Monday, January 04, 2016

Answering two questions from Vincent Torley

Vincent Torley read a post by Jerry Coyne where Jerry wondered if Intelligent Design Creationism was in trouble because the Discovery Institute has lost Bill Dembski and Casey Luskin [Is the Discovery Institute falling apart?].

Torley disagrees, obviously, but he focuses on a couple of the scientific statements in Jerry Coyne's post and comes up with Two quick questions for Professor Coyne.

I hope Professor Coyne won't mind if I answer.

Before answering, let's take note of the fact that Vincent Torley has been convinced by the evidence that most of our genome is junk. I wonder how that will go over in the ID community?

Here's question #1 ...
So my first question is: if (i) Nature contains systems which accomplish a feat (namely, coding for complex structures) in a manner which is far better than what our best computer scientists can do, and (ii) despite diligent searching, scientists have failed to observe any cases in Nature of unguided processes generating a new code from scratch, then why isn’t it reasonable to infer (at least provisionally) that these systems were designed by a super-human Intelligence? You tell me, Professor.
Both of the premises are wrong. I've yet to see any natural system that's as good as what computer scientists can do. Most of the genes that code for complex structures are inefficient and error-prone. Natural systems look like they were designed by a tinkerer who cobbles together odds and ends that just happened to be in reach. They look like they evolved haphazardly. Any intelligent scientist could do better and, in some cases, they have done better by genetically modifying organisms to make them more efficient.

This is an important point. Intelligent Design Creationists never see the big picture so they lack perspective—a fault shared by many non-creationists as well. It's simply not true that complex biological structures are complex because they are very sophisticated and efficient. In many cases, they are complex by accident and it's easy to make better, more simple, systems that can do the same job.

The second premise of Vincent Torley's question is also wrong. We have lots of examples of unguided processes generating new code from scratch. This includes de novo genes. See

Kaessmann, H. (2010) Origins, evolution, and phenotypic impact of new genes. Genome research, 20:1313-1326. [doi: 10.1101/gr.101386.109]

Here's a quotation from the abstract of the Kaessmann review,
Thus, it was shown that novel genes also regularly arose from messenger RNAs of ancestral genes, protein-coding genes metamorphosed into new RNA genes, genomic parasites were coopted as new genes, and that both protein and RNA genes were composed from scratch (i.e., from previously nonfunctional sequences).
This is another case where a little knowledge is a dangerous thing. Vincent Torley and his friends have convinced themselves that the evolution of de novo genes has never been observed. None of them bother to read the scientific literature to see if their stories are correct.

See also:

Carvunis, A.-R., Rolland, T., Wapinski, I., Calderwood, M.A., Yildirim, M.A., Simonis, N., Charloteaux, B., Hidalgo, C.A., Barbette, J., Santhanam, B., Brar, G.A., Weissman, J.S., Regev, A., Thierry-Mieg, N., Cusick, M.E., and Vidal, M. (2012) Proto-genes and de novo gene birth. Nature, 487:370-374. [doi: 10.1038/nature11184]

Long, M., Betran, E., Thornton, K., and Wang, W. (2003) The origin of new genes: glimpses from the young and old. Nat Rev Genet, 4:865-875.

Long, M., VanKuren, N. W., Chen, S., and Vibranovski, M. D. (2013) New gene evolution: little did we know. Annual review of genetics, 47:307. [doi: 10.1146/annurev-genet-111212-133301]

Näsvall, J., Sun, L., Roth, J. R., and Andersson, D. I. (2012) Real-time evolution of new genes by innovation, amplification, and divergence. Science, 338:384-387. [doi: 10.1126/science.1226521 ]

Neme, R., and Tautz, D. (2013) Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. BMC genomics, 14(1), 117. [doi: 10.1186/1471-2164-14-117]

Schlötterer, C. (2015) Genes from scratch–the evolutionary fate of de novo genes. TRENDS in Genetics, 31(4), 215-219. [doi: 10.1016/j.tig.2015.02.007]

Tautz, D., and Domazet-Lošo, T. (2011) The evolutionary origin of orphan genes. Nature Reviews Genetics, 12(10), 692-702. [doi: 10.1038/nrg3053]

Wu, D.-D., Irwin, D.M., and Zhang, Y.-P. (2011) De novo origin of human protein-coding genes. PLoS Genet, 7:e1002379. [doi: 10.1371/journal.pgen.1002379]

Given that both of his "facts" (premises) are wrong, Vincent Torley's question becomes irrelevant. But let's answer it anyway. He asks,
... why isn’t it reasonable to infer (at least provisionally) that these systems were designed by a super-human Intelligence? You tell me, Professor.
It's not reasonable because it raises far more questions than it answers. If Torley's facts were correct (they aren't), it would still be much more reasonable to infer that that new coding information arose by unknown natural processes than to speculate that there are unknown supernatural beings who could have done the job.

In other words, "we don't know" is still a more reasonable answer than "gods did it" because by inferring gods you just shift the questions to another level, e.g. who made the gods?

The problem here is that Torley's question does not reflect his actual logic. Creationists begin with the "knowledge" that omnipotent supernatural beings actually exist and that he/she/it/them is/are responsible for creating us and the universe. That makes it much more "reasonable"—in their eyes— to infer that gaps in our scientific knowledge can be filled by their gods.

