Wednesday, 20 November 2013

Genes are not sections of nucleic-acid

All through the first half of the twentieth century, the term "gene" referred to the heritable aspect of traits. Then, in 1953, the structure of nucleic acids was discovered. It had been discovered that genes were made of nucleic acids!

Not quite. Some genes are made of nucleic acids. Other genes are not made of nucleic acids.

Since the 1950s, some people have got confused about what genes are. When I talk to them they say things like what Massimo Pigliucci said to me last year:

Tim, I'm a geneticist by profession, and let me tell you: genes do not exist inside hard drives, or anywhere else but in living organisms. And they are always made of RNA or DNA.
This isn't just a case of people using words differently - it's a basic science mistake. Watson and Crick never discovered that all genes were made of nucleic acids. They discovered that some genes were made of nucleic acids. Our most-distant ancestors probably had genes which were not made of nucleic acids. Our descendants will probably have genes that are not made of nucleic-acids. Aliens will probably have genes not made of nucleic acids. The belief that all genes are made out of nucleic-acids is just a terribly confused scientific mistake. There is no parallel universe where genetics is the study of nucleic-acid-based inheritance. The genes representing the heritable aspect of the trait of circumcision are not encoded in nucleic acids. Surnames are not encoded in nucleic-acids. Stress levels are not encoded in nucleic acids. Not all traits are encoded in nucleic acids!

I often encounter people who claim that memes are not like genes because of - some difference or other. After a little while it turns out that they think that genes are made of nucleic acids. Nope. Some genes are made of nucleic acids. Other genes are not made of nucleic acids. The idea that all genes are made of nucleic acid is just a basic scientific mistake.

If someone ever claims that memes are not like genes - and it turns out that they think that genes are made of nucleic acids, this page is designed for them. Memes are not just like genes. They are genes. Full stop. Anyone who says otherwise is likely to be perpetuating a decades-old basic scientific mistake about what genes are made of.

Boyd and Richerson are some of the more prominent culprits here. They wrote a whole book titled "Not By Genes Alone". It argued that culture wasn't like genes. Except that this perpetuates the science mistake under discussion here. Memes aren't just like genes. They are genes. Those who promote the idea that genes are made of nucleic acid are peddling a mistaken, pseudoscientific dogma that does not withstand close inspection.

Part of the problem comes from molecular biologists. As Stephen Pinker put it:

Part of the blame goes to molecular biologists, who hijacked the term "gene" for protein-coding sequences, confusing everyone.
If this seems cryptic, Pinker has clarified and elaborated here:

Molecular biologists have appropriated the term "gene" to refer to stretches of DNA that code for a protein. Unfortunately, this sense differs from the one used in population genetics, behavioral genetics, and evolutionary theory, namely any information carrier that is transmissible across generations and has sustained effects on the phenotype.

See also, Against epigenetic inheritance.

Other examples

  • Larry Moran: A gene is a DNA sequence that is transcribed to produce a functional product.
  • P Z Myers: "But what the hell do we mean by a “gene”? Sure, it’s a transcribed sequence in the genome that produces a functional product; it’s activity is dependent to a significant degree on the sequence of nucleotides within it"


