Probabilities And Skepticism

I thought about including this in my previous thread, but it has grown so large that I suspect it would be lost in the abyss. If Skeptical Zone readers are interested I’ll write a series of these posts, in which I’ll develop a number of themes concerning why I abandoned evolutionary orthodoxy and became convinced that an inference to design is most reasonable.

As most of you know, I am a classical musician. All great musical compositions have a theme, and the theme of this site is “think it possible that you may be mistaken.” With that theme in mind, might I suggest some skepticism concerning probabilities?

One doesn’t need precise numbers to recognize when proposed probabilities are way of whack. When I was growing up and learning mathematics my dad (a professor of chemical physics) admonished me to always check my calculations to see if they made sense on the surface (in my engineering department we call this “using the beverage out the nose” test). If I punch 87 x 53 into my calculator and get 46,481 I immediately know something is wrong (in this case I hit the 7 key twice by accident) even if I don’t know exactly what is wrong, because the result should be somewhere in the hundreds, not thousands. I don’t need to know exactly what the problem is in order to recognize that the result makes no sense.

I apply this logic to probabilities concerning evolutionary theory. We have some good empirical evidence that it took about 10^20 reproductive events for malaria to evolve chloroquine resistance. It could be that Lucy turned into Lizzie in 3.2 million years by stochastic Darwinian mechanisms filtered by natural selection, but I apply the beverage-out-the-nose test concerning the probabilities. Even given the most generous assumptions (a few hundred thousand generations with a few million individuals in each generation) the probabilistic Lucy–to-Lizzie resources don’t pass the smell test, in my view.

So, I ask Skeptical Zone readers: Is my skepticism unwarranted, and if so, why?

256 thoughts on “Probabilities And Skepticism

  1. Joe,

    I am an ass, hands, feet, a stomach, shoulders, legs, a head, a heart, etc.

    Please quit speaking like an uneducated donkey!

    “CSI is just an indicator of intentional design” – Joe Schmo

    Tell me, Joe, what FIELD of study does the DI take seriously that is competent in understanding theories of ‘intentional design’? You won’t suggest ‘engineering’ or ‘programming,’ will you please?

    - Gregory

  2. Joe G:
    olegt- You don’t have any idea what you are even talking about.

    CSI is just an indicator of intentional design- that is all. And to refute that claim all you have to do is step up and demonstrate that blind and undirected processes can produce it. However you will never even attempt any such thing because you have intellectual issues.

    Well now. I seem to remember a paper in which a large number of randomly-assembled proteins – each around 80 amino-acids long, IIRC – were produced. When tested, a small (very small) proportion of them were functional – of those. none were matched by anything in the databases. Furthermore, only one function (ATP-binding) was tested for – no-one knows how many more functional proteins would have been found had other functions been tested for.

    So there we are – functional proteins from random assembly. NO information was specified in advance, therefore no CSI present, and ID is blown away

  3. Well now. I seem to remember a paper in which a large number of randomly-assembled proteins – each around 80 amino-acids long, IIRC – were produced.

    Reference please.

  4. Gregory:
    Joe,

    I am an ass, hands, feet, a stomach, shoulders, legs, a head, a heart, etc.

    Please quit speaking like an uneducated donkey!

    “CSI is just an indicator of intentional design” – Joe Schmo

    Tell me, Joe, what FIELD of study does the DI take seriously that is competent in understanding theories of ‘intentional design’? You won’t suggest ‘engineering’ or ‘programming,’ will you please?

    - Gregory

    Science, Gregory- one of the basic questions science asks is “How did it come to be this way (the way it is)?” and design is one possibility.

  5. Joe G: Reference please.

    Here y’go
    Functional proteins from a random-sequence library.
    Keefe AD, Szostak JW.
    Source
    Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston 02114, USA.
    Abstract
    Functional primordial proteins presumably originated from random sequences, but it is not known how frequently functional, or even folded, proteins occur in collections of random sequences. Here we have used in vitro selection of messenger RNA displayed proteins, in which each protein is covalently linked through its carboxy terminus to the 3′ end of its encoding mRNA, to sample a large number of distinct random sequences. Starting from a library of 6 x 1012 proteins each containing 80 contiguous random amino acids, we selected functional proteins by enriching for those that bind to ATP. This selection yielded four new ATP-binding proteins that appear to be unrelated to each other or to anything found in the current databases of biological proteins. The frequency of occurrence of functional proteins in random-sequence libraries appears to be similar to that observed for equivalent RNA libraries.
    Nature. 2001 Apr 5;410(6829):715-8.

