The physics of human walking and considering the wider picture

Gorilla walking like a man. CC talkrational.org
A gorilla walking like a man. Photo by talkrational.org is licensed under CC BY 2.0

Impulsive ankle push-off powers leg swing in human walking
Susanne W. Lipfert, Michael Günther, Daniel Renjewski, and Andre Seyfarth
J Exp Biol 2014 217:1218-1228.

I love papers like this. The extreme level of detail people go to in the quest to discover is fascinating. The question that always comes to my mind is “What made them decide to research this in the first place?” Was it through trying to understand more about where humans come from or was it purely a mathematical and physical curiosity about how we walk? The beauty of science is that it is allowed to be curiosity driven – just like those papers and pieces of research which made it into the IgNobel Awards and have ended up being pivotal in their respective fields.

“Impulsive ankle push-off powers leg swing in human walking” is a rather complicated paper, full of mathematical terminology and notation, but if you can get through the equations you’ll discover a story that shows how human walking has been fine-tuned, linking this physical paper to fundamental questions of human origins. Continue reading “The physics of human walking and considering the wider picture”

The difficulty celebrating my first first-author paper

Sadly I didn't get a paper copy as it's an online-only journal!
My paper

The paper that my thesis worked towards was published last week.

Continue reading “The difficulty celebrating my first first-author paper”

Why have a circadian clock?

Almost every animal and plant on the planet has a circadian clock, even those that live in the depths of the sea and deep underground in caves.

The presence of clocks in almost all life-forms implies that it is a helpful or advantageous characteristic, an evolutionary adaptation, serving to improve the fitness of the organism. This argument makes apparent sense but, without testable hypotheses, has little to support it.

Two main hypotheses have been formed to explain the evolutionary benefit of having a circadian clock. The first is known as the External Synchronisation hypothesis – that the benefit to the circadian clock lies in being coordinated with the external environment, for example, the predictable daily change in light and dark that we call day and night. The second is the Internal Synchronisation hypothesis – here the clock benefits an organism by allowing it organise physiological processes in time in order to avoid conflict between incompatible processes, for example separating the process of photosynthesis from that of nitrogen fixation in the case heterocystous cyanobacteria.

These two hypotheses aren’t mutually exclusive. The internal synchronisation hypothesis doesn’t necessarily require a 24 hour clock; plenty of other periods would suit. But, timing pressure placed on an animal from the external environment could force biological processes to fit within the 24 hour day, for example, the reactions for photosynthesis. These are only necessary in the day when it is light. But since nitrogen fixation and photosynthesis are incompatible, nitrogen fixation gets restricted to the night and internal organisation has been forced on an animal from external pressure. Once established, internal synchronisation could become independent of external pressures. Perhaps, in the origin of circadian timing systems, external synchronisation came first and internal synchronisation second, but now, either one serves as a selective advantage. So, though the two hypotheses propose reasons for selective advantage a circadian clock might give to an organism, and therefore why Clocks may have evolved in the first place, arguments are complicated as whether these are the original selective pressure that formed a circadian timing system.

How might we test which which hypothesis is most important today? One way is to look at animals that live in non-rhythmic environments, those that do not experience the regular and predictable cycle of day and night. These animals offer the chance to directly test the first, external synchrony, hypothesis, since in a non-rhythmic environment, there is no need to synchronise to an absent cycle. 

The deep sea and caves are two environments that fit this description. Interestingly, most studies on organisms that live there give at least some hints that circadian clocks are present and working even here. Although, there are many difficulties interpreting and comparing this research due to the various experimental conditions used, this general observation lends weight to the internal synchronisation hypothesis – in the absence of a no cycling external environment, a ticking clock must be being used for something else, and internal synchrony is the most obvious.

My PhD research looked at one organism that lives in the depths of caves and is highly adapted to life there: the Mexican blind cavefish, Astyanax mexicanus. This fish shows wonderful daily patterns of behaviour and gene expression, confirming that it has a functional circadian clock. It also shows some interesting quirks, which give some insight into why an animal that lives in the dark and has done so for tens to hundreds of thousands of years might keep a system that generates 24 hours rhythms in physiology and behaviour.

