsened by obesity, jumping, rough handling, or intense exercise, which place greater strain on the vertebrae. About 20-25% of Dachshunds will develop IVDD.[40]"

      Looks like things don't fit.

      I understand you to be saying that if you changes one part of a n organism, the rest of the organism changes to compensate. That's a pretty neat trick. How did that evolve? But I digress.

      Now, when you chnage the morphology of a fruit fly, for example, you change the one part of the morphology, e.g. the antenna, but you don't get the rest of the fruit fly to compensate. You just get a freaky, defective fruit fly.

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    15. natschuster the lying homophobic bigot

      This is from the wikipedia rtciel on dachshunds:

      Looks like things don't fit.


      What part "doesn't fit" bigot? Do the bones not match the muscles not match the nerves fibers?

      The animals may not be as reproductively fit as other normally proportioned dogs, but that's due to humans removing natural selection pressures and deliberately breeding them to be that morphology. Nothing to do with any evolutionary "limits".

      But do keep lying about the topic bigot. I never complain when a Creationist makes himself look as stupid as you do.

      Delete
    16. The spine is too long and the ribs are too short. The proportions aren't right. That causes problems.

      Adn their not being reproductively fit is kind of my point. There is something wrong that would not allow these to survive and reproduce, that is, evolve, as well as other dogs without human, that is, intelligent, intervention. Kind of puts a limit on evolution. Just like chanig Hox gene messe up the way a fruit fly is put together.

      Delete
    17. natschuster the lying homophobic bigot

      The spine is too long and the ribs are too short. The proportions aren't right. That causes problems.


      That's a lot different than your earlier stupid claim "the pieces won't fit without millions of coordinated mutations". The pieces fit perfectly.

      These proportions wouldn't even exist except for humans imposing artificial selection on the breed. And even then the proportions would still function just fine if not for the mechanical strength of the biological materials not being able to handle the physical strain. That's the laws of physics being the limit as I pointed out before, not any limit caused by evolutionary processes themselves.

      You're still floundering badly here bigot. Maybe you should go back to one of your other trolls like C14 in dinosaur bones, although you looked pretty stupid on that one too.

      Delete
    18. If the mutation causes the pieces to be out of proportion, so they don't function properly, then that is what I meant be said by "not fitting." The parts have to be proportional. And who cares whether it is artificial or natural selection? The point is that you change the proportions, you get problems.

      Did I say millions of compensatory mutations? I thought I said some simultaneous compensatory mutations. It's like when you try to change a protein to a homologous protein with a different function. The protein looses stability unless you have compensatory mutations.

      Dwarfism in humans can also cause problems like problems with the spine. Things have to be proportioned.

      Delete
    19. natschuster the lying homophobic bigot

      If the mutation causes the pieces to be out of proportion, so they don't function properly, then that is what I meant be said by "not fitting." The parts have to be proportional. And who cares whether it is artificial or natural selection? The point is that you change the proportions, you get problems.


      LOL! Look at the bigot doing the 100 yard goalpost push!

      First it was "You have to change a number of parts simultaneously. " Now it's "things have to be proportioned."

      You still need to work on your memory bigot.

      The bigot still has not provided one iota of evidence for any limits to evolutionary processes. He's only "discovered" the well know fact that some morphological forms will provide better reproductive fitness than others. Guess what usually happens to the less fit ones bigot?

      Delete
  21. I love this quote from Oleg.

    He has just provided the reasoning to support the contention that we need not know the identity of the designer to understand design in nature.

    Therefore, intelligent design biology is scientific after all.

    Thank you, Oleg!

    Oleg: "Are you suggesting that we cannot understand how magnets work without knowing the origin of the weak force? This is pretty bizarre. With an attitude like that, science is impossible."

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    1. You are welcome, Steve.

      Now that you are free from having to identify the designer, tell us something about the design. We're not going to hold our collective breath because ID luminaries have already told us that no answer will be forthcoming: they have no interest in this pathetic level of detail.

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    2. Steve: He has just provided the reasoning to support the contention that we need not know the identity of the designer to understand design in nature.

      Oleg's example illustrates that not all explanations are reductionist in nature. However, this doesn't mean that ID actually serves an explanatory purpose.

      Knowledge is information that tends to remain when embodied in a storage medium.

      The genome contains the knowledge of how to adapt air, water, etc. into the biological features of organisms, encoded into DNA. That's what happens when an organism reproduces, right?

      And it's these very features that you're claiming that needs to be explained, right?

      So, the question is: what is the origin of this knowledge? How do you explain it?

      Some designer that "just was", complete with the knowledge of how to perform these transformations, already present, does not serve an explanatory purpose. This is because, one could more efficiently state that organisms "just appeared" complete with the knowledge of how to perform those transformations already present in their genome.

      Neither add to the explanation. (And no, the latter is not Darwinism)

      So, adding a designer to the mix doesn't actually solve the problem. It merely pushes the problem into an inexplicable realm. It's not even a non-reductionist explanation.

