Sunday, January 01, 2017

The most popular Sandwalk post of 2016

My most popular post last year was: An Intelligent Design Creationist disputes the evolution of citrate utilization in the LTEE ... Lenski responds. It had almost 20,000 views and 227 comments.

The article discussed a paper by Intelligent Design Creationist Scott Minnich who criticized Richard Lenski's ongoing evolution experiment on the grounds that no new information had been created in the evolution of ability to use citrate.
Intelligent Design Creationists are not happy about this experiment because it not only shows evolution in action but it also illustrates features of the process that ID proponents don't understand; features like drift, neutral alleles, and contingency that expose the ignorance of the average creationist. However, there are a few ID proponents who actually understand evolution so they are forced to come up with other kinds of criticism to soften the impact of the results coming out of the Lenksi lab.

One of those creationists is Scott Minnich, a professor and researcher at the University of Idaho in Moscow, Idaho (USA). Minnich wants you to believe that the LTEE isn't significant because no new genetic information was created. This is part of a strategy to accept microevolution but deny that macroevolution can be explained by naturalistic processes.

Minnich's lab did some experiments in order to replay the evolution of citrate utilization in E. coli cultures. They found that they could evolve strains that utilized citrate under aerobic conditions but in their hands it took much less time than it took in the LTEE and it was much more likely to occur. (Recall that the Cit+ phenotype only evolved in one of the twelve cultures in the LTEE and it took 30,000 generations.) Here's the Minnich paper and the abstact.
Lenski and his postdoc, Zachary Blount, responde to the critique. I summarized the exchange as follows,
Evolution works by modifying pre-existing DNA to create new genes or new regulatory elements from sequences that were already present in the genome. Creationists seem to think that new genetic information has to be "poofed" into existence from nothing or it doesn't count as new information. They would like very much to demonstrate that there are real examples of such magic because that would lend support to their claim that goddidit. So far they haven't come up with a single, credible, example of such a gene so they have to be content with denying that evolution can create new genetic information.

It's sad, really.
Surprisingly, some people wanted to debate this point!


52 comments :

  1. Its not like that.
    What is in genes is mysterious. There must be a finale result but its combinations and equations is open to manipulation by natures desire to survive.
    I agree people have different colours but never evolved to different colours but instead instantly changed in a few years for migrating peoples.
    so the genes must have this ability even if not understood how its triggered.
    Why should modifying dNA count as creating new information? its the same information just modified! Indeed all the information could be free agents.
    Hmmm. ID is saying no creation for new information. Its a closed system.
    Evolutionists here are saying the closed system is crating new information.
    I think the evolutionists need to show how thresholds of information can be crossed to create new information.
    anyways ID is saying its a closed system.

    ReplyDelete
    Replies
    1. A closed system, but the enclosure is around DNA that is reactive. Cave species all over the world lose sight and pigment. Does this happen because of random mutations, or because their DNA is prepared to adapt?

      Delete
    2. Robert, if you are going to comment, please turn your brain on.

      "I agree people have different colours but never evolved to different colours but instead instantly changed in a few years for migrating peoples."

      African Americans have been in North America for a few centuries. The last time I looked, they are still black. And the Asians brought over to build the railway in the 1800s are still Asian.

      Please tell us that you don't have a job involved with establishing science policy for Canada.

      Delete
    3. I don't believe Mr. Byers has any such position. However, is it noteworthy that at least some creationists list him among their most illustrious scientific thinkers:

      http://www.rae.org/essay_author.html

      Delete
    4. txpiper,

      "Cave species all over the world lose sight and pigment. Does this happen because of random mutations, or because their DNA is prepared to adapt?"

      How would you go about trying and distinguishing between those two?

      Delete
    5. Does this happen because of random mutations, or because their DNA is prepared to adapt?

      Right, because of "front loading." We also know that there is no junk DNA, and the proof that both of these concepts are true is that bacteria, since they need more "front loading" to prepare for all their descendants, have so much more DNA than we d... - oh, wait....

      Delete
    6. photosynthesis,

      “How would you go about trying and distinguishing between those two?”

      In a word, parsimony.

      This article:

      http://phys.org/news/2013-12-cavefish-evidence-alternative-mechanism-evolutionary.html

      explains why cave species are awkward for the mutation/selection deal:

      “In the classical view of evolution, species experience spontaneous genetic mutations that produce various novel traits—some helpful, some detrimental. Nature then selects for those most beneficial, passing them along to subsequent generations.

      It's an elegant model. It's also an extremely time-consuming process likely to fail organisms needing to cope with sudden, potentially life-threatening changes in their environments. Surely some other mechanism could enable more rapid adaptive response.”


      There is, of course, evolutionary spackling to deal with the problem:

      “Eye loss in these fish is considered to be a demonstration of an evolutionary concept known as "standing genetic variation," which argues that pools of genetic mutations—some potentially helpful—exist in a given population but are normally kept silent.”

      In other words, saving up DNA replication errors for a rainy day. Comical, but who would notice when it is an evolutionary concept?

