Time does not permit a longer response at present, but here are a few thoughts:
The “frozen accident” idea has only ever been a hypothesis - not a prediction.
There is extant evidence for code evolution in the deep past - some of it is in the paper I discuss in this blog post.
The code has evolved, post LUCA, in some lineages. Stephen Meyer evokes it in his writings as a way to claim the code is arbitrary. So, ID can’t really have it both ways.
The idea that a well-adapted code - virtually optimized, even - would then outcompete other codes and become standard post LUCA is a pretty reasonable idea - even if that code was then tweaked in minor ways in some lineages thereafter. Optimize the code prior to LUCA, and that code takes over.
It is reasonable indeed, and there is evidence for that from Steve Freeland, who showed some years ago that the canonical code is far more optimal (in terms of error avoidance and efficiency) than could be expected by chance or a frozen accident compared to almost all other alternative codes.
So this raises the question of falsifiability. If something as prominent and confidently held as the “frozen accident” is demoted to an auxiliary hypothesis, as Lakatos put it, then evolution would seem to be unfalsifiable, in the Lakatosian sense.
There are no extant codes, from the large range of codes that would have had to have evolved. That certainly is strange. We have only a single canonical code, and must imagine that pre LUCA, in the very early stages of evolution, there would have been an enormous range of codes evolved, which have now vanished, and which strangely found a highly optimized code with nuanced features that would be difficult to evolve.
There is simply no comparison between (i) the enormous evolutionary distance you must cover to evolve the DNA code, and (ii) the minor variants we find in biology. I am surprised you would appeal to the latter as evidence for the former.
This view adds additional pressure on the pre LUCA evolution of the code. It must have found a code that really was, as you say, “virtually optimized” so as never to tolerate any additional evolution of the billions of years to follow. So much heavy lifting for evolution, to produce such nuanced complexities, in those early stages of evolutionary history, with only unicellular organisms.
Secondly, not only must the pre LUCA evolution produce an ~optimal code, but it must be quite a spike in the fitness landscape. Over billions of years, it was not possible for any lineage to evolve away to some other code. That is quite a claim.
Following up on this comment, I think there is a contradiction between this comment and the blog post. In the post you note findings that were consistent with expectations, and you refer to those expectations as “predictions.” And yet it is clear that these were never hard predictions. Here is what you write:
Clearly, evolution would not have been dropped if this “prediction” had turned out false. And yet when I ask about the very prominent and confidently held statement that the DNA code is mundane (which turned out to be false), you state it is merely a hypothesis. Am I wrong to think there is a little Monday morning quarterbacking going on here?
In Crick’s original paper (PDF), he presents the “frozen accident theory” (his wording) over against the “stereochemical theory”. These are thus competing “theories” (more properly, hypotheses). Neither is a “prediction” - rather, the two hypotheses make somewhat competing predictions:
A pure “frozen accident” origin of the code would fail to reveal meaningful stereochemical interactions between anticodons and amino acids. Read Crick’s paper - he lays it all out. In 1968, there was little evidence for such affinities.
A pure stereochemical origin would reveal many such correspondences.
As Crick points out in the paper, hybrid models are also possible - stereochemical origins with later “accidents” frozen in.
So, this was not a “confidently held statement” - far from it. Crick himself lays it out as two alternative hypotheses.
That one hypothesis has gone on to garner support over the other is not at all surprising, and hardly a “problem for evolution”.
As Sy has pointed out above, the evidence we have is that the code is quite optimized. As such, it would be a large peak of local fitness. It may not be a global maximum, but it need not be in order to be maintained. All that is needed is that a significant deviation from it would result in lower fitness - which it certainly would do in the current context - since such a shift would be in direct competition with a very well functioning code. The same question could be asked of other core components of all life as we know it - is there something with a higher global fitness than current ribosomes when it comes to assembling proteins? Possibly, but we can be quite sure that even millions of years hence organisms would still be using essentially the same ribosomes we have now. It’s a strong local peak of fitness.
No, not a “significant” deviation. Because of the incredibly high level of conservation, essentially any deviation from the canonical code must result in lower fitness. Essentially no change is allowed. This would be a very steep fitness spike–the Washington Monument of fitness landscapes. I understand the logic you are setting forth here, but it appears you are unaware of the several difficulties you create.
