Sunday, June 17, 2012

An Animated Tour of the Cell: Revealing the Majestic Beauty of Biology

As reported at Evolution News and Views: It is said that a picture speaks a thousand words. An animation speaks at least 10,000.



This animation illustrates a few of the amazing operations that take place in living organisms. Wise men from ages past could only dream of such things but now that we know it evolutionists preach that it is meaningless. They are blind guides who, while professing to be wise, have become fools.

29 comments:

  1. No, we don't "preach that it is meaningless".

    That's misunderstanding caused by people equivocating with the word "random".

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    1. I often wonder what this "meaning" means.

      Too bad biochemistry is so hard to visualise accurately. These videos give no hint of the fuzziness of chemistry, with all the random collisions and unspecific interactions. They don't make justice to the real complexity behind this. All the molecules seem to be actively directed to fit nicely in place, as in an assembly line. But then, Cornelius did label this under "False expectations".

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    2. Wise men from ages past could only dream of such things but now that we know it evolutionists preach that it is meaningless. They are blind guides who, while professing to be wise, have become fools.

      The word "meaning" is meaningless unless you supply the implied to whom. Meaning, like beauty or information, only exists in the mind of a beholder.

      For believers, only the meaning that exists in the mind of their god is valid.

      For non-believers, if there is no god there is no divine meaning. If there is a god, then how do we know what its meaning or purpose might be? How do we know that its meaning or purpose treats us as special or is in any way favorable to us and, since we are also capable of recognizinging meaning, why should its meaning take precedence over any we are able to conceive?

      Finally, the theory of evolution is not about ultimate meaning only how life on Earth has changed and diversified over time after it appeared. It says nothing about the existence of any god, it only offers an explanation for terrestrial life which does not require us to invoke the existence of a god.

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    3. Speaking of "fuzzy", one of the problems we have in creating prosthetic limbs is that human sensory and motor control signals are extremely noisy. Furthermore, this noise is always different even when performing the same motion.

      In fact, our brains must go though an extreme amount of effort to compensate for the negative consequences of this noise to enable the level of coordination we have now. This includes employing "motion simulators" which we use to help isolate external forces from force we ourselves generate. The absence of these additional channels can result in significant errors.

      Daniel Wolpert expands on this, in detail, in his 2011 TED talk.

      So, I'd ask, why would an advanced designer put so much noise in both our sensory input and motor control signals that we must expend a significant amount of effort to compensate for the negative consequences of that noise?

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  2. Elizabeth,

    I'd suggest Cornelius' claim that we "preach that it is meaningless" is a symptom of a deeper underlying assumption, not merely a simple misunderstanding.

    Specifically, Cornelius' posts are geared towards his target audience. And both Cornelius and his audience share same conception of human knowledge. Namely, that reason, knowledge and morality must be justified by an authoritative source: the Christian God. Otherwise, it's meaningless.

    However, as you've pointed out this is a non-sequitur. He's making some other assumption that he hasn't explicitly disclosed. So, I'm suggesting Cornelius doesn't recognize his conception of human knowledge as an idea that would be subject to criticism. If he did, he'd actually acknowledge this is a non-sequitur, then present an argument for his specific conception of knowledge. But he will not.

    At best, he'll repeat the same disingenuous claim that "Evolution is random". At worst, he'll simply ignore the substance of the issue all together.

    So, again, I think you're being charitable in assuming that his claim merely represents a simple misunderstanding over evolutionary theory. That's the symptom, not the underlying cause.

    Of course, Cornelius could easily clear all of this up, once and for all, in a single comment. I won't he holding my breath.

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  3. Let no man deceive himself. If any man among you seemeth to be wise in this world, let him become a fool, that he may be wise.

    1 Corinthians 3:18

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  4. Geoxus
    Too bad biochemistry is so hard to visualise accurately. These videos give no hint of the fuzziness of chemistry, with all the random collisions and unspecific interactions. They don't make justice to the real complexity behind this. All the molecules seem to be actively directed to fit nicely in place, as in an assembly line.

