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If God's word is true, science will show it to be true.

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ORIGINAL: drmark

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If God's word is true, science will show it to be true.

Perhaps better phrased: Since God's Word is true, true science can and will never contradict Scripture.

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Usually one requires a scientific theory to predict phenomena that it claims to address. For example, germ theory makes no predictions about the kinds of microorganisms we will find other than that we will find none that spontaneously generate. So it is not ‘weak’ because it make no such predictions.

ID doesn’t predict what sort of organisms we will find in terms of specific types because ID originated organisms aren’t dependent on the ordinary limits of nature in terms of organization and complexity.

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Again, you seem to think that common descent proves that evolutionary mechanisms work – it doesn’t. If evolution doesn’t work, and common descent doesn’t demonstrate that it works, then all the evidence for common descent in the world doesn’t make the designer of life out to be deceitful. It’s that simple.

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I think you are putting a bit to much stock in what was an April fools joke both by BBC and myself. If the penguins could fly as depicted in the video, they not only would revise my understanding of how life changes, but also our primary understanding of physics.

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Well, not just me, but as genetics is at the heart of biological change, you should be fairly familiar with it (or at least confident of your own knowledge) before you go about debating the subject at all.

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While I agree that not making correct predictions in a certain area isn’t always a weakness of a theory, that generally depends on there not being any other theory which does. So for the example you gave with germ theory, while it can’t predict what specific types of germs will exist, the reason that isn’t a weakness is because there’s no other theory that can, either. If there were a theory that did, it would have an advantage over germ theory in this respect.

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Since this was your response to a line of evidence for UCD, it sounds like what you’re saying is that you don’t actually doubt UCD—what you doubt is just that natural selection acting on random mutations is sufficient to cause the changes associated with UCD. Is that right?

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So in other words, is what you’re saying that you never really found that video convincing at all? When you said you did, that was just your own joke you were playing on the rest of us? I’d sort of suspected that was the case, since it seemed kind of unlike you to be convinced of evolution so easily.

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Can you please answer the two questions I asked you in my last reply to you? One was why confirmed predictions made by the theory that birds are descended from dinosaurs were off-topic by your standards, when Betta challenged me to provide evidence for that, yet whether the feathers preserved in amber were “proto-feathers” was relevant enough for you to bring up.

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And my other question was, what was your problem with my response to your question about whether I was just interested in “winning points”, in which I answered your off-topic question with an off-topic reply? Was it that I went into too much detail, or what?

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ORIGINAL: Agahnim

Since this was your response to a line of evidence for UCD, it sounds like what you’re saying is that you don’t actually doubt UCD—what you doubt is just that natural selection acting on random mutations is sufficient to cause the changes associated with UCD. Is that right?

If it is, there’s a point I’d like to make related to this, but I’d like to make sure I understand your opinion about it first.

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And DanJames: It’s going to take some time for me to find the answer to your question about photosynthesis, but I’ll do my best. In the meantime, if you manage to find the full text of the article about drug resistance in HIV, I’d appreciate you posting it so both Jhud and I can see it.

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Didn’t you bring up the ‘proto-feathers’? I simply didn’t want to have to separate conversations, one about ‘proto-feathers’ which is obviously relevant to a bird thread, and one about whether predictions of ID, which really has nothing to do with a bird thread.

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Dude, that sentence is too convoluted for me to parse.

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ORIGINAL: DanJames
I'll try to find a way to pose the question to my professor without looking like a Creationist sympathizer and maybe I'll post it as a new thread.

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ORIGINAL: Agahnim
We can discuss the rest of what we’re debating after you’ve answered these questions.

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All right, I’ll explain it again:

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ORIGINAL: BVZ

Natural selection works on ANY mutation that has an effect on the phenotype. When taking this into consideration, why separate mutations in regulatory genes, and mutations that are not?

