In our latest paper we demonstrated that magnesium perchlorate can depress the onset of intracellular vitrification in Bacillus subtilis cells. But why did we do that and why does it matter?

Well it comes back to the fact that Mars is a very cold place, and if you want to know whether there’s life on Mars, you need to know whether life could be there. For Mars, temperatures of -70°C are common, both on the surface and in the subsurface. Therefore, one of the central questions in Martian astrobiology is, can you have active life at such low temperatures? To answer this question you have to investigate the mechanisms which are believed to set the limits to life at low temperatures. But what are they?

Well first off, all life needs liquid water in order to survive, and at ambient pressure water freezes at 0°C. So there’s our first constraint. We also know that ice formation inside of cells is a considerable problem for life as ice can easily pierce membranes and rupture cells. But let’s assume you can prevent ice forming, either from the presence of ions in the environment or from the production of molecules such as glycerol, what sets the next low temperature limit for life?

Answering this is where things have gotten a bit more tricky. The current low temperature record holder is Planococcus halocryophilus, a bacterium isolated from the Canadian high arctic. It’s capable of replicating at -15°C and is metabolically active down to -25°C. Beyond that, kinetic data from enzymatic studies suggested that life may be able to maintain itself at any deep subzero temperature, as enzymatic rates of repair always exceeded those of spontaneous molecular damage. Note however that maintaining cellular structure is a world away from growth and division. But beyond P. halocryophilus and the kinetic arguments, it was exceedingly hard to find life much below -20°C. Therefore, in 2013 Andrew Clarke and his co-authors argued that it was the onset of intracellular vitrification occurring at ~-20°C which was setting a physical limit to life at low temperatures. But what is intracellular vitrification?

Intracellular vitrification is the process by which the interior of a cell transitions from being liquid and dynamic, to becoming an incredibly viscous glass-like substance. As biomolecular diffusion ceases beyond the glass transition, so does biochemical processes and as such life is suspended in a cryopreserved state. It’s worth making a distinction here about what is meant exactly by vitrification and glass transitions as these terms are used by multiple fields to mean slightly different things. In the field of cryopreservation, vitrification is used to mean the process by which biological material (cells, seeds, tissue) are preserved without ice formation i.e. your entire sample vitrifies, water and all. This is commonly achieved by using cryoprotectants to depress ice formation, and instead induce a glassy state which lacks sharp ice crystals which cause cellular damage. In the environmental context vitrification is slightly different. In the environment, intracellular vitrification occurs as the extracellular environment begins to freeze, thus concentrating solutes which generates an osmotic gradient across cell membranes. This osmotic gradient forces water out of cells and the cell shrinks. This process of ice formation, solute concentration, and intracellular water loss continues until you reach a point at which there is no longer sufficient intracellular water to maintain biomolecular diffusion, and consequently the intracellular space undergoes a glass transition. Or so goes the theory. Also a quick apology to the physicists and material scientists, we know that “glasses” and “glass transitions” mean very precise and detailed events in your fields, but we’ve simply stolen them as they’re the closest terms to what we’re trying to describe. But now that we know what vitrification is, what does it have to do with life on Mars?

Well if vitrification occurs at roughly -20°C for most unicellular organisms, and Mars is far colder than that, then we’d have to conclude that without some mechanism to depress vitrification, there can be no active life on Mars. Sad. But wait, vitrification requires liquid water to freeze, and as luck would have it Mars is covered in salts which are exceptionally good at depressing the freezing point of water. Here enters perchlorate salts to this story, and the genesis of my research question. If perchlorate salts can depress the freezing point of water, and vitrification only occurs after water has frozen, do perchlorate salts also then depress the onset of intracellular vitrification?