  6. Starting from a library of 6 x 1012 proteins each containing 80 contiguous random amino acids, we selected functional proteins by enriching for those that bind to ATP.

    They started with the proteins- which means the proteins did not arise via blind and undirected processes.

    Try again…

  7. Joe G: Well Lynn didn’t demonstrate anything. All she did was say “Hey these organelles look like bacteria” and she did not account for the nucleus.

    Science is work in progress, Joe.

    BTW there would have been more than one phenomenon- *dumbass*

    One phenomenon, two phenomena was all that I was pointing out. Don’t feel bad, it was an honest mistake. We can all learn something every day.

  8. Yes I know science is a work in progress. And some day it may have some actual scientific data to support that paper you linked to- as in some experiment that demonstrates one prok can engulf another and habe it evolve into mitochondria.

    Right now all you have is “euks are way too complex to have been the first life so euks must have come from proks”

  9. Joe,

    You’re making a serious category mistake, but you don’t have the education to understand this. ‘Natural science’ does *not* study ‘intentional design.’ The DI priviledges natural and applied sciences and you sycophantize on their bias. I know this about the DI much better and more closely than you do, Joe.

    And calling people ‘ass’ and ‘lame-ass’ is not the kind of thing your ‘Mentor’ would do. Is this poddy-language a reflection of how you feel when speaking with ‘skeptics’? It only reflects your low culture and lack of patience.

  10. Joe G:
    What you need is some way for a protein to form without a ribosome.

    Good luck with that…

    Deafening sound of goalposts moving…
    Your failure to deal with the actual point – the refutation of your argument – is noted – as always.

    But I’d be happy to discuss the evolution of ribosomes…perhaps you could regain some credibility

  11. Joe G: They started with the proteins- which means the proteins did not arise via blind and undirected processes.

    Try again…

    Randomly assembled – distinct random sequences.Can’t test for functional proteins without proteins, so they made their own, by blind, undirected processes.
    No need to try again.

  12. Joe, you’ll enjoy this, too.

    Selection and evolution of enzymes from a partially randomized non-catalytic scaffold
    Burckhard Seelig & Jack W. Szostak

    Nature: Vol 448| 16 August 2007| doi:10.1038/nature06032

    From the abstract: “Here we show that genuinely new
    enzymatic activities can be created de novo without the need for
    prior mechanistic information by selection from a naive protein
    library of very high diversity, with product formation as the sole
    selection criterion”

    “Without the need for prior mechanistic information” – that’s interesting

  13. I think it was toronto (among many others, of course) who complained that the specificiation in CSI cannot be determined retroactively, by examining the presumed object meeting the presumed specification. He asked, if you specify a red car and a blue car, and you get delivered two identical blue cars, how can you tell which of them meets the specification and which one does not?

    To determine if information is specified, it is necessary to know the specification BEFORE examining the information. A specification is a statement of intent. Unintended consequences are frequent, so just looking at the consequences cannot tell us if they meet spec.

    Buy hey, maybe this is what gives CSI it’s power – it’s whatever we want it to be, can’t get much more powerful than that.

  14. Joe G,

    Umm no one can tell NS apart from genetic drift. BTW no one has done a complete side-by-side comparison of the two genomes (chimps v humans). And no one knows if changes to the genome can account for the anatomical and physiological differences between the two.

    See: http://en.wikipedia.org/wiki/Ka/Ks_ratio
    http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0030029
    and
    http://www.pnas.org/content/100/12/7181.long

    For human chimp genome comparisons see
    http://www.nature.com/nature/journal/v437/n7055/full/nature04000.html
    http://genome.cshlp.org/content/15/12/1746.long
    http://genome.cshlp.org/content/18/11/1698

  15. Just a few quick comments:

    Gil is not reasoning to a conclusion from anything resembling an informed analysis, but rather rationalizing a foregone conclusion driven by ideology.

    My initial foregone conclusion driven by ideology was that materialistic evolutionary theory just had to be true, almost by definition. However, I found contemporary arguments from design to be compelling, as did Antony Flew.

    No, you certainly aren’t wasting your time, Gil, but I think you misunderstood this comment. We do have gills at a certain point in development – so you did, at one point, have gills, Gil :)

    From what I understand, at no point in human embryonic development do humans have gills; they have pharyngeal artifacts which develop into highly disparate organs in different species. If I am wrong on this point I welcome correction.

    As a result of his comment I assumed Flint was referring to the fish from which I evolved, which do indeed have gills.

