Home » Evolution, Intelligent Design » “Ode to the Code”

“Ode to the Code”

[From a colleague:] There’s an interesting article in the American Scientist from last year that is worth revisiting. It examines whether the genetic code is optimized for reducing the impact of point mutations. Apparently it is according to the author. Given that there are exponentially large numbers of potential codon usages, if the genetic code really is the product of arbitrary events, anti-ID scientist face a serious problem, namely, how is it that this “frozen accident” just happens to be the best code for minimizing point mutations. Favorite quote from the article: “It seems hard to account for these facts without retreating at least part of the way back to the frozen-accident theory, conceding that the code was subject to change only in a former age of miracles, which we’ll never see again in the modern world.” Go here for the article.

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39 Responses to “Ode to the Code”

  1. Of course, the evolutionists will just try to use their evolutionist mind tricks, waving their hands and saying “this isn’t the evidence for ID you are looking for.” This has a strong effect on the weakminded.

  2. I just LOVE this blog.
    Sorry to gush, but this is great stuff!

  3. I agree!

  4. Let’s state it this way: given two theoretical frameworks, which one–ID or evolution–predicts this? Which one predicts a less efficient coding? Which prediction is supported? Which theoretical framework is supported?

    Oh, and don’t forget the mantra. No matter which discoveries may support it, no matter how well its predictions play out, ID is not science. Repeat after me . . . You are getting sleepy . . . ID is not science.

  5. That’s a good one, TomG.

  6. ” ‘It seems hard to account for these facts without retreating at least part of the way back to the frozen-accident theory, conceding that the code was subject to change only in a former age of miracles, which we’ll never see again in the modern world.’ ”

    The genetic code actually has a surprising amount of variability. For instance, the code that our mitochondria uses differs from the code our nuclear genome uses. It is not impossible (even now) for the code to evolve.

    Indeed immediately before the quote, the article states: “The few variant codes known in protozoa and organelles are thought to be offshoots of the standard code, but there is no evidence that the changes to the codon table offer any adaptive advantage. In fact, Freeland, Knight, Landweber and Hurst found that the variants are inferior or at best equal to the standard code.”

    Also, from earlier on: “Using this bootstrap criterion, Freeland and his colleagues compared the biological code with another set of a million random variations. The natural code emerged as the uncontested champion. They wrote of the biological code: ‘…it appears at or very close to a global optimum for error minimization: the best of all possible codes.’ ”

    There are no surprises here. We observe that the code is more or less optimal. We know it is possible to alter the genetic code (and more easily in small genomes such as mitochrondrial genomes). We think that natural selection is pretty good at finding good solutions. So, mutation in some of the earliest living organisms results in a variety of genetic codes, some of which are more optimal than others, then natural selection will choose the optimal code over all of its contenders.

    Of course the code is no longer changing (“conceding that the code was subject to change only in a former age of miracles, which we’ll never see again in the modern world.”). It is optimal. Natural selection has no where to take it.

  7. I always have to wonder when people speak of natural SELECTION how they define that as being a mechanism that means there is no goal, purpose, point, etc. to life. If something is selecting, it must have a goal, a purpose, and meaning. Choosing and selecting are inherent to agents who have a goal in mind, a purpose for their work, etc.

    How could a natural pointless mechanism arise from nothing that actually shows signs of intellect (such as choosing out of a group of mutations.) ?? Nowhere do we see such mechanisms at work unless an intellect is behind it.

  8. Also- I should note that if a mechanism is actually showing signs of intellect and thought and purpose by choosing the best possible mutations, you could hardly call all these mutations happy accidents. How is it an accident, in the end, when a mechanism is supposedly acting in nature but doing so in the way that an engineer or inventor or creator or another sort would?

    I still have to come back to selection- if something is actively selecting things out of a group, it must have purpose and meaning. In any other field of study, such a mechanism operating in such a constructive way would be impossible without an intellect that brought it into being to begin with. Things that act in the manner of showing intellect always come from an intellectual agent…they don’t arise out of nothing. Then again, in the lab and in the field- we have seen that natural selection merely acts to conserve and very little, if anything, else.

