Redundancy and teleology

The Independent reports some research from the “1000 Genome Project”, under the headline “Human genome study reveals certain genes are less essential than previously thought”. The gist is that in 2,500 individual genomes studied (a supererogatory number in terms of the project’s name):

“…we were surprised to see over 200 genes that are missing entirely in some people,” said Jan Korbel of the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, who led one of the genome project’s studies.

The article goes on:

The finding has astonished researchers because it was thought that all the 20,000 or so genes that make up the human genome must be essential for life. However, it may be that some genes are dispensable because of some kind of built-in redundancy to the human genome.

How accurate it is that it was believed that all 20K genes are absolutely indispensible I’m not sure. But what is certain is that the total of coding genes found in the Human Genome Project was already surprisingly niggardly in accounting for our species, especially given the allegedly minor differences from the chimp genome. This doesn’t appear to leave much room for unnecessary genes gathering dust. To put it in perspective, 200 genes is 1% of the total – the same as some of the less conservative estimates of the difference between the human and the chimp genomes.

But surprising numbers aren’t the main issue here – what ought (at least) to put the cat among the pigeons is that one word “redundancy”. It means, in general usage, “superfluity” or even “supererogation”(!), and in the context of entities having functions it is deeply teleological. For redundancy must always be considered with respect to some goal above and beyond the mechanism in question, and evolution doesn’t, it is said, do goals.

All cars, for example, have since early days been required to have two separate braking systems (classically a hydraulic footbrake and a mechanical handbrake). This is because being able to stop was considered so important that redundancy was built in: the goal of stopping was essential to the function of the whole car. Or, more accurately, since a car has no overall goals, being just a collection of parts, we should say that stopping was essential to the aims of the designer who gave it purpose. The existence of both a belt and braces is strong evidence of an important teleological target.

A different example might be the different voicings of chords on a guitar. Completely different hand positions can be used for musically equivalent chords, and I find that, particularly on pieces I don’t know well enough to play automatically, I often use different voicings at the same points of the tune. And that’s because the hand positions are not following their own inbuilt agenda of efficient causation, but the needs of the human target of rendering that particular tune, whatever it takes.

A third common example could be one’s intention to travel to work. Finding the trains cancelled by a strike, you take the car. Finding an accident blocking the main road, you divert down a side street. Or you walk. If your journey were only a train of efficient causes, breaking the sequence ought to stop it. The use of alternatives reveals final causation – a goal. One could plausibly account for the existence of a car, or a tune, or a journey, via efficient causes. But the existence of alternative efficient causes with the same end, within the same system, implies final causation, and an entity capable of aiming at it.

This is particularly applicable in evolution, when it is said to operate entirely by efficient causes, ateleologically. Evolution by natural selection is notoriously short term: if a variation is selected by the environment to reproduce successfully, it continues to exist. If there is even one costly step to be traversed towards some functional fitness, purifying selection screens it out.

In the “selfish gene” concept, the entity rather dubiously analogised as the unit “aiming” to survive is the individual gene. Together with the other genes with which it chances to be thrown together, with no global organising principle, it generates a survival machine called “an organism” to ensure its own propagation. Now quite clearly the findings of the new research make this particular gene-centred view very far-fetched indeed. In many cases, it seems, the selfish gene doesn’t turn up for the game, yet a perfectly good substitute is already in place, or is co-opted from elswehere in the team. This makes it far more likely that the organism is using the genes, rather than the genes using the organism.

It will always be possible, of course, to generate an epicycle to keep the selfish gene concept on the table – perhaps the “back-up” gene always contributes to the function, but at a lower level. Perhaps it serves some other function but absence of the main gene happens to leave a job-opportunity it can fill. Perhaps they are in competition with each other, the second to evolve having pushed the first aside. Anything’s possible – but in these cases the word “redundancy” ought to have been avoided, for there was actually nothing “superfluous” involved. Redundancy was instead thrown off as an accidental by-product – yet apparently as a matter of course, given its frequency. The blind watchmaker whose mistakes always performs useful functions is a possibility. But is he in the least plausible?

On the contrary usually natural selection is understood to do just enough to get by, and there is no reason for it to expend effort and energy developing multiple routes to the same function, especially if (as seems probable in at least many cases) they are only used when, occasionally, the main system is absent. Unlike human research projects, evolution by natural selection has no means of deciding to do something 2,500 times where 1,000 would do: “just to make sure” is teleological and requires some other theory of evolution.