    My apologies to Flint for my misunderstanding.

    However, I know it would be very much appreciated here if at some point you could find time to provide a more detailed account of how you arrived at the conclusion that the probability of life without an ID is too small to be effectively possible, and, indeed, what you find most persuasive about the ID case.

    Liz, I’ll do that. I have a unique perspective on this subject, since I was indoctrinated with Darwinian orthodoxy as a child. I still remember my mother preaching “ontogeny recapitulates phylogeny.” I memorized that phrase as a child.

    Once again Liz, I appreciate your invitation, and what I consider to be your good personal character. That’s not a schmooze, just an observation.

  16. Joe G,

    Well Lynn didn’t demonstrate anything. All she did was say “Hey these organelles look like bacteria” and she did not account for the nucleus.

    No, she didn’t say anything like that: See
    http://www.sciencedirect.com/science/article/pii/0022519367900793
    (note the theory to account for the origin of mitosis)
    more importantly see
    http://www.sciencemag.org/content/283/5407/1476.full
    what part of figures 1 and 2 do not constitute evidence for the endosymbiotic theory of mitochondrial origin?
    Also note that some bacteria, like the Planctomycetes, have their nuclear material enclosed in a double walled membrane.
    http://en.wikipedia.org/wiki/Planctomycetes

  17. We have a good idea of the kinds of differences between chimps and humans, and all involve fairly standard evolutionary mechanisms (naturla selection of single mutations, copy number variation and deletions), not the Beheian highly improbables.

    Let’s see a little evidence. The Darwinists have not be able to account for even one of the 192 human specific genes.

  18. Liz wrote:

    However, I know it would be very much appreciated here if at some point you could find time to provide a more detailed account of how you arrived at the conclusion that the probability of life without an ID is too small to be effectively possible, and, indeed, what you find most persuasive about the ID case.

    Gil responded:

    Liz, I’ll do that.

    Gil,

    Don’t forget to include the “simple probability calculations” that expose, according to you, the absurdity of the Darwinian mechanism.

    I find it necessary to remind you of this yet again, because several years’ experience has taught me that you will try to evade the question if at all possible.

  19. Gil,

    What’s quite striking about what you say is how it’s couched in such relentlessly religious terms. For example

    My initial foregone conclusion driven by ideology was that materialistic evolutionary theory just had to be true, almost by definition.

    But what we have here is a best-fit explanation proposed for a very large body of observations. Nothing in the process of fitting the model to the data is ideological, nor is the theory “materialistic”. It’s just a simple process of evidence leading to most-likely-accurate conclusions.

    I have a unique perspective on this subject, since I was indoctrinated with Darwinian orthodoxy as a child.

    What a suggestive phrase. Did your mother tell you to look both ways before crossing the street? If so, she was indoctrinating you with materialist orthodoxy. SHE might have thought she was concerned for your safety, but she was corrupting your soul! Or perhaps you are offended because scientific theories, unlike religious orthodoxies, do not represent themselves to be Absolute Truth, and keep changing as people learn more. In that case, little wonder you should find an undefined, untestable, unfalsifiable position to be more comfortable. It’s guaranteed evidence-proof, nothng to fear.

    (Incidentally, did humans evolve from fish? I would think humans and fish share a MUCH earlier common ancestor. Fish are quite modern. But as far as I know, that common ancestor was aquatic. Probably pre-Cambrian.)

  20. William J. Murray:
    llanitedave,

    Why say something like this? Obviously, you can’t support such a universal assertion; do you say it just to add significance and weight to what is obviously an a priori ideological position?

    Yes, I can support such a universal assertion — given enough time. But the short answer is that there is a universal consilience between all branches of natural science that together support the conclusion not only of the natural development of all biological species including ourselves, but also the physical development of the cosmos and the planet Earth itself in evolving the necessary physical, chemical, temporal and biological environment. I’ve seen nothing proposed in opposition to this idea that was not full of errors, incredulity, and ideology.

    I did actually have an a priori ideological position on the matter, once upon a time. But it was based on wishful thinking, not scientific fact. I’ve abandoned it since. Any ideological position I ever had on the matter doesn’t help your argument, because at one time it WAS your argument. It was wrong.

    I prefer to believe we are not.

    That belief, as far as I can tell, doesn’t (1) directly contradict any experiential facts or (2) create any internal logical contradictions or other unresolvable problems.

    I’m free to believe whatever I wish as long as I follow those two guidelines.