      However, the article goes on to notice that the adaptation is a reaction to the environment, attributable to a unique protein. It isn’t evolution at all. It just illustrates that genomes include prepared responses.

      "This is the first study showing that this HSP90-mediated mechanism can be applied to vertebrates for real morphological adaptive traits.”

      I expect that this is actually the tip of a genetic iceberg.

      Delete
    7. txpiper,

      That's as far from parsimonious as it could get. I find the "explanations" in that article quite convoluted (the very opposite of parsimonious). I think that the reviewers were as drunk when they reviewed the manuscript as the authors when they wrote it (I actually went and checked the article, rather than the "news" your link points to).

      Now, let's leave that convoluted piece of crap out, and tell me what would be actually parsimonious. What would you check, and what would you expect to see in either case.

      Delete
    8. txpiper,

      "However, the article goes on to notice that the adaptation is a reaction to the environment, attributable to a unique protein. It isn’t evolution at all."

      So what? Me walking down the street is not evolution either. That doesn't mean that evolution doesn't happen.

      "It just illustrates that genomes include prepared responses."

      For that they'd have to prove that there's an actual advantage to the underdeveloped eyes.

      The only thing these guys showed was that in one species of fish, the eyes underdeveloped and the underdevelopment was linked to some shock protein. This didn't matter because the fish live with no light. But where's the actual advantage? What's the big deal? How does that contradict evolution? how does that mean that the eye loss was "preprogrammed"?

      See how that's not parsimonious?

      Again: Now, let's leave that convoluted piece of crap out, and tell me what would be actually parsimonious. What would you check, and what would you expect to see in either case.

      Delete
    9. photosynthesis,

      The Wikipedia entry for Troglofauna says:

      “Troglofaunal species include representatives of many animal groups, including gastropods, millipedes, spiders, pseudoscorpions, harvestmen, isopods, collembolans, diplurans, beetles and salamanders.”

      It also notes that:

      “Troglofauna adaptations and characteristics include a heightened sense of hearing, touch and smell. Loss of under-used senses is apparent in the lack of pigmentation as well as eyesight in most troglofauna. Troglofauna insects may exhibit a lack of wings and longer appendages.”

      Nobody is telling you that you can’t believe that all those specialized adaptations happen in all those species because natural selection is acting on random DNA replication errors. You shouldn’t feel compelled to tag along with Harvard Medical School researchers, or MIT biology professors. Just ignore things that have have unpleasant ideological implications, and read something that don’t make you uncomfortable, like this:

      http://oceanexplorer.noaa.gov/facts/cave-adapt.html

      It even includes a government-sanctioned, taxpayer-funded qualifier to discourage anyone whose curiosity might drift in the wrong direction:

      “Adaptations do not happen because an animal “wants to adapt” or “needs to adapt.” Adaptations happen as random events, and if they provide an advantage, the organism is more likely to survive and reproduce than other organisms with these same adaptations.”

      Feel better?

      -

      “tell me what would be actually parsimonious.”

      Having a DNA profile that doesn’t require accidents to adapt.

      Delete
    10. txpiper,

      I never said that organisms living in caves have no adaptations I said that the guys with the particular species of fish didn't prove that losing sight was advantageous. Did you get that now?

      I also explained how that didn't mean that evolution doesn't happen. It just meant that in that particular case the fish lost sight in a way that wasn't unexpected. But that's it.

      The convoluted explanation by that research group was ridiculous, and you said so yourself! You mocked the idea of mutations waiting there just in case. Yet, that's exactly the position you're defending! You think that those mutations were there waiting just in case! You're a clear case of cognitive dissonance.

      Having a "system" there for losing traits is not parsimonious. Parsimonious is when some trait is no longer of use, and mutations that hurt those no-longer-useful traits don't get selected against (because the traits are no longer useful). That's parsimonious.

      Delete
    11. photosynthesis,

      “I said that the guys with the particular species of fish didn't prove that losing sight was advantageous”

      If you check around, I think you’ll find the prevailing opinion will be about susceptibility to injury and the high cost of repairing a useless organ, or something like that.
      -
      “It just meant that in that particular case the fish lost sight in a way that wasn't unexpected. But that's it.”

      But as the Wikipedia article noted, that isn’t all cave species lose, or gain. The issue is whether or not any of the adaptations are acquired accidentally as a result of random DNA replication errors. That idea obviously didn’t sit well with whoever cooked up the concept of ‘standing genetic variation’, whereby accidental beneficial alleles are on stand-by. Whatever the case, the selection fairy would have its hands full sorting that out.
      -
      “The convoluted explanation by that research group was ridiculous, and you said so yourself!”

      I don’t think that was the research group. That was just an explanatory insertion on the part of the writer.
      -
      “You mocked the idea of mutations waiting there just in case.”

      Check. But that appears to be pretty close to the default concept in regards to rapid evolution. Hell, they had to come up with something.
      -
      “Yet, that's exactly the position you're defending! You think that those mutations were there waiting just in case!”

