The Enigma of Lamarckism

Lamarckism (or Lamarckian inheritance) is the idea that an organism can pass on characteristics that it acquired during its lifetime to its offspring (also known as heritability of acquired characteristics or soft inheritance).

– Wikipedia

Many of us have probably been taught that Lamarkian inheritance is anathema. Heresy. But why would that be the case? Is it for theoretical reasons or simply because of a lack of empirical evidence?

Let’s transition to a hypothetical RNA World.

Must it not have been the case that in the RNA world inheritance was strictly Lamarckian? How could it have been otherwise?

So at some point there must have been a transition from Lamarckian inheritance to Darwinian inheritance. Why would that be an advantage and why would vestiges of Lamarkian inheritance not still be evident?

What do readers think?

74 thoughts on “The Enigma of Lamarckism

  1. Mung: And why?

    The designer wanted it that way. I like ID, it’s so simple. Now, please continue with your “I just want to learn, I’m only asking questions” facade.

  2. Mung: Sequence is a mathematical term. You’re confusing the map with the territory.

    “Sequence” is not an exclusively mathematical term. It is widely used elsewhere, and probably adopted from there into mathematics.

  3. Mung: The typical story goes something like this:

    There was a self-replicating molecule.
    Replication wasn’t perfect.
    Therefore there was Darwinian Selection.
    And that explains everything.
    Therefore Life

    I’ll give you credit for having mastered the ridiculous strawman creationist version of evolution.

  4. keiths: 3. Your knowledge of molecular biology is abysmal.

    Another fact-free statement brought to you by keiths. keiths, your people-skills are abysmal. We’re not talking molecular biology here, because we are not talking about living systems. Do you want to discuss or engage in insults? Your call.

  5. Neil Rickert: I’ll give you credit for having mastered the ridiculous strawman creationist version of evolution.

    Thank you!

    But please try to keep up, Neil. I don’t think we have Darwinian evolution in the RNA world. (Any more than we have Lamarckian inheritance.)

    Feel free to educate me. You and your buddy keiths. Do try.

  6. Neil Rickert: I’ll give you credit for having mastered the ridiculous strawman creationist version of evolution.

    Is this evolution you speak of sort of like the theory of modern medicine?

    Is it unfalsifiable because it is too complex and there are just way too many vagaries to articulate in one place?

    Its kind of hard to make a strawman out of a theory that can’t even be defined isn’t it?

  7. keiths: The nucleotide sequence, Mung. RNA molecules consist of sequences of nucleotides just as protein molecules consist of sequences of amino acids.

    Protein molecules spontaneously fold into a 3D configuration. So do RNA molecules. How do you propose to copy a 3D folded protein?

  8. Neil Rickert,

    “…it’s complex, and detailed, and leaves quite a lot of things unanswered, or answered ambiguously.”

    I believe this is how you all describe your theory, right?

  9. Elizabeth: Oh, I see what Mung is getting at. I thought he was asking how RNA-based life would reproduce.

    Please share it with everyone else. My communication skills must suck.

  10. Elizabeth: I do suggest you check it out, Mung, not to be convinced, but at least to see what the argument is.

    The animations are very clear.

    🙂

    Well, I saw 3D shapes where you saw 2D shapes. So… lol

    I did read the text. I did watch the animations. That’s how I reached the conclusion they were leaving out relevant steps.

    Can you state simply, the steps they offer? For example:

    1. a bunch of RNA molecules can stick to clay.

    I’ll be happy to point out missing steps. Such as, how do a bunch of RNA molecules stuck to clay become a sequence? How do a bunch of RNA molecules stuck to clay become a self-replicating molecule?

  11. Elizabeth: The RNA molecule doesn’t have to “fold” to self-replicate.

    If it does not fold it has no ability to catalyze any reaction. Are you simply unaware of the reasons behind the RNA World hypothesis?

    Wikipedia:

    The RNA world refers to the self-replicating ribonucleic acid (RNA) molecules thought to have been precursors to all current life on Earth. RNA stores genetic information like DNA, and catalyzes chemical reactions like an enzyme protein.

    The two go hand in hand, and I invite you to present evidence to the contrary.

    Elizabeth:

    A single RNA strand can form a double strand without an enzyme in an environment rich in its constituent nucleotides, because each nucleotide on the strand will tend to bind to its matching pair, forming a double strand, where the second strand has the same sequence information as the first (only with the pairs reversed).