    Sure, as long as you don’t address any specifics. Of course, it also doesn’t require you to make any testable predictions or challenge any of your presumptions either, so you’re in the clear. It doesn’t push you to know anything.

    It begs the question, though, of why are you on a web site talking to people who adctually are interested in learning about nature in more depth and with more specificity. Is your ideological position really not so comfortable after all?

  21. William J. Murray:
    llanitedave,

    Why say something like this? Obviously, you can’t support such a universal assertion; do you say it just to add significance and weight to what is obviously an a priori ideological position?

    Yes, I can support such a universal assertion — given enough time. But the short answer is that there is a universal consilience between all branches of natural science that together support the conclusion not only of the natural development of all biological species including ourselves, but also the physical development of the cosmos and the planet Earth itself in evolving the necessary physical, chemical, temporal and biological environment. I’ve seen nothing proposed in opposition to this idea that was not full of errors, incredulity, and ideology.

    I did actually have an a priori ideological position on the matter, once upon a time. But it was based on wishful thinking, not scientific fact. I’ve abandoned it since. Any ideological position I ever had on the matter doesn’t help your argument, because at one time it WAS your argument. It was wrong.

    I prefer to believe we are not.

    That belief, as far as I can tell, doesn’t (1) directly contradict any experiential facts or (2) create any internal logical contradictions or other unresolvable problems.

    I’m free to believe whatever I wish as long as I follow those two guidelines.

    Sure, as long as you don’t address any specifics. Of course, it also doesn’t require you to make any testable predictions or challenge any of your presumptions either, so you’re in the clear. It doesn’t push you to know anything.

    It begs the question, though, of why are you on a web site talking to people who adctually are interested in learning about nature in more depth and with more specificity. Is your ideological position really not so comfortable after all?

  22. William J. Murray:
    llanitedave,

    Why say something like this? Obviously, you can’t support such a universal assertion; do you say it just to add significance and weight to what is obviously an a priori ideological position?

    Yes, I can support such a universal assertion — given enough time. But the short answer is that there is a universal consilience between all branches of natural science that together support the conclusion not only of the natural development of all biological species including ourselves, but also the physical development of the cosmos and the planet Earth itself in evolving the necessary physical, chemical, temporal and biological environment. I’ve seen nothing proposed in opposition to this idea that was not full of errors, incredulity, and ideology.

    I did actually have an a priori ideological position on the matter, once upon a time. But it was based on wishful thinking, not scientific fact. I’ve abandoned it since. Any ideological position I ever had on the matter doesn’t help your argument, because at one time it WAS your argument. It was wrong.

    I prefer to believe we are not.

    That belief, as far as I can tell, doesn’t (1) directly contradict any experiential facts or (2) create any internal logical contradictions or other unresolvable problems.

    I’m free to believe whatever I wish as long as I follow those two guidelines.

    Sure, as long as you don’t address any specifics. Of course, it also doesn’t require you to make any testable predictions or challenge any of your presumptions either, so you’re in the clear. It doesn’t push you to know anything.

    It begs the question, though, of why are you on a web site talking to people who adctually are interested in learning about nature in more depth and with more specificity. Is your ideological position really not so comfortable after all?

    eta: Sorry that there’s no link to the original exchange. There seems to be a frustrating bug in this software.

  23. Ian Musgrave: We have a good idea of the kinds of differences between chimps and humans, and all involve fairly standard evolutionary mechanisms (naturla selection of single mutations, copy number variation and deletions), not the Beheian highly improbables.

    Let’s see some evidence. None of 192 human specific genes have been given a detailed Darwinian account of how they arose.

  24. William J. Murray:
    llanitedave,

    Why say something like this? Obviously, you can’t support such a universal assertion; do you say it just to add significance and weight to what is obviously an a priori ideological position?

    I prefer to believe we are not.

    That belief, as far as I can tell, doesn’t (1) directly contradict any experiential facts or (2) create any internal logical contradictions or other unresolvable problems.

    I’m free to believe whatever I wish as long as I follow those two guidelines.

    Yes, I can support such a universal assertion — given enough time. But the short answer is that there is a universal consilience between all branches of natural science that together support the conclusion not only of the natural development of all biological species including ourselves, but also the physical development of the cosmos and the planet Earth itself in evolving the necessary physical, chemical, temporal and biological environment. I’ve seen nothing proposed in opposition to this idea that was not full of errors, incredulity, and ideology.

    I did actually have an a priori ideological position on the matter, once upon a time. But it was based on wishful thinking, not scientific fact. I’ve abandoned it since. Any ideological position I ever had on the matter doesn’t help your argument, because at one time it WAS your argument. It was wrong.

