The living puddle

The above title  is from (Ehrenvard, 1962), discussed by (Williams, 1966). Ehrenvard believes that life is probably older than organisms. He imagines a stage at which every body of water could be thought of as a single diffuse organism. His view has resonance with Darwin’s warm little pond which I discussed previously McLachlan (2010). The origin of life is one of the most profound mysteries confronting science and rain pools are the quintessential warm little ponds where life may have originated. Furthermore, Strother and colleagues (Strother et al. 2011), present evidence that rain pools and other puddles were the places where life first colonised land. More specifically, the famous palaeontologist Alfred Sherwood Romer's theory suggests that amphibians may have originated in rain pools and used them as a base for the colonization of land (quoted by Dawkins 2004), p251. Thus these humble and much overlooked habitats take on a significance which places them in a new light.

Reference

Dawkins, R. (2004). The Ancestor's Tale: A pilgrimage to the Dawn of Life. Weidenfeld and Nicholson. UK.

Ehrenvard, G. (1962). Life: Its Origin and Development. Minneopolis: Burgess.Williams, G. C. (1966). Adaptation and Natural Selection. Princeton: Princeton University Press.
McLachlan, A. J. (2010). Life in the puddle. http://www.atholmclachlan.blogspot.com./
Strother, P. K., Battison, L., Brasier, M. D. and Wellman, C. H. (2011). Earth’s earliest non-marine eukaryotes. Nature, 473, 505-509.

The Scientific Method

If you find what follows condescending, even insulting - well, in 35 years of university level research and teaching in science I have met only one among all my colleagues and students at Newcastle University able to hold their heads high in this matter. I refer to the Scientific Method which we all think we use in our research. I know there are many examples of beautiful experiments. The careful and inspirational experiments of Richard Lenski and colleagues with Escherichia coli and those of John Endler and colleagues with guppies come to mind (described by Richard Dawkins (2009), pp. 116-139. But, in my experience, these are the exception to the great ground swell of misunderstanding or even scorn for the method.  In his essay, Induction And Intuition in Scientific Thought, Peter Medawar makes the same point with the eloquence we expect of him (Medawar, 1984), p.78, but ends with the conclusion that the method dwells principally in the minds of philosophers. My contention is that this is mistaken. I believe a conscious knowledge and application of the method greatly eases a scientific investigation.

So, how did I escape the general malaise over the scientific method? Many years ago, while browsing in the Newcastle University library, I came across Paul Weisz's textbook for first year biology students (Weisz, 1959). The final chapter concerned the scientific method which had immediate resonance with me.  I supplemented what I learned from Paul Weisz with the excellent book by Beveridge (1950), given to me by my father in law. An appreciation of the method does not come easily but demands thought and practice. So why is the method not part of all undergraduate courses in science? Why had my own realization to wait some 20 years after my PhD? Part of the answer may be that many investigations do actually not benefit from the application of the method. It is true that the method comes into its own only with the design of experiments. Some subjects, for example ecology, a traditionally descriptive science, largely escapes the needs of experimental rigour. For example, preliminary ecological investigations seeking answers such as, in my case, what is living in the mud of newly flooded lakes Kariba and Chilwa in tropical Africa (McLachlan, 1974, 1979)? This investigation could have been framed as a hypothesis such as 'mud samples will reveal something interesting about the colonisation of a newly flooded lake’, but to no great benefit. Later I became interested in mating systems, specifically of chironomid midges, the larvae of which inhabit the mud of lakes in great numbers. It was in the study of the mating systems of these midges that I was to learn  the value of the method.  

Why was I to find colleagues and student so disinterested, even hostile to this indispensable tool?  Since discovering Paul Weisz I have made the four steps of the scientific method; observation, hypothesis, prediction, test; the subject of laboratory classes and field courses from first year on. Examples of the application of the protocol are given below. I cannot say I recall any enthusiasm for this approach from students. Not infrequently, when setting out on a final year research project, I met with the question, "Dr McLachlan - do we really have to do all that scientific method stuff?" But I know from personal experience how difficult it often is to get started on a problem without the conscious effort required to create testable and falsifiable hypotheses. To illustrate the point what follows takes the form of an undergraduate lecture. I consider two famous cases of scientific investigation from history and one from my own research. All fail because of flawed methods. My hope is that these examples will be found instructive. I do not here dwell on the philosophy of the hypothetical/deductive method which underlies the method. The axiom of Karl Popper that any hypothesis must be falsifiable, is taken as given (Popper, 1959 edition). A proper experiment requires one or more treatments, designed to test an hypothesis. A control which omits the test and a treatment control to monitor effects of the treatment are both mandatory. 