    If you were to watch a video of a day in the life of a city, you'd see plenty of randomness there...on the roads, for example; cars stop, start, overtake, have occasional accidents and so on, but nevertheless it is perfectly obvious that the overall system is an organized one
    The same goes for events taking place in living cells

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    1. The cell is certainly an organised system. So are whole organisms.

      I don't think this is in dispute. The issue is where this organisation comes from.

      Evolutionary processes are organising processes.

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    2. That's quite an understatement. If instead of cars you had hordes of people on the streets running away from bears, you'd have a better analogy. Nobody is saying organisms are not organised. What I said is that molecules do not behave as if they were on an assembly line.

      Elizabeth:
      Evolutionary processes are organising processes.

      Well, not necessarily. But they certainly can be.

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    3. Geoxus, darwinists always underestimated the complexity of life and never learn:

      " But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines."
      http://www.ncbi.nlm.nih.gov/books/NBK21054/

      Seems no people running of bears in the cell.

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    4. That quote, from a textbook written by "Darwinists", about research done by "Darwinists" is a cartoon response to another cartoon. It is true that the intracellular space is replete of macromolecular complexes and big proteins that interact with each other and work in a coordinated way. But that doesn't take away the fuzziness of chemistry, and you won't find things as ions, nucleotides, amino acids, and small sugars moving over invisible rails to the active site of enzymes, as often depicted in videos of transcription and translation.

      In any case, this is a far more complex and realistic representation of the cell. You are the ones who cheer at these cartoons, as simplification is one of the causes of resemblance with human machines.
      In any case, this is a far more complex and realistic representation of the cell. You are the ones who cheer at these cartoons, as simplification is one of the causes of resemblance with human machines.

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    5. There was an accidental duplication C&P-ing in my previous comment. But prolly some repetition is appropriate for the circumstances.

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  5. Elizabeth Liddle
    The cell is certainly an organised system. So are whole organisms.

    I don't think this is in dispute. The issue is where this organisation comes from.

    Evolutionary processes are organising processes.


    How do you know that cells are the product of evolutionary processes?

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  6. I don't, for sure. But it's a strong candidate mechanism.

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  7. Biological organisms are self-organizing. Their genome contains the knowledge of how to adapt matter into specific biological features. So, they build themselves. This is in contrast to cars, which do not organize themselves. The knowledge of how to organize raw materials into cars exists in us, and the robots we've programmed to assemble them.

    So, the question is, what is the origin of this knowledge used to perform these adaptions. That's where the organization comes from. In the absence of the knowledge of how to perform these adaptations, no organization would appear.

    Merely stating "that's just what some designer must have wanted" doesn't explain how this knowledge was created, which would have been used to perform the adaptation.

    Returning to your analogy, cities are organized based on knowledge that is present there. Take that knowledge away and there would be no organization.

    Significant changes in our knowledge of transportation has changed how cities are organized, including how cheaply things can be transported, the speed as which things can be transported, how safely they can be transported, how much space the take up when not in use, etc.

    If we had the knowledge to create cheaper, faster, safer vehicles that took significantly less space when not in use, cities would be organized differently. Despite our desire for progress in these areas, our knowledge of how to do so is limited. As such, we can explain the organization of cities based on our knowledge of transportation.

    The specific kind of cars we observe on the roads represent trade offs between safety, performance, fuel economy, etc. We could build safer cars, but they would be slower, consume more fuel and cost significantly more. Tanks are very safe, but driving one to work every day isn't practical.

    However, in the future we will create the knowledge necessary to build cars that are practical, yet are more safe than today's tanks.

    Sports cars trade performance for cost, fuel economy, comfort and even safety. Other vehicles trade cargo space, for performance, etc.

    As such, we can explain the various complexity of vehicles on the road today based on current knowledge of how to build cars and the trade offs they represent.

