Mendel’s Accountant again….

Journal club time: paper by Sanford et al: The Waiting Time Problem in a Model Hominin Population.  I’ve pasted the abstract below.

Have at it guys 🙂

Background

Functional information is normally communicated using specific, context-dependent strings of symbolic characters. This is true within the human realm (texts and computer programs), and also within the biological realm (nucleic acids and proteins). In biology, strings of nucleotides encode much of the information within living cells. How do such information-bearing nucleotide strings arise and become established?

Methods

This paper uses comprehensive numerical simulation to understand what types of nucleotide strings can realistically be established via the mutation/selection process, given a reasonable timeframe. The program Mendel’s Accountant realistically simulates the mutation/selection process, and was modified so that a starting string of nucleotides could be specified, and a corresponding target string of nucleotides could be specified. We simulated a classic pre-human hominin population of at least 10,000 individuals, with a generation time of 20 years, and with very strong selection (50 % selective elimination). Random point mutations were generated within the starting string. Whenever an instance of the target string arose, all individuals carrying the target string were assigned a specified reproductive advantage. When natural selection had successfully amplified an instance of the target string to the point of fixation, the experiment was halted, and the waiting time statistics were tabulated. Using this methodology we tested the effect of mutation rate, string length, fitness benefit, and population size on waiting time to fixation.

Results

Biologically realistic numerical simulations revealed that a population of this type required inordinately long waiting times to establish even the shortest nucleotide strings. To establish a string of two nucleotides required on average 84 million years. To establish a string of five nucleotides required on average 2 billion years. We found that waiting times were reduced by higher mutation rates, stronger fitness benefits, and larger population sizes. However, even using the most generous feasible parameters settings, the waiting time required to establish any specific nucleotide string within this type of population was consistently prohibitive.

Conclusion

We show that the waiting time problem is a significant constraint on the macroevolution of the classic hominin population. Routine establishment of specific beneficial strings of two or more nucleotides becomes very problematic.

844 thoughts on “Mendel’s Accountant again….

  1. Elizabeth,

    “At the other extreme, 50 populations evolved in an environment where only EQU was rewarded, and no simpler function yielded energy. We expected that EQU would evolve much less often because selection would not preserve the simpler functions that provide foundations to build more complex features. Indeed, none of these populations evolved EQU, a highly significant difference from the fraction that did so in the reward-all environment (P ~= 4.3 x 10-9, Fisher’s exact test).”– Lenski. You lose, Elizabeth

  2. Alan Fox: Frankie: I have no idea what that means. Perhaps English isn’t your primary language

    It’s quite simple. Just fill in the acronym; OOL = origin of life. Then the question becomes “what is the origin of life of the intelligent designer?” Of course, on previous form, I guess you will respond that this is something you don’t need to consider. Unfortunately for those wishing to promote ID as a scientific venture, failing to propose hypotheses about how, when and when the “intelligent designer” acts (entailments) means that ID can be asserted to fit any scenario, confirming it as scientifically vacuous.

    Why does the intelligent designer require an OoL? And no, we do not have to say anything about the how, when and when the designer acts. You are obviously scientifically illiterate as archaeology doesn’t have to do that and they cannot until the first determine design exists and then study it.

  3. Frankie:
    Elizabeth,

    “At the other extreme, 50 populations evolved in an environment where only EQU was rewarded, and no simpler function yielded energy. We expected that EQU would evolve much less often because selection would not preserve the simpler functions that provide foundations to build more complex features. Indeed, none of these populations evolved EQU, a highly significant difference from the fraction that did so in the reward-all environment (P ~= 4.3 x 10-9, Fisher’s exact test).”– Lenski. You lose, Elizabeth

    You seem to be still missing my point, Joe.

  4. Frankie: Umm we can detect design without knowing anything about the designer. We don’t even ask about a designer until after we have determined design exists.

    So you know nothing about the designer, nothing about how to that designer implemented his design,nothing about how natural processes may have modified that design, nothing about when the design was created.

    Now you are saying you are not asking questions about the designer because you don’t know yet whether design exists either?

  5. newton: in reply) (Reply)

    ID is about the DESIGN. The only way to make any scientific determination about the questions you ask is by studying the design and all relevant evidence. And guess what? That is exactly how forensics and archaeology do it.

  6. Frankie: You are obviously scientifically illiterate as archaeology doesn’t have to do that and they cannot until the first determine design exists and then study it.

