The blue waters of the Mediterranean

Back in 2005, I published an article in BlueSci, Cambridge University's Science magazine, which publishes science-related articles on various topics to "provide fascinating yet accessible science to everyone". It explains why the waters of the Mediterranean are usually blue and crystal clear. I reproduce it here, enriched with some photographs. The original article can be found on page 19 of BlueSci issue 3.

Have you ever wondered why the waters of the Mediterranean Sea are so blue and crystal clear? Is it because the sun is shining so brightly whenever you go on holiday there? Or because there is little pollution? Well, these factors may have something to do with it, but the main reason is that the Mediterranean Sea is oligotrophic. The word ‘oligotrophic’ comes from the Greek words ολίγον (oligon) meaning "little/few", and τροφή (trophi) meaning "food/nutrition", so it means "little, or not enough, food". Essentially, the waters of the Mediterranean don’t contain enough nutrients to support massive growth of phytoplankton (algae). The word phytoplantkon again comes from the Greek words φυτόν (phyton), meaning "plant", and πλαγκτός (planktos), meaning "wanderer" or "drifter", so it means "wandering plant". Most phytoplankton are too small to be seen with the naked eye. However, when present in high enough numbers, they may appear as a green or redish/brown discoloration of the water due to the presence of chlorophyll and other pigments within their cells.

Many people are more familiar with the opposite effect 'eutrophication' (from the Greek for ‘plenty of food’) which causes excessive phytoplankton growth, turning the water a turbid green. Eutrophication often occurs in lakes and coastal areas when high levels of fertilisers are discharged into the water as waste from nearby human activities. Fertilisers and other organic waste contain high levels of phosphorus and nitrogen which phytoplankton need to grow. Phytoplankton grow by photosynthesis so, very much like plants on land, they need light and carbon dioxide (CO2). There’s always enough carbon dioxide present in the water and enough light, at least in the spring and summer, for plankton to grow efficiently. However, along with the light and carbon dioxide needed for photosynthesis, algae also require nutrients; the two most important, which are often in short supply in marine waters, are nitrogen and phosphorus (in the form of nitrates or ammonia, and phosphates, respectively). When nutrients are in short supply, the organisms are limited in their growth, no matter how abundant light and carbon dioxide. In eutrophic lakes, fertilisers and other organic waste bring high levels of nitrogen and phosphorus into the water. The phytoplankton feast on these nutrients, grow and divide rapidly, and so the population expands. When the phytoplankton die as part of their natural life cycle, they sink to the bottom of the lake where they are broken down by bacteria. Many bacteria use oxygen to release energy from their food by respiration and, soon enough, the bacteria use up all the available oxygen and the bottom of the lake becomes anaerobic — without oxygen. Many of the plants and fish that normally grow in the bottom waters can no longer survive in these anaerobic conditions. Anaerobic respiration by the bacteria also produces foul smelling by-products, such as hydrogen sulphide and methane. The effects of eutrophication are dramatic and can only be reversed by laborious cleaning efforts.

The processes involved in eutrophication point to another factor important to oligotrophication: the water column is stratified both in lakes and in the sea. Most of the time the top of the body of water is effectively separated from the bottom. This is partly because the surface waters tend to be warmer, making them less dense than the colder bottom waters. Mixing of these two layers of water only occurs due to severe weather conditions, or in areas of upwelling and downwelling; this respectively forces the bottom water layers up, or the surface waters down, due to a combination of geographical features and ocean and atmospheric circulation.

So, how does this explain why the Mediterranean is so blue? We have seen that algae need nutrients to grow, and that the lower waters are, for the most part, separated from the surface waters. Since algae need light to grow, they prefer to be in the top waters where the sun shines, but most of the nutrient supply is in the bottom waters, where bacteria decompose organic matter and release nutrients. Looking at a map of the Mediterranean Sea reveals that it’s really more like a big lake — almost landlocked — with very limited water exchange through the Suez Canal to the Red Sea, or to the Black Sea through the Bosphorus Strait.