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    1. Biological organisms are self-organizing. Their genome contains the knowledge of how to adapt matter into specific biological features. So, they build themselves. This is in contrast to cars, which do not organize themselves. The knowledge of how to organize raw materials into cars exists in us, and the robots we've programmed to assemble them.

      I think you have made two very good points here.

      1) That humans, with all their great knowledge, have so far been unable to manufacture self-organizing (also self-repairing and self-perpetuating) units

      2)You acknowledge that the simple objects that humans have been able to manufacture from inanimate matter (simple in comparison to what is found in living organisms)...depend on human knowledge for their existence

      Surely then, those self-organizing biological organisms (which, like human-made products are made up of inanimate matter)...surely they must likewise be the product of some sort of knowledgeable entity?

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  8. Watendlath: 1) That humans, with all their great knowledge, have so far been unable to manufacture self-organizing (also self-repairing and self-perpetuating) units

    We can already do this, in a limited sense. Nano technology will eventual complete the process.

    Watendlath: 2)You acknowledge that the simple objects that humans have been able to manufacture from inanimate matter (simple in comparison to what is found in living organisms)...depend on human knowledge for their existence

    Cars depend on human beings because they do not contain the knowledge to build themselves. Biological organisms do not share this dependency.

    Watendlath: Surely then, those self-organizing biological organisms (which, like human-made products are made up of inanimate matter)...surely they must likewise be the product of some sort of knowledgeable entity?

    Not necessarily.

    People (some sort of knowledgeable entity) can create two kinds of knowledge: explanatory and non-explanatory. This is because people are universal explainers. On the other hand, evolutionary process cannot create explanatory knowledge. This is because natural processes cannot create explanations.

    To illustrate the difference between the two types of knowledge, imagine I had a genetic disease.

    I would expect my doctor to base my treatment on a good explanatory theory, in that changing specific genes in my genome in a specific way would result in specific biological changes that could improve my condition. This would be explanatory knowledge.

    On the other hand, a doctor could base my treatment on a rule of thumb: changing any of my genes in any way could result in some unknown biological change that could improve my condition. This would be non-explanatory knowledge.

    Assuming your doctor had both kinds of knowledge as his disposal, which treatment do you think he would use? Which treatment would you want?

    I don't know about you, but I'd want a treatment based on explanatory knowlege.

    In regard to cars, not only does the knowledge of how to build them exist in us, but it represents explanatory knowledge, which only people can create. Since we are the designers, we know it's explanatory. And, even when it book or electronic form, we can examine it and see that it indeed explanatory. So, this is how we know cars are designed by people.

    On the other hand, the knowledge of how to build biological adaptations exists in an organism's DNA. Not only can we observe organisms being build independently of any particular person, but we can observe the knowledge used to build organisms in the cell and see that it's non-explanatory knowledge. Evolutionary process are essentially useful rules of thumb - just like the treatment latter treatment based on non-explanatory knowledge in my illustration above.

    However, since people can create both kinds of knowledge, you might suggest that people could have created the knowledge found in DNA. However, as I've illustrated above, when both kinds of knowledge are available, we employ explanatory knowledge, in practice.

    In fact, our best, current explanation for our relatively recent and rapid increate in the creation of knowledge in that we've shifted to prefer explanatory knowledge over rules of thumb. So, as intelligent agents, we've improved our ability to make progress by preferring explanatory knowledge.

    In other words, in claiming that some designer put the knowledge in the genome, you're implying that this supposed designer chose to employ non-explanatory knowledge rather than explanatory knowledge. But, if this is the case, then it seems that we know more about how to make progress that a designer which is supposedly more advanced than we are.

    How do you explain this discrepancy?

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  9. Scott said:
    "This is because natural processes cannot create explanations."

    Then as humans can create explanations, humans are not the result of a natural process.

    QED.

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    1. No, the implication is that human creativity is not a natural process. Which is probably true by definition under Scott's terms.