  1. Tim,
    I'll bite. You say:
    "This isn't just a case of people using words differently - it's a basic science mistake. Watson and Crick never discovered that all genes were made of nucleic acids. They discovered that some genes were made of nucleic acids."
    And I see opinion, not scientifically agreed convention. I am somewhat drawn to the memetic camp, but I see no problem with the typical convention:
    Replicon/replicator = a piece of information that, within it's environment, gets replicated (with almost perfect fidelity). The building block on which natural selection acts. This is an abstract concept that in the real world can be found on different substrates.
    Gene = a replicon based on nucleic acids (DNA and sometimes RNA)
    Meme = a replicon based on (??) some neural structure.
    The above works: one word for each concept, allows fast, precise and efficient communication. Saying that Gene = Replicon as you do, leaves us with unneeded redundancy at one level and without a "Single word" for the nucleic acid implementation, that happens to be studied by geneticists. And said geneticists unsurprisingly like to call the things they study "genes". You may not like it, but they will do it just the same, why not go along with them?
    Next: meme. Memes are different from genes on many levels.
    1) we don't really understand the medium that stores them. Nobody has broken the neural code that is used to store memories yet. Moreover, it's likely that each different kind of memory uses it's own code (music, actions, verbal thoughts, and so on). Even more, it's likely that different people will have (at least to some extent) different internal conventions or codes: i.e. the same Meme is encoded differently in different brains.
    2) we don't understand the replication mechanism. For genes, we know a lot about the different polymerases, for memes, not a clue. But we know that memes use a variety of "messengers", other people, media, different languages, written languages, the internet, and so on.
    3) given the first two, we know that we can't even begin to measure the replication fidelity, because each combination of factors (the subject of a meme, the encoding in its current and destination brain, the medium used for it's transmission, including if applicable language) will have a significant effect on it. Plus, of course, once transmission happened, the subject of the meme (what kind of information it stores) will interact with the person that hosts it is such a way that it makes it impossible to reliably verify the transmission fidelity after the transmission is complete.
    4) We know pretty well that memories drift, they change over time, but have only a very vague understanding on the rules that govern this drift. We know enough to be sure that the drift depends on the subject and what happens to the subject. So while genes usually are quite stable between generations, memes keep changing even while hosted on the same brain.
    5) if we can't measure/estimate/evaluate/predict neither the storage stability nor the transmission fidelity (we can, by definition, work only on a case by case way), we can't treat memes like genes, we just can't.

    Does this negate that memes are replicons? No, it does not, memes are replicons that happen to work in much more complex and unpredictable ways than genes.
    You see? I'm using widely accepted conventions and they work. If I was using yours, instead of the two short sentences above I would have needed plenty of explanations.
    Just my 5c, but no, I don't share your view: genes (R/DNA based) don't work like memes. You can see both as replicons, and study how selection acts on them, but it does act in different ways. Saying that genes = replicons is misleading, does not help, is not an accepted convention and would confuse scientists and general public in equal measure.

  2. If you don't see a problem with "replicon/replicator" there are plenty of others who do. This terminology has caused massive confusion and misunderstandings - revolving around the issue of fidelity.

    A "replica" is normally defined as being a high-fidelity copy. However, there's little point in having a science of replicators - since high fidelity copying is a special case of copying - and the same math describes both cases. I go into all this in posts titled: "Replicator rot", "Richard Dawkins - on the definition of the term meme", "Against Replicator Terminology" and "The role of high-fidelity transmission in memetics", "The claim that evolution doesn't require replicators" and "An inherited unit for Universal Darwinism". Replicator terminology definitely has some big shortcomings - even if you are not aware of them.

    I do call the things geneticists study "genes"! Genetics is the study of genes and heredity.

    Aren't you falling into the very trap my post describes? You say memes aren't like genes - and then go on to give a list of reasons why memes aren't like nucleic acids.

    If you define "gene" in the traditional way that I prefer, memes are not just *like* genes, they *are* genes. If you don't, then your conception of "genetics" sucks. We *have* a science of heredity - it's called "genetics". We don't need a new science of "replicatorology" - genetics has the topic covered. "Replicatorology" is a doomed science with no future.

    As for your alleged differences: 1 and 2 are expressions of ignorance, 3 and 5 are wrong (of course we can measure meme copying fidelity!) as for 4: genes in bacteria drift too - while memes in flash drives don't - in other words, you just cherry-picked your examples to match your conclusion.

    I don't agree that understanding that genes are not sections of nucleic-acid would confuse the public - rather it would help to undo decades of confusion on the topic.

    If you don't like my preferred terminology, that's cool. Note that I have, however spent many years thinking about the issue.