    By this exact same logic, the RNA strand will fold on itself and prevent any such binding to other RNA strands which would enable any copy to take place. That is precisely what I have been trying to point out all along.

    At best you get an RNA strand that has folded to itself and to which random other bits of RNA (not a strand) have managed to attach themselves.

    Not a basis for self-replication.

  12. Elizabeth: A polymer with a double strand (like RNA or DNA) can split, and then the two halves attract monomers to complete them. So you then end up with two double strands, with the same sequence.

    We know DNA is a double strand. We also know the strands don’t just separate by magic invocation and magically attract monomers.

    What is the basis for the belief in double-stranded RNA in the RNA World, and what was the mechanism by which the strands were separated and copied such that two identical double-stranded RNA were the result? Heat? Heat is not a mechanism.

  13. Elizabeth: One may, in fact, have properties that cause it to fold, while the other does not.

    1.) If one folds and the other does not we hardly have a self-replicating molecule.

    2.) What is the basis for your belief in non-folding strands of RNA?

  14. RNA is fundamentally a minor variant of DNA (actually, it’s the other way around, if we assume RNA First). It behaves in the same way. If you have double stranded RNA, neither strand will fold due to the presence of the other. Separate the two strands and – if conditions are right – one or both will fold. In that folded configuration, it is true that can’t be replicated, although (compared to peptides) it’s a relatively easy matter to reconstitute a replicatable version.

    But it’s not necessary to imagine a functional single-strand ribozyme being replicated. A simpler version of the modern double-stranded genome with transcription would work in principle: a double stranded RNA genome from which functional transcripts can be extracted in high number. Note that transcription is mechanically almost exactly the same as replication – if you can do one, you are but a tiny step away from being able to do the other.

    It’s actually hard to avoid double stranded RNA – if you could create a template copy of a single strand, the new copy is very likely to anneal to the template. So the first copy of a single strand cannot fold – it’s prevented from doing so by the template. But every subsequent copy can, provided you don’t also copy the antisense strand.

    So in my view double stranded genomes were likely there pretty much at the start, an almost unavoidable consequence of the chemistry of nucleic acids. From this, both replication and bulk generation of enzymes are possible, without a whiff of Lamarckism.

    One might ask how ribozyme extraction was controlled, and obviously I don’t know. Nonetheless, from a double stranded precursor, any short segment that functions as a polymerase is likely to light a powerful fuse, providing as it does both polymerase-in-bulk and replication.

  15. Mung: 1.) If one folds and the other does not we hardly have a self-replicating molecule.

    Well, you get a self-renewing molecule, plus a supply of enzymes. And if one happens to help the replication process, then you may get renewed double strand + enzyme on some occasions and two double strands on others.

    The point is that there is potentially a way for RNA to code for its own replicase.

  16. The point is that there is potentially a way for RNA to code for its own replicase.

    Yes, and there is a great deal of research directed at RNA polymerization, elongation, and replication. One of the most promising, or at least quite interesting, lines of research is the eutectic phases of water which promotes RNA polymerization via increased catalytic activity and kinetics as the freezing process concentrates solutes in the voids between the ice. Additionally, dilute solutions, which contain some lipid components, have been found, with desiccation, to produce the same sort of increased kinetics and polymerization as eutectic phase chemistry.

    http://www.ncbi.nlm.nih.gov/pubmed/12448990

    http://www.nature.com/ncomms/journal/v1/n6/full/ncomms1076.html

    https://mitpress.mit.edu/sites/default/files/titles/alife/0262290758chap4.pdf

    http://flint.sdu.dk/index.php?page=non-enzymatic-replication

    http://www2.mrc-lmb.cam.ac.uk/groups/ph1/rna_self.html

  17. Allan Miller: If you have double stranded RNA, neither strand will fold due to the presence of the other. Separate the two strands and – if conditions are right – one or both will fold.

    OK. But we’re talking RNA.

    What is the basis for Elizabeth’s faith, and yours, that RNA will both fold and not fold? It’s reasonable to assume, is it not, that both strands exist in the same conditions?

    Elizabeth:

    One [strand] may, in fact, have properties that cause it to fold, while the other does not.

    Magical properties? Do tell.

  18. Mung,
    Regarding the folding propensities of RNA polymers, just google tRNA and check out the images. The spacial orientations emerge from the sequences of nucleotides. They don’t need a folder.

