Wednesday, September 23, 2015

How can she go wrong?—let us count the ways ...

There's a very good reason why the creationist website Evolution News & Views (sic) doesn't allow comments but that won't stop us from making comments on Sandwalk. Check out Ann Gauger's latest offering at: Waiting for Mutations: Why Darwinism Won't Work.

There are a few errors in that post. How many? Let us count the ways.1

Theme
Mutation
-definition
-mutation types
-mutation rates
-phylogeny
-controversies
What's interesting about that post is that we've been over the data many times in an attempt to explain mutation to the creationists. Last year I tried to explain why humans and chimpanzees have accumulated about 22 million point mutations since the time they evolved from a common ancestor about 6 million years ago. I thought it would be helpful if they understood why these numbers are perfectly reasonable according to population genetics.

What happened was that the vast majority of commenters on Uncommon Descent called me names and told me I was wrong. A few creationists, Sal Cordova, Vincent Torley, and Branko Kozulic took up the challenge and, for a short while I thought they understood.

That didn't last. As soon as they began to feel the heat from their fellow creationists they started to make up strange stories to prove that the differences between human and chimp genomes can't be explained by evolution.

Here's the initial exchange ...
Here's the followup ....
What this proves is that creationists are remarkably resistant to being taught correct evolutionary theory. They just won't accept anything that doesn't fit into their creationist, anti-evolution, worldview. Ann Gauger is no exception, although she should be. She's a scientist. It's shocking to think that she's the best they've got on the side of the IDiots.

Scientists have even tried to explain how two, or more, mutations can occur within a population. We use dumbed-down language that even some creationists could understand (if their minds were open) [e.g. CCC's and the edge of evolution].

That didn't work either. Nothing seems to work.

That exchange from April 2014 got me thinking about the "big tent" approach of Intelligent Design Creationism. You know what I mean. It's the attempt to make everyone happy about the attack on evolution and the vague allusions to gods intelligent designers. The people under the big tent range from hard-core Young Earth Creationists to those who are almost indistinguishable from theistic evolutionists.

Isn't it strange that they can unite behind the argument that the Cambrian Explosion disproves evolution, for example, when most of them think that all the fossils were created in the Deluge only 4500 years ago? In other words, they deny that the fossil record shows rapid evolution over ten million years or so but they're willing to support Stephen C. Meyer anyway. Strange.

Isn't it strange that they can discuss why evolutionary biologists are wrong about the number of mutations that arose naturally since humans and chimpanzees diverged from a common ancestor when most of them believe that humans and chimps were created separately about 6000 years ago?

I asked five questions that I hoped would provide some answers about this "big tent" approach and Vincent Torley responded' Five questions for Intelligent Design Creationists. It shows, once again, how the creationists resist knowledge.


1. Apologies to Elizabeth Barret Browning.

211 comments :

  1. Actually, humans and chimps have accumulated about 35 million point mutations, not 22 million, plus around 5 million indels. At least according to the chimp genome paper. Do you have another source?

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    1. On of their favorite memes is isolated islands of function. Islands can't be terribly isolated if millions of mutations fail to sink the boat.

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    2. I believe the isolated islands are for proteins, so even if the entire genome is functional, that bit only applies to a couple percent, and even there around 1/3 of mutations are silent. Of course the isolated islands and the whole-genome functionality are both bogus; but at least they aren't mutually contradictory.

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    3. I don't think you can be sure that there are not isolated islands out there in protein space. It is possible (I think likely) that all the evolution that has ever occurred in our biosphere is on one isolated island. There may be far better ways to be, say, a fish than any that we have ever seen. Which is OK because the fish we have do well enough.

      The issue is not whether there are such islands, but whether present-day life is spread over more than one of them. This includes assessing what we count as isolated. The wrong definition is that any island that cannot be reached with a single mutation is isolated. Other processes such as birth of proteins from translating junk DNA (proteins that have low but noticeable ability to catalyze a new reaction) can reach those islands. So they are not isolated.

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    4. John Harshman,

      The difference between human and chimpanzee genomes in aligned regions ranges from 1.1% to 1.4%. These are substitution differences that result from evolution from a common ancestor. See Rogers & Gibbs (2014) "Comparative primate genomics: emerging patterns of genome content and dnamics" [doi:10.1038/nrg3707]

      I took the highest value from Scally et al. (2012). A difference of 1.4% works out to a little less that 45 million differences when extrapolated over the entire genome. That's about 22 million substitutions in each lineage assuming the mutation rate in humans and chimpanzees is identical.

      The human and chimpanzee genomes each contain sequences not found in the other genome. These represent insertions and deletions. Most of them are less than 100bp and many of them are probably artifacts. (The chimp genomes is not "finished.")

      Nevertheless, we can estimate that each lineage accumulated between one and two million indels over the course of their evolution from a common ancestor. Assuming that each of these represent a single mutation event, this increase the total number of mutations from about 22 million to 23 or 24 million.

      I didn't think that was worth mentioning to the creationists. They're confused enough already.

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    5. I think you may have underestimated the number of indels. But I see our numbers differ less than I had supposed, since you intended the numbers to be per lineage, not total differences.

      What are the complete references for Rogers & Gibbs and Scally et al.? (Your doi link seems not to work.)

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    6. Rogers, J. and Gibbs, R.A. (2014) Comparative primate genomics: emerging patterns of genome content and dynamics. Nature Reviews Genetics, 15(5), 347-359. [doi:10.1038/nrg3707]

      Scally, A., Dutheil, J. Y., Hillier, L. D. W., Jordan, G. E., Goodhead, I., Herrero, J., Hobolth, A., Lappalainen, T., Mailund, T., and Marques-Bonet, T. (2012) Insights into hominid evolution from the gorilla genome sequence. Nature, 483(7388), 169-175. [doi: 10.1038/nature10842]

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    7. John Harshman says,

      I think you may have underestimated the number of indels.

      Why do you this this is important? Even if it's 5 million indels per lineage that's less that 25% of the number of substitutions.

      But I see our numbers differ less than I had supposed, since you intended the numbers to be per lineage, not total differences.

      I suspected that this was part of the problem.

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    8. Why do you this this is important?

      It isn't. And it's 5 million total, not per lineage, again from the chimp genome paper. I am merely quibbling about the numbers. The chimp paper also gives a difference of 1.3% (not counting indels) averaged over the entire alienable genome.

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    9. Why are you quibbling about the numbers? Is there a point you're trying to make?

      (I knew that one paper says about five million total differences, I was just saying that even if it was fuve million per lineage it wouldn't make a big difference in the calculation. Or, is that what you mean by " quibbling"?)

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    10. Mostly just curious about where you got your numbers, which were fairly different from the counts I've seen.

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    11. What is the significance of comparing chimp and man, when the data are first prescreened to leave out sequences are >96% dissimilar?

      Answer: you confirm what is generally believed (1-2% difference) by the evo community. Is it science?

      What is the significance of comparing chimp and man, when indels in protein coding parts are not included?

      Answer: you find about 5-6% differences in protein coding genes.

      What is....if we perform an unbiased unfiltered sequence by sequence comparison? In a whole genome comparison.

      Answer: we find the biological difference between man and chimp, which is currently estimated between 8-20 percent (depending on the reported studies). The interesting differences, the information what makes a man man and a chimp chimp, is in this part. Almost nobody is looking for it, since the NSG methods are completely biased towards exonism.


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    12. In all that blather I found something interesting:

      What is the significance of comparing chimp and man, when indels in protein coding parts are not included?

      Answer: you find about 5-6% differences in protein coding genes.


      Is there anyone here who can translate that to English and offer a reference? Is he saying that 5-6% of human and chimp proteins differ by an indel? That seems very unlikely, but I'm ready to learn.

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    13. It sounds to me like he's counting a single insertion of 10 nucleotides as being equivalent to 10 differences.

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    14. Clearly he does that in some of the comparisons. But in protein-coding genes (whatever he means by that)? I doubt that very many protein-coding sequences have indels at all between human and chimp, certainly not enough to cause a 5-6% length difference between average proteins. My notion, some indel or other in 5-6% of proteins, is at least more plausible than that.

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    15. You're right. Wouldn't 2/3 indels within transcribed regions be fatal to the gene since 2 out of every 3 indels would result in a frameshift?

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    16. Yes, though of course a few frameshifts might result in new proteins with altered function, especially if the indel were late in the sequence. But certainly the overwhelming majority of known indels in exons are within frame, simply because there tends to be very strong selection against frameshifts. And even in-frame indels are quite rare. In one gene I've studied within birds, for example, MYC, there are only two known indels (though one of them seems to have happened independently at least twice), both within frame. That's a combined total of around 7 billion years of lineage evolution. How much could we expect in a mere 10 million years (5 million each in chimp and human lineages)?

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  2. Its not strange to back up the CE even while a YEC. Its just proving evolution wrong on its OWN case. Like on the witness stand one is cross examining the witness for the opposition.

    There is no evidence for mutations accumulating. How could there be? All that one can see it what there is now. Its speculation how it came about.
    Its still ONLY comparative genetics as far as i make it out.

    We have like genetics with apes because we have the same body. It would be that way. Yet its not evidence for common ancenstry but only common design/blueprint.
    Otherwise omne puts god in a corner on this.
    He can't have a common blueprint/program but someone is saying it shows common descent.
    What would I do? I would make it like in physics. Common laws for biology and so genes are just a parts department number.
    Its an error to extrapolate a descent from them.
    If man and ape look alike then it could only be you would have like genes.
    Yet created separately. A special case.

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    1. Its not strange to back up the CE even while a YEC. Its just proving evolution wrong on its OWN case.
      Yes it is a bit strange, Robert. Why is disproving mainstream evolutionary theory more important than disproving designed evolution, if you know both to be incorrect? My guess is that that is because of the "religion friendly" implications of DI, correct?

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    2. "We have like genetics with apes because we have the same body. It would be that way. "

      You do understand not a lot of dna actually instructs how the body is built?

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    3. Hey byers, take up a hobby, like finger painting, and leave science to scientists. Your willfully ignorant creationist drool, which you arrogantly slobber on several websites that are devoted to discussing scientific, educational topics, is just a delusional mess.

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    4. "If man and ape look alike then it could only be you would have like genes."

      Like the marsupial wolf and the placental wolf? Oh, wait a minute ------

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    5. @TWT: Not fair. Why should finger painting be more highly regarded as a hobby than word salad beat poetry? What's good enough for Edward Lear is good enough for Byers.

      Now if you're actually _reading_ his drivel, well, isn't the joke on you?

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    6. Confused.
      I understand like dNA with apes is because of like body. now if you say DNA is not/not very much related to looks then thats news to me.
      I'm sure we have like dNA because of like looks without much interference after creation week.

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    7. Christine marie Janis
      The case i make for dna differences between look alike marsupial/placental creatures iS that the marsupialism was a later reaction upon migration to areas. so its reasonable to not just see a few DNA points added on/replacing the origina; but a whole spin of the dNA system of the creatures.
      there is no evidence of DNA origins. only results and then a vextrapolation backwards based on a presumption thats the only option in a very complex system.

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    8. Robert, you mentioned you believe in a creation week. Do you also believe in a flat geocentric earth? If not, then how do you explain the sun supposedly standing still over Joshua's army for 24 hrs?

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    9. Robert, it's clear that you don't understand the marsupial wolf problem. The problem is not just that marsupial wolves are different genetically to placental wolves, the problem is that marsupial wolves are far more similar genetically to koala bears and wallabies than they are to placental wolves.