This is the research question which took me to Fernanda Fonseca’s lab in Paris, one of the original co-authors in the 2013 paper on the low temperature limit for life. The plan was simple, grow some Bacillus subtilis, incubate it in various concentrations of magnesium perchlorate, then measure it’s intracellular vitrification, easy. Why B. subtilis? Practicality. I was on a travelling fellowship so only had two months to complete this work. As such, I needed a workhorse model organism that would grow rapidly to large amounts, and was also well characterised in the literature. B. subtilis ticked both these boxes, and it also helps that we already knew exactly how it behaved in response to perchlorate salts. How do you measure intracellular vitrification? In our case we used a differential scanning calorimeter, or DSC for short. A DSC is a piece of equipment which can measure the difference in energy required to heat or cool a sample compared to a reference, hence the differential part of the name. Briefly, if you heat your sample and it melts, it takes energy to break all those bonds, and a DSC “sees” this by having to put more energy into the sample to keep it at the same temperature as the reference. On the other hand if your sample starts to give out heat, then the DSC works less hard and can then record this as requiring less energy to heat your sample. In our case, we were looking for thermal signals during the heating ramp, and so technically we were measuring de-vitrification. As de-vitrification is going from glass to liquid, an energy requiring process, we were looking for endothermic events in our DSC traces. For B. subtilis, its intracellular vitrification without perchlorate occurred at ~-23°C, so fairly consistent with what Clarke et al. had reported for other microbes. But, as we added magnesium perchlorate, its intracellular vitrification began to depress, so much so that by 2.5 M magnesium perchlorate, the vitrification peak was depressed to -83°C. Therefore, we demonstrated that not only do perchlorate salts depress the freezing point of water, but that in doing so they also depress the onset of intracellular vitrification, the process believed to set the low temperature limit for life.

Does this mean there’s active life on Mars? Of course not. We simply demonstrated that the physical process of vitrification can be depressed by perchlorate salts, which unfortunately bring with them a host of other problems. Chief among these is the fact that there’s no known organism capable of tolerating eutectic concentrations of magnesium perchlorate. Then we have other issues such as protein unfolding at subzero temperatures and membrane stiffness. As ever, these issues will be explored in future research, as will other aspects of intracellular vitrification. But what’s coming out of this research is hopefully an altered view of how we think of perchlorate salts with regards to biology. As an archetype for chaotropicity they’ve always been seen as deleterious towards life, but this is a simplification of a complex web of interactions which change across temperature, pressure, salt concentration and cation species. So going forward we need to determine how life can utilise the benefits of perchlorate salts, while also mitigating their negative effects. Do that, and we might get close to making a Martian.

May 26, 2024

Here I am, back again after a long hiatus talking about the effects of perchlorate salts on chymotrypsin, but this time it’s not bad news! The literature on the effects of chaotropic molecules (perchlorates included) on enzyme activity and stability overwhelmingly shows that they are deleterious to enzymes, something I have been able to show myself through my own research. But this time, I get to write about how perchlorate salts can actually increase enzyme activity at low temperatures.

So how did this research idea even come about? It all started when two of my research interests, extremophilic enzymes and perchlorates, basically collided into each other. All of my previous research has shown that perchlorate salts reduced the enzymatic activity and structural stability of my model enzyme, chymotrypsin. On the face of it, these effects are bad news for biochemistry and life in perchlorate rich environments. But is structural instability always a bad thing?

When might an enzyme being less stable, actually be beneficial for its activity? This brings us to the psychrophilic enzymes, which come from organisms that are uniquely adapted to life in cold environments. Psychrophilic enzymes are generally characterised by a few notable features; they exhibit greater enzymatic activity at low temperatures compared to their mesophilic and thermophilic counterparts, which is obviously beneficial for the organism expressing them. These psychrophilic enzymes also tend to lose their activity at lower temperatures and are more susceptible to unfolding by chaotropic molecules. An important point here is that the structural instability and low temperature activity of psychrophilic enzymes are not separate phenomena, they are linked, and wonderfully so. Because psychrophilic enzymes are less stable, they are routinely reported to have increased flexibility, and it is this flexibility which actually allows them to be active at low temperatures! You can even increase the low temperature activity of an enzyme by simply making it more flexible by introducing a single glycine substitution. Quick caveat: this doesn’t always work, but it works often enough that we can view it as a general rule. We can also look at the flexibility-activity relationship from a thermodynamic viewpoint, which really brings the whole picture together. The key to increasing low temperature enzyme activity is to make the reaction require less activation energy (make ΔH^‡ smaller). As psychrophilic enzymes have less stabilising interactions, fewer of these interactions need to be broken in order to facilitate catalysis and as a result you need less energy input to start the reaction. This isn’t a free meal, the reduced activation energy comes with a price. As there are less stabilising interactions, and the enzyme is more flexible as a result, it means that to form the activated enzyme-substrate complex, you must pay a larger entropic cost (ΔS^‡ becomes more negative). These are the thermodynamic hallmarks of psychrophilic enzymes, a lower energy of activation and a more negative entropy of activation.