First, a typical experiment from somewhere around 1500 AD  to address the apparently inexplicable accuracy achieved by rifled firearms (Trench, 1972), pp.107,108 (Calabi, Helsley, and Sanger, 2013), p46. This example captures the spirit of experiments conducted around that time. Here an hypothesis was created to explain a widely made observation concerning accuracy. The hypothesis was that the devil sits astride the ball fired from a rifled firearm to guide it. To test the hypothesis a set of experimental balls were deeply engraved with the sign of the cross. The assumption here is that the sign of the cross would repel the devil leading to a prediction that the experimental balls would no longer fly true. Control was provided by an equal number of balls, identical to the experimental set but not treated in any way. The devil would therefore be allowed access to these control balls which were predicted to fly true. That is exactly what results showed - control ball, but only those - flew true to target. All well and good.  Here we have an elegant, controlled experiment. It is perhaps not immediately easy to see the flaw. But there is one - a treatment control is lacking. What we need is a treatment control with a third set of balls but with a similar sign other than the cross, deeply engraved. And indeed, musket balls in such a treatment control were subsequently shown to fly erratically, just like experimental balls, hence leading to the rejection of the devil hypothesis. The unbalancing effect of engraving musket balls is quite sufficient alone to cause erratic flight. The devil is not required.

Here is another example from history. Aristotle postulated an idea called Spontaneous Generation which purported to explain that abiding mystery, the origin of life. This hypothesis is readily tested by experiment. It is widely known that flies emerge from rotting meat, evidence it seemed, of spontaneous generation of life in the form of flies. To test the hypothesis of Spontaneous Generation, rotting meat was placed in a bottle, screened to eliminate the possibility of flies arriving from outside. The control was a bottle with decomposing meat, but left unscreened.  The prediction here is that flies would appear in both experiment and control - a prediction fully born out by the result. Flies appeared in all bottles even when screening denied egg laying flies access from outside - thus apparently confirming the hypothesis of spontaneous generation. But to ensure the absence of organisms at the outset, a better experimental design would require the initial sterilisation of meat, eliminating the possibility that flies had laid eggs before the start of the experiment. It took over a hundred years for the compelling spontaneous generation idea to finally be laid to rest by the careful experiments of Louis Pasteur using heat sterilisation of experimental treatments (Fenchel, 2002). Under a heat treatment regime, flies appeared, but only in the unscreened containers. At last the persistent hypothesis of spontaneous generation was demolished.  There are many variants of both these classical experiments. 

To give an example from the work of myself and collaborators; many years were spent studying the extraordinary fly larvae inhabiting rain pools in tropical Africa (McLachlan and Ladle, 2001). There are interesting problems of adaptation associated with extremely ephemeral habitats. One is that each pool harbours essentially one, and only one species - a situation which would appear to persist over geological time. It is a surprising, and rare situation for an ecologist to encounter. I wanted to know if a pool would always harbour the same species. Experiments involved a transplant, that is, the removal of all inhabitants from a pool and either replacing them with a species never before encountered there or refilling pools with tap water and awaiting the outcome of natural invasion by ovipositing females. These experiments are rather vague. While posing some interesting further questions  (McLachlan, 1985; McLachlan and Cantrell, 1980), they would have benefited from a more formal experimental design. I would do it differently now.

A formal experimental design to test one possible hypothesis might look like this:   

Observation: Each pool is inhabited by the larvae of a single species, always the same one. This is an extraordinary situation worthy of attention.

Hypothesis: The species present is determined by chemical characteristics of the pool water conditioned by previous populations of larvae.

Prediction: Conditioned water will determine the species invading a pool.

Test: Experiment: Remove all water from a set of replicate pools. Filter and replace. Leave to allow oviposition by females.

         Control: Filter fresh rain water; add to a replicate set of pools after the removal of original water and occupants. Leave to allow oviposition by females.

        Treatment control: Unfiltered rain water. Leave to allow oviposition by females.

A series of further experiments are required to test other specific hypotheses.     

 

The final point I wish to make is the vexing matter of the reproducibility of experiments carried out by different people. Here we have an unresolved difficulty at the heart of the scientific method which much occupies the minds of the scientific community at present.

The situation has been brought to prominence  by some high profile cases, for example that of the physicist Jan Hendrik Schön (Reich, 2009). Schön was an astonishingly prolific innovator but no one could repeat his experiments. He claimed this was not his fault but that others lacked the skill necessary to succeed. And this is indeed the crux of the matter.  The scientific method is not like a recipe for making a cake that anyone can follow to a successful outcome. It is an art, more like poetry or painting (Medawar, 1984). If no one can reproduce a Mona Lisa, should we conclude that Leonardo da Vinci was a fraud? Furthermore, the Methods section of a scientific paper rarely contains all the minutiae which could bring an independent repetition closer to the original. The cartoon above by Garry Larson encapsulates the difficulty perfectly. The victim's inquisitors are never going to make fire with the method provided. Such difficulties worry us as shown by the frequent appearance of papers concerning replication (Baker, 2016; Editorial, 2015, 2016a, 2016b; N. Editorial, 2016a, 2016b; Nuzzo, 2015; Reardon, 2016; Serewitz, 2015, Kneebore, R., Schlegel, C. and Spivey, A. (2019). The list shows no sign of easing off. Indeed, quite the reverse, it is accelerating.