      So if marsupialism was a later adaptation then why did all these marsupial animals undergo that adaption at the same time? And why did they all undergo exactly the same genome wide reorganisation in exactly the same way (leaving them with similarities compared to placentals across their genomes)?

      And why do they all share genes that placental mammals don't have? I thought the point of Ann Gaugers paper is that new genes don't have enough time to evolve - now you are contradicting her and saying that these new genes must have developed in all marsupials independently at the same time. Do you see how self-contradictory your belief system is?

      Now I could point out exactly the same thing in cetacea. Dolphins and whales are far more similar genetically to ungulates (hippos and horses and deer) than they are to any other fish or shark. The same logic applies here. This can only be because they share a more recent common ancestor.

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    10. She is taking on evolutions claims. Yet other mechanisms can bring genetic change quickly. Who says no?
      i understand the marsupial gene thing.
      Upon migration to certain areas all the creatures were instantly needing important biological change in reproduction and a few other details.
      Therefore , like in a computer doing the math, the genetic system would be "scrambled" and produce likeness for the marsupial traits and no longer alike to their placental cousins.
      The genes are fantastic in complexity and easily can be seen to be flexible in changing. Just seeing them moving along slow is unreasonable and not likely.
      Anyways its clearly obvious that marsupials are just the same creatures as placentals and many other families likewise in the fossil record misclassified. So it proves the DNA trailing is not accurate. Does toi me.

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    11. Byers blubbers :
      She is taking on evolutions claims. Yet other mechanisms can bring genetic change quickly. Who says no?

      People who actually STUDY genetics and DNA, and have catalogued what genetic changes are actually possible.

      NONE known to sane and rational folk cause the changes you decree must have happened - but, then again, sane and rational folk know there was no worldwide flood a few thousand years ago, so no need for such ridiculously accelerated changes.

      i understand the marsupial gene thing.
      Upon migration to certain areas all the creatures were instantly needing important biological change in reproduction and a few other details.


      No, you obviously do NOT understand the 'marsupial gene thing'. There is far more than one gene needed to be a marsupial.

      Therefore , like in a computer doing the math, the genetic system would be "scrambled" and produce likeness for the marsupial traits and no longer alike to their placental cousins.

      That has got to be singlehandedly the most STUPID, ridiculous thing I have ever had the misfortune to read !!

      Only a mind uncluttered with knowledge or understanding could come up with something that astoundingly INANE !

      Genomes do NOT WORK LIKE THAT, BUFFOON !!

      The genes are fantastic in complexity and easily can be seen to be flexible in changing. Just seeing them moving along slow is unreasonable and not likely.


      Researchers have been studying genes for DECADES, twit - genes are nowhere near as fantastical as they are in your deranged imagination.

      Anyways its clearly obvious that marsupials are just the same creatures as placentals and many other families likewise in the fossil record misclassified.


      RiiiIIiiIIiiIIGHT !! Like every researcher on the planet is as hopelessly ignorant as you !

      Upon what basis - other than your willful STUPIDITY and pathological need to grovel before your deluded interpretation of ancient superhero stories - did you 'determine' that everyone else on the planet has misclassified marsupial animals ?

      So it proves the DNA trailing is not accurate. Does toi me.


      So, when REALITY and your delusions conflict, it is REALITY that is in error ? That is some major weapons grade stupidity and arrogance there Byers !

      BTW - Lenski kept samples of his bacteria every few generations. They can DIRECTLY LOOK AND SEE THAT MUTATIONS WERE ACCUMULATING THE WHOLE TIME !

      Sane and rational folk know that mutations can accumulate; in fact, there is nothing to prevent it. Once DNA mutates, there is no magical force field protecting it from further mutations.

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    12. "Upon migration to certain areas all the creatures were instantly needing important biological change in reproduction and a few other details."

      Right --- it suddenly became vitally important to make changes in the ankle joint and to add a little shelf to the inside of the lower jaw.

      As we've noted before, if this need to change on migration were true, then it would be seen in the Australian bats, rodents, and seals, and also in all of the other mammals in South America.

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    13. Ooh, a reflected angular process reference. My favorite.

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  3. Robert said There is no evidence for mutations accumulating. How could there be? All that one can see it what there is now. Its speculation how it came about.

    Wait a minute, we are able to collect DNA from several generations alive. We ar not limited to humans only, mice, lab mice, friut flies, the entire biosphere is availalble for the study of genomes.

    Without being anywhere near any kind of a biologist I assume that there is every amount of evidence available if Robert would bother to learn (or, God forbid, study) a little science. Though I don't recommend that, it might cause some serious problems.

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    1. Its still a extrapolation backwards to dna origins from the present. It need only be a special case that mutations happen in present generations of mice etc but its not evidence that one can count backwards and calcuate how many mutations appeared and when.
      Its like the errors in geology of only seeing slow actions when almost all geology came from fast actions.
      In Canada the whole history of ontario is being rewritten as the result of ice age mega floods and no more about slow glaciers.

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  4. Would any REAL scientist call evolution or evolutionary theory "Darwinism" in this day and age?

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    1. The number of Real Scientists™ that would do so is not zero but it is declining. The word "Darwinism" is still thought of by some evolutionary biologists as a nice way of honoring Darwin and pointing out the continuity of their work with his. But the Discovery Institute successfully poisoned this usage by making out that it means that the biologist is a cultist who follows an infallible guru, rather than someone doing science.

      Once biologists have a little experience with arguing with creationists they may have big second thoughts about using the word.

      There is another usage of "Darwinist", which Larry uses here. Namely someone who thinks that the only force in evolution is natural selection. I am unaware of anyone who actually belongs in that category.

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    2. Honouring people is nice, but an important point to make is that science does not do -isms. None. No Newtonism, Einsteinism, or Felsensteinism.

      Not even Moranism !

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    3. Physicists like to name things after themselves. That's why we have Calabi-Yau spaces, Bose-Einstein condensates and the Schrodinger Wave Equation. If biochemists were more like physicists the enzyme that makes DNA would be Kornbergase, the enzyme that makes Telomeres would be Blackburnase. Spliceosomes would be Sharposomes and the short DNA fragments made during lagging strand synthesis would be Okazaki fragments.............oh wait a second

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    4. Joe says,

      There is another usage of "Darwinist", which Larry uses here. Namely someone who thinks that the only force in evolution is natural selection. I am unaware of anyone who actually belongs in that category.

      I don't know anyone who belongs in that category either. However, I'm reminded of a quotation from the Spandrels paper ...

      At this point, some evolutionists will protest that we are caricaturing their view of adaptation. After all, do they not admit genetic drift, allometry, and a variety of reasons for non-adaptive evolution? They do, to be sure, but we make a different point. In natural history, all possible things happen sometimes; you generally do not support your favored phenomenon by declaring rivals impossible in theory. Rather, you acknowledge the rival but circumscribe its domain of action so narrowly that it cannot have any importance in the affairs of nature. Then, you often congratulate yourself for being such an undogmatic and ecumenical chap. We maintain that alternatives to selection for best overall design have generally been relegated to unimportance by this mode of argument. Have we not all heard the catechism about genetic drift: it can only be important in populations so small that they are likely to become extinct before playing any sustained evolutionary role?

      They're referring to adaptationists but that's just a synonym for "Darwinist" in the way that I use the word.

      The point is that Darwinists may well be aware of the fact that natural selection is not the only force in evolution but that doesn't get them off the hook if all they talk about is selection and adaptation when nobody is looking.

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    5. As long as there is nothing in addition to selection of variation (mutation-selection) to explain the transformation from microbes to man, modern evolutionary theory did not move beyond Darwin.

      Let's see...unique genes is humans. The SRGAP2B, SRGAP2C and SRGAP2D are mot found anywhere but in humans.

      No selection involved? No mutation involved? Drift? Neutral mutations?

      What did I miss?

      Prof Sandwalk, could you please disclose what other evolutionary forces could produce such genes?

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    6. Lemme see, a quick google search and this pops up:
      "Cortical development gene Slit-Robo Rho GTPase-activating protein 2 (SRGAP2) has been highly conserved over mammalian evolution, and human is the only lineage wherein gene duplications have occurred (three times)"

      Your credibility well below 0, has actually dropped even further.

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    7. Wow Peer!

      Read a book or something! SRGAP2C is like 99% identical to SRGAP2 which is found in other mammals!

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  5. > There are a few errors in that post. How many?

    Well for a start she quotes this recent paper by John Sanford to support her claim that it takes 1.5 million years for a single SNP to both appear and become fixed.

    One of the problems with Sanford's paper though is that he is looking for the time it takes to evolve and fix a specific mutation. He calculates this time using a simulation (Mendel's accountant) and by taking the average of 25 runs for a single data point.

    The obvious problem here is that evolution is not directed and it is not searching for a specific mutation. Rather evolution experiments with millions of mutations some of these go on to become fixed in a short space of time and others don't. Most of the mutations that evolution experiments with go extinct and never go on to become fixed.

    This seems to me to be a case of the Texas sharp shooter fallacy.

    It seems to me that he is drawing a target around a specific mutation and then he proceeds to calculate the improbable odds and the ridiculous amount of time it would take (on average) for that specific mutation to occur and become fixed. But evolution is working on millions of mutations in parallel - some of these will become fixed a lot quicker than others and it is these which we will see actualised. By averaging over 25 runs, he is skewing his results towards the vast majority of mutations which will ultimately disappear before becoming fixed.

    Is this not a bit like looking up who won the lottery last week, proceeding to calculate the ridiculous odds against this particular individual winning and then concluding that this person must have won by divine fiat because how else could they possibly overcome those odds?

    Am I misunderstanding something fundamental here?

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    1. In a population of size N diploid individuals, it takes about 4N generations for a neutral mutation to reach fixation once it has occurred. For early human populations of 10,000 individuals, that's 250,000 years. I think Sanford's simulation waits for a particular change to occur, one that is destined to fix, and then asks also how long the fixation takes.

      You are correct that tit is a mistake to build in the waiting for one particular SNP allele to occur. Not only are there many places in a gene where neutral SNP mutations might occur, but we have a great many spots in the genome at which this can happen. All these neutral mutants can undergo genetic drift simultaneously, and essentially independently. You don't have to wait for one to occur and fix, then start waiting for another to occur and fix, and so on.

      So you are right, if the 1.5 million years figure is argued to be for steps in a sequential process, where you have to wait for one particular SNP allele, then wait for another, the argument is fallacious.

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    2. Oops, brain malfunction. 4N generations is 40,000 generations, or a bit under 1 million years.

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    3. Joe, is this the average amount of time it has taken for fixed mutations to become fixed?

      Since fixation is a stochastic process, surely this number is highly variable in practice?

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    4. Why are they still using their sham program? The one they told is was the best ever and totally the most realistic - until they had to re-write the thing. But then THAT version was the best ever and totally the most realistic. The one where no matter what you use as the rate of beneficial v. deleterious mutation, your population goes extinct.

      I wonder whom they think they are fooling?

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    5. The one where no matter what you use as the rate of beneficial v. deleterious mutation, your population goes extinct.

      But that just 'proves' Sanford's point about "genetic entropy". To them this is a feature of the program, not a bug.

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  6. I think your point is correct. The real argument is how many functional protein sequences are there? So if there is no target, success is finding a protein that can do real work. Since it has been experimentally validated that functioning protein space is relatively rare, natural selection is generally believed to be one of the answers, but not the whole show.

