Shaky Foundations

Over at the blog Jesus Creed, RJS writes:

DNA is capable of passing information on from generation to generation – but it is not reactive and requires a complex series of reactions involving proteins for replication. Production of these proteins of require both RNA and additional proteins for transcription, and translation. The interrelated reactions are quite complex. DNA is a fairly stable (unreactive) molecule, making it good for information storage, but the chemistry of DNA is simply not rich enough for life to originate from DNA.

Proteins have a very rich chemistry and can perform many functions. But they are not capable of replication. There are no specific interactions that allow one amino acid chain to produce an identical chain.

Therefore – life did not originate with proteins, nor did it originate with DNA.

What RJS presents is the classic, foundational argument for the RNA world:

  • DNA is inert, but it passes on information across time.
  • Proteins don’t pass on information across time, but are reactive.
  • RNA is both reactive and passes on information across time.
  • Since life requires both reactivity and the ability to transmit information, life must have started with RNA.

But it’s not a simple as this.

First, DNA is not inert.  Scientists have created a whole set of DNA enzymes known as DNAzymes. Here is a short excerpt from just one research article using these DNA-enzymes:

The 10–23 RNA cleaving DNAzyme is a catalytic nucleic acid composed entirely of DNA (Fig. ​(Fig.1)1Figure 1) (1). It was derived from a combinatorial library of sequences by in vitro selection. The tremendous activity and sequence specificity against its target RNA under simulated physiological conditions (2,3) has generated the expectation that it may function in cells as a gene suppression agent.

Yes, the reactivity is limited and man-made, but that is just an observation of our current understanding.  The point that matters is that DNA is not inert.

I would also add that proteins can pass on information – simply consider prions and evolution:

Prions speed evolution

Darwinian Evolution of Prions in Cell Culture

In reality, all three biomolecules (RNA, DNA, and proteins) are reactive and transmit information.  One can make arguments about differing degrees, that are a function of our current  understanding, but the forceful beauty and simplicity of the original argument for the RNA world is gone.

Look, I don’t deny the existence of the RNA world.  But I would remind people that the RNA world is neither a fact nor a well supported theory – it is a hypothesis/speculation that amounts to a vague “looks like” argument supported by strands of circumstantial evidence with a mixed bag of predictive success.  That’s it.  While I cannot deny the RNA world once existed (it sounds plausible and would fit well within a teleological explanation), neither can I cheerlead for the RNA world because of some serious, fundamental concerns.

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7 responses to “Shaky Foundations

  1. I’m curious about two things:

    1. Yarus’s work showing chemical affinity between some amino acids and their codons or anti-codons. Do you think it fits into an RNA world scenario better than into a whole cell (DNA, RNA, proteins, etc.) scenario? Would it fit equally well into a DNA world scenario?

    2. Since you mentioned it, I’m curious how you think an RNA world would fit well within a teleological perspective?

  2. Hi Bilbo,

    1. No, I do not think Yarus’s work fits into an RNA world scenario better than into a whole cell (DNA, RNA, proteins, etc.) scenario.

    2. For starters, consider that an RNA world would clearly front-load the existence of a DNA-world, as even RNA world enthusiasts acknowledge the strong selection pressure for such a transition that would be facilitated by the need for minor biochemical changes. Also, the role of RNA expands tremendously with the appearance of eukaryotic cells and then metazoan life. In fact, I can already make the case that RNA itself (with or without the hypothetical geological RNA world) helped to nudge the appearance of metazoan life.

  3. Mike wrote: “1. No, I do not think Yarus’s work fits into an RNA world scenario better than into a whole cell (DNA, RNA, proteins, etc.) scenario.”

    I think Art and Zachriel would want an explanation for why so many amino acids have affinity with their codons or anti-codons.

  4. Very good. Yarus’s work does add plausibility to the RNA World in the sense that it is one piece of circumstantial evidence that makes it look more like an RNA world once existed. But before getting to why so many amino acids have affinity with their codons or anti-codons, it is a good idea to set the stage.

    First, am I correct in noting that Yarus’s work does add plausibility to the RNA World in the sense that it is one piece of circumstantial evidence that makes it look like an RNA world once existed or does his work go much further, constituting some type of powerful, objective evidence that should compel folks to embrace the RNA world as a historical fact?

    Second, does the RNA World hypothesis predict that such affinities would not serve a current utility in cells? In other words, if such an explanation is found, would this falsify the RNA world? Or at least weaken the hypothesis?

  5. Mike: “…or does his work go much further, constituting some type of powerful, objective evidence that should compel folks to embrace the RNA world as a historical fact?”

    I don’t think so, though Art or Zach would know more about this.

    Second, does the RNA World hypothesis predict that such affinities would not serve a current utility in cells? In other words, if such an explanation is found, would this falsify the RNA world? Or at least weaken the hypothesis?

