Intelligent Design

Atheist biologist makes an excellent case for Intelligent Design

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Matthew Cobb is a professor of zoology at the University of Manchester and a regular contributor over at Why Evolution Is True. Recently, while critiquing a cartoon from xkcd (shown above), he argued that our DNA is the mindless product of a series of historical accidents. But then he let the cat out of the bag, at the end of his post:

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. In Drosophila there is a gene called Dscam, which is involved in neuronal development and has four clusters of exons (bits of the gene that are expressed – hence exon – in contrast to the apparently inert introns).

Each of these exons can be read by the cell in twelve, forty-eight, thirty-three or two alternative ways. As a result, the single stretch of DNA that we call Dscam can encode 38,016 different proteins. (For the moment, this is the record number of alternative proteins produced by a single gene. I suspect there are many even more extreme examples.)

Cobb triumphantly concluded:

In other words, DNA is even more complicated than [xkcd cartoonist] Randall [Munroe] 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!

But the damage was done. Even as he chided cartoonist Randall Munroe for claiming that DNA is subject to “the most aggressive optimisation process in the universe” and insisted that our genes are “a horrible, historical mess” consisting mostly of junk DNA, and that they are really the product of mindless tinkering rather than design, Cobb was forced to concede that amidst all this chaos, there were indeed some “astonishing examples of complexity which do indeed appear to be the result of optimisation” which “would boggle the mind of anyone, not just a cocky computer scientist in a hat.”

Intelligent Design supporters are often accused of appealing to something called an API: an Argument from Personal Incredulity. The acronym comes from Professor Richard Dawkins. The reasoning is supposed to go like this: I cannot imagine how complex structure X could have come about as a result of blind natural processes; therefore an intelligent being must have created it. This, Dawkins rightly points out, is not a rational argument. Certainly it has no place in a science classroom.

But my own conversion to Intelligent Design was not based on an API, but on something which I have decided to call the STOMPS Principle. STOMPS is an acronym for: Smarter Than Our Most Promising Scientists. The reasoning goes like this: if I observe a complex system which is capable of performing a task in a manner which is more ingenious than anything our best and most promising scientists could have ever designed, then it would be rational for me to assume that the system in question was also designed. That is not to say that nothing will shake my conviction, but if you claim that an unguided natural process could have done the job, then I am going to demand that you explain how the process in question could have accomplished this stupendous feat. I shall demand a specification of a mechanism, and a demonstration that this mechanism is at least capable of generating the complex system we are talking about, within the time available, without appealing to mathematical miracles (like winning the Powerball Jackpot ten times in a row). To demand any less would be the height of irrationality.

Professor Matthew Cobb concedes that our junky DNA contains genes which encode for proteins. He concedes that within the “noise” of our junky DNA, there are also “astonishing examples of complexity which do indeed appear to be the result of optimisation,” and that the complexity of this DNA code would “boggle the mind” of even “a cocky computer scientist in a hat.” This sounds like a perfect example of a case where the STOMPS Principle could be legitimately invoked. If Nature contains systems which accomplish a feat in a manner which is far better than what our best scientists can do, then it’s reasonable to infer that these systems were intelligently designed.

At this point, some evolutionists may respond by invoking what philosopher Daniel Dennett has termed Leslie Orgel’s second law: “Evolution is cleverer than you are.” The relevant question here is: cleverer at what? We have seen that all living things employ a genetic code: a set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. Despite diligent inquiry on our part, we have yet to uncover a single instance in Nature of unguided processes generating a code of any sort – let alone one which would “boggle the mind” of even “a cocky computer scientist in a hat.” Whatever else evolution might be clever at, code-making is hardly its forte.

But, we shall be told, evolution refines the code in our DNA all the time – through natural selection winnowing random mutations, as well as purely chance-driven processes such as genetic drift. Who are we to say that it could not have generated this code by an incremental series of refinements, over billions of years?

I used to be a computer programmer, for ten years. I think I know what it means to refine computer code. Evolution doesn’t do anything like that: what it does is corrupt the code in organisms’ cells, in ways that occasionally turn out to improve those organisms’ prospects for survival. That might be good for the organisms, but from a code-bound perspective, it isn’t “good” at all: it’s just the corruption of a code. And corruption is the opposite of generation.

So when I hear someone tell me that “nature, heartless, witless nature” could have not only generated a code, but generated one which even our brightest scientists are in awe of, my response is: “You’re pulling my leg.”

Finally, I’d like to address Professor Matthew Cobb’s argument that “[o]ur genes are not perfectly adapted and beautifully designed,” because our DNA is littered with junk: they are instead the product of “evolution and natural selection.” My response to that argument is: so what? Even if Professor Cobb is right about junk DNA – and I’m inclined to think he is (for reasons I’ll discuss in another post) – that’s beside the point. At most, it shows is that DNA which doesn’t code for anything wasn’t designed. But my question is: what about the DNA which does code for proteins, and which does so in a manner that boggles the ingenuity of our brightest minds? Professor Cobb, it seems, is missing the wood for the trees here.

Junk DNA might be described as degenerate code – but there has to be a code in the first place, before it can degenerate. The existence of junk DNA cannot be used as an argument against design: all it establishes is that the designer of our DNA – whether out of benign neglect, laziness, illness, or ignorance that something has gone amiss – doesn’t always fix the code he created, when it becomes corrupted. Accordingly, junk DNA cannot be used as a legitimate argument against the proposition that the DNA in our cells which codes for genes was designed.

