Friday, October 21, 2011

Gene Expression Evolution: Your Daily Teleology …

Here is a new paper that claims to show the rate of gene expression evolution in a range of different mammalian species. Of course the paper shows no such thing. What it does show are gene expression rates in extant species. And what they found is that those rates are all over the map. The rates are often similar, but in other cases the rates not only vary between species, they also vary between organs and even chromosomes. As usual, the evolutionists describe the findings using teleological language to cover over what evolution really says:

We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation.

Of course there is no such thing as “selective pressure.” This phrase is commonly used to envision an active process that responds to environmental challenges. If natural selection shapes and designs the species according to need, then it sounds more plausible. In reality, all natural selection does is kill off the bad designs.

Although gene expression evolution in mammals was strongly shaped by purifying selection, …

Translation: The evolutionists found that many cases similar genes have similar expression rates.

we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals.

In other words, the evolutionists also found some similar genes that have significantly different expression rates. So the evolutionists must infer a new kind of evolution. Instead of mutations grinding away which, on rare occasion, provide a slightly better design (in terms of reproduction of course), the new kind of evolution states that the genes and their regulation mechanisms are generally already in place. What changes is their expression rates. So evolution created all these genes and regulation mechanisms, no knowing that it had just created the building blocks for all massive biological complexity. All that was needed was some expression rate changes.

Aside from being unlikely, evolution calls for massive serendipity. As usual, it is presented in teleological terms.

16 comments:

  1. CH: "Of course there is no such thing as “selective pressure.” This phrase is commonly used to envision an active process that responds to environmental challenges. If natural selection shapes and designs the species according to need, then it sounds more plausible. In reality, all natural selection does is kill off the bad designs."

    For years I've wondered if this whole blog was an elaborate Poe. Now we have the answer.


    I think.

    ReplyDelete
  2. "Of course there is no such thing as “selective pressure.” This phrase is commonly used to envision an active process that responds to environmental challenges. If natural selection shapes and designs the species according to need, then it sounds more plausible. In reality, all natural selection does is kill off the bad designs."

    Mind-boggling.

    And how, pray tell, does natural selection do anything at all if there is no such thing as a selection pressure?

    You don't understand the theory of evolution at all, do you?

    ReplyDelete
  3. Natural selection, a serious name for simple passive filter "kills off bad design".

    Pardon, who is a bad designer: nature or God?

    I don't understand this.

    ReplyDelete
  4. Ritchie:

    And how, pray tell, does natural selection do anything at all if there is no such thing as a selection pressure?

    Well when it comes to adaptation it is not clear that natural selection does a great deal. Adaptations often arise in response to environmental challenge. In other words, environmental challenges cause the biological variations to arise. This contradicts evolution’s prediction that these are unlinked. So now even evolutionists are having to devise ideas about how evolution created the ability for populations to respond to such challenges. So now when you have an environmental challenge, it is not selection acting on random change that forms the response, but rather something more analogous to physiological change, where the population undergoes a non random change, biased toward addressing the challenge.

    You don't understand the theory of evolution at all, do you?

    The problems with the concept of “selection pressure” are that it masks the problem of undirected change producing new designs and it misses directed change.

    Undirected change is unlikely to produce new designs, but the concept of “selection pressure” assumes that is what happens. The concept simply assumes that when there is a need, such designs will accidentally be produced, and so will succeed while selection kills off the lower-fitness designs. Sure such designs would succeed, but they don’t just happen to arise luckily. That would be incredibly unlikely.

    In fact, populations adapt because they are equipped, a priori, with the equipment to adapt. Thus they undergo change that addresses the environmental challenge. This is not selection pressure. The concept of “selection pressure” says that the change is random with respect to the challenge.

    The authors say that new designs such as organs arose due to “selection pressure.” Of course this would have occurred many millions of years ago when no one was watching. This is no different than Flew’s Gardener. There is no scientific evidence that this could have occurred, and plenty of scientific evidence that it is unlikely. But it sounds good. The term is an evolutionary euphemism.

