A De Novo Gene: Unlikely and Very Unlikely

_{Cornelius Hunter

December 9, 2009

Intelligent Design}

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If you scramble about 90% of a protein sequence—randomly replacing amino acids with different ones—would the protein still work? That is what evolutionists are implying in order to make sense of their theory. The problem is that evolution’s explanations for de novo genes are unlikely and very unlikely. In the case of the T-urf13 de novo gene, the two choices seem to be (i) a one in ten million shot that protein coding sequences just happened to be lying around waiting for use or (ii) only about 10% of the T-urf13 sequence really matters and you can scramble the rest with no effect. Read more

Comments

When there is a trail, the designer "guides" it. When there isn't a trail, the designer also guides it (or more likely, we do not have a complete accounting of evidence). That's interesting. It is easy to measure sequencing data from one generation to the next. Why not look for evidence of a severe mutational discontinuity between generations? Do you have an example of one that's been observed?olin_{December 10, 2009
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"My view: there are actually no possible observations that would decide this, because the ‘non-naturalistic’ (what is that exactly anyway?) is not empirically observable in the first place. Ergo, ID is a metaphysical interpretation of our empirically observable reality." Nonsense. You interestingly assume that there would not be any naturalistic evidence for protein formation which is revealing. But as an ID supporter I would expect to find some and perhaps several. Naturalistic process leave a trail and that is how much of science is practiced, searching for these trails. Much of astronomy and cosmology is based on these trails such as red shifts, luminosity, super novas, parallax angles, movements of light and solar bodies. Geology leaves trails such as mid ocean ridges, changes in magnetic orientation, age of rocks etc. Biology should leave similar trails. When they don't is when people should step up and take notice. Species devolved/evolved from a common ancestor should leave a trail of all the changes that happened over time, including gene formation. If such a trail is not present then what could be the explanation since naturalistic process don't allow for poofing. Dare I say the non metaphysical, scientific answer would be the possibility of intelligent meddling in the process. The metaphysical answer would be to a priori deny the existence of an intelligence. So ID is the non metaphysical approach to science while the current academy is deeply entrenched in limiting metaphysical paradigm to the practice of science.jerry_{December 10, 2009
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"i see you are an advocate of good science. So am I. I see a good deal of very good science being done all the time, they even get Nobel prices. Just tell me, who are doing the good science these days, ID proponents or the despised mainstream scientists?" Why does there have to be a difference. Why can't a particle physicist be an ID advocate? Why can't a evolutionary biologist be an ID advocate? Name the field and tell me why the person working in that field cannot be an ID advocate? There is no reason so the distinction is meaningless.jerry_{December 10, 2009
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What kind of observations would lead one to decide if novel gene development took place via naturalistic means or not? This is a serious question, I think this is the most crucial point in the debate if ID is science or not. My view: there are actually no possible observations that would decide this, because the 'non-naturalistic' (what is that exactly anyway?) is not empirically observable in the first place. Ergo, ID is a metaphysical interpretation of our empirically observable reality. fGfaded_Glory_{December 10, 2009
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olin, I still await the positive evidence that T-urf13 evolved.ellijacket_{December 10, 2009
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If you wish to cherry pick my posts, that is fine, but it is not convincing. Newtonian gravity is a red herring: the discussion is about intelligent design and evolution, how organisms develop. I still await the positive evidence that T-urf13 was designed.olin_{December 10, 2009
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jerry:
There are a lot of hurdles naturalistic evolution has to leap before they really can make their case and this is one of them. I am sure we will find more of them and that is good science, not what is practiced today which is making definitive conclusions without any supporting data.
i see you are an advocate of good science. So am I. I see a good deal of very good science being done all the time, they even get Nobel prices. Just tell me, who are doing the good science these days, ID proponents or the despised mainstream scientists?Cabal_{December 10, 2009
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"You may want to have a look at this one:" I am certainly not qualified to evaluate this type of research but have advocating for quite awhile that it is exactly this type of research that will determine one way or the other whether de nove gene development by naturalistic means is a common occurrence or not. This type of analysis has to show positive results a couple thousand times before the naturalistic evolutionists will have a solid case. There are a lot of hurdles naturalistic evolution has to leap before they really can make their case and this is one of them. I am sure we will find more of them and that is good science, not what is practiced today which is making definitive conclusions without any supporting data.jerry_{December 10, 2009
