Darwinism Natural selection

The Elephant in the Room

Spread the love

We are regularly told by proponents of evolutionary theory, from Darwin right up to the present day, that purely natural processes, such as random mutations and natural selection, have the ability to build, construct, fashion, purpose and create remarkable machines. Machines that rival, and in many cases surpass, our most advanced technologies.

We are assured in no uncertain terms that such natural processes have this great creative power. Yet when examples are sought, we are invariably given examples that either did not come about through purely natural processes (see Berra’s Blunder), or examples that are trivial in scope. But nothing that even comes close to verifying the grand claims of the evolutionary creation story.

There is a huge elephant in the room.

Why, if evolutionary processes are so incredibly adept at producing remarkable technologies that surpass our capabilities, do we not see such evolutionary processes being put to good use on a regular basis?

All around the world, every day, millions upon millions of new inventions, designs, projects, programs, and other creations are being pursued. Yet the most awesome creative force of all, so we are assured, is for some reason notably absent. Occasionally someone will claim that evolutionary processes were responsible for creating this or that product (the NASA antenna being the example most often trotted out, even though it is not a proper example of purely natural evolutionary processes). Sometimes someone will assert that an “evolutionary algorithm” has produced something mildly interesting (like the questionable and potentially flawed Avida results touted several years ago in Nature). But by and large, this alleged remarkable creative force is absent, irrelevant, a “no show,” when it comes to actually creating things in the real world.

Now the evolutionary proponent will no doubt argue that the reason is simple: not enough time. Easily impressed with all the zeroes in a number like the billions of years of Earth’s history, the evolutionist reposes faith in the power of deep time to take what is clearly an impotent process in the short term and turn it into the most potent creative force in the long term. But when the actual numbers are reviewed and the actual requirements for construction of functional creations assessed, it becomes clear that those zeroes in the age of the Earth or even the age of the universe are but a rounding error and are unhelpful in addressing the larger issue.

To be sure, a trial-and-error process like random mutations and natural selection can occasionally do something interesting – if there is a large enough population and a strong enough selective pressure. Behe has spent time searching for this “edge of evolution,” while in stark contrast most evolutionists never even bother thinking about what evolutionary processes can actually accomplish in the real world, simply taking it as an article of faith that “with evolution nothing is impossible.”

More to the point, such minor changes even when they do show up do not constitute evidence for the larger evolutionary claims. Particularly when many of the alleged examples of evolution’s power turn out to be, on closer examination, examples of breaking a machine, rather than building it.

So the elephant in the room remains. Design is a critical aspect of our modern lives. Design occurs across the spectrum of disciplines and across the globe on a near constant basis. Yet the most potent creative force that allegedly ever existed, that of evolutionary mechanisms, is noticeable in its near complete absence – dabbling at the fringes, only occasionally participating, rarely influencing, never doing much of any real consequence.

We might be forgiven for wondering if perhaps this is all the evolutionary mechanisms have to contribute.

Or all that they ever did.

366 Replies to “The Elephant in the Room

  1. 1
    bw says:

    just gonna to leave this here (please ignore the rather annoying narrator – the action starts around 40 seconds)

    Another example in nature that proves the amazing power of random mutations and natural selection.

    “Evolution at its finest” to quote a knowledgeable youtube commenter.

    You only have to look at examples like this, and there are many, and the creative power of mutation + selection becomes most apparent.

    To not see it one must be blind, blinkered if you will.

    You needn’t spend a second thought to the process really when it is so obvious in the first place.
    In fact thinking about such things should be avoided at all costs! Thoughts as we all know can lead to doubts.. and nobody wants that burden.

  2. 2
    Box says:

    Blind unreasonable random stuff that creates inconceivably complex organisms. Disjoint parts that self-organize into larger living wholes for no reason whatsoever.

    Can anyone come up with a stupider, more counterintuitive idea?

  3. 3
    Mapou says:

    Box:

    Can anyone come up with a stupider, more counterintuitive idea?

    No, of course. The stupidity of it all is what boggles the mind. Sometimes, I wonder if the human species has not been infected with stupid memes by alien mind snatchers who enjoy spreading division just for the sake of it.

  4. 4
    Cross says:

    Mapou @ 3

    “I wonder if the human species has not been infected with stupid memes by alien mind snatchers”

    Tom Cruise would tell you it was the evil galactic ruler called Xenu. 😉

    Cheers

  5. 5
    Cross says:

    Box @ 2

    You and I must just lack imagination, here is how evolution created the Bombardier Beetle from http://www.talkorigins.org/faqs/bombardier.html

    “Gish is wrong; a step-by-step evolution of the bombardier system is really not that hard to envision. The scenario below shows a possible step-by-step evolution of the bombardier beetle mechanism from a primitive arthropod.

    Quinones are produced by epidermal cells for tanning the cuticle. This exists commonly in arthropods. [Dettner, 1987]

    Some of the quinones don’t get used up, but sit on the epidermis, making the arthropod distasteful. (Quinones are used as defensive secretions in a variety of modern arthropods, from beetles to millipedes. [Eisner, 1970])

    Small invaginations develop in the epidermis between sclerites (plates of cuticle). By wiggling, the insect can squeeze more quinones onto its surface when they’re needed.

    The invaginations deepen. Muscles are moved around slightly, allowing them to help expel the quinones from some of them. (Many ants have glands similar to this near the end of their abdomen. [Holldobler & Wilson, 1990, pp. 233-237])

    A couple invaginations (now reservoirs) become so deep that the others are inconsequential by comparison. Those gradually revert to the original epidermis.

    In various insects, different defensive chemicals besides quinones appear. (See Eisner, 1970, for a review.) This helps those insects defend against predators which have evolved resistance to quinones. One of the new defensive chemicals is hydroquinone.

    Cells that secrete the hydroquinones develop in multiple layers over part of the reservoir, allowing more hydroquinones to be produced. Channels between cells allow hydroquinones from all layers to reach the reservior.

    The channels become a duct, specialized for transporting the chemicals. The secretory cells withdraw from the reservoir surface, ultimately becoming a separate organ.
    This stage — secretory glands connected by ducts to reservoirs — exists in many beetles. The particular configuration of glands and reservoirs that bombardier beetles have is common to the other beetles in their suborder. [Forsyth, 1970]

    Muscles adapt which close off the reservior, thus preventing the chemicals from leaking out when they’re not needed.

    Hydrogen peroxide, which is a common by-product of cellular metabolism, becomes mixed with the hydroquinones. The two react slowly, so a mixture of quinones and hydroquinones get used for defense.

    Cells secreting a small amount of catalases and peroxidases appear along the output passage of the reservoir, outside the valve which closes it off from the outside. These ensure that more quinones appear in the defensive secretions. Catalases exist in almost all cells, and peroxidases are also common in plants, animals, and bacteria, so those chemicals needn’t be developed from scratch but merely concentrated in one location.

    More catalases and peroxidases are produced, so the discharge is warmer and is expelled faster by the oxygen generated by the reaction. The beetle Metrius contractus provides an example of a bombardier beetle which produces a foamy discharge, not jets, from its reaction chambers. The bubbling of the foam produces a fine mist. [Eisner et al., 2000]

    The walls of that part of the output passage become firmer, allowing them to better withstand the heat and pressure generated by the reaction.

    Still more catalases and peroxidases are produced, and the walls toughen and shape into a reaction chamber. Gradually they become the mechanism of today’s bombardier beetles.

    The tip of the beetle’s abdomen becomes somewhat elongated and more flexible, allowing the beetle to aim its discharge in various directions.”

    Simple really, isn’t it? 😉

    Cheers

  6. 6
    ppolish says:

    The snake that had “walking stick” tail didn’t do as well. Birds ignored it. Now it is shaping those sticks into a bird feeder. Randomly, purposelessly.

  7. 7
    humbled says:

    Mapou @ 3
    I agree, in fact I recently rewatched a movie called “Idiocracy”. In it the population have dumbed down over a period of time leaving morons behind. It is obviously a comedy and when I first watched it many years ago I didn’t think much of it. These days I recognise the prophetic message as well as this very fate rearing its ugly head.

    http://www.imdb.com/title/tt0387808/?ref_=nv_sr_1

  8. 8
    Box says:

    Cross #5,

    My lack of imagination bothers me. I cannot even imagine how blind unreasonable random stuff brings one cell into existence. And even if this happened – for no reason at all – I cannot envision why such a cell doesn’t fall apart the very next moment.
    My problem is that in my understanding of materialism it offers absolutely no cause – no reason, no force – that creates and sustains life. And in my book one cannot explain an effect without a cause.

  9. 9
    bornagain77 says:

    As to Avida, here is a recent video that shows that Avida, when using realistic biological parameters as its default settings, instead of using highly unrealistic default settings as it currently does, actually supports Genetic Entropy instead of Darwinian evolution:

    Biological Information – Mendel’s Accountant and Avida 1-31-2015 by Paul Giem
    https://www.youtube.com/watch?v=cGd0pznOh0A&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ&index=14

    Of related note:

    Panda’s Thumb Richard Hoppe forgot about Humpty Zombie – April 15, 2014
    Excerpt: I discovered if you crank up Avida’s cosmic radiation parameter to maximum and have the Avida genomes utterly scrambled, the Avidian organisms still kept reproducing. If I recall correctly, they died if the radiation was moderate, but just crank it to the max and the creatures come back to life!
    This would be like putting dogs in a microwave oven for 3 days, running it at full blast, and then demanding they reproduce. And guess what, the little Avida critters reproduced. This little discovery in Avida 1.6 was unfortunately not reported in Nature. Why? It was a far more stupendous discovery! Do you think it’s too late for Richard Hoppe and I to co-author a submission?
    Hoppe eventually capitulated that there was indeed this feature of Avida. To his credit he sent a letter to Dr. Adami to inform him of the discovery. Dr. Adami sent Evan Dorn to the Access Research Network forum, and Evan confirmed the feature by posting a reply there.
    http://www.creationevolutionun.....idcs/?p=90

    Of supplemental note:

    LIFE’S CONSERVATION LAW – William Dembski – Robert Marks – Pg. 13
    Excerpt: (Computer) Simulations such as Dawkins’s WEASEL, Adami’s AVIDA, Ray’s Tierra, and Schneider’s ev appear to support Darwinian evolution, but only for lack of clear accounting practices that track the information smuggled into them.,,, Information does not magically materialize. It can be created by intelligence or it can be shunted around by natural forces. But natural forces, and Darwinian processes in particular, do not create information. Active information enables us to see why this is the case.
    http://evoinfo.org/publication.....ation-law/

    Evolutionary Synthesis of Nand Logic: Dissecting a Digital Organism – Dembski – Marks – Dec. 2009
    Excerpt: The effectiveness of a given algorithm can be measured by the active information introduced to the search. We illustrate this by identifying sources of active information in Avida, a software program designed to search for logic functions using nand gates. Avida uses stair step active information by rewarding logic functions using a smaller number of nands to construct functions requiring more. Removing stair steps deteriorates Avida’s performance while removing deleterious instructions improves it.
    http://evoinfo.org/publication.....gic-avida/

  10. 10
    bornagain77 says:

    As to the more sophisticated programs that are used in engineering:

    Applied Darwinism: A New Paper from Bob Marks (W. Dembski) and His Team, in BIO-Complexity – Doug Axe – 2012
    Excerpt: Furthermore, if you dig a bit beyond these papers and look at what kinds of problems this technique (Steiner Tree) is being used for in the engineering world, you quickly find that it is of extremely limited applicability. It works for tasks that are easily accomplished in a huge number of specific ways, but where someone would have to do a lot of mindless fiddling to decide which of these ways is best.,, That’s helpful in the sense that we commonly find computers helpful — they do what we tell them to do very efficiently, without complaining. But in biology we see something altogether different. We see elegant solutions to millions of engineering problems that human ingenuity cannot even begin to solve.
    http://www.evolutionnews.org/2.....58591.html

    There is absolutely nothing surprising about the results of these algorithms. The computer is programmed from the outset to converge on the solution. The programmer designed to do that. What would be surprising is if the program didn’t converge on the solution. That would reflect badly on the skill of the programmer. Everything interesting in the output of the program came as a result of the programmer’s skill-the information input. There are no mysterious outputs.
    Software Engineer – quoted to Stephen Meyer

    Climbing the Steiner Tree–Sources of Active Information in a Genetic Algorithm for Solving the Euclidean Steiner Tree Problem – 2012 – Winston Ewert, William A Dembski, Robert J Marks II
    http://bio-complexity.org/ojs/.....le/view/50

    A.I. Has Grown Up and Left Home – Dec. 19, 2013
    Excerpt: For example, genetic approaches represent algorithms with varying parameters as chromosomal “strings,” and “breed” successful algorithms with one another. These approaches do not improve through better understanding of the problem. All that matters is the fitness of the algorithm with respect to its environment—in other words, how the algorithm behaves. This black-box approach has yielded successful applications in everything from bioinformatics to economics, yet one can never give a concise explanation of just why the fittest algorithm is the most fit.
    Neural networks are another successful subsymbolic technology, and are used for image, facial, and voice recognition applications. No representation of concepts is hardcoded into them, and the factors that they use to identify a particular subclass of images emerge from the operation of the algorithm itself.
    http://nautil.us/issue/8/home/.....-left-home

    Why there is a limit to what computers can do is stated here:

    Algorithmic Information Theory, Free Will and the Turing Test – Douglas S. Robertson
    Excerpt: The basic problem concerning the relation between AIT (Algorithmic Information Theory) and free will can be stated succinctly: Since the theorems of mathematics cannot contain more information than is contained in the axioms used to derive those theorems, it follows that no formal operation in mathematics (and equivalently, no operation performed by a computer) can create new information.

    “For example, the famous “Turing test” for artificial intelligence could be defeated by simply asking for a new axiom in mathematics. Human mathematicians are able to create axioms, but a computer program cannot do this without violating information conservation. Creating new axioms and free will are shown to be different aspects of the same phenomena: the creation of new information.”
    http://cires.colorado.edu/~dou...../info8.pdf

    The Limits Of Reason – Gregory Chaitin – 2006
    Excerpt: an infinite number of true mathematical theorems exist that cannot be proved from any finite system of axioms.,,,
    http://www.umcs.maine.edu/~chaitin/sciamer3.pdf

    Kurt Gödel – Incompleteness Theorem – video
    https://vimeo.com/96082228

    Alan Turing & Kurt Godel – Incompleteness Theorem and Human Intuition – video
    https://vimeo.com/92387854

    “Either mathematics is too big for the human mind or the human mind is more than a machine”
    Kurt Gödel

    And despite this severe limit on natural processes to ever create algoritmic infomation, there are found to be ‘countless thousands of intricate algorithms’ in life:

    To the skeptic, the proposition that the genetic programmes of higher organisms, consisting of something close to a thousand million bits of information, equivalent to the sequence of letters in a small library of one thousand volumes, containing in encoded form countless thousands of intricate algorithms controlling, specifying and ordering the growth and development of billions and billions of cells into the form of a complex organism, were composed by a purely random process is simply an affront to reason. But to the Darwinist the idea is accepted without a ripple of doubt – the paradigm takes precedence!”
    Michael Denton, Evolution: A Theory In Crisis

    Verse and Music:

    John 1:1-4
    In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind.

    Kutless Performs “In Jesus’ Name” Acoustic and Unplugged
    https://www.youtube.com/watch?v=GDwjTURYZxs

  11. 11
    Cross says:

    Box @ 8

    I bothers me too, but I think the problem is we don’t have the right “religion”, people of the materialist evolution religion (or Evo of the gaps)take this stuff “by faith”.

    Cheers

  12. 12
    Cross says:

    ppolish @ 6

    And the snake with the “bird like” tail soon went extinct, it kept eating itself. 😉

    Cheers

  13. 13
    Cross says:

    BA77 @ 10

    Enjoyed the Kutless video.

    Cheers

  14. 14
    JDH says:

    bw @ 1

    It occurs to me that your comment may be sarcasm. If it is, it sounds too much like a real darwinist. I have to admit though I did not think of that before I responded with the following.

    Another example in nature that proves the amazing power of random mutations and natural selection.

    Congratulations! You are a winner for the “cyclic reasoning, video does nothing to support your conclusions unless you assume the premise” award.

  15. 15
    Me_Think says:

    Too bad we don’t know who the ID designer is and how he/she/it accomplishes creation and maintenance of billions of cellular processes. We could revolutionize design with such omnipotent power.

  16. 16
    JDH says:

    Me_Think – Speak for yourself, I happen to know who the ID designer is. He does not share his power with people who wouldn’t have the foggiest idea what to do with it.

  17. 17
    rvb8 says:

    Nevertheless, Evolution remains a fully evidence based scientific theory, along the lines of Germ Theory, Gravitation, and Relativity. Harping on about its failings (there are many, as you would expect, missing links in this evolving field)only begs the question; What do you have? Behe, Dembsky (gone missing apparently), No Free Lunch(aah, down home folksy wisdom), Wells (Heh!) and…….

    All these words to say, “I simply can’t believe it…”
    So what, do science or shut up! Can you not get this simple idea through your collective dense skulls; Science depends upon results, evidence, and promising areas for further research, all of which Evolution has, all of which creationism doesn’t.

    P.S. I’ve given up on using the pointless title ID as it really just means Christian Creationism.

    According to Phillip Johnson, one of your High Priests, he believes that for all of Evoution’s faults it is at least a fully worked out science; he is of course fully correct!

  18. 18
    Cross says:

    rvb8 @ 17

    So the creation story of the Bombardier Beetle is science?

    I would have used it as a bed time story when my kids were younger except there is far too much invagination going on and I fear my constant laughing would keep them awake.

    Cheers

  19. 19
    Me_Think says:

    JDH @ 16

    Speak for yourself, I happen to know who the ID designer is. He does not share his power with people who wouldn’t have the foggiest idea what to do with it

    Well, now look who is admitting ID is creationism.

  20. 20
    Joe says:

    Me Think

    Too bad we don’t know who the ID designer is and how he/she/it accomplishes creation and maintenance of billions of cellular processes.

    Geez computer programmers maintain billions of ones and zeros

    We could revolutionize design with such omnipotent power.

    As if knowing how something was done means we could do it.

  21. 21
    Joe says:

    rvb8

    Nevertheless, Evolution remains a fully evidence based scientific theory

    Nice equivocation. Unguided evolution can’t even be tested.

    Do science or shut up, rvb8- first you have to demonstrate that you understand what science is.

  22. 22
    Mapou says:

    Me_Think:

    Too bad we don’t know who the ID designer is and how he/she/it accomplishes creation and maintenance of billions of cellular processes. We could revolutionize design with such omnipotent power.

    There is nothing really mysterious about intelligent design. Take modern software design, for example. It is a hierarchical process: complex objects are made of simpler objects. It’s called design through inheritance. This can lead to extremely complex systems over time. The same thing is observed in nature. Complex organisms are organized hierarchically. I have no problem sharing genetic material with apes, birds, fish, plants, bugs and germs. We, humans, are the pinnacle of genetic design and engineering.

    And why must genetic design require omnipotent power, pray tell? I can easily imagine an extremely advanced civilization designing life on earth. I can imagine the human species doing the same thing over a couple of hundred millions years. (We, too, are gods.)

    One more thing. Instead of continually harping on who the designer is, like a neurotic parrot, why don’t you tell us how life on earth originated according to materialism, so we can all marvel at your great wisdom? How did the first self-replicating genome come about? Let’s hear it, Mr. Smartypants.

  23. 23
    rvb8 says:

    Joe,

    Science is that which gives promising answers to questions of natural phenomena. Unlike creationism it requires no faith, still less your tiresome emotional baggage joe.

    A dictionary might help Joe; in what way is ‘Evolution remains a fully evidence based scientific theory’, equivocation? There is no ambiguity in my statement. Perhaps I should understand science more deeply, however you should start with what words mean.

    One more thing Joe, computer programmers do not maintain billions of ones and zeros, they are maintained by electrons which when allowed to pass a gate, or not, are given the purely man made notation of a one or a zero. That is, physical understandable, testable material things maintain the ones and zeros, these in turn create the information you stand so pompously, in stupefied, knuckle dragging awe of.

  24. 24
    Mapou says:

    Is there a single evidence for Darwinian evolution that cannot be easily explained by intelligent design?

    The inconvenient truth is that Darwinian evolution cannot explain complex functional systems. Such systems require intelligent planning. Even children can understand this after playing with Lego blocks.

  25. 25
    Mapou says:

    I’m getting tired of a bunch of brain-dead Darwinists acting like they invented science and that science belongs to them. Give it a rest. It’s getting old and it shows you as a bunch of arrogant morons.

  26. 26
    Cross says:

    rvb8 @ 23

    “Unlike creationism it requires no faith”

    Lol, the creation of the Bombardier Beetle has so many gaps that you have to “believe” evolution magically filled you do indeed require a lot of faith.

    Faith in the evo-of-the-gaps is strong in this one.

    Cheers

  27. 27
    Cross says:

    rvb8 @ 23

    “Computer programmers do not maintain billions of ones and zeros, they are maintained by electrons which when allowed to pass a gate, or not, are given the purely man made notation of a one or a zero. That is, physical understandable, testable material things maintain the ones and zeros, these in turn create the information you stand so pompously, in stupefied, knuckle dragging awe of.”

    The programmers (Intelligent agents) create the Information, the physical system only stores the representation of the information according to the way the designers created it.

    Joe, I’m guessing rvb8 does not get the irony of this.

    Cheers

  28. 28
    Joe says:

    rvb8- unguided evolution doesn’t have any answers. Also ID is not anti-evolution- ID is OK with evolution by intelligent design- tat is organisms were intelligently designed to evolve. No one is arguing about mere evolution.

    BTW programmers put those ones and zeros on the buss lines and they control the gates. And unlike you I understand what information is.

  29. 29

    The only logical way in which natural selection might make some sense vis-à-vis to random mutations is this:

    Organisms that have suffered no mutations (or far fewer mutations then others) have better chances of survival.

    Let’s make it even clearer for evolutionists:

    The organisms with no mutations are selected for survival.

    And let’s do the thinking for them also (I don’t trust them as being able to logically connect premises to conclusions):

    There is no Darwinian evolution.

    And no, I did not appeal to the Bible to reach this conclusion.

    It is just simple, 5 years old kids’ logic. Elementary my dear Watson!

  30. 30
    Eric Anderson says:

    Cross @5:

    It is embarrassing to see Mark Isaak post his made up story as though it constituted some kind of explanation. Reminds me of Matzke’s “explanation” for the bacterial flagellum. If I didn’t know better, I would think these kinds of writings were parodies, rather than the serious attempts to reassure the faithful that they are.

    Berlinski in his most famous essay had to remind the reader that the descriptions of the evolutionary storyline were not a parody, but the real deal.

    I’m looking at a tome of Kipling’s just-so stories on my shelf.

    Isaak is in good company.

  31. 31
    Mark Frank says:

    Why, if evolutionary processes are so incredibly adept at producing remarkable technologies that surpass our capabilities, do we not see such evolutionary processes being put to good use on a regular basis?

    They are not incredibly adept. They are very slow and unpredictable. But given enough time they produce solutions. Creating a solution intentionally is much quicker and you can predict what you are going to get. You reproduce the same old argument about there not being enough time for evolution to do the job.   Why dress it up in an argument about us not using evolutionary processes for ourselves?

  32. 32
    Cross says:

    Eric Anderson @ 30

    Yes, perhaps Isaak has missed his calling as a writer of children’s stories like Kipling.

    In any case, maybe even rvb8 is embarrassed as he seems to be avoiding the story altogether.

    Cheers

  33. 33
    rvb8 says:

    Cross,

    Why the fixation on the complexity of the Bombardier beetle? I thought you lot were just as flabbergasted by the infamous flagellum. You look at DNA and look no further. Your argument seems to be one of refusing to follow where the evidence leads, or more sadly trying to get everyone else to become members of your anticuriosity league.

    All of the steps you describe (and no doubt many you missed) seem quite scientific to me, add to this that powerful weeder out of uselessness, Natural Selection, and the steps seem probable.

    Using sarcastic language does not an argument make.

  34. 34
    bornagain77 says:

    as to: “All of the steps you describe (and no doubt many you missed) seem quite scientific to me, add to this that powerful weeder out of uselessness, Natural Selection, and the steps seem probable.

    So ‘you’, (although there is no ‘you’ in atheistic materialism), subjectively think that it ‘seems’ scientific to you? and also ‘you’ subjectively think the steps ‘seem probable’?

    But that is the entire problem that Eric has pointed out. You have no actual empirical evidence that the steps actually are probable or that molecular machines that rival and surpass man-made machines can be had by unguided material processes.
    Your subjective opinion is just that, your own personal subjective opinion! (i.e. an unsubstantiated belief, a position of blind faith in the power deep time and chance to work miracles that would make the blind faith suicide bombers seem rational.)

  35. 35
    sparc says:

    InVivoVeritas:
    It is just simple, 5 years old kids’ logic.

    Obviously.

  36. 36
    Cross says:

    rvb8 @ 33

    Why the fixation on the complexity of the Bombardier beetle?
    Because its defence mechanism is a good example of irreducible complexity.

    I thought you lot were just as flabbergasted by the infamous flagellum.
    No, I’m impressed by all the creation.

    You look at DNA and look no further.
    Actually I’m a fan of science, have been for many years, just not a fan of what passes for science these days.

    Your argument seems to be one of refusing to follow where the evidence leads, or more sadly trying to get everyone else to become members of your anticuriosity league.
    I’m happy to follow where real evidence leads, as BA77 has pointed out above, Isaak’s story contains no actual empirical evidence.

    All of the steps you describe (and no doubt many you missed) seem quite scientific to me,
    Disturbing.

    add to this that powerful weeder out of uselessness, Natural Selection, and the steps seem probable.
    Really disturbing.

    Using sarcastic language does not an argument make.
    And neither do just-so stories with no evidence.

    Cheers

  37. 37
    bw says:

    With regards to the Bombardier beetle and many other examples like it; I have no idea how anyone who claims to be interested in the sciences or worse still an actual paid scientist could ever be even remotely satisfied with the number of maybe/possibly/might/could ‘s that need to be invoked to explain what we observe in nature.
    That just doesn’t cut the mustard for me – yet for seeking better explanations I get labelled as anti-science 🙁
    Even back when I was in education studying Maths and the Sciences, if ever I was told something was true “just because” I was never happy to accept those and am still the same now.

  38. 38
    Eric Anderson says:

    Mark Frank @31:

    Precisely on cue and as predicted, I said the evolutionary response would be deep time. The reason we don’t see evolution working at a practical level all around us today is the lack of time. Sure, I understand that is the theory. But it is not an explanation of how any of it could actually work, just an appeal to the idea that it takes a lot of time. Which is neither an explanation nor evidence, but rather just a restatement of the theory.

    Furthermore, deep time, as I also noted, is but a rounding error. People who don’t think through the issues carefully are easily impressed with millions or even billions of years. Yet such timeframes are completely impotent to produce what is alleged. And deep time certainly doesn’t explain the utterly critical how of the creation’s production, other than the facile and naive “Well, you know, it takes a long time.”

    Traditional evolutionary theory is very convenient in that the alleged wonderful changes always seem to be occurring just outside of our ability to observe. Gould even made a name for himself by centralizing this idea in his punctuated equilibrium concept: evolution generally happens just out of reach of our observations. Then when a skeptical person points out the lack of observational evidence, the evolutionist says, in effect, “Of course there isn’t observational evidence. Evolution usually happens when and where we can’t observe it. We shouldn’t expect any observational evidence. That is just what my theory predicts!”

  39. 39
    Eric Anderson says:

    All of the steps you describe (and no doubt many you missed) seem quite scientific to me, add to this that powerful weeder out of uselessness, Natural Selection, and the steps seem probable.

    And therein lies one of the key differences.

    Some of us would like actual evidence, an actual biology-based and engineering-based explanation. Even a semi-detailed approach would be nice.

    Others are easily impressed with vague generalities (notice none of the steps included actual biochemical or engineering-quality analysis) and general assertions. Stuff happens and natural selection keeps the good stuff.

    Sure.

    The Great Evolutionary Explanation:

    Stuff Happens.

  40. 40
    Mark Frank says:

    #38 EA

    My point was not to debate whether there is enough time for evolution to take place according to neo-darwninian theory. That debate has been had many, many times. I was addressing your OP. We have not used neo-darwinian techniques to address our own problems because there isn’t enough time. Whether there is enough time for these techniques to create life over 4 billion years is a different question.

  41. 41
    Cross says:

    Mark Frank @ 40

    “Whether there is enough time for these techniques to create life over 4 billion years is a different question.”

    If something is impossible to evolve step by step, no amount of time makes it possible.

    The Bombardier Beetle is impossible to evolve by RV + NS. At many steps the poor thing would burn its backside off waiting for a hopeful mutation. The magic of a lot of time does not solve the issue.

    Cheers

  42. 42
    rvb8 says:

    BA, the ‘you’ was Cross, the ‘me’ was me. Sorry for the confusion.

    Being an atheist and a materialist I understand the ‘you’ far better than the religiously inclined, as I know that ‘you’ are a physical being made of material. I can see and fondle (heh!) physical beings, and I enjoy it immensely.

    This spiritual life however is problematic. You BA, say i have no idea of the ‘you’, and yet what you talk to isn’t there. You BA, speak to thin air and try to convince me something is listening.

    It would quite clearly appear it is you who does not understand identity and we materialists who understand identity most intimately.

    I hope you and god have a nice day.

  43. 43
    bornagain77 says:

    Actually rvb8, contrary to what you imagine to be true, your soul and the spiritual realm are ‘even more real than real’. In fact, we have far more observational evidence for the reality of souls than we do for the Darwinian claim that unguided material processes can generate sophisticated functional information:
    http://www.uncommondescent.com.....ent-545518

  44. 44
    rvb8 says:

    ‘More real than real’, besides being redundent is that also tautology? Souls and the spiritual realm, how do you get evidence for the immaterial? Hearsay, near death nonsense, my friend’s brother’s, half sister met a boy who said that….

    BA this is not evidence, it’s wish fulfillment, you wish it is so and you make it so, kind of like ID. ‘More observational evidence for the reality of souls..’, where? youtube, http://www.soulsarereal.com, http://www.isawaghost.org, or any of your other pointless non-evidence sites.

    Oh yeah, do Hindus have souls? I really don’t know, or do they only click on line upon revelation in Christ? In that case what point a soul, if you’re not Christian? I sold mine for 5$ to a friend several years ago in a tipsy bet. I have not asked for it back and the repercussions are, nil. I don’t want it back, it’s a load off my mind, heh!

    Save me a 10000 word ideological rant, there are none more zealous than the converted zealot, or none more proof aghainst reason.

  45. 45
    gpuccio says:

    rvb8:

    I like your style. At least, you are not boring. However, you are probably too passionate in your personal faith to make a real argument.

    You say: ” add to this that powerful weeder out of uselessness, Natural Selection, and the steps seem probable.”

    Well, deciding what is probable and what is not is probably one of the most intimate free choices in an individual’s life. I respect yours, even if you seem not too respectful of others’.

  46. 46
    bornagain77 says:

    rvb8, it is funny that you deny the testimonies of the millions of people who have died for a short while in Near Death Experiences, and have told us that they had survived death, but you readily believe that your brain, which is far more complex than the entire internet combined, came about by unguided material processes,,, even though NO ONE has EVER seen unguided material processes generate ANY non-trivial functional information!?!? ,,, You simply imagine that such unfathomed complexity, as is in your own brain, can arise by unguided processes with no proof whatsoever.

    Moreover, as pointed out previously at post 43, we have excellent empirical evidence from physics backing up the plausibility that the soul survives death. i.e. the ‘physics’ of the human body is consistent with the belief that the soul survives death.

    Thus when you say that there is ‘none more proof against reason’, I am left to wonder exactly what reason, or observational evidence, have you ever presented that I have not fairly considered??

    You, nor any other atheist, has ever presented ANY observation evidence whatsoever for your/their belief that functional information can arise by unguided material processes, and I have presented, not only observational evidence that there is indeed life after death, but also empirical evidence from physics that the physics within the human body is consistent with those testimonies.

    http://www.uncommondescent.com.....ent-545518

    Correlations in special relativity with Near Death Testimonies.
    http://www.uncommondescent.com.....ent-548563

    Thus rvb8 why do you resolutely defend something for which you have no proof, and indeed for which you only imagine to be true, and steadfastly reject that for which we have excellent proof and reason to believe?

    There simply is no ‘reason’ in this.

    Verse:

    Mark 16:14
    Later Jesus appeared to the Eleven as they were eating; he rebuked them for their lack of faith and their stubborn refusal to believe those who had seen him after he had risen.

    Of related note:

    Scientists say Turin Shroud is supernatural – December 2011
    Excerpt: After years of work trying to replicate the colouring on the shroud, a similar image has been created by the scientists.
    However, they only managed the effect by scorching equivalent linen material with high-intensity ultra violet lasers, undermining the arguments of other research, they say, which claims the Turin Shroud is a medieval hoax.
    Such technology, say researchers from the National Agency for New Technologies, Energy and Sustainable Economic Development (Enea), was far beyond the capability of medieval forgers, whom most experts have credited with making the famous relic.
    “The results show that a short and intense burst of UV directional radiation can colour a linen cloth so as to reproduce many of the peculiar characteristics of the body image on the Shroud of Turin,” they said.
    And in case there was any doubt about the preternatural degree of energy needed to make such distinct marks, the Enea report spells it out: “This degree of power cannot be reproduced by any normal UV source built to date.”
    http://www.independent.co.uk/n.....79512.html

    If scientists want to find the source for the supernatural light which made the “3D – photographic negative” image on the Shroud I suggest they look to the thousands of documented Near-Death Experiences (NDE’s) in Judeo-Christian cultures. It is in their testimonies that you will find mention of an indescribably bright ‘Light’ or ‘Being of Light’ who is always described as being of a much brighter intensity of light than the people had ever seen before.