Vincent Torley's second question is no better,
So my second question for you is: will you concede that neo-Darwinism is unable to account for the origin of the epigenetic information needed to create novel body-plans (which must have occurred before the Cambrian explosion took place), and that natural selection therefore doesn’t explain all cases of apparent design in nature, falsifying your previous claim that it’s the “only game in town” for producing adaptations?

Incidentally, are you aware of any good evidence that epigenetic information is not divine in origin? If so, please elaborate.
Torley is using the broad definition of epigenetics: "the study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself." That includes things like the regulation of the lac operon in E. coli and developmental regulation of transcription factor genes in Drosophila melanogaster. It also includes regulatory mechanisms that involve methylation of DNA and modification of histones during the transition from 'open' to 'closed' chromatin configurations.

We know how the transcription of genes is regulated by transcription factors and there's nothing mysterious going on. It's easy to envisage how such regulatory mechanisms can arise by purely naturalistic means. There's nothing about our understanding of evolution, biochemistry, genetics, and molecular biology that precludes the origin of such epigenetic information. It's silly to say that "neo-Darwinism" (whatever that is) is unable to account for the evolution of gene regulation by repressors and activators [see The Extraordinary Human Epigenome].

We know that novel body plans can be created by simply altering the expression of pre-existing genes. That's the main discovery of developmental biology in the 70s and 80s. There's no mystery there, either.

Same with modifications of DNA and histones in eukaryotes. These modifications are associated with a mode of control and regulation at the level of chromatin structure. Much of the eukaryotic genome is effectively silenced by a tight association with nucleosomes (histones) in a three-dimensional structure called the 30nm chromatin fiber (and higher order structures).

The 30nm fiber exists in dynamic equilibrium with an open conformation called the 'beads-on-a-string' structure (see the electron microscope structures below). Transcription factors can recognize and bind to their binding sites in the open conformation but not the closed one. If the transcription factor binds to a functional promoter region then the adjacent gene will be transcribed.

As genomes expanded during the evolution of eukaryotes, it became selectively advantageous to shut down much of the genome that wasn't immediately required for viability. But the gradual evolution of more and more tightly binding nucleosome structures came at the cost of accidentally turning off genes that were needed. Thus, mechanisms for maintaining an open conformation around active genes evolved simultaneously with the evolution of heterochromatin and 'closed' structures. Those mechanisms involved modifying the histones bound to active genes so that they could not associate with each other to form the 30nm chromatin fiber.

The modifications vary from species to species but many of them involve attaching acetyl groups to the ends of individual histone proteins in the nucleosome. When the open configuration needs to revert to the closed configuration the acetyl groups are removed by deacetylation. Thus, the opening and closing of chromatin domains can be triggered by the binding of transcription factors near a promoter.

This mode of regulation at the level of chromatin structure can also be controlled by methylation of DNA at cytosine residues. When transcription of a gene is required, the sequences in the promoter region can be methylated at certain sites and this inhibits formation of the closed structure. Methylation is also reversible so that when the gene is turned off the methyl groups are removed.

Some genes will need to be active for many cell generations so a given promoter region will contain modified histones and methylated DNA for a long time. Some genes will transiently revert to the closed configuration only to be re-activated. (Everything in biology exists in a transient state of dynamic equilibrium.) Thus, epigenetic modifications are 'inherited' from generation to generation.

If the genes are active in germ cells then the activation can be passed to another generation in multicellular species. This is not conceptually different from E. coli cells that "inherit" active transcription of the lac operon or repression of prophage genes. None of those discoveries from the 60s and 70s caused anyone to question our understanding of evolution just like none of the discoveries of other levels of control ( = more epigenetics) in the 80s caused any concern.

The only people who get excited about the evolutionary implications of epigenetics are biologists who don't understand biochemistry, genetics, evolution, and molecular biology and creationists who don't understand any of those subjects and who are looking for god in the gaps of their knowledge.

As for the claim that natural selection can account for all cases of apparent design in nature, that's an exaggeration promoted by Jerry Coyne. It's not far from the truth but there may be non-selective processes that play an important role in adaptation.

But that's not what Vincent Torley is referring to. He's not just questioning whether natural selection can explain all cases of apparent design but whether any kind of evolution can explain it. Torley thinks he's proved the negative; namely, that epigenetic phenomena cannot be explained by naturalistic means. Therefore, gods must have done it.

His claim is absurd. His questions are absurd.


Image credit for histones & chromatin figures: Moran, L.A., Horton, H.R., Scrimgeour, K.G., and Perry, M.D. (2012) Principles of Biochemistry 5th ed., Pearson Education Inc. pages 590 and 591 © Pearson/Prentice Hall

63 comments :

  1. Incidentally, are you aware of any good evidence that epigenetic information is not divine in origin?

    Isn't Torley supposed to be a trained philosopher? What kind of philosopher would ask such an asinine question?

    Thanks for the great summary of epigenetics, regardless. I don't know if Torley will appreciate it, but I certainly do.

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    1. Yeah, I choked on that too. Torley got a PhD in philosophy and I expect better from him than just him flipping the burden of evidence.

      As Carl Sagan used to say: extraordinary claims require extraordinary evidence. We've never seen divine agents caused epigenetic changes, or do anything at all.