    ReplyDelete
  5. CH: The authors say that new designs such as organs arose due to “selection pressure.” Of course this would have occurred many millions of years ago when no one was watching.

    The origin of concrete differences between species is the origin of the knowledge found in the genome, which is used to build each species. As such, what's in question is how that knowledge was created, not merely were it was located before it was place in the genome. In the absence of such an explanation, one could more simply state that organisms "just appeared", complete with the ability to adapt, already present.

    So, how do you explain how the knowledge found in the genome that was created "while no one was looking"?

    CH: This is no different than Flew’s Gardener. There is no scientific evidence that this could have occurred, and plenty of scientific evidence that it is unlikely. But it sounds good. The term is an evolutionary euphemism.

    Evolution falls under a greater umbrella which explains knowledge creation in general. In science, we use conjecture to create theories, test them via observations and discard those with errors. Evolution creates what amounts to "theories" of how to replicate individual genes in a specific environment via genetic variation and tests those "theories" by discarding those with errors via natural selection.

    As such, you might as well have said, "all scientific experiments do is discard theories with errors."

    Of course this analogy is imperfect, otherwise it wouldn't' be an analogy, would it? The key difference is that people can create explanations. Evolution cannot. People can discard a near infinite number of mere possibilities that lack explanations, a priori. However, since it lacks the concept of an explanation, evolution must test every variation.

    Regardless of these differences, both processes still fall under the same explanation of knowledge creation. Neither is "magic."

    Since we seem to be in agreement that the genome contains knowledge, it seems that your objection represents an implicit claim that the genome was created in such a way that makes a theory of how that knowledge was created impossible.

    Would this be an accurate assessment?

    Or perhaps you're claiming that knowledge creation as a whole cannot be explained? For example, how do you explain our relatively recent and rapid increase in the creation of knowledge?

    ReplyDelete
  6. nice blog, i like what u wrote

    ReplyDelete
  7. CH:

    "Adaptations often arise in response to environmental challenge. In other words, environmental challenges cause the biological variations to arise."

    Hang on a moment, I want to be absolutely crystal clear on this: you are saying environmental changes CAUSE biological variations?

    So imagine there is a group of mice living on the banks of the river. If the climate gets wetter, this will actively CAUSE the mice to develop genes which give them adaptations to wetter conditions?

    Do I misrepresent you, or are you actually making this claim? And if you are, what evidence do you have of this? HOW does the environment CAUSE biological adaptations in organisms living within it?

    "Undirected change is unlikely to produce new designs, but the concept of “selection pressure” assumes that is what happens."

    You are massively over-complicating your scientific definitions. Any change in the environment which affects a gene pool's survival chances is a selection pressure. A drought is a selection pressure. A disease is a selection pressure. A new rival species is a selection pressure.

    "In fact, populations adapt because they are equipped, a priori, with the equipment to adapt. Thus they undergo change that addresses the environmental challenge."

    Do they? So there are never any disadvantageous mutations? The previously-mentioned mice living by the river will always adapt in a way which is beneficial to them? Absolutely any mutation which arises will be a mutation which assists them to survive in a wetter environment? Creatures do not throw up mutations which hinder their chances of survival/reproduction?

    ReplyDelete
  8. Ritchie:

    Hang on a moment, I want to be absolutely crystal clear on this: you are saying environmental changes CAUSE biological variations?

    Yes.

    So imagine there is a group of mice living on the banks of the river. If the climate gets wetter, this will actively CAUSE the mice to develop genes which give them adaptations to wetter conditions?

    In principle, yes. (rather than developing genes, adaptations more likely modify genes, or use them differently).

    Do I misrepresent you, or are you actually making this claim? And if you are, what evidence do you have of this?

    Such evidence has been known for the better part of a century, but it has been opposed by evolution. In recent years some evolutionists have recognized they must reckon with it, and try to incorporate it into the theory. So they say evolution created these adaptation mechanisms.

    HOW does the environment CAUSE biological adaptations in organisms living within it?