After researching all this, I realised that I might be able to link the psychrophilic activity-flexibility relationship to my own work with perchlorates and chymotrypsin. My thought was, if perchlorate salts partially unfold my enzyme, thus reducing the number of stabilising interactions, would this make my enzyme more flexible and then potentially more active at low temperatures? I became convinced that this should be the case when I found a couple of rare examples of chaotropic molecules increasing enzyme activity at room temperature. All I had to do now was test the hypothesis.

The resulting data did indeed show that perchlorate salts (0.25M) could increase the activity of chymotrypsin at 5°C by ~10% despite perchlorates lowering chymotrypsin activity at ambient temperatures. The thermodynamic analysis suggested that this stemmed from a reduced enthalpy of activation, as had been predicted, but that the effect was diminished by an increasingly negative entropy of activation. These two facets suggested to me that perchlorate induced flexibility was probably the cause of this increased enzyme activity. However the picture wasn’t that simple. Higher concentrations of perchlorate salts (0.5M) did not increase the enzyme activity over the assayed temperature range, however the results suggested that by ~0°C these higher perchlorate concentrations should confer increased activity. So what emerged was this complex interaction between enzyme activity, temperature, and perchlorate concentrations. It’s worth noting in general that enzymes don’t work frozen in ice, and perchlorate salts depress the freezing point of water, so provided an enzyme can remain sufficiently folded to be active, perchlorate salts effectively offer an avenue for activity where there’d be no activity without them at subzero temperatures.

So perchlorate salts aren’t necessarily as bad for biology as we think, at least in colder environments. But that then raises the question of how cells behave at low temperatures in the presence of perchlorates. A question which will hopefully be answered and published soon.

Jul 8, 2023

In my last blog post I talked about how high pressures can increase enzyme activity even in the presence of perchlorate salts. Well now it is time to talk about the study which led to those results, which, ironically has only just been published. Peer review, what can you do?

My latest paper explored the effects of perchlorate salts on the structure, stability, and activity of my model enzyme α-chymotrypsin. These results essentially formed the benchmark for my understanding of how perchlorate salts affect α-chymotrypsin. This gave me a solid platform from which I can relate all future work back to as a reference point. So what did I find?

Perchlorate salts are bad for biochemistry, but not equally so. The three perchlorate salts examined were sodium, magnesium, and calcium perchlorate. I found that all perchlorate salts reduced the activity and the melting temperature of my enzyme in a concentration dependent manner. In fact the enzyme totally unfolds at room temperature in high enough concentrations of magnesium and calcium perchlorate. The extent to which these salts exerted a deleterious effect followed a fairly standard Hofmeister series, namely that sodium perchlorate exhibits the least deleterious effects, with calcium perchlorate exhibiting the most, and magnesium perchlorate exhibiting intermediate values. However, it is hard to draw solid comparisons between sodium perchlorate and magnesium and calcium perchlorate as they are divalent cations. Due to their stoichiometry, a one molar solution of magnesium or calcium perchlorate has twice as many perchlorate anions in solution as does a one molar solution of sodium perchlorate. You can of course double the amount of sodium perchlorate to equal out the anion concentrations, but now you have twice as many sodium cations in solution as you have magnesium or calcium. Ah the fun times we have trying to understand ionic effects in salt studies… This is why I prefer to look at these effects from a “whole salt” perspective.

Another feature explored in this study was the fact that the perchlorate effect appears to be dominant. On Mars, it is unlikely that an environment would contain only one type of salt, so it makes sense to examine combinations to assess whether they negate, or exacerbate each other. As magnesium sulphate is fairly widespread on Mars, it made sense to include it alongside the perchlorates. I found that magnesium sulphate increased the melting temperature of α-chymotrypsin, i.e. it stabilised the enzyme, but could it still exert this effect in the presence of perchlorates, or at least mitigate some of the perchlorate nastiness? Interestingly the answer was no, the perchlorate salt effect was dominant. This suggests that even if there are stabilising salts in a perchlorate containing solution, the deleterious effect of the perchlorates will still come out on top and exert its effect on biochemistry. This result was a little surprising  as it has been shown previously that stabilising agents can generally negate the effects of a range of deleterious compounds. It is hard to explain why the perchlorate effect is dominant without understanding what is happening at the molecular level, which unfortunately is beyond us for now. If I were to speculate, I would suggest that the mechanism through which perchlorates exert these destabilising effects is not simply just the opposite of how stabilising molecules exert their effects.