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    2. Torley says further down in this comment section that he just meant that as a "cheeky comment" in reply to Coyne's suggestion that the "intelligent designer" of which Torley speaks is a god. The nerve of Coyne, making such a presumption!

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  2. Hi Professor Moran,

    Thank you very much for responding to my post. Just a couple of quick points:

    1. You write: "I've yet to see any natural system that's as good as what computer scientists can do. Most of the genes that code for complex structures are inefficient and error-prone." Regarding our DNA, zoology Professor Matthew Cobb writes: "On a final note, in some cases, within this amazing noise, there are also astonishing examples of complexity which do indeed appear to be the result of optimisation – and they would boggle the mind of anyone, not just a cocky computer scientist in a hat." Whom am I to believe?

    You write: "Natural systems look like they were designed by a tinkerer who cobbles together odds and ends that just happened to be in reach."

    Creationist botanist Alex Williams writes: "DNA information is overlapping-multi-layered and multi-dimensional; it reads both backwards and forwards... No human engineer has ever even imagined, let alone designed an information storage device anything like it...

    * There is no ‘beads on a string’ linear arrangement of genes, but rather an interleaved structure of overlapping segments, with typically five, seven or more transcripts coming from just one segment of code.
    * Not just one strand, but both strands (sense and antisense) of the DNA are fully transcribed.
    * Transcription proceeds not just one way but both backwards and forwards...
    * There is not just one transcription triggering (switching) system for each region, but many." (“Astonishing Complexity of DNA Demolishes Neo-Darwinism.” Journal of Creation, 21(3), 2007. Note: I don't agree with Williams' young-earth arguments based on Haldane's dilemma; nor do I share his enthusiasm for ENCODE. However, I assume that his description of DNA coding is accurate: he is, after all, a botanist.)

    And Bill Gates adds: "Human DNA is like a computer program but far, far more advanced than any software ever created." (The Road Ahead, Penguin: London, Revised Edition, 1996 p. 228.)

    Again I ask: whom am I supposed to believe?

    More to follow...

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    1. Vincent Torley asks, "Whom am I to believe?"

      Me.

      Creationist botanist Alex Williams writes: "DNA information is overlapping-multi-layered and multi-dimensional; it reads both backwards and forwards... No human engineer has ever even imagined, let alone designed an information storage device anything like it...

      Bully for him. He is wrong.

      * There is no ‘beads on a string’ linear arrangement of genes, but rather an interleaved structure of overlapping segments, with typically five, seven or more transcripts coming from just one segment of code.

      He's wrong about that as well.

      * Not just one strand, but both strands (sense and antisense) of the DNA are fully transcribed.

      That's not true. And even if a large proportion of the genome is transcribed it doesn't mean that it's functional.

      * Transcription proceeds not just one way but both backwards and forwards...

      Backwards and forwards with respect to what?

      * There is not just one transcription triggering (switching) system for each region, but many." (“Astonishing Complexity of DNA Demolishes Neo-Darwinism.”

      Some genes, like the lac operon in E. coli, are regulated in multiple ways. I could design a better system in all the cases I'm familiar with.

      And Bill Gates adds: "Human DNA is like a computer program but far, far more advanced than any software ever created." (The Road Ahead, Penguin: London, Revised Edition, 1996 p. 228.)

      Again I ask: whom am I supposed to believe?


      Gee ... that's a tough one. You have to choose between a rich man who builds computers and ran a large company and one who's been teaching this stuff for 40 years and has written several textbooks on the subject.

      Good luck.



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    2. Hi Professor Moran,

      I've just been reading Arthur Hunt's demolition job on Alex Williams' paper at http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?act=ST;f=14;t=6031;st=#entry140101 and I have to concede that Williams makes some scientific howlers. I won't be citing his paper anymore. That's one for the garbage heap.

      Bill Gates, on the other hand, I have to take more seriously. He's not a biologist, but he knows an awful lot about coding, so when he writes that the coding in human DNA is more advanced than any software, I have to ask myself if he's right. And when a Darwinist biologist like Professor Matthew Cobb, after pointing out that at least 85% of our DNA is junk, goes on to add that there are, nevertheless, "astonishing examples of complexity which do indeed appear to be the result of optimisation – and they would boggle the mind of anyone, not just a cocky computer scientist in a hat," then I have to take him very seriously.

      I also have to marvel when I see Dr. Stephen Larson, a neuroscientist, systems biologist and engineer, declare that "life's complex interacting molecular machines" appear to have been "built by an engineer a million times smarter than me" - even though he's a staunch evolutionist
      (see http://www.evolutionnews.org/2015/06/biologist_in_te096761.html ). Very strange.

      I want to get to the bottom of this. What do you think is the point at issue between you and Cobb (or for that matter, Larson)?

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    3. Are you familiar with Orgel's 2nd rule, VJ Torley?

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    4. lutesuite,

      Where's the evidence for it? And cleverer at what, specifically?

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    5. Evidence? You're wanting evidence? I'm sorry, I thought we were just exchanging quotes reflecting the subjective impressions of famous authorities. I must have overlooked where you provided the evidence underlying the statements by Gates and Larson. Perhaps you could point this out for me.

      As for the "cleverer" part, the statement that you, yourself, quoted from Stephen Larson explains this quite nicely.

