Intelligent Design

Which came first: DNA or Protein?

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A commenter quoting George Church on the ribosome in Paul’s thread reminds me of how I came to be on this side of the ID controversy.

For decades I’d uncritically accepted the notion that life could emerge from chemicals bumping together in a primordial soup and that once started it could evolve through mutation and selection into what we see today. In 1991 I read something from the ID camp that, among other things, pointed to some closely related proteins differing by just several point mutations where any of the mutations occurring singly would be fatal and where all of them occurring at once was statistically almost impossible. In other words, there was no path from A to B that natural selection could take. I suspected what they were saying might be true but in 1991 I didn’t have the time to do any due diligence on what was claimed but a seed of doubt about neo-Darwinian evolution had been planted.

I retired in the year 2000 and among other things that I suddenly had much more time for was online debates about religion and politics. I’ve always been agnostic (if not outright positive atheist) on religion. My mother told me I was questioning bible stories almost as soon as I learned to talk. We’d always had a lot of pets so I had a good idea of what’s required in the way of food and care they needed. When I was told the story of Noah and the Ark my immediate comment was that all those animals plus all the food they’d need wouldn’t fit on a wooden boat and there weren’t enough people on board to tend to their needs and clean up after them. So I have a very long history of skepticism when it comes to miraculous claims. At any rate, after a few years of arguing about religion and politics, George W. Bush was elected to a second term and politics suddenly became boring.

One of the people I’d often engaged with was a medical doctor who was also an evangelical Christian. We were both staunch conservatives so there was little disagreement on politics but we locked horns a lot on religion. Eventually the subject of evolution came up and I took the side of consensus science while the doctor took the side of special creation.

Early in the discussion he challenged me: “Dave, replication of DNA requires a lot of very complex protein machinery and that protein machinery needs a lot of DNA to store the instructions for how to make it. If you can show me which came first, DNA or protein, I’d find the rest of the Darwinian narrative a lot more convincing.” At that point I knew the basics about how DNA is transcribed to RNA and that RNA is fed through a ribosome like a paper tape to manufacture proteins. I also knew the central dogma of molecular biology that information only flows one way from DNA to RNA to protein. So off I went in search of an answer to his question. I came back to him with the RNA World hypothesis. He laughed. “Dave”, he said, “the RNA world is science fiction. There are more holes in it than there are in all the highway signs in Texas. None of the chemistry is realistic.” So off I went again to dig deeper into the RNA World hypothesis. I discovered that the doctor was correct.

In the several years since then and very much investigation into the science underlying the neo-Darwinian claims it has become nothing but increasingly more clear that the emperor is wearing no clothes. The so-called overwhelming evidence for evolution is in fact invariably evidence of common descent (nested phenotype and genotype hierarchies) with little evidence supporting the further claim that mutation and selection is the primary mechanism of phenotype and genotype modification. Indeed, the nascent field of evo-devo is putting even nested hierarchy under heavy fire through the discovery of non-homologous development pathways in closely related species!

Which came first, DNA or protein, is literally and figuratvely the mother of all chicken/egg paradoxes. I’ve written here on UD and elsewhere many times in the past that the ribosome, not the flagellum, is the structure that ID proponents should use as the leading example of irreducible complexity. George Church IMO is right. The ribosome should be our focal point. Other ID proponents, Bill Dembski in particular, say that the DNA/protein paradox is too complex for lay persons to easily grasp and the ribosome’s structure doesn’t immediately bring to mind any machines people are familiar with. And so the flagellum remains the icon of ID instead of the ribosome. I see their point but I still think we should point to the ribosome more often and thus this article.

16 Replies to “Which came first: DNA or Protein?

  1. 1
    SCheesman says:

    DaveScot: “I’ve written here on UD and elsewhere many times in the past that the ribosome, not the flagellum, is the structure that ID proponents should use as the leading example of irreducible complexity.”

    And now ATP Synthase has been added for a third archetype of irreducible complexity. I have to agree that the flagellum seems to the most easily understood to the layman of the three, but what an embarrassment of riches!

  2. 2
    bFast says:

    SCheesman:

    I have to agree that the flagellum seems to the most easily understood to the layman of the three, but what an embarrassment of riches!