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    1. It's both relatively rare and surprisingly common! Random peptides exhibit catalytic functions (though obviously catalysis is not the sole protein function) at a frequency sufficient to disable Hoyle-style arguments looking for single targets. Also not appreciated is the multiplicative effect of multiple 'search'. Although a particular enzymatic function may still be unlikely, each locus probes its neighbourhood. The chance of no locus hitting anything beneficial is exponentially diminished by increase in the number of loci. This, in classic paradox, is what some of them think junk DNA is 'for' - a Design feature enabling the very thing they think cannot happen: evolution.

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  7. Am I misunderstanding something fundamental here?

    Not unless your real name is Ann Gauger. :-)

    The first time I saw the lottery example was in one of Sean B. Carroll's books. If you look at practically any creationist mathematical "demonstration" of the impossibility of evolution, you'll find this fallacy lurking there.

    Another way of putting the same fallacy (which is simply calculating chances of one specific goal - always astronomical - rather than the chance that any evolutionary outcome can happen at all - routine) is demonstrating to any creationist that it is absolutely impossible he or she exists. In each generation, what are the chances your particular ancestors meet and have children, out of all the people alive on earth? Then that at least one child would survive from each couple, and that *those* particular children, of all people on earth in the next generation, would meet and have children with each other? Etc., etc., down through every generation at least from the origin of Homo sapiens (somewhere around 50,000 to 6,000 years ago ;-) ) until you. Those chances are pretty microscopic. So you don't exist.

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  8. I thought when I first read some of these exchanges, and after rereading them I still think that some of the posts here at Sandwalk were not as simple and straightforward as might have helped clueless readers understand them. Not that the posts here were wrong, but they were aimed at college students at least, and these IDiots are at the level of clueless high school students, at best. (Not that aiming lower would have helped the IDiots themselves, of course; when they're determined not to learn, they can always accomplish that. And it's hard to be painfully explicit responding to IDiot posts that wander all over as these did, because the responding posts have too be too long, or too many. But it's something to consider.)

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  9. So, you are basically arguing 100 mutations per generation, 500k generations, that's enough material to explain the number of mutations that separate chimps from humans. That is, 22 million fixations are expected via neutral drift.

    Does that imply most neutral drift ended up functional? How does that work? Does lots of neutral drift eventually get co-opted into functional genes? Or does neutral drift eventually co-opt junk DNA to create species-specific genes?

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    1. No. Most neutral fixations happen in junk DNA. It was junk DNA before the mutation happened and it's still junk after the mutation is fixed. The functional part of the human genome (and the chimp genome too) is less than 10%. Occasionally, a bit of junk gets mutations that render it functional; given the size of the genome and the length of time, this can add up to hundreds of examples, but it doesn't significantly affect the percentage of junk in the genome.

      Now you're probably asking about the mutations that make us anatomically different from chimps, some of which happened in the human lineage. Almost all of those happened to functional sequences, which we might call genes. Some of these sequences can be recognized by showing a fixation rate higher than expected from drift. Others are more difficult to detect. But, however important those are, they're a tiny percentage of the total fixations, the overwhelming majority of which have no phenotypic effects.

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    2. The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

      Has anyone seen this 2013 paper from the University of Toronto. From the data shown in the paper the splicing sequences between apes and humans are 50% different. If this is real does it change the discussion of how humans evolved?

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    3. John: How many de novo human genes are there? I read 60 here http://tinyurl.com/ospoak6. If the average number of base pairs per gene is 10k, does that there are about 600k new functional mutations from the chimp-human split? If so, then the ratio of functional to nonfunctional mutations fixed is around 600/50000 or 1%?

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    4. Has anyone seen this 2013 paper from the University of Toronto. From the data shown in the paper the splicing sequences between apes and humans are 50% different. If this is real does it change the discussion of how humans evolved?

      Here's the paper.

      Barbosa-Morais, N.L., Irimia, M., Pan, Q., Xiong, H.Y., Gueroussov, S., Lee, L J., Slobodeniuc, V., Kutter, C., Watt, S., and Çolak, R. (2012) The evolutionary landscape of alternative splicing in vertebrate species. Science, 338(6114), 1587-1593. [doi: 10.1126/science.1230612]

      Here's the abstract.

      How species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level is poorly understood. By comparing organ transcriptomes from vertebrate species spanning ~350 million years of evolution, we observed significant differences in alternative splicing complexity between vertebrate lineages, with the highest complexity in primates. Within 6 million years, the splicing profiles of physiologically equivalent organs diverged such that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are cis-directed. However, a subset of pronounced splicing changes are predicted to remodel protein interactions involving trans-acting regulators. These events likely further contributed to the diversification of splicing and other transcriptomic changes that underlie phenotypic differences among vertebrate species.

      I disagree strongly with the interpretation of my colleagues Ben Blencowe and Brenden Fry. Most so-called "alternative transcripts" are present at very low levels and they represent splicing errors, IMHO. The error rate of the spliceosome complex is almost 1% so you expect lots of "alternative" transcripts if your detection system is very sensitive. (It is.)

      If my interpretation is correct, you don't expect much similarity in the error-prone splicing patterns of the same genes in different species (e.g. humans and chimps) and that's exactly what you see.

      This is why other labs have a different, and much more reasonable, interpretation of the same observations, for example ...

      Pickrell, J.K., Pai, A.A., Gilad, Y., and Pritchard, J.K. (2010) Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet, 6(12), e1001236. [doi: 10.1371/journal.pgen.1001236]

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    5. Hi Eric

      I'm quite familiar with that paper

      First of all: These de-novo genes all tend to be very short (Fewer than 1000 bases each)

      Secondly: Calling them genes is somewhat controversial because we aren't sure at this point whether or not they are functional. They appear to be transcribed and protein products appear to be produced but we don't know whether or not this transcription is spurious.

      Finally and most importantly: These sequences didn't just pop out of nowhere over the last 8 million years. Nearly identical sequences exist in Chimpanzees, Gorillas, Orangutans, Gibbons, etc. On average we only see 1 or 2 mutations separating our version of these sequences from the Chimpanzee version. So at most these 60 de-novo genes represent between 60 - 120 new mutations that have arisen in humans. What has happened in each case is that a frameshift mutation has occurred (an insertion or a deletion) which has in effect extended an open reading frame and allowed these to be transcribed in humans. In all the other apes these sequences were too short to be transcribed (they had premature stop codons). They probably represent junk DNA in other apes.

      So what we see here is intragenic DNA which doesn't appear to do anything in other apes and has had a simple mutation allowing it to be transcribed.

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    6. If the average number of base pairs per gene is 10k

      I think it's much less than that. But anyway, de novo genes are typically much shorter than old ones, and contain few exons. The mean length of a de novo gene is a few hundred BP.

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    7. Eric, it would be worth your while looking at the supporting information for that paper where they provide the actual sequences and also the equivalent sequences in chimps, gorillas and orangutans - pointing out in each case what mutation occurred allowing it to be transcribed.

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    8. Erik: How many de novo human genes are there?

      Me (previously): "Occasionally, a bit of junk gets mutations that render it functional"; and that's what you're asking about, though you may not know it.

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    9. Ace: do you mean, 60-120 mutations per de novo gene, or in total?

      If it's in total, are you saying that basically 50 million mutations fixed in the human branch, and a mere 100 of them were sufficient to make us so different than our chimp-human progenitor, often by rendering, per John H, junk functional?

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    10. and a mere 100 of them were sufficient to make us so different than our chimp-human progenitor, often by rendering, per John H, junk functional?

      I think you may be improperly fixated on the idea that it these new genes that result in the differences between humans and apes.

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    11. oops, meant between humans and chimps.

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    12. SRM: I might be. What would be the primary difference, if not new genes?

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    13. If not new genes, what creates the morphological changes we observe. different muscle structure, different bone structure, different brain capability etc
      The paper I cited and Larry's paper both show alternative splicing sequencing differences between vertebrates. Can this happen without DNA sequencing changes?

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    14. Note Aceofspades comment above: Secondly: Calling them genes is somewhat controversial because we aren't sure at this point whether or not they are functional. They appear to be transcribed and protein products appear to be produced but we don't know whether or not this transcription is spurious.

      Even if all of these "new genes" were functionally important, it doesn't necessarily follow they have anything to do with the obvious differences between humans and chimps.

      Can this happen without DNA sequencing changes?

      Yes, obviously changes in the sequence of DNA are necessary, but there are all sorts of other mutations that could be responsible, particularly in transcription regulatory proteins and in cis-acting sites in DNA that influence gene expression.

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    15. OK, now I'm really confused. We started with 50MM mutations via neutral drift, and about 22 MM 'new' mutations per humans over chimps (or, 44 MM total different now).

      Not all mutations are functional...but has someone estimated how many of these differentiating mutations are? Can you estimate how many functional genetic mutations differentiate chimps and humans, whether they are genes or cis-acting sites or something else?

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    16. Not all mutations are functional...but has someone estimated how many of these differentiating mutations are? Can you estimate how many functional genetic mutations differentiate chimps and humans, whether they are genes or cis-acting sites or something else?

      No. Or rather one could, but it would be a guess with quite wide error bars. Some limits are possible, though: first, only around 10% of the genome is functional, so we're down to 10% of fixations right there. A high proportion of mutations in functional sequences are also neutral. And genetic load arguments would reduce the number considerably more. If I had to guess, I'd say a couple thousand at most, accent on "guess". Some of these are non-silent substitutions in protein-coding sequences; some of them are gains or losses of transcription factor binding sites in promoters. I suspect those are the majority. But there are other things too.

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    17. Evo d said: If not new genes, what creates the morphological changes we observe. different muscle structure, different bone structure, different brain capability etc

      One must be careful in considering the differences - are the muscles and bones and brains of chimps really that different from the human versions? The ultrastuctural differences you are recognizing are probably the result of developmental differences. I don't imagine there are many distinguishing features otherwise between the muscle tissue of the chimp vs human.

      None of this is to say that new genes (de novo in origin or otherwise) can't play a role in differences, but they are not nearly as required as you suspect.

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    18. SRM: If we just looked at one of muscle proteins like actin, myosin and titin it would be interesting to see if the amino acid sequences were similar or not. I have been looking, but have yet to find any credible papers.

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    19. I suspect you will find them similar, as opposed to not similar.

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    20. In fact they well be identical in amino acid sequence, or with one or a few substitutions at most that probably have little impact on the protein structure or function - but I don't know what the sequences look like offhand.

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    21. here's a page linked to a textbook that came up as first hit in a google search... it might be helpful as a general source of info. It does in fact discuss a myosin protein and the consequence of a premature stop codon in human gene. I don't know how accurate all the info is: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/H/HominoidClade.html

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    22. I just noticed the last line on that page talking about the potential importance of alternative splice sites - a contention that might be disputed by several knowledgable people here. Probably it was the height of impudence to link to a general biology text book on this blog, when I should have linked to a much more definitive textbook :-)

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    23. Hi Evo d, here is a link to an alignment between the human and chimp titin proteins:

      http://useast.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog/Alignment?db=core;g=ENSG00000155657;r=2:178798495-178807408;t=ENST00000470257

      Overall, they are quite similar (about 92% identical). At a glance, it looks as if much of that ~8% difference is due to to differences in the lengths of the two sequences (i.e., insertions/deletions). Take a look!

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    24. Thanks Dave...great link. So now we have an interesting discussion point. Titin has 11 versions I know about (trying to verify) for skeletal, heart etc. The one you identified has just under 36k residues. 2.5 k residues were added that have to be mechanically compatible with the smaller version in chimps. The titin you identified is the largest (I think) so the average change will probably be less then the others. The change of the genome would have to be next to the smaller titin version in chimps. This is 2500 changes to a specific location in the genome unless the change was created with alternative splicing. Any other ideas?