This research builds on a long history of deleterious salt effects, otherwise known as chaotropicity. The deleterious nature of perchlorate salts agrees with many other studies, however the dominant nature of these effects was unexpected. Altogether this paints a rather bleak picture for the potential habitability of Mars if we cannot have functioning biochemistry in low molal concentrations of perchlorates. However, my research is all about the weird things that happen when we look at more than just one environmental parameter. We already saw that high pressures increased enzyme activity when in the presence of perchlorates, and I can only hint that we have found another interesting effect when you change a certain physical parameter. For now you will just have to believe me when I say that the possibility of biochemistry in perchlorate brines may not be as bleak as has been previously thought.

Apr 29, 2021

If the surface of Mars is such a hostile place, is the deep subsurface any better for life? This is the question that we have recently started to answer with our new publication in Communications Biology from myself, Michel Jaworek, Roland Winter and Charles Cockell.

So it’s fairly uncontroversial to say that the surface of Mars isn’t a nice place to be. The temperature fluctuates from ok to extremely cold, there’s constant incoming radiation, it’s salty, dusty and maybe most importantly there is essentially no liquid water. All in all, not the first place you would expect to find life on Mars. However, deep beneath the Martian surface there may be environments that are less hostile to life. Examples of such environments would be the subglacial lakes reported by Orosei et. al. in 2018  and Lauro et. al in 2020 or the  deep ground water as suggested in Clifford et. al. 2010.

These deep environments are however not without their own challenges. Firstly, they would be extremely cold, and I mean cold. We are talking about environmental temperatures lower than 210 K (-63 °C), which is pretty far below the freezing point of water. But wait, lakes have been found beneath Mars, so how can they contain liquid water if it’s so cold? Well that leads us to our second problem, the salts. For liquid water to exist at such low temperatures we need salts in the solution to depress the freezing point of water low enough so that it doesn’t freeze. So it’s cold salty water, how bad can it be? Well the reigning champion of freezing point depression is our nasty friend the perchlorates, and for water to be liquid at such temperatures it has to be packed with them. Perchlorate salts aren’t something you come across much on Earth unless you’re from the Atacama or work at a munitions factory. On Mars however, they’re everywhere, and they’re bad news for life. We also have a third contestant in the extreme environmental parameter contest, and that is the high pressures which you would experience in the deep subsurface, and importantly, we just don’t know how life responds to both pressure and perchlorate salts.

So what did we do? Well, being biochemists we immediately ignored life itself and decided to look at a model enzyme and examined how its stability and activity changed with increasing concentrations of magnesium perchlorate and increasing pressures. Unsurprisingly we observed that magnesium perchlorate reduced the activity of our enzyme at ambient pressures, and we can use this as our starting point to compare our further observations to. So what happened when we increased the pressure? We found that the activity of our enzyme increased with pressure, even in the presence of perchlorate salts, and it was interesting to note that the greatest proportional increase happened with 0.25 M magnesium perchlorate. I’ll not go into the detail, but the reason why this happened is due to the fact that our enzyme has something called a “negative activation volume”. This essentially means that throughout the course of the enzymatic reaction, the volume of the enzyme decreases, and pressure loves it when you decrease the volume of something, and so it favours the enzyme reaction, thus increasing the activity. So if life on Mars was trying to avoid the hostility of the surface, it could gradually work its way into the subsurface, and if its vital biochemistry had a negative activation volume, it could expect to see an increase in its biochemical activity, effectively undoing the negative effects of the perchlorate salts.

It wasn’t a complete victory over the perchlorate salts though. We found that the salts reduced the temperature at which our enzyme melted and also lowered the pressure at which it unfolded. So while you can recover enzymatic activity that was lost due to the perchlorate salts, the folded phase space of our enzyme was ultimately constricted in the presence of perchlorates. This may have important implications. When you look at the phase diagram for life, it looks surprisingly similar to the phase diagram of proteins, as opposed to lipids or DNA. This means that protein stability is a good proxy for the feasibility of life, and our results suggest that perchlorate salts will constrict the possible environmental conditions in which life can survive. So it’s not all good news.

As with any study there are caveats. The concentrations of perchlorates that we used were far from the saturation point. This is simply because saturated magnesium perchlorate obliterates life and it will be a monumental amount of work (or a stroke of luck) to find life or biochemistry that can function at such high concentrations of perchlorates. Secondly, we had to ignore the low environmental temperatures and this was largely a technical consideration. Most lab equipment is designed to work really well at room temperature and ambient pressure. So making a spectrophotometer that works at 2 kbar is hard enough without also asking it to cool down to 200 K. However, watch this space, as the low temperature work is underway and will hopefully be coming to a publication near you soon….or however long peer review takes.