    Ask the Experts: What Is a Near-Death Experience (NDE)? – article with video
    Excerpt: “Very often as they’re moving through the tunnel, there’s a very bright mystical light … not like a light we’re used to in our earthly lives. People call this mystical light, brilliant like a million times a million suns…”
    – Jeffery Long M.D. – has studied NDE’s extensively
    http://abcnews.go.com/Nightlin....._gydvW8jbI

    “Suddenly, I was enveloped in this brilliant golden light. The light was more brilliant that the light emanating from the sun, many times more powerful and radiant than the sun itself. Yet, I was not blinded by it nor burned by it. Instead, the light was a source of energy that embraced my being.”
    Ned Dougherty’s – Fast Lane To Heaven – Quoted from “To Heaven and Back” pg. 71 – Mary C. Neal MD

    Life After Life – Raymond Moody – Near Death Experience – The Tunnel, The Light, The Life Review – video
    http://www.youtube.com/watch?v=z56u4wMxNlg

    All people who have been in the presence of ‘The Being of Light’, while having a deep NDE, have no doubt whatsoever that the ‘The Being of Light’ they were in the presence of is none other than ‘The Lord God Almighty’ of heaven and earth.

    In The Presence Of Almighty God – The NDE of Mickey Robinson – video
    https://vimeo.com/92172680

    Verse and Music:

    Acts 26:13-15
    at midday, O king, along the road I saw a light from heaven, brighter than the sun, shining around me and those who journeyed with me. And when we all had fallen to the ground, I heard a voice speaking to me and saying in the Hebrew language, ‘Saul, Saul, why are you persecuting Me? It is hard for you to kick against the goads.’ So I said, ‘Who are You, Lord?’ And He said, ‘I am Jesus, whom you are persecuting.

    Toby Mac (In The Light)
    http://www.youtube.com/watch?v=5_MpGRQRrP0

  47. 47
    Cross says:

    rvb8 @ 44

    “this is not evidence, it’s wish fulfillment, you wish it is so and you make it so”

    Are you sure this does not apply to your view of the Bombardier Beetle creation story? No one else has found it scientific and probable.

    “there are none more zealous than the converted zealot”

    You seem very zealous, are you a convert to atheism?

    Cheers

  48. 48
    bornagain77 says:

    Of semi-related interest, wallstreeter43 has just posted a fairly detailed defense of the authenticity of the Shroud of Turin here:
    http://www.uncommondescent.com.....ent-549413

  49. 49
    Dionisio says:

    Regarding this never-ending OOL debate, here’s a recent comment (#509) within a discussion -started by gpuccio’s very insightful OP- on a very important area of science:
    http://www.uncommondescent.com.....ent-549436

    Personally I don’t know exactly how or when OOL happened, but believe in its supernatural cause. Ancient scriptures (Gen.1; John 1) declare that in the beginning the transcendent Ultimate Reality purposely caused everything that exists, including life.
    I believe that the whole creation is the general revelation of the Ultimate Reality and that the sacred scriptures are His special revelation to us. I also believe that many won’t believe it. For many years I did not believe it either. I was raised and educated within a system that was totally against such a belief. I believe that my current belief has a supernatural cause too. No amount or quality of any kind of education could have done it. That faith must have come from the same transcendent source. No one among us can explain it. As life itself, it’s a most wonderful mystery. And I sing hallelujah!

  50. 50
    Silver Asiatic says:

    ‘More real than real’, besides being redundent is that also tautology? Souls and the spiritual realm, how do you get evidence for the immaterial? Hearsay, near death nonsense, my friend’s brother’s, half sister met a boy who said that….

    Evidence for the immaterial is by negation – we don’t have evidence that certain thing are physical, and yet they exist, so we consider them immaterial. Consciousness, thoughts, aesthetic appreciation, ideas, dreams, memory, inspiration, desire for life-longevity, desire for happiness and love – unending … lots of things are immaterial.

    As for life beyond death – why are you so closed to that possibility? Since it’s a non-physical state, what kind of evidence would convince you that it’s real?

    Oh yeah, do Hindus have souls? I really don’t know, or do they only click on line upon revelation in Christ? In that case what point a soul, if you’re not Christian? I sold mine for 5$ to a friend several years ago in a tipsy bet. I have not asked for it back and the repercussions are, nil. I don’t want it back, it’s a load off my mind, heh!

    Your soul, among other things, is your conscious identity. Again, we have no evidence that this is a physical entity. What evidence do we have that this thing called “you” exists (as an identity)?

    Reason: What is the physical evidence that indicates that reason is of any importance or value?

  51. 51
    logically_speaking says:

    I just watched the video in comment 1, and laughed out loud. Apparently the greatest evolutionary adaptation ever is on the verge of extinction. So much for natural selection.

  52. 52
    PaV says:

    mark frank:

    Creating a solution intentionally is much quicker and you can predict what you are going to get. You reproduce the same old argument about there not being enough time for evolution to do the job. Why dress it up in an argument about us not using evolutionary processes for ourselves?

    IBM has a cpu that runs at 155 billion cycles per second. Let’s say your running through a string 3 billion characters long, I’m not computer guy, but I would guess that you could run that string through 50 times a second. Then let’s say there is a program that ‘mutates’ the string, and let’s say that string is also 3 billion characters long. Then we’re looking at 25 throughputs, with mutations, per second. So, in one day you would have 24 hours x 3600 seconds/hour x 25 =2,160,000 throughputs. Wouldn’t this be equivalent to 2 million plus replications? Over a week: 15 million. Over a year 180 million replications. Isn’t that enough replications for neo-Darwinian evolution to take place?

    (I hope the computer guys step up and give an accurate view of the numbers involved.)

  53. 53
    Zachriel says:

    PaV: Then we’re looking at 25 throughputs, with mutations, per second. So, in one day you would have 24 hours x 3600 seconds/hour x 25 =2,160,000 throughputs.

    In a human gut, there are about 10^14 bacteria, of several thousand species, each with a genome of about 10^6, which can replicate every few minutes.

    Think populations.

  54. 54
    PaV says:

    Zachriel:

    Then why haven’t they “evolved”?

  55. 55
    Mung says:

    From the OP:

    We are regularly told by proponents of evolutionary theory, from Darwin right up to the present day, that purely natural processes, such as random mutations and natural selection, have the ability to build, construct, fashion, purpose and create remarkable machines. Machines that rival, and in many cases surpass, our most advanced technologies.

    And these processes can modeled, using intelligent design!

    Amazing.

  56. 56
    Mung says:

    Mark Frank:

    My point was not to debate whether there is enough time for evolution to take place according to neo-darwninian theory.

    Of course not. We don’t want to actually subject the theory to a TESTABLE HYPOTHESIS! But isn’t that sort of the point of the OP?

  57. 57
    rvb8 says:

    Oh dear PaV,
    they haven’t evolved because their environment is static. Why are crocodiles largely the same as 100 million years ago? No need to their habitat has remained equitable for their reproduction; also the turtle, cockroach, tuatara, and, interestingly enough why monkeys are still in the jungle and not responding to your dimness.

  58. 58
    Mung says:

    Oh dear PaV,
    We know their environment is static because they did not evolve.

  59. 59
    rvb8 says:

    Evolution requires material changes in environment to allow NS to weed out those prodgeny which are less fit Mung. If the selective pressure is minimal, for example a stable environment, then the resulting variety of adaptive answers to that environment are minimal; a shark does not need to be a better shark, it is well suited to its environment.

    I will continue answering the sillyness here until all of the pretenders realise their failed theory is, well, a failed theory. Oddly enough by any dictionary definition it was never even that.

  60. 60
    Mung says:

    rvb8: Evolution requires material changes in environment to allow NS to weed out those prodgeny which are less fit Mung.

    How lucky for you then that the ability to spell is not a requirement. Unless it is. What a grand theory!

  61. 61
    Cross says:

    rvb8 @ 59

    “If the selective pressure is minimal, for example a stable environment, then the resulting variety of adaptive answers to that environment are minimal”

    from http://www.nhm.ac.uk/nature-on.....t-warming/

    “Earth’s unstable climate

    Life on Earth has flourished and evolved for hundreds of millions of years. However, this does not mean that the climate has been stable throughout this time.

    Geological data shows evidence of large-scale climate changes in the past, caused by factors like the tilt of the Earth’s axis and tectonic plate movement (as climate is affected by the distribution of the planet’s continents). Some of these changes were gradual; others were much more rapid.

    Cretaceous world

    In the mid Cretaceous, about 100 million years ago, the distribution of fossil plants, and large herbivorous dinosaurs, suggests sub-tropical conditions extended to Alaska and Antarctica and there were no polar ice caps. The planet was warmer than today – scientists have estimated it was 6 – 8°C warmer. Carbon dioxide levels in the atmosphere were about 5 times higher than today.

    These warm conditions lasted for tens of million of years before the climate started cooling.

    Rapid temperature change

    The geological record also reveals dramatic events when there was much more rapid climate change. One of the fastest changes in Earth’s temperature took place during an event that oceanographers call the Palaeocene-Eocene thermal maximum.

    55 million years ago, global temperatures rose 6°C over a period of 20,000 years or less. Like climate change today, scientists think that an increase in greenhouse gases caused this rapid warming. This was possibly due to a catastrophic release of frozen methane deposits – like carbon dioxide, methane is a greenhouse gas.

    This period of climate change caused major ecosystem changes and extinction of many organisms.

    The ice ages

    In the recent geological past, much of Britain was covered by ice sheets. We know this because the landscape shows many distinctive glacial landforms, especially in North Wales, Scotland and the Lake District. Also, fossils of mammoths and woolly rhinoceroses, which lived in cold climates, have been found across southern Britain.

    This type of evidence, along with marine sediment cores and ice cores, shows that over the past 2 million years, climate fluctuated dramatically between ice ages and warm interglacial periods, similar to today’s climate.

    These major changes were driven by cyclical changes in the Earth’s orbit, which altered the distribution of solar energy between the seasons and across the Earth.

    An inescapable conclusion of this is that the Earth’s climate is unstable and minor changes in the Earth’s energy budget cause large changes in climate.”

    100 million years of stable environment, where?

    Cheers

  62. 62
    Hangonasec says:

    The Bombadier Beetle. Heh heh. You know that one was debunked about 1980 or so?

    But … one thing we don’t tend to find with ‘known’ designs is elaborate solutions to problems the designers themselves created. I have designed an effective predator. So how do I protect its prey? I know! Defences! Is the defence too effective? OK, let’s have a mechanism for getting round it! I thereby maintain the perfect balance, give or take an extinction or two. Because I’m a great one for elaborately unnecessary solutions, me.

    Of course, Multiple Designer Theory gets round that one, but I doubt most here want to go that way. Or we could try the ‘who are we to judge necessity?’ tack.

  63. 63
    gpuccio says:

    Hangonasec:

    “Of course, Multiple Designer Theory gets round that one, but I doubt most here want to go that way.”

    I certainly do. I have stated many times that we can in no way be sure of how many biological designers exist. I can agree with you that some observed properties of the designed beings could be interpreted as in favor of more than one.

    But it is not so clear cut. Think, for example, of a video-game. It could have been designed by a single designer (although I think that most are the result of teams). And yet, you can find contrasting parties there, and difficulties and forms of help, which are part of the game, and in the end are the essence of its meaning and value.

    The same can be said for a book, or a movie, or a painting. All designed things, usually by a single designer.

    So, your “argument” is rather pointless.

  64. 64
    Cross says:

    Hangonasec @ 62

    “The Bombadier Beetle. Heh heh. You know that one was debunked about 1980 or so?”

    The only way to “debunk” is to come up with evidence of the evolution of it’s complex defence mechanism one mutation at a time without burning it’s backside off. Isaak had a go and come up with quite a story, completely devoid of any evidence.

    Care to have a go yourself?

    “I have designed an effective predator. So how do I protect its prey? I know! Defences! Is the defence too effective? OK, let’s have a mechanism for getting round it! I thereby maintain the perfect balance”

    Exactly, it’s called a balanced ecosystem. It was designed that way.

    “A healthy ecosystem has lots of species diversity and is less likely to be seriously damaged by human interaction, natural disasters and climate changes. Every species has a niche in its ecosystem that helps keep the system healthy. We are learning about new species every day, and we are just figuring out the roles they play in the natural world. By studying and maintaining biodiversity, we help keep our planet healthy.” from http://www.nhptv.org/naturewor.....ystems.htm

    You really need to read up a bit on some real science.

    Cheers

  65. 65
    Axel says:

    Me_Think #15

    ‘Too bad we don’t know who the ID designer is and how he/she/it accomplishes creation and maintenance of billions of cellular processes. We could revolutionize design with such omnipotent power.’

    Oh, NO, MT. That kind of power in man’s hot little hands would be disastrous! What am I saying? It is already destroying the earth, starting with the sea, producing a global catastrophe it’s better not to even mention.

    And that’s only a small package of God’s power that He has vouchsafed to his incorrigible children. Are you crazy? For goodness sake, we were talking about something innocuous recently, and you saw a connection with a threat of mind control. I mean it’s very comical, but it’s not really, in its implications for man having divine power, is it?

  66. 66
    Hangonasec says:

    GP @63

    So, your “argument” is rather pointless.

    More an observation than an argument. If you are happy with multiple, competing designers, fair enough, but you are in something of a minority here.

    Your examples of trade-off within a single designer’s output don’t really address the matter. The whole purpose of the tensions between the protagonists in a book or game is to create the dramatic narrative – that which makes the book worth reading, or the game worth playing. Are you saying that the bombardier beetle’s unique defence, and the ability of predators to get round it, form the essence of some arcane plot twist in the glorious Game Of Life (TM)? Who is this story for? Us?

  67. 67
    Hangonasec says:

    Cross @64

    […] quite a story, completely devoid of any evidence.

    Care to have a go yourself?

    Why certainly. Just as soon as you provide an equivalent level of detail as to how the Designer arranged things, and got round the significant difficulties of getting a functional bombardier beetle past the feasibility stage. Seem fair?

    Exactly, it’s called a balanced ecosystem. It was designed that way.

    And your evidence is … the fact that the ecosystem is balanced? Hmmm …

    It is not (on the face of it) necessary to equip a particular beetle with an elaborate couldn’t-possibly-evolve defence, and simultaneously equip predators with the means to evade it. Would the ecosystem with neither defence nor response be unbalanced? Plenty of ecosystems don’t have bombardier beetles in them.

    You really need to read up a bit on some real science.

    Why thanks, Captain Snark, I’ll get onto it right away!

  68. 68
    Joe says:

    Hangonasec is confused. Its position is the one that claims to have a step-by-step process that explains the diversity of life, not ID. Its position can’t account for beetles. It cannot get beyond populations of prokaryotes GIVEN starting populations of prokaryotes.

    ID claims to have a step-by-step process for determining the existence of intelligent design and we have laid it out.

  69. 69
    gpuccio says:

    Hangonasec:

    “If you are happy with multiple, competing designers, fair enough, but you are in something of a minority here.”

    I like being in a minority. And it is not a question of “being happy”. ID is about science. What we observe can be explained both by a single designer and by multiple designers. It is not a question for philosophy or religion, but for science.

    “Your examples of trade-off within a single designer’s output don’t really address the matter. The whole purpose of the tensions between the protagonists in a book or game is to create the dramatic narrative – that which makes the book worth reading, or the game worth playing.”

    And that was exactly my point. The worth of the entire design is the main issue.

    “Are you saying that the bombardier beetle’s unique defence, and the ability of predators to get round it, form the essence of some arcane plot twist in the glorious Game Of Life (TM)? ”

    I am just saying that the Game could really be glorious, and that the plot twists, even if apparently arcane, could be necessary for the glory of the whole picture.

    “Who is this story for? Us?”

    These are, for the moment, more philosophical and religious questions than scientific ones. I am afraid that our scientific data are probably not enough to answer them at that level, For the moment.

    You are entitled to your own answers, including the answer that there is no story. Your choice.

    As for me, I would not ignore the possibility that we have an important role in the whole story.

  70. 70
    gpuccio says:

    Just to remind what we are talking of, from Wikipedia:

    Defense mechanism[edit]
    The two reactant chemical compounds, hydroquinones and hydrogen peroxide, are secreted by specialized glands and are stored in separate reservoirs in the rear tip of its abdomen. When threatened, the beetle contracts muscles that open the valves of these reservoirs and force the two reactants into a thick-walled mixing chamber lined with cells that produce enzymes including catalases and peroxidases.

    In the mixing chamber the enzymes rapidly break down the hydrogen peroxide, releasing free oxygen and catalyzing the oxidation of the hydroquinones into p-quinones.[citation needed] The reaction is very exothermic, and the released energy raises the temperature of the mixture to near 100 °C, vaporizing about a fifth of it. The resultant pressure buildup forces the entrance valves from the reactant storage chambers to close, thus protecting the beetle’s internal organs. The boiling, foul-smelling liquid partially becomes a gas by flash evaporation and is expelled explosively through an outlet valve, with a loud popping sound.

    The flow of reactants into the reaction chamber and subsequent ejection occur in a series of about 70 pulses, at a rate of about 500 pulses per second. The whole sequence of events takes only a fraction of a second.

    Typically the beetle turns its body so as to direct the jet towards whatever triggered the response. The gland openings of some African bombardier beetles can swivel through 270° and thrust between the insect’s legs, discharging the fluid in a wide range of directions with considerable accuracy.[3]

    And here is the “explanation”:

    Evolution of the defense mechanism[edit]
    The unique combination of features of the bombardier beetle’s defense mechanism—strongly exothermic reactions, boiling-hot fluids, and explosive release—have been used by creationists and proponents of intelligent design as examples of irreducible complexity that could not have been produced by evolution.[4] However, while the true evolutionary path is still unknown, biologists have shown that the system could have theoretically evolved from defenses found in other beetles in incremental steps by natural selection.[5][6]

    Specifically, quinone chemicals are a precursor to sclerotin, a brownish substance produced by beetles and other insects to harden their exoskeleton.[7] Some beetles additionally store excess foul-smelling quinones, including hydroquinone, in small sacs below their skin as a natural deterrent against predators—all carabid beetles have this sort of arrangement. Some beetles additionally mix hydrogen peroxide, a common by-product of the metabolism of cells, in with the hydroquinone, and some of the catalases that exist in most cells makes the process more efficient. The chemical reaction produces heat and pressure, and some beetles exploit the latter to push out the chemicals onto the skin; this is the case in the beetle Metrius contractus, which produces a foamy discharge when attacked.[8] In the bombardier beetle, the muscles that prevent leakage from the reservoir additionally developed a valve permitting more controlled discharge of the poison and an elongated abdomen to permit better control over the direction of discharge.[5][6]

    Very clear, isn’t it? 🙂

  71. 71
    Zachriel says:

    gpuccio: Very clear, isn’t it?

    Sure. They say the evolutionary history isn’t known, but that the prerequisites are found in related organisms.

  72. 72
    Mark Frank says:

    #52 Pav
     

    Over a year 180 million replications. Isn’t that enough replications for neo-Darwinian evolution to take place?

     
    You need to do more than replicate to get evolution. You need a inheritance of traits with some variation and selectionary pressure.  If you have all of these I would expect some fairly dramatic changes in the string over that many replications.  Of course you have no way of predicting what those changes will be so they are of limited  use for creating useful solutions to well-defined problems which I guess was the point of the OP.  It would be much quicker and more effective to design a solution yourself using your human faculties to do so.

  73. 73
    Mark Frank says:

    #56 Mung

    We don’t want to actually subject the theory to a TESTABLE HYPOTHESIS! But isn’t that sort of the point of the OP?

    I thought the point of the OP was that there was an elephant in the room which was that we did not use neo-Darwinian techniques to solve problems. Anyhow that was what I was addressing.

  74. 74
    Zachriel says:

    PaV: Then why haven’t they “evolved”?

    They have. See Ley et al., Evolution of mammals and their gut microbes, Science 2008. It’s actually a hot topic right now. Gut microbes and their gut organisms have co-evolved in a close symbiotic relationship, each host species with a particular consortium of microbes.

  75. 75
    Joe says:

    Unguided evolution cannot account for elephants. Heck it can’t even get beyond populations of prokaryotes given starting populations of prokaryotes.

  76. 76
    Andre says:

    WTF is selectionary?

  77. 77
    Zachriel says:

    -ary, thing or person belonging to or connected with
    http://www.merriam-webster.com/dictionary/-ary

    “selctionary pressure” therefore means pressure connected with selection, the ‘push’ of selection that results in changes in an evolving population.

  78. 78
    Hangonasec says:

    Joe @68

    Hangonasec is confused. Its position is the one that claims to have a step-by-step process that explains the diversity of life, not ID. Its position can’t account for beetles. It cannot get beyond populations of prokaryotes GIVEN starting populations of prokaryotes.

    Come back with those goalposts! Bombardier beetles, Joe. Not “heck your position can’t even account for quarks/planets/water/fish”. Bombardier beetles. Focus.

    ID claims to have a step-by-step process for determining the existence of intelligent design and we have laid it out.

    Sure it does.

    Step 1:

    Challenge ‘Darwinism’ to come up with the precise series of mutations and selective advantages involved for a given trait.

    Step 2a – if a scenario is presented, sneer at it; go to step 3.

    Step 2b – if no scenario is presented, sneer anyway and go to step 3.

    Step 3 – Declare victory. It’s designed! THIS is designed and THAT is designed and … yes! All of it! It’s designed if you can’t show otherwise! Because, as gpuccio says, ID is science. Really.

  79. 79
    Joe says:

    Beetles- your position cannot account for beetles- any of them.

    Challenge ‘Darwinism’ to come up with the precise series of mutations and selective advantages involved for a given trait.

    Nope- we ask you to support your claims. Nothing more. And your angry ignorance is amusing but it is still angry ignorance.

  80. 80
    Piotr says:

    #71 Zachriel,

    Sure. They say the evolutionary history isn’t known, but that the prerequisites are found in related organisms.

    There are, by the way, 500+ species of bombardier beetles in two groups which may or may not constitute one clade together. The species Metrius contractus, mentioned in the Wikipedia article, belongs to the less known of the two groups and retains what may resemble the ancestral defensive mechanism. No jet, and the spray is colder than in the more evolved bombardiers.

    http://jeb.biologists.org/content/203/8/1265.long

  81. 81
    Cross says:

    Hangonasec @ 67

    “[…] quite a story, completely devoid of any evidence.

    Care to have a go yourself?

    Why certainly. Just as soon as you provide an equivalent level of detail as to how the Designer arranged things, and got round the significant difficulties of getting a functional bombardier beetle past the feasibility stage. Seem fair?”

    Standard Evo response, I have no explanation, change the subject.

    “And your evidence is … the fact that the ecosystem is balanced? Hmmm …

    It is not (on the face of it) necessary to equip a particular beetle with an elaborate couldn’t-possibly-evolve defence, and simultaneously equip predators with the means to evade it. Would the ecosystem with neither defence nor response be unbalanced? Plenty of ecosystems don’t have bombardier beetles in them.”

    Perhaps if the designer wanted to show that the beetle was designed and could not have evolved, he would do so. Then those that were open minded would think twice about the fairy stories that have been made up to explain away the design.

    “You really need to read up a bit on some real science.

    Why thanks, Captain Snark, I’ll get onto it right away!”

    Glad to be of assistance.

    Cheers

  82. 82
    gpuccio says:

    Zachriel:

    “They say the evolutionary history isn’t known, but that the prerequisites are found in related organisms.”

    Just to be clear: I am not denying that there is an history in the evolution of design. I am denying that what you call “the prerequisites” for an “evolutionary history” which is not known are of any help in explaining the known biological history in terms of RV + NS.

    Of course biological information is generated in time, and there is a continuity of design and of programming and links between solutions and functions. Like in human design. That has sense if we look at the functional choices as designed solutions, while it has no sense at all if we try to explain them in terms of RV + NS.

    Related organisms are related. As you know, I completely accept that. I have never denied CD, indeed I have defended it many times here. But it is common descent by design, just as Windows 8 descends from the old DOS.

    So, the “explanation” presented in Wikipedia for the “Evolution of the defense mechanism” is no explanation at all. If we take it simply as a description of a few facts of natural history, it’s fine, but as an explanation, it is a fairy tale.

  83. 83
    gpuccio says:

    Hangonasec:

    ID is science. Really.

  84. 84
    gpuccio says:

    Piotr:

    I bow to your knowledge of beetles! 🙂

  85. 85
    gpuccio says:

    Hangonasec:

    You are a very good example of the denial of ID that I treasure so much: mere religious motivations, no arguments, no desire to reason, no love for intellectual confrontation: just “mock and scorn”.

    Thank you, we really need the likes of you. 🙂

  86. 86
    Piotr says:

    Gpuccio:

    …as an explanation, it is a fairy tale.

    As opposed to manipulation by a completely unknown intelligent entity (obviously present on Earth but never seen in action or otherwise), with completely unknown techniques, over billions of years. It’s science. Really.

  87. 87
    Piotr says:

    #84 Gpuccio,

    Just pointing out the existence of an “intermediate form” of the bombarding mechanism, described in detail in the literature.

  88. 88
    Hangonasec says:

    Hangonasec:

    You are a very good example of the denial of ID that I treasure so much: mere religious motivations, no arguments, no desire to reason, no love for intellectual confrontation: just “mock and scorn”.

    Thank you, we really need the likes of you. 🙂

    You’re welcome, I aim to please, though my remarks were more in response to Joe’s robotic buffoonery than any argument advanced by yourself (if you in fact did advance an argument). Still, you profess a desire to reason, and yet you dismiss me as ‘religious’, simply because I demand an equivalent rigour from ID to that demanded of ‘Darwinism’. Convenient way to avoid all further requirement to ‘reason’ – “we have all the answers, but you won’t get it because you belong to the Church of Darwin”.

    I think equivalency of explanation a perfectly reasonable expectation. If your cohorts, and you yourself, dismiss the possibility of the ‘Darwinian’ version out of hand, yet have nothing from ID Theory to put in its place, then you don’t look to me to be doing science. It is a simple matter to find something whose evolutionary explanation is unknown. How do you fill that gap?

  89. 89
    Hangonasec says:

    Joe @79

    Nope- we ask you to support your claims. Nothing more.

    But the same does not go for ID? Explain something biological without reference to the failure of ‘Darwinism’.

    And your angry ignorance is amusing but it is still angry ignorance.

    Another irony meter bites the dust.

  90. 90
    Hangonasec says:

    Cross @81

    Standard Evo response, I have no explanation, change the subject.

    Standard Creationist response. Pretend demanding equivalent rigour for the proponent’s favoured explanation of the same thing is ‘changing the subject’.

    Perhaps if the designer wanted to show that the beetle was designed and could not have evolved, he would do so. Then those that were open minded would think twice about the fairy stories that have been made up to explain away the design.

    Gah, I thought the predator-prey interaction was over-egged enough! Now it’s a message too? He really needs to work on his communication skills. But hey, if it means you don’t have to swallow fairy stories … !

  91. 91
    Cross says:

    Hangonasec @ 90

    Although I am a “creationist”, not young earth. I have no problem with microevolution, better described as built in adaption by the designer. Other related beetles with similar or part related defence mechanisms are no problem.

    When I was developing object oriented software, we often reused classes that were previously used and tested for new projects even if all the functions were not needed. This can show a common designer just as easily as common descent.

    The reason I posted the Bombardier Beetle is because it’s defence mechanism is an great example of a system that could not develop by one mutation at a time.

    This IS evidence for design. If neo-darwin evolution is “proven” then it must have an explanation. Even Dawkins admits life looks designed.

    If the explanation for it’s evolution has points where things appear (ie extra chemicals or chambers) but at the time have no selection benefit, or the animal would destroy itself before another beneficial mutation comes along, then the honest thing to admit would be that RV + NS could not have done it.

    I would not expect you to give up your belief system, but you and others here could concede that a further explanation was needed instead of relying on ridiculous just-so stories.

    Cheers

  92. 92
    Hangonasec says:

    Incidentally, the mixture becomes boiling-hot inside the abdomen. It’s this that forces it out. Hydrogen peroxide and hydroquinone exist together in one chamber. They don’t react explosively. Catalase and peroxidase in another chamber cause the explosion.

    Both enzymes, and both reagents, have roles within the body. So … what’s IC about this system? Clearly, you don’t get an explosive mixture at the concentrations more typically found. Peroxide is produced in below-explosive quantities as part of immune defence. Peroxidase rapidly denatures it, to protect the body’s cells. But overproduction of peroxide alone is a plausible defence against external attack, and of course there is no need to denature it ‘out there’. In fact now if you added peroxidase, you’d get explosive release, making the defence more effective.

    Now, I don’t have a detailed audit of course. There are several million species with tens of thousands of genes in each, and not that much to spend on unravelling detailed evolutionary history for Creationist Challenge X. Nonetheless, the components of the system do not all have to be in place for it to work at all. Gish was wrong.

  93. 93
    Cross says:

    Hangonasec @ 92

    “Now, I don’t have a detailed audit of course”

    That is because the devil is in the detail as you full well know.

    To repeat,
    If the explanation for it’s evolution has points where things appear (ie extra chemicals or chambers) but at the time have no selection benefit, or the animal would destroy itself before another beneficial mutation comes along, then the honest thing to admit would be that RV + NS could not have done it.

    To give an example, if I grant you all the steps before, why did the second chamber develop before the reaction of the two chemicals was enabled by an appearing enzyme? What possible selection benefit does it give the beetle? Then, giving you the second chamber and the magically appearing reaction enabler, the beetle burns its backside off until another magical mutation temperature hardens the chamber. Which comes first, the chemical reaction or the temperature hardened chamber to hold it? What selection benefit is there for one without the other?

    “There are several million species with tens of thousands of genes in each, and not that much to spend on unravelling detailed evolutionary history for Creationist Challenge X. ”

    Just one detailed explanation would be enough.

    Cheers

  94. 94
    Me_Think says:

    Cross @ 93

    Just one detailed explanation would be enough.

    There is an explanation- all you need to do is search:

    Quinones are produced by epidermal cells for tanning the cuticle. This exists commonly in arthropods. [Dettner, 1987]

    Some of the quinones don’t get used up, but sit on the epidermis, making the arthropod distasteful. (Quinones are used as defensive secretions in a variety of modern arthropods, from beetles to millipedes. [Eisner, 1970])

    Small invaginations develop in the epidermis between sclerites (plates of cuticle). By wiggling, the insect can squeeze more quinones onto its surface when they’re needed.

    The invaginations deepen. Muscles are moved around slightly, allowing them to help expel the quinones from some of them. (Many ants have glands similar to this near the end of their abdomen. [Holldobler & Wilson, 1990, pp. 233-237])

    A couple invaginations (now reservoirs) become so deep that the others are inconsequential by comparison. Those gradually revert to the original epidermis.

    In various insects, different defensive chemicals besides quinones appear. (See Eisner, 1970, for a review.) This helps those insects defend against predators which have evolved resistance to quinones. One of the new defensive chemicals is hydroquinone.

    Cells that secrete the hydroquinones develop in multiple layers over part of the reservoir, allowing more hydroquinones to be produced. Channels between cells allow hydroquinones from all layers to reach the reservior.

    The channels become a duct, specialized for transporting the chemicals. The secretory cells withdraw from the reservoir surface, ultimately becoming a separate organ.

    This stage — secretory glands connected by ducts to reservoirs — exists in many beetles. The particular configuration of glands and reservoirs that bombardier beetles have is common to the other beetles in their suborder. [Forsyth, 1970]

    Muscles adapt which close off the reservior, thus preventing the chemicals from leaking out when they’re not needed.

    Hydrogen peroxide, which is a common by-product of cellular metabolism, becomes mixed with the hydroquinones. The two react slowly, so a mixture of quinones and hydroquinones get used for defense.

    Cells secreting a small amount of catalases and peroxidases appear along the output passage of the reservoir, outside the valve which closes it off from the outside. These ensure that more quinones appear in the defensive secretions. Catalases exist in almost all cells, and peroxidases are also common in plants, animals, and bacteria, so those chemicals needn’t be developed from scratch but merely concentrated in one location.

    More catalases and peroxidases are produced, so the discharge is warmer and is expelled faster by the oxygen generated by the reaction. The beetle Metrius contractus provides an example of a bombardier beetle which produces a foamy discharge, not jets, from its reaction chambers. The bubbling of the foam produces a fine mist. [Eisner et al., 2000]

    The walls of that part of the output passage become firmer, allowing them to better withstand the heat and pressure generated by the reaction.

    Still more catalases and peroxidases are produced, and the walls toughen and shape into a reaction chamber. Gradually they become the mechanism of today’s bombardier beetles.

  95. 95
    Cross says:

    Me_Think @ 94

    I posted this so called explanation at post 5 myself!

    Explain the detail I posted at 93, details no stories!

    To repeat again,
    To give an example, if I grant you all the steps before, why did the second chamber develop before the reaction of the two chemicals was enabled by an appearing enzyme? What possible selection benefit does it give the beetle? Then, giving you the second chamber and the magically appearing reaction enabler, the beetle burns its backside off until another magical mutation temperature hardens the chamber. Which comes first, the chemical reaction or the temperature hardened chamber to hold it? What selection benefit is there for one without the other?

    Explain with RV + NS one mutation at a time as per neo-darwinism please.

    Cheers

  96. 96
    Me_Think says:

    Cross @95

    To give an example, if I grant you all the steps before, why did the second chamber develop before the reaction of the two chemicals was enabled by an appearing enzyme? What possible selection benefit does it give the beetle?

    Second chamber didn’t develop as a single monolith structure. First secretory cells formed allowing more hydroquinone to be produced, which later become channels which later become the chamber. The advantage here was more hydroquinone.

  97. 97
    Cross says:

    Me_Think @ 96

    The second chamber is not needed to allow more hydroquinone unless you know in the future you will be adding an enzyme to cause a reaction producing rapid heat, expansion and ejection. Evolution is meant to be blind. You still need to answer which comes first, the chemical heat reaction or the heat hardened chamber? One mutation at a time.

    Cheers

  98. 98
    gpuccio says:

    Hangonasec:

    What I mean is that:

    “But … one thing we don’t tend to find with ‘known’ designs is elaborate solutions to problems the designers themselves created. I have designed an effective predator. So how do I protect its prey? I know! Defences! Is the defence too effective? OK, let’s have a mechanism for getting round it! I thereby maintain the perfect balance, give or take an extinction or two. Because I’m a great one for elaborately unnecessary solutions, me.”

    And:

    “Are you saying that the bombardier beetle’s unique defence, and the ability of predators to get round it, form the essence of some arcane plot twist in the glorious Game Of Life (TM)? Who is this story for? Us?”

    are religious arguments, and not scientific ones. I have answered you about that.

    And:

    “Step 1:

    Challenge ‘Darwinism’ to come up with the precise series of mutations and selective advantages involved for a given trait.

    Step 2a – if a scenario is presented, sneer at it; go to step 3.

    Step 2b – if no scenario is presented, sneer anyway and go to step 3.

