Biological Information and Intelligent Design: Signature in the Ribosome

(Dennis Venema) #3

You’re welcome. I’m happy to answer questions folks might have as well.

(sy_garte) #4

Thanks for another great article on this subject, Dennis. Reading your piece made me think of another possible implication of the stereochemical hypothesis. The Johnson and Wang work is very suggestive of another possible strike against an ID theory - the notion of irreducible complexity.

It has been suggested that RNA world ribozymes probably transitioned to RNA plus peptide (small protein chains) which would have been more catalytically active than pure RNA ribozymes. So the amino acid-codon/anticodon stereochemical linkages might have developed as a way to improve ribozyme activity (although how such evolution might occur in the absence of translation is mysterious). Then by the same kind of exaptation process that led to the eye, the flagellum etc, the stereochemical binding between amino acids and their corresponding aptamers became the forerunners of an entirely new process - translation and protein synthesis.

I believe I have seen this hypothesis before, but I havent seen it linked to refutation of IC or ID.

(Dennis Venema) #5

Yep- my thoughts are the same as yours - it’s quite possible that translation was exapted from a stereochemical function. I don’t think I’ve seen that discussed in the context of ID before either - then again, there are very few folks who take on ID and also discuss chemical evolution in detail.

(Roger A. Sawtelle) #6

Specifically, they claim that the genetic code is a “genuine code”—i.e. one constructed directly by an intelligent agent—and not a set of correspondences that arose through a natural process. - See more at: http://biologos.org/blogs/dennis-venema-letters-to-the-duchess/biological-information-and-intelligent-design-signature-in-the-ribosome#sthash.ZE1luOPb.dpuf

@DennisVenema

We are starting an argument based on false premises which invalidates the whole argument, both pro and con. A code is a language. Languages are not directly constructed by an intelligent agent, but they evolves and continue to evolve. This definition appears to be artificially constructed by IDers.

To say that a code or language could not be “a set of correspondences that arose from natural correspondences” means that God could not use a language or code as part of God’s Creation, even though Jesus Who is God is also the Word, which means that God did use language or code for the Creation.

Most people are not aware of it, but math is a language or code. Mario Livio raised the question, Is God a Mathematician? The answer is Yes and one of the languages God speaks is the international language of math. The language of math works because it is based on natural correspondences.

God can create using madth because God designed the universe with “natural” correspondences, and enables humans to recognize these correspondences. The same with the language of DNA.

Nature works because it is rationally structured. Humans can understand how nature works because it is rationally structured. Nature is designed by God because God is Rational, as well as Powerful and Good.

(Vincent Torley) #7

Hi Dennis. I enjoyed reading your informative article. It has made me rethink the “genetic code” argument.

By the way, I wanted to ask you what you think of these articles:

http://www.bbc.com/earth/story/20161026-the-secret-of-how-life-on-earth-began “The Secret of How Life on Earth began” by Michael Marshall)

http://bio-complexity.org/ojs/index.php/main/issue/current (two articles by Hossjer, Gauger and Reeves on human ancestry: in a nutshell, they believe in Adam and Eve but argue that they were created as genetic chimeras, at an unspecified time in the past)

Any comments you’d care to make?

(Dennis Venema) #8

Thanks for those links. Where to begin with the BIO-Complexity paper?

First off, the paper is based on “created diversity” within an original founding couple, who are from the Middle East rather than from Africa. This sounds a whole lot more like special creation than “ID”. Why would an ID advocate care if a designer created humans as a pair (rather than a population), and why would they care that they be created in the Middle East (rather than in Africa)? The obvious answer is to comport with a particular interpretation of Genesis.

Also, how this “created diversity” can explain current genetic diversity is not explained. For example:

“If the first human couple was created with DNA diversity, there are four different copies of each non- sex chromosome; two in the male founder and two in the female one. Their four chromosomes have since then been scrambled by ancestral recombinations, and today each of us has inherited one mosaic of the four founder chromosomes from our father, and another one from our mother.
The DNA blocks can be seen in all human populations, but they tend to be longer for non-Africans than for Africans. This may indicate that African populations are older, but it is also possible that recombinations happen more often among Africans, as some recent research indicates [50].”