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    2. In other words, in claiming that some designer put the knowledge in the genome, you're implying that this supposed designer chose to employ non-explanatory knowledge rather than explanatory knowledge. But, if this is the case, then it seems that we know more about how to make progress that a designer which is supposedly more advanced than we are.

      What evidence do you have that the knowledge contained in the genome is of the 'non-explanatory' type?

      How, for example, did a spider come by the knowledge to build a web?
      How do you know that there has never been a time when spiders did not know how to use the silk they produce?

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    3. Geoxus said
      "No, the implication is that human creativity is not a natural process. Which is probably true by definition under Scott's terms."

      So according to you under Scott`s terms, a natural process lead to humans that are able to make a non natural process?

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    4. As people, we've made the leap to universality in that we are universal explainers. As such, only people can create explanatory knowledge.

      This is not the same as saying only intelligent beings can create universal explainers.

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    5. Watendlath: What evidence do you have that the knowledge contained in the genome is of the 'non-explanatory' type?

      Unlike cars, the knowledge the used to build biological adaptations exists in the genome of organisms. it's right there for us to examine. This is the evidence. And we can compared it to the knowledge of how to perform adaptations to build cars, which exists in us and takes the form of explanatory knowledge. Right?

      What we observe is genetic variation in the genome that is random in respect to passing those genes on into future generations. So, the knowledge created there is based on a rule of thumb, just as the latter form of treatment in the example above.

      On the other hand, a doctor could base my treatment on a rule of thumb: changing any of my genes in any way could result in some unknown biological change that could improve my condition. This would be non-explanatory knowledge.

      If my condition is improved, the doctor wouldn't know the underlying reason why changing those particular genes resulted in that improvement. It's merely a useful rule of thumb. If that's the best we had, then I'd take it, rather than dying.

      This is in contrast to treatment based on an explanation that changing particular genes in a particular way would result in particular changes that would improve my condition, which is explanatory knowledge. This is explanatory knowledge. If I had the option, I would most certainly prefer this treatment over a rule of thumb. Wouldn't you?

      Watendlath: How, for example, did a spider come by the knowledge to build a web?

      I'd suggest that the question isn't merely were was this knowledge previously located, but how was it created. Again, see my car example above, in which the incremental creation of knowledge plays a key role in explaining the particular features we observe in cars today, features of cars in the past and the features of cars in the future.

      Conjecture, in the form of genetic variation, and refutation, in the form of natural selection. This results in non-explanatory knowledge.

      Watendlath: How do you know that there has never been a time when spiders did not know how to use the silk they produce?

      First, you're being unnecessarily vague. Spiders do not hold explanatory knowledge about how to use the silk they produce as they are not people. Rather their DNA contains a rule of thumb that is useful in catching food.

      Second, a spider's DNA contains the knowledge of how to build all of the biological adaptations that make spiders unique as a species, such as the adaptations that create silk, alone with above useful rule of thumb. So if we include the ability to create and use spider silk in the definition of "spider", then it's always contained this knowledge in it's DNA.

      So, what makes a spider a spider in the first place is the non-explanatory knowledge in it's DNA.

      There may have been times where the DNA of an insect similar to a spider contained a rule of thumb for creating silk, but not the same rule of thumb of how spiders use silk today.

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    6. Corrections: So to answer your question, the knowledge was created by conjecture, in the form of genetic variation, and refutation, in the form of natural selection. This results in non-explanatory knowledge.

      Second, a spider's DNA contains the knowledge of how to build all of the biological adaptations that make spiders unique as a species, such as the adaptations that create silk, along with above useful rule of thumb.

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    7. Blas,

      To clarify...

      Our earliest number systems could only represent a limited set of numbers. It was well within our reach to build universal number systems. But despite our ability to do so, we initially did not.

      Later, the Romans created a number system that could represent a larger set of numbers, but it wasn't universal either. Again, they had the ability to do so, but did not because, for the most part, they didn't deal with numbers that were larger.

      It was only when what we now call the Arabic number system, which was ironically devised in India, that we actually created a system that was universal in that it could represent any set of numbers.