    Except that in archaeology we actually do have a substantial background of empirically confirmed general facts about human thought and behavior, and we also have empirically confirmed general facts about culture, technology, etc. (If we found an iron sword in ruins that predated the development of furnaces hot enough to melt iron ore, we would know that something is badly amiss!)

    Since the Intelligent Designer was not (we assume) a human being, we have no such body of general facts to draw upon. Simply stipulating that it was an intelligent being of some kind tells us nothing about its specific capacities or intentions. But without any way of specifying what its capacities or intentions were, over and beyond the bare stipulation of intelligence, there’s nothing testable.

    This is the main point that ID theorists fail to comprehend: the analogy between artifacts and organisms — whether put in Paley’s language of “intricate contrivance” or Dembski’s language of “complex specified information” — does, indeed, furnish us with an inference to the best explanation, or what Peirce called “an abductive leap”. But an inference to the best explanation is not sufficient for a scientific theory; we also need some way of testing the inference. And that is what ID theorists refuse to do. All of the probability calculations carried out by Dembski, Behe, et al. are just versions of the design inference itself; they aren’t tests of the inference.

    I stopped posting at Uncommon Descent because I grew tired of making this same elementary point repeatedly and having it utterly ignored every time.

  7. newton: then it is true, you cannot detect design

    That doesn’t follow. Of course we can detect design as the design has testable entailments. And all you have to do to falsify our design inference is ante up and demonstrate a non-telic process can produce it. Science 101

  8. Kantian Naturalist: Except that in archaeology we actually do have a substantial background of empirically confirmed general facts about human thought and behavior, and we also have empirically confirmed general facts about culture, technology, etc. (If we found an iron sword in ruins that predated the development of furnaces hot enough to melt iron ore, we would know that something is badly amiss!)

    Since the Intelligent Designer was not (we assume) a human being, we have no such body of general facts to draw upon. Simply stipulating that it was an intelligent being of some kind tells us nothing about its specific capacities or intentions. But without any way of specifying what its capacities or intentions were, over and beyond the bare stipulation of intelligence, there’s nothing testable.

    This is the main point that ID theorists fail to comprehend: the analogy between artifacts and organisms — whether put in Paley’s language of “intricate contrivance” or Dembski’s language of “complex specified information” — does, indeed, furnish us with an inference to the best explanation, or what Peirce called “an abductive leap”. But an inference to the best explanation is not sufficient for a scientific theory; we also need some way of testing the inference. And that is what ID theorists refuse to do. All of the probability calculations carried out by Dembski, Behe, et al. are just versions of the design inference itself; they aren’t tests of the inference.

    I stopped posting at Uncommon Descent because I grew tired of making this same elementary point repeatedly and having it utterly ignored every time.

    We have plenty of knowledge of cause and effect relationships. We don’t care about the intentions, motives or capacities. Designers are obviously capable of designing the things they design.

    ID posits testable entailments for the DESIGN.

    We study the design so we can understand it. You see we understand it makes a difference to study something as a designed artifact or as natural formations. Studying Stonehenge as a geological formation would be useless and a waste of time.

    UD ignored your posts because they were irrelevant. Deal with it.

  9. Frankie: ID is about the DESIGN. The only way to make any scientific determination about the questions you ask is by studying the design and all relevant evidence. And guess what? That is exactly how forensics and archaeology do it.

    And the relevant evidence is the nature of the designer, how and when the pattern was created, questions you have not yet undertaken because you are unable even to tell,according to you, whether design exists yet.

    Any timetable on when this Edge of ID might be reached?

  10. newton:

    You don’t get to say what the relevant evidence is. You have no idea nor any qualifications.

    Look if your position had something beyond strawmen and propaganda, ID would be a non-starter. Yet he we are, your strawmen are exposed and your position still has nothing.

    BTW, design has been detected. So please stop putting words in my mouth

  11. Frankie: That doesn’t follow. Of course we can detect design as the design has testable entailments. And all you have to do to falsify our design inference is ante up and demonstrate a non-telic process can produce it. Science 101

    Then what is stopping you from asking questions about the designer?

  12. newton: Then what is stopping you from asking questions about the designer?

    Nothing. It just has nothing to do with ID.

    We don’t even know who built Nan Madol- nor how

  13. Frankie: Nothing. It just has nothing to do with ID.
    We don’t even know who built Nan Madol- nor how

    No human would stack rocks like that.