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    25. John: I'm not a biologist, I do finance, and work a lot with computers, and find genetics fascinating. But the way the genes actually work seems a lot more complicated than we thought (eg, I have about 5 genes suggesting I have blue eyes according to 23andme, far from the single allele I learned in school). So, I figure to the extent one can estimate the number of new functional genes, their size, and then number of new proteins, this might help understand how genes work. That is, we have hard numbers for actual DNA differences between humans and chimps, and perhaps the proteins too. If we think 250k generations separate them, that's a good number. Filling in those other numbers, then, would allow us to calibrate various genetic models, in the way that time series parameters in finance are used to inform structural models of asset pricing.

      Bottom line: it would be good to estimate how many functional DNA mutations and protein differences (de novo and alternative structures) separate chimps and humans. If you are saying 2000, that's a better number than 'I don't know.'

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    26. An allele was never implied to be a single "gene" in the sense of a single protein-coding gene. originally the term referred to a specific pheneotypic effect (such as "long legs" or "blue eyes"). An allele is a version of a locus (or several loci) with some particular phenotypic effect. Some times an allele CAN imply a single gene and a particular version of it (say, one with a single mutation at some specific spot), at other times it might be a whole host of genes that contribute to some particuar phenotype.

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    27. Good point. What I meant to say, was that when I was taught Mendelian genetics in Jr High, we used the example of blue and brown eyes, where a big B was for brown, little b for blue. One gene, one trait.

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    28. An allele is defined as follows [allele] ...

      An allele is one of a number of alternative forms of the same gene or same genetic locus.

      Thus, a single allele ALWAYS refers to different variants of a single gene (or locus) and NEVER to multiple variants in multiple genes.

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    29. SRM: No problem sharing from a biology textbook, I appreciate any information on the subject. The interest in splicing is because it is a mechanism we can observe. IMHO we are making little progress in describing the evolution of new ordered sequences inside DNA (like the ape to man discussion) and I don't think the continued speculation is adding much value to our understanding of evolution. Below is another paper on the spliceosome role in mammalian evolution. In addition on pubmed.gov there are 10k papers on its link to cancer.
      http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568499/

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    30. @Evo d

      The big question about alternative splicing is whether most of it actually exists. In other words, are most of the uncommon transcripts functional or are they nothing but noise?

      Read Questions about alternative splicing.

      The question is related to The Deflated Ego Problem because massive alternative splicing is one of the just-so stories that some scientists promote in order to get over the disappointment of learning that humans have the same number of genes as other mammals.

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    31. ... the disappointment of learning that humans have the same number of genes as other mammals.

      And fewer than the common water flea, though we have much more junk DNA and much longer introns, if that's any consolation.

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    32. Hi Larry...I appreciate your skepticism here. I am attaching a overview of titin for about 16 primates. The database is claiming many allies are alternatively spliced. Do you think they are mis informed? As I posted earlier the comparison of the largest titin and chimp gene and human gene are different by 2500 amino acids. How would genome variation possible account for this?
      The possibility of getting 2500 functionally specific amino acid mutations at a specific point in the genome would be exceedingly small but a splicing variation would seem a lot more likely. Again, I do appreciate your skepticism and do not want to chase a dead end but a I think a fresh look here is worth the potential that alternative splicing brings to evolutionary thinking (with the exception of stroking scientific egos.) http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&c=Gene&l=CCDC141andTTN

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    33. @Evo d says,

      The database is claiming many alleles are alternatively spliced. Do you think they are misinformed?

      The tintin gene has about 350 exons and many of them encode repeated domains that encode a small module that's present in multiple copies in the expressed protein.

      There are many possible ways of splicing these 350 exons and many of them give perfectly respectful long proteins with a few extra or a few less modules. I have no reason to doubt that this is an example of biologically relevant alternative splicing. There are quite a few excellent examples. Most of the proven examples are better than this.

      As I posted earlier the comparison of the largest titin and chimp gene and human gene are different by 2500 amino acids. How would genome variation possible account for this?

      Amazing. I guess the gods must have done it. Where's the nearest mosque ... I feel religion coming on.

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    34. Evo, I'm wondering how you would computer model the alternative actions of a titin gene. I expect it be relatively easy for someone like you who understands the NCBI information to show what that part of the system looks like in code. I'm being serious too, but before I complicate things by explaining the method I would use it seemed best for me to first ask how you would program that part of the process.

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    35. Hi Gary
      I honestly would not know where to start. I am very interested in your thoughts on this. The protein looks like it operates as a counter balance to actin and myosin. The human version has 36000 amino acids but looks like it has lots of repeating amino acid sequences so thats probably what I would sort out first but the actual mechanical tension and how to set the sequences I honestly don't have a clue.

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    36. Hi Larry
      I think I understand your position and appreciate it re AS...you believe it is real but it is exaggerated for non scientific reasons. The challenge on the 2500 amino acid difference was just to suggest that AS seemed like a more logical path then trying to add sequencing information to code an additional 2500 amino acids to the genome.

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    37. In digital systems everything has to (in one way or another) be stored in a RAM chip. But the same basic rules for reading and writing data apply to genetic systems.

      A digital RAM is addressed with a unique pattern of addressing bits. A genetic RAM is addressed with a unique pattern of sensory molecules. Either RAM system can store a data address that specifies a given protein splicing.

      In a genetic system sensory molecules flow through pathways from one gene territoty to another in a 3D nuclear structure, which only requires the computer RAM be dimensioned accordingly. A given sensory molecule does not necessarily have to flow from a point A to influence a point B. In a network structure one gene territory can have a rippling effect on other gene territories around it, its neighbors. As in the navigational network in the ID Lab 5 complex behavior can emerge from the neighbor to neighbor interactions that move like a waves through the network. Instead of what looks like a slow moving 3D river system it's more like brain areas becoming active, which in turn cause other brain areas to become active. In either case the modeling method that is used must be able to behave like a network, where the neighbor to neighbor interactions can produce relatively fast moving waves that ripple outward. It's still just a common ordinary RAM. The self-oscillations (i.e. brain waves) are simply what happens when one place addresses neighboring places in a network. You can say it's normal for a RAM system like this to self-address itself.

      The titin gene would be one place/location in the network. Its output data would be the exact structure (out of many) that gets spliced, which in turn can influece the places in the network it may travel through on its way outside of the cell nucleus.

      There would be one address input connection per sensory molecule that influences what gets spliced at that place. The place each sensory molecule connection comes from will have to be figured out, but that's becoming more easily possible.

      The duration of signals depend on the half-life of the messaging molecule and outward flow to other places.

      More than one place is required for network activity to begin but otherwise the result is not a RAM system that waits for something to happen, it starts self-addressing itself. That alone is not "intelligence" it's more like a zombie, though good start and almost there. Only need to add the ability to take guesses that change network properties and mechanism(s) to gauge success (i.e. replication) for it to take on "a life of its own" that through time learned how to become us and other living things. From the machine intelligence perspective that system qualifies as being intelligent, but it's nothing to get shook up by like it's nuts to say so. Genetic systems requiring the same modeling method I used for cerebral cortex networks only helps make this area of science awesome science fun.

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    38. Hi Gary
      Sorry I am late responding to your ideas. I have been out of town and did not have my laptop. I think you observation here is interesting. A couple of questions: When you say RAM memory do you mean DNA only or do you include proteins as having memory storage capability. Have you identified how addresses are created in the biological network? What is the wave that moves through the network i.e. a photon or a wave traveling through a medium induced through molecular vibration? Do have experimental evidence that you can attach to your concept?

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    39. Evo, the Intelligence Design Labs provide programmable experiments. If you need cell or animal experiments then the ID Lab-5 has information in the Notes folder, while comments of the source code (see .frm files) lists papers and other resources.

      You can click on my name above for a list of information sites I wrote. The only way to currently know why this would work with genetic systems (which includes all molecules in the system not just DNA) is to know how the code works for neural and other complex behaviors. The "waves" can be seen in the second photo of the "Attractor Network" Version 2, which is showing pulses moving through the network (as in bat chirps or clicks moving through air, echo-location).

      http://intelligencegenerator.blogspot.com/

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    1. splicing is evidence of design, not evolution.

      http://reasonandscience.heavenforum.org/t2180-the-spliceosome-the-splicing-code-and-pre-mrna-processing-in-eukaryotic-cells

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    2. The haphazard mechanisms of splicing and the many errors it is prone to, is evidence of evolution. The outrageous and excessive size of the spliceosomal complex combined with the clear nonfunctionality of most introns is overwhelming evidence of this.

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    3. splicing is evidence of design, not evolution

      Sure, Rube Goldberg design.

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    4. The haphazard mechanisms of splicing and the many errors it is prone to, is evidence of evolution.///

      aham. And the proof reading system is what ? LOL....


      Proofreading and spellchecking: A two-tier strategy for pre-mRNA splicing quality control 1

      Multi-tier strategies exist in many biochemical processes to ensure a maximal fidelity of the reactions. In this review, we focus on the two-tier quality control strategy that ensures the quality of the products of the pre-mRNA splicing reactions catalyzed by the spliceosome. The first step in the quality control process relies on kinetic proofreading mechanisms that are internal to the spliceosome and that are performed by ATP-dependent RNA helicases. The second quality control step, spellchecking, involves recognition of unspliced pre-mRNAs or aberrantly spliced mRNAs that have escaped the first proofreading mechanisms, and subsequent degradation of these molecules by degradative enzymes in the nucleus or in the cytoplasm. This two-tier quality control strategy highlights a need for high fidelity and a requirement for degradative activities that eliminate defective molecules. The presence of multiple quality control activities during splicing underscores the importance of this process in the expression of genetic information.

      1) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039138/

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    5. El, you obviously only cherry picked the bit to read which is of interest for you. But, you should've read on, about half a paragraph down, they explain the mechanism, which doesn't involve wands/ magic/ wishful thinking.

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    6. Is Elshamah777 the same person as BornAgain77? Their posts seem to contain similar quantities of rambling nonsense

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    7. http://reasonandscience.heavenforum.org/t2043-dna-repair?highlight=repair

      Its evident that the repair mechanism is essential for the cell to survive. It could not have evolved after life arose, but must have come into existence before. The mechanism is highly complex and elaborated, as consequence, the design inference is justified and seems to be the best way to explain its existence.

      Natural selection cannot act without accurate replication, yet the protein machinery for the level of accuracy required is itself built by the very genetic code it is designed to protect. Thats a catch22 situation. It would have been challenging enough to explain accurate transcription and translation alone by natural means, but as consequence of UV radiation, it would have quickly been destroyed through accumulation of errors. So accurate replication and proofreading are required for the origin of life. How on earth could proofreading enzymes emerge, especially with this degree of fidelity, when they depend on the very information that they are designed to protect? Think about it.... This is one more prima facie example of chicken and egg situation. What is the alternative explanation to design ? Proofreading DNA by chance ? And a complex suite of translation machinery without a designer?

      I enjoy to learn about the wonder of these incredible mechanisms. If the apostle Paul could understand that creation demands a Creator as he wrote in Romans chapter one 18, how much more we today with all the revelations about cell biology and molecular machines?

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    8. ES777, you jumped from some sciency sounding stuff to "the apostle Paul" and "Romans chapter one 18", but isn't 'ID' alleged to be strictly scientific, not religious?