References

Baker, M. (2016). Statisticians issue warning on P values. Statement aimed to halt missteps in the quest for certainty. Nature, 531, 151.
Beveridge, W. I. B. (1950). The Art of Scientific Investigation. William Heinemann Ltd, London.

Calabi, S., Helsley, S., and Sanger, R. (2013). The Gun Book for Girls.: Shooting Sportsman Books.
Dawkings, R. (2009). The Greatest Show on Earth. Bantam Press, London. 

Editorial. (2015). It's good to talk. Nature, 523, 382.

Editorial. (2016a). Repetitive flaws. Strict guidelines to improve reproducibility of experiments are a welcome move. Nature, 529, 256.

Editorial. (2016b). Reproducibility call. Nature 529, 261.

Editorial, N. (2016a). Repetitive flaws. Nature, 529, 256.

Editorial, N. (2016b). Reproducibility call. Nature, 529, 261.

Fenchel, T. (2002). The Origin and Early Evolution of Life. . Oxford: Oxford University Press.
Kneebone, R., Schlegel, C. and Spivey, A. (2019). Science in hand: how craft informs lab work. Nature, 564, 188-189. 

McLachlan, A. J. (1974). Development of Some Lake Ecosystems in Tropical Africa, with Special Refrence to the Invertebrates. Biological Reviews, 49, 365-397.

McLachlan, A. J. (1979). Decline and Recovery of the Benthic Invertebrate communities. In M. Kalk, McLachlan, A. J. and Howard-Williams, C. (Eds.), Lake Chilwa. Studies of change in a Tropical Ecosystem. London: W. Junk. Publishers.

McLachlan, A. J. (1985). What determines the species present in a Rain - pool? Oikos, 45, 1 - 7.

McLachlan, A. J., and Cantrell, M. A. (1980). Survival Strategies in Tropical Rain Pools. Oecologia, 47, 344 - 351.

McLachlan, A. J., and Ladle, R. (2001). Life in the puddle: behavioural and life-cycle adaptations in the Diptera of tropical rain pools. Biological Reviews 76, 377-388.

Medawar, P. (1984). Pluto's Republic. In. Oxford: Oxford University Press.

Nuzzo, R. (2015). Fooling ourselves. Nature, 526, 182-185.

Popper, K. (1959 edition). The Logic of Scientific Discovery.: Routledge Classics.

Reardon, S. (2016). A mouses home may ruin studies. Environmental factors lie behind many irreproducible rodent experiments. . Nature, 530, 264.

Reich, E. S. (2009). Plastic Fantastic. How the Biggest Fraud in Physics Shook the Scientific World. New York: Palgrave MacMillan.

Serewitz, D. (2015). Reproducibility will not cure what ails science. Nature, 525, 159.

Trench, C. C. (1972). A history of Marksmanship. . Norwich: Longman.

Weisz, P. B. (1959). The Science of Biology. (2nd ed.). New York: McGraw-Hill.

The Extended Phenotype

The central theorem of the extended phenotype: An animal’s behaviour tends to maximise the survival ‘for’ the genes for that behaviour, whether or not those genes happen to be in the body of the particular animal performing it.

The quote above is from Richard Dawkins (Dawkins, 1982), p233, and there is no doubt that the idea of the extended phenotype (EP), has changed the way we think about evolution. It requires a rethink of what constitutes an individual and much else besides. My favourite example of EP is to be found in the interaction between the genes of host and parasite.  Here genes of the parasite typically reach outside the body of the parasite to manipulate host behaviour (Poulin, 2010).

By definition parasites reduce host fitness. But the parasite that harms its host may be damaging its own reproductive potential. Hence the parasite has a vested interest in the reproductive success of its host. Indeed, a parasite can enhance it’s own fitness and, at the same time that of its host, through the harmonious collaboration between the genes of host and parasite. So, in practice, parasitism merges into symbiosis and parasitism must be seem to extend from fitness benefit to parasite alone all the way to benefit for both parasite and host. He cites the extreme example of mitochondria and the chloroplasts of plants. Both originate as independent parasites, eventually evolving to an intimate permanent relationship within the cells and life cycle of the host.