A personal story

A few years ago, I came across an article by an Australian botanist (who is also a creationist) named Alex Williams, entitled, “Astonishing Complexity of DNA Demolishes Neo-Darwinism” (Journal of Creation, 21(3), 2007). At the time I knew very little about specified complexity and other terms in the Intelligent Design lexicon. I heartily dislike jargon, and I was having difficulty deciding whether there was any real scientific merit to the Intelligent Design movement’s claim that certain biological systems must have been designed. But when I read Alex Williams’ article, the case for Intelligent Design finally made sense to me. What impressed me most, with my background in computer science, was that the coding in the cell was far, far more efficient than anything that our best scientists could have come up with. Here are some excerpts from the article:

The traditional understanding of DNA has recently been transformed beyond recognition. DNA does not, as we thought, carry a linear, one-dimensional, one-way, sequential code—like the lines of letters and words on this page… 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.

(Bold emphasis mine – VJT.)

I’d like to make it clear that as someone who believes in a 13.8 billion-year-old universe and in common descent, I do not share Williams’ creationist views. In particular, I think his argument for a young cosmos, based on Haldane’s dilemma, rests on faulty premises. But I do think that Williams is on solid scientific ground when he writes that no human engineer has ever even imagined, let alone designed an information storage device anything like DNA. Here we have an appeal to the STOMPS principle: DNA encodes information in a way which is far cleverer than anything that our most intelligent programmers could have designed, so it is reasonable to infer that DNA itself was designed by a superhuman intelligent agent.

I’d like to conclude this post with a quote from someone whose impartiality is not in doubt: Bill Gates, the founder of Microsoft Corporation, who is also an agnostic:

Biological information is the most important information we can discover, because over the next several decades it will revolutionize medicine. 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.)

If an agnostic like Bill Gates, who is an acknowledged expert on computing, thinks that the complexity of human DNA surpasses that of any human software design, then it is surely reasonable to infer that human DNA – or at the very least, its four-billion-year-old progenitor, the DNA in the first living cell, was originally designed by some superhuman Intelligence.

Professor Cobb is undercut by one of his own commenters

We have seen that Professor Matthew Cobb’s argument against DNA having been designed is a philosophically flawed one. But reading through the comments attached to his post, I came across two comments by a reader named Eric (see here and here) which blew Professor Cobb’s case right out of the water, from a computing perspective:

… Matthew’s comment “Our genes are not perfectly adapted and beautifully designed. They are a horrible, historical mess” makes the analogy to human programming better, not worse….

I would guess that the entire etymology of computer programming languages is a result of historical contingency (i.e. a horrible, historical mess) as much as it is a result of optimization or rational choice. The reason Java forms the basis of so many internet-based languages is because that’s what was included in the earliest version of Netscape Navigator, which captured the market at the time. And the reason there are so many Visual Basic type programming languages is because Basic is what ran on the first generation of IBM personal computers. Geez, I know labs that were programming their nuclear physics detector setups in Fortran in the 1990s, and that is a language invented for use with punch cards.

Now computer programming languages will probably always require a more formal and rigorous syntax than natural language, but IMO the specific formal syntaxes that we used today are more due to the vagaries of human history than they are any sort of rational choice of the best options.

For that matter, why the frak do we even bother with www? Http vs. Https? That’s four redundant and therefore worthless letters out of five, the equivalent of 80% “junk DNA” in one of the most common and most recent human-built computer syntaxes. What sense does it make? None. Why do we have it? History.

Eric makes a very interesting point here. What do readers think?

(H/t: Denyse O’Leary.)

46 Replies to “Atheist biologist makes an excellent case for Intelligent Design

  1. 1
    Mapou says:

    Cobb is just another example in a long list of gutless impostors who pretend to be scientists. They knowingly teach lies in order to advance and protect their careers. There is no honor within the scientific community. Almost all biologists are outright liars. The very term “evolutionary biologist” betrays their pseudoscience and complicity in perpetrating the lie. Why? Because it assumes the a priori correctness of the theory (Darwinian evolution) that biology is supposed to be trying to falsify.

    As any programmer can tell you, the combinatorial explosion kills all stochastic search mechanisms (e.g., RM+NS) dead.

  2. 2
    Bob O'H says:

    As any programmer can tell you, the combinatorial explosion kills all stochastic search mechanisms (e.g., RM+NS) dead.

    [citation needed]

  3. 3
    Barry Arrington says:

    Bob,

    Go back and read just about every post Gil Dodgen ever wrote.

  4. 4
    Mapou says:

    @2,

    You actually need a citation to understand that the combinatorial explosion is a show stopper when it comes to random searches? You’re pathetic, Bob. Like all Darwinists, you’re a moron.

  5. 5
    Jack Jones says:

    Would be good to have Mr Dodgen contributing again.

  6. 6

    Mapou and I are a bit of a two-punch on “combinatorial expansion”. But we come at it from two different directions. Mapou’s point is straightforward, coming directly from mathematics. Mine comes from semiotics.

    What is PHYSICALLY REQUIRED to have a formal system of combinatorial expansion?

    – – – – – – – – – – –

    First, you have to have semiotic system. No small thing.

    Second, you have to have the simultaneous appearance of three independent instances of physicochemical arbitrariness, each encoded within the information that they make possible … or the system simply won’t function.

    – – – – – – – – – –

    Mr Cobb should read more. I bet he’s never even considered what is physically required to produce the system he thinks is such a mess.

    🙂

  7. 7
    mike1962 says:

    Enjoyable post, VJT

    “The existence of junk DNA cannot be used as an argument against design: all it establishes is that the designer of our DNA – whether out of benign neglect, laziness, illness, or ignorance”

    Or passive intention, if the productions of the evolutionary system were good enough for the designer’s purposes. For example, if I were using a genetic algorithm to design an antenna, I might prefer that the antenna be extremely optimized and aesthetically pleasing to me. But I may decide an ugly antenna is acceptable if the best antenna turns out to be ugly and the antenna’s efficiency was the top priority.