    Your freedom to believe what you wish, or what you prefer (either way, it’s an interesting and informative confession) is fine, as long as you don’t address any specifics. Of course, it also doesn’t require you to make any testable predictions or challenge any of your presumptions either, so you’re in the clear. It doesn’t push you to know anything.

    It begs the question, though, of why are you on a web site talking to people who adctually are interested in learning about nature in more depth and with more specificity. Is your ideological position really not so comfortable after all?

  25. Noam Ghish: Let’s see some evidence.None of 192 human specific genes have been given a detailed Darwinian account of how they arose.

    Is this a God of the Gaps argument in the making?

  26. llanitedave,

    Ian made an assertion, now let’s see him back it up.

    ID is an argument from knowledge not ignorance. We know that there are only three causes of motion: law, chance and design. Darwinian forces assert that only two causes are responsible for all the diversity of life, chance and law. We can exclude this hypothesis in principle. Organisms exhibit complex specified information and law and chance cannot produce CSI.

    I invite you llanitedave to discuss Darwinism with me over skype. My skype ID is noam.gish76

  27. Noam Ghish:
    llanitedave,

    I invite you llanitedave to discuss Darwinism with me over skype.My skype ID is noam.gish76

    Won’t happen. If the topic is worth arguing, then it’s worth arguing publically, in writing, referenceable, and with access to all the most knowledgable spectators and participants. I’m not in it to score rhetorical points, but if you really think you have something to teach me, then I’m sure all interested readers could share that learning as well.

  28. llanitedave,

    I’ve discussed Darwinism in person with people. There are so many things that they do not understand. You have to really sit down with them for about two hours and correct so many of their assertions before they begin to understand where they go wrong. That sort of thing would take about 8 hours in print, which is time I don’t have. I imagine you consider yourself an honest seeker for the truth. You can only seek truth if you submit your ideas to criticism. Writing and talking both have their pros and cons.

  29. Noam Ghish,

    In case you hadn’t read my reply above, here it is again.

    http://stke.sciencemag.org/cgi/content/full/sigtrans;2/89/pe59

    If you actually read the literature you would see there is a lot of work that goes into explaining these genes. Take the human specific TBC1D3 referenced in the paper you cite. It’s a variant of the RabGTPase family TBC that appears to have evolved along the hominoid-lineage 35 million years ago by segmental duplication.
    http://www.pnas.org/content/100/5/2507.short

    Gene duplication, that’s how these things arise.

  30. Ian Musgrave,

    We both agree that gene duplication happens what we do not agree on is whether gene duplication occurs by chance or design. I have a very difficult time believing that someone like you, Ian, who has been debating with IDers for a very long time have not yet understood that this is what we’re arguing. If gene duplication occurs by chance then you need to show how each mutation conferred a substantive survival coefficient on the organism and given the amount of time and population size such a mutation would have a strong chance of spreading through the population. You then have to show a step by step route from one gene to another gene, pointing out the mutations, their newly acquired functions, and their selective coefficients for each mutations. Given the fact that genes on average are 400 aa long, we can rest assured that no explanation from the Darwinists will ever be forthcoming.

  31. Noam Ghish,

    Well, we *know* gene duplication happens by chance at the roughly the same rate as single base mutations, the Kn/Ks ratios show evidence of natural selection. We see devono duplications of CYP450 enzymes in ppulation screens all the time.

    To show design, you would have to show an excess of BAM1 integration sites (or choose your favourite vector). Where is the evidence that gene duplicates have artificial integration sites?

  32. Ian Musgrave,

    As expected you failed to meet this challenge:

    If gene duplication occurs by chance then you need to show how each mutation conferred a substantive survival coefficient on the organism and given the amount of time and population size such a mutation would have a strong chance of spreading through the population. You then have to show a step by step route from one gene to another gene, pointing out the mutations, their newly acquired functions, and their selective coefficients for each mutations

    The Darwinists can point to no evidence to support their theory that ALL mutations are random.

  33. Noam Ghish,

    You don’t understand biology do you? You do know what neutral drift is? You do understand what Kn/Ks ratios mean? You do understand we can follow duplications/deletions in a range of model organisms?

    Meanwhile, where are your BAM1 sites? How is the Uplift Institute inserting CYP450 duplicates into modern day humans without us noticing? Where is _your_ proof that duplications are non-random?