  9. Josh,

    Let’s take a hypothetical scenario:

    Say we have a number of populations of bacteria. These populations are exactly the same except they differ in their genetic codes. Some happen to have ‘good’ codes, and some happen to have ‘bad’ codes. Bacteria with ‘good’ codes are generally happier and withstand changes in the environment better than bacteria with ‘bad’ codes.

    Are you with me so far? In other words, if I were to create in the lab these different kinds of bacteria, I could seed them in the wild and record which ones grow the best. Are we in agreement?

  10. I’d like to approach something else simultaneously…

    “if something is actively selecting things out of a group, it must have purpose and meaning.”

    What do you mean by this? I can take a magnet and pass it over a group of objects, and the magnet will ‘actively select’ those objects that have the opposite charge. Does the magnet have some ‘purpose’ or ‘meaning’ that I am not aware of?

  11. cambion

    The differences in mitochondrial codon translation tables are trivial.

    http://www.ncbi.nlm.nih.gov/Ta.....e=t%23SG12

    I was writing about it a year ago at PT, trying to argue from your(?) POV that the differences are significant. It was a position I couldn’t really support.

    http://www.pandasthumb.org/pt-.....tml#c12831

  12. “Freeland and his colleagues compared the biological code with another set of a million random variations. The natural code emerged as the uncontested champion. They wrote of the biological code: ‘…it appears at or very close to a global optimum for error minimization: the best of all possible codes.’ ”

    Now it’s realized that the genetic code is optimized for error reduction. And it’s all due to Darwinian evolution?

    Darwinian evolution is also purported to explain non-optimal “apparent” design in nature, too? Which is it? And why wouldn’t Darwinian evolution make a trade-off between error minimization and some other property, such as overall speed of replication, as is done with error detection and correction codes by humans programmers?

  13. Really interesting. A product of mutations which limits mutations. Would we expect to see that?

  14. Can someone (Maybe Cambion) explain to me how an organism could survive a “mutation” in it’s genetic code? Wouldn’t that completly scramble every gene in it’s genome? It’s like reading ASCII with an EBCDIC translator – all you’d get is gibberish.

  15. I think Jay’s point needs repeating: evolution explains optimal genetic coding and suboptimal genetic coding. It explains everything and therefore explains nothing.

  16. Let me try to clarify things a bit…

    Whether or not the genetic code is optimal does not speak to whether evolution by natural selection. It is instead concerned with abiogenesis. I find evolution by natural selection to be strongly supported by the scientific evidence, however I find abiogenesis to be somewhat lacking and more or less on par with its alternatives. To me, it is entirely possible that aliens (or God for that matter) created the very first bacteria that inhabited the earth. Nothing survives of the putative RNA life that abiogenesis calls for. There are inferrences based upon the make up of the cellular machinery (i.e. ribosomes made from RNA), but nothing too strong.

    However, in this case, I think abiogenesis can explain the optimal genetic code observed in extant organisms just as well as extra-terrestrial or divine creation.

    IF genetic codes can mutate and IF some codes work better than others (confer higher fitness), THEN evolution will select for the best possible code it can reach via mutation.

    We know that codes can mutate. See http://www.evolvingcode.net/PDF/rewiring.pdf. In particular look at the phylogeny shown on page 51. You’ll notice around 40 changes to the canonical genetic code that have occured since the LUCA. All of these changes are putatively neutral (or possibly slightly deleterious or slightly advantageous) changes (as we think the canonical code to be optimal).

    For particulars on how one code is swapped for another, please take a look at the PDF.

    “Can someone (Maybe Cambion) explain to me how an organism could survive a “mutation” in it’s genetic code? Wouldn’t that completly scramble every gene in it’s genome? It’s like reading ASCII with an EBCDIC translator – all you’d get is gibberish.”

    The smaller the genome the less scambling there is. In the origin of life (if abiogenesis is true) there would have been a step where most of the cellular machinery was run entirely by RNA, except for maybe a single protein gene that was translated from an early genetic code. Changes to this code, are much less likely to screw things up than changes to a code that is responsible for 20,000 genes.

    “Really interesting. A product of mutations which limits mutations. Would we expect to see that?”

    Yes. Lookup “error catastrophe” and “molecular quasispecies.” If the mutation rate gets above a certain threshold, purifying natural selection cannot control the genome and it wanders off away from the optimal sequence.