      Not at all, because I think adaptability is a deliberate mechanism, not an accumulation of random accidents. As the phys.org article I linked to mentioned, fast-track adaptations like this simply don’t work in the mutations/selection paradigm. Here's a good example:

      https://en.wikipedia.org/wiki/Italian_wall_lizard


      Delete
    12. because I think adaptability is a deliberate mechanism

      Why do you need deliberate? It's the Thermos joke all over again. ("You put something hot in, it stays hot. You put something cold in, it stays cold. How does it know?" The answer of course is that it doesn't have to know, once you understand the scientific concept of insulation. And you don't need adaptability to be a deliberate process if you understand evolution.)

      photosynthesis putly simply and understandably: "[W]hen some trait is no longer of use...mutations that hurt those no-longer-useful traits don't get selected against (because the traits are no longer useful)." Very simple, no faith in unevidenced all-powerful omniscient beings required.

      Delete
    13. We should be grateful to txpiper for providing such a textbook example of how the creationist mind functions (or, more accurately, malfunctions).

      In an earlier post he wrote sarcastically, re: the Lenski LTEE:

      So after 31,000 generations, they got a transport protein that enables E coli to utilize citrate with genes that it had before the experiment began. That's heavy duty stuff right there.

      I guess he expected more to happen, faster. But just above he writes:

      As the phys.org article I linked to mentioned, fast-track adaptations like this simply don’t work in the mutations/selection paradigm. Here's a good example:

      https://en.wikipedia.org/wiki/Italian_wall_lizard


      So now he thinks the relatively rapid morphological changes that occurred in the Mrcau lizards couldn't have been evolutionary, because too much happened too quickly.

      Now, it is true that the changes in the lizards have not been definitively shown to result from mutations or change in allele frequency, so they could instead be examples of plasticity. But that is immaterial to the point txpiper is trying to make. It's pretty clear that he simply won't accept any evidence that demonstrates evolution to be true, because he desperately wants it not to be true.

      Delete
    14. @lutesuite, and of course he also simultaneously holds the ideas that adaptability is planned, i.e., "frontloading," while simultaneously maintaining there is no junk, which should simply on the basis of mathematics mean bacteria (requiring lots of "frontloading" genes) must have more DNA than we do (needing no "frontloading" genes at all, as we are the pinnacle of creation, doncha know).

      It apparently troubles txpiper not at all that the math works exactly opposite to the way his ideas say it should. So, an experiment on creationist ideas, and the result says those ideas must be wrong.

      Delete
    15. lutesuite,

      “I guess he expected more to happen, faster.”

      No, I would not. But it could have.

      Lenski and Blount concur. “We had already shown that if you put the bacteria on petri dishes where citrate was the only carbon source available and they were subject to prolonged starvation on it, we also could get . . . citrate mutants appearing on the order of a few weeks or so,” Lenski told The Scientist. “It’s already known [when mutants appear] depends on the ecological context.” *
      http://www.the-scientist.com/?articles.view/articleNo/45423/title/Similar-Data--Different-Conclusions/
      -
      “…the relatively rapid morphological changes that occurred in the Mrcau lizards couldn't have been evolutionary, because too much happened too quickly.”

      It really doesn’t matter whether it is cave species, Italian wall lizards or polar bears. Adaptation is only adaptation. The problem for you, is that “standing genetic variation”* means having functional, unexpressed contingency genes that can be activated by environmental stress. This is a gross embarrassment for the standard evolutionary paradigm because natural selection, even in full-blown fairy mode, cannot plan ahead.

      None of this is uncomfortable for creationists. We would expect animals with a mandate to be fruitful and multiply, to be equipped with the means to do that.

      *Populations adapt to novel environments in two distinct ways: selection on pre-existing genetic variation and selection on new mutations
      https://pdfs.semanticscholar.org/c259/71e0683d6d9a8733b84a8c321588846c28cc.pdf

      Delete
    16. The problem for you, is that “standing genetic variation”* means having functional, unexpressed contingency genes that can be activated by environmental stress.

      No, it doesn't. But if it'll make you feel better to believe it does, I can't stop you.

      Delete
    17. Hey Tx,

      you're claims still are in the realm of "evolution can't do this, thus goddidit".

      The paper you cite doesn't conclude what you think it does. Your selective reading filter clearly picked up the words "selection on pre-existing genetic variation" but you neglected to understand the paper itself.

      Because the authors further down in the paper write:
      "Another reason is that a beneficial allele present as standing variation is older than a new mutation, and might have been pre-tested by selection in past environments, in another part of the species’ range, or even in another species with which the population has exchanged genes [5]. Such alleles might have multiple advantageous genetic changes [6,7]. In contrast to new mutations, such standing variation has already passed through a ‘selective filter’, which increases the chance that large-effect alleles are advantageous, and the probability of parallel evolution[8]."

      Anyway, could you point me to the bit where the authors state that life forms need to have genes front loaded to be able to adapt to new environments? I also can't seem to find the "IDdidit" conclusion.

      Delete
    18. txpiper doesn't even have a coherent position to defend.