    Your incredulousness is an example of how evolutionary rationalism is at odds with science. The evidence has been known for the better part of a century, and we learning more all the time.

    Regarding how, the general answer is that organisms generate signals that activate various molecular mechanisms of change and adaptation. You could just as easily be demanding evidence for physiological change. Adaptation is similar, but it can be inherited.

    So there are never any disadvantageous mutations?

    No, I didn’t say that.

    ReplyDelete
  9. CH:

    "Such evidence has been known for the better part of a century, but it has been opposed by evolution. In recent years some evolutionists have recognized they must reckon with it, and try to incorporate it into the theory. So they say evolution created these adaptation mechanisms."

    I was hoping for something a little more concrete here, to be honest. What solid evidence can you point to to show this? What studies demonstrate it?

    "Your incredulousness is an example of how evolutionary rationalism is at odds with science."

    My incredulousness is irrelevant. Science deals in evidence. That is all you need to show.

    "Regarding how, the general answer is that organisms generate signals that activate various molecular mechanisms of change and adaptation."

    Can you give me the big print version with pictures, please?

    "So there are never any disadvantageous mutations?

    No, I didn’t say that."

    True, but you did say there was no such thing as selective pressure! And that organisms adapt because they are directed. So how do you account for disadvantageous mutations? Surely a sign of direction would be that mutation gets it right every time? Otherwise this 'directing force' wouldn't be very good/powerful, would it? The alternative - that mutations are completely blind to whether they are advantageous or not and it is merely that advantageous ones are the ones to survive and propagate while deleterious ones die off - is natural selection.

    ReplyDelete
  10. Ritchie:

    I was hoping for something a little more concrete here, to be honest. What solid evidence can you point to show this? What studies demonstrate it?

    OK, sure. Here is a smattering of items:

    http://www.sciencedaily.com/releases/2011/09/110916152401.htm
    http://www.time.com/time/magazine/article/0,9171,1952313,00.html
    http://www.ncbi.nlm.nih.gov/pubmed/11028992
    http://www.ncbi.nlm.nih.gov/pubmed/16959970
    http://www.jstor.org/pss/10.1086/598822
    http://www.sciencedaily.com/releases/2011/07/110701121627.htm
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2989988/
    http://www.sciencedaily.com/releases/2006/08/060807154715.htm
    http://www.sciencedaily.com/releases/2011/07/110724135553.htm
    http://www.ncbi.nlm.nih.gov/pubmed/11944985
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1276013/
    http://darwins-god.blogspot.com/2010/04/amazing-stickleback.html
    http://darwins-god.blogspot.com/2010/02/hopeful-monsters-endless-list-of.html

    ReplyDelete
  11. CH:

    None of these links (apart from the ones to old posts on your own blog) are saying what you want them to say!

    Epigenetics is not a substitute or alternative for random mutation and natural selection. It merely holds that genetic modifiers may be passed down, along with DNA. But it does not give rise to mutations in the genetic code (these are still random) and nor does it explain how these random mutations are propogated/eliminated in the gene pool (that is still natural selection). Thus it is merely an ADDITIONAL source of adaptation. Like HGT, epigenetics complicates ToE, but it does not by any stretch throw doubt onto it.

    And I must also repeat a question I made earlier - why do you have no trouble accepting the conclusions of these evolutionists? Aren't their methods flawed? Aren't they blinkered by their religious beliefs? If ToE is flawed, then so is genetics, and so is epigenetics. Yet you have no trouble accepting it as fact simply because you (erroneously) think it supports your position...?

    ReplyDelete
  12. Ritchie to Hunter:

    And I must also repeat a question I made earlier - why do you have no trouble accepting the conclusions of these evolutionists?

    That's an issue that has puzzled me, also.

    Yet you have no trouble accepting it as fact simply because you (erroneously) think it supports your position...?

    That looks like a good explanation. Dr Hunter wouldn't reference those sources if he thought otherwise.

    ReplyDelete
  13. CH, "bad designs"???