  14. petrushka: n

    What humans? How did they cut the blocks and transport them?

    We have no idea. We can’t test the claim that humans of hundreds or thousands of years ago had the capability. Only the structures they left behind are hints that they may have.

  15. I thought I had agreed with you that no humans would stack rocks like that.

    You win. It was space aliens. Or God.

  16. Frankie: newton:

    You don’t get to say what the relevant evidence is. You have no idea nor any qualifications.

    BTW, design has been detected. So please stop putting words in my mouth

    You cited archeology and forensics as analogs to ID, that is relevant evidence for those disciplines. You seem to have no problem demanding certain evidence from evolutionary sciences, what exactly are your qualifications,Frankie, now that you mention it?

    “We don’t even ask about a designer until after we have determined design exists”

    Sorry I figured the only explanation possible for your disinterest in the designer of life was you had not yet determined whether design exists. Apologies. So why the disinterest?

  17. Frankie: We can’t test the claim that humans of hundreds or thousands of years ago had the capability.

    Why on Earth not? Experiments to try out methods for moving heavy stones – such as are found at Stonehenge – demonstrate that enough people working together with simple tools, rollers, ropes, levers and so on, can achieve the sorts of feats needed to transport and erect large monoliths.

    Flooded and boggy areas in Eastern England had wooden walkways built on timber piles. They date to Anglo-Saxon times. Archaeologists were initially puzzled how large tree trunks could be driven deeply into the substrate without machinery. Then somebody tried tying on a cross beam to a timber pile and getting people to stand on it and jump in rhythm. Seems the technique is still in use today.

    ETA clarity

  18. Frankie: Nothing. It just has nothing to do with ID.

    We don’t even know who built Nan Madol- nor how

    You make ID sound useless and untestable .It is not that ID has not yet asked those questions, ID is by definition incapable of asking those questions. So ID is kinda of a dead end

  19. newton: You cited archeology and forensics as analogs to ID, that is relevant evidence for those disciplines. You seem to have no problem demanding certain evidence from evolutionary sciences, what exactly are your qualifications,Frankie, now that you mention it?

    “We don’t even ask about a designer until after we have determined design exists”

    Sorry I figured the only explanation possible for your disinterest in the designer of life was you had not yet determined whether design exists. Apologies. So why the disinterest?

    Both forensics and archaeology tell us that it is not required to know the designer or the method used before we can determine design/ a crime.

    And who says I am not interested in the designer of life? Why do you have to put words and thoughts onto your opponents? That is a sure sign of desperation.

  20. I find the lack of belief in sky fairies to be disturbing. Joe Frankie has proved his case conclusively.

  21. newton: You make ID sound useless and untestable .It is not that ID has not yet asked those questions, ID is by definition incapable of asking those questions. So ID is kinda of a dead end

    We have said exactly how to test ID. And how is the design inference a dead end when it forces us to ask those other questions? ID isn’t about those questions. That doesn’t mean that other disciplines cannot be formed to take them on.

  22. Alan Fox: Why on Earth not? Experiments to try out methods for moving heavy stones – such as are found at Stonehenge – demonstrate that enough people working together with simple tools, rollers, ropes, levers and so on, can achieve the sorts of feats needed to transport and erect large monoliths.

    Flooded and boggy areas in Eastern England had wooden walkways built on timber piles. They date to Anglo-Saxon times. Archaeologists were initially puzzled how large tree trunks could be driven deeply into the substrate without machinery. Then somebody tried tying on a cross beam to a timber pile and getting people to stand on it and jump in rhythm. Seems the technique is still in use today.

    ETA clarity

    As if the people of TODAY are an example of the people of thousands of years ago.

  23. Frankie: As if the people of TODAY are an example of the people of thousands of years ago.

    Do you think people today are different in any significant way from people living in the Anglo-Saxon period? From people living at the time the construction of Stonehenge began? Modern humans have been around for at least eighty thousand years. Granted some of us may be carrying a little excess weight compared to ancient times…

  24. Alan Fox: Do you think people today are different in any significant way from people living in the Anglo-Saxon period? From people living at the time the construction of Stonehenge began? Modernhumans have been around for at least eighty thousand years. Granted some of us may be carrying a little excess weight compared to ancient times…

    Yes, Alan, I say there are significant differences between the humans of today and humans just 200 years ago. But that isn’t the point.