      Since you apparently believe that scientific stuff is very important (LOL), will you please present the scientific evidence that substantiates biblical fairy tales? How about you start with the scientific evidence that substantiates the existence of yhwh, yeshua, holy-ghost, moses, noah, adam, eve, cain, abel, jonah, a talking snake, and satan (and everything attributed to them in the bible)? And while you're at it, can you show that the scientific evidence substantiates the existence of only your chosen, so-called god (yhwh-yeshua-holy-ghost) and not any of the other thousands of so-called gods?

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    9. This is one more prima facie example of chicken and egg situation.

      The eternal dillema of the creationist - they can never escape the idea that complex things poof into existence, then must suddenly scramble to survive in a hostile environment.

      Similarly, the chicken and the egg conundrum is only a problem for a creationist, who must conclude that god poofed chickens into existence, or played the role of a celestial easter bunny hiding fertilized eggs about the garden of eden.

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    10. Are creationists the last people on earth who seriously believe that the existence of cycles is a problem? What came first, the night or the day?

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    11. ElShamah777 writes:

      Its evident that the repair mechanism is essential for the cell to survive. It could not have evolved after life arose, but must have come into existence before.


      In other words, you are endorsing the notion of a 'designer' that was incapable of designing a genetic system that worked right in the first place.

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    12. yes, id is strictly scientific. But who hinders me to bring creationism into the game ?

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    13. N Manning

      i endorse that the creator cannot make square circles. He cannot make impossible things.

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    14. Oh, c'mon. The Bible is chock-full of impossible things. A global flood, Joshua's long day, a virgin giving birth to a boy, people rising from the dead, etc. If not the creator, who did it?

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    15. the creator cannot make square circles. He cannot make impossible things

      Impossible things like creation ex nihilo?

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    16. He means logically impossible things. Miracles are not logically impossible.

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    17. Whether square circles are impossible depends on what squares and circles we are talking about. If they are geometrical figures in Euclidean space, the statements "X is a square" and "X is a circle" cannot be true of the same X under the standard definition of "square" and "circle", but in what sense does one "make" abstract mathematical objects? Last I heard, maths was a human construct, not something made by gods. It's a matter of convention to call logical contradictions "impossible" (in an abstract world where we ourselves define the rules). By the way, there are logically consistent non-Euclidean geometries in which you can have square circles.

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    18. logic: 1. reasoning conducted or assessed according to strict principles of validity.

      logically: 1. Of, relating to, in accordance with, or of the nature of logic: logical disputation.
      2. Based on earlier or otherwise known statements, events, or conditions; reasonable: Rain was a logical expectation, given the time of year.
      3. Reasoning or capable of reasoning in a clear and consistent manner: a very logical person.

      logically: capable of or reflecting the capability for correct and valid reasoning: a logical mind; an analytic thinker; the ratiocinative process; a rational being.


      Miracles are a part of religious beliefs, and religious beliefs are illogical.

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    19. ES777 said:

      "yes, id is strictly scientific."

      NOT.

      "But who hinders me to bring creationism into the game ?"

      Huh?

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    20. Impossible things like creation ex nihilo? //what alternative do you suggest? That absolutely nothing created the universe ? LOL....

      http://reasonandscience.heavenforum.org/t1877-easy-steps-to-refute-atheism

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    21. I don't know how or if the universe was "created", you're begging the question right there, it might have always been there, who knows! The thing is that the impossibility of ex nihilo creation is your thing, it's your own claimed universal principle, the one you use to "prove" that there must be a being capable of doing exactly that, create everything out of nothing. You retards can't even do basic logic or realise how stupidly fallacious your medieval arguments are

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    22. it might have always been there, who knows! // you conveniently ignore modern science which helds that the universe had a beginning with the Big Bang.

      The thing is that the impossibility of ex nihilo creation is your thing

      Well, either 1. the universe was created by a enormously powerful being, or 2. it was not. What is more rational, that the universe had a cause, or no cause. The Kalaam cosmological argument is greeting you.

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    23. I'm not ignoring modern science. You don't understand modern science at all, and the Big Bang theory doesn't prove everything started there you dimwit.

      The Kalam? Don't make me laugh please. Can you explain how does time "begin to exist"? The Kalam is as ridiculous and useless as your tiny brain

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  12. Ann Gauger said: "Genes operate in networks, and to shift a gene regulatory network would require many mutations, and not just random ones."

    I like her use of the word "networks".

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    1. Is it the lilt in her voice when she says "networks"? What is special about her use of the word "network", other than being wrong about the mutations part?

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    2. I'm sure he thinks of it as a synonym for "complexity", which he can stick "specified" in front of.

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    3. If you must know what I think then study the AC/DC - Who Made Who video.

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    4. When I want to know about gene regulatory networks, I prefer Lynch over music videos: The evolution of genetic networks by non-adaptive processes.

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    5. Paul the music video was sort of a "shove this!" in response to the thought of me being here to stick "specified" in front of "complexity".

      In regards to the origin of gene regulatory networks and how they work I now prefer Sal over "evolution" papers that are stuck behind a paywall anyway: Repetitive DNA and ENCODE.

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  13. What is special to me about her use of the word "networks" is this can indicate a better than average understanding of what gives intelligent systems the ability to have an internal representation of the external environment. The Intelligence Design Lab #5 demonstrates what that adds to a neural brain. Study material is at:

    http://intelligencegenerator.blogspot.com/

    Talking about "mutations" as though that explains how genetic "networks" work indicates a poor understanding of what makes living things alive.

    It is deceptive to claim that the ID movement is just saying "can't be explained by evolution". The issue is not that simple. The problem stems from oversimplified garbage that some find to be an acceptable explanation for how intelligence and evolution works.

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    1. You are an incredibly self-deluded idiot.

      Ups, sorry, not what you expect ... here it goes:

      "Oh, I so admire you Gary! So smart you are!"

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    2. Photosynthesis please stop with the disturbing complements. All together they sound like a cheap pickup line, and I'm happily married thank you..

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    3. If you want an intelligent design perspective to be taken seriously, it will have to engage with the literature. What Ann Gauger does time and time again is create a bullshit version of evolution, and then claim it hasn't/couldn't happen. The reason I directed you to the Lynch paper was because it addresses the issue of regulatory network in a way that Gauger and her colleagues have never meaningfully engaged in. Her mantra about "random" will not get her far precisely because the oversimplified garbage is what she, not mainstream evolutionary biologists, has created.

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  14. what makes living things alive.

    Please tell.

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  15. what makes living things alive

    It has to be the same source of energy that sustains the expansion of the universe.

    Since scientists have no idea what that source of energy is, it follows, that they will never be able create even simple life.

    Just like a battery sustains the movements of a toy dog, the same is required for life forms.

    Some kind of life sustaining energy makes living things alive. There is no other way of explaining it.

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    1. Jojo, we know where the energy comes from. Naturally occurring chemical compounds, geothermal sources, and electromagnetic radiation from the Sun. What "makes living things alive" is spontaneous self-organisation made possible (among other things) by the fact that the Earth system receives energy from the Sun and dissipates it back into cold outer space as thermal radiation, continouosly exporting vast amounts of entropy. A small part of this flow is diverted as free energy available to run all sorts of geochemical processes, atmospheric and oceanic circulation, and of course the biosphere.

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    2. Jojo: You should read Nick Lane's new book The Vital Question: Why is life the way it is?. http://www.nick-lane.net/

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    3. @Jojo

      I bet you're really confused when you hear about volcanic eruptions and hurricanes. Scientists have no idea where that energy comes form. I think it's probably gremlins under the earth and fairies in the air. Or maybe Thor.

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    4. Dang Jojo, I think you win the prize for packing the most that is wrong or utterly clueless in the least space.

      The energy that sustains the expansion of the universe is popularly known as "dark energy." Scientists know quite a bit about it and have measured its effects (thus the fact that you've read about it). Since life is part of the universe, dark energy operates in all life including us. Luckily its effects are overcome by gravity or all the matter that went to make up earth and life would simply have dispersed and done nothing.

      The energy utilized by life to sustain itself is chemical energy. This energy is made available to life on our planet by input from two sources, solar and geophysical (the sun and heat from processes going on within the earth, including radioactivity, tidal forces, and heat left over from earth's formation).

      That's it, pretty prosaic, no magic involved or necessary.

      Delete
    5. Luckily its effects are overcome by gravity in our locale in the universe at this point in time, that is. Over all of space-time, dark energy is "winning out" over gravity, and thus the universe is expanding.

      Delete
    6. Jojo, I agree that living things are powered by the same source of energy that sustains the expansion of the universe. The most precise phrase I can find is "behavior of matter". For example:
      "The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, whereby the behavior of matter powers a coexisting trinity of systematically self-similar (in each other's image, likeness) intelligent systems at the molecular, cellular and multicellular level"

      Delete
    7. And here I thought most life was powered by sunlight. Silly me.

      Delete
    8. "What "makes living things alive" is spontaneous self-organisation made possible (among other things) by the fact that the Earth system receives energy from the Sun and dissipates it back into cold outer space as thermal radiation, continouosly exporting vast amounts of entropy."

      Jojo, don't be fooled by sophistry. The self-organisation of living organisms is programmed in the genetic information present in the genome of the self-organizing organism. It only requires a bit of energy, which is produced by chemo-electro-potential convertors, nanomachines encoded in the genome, which in turn are also encoded in the genome. It all boils down to information. Not energy, but information makes the organization of life possible.

      The problem is: materialism cannot handle information. Naturalism cannot explain beyond matter (and its equivalent energy).

      Delete
    9. Peer Terborg, you've got the priorities wrong:
      "It all boils down to information. Not energy, but information makes the organization of life possible"
      Now explain how you're able to get information or a genome without energy. Or a self-organizing genome without energy. Or a replicating genome without energy. Or even a transposon hopping without energy

      Delete
    10. Naturalism cannot explain beyond matter

      Ahh, the good old "materialism can't account for abstraction", so they invent their own abstract entity to explain abstraction and declare victory. Creatard logic 101

      Delete
    11. Although hydrothermal vent life does not need sunlight to power it: sunlight is produced by the behavior of the matter (that the Sun is made of).

      Delete
  16. "Naturally occurring chemical compounds" ?

    For a second or two I began to question myself whether I have asked the right question. Once I was flooded with the same kind of input, I realized where I've ventured into.

    All of you at one point or another substituted the cause that is absolutely essential to further discussion with naturally or natural which means nature, which is a clever but not sufficient way to omit the cause. In this case to omit an intelligent cause. It is so clear as to what you are trying to accomplish. But this is just a veneer to cover your shortcomings, inadequacies of your belief system.

    ReplyDelete
    Replies
    1. "All of you at one point or another substituted the cause that is absolutely essential to further discussion with naturally or natural which means nature, which is a clever but not sufficient way to omit the cause. In this case to omit an intelligent cause."

      First, assume a can opener.

      Delete
    2. Could be turtles all the way down.

      Now Jojo, let us assume you are correct, as you could be. Now explain to us how you came to know as much as you do about this intelligent cause, and how it dovetails so nicely with your religious/spiritual convictions. I trust you won't be disingenuous.

      Delete
  17. Elshamah777 invokes his incredulity as if it meant something :

    Its evident that the repair mechanism is essential for the cell to survive. It could not have evolved after life arose, but must have come into existence before.

    Much like flashlights had to be invented before darkness ...

    The mechanism is highly complex and elaborated, as consequence, the design inference is justified and seems to be the best way to explain its existence.


    Only if one is intellectually lazy or willfully ignorant, since 'A Magical Sky Pixie DIDIT !!1!!11!1!!' explains absolutely nothing; it is but an irrelevant, meaningless noise squeezed from the bowels of bewildered IDiots, creationuts and theoloons anytime they are confronted with something beyond their willfully limited understanding.