  17. “I think Jay’s point needs repeating: evolution explains optimal genetic coding and suboptimal genetic coding. It explains everything and therefore explains nothing.”

    Scientific theories are ammended all the time. Look at “dark matter” and “dark energy.” This doesn’t mean cosmological physics is falling apart, does it?

    Also, I would object to the phrasing. I think a better statement would run: “evolution via natural selection is consistent with an optimal genetic code, but it would also be consistent with a suboptimal code.” Thus, the observation of what sort of code we have says nothing about whether evolution by natural selection is true or not. Really, as I said earlier, this optimal / subooptimal code thing is about abiogenesis and not evolution (it’s concerned with events before the LUCA).

  18. “IF genetic codes can mutate and IF some codes work better than others (confer higher fitness), THEN evolution will select for the best possible code it can reach via mutation.”

    IF that were true THEN the diversity of life would more resemble the diversity of the code (minimal). If the best possible code comes to dominate in such as way as to exclude virtually all variation on it, and this happens via random mutation and natural selection, then one would also expect that one optimal organism would become dominant in such a way as to exclude virtually all variation on it.

  19. “You’ll notice around 40 changes to the canonical genetic code that have occured since the LUCA.”

    Holy fossilized DNA, Batman! I wasn’t aware we were able to run the LUCA through a DNA sequencer to determine exactly what genetic code it used!

    By what miracle were able to determine the genetic employed by the purported LUCA, Cambion? Or are you letting an article of your faith creep in disguised as a fact in this discussion?

  20. Thought experiment: Let’s call the very first form of life “Proto-Form A”. Now, PF-A has the whole world to itself. Why would it want to change? It would then be competing with whatever it changed into?

    But, some would argue, it had no “choice”. It mutated. So, now there’s Proto-Form A and Proto-Form B. Proto-Form B happens to be superior to Proto-Form A, so Proto-Form B takes over. Proto-Form B is now faced with the same dilemna as Proto-Form A. It has no choice. It mutates. Now there’s Proto-Form C and Proto-Form B. Proto-Form C is superior to Proto-Form B. It out-competes it. Now, there’s only Proto-Form C.

    Now, if there is only, at most, two forms of life at any one time, and NS is operative, then how do we ever move beyond more than two forms?

    It might be argued that Proto-Form B and Proto-Form C, for example, simply co-exist in different niches; so then, let’s presume that we have the possibility of more than one “form” of life.

    However, note this: at the dawn of life, there are incredible amounts of “niches” available to new forms. So, if each of these new forms simply take over new niches, then we have a plethora of different life-forms that have come about without the aid of NS. In fact, it’s because there’s no selection taking place (but simply movement to new ‘niches’) that a multitude of “life-forms” can exist.

    In sum, for “life” to begin, we either have NS working–with the result that we never have more than two-forms of life at any one time; or, we have many forms of new life emerging WITHOUT the ‘assistance’, shall we say, of NS.

    In terms of this post, when the FIRST form of life appears, by definition, it’s code IS “optimal.” And, thus, either it remains “optimal”, or, it BECOMES more “optimal” absent the workings of NS.

    How is this impasse resolved?

  21. Besides varied environmental niches there is also seperation of groups by distance. So if group 1 goes from Proto-Form A to Proto-Form B there isn’t a reason for group 2–which is out of range to be competing with group 1–to do the same unless there is a change in environmental factors universal to all groups.

  22. Gumpngreen: “So if group 1 goes from Proto-Form A to Proto-Form B there isn’t a reason for group 2–which is out of range to be competing with group 1–to do the same unless there is a change in environmental factors universal to all groups.”

    Thus, change is brought about without NS operating. Correct?

  23. By the way, it so happens that Freeland, who’s mentioned in “Ode to the Code” article, was also recently mentioned in an article in the November issue of “Scientific American” (sic) magazine. (The actual article is located at http://www.sciam.com (subscription required).) My greatly abbreviated, satirized version:

    Lean Gene Machine: Ocean Bacterium Has the Most Streamlined Genome [At least the title was accurate]
    By Steven Ashley. [Creative editing to eliminate dogmatic Darwinist bias from the remainder performed by jay.]

