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Assessing Fault

by Bradford

Why Do We Rape, Kill and Sleep Around? The fault, dear Darwin, lies not in our ancestors, but in ourselves, a Newsweek article by Sharon Begley, shows us what happens when evolutionary psychology clashes with powerful social values. The former comes out the worse for it.

This entry was posted on Tuesday, June 30th, 2009 at 12:19 am and is filed under Evolutionary Psychology. You can follow any responses to this entry through the RSS 2.0 feed. Both comments and pings are currently closed.

80 Responses to “Assessing Fault”

  1. The Pixie Again Says:
    June 30th, 2009 at 7:11 am

    This paragraph seems to sum up the article:

    Like other critics, he has no doubt that evolution shaped the human brain. How could it be otherwise, when evolution has shaped every other human organ? But evo psych's claims that human behavior is constrained by mental modules that calcified in the Stone Age make sense "only if the environmental challenges remain static enough to sculpt an instinct over evolutionary time," Pigliucci points out. If the environment, including the social environment, is instead dynamic rather than static—which all evidence suggests—then the only kind of mind that makes humans evolutionarily fit is one that is flexible and responsive, able to figure out a way to make trade-offs, survive, thrive and reproduce in whatever social and physical environment it finds itself in. In some environments it might indeed be adaptive for women to seek sugar daddies. In some, it might be adaptive for stepfathers to kill their stepchildren. In some, it might be adaptive for men to be promiscuous. But not in all. And if that's the case, then there is no universal human nature as evo psych defines it.

    Apparently "evo psych" is an evolving science, and new ideas are replacing old.

  2. Comment by The Pixie Again — June 30, 2009 @ 7:11 am

  3. hrun Says:
    June 30th, 2009 at 7:36 am

    Did anyone actually argue that the fault does not lie within ourselves if we commit crimes?

    Last I looked rape, no matter what your post-hoc reasoning for it you can come up with (tiny pink elephant told me to do it, my cave-man genes told me to do it, my vengeful god told me to do it, …), it remains illegal and you will be punished.

    Or did the person who observed rape occurring in the animal kingdom and speculated how rape in humans could be an adaptation at the same time argue that such rape should be legal and is justified?

  4. Comment by hrun — June 30, 2009 @ 7:36 am

  5. Bradford Says:
    June 30th, 2009 at 10:58 am

    hrun; Or did the person who observed rape occurring in the animal kingdom and speculated how rape in humans could be an adaptation at the same time argue that such rape should be legal and is justified?

    It is not that simplistic. Within legal systems judges have considerable latitude as far as evidentiary rulings and sentencing goes. One who feels moral failures are programmed is apt to act differently than one who views moral failures as something that must be faced up to and changed.

  6. Comment by Bradford — June 30, 2009 @ 10:58 am

  7. hrun Says:
    June 30th, 2009 at 11:46 am

    It is not that simplistic. Within legal systems judges have considerable latitude as far as evidentiary rulings and sentencing goes. One who feels moral failures are programmed is apt to act differently than one who views moral failures as something that must be faced up to and changed.

    Maybe so… so what are we going to do about it? Show that the science is false? Or show that writing a book or advancing a hypothesis can have consequences (irrespective of the correctness of the science)?

  8. Comment by hrun — June 30, 2009 @ 11:46 am

  9. Bradford Says:
    June 30th, 2009 at 11:49 am

    hrun: Maybe so… so what are we going to do about it? Show that the science is false?

    What exactly is the "science" you're referencing.

  10. Comment by Bradford — June 30, 2009 @ 11:49 am

  11. hrun Says:
    June 30th, 2009 at 12:02 pm

    What exactly is the "science" you're referencing.

    I assumed that in this thread we were referring to people claiming that rape (and other undesirable behavior) might actually have been selected for through human evolution. That was the "science" I was referring to.

  12. Comment by hrun — June 30, 2009 @ 12:02 pm

  13. Jean Says:
    June 30th, 2009 at 12:11 pm

    So where's the "science" in that, hrun?

  14. Comment by Jean — June 30, 2009 @ 12:11 pm

  15. Bradford Says:
    June 30th, 2009 at 12:22 pm

    I agree Jean. Where's the science in that claim?

  16. Comment by Bradford — June 30, 2009 @ 12:22 pm

  17. hrun Says:
    June 30th, 2009 at 12:25 pm

    So where's the "science" in that, hrun?

    I don't know. Who do you think I am? Somebody who has time to read up on Evo-Psych research? It seems like Bradford knows. Why not ask him?

  18. Comment by hrun — June 30, 2009 @ 12:25 pm

  19. Bradford Says:
    June 30th, 2009 at 1:22 pm

    hrun: I assumed that in this thread we were referring to people claiming that rape (and other undesirable behavior) might actually have been selected for through human evolution. That was the "science" I was referring to.

    and subsequently in response to the question "So where's the "science" in that, hrun?"

    I don't know. Who do you think I am? Somebody who has time to read up on Evo-Psych research?

    You're confused. Initially you assert that the science you were referring to was the claim "that rape (and other undesirable behavior) might actually have been selected for through human evolution." Then you modify that to "I don't know" when asked for the science in that.

  20. Comment by Bradford — June 30, 2009 @ 1:22 pm

  21. Todd Berkebile Says:
    June 30th, 2009 at 2:48 pm

    Evolution is not a "moral" process, something is not moral just because it evolved. No one I am aware of is claiming otherwise. Of course evolution does tend to select things that work and since morality works there certainly might be selective advantages there. This, however, cannot demonstrate morality.

    In other words, the author doesn't seem to be making any sort of moral case nor would any reasonable person and yet Bradford fears this research, if true, might lead judges to not punish rapists? I don't see the connection between that seemingly unjustified fear and this research.

    PS: Just to be clear, I think most evo-psych is BS. At best they gather interesting correlations but then often jump to wild conclusions.

  22. Comment by Todd Berkebile — June 30, 2009 @ 2:48 pm

  23. Bradford Says:
    June 30th, 2009 at 2:55 pm

    Todd:

    In other words, the author doesn't seem to be making any sort of moral case nor would any reasonable person and yet Bradford fears this research, if true, might lead judges to not punish rapists?

    You need a remedial reading course.

  24. Comment by Bradford — June 30, 2009 @ 2:55 pm

  25. hrun Says:
    June 30th, 2009 at 4:12 pm

    You're confused. Initially you assert that the science you were referring to was the claim "that rape (and other undesirable behavior) might actually have been selected for through human evolution." Then you modify that to "I don't know" when asked for the science in that.

    I am not at all confused, Bradford. There is a branch of research (or science if you will) that is called 'evolutionary psychology'. Typically, what was described (human behavior based on evolution) falls into the purview of evo-psych as I understand it. Hence, I called this 'science'. If you have a beef with this particular hypothesis or if you feel that all of evo-psych is not science… then fine. It doesn't matter much to me either way. I have not informed myself in detail about evo-psych to know if it is science or not.

    If it is not, I am sure that you (or Jean) can make that case.

  26. Comment by hrun — June 30, 2009 @ 4:12 pm

  27. themayan Says:
    July 11th, 2009 at 10:42 pm

    Bradford great article. Whether or not there's any truth to the conclusions of the researchers is something I wont get into, however I will say that Darwinist are always the first ones to give credit to evolution for constructs such as intelligence, altruism, cognitive reasoning etc however, the negative aspects of life are usually ignored. Someone once said that great ideas have many mothers and fathers, but bad ideas are orphans.