First, as you say, the high optimality of the code means it must have evolved from some other starting point. It would be way too lucky for such as code to have arisen right off the bat. Now how one gets a code going in the first place is a problem. But given the astronomical design space of the code, we are talking about an astronomical number of different codes evolution must have evolved, tested, and moved on. That alone is an enormous problem.
But beyond that, even if there was enough time for evolution to generate and test all those codes, you have the fundamental problem changing the code is going to change the translated peptide products. Science tells us you can’t just be changing the code like this. So you are now stuck having to imagine some way that this can happen. The code must be evolvable, in spite of what we know from science.
Next, even if the code was easily evolvable, and evolution had the time to traverse the astronomical design space, this Washington Monument of fitness landscapes means that the very pre LUCA evolutionary process you are calling for would be doubtful simply because, since the code’s fitness degrades so much away from the canonical code, the sequence of codes that evolution would have traversed, would have had terrible fitness.
This is to say nothing of how you are going to evolve the nuanced properties of the code, such as error correction or minimization. Not only do these properties have a rugged fitness landscape (rendering selection ineffective), but some of them are dependent on clever strategies in the gene sequence. IOW, the error correction or minimization works only if the DNA sequence itself is cleverly coded to take advantage of it. So you have no fitness improvement until the DNA sequence luckily has a bunch of mutations, just right to exploit the DNA code feature. Because there is no fitness improvement, it will not be selected for.
(Finally, my statement about “confidently held” was in reference to the post Crick consensus, but I get your point.)
From where did you get the term “mundane”?[quote=“Cornelius_Hunter, post:20, topic:5974”]
Similarly, Alberts, et. al., Molecular Biology of the Cell, 3rd Ed. write: “The code seems to have been selected arbitrarily (subject to some constraints, perhaps).” Obviously this was a false prediction…
[/quote]
It’s neither false nor a prediction.
[quote=“Cornelius_Hunter, post:20, topic:5974”]
Is it an internal contradiction to claim that the code underwent enormous unobserved evolutionary change, with no extant evidence, in the early stages of evolutionary history in some unknown, hypothetical pre LUCA organisms; and yet, the extant code cannot have evolved for billions of years due to heavy constraints?
[/quote]No, which is why Dennis specified LUCA.
[quote=“Cornelius_Hunter, post:27, topic:5974”]
Because of the incredibly high level of conservation, essentially any deviation from the canonical code must result in lower fitness. Essentially no change is allowed.[/quote]
Why would this be a the case on an RNA World foundation?
It appears that you are unaware of basic biology. You seem to place the parsing rhetoric far above any evidence. Is that a fair assessment of your approach?
You haven’t established that an astronomical design space must be explored. We know as an absolute fact that evolution (the same is true of design, if you prefer) has explored very little of the protein design space.
You haven’t established a number, so you haven’t established time either.
Not a problem on the foundation of an RNA World.
I think that only you are telling us anything of the sort, and misattributing it to science.
[quote]…This is to say nothing of how you are going to evolve the nuanced properties of the code, such as error correction or minimization.
[/quote]What error correction?
I would be less sweeping than that – I view models with some caution. If you showed me evidence that the ancestral human population size was 1000, half a million years ago, I would be mildly surprised. For 100 I would be shocked, and 2 I simply wouldn’t believe.
Hi Cornelius, thank you for joining us here! I would like to respond in particular to the following statement you made regarding the genetic code:
There is abundant evidence that directly contradicts your claim. See, for example, the abstract of this Nature paper from 2015 titled 'Genetic code flexibility in microorganisms: novel mechanisms and impact on physiology’:
“The genetic code, initially thought to be universal and immutable, is now known to contain many variations, including biased codon usage, codon reassignment, ambiguous decoding and recoding. As a result of recent advances in the areas of genome sequencing, biochemistry, bioinformatics and structural biology, our understanding of genetic code flexibility has advanced substantially in the past decade. In this Review, we highlight the prevalence, evolution and mechanistic basis of genetic code variations in microorganisms, and we discuss how this flexibility of the genetic code affects microbial physiology.”