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ORIGINAL: DanJames

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ORIGINAL: BVZ

Natural selection works on ANY mutation that has an effect on the phenotype. When taking this into consideration, why separate mutations in regulatory genes, and mutations that are not?

I'll test my understanding, and Jhud can correct me where I mess up. If the only change to the organism is the way that the genes are regulated, then that would mean that no new information was added.

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Clumping the changes that were seen into the term "evolution" gives the thought in the mind of the reader that a new and novel characteristic has been displayed, but in reality, a capability that was already present, though dormant, is simply being expressed.

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This is a strong indication that the organism was designed because all of the information was already present in the organism. It simply wasn't being expressed until there was a stressful situation to cause it to come to the surface through changes in regulatory genes.

My question is, are the changes to the regulatory genes mutations in the way that we normally think of mutations.

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ORIGINAL: BVZ

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ORIGINAL: DanJames

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ORIGINAL: BVZ

Natural selection works on ANY mutation that has an effect on the phenotype. When taking this into consideration, why separate mutations in regulatory genes, and mutations that are not?

I'll test my understanding, and Jhud can correct me where I mess up. If the only change to the organism is the way that the genes are regulated, then that would mean that no new information was added.

Agreed. If ALL in the phenotype are ONLY the result of changes in regulating genes, then what you say would be true.

But the HIV example shows that this condition is not met, so the point is moot.

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Even though the goalposts have been reached (despite them being moved), I think that Juhd did not manage to move them at all, since the two positions seem equivalent to me.

So, I ask again: Why differentiate between mutations in regulatory genes and mutations in genes being regulated and the rest?

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This is very important in this particular discussion. The reason for this is clear when you examine the OP.

Juhd asked for something. He got that something, but then moved the goalpost.

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ORIGINAL: Jhud

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This is very important in this particular discussion. The reason for this is clear when you examine the OP.

Juhd asked for something. He got that something, but then moved the goalpost.

Actually, I was reserving judgement until we knew more about the nature of the change; perhaps you could enlighten us since you seem confident of the how the mutation effected the change. Perhaps you can give us the details?

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If the only change to the organism is the way that the genes are regulated, then that would mean that no new information was added. Clumping the changes that were seen into the term "evolution" gives the thought in the mind of the reader that a new and novel characteristic has been displayed, but in reality, a capability that was already present, though dormant, is simply being expressed. This is a strong indication that the organism was designed because all of the information was already present in the organism. It simply wasn't being expressed until there was a stressful situation to cause it to come to the surface through changes in regulatory genes.

My question is, are the changes to the regulatory genes mutations in the way that we normally think of mutations.

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One note about IDists with regard to mutations.

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ORIGINAL: Jhud

And that is why I would like the details about how the HIV virus is developing resistance; I suspect it reflects a simple mutation which simply disallows a protein from doing what it did before, and not a novel capability in response to the antiviral medications.

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So, regulation of genes is a lot like conventional mutations? Duplication for amplification and deletion for inhibition?

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I ordered the full text. Give me time, man. The interlibrary loan program can take a day or forever and a day.

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ORIGINAL: Jhud

Indeed, the article briefly acknowledges that the mechanisms that actually caused the changes are at this point unknown:

But Dr. Velicer has no idea at the moment how the mutation brought about the remarkable transformation in behavior. The mutated segment of DNA actually lies near, but not inside, a gene. It is possible that proteins latch on to this region and switch the nearby gene on or off. But no one actually knows what the gene normally does.

Mutations like this one, Dr. Velicer said, “make for a much more complicated story.” It is a story he and other scientists are looking forward to revealing.

So to simply place them under the rubric of ‘evolution’ or claim they contradict Behe is premature at best, somewhat disingenuous at worst.

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Living organisms have the capacity to adapt to changing environments without the need to rely on mutations, which are infrequent and thereby slow, to be incorporated into a population in a given environment. In the case of the efflux of toxic compounds, physiological adaptation of a cell to a given substance in a given environment begins with an event that takes place at or within the cell envelope and results in a sensor type of stress response. This eventually results in genetic activity that encodes for additional units of that same efflux pump that extrude a broad range of substrates. The addition of more efflux pumps into the cell envelope increases the survival of the organism.