What is a circadian clock?

Broadly speaking, the circadian clock is a cell and molecular feedback loop – inside the cell, a bunch of proteins that interact with genes and DNA, which in turn interact back with those original proteins. This cellular feedback loop controls those outward and apparent rhythms we are aware of, like jet lag and waking, as well as many more we may be unfamiliar with, but it isn’t just humans who have a body clock, all life on planet Earth has one, although its workings aren’t exactly the same in all life-forms.

The feedback loop. Proteins join together to activate gene transcription of genes that subsequently repress the original proteins. This feedback generates oscillations of gene expression.
The feedback loop. Proteins join together to activate gene transcription of genes that subsequently repress the original proteins. This feedback generates oscillations of gene expression. From Eckel-Mahan and Sassone-Corsi, 2013, Metabolism and the circadian clock converge.

In animals, the key players are genes called clock, bmal, period and cryptochrome. There are actually multiple versions of the genes, named numerically (clock1a, bmal2, period3 etc) and shortened to 3 or 4 letters (clk1a, bmal2, per3 etc). To explain the cycle, we need to start with clock and bmal and go twice around the feedback loop, each stage showing the effect of the previous.

Firstly, CLOCK and BMAL proteins (CLK and BMAL; by consensus gene names are in italics and PROTEIN names are in uppercase), interact in the cell, joining together to turn on period and cryptochrome genes. As the genes are turned on, they are transcribed by the cell, eventually begetting proteins, PER and CRY proteins. These proteins interact with CLK and BMAL proteins to make CLK and BMAL less activating, repressing CLK and BMAL.

Secondly, as CLK and BMAL are now repressed, the turning on of period and cryptochrome genes is stopped. Fewer PER and CRY proteins are generated by the cell. Fewer PER and CRY proteins means less repression of CLK and BMAL, and so CLK and BMAL are released to begin another cycle.

The overall effect is similar in plants and other organisms: Activator proteins turn on repressor genes, these repressor genes are translated into repressor proteins by the cell and repress the activator proteins and so on. These proteins and genes in the clock aren’t the same in all organisms, but they play similar roles turning on or off genes, modifying the activity of proteins, like how David de Gea and Manuel Neuer are not the same player, but play similar roles for their teams. The fact that clocks have a similar feedback mechanism but consist of different components in the different branches of life adds to the idea that circadian clocks must be evolutionarily adaptive. It is an example of convergent evolution, where two separate species look similar without being evolutionarily related, such as how dolphins and sharks look fairly similar and are adapted to the broadly similar environments but are completely different species. In this case, evolution has dictated that the best body shape for fast and efficient swimming in water is a streamlined oval. In the case of circadian clocks, we can suggest that evolution has dictated that the best way of organising your physiology and behaviour is through the use of a molecular feedback loop which acts within the cells of the body.

 

Two illustrations of how the molecular components make up the circadian clock. On the left - in zebrafish. Clock (CLK) and bmal (BMAL) proteins (there are 6 versions) interact to activate (green arrow) transcription of per and cry genes. PER and CRY proteins then interact with CLK and BMAL to repress (green line with flat on top) their activity. Per and cry are also activated by light. On the right - plants. CCA1 and LHY are the CLK and BMAL equivatlents, interacting to activate PRR7 and PRR9 which then repress CCA1 and LHY.
Two illustrations of how the molecular components make up the circadian clock. On the left – in zebrafish. Clock (CLK) and bmal (BMAL) proteins (there are 6 versions) interact to activate (green arrow) transcription of per and cry genes. PER and CRY proteins then interact with CLK and BMAL to repress (green line with flat on top) their activity. Per and cry are also activated by light. Taken from Vatine et al., 2011, It’s time to swim! Zebrafish and the circadian clock. On the right – plants. CCA1 and LHY are the CLK and BMAL equivatlents, interacting to activate PRR7 and PRR9 which then repress CCA1 and LHY. Taken from Harmer lab at UC Davis

Why is Darwin more famous than Wallace? Cultural survival of the fittest

A young Wallace and Darwin

Why is Darwin is more famous than Wallace?