      Consider the situation in which an organism's environment is altered in such a way that would cause positive selection pressure on a particular allele. This allele could have arisen in two ways: By mutation prior to the change in environment, or by mutation after the change in environment. txpiper claims the former represents "frontloading" of the genome by God. But he has no way of distinguishing this from mutations that simply arose randomly. All he has is faith that Goddidit.

      Delete
    19. txpiper,

      "If you check around, I think you’ll find the prevailing opinion will be about susceptibility to injury and the high cost of repairing a useless organ, or something like that."

      I don't care about a prevailing opinion. I care about evidence.

      "But as the Wikipedia article noted, that isn’t all cave species lose, or gain."

      But the specific example in that news article was not each and every trait in each and every cave-dwelling organism. It was a single loss, linked to a stress protein in a specific species of fish. I don't understand why you'd jump to a "therefore every trait."

      "Not at all, because I think adaptability is a deliberate mechanism, not an accumulation of random accidents."

      You're still defending what you first mocked, only worse, since instead of "mutations waiting just in case" yours is "deliberate mutations waiting just in case." The second is worse because you cannot prove that those mutations are deliberate, and nobody has proven that the mutations were there waiting just in case.

      "As the phys.org article I linked to mentioned, fast-track adaptations like this simply don’t work in the mutations/selection paradigm."

      That was a news article, and that was but one kind of loss. They still have to calculate the rate of mutation per generation, from there calculate if that's possible, not just claim it. In either case, you cannot generalize from that single example. Do you really think that every trait is exactly the same in terms of time or number of mutations that can lead there? Why would anybody think that way?

      "Here's a good example: https://en.wikipedia.org/wiki/Italian_wall_lizard"

      A good example of what? Again, what makes you think that the traits gained by those lizards were beyond the mutations already present in the population, or beyond mutation/selection in the time it took? You do know that there's lots of variation in mandible strength and intestinal lengths just within a species, right? So, what's so hard to understand about those lizards that you think they adapted too quickly? How would you know? Have you studied those variabilities? Are they reported? Do you know the genetic and allelic map of the mother and daughter species populations?

      You don't know, but you have to assume your conclusion because you're too ignorant and too committed to your fantasies, so if someone finds a case where mutations/selection were not involved some adaptation, it must mean that the whole of life are but adaptations involving no mutations/selection/drift. Right? All in the name of god-did-it.

      Delete
    20. Simple question, tx:

      If bacteria had to have frontloaded genomes so they could evolve into all the other life forms including us, and there is no junk DNA, why do we have more genes than bacteria?

      Delete
    21. TxPiper puts "standing genetic variation" in scare quotes so he apparently thinks this is hypothetical, not observed. Which is kind of funny. Tx's other points have been demolished by others, but I'll go after this one.

      "The problem for you, is that “standing genetic variation”* means having functional, unexpressed contingency genes that can be activated by environmental stress."

      Of course not. You don't seem to know what it means, and you're getting it confused with ideas of "frontloading" from IDiots like Perry Marshall of Evolution 2.0 infamy.

      But I have to ask you: what experimental evidence made scientists think adaptations were due to standing genetic variation? Because you seem to believe this is a hypothetical and not an observed.

      So I ask Txpiper a simple question: how did the fact (not mere hypothesis) of standing genetic variation win out over the older idea of "programmed evolution" or "frontloading" which nowadays is sold by IDiots like Perry Marshall as if they're new? What EXPERIMENTS led scientists to conclude that mutations were RANDOM, not programmed, and that standing variation usually preceded the appearance of adaptations?

      Because Txpiper, like IDiot Perry Marshall, seems to believe scientists never did the tests. They all seem to know nothing about any tests. They all seem to think this stuff is presumed or assumed and no scientists would ever test it.

      Seriously, these ideas have been kicked around for 80 years by people vastly smarter than Tx or Perry Marshall, and these guys just ASSUME that the world's smartest people would never TEST it.

      Delete
    22. So let me make my question to Txpiper more specific. Back in the 30's an 40's, a lot of microbiologists believed in your dummy idea of "programmed evolution", specifically, that antibiotic resistance appeared quickly in bacteria because they were "programmed" to get antibiotic resistance. They ASSUMED that your "frontloading" shit was true. Your "frontloading", which Perry Marshall stupidly calls "Evolution 2.0" like it's new, was the OLD idea of the 1930's, it was assumed, and when they tested it, they proved it wrong. They showed the mutations were present in standing genetic variation.

      Now I'm asking Txpiper: do you know what experiments I'm talking about? Which experiments of the 1940's (there're more than one) showed specifically that development of antibiotic resistance was NOT due to "frontloading", but due to random mutations already present in standing genetic variation?

      How many experiments can Txpiper (or that IDiot Perry Marshall) name that showed this? You IDiots just ASSUME that scientists ASSUMED there was standing genetic variation. You're accusing the world's smartest people (some got Nobels) of not TESTING it. You don't know that, you just assume.

      So name the $%^&ing experiments that showed it. Don't try to change the subject-- until you answer straight up, I'll be on you like a Republican on a lobbyist.