This appears to be yet another example of how the negative rhetoric of the ID movement keeps being refuted by advances in scientific research. In the final analysis, the ID approach doesn’t seem to help in bringing glory to our “Designer”.
Hi Casper and thanks for your response. Please note, however, that this is not my claim. This is the evolutionary claim that Professor Venema was elucidating. I have no problem with multiple codes, and in fact expect them.
Well I think the key here is that the DNA code evidence is an awkward fit for evolution. I don’t mean that as negative rhetoric. The combination of being an astronomical design space, extremely conserved (Ling, et. al., notwithstanding; btw, for our purposes I don’t think biased codon usage would qualify as a different DNA code), ~optimal, interacting with the coding sequence, and complex and multiple functions, make for a complex evolutionary history.
I’m not saying evolution cannot explain it, period. It seems one can always find an explanation. But explanations can be heroic.
Just a non-moderator flag to the moderating team (@BradKramer) that we have a renegade fascinating Adam discussion hiding out in the ribosome discussion area, #s 7-17 and 30. After a while of ignoring this thread, I said, I wonder why this keeps getting so much traffic, and I looked and behold, not one but two fascinating topics on tap!
@Cornelius_Hunter thanks for joining us here. I’m glad to hear from you.
I want to start by saying that abiogenesis (the rise of the first cell) is separable from evolution. Within the confines of science, we only look for natural mechanisms to explain it. However, outside science when we consider what really happened, it is entirely possible that God created the first cell by first cause: his direct action.
The reason for this is simple. Abiogenesis (the origin of life) is a seperate issue than evolution (the common descent of life from that first set of cells). And there is a tsunami of evidence for common descent.
In one sense, I do agree with @Cornelius_Hunter. @DennisVenema’s argument about the direct templating argument does not really demonstrate that abiogenesis is true. In my view, that is not why the direct templating argument is interesting.
Rather, if the underlying data holds up, it seems to undermine the ID argument that the genetic code is a true arbitrary code. This alone does not make the ultimate conclusions of Meyer’s false, but it does call into question the the confidence placed in the “genetic code” arguments. The point is driven home even more, when it is asserted (against the evidence) that the genetic code is not varied, etc.
Even if Meyers is ultimately right (which I am open to), this is not a terribly strong argument.
This not a contradiction at all. The notion here is that there a lot of changes before the code is optimized. Once it is optimized, there are much less. We see this all the time in evolutionary systems, both real and in simulations. Imagine a ball rolling into a valley. As it rolls down the slope it goes quickly, but as it hits the valley (the optimum) it stops rolling as fast, and then stops entirely. There is no inherent contradiction between its movement towards the valley, and its relative inertia when it reaches there.
Once again, even if @Cornelius_Hunter is ultimately right that the first cell did not arise by natural causes (which I am open to), this is not a terribly strong argument.
Of course, just because these are weak arguments does not necessarily mean that they are ultimately wrong. Perhaps God did create the first cell by first cause. Who knows? Science certainly does not consider this possibility. I do not think, however, that this possibility benefits from strong confidence in weak arguments.
To me, it seems most reasonable to start with is some humility from both sides… Although we do not consider God’s action in science itself, it certainly is not unreasonable (even given the evidence) for some to wonder if God’s direct action was required to create the first cell. And on the part of ID, recognition that the arguments (even if ultimately correct) do not warrant so much confidence. Even if ID is ultimately right about abiogenesis, that does not meant that all the details of the arguments are correct.
The reason for this humility on both sides is the same. There are limits to science. It is a fallible human activity, and we cannot expect it to reliably resolve questions like this. That is part of the reason why we hold to methodological naturalism in science, to keep these resolvable debates outside the gates, where they belong.
Following up and expanding on my previous comment, the high conservation of the DNA code means that (from an evolutionary perspective–this is not my claim) you have to have it in the LUCA. That was a profound finding. It paralleled several other findings which mandated increasing complexity in the LUCA. It was looking more and more like a modern, extant cell. Naturally evolutionists had expected the LUCA to be a primitive cell, but the evidence falsified this view.