      However, one could use some other set of symbols to develop a universal number system. So, universality isn't something that we created. Rather it's an emergent feature of systems that we did not "create" ourselves.

      We can say the same about Universal Turing Machines (UTMs), as defined by Alan Turing. Specifically, UTMs are capable, in principle, of running any program that another UTM can run.

      Before the concept of a UTM was even a glimmer in Alan Turing's eye, we started out with simple mechanical calculators, such as the abacus. As time passed, these computers became more complex, in that they added additional conditional instructions. Eventually, these systems gained the necessary repertoire of computations which represented the leap to universal computation.

      While we can create universal computers, we did not create this universality itself. Universality in computing isn't tied to any particular computation speed, storage capacity, etc. It emerges from a specific repertoire of computations that a UTM can perform, in principle.

      It's the same with our ability to create explanations. We evolved to the extent that we made the leap to universal explainers. In principle, we have the capacity to explain anything, just as UTMs have the ability, in principle, to perform any computation that any other UTM can perform.

      While it's true that we do not yet know how to create computers which can create explanations themselves (which is known as Hard Artificial Intelligence), this doesn't mean we cannot recognize it as an emergent leap to universality - in the same sense as numbers, computation, etc.

      Does that clarify your question?

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    8. Watendlath: What evidence do you have that the knowledge contained in the genome is of the 'non-explanatory' type?

      Also, over 98% of all species that have ever existed have gone extinct. This is the sort of results we would expect if the genome contained useful rules of thumb, rather than explanatory knowledge.

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  10. ScottUnlike cars, the knowledge used to build biological adaptations exists in the genome of organisms. it's right there for us to examine. This is the evidence.

    It is evidence that the genome contains the knowledge to build biological adaptations, and that is all.

    What we observe is genetic variation in the genome that is random in respect to passing those genes on into future generations.

    OK

    So, the knowledge created there is based on a rule of thumb

    What knowledge is created?
    If a black cat gives birth to a black and white kitten it is because of knowledge that already exists in the DNA of the mother or father cat
    No new knowledge is created

    …just as the latter form of treatment in the example above....

    On the other hand, a doctor could base my treatment on a rule of thumb: changing any of my genes in any way could result in some unknown biological change that could improve my condition. This would be non-explanatory knowledge.


    No, that isn’t the same as what you described before...genetic variation in the genome that is random in respect to passing those genes on into future generations

    Here you are talking about DNA recombination, the process that happens during meiosis where already-existing genes are shuffled up and the resulting DNA changes are passed on to the offspring.
    I accept that; there is plenty of evidence for it.

    But your example of the doctor and his rule of thumb is describing something else.

    In this case, you are talking about small random alterations to the genes themselves creating new knowledge, ie new adaptations
    And you are extending that rule of thumb to encompass the entire history of development of life on this planet.

    One problem with that is that DNA has the ability to proof-read itself, to correct its own mistakes

    Another problem is that geneticists, even though they have done so much research and learnt so much, are nevertheless still in the early days of understanding how the genome actually works
    It is therefore pointless at this stage to make the sort of claim you are making….it is just a guess.

    I am not against the concept of evolution; if God wanted to create in that way, so that a fin became a limb and eventually a wing, then why not.
    But what I question is, if that is what happened, then how did it happen?
    As I said before, your rule of thumb claim is turning out to be a bit premature.

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  11. Scott: Unlike cars, the knowledge used to build biological adaptations exists in the genome of organisms. it's right there for us to examine. This is the evidence.

    Watendlath: It is evidence that the genome contains the knowledge to build biological adaptations, and that is all.

    Why is that "all"? Are you denying there is no difference between non-explanatory knowledge and explanatory knowledge?

    Scott: What we observe is genetic variation in the genome that is random in respect to passing those genes on into future generations.

    Watendlath: OK

    Scott: So, the knowledge created there is based on a rule of thumb.

    Watendlath: What knowledge is created?

    The knowledge of how to build features of biological organisms. The origin of this knowledge is a useful rule of thumb.

