So, after an extended break, normal service is resuming, although the post today will be slightly off the usual topic of the evolutionary journey.

As I mentioned yesterday, I have been writing my bachelor project, and I thought I would share with you a little of the topic I have written it on.

I could write a post which would keep my good e-friend Argyle Sock very happy, with lots of statistical stuff in it, but, honestly, if I see the terms “not normally distributed” one more time, my head may go pop!

Also, the actual topic is much cooler than the stats (even though they are very cool too of course!).

I would like to introduce to a group of pigments called anthocyanins.  These are the reason for the colour of blueberries, blackberries, some grape species, olives and many other fruits, and purple or red colourings in flowers, like these pansies:

Violet pansies: The purple colour is caused by anthocyanins in the petals. Image from Wikipedia

The amazing bright red colours you see in autumn leaves is also down to anthocyanins.

So..why have I spent this last semester writing about pretty red colours? is where it gets a little more interesting (not that pretty purple flowers are not interesting of course!)

Anthocyanins are also found in leaves which are not about to fall off the tree.  Some plants have red leaves when they are young, and some plants can turn on and off the red colouring under certain conditions

Sciencey term for the day: This is called phenotypic plasticity….a phenotype is the appearance something has due to certain genes being expressed. If a phenotype is plastic, it means it can change under certain environmental conditions.

So, I have been looking at a particular plant, which is usually green and grows in shallow lakes.  These lakes dry out a bit in the summer (Yes, we have summer in Denmark, sometimes!), and so some of these plants may end up out of the water.  If this happens, 90% of these plants turn red, until the water covers them again.

The reason I have been looking at this plant (with a bunch of other people who are much better at scary maths than me!) is because it is not entirely clear exactly what the red stuff in the leaves does.  In some plants it seems to act a bit like a sunscreen, in others it seems to stop the plant being eaten by insects.

The amazingly awesome Leaf-cutter ants (Several posts on them will come along a bit later in our evolution journey) will not harvest leaves which are red. This may be because insects do not see red the way we do, they do not have the parts in their eyes which can collect red light.

Leaf Cutter Ants carrying leaves off to their underground farm Image from wikipedia

It has also been suggested that anthocyanins can help plants survive during cold or drought conditions, so, there seems to be a whole lot of stuff that this pigment helps with.

The health food industry has even been getting in on it, and you can buy anthocyanin supplements…this is because in plants, they work as anti-oxidants, and we are always hearing about how having free radicals is bad for us, and so we should eat blueberries, or whatever the cool food to eat this week is (its usually the most expensive one!).  I am not entirely sold on this idea, as, last time I checked, I am not a plant.

So anyway, I have been working with an awesome group of my fellow students, and we have been trying to make these poor plants very stressed to see what happens. We grew them under some very bright lights, and then did some tests where we zapped them with..well…an even brighter light, to see what they did.

Personally, I find the plant we have been studying more interesting than the actual pigment we have been looking at, although, that has been fascinating to learn about.  The plant itself has no stomata, which are the holes which plants use for taking in carbon dioxide and giving out oxygen and look like this in extreme close-up:

Stomata on a tomato leaf Image from wikipedia

Because this plant has no stomata, it has to breathe through its roots, which is extremely cool!  This means that it can only live in lakes which do not have a lot of nutrients in them, because, if you increase the amount of nutrients which end up at the bottom of a lake, you decrease the amount of carbon dioxide which is produced by the bacteria eating all the dead stuff at the bottom.

As more dead stuff ends up at the bottom of the lake, the bacteria down there start using up more oxygen than is available, and so the only ones that can live there produce methane (CH4) instead of carbon dioxide (CO2). This is what is found in my favourite land-types, the wetlands, bogs and moors.

Oh, yes, I forgot to show you a picture of the plant!  This is the little thing I have spent 6 weeks growing, and then several weeks cutting up and zapping with bright lights!

Lobelia Dortmanna. Image from wikimedia

So, I hope I did not bore you too much with the slightly off-topic post, and next time we will pick up on the evolutionary trail again, with some weird and wonderful creatures. If you prefer plants, hang in there, we will get to them in a few million years or so!


Collated information on Ash dieback

I have been asked by a few people what they can do about the Ash dieback problem in the UK, and whilst I said yesterday that there was no official guidance for the general public yet, there are some informative documents prepared by the forestry commission.

Most of these are in the original post I made (HERE), but as they are at the end of a long post, I will put them up on here again, with the new information.

