Genes – the language of God 1: Genes as Language

Genome mapping sequence

A common way to talk about genes is as things that have meaning, either as a kind of language (or code, or recipe), or as information about the bodies of the organisms they generate. This has led some, for example, Francis Collins (2010), to speak of genes as the language of the living universe, in much the same way that some physicists talk about the mathematical laws of physics as the language of the physical universe. In this series, I will discuss this way of talking about genes, and consider (1) if it is true or helpful, and (2) what problems arise from thinking about genes as language. Towards the end, Stephen Ames will discuss what this means for thinking about God and genes, responding to Collins’ 2006 book The language of God. As I am not a believer, I cannot say anything helpful to believers about this topic.

Let us look at some examples of genes-as-language talk.

In 1966, George Beadle entitled a book on genetics – then still new to most readers – The Language of Life. It was a metaphor of course, and he did not employ it much in the textbook, but the idea that genes are something language like is very old. The historian of science, Donald Forsdyke, has traced similar ideas back to Darwin’s contemporary, Samuel Butler.

Because we are most familiar with language, describing and explaining things in terms of language and language-like features has real power to convey ideas about science. However, since these things science describes are not actually language, there is a risk that it will cause confusion, and it does.

Collins’ use of this terminology is wildly overblown. For example, he writes, in a chapter he titled “Deciphering God’s Instruction Book”, “I found myself standing next to the President of the United States in the East Room of the White House on June 26, 2000, announcing that the first draft of the human instruction book had been determined. The language of God was revealed.” [2006, 122] Later, he writes “For me as a believer, the uncovering of the human genome held additional significance. This book was written in the DNA language by which God spoke life into being.” [2006, 123]

If these are metaphors, they might be harmless. A metaphor is a figure of speech, in which what we know of one thing can be carried over to another (the Greek word metaphoros today means a shopping trolley!), and the use of metaphors in learning and teaching is unavoidable. But a metaphor is at best the first step up to knowledge. Once you take that step, then you have to understand the new item in its own terms. Here are some other language and informational metaphors regarding genes:

  • Genes as a code. Since the structure of DNA was discovered in 1952, the idea that the DNA is a code for proteins was taken up enthusiastically. By the mid-1960s, biochemists had worked out which three-“letter” combinations “stood for” which amino acids. But, once “the code” was worked out, it turned out in short order there were up to 17 alternate variations. There is nothing about the triplet letter codes that must create the amino acids that they do; in fact what causes the triplet to create an amino acid chain is more to do with the ribosome; all the RNA that the DNA makes does is to trigger the ribosome to add a particular amino acid to the peptide, or chain.
  • Genes as a program or recipe. The computer metaphor and the cook metaphor have been used at different times. The computer metaphor is based on the idea that DNA is an algorithm that is “executed” by the cellular machinery to build a cell or organism. The cook using a recipe metaphor is slightly older, but often these two are used interchangeably. Both involve the idea there is a sequence of steps that is specified by genes to create (“cook” or “output”) an organism.
  • Genes as information. Genes are the patterns of DNA that are “transmitted” from one generation to the next.
  • Genes as a language. Genes “describe” organisms in some fashion.

A metaphor can systematically mislead us. It can mislead members of the general population who think that the Higgs boson really is the “god particle” or that the Big Bang really was an explosion. This might be unavoidable if we don’t teach the facts early enough; and it may be harmless. But consider some other metaphors: we “stimulate” the immune system with this or that drug or vitamin. This dysmetaphor, so to speak, causes people to spend literally billions of dollars on useless vitamin supplements or to avoid vaccination so their kids are “stimulated” by actually contracting measles, which can kill.

These dysmetaphors can have more subtle effects. Some, such as George Lakoff, argue that the metaphors by which we frame issues subtly changes how we process the issues. While it may not be that framing effects really sharply change our thinking, nevertheless, even scientists can be misled by metaphors. I would say that the idea genes are linguistic things – symbols – misleads a great many scientists in a great many ways. It moves our attention from the physical properties of genes and their organisms to abstract properties. We will return to this. And of course there is the misleading such metaphors cause when philosophers take them up.

12 thoughts on “Genes – the language of God 1: Genes as Language

  1. “… all the RNA that the DNA makes does is to trigger the ribosome to make a particular amino acid.”

    No, the messenger RNA doesn’t “make a particular amino acid.” What it does is (1) initiate translation with a specific amino acid (carried by transfer RNA) such as methionine, (2) add more amino acids, one by one, during elongation of the growing polypeptide, and (3) terminate translation when a stop codon enters the ribosome. (Note the “linguistic” verbiage here — “messenger,” “translation,” and “codon” — which is integral to any discussion on genome function, and which, I think, carries a significance that goes beyond mere metaphor.)

    “It can mislead members of the general population who think that the Higgs boson really is the “god particle” or that the Big Bang really was an explosion.”

    The “Big Bang,” as described by those who believe in it, was a rapid, hot, violent expansion — a genuine explosion, I suggest, not a metaphorical one.