    It is estimated that some 25,000 genes code for the proteins required to build each human being, a figure representing only 1 or 2 percent of our entire genome. The remainder is “spare DNA” (sometimes presumptuously and derisively called “junk DNA” by philosophical materialists) — base pair sequences that do not directly code for proteins. But where it makes sense for organisms to operate extremely efficiently, their DNA has been greatly optimized… A new champion in this special class has been discovered. An oceanic bacterium, Pelagibacter ubique (from the Latin for “ubiquitous ocean bacterium), also known as SAR11, one of the smallest self-replicating cells known, has only 1,354 genes, investigators report in the August 19 Science. SAR11 has almost no spare DNA…

    Biologists believe that the overhead required to maintain spare DNA is typically justified because it preserves a reservoir of potentially useful genes for a new or changing environment… Essentially, if it is likely that organisms will be subject to great environmental stresses, then they have been provided with contingency-plan genes to cope with the stresses. However, to save on the metabolic burden of replicating DNA with no immediate or potential benefit, P. ubique’s genome size has been reduced.

    Stephen J. Freeland, an evolutionary biologist at the University of Maryland, Baltimore County, consulted for a philosophical materialist quote with which to conclude this article, has inanely said, “Although natural selection is about the survival of the fittest, what’s fittest changes with the specific circumstances” (sic), thus proving the notion that such people, having no other plausible-sounding material mechanism to which to appeal, will attempt to use the concept to explain anything and everything, no matter how diverse and incongruous the phenomena — from ingenious biological devices, to dearth of complexity.

  24. How can one explain the evolution of “semantics” within the genetic code?

  25. “Biologists believe that the overhead required to maintain spare DNA is typically justified because it preserves a reservoir of potentially useful genes for a new or changing environment…”

    Did the Scientific Armerican article actually say this? No one believes that…

    It’s one of the great cardinal sins in evolutionary theory to posit a mechanism that thinks about the future. Evolution is only concerned with what’s hot NOW.

    “Although natural selection is about the survival of the fittest, what’s fittest changes with the specific circumstances”

    I, too, have a huge problem with just-so-stories. It could be that the mutational spectrum that effects this bacteria is heavily scewed toward DNA losses. No function, just random.

  26. “IF that were true THEN the diversity of life would more resemble the diversity of the code (minimal). If the best possible code comes to dominate in such as way as to exclude virtually all variation on it, and this happens via random mutation and natural selection, then one would also expect that one optimal organism would become dominant in such a way as to exclude virtually all variation on it.”

    There’s been some interesting work along these lines adapting economic game theory to evolutionary situations. ‘Organisms’ repeatedly play games like Prisoner’s Dilemma or the Ultimatum game against each other, using strategies that they pass on to their descendents. Mutations sometimes occur converting on strategy to another.

    In many cases, your best strategy depends upon what strategy your neighbors are using. The system evolves to a point where a number of different strategies coexists in a sort of dynamic equilbrium. ((This speaks some to your comment as well PaV))

  27. “Holy fossilized DNA, Batman! I wasn’t aware we were able to run the LUCA through a DNA sequencer to determine exactly what genetic code it used!”

    Haha… Didn’t mean to sound like we had LUCA DNA on hand…

    The genetic code of the LUCA is inferred from the genetic codes used by extant organisms. When these codes are mapped onto the phylegeny of life, we observe 40 *putative* changes. If common descent is true, there must be some number of changes to the genetic code, maybe not these particular 40, but at least some other isometric set.

  28. “The system evolves to a point where a number of different strategies coexists in a sort of dynamic equilbrium.”

    Exactly. So why didn’t this happen with the genetic code?

  29. Sequenced genetic code of the LUCA was rhetorical.

    In fact the LUCA itself is a hypothetical construct that leaves me sitting in a most unsatisfied manner on the mother of all chicken/egg paradoxes. The similarity of the genetic code amongst all investigated organisms is in fact the only bit of empirical evidence suggesting a LUCA. Even there common descent cannot be distinguished from common design. If one doesn’t dogmatically rule out design then the LUCA could very well have been not a minimal genome that evolved into more complex and diversified genomes but rather an uber-genome that fragmented and devolved into the range of extant organisms today.

    Too bad we don’t incorporate a page from cosmology into biology and instead of referring to “life” we call it “observable life” like the “observable universe” to keep us firmly grounded in the difference between the known and the unknown.