      Delete
    23. And I've got another question for Txpiper on the topic of "standing genetic variation" which he puts in scare quotes, like scientists haven't observed it.

      Here's the question. How much standing genetic variation do you think there is in Homo sapiens? I'm asking you to compute a simple measure (actually an underestimate) of genetic variation.

      Let's see how much you know, OK TxPiper? And if you can't do the very simple math (my kid could do it) you can ask that IDiot Perry Marshall to do it.

      It's a simple math question. Consider the AVERAGE base pair in the human genome (of which there are 3.2 billion). Excluding lethal variations (which should not exist), in the entire human race, population 7 billion, how many INDEPENDENT mutations, new to the individual carrying it, do you think there are at the average base pair in the genome? Again, excluding lethals, which will be rare anyway, and excluding mutations inherited from one's parents or grandparents.

      For example, if a particular base pair in the human genome is typically, say, C, how many independent, de novo appearances of T, G, or A (new to the individual, not inherited from parents) should there in the whole human race alive today?

      Here's a hint. Start with an experimental rate of mutation *per base pair* and *per generation* for humans. Multiply by the human population, 7 billion. Another hint: don't use the mutation rate per cellular multiplication, because humans undergo many cellular divisions before they make babies. Use the rate per human generation.

      And to make the math simple (my kid could do it): For simplicity, assume all mutations are equally probable (e.g C mutating to T, G, or A will all have 33% probability.) Exclude mutations inherited from one's parents or grandparents. Only consider de novo mutations new to that individual, appearing in one generation. Thus, the result will be an underestimate. And ignore lethals.

      Since Txpiper doesn't believe in "standing genetic variation", let's see him compute a measure of how much we'd normally expect there to be. Just in humans. Forget bacteria.

      Delete
    24. photosynthesis,

      “I don't care about a prevailing opinion. I care about evidence.”

      You do? Don’t you recall your sketch about how an early organism would acquire 25 genes? You didn’t mention evidence at all. You just filled up a canyon with total nonsense.
      -
      “You're still defending what you first mocked…you cannot prove that those mutations are deliberate, and nobody has proven that the mutations were there waiting just in case.”

      I don’t think mutations has anything to do with it. My beliefs about DNA replication errors is that they screw things up, because that is what the disease databases show. (By they way, your explanation about why nobody is tracking and recording beneficial mutations was embarrassing.) Your perception of mutations is based on imaginary scenarios that support your theory, not evidence. Nobody ever discovered that natural selection acts on mutations. That is an idea that had to be wormed into the theory when the molecular level stuff came into view. The religious dogma had taken hold long before anybody knew anything about the central dogma.
      -
      “…that was but one kind of loss. They still have to calculate the rate of mutation per generation, from there calculate if that's possible, not just claim it.”

      You’re ignoring that fact that fish, amphibians, mollusks, insects, spiders, millipedes and crustaceans, isolated in caves all over the world, lose the same traits, and acquire similar enhancements. This does not occur accidentally. There is nothing random about it. Mutation rates are irrelevant.
      -
      “So, what's so hard to understand about those lizards that you think they adapted too quickly?”

      Before I answer that, to what mechanisms do you attribute the adaptations?

      ===

      judmarc,

      “If bacteria had to have frontloaded genomes so they could evolve into all the other life forms including us, and there is no junk DNA, why do we have more genes than bacteria?”

      Simple answer. Creationists don’t think bacteria evolved into anything else.

      ===

      Diogenes,

      “Since Txpiper doesn't believe in "standing genetic variation” “

      Oh, I never said I don’t believe that there is such a thing. The animals we’ve been discussing give me every reason to accept that there is. But the article I linked to describes standing genetic variation as

      “an evolutionary concept…which argues that pools of genetic mutations—some potentially helpful—exist in a given population but are normally kept silent.”

      You seem convinced that it is more than just an arguable concept. And I’m supposing that you believe that these pools of potentially helpful mutations, and the protein triggers that can activate mutant alleles, are the result of natural selection acting on random DNA replication errors. So, why would alternate genes that blind the host be selected for?

      Delete
    25. I asked Txpiper to do a simple calculation to get a lower limit on the standing genetic variation in the human race today. You don't know how and can't even guess at a ballpark figure. I asked you what experiment(s) led scientists in the 1940's to conclude that it was standing genetic variation, not "frontloading" of invisible information, that facilitated the development of antibiotic resistance. You clearly have no clue what you're talking about, or why scientists concluded what they did.

      Instead you give me "I’m supposing that you believe that these pools of potentially helpful mutations, and the protein triggers that can activate mutant alleles, are the result of natural selection acting on random DNA replication errors". Jesus no. At least not most of the time. I brought up the 1940's experiments which proved the opposite, at least in that case. I suppose in some other situation there could be standing genetic variation which had been previously selected some generations back, but in the cases I've been discussing the mutation rate is high enough that we can get at least a ballpark figure from random mutation alone.



      As for "the protein triggers that can activate mutant alleles", I don't even know what you mean or where you got that from, and I don't think you know, either. At this point you're just throwing together words and hoping there's a 50-50 chance they'll mean something. "Protein triggers"? This is not translatable into molecular biology.