  28. Comment by themayan — July 11, 2009 @ 10:42 pm

  29. Bradford Says:
    July 12th, 2009 at 7:41 am

    Hi themayan,

    I've been critical of efforts to cite human belief systems and link their origin to an evolutionary process. I think the efforts are laden with mischief. Consider the reaction if a popular or politically correct set of beliefs is cited and linked to a hypothesis which attempts to explain their origin on vague or unspecified evolutionary pathways. My gut instincts signal that there would be resentment and reactions like "it's about justice, not evolution" would surface. The danger of evo/psych research is that it lends itself naturally to politicization.

  30. Comment by Bradford — July 12, 2009 @ 7:41 am

  31. Zachriel Says:
    July 12th, 2009 at 9:38 am

    Bradford: Consider the reaction if a popular or politically correct set of beliefs is cited and linked to a hypothesis which attempts to explain their origin on vague or unspecified evolutionary pathways.

    As we know with a high degree of scientific certainty that life evolved, it becomes a matter of trying to disentangle the biological and cultural aspects of modern humans. However, it is important that such conjectures be testable to be considered more than speculation.

    themayan: Darwinist are always the first ones to give credit to evolution for constructs such as intelligence, altruism, cognitive reasoning etc however, the negative aspects of life are usually ignored.

    Gee whiz. Animals consume other organisms for nourishment. Frankly, you need to try and understand evolution before making such unfounded statements. The Theory of Evolution certainly does involve death and dying, disease, even extinction. Many things humans would consider "negative aspects of life".

  32. Comment by Zachriel — July 12, 2009 @ 9:38 am

  33. themayan Says:
    July 12th, 2009 at 10:30 am

    Zachriel maybe I should have been more specific. I was speaking in terms of the context of the article, rape, murder, cruelty, etc or what most would consider inhumane behaviour. I was speaking of causation not models. Evolution is supposed to be a scientific and natural model of cause and effect, according to the theory.

  34. Comment by themayan — July 12, 2009 @ 10:30 am

  35. Bradford Says:
    July 12th, 2009 at 10:30 am

    Zachriel: As we know with a high degree of scientific certainty that life evolved, it becomes a matter of trying to disentangle the biological and cultural aspects of modern humans.

    Consider the following human urges:

    the urge to rape

    the urge to stereotype

    the urge to ponder the origins of humans and the universe they inhabit

    the urge to use governments to regulate societal behavior

    A researcher with some imagination could fashion theories and attempt to identify genes which influence behavior. What approach would be used "to disentangle the biological and cultural aspects of modern humans?"

  36. Comment by Bradford — July 12, 2009 @ 10:30 am

  37. Zachriel Says:
    July 12th, 2009 at 11:18 am

    themayan: I was speaking in terms of the context of the article, rape, murder, cruelty, etc or what most would consider inhumane behaviour. I was speaking of causation not models. Evolution is supposed to be a scientific and natural model of cause and effect, according to the theory.

    Many aspects of human behavior are not easily explained in biological terms. However, where we can find a continuum with related species, then we have reason to suspect an evolutionary origin. However, all of human behavior is highly influenced by culture, so disentangling causes can be problematic. That is not to say that humans didn't evolve. They did. But culture strongly infuences behavior.

    Humans are social organisms, and one of the most important explanatory aspects of human behavior is the relationship of the individual with their perceived status within the "group".

    Bradford: A researcher with some imagination could fashion theories and attempt to identify genes which influence behavior.

    Imagination is critical to the proposal of interesting hypotheses, however, being able to demonstrate such relationships can be difficult. Few scientists would consider single genes to have much explanatory power; most treating the question on a biological level.

    Bradford: What approach would be used "to disentangle the biological and cultural aspects of modern humans?"

    A fruitful approach might be to isolate heritable behavioral characteristics. In humans, this includes such basics as hunger and sex, but also relationships with others. Peculiar characteristics of humans include the ability to abstract about the past or future or even imaginary worlds.

  38. Comment by Zachriel — July 12, 2009 @ 11:18 am

  39. Bradford Says:
    July 12th, 2009 at 11:38 am

    A fruitful approach might be to isolate heritable behavioral characteristics. In humans, this includes such basics as hunger and sex, but also relationships with others. Peculiar characteristics of humans include the ability to abstract about the past or future or even imaginary worlds.

    Or the ability to abstract about both actual and fantasy worlds like the one in which humans are driven to use governments (actual) to create utopias (fantasies). What heritable characteristics are relevant to this?

  40. Comment by Bradford — July 12, 2009 @ 11:38 am

  41. Zachriel Says:
    July 12th, 2009 at 11:47 am

    Bradford: Or the ability to abstract about both actual and fantasy worlds like the one in which humans are driven to use governments (actual) to create utopias (fantasies). What heritable characteristics are relevant to this?

    You just provided your own answer. It derives from the human ability to abstract.

  42. Comment by Zachriel — July 12, 2009 @ 11:47 am

  43. Bradford Says:
    July 12th, 2009 at 11:50 am

    Zachriel: You just provided your own answer. It derives from the human ability to abstract.

    Hmmm. In view of the fact that this involves a considerable portion of the human brain and many, many genes how could evo/psych approaches be expected to yield useful results about anything attributed to an abstraction capacity?

  44. Comment by Bradford — July 12, 2009 @ 11:50 am

  45. Zachriel Says:
    July 12th, 2009 at 12:04 pm

    Bradford: Hmmm. In view of the fact that this involves a considerable portion of the human brain and many, many genes how could evo/psych approaches be expected to yield useful results about anything attributed to an abstraction capacity?

    You seem to be fixated on genes. Humans clearly inherited a panoply of traits from their hominid ancestors. This includes the use of tools and the formation of social groups and cooperation.

  46. Comment by Zachriel — July 12, 2009 @ 12:04 pm

  47. Bradford Says:
    July 12th, 2009 at 12:07 pm

    Zachriel: You seem to be fixated on genes. Humans clearly inherited a panoply of traits from their hominid ancestors. This includes the use of tools and the formation of social groups and cooperation.

    Are you saying that the use of tools and the formation of social groups and cooperation can be biologically analyzed apart from consideration of gene expression?

  48. Comment by Bradford — July 12, 2009 @ 12:07 pm

  49. Zachriel Says:
    July 12th, 2009 at 12:09 pm

    Bradford: Are you saying that the use of tools and the formation of social groups and cooperation can be biologically analyzed apart from consideration of gene expression?

    Yes. Of course. Do you really think we have to know the molecular basis of the gene to observe that traits, including behavioral traits, can be inherited?

  50. Comment by Zachriel — July 12, 2009 @ 12:09 pm

  51. Bradford Says:
    July 12th, 2009 at 12:19 pm

    Zachriel: Yes. Of course. Do you really think we have to know the molecular basis of the gene to observe that traits, including behavioral traits, can be inherited?

    No. But what I am wondering is how observing primate traits, for example, enables one to state anything about say, rape, which goes beyond it is a related to inheritance. That strikes me as very banal.

  52. Comment by Bradford — July 12, 2009 @ 12:19 pm

  53. Daniel Smith Says:
    July 12th, 2009 at 3:25 pm

    Zachriel:
    As we know with a high degree of scientific certainty that life evolved,

    The only thing we don't know is how life evolved. If the evolutionary pathway cannot be reconstructed "with a high degree of scientific certainty", how can we know that life actually evolved?

    First, of course, you must define "evolved". Do you mean simply that life has 'changed over time'? No one disputes that. Or do you mean that "we know with a high degree of scientific certainty that life" evolved from molecules to man? Herein lies the problem.

    For instance, take one of life's basic features: Paired enzymes. Paired enzymes are unrelated enzymes that influence metabolic cycles by the same allosteric effectors only in opposite ways at branch points. If only one enzyme evolved at a time, the metabolic cycle proceeds in one direction only and has no balancing factor. If two cycles evolved separately, they could both proceed unregulated, competing with each other over the same resources – or worse – synthesizing and degrading the same compound at the same time. Conditions such as this are called 'disease' and ultimately cause death. All of life's metabolic cycles are precisely regulated so that energy is not wasted.