There’s also another important direction these findings force us to take. If the organism governs the genes rather than vice versa, then what is this organism? Clearly it must be more than just the sum of the genes.

When the study uses the word “redundancy” for the missing genes, it is used within the implied reference frame of “human form”. Bits of the human genome are missing, but the individuals still do the “human thing”. It is real people who lack these genes, rather than specimens that are near-human.

If the human appetite-engendering gene Munchmuch is absent in jellyfish, and its function is served by the alternative munchMuch, it’s not surprising because jellyfish are not people. But if we find munchMuch instead of Munchmuch in a small tribe in New Guinea, does that make the tribe less human (or a human-jellyfish hybrid, perhaps)? Of course not. They are simply evidence that the “human genome” does not define “human”.

If the human genome is not a standard, but a spectrum in which all the variations are duly noted, perhaps explained, and filed away, then there is something other than “genome” that defines us as human. We might call it “form” or “formal causation” – but it requires to be explained by something other than the sum total of our genes, for that has been shown to be pretty plastic.

Whatever this “form” is, it continues to do what it takes to maintain human functions when the genes that were formerly alleged to define those functions aren’t even present. There is therefore a “normal” humanity which is more than the genes, because at least 200 of them (and quite probably more, if larger samples were used) are redundant, meaning that “normal” function (ie that tending towards the end of humanness) is maintained without them.

All this is implied in that term “genetic redundancy”. Lack of redundancy, in the case of any particular gene, does not imply that there is no such thing as form, but only that normal form cannot be maintained when the gene is lost, just as the loss of our brain or heart ends human life. But the presence of any redundancy – even in 1% of genes – is evidence for form, teleology, and some kind of global organisation. And global organisation is the antithesis of Darwinian evolution.

That’s why this research seems to me pretty important.

Jon Garvey

About Jon Garvey

Training in medicine (which was my career), social psychology and theology. Interests in most things, but especially the science-faith interface. The rest of my time, though, is spent writing, playing and recording music.
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7 Responses to Redundancy and teleology

  1. JoeCoder says:

    I remember hearing about genetic redundancy in a few other places too:

    1. From the ENCODE team:
    “Loss-of-function tests can also be buffered by functional redundancy, such that double or triple disruptions are required for a phenotypic consequence. Consistent with redundant, contextual, or subtle functions, the deletion of large and highly conserved genomic segments sometimes has no discernible organismal phenotype, and seemingly debilitating mutations in genes thought to be indispensible have been found in the human population”

    2. Third-Way physiologist Dennis Noble had a talk covering redundancy too:
    “Simply by knocking genes out we don’t necessarily reveal function, because the network may buffer what is happening. So you may need to do two knockouts or even three before you finally get through to the phenotype. … If one network doesn’t succeed in producing a component necessary to the functioning of the cell and the organism, then another network is used instead. So most knockouts and mutations are buffered by the network. …
    Is this an unusual result, … or is it general? This study went through all 6000 genes in the organism yeast. knocking them out one by one. 80% of the knockouts were silent. So this physiological process of buffering against gene change is general. It’s usual in fact. Now that doesn’t mean to say that these proteins that are made as a consequence of gene templates for them don’t have a function. Of course they do. If you stress the organism you can reveal the function. .. If the organism can’t make product X by mechanism A, it makes it by mechanism B.”

    3. In C. elegens (worm) a surprising 89% of single-copy and 96% of duplicate genes show no detectable phenotypic effect when they are knocked out.

    John Sanford’s work shows that in human populations, selection should not even be able to maintain genes that are under constant selection. It’s hard to believe that selection could maintain rarely used genes.

  2. Jon Garvey Jon Garvey says:

    Hi Joe – welcome to The Hump.

    Yup – the news article wasn’t the first mention of genetic reducndancy I’d come across, but it was the first to make me consider its teleological implications. Thanks for the figures on yeast and C. elegans, which bring into perspective how common redundancy is and suggests, therefore, that in some way it’s necessary (another teleological word!) rather than merely an occasional accident.