    It appears as if biological organisms are brilliantly optimized in some respects and not so much in others. This may be perfectly acceptable to the designer for a variety of reasons.

    EDIT: an example of intentional noise introduced into a system. In audio engineering, up-converting a lower digital format to a higher one, say from 16 bits to 32 bits, typically uses a technique that introduces random values in the bottom 16 bits of the 32 bit result. Believe it or not, this results in a more natural sound to human listeners. Someone analyzing the system without this understanding of human perception might easily conclude that the system had a serious flaw in it! But the random “junk” in the data is intentional and desirable.

  8. 8
    bFast says:

    “As a result, the single stretch of DNA that we call Dscam can encode 38,016 different proteins.”

    As a software developer of some skill and expertise, I marvel. This is vastly beyond the skill level of anyone I know.

  9. 9
    ppolish says:

    I can’t think of a single Intelligently Designed system/process that does not generate waste ie junk. It’s a Law I think.

  10. 10
    mike1962 says:

    ppolish: I can’t think of a single Intelligently Designed system/process that does not generate waste ie junk. It’s a Law I think.

    Sometimes it’s intention and desireable. See #7

  11. 11
    Barry Arrington says:

    “The existence of junk DNA cannot be used as an argument against design.”

    Even less can it be used as an argument against design by the God of the Bible. To those who believe in the fall and the curse that followed it, degradation of the genome through the accumulation of junk would be unsurprising. I am not endorsing this admittedly speculative view. I am merely pointing it out.

  12. 12
    bornagain says:

    a few notes:

    The Extreme Complexity Of Genes – Dr. Raymond G. Bohlin – video
    http://www.metacafe.com/watch/8593991/

    Landscape of transcription in human cells – Sept. 6, 2012
    Excerpt: Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.,,,
    Isoform expression by a gene does not follow a minimalistic expression strategy, resulting in a tendency for genes to express many isoforms simultaneously, with a plateau at about 10–12 expressed isoforms per gene per cell line.
    http://www.nature.com/nature/j.....11233.html

    Time to Redefine the Concept of a Gene? – Sept. 10, 2012
    Excerpt: As detailed in my second post on alternative splicing, there is one human gene that codes for 576 different proteins, and there is one fruit fly gene that codes for 38,016 different proteins!
    While the fact that a single gene can code for so many proteins is truly astounding, we didn’t really know how prevalent alternative splicing is. Are there only a few genes that participate in it, or do most genes engage in it? The ENCODE data presented in reference 2 indicates that at least 75% of all genes participate in alternative splicing. They also indicate that the number of different proteins each gene makes varies significantly, with most genes producing somewhere between 2 and 25.
    Based on these results, it seems clear that the RNA transcripts are the real carriers of genetic information. This is why some members of the ENCODE team are arguing that an RNA transcript, not a gene, should be considered the fundamental unit of inheritance.
    http://networkedblogs.com/BYdo8

    Duality in the human genome – Nov. 28, 2014
    Excerpt: The gene, as we imagined it, exists only in exceptional cases. “We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel’s time. Moreover, the conventional view of individual mutations is no longer adequate. Instead, we have to consider the two gene forms and their combination of variants,”,,,
    “Our investigations at the protein level have shown that 96 percent of all genes have at least 5 to 20 different protein forms.,,,
    http://medicalxpress.com/news/.....enome.html

    Design In DNA – Alternative Splicing, Duons, and Dual coding genes – video (5:05 minute mark)
    http://www.youtube.com/watch?v=Bm67oXKtH3s#t=305

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013
    Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43].

    38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142.
    39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432.
    40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654.
    41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997.
    42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816.
    43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes

    Conclusions: Our analysis confirms mathematically what would seem intuitively obvious – multiple overlapping codes within the genome must radically change our expectations regarding the rate of beneficial mutations. As the number of overlapping codes increases, the rate of potential beneficial mutation decreases exponentially, quickly approaching zero. Therefore the new evidence for ubiquitous overlapping codes in higher genomes strongly indicates that beneficial mutations should be extremely rare. This evidence combined with increasing evidence that biological systems are highly optimized, and evidence that only relatively high-impact beneficial mutations can be effectively amplified by natural selection, lead us to conclude that mutations which are both selectable and unambiguously beneficial must be vanishingly rare. This conclusion raises serious questions. How might such vanishingly rare beneficial mutations ever be sufficient for genome building? How might genetic degeneration ever be averted, given the continuous accumulation of low impact deleterious mutations?
    http://www.worldscientific.com.....08728_0006

    Biological Information – Overlapping Codes 10-25-2014 by Paul Giem – video
    https://www.youtube.com/watch?v=OytcYD5791k&index=4&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ

    Overlapping Genetic Codes 12-6-2014 by Paul Giem – video
    https://www.youtube.com/watch?v=3WZy0n60_ZU

    Second, third, fourth… genetic codes – One spectacular case of code crowding – Edward N. Trifonov – video
    https://www.youtube.com/watch?v=fDB3fMCfk0E

    In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, “Reading only one message, one gets three more, practically GRATIS!”. And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read.

    Concluding powerpoint of the lecture (at the 1 hour mark):

    “Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages.”
    Edward N. Trifonov – 2010

  13. 13
    computerist says:

    Biology is not quite impossible, it is just incredibly difficult!

    …yet we understand enough to know it evolved via NS+RM, as well as know what is useful and what isn’t?

    Not only that, it’s apparently ever changing, so like technology, what’s relevant today maybe be invalid/irrelevant tomorrow.

    Biology is therefore nothing more than a wild goose chase, because evolution (RM+NS) happens all the time we will always be behind.

    Is biology therefore impossible since we will always be lagging/behind? If not, why not?

