Thursday, April 3, 2014

Mapping the Brain’s Connections—The Connectome

Beyond Belief

As we have seen before the brain has more switches than all the computers and routers and Internet connections on Earth. That is not all the brains on Earth, nor all human brains, but merely a single brain of a single human. With over 100 billion nerve cells, or neurons, and a quadrillion synapses, or connections, it is, as one researcher described, “truly awesome.” Researchers have found that the brain’s complexity is beyond anything they’d imagined, or as one evolutionist admitted, almost to the point of being “beyond belief.” Amidst all these nerve cells and connections, a key question is: “Exactly which nerve cells do all these connections link together?” These connections should reveal a great deal about how the brain works, for while a single nerve cell may be enormously complex, it is in the massive networking of these many neurons that the brain’s fantastic processing and cognitive powers are likely to emerge. Now new research is mapping out all these connections in the mouse brain.

It was a massive imaging job and it has produced almost two petabytes of data. The result is a high-level view of the mouse brain’s wiring diagram. The diagram is like a map of the major freeways and highways between cities, except the brain's mapping is in three dimensions and is far more complex. Future work will zoom in to reveal the city streets, but for now scientists can see the major data flows in the mouse brain. What they see are highly specific patterns in the connections between different brain regions. They also see that the strengths of these connections vary by more than five orders of magnitude. While there is still much to learn and understand about this wiring diagram, it is a fascinating peek at this most complex of structures in the known universe. One finding that has emerged from this, and previous studies of the brain, is that there is no evidence the brain could have arisen spontaneously as evolutionists claim. Indeed, beyond theoretical speculation with no empirical support, evolutionists have no idea how natural selection, acting on random mutations and the like, could have created the brain. But they are certain that the brain must have evolved.

Religion drives science, and it matters.

120 comments:

  1. I would rather pay the mouse to figure these things out RATHER then the evolutionists.!!
    i want the mouse to have a great brain because I'm convinced the brain is 95% etc etc just memory. the glory of our computers is about its memory ability and not its thinking ability.
    Computers can play chess, do math etc which are all just memory operations without intellectual thought.
    Christians should know we think in our souls and this goes with us to the afterlife with no need of the brain joining us.
    Therefore we should first see our brains as just memory machines connecting our souls with our bodies.
    This leading to the conclusion that all mental problems have nothing to do with our thinking or intelligence of our true being, our soul, but only from triggering problems with our memory.
    So savants being the extreme of the spectrum.
    Creationism could have a better direction to healing these problems if we took mental problems AWAY from brain wiring errors and into memory wiring errors.
    I think a more healable target.
    Fighting the evolved brain could lead to fizing the broken memory in the brain.
    Why not??

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  2. Zachriel,

    half a wave at 110kHz

    At 110 kHz the wavelength is about half the 50khz wavelength which was what?? .68 cm, so halve that and you get .34 centimeters, or more closely .3 cm which is how many mm? And realize, that's in cross section. Not head or tail on. Half a wave would be? .15 cm or so? And a gnat is what size? oops.

    That's operating at the limit. The real issue is power output and hearing sensitivity. The wavefront will reflect off any object, unless the returning echo is exactly out of phase with the transmitted signal with no Doppler shift. In that case it will cancel out.

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    1. eklektos: Half a wave would be? .15 cm or so? And a gnat is what size?

      About 0.2 cm or a couple of millimeters, as we said.

      eklektos: The wavefront will reflect off any object, unless the returning echo is exactly out of phase with the transmitted signal with no Doppler shift. In that case it will cancel out.

      Uh, no. Rayleigh Criterion: "This leads to the simplified statement that the limit of resolution of any imaging process is going to be on the order of the wavelength of the wave used to image it."
      http://hyperphysics.phy-astr.gsu.edu/hbase/phyopt/raylei.html

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    2. Zachriel,

      you're confused. and a little late.

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    3. At 100 kHZ, the half-wave is the size of a typical gnat. At 10 kHz, the half-wave is the size of a typical moth. It's almost as if the bat is tuned to its prey.


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    4. Yea, I was off by a factor of ten. Sorry about that. but at 110hz you're operating at the limit, particularly if the gnat is head on. The point is that the listening interval is what's important. Now like I said I don't know if the pulse rate is linear or not.

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  3. And from your favorite reference:

    However, low frequencies are adaptive for some species with different prey and environments. Euderma maculatum, a species that feeds on moths, uses a particularly low frequency of 12.7 kHz that cannot be heard by moths

    That's a 27 cm moth, or almost the size of the bats wingspan. Even a 14cm (half a wave) moth isn't plausible as that's the bats body length. So there must be a flaw in your argument, no?

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    1. eklektos: That's a 27 cm moth

      The speed of sound, c = 340 m/s at 20°C
      Frequency, f = 12.4 kHz
      Wavelength, c/f = 2.7 cm
      Half-wave = 1.35 cm, about the size of a moth

      "Like most Microchiroptera, the Spotted bat is an echolocator, but uses very low frequencies to locate prey (9-12kHz). These frequencies limit the Spotted bat to catching large flying insects, apparently specializing on large moths that cannot detect echolocation calls of such low frequencies."
      http://animaldiversity.ummz.umich.edu/accounts/Euderma_maculatum/

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    2. 3400ms*12700=..27m or 27cm

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    3. Speed of sound is ≈ 340 m/s, depending on air pressure and moisture content.

      https://www.google.com/search?q=speed+of+sound

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  4. Zachriel,

    Oh look, also from your favorite reference:

    For example, a pulse interval of 100 ms (typical of a bat searching for insects) allows sound to travel in air roughly 34 meters so a bat can only detect objects as far away as 17 meters (the sound has to travel out and back).

    Do I really need to post more?

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    1. You're confusing pulse interval with audio frequency.

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    2. Uh yea. it's a little late for that.

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  5. But I will. You are confusing pulse interval with frequency. The signal is not a continuous wave but is pulsed at a given frequency. The time between pulses is listening time, as I pointed out. If the bat is transmitting(vocalizing) when the echo is returning then it won't hear it. That is the meaning of what you were referring to as half wave. The frequency of the transmitted pulse, i.e. the wavelength, is irrelevant. It is the interval between pulses that matters.