    Step 3 – Declare victory. It’s designed! THIS is designed and THAT is designed and … yes! All of it! It’s designed if you can’t show otherwise! Because, as gpuccio says, ID is science. Really.”

    is just “mock and scorn”. Maybe it was not addressed to me, but it quotes me, so I feel involved. 🙂

    My simple point is: you seem reasonable, please behave reasonably.

    My point about the beetle is: we have a very clearly functional complex here, which would be almost impossible to realize by the standards of our design. There is no explanation for its highly functional configuration. All that is offered by Wikipedia and by the interlocutors here is:

    a) a description of historical facts

    b) a description of variants, which may be considered in some way “intermediate”.

    That’s fine, but it is not an “explanation”, in the scientific sense. The evidence of design remains, and the existence of some intermediate or variant forms is not only perfectly compatible, but really normal in a design scenario. Design is not a miracle, but a process of engineering.

    Then you say:

    “I think equivalency of explanation a perfectly reasonable expectation. If your cohorts, and you yourself, dismiss the possibility of the ‘Darwinian’ version out of hand, yet have nothing from ID Theory to put in its place, then you don’t look to me to be doing science. It is a simple matter to find something whose evolutionary explanation is unknown. How do you fill that gap?”

    I am rather surprised. I think that I have been trying to present arguments here for years. I certainly expect that you don’t agree, but not that you deny it.

    Usually, I don’t deal with macroscopic examples, like the beetle. I prefer to discuss molecular issues, like protein emergence, because I believe that all the discussion must be brought at the molecular level, the only one at which we can try to “explain” things.

    Her are a couple of recent OPs where I certainly try to make arguments:

    http://www.uncommondescent.com.....er-things/

    http://www.uncommondescent.com.....-language/

    http://www.uncommondescent.com.....on-part-1/

    Serious interlocutors like Mark Frank, Piotr, Zachriel, Petrushka, DNA_Jock and many others have been arguing here for a long time, and very well. I have enjoyed discussing with them many times. Although we don’t agree, we usually try to understand the other’s reasoning, and to answer. That’s what is called intellectual confrontation, and it is based on respect (and a certain amount of healthy fighting! 🙂 ).

    So the point is: why do you come here? To join the discussion, or just to “mock and scorn”?

  99. 99
    gpuccio says:

    Piotr:

    “As opposed to manipulation by a completely unknown intelligent entity (obviously present on Earth but never seen in action or otherwise), with completely unknown techniques, over billions of years. It’s science. Really.”

    You can do better than that.

    Why do you speck of intelligent entities “never seen in action”? The whole idea is that the tons of functional information in the biological world, that cannot be explained otherwise, are the result of design. If that is true, we have a lot of “action” to be seen.

    I will not discuss here the simple fact that many people believe that non physical intelligent entities are at work, and can be experienced, in many other ways, because that discussion would not be strictly scientific. But, as you probably know, I don’t believe that science is the only form of cognition, because I am not, philosophically, a reductionist.

    The techniques are not really “completely unknown”. Guided mutations, for example by guided transposon activity, is IMO something that we are beginning to detail. Many other details can be discovered.

    And why do you object to the “billions of years”? I don’t understand. That is the time span of biological information and of its appearance. That’s what we must explain, by RV + NS or by design. So, if we conclude for design, we have evidence of design for billions of years. And so?

    By the way, my admiration for your knowledge (of beetles, and of many other things biological) is absolutely sincere! 🙂

  100. 100
    gpuccio says:

    By the way, how would you describe the emergence of a painting on a canvas, if you could not see the painter, but only the canvas?

    You could certainly describe a lot of intermediate states, many of them with some functional properties. That’s exactly what happens in the design process.

    It’s a description of a design process, not an explanation of the painting based on non design laws.

  101. 101
    Piotr says:

    #100 Gpuccio,

    But we are not talking about a painting on a canvas. We are talking about something that you believe is analogous to a painting on a canvas, but others don’t share your belief.

    Why does design predict the existence of intermediate states? Design is teleological, so intermediate stages are dispensable. Why not design the “perfect” bombardier at once (or, if you really have to experiment with imperfect prototypes, destroy them)? In fact, since you don’t propose what the designer is, what methods it uses, or what its objectives are, you can’t make any prediction at all, as regards ancestral/intermediate states.

  102. 102
    gpuccio says:

    Piotr:

    “But we are not talking about a painting on a canvas. We are talking about something that you believe is analogous to a painting on a canvas, but others don’t share your belief.”

    Right. Otherwise we would not be here to discuss. And it is not really a question of beliefs, but of scientific interpretations of data. We certainly differ in our scientific interpretations.

    “Why does design predict the existence of intermediate states? ”

    Intermediate states are observed in all the cases of design we know of.

    They are often necessary at the level of the conscious representation: the form which is designed is often gradually changing during the process, as the cognitive functions of consciousness, and its purposes, act on the inputs which come from the world.

    And they are certainly necessary at the level of implementation: the painter has to prepare the canvas, then draw a ketch to guide the realization of the colours, and so on. That is true, even in the rare case that the designer already has a complete representation of the final work just from the beginning.

    “(or, if you really have to experiment with imperfect prototypes, destroy them)”

    That from you, a linguist? I am surprised. Are you encouraging all artists, including writers, to destroy all “imperfect prototypes”? In name of what?

    “In fact, since you don’t propose what the designer is, what methods it uses, or what its objectives are, you can’t make any prediction at all, as regards ancestral/intermediate states.”

    I do propose what the designer is: a conscious, intelligent, purposeful being, probably not physical, who acts in ways that are similar to the ways we act when we design. That is my prediction, and my argument.

    That’s why all the “arguments” which point to properties which are routinely observed in human design are not arguments against biological design.

  103. 103
    Me_Think says:

    Cross @ 97

    The second chamber is not needed to allow more
    hydroquinone unless you know in the future you will be adding an enzyme.still need to answer which comes first, the chemical heat reaction or the heat hardened chamber

    Of course they are not needed for mixing, but for storing hydroquinone , which makes the beetle more unpalatable to it’s predator. Just as hydroquinone evolved in response to predators developing resistance to quinones, the chamber is an intermediary step to chamber for mixing- evolution doesn’t have a predetermined aim. What ever is available is used as a precursor for the next step in defense. I am sure you have heard of predator-prey arms race evolution.

    You still need to answer which comes first, the chemical heat reaction or the heat hardened chamber

    The chemical heat reaction. Hyderoquinones and quinione byproducts is used in hardening or Sclerotinize of the chamber.
    Mixing hydrogen peroxide and hydroquinone leads to oxidation, not explosion. In fact, without enzymes peroxidase and catalase quinine, oxygen, quinone and water can not form. This again proves the chamber turned from storage space to reaction chamber and didn’t evolve as a irreducible complex structure.

  104. 104
    Cross says:

    Me_Think @ 103

    You don’t seem to be following my point or the problem with RV + NS one mutation at a time.

    Lets try again, below is the explanation of the defence system from rationalwiki an anti creationist site so it is not biased in my favour

    “The proven science behind the beetle’s defenses is that it uses a mixture of hydroquinone and the hydrogen peroxide and that, when two enzymes are added by the beetle (a catalase to decompose the hydrogen peroxide, and a peroxidase to oxidize the hydroquinones and thereby break them down into the simpler quinones), it causes the mixture to heat to nearly 100°C. Inside the insect’s defense system, there are two chambers: the larger inner chamber (called the “reservoir” or “collection bladder”) empties into the smaller outer one (called the “vestibule” or “explosion chamber”), which in turn empties into the outside world through an opening near the anus. There are two sets of these organs, one on each side of the anus. The collection bladder collects hydrogen peroxide and hydroquinone. The explosion chamber collects a brown gooey mixture of the two enzymes and has a thick chitin wall with numerous little holes in it through which single-celled glands secrete and deposit the enzymes into the chamber. When the insect’s defenses become stimulated, a muscle opens up and through this opening, the two chemicals are forced into the explosion chamber, where the enzymes cause them explode out of the insect’s derrière as oxygen, quinone, and water.”

    There are many points that I could address but lets just stick to the second chamber. It is not used to store hydroquinone, the first or storage chamber holds both the hydrogen peroxide and hydroquinone. Therefore, the second chamber serves no purpose until it is able to add the enzimes that cause the reaction (I know it does not explode)that heats, expands and is expelled.

    Therefore, the second chamber has no selective advantage until the whole system works. Not only this but there are valves, hardened linings etc, that have to appear also with no selection advantage before the system works.

    The problem is how this can evolve, one mutation at a time, by only RV + NS.

    Vague steps with out detail are easy to imagine until you get to the detail and order. This is where the just so stories fail to deliver.

    Cheers

  105. 105
    Me_Think says:

    Therefore, the second chamber has no selective advantage until the whole system works. Not only this but there are valves, hardened linings etc, that have to appear also with no selection advantage before the system works.

    That is the whole point. The chamber doesn’t evolve for ‘system’ to work. It evolves from the precursor to the chamber which forms as an extension of secretory cells to produce and store more hydroquinone. The more hydroquinone, the more unpalatable the beetle becomes to the predators,while other beetles with lower hydroquinone’s population decreases, high hydroquinone beetle survives to next generation. It is a case of simple Predator-Prey dynamics.

  106. 106
    Zachriel says:

    gpuccio: I am denying that what you call “the prerequisites” for an “evolutionary history” which is not known are of any help in explaining the known biological history in terms of RV + NS.

    Of course they are. As evolution posits incremental changes, having prerequisites is a prediction of the theory. Finding those prerequisites in extant organisms, as well as intermediate forms, is a confirmation of that prediction. See Darwin 1859.

    gpuccio: So, the “explanation” presented in Wikipedia for the “Evolution of the defense mechanism” is no explanation at all. If we take it simply as a description of a few facts of natural history, it’s fine, but as an explanation, it is a fairy tale.

    A plausible history shows that there is an evolutionary pathway, something denied by ID enthusiasts. (“The reason I posted the Bombardier Beetle is because it’s defence mechanism is an great example of a system that could not develop by one mutation at a time.”) It’s also something that can be tested through further research.

    gpuccio: You could certainly describe a lot of intermediate states, many of them with some functional properties. That’s exactly what happens in the design process.

    The difference is that for most paintings, we can see that it is incomplete until finished. With evolution, every species in a lineage is viable.

  107. 107
    gpuccio says:

    Zachriel:

    Evolution posits incremental changes that can be explained by RV and NS. Incremental changes which are not of that kind will not help.

    A drawing prepared for a painting can be considered “complete”, but it is not the final painting. Viable is not the same as complete. In software development, the different versions of Windows can probably be considered viable (with a little bit of optimism), or “complete” ( with great imagination), but new functions, correction of bugs and different perspectives are added as time goes by.

  108. 108
    Zachriel says:

    gpuccio: Evolution posits incremental changes that can be explained by RV and NS.

    Yes. Part of that is incremental changes. So we are in agreement concerning the history of incremental changes, then?

    gpuccio: A drawing prepared for a painting can be considered “complete”, but it is not the final painting.

    Evolution posits that organisms are not ‘studies’ for some future, but are adapted to their own environment.

    gpuccio: In software development, the different versions of Windows can probably be considered viable (with a little bit of optimism), or “complete” ( with great imagination), but new functions, correction of bugs and different perspectives are added as time goes by.

    Sure, but the steps between versions are too vast to be explained by incremental change. That, and the evidence of human designers, of course.

  109. 109
    gpuccio says:

    Zachriel:

    “Sure, but the steps between versions are too vast to be explained by incremental change.”

    Which is, exactly, ID’s point. The steps can never be explained by simple incremental changes, with the exception of the few documented cases of microevolution.

    That’s why the concept of CSI has been developed and applied.

  110. 110
    Zachriel says:

    gpuccio: Which is, exactly, ID’s point.

    Yes.

    gpuccio: The steps can never be explained by simple incremental changes, with the exception of the few documented cases of microevolution.

    There is a great deal of evidence of incremental change within the parameters of evolutionary history.

  111. 111
    Box says:

    Zachriel: There is a great deal of evidence of incremental change within the parameters of evolutionary history.

    could you provide us with some examples?

  112. 112
    Piotr says:

    #102 Gpuccio,

    Intermediate states are observed in all the cases of design we know of.

    They are often necessary at the level of the conscious representation: the form which is designed is often gradually changing during the process, as the cognitive functions of consciousness, and its purposes, act on the inputs which come from the world.

    And they are certainly necessary at the level of implementation: the painter has to prepare the canvas, then draw a ketch to guide the realization of the colours, and so on. That is true, even in the rare case that the designer already has a complete representation of the final work just from the beginning.

    But “intermediate forms” in biology are not sketches or half-finished prototypes. Every species is fully viable. We call some of them “intermediate” or “transitional” only because they can be used to illustrate an evolutionary sequence, not because they require further development according to some teleological scenario. The existence of transitional forms is predicted by evolutionary biology whatever the mechanism of evolution. I suppose they could be made compatible with guided evolution involving design (depending on how the designer is supposed to work), but they don’t represent the specific prediction of a (currently non-existent) theory of design.

    That from you, a linguist? I am surprised. Are you encouraging all artists, including writers, to destroy all “imperfect prototypes”? In name of what?

    Do you think artists typically document every stage of their work for posterity? Anyway, as I said above, there are no “imperfect prototypes” in biology, because every living species is a finished product. There are many bombardier beetles; their mechanisms of bombardment are similar but not identical; and although the particular mechanism used by Metrius looks less sophisticated, Metrius is not an imperfect prototype of its better-known cousins such as Brachinus

    I do propose what the designer is: a conscious, intelligent, purposeful being, probably not physical, who acts in ways that are similar to the ways we act when we design. That is my prediction, and my argument.

    Let’s test your prediction. Where is the agent of intelligent design? I would like to compare it with your description.

    OK, you needn’t bother. I don’t really think “the ways we act to design” have any relevance to the origin and evolution of life. If you were to “design” a cat, how would you go about it? How do we humans design cats?

  113. 113
    gpuccio says:

    Piotr:

    There are “intermediate forms” and variants, both in biology and in human design. Different species can be considered variants, like different vesions of Windows. But the gradual emergence of new proteins and pathways could configure intermediate forms, like when we find a new gene gradually arising by transposon activity, and finally activated in a new species (as you know, there are examples even in primates).

    You say:

    “I suppose they could be made compatible with guided evolution involving design”

    Indeed, they are perfectly compatible with it.

    And again, you say:

    “The existence of transitional forms is predicted by evolutionary biology whatever the mechanism of evolution.”

    The existence of intermediates and variants is predicted by common descent. They exist, and CD is the best explanation. The specific mechanism of RV + NS, instead, makes other predictions: intermediates that are naturally selectable, and which can be reasonably explained by RV in the range of what RV can do at the molecular level.

    Those intermediates are exactly what is missing, as I have discussed many times.

    You say:

    “Do you think artists typically document every stage of their work for posterity? ”

    Not every stage, but they often document stages. And we know that many things in biology have been cancelled. So, where is the difference?

    You say:

    “Anyway, as I said above, there are no “imperfect prototypes” in biology, because every living species is a finished product.”

    That is a strange statement. One of the recurrent arguments of neo darwinists against design is that there are many imperfect implementations in nature. I agree, and I have often argued that design needs not be perfect design, except in the imagination of pseudo criticists who only want, for their reasons, to exclude a perfect designer (God, I suppose).

    So, do you really think that every “product” is perfect in biology? And it is strange that you speak of species as “finished products”. Isn’t evolution a constant process? Design certainly is, IMO.

    You say:

    “Metrius is not an imperfect prototype of its better-known cousins such as Brachinus”

    It’s a different implementation, but, if I understand what you say, it is also less efficient. Where do you draw a line which divides diversity from imperfect implementation?

    You say:

    “Let’s test your prediction. Where is the agent of intelligent design? I would like to compare it with your description.”

    The agent of Intelligent Design is wherever we can observe an act of biological design (not human). Our growing understanding of biology will test my prediction. And it will test the false explanations of neo darwinism, too.

    You say:

    “OK, you needn’t bother. I don’t really think “the ways we act to design” have any relevance to the origin and evolution of life. If you were to “design” a cat, how would you go about it? How do we humans design cats?”

    I really don’t understand what you mean. Humans design simpler things: computers, cars, proteins sometimes, biological tests, paintings, books. We cannot yet design a cat. And I cannot paint Leonardo’s Virgin of the rocks. And so?

    Each designer has his specificities, talents and limitations.

    Now, the simple point is: if design has relevance to the origin and evolution of life, then “the ways we act to design” certainly have relevance too, because all we know of the design process comes from human design.

    I understand that you don’t believe that, but then why do you come here to discuss, and then you tell me that I “needn’t bother” to express my point of view?

  114. 114
    Joe says:

    Hangonasec:

    Explain something biological without reference to the failure of ‘Darwinism’.

    First off science mandates the elimination of necessity and chance before the design inference is considered. That means if Darwinian processes can explain it then we don’t infer an intelligent designer was required.

    Next start with ATP synthase- two unrelated functional subsystems coming together to perform a function neither one could by itself. ATP synthase has ALL of the hallmarks of intelligent design.

  115. 115
    Hangonasec says:

    Cross @104:

    Vague steps with out detail are easy to imagine until you get to the detail and order. This is where the just so stories fail to deliver.

    A statement dripping with irony, for the critic of ID theory!

    Hydroquinone does not need to be expelled by forceful reaction to be noxious. It can merely collect in a sac and be secreted. The addition of catalase/peroxidase can wait. Gish made the error of insisting that a de-inhibitor and an inhibitor were required to provide IC. He was wrong. It isn’t IC. If hydroquinone and peroxide can be separately defensive, without accelerant enzymes, where’s the IC bit come in?

    Of course, you can just keep saying ‘no, doesn’t work’ to any and all possibilities.

  116. 116
    Zachriel says:

    Box: could you provide us with some examples?

    Try looking at a phylogenetic tree; dinosauria, for instance.
    http://www.gavinrymill.com/din.....mplete.jpg

    gpuccio: The specific mechanism of RV + NS, instead, makes other predictions: intermediates that are naturally selectable, and which can be reasonably explained by RV in the range of what RV can do at the molecular level.

    Sure. A canonical example is the mammalian middle ear, where each step increased auditory sensitivity while maintaining jaw function. First predicted from studies of embryos, it is also supported by paleontological and molecular data.

  117. 117
    gpuccio says:

    Zachriel:

    Did you miss “at the molecular level”?

  118. 118
    gpuccio says:

    Zachriel:

    To be more clear, molecular steps which are naturally selectable and in the range of reasonable RV, and which, cumulatively, bring about new complex functional information.

    Such as intermediates to ATP synthase, ordered in a sequence of small molecular variations (let’s say 2-3 AAs), with each step functional and naturally selectable?

  119. 119
    Zachriel says:

    gpuccio: Did you miss “at the molecular level”?

    “First predicted from studies of embryos, it is also supported by paleontological and molecular data.” How else did you think hereditary morphological changes occur other than by changes in developmental genes?

    However, more broadly, morphological evolution demonstrates the power of evolution to create complex structures, contrary to claims that evolution is insufficient. The direct evidence for molecular transitions will necessarily be limited.

  120. 120
    Zachriel says:

    gpuccio: Such as intermediates to ATP synthase, ordered in a sequence of small molecular variations (let’s say 2-3 AAs), with each step functional and naturally selectable?

    Notably you point to a very ancient transition. ID resides in the gaps. In any case, molecular variations can include more than simple mutations. ATP synthase is thought to be a combination of two more primitive molecules.

  121. 121
    Piotr says:

    The existence of intermediates and variants is predicted by common descent. They exist, and CD is the best explanation. The specific mechanism of RV + NS, instead, makes other predictions: intermediates that are naturally selectable, and which can be reasonably explained by RV in the range of what RV can do at the molecular level.

    What predictions does intelligent design make instead?

    Those intermediates are exactly what is missing, as I have discussed many times.

    There are plenty of examples; Zachriel has just given one, and it would be easy to find others — e.g. the evolution of internal fertilisation and viviparity in poeciliid fish, where various transitional stages are still retained in different members of the family.

  122. 122
    Joe says:

    By Zachriel’s “logic” archaeology and forensic science reside in the gaps. And no, there isn’t any genetic evidence to support the alleged evolution of the mammalian middle ear. Let alone evolving via differing accumulations of genetic accidents, errors and mistakes.

  123. 123
    Joe says:

    Intelligent Design predicts we will observe structures that can only be explained by intelligent agency activity.

  124. 124
    CHartsil says:

    “Intelligent Design predict we will observe structures that can only be explained by intelligent agency activity.”

    Even if that were a valid prediction, you still have yet to show that they were produced by intelligence in the first place. Just asserting “They’re really complex, so they must have been designed” does not make it so

  125. 125
    Joe says:

    CH- What does unguided evolution predict?

    And ID has a methodology for determining design. Your position doesn’t even have a methodology

  126. 126
    Box says:

    Zachriel #116,
    Could you provide other ‘evidence’ for incremental change besides cladistics, because that stuff is build on the assumption that the groups are related by common descent and often ignores the fossil record?

  127. 127
    Hangonasec says:

    Box @126 – molecular cladistics may legitimately ignore the fossil record (and may not have one anyway), and typically takes as a null hypothesis that the data are not related, with all similarites due to ‘chance’. The null is rejected if there is strong support for doing so – ie, if the data indicate relatedness. ‘Assuming relatedness’, as a failing of cladistic analysis, is a Creationist canard.

  128. 128
    Box says:

    Hangonasec: ‘Assuming relatedness’, as a failing of cladistic analysis, is a Creationist canard.

    And I’m not even a creationist. The point here is that Zachriel is going to provide “evidence of incremental change within the parameters of evolutionary history” and cladistics seems inappropriate for reasons given. Would you accept as evidence for the existence of God the cataloging of lightning strikes by a religious group that assumes that every strike of lightning is proof of His existence?
    I’m expecting something like Darwin’s finches 🙂

  129. 129
    gpuccio says:

    Zachriel:

    Could you please detail the molecular data and the changes in developmental genes you refer to?

    Thank you.

  130. 130
    gpuccio says:

    Piotr:

    “What predictions does intelligent design make instead?”

    Easy. That the complex functional information we observe is beyond any explanation by RV and NS. That the growing understanding of biological complexity at all levels, especially at the regulation level (epigenetics) will unravel ever new levels of organized functional complexity, ever more beyond any explanation by RV and NS. That the input of active functional information into biological molecules and systems in the course of natural history will be growingly evident as our understanding of biological system increases. That the functional space of proteins will be shown to be made of functional islands beyond the power of any unguided evolutionary search. And so on.

  131. 131
    gpuccio says:

    Piotr:

    “the evolution of internal fertilisation and viviparity in poeciliid fish, where various transitional stages are still retained in different members of the family”

    Molecular details, please.

  132. 132
    Cross says:

    Me_Think @ 105

    “That is the whole point. The chamber doesn’t evolve for ‘system’ to work. It evolves from the precursor to the chamber which forms as an extension of secretory cells to produce and store more hydroquinone. The more hydroquinone, the more unpalatable the beetle becomes to the predators,while other beetles with lower hydroquinone’s population decreases, high hydroquinone beetle survives to next generation. It is a case of simple Predator-Prey dynamics.”

    So we are now at co-option, another of evolution’s magic tricks. Next I suppose is HGT? I would guess then that the beetle had two extra anus before the defense mechanism worked and this helped it crap itself quicker and run, they were later co-opted for use as targeting apparatus? 😉

    Anyway, I reinterate, the second chamber does not hold hydroquinone. It holds the excretion glans for the enzimes which are only needed for the final system.

    Thanks for the debate but it’s clear we are not going to get anywhere.

    I am just glad that airliners are designed by engineers and not darwinists. 😉

    Cheers

  133. 133
    Cross says:

    Hangonasec @ 115

    “If hydroquinone and peroxide can be separately defensive, without accelerant enzymes, where’s the IC bit come in?”

    Then if it is successful without the enzymes, why does the complicated additional system evolve at all?

    Anyway, see my post above to Me_think, we are not going to get anywhere if we don’t get into the detail.

    Cheers

  134. 134
    PaV says:

    Zachriel:

    They have. See Ley et al., Evolution of mammals and their gut microbes, Science 2008.

    Have they “evolved,” or simply “changed”?

    I’ve looked at the abstract, and there they talk about “co-evolution.” How could they know this has happened? They only know present day differences as they were examining the fecal products of modern-day mammals.

    Even if we could go back in time and show that these “populations” have changed with time, you start with a mammal, you end up with the same mammal; you start with a gut bacteria and you end up with a gut bacteria. To call this “evolution” is to trivialize the common-sense understanding of “evolution.”

    Wouldn’t it better to say that caterpillars “evolve” into butterflies? Yet, I don’t hear anyone speak like this. Why not?

    So much mischief comes from the misuse of language.
    The Devil is the Prince of Lies.

  135. 135
    Piotr says:

    #131 Gpuccio,

    Ask fish geneticists — I’m not one. It’s ironic that you demand an excruciatingly detailed molecular scenario for every example we discuss while remaining conveniently non-commitant about “the designer” and its methodology. Design details, please. Show us the evidence of teleological manipulation, and explain how it was done.

    Suppose I were able to lay out the molecular details and identify the crucial mutation in various poeciliid lineages: would you then ask me to prove that the mutations were not “designed”? What would prevent you from claiming that the mutations took place according to an unknown designer’s unspecified plan?

    How do you read the designer’s mind? Why should the designer have wanted to make most (though not all) New World poeciliids live-bearers while leaving all the stay-at-home African lineages oviparous? Did design fail in Africa, or was the plan restricted to the New World (and how do you know which was the case)?

  136. 136
    Piotr says:

    #134 PaV,

    So much mischief comes from the misuse of language.
    The Devil is the Prince of Lies.

    The mischief is all yours. “Evolution” has a well-established technical meaning in biology, so why do you equivocate, creating unnecessary confusion? You must be the devil’s minion.

  137. 137
    Zachriel says:

    Box: Could you provide other ‘evidence’ for incremental change besides cladistics, because that stuff is build on the assumption that the groups are related by common descent and often ignores the fossil record?

    Common descent provides the historical context to evaluate the evidence concerning mechanisms of change. If you reject common descent, then we have to start with that. Do you accept the evidence of the historical progression of first appearance over hundreds-of-millions of years from single-celled organisms to colonial organisms to chordates to vertebrates to gnathostomes to land vertebrates to amniotes to mammals to primates?

    gpuccio: Could you please detail the molecular data and the changes in developmental genes you refer to?

    Really? You don’t accept that changes to genes cause developmental changes? It’s an entire field of study. Did you want an overview, or were you asking for seminal studies in the field? For the former, try Moody (editor), Principles of Developmental Genetics, Academic Press 2007. For the latter, it was a long process of accumulating knowledge, but it was Edward B. Lewis who discovered homeotic genes, which was crucial for forging the relationship between development and genetics. See also, the review issue, The evolution of evo-devo biology, PNAS 2000.
    http://www.pnas.org/content/97.....ialFeature

    PaV: How could they know this has happened?

    While bacterial host specificity suggests coevolution, they considered the possibility that it was due to dietary preference. They searched for evidence of codiversification, and found that the bacterial phylogeny matched the mammalian phylogeny more often than expected by chance alone.

    PaV: Wouldn’t it better to say that caterpillars “evolve” into butterflies?

    No. That process is called metamorphosis, a part of the developmental life cycle of the butterfly.

  138. 138
    Eric Anderson says:

    Mark Frank @40:

    We have not used neo-darwinian techniques to address our own problems because there isn’t enough time. Whether there is enough time for these techniques to create life over 4 billion years is a different question.

    Fair enough and thank you for the clarification.

    Yet this is where the computer is supposed to step in. What would take millions of years in real life can be simulated in hours or days on a computer. So, again, the question remains: Why do these (allegedly simple and straight-forward) processes of Neo-Darwinism not produce much of interest when run in silico? The computer is supposed to deal with the time issue.

    So we have two options, really:

    1. The evolutionary algorithms (including those that have received much attention and fanfare), don’t in fact really simulate evolutionary processes accurately. That is why nothing much of interest occurs, even over the simulated timeframes that would be relevant for evolution.

    or

    2. Evolutionary processes are impotent to produce much, even when properly-configured algorithms provide ample simulated time.

    Or perhaps both.

  139. 139
    Box says:

    Zachriel: Common descent provides the historical context to evaluate the evidence concerning mechanisms of change.

    So, one has to accept CD in order to evaluate the evidence for CD? At least, that seems to be what you are saying, because your “incremental change within the parameters of evolutionary history” (#110) more or less equates with CD, right? Or to put it differently, CD more or less implies incremental change – the very thing that needs to be evidenced.

    I disagree with your assessment that I have to accept CD first, before you can present your evidence for “incremental change within the parameters of evolutionary history”. Why should it matter whether I believe in CD or not? Why should it stop you presenting that evidence? Just don’t start off with cladistics, because of reasons given.

    Zachriel: If you reject common descent, then we have to start with that.

    I’m not saying that I do or don’t. However, to be clear, I reject any blind watchmaker evolution nonsense.

    Zachriel: Do you accept the evidence of the historical progression of first appearance over hundreds-of-millions of years from single-celled organisms to colonial organisms to chordates to vertebrates to gnathostomes to land vertebrates to amniotes to mammals to primates?

    For now I reject the idea of a smooth progression. The fossile record doesn’t allow me to.

  140. 140
    franklin says:

    Box

    I’m not saying that I do or don’t. However, to be clear, I reject any blind watchmaker evolution nonsense.

    How do you determine what is ‘blind watchmaker evolution’ and what is not ‘blind watchmaker evolution’?

    Box

    For now I reject the idea of a smooth progression. The fossile record doesn’t allow me to.

    If the fossil record does not allow you to reject a smooth progression on what grounds are you rejecting the fossil evidence of a smooth progression?

  141. 141
    Box says:

    Franklin: How do you determine what is ‘blind watchmaker evolution’ and what is not ‘blind watchmaker evolution’?

    IMO the concept “blind watchmaker evolution” – a purposeless and undirected process that produced life and mankind accidentally – is nonsense.

    Franklin: If the fossil record does not allow you to reject a smooth progression on what grounds are you rejecting the fossil evidence of a smooth progression?

    You got me wrong. The fossil record does not allow me to accept a smooth progression. There is no fossil evidence of a smooth progression.


    edit: only now I notice that in #139 I did not write coherently (last sentence). I thank Franklin for the chance to clear matters up.

  142. 142
    franklin says:

    Box

    IMO the concept “blind watchmaker evolution” – a purposeless and undirected process that produced life and mankind accidentally – is nonsense.

    your, reply does not answer the question I asked. Let me post it again in hope that you will answer it:

    How do you determine what is ‘blind watchmaker evolution’ and what is’ not blind watchmaker evolution?’

    Box

    The fossil record does not allow me to accept a smooth progression.

    so what is your ‘rabbit in the cambrian’ that disrupts the smooth progression?

    :

  143. 143
    gpuccio says:

    franklin:

    “How do you determine what is ‘blind watchmaker evolution’ and what is’ not blind watchmaker evolution?’”

    CSI is the key. As you should know, if you are familiar with ID theory.

  144. 144
    gpuccio says:

    Zachriel:

    “You don’t accept that changes to genes cause developmental changes?”

    I am surprised that you don’t understand. Understanding is not your problem, usually.

    Of course I accept that changes to genes cause developmental changes. So, your encouragement to pusrue better knowledge of evo devo is completely out of context.

    What I asked was:

    “Could you please detail the molecular data and the changes in developmental genes you refer to?”

    It was you who said that:

    “A canonical example is the mammalian middle ear, where each step increased auditory sensitivity while maintaining jaw function. First predicted from studies of embryos, it is also supported by paleontological and molecular data.”

    So, I was just asking for references to the molecular data which support that specific transition.

    Why? Because, as you can see if you look at my answer to franklin in post #143, in ID “CSI is the key”.

    My point is simple: we can evaluate a transition from the point of view of ID and of neo darwinist plausibility only if we know the molecular basis of that transition. Why? Because, as you say, it’s “changes to genes” that cause developmental changes

    ID theory and neo darwinism are attempts at exlaining the causes of those “changes to genes”. IOWs, they are theories about the possible causes of known causes.

    That’s why we cannot reason about the developmental changes, unless we know the molecular transitions which cause them. It’s those molecular transitions which must be evaluated for their information content, smooth gradualism or lack of it, and explanatory power of the respective theories.

    That’s why I asked you references about the details of the molecular transitions which, according to what you have said, support the developmental changes that, in your opinion, are good examples in favor of your theory.

  145. 145
    gpuccio says:

    Piotr at #135:

    Even if it may seem rude, I would ask you to read my previous two posts (#143 to franklin and #144 to Zachriel), because in principle they answer all your comments.

    You say:

    Ask fish geneticists — I’m not one.

    But it was not “fish geneticists” who came to this blog to comment on my statement:

    “Those intermediates are exactly what is missing, as I have discussed many times.”

    It was you who, answering that specific line, stated:

    There are plenty of examples; Zachriel has just given one, and it would be easy to find others — e.g. the evolution of internal fertilisation and viviparity in poeciliid fish, where various transitional stages are still retained in different members of the family.

    So I ask you, and not fish geneticists, as it is my natural right in a discussion.

    You say:

    It’s ironic that you demand an excruciatingly detailed molecular scenario for every example we discuss while remaining conveniently non-commitant about “the designer” and its methodology.

    I love irony, but I am afraid that I can see none here. I have never demanded an “excruciatingly detailed molecular scenario”. I have just asked for a molecular scenario, of any kind and quality. None has ever materialized.

    If you give me a molecular scenario, I can discuss it. If you give me none, I cannot discuss anything. That’s why I ask.

    It’s you and Zachriel who suggest that you have molecular scenarios, and then refuse to say what it is. It’s not my fault. Next time, please consider, before writing, that some intelligent readers may be there, and that they will ask natural questions about what you wrote.

    And, frankly, I think that it is unfair of you to say that I remain “conveniently non-commitant about “the designer” and its methodology”. I think that I have always discussed openly what we can say of the designer from an ID scientific point of view, and what we can’t, including what IMO we will be able to say in the future, as information accumulates. IN this same thread, for example, I have answered to you:

    “The techniques are not really “completely unknown”. Guided mutations, for example by guided transposon activity, is IMO something that we are beginning to detail. Many other details can be discovered.”