The main point of water exchange for the Mediterranean is through the Strait of Gibraltar to the Atlantic Ocean. The Atlantic has plenty of nutrients to offer, but these are mostly found in the deep waters because algae out in the ocean greedily consume the surface nutrients. The Gibraltar Strait is relatively shallow though, so very little deep-water exchange — and thus nutrient exchange — takes place. In addition, the Mediterranean surface waters are more salty than those of the Atlantic because the Mediterranean is relatively warm and its surface water tends to evaporate in the summer leaving the salt behind. (You can definitely taste this if you swim at a beach off the Atlantic coast, compared to Mediterranean waters.) This more salty water ‘attracts’ freshwater, which means surface waters from the Atlantic rush into the Mediterranean at the Strait of Gibraltar, and in return bottom waters from the Mediterranean exit into the Atlantic. A cross-section of the Gibraltar Strait looks something like this:

Hence the vital nutrients required for growth by algae are constantly depleted from the waters of the Mediterranean. This makes the waters of the Mediterranean oligotrophic, so they don’t support high growth of phytoplankton. In turn fewer predators that feed on these, such as zooplankton, can survive. Thus there are fewer zooplankton in the Mediterranean, and the fish tend to be smaller than in the open ocean. With fewer plankton present, the waters of the Mediterranean don’t turn green and murky, and are crystal clear and stunningly blue instead. Perfect for swimming and taking lovely photos!

Arsenic in Space

NASA's major announcement on December 2nd is old news by now, but I decided to write something about it anyway. It was heralded as changing the fate of Astrobiology, but it fizzled out from the news surprisingly quickly I thought. Maybe it's because it didn't capture people's imagination, or most people didn't really understand what the big deal was. Maybe it's because it wasn't really a big deal... I'll try to explain it, and you can make up your own mind.

I'll start by explaining why arsenic is a poison, and what that has to do with life in other planets. Arsenic is a notorious poison: Napoleon is probably the most famous person to have died from it. The reason why arsenic is a poison is because of it's chemical nature. Arsenic is similar to phosphorus, and since phosphorus is vital to life (it's one of the building blocks of DNA and proteins), arsenic goes where phosphorus should be, and the whole living machine breaks down.

As an analogy, think of a bicycle chain. It's made up of maybe a hundred "rings", that fit with each other, the chain fits onto the bicycle gears, and the whole bicycle works. Let's say the rings of the chain are like phosphorus. Now imagine someone comes along and changes one of the rings in the chain with one that's different (like arsenic), maybe just a bit wider on the sides. It still fits with the other rings, so the chain is not broken, but it has a different shape in the middle, with bits sticking out left and right. When the chain passes over the cogs of the gears, this different ring gets stuck, so the whole chain gets stuck, so the whole bicycle doesn't work.

Getting back to chemistry, if you look at the periodic table, arsenic (As) is just below phosphorus (P), meaning that it has the same number of free electrons, but with a bigger nucleus. Which means it can make the same number of bonds. Phosphorus is a major part of DNA and proteins, and even the cell membrane lipids. So phosphorus is important to life. When arsenic comes along, it fits into most of the places where phosphorus can fit, but not all, so once you have arsenic instead of phosphorus in DNA and other molecules, things get stuck and the whole organism doesn't work; like the bicycle chain getting stuck on the gears when one ring is changed.

So, based on this property of arsenic, there was a theory around that maybe there could be life forms out there that used arsenic instead of phosphorus, the same way that life forms based on silicon instead of carbon have been proposed. Essentially, imagine you designed a bicycle (organism) with gears and cogs (enzymes) that fit the weird chain rings (arsenic). You would ultimately have a working bicycle, the parts would just look a bit different than normal.

Ok, after this lengthy introduction, we can get back to NASA's announcement. What the scientists set out to do was find one of these weird life forms that use arsenic instead of phosphorus. And they found some cells that arguably can at least survive with arsenic in their DNA and proteins. Although there is a lot of debate about the methods and the interpretation of the results, this finding supports the theory that there could be life forms out there that use arsenic instead of phosphorus!

This does affect the astrobiology field quite a lot. When we send spaceships to look for life on other planets, they're not just looking around to see what's there, they're trying to detect specific things. So when we setup the whole mission to look for "life as we know it" with DNA, proteins, and lipids with the same structure as what we find on Earth, we are necessarily restricting the search. This means we may be missing other interesting things, that are slightly different to what we know, but are still evidence of life. So, should we be looking for organisms with arsenic in their DNA? Maybe... it's still a bit early to tell, but the whole arsenic story should remind us that we don't know everything, and looking for something that we're not used to seeing is tricky. To borrow a more eloquent expression from Marcel Proust, "the voyage of discovery consists not in seeking new landscapes but in having new eyes". How much should we expand our search? What exotic molecules and organisms might we find, and how do we look for them if we can't even imagine them?

Cafe Scientifique

Since I don't have much to write this week, I thought I'd point you to a valuable link:
the podcast series from the Cafe Scientifique lectures in Cambridge, UK

Cafe Scientifique is a forum for debating science in a relaxed setting
"a place where, for the price of a cup of coffee or a glass of wine, anyone can come to explore the latest ideas in science and technology. Meetings take place in cafes, bars, restaurants and even theatres, but always outside a traditional academic context."
If there is a Cafe Scientifique in your area, I do recommend you try it.
One of these days I'll organise Cafe Scientifique in Athens, Greece!