    No one (to my knowledge) knows how paired enzymes evolved.

    What I've found in my time discussing this issue is that virtually all atheists believe in molecules to man evolution but none of them want to discuss the details of that evolution. They usually say something like "Read the scientific literature yourself" and "I can't help it if you don't understand it", all the while dodging the fact that they have no clue how this process they so firmly believe in produced anything we see today.

    Do you actually know "with a high degree of scientific certainty" how anything evolved Zachriel?

    Or is this all smoke and mirrors?

  54. Comment by Daniel Smith — July 12, 2009 @ 3:25 pm

  55. Zachriel Says:
    July 12th, 2009 at 6:02 pm

    Daniel Smith: First, of course, you must define "evolved".

    Evolution refers to the change and divergence in the genetic compositions of populations. The Theory of Evolution explains how these changes occur. The most fundamental patterns in biology are due to Common Descent.

    Daniel Smith: Or do you mean that "we know with a high degree of scientific certainty that life" evolved from molecules to man? Herein lies the problem.

    Yes. The problem is the strawman. The Theory of Evolution doesn't make claims about "molecules to man".

    Daniel Smith: What I've found in my time discussing this issue is that virtually all atheists believe in molecules to man evolution but none of them want to discuss the details of that evolution.

    I would be happy to discuss the Theory of Evolution. It's best to start with what is most strongly established. We might start with the fact that humans and monkeys and fishes share a common ancestor and (first-order approximation) they evolved by gradual, selectable steps.

    Daniel Smith: Do you actually know "with a high degree of scientific certainty" how anything evolved

    Evolution can be directly observed. And many historical transitions are well-researched. You might consider equine evolution.

  56. Comment by Zachriel — July 12, 2009 @ 6:02 pm

  57. Daniel Smith Says:
    July 13th, 2009 at 2:55 pm

    Zachriel: I would be happy to discuss the Theory of Evolution. It's best to start with what is most strongly established.

    Let's do that then.

    Zachriel:We might start with the fact that humans and monkeys and fishes share a common ancestor and (first-order approximation) they evolved by gradual, selectable steps.

    And what were those steps then? Are they actually known "with a high degree of scientific certainty"?

    Zachriel: Evolution can be directly observed.

    No disputing that.

    Zachriel: And many historical transitions are well-researched.

    Good!

    Zachriel:You might consider equine evolution.

    OK… How did we get from one transitional to another? What were the steps? What is actually known "with a high degree of scientific certainty" about these individual, selectable steps? Or is it assumption that fuels the evolutionary engine?

  58. Comment by Daniel Smith — July 13, 2009 @ 2:55 pm

  59. Zachriel Says:
    July 13th, 2009 at 2:57 pm

    Daniel Smith: How did we get from one transitional to another?

    We observe natural variation in populations.
    We observe sources of novel variation.
    We observe natural selection.
    We observe varying degrees of reproductive isolation.
    We observe the nested hierarchy.
    We predict and observe the existence of intermediate structures and organisms.

    We see (first-order approximation) gradual, selectable adaptation and diversification of ancestral structures for most taxa.

  60. Comment by Zachriel — July 13, 2009 @ 2:57 pm

  61. don provan Says:
    July 13th, 2009 at 3:44 pm

    Daniel Smith: Do you actually know "with a high degree of scientific certainty" how anything evolved Zachriel?

    Or is this all smoke and mirrors?

    This is like the magician objecting that people saying his magic isn't real are using smoke and mirrors to prove it. "I've performed this trick 1000 times, and only once have they shown that the rabbit got into the hat through trickery. And they want you to believe that the rabbit got into the hat through trickery the other 999 times, but they can't prove it! That makes it plausible that it was real magic."

  62. Comment by don provan — July 13, 2009 @ 3:44 pm

  63. Daniel Smith Says:
    July 14th, 2009 at 11:56 am

    IOW, Zachriel and don provan, you have no clue how anything actually evolved.

  64. Comment by Daniel Smith — July 14, 2009 @ 11:56 am

  65. Zachriel Says:
    July 14th, 2009 at 12:00 pm

    Daniel Smith: IOW, Zachriel and don provan, you have no clue how anything actually evolved.

    The how is through variation and selection, descent with modification from common ancestors. If any of these terms are unclear, I would be happy to elaborate. You might also look at a specific example.

    Blount, Borland & Lenski, Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli, PNAS 2008.

  66. Comment by Zachriel — July 14, 2009 @ 12:00 pm

  67. Daniel Smith Says:
    July 14th, 2009 at 8:13 pm

    If any of these terms are unclear, I would be happy to elaborate.

    Condescension?

    Blount, Borland & Lenski, Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

    I am printing this paper out right now. I will read it and get back to you.

  68. Comment by Daniel Smith — July 14, 2009 @ 8:13 pm

  69. kornbelt888 Says:
    July 15th, 2009 at 1:40 pm

    Daniel Smith: IOW, Zachriel and don provan, you have no clue how anything actually evolved.

    Zachriel: The how is through variation and selection, descent with modification from common ancestors.

    Back from vacation. Nice to see you two still at it.

    Question: "How are airplanes made?"

    Answer: "by people in factories using drills, screwdrivers, metal fabricators, and other well known tools."

    This is an explanation. But it's not very precise.

    When Daniel asks "how?", I suspect he wants to know "what?" IOW, what specific variations were chained together to get from, say, an ape-like brain to a modern human brain? You can't tell us, Zachriel. Science is of no help. Moreover, germane to this blog, it is unknown to what extent intelligent intervention would be required in the evolution path.

    Consider an airplane. We can all agree that, given known laws and properties of nature, it's existence would be extremely improbable if human-like engineers did not exist. The path from non-intelligent matter and energy to airplanes is extremely improbable unless it routes through human-like engineers. Another way of saying this is: airplanes are dependent on human-like engineers, something more complex than the airplanes. Daniel (and I) want to know if the path from, say, ape-like brain to human brain, or from primordial elements to human brain, is dependent on something more complex than the product. Science cannot answer that presently.

  70. Comment by kornbelt888 — July 15, 2009 @ 1:40 pm

  71. Zachriel Says:
    July 15th, 2009 at 2:04 pm

    kornbelt888:

    Question: "How are airplanes made?"

    Answer: "by people in factories using drills, screwdrivers, metal fabricators, and other well known tools."

    This is an explanation. But it's not very precise.

    That's right. Terms and methods may need elaboration.

    kornbelt888: IOW, what specific variations were chained together to get from, say, an ape-like brain to a modern human brain?

    The concern was "how anything actually evolved". Though brains don't normally fossilize, we do have a great deal of fossil evidence revealing the long evolutionary history of chordates. But let's try a few other transitions first. Perhaps the radiation of dinosaurs, or the development of the mammalian middle ear from reptilian jaw bones, or antibiotic resistance in laboratory bacteria. Or are you saying we have no idea the steps related to the evolution of any historical transition?

  72. Comment by Zachriel — July 15, 2009 @ 2:04 pm

  73. kornbelt888 Says:
    July 15th, 2009 at 2:12 pm

    Zachriel: Or are you saying we have no idea the steps related to the evolution of any historical transition?