    You say:

    Suppose I were able to lay out the molecular details and identify the crucial mutation in various poeciliid lineages: would you then ask me to prove that the mutations were not “designed”? What would prevent you from claiming that the mutations took place according to an unknown designer’s unspecified plan?

    Sometimes I wonder if you remember the many discussion we had in the past. You should know very well that I would never ask you “to prove that the mutations were not designed”. Why do you say such nonsense?

    You should know my methodology, which is simply ID methodology:

    a) I would test the known data for dFSCI in the object.

    b) If dFSCI is appropriately detected, I would infer design for the object.

    c) You are free to show that I am wrong, explaining how the observed object can be explained in other credible ways, which do not include a design process. IOWs, you are free to falsify my scientific inference, if you can. And Popper will be happy that you can try, either you succeed or not. That’s how science works.

    As you can see, nowhere in my methodology I am asking you to “prove that the mutations were not designed”.

    It’s usually neo darwinists who ask us to “prove that the mutations were not the result of some unknown non design process”. It’s neo darwinists who use a bad epistemology, not us.

    So, when you say:

    What would prevent you from claiming that the mutations took place according to an unknown designer’s unspecified plan?

    The answer is simple: I would never do that. If dFSCI is not present, I will never infer design. It’s because dFSCI is present that I infer design. So, if no dFSCI is there, you can be quiet and happy: no design inference will be proposed.

    And, as you should know, the evaluation of dFSCI has nothing to do with the designer’s “plan”, either specified or unspecified. It only requires that any observer (not the designer) may give an objective definition of a function that can be implemented using the object, and that the measure of the digital information necessary to implement that function be beyond an appropriate threshold for the system we are evaluating, where the object originated.

    As you can see, there is absolutely no mention of designer’s plans in this procedure.

    That said, it is obvious that your last paragraph:

    How do you read the designer’s mind? Why should the designer have wanted to make most (though not all) New World poeciliids live-bearers while leaving all the stay-at-home African lineages oviparous? Did design fail in Africa, or was the plan restricted to the New World (and how do you know which was the case)?

    has no relevance at all to my discussion.

    Just a final comment. It is sad to see that intelligent interlocutors like you and Zachriel seem to ignore completely the theory you are criticizing (at least when that is convenient for your discussion), and go back to generic and false arguments, while in other cases you are certainly able to make more specific and relevant points.

  146. 146
    Piotr says:

    Gpuccio:

    If you give me a molecular scenario, I can discuss it. If you give me none, I cannot discuss anything. That’s why I ask.

    Can you, really? And what do you mean by a molecular scenario? The sequence of mutations enabling an innovation? Or maybe the full molecular history of the whole population, so that we can see all the alternative developments, including all the neutral and deleterious ones (otherwise you could always claim that what we see confirms directed evolution)?

    What would you do with those data, even if it were humanly possible to provide them? Can you do the maths you’d have to do to show that there has been a significantly-larger-than-predicted proportion of mutations, transposon activity, etc., conspiring to achieve a putative functional objective?

    You would probably fall back on the same weary references to Axe and Gauger & Axe, “disproving” the unguided evolvability of any non-trivial function a priori. As long as you believe their results are established science, you won’t be convinced by any molecular scenario, or rather you will interpret any scenario resulting in evolutionary novelty as “evidence of design”.

    It’s usually neo darwinists who ask us to “prove that the mutations were not the result of some unknown non design process”. It’s neo darwinists who use a bad epistemology, not us.

    Bad epistemology? Absence of design (or teleology in general) is the default possibility. You can falsify it by demonstrating design or purpose.

    The answer is simple: I would never do that. If dFSCI is not present, I will never infer design. It’s because dFSCI is present that I infer design. So, if no dFSCI is there, you can be quiet and happy: no design inference will be proposed.

    OK, but if there is a whole bunch of novel functions connected with viviparity (internal fertilisation, requiring rather complex anatomical and behavioral changes in both sexes, and matrotrophy, complete with the development of a sort of placenta), I’m pretty sure you’ll invoke dFSCI and “infer design”. Any transitional state will then become additional evidence of the designer’s work (experimenting with prototypes). Not that I care much, because I don’t think dFSCI (or CSI, or anything of the sort) is a valid notion in the first place. The “digital information” can’t be reliably measured for any real-life situation, and you really “infer design” by eyeballing the evidence, not by doing the maths. You may impress some of the UD readership, but you are preaching to the choir here.

  147. 147
    Joe says:

    Zachriel:

    That process is called metamorphosis, a part of the developmental life cycle of the butterfly.

    And ANOTHER biological process unguided evolution cannot explain.

    Thanks again Zachriel!

  148. 148
    gpuccio says:

    Piotr:

    Can you, really?

    Yes. Test me. Give me the molecular scenario.

    Bad epistemology? Absence of design (or teleology in general) is the default possibility. You can falsify it by demonstrating design or purpose.

    Bad epistemology. The null hypothesis is an explanation based on reasonable random variation. Alternative hypotheses can be explanations based on known laws, or design. Your epistemology is bad.

    OK, but if there is a whole bunch of novel functions connected with viviparity (internal fertilisation, requiring rather complex anatomical and behavioral changes in both sexes, and matrotrophy, complete with the development of a sort of placenta), I’m pretty sure you’ll invoke dFSCI and “infer design”.

    Only if dFSCI is present in the proteins or molecules implementing the new functions.

    Any transitional state will then become additional evidence of the designer’s work (experimenting with prototypes).

    Not if you give me a series of transitional states which are naturally selectable, each of which could arise by reasonable RV (IOWs, naturally selectable transitions which do not exhibit dFSCI).

    Not that I care much, because I don’t think dFSCI (or CSI, or anything of the sort) is a valid notion in the first place.

    Your choice.

    The “digital information” can’t be reliably measured for any real-life situation, and you really “infer design” by eyeballing the evidence, not by doing the maths.

    That is simply not true. I have done the math many times. If you don’t agree with my math and methodology, that’s your choice, but you cannot say that I haven’t done the math, because I have.

    You may impress some of the UD readership, but you are preaching to the choir here.

    I don’t want to impress anyone. And I am not preaching. I am just expressing my ideas to all intelligent people who want to discuss them. The same as you, I suppose.

  149. 149
    Joe says:

    Piotr, It is very telling that you and your ilk cannot lead by example. You cannot produce testable hypotheses for unguided evolution. You cannot produce a model for it. When checked against observation and experiment evolutionism is impotent.

    BTW “we don’t know” is the default position. Are you really that out of it tat you think your position is the default and can “win” without supporting evidence and science?

  150. 150
    Joe says:

    Zachriel:

    Common descent provides the historical context to evaluate the evidence concerning mechanisms of change.

    Anyone wishing for UCD needs to deal with the following:

    Loci that are obviously variable within natural populations do not seem to lie at the basis of many major adaptive changes, while those loci that seemingly do constitute the foundation of many if not most major adaptive changes are not variable.- John McDonald, “The Molecular Basis of Adaptation: A Critical Review of Relevant Ideas and Observation”, Annual Review of Ecology and Systematics: 14, 1983, p77-102

    Strange how they just ignore those facts.

  151. 151
    Joe says:

    Piotr:

    Design details, please.

    That doesn’t have anything to do with ID. Please grow up.

  152. 152
    Zachriel says:

    Eric Anderson: What would take millions of years in real life can be simulated in hours or days on a computer.

    As pointed out, the computational resources of a computer are very limited. In a human gut, there are about 10^14 bacteria, of several thousand species, each with a genome of about 10^6, which can replicate every few minutes. There are about 10^10 human guts, and a like number of cattle. Now, add in the gut bacteria in termites.

    Box: one has to accept CD in order to evaluate the evidence for CD?

    One should not ignore the evidence for an historical progression. That history is important for evaluating the mechanisms of that progression.

    Box: Why should it matter whether I believe in CD or not?

    Because it’s a well-supported scientific finding, and forms the basis for determining the mechanisms of adaptation.

    Box: I’m not saying that I do or don’t.

    Can any of your neighbors tell, Box? I’ll ask them.

    Box: For now I reject the idea of a smooth progression.

    That wasn’t the question. Do you accept the evidence of the historical progression of first appearance over hundreds-of-millions of years from single-celled organisms to colonial organisms to chordates to vertebrates to gnathostomes to land vertebrates to amniotes to mammals to primates?

  153. 153
    Box says:

    Franklin #142,

    Franklin: How do you determine what is ‘blind watchmaker evolution’ and what is’ not blind watchmaker evolution?’

    Franklin, for me blind watchmaker evolution is a non-starter. Philosophical arguments against naturalism and a naturalistic account of life prevent me to consider blind watchmaker evolution as a viable option.
    To name one such argument: under naturalism there is no force that accounts for the wholeness of an organism. IOW under naturalism there is no reason as to why distinct parts organize in a (supposedly non-existent) whole – the organism. Moreover under naturalism there is no reason for the continued existence of organisms – to not fall apart. Think about it: under naturalism organisms are an effect without a cause..
    Bottom line: it’s clear to me that organisms are not reducible to chemistry – are not bags of chemicals.
    So I’m not as kind to naturalism as many ID-proponents who, for the sake of argument, are willing to tag along with a naturalistic account of organisms and go on showing naturalism wrong even under its incoherent assumption.

    Franklin: so what is your ‘rabbit in the cambrian’ that disrupts the smooth progression?

    The Cambrian explosion is by no means the only explosion of life recorded in the fossil record. To name but a few sudden appearances: major fish groups, land plants, birds.

  154. 154
    Zachriel says:

    gpuccio: So, I was just asking for references to the molecular data which support that specific transition.

    Among several such studies, see Wilson & Tucker, Fgf and Bmp signals repress the expression of Bapx1 in the mandibular mesenchyme and control the position of the developing jaw joint, Developmental Biology 2004; Tucker et al., Bapx1 regulates patterning in the middle ear: altered regulatory role in the transition from the proximal jaw during vertebrate evolution, Development 2004.

    gpuccio: My point is simple: we can evaluate a transition from the point of view of ID and of neo darwinist plausibility only if we know the molecular basis of that transition. Why? Because, as you say, it’s “changes to genes” that cause developmental changes.

    If we see gradual change in structure, they are due to incremental changes in the underlying gene patterns.

    gpuccio: It’s those molecular transitions which must be evaluated for their information content, smooth gradualism or lack of it, and explanatory power of the respective theories.

    Are you suggesting that incremental changes in structure require non-incremental changes in genes?

  155. 155
    Piotr says:

    Yes. Test me. Give me the molecular scenario.

    What molecular scenario? There are about 30 genera and about 200 species of Poeciliidae, some oviparous, some viviparous, and some kind of in-between. Do you want me to show you the genome of the MRCA of the family (dating back at least to the Cretaceous) and all the transitions leading to one of the modern species over 100 million years? All we have is the modern genomes, and it would probably take years of and research to identify some of the genomic changes involved in viviparity and sketch their hypothetical sequence in time. So you are demanding something you know in advance nobody can provide. Then, since evolution (as normally understood) is opportunistic and not goal-oriented, which particular trait(s) would you treat as “the solution” in the search space?

  156. 156
    Zachriel says:

    Box: under naturalism there is no reason for the continued existence of organisms – to not fall apart.

    Really? Thought it was integumen and connective tissues.

    Box: it’s clear to me that organisms are not reducible to chemistry – are not bags of chemicals.

    Can you point to any observational evidence of something other than physical causes which keep organisms from “falling apart”?

  157. 157
    gpuccio says:

    Zachriel:

    I am not suggesting anything. I am asking for data and references, to evaluate and discuss. I will look at the one you have given, thank you.

  158. 158
    Joe says:

    Zachriel:

    Because it’s a well-supported scientific finding, and forms the basis for determining the mechanisms of adaptation.

    That is incorrect as the claim is not scientific. It cannot be tested.

    BTW unguided evolution cannot account for Bapx1- so tat would be a problem and we are sure you will continue to ignore it.

  159. 159
    gpuccio says:

    Piotr:

    “All we have is the modern genomes, and it would probably take years of and research to identify some of the genomic changes involved in viviparity and sketch their hypothetical sequence in time. ”

    I can wait.

    “So you are demanding something you know in advance nobody can provide.”

    No. I know nothing in advance, because I know nothing of the specific example you brought up. I just asked how we could evaluate your example and see if it is really a valid example. That’s all.

    If you have other examples, for which the research has been done, please point to them.

    If you have no examples, just say it.

    “Then, since evolution (as normally understood) is opportunistic and not goal-oriented, which particular trait(s) would you treat as “the solution” in the search space?”

    Those for which we can define complex functions, requiring complex specific information, according to my definition of dFSCI. Any function will do.

  160. 160
    Piotr says:

    #130 Gpuccio,

    That the input of active functional information into biological molecules and systems in the course of natural history will be growingly evident as our understanding of biological system increases. That the functional space of proteins will be shown to be made of functional islands beyond the power of any unguided evolutionary search.

    The former is ambiguous ID-speak. The latter has already been falsified e.g. by Andreas Wagner’s research, which you chose to shrug off, exchanging patronising jokes about multi-dimensional mumbo-jumbo with Dionisio. The maths there is difficult (for good reasons), but the gist of the argument is not difficult to understand.

  161. 161
    Piotr says:

    Gpuccio:

    No. I know nothing in advance, because I know nothing of the specific example you brought up. I just asked how we could evaluate your example and see if it is really a valid example. That’s all.

    This is more or less what is currently known about the molecular underpinnings of the evolution of viviparity in one poeciliid species (the platyfish):

    http://www.ncbi.nlm.nih.gov/pm.....474895.pdf

    Any signature of design there?

  162. 162
    gpuccio says:

    Piotr:

    “The maths there is difficult (for good reasons), but the gist of the argument is not difficult to understand.”

    Then please explain it to me. I made specific questions, and nobody cared to try to defend the argument. Do you?

  163. 163
    gpuccio says:

    Piotr:

    Thank you for the reference. I will look at it, and come back to you.

    Was it so difficult?

  164. 164
    gpuccio says:

    Piotr:

    By the way, ID-speak is what we IDists speak, just as Englishmen speak English. But you are a linguist, and I must certainly not explain that to you.

    That you find our language ambiguous is your respected opinion. As you certainly know, human languages are never context independent. If the unavoidable ambiguity is good or bad remains a personal choice.

  165. 165
    Piotr says:

    #163 Gpuccio,

    Was it so difficult?

    No, but I doubt if you will accept it as a “scenario”. The authors identify some of the genes that may be involved, they find evidence of selection acting on them, but of course they can’t offer a detailed step-by-step account of mutations occurring over tens of millions of years. Nobody can.

  166. 166
    Piotr says:

    #162 Gpuccio,

    The articles are highly technical; the book Arrival of the fittest (2014) is aimed at the interested (and moderately informed) non-specialist. Have you seen Richard Hoppe’s review on “Panda’s Thunb”?

    http://pandasthumb.org/archive.....agner.html

    It’s brief, but followed by an interesting discussion. It’s far more useful, IMO, than Mark Pagel’s review in Nature (I cringed at the “squid-to-albatross” example, which is Pagel’s, not Wagner’s, so you can’t blame the book for it).

    Many detailed “molecular scenarios” can be found in Robustness and evolvability in living systems, another semi-technical book by the same author (2013).

  167. 167
    Hangonasec says:

    Cross @133

    Hangonasec @ 115

    Me: “If hydroquinone and peroxide can be separately defensive, without accelerant enzymes, where’s the IC bit come in?”

    You: Then if it is successful without the enzymes, why does the complicated additional system evolve at all?

    Evolution does not postulate that adaptation finds an adaptive peak and remains there for eternity. Systems can be improved (measured in the currency of increased offspring numbers vs your conspecifics), which is the whole point of a directional selection scenario. And note that predators evolve too.

    Anyway, see my post above to Me_think, we are not going to get anywhere if we don’t get into the detail.

    Fair enough, but if you are going to declare a system IC, you need to consider – seriously consider – mechanisms that could achieve it without the requirement for complete assemblage on Day 1. “It’s IC because you have no hard evidence that it isn’t” is a somewhat dubious approach, isn’t it? There are numerous ways in which an apparently IC structure can arise. In order to be clear that IC is in fact present, one would have to satisfy oneself on those very ‘details’.

  168. 168
    markf says:

    EA

    Why do these (allegedly simple and straight-forward) processes of Neo-Darwinism not produce much of interest when run in silico?  –  – The computer is supposed to deal with the time issue.
    So we have two options, really:

    1. The evolutionary algorithms (including those that have received much attention and fanfare), don’t in fact really simulate evolutionary processes accurately. That is why nothing much of interest occurs, even over the simulated timeframes that would be relevant for evolution.

    or
    2. Evolutionary processes are impotent to produce much, even when properly-configured algorithms provide ample simulated time.

    It is option 1. Computer algorithms have never pretended to simulate all aspects of evolutionary processes. What they do is show is that darwinian-like processes can lead to unexpected, complicated responses to selectionary pressures.  This is not the same as creating solutions to mankind’s own problems and certainly not the same as creating solutions more quickly and elegantly than we can using our own expertise. For a start they are working within the physical limitations of a computer which places enormous limitations on the kind of solution that can come out of it.

  169. 169
    Box says:

    Zachriel: Can you point to any observational evidence of something other than physical causes which keep organisms from “falling apart”?

    Specifically organization and information. More generally, whenever we observe an organism we witness a whole – the organism – performing a dynamic balancing act or homeostasis. Naturalism offers no reason – no cause – whatsoever for this observation. If an organism is just a bag of chemicals, why does it behave that way?
    What force prevents the organism to simply fall apart? What force keeps things together for exactly a life time and not a moment longer?

    Naturalism offers us no answer.

  170. 170
    bornagain77 says:

    as to: “Can you point to any observational evidence of something other than physical causes which keep organisms from “falling apart”?”

    If you mean non-material causes that arise from outside space time, then Yes! There is observational evidence for non-local, beyond space and time, quantum entanglement ’causes’ within DNA (and even within proteins) which keep them from “falling apart”:

    Quantum entanglement in hot systems – 2011
    Excerpt: The authors remark that this reverses the previous orthodoxy, which held that quantum effects could not exist in biological systems because of the amount of noise in these systems.,,, Environmental noise here drives a persistent and cyclic generation of new entanglement.,,, In summary, the authors say that they have demonstrated that entanglement can recur even in a hot noisy environment. In biological systems this can be related to changes in the conformation of macromolecules.
    http://quantum-mind.co.uk/quan.....t-systems/

    Quantum entanglement holds together life’s blueprint – 2010
    Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours. “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford.
    http://neshealthblog.wordpress.....blueprint/

    Does DNA Have Telepathic Properties?-A Galaxy Insight – 2009
    Excerpt: DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn’t be able to.,,, The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible.
    per daily galaxy

    DNA Can Discern Between Two Quantum States, Research Shows – June 2011
    Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property.
    http://www.sciencedaily.com/re.....104014.htm

    Quantum Information/Entanglement In DNA – short video
    https://vimeo.com/92405752

    That ‘non-local’ quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints (Bell, Aspect, Leggett, Zeilinger, etc..), should be found in molecular biology on such a massive scale, in every DNA and protein molecule, is a direct empirical falsification of Darwinian claims, for how can the ‘non-local’ quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy) cause when the quantum entanglement effect falsified material particles as its own causation in the first place? Appealing to the probability of various ‘random’ configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply!

    Looking beyond space and time to cope with quantum theory – 29 October 2012
    Excerpt: “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,”
    http://www.quantumlah.org/high.....uences.php

    Closing the last Bell-test loophole for photons – Jun 11, 2013
    Excerpt:– requiring no assumptions or correction of count rates – that confirmed quantum entanglement to nearly 70 standard deviations.,,,
    http://phys.org/news/2013-06-b.....otons.html

    etc.. etc..

    In other words, to give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘special’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!

    And although Naturalists have proposed various, far fetched, naturalistic scenarios to try to get around the Theistic implications of quantum non-locality, none of the ‘far fetched’ naturalistic solutions, in themselves, are compatible with the reductive materialism that undergirds neo-Darwinian thought.

    “[while a number of philosophical ideas] may be logically consistent with present quantum mechanics, …materialism is not.”
    Eugene Wigner
    Quantum Physics Debunks Materialism – video playlist
    https://www.youtube.com/watch?list=PL1mr9ZTZb3TViAqtowpvZy5PZpn-MoSK_&v=4C5pq7W5yRM

    Why Quantum Theory Does Not Support Materialism By Bruce L Gordon, Ph.D
    Excerpt: The underlying problem is this: there are correlations in nature that require a causal explanation but for which no physical explanation is in principle possible. Furthermore, the nonlocalizability of field quanta entails that these entities, whatever they are, fail the criterion of material individuality. So, paradoxically and ironically, the most fundamental constituents and relations of the material world cannot, in principle, be understood in terms of material substances. Since there must be some explanation for these things, the correct explanation will have to be one which is non-physical – and this is plainly incompatible with any and all varieties of materialism.
    http://www.4truth.net/fourtrut.....8589952939

    Moreover, since quantum entanglement can be used as a ‘quantum information channel’ to perform quantum computation, then, as far as empirical science itself is concerned, Neo-Darwinism is falsified in its claim that information is ‘emergent’ from a material basis.

    Verse and Music:

    Colossians 1:17
    He is before all things, and in him all things hold together.

    ROYAL TAILOR – HOLD ME TOGETHER = music
    https://www.youtube.com/watch?v=vbpJ2FeeJgw

  171. 171
    Zachriel says:

    Zachriel: Can you point to any observational evidence of something other than physical causes which keep organisms from “falling apart”?

    Box: Specifically organization and information.

    Physical causes include how physical forces are organized.

    Box: What force prevents the organism to simply fall apart?

    The molecular forces in the integumen, among other things.

  172. 172
    Silver Asiatic says:

    What force keeps things together for exactly a life time and not a moment longer?

    Supposedly, there is this chemical thing called “life”. It’s the very same ‘property’ in a living cell, a tree, an elephant (in the room), and a human being. This supposed chemical property holds things together as ‘living organisms’. Then it goes away and ‘organisms’ become non-living chemicals again. Before this, the chemicals struggled to survive because chemicals want to live. They competed and diversified to become bombardier beetles, orchids, crocodiles – and to paint the Sistine Chapel ceiling. Then they went back to what they were before – just chemicals, no longer interested in surviving any more.

    As Zachriel said before, this is all explained by cell walls and skin.

  173. 173
    Zachriel says:

    Silver Asiatic: this is all explained by cell walls and skin.

    No, but it is the reason organisms don’t just “fall apart”.

  174. 174
    Box says:

    Zachriel: The molecular forces in the integumen, among other things.

    Do they prevent death – the disruption of homeostasis? Do you even contemplate the possibility that I might be talking about something else before you come up with one of your flimsy responses?

  175. 175
    Zachriel says:

    Box: Do they prevent death – the disruption of homeostasis?

    They are certainly one of the critical systems to maintaining homeostasis.

  176. 176
    bornagain77 says:

    SA at 172, that comment got a big smile out of me 🙂

    classic!

  177. 177
    Box says:

    BA77 #176,

    I second that 🙂

  178. 178
    gpuccio says:

    Piotr:

    Can’t you just simply explain the meaning of the argument, if you understand it and agree with it?

    From what I have heard up to now, I am really not interested in Wagner’s ideas, and up to now none of his (very few) fans here has offered anything to change my mind. Would you like to try?

  179. 179
    gpuccio says:

    Silver Asiatic:

    Maybe Zachriel’s is a skin-deep explanation. 🙂

  180. 180
    Box says:

    Zachriel: They [integumen, among other things] are certainly one of the critical systems to maintaining homeostasis.

    An incredible number of things is responsible of maintaining homeostasis. What we see is that all these quarks, atoms and molecules act as if they are coerced into perfect harmony with one goal in mind: to serve the organism. As if there is a conductor with overview(!) ordering them around. As if they are subordinate to the whole organism.
    Not only do we see this functional subordination in the cell, but also on macro-level. All the parts (organs, limbs and so forth) are all functionally subordinate to the whole organism.
    One could say that it is as if something immaterial, or rather someone, manifests itself in matter – yes even subjugates matter.

    However naturalism informs us that the whole thing is just appearance and accidental and that there is nothing but particles in motion without a common goal in mind.

  181. 181
    Zachriel says:

    Box: An incredible number of things is responsible of maintaining homeostasis.

    Yes, all of them apparently physical processes.

  182. 182
    Silver Asiatic says:

    Thanks, BA, Box & gpuccio 🙂

  183. 183
    Piotr says:

    Gpuccio:

    From what I have heard up to now, I am really not interested in Wagner’s ideas, and up to now none of his (very few) fans here has offered anything to change my mind. Would you like to try?

    If you are “not really interested” in something that might shatter the ID image of lonely islands of functionality amidst the hostile ocean of non-function, your mind may be made up so firmly that I shouldn’t bother. I’ll try nevertheless, though not tonight, Giuseppe.

  184. 184
    gpuccio says:

    Piotr:

    Thank you.

    No, my mind is not “made up so firmly”: I am open to all interesting contributions, either in favor of my ideas or against them.

    But I have many things to do and many interests, and only a little time, so I have to choose what I read or what I try to understand better. I rely very much on my intuition and my impressions.

    So far, I have really no good impressions about Wagner’s ideas. Least of all I have the impression that they “might shatter the ID image of lonely islands of functionality amidst the hostile ocean of non-function”. Not at all.

    Otherwise, I would read Wagner’s works very carefully, be sure of that.

    However, I will wait for your attempt to change my mind, seeing that the only other “Wagner fan” here, Me_Think, has apparently abandoned the field.

  185. 185
    Cross says:

    Hangonasec @ 157

    “Fair enough, but if you are going to declare a system IC, you need to consider – seriously consider – mechanisms that could achieve it without the requirement for complete assemblage on Day 1. “It’s IC because you have no hard evidence that it isn’t” is a somewhat dubious approach, isn’t it? There are numerous ways in which an apparently IC structure can arise. In order to be clear that IC is in fact present, one would have to satisfy oneself on those very ‘details’.”

    Believe it or not I have considered (over many years) the mechanisms that could achieve complex defense systems like the beetle and find RV + NS one mutation at a time sadly lacking when you look at the details. I should add that I have no problem with microevolution or adaption within very confined boundaries.

    On the surface some evo explanations look plausible (though not the beetle) until you look at the details. Where there are large gaps in the detail, the standard answer is “we don’t know” as if that is a scientific answer. The scientific answer should be, evolution as we understand it has a problem here, what are the alternatives.

    In the case in life where I see a complex system like say a jet engine, I conclude rightly that it was designed. Same with the beetles defense system, many parts that are all required to work together for the system to function. The evolution story needs to be detailed if you expect it to be believed possible. ie. the order of the assembly of the system, one mutation at a time that provides real selection advantage at each step, and the viability of the creature also at each step.

    This is where the evo story fails. The OOL, single to muli cell, cell division to sexual reproduction and many other “gaps” are left right out of evo stories because RV + NS one mutation at a time can not account for them.

    I suggest that you also, look into the details of what you believe and see if it fits. See if it fits in the hard bits to explain, not just the easy ones.

    Cheers

  186. 186
    Eric Anderson says:

    Piotr @136:

    “Evolution” has a well-established technical meaning in biology, so why do you equivocate, creating unnecessary confusion?

    Please, pray tell, what is this well-established technical definition?

  187. 187
    Eric Anderson says:

    gpuccio @184:

    Apologies for jumping in, but thought I would mention a couple of quick thoughts.

    I have not read Andreas Wagner’s new book, but if he has indeed succeeded in “solving evolution’s greatest puzzle,” as his book title claims, then I am sure a Nobel Prize awaits. 🙂

    In all seriousness, it looks like Wagner has done some interesting work, but I’m not sure why anyone would think that it somehow would overthrow intelligent design. Typical materialist propaganda, as far as I can tell, from those who tout every new finding as finally being the answer to the evolutionary puzzle — that is, until people look more closely and realize it isn’t.

    Just from the official description on Amazon, it looks like Wagner’s book focuses on potential mechanisms for doing what he acknowledges random mutations and natural selection cannot do within the timeframe available (a good acknowledgement, to be sure). Wagner argues that adaptations are driven “by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take.”

    By “set of laws,” presumably he is not referring to physical laws so much, but to the way things are set up in biological systems. I can’t quite tell from the description, but if he is arguing that organisms are set up in such a way that they can adapt quickly to their environment by sampling a subset of all theoretical possibilities, then that is an interesting result. Not particularly new. And not anything that would contract intelligent design. But no doubt some new good examples and analysis of recent research are provided.

    For some reason the old example of the antifreeze protein in the Arctic cod is offered as “an archetypal example of nature’s enormous powers of creativity.” So that perhaps gives us some feel for whether he has in fact offered up “the final puzzle piece in the mystery of life’s rich diversity.”

    Finally, I should say that (notwithstanding Wagner’s over-the-top title and descriptions of his work) it is perhaps the case that the materialist cheerleaders are claiming much more for his work than he claims himself. That happens all too often.

  188. 188
    Piotr says:

    #186 Eric Anderson,

    A short definition would be like this:

    Change in heritable traits in a population over successive generations

    You can develop it in various ways depending on what class of traits, what time depths and what aspects of the process you are interested in, but it captures the most important points: it’s populations, not individual organisms that evolve, and only heritable modifications (and changes in their frequency) count.

  189. 189
    bornagain77 says:

    gpuccio, Wagner’s model and book is a joke:

    Arrival of the Fittest: Natural Selection as an Incantation – November 17, 2014
    Excerpt: Once again, as with Avida and all the other computer models, we find that Wagner has snuck extra information into the system. As Dembski showed in No Free Lunch, no evolutionary algorithm is superior to blind search. Without design, there is no shortcut to the treasure.

    To make the hunt easier for evolution, Wagner imagines a fantasy land with treasures all over the place, right near each other: “Wagner finds that he does not have to travel very far along these mutational pathways before he encounters new neighbourhoods, where the networks produce different products,” Pagel explains sympathetically while personifying evolution. “For instance, a network that can consume glucose might lie near one that can consume other fuels, such as acetate.” Yes, and if a squid had wings, it could fly like an albatross. After all, they are neighbors.
    http://www.evolutionnews.org/2.....91261.html

  190. 190
    Joe says:

    Piotr:

    Change in heritable traits in a population over successive generations

    No one debates that, Piotr.

  191. 191
    bornagain77 says:

    as to

    “Change in heritable traits in a population over successive generations,,, it’s populations, not individual organisms that evolve, and only heritable modifications (and changes in their frequency) count.”

    Neutral Theory: The Null Hypothesis of Molecular Evolution
    The evolution of living organisms is the consequence of two processes. First, evolution depends on the genetic variability generated by mutations, which continuously arise within populations. Second, it also relies on changes in the frequency of alleles within populations over time.
    The fate of those mutations that affect the fitness of their carrier is partly determined by natural selection. On one hand, new alleles that confer a higher fitness tend to increase in frequency over time until they reach fixation, thus replacing the ancestral allele in the population. ,,,
    http://www.nature.com/scitable.....ecular-839

    Trouble with all that is that is not what we find in the empirical evidence:

    Study demonstrates evolutionary ‘fitness’ not the most important determinant of success – February 7, 2014 – with illustration
    Excerpt: An illustration of the possible mutations available to an RNA molecule. The blue lines represent mutations that will not change its function (phenotype), the grey are mutations to an alternative phenotype with slightly higher fitness and the red are the ‘fittest’ mutations. As there are so few possible mutations resulting in the fittest phenotype in red, the odds of this mutation are a mere 0.15%. The odds for the slightly fitter mutation in grey are 6.7% and so this is far more likely to fix, and thus to be found and survive, even though it is much less fit than the red phenotype.,,,
    By modelling populations over long timescales, the study showed that the ‘fitness’ of their traits was not the most important determinant of success. Instead, the most genetically available mutations dominated the changes in traits. The researchers found that the ‘fittest’ simply did not have time to be found, or to fix in the population over evolutionary timescales.
    http://phys.org/news/2014-02-e.....ccess.html

    This following headline sums the preceding finding up very nicely:

    Fittest Can’t Survive If They Never Arrive – February 7, 2014
    http://crev.info/2014/02/fitte.....er-arrive/

    In fact, despite decades of trying to ‘fix’ beneficial mutations in fruit flies, ‘selection did not lead to the fixation of newly arising unconditionally advantageous alleles’,,

    Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010
    Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator.
    http://www.arn.org/blogs/index.....ruit_flies

    More problems with neutral theory are outlined here:

    Natural Selection Struggles to Fix Advantageous Traits in Populations – Casey Luskin – October 23, 2014
    Excerpt: Michael Lynch, an evolutionary biologist at Indiana University,, writes that “random genetic drift can impose a strong barrier to the advancement of molecular refinements by adaptive processes.”2 He notes that the effect of drift is “encouraging the fixation of mildly deleterious mutations and discouraging the promotion of beneficial mutations.”3 Likewise, Eugene Koonin, a leading scientist at the National Institutes of Health, explains that genetic drift leads to “random fixation of neutral or even deleterious changes.”4
    http://www.evolutionnews.org/2.....90571.html

    Moreover, mutations aren’t ‘random’, as is presupposed in neutral theory (and in the modern synthesis in general), but are, for the vast majority of times, mediated by in a non-random fashion by sophisticated molecular machines:

    “It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works’
    James Shapiro – Evolution: A View From The 21st Century – (Page 82)

    WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Fully Random Mutations – Kevin Kelly – 2014
    Excerpt: What is commonly called “random mutation” does not in fact occur in a mathematically random pattern. The process of genetic mutation is extremely complex, with multiple pathways, involving more than one system. Current research suggests most spontaneous mutations occur as errors in the repair process for damaged DNA. Neither the damage nor the errors in repair have been shown to be random in where they occur, how they occur, or when they occur. Rather, the idea that mutations are random is simply a widely held assumption by non-specialists and even many teachers of biology. There is no direct evidence for it.
    On the contrary, there’s much evidence that genetic mutation vary in patterns. For instance it is pretty much accepted that mutation rates increase or decrease as stress on the cells increases or decreases. These variable rates of mutation include mutations induced by stress from an organism’s predators and competition, and as well as increased mutations brought on by environmental and epigenetic factors. Mutations have also been shown to have a higher chance of occurring near a place in DNA where mutations have already occurred, creating mutation hotspot clusters—a non-random pattern.
    http://edge.org/response-detail/25264

  192. 192
    CHartsil says:

    Notice that the notion of directed mutations hasn’t really gained any ground? That’s because it’s mostly nonsense. There are loci that can be driven to mutation in response to external stimuli, but even then they’re non-directional. That’s as close as you’ve gotten

  193. 193
    bornagain77 says:

    Duality in the human genome – November 28, 2014
    Excerpt: The results show that most genes can occur in many different forms within a population: On average, about 250 different forms of each gene exist. The researchers found around four million different gene forms just in the 400 or so genomes they analysed. This figure is certain to increase as more human genomes are examined. More than 85 percent of all genes have no predominant form which occurs in more than half of all individuals. This enormous diversity means that over half of all genes in an individual, around 9,000 of 17,500, occur uniquely in that one person – and are therefore individual in the truest sense of the word.
    The gene, as we imagined it, exists only in exceptional cases. “We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel’s time.,,,
    According to the researchers, mutations of genes are not randomly distributed between the parental chromosomes. They found that 60 percent of mutations affect the same chromosome set and 40 percent both sets. Scientists refer to these as cis and trans mutations, respectively. Evidently, an organism must have more cis mutations, where the second gene form remains intact. “It’s amazing how precisely the 60:40 ratio is maintained. It occurs in the genome of every individual – almost like a magic formula,” says Hoehe.
    http://medicalxpress.com/news/.....enome.html

    Majority of mutations are directed (non-random) – Jonathan Bartlett – video
    http://www.youtube.com/watch?v=YJwWhhpua_o

    Here is a simplified list of ‘non-random’ mechanisms which confer antibiotic resistance:

    Antibiotic Resistance Is Prevalent in an Isolated Cave (4 million year old) Microbiome – April 2012
    Excerpt: ‘Antibiotic resistance is manifested through a number of different mechanisms including target alteration, control of drug influx and efflux, and through highly efficient enzyme-mediated inactivation. Resistance can emerge relatively quickly in the case of some mutations in target genes and there is evidence that antibiotics themselves can promote such mutations [43], [44], [45], [46]; however, resistance to most antibiotics occurs through the aegis of extremely efficient enzymes, efflux proteins and other transport systems that often are highly specialized towards specific antibiotic molecules.’
    http://www.plosone.org/article.....ne.0034953

    from the ‘non-Darwinian’ evolutionist, James A. Shapiro PhD. Genetics

    How life changes itself: the Read-Write (RW) genome. – 2013
    Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.
    http://www.ncbi.nlm.nih.gov/pubmed/23876611

    “What I ask others interested in evolution to give up is the notion of random accidental mutation.”
    http://www.huffingtonpost.com/.....11144.html

    etc.. etc..