  3. Thanks Tim,
    Sorry for the late reply, I had to track down all your articles and then find the time to read them!
    It seems we disagree in more than one way. I will gloss over the small details and address the core only, I'm sure you are able to fill in the blanks as/if needed.
    I understand the first, fundamental disagreement in this way:
    I think that "replicator" is a good term for the overarching concept (the one that encompasses DNA-genes and memes), you think that it's not, because it intuitively suggests high fidelity.
    In a specular way, you think that the word gene should be used as the overarching concept and don't feel the need to have a specific term for nucleic-acid-based genes; I think that gene is currently used for the latter and don't think it's feasible to change this convention.
    So it boils down to the difficulty of changing the collectively agreed meaning of words: you want to ditch "replicator" and change the typical meaning of gene (in current understanding, I will not argue with you about the scientific correctness), I want "replicator" to be understood as a scientific term, stripping it from the intuitive and incorrect implication of fidelity. Will either of us succeed? It's likely that we won't even change each other's mind, so no, I expect that we won't be able to change the public perception as a whole (would be glad to be surprised by one of us in equal measure).
    In your own terms, yes, I fall fair and square in "the error" you describe (of course, I don't see it as an error) and that's exactly why I've written my original comment. I am happy to accept the definition nucleic-acid-based-replicators <=> genes, and I do so because:
    a) people understand the word gene is this way
    b) it works, it makes it easier to explain the different concepts.
    So I've posted my original to explain why I think accepting the currently used convention would make your own argument simpler to explain and disseminate. And I wanted to do so because in my opinion the ideas of memetics and Universal Darwinism do have something to offer and I agree with you, they are both too young to dismiss them completely.

    You then go into the specifics, but omit to address my main point, that's where I say "Does this negate that memes are replicons? No, it does not, memes are replicons that happen to work in much more complex and unpredictable ways than genes. You see? I'm using widely accepted conventions and they work". My points 1-5 can be used to address the objections of those that say that memetics is a pointless science (or pseudoscience), and explain why it has not flourished so far (we are ignorant, and this ignorance prevents the creation of useful predictive models based on memetics). To do so, having an overarching concept (replicator for me, gene for you) is useful, and having a single-word for "nucleic-acid-based-replicator" is equally handy. That's all.
    Clearly, I've failed completely in my intent. I hope this clarifies, if it does not, I'll have to live with it (life is short and I have to carefully direct my little amounts of spare energy).

  4. "Replicator" - as you defined it above - is an unsuitable entity to act as a foundation for evolutionary theory. As has been endlessly gone over by myself and others, high-fidelity copying and low-fidelity copying both occur in evolutionary processes, and they share the same mathematical models and dynamics. You can have a science of reproduced entities - and any proposed science of entities copied with high-fidelity is a subset of this. People have proposed a science of high-fidelity copying in the past (e.g. see David Hull). However proponents of a more general science of reproduced entities just snort and ridicule the idea as insufficiently general - and so not properly scientific. They correct about this - and I am with them.

    The ways forward scientifically for the replicator proponents are to have a not-very general science that only covers some evolutionary processes - or to redefine "replicator" to refer to anything that is copied (as has been done by Dawkins and Szathmary). That results in very confusing and counter-intuitive terminology - due to the etymology of the word "replicator". Neither path is very attractive. The "replicator" terminology has other drawbacks: genes are "replicatees" not "replicators". I go over all this in chapter 13 of my book.

    I propose that biologists go on using "gene" for nucleic acid sections - since everyone agrees that these are genes. For those who *really* want a term that *specifically* refers to DNA or RNA, "DNA gene" and "RNA gene" are available. For those who want to refer to nucleic acids I propose "nuclear gene". Or maybe we can have "Deme", "Reme" and "Neme" for these.

    I think that the most important concept should have the best term - and the most important concept - by far - is the inherited unit in universal Darwinism. Those who propose "gene" and "genetics" be confined to DNA - or to nucleic acids - have a parochial view of science. Science often prefers the general to the specific. When our descendants switch to storing their heritable material in 3D crystals they'll have to trash their supposed "science of heredity" - and start again. We can foresee this mistake and avoid it now. We should avoid this mistake - rather than lumbering our descendants with a terminological mess.