      You sound like the people who read Perry Marshall's Evolution 2.0 crap on Facebook.

      Delete
    26. txpiper,

      "You didn’t mention evidence at all. You just filled up a canyon with total nonsense"

      I mentioned evidence. Which this comment you just revealed is that you don't actually read the answers, you just skim through them, if at all. No wonder you would not understand any of it. You just don't pay attention (or maybe you only care and read if you can add a god-did-it in the middle). You should not be so quick to call anything nonsense if you haven't even read it.

      "I don’t think mutations has anything to do with it."

      Whatever you want to call them, they're still waiting-just-in-case. Changing the names won't change the fact that you're defending what you mocked with additions that are even more mockable.

      "My beliefs about DNA replication errors is that they screw things up,"

      Beliefs shouldn't have anything to do with it. I prefer checking things up. Imagine this: since each human is born with 100-200 mutations not in their parents, if you were right, we would already be extinct.

      "because that is what the disease databases show. (By they way, your explanation about why nobody is tracking and recording beneficial mutations was embarrassing.)"

      That you refuse to follow the logic is what's embarrassing. But, please, show me the hospital records of people getting "treatment" for having beneficial mutations.

      What's pretty much stupid is to think that databases about harmful mutations also record, without any bias, neutral, semi-neutral, and beneficial mutations.

      "Your perception of mutations is based on imaginary scenarios that support your theory, not evidence."

      Don't be silly. Mutation rates have been measured, and now, with DNA sequencing becoming so common, scientists have been reporting mutation rates, confirming previous estimates (like the one in humans). But, if you still doubt my words, all you have to do, actually, is look around. Not every person is identical. This means that a lot of mutations have harmless, even if visible, effects.

      "Nobody ever discovered that natural selection acts on mutations. That is an idea that had to be wormed into the theory when the molecular level stuff came into view."

      Sure. But it has also been very well demonstrated. Whenever there's a selection sweep, we see what we expect. For example, lots of "carried-over" fixed mutations that came with the beneficial one. Studies in breeding crops show the very same, what's called a bottleneck effect. Your ignorance is no measure of scientific progress. Before claiming that kind of crap, you should get better informed. But we both know that you don't really care. Right?

      "You’re ignoring that fact that fish, amphibians, mollusks, insects, spiders, millipedes and crustaceans, isolated in caves all over the world, lose the same traits, and acquire similar enhancements."

      I'm not ignoring anything. I'm telling you that such thing doesn't mean they lost or gained traits by the very same mechanisms as that single species of fish.

      "This does not occur accidentally. There is nothing random about it."

      You cannot possibly know that. You're just assuming out of desperation for god-did-it. Sorry, but imaginary friends remain imaginary regardless of how hard something might be for you to understand.

      "Mutation rates are irrelevant."

      This claim shows that you have no idea what you're talking about. Yet, you're saying so and your lack of understanding don't make it so.

      [me:] “So, what's so hard to understand about those lizards that you think they adapted too quickly?"
      [tx:] "Before I answer that, to what mechanisms do you attribute the adaptations?"

      To natural selection, what did you expect? Did you even try and read my complete answer? Oh, sorry, of course you didn't.

      Delete
    27. Simple answer. Creationists don’t think bacteria evolved into anything else.


      HAHAHAHAHA! I didn't know you were such a comedian. Then what were they "frontloaded" for?

      Delete
    28. Txpiper actually wrote: "Your perception of mutations is based on imaginary scenarios that support your theory, not evidence. Nobody ever discovered that natural selection acts on mutations."

      Jesus tapdancing Christ, where do creos get universal negatives like that one. (And their belief that universal negs are so easily provable.) No, scientists have studied this extensively and have *observed* not assumed that NS acts on mutations. You don't know anything about experimentation so you just ASSUME that scientists assume such things. No, scientists observed it in experiments that you have never heard of.

      Lenski's LTEE experiment has already been mentioned. So instead I'll give another. What do you think happens in MA experiments? Natural selection is turned off. So what accumulates? Mutations. Lots of them.

      And most of them are neutral or deleterious. About 3% are beneficial (at least in bacteria.) Recent experimental results have shown that we've been underestimating, not overestimating, the rates of beneficial mutations.

      These mutations pile up if NS is turned off. (Do you know how they do it?) When NS is turned back on, the beneficial mutations are amplified and the deleterious ones are mostly selected out.

      Now suppose creationists were right about pre-programmed "adaption", that is, front-loaded evolution based on invisible, esoteric information that creationists won't define and can't compute.

      If beneficial adaptions were "frontloaded" into bacteria, then, in MA experiments, when NS is turned off, most if not all changes (call them "adaptations" if you like) would be beneficial. That's not what we observe. When NS is off, most changes are neutral or deleterious. So there is no front-loading, no pre-programmed adaptation. When NS is turned back on, the beneficial mutations amplify and the deleterious are mostly selected out.