    Not at all

  74. Comment by kornbelt888 — July 15, 2009 @ 2:12 pm

  75. Daniel Smith Says:
    July 15th, 2009 at 2:22 pm

    Blount, Borland & Lenski, Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

    Zachriel has cited this paper as an example of evolution in action – and that it is. Let's examine the details:
    The paper examines the evolution, after 30,000+ generations, of a strain of E. coli that gained the ability to exploit citrate as an energy source.
    The first thing I noticed was that E. coli already has much of the machinery in place to use citrate:

    The inability to use citrate as an energy source under oxic conditions has long been a defining characteristic of E. coli as a species (35, 36). Nevertheless, E. coli is not wholly indifferent to citrate. It uses a ferric dicitrate transport system for iron acquisition, although citrate does not enter the cell in this process (37, 38). It also has a complete tricarboxylic acid cycle, and can thus metabolize citrate internally during aerobic growth on other substrates (39). E. coli is able to ferment citrate under anoxic conditions if a cosubstrate is available for reducing power (40). The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions (41–43). Indeed, atypical E. coli that grow aerobically on citrate (Cit+) have been isolated from agricultural and clinical settings, and were found to harbor plasmids, presumably acquired from other species, that encode citrate transporters (44, 45).

    In spite of all this potential, it still took 31,500 generations for some method of citrate utilization to evolve under lab conditions. The mutation rate to Cit+ is so low, they posit that

    Such a low rate suggests that the final mutation to Cit+ is not a point mutation but instead involves some rarer class of mutation or perhaps multiple mutations.

    They show through experimental "replays" that the evolution of this function is "historically contingent", IOW it only happens in strains of E. coli that have followed one historical path – thus confirming one of the tenets of the non-Darwinian evolutionary theories of people like Otto Schindewolf and Leo Berg – who held that evolution was constrained along certain pathways. I'm sure Zachriel is probably unaware of that though. Most atheists I've encountered show a reluctance to explore anything outside the Darwinian landscape.
    What I get out of this is that:
    A) Evolution (as presented here) is slow and extremely inefficient. 30,000+ generations may not take long for E. coli, but when we're talking about humans, fish, monkeys and horses, 30,000+ generations to develop the ability to transport one type of molecule into a cell leaves much to be desired when proffering an explanation for the differences between those species.
    B) Evolution (as presented here) requires pre-existing elements. What evolved here was not the tricarboxylic acid cycle that metabolizes citrate, but simply the means to utilize it via (most likely) an also pre-existing transport system.
    C) Evolution (as presented here) is historically contingent. Most populations did not evolve this ability, but only those within a certain 'family'. This further lessens the odds of said evolution occurring. In fact the authors noted that the rate of mutation for Cit+ amongst the pre-30,000 gen samples was "the lowest upper bound ever reported for a mutation rate that has been experimentally measured".
    In short Zachriel, if you want to present this as an example of evolution in action, you're essentially shooting your cause in the foot by doing so.

  76. Comment by Daniel Smith — July 15, 2009 @ 2:22 pm

  77. Zachriel Says:
    July 15th, 2009 at 3:02 pm

    Daniel Smith: Evolution (as presented here) is slow and extremely inefficient.

    Actually, lots of evolution happens in Lenski's experiments. This particular transition is rare and contingent, and that's what makes it interesting enough for a separate paper. You had said, "you have no clue how anything actually evolved". And this paper answers your objection.

    Now, we might consider next the Lederberg Experiment which demonstrates that mutations are random with respect to fitness.

  78. Comment by Zachriel — July 15, 2009 @ 3:02 pm

  79. kornbelt888 Says:
    July 15th, 2009 at 4:58 pm

    Zachriel: Now, we might consider next the Lederberg Experiment which demonstrates that mutations are random with respect to fitness.

    While mutations are random, doesn't Barry Hall's work strongly suggest that with the ebg operon the mechanism generating the mutations appears to be responding to environmental cues?

  80. Comment by kornbelt888 — July 15, 2009 @ 4:58 pm

  81. don provan Says:
    July 15th, 2009 at 5:08 pm

    kornbelt888: When Daniel asks "how?", I suspect he wants to know "what?"

    I don't think Daniel actually wants to know anything.

    IOW, what specific variations were chained together to get from, say, an ape-like brain to a modern human brain?

    Isn't this something like objecting that we don't really know how oxygen and hydrogen combine into water because we do not know which specific atoms will come together? Zachriel has given him the "H2 + H2 + O2 = H2O + H2O" equivalent of evolution, but he isn't satisfied with that. When will he be satisfied? I suspect never, because he isn't seeking answers, he's only seeking reasons to deny.

  82. Comment by don provan — July 15, 2009 @ 5:08 pm

  83. kornbelt888 Says:
    July 15th, 2009 at 5:38 pm

    Kornbelt: IOW, what specific variations were chained together to get from, say, an ape-like brain to a modern human brain?

    Don Provan: Isn't this something like objecting that we don't really know how oxygen and hydrogen combine into water because we do not know which specific atoms will come together?

    No.

    What path is required to get water from hydrogen and oxygen?

    What path is required to get a human brain from an ape brain?

    Very different answers. The former is well known, and the latter is not known. "Random variation and natural selection" is not an answer to the second question. RV+NS is a mechanism, not a path. A path pertains to an actual sequence of steps that occured, not simply a mechanism. Me twisting a Rubic's Cube is a mechanism. The order of the twists is a path.

  84. Comment by kornbelt888 — July 15, 2009 @ 5:38 pm

  85. don provan Says:
    July 15th, 2009 at 7:21 pm

    What path is required to get water from hydrogen and oxygen?

    What path is required to get a human brain from an ape brain?

    Exactly. I cannot tell you the exact path hydrogen and oxygen atoms take when combining to make water, I can only explain the process. I could, conceptually, take specific atoms and show you them combining into a water molecule, just as we understand specific evolutionary steps. In both cases, there's a certain level of detail we cannot describe, and don't need to describe in order to show that our general description is valid.

    "Random variation and natural selection" is not an answer to the second question. RV+NS is a mechanism, not a path. A path pertains to an actual sequence of steps that occured, not simply a mechanism.

    Correct. H2 + H2 + O2 = H2O is not a sequence of steps, either, it is a mechanism. If I were to demonstrate it for you, I'd be able to explain in general terms what happened, but I wouldn't be able to describe the individual steps involving each atom.

    Mind you, I do not mean to claim here that the specific modification being requested can be explained, I'm merely questioning whether Daniel is making a demand that could be satisfied under any conditions.

  86. Comment by don provan — July 15, 2009 @ 7:21 pm

  87. Zachriel Says:
    July 15th, 2009 at 7:57 pm

    kornbelt888: A path pertains to an actual sequence of steps that occured, not simply a mechanism.

    Many pathways in evolutionary history are quite well known, others less so. Still, we can look at the overall pattern and determine that life shares common ancestors and that for a great many transitions, there are selectable pathways. We can also directly observe the mechanisms of evolution, including natural selection and novel sources of variation.

    ID just points to supposed Gaps and claims it couldn't have happened.

    Consider the repeated example of the human brain. Well, there's somewhat of a Gap in extant organisms between humans and other apes. Nevertheless, we can compare various related species and see that brains fit the very same nested hierarchy as expected from Common Descent. We can also see that the human brain is comprised of modified components found in other organisms. We can trace the evolution of brains from primitive craniates through fishes, land vertebrates and mammals. Then to the hominid line where we see further enlarging of brain capacity accompanied by sophisticated use of tools. So we do see the expected pattern of descent with modification.

  88. Comment by Zachriel — July 15, 2009 @ 7:57 pm

  89. kornbelt888 Says:
    July 15th, 2009 at 8:31 pm

    Kornbelt: What path is required to get water from hydrogen and oxygen? What path is required to get a human brain from an ape brain?

    Don P: Exactly. I cannot tell you the exact path hydrogen and oxygen atoms take when combining to make water, I can only explain the process. I could, conceptually, take specific atoms and show you them combining into a water molecule, just as we understand specific evolutionary steps.