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    1. Zachriel,

      Also realize that pulse need not be equal re; transmission vs listening. The burst can be(I give this for example only) 2us and the listening time 10us. I'm not that sure of exactly how a bat times it's clicks. But those clicks have frequency. And that frequency must be far higher than the pulse interval. This is how you jam a radar, you return an out of phase signal which cancels the transmitter frequency. This is why radars sweep their frequency. I hope this helps you understand the principles involved.

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    2. eklektos: And that frequency must be far higher than the pulse interval.

      At a distance of 50 cm, the maximum pulse rate would be about 340/s. At 5 cm, the maximum pulse rate would be about 3400/sec. These are much lower than the frequency of the signal itself, which ranges from 10 kHz to 100 kHz.

      None of this changes Rayleigh criterion.

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    4. Yeah, it's almost as if the bat is tuned to its prey.

      "These frequencies limit the Spotted bat to catching large flying insects"
      http://animaldiversity.ummz.umich.edu/accounts/Euderma_maculatum/

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    5. By the way, from Rayleigh criterion, we can probably determine that conventional AM frequencies are not used for aviation radar.

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    6. Zachriel,

      Well radar has other problems. It operates in the microwave frequency band, but it cannot pick-up small objects like gnats even though it operates at far higher frequencies. One of the issues is receiver sensitivity. Besides, you wouldn't want to be a gnat directly in front of the antenna, or anything else.

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    7. eklektos: It operates in the microwave frequency band, but it cannot pick-up small objects like gnats even though it operates at far higher frequencies.

      Well, let's look at that. Air traffic terminals use wavelengths of about 10 cm. No, they can't see gnats, nor would they want to. It would rather clutter the monitors.

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    9. The difference being that at microwave levels the signal travels at the speed of light and not the speed of sound.

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    10. eklektos: The difference being that at microwave levels the signal travels at the speed of light and not the speed of sound.

      That's correct, but the Rayleigh criterion still applies.

      Speed of light, c = 300 million m/s
      Frequency of air traffic terminal radar, f = 3 GHz

      Wavelength, c/f = 10 cm, too long to detect gnats

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    11. Actually it usually won't even pick up birds. It will however pick up flocks of birds.

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    12. Glad we resolved that. So toothed whales and bats use a similar high range of frequencies. They share the same adaptations to the prestin gene, while the prestin gene is otherwise largely conserved in mammals.

      If you look at the non-homologous bases in the prestin gene, it shows toothed whales and bats close together. However, if you look at homologous bases in the prestin gene, they support the standard phylogeny. Evolution by natural selection explains both facts very neatly.

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    13. Zachriel,

      I have to admit you were correct about the frequency. I humbly apologize.

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    14. eklektos: I have to admit you were correct about the frequency.

      No problem. Sometimes we've believed as many as six wrong things before breakfast.

      Glad we resolved that, so we can return to the original point. Toothed whales and bats use a similar high range of frequencies. They share the same adaptations to the prestin gene, while the prestin gene is otherwise largely conserved in mammals.

      If you look at the non-homologous bases in the prestin gene, it shows toothed whales and bats anomalously close together. However, if you look at homologous bases in the prestin gene, they support the standard phylogeny. Evolution by natural selection explains both facts very neatly.

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    15. Evolution by natural selection explains both facts very neatly without ever addressing how you got from one to the other. Twice. It's assumed, not proven, or even adequately explained. You are talking about building novel structures. That requires changing the very developmental pathways which all experimentation, greatly compressing time, have demonstrated you can't change. You fault Axe for choosing the starting point and end, which is exactly what genetic experiments are trying to do. Sauce for the goose Saavik.

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    16. eklektos: Evolution by natural selection explains both facts very neatly without ever addressing how you got from one to the other.

      Of course it does. There are about two dozen base changes involved in the evolution of prestin in bats and whales. Evolution is quite adept at finding such sequences—as long as there is a selectable pathway. Phylogeny supports that such a selectable pathway is available. See Liu et al., Cetaceans on a Molecular Fast Track to Ultrasonic Hearing, Current Biology 2010. Pay particular attention to the phylogenies.

      eklektos: You are talking about building novel structures.

      No, prestin is not novel to bats or toothed whales. All mammals have prestin, and it has orthologs in non-mammalian species.

      (Above, we meant to write synonymous and non-synonymous. We apologize if there was confusion.)

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    17. Doesn't echolocation require a lot more stuff than just prestin? For example. bats and whales have to know how to use it. So changing the prestin by itself is not enough.

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    18. natschuster: Doesn't echolocation require a lot more stuff than just prestin?

      The basic mechanisms are already in place, which are normally used to suppress echos. For instance, humans have a rudimentary echolocation ability, which can improve with use, and can come naturally. Indeed, most people can sense their basic surrounding, such as if they are in a closed space, or an open one.

      "I was using echolocation from the age of two."
      http://www.youtube.com/watch?v=A8lztr1tu4o

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    19. Is the rudimentary mechanism useful for catching insects? Or did a lot stuff have to evolve simultaneously before that could happen?

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    20. natschuster: Is the rudimentary mechanism useful for catching insects?

      As we just pointed out, the rudimentary mechanism is useful for suppressing echos.

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    21. But to go from a system that suppresses echos to a system that can catch insects requires a lot of simultaneous changes to the whole animal. And isn't echo suppression kind of the opposite of echolocation? Don't bats have special wring in their brain? You need all of these changes simultaneously. Then the same thing happened in whales. They need that forehead melon to focus the sound.

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    22. natschuster: But to go from a system that suppresses echos to a system that can catch insects requires a lot of simultaneous changes to the whole animal.

      There's much unknown about bat evolution as they don't fossilize well, but the evidence we do have suggests they developed flight before echolocation, and that they developed flight from gliding (Onychonycteris finneyi). It is likely they were already insectivores before the development of sonar, hunting at dawn and dusk, then slowly developing the ability to hunt in darker conditions.

      natschuster: And isn't echo suppression kind of the opposite of echolocation? Don't bats have special wring in their brain?

      As we pointed out, primitive echolocation exists in other mammals. For instance, humans have a rudimentary echolocation ability, which can improve with use, and can come naturally. Indeed, most people can sense their basic surrounding, such as if they are in a closed space, or an open one.

      "I was using echolocation from the age of two."
      http://www.youtube.com/watch?v=A8lztr1tu4o

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    23. A lot is unknown, yes. That's kinda my point. How do you go from a system that is useful for navigating around big objects in the dark to one that can allow the organism to catch flying insets or fast fish require changes simultanious changes in the whole organism, not just the prestin. And it happened not once, but twice.