 

Oct 19, 2020

As most labs have been shut down due to COVID-19, it has been pretty hard to do research the past few months. Instead, I have been using this time for reading, writing, and familiarising myself with online bioinformatics software. Normally I get a bit scared when I hear about computational biology or chemistry, largely because the world of coding and modelling is still quite foreign to me. So it has come as a relief to find online bioinformatics software that is easy to use and interpret. I thought that it would be a good idea to run through some of the things I have been using recently, the databases they rely on and explain how to use them and interpret their results.

1. PDB

The Protein Data Bank (PDB) is a phenomenal database of over 160,000 protein crystal structures and all the bioinformatic software that I have used relies heavily on this great tool. The PDB is easily searchable and its greatest limitation is that you have to hope someone has determined the structure of your target protein. The PDB stores protein structure entries as 4 figure code, for example the SARS-CoV-2 spike protein is stored under 6VXX and this is its PDB ID. On the structure’s page you can then get lots of information about your target protein including, the year it was determined, the paper associated with it, its crystal score, its UniProt ID (more on this later) and perhaps coolest of all, the 3D view of your protein. The 3D viewer is great for understanding more about the actual structure of the protein you are interested in. You will be able to see the alpha helices, beta sheets, hydrogen bonds, bound cofactors etc. You can change the view from cartoon to molecular surface which is a great way to visualise active sites and deep binding pockets (which is especially nice if the structure comes bound with a ligand, you will see exactly how it fits in). The PDB is a great starting place for protein based bioinformatics projects.

 

2. UniProt

UniProt is the second bioinformatics tool on the list and like the PDB, it is absolutely massive. There are so many functions and uses for UniProt and I only know some, so hopefully I can do it justice. UniProt will provide you with a wealth of information about your protein of interest, provided the information exists. When I do enzymatic studies, I use bovine chymotrypsin, and you can see its UniProt entry here. On the page you can see that there is information such as its active site residues, where it acts in relation to the cell, post-translational modifications, multiple solved protein structures and the amino acid sequence. So obviously this is a quick and simple way to see what your enzyme does, what it acts on and where it does this. UniProt also has an align tool which essentially lines up proteins of your choice and tells you what residues are conserved, and which ones are biologically similar (pretty handy for approximating active sites).  The align tool also draws a phylogenetic tree which is kind of cool, but I haven’t had a use for it yet. All in all it is great for getting more information about your protein of interest.

 

3. PoPMuSiC and HoTMuSiC

PoPMuSiC and HoTMuSiC are two pieces of protein stability prediction software which are incredibly useful beyond being brilliantly named. Both pieces of software are available as webservers at this link. PoPMuSiC is a protein stability predictor in terms of changes to the free energy of folding (ΔG_F)upon point mutation, whereas HoTMuSiC predicts changes to protein melting temperature (ΔT_m) upon point mutation. To use the software you have to enter the PDB ID for your target protein (as it’s a structure based predictor), you can then select to either get the results from a single, user defined mutation, or you can do a systematic run which provides you with the stability changes for each amino acid residue replaced by the 19 other possibilities. As predicting greater stability was the original aim for the software, it also produces a handy graphical output of the sum of the stabilising mutations at each respective residue. If you happen to know the melting temperature of your protein you can enter it into the HoTMuSiC software, which slightly increases the accuracy of the results. Some of the papers from the makers of the software can found here, here and here so that you can see some of the work you can do with the software.

 

4. SCooP

SCooP is another piece of protein stability software, made by the same makers of PoPMuSiC and HoTMuSiC. SCooP is different in that it will provide you with a predicted protein stability curve along with values for the upper melting temperature, the free energy of folding (at room temp), the heat capacity and the enthalpy change. What I really like about SCooP is that it is very visual, I really like being able to see something tangible and it is extremely intuitive. Here is a little demonstration of how it works which you can try for yourself using carbonic anhydrase as our example protein. Go to the site and enter these two PDB IDs, 4COQ and 5HPJ. These two proteins are homologous but come from different organisms. From the results see if you can tell which protein comes from an organism which lives in the cold depths of the ocean, and which one lives beside boiling hot water. You will see for yourself that SCooP is a great tool and the paper for it can be found here.

