What was going on? What was it that suddenly happened to Tribe Ara-3? Lenski and two colleagues investigated further, and worked it out. It is a fascinating story. You remember I said that glucose was the limiting resource, and any mutant that 'discovered' how to deal more efficiently with glucose would have an advantage. That indeed is what happened in the evolution of all twelve tribes. But I also told you that glucose was not the only nutrient in the broth. Another one was citrate (related to the substance that makes lemons sour). The broth contained plenty of citrate, but E. colinormally can't use it, at least not where there is oxygen in the water, as there was in Lenski's flasks. But if only a mutant could 'discover' how to deal with citrate, a bonanza would open up for it. This is exactly what happened with Ara-3. This tribe, and this tribe alone, suddenly acquired the ability to eat citrate as well as glucose, rather than only glucose. The amount of available food in each successive flask in the lineage therefore shot up. And so did the plateau at which the population in each successive flask daily stabilized.
Having discovered what was special about the Ara-3 tribe, Lenski and his colleagues went on to ask an even more interesting question. Was this sudden improvement in ability to draw nourishment all due to a single dramatic mutation, one so rare that only one of the twelve lineages was fortunate enough to undergo it? Was it, in other words, just another mutational step, like the ones that seemed to be demonstrated in the small steps of the fitness graph on page 125? This seemed to Lenski unlikely, for an interesting reason. Knowing the average mutation rate of each gene in the genome of these bacteria, he calculated that 30,000 generations was long enough for every gene to have mutated at least once in each of the twelve lines. So it seemed unlikely that it was the rarity of the mutation that singled Ara-3 out. It should have been 'discovered' by several other tribes.
There was another theoretical possibility, and an extremely tantalizing one. This is where the story starts to get quite complicated so, if it is late at night, it might be an idea to resume reading tomorrow . . .
What if the necessary biochemical wizardry to feed on citrate requires not just one mutation but two (or three)? We are not now talking about two mutations that build on each other in a simple additive way. If we were, it would be enough to get the two mutations in any order. Either one, on its own, would take you halfway (say) to the goal; and either one on its own would confer an ability to get some nourishment from citrate, but not as much as both mutations together would. That would be on a par with the mutations we have already discussed for increasing body size. But such a circumstance would not be rare enough to account for the dramatic uniqueness of Tribe Ara-3. No, the rarity of citrate metabolism suggests that we are looking for something more like the 'irreducible complexity' of creationist propaganda. This might be a biochemical pathway in which the product of one chemical reaction feeds into a second chemical reaction, and neither can make any inroads at all without the other. This would require two mutations, call them A and B, to catalyse the two reactions. On this hypothesis, you really would need both mutations before there is any improvement whatsoever, and that really would be improbable enough to account for the observed result that only one out of the twelve tribes achieved the feat.
That's all hypothetical. Could the Lenski group find out by experiment what was actually going on? Well, they could take great strides in that direction, making brilliant use of the frozen 'fossils', which are such a continual boon in this research. The hypothesis, to repeat, is that, at some time unknown, Tribe Ara-3 chanced to undergo a mutation, mutation A. This had no detectable effect because the other necessary mutation, B, was still lacking. Mutation B is equally likely to crop up in any one of the twelve tribes. Indeed, it probably did. But B is no use - has absolutely no beneficial effect at all - unless the tribe happens to be primed by the previous occurrence of mutation A. And only tribe Ara-3, as it happened, was so primed.
Lenski could even have phrased his hypothesis in the form of a testable prediction - and it is interesting to put it like this because it really is a prediction even though, in a sense, it is about the past. Here's how I would have put the prediction, if I had been Lenski:
I shall thaw out fossils from Tribe Ara-3, dating from various points, strategically chosen, going back in time. Each of these 'Lazarus clones' will then be allowed to evolve further, on a similar regimen to the main evolution experiment, from which, of course, they will be completely isolated. And now, here's my prediction. Some of these Lazarus clones will 'discover' how to deal with citrate, but only if they were thawed out of the fossil record after a particular, critical generation in the original evolution experiment. We don't know - yet - when that magic generation was but we shall identify it, with hindsight, as the moment when, according to our hypothesis, mutation A entered the tribe.
You will be delighted to hear that this is exactly what Lenski's student Zachary Blount found, when he ran a gruelling set of experiments involving some forty trillion - 40,000,000,000,000 - E. coli cells from across the generations. The magic moment turned out to be approximately generation 20,000. Thawed-out clones of Ara-3 that dated from after generation 20,000 in the 'fossil record' showed increased probability of subsequently evolving citrate capability. No clones that dated from before generation 20,000 did. According to the hypothesis, after generation 20,000 the clones were now 'primed' to take advantage of mutation B whenever it came along. And there was no subsequent change in likelihood, in either direction, once the fossils' 'resurrection day' was later than the magic date of generation 20,000: whichever generation after 20,000 Blount sampled, the increased likelihood of those thawed fossils subsequently acquiring citrate capability remained the same. But thawed fossils from before generation 20,000 had no increased likelihood of developing citrate capability at all. Tribe Ara-3, before generation 20,000, was just like all the other tribes. Although its members belonged to Tribe Ara-3, they did not possess mutation A. But after generation 20,000, Tribe Ara-3 were 'primed'. Only they were able to take advantage of 'mutation B' when it turned up - as it probably did in several of the other tribes, but to no good effect. There are moments of great joy in scientific research, and this must surely have been one of them.