    Natural selection cannot act without accurate replication, yet the protein machinery for the level of accuracy required is itself built by the very genetic code it is designed to protect.


    You seem to be under the delusion that ANY mutation is fatal - they aren't.

    You can change the third base of a protein coding region and NOT CHANGE THE PROTEIN AT ALL. 33% of a DNA sequence can be changed to no effect !

    Plus the FACT that protein sequences aren't as fragile as your limited imagination - a basic examination of REALITY show that there can be many sequences that do the same thing.

    Plus the FACT that small, simpler genomes can tolerate higher error rates - the max is about 1/L, where L is the number of based needed for life.

    A viroid with a genome of 300 bases can survive a mutation rate of 1 per 299 bases per replication.

    Plus the FACT that improved replication fidelity would be a feature natural selection can operate on.

    Thats a catch22 situation. It would have been challenging enough to explain accurate transcription and translation alone by natural means, but as consequence of UV radiation, it would have quickly been destroyed through accumulation of errors.


    Not really - a few meters of ocean water is an excellent UV blocker.

    So accurate replication and proofreading are required for the origin of life. How on earth could proofreading enzymes emerge, especially with this degree of fidelity, when they depend on the very information that they are designed to protect?


    They didn't need high fidelity to start with, twit !

    "Real ribozymes suggest a relaxed error threshold", Kun A, Santos M, Szathmary E, Nature Genetics 2005; Sept 37(9): 1008-11
    doi:10.1038/ng1621

    An error rate of 1 per 1000 bases could support a genome 7000-8000 bases long (about 100 70mer genes, or 70 100mer genes) Close to the minimal viable genome.

    Think about it.... This is one more prima facie example of chicken and egg situation. What is the alternative explanation to design ? Proofreading DNA by chance ? And a complex suite of translation machinery without a designer?


    Yes, given the FACT that random RNA sequences can be selected for functions - the ribosome is a ribozyme (can still function at reduced efficiency without proteins).

    I enjoy to learn about the wonder of these incredible mechanisms. If the apostle Paul could understand that creation demands a Creator as he wrote in Romans chapter one 18, how much more we today with all the revelations about cell biology and molecular machines?


    Blubbering about Magical Sky Pixies is not understanding; it is a glorification of ignorance, and an excuse to simply sit on your arse and NOT try to understand the world as it really is.

    ReplyDelete
  18. PeePee says: "You can change the third base of a protein coding region and NOT CHANGE THE PROTEIN AT ALL. 33% of a DNA sequence can be changed to no effect !"

    Yeah, in the old days of Watson and Crick. Now we have discovered several additional codes overlapping the first identified protein-code.

    Further, an error rate of 1/1000 will be absolutely desastrous to any coding genome. Never heard of Muller?

    "Only if one is intellectually lazy or willfully ignorant, since 'SelectionDIDIT or NOTHINGdidit !!1!!11!1!!' explains absolutely nothing; it is but an irrelevant, meaningless noise squeezed from the bowels of bewildered Darwimps, evolunatics and atheloons anytime they are confronted with something beyond their willfully limited understanding."

    In other words, Poland Paul you're the best example never to convert.

    ReplyDelete
    Replies
    1. Ladies & gentlemen, Peter Borger, the not-over-the-top creationist. LMFAO

      Delete
    2. Natural selection cannot act without accurate replication, yet the protein machinery for the level of accuracy required is itself built by the very genetic code it is designed to protect.

      You seem to be under the delusion that ANY mutation is fatal - they aren't.

      Rod Carty: DNA repair mechanisms make no sense in an evolutionary presupposition. Error correction requires error detection, and that requires the detection process to be able to compare the DNA as it is to the way it ought to be.

      DNA repair is regarded as one of the essential events in all life forms.

      The stability of the genome is essential for the proper function and survival of all organisms. DNA damage is very frequent and appears to be a fundamental problem for life. DNA damage can trigger the development of cancer, and accelerate aging.

      Plus the FACT that protein sequences aren't as fragile as your limited imagination - a basic examination of REALITY show that there can be many sequences that do the same thing.



      Protein-protein interactions drive the operation and function of cells. These interactions involve a molecular interface formed by a subset of amino acids from each protein. Interfacial residues often vary between orthologs, indicating some mutational tolerance or degeneracy, but such natural variability may not capture the full plasticity of interfaces. Thus, it remains unclear how many combinations of interface residues will support a given interactionand how these combinations are distributed and connected in sequence space (3) (fig. S1A). It is also unknown whether all functional variants can be reached through a series of mutations that retain function, or whether evolution is fundamentally constrained, limiting the natural diversity in orthologous proteins.
      The test results are clear. We've dropped from 20N variants in sequence space to 160,000 possible sequences for just four key residues, to 1659 functional variants of those, to 57 that are accessible to unguided natural processes, to 13 that could actually compete in the wild. In summary, functional space is a tiny, tiny fraction of sequence space. And "practical" functional space is another tiny fraction of theoretical functional space. We might put it this way: nature abhors the edge of evolution.
      Seeing that the "wiggle room" for our spare tire on the axle is so small, we might return to the old, tried-and-true explanation that the car was designed after all.

      Delete
    3. link to the text above:

      http://reasonandscience.heavenforum.org/t2062-proteins-how-they-provide-striking-evidence-of-design#4058

      Yes, given the FACT that random RNA sequences can be selected for functions - the ribosome is a ribozyme (can still function at reduced efficiency without proteins).

      LOL.... no kidding. Your credulity is remarkable.

      http://reasonandscience.heavenforum.org/t2024-the-rna-world-and-the-origins-of-life

      http://reasonandscience.heavenforum.org/t2024-the-rna-world-and-the-origins-of-life

      There are problems in imagining an RNA-catalysed metabolic network 1

      The question about the initial trigger is not trivial: to form an RNA nucleotide, not only one, but a series of reactions is necessary. An initial RNA-catalysed reaction system needed, in essence, to provide some sort of function, in order that genetics could select for it and improve catalysis and efficiency. In other words, evolution is selecting for the (functional) product and not for an intermediate step, so an initial RNA-based network could not have come into place one reaction at a time, but only as an already operational entity. This argument renders the origin of metabolism as an RNA-based metabolic reaction system not impossible, but substantially less probable. This problem is amplified by the notion that the least self-sustaining chemical networks lack evolvability, and evolutionary selection cannot change the chemistry in a reaction system, neither are the thermodynamic properties of metabolites subject to genetic selection. Thus RNA genetics has its limitations in optimizing chemical reaction networks.

      Delete
    4. Peer loses his sh*t with :

      PeePee says: "You can change the third base of a protein coding region and NOT CHANGE THE PROTEIN AT ALL. 33% of a DNA sequence can be changed to no effect !"


      Yeah, in the old days of Watson and Crick. Now we have discovered several additional codes overlapping the first identified protein-code.


      Well, if you close one eye, hold you head JUST right, and wish really, REALLY hard, you can 'discover' codes anywhere you need them !

      Got a reference for your assertion there are other codes besides 'Personal Incredulity Illustrated', 'Mathematical Meanderings Weekly', 'Vanity Press' or 'Cranks Quarterly' ?

      If what you whined were true, it would be nearly impossible for ANY mutations to arise - even a single base change would affect 5 magical codes; can you imagine what inserting a few HUNDRED base transposable element would do ?

      Oh, right - transposable elements are MAGICAL !

      Further, an error rate of 1/1000 will be absolutely desastrous to any coding genome. Never heard of Muller?


      Have you ? A mutation rate of 1 per 1000 bases per replication is QUITE survivable to an organism with a genome of 500 bases. After all, in REALITY, it is not possible to have a mutation rate of 0.

      Viroids have a genome from 249 to 467 bases, and they routinely have mutation rates on the order of 1 per 500 bases per replication, and survive quite well.

      From what you've posted, you seem to have heard of transposable elements, but have no real understanding of what they are or how they work, and so have given them near magical powers.

      One of the types of mutations TEs don't do is point mutations - like those in HAR1F and FOXP2. Where, EXACTLY, are your magical TEs that magically directed changes to these genes ?

      Screaming Peer bellows :

      "Only if one is intellectually lazy or willfully ignorant, since 'SelectionDIDIT or NOTHINGdidit !!1!!11!1!!' explains absolutely nothing; it is but an irrelevant, meaningless noise squeezed from the bowels of bewildered Darwimps, evolunatics and atheloons anytime they are confronted with something beyond their willfully limited understanding."

      In other words, Poland Paul you're the best example never to convert.


      Translation : Me have no coherent response, so me just twist your words !

      How, EXACTLY, does blubbering about the unknowable whims of unknowable beings explain anything ?

      You are one of only two blowhards I have ever had the misfortune to encounter that 'thinks' selection does not exist.

      Whether a mutation is beneficial, deleterious or neutral is context dependent - mutations that grant an advantage are under postive SELECTION (and tend to become more common in a population), mutations that reduce fitness tend to become extinct, while neutrals can hang around for quite some time.

      Delete
    5. Codes Within Codes: How Dual-Use Codons Challenge Statistical Methods for Inferring Natural Selection

      http://www.evolutionnews.org/2013/12/codes_within_co080381.html

      And furthermore , there is the the histone binding code, transcription factor binding code, the splicing code, and Tubulin code...

      http://reasonandscience.heavenforum.org/t2096-the-astonishing-language-written-on-microtubules-amazing-evidence-of-design

      Delete
    6. Peepee, I studied the internal structures of the intronless CEBPA gene for several years to find out the codes determining truncated forms of the protein. I published a paper on it, recently. Look it up. Inform yourself.

      Delete
    7. Peepee peeps: "You are one of only two blowhards I have ever had the misfortune to encounter that 'thinks' selection does not exist."

      Of course NS exists. It was first described and explained that it does not play a role of significance in evolutionary processes by Edward Blyth. It guards the genome for too fast burnouts. It stabilizes. Everybody, all biologists knew that, except theologian Darwin...who thought it had magical powers.

      Delete
    8. Here, Peepee antiscience attitude exposed: "Well, if you close one eye, hold you head JUST right, and wish really, REALLY hard, you can 'discover' codes anywhere you need them !"

      A colleague of mine spent ten years of his life to find all alternative protein-translation codes in CEBPA and CEBPB.

      You should be ashamed of yourself. If all Darwinians think as you do, we begin to understand why Mendels genetics had to be rediscovered, why McClintock was ignored, junkDNA, etc.

      Delete
    9. " It was first described and explained that it does not play a role of significance in evolutionary processes by Edward Blyth. It guards the genome for too fast burnouts. It stabilizes. Everybody, all biologists knew that, except theologian Darwin...who thought it had magical powers. "

      Wow, so many lies in just a few sentences.
      Perhaps you should look up who Blyth was and what he really did, instead of lying through your teeth what you hoped he had done.

      Delete
    10. Edward Blyth was a biologist, Darwin a theologist.

      Delete
    11. Interesting - a guy that 'thinks' life was created by a Magical Sky Pixie calls me 'unscientific' !!

      Mendel and McClintoch had advantages over you - they had EVIDENCE to support what they were saying; they were not relying on gibbering ignorance the way you are.

      It took you YEARS to figure out the coding of CEBPA ? It only has 3 start methionines with good Kozak sequences - and all proteins are in the same frame !

      DECLARING something you observe a 'code' is easy; DEMONSTRATING that it is actually relevant is much more difficult.

      But I guess you wouldn't know about that, would you ? The moment things become difficult, you can just give up and whine 'OBVIOUSLY front loaded in by a Magical Sky Pixie !'