    You are the master of understatement, aren’t you.

    I actually think that the flagellum is the better candidate to the ribosome and to ATP Synthase because we have a picture of what came before the flagellum, but not the other two are there in all life. As such, if either of the other two examples were selected, Behe would be accused of selecting them simply because all precursors are lost to us. The flagellum makes for a much more fruitful discussion, despite the fact that the other two are probably way more complex than the flagellum.

    I, personally, would like the discussion to be focused on the HAR1F gene. It is ultra-conserved in all mammals, possibly all quadrupeds, yet it has 18 mutations in humans. It is one of those genes (an RNA gene) that requires all 18 mutations to have occurred simultaneously. Further, it appears that the gene plays a significant role in giving humans a superior intelligence. If you look on wikipedia, you will find discussion about HAR1F, but not about the challenge of evolving the dear thing.

    Alas, Dave, even if RNA world could be proved, even if it “evolved” we still would have the problem of which came first, the machinery that translates raw code (potentially RNA) into proteins or the proteins that make up that machinery. Even if we bite deep into the RNA world hypothesis, we get no closer to solving the chicken and egg problem.

    About the “central dogma”, if you check your link carefully, it does discuss the fact that RNA can be converted to DNA. However, even this seems to be advanced lifeforms(eukaryotes). Even then, protein is never translated into information — that level of decompiling is not known to exist.

  3. 3
    DLH says:

    DaveScott

    Another chicken/egg is:

    Which came first? the ATP Synthase or RNA?
    The ATP synthase is essential to make ATP, and the ATP is essential to carry the energy needed to drive the RNA/DNA replication processes, AND for the protein expression that is essential to making the ATP Synthase etc.

    See: Are ATP energy cycles essential to life?

    ATP energy flows are ubiquitous and apparently essential to (almost all?) biochemical processes. Consequently ATP synthase is essential to (almost all?) biochemical processes.

    ATP synthase is more obviously essential than the flagellum. Models of ATP synthase generator/motor are reasonably easy to picture and explain than the RNA/DNA or even the flagellum. It is much harder to explain its origins, and much harder to explain the origin of life without it.

    Accordingly, I would recommend ATP Synthesis to be considered as a more suitable ID mascot.

  4. 4
    mike1962 says:

    Davescot: “there weren’t enough people on board to tend to their needs and clean up after them. So I have a very long history of skepticism when it comes to miraculous claims.” [Ephesis added.]

    You seem to be guilty of the Humean error.

  5. 5
    mike1962 says:

    Great article.

  6. 6
    Semprini says:

    “For decades I’d uncritically accepted the notion that life could emerge from chemicals bumping together in a primordial soup” – well nobody can blame you for that, seeing as it’s all the schools are allowed to teach; ‘just dumb molecules dumbly bumping together and turning into bacteria but it was so long ago we can;t go into details’. Here’s hoping Expelled will open some minds on that one, exposing the nonsense of lightning and mud puddles.

  7. 7
    Unlettered and Ordinary says:

    Greetings!

    I am a layman and I understand the DNA, RNA and protein paradox just fine.

    ATP is over my head.

    But back to RNA world, where on earth could you form RNA, all the hypothesis together and by a process of elimination that leaves only thermal vents deep in the ocean with tempatures way to high to make RNA. several more paradoxes. None of which are plausable, or probable.

    I just love the “fact” that we cannot make DNA or RNA through chemical reactions. Amino acids have there own problems just as complex if not more, not to even mention protiens.

    flagellum = out board motor… It is the easiest to visualize.

  8. 8
    rna says:

    SCheesman #1:

    I would not think that the ribosome fits the definition of an irreducible complex macromolecular machine since it is long known that one can take away individual parts (ribosomal proteins) without destroying core functions of the ribosome such as peptide bond formation. See: Noller and cowokers,
    Science 1992, vol. 256, 1416-1419, which gives an extreme example for this. It is also known that RNA molecules much less complex then ribosomal RNA can catalyze peptide bond formation in a chemical reaction similar to that occuring on ribosomes. See Zhang et al., Nature 1997, vol. 390, pages 96-100.