      On the other hand Darwinism is the theory that this knowledge was genuinely created, rather than having always existed. Biological complexity emerges from variation and selection. It *is* a non-reductionist explanation, which is part of our current, best explanation for the universal growth of knowledge.

      Other examples of emergent phenomena include Universal Turing machines, which can, in principle run any program that any other UTM can run. No one set out to design an UTM. Rather, this universality emerged from a specific repertoire of computations. We can say the same about the universality of the Arabic number system to represent any number, etc.

      Delete
  22. But wait Oleg, if Im not mistaken neither are we allowed to ask for any level of empirical detail for how natural selection builds genomes. We are supposed to take it on faith that incremental, step-wise fortuitous mutations builds stuff.

    Once the basic proto-cell with nucleus and lipid membrane got started (your abiogenesis concession), does neo-darwinism have empirical evidence for how NS built the first systems?...the sensory, digestive, endocrine, defensive, nervous etc etc.

    Is there any evidence besides speculative guesswork? Is there any explanation not assuming evolution?

    As for ID, it assumes the first complete multi-cell organism was front-loaded with information. It is this starter kit that life built stuff with.

    James Shapiro's work provides a lot of evidence for the genome modifying itself in response to environmental change, providing evidence that the genome is not a boat sailing on a whim, but in fact utilized the information stored within the organism.

    These observations do lend supporting evidence that the genome is in fact front loaded with information; in contrast to the neo-darwinian take that information is an emergent property resulting from NS's activity.

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    1. Steven,

      The tu quoque tactic won't get you very far. Evolutionary biology may not have all answers, but it has provided some answers.

      But whatever the failures of evolutionary biology (real or perceived), ID has to stand on its own as an alternative scientific theory. Yet ID refuses to provide any answers. The equivalence is simply not there.

      Delete
    2. Steve

      As for ID, it assumes the first complete multi-cell organism was front-loaded with information. It is this starter kit that life built stuff with.


      What is the basis for that assumption?

      The oldest fossilized multi-celled organisms known are approx. 2.1 billion years old. Is that when the Designer did his thing? What about the single celled organisms that were around for at least 1 billion years before then?

      Did all subsequent life evolve from this 2.1 billion year old ancestor? That kinda screws Meyer's Cambrian claims, right?

      Where was this information for all the subsequent hundreds of millions of species (both extant and extinct) stored, and how? Don't say "in the genome" unless you have some evidence to back it up.

      How did the 'front-loaded' design account for major mass extinction events like the Chicxulub impact 65 million years ago?

      So far it looks like you're just making up stuff as you go. Can you support any of it, even a little?

      Delete
    3. Steve

      These observations do lend supporting evidence that the genome is in fact front loaded with information; in contrast to the neo-darwinian take that information is an emergent property resulting from NS's activity.


      This idea has been pretty thoroughly falsified by Lenski's Long Term E coli Experiment. 12 identical colonies were cloned from the same individual organism and subjected to identical environments. All were monitored for over 50,000 generations and each colony has followed its own unique evolutionary path, including the well known one that evolved the ability to digest citrates. If they were all 'front-loaded', all should have followed nearly identical developmental trajectories, but they didn't.

      Samples taken at each generation were frozen and some were used to 'run the film over'. Those samples also each followed a different evolutionary path than the first time.

      The results are exactly what you'd expect from a process of RM+NS, and completely opposite of what you'd expect from 'front-loading'.

      Delete
    4. Simple; the logical observation that you need tools to make tools. Its a bridge that can't be crossed by darwinian means. So pre-existing elements is the only logical conclusion.

      Besides, when we observe genomes in action, we see that they are exhibiting intelligent activity. So where does that intelligence come from if not front-loading? It makes the most sense.

      Regarding the origin of information, as Oleg pointed out, we don't need to ask what the source of the weak magnetic force is; only that it exists.

      In the same vein, we need not ask what is the source of the information in the genome. We only need to know that it exists. And we move on from there.

      Sure, figuring out where and how information is stored in the genome and how genomes utilize it is a tough nut to crack but that's what makes intelligent design biology that more interesting and promising than evolutionary biology's blanket denials of pre-existing information.



      Thorton: "What is the basis for that assumption?"

      Delete
    5. OK, so Steve is going to ignore the details of the questions I asked and go with the usual ID empty bluster and hand waving.

      No surprises here folks.

      Delete
  23. Not only does it not have all the answers, it has very few answers. It cannot answer any of the core developments of life after abiogenesis. Its theory rests of a series of unexplained phenomena (in addition to all the internal systems like sensory, defense, digestive, etc) like endosymbiosis, sexual reproduction, horizonal gene transfer, recombination; they are all co-oped as if evolution did it so no need to explain them; just incorporate them in your theory and act as if nothing happened.