  34. damitall: Here y’go
    Functional proteins from a random-sequence library.
    Keefe AD, Szostak JW.
    Source
    Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston 02114, USA.
    Abstract
    Functional primordial proteins presumably originated from random sequences, but it is not known how frequently functional, or even folded, proteins occur in collections of random sequences. Here we have used in vitro selection of messenger RNA displayed proteins, in which each protein is covalently linked through its carboxy terminus to the 3′ end of its encoding mRNA, to sample a large number of distinct random sequences. Starting from a library of 6 x 1012 proteins each containing 80 contiguous random amino acids, we selected functional proteins by enriching for those that bind to ATP. This selection yielded four new ATP-binding proteins that appear to be unrelated to each other or to anything found in the current databases of biological proteins. The frequency of occurrence of functional proteins in random-sequence libraries appears to be similar to that observed for equivalent RNA libraries.
    Nature. 2001 Apr 5;410(6829):715-8.

    The function is it sticks to something? What would that make, a sticky lump of ATP? Function? Hey I may be missing something that I don’t know about but this sounds like a symptom of a core flaw in evolutionary thinking – a massively colossal and unrealistic underestimation of the difficulty of assembling things, of putting things together, of making things work. Were the stickiness used in a multi step tightly constrained mechanical-chemical process or ‘machine’ you could say it had function. This sounds like throwing a bunch of shapes out and noting they come to rest in depressions in which they fit. Throw some long and short bits around and a long may land on a short like a lever – has a machine been built? Yes. Can this get to an aircraft carrier? ? Surely this is the trivial zero point of function.

  35. damitall:
    Joe, you’ll enjoy this, too.

    Selection and evolution of enzymes from a partially randomized non-catalytic scaffold
    Burckhard Seelig & Jack W. Szostak

    Nature: Vol 448| 16 August 2007| doi:10.1038/nature06032

    From the abstract: “Here we show that genuinely new
    enzymatic activities can be created de novo without the need for
    prior mechanistic information by selection from a naive protein
    library of very high diversity, with product formation as the sole
    selection criterion”

    “Without the need for prior mechanistic information”- that’s interesting

    Again, enzymatic activity is a chemical property. Could it be given a function, yes. Is it a functional protein, no, it’s a chemically active protein which, by itself can act only chemically. Maybe burning up a cell it was in?

  36. Butifnot,

    Surely this is the trivial zero point of function.

    You and gpuccio should get together on this. He and Durston are the ones defining dFSCI as absolutely objective measures based on this “trivial” but objective definition of function.

    If you wish to define function in terms of utility for an organism, you are in the realm of natural selection.

    But how do you know whether or not a particular kind of stickiness would have utility in some system or another? When you invoke the magic word “design” what do u mean? What does the designer do in order to figure out what has utility and what does not? Describe the steps a designer takes when designing.

    I could describe the steps taken by Edison for any number of inventions. When you say design, do you mean magic, or something analogous to what human designers do?

  37. Butifnot: Again, enzymatic activity is a chemical property. Could it be given a function, yes. Is it a functional protein, no, it’s a chemically active protein which, by itself can act only chemically. Maybe burning up a cell it was in?

    If you were to actually read the reference, butifnot, you’d see that these were RNA ligases, not noted for “burning up cells”
    Functional.
    n fact, enzymes are by definition functional
    And ATP binding is a very important function in the cell, exhibited by many proteins.
    If you think that binding of proteins to other molecules not important functions, don’t tell your immune system.

    It’s a common misconception amongst goddiditists that only an invariant, highly specified, one-change-and-it’s-dead, sequence of aminoacids can be associated with a given function. This is by no means always true, as that poster-boy of ID, Douglas Axe, has neatly demonstrated in Proc Natl Acad Sci U S A. 1996 May 28; 93(11): 5590–5594.

  38. Noam Ghish:
    llanitedave,

    I’ve discussed Darwinism in person with people.There are so many things that they do not understand.You have to really sit down with them for about two hours and correct so many of their assertions before they begin to understand where they go wrong.That sort of thing would take about 8 hours in print, which is time I don’t have.I imagine you consider yourself an honest seeker for the truth.You can only seek truth if you submit your ideas to criticism.Writing and talking both have their pros and cons.

    How can you submit your ideas to criticism if they aren’t being publically reviewed?

    I think, considering the amount of time you spend here, you DO have time to do it right. And judging by your interactions with knowledgable people here, there also seems plenty that YOU don’t understand.

    I would more expect an honest seeker for truth to search for truth where he can find it, and to gather as much exposure for the search as possible, rather than to closet himself with a person while limiting the exchange to vocal rhetoric.