    Watendlath: If a black cat gives birth to a black and white kitten it is because of knowledge that already exists in the DNA of the mother or father cat. No new knowledge is created.

    If we follow the fossil record back far enough, we find mammals that are cat-like, but do not represent modern day cats. Eventually, we find there are no mammals at all, etc.

    What is the origin of this knowledge? How was it created?

    Again, the claim that some designer "Just was" complete with the knowledge of how to perform the necessary adaptations of matter to build cats, already present, serves no explanatory purpose. This is because one could more economically state that cats "just appeared" complete with the knowledge of how to perform the necessary adaptations of matter to build themselves, already present.

    All you've done is push the problem into some inexplicable realm.

    Scott: On the other hand, a doctor could base my treatment on a rule of thumb: changing any of my genes in any way could result in some unknown biological change that could improve my condition. This would be non-explanatory knowledge.

    Watendlath: No, that isn’t the same as what you described before...genetic variation in the genome that is random in respect to passing those genes on into future generations.

    I did not say they were the exact same thing. I said evolutionary process and the specific treatment plan were both examples of creating non-explanatory knowledge though a rule of thumb. Neither results in explanatory knowledge of why changing those genes results in the expression of specific features.

    So, they can both be explained in that they are forms of conjecture and refutation. They fall under the same theory.

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  12. Watendlath: Here you are talking about DNA recombination, the process that happens during meiosis where already-existing genes are shuffled up and the resulting DNA changes are passed on to the offspring. I accept that; there is plenty of evidence for it.

    No, I'm tanking about genetic variations that is random in respect to passing genes on to future generations (in the case of evolution) and genetic variations that are random in respect to improving my condition (in the case of the doctor forming a treatment.)

    Again, if the doctor had conjectured changing specific genes in a specific way which would change specific features, then this would be an explanatory theory. If successful, this would result in the creation of explanatory knowledge.

    Watendlath: But your example of the doctor and his rule of thumb is describing something else.

    Describing the addition of number using an abacus is different than describing the addition of a number using a computer. This doesn't mean the results they both achieve cannot be explained though mathematics.

    Watendlath: In this case, you are talking about small random alterations to the genes themselves creating new knowledge, ie new adaptations. And you are extending that rule of thumb to encompass the entire history of development of life on this planet.

    Yes, I'm suggesting they both create non-explanatory knowledge using the same useful rule of thumb.

    Watendlath: One problem with that is that DNA has the ability to proof-read itself, to correct its own mistakes.

    This would only be a problem if DNA repair mechanisms were 100% effective. Not are you taking into account other means of genetic variation, such as horizontal gene transfer, etc.

    Watendlath: Another problem is that geneticists, even though they have done so much research and learnt so much, are nevertheless still in the early days of understanding how the genome actually works. It is therefore pointless at this stage to make the sort of claim you are making….it is just a guess.

    This is precisely my point. Being in the early days of understanding how the genome works means there are areas were we lack explanatory knowledge. In the absence of explanatory knowledge, what do we do? We employ useful rules of thumb, as described in the treatment I described. Right?

    So, no, it's not "just a guess". Again, are you denying there is a difference between explanatory and non-explanatory knowledge?

    Watendlath: I am not against the concept of evolution; if God wanted to create in that way, so that a fin became a limb and eventually a wing, then why not.

    We can explain our relatively recent and rapid increase in the creation of knowledge in the shift to use good explanations as a criteria for what logical possibilities to test. In other words, as intelligent designers, we've made process in our ability to make progress.

    Yet, you're suggesting that some designer that is supposedly more advanced that us knows less about how to make progress than we do. How do you explain this discrepancy?

    Watendlath: But what I question is, if that is what happened, then how did it happen?

    We can explain the origin of this knowledge in that it was creating conjecture, in the form of genitive variation, and refutation, in the form of natural selection. It's form of the same umbrella theory as to how we crate both explanatory and not explanatory knowledge.

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