    Yes, I think if we found that such affinities served a current utility this would weaken the RNA world hypothesis. Or at least, Yarus’s evidence for it.

  6. I don’t think so, though Art or Zach would know more about this.

    I agree. Though the critics will struggle in agreeing with us because they are invested in the notion that my approach is nonsense because it boils down to subjective appearances. Thus, it would be hypocritical to naysay my approach while admitting they employ it to support the RNA world. As such, you can expect them to engage in all sorts of rationalizations to explain why their approach is something more than citing clues that make it look like the RNA world once existed.

    Yes, I think if we found that such affinities served a current utility this would weaken the RNA world hypothesis. Or at least, Yarus’s evidence for it.

    You are moving too fast here. Does the RNA world hypothesis predict that such affinities would not serve a current utility in cells? I’ve never seen this prediction. That’s because, the RNA world hypothesis can easily co-exist with cells making later use of these intrinsic affinities. In other words, the RNA world makes no prediction here. Whether cells currently make use of these affinities or not, the RNA world fits both findings equally well.

    So you began by noting, “I think Art and Zachriel would want an explanation for why so many amino acids have affinity with their codons or anti-codons.”

    Yeah, they probably would. But it’s not the RNA world hypothesis that is being tested with such a demand. So what would they be trying to test?

  7. On RNA Cell Faring Programs

    The chicken and egg story…
    RNAs are still Earth’s primal organisms, who made the genome as their functional working templates…(BTW, they also made the cell enclosing membranes as their functional organs…)

    Cell Faring Programs Involve Transcription Factors,
    Made By RNA Genes From DNA Templates Made By The Genes,
    Transcription Factors That Activate Genes,
    The RNA genes.

    A. TGF-beta acts as a transcription factor
    http://www.answers.com/topic/tgf-beta
    Transforming growth factor beta (TGF-beta) is a protein synthesized by skeletal cells, found in most species, that controls proliferation, cellular differentiation, and other functions in most cells.

    B. Myc produces DNA binding protein
    http://www.answers.com/topic/myc-2
    myc = Any of a group of vertebrate oncogenes whose product, a DNA binding protein, is thought to promote the growth of tumor cells. Possibly from my(elo)c(ytomatosis virus).

    C. From “How Cells Protect Themselves from Cancer”
    http://www.sciencedaily.com/releases/2010/03/100316101653.htm

    – Two protection programs work together, through an interaction with normal immune cells, to prevent tumors.

    – The oncogenes themselves can activate these cell protection programs in an early developmental stage of the disease. They trigger apoptosis (programmed cell death), and senescence (biological aging) is triggered by another oncogene, the ras gene. Senescence stops the cell cycle, and the cell no longer divides.

    – First Myc oncogene triggers apoptosis in the lymphoma cells. The dying cells attract macrophages of the immune system, which devour and dispose of the dead lymphoma cells. The thus activated macrophages secrete messenger molecules (cytokines), including the cytokine TGF-beta, which can block the growth of cancer cells in the early stage of a tumor disease, by switching on the senescence program.

    D. From “Red and white blood cells come from different sources” ???
    http://www.sciencenews.org/index/generic/activity/view/id/56929/title/Researchers_distinguish_two_different_types_of_blood_stem_cells_
    Researchers (in mice) distinguish two different types of blood stem cells??? All stem cells are not created equal???

    – In the blood, millions of diverse cells die every second. To keep up with this loss, stem cells continually divide to create the correct balance of cell types, which include oxygen-carrying red blood cells and a menagerie of immune cells.

    – The hitherto thought was that one single type of blood stem cell in the bone marrow continually replenish the blood system throughout a person’s life. Recent studies hinted that blood stem cells have distinct behaviors, but the different kinds of cells were pinpointed only now, using different dye stain markers.

    – While each type of stem cell was able to produce every kind of blood cell, the team found a clear difference in end-products ratio: One type of stem cell produced many more red blood cells than immune cells, and vice versa.

    – What’s more, as the mice aged, the relative amounts of these stem cell types shifted. As mice got older, the stem cells that create more red blood cells made up a larger proportion of all stem cells, beating out the immune-cell–biased stem cells.

    – The researchers also observed that TGF-beta1 spurs red blood cell–producing stem cells to divide and at the same time represses division of their immune cell–producing counterparts. They suggest that these different actions of TGF-beta1 may allow fine-tuning of the ratio of different stem cell “subtypes”.

    Dov Henis
    (Comments From The 22nd Century)
    03.2010 Updated Life Manifest
    http://www.the-scientist.com/community/posts/list/54.page#5065
    Genomes Are RNAs-Made Patterns-Manuals
    http://www.the-scientist.com/community/posts/list/260/122.page#4819

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