In Our Time: Extremophiles

“Extremophiles” is a bit of a parochial term – this is the name for organisms that live happily in environments that we consider extreme. Too cold, too hot, too acid, too something to support life, in our terms. Studying the lifeforms that disagree with us on what is a good place to live has started a new field of astrobiology and a new appreciation of the possibility of life existing in the wider universe. Discussing this on In Our Time were Monica Grady (Open University), Ian Crawford (Birkbeck University of London) and Nick Lane (University College London).

The study of extremophiles started with the discovery of a rich ecosystem based on extremophiles living at hydrothermal vents in the sea floor near the Galapagos Islands (an amusing coincidence that it’s these islands in particular). The discovery was made by the scientific crew of a submersible called Alvin in 1977, and was a revelation as although extremophiles were known to exist this was the first evidence that there were more than a few outlier species. Previous assumptions about the requirements for life were shaken up by this discovery. The experts emphasised that we (and organisms like us) live in the “extreme” environments when compared to the universe as a whole – we require conditions that generally don’t exist. So the discovery that life could exist in more “usual” conditions meant that it’s more plausible that life might exist somewhere other than on Earth.

The science of astrobiology was started by these discoveries – this is a multidisciplinary field, which the experts positioned as being part of a trend in modern science. The 20th Century was in many ways about increasing specialisation in the sciences, but now there is a move towards seeing the bigger picture with more collaborations between groups with different specialities. Astrobiology is not exobiology – that would be the study of alien lifeforms and we haven’t found any (yet). Instead astrobiology is the search for life elsewhere.

One of the assumptions that was overturned by the extremophiles found by Alvin was that sunlight was critical for life. Knowing that it’s possible for life to cope with no sun* opens up the possibility that life might exist on Jupiter’s moon Europa, for instance. Europa has a hot core (due to the friction generated by the various gravitational forces exerted on it) and an icy shell, with liquid in between. It also probably has hydrothermal vents. It just wouldn’t have sunlight under the shell, but that might not matter after all.

*They did mention in passing later in the programme that parts of the ecosystem at those vents makes use of the oxygen dissolved in the sea, which wouldn’t be there without sunlight (as it’s a by-product of photosynthesis, which uses the sun for energy). So the current population is evolved to handle a post-photosynthesis world. But I think the idea is that if there wasn’t any dissolved oxygen then it’d just be a different ecosystem of extremophiles rather than no ecosystem at all.

Another foundational insight for the field of astrobiology was the work of Carl Woese in the 1970s on developing a Tree of Life based on genetic data. The traditional view of the high level groupings of organisms is five kingdoms: animals, plants, fungi, protists, bacteria. But Woese’s work showed that the real high level division is into 3 kingdoms: bacteria, archaebacteria and eukaryotes. Eukaryotes include all multicellular organisms (plus some single celled ones). Archaebacteria include the extremophiles and were once thought to be just a subset of bacteria – but the genetic data shows that they are as unrelated to bacteria as we are. They also arose first – bacteria and eukaryotes diverged from them later.

Astrobiology is not the same as SETI – the latter is searching for signs of intelligent life elsewhere in the universe, but astrobiologists will be overjoyed to discover a single celled organism existing somewhere other than Earth. The experts spent a bit of time discussing the Drake Equation and how astrobiology fits within that framework. The Drake Equation is an answer (of sorts) to the question of how many extraterrestrial civilisations we might be able to communicate with. I say “of sorts” because, as Bragg pointed out on the programme, the terms of the equation started out as all unknowns. What the equation is useful for is breaking down the question into manageable chunks that can then be investigated. So one term is “how many stars have planets”, and since Drake formulated his equation it’s been found that pretty much all stars have planets – so clearly that’s not a limiting factor. The question that astrobiologists are working on is “how common is life of any sort?” – which is a couple of the terms in the Drake Equation: the average number of planets that are capable of supporting life per star that has planets and the number of these capable planets that actually develop life.