    Noble, of course, is essentially a self-organisation theorist (his book, Music of Life is worth a read), and though he denies creatorial intent, I think teleology (or teleonomy or whatever term he prefers) is part of his system. He just considers it to be natural teleology, in the tradition of Aristotle. So my reponse to him would be (a) Does his proposed self-organisation for for complexity amount to much more than vague hopes? And (b) Though teleology does not entail design of necessity, as in Thomas Nagel’s case it is hard to build a case without it. If nothing else one has to account for a Universe in which the dice are so loaded that stuff comes together to make organised systems.

    I agree that accounting for the maintenance of secondary or back-up systems by adaptive selection stretches credulity.

  3. Sy Garte Sy Garte says:

    Jon,

    As chance (I refuse to believe its random in this instance) would have it, I have finally returned to your blog after too long an absence to find a post that is perfectly timed for my own interests. Not for the first time. I am currently working on a project to study the way that gene regulatory networks (GRN) could lead to gene buffering, convergence and pleiotropy. All of which in my mind, (and it appears in yours as well) have some relation to real teleology. This is quite similar to Joe’s quote from Dennis Noble above. I clearly agree with your comment that this research seems pretty important. My own work is theoretical using model networks, but I am optimistic that some light might be shed.

    As for redundancy (which is a built in feature of the complex GRNs that govern animal development), it is a common feature of all cellular systems, including biochemical pathways. So when the cell needs to turn off an enzyme there are generally several ways to do it simultaneously, including feedback inhibition, repression of the gene that produces the enzyme and so on. I am not sure that this tendency to redundancy is something that lies outside of adaptive selection. Things do tend to wrong. In cells as well as in autos, appliances and the internet. So organisms with lots of backup probably can claim a selective advantage.

    On the other hand, and here was are back in agreement, this should only go so far. The entire idea of complex interactive regulatory networks is something that is really clever. I dont think normal evolutionary processes can be ruled out, but the lovely aroma of purpose is hard to ignore. I am very excited to be working on this issue.

    As part of the project (funded by the John Templeton Foundation) I will be reporting on my progress on my new blog . I have some other stuff on there you might get a kick out of.

    Anyway, I have retired from the NIH, and am now free to say anything I want to anywhere, without worry. I have also returned to Biologos, which has a whole new website. Havent seen you there. Hope all is well.

    Sy

    • Jon Garvey Jon Garvey says:

      Thanks for this Sy (and welcome back!).

      As you say, though there can be no absolute answer, at present state of knowledge anyway, about how much teleology can be explained without teleology, there comes a point when you begin to think, “This isn’t looking simple and self-evident any more.”

      I’ll search your site when it’s not so late at night here. I’ve seen the new BL site but haven’t been reading or posting much there recently – I confess partly because I can’t find my way round the new gleaming website. Simple soul, me.

      Anyway, since the next post is also in the same ballpark, I may as well put it up now before I turn in.

      Jon

      • Jon Garvey Jon Garvey says:

        Sy

        Further to above, have thought about your first comments after a good night’s sleep.

        I am not sure that this tendency to redundancy is something that lies outside of adaptive selection. Things do tend to wrong.

        The key word there is “wrong”. It seems to me that what you’re actually implying is that an organism that can display final causation (aka internal teleology, or targeted planning: a “right” result) has a selective advantage. That is undoubtedly true, but it raises the question of whether it’s philosophically possible for a chain of efficient causes to lead to an entirely new kind of causation, ie finality. The undirected purposeless process produces purpose and direction – how does that work?

        In other words, it’s like biologists denying Aristotelian forms in favour of purely efficient causes, and then suggesting that organisms that evolve a global form have a selective advantage.

        Noble, of course, sees no problem with that on the basis of self-organising complexity “laws”, but they have yet to be demonstrated on the ground, I think.

        I like the website – astonishingly on my first visit I found comments by an old friend from my last church, who moved to America many years ago. She happens to be the one person in the world who’s used the material I did on the Book of Revelation that I’m using in the current course I have mentioned in a couple of recent posts.

      • Edward Robinson Edward Robinson says:

        Hi, Jon.

        I haven’t figured out how the new BL site works, either, but you can still go directly to the Forum page, which works the same it has for the past several months:

        https://discourse.biologos.org/

        So you don’t need to use any of the new pages at all.