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    24. natschuster: How do you go from a system that is useful for navigating around big objects in the dark to one that can allow the organism to catch flying insets or fast fish require changes simultanious changes in the whole organism, not just the prestin.

      You don't seem to be reading our responses. The basic mechanisms are already in place in mammals. Bats already caught insects. Bats already had primitive echolocation. It just had to be incrementally improved.

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    25. But each part, e.g. the brain, had to be improved at the same time.

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    26. natschuster: But each part, e.g. the brain, had to be improved at the same time.

      You don't seem to be reading our responses. As we already mentioned above, the general ability is already there in mammals.

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    27. The brain is optimized for echolocation, but evolution is excellent at optimization. Those bats that could navigate best in the dusk had an advantage.

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    28. How do we go from navigation to catching insects in bats, and fish in whales, who have that melon in their forehead, and special stuff in the lower jaws? And then there is the special stuff in the ears of bats. And they have to somehow know how to use it as well. There is a behavior component as well

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    29. natschuster: How do we go from navigation to catching insects in bats, and fish in whales, who have that melon in their forehead, and special stuff in the lower jaws?

      The original question was about the parallel evolution of prestin to which we have already responded.

      Catching insects and fish predate echolocation. In bats, there were many changes, lengthening of the wings, shortening of the hind limbs, reduction in claws, enlarged cochlea, greater sensitivity of the inner ear hairs, etc.

      As for the "special stuff", do you think, if we looked carefully, that the "special stuff" is actually a modification of existing "stuff"?

      natschuster: And they have to somehow know how to use it as well.

      "I was using echolocation from the age of two."
      http://www.youtube.com/watch?v=A8lztr1tu4o

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  6. CH: One finding that has emerged from this, and previous studies of the brain, is that there is no evidence the brain could have arisen spontaneously as evolutionists claim.

    What makes a denier a denier is the claim that there is no evidence for evolutionary theory. Absolutely none. Nada. Once you make that claim, it’s unclear why you expect people to take you seriously.

    CH: Indeed, beyond theoretical speculation with no empirical support, evolutionists have no idea how natural selection, acting on random mutations and the like, could have created the brain.

    First, If by “no empirical support”, you mean no empirical evidence proves evolution created a brain, that’s a distinction without a difference. “Theory X is not empirically proven via observations” is a bad criticism because no theories are empirical proven via observations. This is merely handwaving.

    Second, as I’ve pointed out elsewhere, evolutionary theory does have scientific character.

    From: http://ncse.com/cej/6/2/what-did-karl-popper-really-say-evolution

    What Popper calls the historical sciences do not make predictions about long past unique events (postdictions), which obviously would not be testable. (Several recent authors—including Stephen Jay Gould in Discover, July 1982—make this mistake.) These sciences make hypotheses involving past events which must predict (that is, have logical consequences) for the present state of the system in question. Here the testing procedure takes for granted the general laws and theories and is testing the specific conditions (or initial conditions, as Popper usually calls them) that held for the system.

    A scientist, on the basis of much comparative anatomy and physiology, might hypothesize that, in the distant past, mammals evolved from reptiles. This would have testable consequences for the present state of the system (earth's surface with the geological strata in it and the animal and plant species living on it) in the form of reptile-mammal transition fossils that should exist, in addition to other necessary features of the DNA, developmental systems, and so forth, of the present-day reptiles and mammals.


    Cornelius has yet to even acknowledge this, let alone provide any genuine criticism of it.

    Again, one clearly put themselves in the denier category when they deny there is no practical, rational conception of science in which evolutionary theory has scientific character. Absolutely none. Nada.

    For example, what’s problematic for such a denial is the existence of a wide spectrum of nervous systems with varying degrees of complexity; just as we see a wide spectrum of light sensitive biological adaptations - the appearance of both are necessary consequences of evolutionary theory which we can empirically observe.

    Furthermore, *initial* brain development can be explained not as evolving to think or feel, but to control movement.

    http://www.ted.com/talks/daniel_wolpert_the_real_reason_for_brains

    Mammalian neuron connectivity can be virtually reconstructed on a large scale by using a few key principles.

    https://www.youtube.com/watch?v=ySgmZOTkQA8

    Again, I have yet to see anyone actually acknowledge the arguments made in this videos, let alone criticized them. (here’s a hint, Incredulity is not an argument.)

    IOW, it’s unclear how one can simultaneously hold the position that there is absolutely no evidence, yet have absolutely no criticism of the above. This is the very definition of denial.

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    1. Scott,

      RE; the guy in the video, which was interesting thanks. How many times did the guy say "design principles"? Nor does the connectivity explain the origin of the molecular composition of the neurons. We know that wiring of the brain is a developmental process. When he says the neuron decides where it's going to go or what it's supposed to be like that he's simply saying the neuron will grow until it connects with another neuron. Note he says that the locations are very similar within species, not across. We also know if one portion of the brain is damaged it will rewire itself, within limits. We see this with stroke victims all the time. We also know that the brain continues to wire itself into the mid twenties.

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    2. eklektos: How many times did the guy say "design principles"?

      How many times did the guy say brain, or any other word? How is that relevant?

      Natural structures are grouped by type of “design”, despite being formed naturally. For example, natural arches can be categorized in to at least two different designs: those constructed from a single rock or multiple rocks. Use of the terms “designs” and “constructed” is not a argument that either type were actually designed or constructed by an intelligent agent.

      eklektos: Nor does the connectivity explain the origin of the molecular composition of the neurons.

      Where did I suggest that specific video did? How would that even be possible in an exhaustive sense? Every explanation is incomplete and contains errors to some degree. However, other explanations have been provided elsewhere.

      eklektos: When he says the neuron decides where it's going to go or what it's supposed to be like that he's simply saying the neuron will grow until it connects with another neuron.

      Rather than a complex chemical process that determines how individual neurons are placed and oriented there is a simple, general rule that can be used to virtually layout millions of neurons for the purpose of simulation that conforms to observations of actual neurons. If we delete, change the orientation of neurons in a non-determinist way, this doesn’t have much of a statistical impact on where synapses will be formed.

      eklektos: Note he says that the locations are very similar within species, not across.