  25. Frankie: I say there are significant differences between the humans of today and humans just 200 years ago.

    Do you attribute theses differences to evolutionary change?

  26. How do we “know” that the humans of thousands of years ago had the capability to build Stonehenge?

    Stonehenge! Without the Antikythera Mechanism no one would think the ancients had the capability of building such a device.

    The point is we determine design exists first. That is what ID is- the detection and study of design in nature.

  27. Moved a post of Frankie’s to guano. Frankie can of course repost the substantive part of that comment minus the rule-breaking element.

  28. Frankie: Not undirected evolutionary change.

    But directed evolutionary change? You claim there are differences between people living now compared to 200 years ago attributable to evolutionary change? I’m curious. Can you be more specific?

  29. Alan Fox: But directed evolutionary change? You claim there are differences between people living now compared to 200 years ago attributable to evolutionary change? I’m curious. Can you be more specific?

    I can be as specific as evolutionists are in describing the genetic changes required to support their ideas. 😛

  30. Alan Fox:

    Alan, you claimed that modern humans have been around for some 80,000 years. In the last 200 humanity has seen monumental growth technologically speaking.

  31. Frankie:
    How do we “know” that the humans of thousands of years ago had the capability to build Stonehenge?

    Stonehenge!

    Excellent point! Where would we be without the artefacts that demonstrate the development of the power of human cultural and social organisation.

    Without the Antikythera Mechanism no one would think the ancients had the capability of building such a device.

    Excellent point again. The existence of the artefact demands an explanation both for its purpose and how it could have been manufactured. And there seem to be such explanations.

    The point is we determine design exists first. That is what ID is- the detection and study of design in nature.

    Can you give me an example of a bit of design in nature that has been detected and studied? And could you contrast it with an example of a bit of un-design in nature so we can see the difference. I ask because I have previously met with the assertion that all nature is designed. In which case studying “design” seems a bit pointless.

  32. Frankie: Alan, you claimed that modern humans have been around for some 80,000 years. In the last 200 humanity has seen monumental growth technologically speaking.

    So you are not claiming humans living today are significantly different from those living 200 years ago? What about 5,000 years ago when evidence suggests humans first started work on Stonehenge?

  33. I think the “intelligent” part of Intelligent Design is really all that one has to know about the designer.

    Like, how would we know if intelligence exists on (or at least having visited, or sent something to) a planet? Find some machines, some monoliths, whatever, just something rationally planned and thought out. Oh yes, it would be quite different from determining if life exists on the planet. Find life constrained by heredity on a planet and it hardly indicates intelligence, unless one were to find evidence of genetic engineering or some such thing (plant breeding, although that remains constrained by heredity for obvious reasons).

    We know things about intelligence, like that it thinks rationally, at least at times. True, this is really only known about human intelligence, but we generalize it to at least humanoid intelligence.

    What we do know about life on earth is that it has not been rationally designed. Intelligence isn’t constrained by heredity, evolution is. In order to discover the involvement of intelligence in the “design of life” it’s relatively simple, just find where rational choice has superseded the limits of evolution.

    It’s the simple and obvious test for intelligent design in life that IDists studiously avoid, because it tells decisively against life having been designed. Make the test anything other than the good one, the test of whether or not intelligence has generally transcended evolutionary limits (we know the pretense regarding flagella (esp. bacterial), which, even if it indicated what they claim would not generalize to, say, human evolution). Yes, we have the means to test for any intelligent intervention that fits the typical definition, and the test indicates that all credible intelligent intervention has been human, and/or animal, under a broader definition of “intelligent.”

    Glen Davidson

  34. Alan Fox: So you are not claiming humans living today are significantly different from those living 200 years ago? What about 5,000 years ago when evidence suggests humans first started work on Stonehenge?

    I said there is a significant difference between us and the humans of 200 years ago

  35. Alan Fox: Excellent point! Where would we be without the artefacts that demonstrate the development of the power of human cultural and social organisation.

    Excellent point again. The existence of the artefact demands an explanation both for its purpose and how it could have been manufactured. And there seem to be such explanations.

    Can you give me an example of a bit of design in nature that has been detected and studied? And could you contrast it with an example of a bit of un-design in nature so we can see the difference. I ask because I have previously met with the assertion that all nature is designed. In which case studying “design” seems a bit pointless.