    Agreed. But with H2O, you can provide a path that would work given the laws of chemistry as we know them. There is proof of concept. No such proof of concept exists to turn an ape brain into a human brain in a series of unguided variations. I think it would sufficiently shut the mouth of any skeptic (mine, certainly) if such a path could be demonstrated, never mind the actual path.

  90. Comment by kornbelt888 — July 15, 2009 @ 8:31 pm

  91. kornbelt888 Says:
    July 15th, 2009 at 8:45 pm

    kornbelt888: A path pertains to an actual sequence of steps that occured, not simply a mechanism.

    Zachriel: Many pathways in evolutionary history are quite well known, others less so. Still, we can look at the overall pattern and determine that life shares common ancestors and that for a great many transitions, there are selectable pathways. We can also directly observe the mechanisms of evolution, including natural selection and novel sources of variation.

    I agree.

    ID just points to supposed Gaps and claims it couldn't have happened.

    Well, I haven't been talking about ID in this thread. And I, personally, have never made the claim that "it couldn't have happened." My point is that not enough is known about what's in the gaps to know one way or the other yet. (I'm comfortable with any answer.)

    Consider the repeated example of the human brain. Well, there's somewhat of a Gap in extant organisms between humans and other apes. Nevertheless, we can compare various related species and see that brains fit the very same nested hierarchy as expected from Common Descent.

    Agreed. Common descent is not a particularly live issue for me personally, although the tree of life is not as tidy as some seem to assert. What is a live issue for me is the nature and cause of the incremental steps. Some are known. Some are obviously not.

    We can also see that the human brain is comprised of modified components found in other organisms. We can trace the evolution of brains from primitive craniates through fishes, land vertebrates and mammals. Then to the hominid line where we see further enlarging of brain capacity accompanied by sophisticated use of tools. So we do see the expected pattern of descent with modification.

    Agreed. But brain size is a very limited metric and tells us little of the actual neural pathways (the "programming") that make one kind of brain have different processing capabilities compared to another. There is a vast dearth of information.

  92. Comment by kornbelt888 — July 15, 2009 @ 8:45 pm

  93. Zachriel Says:
    July 15th, 2009 at 9:00 pm

    kornbelt888: What is a live issue for me is the nature and cause of the incremental steps.

    There is significant evidence that transitional structures are selectable, that is, each organism is adapted to its own environment. Consider the evolution of the reptilian jaw bones into the mammalian middle ear.

    kornbelt888: But brain size is a very limited metric and tells us little of the actual neural pathways (the "programming") that make one kind of brain have different processing capabilities compared to another.

    Brains don't normally fossilize, but we know that human brains fit the nested hierarchy, that human brains are comprised of modifications of structures found in related organisms, that craniates follow a long, diversifying path of evolutionary history, and that humans are derived hominids. In other words, each bit of evidence, from the most ancient craniate fossil to the molecular structure of neurons, fits the hypothesis of evolutionary descent.

  94. Comment by Zachriel — July 15, 2009 @ 9:00 pm

  95. don provan Says:
    July 15th, 2009 at 9:00 pm

    kornbelt888: No such proof of concept exists to turn an ape brain into a human brain in a series of unguided variations.

    Certainly we know some things about this path, so the question becomes one of how much we need to know to meet your requirement of "proof of concept". From my point of view, there's no limit to what you could require. It's nice of you to grant a potential path rather than the actual path, but I'm sure you could find several potential paths already, so you're already rejecting them for some reason.

    But beyond that, even if someone could show you an acceptable path, meeting your proof of concept, would you just turn your attention elsewhere? "Well, ok, but what about the thumb? How did that develop? If you can't show me that, then you can't say God didn't do it."

    My concern is that you and Daniel could go on forever no matter what anyone showed you. If, instead, you could come up with a concrete requirement, then we could send you to the biologists to see if they can satisfy it. (Hint: Almost all biologist think there are sufficiently well understood pathways to make the general case. Why does Daniel think he's better at defining the requirement then they are?)

    As long as Daniel's requirements are open ended, there's no reason to actually engage anyone that actually knows something about these pathways since we'd be wasting their time. Dawkins wrote a book (The Ancestors Tale) providing all kinds of examples of this type, in various levels of details. Perhaps we could start by Daniel explaining why none of that is sufficient. But I think the answer will be something that amounts to "not enough detail", a complaint that can always be made.

  96. Comment by don provan — July 15, 2009 @ 9:00 pm

  97. Zachriel Says:
    July 15th, 2009 at 9:10 pm

    kornbelt888: My point is that not enough is known about what's in the gaps to know one way or the other yet.

    You have to look at the overall pattern, and the predictive capability of the Theory of Evolution. What is posited is a long continuum of descent and diversification from common ancestors. And what we have is a huge amount of data, from many different of study, from geology to genomics, each datum representing a point on the continuum.

    When scientists propose testable hypotheses and make empirical predictions, these predictions confirm and extend our knowledge of this continuum. You can wave you hands at Gaps forever because data-points will never fill a continuum.

  98. Comment by Zachriel — July 15, 2009 @ 9:10 pm

  99. kornbelt888 Says:
    July 15th, 2009 at 9:48 pm

    kornbelt888: What is a live issue for me is the nature and cause of the incremental steps.

    Zachriel: There is significant evidence that transitional structures are selectable, that is, each organism is adapted to its own environment.

    You seem to be implying that I asserted the opposite. Why would you think that?

    kornbelt888: But brain size is a very limited metric and tells us little of the actual neural pathways (the "programming") that make one kind of brain have different processing capabilities compared to another.

    Zachriel: Brains don't normally fossilize, but we know that human brains fit the nested hierarchy, that human brains are comprised of modifications of structures found in related organisms, that craniates follow a long, diversifying path of evolutionary history, and that humans are derived hominids. In other words, each bit of evidence, from the most ancient craniate fossil to the molecular structure of neurons, fits the hypothesis of evolutionary descent.

    Agreed. So you agree with my statement?

  100. Comment by kornbelt888 — July 15, 2009 @ 9:48 pm

  101. kornbelt888 Says:
    July 15th, 2009 at 10:05 pm

    kornbelt888: No such proof of concept exists to turn an ape brain into a human brain in a series of unguided variations.

    Don P: Certainly we know some things about this path, so the question becomes one of how much we need to know to meet your requirement of "proof of concept".

    An account with no gaps that is reproducible. What else?

    I'm sure you could find several potential paths already, so you're already rejecting them for some reason.

    Where? Before you can create an transitional account from ape brain to human brain you'd have to have a solid handle on how both function, down to the way the precise neural networks operate that are responsible for the function we see in both. Science is a long ways off from that. Given that, where is there a gap-free incremental account for such a transition?

    But beyond that, even if someone could show you an acceptable path, meeting your proof of concept, would you just turn your attention elsewhere? "Well, ok, but what about the thumb? How did that develop? If you can't show me that, then you can't say God didn't do it."

    This thread has nothing to do with God or designers. You seem to be implying that I'm hunting for gaps just to feel good about my religion or something. Fuggedaboutit.

    If, instead, you could come up with a concrete requirement, then we could send you to the biologists to see if they can satisfy it.

    An account with no gaps that is reproducible. What else?

    (Hint: Almost all biologist think there are sufficiently well understood pathways to make the general case. Why does Daniel think he's better at defining the requirement then they are?)

    I'm afraid general cases won't do for a skeptic like me when it comes to the human brain. I can't answer for Daniel.

    As long as Daniel's requirements are open ended, there's no reason to actually engage anyone that actually knows something about these pathways since we'd be wasting their time.

    As for me, I can only say that what we know about evolution and what we know about ape brains and human brains is so little that any attempt to make a case would be the waste of time.