    It should be needless to say, but to say it anyway, Highly sophisticated machines rearranging the genome is NOT a Darwinian presupposition.

  194. 194
    Me_Think says:

    bornagain77 @ 189

    gpuccio, Wagner’s model and book is a joke:
    As Dembski showed in No Free Lunch, no evolutionary algorithm is superior to blind search. Without design, there is no shortcut to the treasure. To make the hunt easier for evolution, Wagner imagines a fantasy land with treasures

    My posts about Wagner are all over UD. I did post even in thread started by GP. I will copy paste from that thread. Wagner’s concept is very simple. It posits a multidimensional network search, instead of landscape search advocated by Demski, Axe et al.
    See how the search space reduces:

    Imagine a solution circle (the circle within which solution exists) of 10 cm inside a 100 cm square search space.
    The area which needs to be searched for solution is pi x 10 ^2 = 314.15
    The total Search area is 100 x 100 = 10000.
    The % area to be searched is (314.15/10000) x 100 = 3.14%

    In 3 dimensions,the search area will be 4/3 x pi x 10^3
    Area to search is now cube (because of 3 dimensions) = 100^3.
    Thus the % of area to be searched falls to just 4188.79/100^3 = 0.41 % only.
    Hypervolume of sphere with dimension d and radius r is:
    (Pi^d/2 x r^d)/Gamma(d/2+1)
    HyperVolume of Cube = r^d
    At 10 dimensions, the volume to search reduces to just: 0.000015608 %
    But in nature, the actual search area is incredibly small. As wagner points out in Chapter six,

    In the number of dimensions where our circuit library exists—get ready for this—the sphere contains neither 0.1 percent, 0.01 percent, nor 0.001 percent. It contains less than one 10^ -100th of the library

    The library that wagner talks about is based on actual metabolic pathways. There are 5,500 metabolic pathways. You can explore all the pathways at biocyc.org
    These are represented by the hypothetical library (Just like landscapes in Dembski, Axe papers). The library is an analogy – See Chapter Three Notes:

    This analogy is inspired by a famous short story of the Argentine author Jorge Luis Borges entitled “The Library of Babel” (Spanish original: “La biblioteca de Babel”), published in English translation in Borges (1962). The idea behind this short story, however, predates Borges. It has been used by many other authors, including Umberto Eco and Daniel Dennett

    Here’s another example of how RNA enzyme called hammerhead ribozyme search is made easy:

    This particular RNA enzyme happens to have 129 neighbors, and because we can compute their shapes, we can determine that there are forty-six new shapes in this neighborhood. That’s the number of shapes evolution can explore without genotype networks.
    And with them? If we only step to the text’s neutral neighbors—those with the same hammerhead shape—and determine the shape of all their neighbors, we already find 962 new shapes. And if we just walk one step further, to those neighbors’ neutral neighbors, we find 1,752 new shapes. Just two steps along this ribozyme’s genotype network, we can access almost forty times more shapes than in its immediate vicinity. The genotype network of the hammerhead shape of course extends much further than just two steps, and it has more than 1019 members

    P.S: Ha, just noticed there is some confusion about dimensions in the other thread. Dimensions are mathematical representation of the structure/process features under study. It has got nothing to do with spatial dimension. I can represent the search hills in search landscape in “height and coordinate dimensions” too. Note that polytope naturally forms network. (Hyper cube is family of polytope).

  195. 195
    bornagain77 says:

    Me_Think, I’m a empirical evidence kind of guy. ‘Just so stories’ with no basis in reality are part and parcel for Darwinists.

    Tell you what, show me one molecular machine that has been generated by Darwinian processes and then perhaps your imaginations will have a basis in reality. Until then they are ‘not even wrong’!

    Of related note:

    “Enzyme Families — Shared Evolutionary History or Shared Design?” – Ann Gauger – December 4, 2014
    Excerpt: If enzymes can’t be recruited to genuinely new functions by unguided means, no matter how similar they are, the evolutionary story is false.,,,
    Taken together, since we found no enzyme that was within one mutation of cooption, the total number of mutations needed is at least four: one for duplication, one for over-production, and two or more single base changes. The waiting time required to achieve four mutations is 10^15 years. That’s longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations.
    We have now addressed two objections raised by our critics: that we didn’t test the right mutation(s), and that we didn’t use the right starting point. We tested all possible single base changes in nine different enzymes, Those nine enzymes are the most structurally similar of BioF’s entire family We also tested 70 percent of double mutations in the two closest enzymes of those nine.
    Finally, some have said we should have used the ancestral enzyme as our starting point, because they believe modern enzymes are somehow different from ancient ones. Why do they think that? It’s because modern enzymes can’t be coopted to anything except trivial changes in function. In other words, they don’t evolve!
    That is precisely the point we are making.
    http://www.evolutionnews.org/2.....91701.html

    “Shared Evolutionary History or Shared Design?” – Ann Gauger – January 1, 2015
    Excerpt: The waiting time required to achieve four mutations is 10^15 years. That’s longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations.
    http://www.evolutionnews.org/2.....92291.html

  196. 196
    gpuccio says:

    Me_Think:

    Here is my last post about Wagner in the other thread, when you apparently “abandoned the field”:

    Box and Zachriel:

    Excuse me, but apparently what I can understand of Wagner’s “argument” is the following:

    a) If we have a set of 5000 metabolic pathways

    b) If we describe each member of the set as “off” (0) or “on” (1)

    c) We have a set of 2^5000 states and

    d) We can go from one state to another one by turning on or off a single metabolic pathway.

    Is that all? Is it really that trivial? And what has that to do with the search for a functional state in a search space which is huge?

    A few simple questions:

    1) The set of 5000 metabolisms is a hugely complex dictionary. Where did it come from?

    2) Turning on or off a metabolic pathway can be a one bit operation, if the metabolic pathway is there and there is a one bit switch which can turn it on or off. That’s what happened with the citrate pathway in the Lenski experiment. But where did the metabolic pathway come from?

    3) Again, I cannot see the “multidimensional space”. We have a set of 2^5000 states. We imagine that we can change the bits of each state. That is similar to a search for a functional protein in the sequence space, but the sequence space is made of random aminoacid sequences, while this “space” is made of complex and functional metabolisms.

    4) That said, it remains to be seen how many of the 2^5000 combinations are functional, and naturally selectable. Frankly, I could not care less. The whole discourse is, up to now, utterly senseless.

    If anyone can make sense of it, please talk!

    Could you please go on from that, and explain this mysterious Wagner argument, as you understand it?

  197. 197
    Me_Think says:

    bornagain77 @ 195

    I’m a empirical evidence kind of guy

    No. You are the ‘Philosopher kind’. You have identified ID agent as God, so unless you can scientifically describe omniscient and omnipotent (may be in terms of energy, field or force) God can’t be scientific hypothesis.

    Tell you what, show me one molecular machine that has been generated by Darwinian processes

    Scientific consensus is every molecular machine is created by Natural process (of which ‘Darwinism’ is a part. Physical structure, ionic, chemical and Quantum effect too is part of Natural process). You may say everything is created and managed by ID agent- that’s your view, not a scientific consensus.

  198. 198
    Me_Think says:

    gpuccio @ 196

    Here is my last post about Wagner in the other thread, when you apparently “abandoned the field”:

    I didn’t notice it till I started searching for my comments to reply to BA77.

    1) The set of 5000 metabolisms is a hugely complex dictionary. Where did it come from?

    answered in comment # 194:

    The library that Wagner talks about is based on actual metabolic pathways. There are 5,500 metabolic pathways. You can explore all the pathways at biocyc.org

    These are represented by the hypothetical library (Just like landscapes in Dembski, Axe papers). The library is an analogy – See Chapter Three Notes:
    This analogy is inspired by a famous short story of the Argentine author Jorge Luis Borges entitled “The Library of Babel” (Spanish original: “La biblioteca de Babel”), published in English translation in Borges (1962). The idea behind this short story, however, predates Borges. It has been used by many other authors, including Umberto Eco and Daniel Dennett

    2)Turning on or off a metabolic pathway can be a one bit operation, if the metabolic pathway is there and there is a one bit switch which can turn it on or off. That’s what happened with the citrate pathway in the Lenski experiment. But where did the metabolic pathway come from?

    What you are referring to is Andreas Wagner’s decades old artificial gene network model developed as a computational model of artificial gene networks. It was made more useful by Jörg (joerg) Stelling. Wagner’s current book refers to it as a future project based on digital circuits being developed by Karthik.

    Circuit networks thus have all it takes to become the warp drives of programmable hardware, in precisely the same way that genotype networks are the warp drives of evolution. They have the potential to help future generations of YaMoRs learn many new skills, from simple self-preservation like avoiding deadly staircases to complex skills like doing the dishes or playing ball with children. In this vision, their digital brains can rewire themselves step by little step, and explore many new behaviors, while being able to preserve old behavior—conserving the old while exploring the new

    3)Again, I cannot see the “multidimensional space”. We have a set of 2^5000 states.

    answered in comment # 194:

    P.S: Ha, just noticed there is some confusion about dimensions in the other thread. Dimensions are mathematical representation of the structure/process features under study. It has got nothing to do with spatial dimension. I can represent the search hills in search landscape in “height and coordinate dimensions” too. Note that polytope naturally forms network. (Hyper cube is family of polytope).

    4) That said, it remains to be seen how many of the 2^5000 combinations are functional, and naturally selectable.

    answered in comment # 194:
    Eg of how it is easy to search and select (compared to landscape search)

    Imagine a solution circle (the circle within which solution exists) of 10 cm inside a 100 cm square search space.
    The area which needs to be searched for solution is pi x 10 ^2 = 314.15
    The total Search area is 100 x 100 = 10000.
    The % area to be searched is (314.15/10000) x 100 = 3.14%
    In 3 dimensions, the search area will be 4/3 x pi x 10^3
    Area to search is now cube (because of 3 dimensions) = 100^3.
    Thus the % of area to be searched falls to just 4188.79/100^3 = 0.41 % only.
    Hypervolume of sphere with dimension d and radius r is:
    (Pi^d/2 x r^d)/Gamma(d/2+1)
    HyperVolume of Cube = r^d
    At 10 dimensions, the volume to search reduces to just: 0.000015608 %
    =====
    Here’s another example of how RNA enzyme called hammerhead ribozyme search is made easy:
    This particular RNA enzyme happens to have 129 neighbors, and because we can compute their shapes, we can determine that there are forty-six new shapes in this neighborhood. That’s the number of shapes evolution can explore without genotype networks. And with them? If we only step to the text’s neutral neighbors—those with the same hammerhead shape—and determine the shape of all their neighbors, we already find 962 new shapes. And if we just walk one step further, to those neighbors’ neutral neighbors, we find 1,752 new shapes. Just two steps along this ribozyme’s genotype network, we can access almost forty times more shapes than in its immediate vicinity. The genotype network of the hammerhead shape of course extends much further than just two steps, and it has more than 10^19 members

    Frankly, I could not care less. The whole discourse is, up to now, utterly senseless.

    One guy has the book but has to be shown which page to be read. The other guy doesn’t want to read either the book or papers of Wagner or try out the Matlab module – he couldn’t care less.
    OK, I am not going to waste any more time. If you want answers read the book, papers or check out software code or database. at Wagner’s zurich univ page

  199. 199
    bornagain77 says:

    as to: “Scientific consensus is every molecular machine is created by Natural process”

    Hmmm, I didn’t ask you what you and your atheistic buddies believed, I asked you for ONE example of a molecular machine arising by unguided processes (i.e. I asked for empirical evidence not an opinion):

    Dr. James Tour, who, in my honest opinion, currently builds the most sophisticated man-made molecular machines in the world, will buy lunch for anyone who can explain to him exactly how Darwinian evolution works:

    Top Ten Most Cited Chemist in the World Knows Darwinian Evolution Does Not Work – James Tour, Phd. – video
    https://www.youtube.com/watch?v=_Y5-VNg-S0s

    “I build molecules for a living, I can’t begin to tell you how difficult that job is. I stand in awe of God because of what he has done through his creation. Only a rookie who knows nothing about science would say science takes away from faith. If you really study science, it will bring you closer to God.”
    James Tour – one of the leading nano-tech engineers in the world – Strobel, Lee (2000), The Case For Faith, p. 111

    Science & Faith — Dr. James Tour – video (At the two minute mark of the following video, you can see a nano-car that was built by Dr. James Tour’s team)
    https://www.youtube.com/watch?v=pR4QhNFTtyw

    OF note: your reply to gpuccio is also evidence free.,,, Speculation built on Conjecture built on Imagination.

    Imagination does not constitute evidence:

    see Axe and Gauger’s paper(s) which were already referenced here:
    http://www.uncommondescent.com.....ent-550177

  200. 200
    Joe says:

    Wagner’s book does not make a case for natural selection. It does not make a case for unguided evolution.

    Scientific consensus is every molecular machine is created by Natural process (of which ‘Darwinism’ is a part. Physical structure, ionic, chemical and Quantum effect too is part of Natural process).

    Evidence, not consensus, is the key to science. And that claim doesn’t have any supporting evidence.

  201. 201
    Joe says:

    CHartsil- Unguided evolution cannot be tested. It hasn’t gained any ground since 1859

  202. 202
    Me_Think says:

    BA77,

    Imagination does not constitute evidence:
    see Axe and Gauger’s paper(s) which were already referenced here:http://www.uncommondescent.com…..ent-550177

    Axe uses the white noise landscape search. Wagner advocates multidimensional Network search – I have already shown how it reduces search space. You can do your own calculation if you want.

  203. 203
    bornagain77 says:

    Me_Think, you have NOT proved anything. Go into the lab and prove it empirically as Axe and Gauger did with their work.

    i.e.

    The Scientific Method – Richard Feynman – video
    Quote: ‘If it disagrees with experiment, it’s wrong. In that simple statement is the key to science. It doesn’t make any difference how beautiful your guess is, it doesn’t matter how smart you are who made the guess, or what his name is… If it disagrees with experiment, it’s wrong. That’s all there is to it.”
    https://www.youtube.com/watch?v=OL6-x0modwY

    “In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.”
    Karl Popper – The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge
    http://izquotes.com/quote/147518

    It’s (Much) Easier to Falsify Intelligent Design than Darwinian Evolution – Michael Behe, PhD
    https://www.youtube.com/watch?v=_T1v_VLueGk

    The Law of Physicodynamic Incompleteness – David L. Abel
    Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”
    If only one exception to this null hypothesis were published, the hypothesis would be falsified. Falsification would require an experiment devoid of behind-the-scenes steering. Any artificial selection hidden in the experimental design would disqualify the experimental falsification. After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided.
    The time has come to extend this null hypothesis into a formal scientific prediction:
    “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”
    https://www.academia.edu/9957206/The_Law_of_Physicodynamic_Incompleteness_Scirus_Topic_Page_

  204. 204
    Box says:

    Me_Think,

    can you show how Wagner’s “multidimensional network search” relates to reality – other than by pointing to the fantasies of Jorge Luis Borges or computer stuff?

  205. 205
    Me_Think says:

    Box @ 204
    Please read the book – you have it.

  206. 206
    Box says:

    Me_Think #205,

    IOW you cannot. Same here.

  207. 207
    Me_Think says:

    bornagain77 @ 203

    Me_Think, you have NOT proved anything. Go into the lab and prove it empirically as Axe and Gauger did with their work.

    Prove Nature in lab ?! What do you think Axe has proved ? All he has done is assert that the probability of a process which he carried out in a lab is low. He derived the low probability by using white noise landscape search. Just use Wagner’s network search to see that it’s probability is not low.

  208. 208
    Me_Think says:

    Box @ 206,
    See Comment # 198:

    One guy has the book but has to be shown which page to be read. The other guy doesn’t want to read either the book or papers of Wagner or try out the Matlab module – he couldn’t care less.
    OK, I am not going to waste any more time. If you want answers read the book, papers or check out software code or database. at Wagner’s zurich univ page

  209. 209
    Box says:

    Me_Think,

    You leave the impression of someone who hasn’t got the foggiest idea how Wagner’s multidimensional stuff relates to reality, but doesn’t want to admit it. After reading the book I too haven’t got a clue. And I suppose that your suggestion – checking out software code or database – isn’t helpful either.

  210. 210
    bornagain77 says:

    Me_Think, in science empirical evidence has the last word. You may imagine that a multidimensional search space greatly eases the search, and perhaps it does,,,

    Dr Quantum Flatland – video
    https://www.youtube.com/watch?v=imt-_SCP2yg

    But we, at least our material bodies, do not live in your imaginary multidimensional search space. The REAL world that we, our material bodies, actually live in is 3 dimensions of space and 1 dimension of time. And in that REAL ‘natural’ world in which we currently live, you have ZERO empirical evidence that unguided material processes can create sufficient functional information for even a single functional protein, nor do you have ANY evidence that unguided processes can transform the functional information of a existing functional protein into another protein of a similar sequence but slightly different function.

    There are principled reasons why this can’t be done by unguided material processes. The main reason for why this cannot be accomplished by unguided processes is what is termed ‘contextuality’:

    (A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics – 2012
    Excerpt (Page 4): The Probabilities Get Worse
    This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent, (i.e. context dependent), with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search.
    http://powertochange.com/wp-co.....Myers_.pdf

    Why Proteins (Protein Domains) Aren’t Easily Recombined – Ann Gauger – May 2012
    Excerpt: each particular helix or sheet has a distinct set of side chains sticking out from it, requiring a distinct set of chemical interactions with any nearby protein sequence. Thus, helices and sheets are sequence-dependent structural elements within protein folds. You can’t swap them around like lego bricks. This necessarily means that when you bring new secondary structure elements into contact by some sort of rearrangement, they will be unlikely to form a stable three dimensional fold without significant modification.
    http://www.biologicinstitute.o.....recombined

    “Why Proteins Aren’t Easily Recombined, Part 2” – Ann Gauger – May 2012
    Excerpt: “So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required.”
    http://www.biologicinstitute.o.....ned-part-2

    Explaining Innovation – Ann Gauger – January 20, 2015
    Excerpt: Even though the two enzymes (Kbl2 and BioF2) we worked with look alike, the way they are put together is distinct. The particular amino acids that cause them each to fold into the same structure are unique in sequence and holistic in their interactions. Each requires high-level, top-down design.
    As we discuss in our recent paper:
    “It may be that our prior attempts to convert Kbl2 to perform the function of BioF2 failed not because we made the wrong alterations but rather because it is misguided even to think of this as an exercise in alteration.
    … They use similar structures not because they are both adjusted versions of some older enzyme, but instead because the purposes they serve happen to call for similar structures. As we found in this work, it is not that Kbl has amino acid residues that are incompatible with the function of BioF2, but rather that Kbl2 is comprehensively suited to one function, while BioF2 is comprehensively suited to another.”
    ,,, Kbl2 and BioF2 represent two distinct ideas or concepts requiring holistic design.
    http://www.evolutionnews.org/2.....92861.html

  211. 211
    gpuccio says:

    Me_Think:

    Thanks for trying, but unfortunately I have not changed my mind at all. If possible, my judgement about Wagner (as it filters through you) has worsened. What a pile of nonsense!

    You say that you are not going to waste any more time with me. That is certainly true of me too.

  212. 212
    Me_Think says:

    Box @ 209

    You leave the impression of someone who hasn’t got the foggiest idea how Wagner’s multidimensional stuff relates to reality, but doesn’t want to admit it…And I suppose that your suggestion – checking out software code or database – isn’t helpful either.

    bornagain77 @ 210

    You may imagine that a multidimensional search space greatly eases the search

    Hi Box, BA77
    I was under the impression you guys knew something about search since you always brought up Axe and Dembski.It seems not only do you have no clue about Wagner, you have no clue about Axe and Dembski’s landscape search too !. I hope you guys don’t think Axe’s desert and mountains are real ! Can you explain in your own words what you understand by mountains in Axe landscape? No wonder you didn’t understand Wagner.

  213. 213
    bornagain77 says:

    Me_Think, you are the one making the claim that unguided processes can easily find functional proteins. The burden is on you to empirically substantiate your claim. i.e. You have ZERO empirical evidence that what you claim to be true is actually true for the REAL world. The burden is not on me to prove that your imaginary landscapes are imaginary instead of real. You are the one making the claim that your imaginary landscapes are real and thus you are the one that must substantiate the claim that they are real!

    Moreover, there is actually some empirical evidence of ‘multidimensional’ search in biology. But this multidimensional search is accomplished via quantum computation and is only useful for repairing the genome and helping a protein find its final folded form. The multidimensional search, according to theory and empirics, does not entail finding new functional sequences in sequence space. Moreover, quantum computation is accomplished via ‘non-local’, beyond space and time, means and is thus of no empirical use as to substantiating the materialistic claims of neo-Darwinism. In fact, finding non-local, beyond space and time, quantum computation in molecular biology falsifies the materialistic claims of neo-Darwiism!

  214. 214
    CHartsil says:

    @BA77 Source for anything at all in the last half of your post.

  215. 215
    bornagain77 says:

    CHartsil, I would, but I’ve been told that you are a bit of a troll. So I decline.

  216. 216
    Me_Think says:

    GP @ 211

    What a pile of nonsense!

    May be like Box ,BA77 and (I suspect) pretty much every IDer, you too have no clue about Axe’s Landscape search and what the mountains and deserts represent. You all are surprised by mathematical constructs ! I wonder what you will say about neural search , Bi Stability landscape….I am sure Axe, Dembski will be surprised to see how no UDer understands their own search model.

  217. 217
    CHartsil says:

    So a personal attack and you’re completely unable to defend anything you said. Got it

  218. 218
    Eric Anderson says:

    Piotr @188:

    Change in heritable traits in a population over successive generations.

    So, if that is what evolution is, then evolution doesn’t result in new species, new types of organisms? Also, evolution would accept the idea that life was created by an intelligent being?

    Thanks,

  219. 219
    Piotr says:

    #218 Eric Anderson,

    So, if that is what evolution is, then evolution doesn’t result in new species, new types of organisms?

    I gave a very general definition of evolution. Of course depending on the nature of the replicators, their population structure, the influence of the environment, and the number of generations evolution eventually leads to divergence and speciation.

    Also, evolution would accept the idea that life was created by an intelligent being?

    Evolution would happen whatever the origin of the first living things, also if they had been created by an intelligent being. One could also imagine guided evolution with an intelligent being intervening from time to time to tinker with the DNA of some or all species. But I would claim that there is no evidence of any such thing.

  220. 220
    Piotr says:

    Gpuccio,

    Do you mind if I begin with a simple illustrative example? Let’s consider all five-letter alphabetic strings (AAAAA, QWERT, HGROF, etc.). By convention, a string will be “functional” if it’s a meaningful English word (BREAD, WATER, GLASS, etc.). Functionality is therefore not a formal property of the string but something dictated by the environment. There are 26^5 = 11881376 (almost 12 million) possible five-letter strings. The number of five-letter words in English (excluding proper nouns and extremely rare, dialectal or archaic words) is about 6000, so the probability that any randomly generated string is functional is about 0.0005.

    Any five-letter string S can produce 5×25 = 125 “mutants” differing from S by exactly one letter. If you represent the sequence space as a five-dimensional hypercube (26x26x26x26x26), a mutation can be defined as a translation along any of the five axes.

    It would appear that the odds of finding a functional mutant for a given string should be about 125×0.0005 = 1/16 on the average. In fact, however, it depends where you start. If S is functional, the existence of at least one functional mutant is almost guaranteed (close to 90%). For most English words there are more than one functional mutants. For example, from SNARE wer get {SCARE, SHARE, SPARE, STARE, SNORE, SNAKE, SNARK…}. Though some functional sequences are isolated or form small clusters in the sequence space, most of them are members of one huge, quite densely interconnected network. You can get from one to another in just a few steps (often in more than one way), which is of course what Lewis Carroll’s “word ladder” puzzle is about:

    FLOUR > FLOOR > FLOOD > BLOOD > BROOD > BROAD > BREAD

    You can ponder the example for a moment; I’ll return to it later.

  221. 221
    Piotr says:

    (#220, continued)

    If “functionality” wasn’t defined as a formal property of 5-strings but something based on external criteria, why does it produce this network effect? The reason is simple: the structure of English words (and, indeed, words in any natural language) is not quite arbitrary. Their spelling reflects to a considerable extent their pronunciation, and pronunciation patterns are shaped by some natural restrictions on preferred sound combinations. In the last analysis, they depend on things like the anatomy of the vocal tract and the aerodynamics of sound production. There are certain recurrent “motifs” and rules of well-formedness which make some sound combinations (and the corresponding spellings) permissible, while forbidding others. For example, FLOST would be acceptable as an English word (so it’s potentially functional), but ARHGM or ZZZZO are ill-formed. Note that FLOST can easily mutate into English words (FLOST > FLOAT > GLOAT > GLOOM > BLOOM > BLOOD, and further into BREAD or FLOUR), but there’s no way to reach the web of functionality starting from ARGHM or ZZZZO.

    Does it mean that the structure of functional 5-strings is “designed”? I wouldn’t say so. English sound combinations have been shaped by something similar to natural selection. An important part of the “environment” that enforces a patterned structure is the human articulatory system with its mechanics. There are biasses and regularities, but they are not the result of anyone’s conscious planning (though language users are intelligent and conscious). Language self-adapts to the communicative behaviour of its users: words must be pronounceable.

    Note also that words are rarely formed from scratch, and even if they are, they conform to the same structural restrictions as vocabulary inherited from earlier generations of speakers (LASER or GOOGLE are structurally similar to POKER or PEOPLE — here I ignore the 5-letter constraint, which was arbitrary and used only for convenience). Words derived from others (like TOOTHBRUSH from TOOTH + BRUSH or CLEVERNESS from CLEVER + -NESS [suffix]) inherit their structural properties. Well-formedness is partly language-specific (and can change in the historical development of languages), but it also has universal components. If C stands for a consonant and V for a vowel, CVCCV or CCVCV are far more likely word-templates than CCCVV or VVVVC cross-linguistically. That’s why the “web of words” described above exists not only in English, but also in any other language, and evolves more or less gradually when languages are affected by sound changes over centuries. One could say that it is characterised by a certain historical robustness.

    (to be continued; comments welcome)

  222. 222
    Eric Anderson says:

    Piotr @219:

    Of course depending on the nature of the replicators, their population structure, the influence of the environment, and the number of generations evolution eventually leads to divergence and speciation.

    Well, there is the rub, isn’t it.

    So evolution is not just “heritable traits in a population over successive generations,” but heritable traits in a population over successive generations that leads to divergence and speciation.

    And given that the “leads to divergence and speciation” in your statement is not a logical conclusion of “heritable traits in a population over successive generations,” it must stand independent on its own as to the evidence. After all, what if heritable traits in a population don’t lead to speciation? Or new functionally-integrated machinery? Or new body plans? Or whole new types of organisms?

    That is where the interesting questions lie. No-one disputes that there are heritable traits in populations. The question is what these heritable traits can accomplish. The bait-and-switch of evolutionary rhetoric, is to point to the minor variations that obviously exist within a population and then claim that those minor variations prove the larger creation story. They don’t. The larger creation story has to stand on its own evidence.

    And what is the evidence that these minor, even cyclical, changes can do all this work of creating? That is the question. So far, after well over a century of intense research and study, we’ve made a handful of slightly interesting observations: moth coloration and finch beaks and antifreeze proteins and so forth. But none of these helps in the slightest to explain how the moth, or the finch, or the Arctic cod could have arisen in the first place.

    Anyway, that is a bit of a tangent, but with respect to your specific comment that caught my eye, no, “evolution” is not a well-defined technical term. It is all over the map. It encompasses ideas that range from the obvious and the well-supported to the outrageous and the wildly-spectacular. It is an extremely slippery term, which fact is used to great advantage by those who are pulling a definitional and rhetorical bait-and-switch, whether intentionally or unknowingly.

  223. 223
    Piotr says:

    EA,

    I have classes in the morning, and it’s past midnight here. If I find the time, I’ll comment tomorrow.

  224. 224
    gpuccio says:

    Piotr:

    I am following you with interest. You are the first person who is trying to make a meaningful discourse. Please, go on.

    I prefer not to comment until I understand really what you want to say, but I really appreciate your work. Thank you.

  225. 225
    Joe says:

    Word ladder puzzle? Really??? Words are usually part of sentences. Mutate a word and you will most likely change the meaning of the sentence.

  226. 226
    kairosfocus says:

    Piotr,

    pardon but a word like FLOAT has in it 5 letters, 26^5 = 1.19*10^7, or if you go for full ASCII 128^5 = 3.44*10^10, both much less than the 10^150 – 10^301 that is the relevant threshold for the design inference on FSCO/I as sign. A typical protein is 300 20-state aa’s long or comes from a space of 2.04*10^390; where hundreds of proteins are required for basic cell viability. (As in, words vs sentences — or, better yet, functional programs. D/RNA is object code.)

    This is a case where scope of config space is directly and materially related to isolation . . . Hamming distance sense . . . of islands of function and relative paucity of search resources on sol system or observed cosmos scale.

    KF

  227. 227
    Piotr says:

    #225 Joe,

    I’m using it as an illustrative analogy (to show how functionality can be distributed in the search space). It isn’t supposed to be a model of language evolution. Besides, you are wrong. Real-world “word mutations” (such as variant pronunciations, mispronunciations, slips of the tongue, phonetic reductions, etc.) rarely do any serious harm. Linguistic messages are highly redundant; otherwise you wouldn’t even be able to understand an accent of English different from yours.

  228. 228
    kairosfocus says:

    Piotr, while skip distance games for short English words are fine, the material issues relate to much more complex informational elements as I just noted. And, the more relevant case is random mutations of computer code to transform one complex function into an even more elaborate one without crashing the machine at any step. KF

  229. 229
    Joe says:

    Piotr:

    Real-world “word mutations” (such as variant pronunciations, mispronunciations, slips of the tongue, phonetic reductions, etc.) rarely do any serious harm.

    Evidence-free assertion.

  230. 230
    Zachriel says:

    kairosfocus: while skip distance games for short English words are fine, the material issues relate to much more complex informational elements as I just noted.

    Much longer words can be had with populations exhibiting mutation and recombination.

  231. 231
    Piotr says:

    #226 KF,

    Have you noticed I’m discussing a greatly simplified model for the sake of easier exposition? There are lots of side issues I must skip, but thresholds don’t play any role at this stage. I haven’t yet begun to talk about biology.

    This is what’s worth keeping in mind: — For a randomly chosen 5-sequence the odds that at least one of its 125 “mutants” is a meaningful English word are about 0.06. However, if the sequence itself is an English word (or even a nonce-word that might be English), the probability is immediately amplified 150 times, to about 0.9, and there are usually several English words among the mutants (for SNARE, I found about ten) — hence the “web effect”.

  232. 232
    Piotr says:

    #229 Joe,

    Everyday observation. If someone says “Febuary” and “nucular” for “February” and “nuclear”, confuses “adopt” with “adapt” in a context that clarifies the meaning, or speaks with a Geordie or Texan accent — is it a great comprehension problem for you?

  233. 233
    kairosfocus says:

    Piotr,

    the issue of a threshold of sufficient complexity that functionally specific complex organisation occurs in islands in config spaces that are deeply isolated relative to blind search resources is highly material.

    Indeed, you will see a discussion of just that point using words in English, in Denton’s Evolution, a Theory in Crisis, c 1985. You will see that he discusses how distance between valid words starts to shoot up as they become longer.

    That is we are looking at much deeper skip distances and isolation issues.

    I have no problem with stepwise increments in islands of function, the issue is to find them by blind search processes.

    And so, simple extrapolation from toy cases is not a reasonable procedure.

    Proteins typically come in at about 300 AAs, the fold-function domains are known to be deeply isolated in AA sequence space, and you need hundreds to function in a viable cell.

    So, complexity and functional specificity are highly material considerations.

    KF

  234. 234
    kairosfocus says:

    Z, the same pattern of deep isolation of islands of function applies to your remark. Recall, Axe and Gauger on the 6 – 7 AA threshold issue. KF

  235. 235
    Zachriel says:

    kairosfocus: You will see that he discusses how distance between valid words starts to shoot up as they become longer.