  14. 14
    Seversky says:

    Sounds like another API to me.

  15. 15
    steveh says:

    Go back and read just about every post Gil Dodgen ever wrote.

    Gil is a gifted musician, computer programmer and former atheist who was Richard Dawkin’s worst nightmare, and who single-handedly exposed the vacuity of Darwinism using ground-breaking simulations such as throwing computers out of airplanes.

    Granville Sewell

    Gil’s point is simple and brilliant. If you are trying to model how molecular errors could accumulate to produce animals and plants, why assume that the only molecules in the cell subjected to errors are the DNA? If you really want to see what unintelligent forces alone can accomplish, through accidents, you should assume accidents can occur in other parts of the organism.

  16. 16
    Mapou says:

    The most mind boggling thing about Darwinism is how utterly stupid it is. Darwinists are all a bunch of mental midgets playing scientists. How did this chicken-shit voodoo religion become the state religion?

  17. 17
    mike1962 says:

    Seversky: Sounds like another API to me.

    Perhaps, but it is not a more developed one? Incredulity based on the fact that our best and brightest can’t get anywhere near inventing a thing is hardly the same thing as mere incredulity.

    When a materialist is sure there is no creator, isn’t that the ultimate API? I think it’s fair to say that there is enough API to go around for everyone to pass the bottle around for a swig. Atheists have theirs. Creationists have theirs. Dogs have theirs. Cats have theirs. Some of us even have incredulity based on that pesky lack of empirical evidence for some of the more wild proffered “explanations.”

  18. 18
    mike1962 says:

    Mapou: The most mind boggling thing about Darwinism is how utterly stupid it is. Darwinists are all a bunch of mental midgets playing scientists.

    Honestly, I’ve actually come to respect psychologists more than evolutionary biologists.

    That’s sinking pretty damn low.

  19. 19
    Jack Jones says:

    Lynn marguilis “Population geneticist Richard Lewontin gave a talk here at UMass Amherst about six years ago, and he mathematized all of it — changes in the population, random mutation, sexual selection, cost and benefit. At the end of his talk he said, “You know, we’ve tried to test these ideas in the field and the lab, and there are really no measurements that match the quantities I’ve told you about.” This just appalled me. So I said, “Richard Lewontin, you are a great lecturer to have the courage to say it’s gotten you nowhere. But then why do you continue to do this work?” And he looked around and said, “It’s the only thing I know how to do, and if don’t do it I won’t get my grant money.” So he’s an honest man, and that’s an honest answer.”

  20. 20
    Mung says:

    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.

    What does noise have to do with anything? Is noise a term of modern physics and chemistry? What are it’s units? Is noise even a term of biochemistry?

    It is impossible to eliminate completely the noise in any real system, especially one as complicated as the living system, and it is at this point that the second theorem of Shannon intervenes. The essential concept is this: we cannot eliminate noise in the channel, but we can under certain conditions transmit a message without error and without loss of message rate in spite of this noise if the message has been properly encoded at the source.The code is the crux of the matter.

    – Lila L. Gatlin. Information Theory and the Living System. 1972

    Figure 20 and equation (70) constitute the first mathematical evidence I have seen which suggests (but does not prove) that the present genetic code is an optimum code rather than an arbitrary code. The reasons for this optimization must be sought in mathematical terms rather than in any physical interaction between amino acids and nucleic acids.

    – Lila L. Gatlin. Information Theory and the Living System. 1972

  21. 21
    Andre says:

    This ties in with the discussion I had with Prof Moran the other day. Junk accumulating over time as the result of system operations actually make junk DNA a no big deal. Design is perfectly fine with accumulation of such junk.

  22. 22
    Zachriel says:

    Jack Jones: “You know, we’ve tried to test these ideas in the field and the lab, and there are really no measurements that match the quantities I’ve told you about.”

    Population genetics are constantly tested and verified in the lab and in nature. They are the basis of all population studies. Margulis was a great scientist, but a secondary source with an agenda.

    Margulis was an avowed Darwinist, by the way. Do you accept Darwinism on her authority as you do this second hand quote?

    Mung: the first mathematical evidence I have seen which suggests (but does not prove) that the present genetic code is an optimum code rather than an arbitrary code.

    Among all genetic codes, the canonical code is on a high peak, but is not optimal for reduction of noise (minimizing the effects of mistranslation). See Novozhilov et al., Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape, Biology Direct 2007.

  23. 23
    Jack Jones says:

    “Margulis was an avowed Darwinist, by the way. Do you accept Darwinism on her authority as you do this second hand quote?”

    She may well have called herself a Darwinist, When it came to her faith. She also revealed that Lewontin told her that what he was doing did not work and he wouldn’t get his grant money if he didn’t do what he did.

    ” Margulis was a great scientist, but a secondary source with an agenda.”

    Fallacy of attacking the motive.

    You have an agenda but still we will deal with your posts rather than dismiss what you say because of your agenda.

  24. 24
    Virgil Cain says:

    Zachriel:

    Population genetics are constantly tested and verified in the lab and in nature.

    Pop gen has nothing to do with what is being debated. Pop gen cannot say how many generations it takes to get a bacterial flagellum in a population that never had one.

    Pop gen is only good for singular populations and cannot be applied to the debate.

    Among all genetic codes

    Yours cannot account for any genetic codes- nor any codes. You lose, again.

  25. 25
    cantor says:

    22 Zachriel November 20, 2015 at 5:57 am

    Margulis was an avowed Darwinist

    .

    Margulis: “[neo-Darwinism] is a minor twentieth century religious sect within the sprawling religious persuasion of Anglo-Saxon Biology”

    .

