Adding information to the genome.

This article at Science Daily describes a research study related to gene duplication: The article describes a study of the genomes of animals relevant to human evolution that specifically looked at gene duplications. They found evidence that there was an increase in the rate of gene duplication leading up to chimps and humans. There's a reference to the journal article from Nature at the end of the article.--Percy

Whether you define evolution as Darwin did (descent with modification and natural selection) or in a more modern way (change in allele frequency over time), Kimura's neutral theory had no impact on either. His work addressed some underlying genetic mechanisms behind one type of evolutionary change, not the basic structure of evolutionary theory.--Percy

Cavediver was just pointing out that you've been ignoring the "at the molecular level" portion of your Kimura quote. Kimura showed that most mutations cause little or no phenotypic change. Obviously that means that the rest of the mutations do cause phenotypic change.It comes up in discussions here over and over again that most mutations don't have much if any detectable effect, and Kimura's research is one way we've come to understand this. But you seem to be misinterpreting his research as showing that mutations cannot cause any phenotypic change.--PercyEdited by Percy, : Typo.

Hi Kaichos Man,Your position is that though the fossil record indicates that some bones in the jaw evolved to become bones in the ear, the mutations and allele remixing that occur during reproduction are insufficient due to low probability to have caused this change. But yoru position is based upon a faulty understanding of how genes control growth and development.Let's say, for the sake of discussion, that you're completely correct that evolution could not have caused this change. You're still completely wrong about two things. First this: Phenotypic change, even extremely significant phenotypic change, is not often caused by simultaneous coordinated mutations. Genes communicate instructions to the developing and growing body by generating proteins that carry "messages." Genetic changes can cause changes to these "messages" that can in turn cause changes in some or all of these three areas:

• The concentration level of the protein.
• The timing of production and delivery of the protein.
• The nature of the protein.

A single point mutation can easily cause a change in just one of these three areas which can in turn cause significant phenotypic change throughout the organism. It is certainly sufficient to minutely change the position and size of a few bones in the jaw.Now on to your second error: Genes are not specifications of position, shape, size and orientation. There is no gene or set of genes saying that the malleus is this long, this wide and that high with this shape, and that it is positioned at these (x,y,z) coordinates. The malleus, like all structures of organisms, is the result of the timing and concentrations of proteins and raw materials acting together in a complex dance of chemical reactions. Proteins are not carriers of messages like, "You have to move 3 centimeters to the left and grow a little spur at the bottom," and so there are no genes generating proteins to carry these messages that don't exist.There are a number of genetically based hearing impairment problems, many caused by a single mutation, that are responsible for morphological changes ranging from the subtle to the profound. Here's a picture I found at Wikipedia of someone with Waardenburg syndrome. It is usually caused by a single mutation in one of a set of related genes, and it causes widespread morphological changes such as widespread eyes, premature graying of the hair, and significant hearing impairment: There must be many mutations and genetic variations affecting hearing, but ones that don't cause significant problems don't get studied or even noticed. Our bedroom is on the second floor, so is it some genetic difference that allows me to be kept awake by a water drip in the basement while my wife sleeps blissfully on? Did genes cause my malleus to be just a millimeter better positioned, or my stapes to be tapered in just the exact best way? Was it just normal developmental variation? Could be, but we'll never know. The point is that, even just a single point mutation can cause changes ranging from the non-existent to the subtle to the dramatic. A coordinated set of simultaneous mutations, though not impossible, is neither required, nor likely, nor thought to occur to any significant degree.--Percy

No, of course not. I was responding to the errors in your position regarding how phenotypic change occurs through mutations and allele remixing, not making an argument about cynodonts.You mistakenly believe that each tiny little incremental change, say moving three tiny bones of the jaw by a millimeter, requires a coordinated set of simultaneous mutations. It doesn't. A single mutation can easily accomplish that much change and even far more. We see evidence of it all the time.What you need to do is examine your position in light of the fact that your supporting argument of coordinated simultaneous mutations with its associated extremely low probability is not the way anyone within biology thinks evolutionary change occurs. You can argue till the cows come home that this scenario is very unlikely, and all we can do is agree with you. That's why it isn't a scenario given any serious consideration by biologists.In other words, even if evolution is wrong, one of the things it can't possibly be wrong about is that evolutionary change occurs through multiple simultaneous coordinated mutations because that isn't a proposition that evolution accepts. It therefore makes no sense for you to offer this proposition as a reason why evolution is wrong.Or to beat this dead horse even more, it would make as much sense to argue that Christianity is wrong because Jesus didn't really spin straw into gold.You continue to make the same fundamental mistake of mustering complaints against evolution about things it doesn't say. If evolution is wrong then it can only be wrong about things it actually says, not about things you mistakenly think it says.--Percy