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    6. Vincent Torley writes,

      And when a Darwinist biologist like Professor Matthew Cobb, after pointing out that at least 85% of our DNA is junk, goes on to add that there are, nevertheless, "astonishing examples of complexity which do indeed appear to be the result of optimisation – and they would boggle the mind of anyone, not just a cocky computer scientist in a hat," then I have to take him very seriously.

      You are quoting from a blog post in November 2015 [DNA: optimised source code?].

      Mathew concludes with ...

      In other words, DNA is even more complicated than Randall imagines – it is historical, messy, undesigned. And when occasionally it is optimised, the degree of complexity is mind-boggling. Biology is not quite impossible, it is just incredibly difficult!

      You are confused about the difference between "complex" and "designed." Just because something is complex does not mean that it is well-designed. Think of the Rube Goldberg metaphor.

      However, I'm pleased that you accept atheist Mathew Cobb as an authority on biology. As you probably know, he is no fan of creationism. You should read his latest book "Life's Greatest Secret" in order to understand the role of information in biology and why we don't need gods to explain evolution.

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    7. Torley,

      DNA transcription could be trivially represented by code using a state machine. This is basic CS.

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    8. It's very odd that Torley is unable to realize that when he attempts to support his position that only intelligent design can produce something as complex as the genetic code, it is fallacious to simply argue: "Look how complex the genetic code is! Only intelligent design can produce something that complex!" You'd think a philosopher would be able to recognize a begged question when he sees it. (OTOH, you'd also expect a doctor to know that keratin is protein, so I guess he and I are both guilty in that regard.)

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    9. Re Larry Moran

      It should also be pointed out that Matthew Cobb sometimes blogs on Jerry Coyne's web site.

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    10. You are confused about the difference between "complex" and "designed." Just because something is complex does not mean that it is well-designed. Think of the Rube Goldberg metaphor.

      Or think of the coastline of the Mississippi (pre-Army Corps of Engineers). Incredibly complex. It would be fabulously difficult for a human to design anything half so complex, with thousands of miles of swerves, turns, twists, and loops, constantly changing.

      Does this mean God must have done it (or Slartibartfast - but no, he did the fjords)?

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  3. Hi Professor Moran,

    Back again.

    2. Regarding de novo genes, I don't hold that they were "made by gods," or even by alien intelligences. I wouldn't call the appearance of a de novo gene a case of coding from scratch, for two reasons.

    I wrote a post on Uncommon Descent in October: http://www.uncommondescent.com/intelligent-design/double-debunking-glenn-williamson-on-human-chimp-dna-similarity-and-genes-unique-to-human-beings/ . In my post, I pointed out that 60 de novo protein coding genes said to be unique to human beings actually have 98% similar counterparts in apes. I wouldn't call a change from 98% similar to 100% identical a case of "coding from scratch." Would you?

    What's more, the abstract of the Kaessmann review freely acknowledges that de novo genes have ancestral genes. That's hardly a case of coding from scratch.

    I'm willing to grant the possibility of unguided processes transforming a code for one kind of structure into a code for another kind of structure. My question, however, concerns the original set of codes that were found in the first living things. Even if we see Nature adapting existing codes, we don't see Nature generating new ones. That was my point.

    Regarding the legitimacy of inferring to an intelligent designer, you reject that inference because it raises more questions than it answers. I reply: even if that's true, so what? The point is that the questions that it raises are secondary questions: we can answer them later on. If you found a monolith on the Moon (like the one in the novel, "2001"), you wouldn't rule out intelligent design simply because it raises more questions than it answers. No; you'd say, "Aliens did it, and we'll figure out the answers to our new questions about the aliens, when and if we meet them." That would be the sensible approach to take.

    Regarding epigenetics, I don't pretend to have any in-depth knowledge of the subject. My argument was based heavily on Sr. Stephen Meyer's book, "Darwin's Doubt," which in turn bases itself on the work of Dr. Jonathan Wells, who is a developmental biologist. I presume he knows what he is talking about when it comes to his own specialty. Wells contends that neo-Darwinian mechanisms are unable to account for the origin of novel animal body plans, such as those that appeared during or shortly before the Cambrian period.

    I'm afraid your technical comments about chromatin and histones went a little over my head, but I noticed that you declared that novel body plans can be created by simply altering the expression of existing genes, whereas Dr. Meyer asserts: "...[B]uilding a new body plan requires more than just genetic information. It requires both genetic and epigenetic information." He thanks Dr. Wells in his acknowledgments, so I presume Wells would endorse what he says. This is an open-and-shut, black-and-white issue. Someone's wrong here. who is it?

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    1. . I wouldn't call a change from 98% similar to 100% identical a case of "coding from scratch." Would you?

      Nope. That's why I gave you all those references so you could see that there are some true examples of genes built from scratch.

      My question, however, concerns the original set of codes that were found in the first living things.

      Then you should have made it clear that you were only referring to the origin of life. This looks a lot like moving the goalposts.

      I reply: even if that's true, so what?

      The goal is to solve the problem, not create more problems.

      Regarding epigenetics, I don't pretend to have any in-depth knowledge of the subject.

      That's not true. Any outside observer would assume that you knew what you were talking about. Otherwise, you would be asking questions to help you understand and not posing challenges that question naturalism and evolution.

      My argument was based heavily on Sr. Stephen Meyer's book, "Darwin's Doubt," which in turn bases itself on the work of Dr. Jonathan Wells, who is a developmental biologist. I presume he knows what he is talking about when it comes to his own specialty.