    And yet long words can evolve from populations that undergo letter mutation and recombination.

  236. 236
    Zachriel says:

    kairosfocus: the same pattern of deep isolation of islands of function applies to your remark.

    We can show that is incorrect, given populations of sequences that undergo mutation and recombination, with every sequence in the population being a proper word.

  237. 237
    kairosfocus says:

    Z, you are talking in effect about moving within islands of function and/or special cases. The material issue linked to the real challenge is to FIND such starting with the very first one, i.e. OOL. For this root of ToL case brings to bear the fundamentals in a context where self-replication itself has to be explained. KF

  238. 238
    Zachriel says:

    kairosfocus: The material issue linked to the real challenge is to FIND such starting with the very first one, i.e. OOL.

    Your claim was that “the same pattern of deep isolation of islands of function applies to your remark,” which concerned word evolution.

    Evolutionary theory, including the toy model, assume reproduction. So you grant that once there are replicators, then complexity can evolve?

  239. 239
    Me_Think says:

    Piotr @ 220,

    If you represent the sequence space as a five-dimensional hypercube (26x26x26x26x26), a mutation can be defined as a translation along any of the five axes

    Hi Piotr could you check your math? 5 dimension hypercube will have only 2^5 = 32 nodes and 2^(5-1) = 16 edges .Remember, the 5,000 metabolic pathways are represented in 5,000 dimensions by Wagner (which would give 1.41 x 10^1505 nodes and 7.062 x 10^1504 edges . I am not sure where you are representing the 6,000 viable words that you talk about in your example.
    If you are not explaining Wagner’s hyper dimensional search network, then your methodology may be right.

  240. 240
    Eric Anderson says:

    Piotr:

    I also appreciate you fleshing out your example, so please keep at it.

    One quick question: If we talk about 3-letter words, we will have many more functional English words, as well as far fewer possibilities, both of which would increase the odds of mutating into another functional 3-letter word. However, if we talk about 7-letter words, just the opposite would be true.

    So the existence of islands of function becomes reduced with increasing complexity and the number of theoretical possibilities also goes up exponentially, true?

  241. 241
    Me_Think says:

    P.S : comment#239: Multiply the number of dimension with the edges

  242. 242
    Eric Anderson says:

    Zachriel @238:

    Just curious, what does reproduction bring to the table? Presumably there are mutations that happen in vivo and that could, in theory, alter the organism. Is reproduction necessary just to provide more mutations or is there something else that reproduction adds? (Assume we are talking about a single-celled organism.)

    Thanks,

  243. 243
    wd400 says:

    This is a strange question. Without reproduction there is no chance for a mutation to outlive its host and very little chance to create competition. In a non-reproductive world you’d have very weak “single-generation” selection (like a sieve filtering the good and the bad ) but no way for the “good” mutations to fill the spots left behind by “bad” ones.

    Compare that to compounded generations of differential reproductive success and you end up with a very different picture.

  244. 244
    Zachriel says:

    Eric Anderson: Is reproduction necessary just to provide more mutations or is there something else that reproduction adds?

    There is a difference between a few replicators taking a large number of steps, and a large number of replicators taking just a few steps. In addition, recombination allows a population to avoid local fitness maxima, and explore farther afield.

  245. 245
    wd400 says:

    More stangeness from this thread.

    So evolution is not just “heritable traits in a population over successive generations,” but heritable traits in a population over successive generations that leads to divergence and speciation.

    Evolution is heritable traits in a population over successive generations. An almost inevitable consequence of such a process is that some populations stop sharing genes with each other. Once that happens you get divergence and speciation.

  246. 246
    Box says:

    WD400: Evolution is heritable traits in a population over successive generations. An almost inevitable consequence of such a process is that some populations stop sharing genes with each other. Once that happens you get divergence and speciation.

    Due to genetic entropy? That would mean that evolution is about the degeneration of species.

  247. 247
    wd400 says:

    No.

    Genes pools split due to patchy habitats, changing environments, mountains, rivers…

    Lineages diverge after gene pools split because change is the ground state of evolutionary processes. One changes can’t move from one population to another you get divergence

  248. 248
    Box says:

    WD400: Genes pools split due to patchy habitats, changing environments, mountains, rivers…

    Aha. So this is how we get from chemicals to humans. I can see it now. Thank you, that was most elucidating.

  249. 249
    wd400 says:

    The question was how do speciation and divergence arise form the simplest description of an evolutionary system. The answer is above.

  250. 250
    Piotr says:

    #240 EA,

    One quick question: If we talk about 3-letter words, we will have many more functional English words, as well as far fewer possibilities, both of which would increase the odds of mutating into another functional 3-letter word.

    There are relatively few three-letter words in English (if you count types, not tokens) — about 2500. On the other hand, their space is smaller (26^3 = 17576), which means that 1/7 of the space is “functional”.

    However, if we talk about 7-letter words, just the opposite would be true.

    There are more 7-letter words than 5-letter ones (the mean word length in English is a little about 8), but of course the search space is 26×26 = 676 times larger, so the density of “functional” strings is lower (about 500 times, roughly). The number of disconnected words grows with word length, though for 7-letter words connectivity is still high

    So the existence of islands of function becomes reduced with increasing complexity and the number of theoretical possibilities also goes up exponentially, true?

    Yes, but note that the example has its artificial limitations. Only “point substitutions” are allowed, and all words must be of equal length. If we permit the addition or deletion of a single character, we enormously increase the number of possible mutations and the connectivity of words. Likewise if we allow sequences of words, or don’t insist that the entire string has to be functional. There are many ways in which a web of functionality can “colonise” even a really vast space of sequences.

  251. 251
    Piotr says:

    #239 Me_Think

    If you are not explaining Wagner’s hyper dimensional search network, then your methodology may be right.

    I’m trying to look at it from a different angle. The elements of the search space considered here are sequences (in biology, they would be DNA sequences), not Cartesian products of types of functionality (identified with metabolic pathways by Wagner).

  252. 252
    Eric Anderson says:

    wd400 @243:

    This is a strange question. Without reproduction there is no chance for a mutation to outlive its host and very little chance to create competition. In a non-reproductive world you’d have very weak “single-generation” selection (like a sieve filtering the good and the bad ) but no way for the “good” mutations to fill the spots left behind by “bad” ones.

    Yes, it would seem like a heretical question to even bring up to those steeped in evolutionary thought. 🙂 But it is a legitimate question. I hesitated whether to bring it up without properly outlining the backdrop of the question, so let’s leave it at that for now. I’m hoping to do a full post on the issue sometime, but it probably won’t be soon due to other commitments. I’d love to get your thoughts and experience then.

  253. 253
    Eric Anderson says:

    Zachriel @244:

    There is a difference between a few replicators taking a large number of steps, and a large number of replicators taking just a few steps. In addition, recombination allows a population to avoid local fitness maxima, and explore farther afield.

    In other words, it provides more probabilistic opportunities for the population to find that advantageous island.

  254. 254
    wd400 says:

    It’s not “heretical”, it just… weird that someone who thnks about evolution thinks it’s even a question.

    Why don’t you coding up the “weasel” example without replication (just n strings changing at random), and see how fundamentally different the process is. Or maybe, read The Blind Watchmaker.

  255. 255
    Eric Anderson says:

    wd400 @249:

    The question was how do speciation and divergence arise form the simplest description of an evolutionary system. The answer is above.

    No. The question was, what is the definition (a definition that was asserted to be technical, clear and unambiguous) of the word “evolution.”

    As is typically the case in evolutionary rhetoric, a definition was offered that was simple and uncontroversial: heritable traits get passed on. Yet, as soon as we began to press a bit, the definition expanded. And if we were to continue the discussion, it would expand further from just divergence and speciation to encompass major new physical structures, completely new organisms, new body plans, the origin of man, etc. None of these follow necessarily from “heritable traits in a population” over generations. The great evolutionary rhetorical game is to pretend that they do follow as some kind of logical necessity and that witnessing something at one end of the spectrum (minor changes in finch beaks or moth wings) is somehow evidence for the grand claims at the other end of the spectrum. It is not. Those grand claims must stand on their own.

  256. 256
    wd400 says:

    No one thinks the existence of particular craters on the moon should “follow necessarily” from the definition of subatomic particles or gravity or movement.

    That’s a pretty good definition of what evolution is. With that in hand it’s easy to see that speciation and therefore divergence are inevitable. That heritable traits can get passed down distinct lineages doesn’t “change” the definition of evolution, as you claim.

    If you want to explain more specific outcomes (a particular crater on the moon, the wider beak of a finch, or indeed the existence of finches) then you need more details.

  257. 257
    Zachriel says:

    Zachriel: There is a difference between a few replicators taking a large number of steps, and a large number of replicators taking just a few steps. In addition, recombination allows a population to avoid local fitness maxima, and explore farther afield.

    Eric Anderson: In other words, it provides more probabilistic opportunities for the population to find that advantageous island.

    You’re not being clear here. Does “it” refer to recombination? If so, recombination allows the population to leap beyond local fitness peaks or islands (which are not necessarily the same thing).

    Returning to your original statement.

    Eric Anderson: Is reproduction necessary just to provide more mutations or is there something else that reproduction adds?

    Reproduction not only provides probabilistic resources and the possibility of recombination, but also encourages a ratchet effect. If at least some progeny are at least as fit as their parents, then at least some members of the next generation will be at least as fit or more fit than the parent generation.

  258. 258
    Box says:

    WD400: No one thinks the existence of particular craters on the moon should “follow necessarily” from the definition of subatomic particles or gravity or movement.

    And certainly no one thinks that the existence of the works of William Shakespeare should “follow necessarily” from the definition of subatomic particles or gravity or movement.

  259. 259
    wd400 says:

    Box,

    True. So why should specific outcomes of evolutionary processes “follow necessarily” from the definition of evolution?

  260. 260
    Piotr says:

    OK, to continue.

    Let’s now move to a different domain — DNA sequences. Here we have four nucleobases (A, C, G, T) instead of the 26 letters of the Latin alphabet. For simplicity, let’s consider a DNA chain comparable to a middle-sized bacterial genome (say, 3 Mbp). Also for simplicity, a continuous substring of the full chain will be regarded as functional if it yields a protein which can play an active role in one of the known bacterial metabolic reactions (“has a metabolic meaning”). This is of course only one of the many ways in which a DNA sequence can be “functional”. I will for the time being ignore regulatory sequences and RNA genes, for example. A typical bacterial gene may be about 900 bp long (with 300 codons). There are 4^900 = 7×10^541 possible DNA sequences of that length, but only 22^300 = 5×10^420 corresponding proteins, which means that, on an average, there are about 1.4×10^121 synonymous sequences yielding the same protein consisting of 300 standard amino acids. If we restrict our attention to point-mutations affecting one nucleotide at a time, there are 2700 possible substitutions for any sequence of 900 base-pairs. Non-synonymous substitutions are more likely to be deleterious (damaging the functionality of the protein) than neutral or beneficial.

    (to be continued)

  261. 261
    Joe says:

    Piotr, For all the changes you can do to your bacteria it will never become anything other than bacteria (or dead).

  262. 262
    Eric Anderson says:

    wd400:

    With that in hand it’s easy to see that speciation and therefore divergence are inevitable.

    Sorry, but this is simply false on both evidentiary and logical grounds.

    First, it is quite clear from even a brief examination of the natural world that the inheritance of traits across generations does not, in the vast majority of the cases, lead to new species. We see literally millions of examples of inherited traits every single day all around us. Meanwhile, the alleged speciation events lie at the very periphery of our ability to detect, both in time and in scope. There are no doubt some speciation events that owe their source to inherited traits across generations, but it is not true that inheritance of traits across generations inevitably leads to speciation. More likely, inherited traits simply lead to variations within a species (which is what is actually observed almost all the time); or perhaps to extinction, just as much as speciation.

    A much more accurate statement would be: “Heritable traits in a population over successive generations rarely lead to speciation; however in rare cases with particular population makeups or under extreme selective pressure they can lead to speciation.”

    And given that inheritance of traits across generations does not usually lead to speciation, we are certainly justified in asking just when it does, and if in particular cases we can be sure that it actually did.

    More important, however, is the logical point:

    You are arguing that “heritable traits in a population over successive generations” inevitably leads to new speciation events.

    We can see that this does not follow logically, simply by asking the question: What if they don’t?

    There is no inevitable logical tie between inheritance of traits across generations and new species arising. To be sure, the materialistic evolutionary paradigm requires, nay, demands it. But it simply does not follow as a matter of logic. They are two separate issues, each of which must stand on its own evidence.

    I realize that in the mind of the evolutionist the significant creative changes are simply small ones writ large. Thus, many proponents of evolution operate under the misimpression that evidence of tiny, even cyclical, changes are evidence for the whole grand creative process. They are not.

    When we escape from the mental trap of assuming that x inevitably leads to y, it becomes clear that it is entirely an open question of when, or if, it actually does. Furthermore, when we move beyond the concept of species, with its notoriously slippery definition that is often in the eye of the beholder, and consider larger scale changes, new organisms, and new body plans, it is even more obvious that “heritable traits in a population over successive generations” do not inevitably lead to such changes, and therefore, simply cannot be counted as evidence of such.

  263. 263
    Eric Anderson says:

    Zachriel @257:

    Reproduction not only provides probabilistic resources and the possibility of recombination, but also encourages a ratchet effect. If at least some progeny are at least as fit as their parents, then at least some members of the next generation will be at least as fit or more fit than the parent generation.

    Thanks, I like that description.

    Just a couple of follow up thoughts:

    I was purposely referring to a single-celled organism that self-replicates to set aside the recombination factor for a moment. But I agree with you it is important in situations of an offspring from two parents.

    As to the ratchet effect, it seems this is essentially a subset of the “more probabilistic resources” category. In other words, if an organism only has one offspring during its lifetime, this effect is nonexistent. However, if the organism has multiple offspring, then the odds of a favorable variation are proportionally increased.

  264. 264
    Zachriel says:

    Eric Anderson: I was purposely referring to a single-celled organism that self-replicates to set aside the recombination factor for a moment.

    Yet keeping in mind that single-celled organisms often recombine.

    Eric Anderson: As to the ratchet effect, it seems this is essentially a subset of the “more probabilistic resources” category.

    There’s still a distinction between a small number taking a large number of steps, and a large number taking a small number of steps. And a distinction between a highly-optimized genome and one with more ‘fluff’.

  265. 265
    wd400 says:

    First, it is quite clear from even a brief examination of the natural world that the inheritance of traits across generations does not, in the vast majority of the cases, lead to new species

    I said inevitable, not common.

    There is no inevitable logical tie between inheritance of traits across generations and new species arising

    In any realized world speciation and divergence will arise if traits are inherited (unless you think real populations can maintain gene flow for ever?) .

    I see no point in playing philosophical games about this.

  266. 266
    Eric Anderson says:

    Zachriel @264:

    Yet keeping in mind that single-celled organisms often recombine.

    In what sense? Are you talking about swapping genetic material and HGT? I’m not sure that relates to reproduction.

    There’s still a distinction between a small number taking a large number of steps, and a large number taking a small number of steps.

    I want to make sure I understand your point. Is the distinction you are drawing just a probabilistic one? Or is there a substantive difference that would impact how the changes arise?

    Thanks,

  267. 267
    Mung says:

    wd400: So why should specific outcomes of evolutionary processes “follow necessarily” from the definition of evolution?

    If evolution isn’t science then there’s no reason at all.

    If nothing follows from saying “evolutiondidit” then it’s pretty much meaningless to say “evolutiondidit.”

  268. 268
    Zachriel says:

    Eric Anderson: Are you talking about swapping genetic material and HGT? I’m not sure that relates to reproduction.

    It creates new genetic combinations, which requires populations, not single organisms.

    Eric Anderson: Is the distinction you are drawing just a probabilistic one? Or is there a substantive difference that would impact how the changes arise?

    There’s a substantive difference. For illustrative purposes, consider the sequence space to be explored to be a typical landscape with hill and dale, copse and glade. You command an outpost. You send a thousand troopers out to reconnoiter, each taking ten steps. You send ten rangers out to explore, each taking a thousand steps. The total steps are the same in both cases, but the results are considerably different. The former exhaustively explores the nearby landscape, leaving no stone unturned. The latter may miss some features nearby, but return with news of distant places.

    Mung: If nothing follows from saying “evolutiondidit” then it’s pretty much meaningless to say “evolutiondidit.”

    The fossil succession and the nested hierarchy follow from the hypothesis of evolution.

  269. 269
    Joe says:

    Zachriel:

    The fossil succession and the nested hierarchy follow from the hypothesis of evolution

    And yet evolutionary biologists say that evolution is too messy to produce a nested hierarchy. Obviously Zachriel doesn’t know what it is talking about.

    And the fossil succession has fish->tetrapods-> fishapods. I doubt that is what evolutionism predicts.

  270. 270
    Joe says:

    Easily refuting Zachriel wrt nested hierarchies:

    The goals of scientists like Linnaeus and Cuvier- to organize the chaos of life’s diversity- are much easier to achieve if each species has a Platonic essence that distinguishes it from all others, in the same way that the absence of legs and eyelids is essential to snakes and distinguishes it from other reptiles. In this Platonic worldview, the task of naturalists is to find the essence of each species. Actually, that understates the case: In an essentialist world, the essence really [I]is[/I] the species. Contrast this with an ever-changing evolving world, where species incessantly spew forth new species that can blend with each other. The snake [I]Eupodophis[/I] from the late Cretaceous period, which had rudimentary legs, and the glass lizard, which is alive today and lacks legs, are just two of many witnesses to the blurry boundaries of species. Evolution’s messy world is anathema to the clear, pristine order essentialism craves. It is thus no accident that Plato and his essentialism became the “great antihero of evolutionism,” as the twentieth century zoologist Ernst Mayr called it.- Andreas Wagner, “Arrival of the Fittest”, pages 9-10

    Let the flailing and/ or willful ignorance begin…

  271. 271
    gpuccio says:

    Piotr:

    Again, thank you for trying to make an argument. I will wait for you to go on, take your time. 🙂

    I would like to make some comments in the meantime, but there is no need for you to answer them now, just go on with your reasoning.

    My comments are about your example with words, and obviously I understand that it is only an example, and that each functional space is different.

    However, I think that some general considerations can be made.

    a) I believe that, in all functional spaces, the search space grows faster than the functional space, as the “length” of the information unit increases. Much faster.

    Both KF and Eric have pointed to that simple fact, and I absolutely agree with them.

    A very simple consequence of that is that the functional complexity of an information unit is bound to increase with the length of the unit, even if with some great residual variance.

    Another consequence is that any eventual natural network of “connections” between functional values, if present, is bound to be drastically “diluted” as the length of the information unit increases, leading to isolated functional islands even when for short units some connections existed.

    So, even if you say that it is rather easy to go from FLOUR to BREAD (but please, see next point), is it equally “easy” to go from QUIXOTICALLY to EXTEMPORIZER? I have not tried, but I would say that the task would be much harder.

    12 letter words are, it seems, about 11400 in English (I confess that I am using Word Finder 🙂 ). The combinations are 26^12, that is 9.542896e+16. The target space/search space ratio is 1.194606e-13.

    In your 5 letter example, with your numbers, the ratio is 0.0005.

    IOWs, going from 5 letters to 12 letters, the target space has approximately doubled (6000 to 11400), while the search space has become more than 8 billion times greater. The ratio is therefore approximately 8 billion times smaller.

    These are simple numbers. Do you really believe that your network of connections is as strong in a 12 letter space as it is in a 5 letter space?

    b) Another very important point. You can “easily” go from FLOUR to BREAD (two states which are not connected at sequence level) through the steps you highlighted, but only if each of the intermediate steps is “selectable”. IOWs, if the network of connections you refer to must be of any relevance to connect to sequence unrelated states, it is absolutely necessary that the system operates through some oracle: in this case, an English dictionary. In this way, English words are recognized as “functional”, and fixed (IOWs, they undergo some form of selection, negative or positive or both).

    I fully agree with you that a system of connections can help a search, but for that to happen we need three different conditions:

    1) The network must be there

    2) Each intermediate functional step must be selectable by an oracle, and negative/positive/mixed selection of the intermediate must follow.

    3) The distance at sequence level between functional selectable intermediates must be in the range of the probabilistic resources of the random variation in the system.

    Now, all three conditions must be verified. While you go on trying to show that condition 1) exists in the protein space (which I don’t believe to be true), I would like to remind that the only oracle admitted in the neo darwinian algorithm is NS, and that NS can only recognize a reproductive advantage, and nothing else.

    Well, for the moment I would say that’s enough.

  272. 272
    Zachriel says:

    gpuccio: a) I believe that, in all functional spaces, the search space grows faster than the functional space, as the “length” of the information unit increases. Much faster.

    Sure.

    gpuccio: A very simple consequence of that is that the functional complexity of an information unit is bound to increase with the length of the unit, even if with some great residual variance.

    Not necessarily. That would depend on the landscape, such as whether it was rolling hills or jagged peaks.

    gpuccio: Another consequence is that any eventual natural network of “connections” between functional values, if present, is bound to be drastically “diluted” as the length of the information unit increases, leading to isolated functional islands even when for short units some connections existed.

    Again, not necessarily the case. A landscape may include tiny islands or vast continents.

    gpuccio: So, even if you say that it is rather easy to go from FLOUR to BREAD (but please, see next point), is it equally “easy” to go from QUIXOTICALLY to EXTEMPORIZER?

    With word evolution—populations of words subject to mutation and recombination—even longer words can evolve.

    The potential space of a 14-letter word is over 100 million trillion. We have used a quite inefficient computer algorithm to evolve many 14-letter words in just minutes. Even though there are ~29,000,000,000,000,000,000,000,000 possible 18 letter combinations, and only 3786 such words in our dictionary, the program found “denominationalists” in less than the lifetime of a mayfly.

    gpuccio: b) Another very important point. You can “easily” go from FLOUR to BREAD (two states which are not connected at sequence level) through the steps you highlighted, but only if each of the intermediate steps is “selectable”.

    That’s right. Again, whether they are connected depends on the landscape.

    gpuccio: I would like to remind that the only oracle admitted in the neo darwinian algorithm is NS, and that NS can only recognize a reproductive advantage, and nothing else.

    Of course. The primary evidence is the nested hierarchy showing common descent, and then functional analysis of protein evolution. We can show selection gradients for gross morphological characteristics, and we can show selection gradients for protein function with experiments such as Lenski’s. We can even occasionally show direct observation of protein evolution, such as nylonase.

  273. 273
    gpuccio says:

    Zachriel:

    You can find anything with a suitable oracle. I have no doubt that you can find the whole Hamlet text by random variation, if you just use Hamlet as an oracle. Do you really believe that such things are evidence of something?

    The nested hierarchy showing common descent is evidence of common descent, and of nothing else. So much for your “primary evidence”.

    What are the “selection gradients for protein function” in Lenski’s experiment?

    Of nylonase we have already discussed in detail (with Piotr, in particular). If I were you, I would avoid mentioning it at all. 🙂

  274. 274
    Joe says:

    Zacho:

    The primary evidence is the nested hierarchy showing common descent

    You are deluded, ignorant or a liar. Given evolution we should not expect a nested hierarchy.

  275. 275
    Joe says:

    gpuccio- Please don’t be fooled by Zachriel’s ignorance. Common descent does NOT predict a nested hierarchy and evos since Darwin have been saying it does not. Only the willfully ignorant think common descent predicts a nested hierarchy.

  276. 276
    Zachriel says:

    gpuccio: You can find anything with a suitable oracle.

    While you didn’t introduce word evolution, we were responding to your own statements on the subject, such as “So, even if you say that it is rather easy to go from FLOUR to BREAD (but please, see next point), is it equally “easy” to go from QUIXOTICALLY to EXTEMPORIZER?”

    gpuccio: The nested hierarchy showing common descent is evidence of common descent, and of nothing else.

    Common descent provides the historical context, including the contours of evolutionary change.

    gpuccio: What are the “selection gradients for protein function” in Lenski’s experiment?

    Not sure your question. Mutation and selection results in improved function, showing there is a stepwise path from low function to high function.

    gpuccio: Of nylonase we have already discussed in detail (with Piotr, in particular).

    Are you saying nylonase was not a new function?

  277. 277
    Joe says:

    Nylonase? Another thing evolutionism cannot explain. No one knows if that arose via blind watchmaker processes.

    Evos are nothing but grand equivocators as to them all evidence for evolution is also evidence for unguided evolution. Typical but still pathetic

  278. 278
    gpuccio says:

    Joe:

    I am really not interested in nested hierarchies, and never have been. I have my reasons to believe in common descent, but they are different.

  279. 279
    gpuccio says:

    Zachriel:

    “While you didn’t introduce word evolution, we were responding to your own statements on the subject, such as “So, even if you say that it is rather easy to go from FLOUR to BREAD (but please, see next point), is it equally “easy” to go from QUIXOTICALLY to EXTEMPORIZER?” ”

    It depends on the search you use, and the algorithm you use. If you fix any variation that brings you nearer to a known word, it is easy to go wherever you like. Piotr’s point was that you can go there by single letter variations yielding each time an existing word, if I understand it well. Is that what your algorithm does?

    “Not sure your question. Mutation and selection results in improved function, showing there is a stepwise path from low function to high function. ”

    What function? Are you referring to the reactivation of the citrate pathway? That looks like a simple regulatory change, rather than a “gradient for protein function”. What do you mean exactly?

    “Are you saying nylonase was not a new function?”

    No. I am saying that nylonase is a rather simple transition at the molecular level, probably in the context of bacterial adaptational algorithms involving plasmids, and certainly not the result of a frameshift mutation, as you (and many others) have argued for a long time. You have done that with me personally, years ago. My memory is still good.

  280. 280
    Zachriel says:

    gpuccio: If you fix any variation that brings you nearer to a known word, it is easy to go wherever you like.

    The word evolution we have been discussing only allows for properly spelled words throughout the history.

    gpuccio: Are you referring to the reactivation of the citrate pathway?

    No, the optimization of citrate utilization, which occurred during generations 33000 to 33500.

    gpuccio: I am saying that nylonase is a rather simple transition at the molecular level

    So nylonase is a new function that came about through a stepwise process then became fixed through selection.

  281. 281
    Eric Anderson says:

    Zachriel @268:

    It creates new genetic combinations, which requires populations, not single organisms.

    Agreed. So this would be an example of additional probabilistic resources being brought to bear, but not involving reproduction. Essentially what we are doing is allowing organism A to take advantage of the (presumably successful) search that organism B has already performed.

    You send a thousand troopers out to reconnoiter, each taking ten steps. You send ten rangers out to explore, each taking a thousand steps. The total steps are the same in both cases, but the results are considerably different. The former exhaustively explores the nearby landscape, leaving no stone unturned. The latter may miss some features nearby, but return with news of distant places.

    I love the imagery, and you might be on to something here. I’ll have to think about it further.

    I’m wondering, though, about what it might mean for evolution. If I pursue your analogy, we seem to have the following:

    1000 organisms exploring 10 steps each would give us a greater likelihood of stumbling across something relatively close to home, meaning, something only slightly different from the current genotype. Whereas with 10 organisms exploring 1000 steps each we have a greater chance of finding a more distant place, something more substantively different from our current genotype, however at the cost that we have fewer chances of finding it.

    Again, interesting analogy and I’ll think about it some more. In either case, at the end of the day what a population provides is more probabilistic resources to go out and search the space, whether lots of organisms close by, or a smaller of organisms number farther afield.

  282. 282
    Mung says:

    Zachriel: The fossil succession and the nested hierarchy follow from the hypothesis of evolution.

    So?

    Zachriel: The fossil succession and the nested hierarchy follow from the hypothesis of evolution.

    Evolutionary theory does not predict the existence of fossils. It follows that evolutionary theory does not predict any particular succession of fossils.

    Evolutionary theory does not predict a nested hierarchy.

    Zachriel: The fossil succession and the nested hierarchy follow from the hypothesis of evolution.

    What’s your point, if you have one?

  283. 283
    Me_Think says:

    Eric Anderson @ 281

    I love the imagery, and you might be on to something here. I’ll have to think about it further…we have a greater chance of finding a more distant place, something more substantively different from our current genotype, however at the cost that we have fewer chances of finding it.

    No. If you represent the genotype as a hyper dimension network, the search space falls down drastically (As shown in various threads on UD):

    Imagine a solution circle (the circle within which solution exists) of 10 cm inside a 100 cm square search space.

    The area which needs to be searched for solution is pi x 10 ^2 = 314.15
    The total Search area is 100 x 100 = 10000.
    The % area to be searched is (314.15/10000) x 100 = 3.14%

    In 3 dimensions, the search area will be 4/3 x pi x 10^3
    Area to search is now cube (because of 3 dimensions) = 100^3.
    Thus the % of area to be searched falls to just 4188.79/100^3 = 0.41 % only.

    Hyper volume of sphere with dimension d and radius r is:
    (Pi^d/2 x r^d)/Gamma(d/2+1)
    HyperVolume of Cube = r^d

    At 10 dimensions, the volume to search reduces to just: 0.000015608 %
    If we take the total 5,500 metabolic reactions in Nature, the search space in hyperdimension is only 1.7234*10^-10926

  284. 284
    Box says:

    Me_Think #283,

    Me_Think: No. If you represent the genotype as a hyper dimension network, the search space falls down drastically (As shown in various threads on UD).

    “As shown”? You have been asked in those threads how Wagner’s ideas (“hyper-astronomical-libraries” and “hyper-dimensional-space” among other things) correlate to reality. We are still waiting for your answer.

  285. 285
    Me_Think says:

    Box @ 284

    “As shown”? You have been asked in those threads how Wagner’s ideas (“hyper-astronomical-libraries” and “hyper-dimensional-space” among other things) correlate to reality. We are still waiting for your answer.

    What do you mean? How much more explanation can me or wagner’s book give you. I have quoted how Metabolic pathways relate to reality, I have quoted how hammer head ribozyme relate to reality and I have asked you what you understand by Axe’s landscape search and hills in his landscape, so I can relate to what you understand (search the various thread on which we and GP discussed this. In fact Poitr joined later to show a simpler approach too). It is you who has to answer- not me.

  286. 286
    gpuccio says:

    Zachriel:

    “No, the optimization of citrate utilization, which occurred during generations 33000 to 33500.”

    I will look at it.

    “So nylonase is a new function that came about through a stepwise process then became fixed through selection.”

    Probably. A simple function. Which is absolutely compatible with ID theory.

  287. 287
    gpuccio says:

    Zachriel and Piotr:

    Going back to the real issue, that you (Zachriel) seem to elude, I will ask an explicit question, to which I hope to receive an answer.

    In post #220, Piotr gives a sequence of 5 letter English words, separated each by a single letter variation. Here it is:

    FLOUR > FLOOR > FLOOD > BLOOD > BROOD > BROAD > BREAD

    In this way he shows that it is possible, at least in some cases, to go from 5 letter word to another, sequence unrelated, 5 letter word, through a series of one letter transitions (6 in this case), where each step is a correct English 5 letter word.

    If I understand well, what he mean is that, if we have an oracle which recognizes English words and fixes them, it is possible to go from FLOUR to BREAD quite easily by single letter variation. That means that there is some good interconnection in the functional space of English 5 letter words.

    OK, I can agree. Obviously, you always need a dictionary as an oracle, and a fixation procedure, but let’s ignore that for the moment.

    In my post #271 I comment:

    a) I believe that, in all functional spaces, the search space grows faster than the functional space, as the “length” of the information unit increases. Much faster.

    Both KF and Eric have pointed to that simple fact, and I absolutely agree with them.

    A very simple consequence of that is that the functional complexity of an information unit is bound to increase with the length of the unit, even if with some great residual variance.

    Another consequence is that any eventual natural network of “connections” between functional values, if present, is bound to be drastically “diluted” as the length of the information unit increases, leading to isolated functional islands even when for short units some connections existed.

    So, even if you say that it is rather easy to go from FLOUR to BREAD (but please, see next point), is it equally “easy” to go from QUIXOTICALLY to EXTEMPORIZER? I have not tried, but I would say that the task would be much harder.

    12 letter words are, it seems, about 11400 in English (I confess that I am using Word Finder 🙂 ). The combinations are 26^12, that is 9.542896e+16. The target space/search space ratio is 1.194606e-13.

    In your 5 letter example, with your numbers, the ratio is 0.0005.

    IOWs, going from 5 letters to 12 letters, the target space has approximately doubled (6000 to 11400), while the search space has become more than 8 billion times greater. The ratio is therefore approximately 8 billion times smaller.

    These are simple numbers. Do you really believe that your network of connections is as strong in a 12 letter space as it is in a 5 letter space?

    In his post #272, Zachriel “answers”:

    not necessarily the case. A landscape may include tiny islands or vast continents.

    and:

    With word evolution—populations of words subject to mutation and recombination—even longer words can evolve.

    I am not satisfied of these “answers”, which IMO are nothing more than vague and non committal statements. So, I ask more explicitly, to Zachriel and to anyone:

    Can you give me a detailed list of words of 12 letters which go from QUIXOTICALLY to EXTEMPORIZER, where each word is a correct English word, and each word differs from the previous one only of one letter?

    IOWs, is the space of 12 letter words as interconnected as the space of 5 letter words?

    As I have already said, I have not even tried. Maybe it is possible, but it seems rather difficult to me, at first sight. You are the fans of word connections, so again I ask: can you do it?

  288. 288
    Box says:

    Me_Think: I have quoted how Metabolic pathways relate to reality. (…) ribozome (..).

    Don’t play stupid with me. Metabolic pathways and ribozomes were neither the problem nor the question, now was it?
    My question was about the relation between reality and stuff like “hyper-astronomical-libraries” and “hyper-dimensional-space”.

  289. 289
    Me_Think says:

    Wellllllll Box,
    You are obviously stupid. I have explained what hyperdimension and hyperastronmical libraries are ( It is even in the book). If GP is honest, he can vouch for me since I don’t want to go searching for all those comments.

  290. 290
    Piotr says:

    #287 gpuccio,

    One problem with the word ladder puzzle as an analogy is that English words are of limited length. The mean length of dictionary headwords is about 8, and the number of words with n letters drops rather quickly as n increases. That’s part of the reason why the web of words becomes rather fragmented for large values of n. If, however, you permit other kinds of mutations beside single letter substitutions (letter addition or deletion, recombination, concatenation), connectivity is largely restored.