The Forestry Commission has published a visual guide to symptoms: Ash Dieback Disease

The Forestry Commission has also updated its guidance, with information that this is now a quarantine pest, and gives contact details if you think you have come across a site of infection. It also outlines how it is thought that the ancient woodlands have become infected. HERE

I used this Forestry Commission PDF in my original post, it is fairly easy to read and gives an overview: Chalara Fraxinea

The Woodland Trust has updated their guidance since I last read it, with the advice that any suspected infections should be reported at once: HERE

The Government has said that 50,000 trees have already been destroyed: (BBC source HERE)

EDIT for update: There is a website which will be launching Monday at ASHTAG and there will be a smartphone app launching Monday too.  I will post details of that when it arrives.

I mentioned on my fellow blogger Argylesocks post (HERE) that my concern is that with the onset of autumn, we will not know until next year what the extent of the infection is, as the fungus is now in the leaf litter over the winter.

I hope that these are isolated cases in woodlands, but I do not understand why it took from February til late September for this to get attention, or be publicised.

For my non-UK readers, I apologise for the UK-centric posting the last few days.  I am currently writing a post relating to a US issue, so will put that up over the soon.  I will be returning to my evolution based posting next week, but will keep putting up posts of interest to current environmental issues, to go a little more in depth into those.  If you have a story from anywhere relating to environmental or ecological issues which you would like to read a bit more in depth on, you can chuck me an email at squirrellyskeptic at gmail dot com.

Leaves, keys and fungi

So, there was this story yesterday in the Guardian about how ash trees are at risk from a fungus:

This topic has been in the media a fair bit lately, but very few of the stories have gone into the mechanisms and details, so I thought I would write briefly about those, as they are fascinating, and can help with understanding the problem better.

Most of the stories in the media have just said that it affects leaves, which is a very vague description.

So, first of all, to make sure we all know the tree we are talking about, this is an Ash tree, otherwise known as Fraxinus excelsior:

Fraxinus excelsior, the common Ash. Image from Wikipedia

And here is it’s close-up (It doesnt get red-eye like I do, and is always photogenic!)

Close up of the leaves and “keys” (fruit) of the common Ash. Image from Wikipedia

So, now we have met the victim, lets meet the perpetrator (Sorry, I am catching up on CSI episodes at the moment, so excuse me if I go a bit Horatio Caine).

This is where it can appear a bit confusing, because this fungus actually has two names:  The one most mentioned in the media is Chalara Fraxinea and it looks like this when it is grown in a lab:

Chalara fraxinea, politely posing in a petri dish. Image from Federal Institute of Technology Zurich

This is the fungus mentioned in the Forestry Commission factsheet about this problem (See further reading for link).

This is what is known as an anamorph, which means it is the asexual reproductive phase of this fungus.

I think the reproduction of plants, fungi and small micro-organisms is really cool, so I am going to explain it a bit here as it can seem a bit confusing (I remember getting tied in knots trying to revise this for functional biology!)

The asexual reproduction of fungi such as this species involves producing spores (from the greek spora, which means seeding, or sowing), which you might know from the puffball mushroom, when you kick it, it gives off a load of dust-like stuff, which is actually the spores for the next generation of the fungus, which looks like this:

Puffball mushroom releasing its spores. Image from wikipedia

Each of those spores is a potential new fungus, provided it lands in a suitable environment for growth.  This method of dispersal is very haphazard, and this is why these organisms produce so many spores.  It is a bit like closing your eyes and throwing a handful of seeds randomly out on a bit of ground and hoping for the best.

They are formed by mitosis, which is also how our cells in our body are replaced and is in itself a really really cool process (especially when you see slides of it), and which I will cover in depth in a later post.

As I mentioned earlier in this post, this fungus has two names, the asexual form C.fraxinea and the sexual form Hymenoscyphus pseudoalbidus. Now, maybe it is just me, but I found it a little confusing initially to understand how one organism can have two names, or even two life cycles when I first started reading about this.

This image shows the life cycle of an Ascomycete, which is the group of fungi which this particular one belongs to.  The asexual cycle is the loop off to the left of the diagram.

General life cycle of an ascomycete. Image from Penn State University

From what I gather from reading several journal articles on this species, it seems that the asexual form is on the leaf litter, and dead wood on the forest floor, and this is not infectious (or pathenogenic to use the sciencey word).

It all goes a bit nasty for our Ash trees when it is in the sexual form, H.pseudoalbidus .  It is called “pseudoalbidus” because there is another species called H.albidus which is not responsible for this problem in Ash trees, but appears physically similar.