      You presume wrong. You are (usually) smart enough to know better than to trust the word of an Intelligent Design Creationist without checking the facts for yourself.

      By now you've encountered many instances where your ID friends have been wrong (e.g. junk DNA) so a little more skepticism is in order.

      I'm afraid your technical comments about chromatin and histones went a little over my head, ...

      Then why are you presuming to understand these issues well enough to challenge Jerry Coyne?

      Dr. Meyer asserts: "...[B]uilding a new body plan requires more than just genetic information. It requires both genetic and epigenetic information." He thanks Dr. Wells in his acknowledgments, so I presume Wells would endorse what he says. This is an open-and-shut, black-and-white issue. Someone's wrong here. who is it?

      I think that you know the answer but you're afraid to admit it, even to yourself. You could start by asking Stephen Meyer what he means by "epigenetic information." If it's just regulation of gene expression then why is that a big deal? Most of us think that new body plans evolve almost always by altering regulation (epigenetics). That's what Stephen Jay Gould wrote about in his book "Ontology and Phylogeny" back in 1977.

      Try and keep up.







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    2. Larry, I think your reply to Vincent Torley might have been easy to misunderstand for someone who isn't clear on the concept, i.e. when you said "Most of us think that new body plans evolve almost always by altering regulation (epigenetics)", he might have thought you were referring to epigenetic inheritance rather than changes in regulatory sequences. I think a lot of creationists are confused about that.

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    3. Even if we see Nature adapting existing codes, we don't see Nature generating new ones.

      Indeed, and no one's saying any different with regard to the origins of life. The first living cells (or virus-like particles) would have utilized extant chemistry, such as self-replicating molecules, amino acids, etc. No one I've read, other than creationists, is holding out for poofing anything complex into existence on a de novo basis.

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    4. John Harshman said,

      Larry, I think your reply to Vincent Torley might have been easy to misunderstand for someone who isn't clear on the concept ...

      How could he misunderstand? He's the one who quoted the definition of epigenetics that includes regulation of gene expression by transcription factors. That seems very clear to me.

      Only an idiot would ....

      Oops. Now I get it.

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    5. Even if we see Nature adapting existing codes, we don't see Nature generating new ones. That was my point.

      We don't see "intelligent designers" doing it in biology, either. In fact, we don't see it happening at all. So what makes you believe it happened?

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    6. I've yet to see any natural system that's as good as what computer scientists can do.

      Well, professor Moran, you haven't seen any "natural system" as good as what computer scientists can do because you have no idea how human brain works. I will give you the benefit of the doubt on this one because all experts in the field don't know it either. It is beyond human comprehension at the moment to even imagine how many operations at the same time human brain can preform but scientists hope that one day they will be able to catch up at least to a very small degree.

      "Most of the genes that code for complex structures are inefficient and error-prone."

      Can you provide specific examples?

      "Natural systems look like they were designed by a tinkerer who cobbles together odds and ends that just happened to be in reach. They look like they evolved haphazardly. Any intelligent scientist could do better and, in some cases, they have done better by genetically modifying organisms to make them more efficient. "

      Can you also provide specific examples of how intelligent scientists could do better but they didn't and how in "some cases" that they did better than nature, especially genetically modifying an organism that are more efficient? If that is true, can the improved efficiency of some organisms have a negative side-effect, say on environment, evolution, procreation?

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    7. Hi Professor Moran,

      I'll keep this brief. I was intrigued by your remark on Intelligent Design inferences: "The goal is to solve the problem, not create more problems." Usually, solving one problem does involve creating other problems, which are then solved further down the line: in fact, I'd even call it a trademark feature of human progress. But let that pass. Am I right in supposing that you would resist making a design inference for a lunar monolith? Seriously?

      The thrust of Dr. Meyer's argument in Darwin's Doubt (pp. 272-282) is that animal body plans are not determined solely by the genetic material in the nucleus, but also, in large part, by factors such as microtubule arrays, the centrosome, and patterns of proteins (and even sugars) in cell membranes. Meyer uses the term "epigenetic information" to refer to all these kinds of information outside our DNA. As I read him, his general point is that since DNA doesn't direct body plan formation, any theory of evolution which focuses on DNA mutations and fails to explain how the other kinds of information in the cell originate (and evolve over time) will be incomplete at best and seriously flawed at worst. On that point, I think even an ID skeptic might well agree with him.

      Re the origin of codes from scratch: I'll have to get in touch with some biologists in the ID camp, but I've had a look at Christian Schlotterer's paper, and I'm intrigued by his two models for the birth of de novo genes. The speculation looks interesting, but one of his models assumes the existence of ORFs (which have the potential to code for a protein or a peptide), while the other model assumes that short peptides can mutate, grow and result in the formation of functional de novo genes. The problem, as I see it, is that if the figures cited by Dr. Douglas Axe in his paper, "The Case Against a Darwinian Origin of Protein Folds," are correct, the latter scenario sounds like a miracle, while the former scenario assumes the existence of something it needs to explain: ORFs.

      I am aware that ORFs of de novo genes tend to be short, so their spontaneous origin may not not be excluded by Axe's calculations. However, with regard to genes coding for long-chain proteins (some of which are found in all living things), I'm a lot more skeptical.