  26. 26
    cantor says:

    Lynn Margulis, Discover Magazine, page 68 April, 2011:

    This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn’t create…. [N]eo-Darwinists say that new species emerge when mutations occur and modify an organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change — led to new species. I believed it until I looked for evidence.

  27. 27
    vjtorley says:

    Hi Zachriel,

    You write: “Among all genetic codes, the canonical code is on a high peak, but is not optimal for reduction of noise (minimizing the effects of mistranslation).”

    May I remind you that (a) being optimally designed is not a requirement for being intelligently designed, and (b) it would be unwise to describe the code we have as sub-optimal unless we know what biological goals it is supposed to satisfy. You mentioned noise reduction, but I’m sure that there are other goals served by the code as well. Some of these goals may also conflict with one another, to some degree. The genetic code that we have may turn out to be the best overall “compromise candidate.”

  28. 28
    Barry Arrington says:

    Dr. Torley at 27.

    Would you rather have an AK-47 or an M16A1?

    That question cannot be answered in a vacuum. Do you value robustness under extreme environmental conditions with users you cannot expect to be very good at maintenance? Go with the AK.

    Do you value accuracy and expect to have relatively sophisticated users well trained to maintain the weapon? Go with the M16.

    I’m wondering if the genetic code is not more analogous to the AK. The designer traded off exquisite fine tuning against robustness after taking a beating from the environment. Or perhaps the whole analogy is bad. It just came to me and I’m thinking out loud.

  29. 29
    bFast says:

    bornagain (12) Thanks for the video link to Dr. Raymond G. Bohlin. I have followed the link to an extended discussion (about 2 hours) from this fellow. Wow!

    May I just rehearse what Mapou (16) said, “The most mind boggling thing about Darwinism is how utterly stupid it is. Darwinists are all a bunch of mental midgets playing scientists. How did this chicken-shit voodoo religion become the state religion?”

  30. 30
    Mung says:

    Zachriel: Among all genetic codes, the canonical code is on a high peak, but is not optimal for reduction of noise (minimizing the effects of mistranslation).

    So?

    Here it is again, this time with text in bold to help you out:

    The essential concept is this: we cannot eliminate noise in the channel, but we can under certain conditions transmit a message without error and without loss of message rate in spite of this noise if the message has been properly encoded at the source.The code is the crux of the matter.

    Do you have any intention of attempting to answer the question about what noise even means in physics and chemistry?

  31. 31
    Seversky says:

    cantor @ 26

    Lynn Margulis, Discover Magazine, page 68 April, 2011:

    This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn’t create…. [N]eo-Darwinists say that new species emerge when mutations occur and modify an organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change — led to new species. I believed it until I looked for evidence.

    This was Margulis’s view but she didn’t speak for all evolutionary biology. Jerry Coyne took a rather different view in this comment in his blog

    You don’t always get creatures that are so defective under artificial selection: house cats are doing pretty well, so long as you don’t screw with their faces to create Persians. True, many artificially selected species wouldn’t survive in nature, for humans often desire traits that would be maladaptive in the wild. Corn, for example, has been selected to keep its seeds on the cob rather than “shatter”, or scatter them about. Not scattering your seeds is about the worst thing you can do as a plant in nature.

    But where on earth does Margulis get the idea that artificial selection shows that “natural selection doesn’t create”? Artificial selection, of course, does create, in that, as Darwin famously noted, humans can mold animals or plants into pretty much anything they like. This shows that combining different mutations can make something new: it can turn an ancestral plant into either a cauliflower, a kohlrabi, a Brussels sprout, or a cabbage (all derived from the same species). And if those changes increased fitness in nature, as for example the combination of traits that turned an ancestral artiodactyl into a whale, why wouldn’t natural selection create something new? The fossil record for the evolution of major taxa attests to this completely—unless Margulis thinks that flippers, feathers, and the like all arose by symbiosis or hybridization. I suspect that she does, which would be a ludicrous and unsupported point of view. After all, that is how, in her speciation book with Dorion Sagan, she suggested that most new species arise.

    Further on in the Discover interview she makes a more specific claim which Coyne discovers is way off-target:

    Finally, Margulis said something about my Ph.D. advisor, Dick Lewontin, that really bothered me. She characterized him as a money-grubbing scientist driven to take grant money for work that he knows is meaningless:

    Population geneticist Richard Lewontin gave a talk here at UMass Amherst about six years ago, and he mathematized all of it—changes in the population, random mutation, sexual selection, cost and benefit. At the end of the talk he said, “You know, we’ve tried to test these ideas in the field and the lab, and there are really no measurements that match the quantities I’ve told you about.” This just appalled me. So I said, “Richard Lewontin, you are a great lecturer to have the courage to say it’s gotten you nowhere. But then why do you continue to do this work?” And he looked around and said, “It’s the only thing I know how to do, and if I don’t do it I won’t get my grant money.”

    Well, fortunately I have a good relationship with Dick, and, like Woody Allen with Marshall McLuhan, I have him here behind the sign. And, like Marshall McLuhan, Lewontin affirms that Margulis knows nothing of his work. (Yes, life can be like that!)

    I called up Dick this morning and read him Margulis’s quote. He said that it completely mischaracterized his views and what he must have said at Amherst. Lewontin said that he thinks that purely mathematical models of population genetics have largely failed to help us understand the distribution of gene frequencies in nature, because those models often make assumptions that are either incorrect or untestable. So while mathematical theory in population genetics has had some successes, he said, it hasn’t been nearly as useful as we hoped. That’s why, Dick claimed, he stopped doing pure equations and started doing computer simulations, which he considers a more realistic way to see what can happen in nature. In simulations one can vary the parameters more easily and check the models’ sensitivity to varied conditions. In fact, Dick said that ages ago he stopped submitting grants that proposed purely mathematical approaches. So Margulis’s characterization of Lewontin as a dishonest huckster trying to fund work that he knew was bogus is inaccurate and unfair.