Hi Kaichos Man,Your concluding question is answered by your opening quote. You end asking: And you began with the answer when you quoted me saying: You're working so hard at not understanding evolution that in just the last couple posts alone you thought I was arguing both for hopeful monsters caused by genetic changes, and for significant phenotypic changes with no genetic basis at all.I'm not really aware of any evolutionists here who understand evolution so poorly that they would argue for either one. Whenever you think an evolutionist is arguing counter to how evolution works then I think you can safely assume you're misinterpreting him.When I say that there are no genes specifying the position, shape, size and orientation of morphological structures like the bones of the inner ear I do not mean that genes are not the controlling elements. I just mean that the way they exercise control is not by explicit specification of parameters like these. In other words and for example, there is no gene with the x-coordinate of the malleus bone.Genes produce proteins that go everywhere throughout the body driving a complex dance of chemical reactions that can result in widespread change and development. In all likelihood there is no mutation that would move just the malleus bone one millimeter during development while leaving the incus and stapes in place. Whatever proteins or complex of proteins that drive their position will likely affect all of them at the same time, and other things as well. That's why there is no requirement for a coordinated set of simultaneous mutations.--Percy

Nothing does. There is no such thing as parameters for position, shape, size and orientation in the genes. Since these parameters don't exist, they aren't specified.When scientists first began studying ant colonies they believed that there had to be some central control. They didn't began making progress on ant behavior until they finally accepted that there wasn't any central control, that each ant was an autonomous unit responding to external stimuli.You're not going to make any progress on understanding how genes are expressed until you finally accept that there isn't any specification of specific parameters.Genes produce proteins that travel throughout the body driving growth and metabolism through a complex dance of chemical reactions. There is no gene and therefore no protein that specifies the x-coordinate of the malleus bone. There's only proteins working in concert to drive chemical reactions that result in certain outcomes. A single mutation that changes a single protein level or timing of delivery or modifying it slightly will affect growth and development of many things at the same time.--Percy

This is a public thread, not a private chat room with just you and me. Everyone can read what everyone says, and so, for example, I saw what you said in response to NosyNed's recipe analogy: "Yes, that seems to be what Percy's getting at."Clearly you played dumb with me, but then you forgot to maintain the ruse in reply to NosyNed. So given that you really did understand what I meant in Message 114, why don't you try again?--Percy

Ignoring your errors concerning the history of genetics, your argument seems to be that future discoveries will prove you right, a sort of, "I am too right and someday you'll see," type of argument.Is there any evidence currently in hand supporting what you believe? Or do you reach all your conclusions using information you don't have?--Percy

Normally I don't demur on requests like this, but I've explained this several times in this very thread, and so have others. I think you've convinced me that this isn't an act.--Percy

The Kimura quote, the Dawkins weasel program, and the means of genetic control over development and metabolism are three examples where you've repeated the same errors over and over again. We're still explaining the same things to you now as a month ago. Disagreeing with our explanations is fine, but there seems to be no hint of comprehension because you continue to repeat the exact same errors with no discernible modification.Debates aren't won by failing to be convinced through a campaign of uncomprehension. They're won by grasping your opponents arguments and composing effective rebuttals.--Percy

Hi LucyTheApe,Science means having evidence for what you believe. Religion means having faith for what you believe. In this thread we're talking about what the evidence says about how information is added to the genome.--Percy

A good topic for another thread.--Percy

Reality *is* an information system. For example, every ray of sunshine striking a leaf is a transmission of information from the sun to the leaf. I'm talking about Shannon information, of course.I am already aware of your misimpression that Shannon information requires intelligence from the Evolving New Information thread, so there's no need for you to go over this again.--Percy

Hi Kaichos Man, Wounded King's reply in Message 161 pretty much sums it up, and here's a specific example of what we're talking about: And you never will get an answer to that specific question, because neither I nor Coyote nor anyone else on the evolution side thinks there are two different methods of evolution, one that changes the genome and some other one that changes the phenotype. Barring environmental and random developmental influences, the genes control the phenotype.What's baffling is that you keep asking this question no matter how many times we keep explaining to you that there aren't two different mechanisms at work. Rather than just repeating your original question, why don't you ask questions that are responses to and are informed by the explanations? If you ask a question and receive an explanation you don't understand, repeating the question doesn't tell us anything about what you didn't understand.Experience tells us that once you find yourself explaining how to debate or how to think or how to problem solve that the situation is already hopeless, though this isn't invariably true. You don't have to agree with our explanations, but you do have to understand them, or at least work toward understanding them.--PercyEdited by Percy, : Fix member name.Edited by Percy, : Grammar.