Now add to this the ~optimality of the DNA code, and you now have an enormous problem. Not only must the canonical code have been present in the LUCA, but it could not have been an accident. It must have been the result of an astronomical search. It is extremely difficult to see how this could happen given the dependencies of coding sequences on the code, the rugged fitness landscape and fitness spike of the canonical code, the nuanced functions of the code which sometimes do not provide immediate fitness advantage. Also note that the RNA world doesn’t help these problems much. Aside from the fact that for many it has fallen out of favor, you can’t just have the RNA world take you up to the canonical code and then quickly switch over to DNA.
So the DNA code is another example of complexity being pushed farther and farther back in evolutionary history, and more and more evolutionary change being pushed into smaller, unobservable, time periods (think punctuated equilibrium).
The paper that Prof. Venema cites is written by evolutionists who take evolution as their starting point. They are assuming evolution is true, a priori, and working from there. So these issues tend to go unnoticed.
I’m sorry, but this does not appear correct from an evolutionary point of view. We do not know to what extent convergent evolution was at play, which would mean that the DNA code did not have to be entirely intact in the LUCA.
This seems to be false too. This seems to rest on a subtle but incorrect conflation.
The first cell is not the LUCA. The first cell (if it arose by natural causes, abiogenesis) would not be the LUCA at all. These are totally different entities, separated by time and space. The LUCA would be much more advanced than the first cell, and more recent too.
And regarding astronomical search, when we are talking about the origin of life, we certainly can invoke astronomical searches. Because, you know, we are in an astronomically large universe, by definition. =)
No, I think it is correct. The idea that the canonical DNA code is the result of convergence is a monumental stretch. It would be even beyond, as I mentioned above, a very heroic explanation. No leading evolutionist advocates such as view. I’ve never seen it even entertained, and would be interested if anyone has a citation for it.
In any case, in biology, when we see convergence, we also see variety. The mammalian and cephalopod eyes are considered to be convergent, but they also have fundamental differences. And in other species, there are all kinds of different vision systems. The idea that the universal DNA code is the result of convergence would be very suspect. Why are there no other canonical codes found? Why are there not more variants of the code? To have that much evolutionary distance covered, and converge with that level of precision would really be heroic.
It also would raise the enormous problem of how that much evolutionary distance could be covered when you have so many dependencies with coding sequences. And of course it would place that much more of a burden on the fitness spike of the canonical code. For instance, it would have to be a global optimum, with no completing local optimums, which is not what the findings have been saying. And the fitness would have to be easily tracked by natural selection which, again, is not what the findings show.
Increased complexity compared to what? All modern cells are complex, with a shared core of complexity, and the default assumption should be that the LUCA was the source of all of it.
Agreed.
A statement you have repeated without any argument or evidence. I see no reason that it should be true. I’ve yet to see the enormous problem here.
How large was the coding sequence when this evolution was taking place? How rugged was the fitness landscape?
What nuanced functions of the code? You previously mentioned error correction. There is no error correction in the code.
Thank you for the question Steve. The reason why the search is so large is that the number of possible codes is so large, and we assume the starting point has no a priori knowledge of the fitness landscape. Does this make sense to you, or should I expand further on this?
First, thank you for joining us with a reasoned defense of your views. I appreciate you taking the time. However, the statement above is a red herring that is often waved in front of Christians to cast doubt where none should exist.
You imply that because the researchers were “evolutionists,” they were biased. But the vast majority of biologists are “evolutionists.” Should research on evolutionary topics be limited only to scientists who don’t accept evolution? Would that qualify as “unbiased” in your mind? The fact is, the research that “evolutionist” scientists perform is reviewed and checked by evolutionists and non-evolutionists alike. That is how “bias” is weeded out, not by crying wolf.
Similarly, the vast majority of the scientific community accept evolution as “true” in the same way that they accept Relativity or Quantum Theory or the Big Bang – on the strength of the evidence and the explanatory and predictive power of the theory. A physicist working in those fields today may take those theories as a “starting point” and work from there without having to go back to the beginning and prove all over again that Relativity, for example, is true. Expecting a biologist to begin every research paper on an evolutionary topic to go back to the beginning and prove all over again the reasons to accept that evolution is true – which almost everyone working within the field already agrees with and believes anyway – is unreasonable and, if I may say so, a silly objection.