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    8. Douglas Axe is either an incompetent ignoramus, or writes papers that make it appear that he is one. So you could save yourself a lot of trouble by simply ignoring any of his "research." Just as the rest of the scientific community does. You're welcome.

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    9. As I read him, his general point is that since DNA doesn't direct body plan formation, any theory of evolution which focuses on DNA mutations and fails to explain how the other kinds of information in the cell originate (and evolve over time) will be incomplete at best and seriously flawed at worst. On that point, I think even an ID skeptic might well agree with him.
      That may be what Meyer believes, but not many biologists would agree. Epigenetic inheritance lasts for a few generations at most and thus can't be important in evolution. Differences in epigenesis among species are the result of differences in their genomes. The proteins in the cell membranes are of course coded for by DNA, and their placements and glycosilations are the result of processes mediated by proteins. Differences in protein expression among species are due to differences in regulatory sequences. Even the maternal transcripts and proteins responsible for some signaling in early development are the result of DNA sequences. Etc.

      Also, you should avoid using the term "origin of codes" unless you are actually referring to the genetic code or some epigenetic code; you seem to be using it to refer to sequences, which is something else. ORFs are nothing more than sequences of some length that lack any stop codons in some reading frame; that sort of thing clearly can occur by chance, given that a random triplet has only a 3/64 chance of being a stop codon; the probability that any random sequence of length n triplets is an ORF is thus (61/64)^n. That's 0.8% in a sequence of 100 triplets, and given three reading frames should probably really be considered 2.4%.

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    10. It seems that the IDiots consider things like fingernails to be "epigenetic" since they aren't made of protein and therefore aren't a direct product of genes.

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    11. Vincent,
      Please tell us - exactly what are the properties that a "lunar monolith" has in common with biological organisms, that make you think this is, in any way, a valid analogy for you to use to support ID or to question Prof. Moran's reasoning skills ?

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    12. That's one of the weird misrepresentations that IDiots often make: They seem to think that by rejecting ID, one is saying that design cannot ever be detected in any circumstance.

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    13. Lutesuite: Fingernails are made of protein.

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    14. What I should have said: They think something like the skeletal system is "epigenetic" because it requires inorganic elements like calcium in addition to an organic matrix. Better?

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    15. @Vincent Torley

      You might be interested in the following paper on the generation of function from the scratch:

      Functional proteins from a random-sequence library.
      Keefe AD, Szostak JW.,
      Nature. 2001 Apr 5;410(6829):715-8.

      P.S. Read one or two introductory textbooks, please.

      Delete
    16. I wonder if part of the problem is that, when Torley speaks of functional sequences arising "from scratch", he is thinking of them literally popping out of thin air, with no physical antecedents whatsoever. That's what several of his fellow IDiots seem to believe:

      http://sandwalk.blogspot.ca/2013/12/how-do-creationists-interpret-lenskis.html

      Delete
    17. Vincent,
      The problem, as I see it, is that if the figures cited by Dr. Douglas Axe in his paper
      You've hit on a very important issue here. Axe calculates the odds of deriving at random a fold ( which he equates with function) as, iirc, 1 in 10^70.
      Consider the following calculation. There are about 10 million species on earth with on average 10,000 proteins... so 10^11 proteins. Now consider earth along with a billion other planets as rich in life as earth. The odds that a single de novo protein could form in any species on any one of a billion worlds is 1 in 10^50. In other words its never, never ever going to happen. But in every species we look at we see several de novo proteins. So Axe is a bit off, to put it mildly. This little observation profoundly undermines the basic assumptions of ID

      Delete
    18. " It doesn't matter how beautiful your theory is, it doesn't matter how smart you are. If it doesn't agree with experiment, it's wrong."

      (Feynman)

      IDiots and their ilk have great difficulty internalizing that.

      Delete
    19. Looking for Vincent Torley...

      Where is he now ?
      No comment?
      Did he finally start informing himself ?

      Or:
      Did he start levitating & did not yet find out how to come down?
      (Any witnesses to calculate a probability for that ?)

      Delete
  4. lutesuite,

    My "asinine question" was a cheeky comment in response to Professor Jerry Coyne's remarks on what ID supposedly says about the source of epigenetic information. You might want to read Coyne's post for context. Cheers.

    ReplyDelete
    Replies
    1. I'd already read Coyne's post, thank you.

      Do you really think you IDiots are fooling anyone by claiming you think the origin of "biological information" is anything but God? Please, don't insult my intelligence.

      Delete
    2. Yeah, sorry, but this is why ID proponents end up being put down. They try to move the goal post. "Evolution can't explain epigenetics, so we ID people who think God is responsible for everything theorize that it must be from something else!"

      "Well, here's how something not God could have created epigenetic processes...."

      "I never said God!! Strawman!!"

      Delete
  5. While you're here, VJ Torley, I wonder if you could clarify a statement made by Casey Luskin:

    The burgeoning field of epigenetics has also validated ID's prediction of new layers of information, code, and complex regulatory mechanisms in life.

    Could you provide a citation to where this prediction was made? TIA.

    ReplyDelete
    Replies
    1. "Could you provide a citation to where this prediction was made?"

      And from what unique tenet of ID/creationist theory does this prediction logically emanate?