      He does not say how the locations differ or why. For example, individual neurons in different species could still follow general rules, despite synapses forming at different locations.

      eklektos: We also know if one portion of the brain is damaged it will rewire itself, within limits. We see this with stroke victims all the time. We also know that the brain continues to wire itself into the mid twenties.

      It’s unclear how this supports your argument.

      For example, would the discontinuance of this process at the age of 18 disprove design, while the continuance does?

      Salamanders can grow entire limbs, including nerves and bone. Yet, when we find ourselves in an environment where no sources are available, a human’s genome does not repair the single broken gene necessarily for us to synthesize vitamin C, resulting in death.

      If our genomes are pre-programmed to react to our external environment, how do you explain this disconnect?

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    3. What are you arguing, that what the gentleman says is irrelevant?

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    4. What are you arguing?

      That asking you to explain how the frequency of which Markram used the phrase "design principle" was relevant, implies I thought what Markram said was irrelevant in a universal sense?

      Really?

      Here's a tip. When you find your self in a hole of bad arguments, stop digging.

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    5. It doesn't trouble you that he kept referring to a design principle? It looks like a very good solution to a problem, but you have to remind yourself that it's not actually designed? That's doublethink.

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    6. ekletos: It doesn't trouble you that he kept referring to a design principle?

      Why would I? Again, how is the frequency of which Markram used the phrase "design principle" actually relevant?

      ekletos: It looks like a very good solution to a problem, but you have to remind yourself that it's not actually designed? That's doublethink.

      Again, you appear unable to even conceive of a non-foundationalist epistemology long enough to accurately reflect my position. Good designs are good regardless of their source. As such, providence is not relevant. I don’t have to remind myself of something I’m not concerned about in the first place.

      http://nautil.us/issue/2/uncertainty/why-its-good-to-be-wrong

      The absence of foundation, whether infallible or probable, is no loss to anyone except tyrants and charlatans, because what the rest of us want from ideas is their content, not their provenance: If your disease has been cured by medical science, and you then become aware that science never proves anything but only disproves theories (and then only tentatively), you do not respond “oh dear, I’ll just have to die, then.”

      The human brain could reflect a compromise by a committee of designers with different goals or represent a battle between God and his equally powerful, yet perfectly evil twin brother. The law of unexpected consequences could result in designs proposed to solve one problem which fail completely, yet end up solving some other problem it was never intended to, etc. IOW, good design need not logically necessitate an intentional outcome.

      What I find ironic is how you completely discard this possibility arbitrarily, yet chastise us for lacking imagination about the origin of biological features.

      Nor would I want to design a brain to operate exactly like those found in nature, as damaged brain cells do not regenerate to the extent as even cells in other parts of our bodies do. See….

      http://news.psu.edu/story/298921/2013/12/19/research/neuron-regeneration-may-help-sufferers-brain-injury-alzheimers

      Assuming human brains are designed, would we adopt this very same design, including this lack of regeneration, based on its providence or would we only adopt specific aspects of this design because those aspects represent a good solution, regardless of their source? (based on their content)

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    7. Look, he discovered a "design principle", that's what the man said. You can spin it till the cows come home. You can write a fifty page response to a simple statement. It doesn't change anything. When you start talking about what God would or wouldn't do, what providence would or wouldn't do, but that is not science. And as to your non-foundationalism gain you are floating in mid-air. You're particular opinion is meaningless. I realize you like ambiguity, but again, what is your foundation for the claim there is no foundation for knowledge?

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    8. eklektos: Look, he discovered a "design principle", that's what the man said. You can spin it till the cows come home. You can write a fifty page response to a simple statement. It doesn't change anything.

      Again, so what? I asked you to explain to me how Markram using the phrase "design principle" is actually relevant to the issue at hand. Several paragraphs later, you still haven’t explained it. Your bad argument hasn’t magically changed in to a good one.

      Furthermore, I provided criticism, not spin, which you have yet to actually respond to. Apparently, “spin”, along with “bait and switch”, are vague terms you use when you simply have no response to criticism.

      This criticism took the form of taking your own argument seriously for the purpose of criticism, in that *all* usage of the phrase “design principle” should conform to it, including use of the phrase in respect to geological structures found in nature.

      Specifically, geological structures can be classified into architectural designs, such as arches, pillars, etc. Geological arches can be sub classified into at least two designs, solids and composites. They operate based on the same universal structural principles human beings leverage while designing buildings, bridges, etc. However, use of the phrase “design principle” in relation to theses geological structures does not necessitate them actually having been designed, right?

      IOW, it would seem implications of the phrase “design principle” is dependent on whether we the subject in question was thought to be deigned, not vice versa.

      Or are you claiming use of this phrase has the same implication for all structures? Is that really what you’re arguing? Or perhaps you simply do not take your own arguments remotely seriously?

      In addition, Markram’s goal is to layout virtual neurons to build a virtual brain; just like architects leverage design principles in their structures. It would be uncontroversial that any resulting virtual brain would be designed.

      eklektos: When you start talking about what God would or wouldn't do, what providence would or wouldn't do, but that is not science.

      You’re not disagreeing with me, as I’ve asked Cornelius to explain what he means by “science” over and over again. He has yet to clarify, despite continuing to use the term “the science” as if the question of what science *is* or what scientists actually do to make progress is not a question at all, or is somehow scientific.

      If by “science”, Cornelius means logical positivism, then it would be uncontroversial that evolutionary theory isn’t science. But then, who cares? We’ve made progress since then. This would be merely hand waving.

      You think evolutionary theory is a waste of time and money because you dogmatically believe the biosphere was designed. The means, method, etc of the designer cannot be explained because this designer is the supernatural Christian God. As such, you find the very idea that any progress can be made, well, personally offensive and objectionable.

      But we still keep making progress. Denying this progress is what makes you, and others like you a denier. You employ general purpose strategies that could be used to deny anything and claim no progress can be made.

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    9. eklektos: And as to your non-foundationalism gain you are floating in mid-air. You're particular opinion is meaningless. I realize you like ambiguity, but again, what is your foundation for the claim there is no foundation for knowledge?

      Again, it seems you cannot conceive of a non-foundationalist epistemology long enough to accurately reflect my position. Specifically, you are confusing me with a disappointed foundationalist.