        Regarding your discussion with Sy, I would say: Sure, a Darwinian can always argue that, since backup systems would give a selective advantage, random mutations plus natural selection would tend to produce them. But this conclusion, however logical it sounds, doesn’t follow. In 1980 a computer capable of running, and equipped with, Microsoft Word and Adobe Acrobat would have a “selective advantage”, and writers and office people would snap the hardware and software up like hotcakes, and the manufacturers of other computers and software would be driven out of business (natural selection). The problem is that none of those programs existed then, nor did computers of the era have the memory, storage, or operating systems to make use of them, had they existed. And in fact all the advances in operating systems, memory, storage, and software that have been made since then were achieved by design, not by trying out random errors in programming code to see if they generated any new useful software or by trying out random physical changes to the motherboard and storage media to see if they improved the computer’s physical possibilities.

        Evolution has to account for not only survival of the fittest, but arrival of the fittest. It’s not enough to say that an organism with a complex set of regulatory networks would have a survival advantage; of course it would. But regulatory networks don’t pop into existence ex nihilo, and it’s not clear that they could have evolved in a stepwise manner — even though Darwinians routinely claim that everything can evolve in a stepwise manner. They still claim that the bacterial flagellum evolved in stepwise manner, but none of them has explained in detail how this could have happened. And some of the regulatory networks and feedback systems etc. in living things are, I believe, more complex and integrated than the flagellum. I’m also told that they are more complicated and integrated than any computer or software ever devised. It’s Behe’s mousetrap problem taken to the nth power. It might be *logically* possible for such things to develop in a stepwise manner, and we might be able to imagine in vague outline, speaking in generalities, how this could happen, but as for actually showing the steps — I see the Darwinian account as bankrupt.

        Of course, in bashing Darwinian accounts I’m not bashing “evolution.” As regulars here know, I think that the classic neo-Darwinian account is a gross oversimplification (at best) of how evolution would have to work to produce complex, integrated systems. In my view there must be *much* more going on than the filtering of random mutations which just pop up due to chance blasts of radiation, etc. And it’s all very well to talk about self-organization, which I believe could account for some features of evolution, but even self-organizational abilities have to come from somewhere. Is it just chance that the universe has self-organizational tendencies? Given all the universes that might have existed that had no such tendencies, is it just luck that such a universe exists? Is it just luck that teleology is built in? I’m grateful to the self-organization theorists for challenging the neo-Darwinians, but I think that a programmatic atheism/agnosticism prevents them from seriously considering the possibility that such self-organization as exists was programmed into nature by a mind.

        • Jon Garvey Jon Garvey says:

          Thanks for that link, Eddie – if you could provide an equally helpful one for my bank’s labyrinthine online banking system it would be great! 🙂

          Design, in the broad sense you maintain – that is, that any “mechanism” that will produce the functions of life requires, at least, a universe that’s full of loaded dice – is the central issue, as we both know.

          From his own different approach (from within genetics) Sy affirms much the same thing – “the lovely aroma of purpose is hard to ignore”. It changes the question from “Could this be construed to happen without God?” to “How did God do this?”

          What that does is to put all mechanisms or possible mechanisms into the category of instruments or agents of God’s will. We affirm God’s governance whether in the mechanisms, behind the mechanisms or instead of the mechanisms.

          Once that is granted, all arguments about the adequacy or nature of particular theories like natural selection become topics of specialist interest – and maybe practical application – but not public controversy. Not many people care whether their car was assembled by hand or by some robot, so long as the brand is reliable.

          If I’m a believing NT scholar, I’ll be interested in the extent to which amanuenses affect the style and content of various epistles. It could cast light on their meaning and application, but not imply anything regarding fundamental authority if I believe that Paul or Peter’s supervision stands behind them, and the Holy Spirit’s behind that.

          What makes it controversial is the contention that if I find a non-apostolic hand in the last stage of composition, I have somehow excluded the involvement of the apostle, or the Spirit. Suddenly the man in the pew has a stake in what would otherwise be a peripheral scribal debate.

          So with biology – once the claim was made that evolution made God unnecessary, not only were culture wars engendered between “science” and “religion”, but scientists were under pressure to stake a lot more confidence in properly provisional theories than was warranted (cf imminently forthcoming post regarding the long usurpation of phyletic gradualism on evolutionary theory, probably because it was the furthest point from “special creation”).

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