      Delete
    29. Incredibly (or not), 11 months ago (Feb. 2016), Txpiper and the rest of us had this same argument about beneficial mutations in this same forum. I proved Tx wrong by citing experiments that measured rates of beneficial mutations, and gave Tx some links to read. He didn't, he's just back repeating the same false assertions.

      Here's part of a review that 11 months ago, I suggested Txpiper read, but he didn't.

      Kassen and Bataillon (2006) [5] took a wild-type Pseudomonas flourescens bacterium, and exposed it to an antibiotic. They obtained over 600 antibiotic-resistant strains, with an estimated frequency of 2.4 x 10-9 beneficial mutations per cell division. That seems like a tiny number, yet it was adequate to drive the evolution of fitter bacteria. These antibiotic-resistant strains were much fitter in the new environment than the parent wild-type bacteria, which could not survive at all in the presence of the antibiotic. Interestingly, even in the absence of antibiotic, at least 2.7% of the mutants were superior to the wild-type. This is just one of the examples we have mentioned where mutant organisms can be superior to the parent in both the new environment and in the original environment.

      This Kassen and Bataillon study was not available when Sanford wrote Genetic Entropy. Neither were studies by Perfeito et al. [37] which found that 1 out of every 150 mutations were beneficial in small populations of E. coli, or by Joseph and Hall [38] who found 13% of the mutations in yeast were beneficial.


      "Letters to a Creationist" reviews literature on beneficial mutation rates

      Some more "Letters to a Creationist" on beneficial mutation rates

      Delete
    30. photosynthesis,

      “I mentioned evidence…”

      Honestly, I couldn’t find it. Perhaps we use different definitions. Here’s what you said:

      “As a mixture of random events combined with the nature of chemical and physical phenomena that resulted in metabolisms energized by chemical/sun energy, and the gathering of catalysts and information carrying molecules, perhaps some molecules that did both (catalysis and information carrying), and a plethora of events that, in the end, left a genome with a set of 25 genes that are much more co-dependent than they were at the beginning of this beautiful mess.”

      Delete
  2. ALL innovation consists of rearranging things that ALREADY EXIST.

    Once again creationists demonstrate that they are ignorant of how the world works.


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  3. Robert Byers, how can you say: "its the same information just modified"? That is a self-contradiction. If information is changed, then it is new information.
    Fair Witness says "ALL innovation consists of rearranging things that ALREADY EXIST". That is no better. Innovation is based on modification of existing information, and then it is new information.

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    Replies
    1. Jarie
      Hmmm. Its not new created information but the same rearranged.
      So one can say its not new created.
      At a greater or lower level its the same information bits. the arranging is flexible as a option.
      A closed system but fantastic possibilities including triggering mechanisms. biology teaches change comes fast and not slow.
      Biology teaches a glorious ability to change. without evolutionary concepts.
      in fact evolutionary concepts exist because of a rejection of biological ability to rearrange information.
      They make it dull and chancy.

      Delete
    2. Robert,
      You are right that at some level it is the same information. If it is a gene coding amino acids, it consists essentially of the same codons. There are 20 different amino acids. You can say the same about English words. They all consist of the same 26 letters, so it is the same information, just in different sequence.

      You should not listen too much to biology teaching. There is a far too high confidence that selection can do miracles, and that new features can be created in very short time. But you should compare to the time that has passed since most of our features were created. This time is for most features hundreds of millions of years. Even though each feature is first created, and afterwards maintained by selection, the creation time is normally millions of years. Some of our systems are constantly evolving. Our immunity and our olfactory (smell) system evolves very fast. For humans there is typical loss of olfactory genes, but for mice such genes are created in a large tempo, maybe even more than one new gene each one million years. Still each creation can take millions of years, as this processes are active all the time, and a lot of them in parallel.

      Delete
  4. Txpiper.
    Cave fish etc are a good case. It happens everywhere and seems unlikely its from random mutations. in fact the researchers you mention INVOKE another idea. This lingering mutations in a box concept. They need this.
    the mutation already there did not suddenly come. YES they say its selected on but this is not what evolution is said to do.
    I think cave creatures show there is a different mechanism going on.

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  5. photosynthesis
    The cave fish example is making a different mechanism.
    The researchers are saying the mutations are already in the creatures body. Something triggers the mutation to get it to lose eyes etc for cave life.
    This is a correction to usual evolution claims.
    It means there never need be selection on any creatures like this from a chance mutation. they already have it. They just get it selected on after it kicks in.
    I think careful research has shown that another mechanism is changing cave creatures instantly. In fact its probably not a mutation lingering around but another triggering mechanism.
    Just like , i say, in how human colour etc changed upon migrating peoples.
    no deaths are involved.
    Cave creatures changing happens too quick and well for old time evolution concepts.

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    Replies
    1. I think careful research has shown that another mechanism is changing cave creatures instantly. In fact its probably not a mutation lingering around but another triggering mechanism.
      Just like , i say, in how human colour etc changed upon migrating peoples.


      Cool! I, for one, want to hear more about this "careful research" that shows humans instantly changing "colour etc" when emigrating to a new land.