      Delete
  6. "Vincent Torley read a post by Jerry Coyne where Jerry wondered if Intelligent Design Creationism was in trouble because the Discovery Institute has lost Bill Dembski and Casey Luskin"

    But they still have Michael Egnor, they are safe.

    ReplyDelete
    Replies
    1. And Dr. Ben Carson may soon be available.

      Delete
  7. Moran: "Both of the premises are wrong. I've yet to see any natural system that's as good as what computer scientists can do. Most of the genes that code for complex structures are inefficient and error-prone. Natural systems look like they were designed by a tinkerer who cobbles together odds and ends that just happened to be in reach. "

    What an idiotic statement!! Moran assumes that because he observes inefficient and error-prone genes that they were ALWAYS like this; that genes started out inefficient and error-prone and have gone further downhill from there.

    Moran's premise is an amateur's mistake.


    Moran: "This is an important point. Intelligent Design Creationists never see the big picture so they lack perspective—a fault shared by many non-creationists as well. It's simply not true that complex biological structures are complex because they are very sophisticated and efficient. In many cases, they are complex by accident and it's easy to make better, more simple, systems that can do the same job. "

    Another howler from Moran!!! Creationist don't see the big picture, is it??!!! And what big picture does Moran see?? Last time I checked, it took an excruciating amount of sweat for Edison to 'accidently' come up with just the right material for his light bulb filament. The last time I checked, Steve Jobs lost his job because of his incompetence and lack of ability to steer Apple and well, we all know the rest of the story.

    What is really happening here is Moran forgetting that human ingenuity and design capabilities are the product of none other than nature herself.

    So Moran's nature is grossly incompetence; BUT, BUT at the same time awesomely competent.

    Methinks Moran's big picture is more like the elephant's tail.

    Moran: "It's easy to envisage how such regulatory mechanisms can arise by purely naturalistic means.

    And there you have it folks!!! A truly devastating rebuttal.

    Evolution in a nutshell: "I can envisage it, therefore it exists".









    ReplyDelete
    Replies
    1. > Moran assumes that because he observes inefficient and error-prone genes that they were ALWAYS like this;

      It's reasonable to assume that because there's no empirical evidence to show other wise. What we see now is full of junk and errors. We've never seen anything else. Can you show us any cells in history where the genetic replication isn't full of errors?

      Delete
    2. Steve wrote:
      "Moran assumes that because he observes inefficient and error-prone genes that they were ALWAYS like this; that genes started out inefficient and error-prone and have gone further downhill from there.

      Moran's premise is an amateur's mistake."

      Actually, what you wrote is what creationists call the result of the fall. You know the stuff which happened after Adam and Eve munched an apple. Nice to see you agree this premise is BS.

      But that's not what prof. Moran wrote, but nice try Steve cherry picking what you think he wrote.

      Delete
    3. What is really happening here is Moran forgetting that human ingenuity and design capabilities are the product of none other than nature herself.

      Let me get this straight now, Steve - your reading is that it's Dr. Moran who's "forgetting" that humans arose by natural means?

      Delete
    4. Steve "Evolution in a nutshell:I can envisage it, therefore it exists".

      As many creationists do, you confuse "connecting the dots" with "making stuff up". Probably because you are good at the latter and not so good at the former?

      Delete
    5. Creationism in a nutshell:
      "I can't envisage it, therefore God did it (and exists)."

      Delete
    6. Steve,

      You said: "What an idiotic statement!! Moran assumes that because he observes inefficient and error-prone genes that they were ALWAYS like this; that genes started out inefficient and error-prone and have gone further downhill from there.

      Moran's premise is an amateur's mistake."

      What is your alternative premise, then?

      Delete
    7. I don't believe that is Larry's premise, either. I'm not aware of any model by which genes become more "inefficient and error-prone" over time. Other than the Christian Original Sin model, that is.

      Delete
    8. Genes demonstrably become more efficient over time, per Lenski. Game, set, match.

      Delete
    9. Genes demonstrably become more efficient over time, per Lenski.

      Huh?

      Delete
  8. Torley:

    "The problem, as I see it, is that if the figures cited by Dr. Douglas Axe in his paper, "The Case Against a Darwinian Origin of Protein Folds," are correct"

    They're not. There was an excellent retort to one of other papers on the very same subject here:
    http://pandasthumb.org/archives/2007/01/92-second-st-fa.html

    Douglas Axe's reply to this is found:
    http://www.biologicinstitute.org/post/19310918874/correcting-four-misconceptions-about-my-2004

    but you'll see he ignore almost half of the important points that Arthur Hunt brought up. Ignoring such crucial points like that can only be taken as a sign that he can't rationalize them.

    ReplyDelete
    Replies
    1. The problem Torley has, which he shares with many other ID supporters, is that he is unable or unwilling to follow the evidence and logic supporting an argument, so he is left saying "Hunt says Axe is wrong, but then Axe says Hunt is wrong. Who am I to believe?" The answer should be simple: You believe the one who makes an argument that is actually consistent with the available evidence. I fail to see why that is so difficult.

      Delete
    2. I think that's rather unfair. I just read comments at UD with Torley saying Professor Moran makes the best arguments for junk dna being just that. He seems to have accepted that.

      Delete
    3. Only once he figured out a way to reconcile the existence of junk DNA with ID. Ideology always come first with the IDiots.