      Hayek, Bartley, Popper
      Justificationism and the
      Abuse of Reason
      - - - - - - - - - - - - - - - - - - - - -
      http://www.the-rathouse.com/Bartley/Leeson-vol.html

      In the light of the dilemma of the infinite regress versus dogmatism, we can discern three attitudes towards positions: relativism, “true belief” and critical rationalism [Note 3]

      Relativists tend to be disappointed justificationists who realise that positive justification cannot be achieved. From this premise they proceed to the conclusion that all positions are pretty much the same and none can really claim to be better than any other. There is no such thing as the truth, no way to get nearer to the truth and there is no such thing as a rational position.

      True believers embrace justificationism. They insist that some positions are better than others though they accept that there is no logical way to establish a positive justification for an belief. They accept that we make our choice regardless of reason: "Here I stand!". Most forms of rationalism up to date have, at rock bottom, shared this attitude with the irrationalists and other dogmatists because they share the theory of justificationism.

      According to the critical rationalists, the exponents of critical preference, no position can be positively justified but it is quite likely that one (or more) will turn out to be better than others in the light of critical discussion and tests. This type of rationality holds all its positions and propositions open to criticism and a standard objection to this stance is that it is empty; just holding our positions open to criticism provides no guidance as to what position we should adopt in any particular situation. This criticism misses its mark for two reasons. First, critical rationalism is not a position. It is not directed at solving the kind of problems that are solved by fixing on a position. It is concerned with the way that such positions are adopted, criticised, defended and relinquished. Second, Bartley did provide guidance on adopting positions; we may adopt the position that to this moment has stood up to criticism most effectively. Of course this is no help for people who seek stronger reasons for belief, but that is a problem for them, and it does not undermine the logic of critical preference.


      Is there something about the above that you do not understand?

      Delete
  7. Zachriel,

    Now let's talk about your ridiculous assertion about the ease of functional protein folds. Let's take up lysozyme. This is a critical protein which catalyzes polysaccharides. It is formed by a DNA sequence which is 5kb long containing 4 exons and 3 introns. The 3 dimensional structure of this protein is critical. It must not only have the right shape, but the catalyzing molecules must be in exactly the right position. Also the amino acid side chain must be in exactly the right sequence to fold the protein properly. The introns must be of the right length and have the binding sites in the right place. Anything out of whack and it won't work. So Axe was very conservative in his estimate. Also you are wrong about cutting out pieces of exons and splicing them somewhere else. If you cut out sections of the exon the fold will lose it's shape. And the exons must be of the right type placed in the right order and with the right introns. Mutation will not accomplish this, nor will recombination because if the exons are placed incorrectly the cell dies, or the chromosome is defective and the developing organism is diseased or dies. Now you can go to Wikipedia and read about the enzyme, but I honestly don't think you understand it. And remember, proteins have many functions besides catalyzation. So as you see Axe didn't undercut his own assertion, despite your claiming he did.

    ReplyDelete
    Replies
    1. eklektos: Let's take up lysozyme.

      You seem to think that because we can't explain every event in evolutionary history that this means evolution didn't happen.

      Lysozymes support the standard phylogeny.

      See Irwin, Biegel & Stewart, Evolution of the mammalian lysozyme gene family, BMC Evolutionary Biology, 2011.
      http://www.biomedcentral.com/1471-2148/11/166/figure/F2

      Lysozymes are very ancient, and probably trace back to the origin of bilateria.

      See Bachali et al., Phylogenetic Analysis of Invertebrate Lysozymes and the Evolution of Lysozyme Function, Journal of Molecular Evolution 2001.

      eklektos: Also you are wrong about cutting out pieces of exons and splicing them somewhere else.

      They don't have to be cut to be copied elsewhere in the genome.

      Delete
    2. Doesn't the whole system of introns and exons depend on a very complex cut and paste system? Doesn't shuffling the exons to get a new protein also require that the whole system be changed as well? How else will it know where to cut and paste?

      Delete
    3. And it isn't just a question of protein evolution being unexplained. Its a question of it being so unlikely that it borders on the impossible.

      Delete
    4. natschuster: Doesn't the whole system of introns and exons depend on a very complex cut and paste system?

      Yes.

      natschuster: Doesn't shuffling the exons to get a new protein also require that the whole system be changed as well?

      No. For an overview, see Long, Thornton, & Wang,The origin of new genes: glimpses from the young and old, Nat Rev Genet 2003.

      natschuster: And it isn't just a question of protein evolution being unexplained.

      A lot is already known about protein evolution. The origins of the first proteins is still a mystery.

      Delete
    5. Zachriel,

      the question is not their supposed age. The question is whether there is an actual possibility of them arising by chance. And that actually makes the case worse.

      Delete
    6. Zach:

      "No. For an overview, see Long, Thornton, & Wang,The origin of new genes: glimpses from the young and old, Nat Rev Genet 2003."

      I didn't see anything that addressed my question. Maybe I missed it,

      Delete
    7. Zachriel,

      yea, you missed it. Current calculations of the probability of a complex protein fold are based on the currently known rate of mutation, population, and time. Decrease the time and population and the odds go up exponentially. So if the protein arose during the Cambrian, as you assert the odds are even higher. And to make matters worse the time of the Cambrian explosion, while you claim them as large because it's 6-10 million years, is actually too small to accomplish the task. With only 6-10 million years the odds are 10/infinity for all practical purposes. As in statistically zero.

      Delete
    8. natschuster: Doesn't shuffling the exons to get a new protein also require that the whole system be changed as well?

      The review lists various mechanisms by which new proteins can be created which don't require the whole system to be change, including exon shuffling and gene duplication.



      Delete
    9. eklektos: So if the protein arose during the Cambrian, as you assert the odds are even higher.

      Most protein families, including those associated with homeobox genes, are thought to have evolved in the Precambrian.

      Delete
  8. Zachriel,

    Now lets talk about Dembski's analogy. As I remember, and it's been a while, it involved dropping scrabble letters onto a board and checking them with a dictionary. Is this the example you're alluding to?

    ReplyDelete
    Replies
    1. That's not quite right. Dembski has avoided making specific claims. Dr. Sean Pitman, as part of an argument about the limits of evolution, claimed that word evolution couldn't result in words longer than about seven letters. That was incorrect.

      Delete
    2. Well, Dembski was simply making an analogy. What Shawn said I'm unaware of. But the real example would be building a complex protein like lysozyme. So you're talking a 5k word, not 20 or 30 characters. You odds would only be slightly better because you're only using a 20 letter alphabet. That's quite a different matter than the scrabble analogy. .