BBC – Why does Charles Darwin eclipse Alfred Russel Wallace?

Why Evolution is True – Why is Darwin more famous than Wallace?

Essentially it was because of the impact of Origin of Species.

With their joint paper, Darwin and Wallace can be thought of a co-proposers of evolution by natural selection. Unfortunately for Wallace’s fame stakes, this joint paper did not arouse much interest at the time. Origin, a year later, with Darwin’s name at the forefront and Wallace being deferential to his colleague, captured both scientist and public imagination. From this, Darwin was the one being ridiculed in cartoons as a half-ape, and Darwin was the name people associated with evolution. It’s also interesting to note that natural selection (but not evolution) went through somewhat of a out-of-fashion period in the early 1900s, which affected Wallace’s fame while not as severely affecting Darwin’s, whose fame stemmed from bringing evolution as a whole to the attention of the world. Later, the Modern Synthesis, a sort of union (or reunion) of evolution, natural selection and genetics in the 1930s, seems to have remembered the contributions of Darwin whilst largely forgetting Wallace’s. As we inherit this synthesis of evolutionary thought and its associated history, we cast Wallace’s role by the wayside – a fitting and ironic example of cultural evolution and survival of the fittest.

Lamarck and Buffon – evolutionary heroes in the Jardin des Plantes, Paris

The Muséum national d'Histoire naturelle in the wintertime Jardin des Plantes, Paris
The Muséum national d’Histoire naturelle in the wintertime Jardin des Plantes, Paris

I recently visited Paris and made a quick trip to the Jardin des Plantes, the site of the Natural History Museum of Paris. Immediately facing you as you enter the park is a statue of Jean-Baptiste Lamarck. Lamarck’s theories are now mostly abandoned, as Darwin and Wallace’s theory of Evolution by Natural Selection has become the basis of biological science. However, Lamarck deserves credit for his contribution to evolutionary ideas as he was the first to propose a theory to explain evolution, that animals change in response to the environment. Paris recognises this with this statue, in which Lamarck is heralded as “Fondateur de la Doctrine de L’Evolution” or “Founder of the Doctrine of Evolution”.

A statue of Jean-Baptiste Lamarck at the entrance to the Jardin des Plantes
A statue of Jean-Baptiste Lamarck at the entrance to the Jardin des Plantes

At the other end of the gardens Buffon and his work is also recognised with a statue. Buffon’s work in natural history, published in an incredible 36 volumes over 39 years, influenced future naturalists such as Lamarck, and discussed a number of evolutionary problems – “he brought them to the attention of the scientific world”. He also was at the forefront of making the Jardin des Plants the Kew Gardens of Paris, with research and the associated museum.

A statue of French naturalist Georges-Louis Leclerc, Comte de Buffon, in the Jardin des Plantes
A statue of French naturalist Georges-Louis Leclerc, Comte de Buffon, in the Jardin des Plantes

Science is a step-by-step process, always building on previous theories and data. Parisiens recognise these two scientists for their work in the field of natural history, and despite many of their ideas now being understood as incorrect, their work is part of the formation of evolutionary theory, the unifying concept of the life sciences.

Le Grande Galerie de L'Evolution

Evolution: What did Darwin, Wallace and Lamarck contribute?

To start this blog off, a little bit of history.

Do you know who Charles Darwin is? How about Alfred Wallace? Jean-Baptiste Lamarck? You’ve probably heard of the first guy. The second, maybe. The third? Perhaps if you’re interested in biology, or French science.

All three men are important in the development of evolution by natural selection as an idea. Darwin is the most famous because of his grand work, Origin of Species, which contributed not just to evolutionary theory but also to the communication of science both then and now. But Wallace and Lamarck should not be forgotten; both have their place in the history of the evolutionary theory, and therefore, are important to the content of this blog. Here is a little summary:

Charles Darwin, Alfred Wallace and Jean-Baptiste Lamarck. Important contributors in the history of evolutionary theory
Charles Darwin, Alfred Wallace and Jean-Baptiste Lamarck. Important contributors in the history of evolutionary theory

Continue reading “Evolution: What did Darwin, Wallace and Lamarck contribute?”