There’s still only one example of a life-bearing planet, so it’s hard to extrapolate much about the origins of life and how common an occurrence it might be. One thing that might have bearing on the problem is that life only arose once on Earth – all organisms share a common ancestor. I did wonder, although they didn’t discuss it, if we can be sure it only arose once – is it possible to disambiguate that from multiple origins only one of which survived? But even if we are sure that it was a one-off event on Earth this may not be because it’s hard to do per se. It might be that once life gets going once it uses up the raw materials that it arose from, preventing subsequent developments of life. This is an idea that goes back even to Darwin although other parts of his “small warm pond” concept of the origin of life are no longer thought plausible.

The origins of life aren’t the only thing that we only have one example of on Earth (with relevance to the Drake Equation). The jump from the simpler cells of archaebacteria and bacteria to the more complex cells of eukaryotes has only occurred once. Multicellular organisms have also only evolved once, ditto intelligence capable of building a technological civilisation. So even if it turns out that there are many planets supporting life of a sort out there in the universe, intelligence may still be very rare or even unique.

Panspermia is another hypothesis about how life got to Earth – or conversely how it may have got/will get to other places. This is the idea that life is spread through the universe via meteors etc, and so life may not’ve originated on Earth. There are several things that suggest that this is possible, even if we don’t know if it actually happened. For instance we do find bits of rocks on Earth that originated on other planets (the Manchester Museum has a small piece of the Moon and a small piece of Mars that got to Earth as meteorites). There are also micro-organisms on Earth that can live within rocks. And we know from experiments done on space missions that some micro-organisms can live through the heat of entry into the Earth’s atmosphere. At this point in the discussion Bragg mentioned Fred Hoyle had been laughed out of the scientific community for proposing something similar many decades ago. Grady pointed out that one reason this sort of theory is looked down is that all it does is shift the question up one level: What’s the origin of life on Earth? Space! What’s the origin of life in space? Dunno. The modern concept of panspermia is also not the same as Hoyle’s – which involved free-floating life seeds travelling over large distances, rather than accidental transfer between planets via meteorite. (This whole section of the discussion made me think of the start of the film Prometheus, which of course is another reason people raise their eyebrows at panspermia – all too often it comes with a side order of “and that’s how the aliens made us”.)

Finding life on other planets is made more difficult because we don’t entirely know what we’re looking for. There was a meteorite discovered in Australia that was thought might have fossil micro-organisms in it that hadn’t originated on Earth. Eventually it was decided that these weren’t the first signs of extraterrestrial life, but it was controversial for a long time. Grady noted that it was easier to figure out in that particular case because it was a rock that had landed on Earth – the task gets much more difficult when another sample means another round trip to Mars. However the only way we’re likely to find out if there’s life elsewhere is by going and looking – whether that’s with robotic explorers or human explorers.

As the Australian meteorite case shows there is a high level of proof required before astrobiologists will be willing to agree that they have found signs of life that are definitely of non-Earth origin. However the experts felt that they (as a field) are getting better at figuring out what to look for. The essential requirements for life are now thought to be water and carbon, but even with those requirements in common with Earth life extraterrestrial life might look very different. The experts emphasised how much chance is involved in evolution – even if you could re-run the history of the Earth it would look completely different despite starting with the same conditions.

This programme felt oddly mis-named – not often the case for In Our Time episodes which generally stay on topic rather well. But this wasn’t really about extremophiles, it was about the search for non-Earth life.

In Our Time: Photosynthesis

In the end nearly all life on Earth depends on sunlight for its energy source. Heterotrophs like ourselves are a step or two away from the sunlight, but ultimately it’s the process of photosynthesis that fuels our food and thus ourselves. Photosynthesis also, as a byproduct, provides the air we breathe. The three experts who talked about it on In Our Time were Nick Lane (University College London), Sandra Knapp (Natural History Museum) and John Allen (Queen Mary, University of London).