      Delete
    3. eklektos: So you're talking a 5k word, not 20 or 30 characters.

      Evolution doesn't posit that large structures suddenly came together, but that they evolved from less complex structures. The equivalent would be whether longer words or phrases can evolve from short words by single letter changes and recombinations, and all intermediates being valid words or phrases.

      Delete
    4. Zachriel,

      yea, you posit making them from smaller structures. But that doesn't actually help. It reminds me of an old Wendys commercial about chicken sandwiches. " See you take the little chicken parts and you put them together to make bigger parts, and parts is parts". It's a just so story. We don't observe this, all we actually see is that when you take this a put it with this you degrade function. Because all of the DNA serves some purpose. And when you examine particular claims, like the 2Q13 fusion you see it's actually implausible. All you do is then claim your weak hypothesis is true because "it fits neatly with our phylogeny". More circular arguments. When it's pointed out it's circular you bring in a totally irrelevant subject, like radiometric dating is true because of cosmology. No, the cosmology could be true and radiometric dating false. That's ad hoc logic.

      Delete
    5. eklektos: yea, you posit making them from smaller structures. But that doesn't actually help.

      Of course it does. If there is an incremental, selectable pathway, then an evolutionary process is quite effective.

      eklektos: When it's pointed out it's circular you bring in a totally irrelevant subject, like radiometric dating is true because of cosmology. No, the cosmology could be true and radiometric dating false.

      If the cosmology and radiometrics independently confirm the same age, then it lends support to that age.

      Delete
    6. There's a just so story which is contra-indicated by actual observation.

      If radiometrics is the thing in doubt then you cannot bring in an unrelated matter. The method is in question. As I said, it does not support it. In fact it's a classic case of ad hoc reasoning.

      Delete
    7. eklektos: If radiometrics is the thing in doubt then you cannot bring in an unrelated matter.

      Of course you can. Indeed, that's what you're supposed to do, bring in independent lines of evidence. The more independent lines of evidence that support a hypothesis, the wider the confirmation, the stronger our confidence in that hypothesis.

      Delete
    8. No, you can't no matter how many times you claim you can. Radiometrics cannot be claimed to be true because it agrees with assumed ages based on a calibration done using assumed ages. That's circular. Or did you forget that you admitted that the method does not work on material where the age is known?

      Delete
    9. eklektos: No, you can't no matter how many times you claim you can. Radiometrics cannot be claimed to be true because it agrees with assumed ages based on a calibration done using assumed ages.

      But that's not what we said, or what we have said. Rather, we said that independent lines of evidence can lend support to the claim. So if independent researchers, making independent observations, using independent methodologies, reach the same conclusion, it strengthens support for the claim. In the case of the old Earth, those observations include everything from the decay of atoms to the life cycle of stars.

      Pliny the Younger wrote that Pompeii was buried in 79 CE, which in agreement with radiometric dating.
      Renne et al., 40Ar/39Ar Dating into the Historical Realm: Calibration Against Pliny the Younger, Science 1997.

      Delete
    10. Excess 40Ar is present in the sanidine in concentrations that would cause significant errors if ignored in dating Holocene samples

      ??

      Delete
    11. eklektos: Excess 40Ar is present in the sanidine in concentrations that would cause significant errors if ignored in dating Holocene samples

      Right. So the lesson is to not ignore the excess 40Ar if you want an accurate date.

      Delete
    12. The lesson is that you have to adjust you're method to get the date you want. It's accurate if you know the initial conditions, which you don't. Therefore the method is not calibrated.

      Delete
    13. eklektos: The lesson is that you have to adjust you're method to get the date you want.

      No. They could determine the excess argon from the amount of 36-Ar. See Renne et al., 40Ar/39Ar Dating into the Historical Realm: Calibration Against Pliny the Younger, Science 1997.

      Delete
  9. Ok, this to me has quite a bit of humor in it:

    http://drmsh.com/2014/04/03/impressions-on-the-noah-movie/

    I particularly found this funny, "Gnostic cosmologies tend to read like the authors were on hallucinogens"

    Which is similar to what a Catholic historian once said of the gnostic Gospels, "They will make your brain itch".

    ReplyDelete
  10. ' Indeed, beyond theoretical speculation with no empirical support, evolutionists have no idea how natural selection, acting on random mutations and the like, could have created the brain. But they are certain that the brain must have evolved.'

    Don't worry, Cornelius. Their remarkable intellects and intellectual integrity are the guarantors of their 'promissory note'. You can take that to the bank.

    ReplyDelete
  11. Well, if an evolutionist can believe that everything came from nothing then the 2 petabytes (2,097,000 gigabytes) of data required to map a mouse's brain are just a drop in the bucket. Yeah, religion drives science all right.

    ReplyDelete
  12. So, can you post the citation about evolutionists stating that the brain appeared spontaneously?

    Didn't think so.

    ReplyDelete
    Replies
    1. Paul:

      Yes, here is an example from Ernst Mayr: "It is now actually misleading to refer to evolution as a theory, considering the massive evidence that has been discovered over the last 140 years documenting its existence. Evolution is no longer a theory, it is simply a fact."

      Delete
    2. "Well, evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts do not go away when scientists debate rival theories to explain them." — Stephen J Gould
      http://www.stephenjaygould.org/library/gould_fact-and-theory.html

      Delete
    3. Zachriel,

      Yes, I realize that you, like Gould want to blur the lines. I think that has actually been destructive. It has sent us off on innumerable wild goose chases over the last decade. Like Alar, Saccharine, Cyclamates, Junk DNA, slowing universal expansion, on and on and on. Science should be empirical, you don't claim something as a fact until you know it's a fact. Evolution is a theory, and not a very robust one. But because that's actually the state of things evolutionist must claim it's a fact even though unproven. We see this all the time. So when you evaluate particular claims you get the bait and switch. You do it all the time.

      Delete
    4. eklektos: Yes, I realize that you, like Gould want to blur the lines.

      Gould didn't blur the lines, but drew them clearly. There is a difference between a set of facts, and a theory that explains those facts. We observe the effects of gravity. The Theory of Gravity explains those observations. We observe evolution and the nested hierarchy. The Theory of Evolution explains those observations.

      Delete
    5. I'm sorry, but that's blurring the lines. Interpretation of the facts is what's in dispute. A theory is not a fact, and Darwinism is not a fact. It's not even a good theory. The discontinuities are glaring.