      Blythe was a creationist; you CLAIM you aren't one, yet cite someone that thought life was crafted by a Magical Sky Pixie exactly as it was seen then, and the ONLY role for selection was to maintain the God-ordained forms ? Another mind strangled by the dead hand of Plato.

      You and he have two presumptions - 1) life was crafted EXACTLY in forms we see today, and 2) selection can only maintain the divine forms.

      Premise #1 is irrelevant, evidence-free twaddle; premise #2 is wrong, given 150+ years of real world observations.

      But you are running a great scam - sane and rational people know of many ways for a genome to gain information. You just steal them, relabel them 'front loading', then try to re-sell them to the scientific community.

      Then throw a fit when people see through the ruse ...

      Then we have ElShamah77 the undead parrot, gibbering about things he literally does not understand as if his ignorance means something.

      An argument from analogy is only strong if the things being compared are similar - life and nonliving things are about as different as things can get !

      Just because two thing share one quality does not mean they share others - dollar bills and lime peels share the quality of being green, but lime peels are not manufactured on printing presses.

      But, then again, he drops to his knees in gibbering incomprehension the moment he sees something more complicated than a stick - his trained inability to follow any process of more than one step pretty much means any scientific finding of the last 1500 years is beyond him.

      Delete
    12. Yes, peepee, you are unscientific. And not even updated unscientific, but completely out of date and out of data.

      There is so much evidence that TEs are simply a part of the regulatory genome and not the remnants of viruses. It is just the opposite: RNA virsue simply have their origin in TEs. To be precise in what has been coinde retro-transposons. There is ample evidence for this view. For instance, the RSV virus. It is trasposon machinery is almost identical to that of an endogenous ERV-H, but it has picked up small part (the on-switch) of the proto-onco known as SRC. Thus it became an oncovirus. A harmless variation-inducing genetic element transformed (evolved if you like that word better) into an RNA virus.

      You, together with all the nonsense-sellers here, believe that RNA virusen are from space. Or leftovers from an utterly hypothetical RNA world (which there is not a scintilla of evidence).

      I do not need the RNA world or out-of-space stories to explain RNA viruses. Belief in the unseen and undemonstrable is nice, but it is not science.

      But anyway, as a non-scientist you may not understand what I mean.

      Delete
    13. Peepee peeps: "It took you YEARS to figure out the coding of CEBPA ? It only has 3 start methionines with good Kozak sequences - and all proteins are in the same frame !"

      This indeed shows you are not a scientist. You probably know a bit of in silico sequences, but to identify how the code works in vivo is rather elaborate, peepee. It needs hundreds of experiments. In particular because the detection of the proteins is so hard.

      That is why the "junk DNA" of the Darwinians is such a hopeless and non-scientific approach to unknown sequences.

      Tell me, peepee, how do you identify unique functional code in the human genome with your big fat computer?

      You cannot because you are miles away from an experiment. Go to the wetlab and design AND perform an experiment, before you start peeping again. Thanks.

      The problem nowadays: belief in in silico models, rather than in observations. The observations killed NeoDarwinism, any kind of evolution by random mutations. That the hard facts you have to live with. So they turn to in silico models.

      But I understand why you are so upset: Biology killed your god. Too bad. But don't blame me or the creationist...blame science.

      Delete
    14. Peepee peeps: "It took you YEARS to figure out the coding of CEBPA ? It only has 3 start methionines with good Kozak sequences - and all proteins are in the same frame !"

      This indeed shows you do not know anything about the CEBPA gene. Upstream of the proteincoding frame of CEBPalpha, the gene codes for an out of frame peptide with a startcodon in a strong Kozak position, which regulates the expression of several different CEBPA proteins from one single intronless gene.

      Su much for peepee's folly.

      Delete
  19. Peter Borger now seems to have lost sense completely. And I said somethong about asthma on the other comment thread. Care to comment?

    "Only if one is intellectually lazy or willfully ignorant, since 'SelectionDIDIT or NOTHINGdidit !!1!!11!1!!' explains absolutely nothing; it is but an irrelevant, meaningless noise squeezed from the bowels of bewildered Darwimps, evolunatics and atheloons anytime they are confronted with something beyond their willfully limited understanding."

    ReplyDelete
    Replies
    1. That's not me...it's peepee's randomly evolved peep.

      Delete
    2. Retracting your words, 'Peer Terborg' ? That would be a first ...

      Of course it was you, who very unimaginatively twisted someone else's words around (and not randomly, but designed). Is this the only sort of intelligent (well ... not really intelligent) design you can come up with ? That might be telling ...

      Delete
  20. For some reason I'm not able to post a reply where I wanted to post it, so I'll post it here;

    Peer said:

    "The self-organisation of living organisms is programmed in the genetic information present in the genome of the self-organizing organism."

    Based on many of your other comments, it should be safe to say that you believe that the programmer is 'the designer', which is 'God', which to most IDiots is the so-called 'Abrahamic God'. The 'Abrahamic God' is allegedly omnipotent, omniscient, omnipresent, omnibenevolent, and perfect. And even if you believe that 'the designer' is some other so-called 'God' I have the same question for you and all other ID-God pushers:

    If "The self-organisation of living organisms is programmed in the genetic information present in the genome of the self-organizing organism." was/is programmed by 'God', then why are there 'flaws' in the programmed, self-organizing information? For example, why are many people and animals born deformed, disabled, diseased, or dead? Why are any?

    ReplyDelete
    Replies
    1. Genetic entropy, mate. Random accumultaion of mutations...the NeoDarwinian engine.

      Read: John Sandford (Genetic Entropy) and you will, like me, understand that all designed systems are going downhill due to genetic entropy.

      All honest scientists who worked on this, know it. From Haldane to Muller to Kimura to Kondrashov, Crow and Lynch. Many, many publications obliterate what you guys believe.



      Delete
    2. But Peer, how can there be "Genetic entropy, mate. Random accumultaion of mutations...the NeoDarwinian engine." if everything was/is intelligently designed and programmed (front-loaded) with self-organizing information?

      You ID pushers sure are inconsistent. You IDiots claim that there's no such thing as random mutations, random accumulation of mutations, natural selection (the 'NeoDarwinian engine", as you put it) and you claim that everything was/is intelligently-designed-front-loaded-programmed-guided by 'the designer' (aka your chosen, so-called 'God') but when you're asked about 'flaws' you blame them on the very thing that you claim doesn't exist ('Darwinian' evolution).

      Tell me, Peer, does "genetic entropy" occur because of 'the fall'?

      Delete
    3. It is a law, Thuthyboy....Entropy...thermodynamics.

      Everybody knows that. If you don't know the basics of physics...why discuss the derived?

      Delete
    4. Peer, yours is a typical, diversionary, IDiotic response to legitimate questions. What a surprise, not.

      Delete
    5. Ah, do elaborate, 'Peer' - your infinite knowledge of biology is well-known, and much admired in all corners of the Universe, but now we learn that you know 'the basics of physics' as well ?

      Enlighten us !

      Creationists have never understood thermodynamics, but surely you are the exception ?

      Delete
    6. "It is a law, Thuthyboy....Entropy...thermodynamics.

      Everybody knows that. If you don't know the basics of physics...why discuss the derived?"


      Peer you moron, the laws of thermodynamics merely state that it requires the conversion of energy into less usable forms to maintain a state of order, or create more order. Have you noticed how it is a fact that all organisms eat? That's why evolution is possible according to thermodynamics. As long as living things are expending energy to stay alive and reproduce, then information or ordered structures or what have you can be maintained and produced. There's this big yellow-white and hot shining object in the sky, and plants seem to grow towards it. It's like they get something out of it. And other living things eat plants. I wonder why?

      Delete
    7. Peer, Peer, such arrogance and you dare to call yourself an honest scientist and realistic biologist? Most if not all honest and realistic scientists I've met, ranging from lab techs to professors, realize they don't know everything and they behave as such.

      Your behavior fits the creationist profile 100%.

      Delete
    8. Peer you moron, the laws of thermodynamics merely state that it requires the conversion of energy into less usable forms to maintain a state of order, or create more order. Have you noticed how it is a fact that all organisms eat?

      My thoughts exactly. How can anybody be this ignorant? Let along somebody that bases so much of their arguments on the concept of entropy?

      Peter, you wrote:

      Read: John Sandford (Genetic Entropy) and you will, like me, understand that all designed systems are going downhill due to genetic entropy.

      If all genetic entropy is leading to the destruction of all genomes, then how come humans and chimpanzees have survived long enough to share a common ancestor while developing novel traits in the mean time?

      Has a magical being kept our genomes intact all this time?

      I assume of course that you are educated enough to be familiar with the overwhelming mollecular evidence that humans and chimpanzees share a common ancestor?

      For example, I assume you don't deny the existence of the hundreds of thousands of transposable elements that we share in identical locations?

      Please tell me you've at least looked into this? This is basic stuff and you're supposed to be a practising scientist!

      You could make a start here is you need a hint

      Delete
    9. Yeah, we defiinitely seem to be struggling to maintain our numbers. Damn this genetic entropy!

      Delete
    10. Thermodynamics, incidentally, has pretty much knob all to due with the mutation or fixation rate.

      Delete
    11. That's why evolution is possible according to thermodynamics

      Slight correction needed: evolution and life are possible because of thermodynamics.

      Carry on.

      Delete
    12. Mikkel you moron,

      When did the first organism "realize" it would eventually die?

      When did it 'realize' it would need to do something about death?

      When did it 'realize' the solution it would needis to reproduce? When did it "realize" it had to eat?

      did the sun provide the answers???

      Geez, evolution is dumb and dumber walking hand in hand.

      Evolution wags its little finger telling creationists its not nice to ask hard questions like that.

      Evolution doesnt need to answer those questions, because well evolution doesnt have to answer them, see.

      Evolution starts after all the heavy lifting has been done.



      〞Peer you moron, the laws of thermodynamics merely state that it requires the conversion of energy into less usable forms to maintain a state of order, or create more order. Have you noticed how it is a fact that all organisms eat? That's why evolution is possible according to thermodynamics. As long as living things are expending energy to stay alive and reproduce, then information or ordered structures or what have you can be maintained and produced. There's this big yellow-white and hot shining object in the sky, and plants seem to grow towards it. It's like they get something out of it. And other living things eat plants. I wonder why?〞

      Delete
    13. Steve, I can't believe I need to tell you this, but simple organisms don't realise anything. They operate simply through stimulus and response.

      We can estimate when this happened (between 4100 - 2500 Ma). But just because we don't know what that organism was, has nothing to do with the overwhelming evidence for evolution.

      If you want to believe that organism was created through magic then go right ahead but when it comes to the question we are actually discussing (like did the organisms we see today evolve from a common ancestor), then we stick to science and evidence.

      Delete
    14. Steve, Steve, Steve.
      Those are not hard questions, they are too simple to answer: You're thinking this very poorly.

      Delete
    15. Hence ACE, the quotation marks around "realize". Duh.

      Evolution without reference to intelligence explains only the most superficial of observations.

      BTW, there is diddly squat in the way of evidence for unintelligent evolution. Evolution has been forced to co-opt a slew of designed objects to make any attempt at an explanation.

      And these are a good sample of the designed objects which evolution tries to claim for itself....well because....it has not other choice:

      1. Reproduction.
      2. Digestive mechanism
      3. Sensory mechanism
      4. Threat detection mechanism
      5. Damage control mechanism
      6. Intra-cellular communication mechanism
      7. Inter-cellular communication mechanism
      8. Extra-cellular communication mechanism
      9. Energy production mechanism
      10. Endo-symbiosis.