Photosynthesis happens in plants, in structures called chloroplasts inside plant cells. At the botanical level Knapp explained that photosynthesis is the plant taking in CO2 and water, and turning those into oxygen and sugars using the energy from sunlight. After she had set the scene the two biochemists moved on to talk a bit about the molecules involved in making this process work. Lane explained the complexity of the protein complexes that are needed, in terms of their size. On the one had they’re very small – each chloroplast is less than a tenth of a millimetre across, yet they are packed full of thousands of clusters of photosynthetic apparatus. But from another perspective they’re very big – if you were to be shrunk to the size of an oxygen atom then the photosynthetic complexes would look like vast industrial cities.

Chlorophyll is a critical component of the process, it does the actual light harvesting. Allen gave quite a good verbal description of a chlorophyll molecule – first imagine a line of four carbon atoms with a nitrogen at the end, and then imagine this formed into a ring (a pentagon). Then imagine four of those in a line, then form them into a ring with the nitrogens all in the centre. This is the head of the chlorophyll molecule, and in the centre spot sits a magnesium atom which is essential to the process. One of the four rings has a tail which is insoluble in water but soluble in fats, and so it is what anchors the chlorophyll in the chloroplast membrane (which is made up of fats).

There are actually 300 or so chlorophyll molecules involved in each photosynthetic operation. The light is absorbed by one and then an electron is excited and leaves the chlorophyll molecule. This bumps into another and detaches an electron from it, and it bumps around a bit like a ball in a pinball table. Eventually it reaches one special chlorophyll molecules which uses the energy to “crack” a water atom. They didn’t really explain the details of the process (and I have long since forgotten them from the days when I had it memorised!), but from here you either follow a process that ends up with glucose (stored energy) and oxygen (toxic waste) or you use the protons from the water (protons are hydrogen nuclei, so that’s what you get if you break up the water and strip the electron off the hydrogen atom) to generate ATP (the energy currency of all cells).

One of the biochemists (Lane, I think) said that ATP is a bit like the coins you put in a coin operated machine. Any time a cell needs energy to do something it uses ATP to power the process. ATP is made either during photosynthesis, or by a process called respiration that both plants and animals do. In essence both do the same thing, but photosynthesis starts with light and respiration starts with glucose. Both processes build up a proton gradient across a membrane – on one side of the membrane there are lots of protons (generated from the H2O or glucose), on one side there are very few. Movement of these protons through the membrane only occurs in channels created by protein complexes that use the energy of this potential difference to generate ATP.

So that’s, in basic terms, the process. They also talked a bit about why plants are green – which is one of those “that’s a good question, but we’re not sure” moments. In one sense (which Knapp pointed out) chlorophyll is green because that’s the wavelength of light it reflects. But more interesting is why plants aren’t black – surely it would be most efficient to absorb all the light? There is some idea that higher wavelengths of light might damage the plants, so are reflected, but it’s not that simple because they don’t just absorb red light (which would be safest). In this bit of the discussion they also mentioned the nifty reason why rainforest plants tend to have red undersides to their leaves. Not much light makes it down to the leaves of plants that aren’t up in the canopy, so it’s important to get as much as you can out of the light you do get. So the red underside reflects red light back up to the top surface of the leaf for another chance of using the energy from it.

Another subject covered was the evolution of photosynthesis, and how plants acquired the ability. And what effect this had on the planet. Photosynthesis evolved in cyanobacteria, which are single celled organisms. Chloroplasts are actually descendants of these free living organisms, which were absorbed or engulfed by ancestral plant cells. So plants didn’t evolve the ability to photosynthesise themselves, instead they make use of a cell that already had the ability. The evolution of photosynthesis had a huge effect on the planet – using up the CO2 in the atmosphere had a cooling effect, and actually led to an ice age, a snowball earth. Release of O2 was also not good – it is very reactive, and was actually toxic to most organisms at the time. Bragg was fascinated by the idea that something that’s so essential to most life nowadays was once a toxic waste product.