 

5. ProteinVolume

ProteinVolume is a bioinformatics tool which allows you to calculate the total volume, Van der Waals volume, void volume and packing density of your target protein. This is a great piece of software which is again incredibly easy to use. All you need to do is upload a PDB file to the server click go and wait for your results. The makers of the software have published some interesting pieces of work using the software which you can find here, here, and here.

 

This is just a short list of the bioinformatics tools and software that I have been using during the lockdown. There is plenty more out there, and websites such as OmicX and bio.tools are great resources for finding the right tool for your project.

 

I don’t think I’ve been totally converted to the ways of bioinformatics as I can’t wait to get back into the lab. I am however excited to keep up to date with bioinformatics as a field as I think the tools that come from it can really supplement my work and will hopefully provide directions for future experimental work and maybe even collaborations.

Jun 16, 2020

I often see posts online asking for advice on how to get into the field of astrobiology and have even had people reach out to me personally asking for advice. So I thought it might be useful to put all my advice into one place. Professor Lewis Dartnell also detailed his advice on his blog here. NASA’’s advice can be found here. To make it as applicable as possible I will cover things you can do when you are in school and then also at university. At this point it is important to note that my route to science has been very typical and focused and it is far from the only route into science. I will have posts in the future discussing atypical routes into science and astrobiology that my colleagues have taken. Most of this advice will be specifically relevant to science students, but hopefully non- scientists also find this useful. For now, here is my advice and my personal experiences with it.

#1 – Choose the Sciences and Keep Them for as Long as Possible

The easiest way to become a scientist is to study the sciences at school and for as long as possible. I know, fairly obvious. But I came very close to not studying biology for my GCSEs, the topic which would later become my career.

In third year I was picking my GCSEs and had provisionally picked physics and chemistry as my sciences. At the time I had no desire to keep on biology (I fully blame the curriculum for this situation) and had in fact chosen PE instead. It was then after a fateful PTA (Parent Teacher Association) meeting that my parents came home and told me that my biology teacher basically pleaded with them to have me pick biology as a GCSE subject. In the end I didn’t take much convincing and dropped PE in favour of biology. A decision, which in retrospect, set me up for the rest of my life so far. So thank you to my 3^rd Year biology teacher, I owe it all to you. This forms the first part of my advice to you if you are at this early stage. Keep as many science subjects on as possible and for as long as possible. The doors these subjects open are vast and will give you plenty of options to pick for your A- levels and for university courses.

#2 – Know What Subjects you need for University

University is where you begin to become a specialist, therefore the courses have pre-requisites. Knowing what these are, is extremely important in picking your A- levels. Thankfully the sciences keep your options open and can branch into a large collection of degree courses.

For my A- levels, I broke from my own advice and picked biology, chemistry, history and politics. During my GCSEs I realised that physics and maths were just languages I couldn’t speak and so they had to go. This was somewhat of a departure from what a lot of my science/ medicine orientated peers picked, namely all three sciences and maths. My advice for picking your A- levels is to think about what you might apply to study at university and see what requirements those courses have.

#3 – Time for University

University is the gateway for most people into the world of science. Assuming you already know what subjects you are roughly interested in, your university degree should largely reflect those interests. People frequently ask what degree they should study to become an astrobiologist. I’ll explain later why it doesn’t really matter what you study specifically, just that you are interested in it. Being interested in your area will make all the work that much more bearable.

For university I applied to both UK and Irish institutions. I chose to attend Trinity College Dublin where I studied “science” for the first two years before specialising in biochemistry in my final two years.  Here I was able to further develop my interests in science and learnt some of the key techniques that I would need for research in my field.

#4 – What to Study to Become an Astrobiologist?

The answer to this, is that it doesn’t really matter. Astrobiologists study everything from the formation of planets and stars to the potential for human exploration of space. You can take almost any topic and apply it to space. So the key to becoming an astrobiologist is to find how your specific field of interest can answer questions related to astrobiology. If you like geology then there is plenty of rocks in the solar system to keep you interested, if you are a biologist like me there are plenty of habitats to interrogate for their habitability or even if you are a lawyer there is the ever looming question as to the legality of the actions of nations in space. Becoming an astrobiologist is then about how you frame the questions you want to answer.

I studied biochemistry at university. The main topics of my lectures were subjects like human health and disease, signalling pathways, metabolism and genetics. Not exactly astrobiology was it? The important thing was to then take the skills and knowledge gained from a primarily biomedical focused degree and apply them to astrobiology. This is what will allow you to become an astrobiologist. Very few places formally teach or lecture on astrobiology, so the key to becoming an astrobiologist is to apply your own skills and questions to the field.