Meetings in Cambridge take place about once a month and the speakers are usually faculty members and researchers from the University of Cambridge. They are amazingly knowledgeable, but presentations are always fun and approachable, and the Q&A session, as well as the chance to socialise over a drink afterwards, make the whole evening even more enjoyable. The podcast series, while not presenting the full talk, includes an interview with the speaker, presenting their main points, as well as excerpts from the audience questions afterwards.
Topics currently available include the study of obesity, gambling, cancer, dementia, synthetic biology, and many more.

Podcasts are produced by the Naked Scientists team, who also run a weekly radio show, that is definitely worth following.
"Each week, listeners of all ages and backgrounds tune in on a Sunday evening to hear creator Dr. Chris Smith, together with his entertaining sidekicks, interview renowned scientists and researchers from all over the world and take science questions on any subject live from the listening public."
More podcasts are available from that.

Happy listening!

Allegory of the genome

This is something I wrote a little while ago, after reading Craig Venter's interview at Der Spiegel entitled "We have learned nothing from the genome". It's my attempt to explain (in less than 1000 words) what the genome is, why it is important, and why it doesn’t provide all the answers.


Imagine you had a library of thousands of books all piled randomly in a number of rooms. You don't even know how many books you have. So, one day you decide to sit down and catalog all the books, and put them in, like, alphabetical order by author. It's a difficult task but eventually you manage. Now once you have that catalog, and you know exctly how many books you have, where every book is, you can sort it by author, by subject, by year of publication, whatever. It's cool. This catalog is something like what we have now that we've decoded the genome.

However, the information in all the books in the library is not really contained in the catalog you made. If you want to get all the information in the library, you'd have to read every single book, and remember every line of it, which is a much more difficult task than just making the catalog. It's probably even impossible for a single person.

For example,if someone asks, "what does it say at the second half of page 52 of that book you bought on 12 March 1998?" it's very unlikely that you'll be able to recite the text. But the catalog does help you to find the book (if you've included information about when you bought each one) so you can open it on page 52, and read what it says. In a similar sense, having the genome has helped us to organise information so we can retrieve it faster. But the genome (the catalog) is like a list of the information of the whole library, it's no substitute for reading every book.

Also, imagine that your library doesn't just contain books, but also notebooks, or even loose pages. When you make the catalog, to speed up things, you decide that you're only going to look at the cover of each book, maybe the first few pages, so you get the title, the author, the year it was published, the publisher. So, for the notebooks, again you just catalog whatever is written in the cover, not everything that's written inside. So, in the end your catalog tells you that you have, for example, 8 notebooks, written by your grandmother during World War II. Again, the catalog doesn't tell you anything about the content, and since noone else has read these notebooks, if you want to know what's in them you'd have to read each and every page. Or for the loose pages, you don't even know how to categorise them sometimes. The notebooks that no-one has ever looked at and the loose pages are a bit like genes of unknown function, or like "junk DNA". Maybe they're very important, but you don't know unless you really read them in detail, and until you do you don't even know what they're important for... For example, your grandmothers notebooks could be her diary, or they could be full of cooking recipes (yummy!) or they could be an account of her activities as a spy for the Russians! Unless you open them and read them, you won't know, and the catalog (the genome) won't give you this level of detail. So, opening and reading every book and notebook, is like studying a gene in the laboratory or the clinic, it takes years before you really know what it does, and the catalog (the genome) only gives you limited clues, but still very valuable ones. Similarly, your library may include books written in ancient foreign languages that noone speaks anymore, or in a secret code (like Morse code) but for which noone has a key. Again, these books are a bit like “junk DNA”, as they may contain useful information, but unless you figure out a way to read them, you don’t know what this information is.

Finally, your catalog doesn't really help to answer meaningful/complicated questions, such as "What did the ancient Egyptians know about the sun" or "What did Tolstoy think about women?" It helps you to start looking for these answers (find all the relevant books), but again to get the answer you'd have to read all the relevant books, take notes, decide what's more important, and essentially write a summary report that answers the specific question. So, again, scientific research to answer the important questions (like, "which genes cause cancer?") is still necessary, and difficult, and it takes time, but the catalog (the genome) is a very important first step in answering these questions.

So, what I'm saying is, the genome (the catalog) is great, it's a big achievement, it speeds up things and it means you have some hope of finding what you're looking for in the library, compared to when it was all a pile of books on the floor. But it's not the answer to everything, in and of itself.