    The genetic code is an example of a bit of design in nature that has been detected and studied. Living organisms are another example.

    And the universe can be designed without having everything in it having to be designed. Accidents do happen.

  36. GlenDavidson:
    I think the “intelligent” part of Intelligent Design is really all that one has to know about the designer.

    Like, how would we know if intelligence exists on (or at least having visited, or sent something to) a planet?Find some machines, some monoliths, whatever, just something rationally planned and thought out.Oh yes, it would be quite different from determining if life exists on the planet.Find life constrained by heredity on a planet and it hardly indicates intelligence, unless one were to find evidence of genetic engineering or some such thing (plant breeding, although that remains constrained by heredity for obvious reasons).

    We know things about intelligence, like that it thinks rationally, at least at times.True, this is really only known about human intelligence, but we generalize it to at least humanoid intelligence.

    What we do know about life on earth is that it has not been rationally designed.Intelligence isn’t constrained by heredity, evolution is.In order to discover the involvement of intelligence in the “design of life” it’s relatively simple, just find where rational choice has superseded the limits of evolution.

    It’s the simple and obvious test for intelligent design in life that IDists studiously avoid, because it tells decisively against life having been designed.Make the test anything other than the good one, the test of whether or not intelligence has generally transcended evolutionary limits (we know the pretense regarding flagella (esp. bacterial), which, even if it indicated what they claim would not generalize to, say, human evolution).Yes, we have the means to test for any intelligent intervention that fits the typical definition, and the test indicates that all credible intelligent intervention has been human, and/or animal, under a broader definition of “intelligent.”

    Glen Davidson

    Glen, You cannot explain life. You cannot explain the genetic code. Your explanation for earth is accretion via cosmic collisions- it is accidents all the way down.

  37. Frankie: I said there is a significant difference between us and the humans of 200 years ago.

    Well, I don’t see any significant physical difference between people today and of 200 years ago. You qualified your earlier statement making apparent you were referring to cultural change, and, if you are, I’d agree there has been rapid and accelerating change in human culture but then I wonder about the relevance in a thread on computer simulations purporting to emulate evolutionary processes.

  38. Alan Fox: Well, I don’t see any significant physical difference between peopletoday and of 200 years ago. You qualified your earlier statement making apparent you were referring to cultural change, and, if you are, I’d agree there has been rapid and accelerating change in human culturebut then I wonder about the relevance in a thread on computer simulations purporting to emulate evolutionary processes.

    Change in behavior is an evolutionary process. Change in behavior is easier than waiting for a lucky genetic accident. Also just watching American football says there has been a big physical change in the last 100 years. The best players of the 1960s couldn’t compete today

  39. Frankie: The genetic code is an example of a bit of design in nature that has been detected and studied.

    Biochemists have certainly worked hard at elucidating the mechanisms of DNA replication and translation. I can’t recall any research into how Design factored in the ways that these mechanisms came to be.

    Living organisms are another example.

    I see. According to Frankie, all living organisms are designed. So why bother to mention the genetic code separately if all life is designed?

  40. Alan Fox: Biochemists have certainly worked hard at elucidating the mechanisms of DNA replication and translation. I can’t recall any research into how Design factored in the ways that these mechanisms came to be.I see. According to Frankie, all living organisms are designed. So why bother to mention the genetic code separately if all life is designed?

    And biochemists will have as much luck explaining the genetic code as a result of some chemical processes as geologists will have explaining Stonehenge as a geological formation.

  41. Frankie: Glen, You cannot explain life. You cannot explain the genetic code. Your explanation for earth is accretion via cosmic collisions- it is accidents all the way down.

    Follow the evidence.

    It’s better to explain much than to explain nothing (saying that evolutionary theory doesn’t exist means nothing, btw). That’s why ID is ignored by science.

    Glen Davidson

  42. Frankie: Both forensics and archaeology tell us that it is not required to know the designer or the method used before we can determine design/ a crime.

    Without knowing the method of death how does one determine whether a crime has been committed ,Frankie?

    Frankie: And who says I am not interested in the designer of life? Why do you have to put words and thoughts onto your opponents? That is a sure sign of desperation

    Really, go on, what has your interest in the designer of life uncovered?

    They are your words ,Frankie. As for thoughts, aren’t you putting thoughts in the unknown designer’s head when you assume his goals, that is if he has a head or thoughts.You ,of course, know neither. Are you desperate, then?

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