    As for your concrete examples, QUIXOTICALLY is based on a foreing proper name, and so is likely to turn out to be “aloof” word (to use Lewis Carroll’s terminology). So is even the shorter adjective QUIXOTIC.

  291. 291
    bornagain77 says:

    Me_Think, so you have ZERO empirical evidence that what you claim is true for reality actually is true for reality and your response for being called on your bluff is to call someone stupid?
    I think the proper response of the UD administrators should be to ban you for such childish invective! But if they did that then we would soon have no neo-Darwinists to argue with since ad hominem is, in the end, all they have got! 🙂

  292. 292
    Me_Think says:

    bornagain77 @ 291

    you have ZERO empirical evidence that what you claim is true for reality actually is true for reality and your response for being called on your bluff is to call someone stupid?

    Wagner is an Evolutionary Biologist . He has over 150 peer reviewed papers (not in buddy reviewed journal like Bio-Complexity). If you think such an evolutionary biologist is bluffing then I invite you to critic the papers given below:

    160. Payne, J.L., Wagner, A. (2014) The robustness and evolvability of transcription factor binding sites. Science 343, 875-877.[link]

    159. Wagner, A. (2014) A genotype network reveals homoplastic cycles of convergent evolution in influenza A (H3N2) evolution. Proceedings of the Royal Society B: Biological Sciences 281, 20132763. [reprint request]

    158. Szovenyi, P., Devos, N., Weston, D.J., Yang, X., Hock, Z., Shaw, J.A., Shimizu, K.K., McDaniel, S., Wagner, A. Efficient purging of deleterious mutations in plants with
    haploid selfing. Genome Biology and Evolution 6, 1238-1252. [reprint request]

    157. Wagner, A., Rosen, W. (2014) Spaces of the possible: universal Darwinism and the wall between technological and biological innovation. Journal of the Royal Society Interface 11, 20131190. [reprint request]

    156. Payne, J.L., Wagner, A. Latent phenotypes pervade gene regulatory circuits. BMC Systems Biology 8 (1), 64. [reprint request]

    155. Dhar, R., Bergmiller, T., Wagner, A. (2014) Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution 68, 1775-1791. [reprint request]

    154. Hayden, E., Bratulic, S., Konig, I., Ferrada, E., Wagner, A. (2014) The effects of stabilizing and directional selection on phenotypic and genotypic variation in a population of RNA enzymes. Journal of Molecular Evolution 78, 101-108. [reprint request]

    153. Barve, A., Hosseini, S.-R., Martin, O.C., Wagner, A. Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms. BMC Systems Biology 2014, 8:48. [reprint request]

    152. Wagner, A. (2014) Mutational robustness accelerates the origin of novel RNA phenotypes through phenotypic plasticity. Biophysical Journal 106, 955-965. [reprint request]

    151. Sunnaker, M., Zamora-Sillero, E., Garcia de Lomana, A.L., Rudroff, F., Sauer, U., Stelling, J., Wagner, A. (2014) Topological augmentation to infer hidden processes in biological systems. Bioinformatics 30, 221-227. [reprint request]

    150. Wagner, A., Andriasyan, V., Barve, A. (2014) The organization of metabolic genotype space facilitates adaptive evolution in nitrogen metabolism. Journal of Molecular Biochemistry 3: 2-13. [reprint request]

    149. Payne, J.L., Moore, J.H., Wagner, A. (2014) Robustness, evolvability, and the
    logic of genetic regulation. Artificial Life 20, 111-126. [reprint request]

    2013

    148. Barve, A., Wagner, A. (2013) A latent capacity for evolutionary innovation through exaptation in metabolic systems. Nature 500, 203-206. [reprint request]

    147. Sunnaker, M., Zamora-Sillero, E., Dechant, R., Ludwig, C., Busetto, A.G., Wagner, A., Stelling, J. (2013) Automatic generation of predictive dynamic models reveals nuclear phosphorylation as the key Msn2 control mechanism. Science Signaling 6, ra41. [reprint request]

    146. Szovenyi, P., Ricca, M., Hock, Z., Shaw, J.A., Shimizu, K.K., Wagner, A. (2013) Selection is no more efficient in haploid than in diploid life stages of an angiosperm and a moss. Molecular Biology and Evolution 30: 1929-1939. [reprint request]

    145. Payne, J.A., Wagner, A. (2013) Constraint and contingency in multifunctional gene regulatory circuits. PLoS Computational Biology 9 (6), e1003071. [reprint request]

    144. Dhar, R., Saegesser, R., Weikert, C., Wagner, A. (2013) Yeast adapts to a changing stressful environment by evolving cross-protection and anticipatory gene regulation. Molecular Biology and Evolution 30, 573-588. [reprint request]

    143. Sabath, N., Ferrada, E., Barve, A., Wagner, A., (2013) Growth temperature and genome size in bacteria are negatively correlated, suggesting genomic streamlining during thermal adaptation. Genome Biology and Evolution 5, 966-977. [reprint request] .

    142. Bilgin, T., Kurnaz, I.A., Wagner, A. (2013) Selection shapes the robustness of ligand-binding amino acids. Journal of Molecular Evolution 76, 343-349. [reprint request] .

    141. Bichsel, M., Barbour, A.D., Wagner, A. (2013) Estimating the fitness effect of insertion sequences. Journal of Mathematical Biology 66, 95-114. [reprint request]

    140. Wagner, A. (2013) Genotype networks and evolutionary innovations in biological systems. In Handbook of Systems Biology. Eds: Walhout, A.J.M., Vidal, M., Dekker, J., Academic Press, London, p 251-264. [reprint request]

    139. Wagner, A. (2013) Metabolic networks and their evolution. In Encyclopedia of Systems Biology; p 1256-1259; Dubitzky, W., Wolkenhauer, O., Yokota, H., Cho, K.-H. (eds) Springer, New York.

    2012

    138. Barve, A., Rodrigues, J.F.M., Wagner, A. (2012) Superessential reactions in metabolic networks. Proceedings of the National Academy of Sciences of the U.S.A. 109 (18), E1121-E1130. [reprint request]

    137. Wagner, A. (2012) The role of robustness in phenotypic adaptation and innovation. Proceedings of the Royal Society B: Biological Sciences 279, 1249-1258.[reprint request]

    136. Hayden, E.J., Wagner, A. (2012) Environmental change exposes beneficial epistatic interactions in a catalytic RNA. Proceedings of the Royal Society B: Biological Sciences 279, 3418-3425.   Â

    135. Chen, B., Wagner, A. (2012) Hsp90 is important for fecundity, longevity, and buffering of cryptic deleterious variation in wild fly populations. BMC Evolutionary Biology 12, 25. [reprint request]

    134. Wagner, A. (2012) The role of randomness in Darwinian evolution. Philosophy of Science 79, 95-119. [reprint request]

    133. Sabath, N., Wagner, A., Karlin, D. (2012) Evolution of viral proteins originated de novo by overprinting. Molecular Biology and Evoluion 29, 3767-3780.

    132. Guo, B., Zuo, M., Wagner, A. (2012) Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication. Molecular Biology and Evolution. doi: 10.1093/molbev/mss108. [reprint request]

    131. Bragg, J.G., Quigg, A., Raven, J.A., Wagner, A. (2012) Protein elemental sparing and codon usage bias are correlated among bacteria. Molecular Ecology 21, 2480–248. [reprint request]

    130. Ferrada, E., Wagner, A. (2012) A comparison of genotype-phenotype maps for RNA and proteins. Biophysical Journal 102, 1916-1925. [reprint request]

    129. Matias Rodrigues, J.F., Rankin, D., Rossetti, V., Wagner, A., Bagheri, H.C. (2012) Differences in cell division rates drive the evolution of terminal and differentiation in microbes. PLoS Computational Biology 8 (4), e1002468. [reprint request]

    128. De la Chaux, N., Tsuchimatsu, T., Shimizu, K.K., Wagner, A. (2012) The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata. Mobile DNA 3, 2. [reprint request]

    127. Bilgin, T., Wagner, A. (2012) Design constraints on a synthetic metabolism. PLoS ONE 7(6): e39903. [reprint request]

    126. Wagner, A. (2012) Metabolic networks and their evolution. Evolutionary Systems Biology/Advances in Experimental Medicine and Biology 751: 29-52. [reprint request]

    125. Wagner, A. (2012) High dimensional adaptive landscapes facilitate evolutionary innovation p271-282 in Svensson, E.I., Calsbeek, R. (eds) The adaptive landscape in evolutionary biology. Oxford University Press, Oxford, UK. [reprint request]

    124. Wagner, A., Weikert, C. (2012) Phenotypic constraints and phenotypic hitchhiking in a promiscuous enzyme. The Open Evolution Journal 6, 14-28. [reprint request]

    123. Hayden, E., Wagner, A. (2012) Directional selection causes decanalization in a catalytic RNA. PLoS ONE 7(9), e45351. [reprint request]

    2011

    122. Hayden, E.J., Ferrada, E., Wagner, A. (2011) Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme. Nature 474, 92-95.[reprint request]

    121. Wagner, A. (2011) The molecular origins of evolutionary innovations. Trends in Genetics 27, 397-410. [reprint request]

    120. Wagner, A. (2011) Genotype networks shed light on evolutionary constraints. Trends in Ecology and Evolution 26, 577-584. [reprint request]

    119. Dhar, R., Sägesser, R., Weikert, C., Yuan, J., Wagner, A. (2011) Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution. Journal of Evolutionary Biology 5, 1135-1153. [reprint request]

    118. Wagner, A. (2011) The low cost of recombination in creating novel phenotypes. Bioessays 33, 636-646. [reprint request]

    117. Zamora-Sillero, E. Hafner, M., Ibig, A., Stelling, J., Wagner, A. (2011) Efficient characterization of high-dimensional parameter spaces for systems biology. BMC Systems Biology 5, 142. [reprint request]

    116. Samal, A., Wagner, A., Martin, O.C. (2011) Environmental versatility promotes modularity in large scale metabolic networks. BMC Systems Biology 5,135.[reprint request]

    115. Espinosa-Soto, C. Martin, O.C., Wagner, A. (2011) Phenotypic plasticity can facilitate adaptive evolution in gene regulatory circuits. BMC Evolutionary Biology 11:5, doi:10.1186/1471-2148-11-5. [reprint request]

    114. Rodrigues, J.F.M., Wagner, A. (2011) Genotype networks, innovation, and robustness in sulfur metabolism. BMC Systems Biology 5:39. [reprint request]

    113. Raman, K., Wagner, A. (2011) The evolvability of programmable hardware. Journal of the Royal Society Interface 8: 269-281. [reprint request]

    112. Raman, K., Wagner, A. (2011) Evolvability and robustness in a complex signaling circuit. Molecular BioSystems 7, 1081-1092. [reprint request]

    111. De la Chaux, N., Wagner, A. (2011) BEL/Pao retrotransposons in metazoan genomes. BMC Evolutionary Biology 11 :154. [reprint request]

    110. Wright, J., Bellissimi, E., de Hulster, E., Wagner, A., Pronk, J.T., van Maris, A.J.A. (2011) Batch and continuous culture-based selection strategies for acetic acid tolerance in xylose-fermenting Saccharomyces cerevisiae. FEMS Yeast Research 11,299–306. [reprint request]

    109. Espinosa-Soto, C., Martin, O.C., Wagner, A. (2011) Phenotypic plasticity can increase phenotypic variability after non-genetic perturbations in gene regulatory circuits. Journal of Evolutionary Biology 24, 1284-1297. [reprint request

    More here

  293. 293
    Zachriel says:

    Eric Anderson: Essentially what we are doing is allowing organism A to take advantage of the (presumably successful) search that organism B has already performed.

    Somewhat more than that. It’s not just sharing of traits, but the many unique combinations of traits that would otherwise be unavailable. “Your father’s nose. Your mother’s eyes.”

    Mung: Evolutionary theory does not predict the existence of fossils. It follows that evolutionary theory does not predict any particular succession of fossils.

    Gee whiz, Mung. There are fossils, in fact, so they can be tested to see if they fit the expected pattern.

    Mung: Evolutionary theory does not predict a nested hierarchy.

    Evolutionary theory states that organisms diverge from common ancestors generally through vertical inheritance, and therefore, organisms will generally form a nested hierarchy.

    Mung: What’s your point, if you have one?

    Hypothetico-deduction, a.k.a. the scientific method.

    gpuccio: Probably. A simple function.

    A few hundred amino acids, that’s all. And to the organisms, crucial. If you could eat plastic residues while everyone else starved, you would think it was the most important trait in the world.

    gpuccio: Can you give me a detailed list of words of 12 letters which go from QUIXOTICALLY to EXTEMPORIZER, where each word is a correct English word, and each word differs from the previous one only of one letter?

    As pointed out several times, we include recombination along with mutation in our word evolution. Given that, then they are probably connected. Also, the claim isn’t that every word is connected, just that many 12-letter words can evolve. Evolution is opportunistic, not necessarily thorough.

  294. 294
    bornagain77 says:

    Me_Think, pointing to adaptations that are, in many instances, non-Darwinian, and that do not exceed the UPB of Dembski is, regardless of what you imagine to be true, NOT providing empirical evidence that search space is, as you claim, multidimensional and that novel functional sequences are within easy reach of each other as a result of being in your imaginary multidimensional search space.

    to reiterate what the real world empirical evidence states:

    four decades worth of laboratory evolution experiments are surveyed here, and no evidence for neo-Darwinian evolution surfaces:

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
    http://behe.uncommondescent.co.....evolution/

    How about the oft cited example for neo-Darwinism of antibiotic resistance?

    List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria:
    Excerpt: Resistance to antibiotics and other antimicrobials is often claimed to be a clear demonstration of “evolution in a Petri dish.” ,,, all known examples of antibiotic resistance via mutation are inconsistent with the genetic requirements of evolution. These mutations result in the loss of pre-existing cellular systems/activities, such as porins and other transport systems, regulatory systems, enzyme activity, and protein binding.
    http://www.trueorigin.org/bacteria01.asp

    That doesn’t seem to be helping! How about we look really, really, close at very sensitive growth rates and see if we can catch almighty evolution in action?

    Unexpectedly small effects of mutations in bacteria bring new perspectives – November 2010
    Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed.
    http://www.physorg.com/news/20.....teria.html

    Shoot that doesn’t seem to be helping either! How about if we just try to ‘fix’ a ‘beneficial’ mutation:

    Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010
    Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator.
    http://www.arn.org/blogs/index.....ruit_flies

    Well that certainly didn’t help. How about if just try to help evolution out a little and saturate genomes with mutations until we can actually see some ‘evolution’?

    Response to John Wise – October 2010
    Excerpt: A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism.
    http://www.evolutionnews.org/2.....38811.html

    Well now its getting frustrating, how about if we try to force bacteria to adapt to a new environment?

    Researchers Ran a Massive Yearlong Experiment to Get Bacteria to Evolve. Guess What Happened? – August 22, 2014
    Excerpt: (the problem the researchers tried to address???)
    “the general inability to connect phenotype to genotype in the context of environmental adaptation has been a major failing in the field of evolution.,,,”
    (Their results in addressing this major failing???)
    ‘In short, it was hard to find anything beyond a “suggestion” or a “scenario” that these bacteria improved their fitness in any way by genetic mutations, other than the gross observation that some of the clones managed to survive at 45 °C. But even the ancestor could do that sometimes through the “Lazarus effect.”‘
    http://www.evolutionnews.org/2.....89231.html

    Shoot that doesn’t seem to be helping either! Perhaps we just have to give the almighty power of neo-Darwinism ‘room to breathe’? How about we ‘open the floodgates’ to the almighty power of Darwinian Evolution and look at Lenski’s Long Term Evolution Experiment and see what we can find after 50,000 generations, which is equivalent to somewhere around 1,000,000 years of human evolution???

    “The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski’s research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address other longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT.”
    (Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).)

    Lenski’s Long-Term Evolution Experiment: 25 Years and Counting – Michael Behe – November 21, 2013
    Excerpt: Twenty-five years later the culture — a cumulative total of trillions of cells — has been going for an astounding 58,000 generations and counting. As the article points out, that’s equivalent to a million years in the lineage of a large animal such as humans. Combined with an ability to track down the exact identities of bacterial mutations at the DNA level, that makes Lenski’s project the best, most detailed source of information on evolutionary processes available anywhere,,,
    ,,,for proponents of intelligent design the bottom line is that the great majority of even beneficial mutations have turned out to be due to the breaking, degrading, or minor tweaking of pre-existing genes or regulatory regions (Behe 2010). There have been no mutations or series of mutations identified that appear to be on their way to constructing elegant new molecular machinery of the kind that fills every cell. For example, the genes making the bacterial flagellum are consistently turned off by a beneficial mutation (apparently it saves cells energy used in constructing flagella). The suite of genes used to make the sugar ribose is the uniform target of a destructive mutation, which somehow helps the bacterium grow more quickly in the laboratory. Degrading a host of other genes leads to beneficial effects, too.,,, –
    http://www.evolutionnews.org/2.....79401.html

    Now this just can’t be right!! Man we should really start to be seeing some neo-Darwinian fireworks by 50,000 generations!?! Hey I know what we can do! How about we see what happened when the ‘top five’ mutations from Lenski’s experiment were combined??? Surely now the Darwinian magic will start flowing!!!

    Mutations : when benefits level off – June 2011 – (Lenski’s e-coli after 50,000 generations)
    Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually.
    http://www2.cnrs.fr/en/1867.htm?theme1=7

    Now something is going terribly wrong here! Tell you what, let’s just forget trying to observe evolution in the lab, I mean it really is kind of cramped in the lab you know, and now let’s REALLY open the floodgates and let’s see what the almighty power of neo-Darwinian evolution can do with the ENTIRE WORLD at its disposal? Surely now almighty neo-Darwinian evolution will flex its awesomely powerful muscles and forever make those IDiots, who believe in Intelligent Design, cower in terror!

    A review of : The Search for the Limits of Darwinism
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’
    Michael Behe The Edge of Evolution p. 155

    “The immediate, most important implication is that complexes with more than two different binding sites-ones that require three or more proteins-are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable.”
    – Michael Behe – The Edge of Evolution – page 146

    “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.”
    Michael Behe, The Edge of Evolution, pg. 162

    Kenneth Miller Steps on Darwin’s Achilles Heel – Michael Behe – January 17, 2015
    Excerpt: Enter Achilles and his heel. It turns out that the odds are much better for atovaquone resistance because only one particular malaria mutation is required for resistance. The odds are astronomical for chloroquine because a minimum of two particular malaria mutations are required for resistance. Just one mutation won’t do it. For Darwinism, that is the troublesome significance of Summers et al.: “The findings presented here reveal that the minimum requirement for (low) CQ transport activity … is two mutations.”
    Darwinism is hounded relentlessly by an unshakeable limitation: if it has to skip even a single tiny step — that is, if an evolutionary pathway includes a deleterious or even neutral mutation — then the probability of finding the pathway by random mutation decreases exponentially. If even a few more unselected mutations are needed, the likelihood rapidly fades away.,,,
    So what should we conclude from all this? Miller grants for purposes of discussion that the likelihood of developing a new protein binding site is 1 in 10^20. Now, suppose that, in order to acquire some new, useful property, not just one but two new protein-binding sites had to develop. In that case the odds would be the multiple of the two separate events — about 1 in 10^40, which is somewhat more than the number of cells that have existed on earth in the history of life. That seems like a reasonable place to set the likely limit to Darwinism, to draw the edge of evolution.
    http://www.evolutionnews.org/2.....92771.html

    Now, there is something terribly wrong here! After looking high and low and everywhere in between, we can’t seem to find the almighty power of neo-Darwinism anywhere!! Shoot we can’t even find ANY power of neo-Darwinism whatsoever!!! It is as if the whole neo-Darwinian theory, relentlessly sold to the general public as it was the gospel truth, is nothing but a big fat lie!

  295. 295
    bornagain77 says:

    But to save us all a bunch of time, how about even one molecular machine produced by unguided Darwinian processes so as to falsify ID?

    Dr. James Tour, who, in my honest opinion, currently builds the most sophisticated man-made molecular machines in the world, will buy lunch for anyone who can explain to him exactly how Darwinian evolution works:

    Top Ten Most Cited Chemist in the World Knows Darwinian Evolution Does Not Work – James Tour, Phd. – video
    https://www.youtube.com/watch?v=_Y5-VNg-S0s

    “I build molecules for a living, I can’t begin to tell you how difficult that job is. I stand in awe of God because of what he has done through his creation. Only a rookie who knows nothing about science would say science takes away from faith. If you really study science, it will bring you closer to God.”
    James Tour – one of the leading nano-tech engineers in the world – Strobel, Lee (2000), The Case For Faith, p. 111

    Science & Faith — Dr. James Tour – video (At the two minute mark of the following video, you can see a nano-car that was built by Dr. James Tour’s team)
    https://www.youtube.com/watch?v=pR4QhNFTtyw

    as to empirical falsification in general, it is far easier to falsify ID than it is to falsify the pseudo-science of Darwinism:

    “In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.”
    Karl Popper – The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge
    http://izquotes.com/quote/147518

    It’s (Much) Easier to Falsify Intelligent Design than Darwinian Evolution – Michael Behe, PhD
    https://www.youtube.com/watch?v=_T1v_VLueGk

    The Law of Physicodynamic Incompleteness – David L. Abel
    Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”
    If only one exception to this null hypothesis were published, the hypothesis would be falsified. Falsification would require an experiment devoid of behind-the-scenes steering. Any artificial selection hidden in the experimental design would disqualify the experimental falsification. After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided.
    The time has come to extend this null hypothesis into a formal scientific prediction:
    “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”
    https://www.academia.edu/9957206/The_Law_of_Physicodynamic_Incompleteness_Scirus_Topic_Page_

  296. 296
    Me_Think says:

    BA,
    Did you read even a Single paper posted in the long list ? Why are Axe,Dembski and Behe who are not evolutionary biologist more credible than an evolutionary biologist?

  297. 297
    gpuccio says:

    Zachriel:

    “A few hundred amino acids, that’s all.”

    Not at all! Just a transition of a couple of AAs from an existing functional molecule.

  298. 298
    Zachriel says:

    gpuccio: Not at all! Just a transition of a couple of AAs from an existing functional molecule.

    Now you got it!

    That’s evolution for ya!

  299. 299
    bornagain77 says:

    Me_Think, I call your (and Wagner’s) literature bluff. Provide real world empirical evidence that falsifies ID. A single molecular machine produced by unguided Darwinian processes will do the trick:

    “Grand Darwinian claims rest on undisciplined imagination”
    Dr. Michael Behe

    Michael Behe – No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines
    http://www.metacafe.com/watch/5302950/

    Calling Nick Matzke’s literature bluff on molecular machines – DonaldM UD blogger – April 2013
    Excerpt: So now, 10 years later in 2006 Matzke and Pallen come along with this review article. The interesting thing about this article is that, despite all the hand waving claims about all these dozens if not hundreds of peer reviewed research studies showing how evolution built a flagellum, Matzke and Pallen didn’t have a single such reference in their bibliography. Nor did they reference any such study in the article. Rather, the article went into great lengths to explain how a researcher might go about conducting a study to show how evolution could have produced the system. Well, if all those articles and studies were already there, why not just point them all out? In shorty, the entire article was a tacit admission that Behe had been right all along.
    Fast forward to now and Andre’s question directed to Matzke. We’re now some 17 years after Behe’s book came out where he made that famous claim. And, no surprise, there still is not a single peer reviewed research study that provides the Darwinian explanation for a bacterial flagellum (or any of the other irreducibly complex biological systems Behe mentioned in the book). We’re almost 7 years after the Matzke & Pallen article. So where are all these research studies? There’s been ample time for someone to do something in this regard.
    Matzke will not answer the question because there is no answer he can give…no peer reviewed research study he can reference, other than the usual literature bluffing he’s done in the past.
    http://www.uncommondescent.com.....ent-453291

    ,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’
    Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205.
    *Professor Emeritus of Biochemistry, Colorado State University, USA

    And yet, despite rejecting Intelligent Design as a ‘matter of principle’, in 2014 Franklin Harold admitted:

    “we may still be missing some essential insight”
    Franklin Harold – 2014

    the ‘non-Darwinian’, natural genetic engineering, James Shapiro admits the same lack of evidence:

    “The argument that random variation and Darwinian gradualism may not be adequate to explain complex biological systems is hardly new […} in fact, there are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation for such a vast subject — evolution — with so little rigorous examination of how well its basic theses works in illuminating specific instances of biological adaptation or diversity.”
    Prof. James Shapiro – “In the Details…What?” National Review, 19 September 1996, pp. 64.

    Talking Back to Goliath: Some Advice for Students in the Evolutionary Biology Classroom – Paul Nelson – September 30, 2014
    Excerpt: (if neo-Darwinism) is true, we should be able to find in the scientific literature the detailed explanations for the origin of complex structures and behaviors, rendered strictly in terms of random variation plus natural selection.
    Guess what? Those explanations aren’t there; they don’t exist. If anyone doubts this, he should try looking for himself. Choose any complex structure or behavior, and look in the biological literature for the step-by-step causal account where the origin of that structure (that is, its coming-to-be where it did not exist before) is explained via random variation and natural selection.
    You’ll be looking a long time. The explanations just aren’t there, and this fact is well known to evolutionary biologists who have become disenchanted with received neo-Darwinian theory. When proponents of the received theory, such as Richard Dawkins, face the task of making random variation and natural selection work, they resort to fictional entities like Dawkins’s “biomorphs” — see Chapter 3 of The Blind Watchmaker (1986) — or flawed analogies such as the “methinks it is like a weasel” search algorithm scenario. No one would have to employ these toy stories, of course, if evidence were available showing the efficacy of random variation and selection to construct novel complexity.
    “Research on selection and adaptation,” notes Mary Jane West-Eberhard, a disenchanted evolutionary theorist, “may tell us why a trait persisted and spread, but it will not tell us where a trait came from….This transformational aspect of evolutionary change has been oddly neglected in modern evolutionary biology” (2003, p. 197).
    http://www.evolutionnews.org/2.....90141.html

    “The response I have received from repeating Behe’s claim about the evolutionary literature, which simply brings out the point being made implicitly by many others, such as Chris Dutton and so on, is that I obviously have not read the right books. There are, I am sure, evolutionists who have described how the transitions in question could have occurred.” And he continues, “When I ask in which books I can find these discussions, however, I either get no answer or else some titles that, upon examination, do not, in fact, contain the promised accounts. That such accounts exist seems to be something that is widely known, but I have yet to encounter anyone who knows where they exist.”
    David Ray Griffin – retired professor of philosophy of religion and theology

    etc.. etc…

  300. 300
    gpuccio says:

    Piotr:

    Before I comment on the other points, are you saying that you cannot do with 12 letter words what you did with 5 letter words? Because, you know, that was exactly my point! 🙂

    Zachriel seems unable to do that too.

    OK, let’s go to your other points. The number of 12 letter words, IOWs my example, is about double than the number of 5 letter words (your example). So, you cannot justify the impossibility with the concept that “the number of words with n letters drops rather quickly as n increases”. After all, I have not taken 30 letter words.

    Obviously, it’s the huge increase in the search space which is the cause of the impossibility. Which is my point.

    And I don’t believe at all that if you add “letter addition or deletion, recombination, concatenation” connectivity is restored. Please show that it is true. But remember that you have to work with simple variation (possibly simple events), and that the search space increases too (just think what letter addition means).

    Now, Zachriel has obviously stated that he can evolve anything he likes. And he is correct. Me too. As I have said, I can evolve the full text of Hamlet. It’s easy:

    a) I have the full text of Hamlet as an oracle.

    b) I take a random string of the same length.

    c) I change the first letter randomly, checking with the first letter in the oracle.

    d) As soon as it is the same, I fix it.

    e) I pass to the second letter, and so on.

    I am sure that any old computer would evolve the result in a very short computational time. As Zachriel would say, “in less than the lifetime of a mayfly”. 🙂

    See how powerful an evolutionary search is?

    Finally, I see that you don’t like QUIXOTICALLY. A pity, it was a fascinating word!

    OK, why don’t you try with SUBJECTIVISM? I suppose we can leave EXTEMPORIZER as an outcome, can’t we?

  301. 301
    gpuccio says:

    Zachriel:

    It’s beautiful to agree with your interlocutor, even if he is a talented discussant for whom “a few hundred amino acids” and “a couple of aminoacids” are essentially the same thing. 🙂

    By the way, why don’t you take a look at my many posts about dFSCI and the design inference? So I could be able to tell you:

    “That’s ID theory for ya!”

    It would simply be fair…

  302. 302
    Zachriel says:

    guppcio: And I don’t believe at all that if you add “letter addition or deletion, recombination, concatenation” connectivity is restored.

    With every member of the population being a properly spelled word. After about three minutes of churning with a population of 1000, this is what the algorithm came up with:

    word, length, Scrabble®

    breakfasters; 12, 21
    deliberating; 12, 16
    lockstitches; 12, 23
    characterless; 13, 20
    denominations; 13, 16
    characterizing; 14, 31

    In the dictionary we used, there are only about 6e3 words of length 12, 13, 14 each. The search space for a 14-letter word is about 4e16, but the total number of mutants tested was only about 5e6 or just the tiniest sliver of possible combinations.

    gpuccio: a) I have the full text of Hamlet as an oracle. b) I take a random string of the same length. c) I change the first letter randomly, checking with the first letter in the oracle. d) As soon as it is the same, I fix it. e) I pass to the second letter, and so on.

    That doesn’t meet the requirements of the algorithm, which is that each word must be properly spelled, or the sequence is stillborn.

  303. 303
    Zachriel says:

    gpuccio: It’s beautiful to agree with your interlocutor, even if he is a talented discussant for whom “a few hundred amino acids” and “a couple of aminoacids” are essentially the same thing.

    They are measures of very different things. If you didn’t know the origin of nylonase, the ID theorist might consider it some incredible feat of engineering! But we ‘saw’ the origin of nylonase, and we do know its origin. It’s within a few steps of a known biological structure. That’s the whole point!

  304. 304
    bornagain77 says:

    It’s within a few steps of a known biological structure. “That’s the whole point!”

    The whole point being exactly what pray tell? 🙂

    That Darwinists erroneously believe such trivial adaptations prove that unguided material processes can build the unfathomed complexity we find in life?

    Well if that is ‘the whole point’ then you Darwinists had me when you erroneously claimed the same thing for varying bird beaks! 🙂

  305. 305
    gpuccio says:

    Zachriel:

    “That doesn’t meet the requirements of the algorithm”

    What algorithm? Why is my Hamlet algorithm less valid than yours?

    My point is that you can always build an algorithm which does what you want: it all depends on how much added information you use.

    If you choose to ignore that your algorithms add a lot of information that could not be present in any “natural” system, then my Hamlet algorithm is as valid as yours.

    So, the point is simple:

    a) If you already know the solution, you can easily find it by an “evolutionary” search (see also the famous Weasel algorithm. Amazing! You only have to add some handicaps (some random search, for example), just to avoid writing down the solution directly.

    b) If you don’t know the solution, but know a lot of things about it, you can find the solution with some ease, according to how much you know. You just have to add the information you know in your algorithm.

    What is new in all this? What has this to do with Wagner’s statements, which were the beginning of the discussion? I still wonder…

    However, can you go from SUBJECTIVISM to EXTEMPORIZER by one letter changes, and through a sequence of correct 12 letter words? That was my question. And beware, I am not at all sure that it is not possible. Just curious.

    A simple yes (with the list of words) or no will do.

  306. 306
    Zachriel says:

    bornagain77: That Darwinists erroneously believe such trivial adaptations prove that unguided material processes can build the unfathomed complexity we find in life?

    It’s hardly trivial. If you could eat plastic residues while everyone else starved, you would think it was the most important trait in the world!

    And if you didn’t know its origin, you would say it was a marvel of engineering, well beyond what could be expected from chance alone.

  307. 307
    gpuccio says:

    Zachriel:

    “If you didn’t know the origin of nylonase, the ID theorist might consider it some incredible feat of engineering!”

    And neo darwinist theorists (including you) have considered it some incredible feat of random frameshift variation for a very long time.

    “But we ‘saw’ the origin of nylonase, and we do know its origin”

    Luckily. We can still believe that, in time, truth emerges.

    “It’s within a few steps of a known biological structure. That’s the whole point!”

    Indeed! The whole point is that neo darwinists were wrong, that their propaganda against ID based on the Ohno conjecture was, indeed, propaganda and nothing else, and that the origin of nylonase is perfectly compatible with ID theory as a form of non designed, maybe adaptational, microevolutionary transition.

  308. 308
    Eric Anderson says:

    Zachriel @293:

    Somewhat more than that. It’s not just sharing of traits, but the many unique combinations of traits that would otherwise be unavailable. “Your father’s nose. Your mother’s eyes.”

    Why would they be otherwise unavailable? I could have the father’s nose and evolve the mother’s eyes on my own later. It might just take longer and be less probable. Again, all we are bringing to the table with recombination is more probabilistic resources — we’re just tweaking the numerator. It doesn’t substantively change what can appear through the evolutionary process.

  309. 309
    Zachriel says:

    gpuccio: What algorithm?

    The algorithm we have been discussing when you said “And I don’t believe at all that if you add ‘letter addition or deletion, recombination, concatenation’ connectivity is restored.” That statement was demonstrably incorrect.

  310. 310
    Zachriel says:

    gpuccio: And neo darwinist theorists (including you) have considered it some incredible feat of random frameshift variation for a very long time.

    Frameshifts are just another type of mutation.

    gpuccio: the origin of nylonase is perfectly compatible with ID theory as a form of non designed, maybe adaptational, microevolutionary transition.

    Mutation and selection. That’s evolution for ya!

  311. 311
    Zachriel says:

    Eric Anderson: Why would they be otherwise unavailable? I could have the father’s nose and evolve the mother’s eyes on my own later.

    Individual don’t evolve. Nor is it certain that a particular trait will evolve in a lineage. Recombination allows for these combinations to be tested in each generation. Some combinations will provide benefits that are not available to the individual traits.

  312. 312
    Eric Anderson says:

    gpuccio @307:

    . . . the origin of nylonase is perfectly compatible with ID theory as a form of non designed, maybe adaptational, microevolutionary transition.

    Exactly. As is every real-world example of “evolution” that has ever been offered. The elephant in the room is that no observable evidence beyond that ever seems to be offered.