  39. DLH suggested downloading “Mendel’s Accountant”:

    You may download the program at http://breaklinksourceforge.net/projects/mendelsaccount.

    I would recommend that users do NOT download this – I did and ended up with an unwanted browser hijacker that also destroyed the rather nice homely fireside theme I have on Firefox. I was able to remove it by using System Restore (I hope). It may be unrelated to Mendel’s Accountant, but this is the only download I did today.

    I’d also be wary of broad evolutionary conclusions drawn from population-genetic programs with invisible source, sponsored by ICR and with a population cap of 1000. Typically, 1000-or-fewer-member populations are doomed (though not the N=2 populations that came off the ark, it would seem).

  40. Ian Musgrave: You don’t understand biology do you?

    This is a nonargument and hence shows inability to understand what counts as logical.

    You do know what neutral drift is?

    Once again, asking a question is a non-argument. GD is incapable of building new genes. The odds are vanishingly small.

    You do understand what Kn/Ks ratios mean? You do understand we can follow duplications/deletions in a range of model organisms?

    Yes I know what the kn/ks ratio is. Sure, we can follow duplication/deletions in a range of organisms. How does that prove that all mutations are random? (by model do you mean computer generated organisms?)

    How is the Uplift Institute inserting CYP450 duplicates into modern day humans without us noticing?

    I’m not sure what you mean by Uplift Inst, maybe the intelligent designer. You can’t see an immaterial force. Can you see gravity? No. We see the effects of intelligence, not intelligence itself. I don’t know why anyone would expect to see God.

    I don’t see how Bam1 sites proves anything. Please elaborate.

    Where is _your_ proof that duplications are non-random?

    It’s the same proof that the Rosetta Stone was not created by erosion. 192 human specific genes, arising in 5 million years. Let’s calculate the odds of that. The average human gene is 400 aa long. Let’s be generous and imagine that only 300 of those aa are absolutely necessary which is probably not true. So what’s 20^300, that’s 1 in 10^360? Well beyond Dembski’s probability bound of 1 in 10^150. There’s my proof, now let’s see yours.

    For your proof I would like to see a detailed account, first of the names of the amino acids of the genes that you’re trying to explain and their sequence. Second, I would like to see the function of the gene when it only had 20 amino acids, then 21, then 22. I would like to see reasonable statistics for how such a gene could overcome the odds against its coming into existence by chance.

    Ian, I’ve asked you for this evidence three times. There is no point in debating with someone who will not answer questions. I invite you to participate with me in a broad discussion regarding atheism and physicalism through Skype. Skype ID: noam.gish76

  41. llanitedave: How can you submit your ideas to criticism if they aren’t being publically reviewed? I would more expect an honest seeker for truth to search for truth where he can find it, and to gather as much exposure for the search as possible, rather than to closet himself with a person while limiting the exchange to vocal rhetoric

    both writing and speaking have their pros and cons.
    I would more expect an honest seeker for truth to search for truth where he can find it, and to gather as much exposure for the search as possible, rather than to closet himself with a person while limiting the exchange to written rhetoric.

    judging by your interactions with knowledgable people here, there also seems plenty that YOU don’t understand.

    Such assertions have no place in logical argument. To prove someone does not understand something you first have to show that they’re wrong on a certain issue. Since it’s very difficult to prove anything in philosophy beyond a shadow of a doubt, one might as well not even bother.

    .

  42. Lizzie noted that

    … to address the plausibility of Lizzie-to-Lucy in 129,000 generations, what we need to find out is:

    what the variance generation mechanisms are
    what environmental conditions might have favoured the differences between Lucy and me.

    We also need to have a pretty good idea of what is required to get from Lucy to Lizzie at the relevant level of analysis. Intuitive comparisons of gross morphology don’t do the trick.

  43. RBH:
    Lizzie noted that

    We also need to have a pretty good idea of what is required to get from Lucy to Lizzie at the relevant level of analysis. Intuitive comparisons of gross morphology don’t do the trick.

    Yes, indeed. Specifically genetic variations involved in brain development. There are some potentially interesting candidates.

  44. Noam Ghish,

    ..192 human specific genes, arising in 5 million years. Let’s calculate the odds of that. The average human gene is 400 aa long. Let’s be generous and imagine that only 300 of those aa are absolutely necessary which is probably not true. So what’s 20^300, that’s 1 in 10^360? Well beyond Dembski’s probability bound of 1 in 10^150. There’s my proof, now let’s see yours.