    Lewontin wanted me to add (for I have permission to quote him here), that his purpose in getting grant money was not simply to fund designated projects described in his research proposals, but to “run an institution”: to “fund a group of creative people to do what they want.” And indeed, that’s what he did—and that’s what many grant-funded investigators do. We can’t always predict how our proposed research will turn out; in fact, we know it will turn out differently from the projects we describe in our proposals. And the granting agencies like the NIH also know this well. In many ways, grants are not just given for proposed projects, but for demonstrated accomplishments of a group of investigators. For many years Lewontin ran one of the most productive groups in modern evolutionary genetics. I was proud to be a part of it.

    When I read him Margulis’s statement, designed to denigrate population genetics, Lewontin didn’t recognize at all the caricature she had drawn. Margulis simply distorted his views, which I’ve just described, as another way of dismissing modern evolutionary biology

    Margulis may have said things that are music to the ears of some here but, while she expressed strong opinions, that doesn’t make her right and there are many who take a different, and equally strongly held, view.

  32. 32
    cantor says:

    31 Seversky November 20, 2015 at 7:11 pm

    This was Margulis’s view but she didn’t speak for all evolutionary biology.

    .

    Your response is totally irrelevant. Go back and read the thread properly before you post again.

    .

  33. 33
    Seversky says:

    vjtorley @ 27

    May I remind you that (a) being optimally designed is not a requirement for being intelligently designed, and (b) it would be unwise to describe the code we have as sub-optimal unless we know what biological goals it is supposed to satisfy. You mentioned noise reduction, but I’m sure that there are other goals served by the code as well. Some of these goals may also conflict with one another, to some degree. The genetic code that we have may turn out to be the best overall “compromise candidate.”

    Let us suppose, for the sake of argument, that we find persuasive evidence for the signature of intelligent design in the genetic code. In other words, at some time in our past an intelligent agency has intervened in the course of life on Earth.

    Of itself, this would be a huge discovery, perhaps the most momentous in the history of science thus far. We would now have evidence, not only for non-human intelligent design playing a role in life on Earth but, since there is no evidence that this intelligent agency originated here, also for the existence of extra-terrestrial life itself. It would also imply an ET that, at that time, was far more advanced than we are now, which would not bode well for some human pretensions to being some sort of pinnacle of creation.

    Once that is all said and done, however, what ground have we gained on answering the question of the origin of life itself? Would we know whether this intelligent agency simply tweaked or tinkered with life that already existed on Earth at that time? Would we be able to tell if the intelligent agency created life from scratch on a previously barren Earth or whether they brought it here to seed the planet with life?

    The fact is that, even if the dreams of intelligent design proponents were fulfilled by the discovery of evidence of ID, it would not necessarily have any bearing on abiogenesis research at all. At root, the question would still be, as it has always been, from an OOL perspective who or what designed or created the intelligent designer?

  34. 34
    Jack Jones says:

    “The fact is that, even if the dreams of intelligent design proponents were fulfilled by the discovery of evidence of ID”

    Incorrect.

    We accept the evidence is for Design, Since when did you presuppose that the evidence is for dumb luck and that people who accept ID had to prove anything to you?

    It’s the other way round kid.

    One thing among others that you have to show is how you could have reached this moment in time if there were an infinite amount of past natural events.

    You have to show when a living organism was observed to originate spontaneously from non living matter in a natural environment.

    It is not possible for you to do either but you are welcome to hold your faith.

  35. 35
    Mung says:

    Seversky:

    Let us suppose, for the sake of argument, that we find persuasive evidence for the signature of intelligent design in the genetic code.

    Why should anyone bother to suppose such a thing if intelligent design has no signature?

    Why is the existence of a code not itself evidence sufficient evidence? What is the mechanism underlying the construction of a code?

  36. 36
    Zachriel says:

    cantor: Margulis: “[neo-Darwinism] is a minor twentieth century religious sect within the sprawling religious persuasion of Anglo-Saxon Biology”

    That’s right Margulis was a Darwinist, but rejected Neodarwinism.

    vjtorley: May I remind you that (a) being optimally designed is not a requirement for being intelligently designed, and (b) it would be unwise to describe the code we have as sub-optimal unless we know what biological goals it is supposed to satisfy.

    It was an appropriate response to the claim was that “the present genetic code is an optimum code rather than an arbitrary code.”

    Mung: “The essential concept is this: we cannot eliminate noise in the channel, but we can under certain conditions transmit a message without error and without loss of message rate in spite of this noise if the message has been properly encoded at the source.The code is the crux of the matter.

    There is no such thing as a perfect transmission system, and protein synthesis is not a noiseless channel. In any case, the canonical code is on a high peak, but is not optimal for reduction of noise (minimizing the effects of mistranslation).

    Mung: Do you have any intention of attempting to answer the question about what noise even means in physics and chemistry?

    There’s obviously information transmitted during protein synthesis. Treating it as an information channel implies the existence of noise.

  37. 37
    Jack Jones says:

    “That’s right Margulis was a Darwinist, but rejected Neodarwinism.”

    Just showed more division among evolutionists over what the theory of evolution is.

  38. 38
    Zachriel says:

    Jack Jones: Just showed more division among evolutionists over what the theory of evolution is.

    A hypothesis entails testable empirical implications. A good theory leads to many testable results. A great theory generates entire new fields of study. The Theory of Evolution is an example of the last.

  39. 39
    Jack Jones says:

    “The Theory of Evolution is an example of the last.”

    What theory of evolution?

    Evolutionists can’t agree on just what it is.