    Dawkins wrote a book (The Ancestors Tale) providing all kinds of examples of this type, in various levels of details. Perhaps we could start by Daniel explaining why none of that is sufficient. But I think the answer will be something that amounts to "not enough detail", a complaint that can always be made.

    Does Daniel deny all evolution? If so, I was not aware of that. That is not my position. Not even close. Never has been.

  102. Comment by kornbelt888 — July 15, 2009 @ 10:05 pm

  103. kornbelt888 Says:
    July 15th, 2009 at 10:08 pm

    kornbelt888: My point is that not enough is known about what's in the gaps to know one way or the other yet.

    Zachriel: You have to look at the overall pattern, and the predictive capability of the Theory of Evolution. What is posited is a long continuum of descent and diversification from common ancestors. And what we have is a huge amount of data, from many different of study, from geology to genomics, each datum representing a point on the continuum. When scientists propose testable hypotheses and make empirical predictions, these predictions confirm and extend our knowledge of this continuum.

    I agree, of course. (What makes you think I wouldn't?) Now, what specific predictions are you willing to make about the evolutionary path from ape brains to human brains regarding the neurological networks that give rise to the uniquely human functions?

    You can wave you hands at Gaps forever because data-points will never fill a continuum.

    Exactly how am I waving my hands?

  104. Comment by kornbelt888 — July 15, 2009 @ 10:08 pm

  105. Zachriel Says:
    July 15th, 2009 at 10:09 pm

    kornbelt888: You seem to be implying that I asserted the opposite.

    This is what you said.

    kornbelt888: My point is that not enough is known about what's in the gaps to know one way or the other yet.

    Not all historical details are known, but the pattern of descent with modification is very well established. Are you only concerned with the human brain? Or do you simply question evolution for every Gap in knowledge.

  106. Comment by Zachriel — July 15, 2009 @ 10:09 pm

  107. Zachriel Says:
    July 15th, 2009 at 10:13 pm

    kornbelt888: An account with no gaps that is reproducible.

    Every Gap then. No amount of evidence would be sufficient for any historical claim. Even when we can make bold and verifiable predictions, you will wave your hands because every time we fill a Gap, two new Gaps appear.

    Zachriel: You have to look at the overall pattern, and the predictive capability of the Theory of Evolution.

    kornbelt888: I agree, of course.

    You say you agree, but apparently don't comprehend.

  108. Comment by Zachriel — July 15, 2009 @ 10:13 pm

  109. kornbelt888 Says:
    July 15th, 2009 at 10:15 pm

    Zachriel: There is significant evidence that transitional structures are selectable, that is, each organism is adapted to its own environment.

    I said that opposite of that? So you're saying that I said in effect that "transitional structures are not selectable, that is, each organism is not adapted to its own environment" ?

    Where did I say or imply that?

  110. Comment by kornbelt888 — July 15, 2009 @ 10:15 pm

  111. Zachriel Says:
    July 15th, 2009 at 10:19 pm

    kornbelt888: Now, what specific predictions are you willing to make about the evolutionary path from ape brains to human brains regarding the neurological networks that give rise to the uniquely human functions?

    That humans brains descended with modification from ancestors common with other craniates. This will mean a nested hierarchy that includes the molecular and macroscopic structures of the brain.

  112. Comment by Zachriel — July 15, 2009 @ 10:19 pm

  113. kornbelt888 Says:
    July 15th, 2009 at 10:24 pm

    kornbelt888: An account with no gaps that is reproducible.

    Zachriel: Every Gap then. No amount of evidence would be sufficient for any historical claim.

    As I said, I don't require a historical claim. I merely require a path that would work, a proof of concept, regardless if it were the actual path or not.

    Even when we can make bold and verifiable predictions, you will wave your hands because every time we fill a Gap, two new Gaps appear.

    Well, make some "bold and verifiable predictions" about ape-to-human evolutionary neural network programming and I'll definitely give serious thought to it.

    Zachriel: You have to look at the overall pattern, and the predictive capability of the Theory of Evolution.

    kornbelt888: I agree, of course. (What makes you think I wouldn't?) Now, what specific predictions are you willing to make about the evolutionary path from ape brains to human brains regarding the neurological networks that give rise to the uniquely human functions?

    Z: You say you agree, but apparently don't comprehend.

    Test me. What about "the overall pattern, and the predictive capability of the Theory of Evolution" compels you to accept the speculation that random variation and natural selection provided a sufficient mechanism to create a evolutionary path from an ape-like brain to a human brain.

  114. Comment by kornbelt888 — July 15, 2009 @ 10:24 pm

  115. Zachriel Says:
    July 15th, 2009 at 10:26 pm

    Zachriel: There is significant evidence that transitional structures are selectable …

    kornbelt888: Where did I say or imply {otherwise}?

    You said, "What is a live issue for me is the nature and cause of the incremental steps," hence my response. The answer is selection, as in Natural Selection.

    You also said is that you require a Gapless pathway for historical claims, even when scientists can make bold and verifiable empirical predictions, such as important intermediate fossil organisms.

  116. Comment by Zachriel — July 15, 2009 @ 10:26 pm

  117. kornbelt888 Says:
    July 15th, 2009 at 10:47 pm

    kornbelt888: Now, what specific predictions are you willing to make about the evolutionary path from ape brains to human brains regarding the neurological networks that give rise to the uniquely human functions?

    Zachriel: That humans brains descended with modification from ancestors common with other craniates.

    This has evidential support from several angles. For example, we know that things like relatively small changes to regulatory genes can be responsible for things like differing skull size. There is proof of concept.

    This will mean a nested hierarchy that includes the molecular and macroscopic structures of the brain.

    I don't dispute any notion of a "nested hierarchy." I expect that if and when ape brains and human brains are fully understood there will not be anything particularly surprising molecularly and in the general macroscopic structures. We already know a fair amount about those. (And say we find any frozen brains of any transitional species, they will fit into the hierarchy without much fanfare.)

    No, where my interest lies is the uncharted waters that make up the distinctive neural networks between humans and our predecessors. The dearth of understanding in this area is so great that nothing that you've said or can offer even gets in the ballpark. It is utterly unknown whether or not the evolutionary mechanisms are sufficient to "program" these networks. There is no basis on which to infer that they reasonably can. It's a wide open field of inquiry. It may be unique in all of time and space. That's not hand waving, it's simply the humble acknowledgment of the state of the art.

  118. Comment by kornbelt888 — July 15, 2009 @ 10:47 pm

  119. kornbelt888 Says:
    July 15th, 2009 at 11:09 pm

    Zachriel: You said, "What is a live issue for me is the nature and cause of the incremental steps," hence my response. The answer is selection, as in Natural Selection.

    Let me clarify. By "nature and cause" I mean whether or not the variations are all random variations or non-random variations or a combination. I do not mean to imply that selection is not involved.

    You also said is that you require a Gapless pathway for historical claims,

    I do not require a historical gapless pathway. Only a gapless pathway. It need not be the historical one. What would suffice is a gapless pathway where there all chains of development have proof-of-concept established from random variation and natural selection. For example, if it could be demonstrated that the neural networks responsible for recognition of musical sequences could be generated from RV+NS, I would be satisfied enough not to press for evidence that it could generate perfect pitch recognition, etc.

    even when scientists can make bold and verifiable empirical predictions, such as important intermediate fossil organisms.

    Well, let's test this. What bold and verifiable empirical prediction can you make based on RV+NS (or the MS) regarding the emergence of the ability of humans to create the theory of gravity? What kind of neural network evolutionary steps should we expect to find in the evidential record, if we could find them?

  120. Comment by kornbelt888 — July 15, 2009 @ 11:09 pm

  121. don provan Says:
    July 16th, 2009 at 3:20 am

    kornbelt888: An account with no gaps that is reproducible.