    The only place the transition from minor adaptive change to large-scale organismal change ever takes place is in the minds of the faithful.

  313. 313
    gpuccio says:

    Zachriel:

    You have still not answered my question about the two words. And we don’t know the details of your algorithm, and how it works. And your algorithm has not brought us from SUBJECTIVISM to EXTEMPORIZER, showing that connectivity has been restored, whatever that means.

    I have a lot of other comments to do about Piotr’s statements and yours, but I prefer to wait to see if Piotr concludes his reasoning, and how it relates to Wagner’s ideas. So, I will take a little rest.

  314. 314
    gpuccio says:

    Eric:

    “The only place the transition from minor adaptive change to large-scale organismal change ever takes place is in the minds of the faithful.”

    Perfectly correct!

    And, I would say, in the discussions of the tricky…

  315. 315
    Eric Anderson says:

    Zachriel:

    Individual don’t evolve.

    This is far from certain, but let’s leave that question for another post another time. We’ve been talking about the difference between a single-celled organism that reproduces itself asexually, versus a large population with sexual reproduction. The single organism reproducing asexually can certainly evolve.

    Nor is it certain that a particular trait will evolve in a lineage.

    Of course it isn’t certain. And it isn’t certain that a particular trait will arise with recombination either. The only difference is that it gives more probabilistic resources.

    Any way you cut it, we are dealing with more probabilistic resources. That is it.

  316. 316
    Zachriel says:

    gpuccio: You have still not answered my question about the two words. {SUBJECTIVISM to EXTEMPORIZER}

    Don’t know. It’s doubtful. However, many 12-letter words are easily available with populations and recombination.

    gpuccio: And we don’t know the details of your algorithm, and how it works.

    Sure you do. We already explained it. We have a population of words. They are subjected to either random mutation or random “addition or deletion, recombination, concatenation”. If the result forms a new word, it can enter the population, otherwise, it’s stillborn. Most are stillborn. But over time, longer and longer words evolve.

    gpuccio: And your algorithm has not brought us from SUBJECTIVISM to EXTEMPORIZER, showing that connectivity has been restored, whatever that means.

    Some words will be out of reach. Evolution is opportunistic, and it’s easy to show that 12- or even 14-letter words quickly evolve.

  317. 317
    Zachriel says:

    Eric Anderson: The single organism reproducing asexually can certainly evolve.

    Sure, but simple mutation will always be limited.

    Eric Anderson: The only difference is that it gives more probabilistic resources.

    That is incorrect. Assuming only single-point mutation, there are many structures that are out of reach that are available to mutation plus recombination.

  318. 318
    Piotr says:

    gpuccio:

    Before I comment on the other points, are you saying that you cannot do with 12 letter words what you did with 5 letter words? Because, you know, that was exactly my point! 🙂

    I can’t. There isn’t much I can do with ANTIDISESTABLISHMENTARIANISM either, and I can’t do anything with 47-letter words, because there are none in English. Moreover, QUIXOTE is only seven letters long and still “aloof” — among other things because it’s a word borrowed from a different language, with no detectable historical connection with anything in English, and so its structure stands out as somewhat exotic. Its “aloofness” is inherited by its derivatives.

    This, however, has to do more with the structural limitations of the English lexicon and the distribution of possible word lengths than with the nature of the search. The word-ladder thought-experiment wasn’t supposed to be an exact analogy of evolutionary “searches” (for one thing, “functional” DNA sequences are of neither fixed nor limited length; for another, there are many possible types of mutations beside single point substitutions). I just wanted to highlight one point: if functionality obeys some external constraints (here, the “Englishness” of words), functional structures are not randomly dispersed in the sequence space. They tend to cluster together and to form an interconnected web, rather than a rugged landscape with towering lonely peaks. That’s also part of Andreas Wagner’s message.

  319. 319
    wd400 says:

    The single organism reproducing asexually can certainly evolve.

    Nah, a single organism reproducing asexually makes a population.

    . The only difference is that it gives more probabilistic resources.

    Is there a process that does more than this? Something like Mt Rushmore might arise by erosion, having someone plan and sculpt a mountain merely increases the probability that it will do so.

  320. 320
    gpuccio says:

    Piotr:

    By the way, your statement that:

    “As for your concrete examples, QUIXOTICALLY is based on a foreign proper name, and so is likely to turn out to be “aloof” word (to use Lewis Carroll’s terminology). So is even the shorter adjective QUIXOTIC.”

    allows me to anticipate a comment which I had thought of, but not expressed for the moment.

    You same statement shows that words are not only connected because of “natural” constraints (like the pronunciation patterns shaped by some natural restrictions on preferred sound combinations, or the anatomy of the vocal tract and the aerodynamics of sound production). They are also connected because of their origin and cultural context.

    That kind of connectivity is based on design factors, and has nothing to do with natural functional constraints. And it is certainly responsible for much of the “connectivity” you observe in words.

  321. 321
    gpuccio says:

    Piotr:

    “I just wanted to highlight one point: if functionality obeys some external constraints (here, the “Englishness” of words), functional structures are not randomly dispersed in the sequence space. They tend to cluster together and to form an interconnected web, rather than a rugged landscape with towering lonely peaks. That’s also part of Andreas Wagner’s message.”

    And I disagree. You are completely ignoring the basic importance of the search space size. Which was the essential point in my arguments.

    As the search space becomes huge, the functional states do become dispersed in it. For proteins, we can check that simple fact by comparing the sequences of basic superfamilies, which are not related.

    And I am really surprised that you think that the functional landscape of proteins is not a rugged landscape, because that is exactly the model that what we know about it definitely favors.

    See this paper, for example:

    http://www.plosone.org/article.....tation=PDF

    I understand that your example with words is not an exact analogy. But, as an analogy, it supports exactly my point: as the search space grows, the connectivity (if ever there was one) fades. Dramatically.

  322. 322
    Piotr says:

    That kind of connectivity is based on design factors, and has nothing to do with natural functional constraints. And it is certainly responsible for much of the “connectivity” you observe in words.

    Not quite. Connectivity via point mutation is almost never due to etymology, but mostly to so-called phonotactic constraints, defining the characteristic pronunciation patterns of a given language. Two adjacent words in a word ladder are rarely related: from LORD you can get LARD, WORD, FORD, LOAD, LORE, etc., none of which is related to LORD. Interestingly, in the chain LORD > LOAD > LOAF the first and last words do have a remote historical relationship (check up the etymologies of LORD and LADY), but this fact doesn’t explain their being connectible. One possible counterexample is words formed by vowel alternation (MAN > MEN, SING > SANG, WRITE > WROTE), but here again the relatedness of connectible words is accidental rather than typical, at least in English.

    Likewise if you allow letter insertions. WRITER is morphologically derived from WRITE, but in a chain like ATE > RATE > IRATE > PIRATE no two words are related.

    Origin may play play a role if you allow concatenation (TOOTH + BRUSH > TOOTHBRUSH). But the fact that a combination of two functional elements may be functional too is hardly a matter of design. We can quite mechanically try out all sorts of combibnations and check if they are correct English words: thus, TOOTHBRUSH, TOOTHACHE, TOOTHPICK, TOOTHLESS and a few others happen to be lexicalised, but TOOTHROOM or TOOTHPAIN aren’t. Note, however, that compounding is a productive process in English, and neologisms of this type are often co-opted as real words before they get recognised by dictionary editors.

  323. 323
    Piotr says:

    P.S. Common origin does not imply “design factors”. SING and SONG are related, but it’s merely a statement about their (rather remote) history. An average language user with no linguistic expertise is vaguely aware of the relationship but can’t even explain how and why they are related, let alone “design” such pairs.

  324. 324
    Phinehas says:

    Piotr:

    I just wanted to highlight one point: if functionality obeys some external constraints (here, the “Englishness” of words), functional structures are not randomly dispersed in the sequence space. They tend to cluster together and to form an interconnected web, rather than a rugged landscape with towering lonely peaks.

    But your analogy has additional arbitrary constraints (like the length of the word) that, when removed, tend to lead us right back to a rugged landscape with towering lonely peaks. It certainly doesn’t demonstrate that it is the external constraint and not the simplicity that is leading to an interconnected web, since with the same external constraint, but the addition of complexity, the connectivity disappears.

    I actually think that language is a very interesting and appropriate analogy. We are just talking about spelling at this point in the thread, but when you extend the analogy to the evolution of sentences, then you have to layer in things like grammar in addition to spelling. And when we expand it to literature, you need to layer in things like foreshadowing, allusions, irony, etc. Again, all in addition to grammar and spelling. Can you go from Hamlet to A Tale of Two Cities with your additions, deletions, recombinations, etc.? For me, this is a much closer analogy to what we actually see with life. Layers of information and coordination and regulation. Complex interrelatedness that boggles the mind.

  325. 325
    Piotr says:

    gpuccio,

    From the article you have linked:

    The landscape structure has a number of implications for initial functional evolution of proteins and for molecular evolutionary engineering. First, the smooth surface of the mountainous structure from the foot to at least a relative fitness of 0.4 means that it is possible for most random or primordial sequences to evolve with relative ease up to the middle region of the fitness landscape by adaptive walking with only single substitutions. In fact, in addition to infectivity, we have succeeded in evolving esterase activity from ten arbitrarily chosen initial random sequences [17]. Thus, the primordial functional evolution of proteins may have proceeded from a population with only a small degree of sequence diversity.

    What they found is not an ocean of dysfuctionality in which you drown as you try to move away from a fitness peak. The landscape is smooth and traversible by (nearly) neutral evolution, while adaptive walks can easily ascend its slopes up to a certain level. Improving the functionality a protein’s sequence further gets difficult because the landscape becomes rugged when the fitness factor is already pretty high. Who cares? Fitness is relative. As long as the organism is viable, it doesn’t have to be perfect in every respect.

  326. 326
    Piotr says:

    Phinehas

    Can you go from Hamlet to A Tale of Two Cities with your additions, deletions, recombinations, etc.?

    Why should I? The real linguistic replicators (more or less analogous to DNA sequences) are words, not sentences (except fixed phrases, which behave like vocabulary units), let alone literary texts. A word can be used millions of times by the same person, and is handed down from generation to generation (slowly changing its form over centuries and millennia). A sentence of ordinary spoken language (not to mention longer utterances) is meant for one-time use and and is rarely repeated in the same form ever again. We do design sentences and texts, but we inherit or borrow the building blocks (words, set phrases). You may try to “design” a word de novo from time to time, but unless you manage to make other people use it, it won’t become part of language evolution.

  327. 327
    Phinehas says:

    Piotr:

    Phin: Can you go from Hamlet to A Tale of Two Cities with your additions, deletions, recombinations, etc.?

    Piotr: Why should I?

    If you hadn’t clipped the next few sentences, you’d already have my answer. To claim that life is just lots of DNA is at least as reductionist as to claim that literature is just lots of letters. There are layers of complexity to both life and literature.

    I also note that you avoided this:

    Phin: But your analogy has additional arbitrary constraints (like the length of the word) that, when removed, tend to lead us right back to a rugged landscape with towering lonely peaks. It certainly doesn’t demonstrate that it is the external constraint and not the simplicity that is leading to an interconnected web, since with the same external constraint, but the addition of complexity, the connectivity disappears.

    One explanation might be that you have nearly as little confidence in the fitness of your analogy as I do.

  328. 328
    Piotr says:

    To claim that life is just lots of DNA is at least as reductionist as to claim that literature is just lots of letters.

    Perhaps. It doesn’t worry me because I’ve never claimed life is just lots of DNA.

  329. 329
    Eric Anderson says:

    Zachriel @317:

    Sure, but simple mutation will always be limited.

    Based on what? It is supposed to have given rise to all manner of wonderful creations, certainly before all of the population-based swaps and sexual recombinations arose. Again, it is just a question of probabilities. Simple mutation has less likelihood of causing a change than a larger genetic change. Sure. Also less likelihood of catastrophic failure. Pick your poison. The fact is that swapping large amounts of genetic material is not some panacea for the limited powers of “simple mutations.”

    That is incorrect. Assuming only single-point mutation, there are many structures that are out of reach that are available to mutation plus recombination.

    Why would we assume only single-point mutation within a single reproducing organism?* Surely the organism could also have, if not recombination from parents, then larger changes in genetic blocks during its lifetime or during the reproduction process. Further, how did those additional pieces of recombining parental DNA come about, if not, at some point in deep time, through “simple mutations”?

    And what it is it about a particular structure that puts it out of reach of point mutations? Either you are claiming that point mutations cannot produce X because it is: (i) not possible due to general lack of probabilistic resources, or (ii) not possible due to the irreducible complexity issue (i.e., cannot be built from slight, successive changes, so some larger, sudden change is required).

    Slightly different angles. But both are still subsets of the probabilistic resources issue.

    —-

    * For wd400’s benefit: again, talking about a single organism that reproduces asexually once and then dies; no large population ever exists; no outside swapping; no parental recombination; just the same genetic material from generation to generation (with whatever point mutations, copying errors, splicing errors, etc. may arise).

  330. 330
    Zachriel says:

    Zachriel: Sure, but simple mutation will always be limited.

    Eric Anderson: Based on what?

    Simple inspection. For instance, “quixotic” is aloof. There are no single step mutations (point change, insertion, or deletion) which yield another word. By the way, this answers gpuccio’s question above.

    However, if there is a population of words, and snippets and recombination are included, then “quixotic” can evolve. A simple snippet is “tic” (twitch) then mutation “tick” (insect) then mutation “tock” (bird) then concatenation “ticktock” (sound).

    Another example, not requiring snippets is “ticktock”. “Ticktock” is aloof. (* According to our dictionary and search, it’s a small island with the verbal forms of “ticktock” as well as the nounal forms of “ticktack”.) That means it can’t evolve from any other word, given only single mutation. However, if the population includes “tick” and “tock”, then it can evolve by concatenation.

    In other words, recombination provides access to areas of the word-space that simple mutation cannot.

  331. 331
    gpuccio says:

    Piotr:

    From the paper:

    In practice, the maximum library size that can be prepared is about 10^13 [28,29]. Even with a huge library size, adaptive walking could increase the fitness, ~W, up to only 0.55. The question remains regarding how large a population is required to reach the fitness of the wild-type phage. The relative fitness of the wild-type phage, or rather the native D2 domain, is almost equivalent to the global peak of the fitness landscape. By extrapolation, we estimated that adaptive walking requires a library size of 10^70 with 35 substitutions to reach comparable fitness.

    You say:

    “What they found is not an ocean of dysfuctionality in which you drown as you try to move away from a fitness peak. The landscape is smooth and traversible by (nearly) neutral evolution, while adaptive walks can easily ascend its slopes up to a certain level.”

    OK, but from that level on, the landscape is extremely rugged.

    The problem is, the whole experiment is of the kind “function retrieval”. They produced a defective phage my substituting a random sequence in a domain, in a protein involved in the infectivity process. This kind of scenario is very good to test the ability of variation and NS to “optimize” a defective function, which however must be present even at the initial low level.

    So, what we see is that variation and NS can “optimize” the defective situation up to a certain level. At the same time, they cannot realistically optimize it even near the wildtype level.

    Why?. Because the rugged landscape cannot be traversed. You need an extremely big starting library (10^70, according to the estimate of the authors) to have a chance of finding the optimal level, even with all the process of variation and NS taking place.

    You say:

    “Improving the functionality a protein’s sequence further gets difficult because the landscape becomes rugged when the fitness factor is already pretty high. Who cares? Fitness is relative. As long as the organism is viable, it doesn’t have to be perfect in every respect.”

    Wrong. First of all, the fitness factor is not high at all, in that experiment. Remember, we are only retrieving an existing function. We are optimizing a single damaged domain of a single protein. The infectivity is made possible by the whole protein, and by all the rest which acts in the infective process. We have just damaged a bit of the machinery, and still we cannot retrieve the function, even with all the focused power of variation and NS.

    The simple point is, the biochemical and biological functions that we see in living beings are extremely optimal. They are the peaks of so many rugged landscapes, exactly as the wild type domain of the protein is the peak of this rugged landscape. Those local optima could never be found by random search and NS, because the connectivity you dream of is not real.

  332. 332
    Zachriel says:

    gpuccio: Why?. Because the rugged landscape cannot be traversed.

    Why? Because they only used point mutation. Recombination can allow the search to move between local maxima. In any case, the experiment shows that a random sequence can have function, and that the degree of function can be substantially increased through natural selection.

  333. 333
    Joe says:

    In any case, experiments demonstrate that natural selection, drift and all other blind watchmaker-type processes are impotent and incapable of producing anything of note.

  334. 334
    Joe says:

    Language evolution is another example of evolution via intelligent design. Why do evos think that everything “evolution” is automatically blind watchmaker evolution?

  335. 335
    Me_Think says:

    I plotted 3,933 twelve letter words and created a communality graph here As you can see the words form disjointed island and search would be difficult if this is represented in 2 dimensional landscape search.
    The graph has vertex count = 586, so it can be represented on 9 dimensional Hypercube 586=2^d. Solving for d, we get d=9.19 so the graph can be represented on 9 dimensional Hypercube. which brings even the distance ‘functions’ near each other.
    Landscape is 1930s concept. The 2 dimensional representation was for simplicity and even Wright acknowledged true landscape can be represented at higher dimensions only. With today’s computational power, there is no need to confine our self to 2 dimensional landscapes.

  336. 336
    Piotr says:

    gpuccio:

    They are the peaks of so many rugged landscapes, exactly as the wild type domain of the protein is the peak of this rugged landscape.

    The wild type is the product of vast populations, millions of generations, and a greater variety of mutation types (ignored in the study for simplicity, as the authors say). It can certainly achieve much more fine-tuning than in-vitro experiments. Relative fitness lower than that of the wild type does not mean “no infectivity”; it means lower infectivity. The mutants would be outcompeted in the wild, which is hardly surprising. The descendants of the successful survivors of innumerable rounds of selection must be tough.

  337. 337
    wd400 says:

    * For wd400?s benefit: again, talking about a single organism that reproduces asexually once and then dies; no large population ever exists

    OK, but you were claiming an individual evolves. In this highly contrived case you would have a lineage not an individual.

    The wider point still seems to be a distraction. Of course mutation+reproduction+selection “only” increases the probability of a given outcome compare to mutation alone. What else could it do? What outcome would be impossible to achieve my mutation alone, or indeed by atoms hitting each other at random? Increasing the probability is the only show in town.

    EA: I must have missed this earlier in the discussion, but ran across it now. It sounds like we are in agreement that the key thing brought to the table is additional probabilistic resources. As far as evolution is concerned, the fundamental, key aspect of reproduction/recombination/and so on, is helping to increase the probabilities.

    As I said earlier. If you doubt that reproducton/selection are important to evolutionary processes you ought to code up a “weasel” program with and without reproduction and see how long each takes to find the target.

  338. 338
    Piotr says:

    #337

    One can treat one individual as a degenerate population. The problem here is that such a population is inevitably doomed. Sooner or later either a fatal accident will befall its sole representative before it produces its single descendant, or enough deleterious mutations will accumulate to kill it. In a viable population harmful mutations are kept in check by natural selection, but in a one-member population the effect of natural selection is instant extinction.

  339. 339
    Eric Anderson says:

    wd400:

    As I said earlier. If you doubt that reproducton/selection are important to evolutionary processes you ought to code up a “weasel” program with and without reproduction and see how long each takes to find the target.

    Why? Because with reproduction it would have more opportunities to find the target?

  340. 340
    Me_Think says:

    Eric Anderson @ 339
    Reproduction increases the available gene pool, which means a bigger genotype network, which in turn means more opportunity to find a new phenotype – the higher the number of vertices, the higher will be the hyperdimensions ( Number of vertices = 2^d, d = dimensions) of the network so it is easier to find a new phenotype.

  341. 341
    wd400 says:

    Why? Because with reproduction it would have more opportunities to find the target?

    No. It will take many orders of magnitude fewer “opportunities” for the target to be achieved.

    Methink,

    That the gene pool is larger is only a small part of importance of reproduction. “reproductive excess” does mean more of the fitness landscape is explored in a given generation. But more importantly, reproduction allows (future) populations the advantage o individually-improbably “good” mutations. That makes navigation through the fitness landscape a very different prospect.

  342. 342
    Eric Anderson says:

    wd400 @341:

    No. It will take many orders of magnitude fewer “opportunities” for the target to be achieved.

    What does this mean? Are you saying that the search landscape changes with a larger population?

    But more importantly, reproduction allows (future) populations the advantage o individually-improbably “good” mutations. That makes navigation through the fitness landscape a very different prospect.

    Can you explain this a bit more? One population might have a mutation that helps with environment x, while another might have a mutation that helps with environment y. And because we now have two populations they somehow navigate differently through the landscape to find a mutation that will help with environment z?

  343. 343
    gpuccio says:

    Zachriel:

    “Why? Because they only used point mutation. Recombination can allow the search to move between local maxima.”

    I don’t agree. Recombination can only work if modular function is present. And recombination has a huge search space too. And recombination can be detected by homology.

    IOWs, 3 good motives not to believe in recombination as the explanation for complex functional information in biology.

    Beware, I am not denying that recombination can have some role. It is, in itself, one of the main modalities of design (modular design, object oriented programming).

    But, as an attempt at explaining biological information by RV + NS, it is really a fairy tale.

    “In any case, the experiment shows that a random sequence can have function, and that the degree of function can be substantially increased through natural selection.”

    I agree. That’s why I say that the rugged landscape paper is a good paper. It shows many interesting things, and it is a fair attempt (with some limitations) to establish the powers and limits of RV and NS in a context where they are extremely favored.

  344. 344
    gpuccio says:

    Me_Think at #335:

    So, you can easily show us how to go from SUBJECTIVISM to EXTEMPORIZER through one letter variation and functional intermediates. Piece of cake for you.

  345. 345
    gpuccio says:

    Piotr:

    The wild type is the product of vast populations, millions of generations, and a greater variety of mutation types (ignored in the study for simplicity, as the authors say). It can certainly achieve much more fine-tuning than in-vitro experiments. Relative fitness lower than that of the wild type does not mean “no infectivity”; it means lower infectivity. The mutants would be outcompeted in the wild, which is hardly surprising. The descendants of the successful survivors of innumerable rounds of selection must be tough.

    Of course, you are free to dream on, even when evidence is against your theory. The paper estimates a starting library of 10^70 sequences to reach the wild type by mutations. That is not realistic, even with “vast populations, millions of generations”. The point is that after a short time the landscape just prevents the traversing to a very specific, isolated local optimum. IOWs, the wildtype optimum, the very efficient optimum we observe in reality, is a tiny island in the ocean, and cannot be realistically reached.

    The supposed role of recombination is just wishful thinking: they had to say something, of course. It is not ignored “for simplicity”, but because the paper can offer exactly nothing about that hoped future explanations, because they have exactly nothing. Since when is the lack of any evidence for an argument called “simplicity”?

    Again, recombination is just a form of random variation. It tests states, exactly like SNP, deletion, insertion, frameshift mutation, and so on. A single event is a single event, and a single new state is tested, either it differs from the previous of one AA, or of all. The only difference in recombination is that it can retain in some measure existing functional sequences. By the way, it is the simplest mechanism to be tested: homologies are there for that purpose.

    That said, I must say again that I appreciate your discourse. You are trying to make reasonable arguments, and even if I don’t agree with them, it is refreshing for me. However, I still can’t see any “connection” ( 🙂 ) between your arguments (which, in essence, are about the topology of functional proteins in the search space, an old an important controversial issue in our discussions here) and Wagner’s ideas. Am I missing something?

  346. 346
    Me_Think says:

    gpuccio @ 344,

    So, you can easily show us how to go from SUBJECTIVISM to EXTEMPORIZER through one letter variation and functional intermediates. Piece of cake for you.

    Don’t you think I tried ? 🙂 There is no pathway (Although if you calculate the Levenshtein distance or Edit distance between your 2 strings, the value obtained is 11)

  347. 347
    Piotr says:

    #354 gpuccio,

    Of course, you are free to dream on, even when evidence is against your theory. The paper estimates a starting library of 10^70 sequences to reach the wild type by mutations. That is not realistic, even with “vast populations, millions of generations”.

    The estimate is based on a simplified theoretical landscape model which implements ruggedness but doesn’t implement (quasi-)neutrality or any type of non-point mutations (to begin with); it should therefore be taken with a rather large grain of salt. Phages are arguably the most numerous “life forms” on earth, easily outnumbering their bacterial hosts by an order of magnitude. A coliphage can repeat its replication cycle many times a day, producing dozens if not hundreds of copies per lytic cycle. Exploiting the brute force of large numbers is something that phages must be very good at.

    The point is that after a short time the landscape just prevents the traversing to a very specific, isolated local optimum. IOWs, the wildtype optimum, the very efficient optimum we observe in reality, is a tiny island in the ocean, and cannot be realistically reached.

    Rather than that, it’s one in a large archipelago of such islands which are isolated from one another if you consider only single point mutations and require every step to be advantageous (ignoring nearly-neutral walks).

    The supposed role of recombination is just wishful thinking: they had to say something, of course. It is not ignored “for simplicity”, but because the paper can offer exactly nothing about that hoped future explanations, because they have exactly nothing. Since when is the lack of any evidence for an argument called “simplicity”?

    The objective of the study was to see if random point mutations plus selection were enough for the phage to regain a fitness index comparable with that of the wild type. If they don’t seem to suffice, some of the simplifying assumptions are probably unrealistic. That’s what the authors really conclude. It wasn’t their purpose to come up with a more sophisticated model, but such models are being developed:

    http://journals.plos.org/plosg.....en.1002551

    Again, recombination is just a form of random variation. It tests states, exactly like SNP, deletion, insertion, frameshift mutation, and so on. A single event is a single event, and a single new state is tested, either it differs from the previous of one AA, or of all. The only difference in recombination is that it can retain in some measure existing functional sequences. By the way, it is the simplest mechanism to be tested: homologies are there for that purpose.

    If your search space is the DNA sequence space, point mutations differ radically from all types of DNA shuffling, and even from simultaneous double mutations: they can only cover one Hamming distance in each step. It’s a very serious limitation in a highly rugged landscape.

    That said, I must say again that I appreciate your discourse. You are trying to make reasonable arguments, and even if I don’t agree with them, it is refreshing for me. However, I still can’t see any “connection” ( 🙂 ) between your arguments (which, in essence, are about the topology of functional proteins in the search space, an old an important controversial issue in our discussions here) and Wagner’s ideas. Am I missing something?

    Thank you for your kind words. I’m slowly getting to the point, as regards Wagner’s ideas. I hope we are not in a hurry (I’m having a hectic time at work).

  348. 348
    Joe says:

    If rivers evolve then so do individuals.

  349. 349
    gpuccio says:

    Piotr:

    We are in no hurry at all! I am very busy too. 🙂

  350. 350
    gpuccio says:

    Piotr:

    By the way, I don’t agree that the paper does not evaluate neutral or quasi neutral walks:

    “Although each sequence at the foot has the potential for
    evolution, adaptive walking may cease above a relative fitness of 0.4 due to mutation-selection-drift balance or trapping by local optima.”

    Emphasis added.

  351. 351
    Piotr says:

    #350 gpuccio,

    I don’t think their model implements quasi-neutrality (where fitness is allowed to vary minimally within some small threshold). The paper by Kouyos et al. (2012; see above) shows that for a threshold of 10^(-3) a nearly neutral walk in a rugged landscape can reach a distance of about 100 mutations.

    By the way, there are other reasons why the study is not very realistic in its simplicity. For example, it assumes a fixed, stationary landscape, while real fitness landscapes can and do change, tracing changes in the environment (in this case, the host, Escherichia coli keeps evolving as well), and forcing the phage to re-adapt to any changes that affect its reproductive success. Perhaps more importantly, the authors start with a randomly generated polypeptide. In natural conditions, any starting sequence would in all likelihood already confer a higher-than-random fitness — or, in the spirit of Wagner, would be fine-tuned for some other functions with a potential for exaptation via minimal nearly neutral modifications. The evolution of new functions does not start in a “fitness vacuum”.

  352. 352
    Zachriel says:

    Eric Anderson: One population might have a mutation that helps with environment x, while another might have a mutation that helps with environment y. And because we now have two populations they somehow navigate differently through the landscape to find a mutation that will help with environment z?

    Yes. Recombination can explores areas of the landscape otherwise unavailable. A simple example above was provided above.

    gpuccio: Recombination can only work if modular function is present.

    Without recombination, word evolution is very limited, and gets stuck on local maxima. With recombination, most the dictionary becomes available.

    gpuccio: So, you can easily show us how to go from SUBJECTIVISM to EXTEMPORIZER through one letter variation and functional intermediates.

    Twelve-letter words easily evolve if you include a population with recombination.

  353. 353
    Joe says:

    Unguided evolution cannot account for recombination.

  354. 354
    wd400 says:

    EA @342,

    I really don’t think it can be explained more simply than it already has been.

  355. 355
    Eric Anderson says:

    Piotr @338:

    The problem here is that such a population is inevitably doomed. Sooner or later either a fatal accident will befall its sole representative before it produces its single descendant, or enough deleterious mutations will accumulate to kill it. In a viable population harmful mutations are kept in check by natural selection, but in a one-member population the effect of natural selection is instant extinction.

    Agreed. A (somewhat) large population protects the species against the nearly-inevitable destruction by mutation or the hazards of nature that would befall a single lineage. Thus, a population makes the likelihood of surviving, and therefore potentially finding, a new functional evolutionary change greater.

  356. 356
    Eric Anderson says:

    wd400 @354:

    I really don’t think it can be explained more simply than it already has been.

    We have probably gotten where we need to in the discussion.

    I am focusing on a very nuanced issue: what does reproduction itself bring to the table. It is a question that it seems most evolutionary proponents never stop to take time to think through carefully, because it is just assumed to be such a fundamental aspect of evolution that no-one would ever even think of asking the question.

    All of the answers that have been provided (you, Zachriel, Piotr, Me_Think) — answers which are perfectly valid, by the way, and most of which I agree with — boil down to one thing: additional probabilistic resources. So far without exception they have been subsets of that issue. It is important to recognize that this is the case.

    Again, let me be clear that I completely agree that a (substantial) population will have a much greater likelihood of stumbling across a favorable mutation (or other advantageous evolutionary change) than will a single lineage. In most cases by several orders of magnitude.

    Whether a population in fact stumbling across such a favorable change is now likely or plausible depends on the numbers. Whether that change will persevere and become fixed in the population is yet an additional question.

    But what reproduction (and a large population) ultimately brings to the table in the blind search for advantageous change is additional resources.

  357. 357
    Zachriel says:

    Eric Anderson: what does reproduction itself bring to the table

    Continuity. Even with simple mutation, a non-reproducing entity will almost inevitably go extinct before exploring much of the search space. The time to extinction can be calculated based on the landscape. For instance, if 1% of mutations are fatal, then the chance of survival is tiny after a thousand generations, and negligible after several thousand generations. With reasonable fecundity, the line can continue indefinitely.

    Eric Anderson: All of the answers that have been provided (you, Zachriel, Piotr, Me_Think) — answers which are perfectly valid, by the way, and most of which I agree with — boil down to one thing: additional probabilistic resources.

    That is incorrect. Recombination within a population allows exploration of areas of the search space not available to mutation alone. We’ve pointed this out before, but your latest comment indicates you have yet to digest it. A simple example was provided above.

  358. 358
    Joe says:

    Unguided evolution cannot account for biological reproduction. And recombination is a mutation.

  359. 359
    CHartsil says:

    “Unguided evolution cannot account for biological reproduction. And recombination is a mutation.”

    So exactly which step is the result of exactly what design mechanism? Be specific.

  360. 360
    Joe says:

    Design is a mechanism. And ID’s specifics come in the design detection methodology.

    OTOH your position doesn’t have any specifics, doesn’t have a methodology and can’t even be tested.

  361. 361
    wd400 says:

    I am focusing on a very nuanced issue: what does reproduction itself bring to the table. It is a question that it seems most evolutionary proponents never stop to take time to think through carefully, because it is just assumed to be such a fundamental aspect of evolution that no-one would ever even think of asking the question.

    Nah, it’s a question evolutionary biologists learn the answer to very early on. Reproductive excess (that there are more possible organisms than an environment can carry) does increase the “probabilistic resources” available (if that phrase can be construed to mean something). But the more important consquence is that “good
    alleles can outlive their host. Members of a population today start out with all of the benifiests of many previous rounds of selection.

    You could try reading The Blindwatchmakerif this is still not clear to you. Or, as I have suggested, make your own “weasel” program. You will probably win the lottery several times before a non-reproduction version hits the target whereas it will takes seconds with reproduction.

  362. 362
    CHartsil says:

    “Design is a mechanism. And ID’s specifics come in the design detection methodology.”

    No, design is the claim. You have to actually evidence it

  363. 363
    Joe says:

    Design is a mechanism, too. And we have evidence for intelligent design in biology. OTOH your position has nothing but promissory notes.

  364. 364
    Joe says:

    wd400:

    You will probably win the lottery several times before a non-reproduction version hits the target whereas it will takes seconds with reproduction.

    All the reproduction in the universe will not help unguided evolution reach any biological targets that involve multiple protein interactions.

  365. 365
    CHartsil says:

    “Design is a mechanism, too. And we have evidence for intelligent design in biology. OTOH your position has nothing but promissory notes.”

    No, design is the claim. You actually have to have a model to test it

  366. 366
    Eric Anderson says:

    Zachriel @357:

    Continuity. Even with simple mutation, a non-reproducing entity will almost inevitably go extinct before exploring much of the search space.

    Agreed. So reproduction increases the amount of the search space that can be explored before extinction. Which means we are increasing our probabilistic resources brought to the table.

    Recombination within a population allows exploration of areas of the search space not available to mutation alone. We’ve pointed this out before, but your latest comment indicates you have yet to digest it. A simple example was provided above.

    Nope. You haven’t explained any such thing. You’ve pointed to recombination as though it does something intrinsically different. Yet all recombination does is quickly bring together two areas of the search space that were explored by two different organisms/lineages. You have not provided a single reason to think that such search space would be “unavailable” to simple mutation. It is just a question of time and resources. So, again, we are back to the basic point that recombination arguably provides a chance to explore a larger portion of the search space within the time allotted.

    I don’t know, maybe we are saying the same thing. Are you just saying that recombination allows us to explore part of the search space that would be unavailable to simple mutation in the same amount of time? Or that that part of the search space would be unavailable to simple mutation ever?

    The first is correct. The second isn’t.

Leave a Reply