  40. 40
    Zachriel says:

    Jack Jones: What theory of evolution?

    The basic theory of evolution has been established since Darwin (1859). This includes descent with modification, divergence from common ancestors, and natural selection. The unification of Darwin’s theory with genetics was a major step forward. There are still questions about how much divergence occurs through bifurcation, and the relative importance of natural selection and other known mechanisms. Evolutionary theory includes an historical component, so there is always going to be significant questions about the exact history.

  41. 41
    AnimatedDust says:

    OT: Bornagain,

    I am hoping you can help me. On a different discussion I found a link I believe of yours, that dealt with time perception and relativity in a PowerPoint presentation of more than 100 slides. Do you know what I’m talking about? If so can you redirect me to the link? Much appreciated.

    I believe the presenter was female.

    AD

  42. 42
    Jack Jones says:

    @40 “Evolutionary theory ”

    There is no agreement on an Evolutionary theory, Evolutionists can’t agree on just what it is.

    There is a philosophy of evolution and evolutionists might have their own speculative hypothesis that they hold to within the Philosophy of evolution.

    But there is no ” the theory of evolution”

    @38 “A hypothesis entails testable empirical implications. A good theory leads to many testable results. A great theory generates entire new fields of study. The Theory of Evolution is an example of the last.”

    And yet the evolutionary community is divided, evolutionists have come out and said neo darwinism has failed.

    Others hold to the hypothesis of neo darwinism.

    Discoveries have only made the evolutionary community more divided.

    Whenever an evolutionist talks about “theory of evolution” then they are talking about the speculative hypothesis that they hold to.

    But as the popular hypothesis of neo darwinism has collapsed then the evolutionary community is more divided than ever before.

    Evolution is a philosophy which accommodates any finding and as it can accommodate the failure of neo darwinism then it can accommodate anything.

  43. 43
    bornagain says:

    AnimatedDust @41, female presenter? 100 slides? Hmmm doesn’t ring a bell. But here are a few of my notes on the subject if it helps:

    Einstein: Einstein’s Miracle Year (‘Insight into Eternity’ – Thought Experiment 55 second mark) – video
    http://www.history.com/topics/.....racle-year

    “I’ve just developed a new theory of eternity.”
    Albert Einstein – The Einstein Factor – Reader’s Digest – 2005

    “..the distinction between past, present, and future is only an illusion, however tenacious this illusion may be.”
    – Albert Einstein – March 1955 (of note: he passed away in April of that year)

    “The laws of relativity have changed timeless existence from a theological claim to a physical reality. Light, you see, is outside of time, a fact of nature proven in thousands of experiments at hundreds of universities. I don’t pretend to know how tomorrow can exist simultaneously with today and yesterday. But at the speed of light they actually and rigorously do. Time does not pass.”
    Richard Swenson – More Than Meets The Eye, Chpt. 12

    Time Dilation | Einstein’s Relativity – video
    https://www.youtube.com/watch?v=G-R8LGy-OVs

    “Recent experiments have confirmed, to within one part in one hundred million billion (10^17), that the speed of light does not change when an observer is in motion.”
    Douglas Ell – “Counting To God” – pg. 41 – 2014

    Experiment with speeding ions verifies relativistic time dilation to new level of precision – Sept. 19, 2014
    Excerpt: A team of researchers,, have conducted an experiment using ions pushed to 40 percent of the speed of light to verify time dilation to a new level of precision.,,
    the team describes how their experiment was conducted and how it allowed them to validate the time dilation prediction to just a few parts per billion.,,,
    The experiment allowed for measuring the shift in laser frequencies relative to what the transition frequencies would be for ions that had not been accelerated. By combining the two frequency shifts, uncertainties could be eliminated making it possible to validate time dilation predictions to an order of precision much higher than previous limits,,
    http://phys.org/news/2014-09-i.....ision.html

    Einstein’s Special Theory of Relativity – infographic
    http://labroots.com/user/infog.....ails/id/14

    Science vs God: Bryan Enderle at TEDxUCDavis – video
    http://www.youtube.com/watch?v=sn7YQOzNuSc

    God, The Universe, and Everything – Special Relativity and Quantum Entanglement Reflect Some Characteristics Of God
    Excerpt: Albert Einstein taught us that time and space are related by light. Imagine that you and I hitch a ride on the Star ship Enterprise, traveling at the speed of light. Now remember, at the speed of light time stops. So if we look out the window while traveling at this speed, we would be aware of the past, the present and the future all at once. This bizarre universe which seems absurd to us is the very universe described by quantum physics.,,,
    The concept that there is something outside the material world becomes even more evident when you consider light. You see light has the ability to behave in a singularly conscious manner. To actually transmit information across the entire universe instantly. Consider this. In 1997 a Geneva researcher created a pair of twin light photons and sent them flying in opposite directions along optical fibers. When one photon hit a mirror it was forced to make a random choice to go one way or the other. Which ever way it went it’s twin photon already seven miles away always instantaneously took the very same option. Instantaneous is the key word here. The reaction of the twin photon was not delayed by the amount of time it takes light to travel seven miles. Other more recent experiments support this finding. In fact, physicists now believe that an entangled twin particle will know what it’s partner is doing and instantaneously mimic it’s actions even if the pair live in separate galaxies billions of light years apart. Since we’ve been told that nothing can travel faster than the speed of light, how does one photon on one side of the universe know what the other photon on the other side of the universe is doing? Instantly?
    – Dwight Nelson
    http://www.theevidence.org/art.....rything-v2

    This higher dimension, ‘eternal’, inference for the time framework of light is also warranted, by logic, because light is not ‘frozen within time’, i.e. light appears to move to us in our temporal framework of time, yet it is shown that time, as we understand it, does not pass for light. The only way this is possible is if light is indeed of a higher dimensional value of time than our temporal time is otherwise light would simply be ‘frozen in time’ to our temporal frame of reference.