      Delete
    4. But, fair enough, give Torley credit for doing something rarely that most other creationists never do at all.

      Delete
  9. Vincent, please try to use the “theory of intelligent design” that you represent to first qualify what is (or is not) “intelligent” then explain how “intelligent cause” works and/or worked through biology.

    Changing the subject to theory that generalizes using the word “evolution” will only help confirm that whether you know or not you are instead promoting a strict version of theistic evolution (evolutionary creationism) where many people believe that God made it all including simple life, then let evolution take over.

    Scientific theories explain how something works or happened. What do you have for the phenomenon of “intelligent cause” that the premise of your own theory obliges you to scientifically explain?

    ReplyDelete
  10. I think there are some serious points being ignored on both sides. Evolution tinkers because thers is no other way to simultaneously juggle thousands of dimensions of fitness, and no other way to design proteins and regulatory networks. There is no grammar that allows you to design novel protein folds without trial and error. There are no sequences that can be examined for syntax before trying them out.

    I don't think humans can do better than evolution. In fact we mimic evolution to solve things like the traveling salesman problem. It's not evolution or design. Evolution is the only way to design.

    ReplyDelete
  11. Hey vince, have you seen any conventual franciscan friars/catholic priests levitate and fly around lately?

    http://sandwalk.blogspot.com/2015/02/vincent-torley-and-evidence-for-gods.html

    ReplyDelete
  12. Vincent,
    I think you're question earlier about why it was unreasonable to invoke an intelligent designer is worth considering.
    I think design explanations are like any other explanations in that they link the thing under consideration as much as possible to other things that we understand. Three examples:

    Anthropologists tell us that a certain remote island in the Pacific has never been inhabited. If we then find stone tools and other artifacts buried near a cave on the island its unreasonable to dismiss them as natural products. We have precedent for invoking design and we know who the designers are: people. We know they can build boats and have settled many islands in the Pacific. We just didn't know that this particular island had been settled. In this case the designed object is evidence of the designer.
    You may have heard that astromomers recently detected anomalous readings from a star that cant be explained by natural phenomena. One astronomer half jokingly suggested its due to alien technology. If there is intelligent life elsewhere in the galaxy its probably exceedingly rare, so invoking aliens without independent evidence of their existence is unreasonable. On the other hand we do have some precedent; we know that intelligent creatures can evolve on the surface of planets (us) and by extrapolating from our own history its possible we one day may have equivalent technology. But for now its better to wait for a natural explanation.
    Invoking a designer god fails completely as an explanation. Its not just that we have absolutely no precedent at all for such a being, and its not just that we should be suspicious of the reason for invoking it- to support Bronze age religious mythology. Its that such a god contradicts what we do know about the world. WL Craig says god is a 'time-less, spaceless immaterial being'. But everything we know about minds tells us that minds must have a medium to operate on and minds by definition must operate in time. He might as well have invoked a timeless, spaceless, immaterial clock.

    ReplyDelete
    Replies
    1. Pedantically, hasn't rather than can't be explained natural phenomena. "The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' but 'That's funny...' ". (Asimov)

      Delete
  13. > As genomes expanded during the evolution of eukaryotes, it became selectively advantageous to shut down much of the genome that wasn't immediately required for viability. But the gradual evolution of more and more tightly binding nucleosome structures came at the cost of accidentally turning off genes that were needed.

    Does "genomes expanded" refer to the large increase in junk dna, or the moderate increase in number of genes? From reading a little, archaea use nucleosomes for gene regulation, but do not use histone modifications. So nucleosomes were already used to turn genes on and off, and eukaryotes just evolved a more complex way of doing so. With respect to genome size, I could imagine this was driven by the need to stop spurious binding to junk dna, but also by the need for more precise regulation if there are more genes that might interfere with each other.

    I found one paper arguing "chromatin modifications may have evolved to suppress the integration of parasitic elements into essential genes by maintaining nucleosome density to as high a degree as possible." Another review suggests a link with genome size but does not discuss it. Another review article suggests the relation to genome size is unclear: "is there a correlation between genome size, complexity and positive or negative supercoiling on the one hand and the presence of distinct classes of architectural chromatin proteins on the other?"

    In the case that histone modification evolved as a response to junk DNA, it's interesting that instead of evolving a mechanism to remove the junk DNA, eukaryotes developed an epigenetic mechanism to dynamically account for it.

    PS I do not know much about this except from reading just now. I'm curious if anyone has a more informed opinion about the origin of chromatin regulation.

    Here's what I read:

    Chromatin is an ancient innovation conserved between Archaea and Eukarya, Ammar et al. Elife 2012 http://dx.doi.org/10.7554/eLife.00078.001. See also http://phylogenomics.blogspot.co.uk/2012/12/story-behind-paper-corey-nislow-on.html

    The Frustrated Gene: Origins of Eukaryotic Gene Expression, Madhani. Cell 2013 http://dx.doi.org/10.1016/j.cell.2013.10.003

    Genesis of Chromatin and Transcription Dynamics in the Origin of Species. Koster et al. Cell 2015 http://dx.doi.org/10.1016/j.cell.2015.04.033

    The interplay between nucleoid organization and transcription in archaeal genomes. Peeters et al. Nature Reviews Microbiology 2015 dx.doi.org/10.1038/nrmicro3467

    ReplyDelete