    I don't think that is an accurate description of what natural selection does. Some members of a species may possess the genetics that make them more fit to reproduce and prosper under specific environmental conditions, while other members would prosper in other conditions. Neither is a "bad design", just different.

    ReplyDelete
  14. Ritchie:

    Epigenetics is not a substitute or alternative for random mutation and natural selection.

    Yes, that certainly is true.

    It merely holds that genetic modifiers may be passed down, along with DNA. But it does not give rise to mutations in the genetic code (these are still random)

    Actually you can also have DNA sequence changes. It is not limited to merely the “modifiers.”

    and nor does it explain how these random mutations are propogated/eliminated in the gene pool (that is still natural selection).

    Well no, random mutations can be propagated in the absence of selection (neutral drift).

    Like HGT, epigenetics complicates ToE, but it does not by any stretch throw doubt onto it.

    This is an example of the robustness of evolutionary theory. Falsified predictions, one after the other, mean nothing to evolutionists. Adaptation occurs rapidly and in response to the environment via complex mechanisms. Not only does this falsify a fundamental prediction of neo Darwinism, evolution doesn’t even explain scientifically how the mechanisms arose.

    And I must also repeat a question I made earlier - why do you have no trouble accepting the conclusions of these evolutionists?

    I don’t accept their conclusions.

    Aren't their methods flawed? Aren't they blinkered by their religious beliefs? If ToE is flawed, then so is genetics, and so is epigenetics.

    No, you are conflating different things. Evolution is not the same as genetics.

    ReplyDelete
  15. Cornelius Hunter: Actually you can also have DNA sequence changes. It is not limited to merely the “modifiers.”

    Epigenetics is defined as changes other than those in genes, otherwise it wouldn't be epi- genetics. Some epigenetic characters can be inherited over generations, but it's not clear if they can become a permanent part of the germ line. Epigenetics can also change the localized mutation rate. Are you referring to something specific?

    Cornelius Hunter: Falsified predictions, one after the other, mean nothing to evolutionists.

    Not all falsifications require discarding an entire theory. If we find out that birds are descended from theropods rather than some other lineage of archosaurs, that no more calls into question common descent, than someone finding out they were adopted means that they weren't born of woman.

    Like all scientific theories, the Theory of Evolution is modified in the light of new evidence. That's what's supposed to happen.

    ReplyDelete
  16. CH:

    "Yes, that certainly is true."

    Well exactly. So Epigenetics doesn't call natural selection into doubt at all, does it?

    "Well no, random mutations can be propagated in the absence of selection (neutral drift)."

    That is true. But this requires the mutations to be beneficially neutral. What about mutations which are not beneficially neutral?

    "This is an example of the robustness of evolutionary theory. Falsified predictions, one after the other, mean nothing to evolutionists."

    No, this is yet another example of you crying 'falsified prediction' at every new discovery biologists make. Unexpected discoveries are not falsified predictions. Added complications are not falsified predictions. It is not ToE which is defended at all costs, it is you who keeps throwing up entirely irrelevant tangental evidence and declaring it a killer blow! You might as well be saying "I had steak and chips for dinner! ToE didn't predict that! Therefore it's wrong! Evolutionists will laugh this off as irrelevant but that is because they are so blind they will never accept their theory is dead."

    If you want to show ToE has feet of clay then you need to come up with some RELEVANT evidence which ACTUALLY shows this - something you have never successfully done.

    "I don’t accept their conclusions."

    But you do! You have just cited their experiments as supporting evidence. But if you are correct and ToE really is fatally flawed, then this evidence crumbles too. Genetics - and epigenetics - is utterly flawed.

    Or, put another way, perhaps there is no such thing as epigenetics. These genetic markers they think they have found were actually just put there by a supernatural agent who intervened miraculously. You believe in things like that, don't you?

    "No, you are conflating different things. Evolution is not the same as genetics."

    No, they are not nearly as seperate as you apparently think.

    If ToE is flawed, then genetics as an entire field is too. If it turns out tomorrow that ToE is not true then we must bin genetics as a field entirely. There would be absolutely no reason why any of it would be true.

    ReplyDelete