#5 – Try to get Experience in the Lab

It’s one thing to be interested in science, but it’s another to actually do it. The day to day life of a scientist is extremely variable across fields, disciplines and individual projects. If you have an idea of an area that you are interested in, try to get a summer placement with a lab in that field, or even just a few days. This will expose you to some of the realities of research. You will get to meet and talk with active scientists and hear their advice. You will also see that the scientific method is a rather messy affair. Experiments fail for unknown reasons, equipment breaks, orders are delayed amongst other unpredictable chaotic events. It’s rarely a smooth road in research. Having research experience also looks good on PhD applications.

I was lucky enough to secure a few summer research placements and can truly say they were a massive benefit. I was able to get hands on experience with techniques that I didn’t have access to, either at school or university. The placements also afforded me the opportunity to discover that I actually enjoyed doing research.

For examples of funding sources for summer research placements, see the Nuffield Research Placement, BBSRC Research Experience Placement and this list compiled by the BNA for examples. This is a non-exhaustive list and more sources of funding exist. Also note that labs may already have funding allocated for summer placements and they just need people to reach out to them to fill those spots.

#6 – Find Your Passion

One day you will be sitting in a lecture hall, probably half asleep, and the lecturer will say something that absolutely blows your mind. If the nugget of information that they just professed utterly consumes you for days on end and all you can do is think about it, then you have just found your passion in science. Finding something like this in your field of study gives you an avenue to formulate questions through.

For me, this happened when I got a copy of “On the Origin of Species” in school and was blown away. As I am sure you know, the school curriculums are rather focused on presenting facts which you can recite in an exam to the best of your ability. The topic of evolution was also taught terribly in Northern Ireland, as in, it was largely absent. So when I came across Darwin’s seminal work, I discovered my passion. I became obsessed with evolution and how, if there is an evolution there must be an origin, and if there was an origin here on Earth, could it have happened elsewhere. That final question is what lead me to the field of astrobiology.

On a quick side note, when you google UK astrobiology, the top result is the UK Centre for Astrobiology (UKCA) at the University of Edinburgh. I called this blog “The Irish Astrobiologist” because when you google Irish astrobiology, there is nothing, nada, zilch. Just links to the UKCA. I wanted to then have something to appear for my fellow students from Ireland, north and south, when they went to investigate this topic and to act as a focal point where people could reach out to ask me about astrobiology. Anyway, moving on.

#7 – What to do After Undergrad?

Once you have obtained your undergraduate degree, there are a multitude of things you can do. You can take time away from academia and studying in general. This time can be used to travel, work or even take some much needed time for yourself.

If you wanted to work but keep it orientated with your long-term career goals, a position such as a research assistant might interest  you.

If you want to continue studying, then consider something like a master’s degree. They are becoming increasingly common in the UK and sometimes needed if you want to do a PhD in Europe. They can be a good opportunity to study something that is a little bit outside of your field to help you broaden and expand your knowledge and to get more time in the lab. They can also be useful to start generating ideas for future PhD projects and gaining skills and experience that can help you in the future.

Taking some time to figure out exactly what it is you want to do with your future can also be extremely beneficial in the long run. The decision over whether or not to do a PhD is one that should not be taken lightly. A PhD is a multi-year commitment and it may involve moving away from home to a new city or even country. In the end, you need to be sure that it is the right choice for you and that you are choosing to do one for the right reasons.

Ultimately there are many things you can do, and some things you may need to do due to personal circumstances. The main point I want to get across is that there isn’t any time pressure at this stage. You can take the time that you need before moving on to the next stage of becoming an astrobiologist. I will post interviews with colleagues who have taken breaks from university and academia to illustrate this point in the future.

#8 – Apply for a PhD

Obtaining a PhD is a goal for most scientists wanting to stay in academia. You will want to reach out to as many research groups as possible to enquire about PhD positions and the earlier the better,  roughly a year before you plan to start. To find labs, look at papers which you found interesting and scan the author list to see which institutions the groups came from. The Astrobiology Society of Britain lists institutions which partake in UK based astrobiology research here, but it is unlikely to be an exhaustive list. NASA Astrobiology have their own list here, as does the European Astrobiology Network Association, EANA, here.