  19. Alan Fox: They don’t need a folder.

    I don’t even know what that means. Where did I ever say that RNA (or tRNA) requires “a folder”?

    My entire argument in this thread has been based upon the observation that RNA folds. Spontaneously. Without “a folder.”

    Elizabeth says RNA folds into a 2D shape. I claim RNA folds into a 3D shape.

  20. Mung,

    OK. But we’re talking RNA.

    You seem to be under the common misapprehension that RNA only exists in single stranded form. That is incorrect. Whenever base pairing occurs, it’s double stranded. We tend to think of ds DNA and ss mRNA/tRNA, but the latter are only single stranded because there happens not to be a complement around, while the former are double stranded because there is. A bare strand means simply that there is an odd number of complementary sequences.

    RNA very readily forms the double stranded structure – it’s the basis of PCR, of RNA probes, of binding of RNA inhibitors and promoters. It’s also the basis of folding.

    What is the basis for Elizabeth’s faith, and yours, that RNA will both fold and not fold? It’s reasonable to assume, is it not, that both strands exist in the same conditions?

    There’s either one or two strands, and you get different behaviour depending on that. Complementary sequence in two antiparallel stretches of nucleic acid tend to find and bind to each other. Those antiparallel stretches can be two different strands – such as a template and its recently-synthesised complement – in which case the structure is unfolded. Folding is inhibited by the double stranded form.

    Alternatively, the sequences may be on different parts of the same strand, in which case the result is a folded RNA molecule. If you look at this piece on tRNA structure, you will see that G-C A-T base pairing occurs at various parts of the molecule. If there were a full complementary strand floating about, the tRNA would not fold, because the binding energy would be stronger between the full complements than between the internal short stretches of complementarity in the tRNA. ‘anti-tRNA’ is inhibitory to tRNA folding.

    So, depending on the length and location of available complementary stretches, RNA may be rendered folded or unfolded by the same mechanism – base pairing. And that’s how you can have both a genome and ribozymes, all made of RNA.

  21. Allan Miller: You seem to be under the common misapprehension that RNA only exists in single stranded form.

    Hardly. I have difficulty understanding where you even came up with this idea.

    https://en.wikipedia.org/wiki/Double-stranded_RNA_viruses

    You seem to be under the common misapprehension that RNA only exists in single stranded form. That is incorrect. Whenever base pairing occurs, it’s double stranded.

    Which of my statements that RNA folds on itself spontaneously did you not understand? By your definition, that would make it double-stranded. Right?

    My argument, if you’ve been paying attention, depends on RNA not just magically existing as a single strand sitting around waiting to be copied.

  22. Mung,

    Me: You seem to be under the common misapprehension that RNA only exists in single stranded form.

    Mung: Hardly. I have difficulty understanding where you even came up with this idea.

    It was the only way I could make sense of your response in the following:

    Me: If you have double stranded RNA, neither strand will fold due to the presence of the other. Separate the two strands and – if conditions are right – one or both will fold.

    Mung: OK. But we’re talking RNA.

    It looked as if you has misread RNA as DNA. Otherwise, ” OK. But we’re talking RNA” is simply redundant as a response.

    My argument, if you’ve been paying attention, depends on RNA not just magically existing as a single strand sitting around waiting to be copied.

    I see no evidence that you paid attention to my prior post. I explained therein how the presence of RNA in single or double stranded form is critically important to folding. It was in answer to the following:

    What is the basis for Elizabeth’s faith, and yours, that RNA will both fold and not fold? It’s reasonable to assume, is it not, that both strands exist in the same conditions?

    Just to be clear, folding is caused by local stretches of complementarity, but folding is prevented by the entire strand having a complement. You seem to wish to word-game on ‘double-stranded’. The term ‘double stranded’ tends to refer to the entire strand having a complement, although clearly (and as I said) folding itself is caused by local dsRNA pairing.

    Which strawman position are you currently attacking? You have given two summaries of what your ‘entire argument’ is about (having quietly dropped the reference to ‘Lamarckism’), and it looks as if you think a ribozyme cannot be copied because it folds. However, it only folds when single stranded. A double stranded genome can produce functional ribozymes in much the same way a modern DNA-RNA one does. I’m betting you want a detailed explanation of how a functional ds genome can arise in the first place. Dunno (my own bet is random hybridisation of short oligonucleotides). But this is not a problem for RNA World per se, contra your original post.

    Funny how we always end up back at the OoL.

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