There are several issues here: African DNA is much more diverse than non-African DNA, both in allele diversity at single loci and in haplotypes of linked alleles. This type of handwaving (and no, the cited paper does not offer a reasonable explanation) does not explain away the problems.

So, short answer: the paper is a (poor) attempt to argue for a predetermined conclusion that humans were specially created as a pair in the Middle East. It does not offer a mechanism to deal with the obvious problems of such an approach other than an appeal to “created diversity” - but even that appeal does not explain how present-day diversity could have largely resided in two individuals.

Perhaps Steve @glipsnort might offer more comments if he has the time.

(Benjamin Kirk) #9

And to give the most charitable interpretation, the authors simply don’t understand the fundamentals of genetic diversity (polymorphism). They particularly don’t understand the role of recombination.

(Steve Schaffner) #10

Yeah, there are many problems with the paper. Its descriptions of previous work is often inaccurate. For example, it cites ref. 49 to claim that Y chromosome diversity is smaller than previously believed. Ref. 49 doesn’t say that at all, and in reality the relevant Y chromosome diversity – the length of the oldest branches – was shown in 2013 to be much higher than previously thought, when a new, highly divergent branch was discovered.

Other examples: Sanford’s paper on waiting times in hominids does not show that that hasn’t been enough time since human-chimpanzee speciation for evolution to work (unless you make idiotic assumptions, that is). Haplotype blocks, to the extent that they’re a real thing, cannot be explained by single early instances of recombination; since their first description (their ref. 60(*)), their characteristic feature has been that multiple recombination events were required at their ends, to break up multiple haplotypes.

More seriously, the paper simply does not address the actual genetic evidence for a large ancestral population size. As we have discussed previously in another thread here, you can inject any amount of genetic diversity into Adam and Eve, but that diversity won’t look anything like the actual diversity we see. What we see has a characteristic frequency distribution that falls off as 1/frequency, so that there are many more rare variants than common ones. Genetic variants in Adam and Eve would all be at high frequency, since the lowest frequency variant you can have with 2 individuals is 25%.

The other strong piece of evidence that human genetic variation is the result of accumulated mutations is that it looks like accumulated mutations. That is, kinds of mutations that we know happen very frequently also appear very frequently in modern genetic variation, and kinds of mutations that occur rarely are seen in variants. (Strikingly, exactly the same pattern is also seen in genetic differences between humans and chimpanzees. My prediction is that you will never see a creationist address this simple fact.)

Really not a good paper.

The second paper strikes me as nuts, by the way: complete overkill in fitting out a highly detailed model when they have no idea whether they can get the coarsest features right with their proposed solution.

(*) I will note that I was, for inexplicable reasons, included as an author on that paper, to which I contributed very little. (On the other hand, I worked my butt off on ref. 61.)

Glipsnort responds to a critical article
(Chris Falter) #11

Dr. Torley -

Hope you are doing well by God’s grace today. Thanks for sharing the links. I am not a biologist, so I cannot provide the same kind of feedback as the others who have already responded. However, the Bio-Complexity papers do not address the strong evidence for common descent of humans and other primates that pseudogenes and endogenous retroviruses provide. In case you have not already seen it, our friend Steve Schaffner has posted a video analysis of his own research on how pseudogenes and ERVs point to common descent among primates.

Assuming for the sake of argument that it were possible that all of humanity descended from a single mating pair who lived ~50,000 years ago, I would still have to conclude on the basis of evidence from pseudogenes and ERVs that the ancient “Adam and Eve” were descendents of a common ancestor with other primates. Or I would have to believe the omphalos theory – i.e., God created that single pair to look as if they evolved from earlier primates.

How much Human and Chimp DNA have we compared?
(Vincent Torley) #12

Hi Dennis, Ben, Steve and Chris,

Thank you very much for your kind responses. With regard to the “created diversity” of the original couple: I assume that the authors of the paper would be willing to countenance the possibility that Adam and Eve may have been genetically engineered over a span of millions of years, via intelligently guided mutations occurring in the genes of their hominid ancestors. One could even call that special creation, if one wanted to. The question which interests me is whether the hypothesis of an original pair (however created), each of whom was a genetic chimera, is consistent with the evidence we observe today. From what you’re telling me, it isn’t.