    That's an impractical demand. We don't have 100% explanation of any historical sequence of events, and explanations that are not 100% are not worthless. In addition, you get to define "gap", and as I pointed out with my H2O example, a gap can be defined to be ridiculously small.

    Before you can create an transitional account from ape brain to human brain you'd have to have a solid handle on how both function, down to the way the precise neural networks operate that are responsible for the function we see in both.

    Oh, yeah, and that's another thing: if we give you a pathway explaining the development, you'll just point out other things we don't know and demand that they must be explained also in order to satisfy your requirements.

    This thread has nothing to do with God or designers. You seem to be implying that I'm hunting for gaps just to feel good about my religion or something. Fuggedaboutit.

    We started out discussing how Daniel does, in fact, appear to be hunting for gaps just to feel good about his religion. We have ended up discussing your search for gaps. That made me think the gaps were significant to you for some reason. If your only point is that there's more we could know about how the human brain developed, then we are in complete agreement. In fact, I can't imagine anyone disagreeing with that.

  122. Comment by don provan — July 16, 2009 @ 3:20 am

  123. Zachriel Says:
    July 16th, 2009 at 7:16 am

    kornbelt888: I expect that if and when ape brains and human brains are fully understood there will not be anything particularly surprising molecularly and in the general macroscopic structures. We already know a fair amount about those. (And say we find any frozen brains of any transitional species, they will fit into the hierarchy without much fanfare.)

    And because they are incremental changes and because they are selectable, they are therefore evolvable.

    kornbelt888: No, where my interest lies is the uncharted waters that make up the distinctive neural networks between humans and our predecessors.

    Ah, but you demanded an "account with no gaps that is reproducible". Now, you seem to be merely concerned with one particular purported Gap. So your position is that everything else evolved but the human brain, even though it also fits the nested hierarchy and that any detail we find will fit the hypothesis of a selectable transition. Furthermore, we have a branching pattern with most lineages going extinct demonstrating the happenstance nature of the process. In other words, all the evidence is consistent with natural variation and selection.

    As for a pathway from a simple notochord to a human brain, you need only study the developing human embryo. This will give you a first-order approximation. For a more detailed look, determine the divergence in the development of the human brain from the development of related species.

  124. Comment by Zachriel — July 16, 2009 @ 7:16 am

  125. Daniel Smith Says:
    July 16th, 2009 at 2:39 pm

    Daniel Smith: Evolution (as presented here) is slow and extremely inefficient.

    Zachriel: Actually, lots of evolution happens in Lenski's experiments. This particular transition is rare and contingent, and that's what makes it interesting enough for a separate paper. You had said, "you have no clue how anything actually evolved". And this paper answers your objection.

    You still have no clue how this evolved. You only know that it did.

    Now, we might consider next the Lederberg Experiment which demonstrates that mutations are random with respect to fitness.

    You completely bypassed all my comments (save one) on the first paper and now you're ready to go on to another? I don't think so.

  126. Comment by Daniel Smith — July 16, 2009 @ 2:39 pm

  127. Daniel Smith Says:
    July 16th, 2009 at 2:58 pm

    To reiterate:

    The paper Zachriel cited referenced a demonstrated instance of the evolution of a new function. This mechanism (whatever it turns out to be) was demonstrated to be historically contingent and it took 30,000+ generations to cause enough change to begin the new function.

    The obvious question is: Is this demonstrated mechanism sufficient to account for the observed differences between the species he wants to talk about – namely; fish, monkeys, humans and horses?

  128. Comment by Daniel Smith — July 16, 2009 @ 2:58 pm

  129. don provan Says:
    July 16th, 2009 at 5:03 pm

    The obvious question is: Is this demonstrated mechanism sufficient to account for the observed differences between the species he wants to talk about – namely; fish, monkeys, humans and horses?

    Experts that consider the matter say it is sufficient. I admit that I'm not one of those experts, but I also have no reason to doubt their assessment. Are you one of those experts? Can you give me any good reasons to doubt their assessment beyond the fact that you don't like it?

  130. Comment by don provan — July 16, 2009 @ 5:03 pm

  131. Zachriel Says:
    July 16th, 2009 at 5:40 pm

    Daniel Smith: You still have no clue how this evolved. You only know that it did.

    Clues were provided that supported the hypothesis of evolution by variation and selection. Frankly, I have no idea what point you are trying to make.

    Daniel Smith: You completely bypassed all my comments (save one) on the first paper and now you're ready to go on to another? I don't think so.

    Sigh.

    Daniel Smith: A) Evolution (as presented here) is slow and extremely inefficient.

    A description of the history of the populations involved is part of the answer as to how. A clue.

    Daniel Smith: B) Evolution (as presented here) requires pre-existing elements.

    Pre-existing elements are part of the answer as to how. A clue.

    Daniel Smith: C) Evolution (as presented here) is historically contingent.

    Historical contingency is part of the answer as to how. A clue.

  132. Comment by Zachriel — July 16, 2009 @ 5:40 pm

  133. Daniel Smith Says:
    July 16th, 2009 at 7:25 pm

    don provan: Experts that consider the matter say it is sufficient.

    Not all of them do don.

    Zachriel: _________ is part of the answer as to how. A clue.

    I have been going out of my way to read everything I can about biology and evolution. I have a stack of papers on evolution (most recommended by people like you – on forums like this) and I've read them all. I'm also reading a biochemistry textbook in my spare time and have several more textbooks on molecular biology on order. While I'll be the first to admit that I'm no expert, I am seeking to educate myself and I am very familiar with the evidence and the arguments for evolution (both Darwinian and non-Darwinian). In fact I'm probably more familiar with the non-Darwinian theories of evolution than you, so you don't need to pretend that my reasons for not accepting the currently held theory are because of some profound ignorance. I find the case unconvincing because I'm familiar with (what I consider to be) a better explanation.

  134. Comment by Daniel Smith — July 16, 2009 @ 7:25 pm

  135. Zachriel Says:
    July 16th, 2009 at 7:41 pm

    Daniel Smith: you don't need to pretend that my reasons for not accepting the currently held theory are because of some profound ignorance.

    It's not a matter of ignorance. Frankly, your answers are too vague to advance the discussion, such as the overstatement "You still have no clue how this evolved."

    Daniel Smith: I find the case unconvincing because I'm familiar with (what I consider to be) a better explanation.

    Yet, you don't provide a better explanation for Lenski's results and an empirical test to distinguish your hypothesis.

    You may want to start with a simpler example. Take a bacterium and allow it to reproduce. Expose the colony to antibiotics. Even though they are all descendents of the original bacterium, some live and some die. If you take the survivors and allow them to reproduce, their offspring are also resistant to the antibiotic. The change is heritable. The question then is, did the bacteria develop this resistance because you exposed them to the antibiotic?

  136. Comment by Zachriel — July 16, 2009 @ 7:41 pm

  137. don provan Says:
    July 16th, 2009 at 7:54 pm

    Not all of them do don.

    If there's a healthy debate, then what's the problem?

  138. Comment by don provan — July 16, 2009 @ 7:54 pm

  139. Daniel Smith Says:
    July 16th, 2009 at 9:35 pm

    How about this Zachriel?
    From the same paper:

    What physiological mechanism has evolved that allows aerobic growth on citrate? E. coli should be able to use citrate as an energy source after it enters the cell, but it lacks a citrate transporter that functions in an oxygen-rich environment. One possibility is that the Cit+ lineage activated a ‘‘cryptic’’ transporter (41), that is, some once-functional gene that has been silenced by mutation accumulation. This explanation seems unlikely to us because the Cit+ phenotype is characteristic of the entire species, one that is very diverse and therefore very old. We would expect a cryptic gene to be degraded beyond recovery after millions of years of disuse. A more likely possibility, in our view, is that an existing transporter has been coopted for citrate transport under oxic conditions. This transporter may previously have transported citrate under anoxic conditions (43) or, alternatively, it may have transported another substrate in the presence of oxygen. The evolved changes might involve gene regulation, protein structure, or both (61).