Lenski's research shows, in microcosm and in the lab, massively speeded up so that it happened before our very eyes, many of the essential components of evolution by natural selection: random mutation followed by non-random natural selection; adaptation to the same environment by separate routes independently; the way successive mutations build on their predecessors to produce evolutionary change; the way some genes rely, for their effects, on the presence of other genes. Yet it all happened in a tiny fraction of the time evolution normally takes.
There is a comic sequel to this triumphant tale of scientific endeavour. Creationists hate it. Not only does it show evolution in action; not only does it show new information entering genomes without the intervention of a designer, which is something they have all been told to deny is possible ('told to' because most of them don't understand what 'information' means); not only does it demonstrate the power of natural selection to put together combinations of genes that, by the naive calculations so beloved of creationists, should be tantamount to impossible; it also undermines their central dogma of 'irreducible complexity'. So it is no wonder they are disconcerted by the Lenski research, and eager to find fault with it.
Andrew Schlafly, creationist editor of 'Conservapedia', the notoriously misleading imitation of Wikipedia, wrote to Dr Lenski demanding access to his original data, presumably implying that there was some doubt as to their veracity. Lenski had absolutely no obligation even to reply to this impertinent suggestion but, in a very gentlemanly way, he did so, mildly suggesting that Schlafly might make the effort to read his paper before criticizing it. Lenski went on to make the telling point that his best data are stored in the form of frozen bacterial cultures, which anybody could, in principle, examine to verify his conclusions. He would be happy to send samples to any bacteriologist qualified to handle them, pointing out that in unqualified hands they might be quite dangerous. Lenski listed these qualifications in merciless detail, and one can almost hear the relish with which he did so, knowing full well that Schlafly - a lawyer, if you please, not a scientist at all - would hardly be able to spell his way through the words, let alone qualify as a bacteriologist competent to carry out advanced and safe laboratory procedures, followed by statistical analysis of the results. The whole matter was trenchantly summed up by the celebrated scientific blogwit PZ Myers, in a passage beginning, 'Once again, Richard Lenski has replied to the goons and fools at Conservapedia, and boy, does he ever outclass them.'
Lenski's experiments, especially with the ingenious 'fossilization' technique, show the power of natural selection to wreak evolutionary change on a timescale that we can appreciate in a human lifetime, before our very eyes. But bacteria provide other impressive, if less clearly worked-out, examples. Many bacterial strains have evolved resistance to antibiotics in spectacularly short periods. After all, the first antibiotic, penicillin, was developed, heroically, by Florey and Chain as recently as the Second World War. New antibiotics have been coming out at frequent intervals since then, and bacteria have evolved resistance to just about every one of them. Nowadays, the most ominous example is MRSA (methycillin-resistant Staphylococcus aureus), which has succeeded in making many hospitals positively dangerous places to visit. Another menace is ' C. diff.' (Clostridium difficile). Here again, we have natural selection favouring strains that are resistant to antibiotics; but the effect is overlain by another one. Prolonged use of antibiotics tends to kill 'good' bacteria in the gut, along with the bad ones. C. diff., being resistant to most antibiotics, is greatly helped by the absence of other species of bacteria with which it would normally compete. It is the principle of 'my enemy's enemy is my friend'.
I was mildly irritated to read a pamphlet in my doctor's waiting room warning of the danger of failing to finish a course of antibiotic pills. Nothing wrong with that warning; but it was the reason given that worried me. The pamphlet explained that bacteria are 'clever'; they 'learn' to cope with antibiotics. Presumably the authors thought the phenomenon of antibiotic resistance would be easier to grasp if they called it learning rather than natural selection. But to talk of bacteria being clever, and of learning, is downright confusing, and above all it doesn't help the patient to make sense of the instruction to carry on taking the pills until they are finished. Any fool can see that it is not plausible to describe a bacterium as clever. Even if there were clever bacteria, why would stopping prematurely make any difference to the learning prowess of a clever bacterium? But as soon as you start thinking in terms of natural selection, it makes perfect sense.
Like any poison, antibiotics are likely to be dosage dependent. A sufficiently high dose will kill all the bacteria. A sufficiently low dose will kill none. An intermediate dose will kill some, but not all. If there is genetic variation among bacteria, such that some are more susceptible to the antibiotic than others, an intermediate dose will be tailor-made to select in favour of genes for resistance. When the doctor tells you to finish taking the pills, it is to increase the chances of killing all the bacteria and avoid leaving behind resistant, or semi-resistant, mutants. With hindsight we might say that if only we had all been better educated in Darwinian thinking, we would have woken up sooner to the dangers of resistant strains being selected. Pamphlets like the one in my doctor's waiting room don't help with that education - and what a sadly missed opportunity to teach something of the wondrous power of natural selection.
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