Let’s leave aside the issue of where this original couple lived: there’s enough ambiguity in Genesis 2 to include the possibility that part of the Garden of Eden was in Ethiopia (the land of Cush). That doesn’t interest me so much.

Dennis seems to be arguing that “created diversity” is scientifically ad hoc (I agree, but I don’t think that’s a fatal flaw), and that this hypothesis fails to explain “how present-day diversity could have largely resided in two individuals.” Ben accuses the authors of misunderstanding the role of recombination in generating genetic diversity. Steve points out an error in the paper regarding Y chromosome diversity, and another error relating to waiting times in the hominid line. More tellingly, “chimera” models of Adam and Eve fail to account for the actual pattern of genetic diversity we observe today - in particular, the existence of rare variants. Additionally, human (and chimp) genetic variation appears to be the result of accumulated mutations. Finally, Chris contends that regardless of whether Adam and Eve were real people, they must have shared a common ancestor with other primates (I agree).

So it looks like monogenism (or monogenesis, as some prefer to call it) - i.e. the hypothesis that there was a single original couple from whom all other humans are descended - is ruled out by the scientific evidence. I’d now like to discuss two other hypotheses.

Back in the sixties, it was common for “progressive” Catholic theologians to argue that Adam may have simply been the leader of a small tribe of people, who were willing to abide by his decision regarding the fate of the human race. Hence, “in Adam all sinned.” That suggestion would work if the set of original ancestors numbered less than 100. But if it numbered 5,000, as Steve is suggesting, then it’s far less plausible. However, Steve appeared to hedge his bets in his video, regarding times beyond about one million years ago. Personally, I firmly believe that Neanderthal man and Denisovan man were truly human, as well as their presumed common ancestor (either Heidelberg man or Homo antecessor) but I’m unpersuaded that the smaller-brained Homo erectus was - which would imply that the first human beings must have lived around one million years ago. So my question is: how sure are we that the size of the human population back then was always more than 1,000 (or for that matter, 100)? What’s the lowest it could plausibly have been, in the light of the genetic evidence?

The other hypothesis I’d like to mention is that proposed by Kenneth Kemp: God infused a rational soul into two particular hominids at the beginning, making them truly human, but He refrained from infusing a rational soul into Adam and Eve’s hominid relatives: theologically speaking, they were just beasts. After the Fall, Adam and Eve mated with these beasts, generating the genetic diversity we observe today in humans. Can anyone see any problems with Kemp’s hypothesis?

(Jay Johnson) #13

It depends what you think of the soul. If the literal Adam and Eve possessed a soul, and their offspring had a soul, as did theirs, etc., then you have a situation where some humans who happened to have the literal Adam and Eve in their lineage would possess a soul, while other humans who did not descend directly from A&E wouldn’t. How long did this situation persist? Seems to me to open the possibility of some “soulless” human beings walking the planet right now. Which, come to think of it, could explain a lot …[quote=“vjtorley, post:12, topic:5974”]
Personally, I firmly believe that Neanderthal man and Denisovan man were truly human, as well as their presumed common ancestor (either Heidelberg man or Homo antecessor) but I’m unpersuaded that the smaller-brained Homo erectus was - which would imply that the first human beings must have lived around one million years ago.
[/quote]

You may be right, if we judge “human” by brain size alone. I’m more intrigued by the population bottleneck about the time that Neanderthal died out. The so-called “Great Leap Forward.” But, that still leaves a lot to be worked out…

(Dennis Venema) #14

On issue with this view is that there is no clear line of demarcation between erectus and other hominins with respect to brain size. It’s a continuum, with no easy place to draw a line.