      Delete
    2. Robert and lutesuite,
      There is no need for any special mechanism or any resident mutation to trigger loss of a function. New mutations are constantly threatening to destroy any feature. Once selection is not actively maintaining it, it will soon be degraded. These processes are probably much faster than creation processes. That is quite natural. Just think of how much easier it is to destroy something than to build something.

      Delete
    3. Robert,

      Since I am quite convinced that you're a Poe, I never know if I should answer your stuff.

      Anyway, Evolution is not about mutations happening "suddenly," let alone as if responding to some environmental change.

      Because mutations happen constantly, any species' population is bound to contain genetic variation. Therefore, that natural selection might have something to select from, already there, is not a surprise to anybody, except, perhaps, people who do not understand these concepts all too well, such as yourself.

      Delete
    4. Jarle
      Losing eyes in caves and saying selection just FAILED to maintain them is a unlikely thing as i see it.
      First, all of them lose their eyes. Your idea would mean its chancy only if eyes atrophied. Some species could keep their eyes. however all cave creatures lose ability and even the eye itself.
      I don't think mutations are constantly trying to destroy features in creatures.
      They don't in mankind or matter to our populations. nor even in cave populations.
      I think the loss of features in cave creatures is a clue to biological change.
      There is something else going on.

      Delete
  6. photo. i barely know what a poe is but i'm not.
    Saying mutations are always in storage in creatures and so just waiting to be selected on is too easy to explain things confidently.
    los of features in cave creatures is so common that its a law of biology. nobody escapes. its like its demanding they lose eyes/colour etc etc. I understand they gain greater use of other senses.
    The atrophy in eyes is not giving a advantage to be selected on. its like another mechanism is driving the senses functions.

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    Replies
    1. Hi, Robert. When are you going to provide a citation to the "careful research" that demonstrates that humans "suddenly change colour" when they move to a new environment? I'm really looking forward to hearing more about this astounding scientific discovery!

      Delete
    2. Robert,

      I didn't say that mutations are there in storage. I said that there's always variation within populations, and that such variation can be selected from. The variation is not "storage" is just happenstance. Do you get it now?

      Losing a trait that's no longer useful by genetic drift is very easy. If the trait is not needed, sooner or later a mutation will arise that destroys the trait. Nobody is trying to destroy it, it just happens because it is not selected against. Do you get it now?

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    3. Lutesuite
      A secondary point however we see greast colour differences, based on the envirorments people migrated to, biblical boundaries of timelines, and so its a first and clear conclusion human colours suddenly developed in a exusting population without selection influence.
      nobody watched. its in a gear and doesn't leave that gear unless a threshold is crossed to trigger change again. today there is no reason for triggering.
      Just like human hair at puberty. its from a old triggering event and stays in gear despite being irrelevant now.

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    4. I don't think its easy. its never been shown either by experiment.
      It is so common, constant, probably quick that these marauding mutations are unlikely to be the origin. Indeed why should a mutation destroy a eye? Why would it, a mutation, be frustrated by the use of an eye.? Whether mutations or your variation it still is asking for a sniper to get rid of those eyes, colour etc.
      I suspect something else.

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    5. I really can't understand the points you're trying to make, Robert. Obviously Creation Science is very exalted and difficult subject, beyond my humble level comprehension, and only penetrable to someone possessed of an intellect such as that of yourself.

      Delete
    6. Luresuite
      its just saying human colours were from a triggering mechanism, after the flood, upon migrating peoples who needed help to survive. the bodies needed to adapt.
      whites had to be that way to grasp vitamins etc from the sun and blacks avoid to much sun etc etc.
      yet this was not from selection and deaths of losers but happened instantly

      Delete
  7. Robert
    The problem is you think that selection or some other force shall make any changes. Selection is just deleting bad mutations. Thereby the existing is maintained quite unchanged. But if selection pressure is reduced, as in a cave, when there is no need for vision, then anything can happen, because without selection there is constantly changes happening. And most of them are of the kinds that would be deleterious for animals outside the cave.

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    1. Your still saying mutations are aiming to get rid of eyes in cave creatures.
      I know you just mean chance mutations but who says there is these mutations/ Its a guess. Its a need to explain the loss of eyes in cave creatures.
      If such mutations happen in a few then why should the whole population be effected? Yet always its the norm they have lose use/or actual eyes. An atrophy.
      i think it is a atrophy, like with flightless birds, and unrelated to mutations and selection.
      I think its just disuse after all.
      i think you need to show a selective advantage for a creature who has lost eyes etc by a mutation in order to change large populations.
      You need selection to bring a result otherwise chance more likely would leave eyed creatures then deeeye them in caves.

      Delete
  8. Robert
    You should also look at animals under domestication. They are protected from predators, and thereby they do not need any camouflage color. Darwin did not understand why these animals changed their coloration and size so readily. This was probably because he looked at variation and selection as positively responding to new needs. His variation was Lamarckian use/disuse, and he saw selection as survival of the fittest among these improved variants. If you stop thinking in the way Darwin did, and instead see changing as the normal and constancy as the effect of selection, then it is much easier to understand these matters.

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