    There are two possibilities mentioned here. The first is deemed "unlikely" based on the assumption that evolution degrades unused genes. The second is called "more likely".

    From a FLE perspective, I would not be surprised at all by the discovery that it was a cryptic gene even though – from a NFLE perspective – these scientists would. In fact, I'll go out on a limb and predict that it will be a cryptic gene after all.

    How about it Zachriel? Care to go on record before the research is done and pick a side?

  140. Comment by Daniel Smith — July 16, 2009 @ 9:35 pm

  141. Zachriel Says:
    July 17th, 2009 at 7:43 am

    Daniel Smith: From a FLE perspective, I would not be surprised at all by the discovery that it was a cryptic gene even though – from a NFLE perspective – these scientists would.

    I'm not quite sure of your "FLE" hypothesis. We start with a single bacterium which reproduces asexually: they're clones. Yet some of the descendants have a heritable trait that others don't, and this trait leads to a selective differential. Why, according to "FLE", are some of the descendants different? Do they sense the environment and initiate the change? If so, then why don't all of them gain the trait?

    You may want to consider the simpler case from my previous comment.

  142. Comment by Zachriel — July 17, 2009 @ 7:43 am

  143. Daniel Smith Says:
    July 17th, 2009 at 7:32 pm

    I've been thinking a lot about this since my last reply Zachriel, and I think I spoke too soon. If this was indeed a front-loaded gene, I doubt it would take 30,000+ generations to re-enable it. This seems more like an example of real Darwinian evolution via the mechanisms of variation and selection.

    That said, I'd like to point out that, because this function is unattainable via a single point mutation (per the paper), it is highly contingent upon a certain evolutionary history.

    Despite this potential, none of the 12 LTEE populations evolved the capacity to use the citrate that was present in their environment for over 30,000 generations. During that time, each population experienced billions of mutations (22), far more than the number of possible point mutations in the ~4.6-million-bp genome. This ratio implies, to a first approximation, that each population tried every typical one-step mutation many times.

    I believe this type of contingency therefore, to be a necessary condition for any change in phenotype requiring more than rudimentary changes genetically, (more than single point mutations certainly), IF, (and that's a big "IF"), those changes occur via the Darwinian mechanism.

    This is the central issue of the paper IMO. It's one also, that you seem willing to skip over. But this is key. The differences between the species you want to talk about are significant. Is this mechanism – for which we now have a real life observed example – capable of producing all the differences we see between the species in the timeframe necessary?

    I don't think so. I'm sure you have no doubts however.

  144. Comment by Daniel Smith — July 17, 2009 @ 7:32 pm

  145. Zachriel Says:
    July 17th, 2009 at 10:03 pm

    Daniel Smith: I believe this type of contingency therefore, to be a necessary condition for any change in phenotype requiring more than rudimentary changes genetically, (more than single point mutations certainly), IF, (and that's a big "IF"), those changes occur via the Darwinian mechanism.

    I'm not sure what you mean. If you mean something that takes more than single point mutations takes more than single point mutations, then yes. If you mean something that takes more than rudimentary changes geneticially takes more than rudimentary changes genetically, then yes. There are many types of genetic mutations beyond point mutations (such as those due to insertion sequences), and populations in the Lenski studies become highly diverse, genetically and phenotypically, over time.

  146. Comment by Zachriel — July 17, 2009 @ 10:03 pm

  147. Zachriel Says:
    July 17th, 2009 at 10:04 pm

    Blount, Borland & Lenski, Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli, PNAS 2008.

    Daniel Smith: This is the central issue of the paper IMO. It's one also, that you seem willing to skip over.

    Contingency is in the title. It's kinda hard to overlook. The paper is interesting because non-contingent evolution has already been observed in this and other studies.

    I don't see the answer to my previous query.

  148. Comment by Zachriel — July 17, 2009 @ 10:04 pm

  149. Zachriel Says:
    July 17th, 2009 at 10:13 pm

    Daniel Smith: The differences between the species you want to talk about are significant. Is this mechanism – for which we now have a real life observed example – capable of producing all the differences we see between the species in the timeframe necessary?

    I assume then we can lay to rest your overstatement about not having a clue about how things evolve.

    Genetics is still a relatively new field. There are bound to be many surprises. But genetics provides strong evidence of descent with modification. In particular, the evidence indicates that genomes are cobbled together by historical events, not designed. Nor do we have to have a theory of genetics to find strong confirmation of the Theory of Evolution.

  150. Comment by Zachriel — July 17, 2009 @ 10:13 pm

  151. kornbelt888 Says:
    July 18th, 2009 at 3:05 pm

    kornbelt888: I expect that if and when ape brains and human brains are fully understood there will not be anything particularly surprising molecularly and in the general macroscopic structures. We already know a fair amount about those. (And say we find any frozen brains of any transitional species, they will fit into the hierarchy without much fanfare.)

    Zachriel: And because they are incremental changes and because they are selectable, they are therefore evolvable.

    When I read your replies to me I am often struck with the feeling that either you are arguing with someone else, are incapable of understanding my views, are somewhat insane, and/or I'm a crappy writer and cannot express myself well in this forum. Whatever the case, I'm going to bow out for now.

  152. Comment by kornbelt888 — July 18, 2009 @ 3:05 pm

  153. Zachriel Says:
    July 18th, 2009 at 3:58 pm

    kornbelt888: When I read your replies to me I am often struck with the feeling that either you are arguing with someone else, are incapable of understanding my views, are somewhat insane, and/or I'm a crappy writer and cannot express myself well in this forum.

    The Theory of Evolution posits a (rough) continuum, i.e. descent with modification, and a branching pattern with extinctions, i.e. Common Descent, that we can explore. When I read your reply, you indicated we would see exactly what is expected from the Theory of Evolution. Then you said "where my interest lies is the uncharted waters that make up the distinctive neural networks between humans and our predecessors." So apparently everything else evolved from primitive cells to hominids over hundreds of millions of years. And brains clearly evolved from primitive organisms up to and including humans. And there is evidence that non-sapien hominids had culture and primitive technology.

    But there's a Gap. And it interests you. That's fine.

  154. Comment by Zachriel — July 18, 2009 @ 3:58 pm

  155. Daniel Smith Says:
    July 19th, 2009 at 11:28 am

    Zachriel,

    This is why debates about origins are useless. You are heavily invested in your bias, and I am heavily invested in mine. We both look at the same paper and come away convinced that the evidence supports our views. I am not going to change my mind, neither are you. So, what's the point?

  156. Comment by Daniel Smith — July 19, 2009 @ 11:28 am

  157. Zachriel Says:
    July 19th, 2009 at 1:25 pm

    Daniel Smith: I am not going to change my mind, neither are you.

    In science, minds are changed by proposing new hypotheses that entail specific and distinguishing empirical observations.

  158. Comment by Zachriel — July 19, 2009 @ 1:25 pm

  159. Daniel Smith Says:
    July 19th, 2009 at 2:32 pm

    Zachriel: In science, minds are changed by proposing new hypotheses that entail specific and distinguishing empirical observations.

    Blah blah blah. You're not going to change your mind because you've already settled on a worldview by which you interpret all relevant evidence. So have I. (Rare is the individual who hasn't). Why can't you admit that?

  160. Comment by Daniel Smith — July 19, 2009 @ 2:32 pm

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