My aim is to apply Dawkins' EP reasoning to a host/parasite system I have spent several years studying. I refer to the relationship between a common chironomid midge, Paratrichocladius rufiventris and two parasites, a mite Unionicola ypsilophora and a mermithid worm, probably Gastromermis rosea (McLachlan, 2006), (Figs. 1 and 2). I consider only the female host midge. For my present  purpose the male can be left aside except for his role as a mate. The part the male plays  is considered elsewhere (McLachlan, 1999). I therefore consider only three interactors; female midge, mite and worm. I do not distinguish sex in the parasites. I use the term fitness in its original sense as used by Darwin and Wallace, i.e. the capacity to reproduce (Dawkins, 1982), pp181-182.

For the host female mating is a necessary prerequisite to send her to water to oviposit. And it is in the water that both parasites find their definitive hosts; a bivalve snail for the worm and midge pupa for the mite. So, both female host and her two parasites can only close their life cycles if the host has mated (McLachlan, 1999). Furthermore, the mite appears to enhance the mating success of the host, thus promoting fitness gains, both for its self and for both parasites.

How might the midge/mite relationship have evolved? We are not dealing with an arms race where gains for interactors are apposed (Dawkins, 2006). Rather we appear to be dealing with a case where both interactors gain - aptly been termed the Jack Sprat principle by Richard Dawkins (Dawkins, 1982), pp. 239-240. It is easiest to understand the Jack Spat principle if  attention is focused on genes rather that phenotypes.  “Selection goes on at that lower level - the level of the component parts of a harmonious complex”. This is Dawkins’ model 2. In model 2 it is the genes that are the target of selection (Cronin, 1991), p1007). How do the genes of the midge gain from cooperation with those of the mite and visa versa?

Jack Sprat model 2 is essentially a frequency dependent model (Dawkins, 2006), p240). The genes at the lower frequency, in whatever player they are found, automatically carry a selective advantage due to their rarity, so increase in frequency until an Evolutionarily Stable Strategy  (ESS), is achieved (Maynard Smith, 1982). Mites are bright red which could be acting as a supranormal signal of the normal red ventral surface of the female (species name rufiventris). The male midge that mates with a female lacking a worm gains in fitness (McLachlan, 2006). Thus a gene in a male that enables him to recognise the supranormal signal of a female with a mite, would spread in the population until competition with rivals lead to an ESS. The end result is harmonious cooperation of midge and mite genes outside the bodies of each - that is, the extended phenotype in operation.

Fig. 1. Parastic mites on a female midge host. (From (McLachlan, 2012).

Now to introduce the second parasite, the mermithid worm. The worm infects only the female midge and renders her sterile. The infected female thus has zero fitness but there is something else here. Remember that worm gains when an infected female returns to water. So there is theoretical possibility of adaptive manipulation by the worm. For instance, could the worm manipulate the physiology of his host to shift resources normally put to eggs into flight muscle. Such a manipulation would  lead to improved flight range in the search for water, like the case of crabs infected with the parasite Sacculina (Dawkins, 1982), p. 214). Here we have the testable prediction that flight muscle mass is greater in worm infected females.  I wish I had carried out test.

Fig. 2.  Mermithid worm emerging from female host. g, mass of  a single worm. Scale bar 0.5mm. (From (McLachlan, 2012).

To summarise, I view manipulation between a midge and its parasites in the light of EP. The EP approach extends understanding beyond reasoning limited to manipulation (McLachlan, 1999). What new insights does EP offer in understanding the adaptive strategies of the midge and its two parasites? I suggest that EP provides something beyond the standard idea of manipulation because it includes an explanation of how manipulation happens. EP also has the power to change how we see an individual. A  midge with a mite or worm is no longer a midge but something else - rather like a rabid dog manipulated by the rabies virus. Such a dog is not longer a dog but a different organic being. So, the debate over at what level selection acts is not over (Dawkins, 1982), p.121. Because EP has focused attention on genes, I have been lead to frequency dependent selection thinking and a better understanding of how the midge system could have evolved as an ESS. 

References

Cronin, H. (1991). The Ant and the Peacock (1993 ed.). Cambridge: Cambridge University Press

Dawkins, R. (1982). The Extended Phenotype. (1999 edition ed.). Oxford: Oxford University Press

Dawkins, R. (2006). The Selfish Gene. Oxford: Oxford University Press.

Maynard Smith, J. (1982). Evolution and the Theory of Games. Cambridge, UK: Cambridge University Press.

McLachlan, A. J. (1999). Parasites promote mating success: the case of a midge and a mite. Animal Behaviour, 57, 1199-1205.

McLachlan, A. J. (2006). You are looking mitey fine: parasites as direct indicators of fitness in the mating system of a host species. Ethology Ecology and Evolution 18, 233-239.

McLachlan, A. J. (2012). Phenotypic plasticity and adaptation in a holometabolous insect, the chironomid midge. ISRN Zoology. 2012, 8 pages.

Poulin, R. (2010). Parasite manipulation of host behaviour: an update and frequently asked questions. In H. J. Brockman (Ed.), Advances in the study of behaviour. (pp. 151- 186). Burlington, MA: Academic Press.