    I’m looking forward to your further discussion in this series.

    1. I said the ribosome makes the amino acid; but I should have said it makes the amino acids form a chain. I will correct it.

      The Big Bang was not an explosion; and the fact that the early universe was hot did not, so far as I can tell from reading various sources, make the universe expand rapidly. It’s a metaphor.

      1. “The Big Bang was not an explosion; and the fact that the early universe was hot did not, so far as I can tell from reading various sources, make the universe expand rapidly. It’s a metaphor.”

        Heat per se doesn’t directly cause explosions we’re familiar with today, either. The typical cause is a chemical reaction producing a gas at a fast enough rate to generate a sudden pressure increase leading to a rapid, destructive expansion.

        As for the purported “Big Bang,” nobody knows what caused its expansion. (“Inflaton”?? What’s that?)

        I do not say the “Big Bang” was a typical explosion, matching all aspects of explosions we experience today. But it matches key features. Like today’s explosions, it is described as a hot, rapid, violent expansion. It’s rightly termed an explosion. So it’s not just a metaphor (as, say, “Cambrian explosion” is).

      2. Further regarding my earlier statement about heat:

        Explosions tend to result from exothermic (heat-generating) chemical reactions. Those reactions may require some added heat to start them proceeding (i.e., activation energy), but a continual heat source is not needed since after initiation they release heat.

        But some explosions don’t require added heat at all — the simple mixing of the reactants, with the kinetic energy already possessed by reactant particles (molecules or ions) at ambient temperatures, is sufficient to start the reaction.

          1. OK, John, I have carefully reviewed each of your links. Before I respond to them, I will just note that two very well-known physicists had no problem applying the term “explosion” — evidently non-metaphorically — to the “Big Bang.”

            Nobel laureate Steven Weinberg, in the updated edition of The First Three Minutes (1993), wrote: “In the beginning there was an explosion. Not an explosion like those familiar on earth, starting from a definite center and spreading out to engulf more and more of the circumambient air, but an explosion which occurred simultaneously everywhere, filling all space from the beginning, with every particle of matter rushing apart from every other particle. . . . the matter rushing apart in this explosion consisted of various types of the so-called elementary particles, which are the subject of modern high-energy nuclear physics.” (p. 5)

            Similarly, Carl Sagan in Cosmos (1980) spoke of “. . . a remarkable explosive event called the Big Bang. At the beginning of this universe, there were no galaxies, stars or planets, no life or civilizations, merely a uniform, radiant fireball filling all of space.” (p. 21) Again, Sagan mentioned “. . . the Big Bang, the explosion that began the Cosmos.” (p. 218) And again, he wrote: “In that titanic cosmic explosion, the universe began an expansion which has never ceased.” (p. 246) And again, he highlighted “. . . the explosive outpouring of matter and energy of the Big Bang. . . .” (p. 337)

            The foregoing citations should not be considered an “argument from authority,” but they’re certainly an indication that describing the “Big Bang” as a (non-metaphorical) “explosion” is not a proof of ignorance. Now to your links.

            http://www.livescience.com/32278-was-the-big-bang-really-an-explosion.html

            At this link, science writer Clara Moskowitz states: “An explosion implies that something exploded, or expanded, from one center point outward into space. In fact, the Big Bang theory suggests that space itself expanded. ‘If it were an explosion it would have a center,’ said physicist Paul Steinhardt, director of the Princeton Center for Theoretical Science at Princeton University in Princeton, N.J. ‘We actually observe that everything is moving away from everything else. It’s really about an expansion of the universe.’ [Note that Weinberg decades ago acknowledged this distinction between the “Big Bang” and more familiar explosions, but nonetheless applied the term “explosion” to the “Big Bang.”]

            Moskowitz then quotes another highly qualified cosmologist, Andreas Albrecht, who demurs from Steinhardt’s view: “‘I think anything that starts out at 10 to the 40th degrees, and is doubling in size every tiny, tiny fraction of a second – I think you’d want to call that an explosion,’ Albrecht said. ‘But it has different features than someone setting off a bomb in the desert.'” [Which is essentially what I said in my earlier comment.]

            http://www.science20.com/quantum_gravity/blog/big_bang_was_not_explosion_however_explosion_metaphor_what_big_bang_was-78575

            At this link, Hontas Farmer writes, “Explosions are the free expansion of material from higher pressure, temperature and density to lower pressure, temperature and density in a short amount of time.”

            So how does that not describe the early “Big Bang”? Farmer continues: “The big bang was not an explosion because no material was involved. None existed yet. The big bang was the sudden expansion of space-time. That is not the same as an explosion in any physical sense.”