I reached out to many labs, some replied, some didn’t. I applied for five PhD programmes and was initially rejected from all of them, even the one I am in today. Thankfully another pot of funding appeared, and I was fortuitousness enough to then be accepted into the University of Edinburgh as a PhD student. Ask your lecturers and professors for help with applications, they have all been through this before and likely receive applications every year, so they know what they are talking about.

Your PhD project doesn’t have to be exactly what you did at undergrad, there is room to grow and develop your knowledge and skill. You aren’t meant to know everything going into your PhD and no one will expect you to.

#9 – Enjoy Yourself

The most important thing is to enjoy yourself. The road from school to university and beyond is a long one. You have to look after yourself. It can be easy to get obsessed with trying to achieve every metric of success or to compare yourself with the progress of others. This is bound to end in burnout. Mental health is rightfully becoming a prominent topic of discussion in academia. I consider myself lucky in that I have not had to brunt the worst that academia has to offer. I know amazing scientists and truly wonderful people who have been hurt by this system. The system is broken, so the most important thing you can do is look after yourself and those around you.

Hobbies, sports and other pursuits will help you stay grounded and give you an escape from the constant academic demands. For me, friends have been an invaluable source of joy and inspiration, without whom, I would never have completed my undergrad. We are all human and we are just doing the best we can.

In summary, if science is your thing, then study it as far and as wide as you can. Find something about astrobiology that you are passionately interested in and the research questions will come to you. It also does not matter what your background is, space is an astonishingly big place, and there is almost certainly an astrobiology question that can be answered by your area of interest. Enjoy the journey.

Mar 15, 2020

When asked what I research, the response “astrobiology” normally raises an eyebrow or two. It is then invariably followed by the question as to what exactly is astrobiology? Normally I’d wheel out the description employed by NASA that it’s the study of the origin, evolution and distribution of life in the universe and we would move on from there. However, I always feel like that description is one made from necessity for writing grants and other administrative literature. It fails to find what is truly exciting and interesting in what is an utterly wonderful field of research to be in. To give you my perspective, I will try and elaborate on why I find Astrobiology so interesting and what questions I seek to answer in my research. To achieve this, it is easiest to explain what I study and then hopefully convince you that it is interesting.

The question that I spend most of my time thinking about is, if life exists on Mars, what might it look like biochemically? As a biochemist, my interests are naturally biased towards such a question. What I find fascinating about Mars is that it harbours environments unlike any seen here on Earth. Therefore, it asks questions of biology which make no sense to ask if we were to solely focus on terrestrial life. Fortuitously for me, as it makes no sense to ask these questions, it means nobody has answered them, which produces a perfect little niche to fill with my PhD thesis.

So what environments am I talking about and what do they look like? The environments that I mainly focus on are concentrated perchlorate brines which are aqueous environments with high concentrations of perchlorate salts. Perchlorates salts are strong oxidising agents and are particularly lethal to life (unless you happen to be the subset of life that can eat small quantities of perchlorate). These environments have been hypothesised to exist deep underground in the Martian groundwater or even as a subglacial lake under the Martian south pole due o their extremely low freezing points (roughly -70 °C). So in addition to being rich in perchlorate salts, these environments have two other factors to keep in mind, namely the high pressures and the extremely low temperatures. This interplay between perchlorate concentration, pressure and temperature is something that we just fundamentally do not see here on Earth.

Recently, I have been studying how the perchlorate and pressure interplay affects a model enzyme. From this work (which will hopefully soon find its way past peer review) and the work of others, I have been able to develop a hypothesis about the biochemical nature of potential Martian life. This is the part of astrobiology that I find amazing. From the results of simple benchtop experiments, the application of biophysics and a sprinkling of evolutionary theory we are then able to derive scientifically valid conclusions about what might be happening deep underground on a rocky red planet millions of kilometres away. What is more amazing is that I can then go on and test this hypothesis and I thoroughly plan to do so. So whilst life on Mars may be totally novel in its biochemical ways (although I doubt it’s anything too novel), the fact that we are at a place in time where these questions can escape from the prison of thought experiment and have life breathed into them through experiment is utterly astounding to me. If and when the results get published, I can then go into them in greater length, so for now you’ll have to bear with me.

Therefore astrobiology is, to me, a scientific mindset from which we can explore questions about biology which we would never have asked, had we not looked out into the night sky. Along this line of enquiry we are bound to find weird and wonderful facets of biology and biochemistry not previously thought possible. It would be even more interesting though to find that the answers should not have been as unexpected all along.

Feb 19, 2020