      Delete
    6. eklektos: I'm sorry, but that's blurring the lines.

      No, it makes a clear distinction between fact and theory.

      eklektos: Interpretation of the facts is what's in dispute.

      Sure, at least there's a dispute in the political and cultural realm.

      eklektos: A theory is not a fact

      That's what Gould said.

      eklektos: Darwinism is not a fact.

      We directly observe evolution, so evolution is a fact.

      Delete
    7. We do not directly observe Darwinism, that's a bait and switch. We observe variations within a species. We do not observe jumps from one genus to the other. The only way you can claim that is to make unproven claims about fossils. Which are nothing more than just so stories. Not to mention they are constantly being changed. Rodhocetus being a perfect example. First it had a fluke based on? The it had front flippers based on? Now it has feet, a tail with no fluke. It had fur, and no blowhole. But it is still claimed as a proto whale? Why? Because Darwinism has to fill in those holes in their charts that's why. This is not science. This is desperately trying to support an incorrect theory based on self delusion. Like classifying a human metatarsal and human footprints as afarensis. Or claiming that a human jawbone washed wash into the same layer as an afarensis skeleton because people lived in the cave. Or buried. Or whatever the latest just so story is.

      Delete
    8. eklektos: We do not directly observe Darwinism, that's a bait and switch.

      What the heck do you mean "darwinism"? How the heck do you observe a theoretical position?

      eklektos: We observe variations within a species.

      Yes, we do. And we also observe there is often no distinct line between species.

      eklektos: We do not observe jumps from one genus to the other.

      If you mean monkeys don't suddenly become humans, sure. Evolution posits relatively gradual change, so sudden "jumps" would contradict evolution.

      eklektos: But {Rodhocetus} is still claimed as a proto whale? Why?

      Rodhocetus has large, dense auditory bullae, which is a defining characteristic of cetaceans. But also because it exhibits the expected transitional characteristics.

      Unfused sacral vertebrae
      Lumbar vertebrae with dorsal spines
      Simplified molar crowns
      Robust tail vertebrae
      Small pelvis, but still connected to the sacral vertebrae
      Nostrils above the canines
      Premaxillae and dentaries extended forward

      Delete
    9. Ok, it's a unique animal. It's not a whale. That is once again ad hoc. Ad hoc seems to be evolutions guiding principle. There are as many differences as similarities. But of course those are ignored. Nostrils, not a blowhole, nor anywhere near being a blowhole. And a host of other differences. An alligator has many of the same characteristics, so whales must have evolved from alligators. But of course they didn't. They're just so stories. All you've got is an extinct animal and a fairy tale.

      Delete
    10. eklektos: it's a unique animal.

      Of course it's a unique animal, suited to its own habitat.

      eklektos: It's not a whale.

      It's a cetacean, with a large, dense auditory bullae.

      eklektos: Nostrils, not a blowhole, nor anywhere near being a blowhole.

      Blowholes are nares. They are in a transitional position.

      eklektos: An alligator has many of the same characteristics, so whales must have evolved from alligators.

      Rodhocetus is clearly a derived mammals, with a single lower jaw bone; and not just mammals, but artiodactyls with their distinctive ear. See Thewissen, Whales originated from aquatic
      artiodactyls in the Eocene epoch of India, Nature 2007.

      The problem is you still don't get the nested hierarchy. For instance, Rodhocetus almost certainly had mammary glands.

      Delete
    11. You have skeleton, that's all. I reject your "nested hierarchies" for the same reasons given before. They are "nested" according to evolutionary assumptions. Again, you assume what you seek to prove.

      Delete
    12. eklektos: You have skeleton, that's all.

      Really? You don't think Rodhocetus was a mammal?

      eklektos: They are "nested" according to evolutionary assumptions.

      No, they are nested according to traits. See Linnaeus c. 1738.

      Delete
    13. Paul: So, can you post the citation about evolutionists stating that the brain appeared spontaneously?

      CH: Yes, here is an example from Ernst Mayr: "It is now actually misleading to refer to evolution as a theory, considering the massive evidence that has been discovered over the last 140 years documenting its existence. Evolution is no longer a theory, it is simply a fact."

      That’s odd. I don’t see the word “spontaneous” in that quote. Nor have you explained what you mean by the term “assistance” in a useful, explanatory way, by which to make use of the term "spontaneous" a meaningful distinction.

      So, no I don’t think you have or will either.

      Delete
  13. @"Evolution is no longer a theory, it is simply a fact" Might refer to accommodation. A grasshopper develops the same green color as surrounding grass for better camouflage. That some of these grasshoppers evolved into a bird is rather not the case. Same like some monkeys suddenly gave birth to human children. If this happened in the past it should also happen today. There are presently millions of monkeys. So this is rather false statement that one specie evolves into a totally different form. Slight degree of adaptation, but no quantum jump from monkey to human.

    ReplyDelete
    Replies
    1. rm: That some of these grasshoppers evolved into a bird is rather not the case.

      Birds did not descend from insects, much less grasshoppers.

      rm: Same like some monkeys suddenly gave birth to human children.

      If monkeys suddenly gave birth to humans, it would falsify the theory of evolution. Rather, modern monkeys and humans share a common ancestor, and the divergence occurred over millions of years.



      Delete
    2. Birds did not descend from insects, much less grasshoppers.

      It was rhetorical. They didn't evolve from dinosaurs either.

      If monkeys suddenly gave birth to humans, it would falsify the theory of evolution. Rather, modern monkeys and humans share a common ancestor, and the divergence occurred over millions of years.

      They're not diverging into anything else either. We can't even properly define a species. evolutionist are always seeking to define animals that are slightly different into different species. Like Darwin's finches, which are all one species in actuality. What we should see if evolution was actually true is jumps in genus, not species, which we can't even seem to define. We however don't see that. What are you going to believe, you're lying eyes?


      Delete
    3. eklektos: We can't even properly define a species.

      There are several workable definitions. That species have chaotic boundaries is important evidence in support of evolutionary theory. We expect the borders to be gray.

      eklektos: Like Darwin's finches, which are all one species in actuality.

      Um, no. They clearly have persistent and distinguishing characteristics. Can you name a professional ornithologist who classifies them as a single species?

      eklektos: What we should see if evolution was actually true is jumps in genus, not species

      Um, no. See Darwin 1859.