      None of the above can be explains without reference to intelligence.

      NONE of them!



      Delete
    16. OK, photo. Here's your chance to answer those simple questions.

      Explain the above list of designed object without reference to intelligence.

      But WAIT....i gotta go to 7-11 for the popcorn first. So you've a got a few minutes headstart.

      Delete
    17. But Steve ... you already assume these 'objects' to be designed ... that is not how questions work.

      Also, you seem to confuse the engineering definition of 'mechanism' with the biological one (see top two items at https://en.wikipedia.org/wiki/Mechanism )

      Delete
    18. > BTW, there is diddly squat in the way of evidence for unintelligent evolution.

      Steve I get the feeling that if I gave you evidence for evolution, you would just slap the word "intelligent" in front of it and say "but that's also evidence for intelligent evolution".

      In any case if you're going to make the claim that a magical invisible man guided evolution each step of the way, then you are the one that will need to provide evidence for that.

      All I presume are the things we are already familiar with - the natural forces we see around us today. Pointing out "flaws" in a theory doesn't make what you're doing science. You need to propose an alternative and then suggest a way that this alternative can be tested.

      There are plenty of hypotheses for the origin of sexual reproduction. The problem isn't that we think these are all too unlikely to have evolved with out a magical being waving a wand. The problem is that all scientific ideas need to be tested (something IDists haven't cottoned on to yet) and it's kind of difficult to test the evolution of sexual reproduction given the time scales that we work with in the lab.

      So right off the bat - in your first point we see that you are talking shit. Given that you can't even take 2 seconds to Google a problem, I don't see why it is worth my time to do all your homework for you. Your gish-gallop won't work here - I'll let you find out for yourself what the current hypotheses are for the other points you listed.

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  21. This is a good time to try getting on the same page in regards to what the Discovery Institute has long stated. Please study this video:

    Is Intelligent Design Theory Incompatible with Evolution? - Casey Luskin

    Thank you..

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    1. Gary, aligning yourself with the theocratic liars of the discotoot in any way, shape, or form is a surefire way to destroy any scientific and moral credibility that you may ever hope to have.

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    2. I doubt that Gary can go any lower in credibility than he's managed to get so far. So, aligning himself with the IDiots does nothing to his reputation. He's the very same self-deluded imbecile, who thinks we should worship him for his "amazing" insights.

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    3. The whole truth is found by going back to the original source, which in this case has long stated:

      Frequently Asked Questions
      http://www.discovery.org/id/faqs/
      Questions about Intelligent Design

      5. Is intelligent design theory incompatible with evolution?
      It depends on what one means by the word “evolution.” If one simply means “change over time,” or even that living things are related by common ancestry, then there is no inherent conflict between evolutionary theory and intelligent design theory. However, the dominant theory of evolution today is neo-Darwinism, which contends that evolution is driven by natural selection acting on random mutations, an unpredictable and purposeless process that “has no discernable direction or goal, including survival of a species.” (2000 NABT Statement on Teaching Evolution). It is this specific claim made by neo-Darwinism that intelligent design theory directly challenges. For a more thorough treatment see the article “Meanings of Evolution” by Center Fellows Stephen C. Meyer & Michael Newton Keas.


      The “Meanings of Evolution” only helps explain why it's true that "Evolution and the theories of evolution are fundamentally different things".

      I prefer to be precise in regards to what is stated. At least this way I do not become one of the unfortunates who are destined to have no credibility at all (with anyone) after having been found to be misrepresenting the facts.

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    4. Gary, if you prefer to be precise in regard to representing the facts, stay as far away from the discotooters as possible unless you don't mind being thought of as precisely dishonest and nuts.

      There is plenty of deliberate misrepresentation (lies and BS) in what you quoted from the discotoot site. For example, there's no such thing as "intelligent design theory", most or all IDiots do NOT accept common descent (especially in regard to humans), there's more to evolutionary theory than "neo-Darwinism", and the stuff about "an unpredictable and purposeless process that “has no discernable direction or goal, including survival of a species"" is wrong in some ways and it reveals the theobotic 'God has a purpose for us' beliefs that drive the ID agenda.

      Hey Gary, take a look at the discotoot Center on Human Exceptionalism site and notice these words under Our Mission and What We Do: "unique human personhood", and "the unique and intrinsic moral worth of human life". So much for accepting common descent.

      And what is the name of the site that was founded by dembski (probably the most well known IDiot and discotooter)? You know which site I mean, don't you? The initials for the site name are UD.

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    5. The whole truth you are now arguing that people taking a scientific theory religiously (i.e. Theistic Evolutionists, Evolutionary Creationists) makes a scientific theory unscientific. You at least need to set a good example and do the same to "evolutionary theory" by protesting for it to likewise be kept out of science and the public schools.

      The only scientific way for me to NOT take sides is to keep the rules the same, by NOT throwing out an excellent premise for a scientific theory just because it's too religion-friendly for you. I must show what discovery the theory leads to or else science gets dragged down by all the divisive religious agendas that are being served by not having done so.

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    6. The only scientific way is to go where the evidence leads you, dimwit. OTOH you have a premise, and of course it's an excellent one! How convenient. And since you have an excellent premise you can ignore any piece of evidence that may conflict with it, and still pretend that you are being "scientific". What a moron

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  22. Premise = "The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection."



    Theory = https://sites.google.com/site/theoryofid/home/TheoryOfIntelligentDesign.pdf

    Done...

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    1. You don't even understand the difference between premises and hypothesis. smfh

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    2. Hypothesis: An idea you can test.

      Premise: A statement or idea that is accepted as being true and that is used as the basis of an argument.
      merriam-webster.com/dictionary/premise

      Theory: An explanation of how something works or happened.

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    3. So by calling it "premise" you accept as true, without needing to prove it, that ID is the best explanation for "certain features" of the universe. How is that scientific? Fail #1

      And read that definition of theory again:

      An explanation of how something works or happened

      Claiming that "certain features" are best explained by design is not explaining how or what anything was designed. So it's not a theory, it's just your stupid, unscientific premise that doesn't explain anything.

      And no, your retard lab doesn't explain anything either

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    4. Damn, we need an edit button. Everyone please excuse my terrible wording there

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  23. Dazz, you are so "dense" that at this point I could consider you a lost cause. But it's easy enough to show what the premise looks like after adding theory that explains how biological "intelligent cause" works, which begins by stating the following:

    The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, whereby the behavior of matter powers a coexisting trinity of systematically self-similar (in each other's image, likeness) intelligent systems at the molecular, cellular and multicellular level as follows:

    [1] Molecular Level Intelligence: Behavior of matter causes self-assembly of molecular systems that in time become molecular level intelligence, where biological RNA and DNA memory systems learn over time by replication of their accumulated genetic knowledge through a lineage of successive offspring. This intelligence level controls basic growth and division of our cells, is a primary source of our instinctual behaviors, and causes molecular level social differentiation (i.e. speciation).

    [2] Cellular Level Intelligence: Molecular level intelligence is the intelligent cause of cellular level intelligence. This intelligence level controls moment to moment cellular responses such as locomotion/migration and cellular level social differentiation (i.e. neural plasticity). At our conception we were only at the cellular intelligence level. Two molecular intelligence systems (egg and sperm) which are on their own unable to self-replicate combined into a single self-replicating cell, a zygote. The zygote then divided to become a colony of cells, an embryo. Later during fetal development we made it to the multicellular intelligence level which requires a self-learning neural brain to control motor muscle movements1 (also sweat gland motor muscles).

    [3] Multicellular Level Intelligence: Cellular level intelligence is the intelligent cause of multicellular level intelligence. In this case a multicellular body is controlled by an intelligent neural brain expressing all three intelligence levels at once, resulting in our complex and powerful paternal (fatherly), maternal (motherly) and other behaviors. This intelligence level controls our moment to moment multicellular responses, locomotion/migration and multicellular level social differentiation (i.e. occupation). Successful designs remain in the biosphere’s interconnected collective (RNA/DNA) memory to help keep going the billions year old cycle of life, where in our case not all individuals must reproduce for the human lineage to benefit from all in society.

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    1. I don't give a rats ass for your nonsensical drivel about biological "intelligent cause".

      Theories and hypothesis need explanatory power, and evidence to back them up. You have none of that and nobody cares if you think it's ok to call that a premise to part with the burden of proof you retard.

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    2. But what is more damning for your "theory", as already pointed out at antievolution.org, is that neither Molecular, Cellular or Multicellular Level Intelligence allow for any kind of disembodied Intelligent Designer, AKA God. You're essentially shooting yourself in the foot, it's plain to see, unless you're an IDiot, of course

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    3. Then after that the theory states:

      Reciprocal cause/causation goes in both the forward and reverse direction. These communicative behavioral pathways cause all of our complex intelligence related behaviors to connect back to the behavior of matter, which does not necessarily need to be intelligent to be the fundamental source of consciousness.

      Behavior from a system or device qualifies as intelligent by meeting all four circuit requirements for this ability, which are: [1] Something to control (a body, either real or virtual representation) with motor muscles (proteins, electric speaker, electronic write to a screen). [2] Random Access Memory (RAM) addressed by its sensory sensors where each motor action and its associated confidence value are stored as separate data elements. [3] Confidence (central hedonic) system that increments the confidence level of successful motor actions and decrements the confidence value of actions that fail. [4] Ability to guess a new memory action when associated confidence level sufficiently decreases. For flagella powered cells a random guess response (to a new heading) is designed into the motor system by the action of reversing motor direction causing it to “tumble”.

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    4. And as I already told you, that's even worse. Not only you tie "intelligence" to "motor muscles", "sensory sensors" and all kind of material stuff, you also claim that the designer's confidence decreases as he fails.

      But of course if you believe in a god that created you in his own image, a god that fails certainly fits the bill, LOL

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    5. I never realized that "material stuff" is now off-limits in science. But I have a feeling that your new rule only applies to a certain theory that further states:

      At all biological intelligence levels whatever sensory the system has to work with addresses a memory that works like a random access memory chip used in a computer. It is possible to put the contents of a RAM into a Read Only Memory (ROM) but using a ROM instead of RAM takes away the system's ability to self-learn, it cannot form new memories that are needed to adapt to new environments. The result is more of a zombie that may at first appear to be a fully functional intelligence but they are missing something necessary, a RAM in the circuit, not a ROM. Behavior of matter does not need to be intelligent, a fully trained (all knowing) ROM could be used to produce atomic/molecular behavior. But a ROM would not work where intelligent behavior is needed. Unless the ROM contains all-knowing knowledge of the future and all the humans it will ever meet in its lifetime it can never recall memories of meeting them, or their name and what they look like.

      For machine intelligence the IBM Watson system that won at Jeopardy qualifies as intelligent. Word combinations for hypotheses were guessed then tested against memory for confidence in each being a hypothesis that is true and whether confident enough in its best answer to push a button/buzzer. The Watson platform had a speaker (for vocal muscles) and muscles guiding a pen was simulated by an electric powered writing device.

      For computer modeling purposes the behavior of matter can be thought of as being “all-knowing” in the sense that the behavior is inherent, does not have to learn its responses. A computer model then starts off with this behavior already in memory and has no GUESS or CONFIDENCE included in the algorithm, as does intelligence. Memory contents then never changes. Only a GUESS can write new data to memory and GUESS must here be taken out of the algorithm. But it is possible to leave the CONFIDENCE in the algorithm, it will still work the exact same way. Where this in time proves to be true for real matter it would be a valuable clue as to how consciousness works and possibly how to model it, which may in turn help answer the “big questions” including those pertaining to afterlife.

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