    Oh, and the non tu quoque part is in the fact that our theory is not lesser in explanatory power. In fact, front-loading, genomic self-adaptation is a better explanation. We are not knocking down ND to give ID a boost, but to draw a clear picture of ND as explaining no more than ID can explain, showing that ID is at least on par with ND.

    We are chipping away bit by bit. No, I won't make any prediction of when ND will die, cuz it wont die; it'll just fade away, be ignored, end up as an interesting foot note, attributed to our lack of understanding biology in the 20th century.


    Oleg: "The tu quoque tactic won't get you very far. Evolutionary biology may not have all answers, but it has provided some answers.

    But whatever the failures of evolutionary biology (real or perceived), ID has to stand on its own as an alternative scientific theory. Yet ID refuses to provide any answers. The equivalence is simply not there."

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    1. Steve

      Not only does it not have all the answers, it has very few answers.


      Which still puts ToE light years ahead of ID, which has zero answers.

      Oh, and the non tu quoque part is in the fact that our theory is not lesser in explanatory power.

      ID isn't a theory. It's not even a testable scientific hypothesis. Right now it's nothing more than idle philosophical speculation. And "POOF, an unknown intelligence at an unknown time using unknown methods and for unknown reasons did it" has zero explanatory power.

      In fact, front-loading, genomic self-adaptation is a better explanation.

      Except the idea has already been falsified. See the Lenski LTEE as described above.

      We are not knocking down ND to give ID a boost, but to draw a clear picture of ND as explaining no more than ID can explain, showing that ID is at least on par with ND.

      You're failing, and pretty miserably too.

      How about answering my questions about timelines for the last 3+ billion years and mass extinction events?

      Delete
    2. Thorton, timelines is only an issue for evoltionary biology that depends on them for step-wise, incremental change.

      If early life was utilized for developing the atmosphere, it makes sense that there would be periodic extinctions.

      As for failing, not quite. I'd rather admit no answer then sing a litany of ad-hoc rationalizations that is evolutionary biology.

      by the way, front-loading is not falsified by Lenski's experiments. Your reasoning is faulty here. You are assuming that if a genome is front-loaded, that it should react in the same way for each colony. But why should that be? We know that bacterial colonies act as a single organism, with cross-communication and collective-decision making capabilities. So a bacterial colony dividing itself into several modified versions that ensures at least a single colony survives is in fact intelligent activity.

      So on the contrary, Lenski's experiments only lend more supporting evidence for the hardiness of the programming in bacteria which allows them the ability to withstand much if not most of what we throw at them; hardly the reaction non-intelligent entities could must.


      Delete
    3. Steve: "by the way, front-loading is not falsified by Lenski's experiments. Your reasoning is faulty here. You are assuming that if a genome is front-loaded, that it should react in the same way for each colony. But why should that be?"

      Steve,

      You have just demonstrated (yet again) that ID is not falsifiable in principle. A designer could do whatever he or she pleases. End of theory.

      Delete
    4. Steve

      Thorton, timelines is only an issue for evoltionary biology that depends on them for step-wise, incremental change.


      Steve, evidence for the 3+ billion year history of life on Earth is here, it's real. If you don't like ToE then your replacement needs to provide your own explanation for it. ALL of it. All the major and minor mass extinctions, all the subsequent radiations, the observed nested hierarchies, ALL of it. You don't have the faintest sniff of a clue.

      If early life was utilized for developing the atmosphere, it makes sense that there would be periodic extinctions.

      Where is your evidence the Chicxulub impactor 65 million years ago was done to develop the atmosphere? What about the other four major mass extinction events? How did the 'front-loading' plan for them?

      As for failing, not quite. I'd rather admit no answer then sing a litany of ad-hoc rationalizations that is evolutionary biology.

      OK, so you have zero scientific training in the subject and don't have any idea what you're blithering about. Got it.

      You are assuming that if a genome is front-loaded, that it should react in the same way for each colony. But why should that be?

      Go read the papers. Because all 12 colonies were started from the same single organism. They all started with the identical genome. Why would the identical genome react in 12 different ways to the identical selection pressure? You have no answer, only more empty hand waving.

      We know that bacterial colonies act as a single organism, with cross-communication and collective-decision making capabilities. So a bacterial colony dividing itself into several modified versions that ensures at least a single colony survives is in fact intelligent activity.

      The bacterial colony didn't divide itself into 12 modified versions. The 12 groups were each started independently from the same identical source by the researchers. That was the point, to see if they would evolve independently, which they did. In your fantasy scenario how did each group even know about the other 11? You haven't thought this through at all, have you?

      So on the contrary, Lenski's experiments only lend more supporting evidence for the hardiness of the programming in bacteria which allows them the ability to withstand much if not most of what we throw at them; hardly the reaction non-intelligent entities could must

      What happened to your earlier claim that the first life was a "complete multi-cell organism front-loaded with information."?

      That sure didn't last long.

      You seem to be just another misinformed Creationist making up crap as you go. There's way too much of that going on I'm afraid.

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