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Genes encoding molecular chaperones and ATP-dependent proteases, key components of the cytoplasmic stress response, exhibit relatively little expression change; whereas genes with periplasmic functions exhibit significant expression changes suggesting a key role for the extracytoplasmic stress response in the adaptation to high temperature. Following acclimation at 41.5°C, two of the three lines exhibited significantly improved survival at 50°C, indicating changes in inducible thermotolerance. Thus evolution at high temperature led to significant changes at the molecular level in heat-inducible gene expression and at the organismal level in inducible thermotolerance and fitness.

So I would say that no, this isn’t indicative of the evolutionary change one should expect if neo-Darwinism is true.

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So I would say that while the NYTs article presents intriguing possibilities, on closer inspection it provides little support for Neo-Darwinism. Indeed, it doesn't even proffer that any of the organisms speciated, much less followed unique evolutionary paths.

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ORIGINAL: Jhud
In terms of gene regulation, a mutation like a gene duplication can indeed affect the way a gene is expressed (and incidentally that is primarily what gene regulation does; changes the product of a gene in some way), often increasing the expression of something that the gene produces.

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That being said, the cell has built into it many regulators, some of which are in the structure of the DNA itself, some of which is a product of transcription by RNAs, and some of which are the product of proteins in the cell itself.

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In fact, it can be applied to presumed examples of evolution cited around here recently, namely the changes that occurred in the ‘domestication’ of foxes in Russia. Many of the changes there are thought to be the result of the regulation of the development of characteristics of typically mature foxes; in short the foxes retain those aspects of immature foxes – docility, playfulness, larger heads in comparison to there bodies, etc. It a regulation to the development of the foxes in response to the selection factors – but it isn’t the development of novel structures and capabilities.

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New regulatory processes are being discovered and described. Many phenomena that were previously thought to be classic cases of evolution are now known to be the product of such processes; antibiotic resistance, the size and thickness of Galapagos finch beaks, the patterning in butterfly wings, etc.

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Another distinction is that evolution is typically seen as an arms race; organisms competing for survival develop increasingly sophisticated structures to deal with those forces that would eliminate them.

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Behe systematically laid out the case that this is not what we actually observe; instead we see ‘trench warfare’ where organisms will employ either extant capabilities in novel ways, or even diminish capabilities in an all out attempt to deal with obstacles to survival.

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And that is why I would like the details about how the HIV virus is developing resistance; I suspect it reflects a simple mutation which simply disallows a protein from doing what it did before, and not a novel capability in response to the antiviral medications.

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I am not sure what the objection is to placing this change under the rubric of evolution. The mutation is documented. The transformation in behaviour is documented. The dispersion of the mutation and the transformation through (part of) the bacterial population is documented and the successful establishment of the new behaviour is documented.

Looks like all the classical necessities of evolution are there.

Yes, there are some matters not yet understood. How does the mutation relate to the transformation of behavior? Since the mutated segment is not part of the gene, is it a regulatory mechanism rather than the gene proper that is directly affected? What is the function of this gene in an unmutated environment?

However, even without answers to these questions, we can see two essentials of evolution: 1. a change in DNA triggers a change in the behavior of a gene, if not directly, then indirectly through some form of regulation or other mechanism. 2. This change is dispersed through the population in a manner consistent with positive selection and contributes to the ongoing survival of the population.

Sounds like evolution to me.

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Sounds like evolution to me.

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How is this not evolution?

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That sounds to me like pseudo-criteria.

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I don't understand why this is referred to as a "presumed" example of evolution.

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But that is still evolution isn't it?

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ORIGINAL: drmark
Do you understand the difference between neo-Darwinian evolution and adaptation, gluadys?