      Delete
    4. Zachriel,

      There are several workable definitions, so that means we can define it, or we can define to suit whatever argument we're making? They can interbreed, they are genetically the same within a normal range of variation, they are in fact one species. So why classify them as separate species? To support Darwinism of course. bah. Darwin was wrong. Law of use and disuse? wrong. Recapitulation? wrong. ect ect ect

      Delete
    5. eklektos: There are several workable definitions, so that means we can define it, or we can define to suit whatever argument we're making?

      As we said, the edge of the category are chaotic. Different fields use slightly different definitions, but they all come down to a population that has persistent and distinct characteristics with little gene flow between populations.

      Is there really a dispute within ornithology about whether Darwin's finches represent a single species?

      eklektos: They can interbreed, they are genetically the same within a normal range of variation, they are in fact one species.

      It depends. If they maintain a persistent and distinct identity with little gene flow between populations, then they are usually considered separate species. Polar bears are a distinct species from brown bears, even though they occasionally hybridize.

      But remember, the fact that species have indistinct boundaries was an important piece of evidence for Darwin. Do you understand why he did?

      Delete
    6. Zachriel,

      You can't put a happy face on it. They may not hybridize because of population isolation. Humans are also isolated into family groups with distinct familial traits, but when you have movement among the groups these traits lose their distinctiveness. And of course you see this today. But humans are more mobile than bears today. What you actually see is homogenization. Were we ever different species? No. What ornithologist do or do not believe is irrelevant. What we actually observe with the finches is what's important. These are categories we make. Nature doesn't know of such categories. The finches have the same genetic makeup and can interbreed. So what is the justification for the classification? Our ease of classifying familial groups and nothing more.

      Delete
    7. eklektos: They may not hybridize because of population isolation.

      The ranges of polar bears and brown bears overlap, but they rarely hybridize for behavioral reasons.

      Not that you are really interested, but there's Grant & Grant on hybridization in Darwin's Finches, Fission and fusion of Darwin's finches populations, Philosophical Transactions of the Royal Society 2008.

      eklektos: Humans are also isolated into family groups with distinct familial traits

      Humans only recently diversified, groups have rarely been isolated for long in biological terms, and they readily produce offspring between groups.

      eklektos: What ornithologist do or do not believe is irrelevant.

      Yeah, what would ornithologists know about bird species. You're funny.

      According to your standard, mallards, wigeons, shovelers, teals, cinnamon teal, black ducks, and gadwalls, are only one species. As are buffalo and domestic cows. As are wolves, coyotes, dingoes, jackals and domestic dogs.

      The term 'species' has a scientific meaning that doesn't change simply because you redefine the word.

      eklektos: So what is the justification for the classification?

      They have persistent and distinct characteristics. In genetic terms, that means there is little gene flow between them.

      Delete
    8. Yeah, what would ornithologists know about bird species. You're funny

      You're not, deal with the argument. Don't run off to authority

      They have persistent and distinct characteristics. In genetic terms, that means there is little gene flow between them

      Again you're avoiding the argument. The reason for that is population isolation. As soon as the isolation is removed the populations hybridize.

      Delete
    9. eklektos: You're not, deal with the argument. Don't run off to authority

      Words are defined by usage. Scientific words are defined by scientific usage. But seriously. We understand the evolutionists are in on the conspiracy. And the geologists. And apparently, the astronomers and physicists. And don't their ringleader, Pliny the Younger. But

      Et tu ornithologists!
      http://fieldmuseum.org/sites/default/files/styles/gallery-large/public/10.%20Ornithologists.jpg

      eklektos: The reason for that is population isolation.

      It's called allopatric speciation. Speciation is a process, not an event. And that is exactly what we would expect from evolution.

      Darwin's Finches are not isolated by geography, by the way, but by behavioral adaptations.

      According to your standard, mallards, wigeons, shovelers, teals, cinnamon teal, black ducks, and gadwalls, are only one species. As are buffalo and domestic cows. As are wolves, coyotes, dingoes, jackals and domestic dogs. Is this correct?

      Delete
    10. They are distinct types. I'm not an expert on buffalo, so I couldn't say. As to ducks I'm not sure of how genetically related they actually are. We were talking about finches. But we know that if a population is isolated long enough they may lose enough genetic information that they cannot interbreed. The finches obviously haven't been behaviorally isolated, they are merging. It's exactly what evolution claims, whether there is actual evidence for it is another question.

      Delete
    11. eklektos: We were talking about finches.

      We were talking about your heterodox usage of the term species.

      eklektos: As to ducks I'm not sure of how genetically related they actually are.

      They have persistent and distinctive characteristics. Using your definition, they are the same species, which is just not a supportable claim.

      Delete
    12. Darwin had a whole chapter on hybridization. That inter-fertility varies in degrees is exactly the pattern expected of an evolutionary process.

      Delete
    13. Darwin also believed in the "law" of use and disuse. And a host of other disproven things. I wouldn't drag your idol into the discussion. The simple problem is that none of this deals with the problem that the finches are basically genetically identical. I'm not running down your rabbit trails.

      Delete
    14. And none of this gets you across the genus barrier. They are all still ducks. As to their genetic similarity like I said I'm not a duck expert. I don't know if they are genetically as similar as the finches. They may not be.

      Delete
    15. eklektos: Darwin also believed in the "law" of use and disuse.

      Darwin didn't have access to a working theory of inheritance. He also proposed a poorly supported theory, pangenesis.

      eklektos: I wouldn't drag your idol into the discussion.

      Darwin is certainly not an idol. Rather, you don't seem to have a rudimentary understanding of the theory you reject. Inter-fertility varying in degree is exactly what is expected of an evolutionary process. Try to grasp that concept.

      eklektos: I'm not a duck expert.

      But you're an expert on defining species, while rejecting the expert opinion of those who are duck experts.

      eklektos: And none of this gets you across the genus barrier.

      What barrier is that?

      Delete
    16. Again, authority. Ad hoc, authority, majority. Not an argument.

      Delete
    17. eklektos: Again, authority.

      How many legs does a dog have if you call the tail a leg?

      What is the "genus barrier"?

      Delete
  14. If anyone is actually interested in the nature of species they should visit Evolving Thoughts, the blog of Australian philosopher of science, John Wilkins. He has written and published extensively on the subject.

    ReplyDelete
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