This was a bit of an odd subject for me to write up – I think I’ve mostly covered what they talked about, but I’m very aware that I used to know a lot more about it. I can remember having the photosynthetic pathway memorised (along with the various steps in respiration too), I just can’t remember any of it! So I know the above is simplified, but I no longer know what the details should be. A bit of a weird sensation.

In Our Time: The Cell

This week we listened to the In Our Time programme on the cell while we had our Sunday morning breakfast. This is a subject about which I know rather more than the average educated layperson*, so I was curious to see if it’d hold up as still being interesting. It did 🙂

In the 45 minutes they managed to cover an impressively large amount of ground. Starting with a brief intro on what a cell is (building block of biological organisms, but just like the atom once you look more closely there’s a lot more going on inside than you thought), then moving on to how big (not very) and how many in a person (a lot, but even all those human cells still only add up to 10% of the cells in your body, the rest are bacterial). They then covered in chronological order the three main stages in life on earth (if you’re thinking from a cellular perspective). First there were prokaryotes – bacteria are this sort of cell. These are the simplest sort of cell – a membrane bag that makes the important chemicals be more concentrated inside than they are in the sea. They have DNA (the metaphor they used was of a library), RNA (copies of blueprints from the library) and proteins (built from the blueprints), and they make the needed energy to do their internal chemistry by transporting protons across the outside membrane. But they don’t have any divisions on the inside of the cell, everything’s in the bag together.

Then about a billion years later the eukaryotes appear (an amoeba is a single-celled eukaryote) … and Melvyn Bragg managed to mispronounce eukaryote more ways than I could count in 45 minutes – the best was when he turned it into something resembling “erotic” 😉 Eukaryotic cells have subdivisions inside them – they’re named for having a nucleus which is a compartment that holds the DNA, they also have mitochondria which were originally free living prokaryotic bacteria. These are the true determinant of eukaryotic cells – they evolved by one cell type engulfing another type, and then living in a symbiotic relationship where the internal bacteria provide energy for the outer cell. It’s thought this arose once and only once. So having more energy and having separate compartments (many of them, not just the two I mentioned) lets them maintain a bigger genome (the fragile DNA is kept away from the rest of the machinery, they have enough energy to do more reactions) and do more complex chemistry.

Next stage (after about another billion years) is the arise of multicellular organisms (like people! tho that took a while) – which are lots of eukaryotic cells stuck together. In this last section they managed to touch on the two sorts of cell division, cell specialisation by controlling which genes are switched on or off, and even some relatively recent research that shows that the control switches for the genes might be quite a long way away on the DNA strand so the way the DNA folds up in the nucleus is important (now that’s a hard problem to solve)**. Oh, and also to mention the true distinction between male & female (female gametes provide the mitochondria).

The experts on the programme were Steve Jones from UCL, Nick Lane (also UCL) and Cathie Martin (JIC and UEA). Unfortunately Prof. Martin wasn’t quite up to the normal standard – she was both nervous & used too much jargon. Either one alone would’ve been OK, but the two together made her contributions somewhat confusing to follow. Which is a shame, because she came across as someone who knew her stuff (as did the other two) but wasn’t comfortable with explaining it to non-scientists (in contrast to the other two).

But that quibble aside, it was interesting to listen to, and I thought it provided a very good high-level run through a complicated subject. It’s always nice when things like this hold up even if you already know what they’re talking about, gives you confidence that the ones you don’t know are equally accurate 🙂

*Amusingly one of the further reading suggestions on the Radio 4 website for the programme is for a textbook I had to buy for my first year undergrad – Alberts et. al. “Molecular Biology of the Cell” … it’s the 2nd edition I have on the bookshelf upstairs, seems they’re up to a 5th edition now.

**One of the things I was doing during my last post-doc was looking for the β-catenin promoter, so this was particularly interesting. Mapping the 3D structure of the DNA to make sure all the various bits line up with the right genes has got to be complicated. And I bet it changes based on what cell type, which other genes are switched on or off etc.