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Jerry
One way to test the de novo theory is to track genes across classes and orders.
You may want to have a look at this one: Heinen TJ, Staubach F, Häming D, Tautz D.(2009): Emergence of a new gene from an intergenic region.Curr Biol 19(18):1527-31
It is generally assumed that new genes would arise by gene duplication mechanisms, because the signals for regulation and ranscript processing would be unlikely to evolve in parallel with a new gene function. We have identified here a transcript in the house mouse (Mus musculus) that has arisen within the past 2.5-3.5 million years in a large intergenic region. The region is present in many mammals, including humans, allowing us to exclude the involvement of gene duplication, transposable elements, or other genome rearrangements, which are typically found for other cases of newly evolved genes. The gene has three exons, shows alternative splicing, and is specifically expressed in postmeiotic cells of the testis. The transcript is restricted to species within the genus Mus and its emergence correlates with indel mutations in the 5' regulatory region of the transcript. A recent selective sweep is associated with the transcript region in M. m. musculus populations. A knockout in the laboratory strain BL6 results in reduced sperm motility and reduced testis weight. Our results show that cryptic signals for transcript regulation and processing exist in intergenic regions and can become the basis for the evolution of a new functional gene.
osteonectin_{December 9, 2009
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Olin-6:
If ID has no idea as to biological mechanism by your own advocates’ admission, how can it be science?
So Newtonian physics was not science because it had no mechanism for gravity?Cornelius Hunter_{December 9, 2009
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I have the same question: Where does ID say genes come from? What story, explanation or mechanism does ID have at all? Did genes just appear? When, and how did you know? How is that not a just-so story? If ID has no idea as to biological mechanism by your own advocates' admission, how can it be science? (There must be a means to come into existence, after all, as life didn't always exist.)olin_{December 9, 2009
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olin, I'm curious exactly where genes came from. Please no just-so stories.ellijacket_{December 9, 2009
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I’m curious if Cornelius Hunter could provide us with the mechanism that he as an intelligent design proponent proposes for this gene...
I don't know that Cornelius is claiming this gene was intelligently designed. What evidence do you have that he is? I certainly don't find any such claim in his article. Also, last time I checked, ID isn't "a mechanistic theory of desiqn." Why do you think it is? Lastly, so what if he has no mechanistic theory of design to offer. Does that make your theory correct? As Elliott Sober writes:
The lazy way to test a hypothesis H is to focus on one of its possible competitors H0, claim that the data refute H0, and then declare that H is the only hypothesis left standing.
An even lazier way to test a hypothesis is to claim that there is no "scientific" alternative to H, and then declare that H is the only hypothesis left standing. Sober:
This is an attractive strategy if you are fond of the hypothesis H but are unable to say what testable predictions H makes.
Mung_{December 9, 2009
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I'm curious if Cornelius Hunter could provide us with the mechanism that he as an intelligent design proponent proposes for this gene, or for that matter, any gene, and how it differs from the perspective of evolutionary biology. When did the designer generate T-urf13 (suddenly, over time, how many years ago, etc.), and what mechanism did the designer do? How do you distinguish this mechanism from the regular mutations and natural selection? Did the gene spontaneously appear in the whole population? After the proposal, I'd be interested in the evidence that the proposal is valid as well.olin_{December 9, 2009
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One way to test the de novo theory is to track genes across classes and orders. Their rise should be visible in like organisms with stubs in some and functioning ones in others if they arose naturally. There should be thousands of genes that different from genera to genera across wide spectrums of organisms. Genomic mapping of these in the near future will enable biologist to see where they could have possibly originated and if there is any naturalistic trace for the genes and the regulatory mechanisms in the various genomes. So in about 20-30 years we will have a good grip on the possible origin or non origin of genes.jerry_{December 9, 2009
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Evolutionists usually say that these resulted from the reuse of existing protein coding genes. For instance, we are able to see in color because the photocells in our retina contain different proteins that are sensitive to different colors of light.
Does this mean that evolutionary theory predicts a "nested hierarchy" of the genes within the genome of each species?Mung_{December 9, 2009
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