            But to say the least, matter came to exist very early in the process and then it was involved in the ongoing explosion (as both Weinberg and Sagan noted). Farmer brings her argument to a curious conclusion: “That said, in terms of the accurate, grammatically correct usage of the language in the sense that any English teacher would agree with, writing the big bang ‘was’ an explosion is correct.”

            http://en.wikipedia.org/wiki/Big_Bang#Expansion_of_space

            This anonymous Wikipedia writer states, “The Big Bang is not an explosion of matter moving outward to fill an empty universe. Instead, space itself expands with time everywhere and increases the physical distance between two comoving points.” [No new argumentation is introduced here.]

            https://au.answers.yahoo.com/question/index?qid=20110818051941AAoYo3u

            This anonymous Yahoo writer states, “No, the Big Bang was not an explosion. We don’t know what, exactly, happened in the earliest times, but it was not an explosion in the usual way that people picture explosions.” [Nothing new here.]

            http://www.exploratorium.edu/origins/cern/ideas/bang.html

            I’m rather surprised that you provided this link, John! Here’s what the anonymous CERN writer says: “This extremely dense point exploded [N.B.] with unimaginable force, creating matter and propelling it outward to make the billions of galaxies of our vast universe. Astrophysicists dubbed this titanic explosion [N.B.] the Big Bang. The Big Bang was like no explosion you might witness on earth today. For instance, a hydrogen bomb explosion, whose center registers approximately 100 million degrees Celsius, moves through the air at about 300 meters per second. In contrast, cosmologists believe the Big Bang flung energy in all directions at the speed of light (300,000,000 meters per second, a million times faster than the H-bomb) and estimate that the temperature of the entire universe was 1000 trillion degrees Celsius at just a tiny fraction of a second after the explosion [N.B.].”

            http://www.big-bang-theory.com/

            This anonymous, apparently non-expert writer states: “There are many misconceptions surrounding the Big Bang theory. For example, we tend to imagine a giant explosion. Experts however say that there was no explosion; there was (and continues to be) an expansion.” [Nothing new here. By the way, this anonymous website seems to be associated with “AllAboutGOD.com”, according to the “About Us” page of the website.]

            https://suite.io/paul-a-heckert/67e2dj

            At this link, astrophysicist Paul Heckert writes: “In the big bang theory, the universe formed as a primeval fireball [N.B.] about 15 (or so) billion years ago. Initially the entire universe was compressed to the size of an infinitesimal point. At the moment of formation this primeval fireball began expanding and has been expanding ever since. The initial expansion of this primeval fireball is almost universally described as a huge explosion. An explosion however is not the best analogy to describe this expansion.”

            Well, I think a “fireball” (Sagan also used this term) that expands rapidly and violently (a lot of matter self-annihilated) is rightly termed an “explosion.” No wonder the “Big Bang” is “almost universally described” in this way. Heckert concludes: “An explosion did not fill the universe with matter, rather the universe itself began expanding. Rather than thinking of the big bang as a giant explosion, compare it to rising raisin bread dough or blowing up a balloon.”

            John, may I suggest that a bowl of raisin bread that expanded as rapidly, violently, and hotly as the alleged “Big Bang” would also be “universally described” as an explosion!

            Now, regarding the alleged “expansion of space-time,” I confess I have always been totally mystified by this concept. Have you ever seen a good, comprehensible explanation of it?

  2. Data underdetermine theories; but it’s also true that theories underdetermine the metaphors we use to imagine them. A variety of dreams can flesh out the armature of equations that a purist might claim is the only real result. Consequently, something other than the evidence and theorems must determine how we imagine things. Gerald Holton wrote some memorable essays on the thematic origins of modern science that illustrate this idea. My favorite example from his work is Einstein’s decision to call his theory relativity instead of the theory of invariance, which would have been just as apt technically but wouldn’t have suited the Zeitgeist as well.

    The thing about metaphorical thinking is that although it’s the source of a great deal of nonsense and error, it is also the medium in which science is conducted, at least by sublunary scientists—angels or supercomputers may transcend the requirement. Imagination: you can’t live with it, but you can’t live without it. To focus exclusively on the way figures and images bewitch us would be to speak like an irritated fish who complained that the water was keeping him from swimming faster.

    1. Your mention of metaphor brought to mind the observation that one of the characteristics of language is metaphor. It is (nearly) impossible to speak without the use of metaphor. Yet metaphor is lacking in DNA.

  3. I’ve taught and worked with biology undergrads, and I’ve seen many, many times students that are unclear on the basic concepts. Many of these confusions are directly based on the language used to teach biology. I don’t know whether the language is the cause of their confusion, but for many students their understanding has frozen around the analogies.

    They don’t have useful internal models of the cell, or of DNA or protein. When they think about DNA, they think information, or a series of letters, or just a concept, DNA is a gene. Not a polymer, a long macromolecule.

    Students have trouble remembering whether a chromosome is bigger or smaller than a gene or a protein, these are all just words to them. They can’t think usefully about what is happening during transcription–they don’t know the relative sizes or amounts of various components, and can’t picture them floating around, bumping into each other, and sticking together or not.

    1. I have read both Shannon’s original paper, Weaver’s book, and various other treatments, including Dretkse’s _Knowledge and the Flow of Information_. I suspect you think the term is singular in definition – if so, it is you who are wrong here.

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