    Once again, lets go back to the human specific TBC1D3 referenced in the paper you cited originally.
    http://stke.sciencemag.org/cgi/content/full/sigtrans;2/89/pe59
    TBC1D3 is a variant of the RabGTPase family TBC that appears to have evolved along the hominoid-lineage 35 million years ago by segmental duplication.
    http://www.pnas.org/content/100/5/2507.short
    Importantly, it’s human specific in that there has been a significant increase in *copy number*. Humans have 6 copies of the TBC1D3, chimps and orang-outangs have only two copies of this gene (go to PubMed protein, and do a BLAST search, then a similarity tree on BAK63846.1 TBC1 domain family member 3 [Pan troglodytes]).

    Here’s the first 60 amino acids of the Human vs chimp TBC1D3
    Query 1 MDVVEVAGSWWAQEREDIIMKYEKGHRAGLPEDKGPKPFGRYNNNVDHLGIVHETELPPL 60
    MDVVEVAGSWWAQEREDIIMKYEKGHRAGLPEDKGPKPF YNNNVDHLGIVHETELPPL
    Sbjct 1 MDVVEVAGSWWAQEREDIIMKYEKGHRAGLPEDKGPKPFRSYNNNVDHLGIVHETELPPL 60

    Your “probability” calculations are completely meaningless, we know gene duplications occur, we know the rates they occur at. You are carrying around at least a couple of gene duplications your parents didn’t have. Mutations that expand the copy numbers of the CYP450 genes are well known in medicine because they have important impacts on drug metabolism.

    Indeed if you look at the vast majority of “human specific” genes (and there was only 168 referenced in that paper), the story is the same one as for TBC1D3, where a human variant of an existing protein is expanded (in some cases not even expanded).
    http://www.broadinstitute.org/mammals/alpheus/data/human_specific_genes.txt

    Choosing a random gene from the above list, ENSG00000101446, this is the protein Kinase inhibitor SPINT3, a member of the KU superfamily. There are highly similar SPINT3 genes (better than 95% similarity) in chimps and orang-outangs, and very similar ones in other primates.

    Same for ENSG00000204919 (a proline rich protein of as yet unassigned function), and so on.

    There are three proteins that *are* unique to humans, which are frame shifts of genes that were present in the common ancestor of chimps and humans.
    http://genome.cshlp.org/content/19/10/1752.full

    Again, your “probability” calculations are irrelevant to the origin of these genes.

    Second, I would like to see the function of the gene when it only had 20 amino acids, then 21, then 22. I would like to see reasonable statistics for how such a gene could overcome the odds against its coming into existence by chance.

    Since no new gene originates this way, why would you like to see this?

    You conception of how new genes arise is a fantasy, which has no relationship to real biology.

  45. Petrushka:
    Butifnot,

    You and gpuccio should get together on this. He and Durston are the ones defining dFSCI as absolutely objective measures based on this “trivial” but objective definition of function.

    If you wish to define function in terms of utility for an organism, you are in the realm of natural selection.

    But how do you know whether or not a particular kind of stickiness would have utility in some system or another? When you invoke the magic word “design” what do u mean? What does the designer do in order to figure out what has utility and what does not? Describe the steps a designer takes when designing.

    I could describe the steps taken by Edison for any number of inventions. When you say design, do you mean magic, or something analogous to what human designers do?

    I think there is a fundamental error at the base of much evolutionary thinking – a ‘confusion’ between what something is and what it does. Utility – that’s the point, not that something is sticky, but how the stickiness is ‘used’. Stickiness = lump, stickiness as part of a system could be endlessly useful.

  46. damitall,

    Damitall you’re way off the page. Binding proteins is exactly nothing, let alone an immune “system”. Enzymes are what they are, to have function they have to be used.

  47. Noam Ghish: both writing and speaking have their pros and cons.
    I would more expect an honest seeker for truth to search for truth where he can find it, and to gather as much exposure for the search as possible, rather than to closet himself with a person while limiting the exchange to written rhetoric.

    Such assertions have no place in logical argument.To prove someone does not understand something you first have to show that they’re wrong on a certain issue.Since it’s very difficult to prove anything in philosophy beyond a shadow of a doubt, one might as well not even bother.

    That also applies to your claimed attempts to correct the misunderstandings of others. I have little interest in discussion with one who cannot separate his philosophy from empirical study.

  48. Pingback: Uncommon Descent | Our Gil Dodgen now contributes at Elizabeth Liddle’s Skeptical Zone

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