  9. 9
    andrew says:

    Hi Dave,

    Nice little article. However, I think you should do some due diligence on your little wooden boat idea – might save you some embarrassment at some future stage. From calculations/estimates I have seen, the ark was only 1/3 full on its maiden voyage – i.e. there was plenty of space for many more humans if they had wanted to get on board. As to sanitation, do you not think that if someone was able to engineer the boat in the first place, they might not have been able to devise some clever ways to clean up the mess, especially seeing they were not lacking water?

  10. 10
    DaveScot says:

    andrew

    Cut me some slack. I was 4 years old when I voiced skepticism of Noah and the Ark.

  11. 11
    Lutepisc says:

    Dave, your presentation of the whole Noah-and-the-Ark thing makes it sound as if it’s so preposterous that even a four-year-old could debunk it. Andrew is suggesting it might be more complicated than that. Can you cut him some slack as well?

  12. 12
    JGuy says:

    bFast:

    SCheesman:

    I have to agree that the flagellum seems to the most easily understood to the layman of the three,but what an embarrassment of riches!

    You are the master of understatement, aren’t you.

    I actually think that the flagellum is the better candidate to the ribosome and to ATP Synthase because we have a picture of what came before the flagellum, but not the other two are there in all life.

    Dave, Dr Cheeseman & bFast…

    It’s interesting that the best examples of IC and complexity are being voted on as some of the more complex things we can find.

    However, one scientist where I use to work stated that water was sufficient evidence of ID.

    And I believe Isaac Newton once claimed that if it were the only evidence provided, the thumb alone would be sufficient evidence of a creator.

    Anyway.. carry on. 😉

  13. 13
    DaveScot says:

    re; Noah and the Ark.

    Anyone care to explain how Noah transported pairs of animals not found locally? Start with how he obtained Australian marsupials and finish with how those marsupials got back to Australia after the flood subsided. 😆

    Here’s another one. What did the carnivores on the ark eat after they were released if not their normal prey? The prey animals only existed as a single pair so if one lion dined on one gazelle – game over for the gazelles. If one cat ate one mouse – game over for mice. If one hawk ate one pigeon – game over for the pigeon. And so forth and so on. Anyone? Bueller? Anyone?

  14. 14
    Mapou says:

    DaveScot wrote: Anyone care to explain how Noah transported pairs of animals not found locally? Start with Australian marsupials.

    LOL. Funny. Dave, the Noah story was not primarily about a flood but about how God tested the faith of one man. Noah suffered forty years of indignation and ridicule while building the ark in a dried land and he never lost faith. It is unlikely that God would jeopardize the entire ecosystem of the earth to test the faith of one man. There are less drastic methods I would think.

    I’ve heard some Hebrew scholars convincingly argue that the flood was a local flood and that only a very small part of the earth was inhabited by man at the time. In fact, in 1996, some scientists proposed that the Black sea suddenly became innundated around 6000 BC supposedly due to a rise in ocean levels. I’m sure that other massive floods have occured in the distant past. Besides, it is unlikely that the whole world would fill up with water in just 40 days from precipitation alone. Just a thought.

    At any rate, do not let errors or contradictions in the Bible be a barrier to your faith. After all, errors and inconsistencies in the scientific literature (especially darwinian theory) does not seem to affect the faith of atheists. The Bible is not the object of our worship. It is only a research document, a tool; and not the only one by any stretch of the imagination. Now we have other tools that we can use to study DNA or the cosmos, for examples.

    I am a Christian and yet I believe that anybody who claims that the Bible is infallible is an idol worshipper of sorts. Sorry, if I offend anyone in this group as I am not judging anyone’s faith including that of young earth creationists. The kingdom of God will be filled with former idolaters, murderers, fornicators, thieves, homosexuals, liars, ignoramuses, and even atheists and Darwinists. ahahaha… One man’s opinion, of course.

  15. 15
    tribune7 says:

    At any rate, do not let errors or contradictions in the Bible be a barrier to your faith.

    It was the rather minor contradictions in the NT that helped convince me the important parts were true.

    Clearly there was no attempt to collaborate among the Gospel writers, and clearly the religious authorities felt the works were authentic enough not to re-write them to make them match when the matter stabilized.

  16. 16

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