(Jay Johnson) #15

Perhaps someone can explain this to me, since I am ignorant of “normal” procedure in peer-reviewed scientific journals. BIO-Complexity explains its peer review process thus:

“The most significant form of peer review begins when a completed work is made publically (sic) available for examination and response. The goal of pre-publication peer review should therefore be to decide whether the work in question merits the attention of experts, rather than to predict the final result of that attention.”

To me, the standard of “merits the attention of experts” seems like a pretty low bar. It also seems odd that the journal promises that “each Research Article will be followed by a brief published Critique when this becomes available,” but I could not find a single published Critique (this “most significant form of peer review”?) for a single Research Article. Perhaps none have become available since 2010, when BIO-Complexity started publishing?

(sy_garte) #16

I agree with this Jay, based not on brain size (which as Dennis points out is a tricky metric) but on anthropological evidence of cultural advance. More recent work suggests that the Great Leap Forward or Upper Paleolithic Revolution of 50,000 ya was not really a revolution, but a much slower and more gradual change starting around 100,000 ya, but only in Africa among H. Sapiens. This is not to say that Neanderthals and the other humanoid groups were inferior intellectually, but they were lacking in several cultural attainments (advanced tool making, fishing, art work).

I agree with the Kemp theory, which unlike Jay’s point, and my response to it above is as much a theological as it is a scientific idea. It does have the advantage of being scientifically valid, and falls into the “Federal Headship” category of beliefs about A and E. I would not necessarily consider the other Sapiens at the time to be beasts, however, but simply not fully formed humans, perhaps with some degree less consciousness (or soul, or Godly input).

Because of pedigree collapse, all human beings alive today (and also alive at the time of the rise of civilization) would be direct (biological) ancestors of Adam and Eve, if they lived (as we are assuming they did) 50,000 ya or earlier, before the start of the major migrations out of Africa of H. Sapiens.

(Jay Johnson) #17

Interesting. Does this explain why past lives regression always winds up a king or queen, rather than a serf? haha. I assumed that sooner or later something like pedigree collapse would kick in (even though I didn’t know what it was called), which is why I just left open the possibility of present-day soulless humans. It still seems that many generations would be required before pedigree collapse kicked in and everyone could count Adam and Eve in their lineage. Possible, but it just seems odd to postulate a time, and possibly a long time, when some humans had a soul and others didn’t.

Anyway, it’s interesting to speculate, but I think science is ruling out the possibility of a literal Adam & Eve. Gen. 2-3 seem to demand a non-literal reading. The only reason not to interpret it that way is because of NT references that seem to require a literal Adam, such as Rom. 5. The issue then becomes one of hermeneutics, interpretation, and the myriad ways the NT authors use the OT. I haven’t got it all worked out yet, but stay tuned … Lol

Edit: added a bit to the first paragraph and fixed typos

(Cornelius_Hunter) #18

Is it a problem that whereas evolutionists predicted the code to be mundane, it was found to be special code (e.g., “1 in a million”)?

(Dennis Venema) #19

Hello Cornelius,

I’m not sure what you mean by “predicted the code to be mundane”.

There is evidence that the code we now have was optimized, through natural selection, after an initial code was established. The paper I discuss in this post is relevant to that hypothesis - this paper strongly suggests that codons were reassigned over time. So, the code we have is optimized, yes - but it did not come about all at once.

(Cornelius_Hunter) #20

Sorry, I thought you would be familiar with this prediction. It can be traced back to Francis Crick’s well known phrase that the DNA code is “a frozen accident,” and was elaborated on and amplified by later evolutionists. If you are familiar with Mark Ridley’s Evolution text, for example, he writes: “The code is then what Crick called a ‘frozen accident.’ The original choice of a code was an accident; but once it had evolved, it would be strongly maintained.” 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 and my question for you was: Does that count as a problem?

Well this brings me to a related question. Since the code is strongly conserved, across the species and billions of years, evolutionists must conclude that the code cannot evolve (hence Crick’s “frozen” description). So my question is, regarding your comment: 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?

(Dennis Venema) #21

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.

Perhaps @Sy_Garte, @Swamidass, or @glipsnort might have other thoughts.

Best,

Dennis

(sy_garte) #22

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.