  30. Common genetic code, observable life, complex specified information, and modern engineering practice suggests the LUCA genome was a template library where all CSI existed in template form to be called upon for instantiation (realization) on an as-needed and/or trial-and-error basis. If one were to devise a generic seed for life that could work in a wide ranging and unpredictably changing environment this would be a good design philosophy. One would need to define a syntax for template storage that would endure so that unused templates could be instantiated at any future date in the manner envisioned when the template was created. This syntax would be the genetic code. It all makes perfect sense from an enlightened scientific/engineering point of view. Unfortunately most scientists seem to be unenlightened clods that can’t tell design from shinola and in defense of their ignorance dogmatically refuse to acknowledge the possibility of design in nature. What a shame. Maybe they’ll evolve into a higher form that can recognize design when they see it.

  31. “Exactly. So why didn’t this happen with the genetic code?”

    Let’s say the world is populated solely by organisms that derive their energy by photosynethesis, it may be my best move in that case to become herbivorous and prey upon these organisms. Or to prey upon a specific organism. Many different moves and many different situations.

    However, with the genetic code, there is always a single optimal move regardless of whether I photosynthesize, or consume those that photosynthesize. No matter the situation, only one code is optimal.

  32. cambion (in post #25): “Biologists believe that the overhead required to maintain spare DNA is typically justified because it preserves a reservoir of potentially useful genes for a new or changing environment…” Did the Scientific Armerican article actually say this? No one believes that…

    The SciAm article actually reads, “Evolutionary biologists believe that the overhead required to maintain junk DNA is justified because it preserves a reservoir of potentially useful genes for a new or changing environment…” Seems that the author and the editors at SciAm beleive it. Some people want so bady to attribute to Darwinian evolution powers it just ain’t got.

  33. “However, with the genetic code, there is always a single optimal move regardless of whether I photosynthesize, or consume those that photosynthesize. No matter the situation, only one code is optimal.”

    Are you really trying to tell me with a straight face that only one code is optimal in all situations? I’d thought better of you.

  34. Many reasonable inferrals can be made from the exclusivity of the genetic code over the virtually infinite number of equally functional permutations available:

    1) common origin for life – all life has a common origin whether it be a single instance of abiogenesis, a common designer, or a single seed that found its way to the earth from elsewhere

    2) rarity of origin – by whatever means it only happened one time on this planet

    3) no laws making life inevitable – there are no laws of nature such as structuralists posit that make the origin of life inevitable or common

    The total failure of SETI and space exploration to find any sign of life anywhere else in the universe when the Copernican Principle of Mediocrity predicted that the universe be awash in living things independently reinforces the inferences drawn above.

  35. “Are you really trying to tell me with a straight face that only one code is optimal in all situations? I’d thought better of you.”

    Surprising to me to, and I’m not sure if I entirely believe it. Although I think it does make a decent hypothesis. Note that it appears the code is optimal in all situations if all you ever care about is reducing the damage of spontaneous mutation…

  36. “Seems that the author and the editors at SciAm beleive it. Some people want so bady to attribute to Darwinian evolution powers it just ain’t got.”

    It’s funny, at many of the molecular biology talks I attend, people make the same mistake. Saying things like: “evolution keeps duplicate genes around because they may be useful in the future.” I don’t say this often, but I think the author of that SciAm paper is a fool…

  37. DaveScot,

    I think post #34 is dead-on. If life is easy to make, and abiogenesis is fairly trivial, then we would expect genetic systems in exant organisms that are wildly different from one another.

    “Common genetic code, observable life, complex specified information, and modern engineering practice suggests the LUCA genome was a template library where all CSI existed in template form to be called upon for instantiation (realization) on an as-needed and/or trial-and-error basis.”

    It’s amazing how close we are to the same page. The only reason science has put forward a very simple bacterial LUCA is because it fits the abiogenesis narrative, as well as a bit of microfossil evidence (which as you pointed out to me before, may not be accurate). The tree of life (as inferred from rRNA sequences) could easily have a eukaryotic LUCA.

    Your model of “instantiation (realization) on a … trial-and-error basis” is very similar to my model of RM + NS. In your case, NS begins with more to play with so to speak. But the mechanism remains more or less the same.

  38. DaveScot,

    You’re referring to the Latent Library idea in post #30, right?

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