    Another line of evidence that supports the inference that ‘tomorrow can exist simultaneously with today and yesterday’, at the ‘eternal’ speed of light, is visualizing what would happen if a hypothetical observer were to approach the speed of light. Please note, at the 3:22 minute mark of the following video, when the 3-Dimensional world ‘folds and collapses’ into a tunnel shape as a ‘hypothetical’ observer moves towards the ‘higher dimension’ of the speed of light, (Of note: This following video was made by two Australian University Physics Professors with a supercomputer.).

    Approaching The Speed Of Light – Optical Effects – video
    https://www.youtube.com/watch?v=JQnHTKZBTI4

    This following confirmation of the time dilation of light is my favorite since they have actually caught the time dilation of light on film
    (of note: light travels approx. 1 foot in a nanosecond (billionth of a second) whilst the camera used in the experiment takes a trillion pictures a second):

    Amazing — light filmed at 1,000,000,000,000 Frames/Second! – video (so fast that at 9:00 Minute mark of video the time dilation effect of relativity is caught on film)
    http://www.youtube.com/watch?v=Y_9vd4HWlVA

    Of related interest, the ‘Dr. Quantum in Flatland’ video is very useful for giving us a small glimpse as to what it would be like to live in a higher ‘eternal’ dimension:

    Dr. Quantum in Flatland – video
    https://www.youtube.com/watch?v=takn4FPkId4

    It is also very interesting to note that this strange higher ‘eternal’ dimension of time finds corroboration in Near Death Experience testimonies:

    ‘Earthly time has no meaning in the spirit realm. There is no concept of before or after. Everything – past, present, future – exists simultaneously.’
    – Kimberly Clark Sharp – NDE Experiencer

    ‘There is no way to tell whether minutes, hours or years go by. Existence is the only reality and it is inseparable from the eternal now.’
    • John Star – NDE Experiencer

    ‘When you die, you enter eternity. It feels like you were always there, and you will always be there. You realize that existence on Earth is only just a brief instant.’
    Dr. Ken Ring – has extensively studied Near Death Experiences

    ‘In the ‘spirit world,,, instantly, there was no sense of time. See, everything on earth is related to time. You got up this morning, you are going to go to bed tonight. Something is new, it will get old. Something is born, it’s going to die. Everything on the physical plane is relative to time, but everything in the spiritual plane is relative to eternity. Instantly I was in total consciousness and awareness of eternity, and you and I as we live in this earth cannot even comprehend it, because everything that we have here is filled within the veil of the temporal life. In the spirit life that is more real than anything else and it is awesome. Eternity as a concept is awesome. There is no such thing as time. I knew that whatever happened was going to go on and on.’
    Mickey Robinson – Near Death Experience testimony

    “Very often as they’re moving through the tunnel, there’s a very bright mystical light … not like a light we’re used to in our earthly lives. People call this mystical light, brilliant like a million times a million suns…”
    • Jeffrey Long M.D. – has studied NDE’s extensively

    “I started to move toward the light. The way I moved, the physics, was completely different than it is here on Earth. It was something I had never felt before and never felt since. It was a whole different sensation of motion. I obviously wasn’t walking or skipping or crawling. I was not floating. I was flowing. I was flowing toward the light. I was accelerating and I knew I was accelerating, but then again, I didn’t really feel the acceleration. I just knew I was accelerating toward the light. Again, the physics was different – the physics of motion of time, space, travel. It was completely different in that tunnel, than it is here on Earth. I came out into the light and when I came out into the light, I realized that I was in heaven.”
    Barbara Springer – Near Death Experience

    “Regardless, it is impossible for me to adequately describe what I saw and felt. When I try to recount my experiences now, the description feels very pale. I feel as though I’m trying to describe a three-dimensional experience while living in a two-dimensional world. The appropriate words, descriptions and concepts don’t even exist in our current language. I have subsequently read the accounts of other people’s near-death experiences and their portrayals of heaven and I able to see the same limitations in their descriptions and vocabulary that I see in my own.”
    Mary C. Neal, MD – To Heaven And Back pg. 71

    “Well, when I was taking geometry, they always told me there were only three dimensions, and I always just accepted that. But they were wrong. There are more… And that is why so hard for me to tell you this. I have to describe with words that are three-dimensional. That’s as close as I can get to it, but it’s really not adequate.”
    John Burke – Imagine Heaven pg. 51 – quoting a Near Death Experiencer

  44. 44
    Virgil Cain says:

    Zachriel:

    The basic theory of evolution has been established since Darwin (1859). This includes descent with modification, divergence from common ancestors, and natural selection.

    That isn’t a theory, however-> Baraminology has been established since Creation. This includes descent with modification, divergence from common ancestors, natural selection, drift but mostly by built-in responses to environmental cues. 😛

  45. 45
    Virgil Cain says:

    Zachriel:

    There’s obviously information transmitted during protein synthesis. Treating it as an information channel implies the existence of noise.

    That doesn’t follow, however random mutations are noise.

  46. 46
    Virgil Cain says:

    Seversky:

    Let us suppose, for the sake of argument, that we find persuasive evidence for the signature of intelligent design in the genetic code.

    We already found such evidence in the code itself.

    Once that is all said and done, however, what ground have we gained on answering the question of the origin of life itself?

    One step at a time, young grasshopper.

    At root, the question would still be, as it has always been, from an OOL perspective who or what designed or created the intelligent designer?

    Ultimate questions are best for theology and philosophy.

    The design inference would mean, at a minimum, that we are here for a purpose other than the mundane. It would also mean that there is more to life than physicochemical processes.

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