This is what the fungus looks like:

H.pseudoalbidus on a branch. Image from Institute of Technology, Zurich

This confusion with two different names for the sexual and asexual form of fungi will be less confusing soon, as in 2013 they are changing the naming structure, so that there is one name for a species of fungi, regardless of which stage of the life cycle it is in.

As you can see from the diagram, the asexual form of the fungus only refers to the spores,  everything else within its lifecycle is classified as H.pseudoalbidus. Calling this C.fraxinea in the media is quite confusing, but understandable, as many journals refer to this fungus as C.fraxinea.

The cycle of infection appears to be, that the spores remain in the litter, or on dead branches over the winter, and then, in the summer, it germinates, and becomes the white mushroom thingies.  These release spores, which are spread by the wind, and some end up on the leaves of Ash trees, and on the branches.  These form structures known as mycelium which are basically a mass of threads, and it is these which are responsible for the damage to leaves and branches, if they get into a gap in the bark, they form lesions like on this branch:

Necrotic lesions on a branch. Image from EPPO (European Plant Protection Organisation)

These are also known as cankers, and result from the death of the tissues.

The fungus also damages the leaves, as shown in this image:

Leaf dieback as a result of fungal infection. Image from EOL

The dead branches and leaves then fall to the floor, and the cycle begins again.

This is a relatively new infection in Ash trees, first being noticed in the mid 1990s.

There are ongoing discussions as to why this has arisen, as this fungus has been known since the late 1800s, but as the non-infectious H.albidus.  There is discussion about whether climatic stress has weakened the trees resistance to infection, or whether the infectious version of this fungus is better suited to the milder climate conditions over recent years, or whether this new infectious form is a mutuation which has arisen recently.

Whatever the cause, the result is devastating. Denmark has lost around 90% of its Ash trees since the infection arrived, and other European nations are reporting large scale losses of Ash trees.  The infection appears to have arrived in the UK (Which is usually protected from these types of infection because of its island status) by importing of young trees which were carrying the fungus.

So far, it seems that the fungus has not managed to infect “wild” trees in the UK, and the government has begun a consultation, which will end on the 26th of October, which could lead to a ban on imports of Ash (and given the severity of the threat, I would hope that a ban is imposed).

Further Reading: (Most are very easy to read, with the exception of the journal article at the end, they are mostly from the Forestry Commission, and similar bodies) (Rapid Risk Assessment)$FILE/pest-alert-ash-dieback-2012.pdf

Krautler & Kirisits: The ash dieback pathogen Hymenoscyphus pseudoalbidus is associated with leaf symptoms on Ash species (2012)



To pea, or not to pea

Ok, so, as I mentioned in the last post, I have just been on a botany field course, and so taking a little diversion from the evolution of life on earth to write about plants. (Got a bit distracted on the course, so forgot to finish writing this post, so apologies for the delay!)

This is a pea, we all know and eat these regularly, across the whole range of dining experiences, from high end restaurants to mushy peas and chips.

A pea plant (img from wikipedia)

This is the pea within the pod

Peas in the pod, ready to be eaten! (img from wikipedia)

The final image is of a pea plant in flower.

A pea plant (Pisum sativum) in flower. Image from Encyclopedia of Life

Peas are in the family Fabacae (from latin “faba” meaning bean, the word became fava over time, and broad beans are known as fava in Italy, they are also the type of bean that Hannibal Lector likes!)

In English, this family is known as the Pea Family, and the fruit they produce (the pea pods in the picture above) are known as legumes.  An alternative (less used now, but more common in the past) name for this family is Leguminosae.

This family is quite a big one, there are 19000 or so species (specific plants) within it.  I found one of the most interesting parts of the course I was just on was looking at a plant and thinking “How the hell did they know that was in the same family as this other plant”, and I am going to try to illustrate that a bit with this post, as well as try to explain how to recognise when a plant is in this family.

This family of plants has been around since the Paleocene era (approx 65-56 million years ago), and the 3rd and 4th images below show a modern Fabaceae plant, and a fossil one from the Paleocene.

Fossil plants compared with modern versions. The centre two images show a modern pea family plant, and a fossil one from the end of the Paleocene era. Image from American Journal of Botany

The modern species within this family are very diverse, and the following images are all of various plants within this family.  The first one is the gorse bush (Ulex europaeus, Ulex is the term Pliny the Elder used for heather (Pliny was an Ancient Greek guy who wrote one of the books which is on my very geeky “Must own this” list, Naturalis Historia) and europaeus means it is found in Europe), which is found on heaths, sandy dunes, and is an extremely annoying plant if you start wandering through some countryside and don’t spot the fallen thorns on the ground around it, or do not notice little bushes of it sprouting up as you climb through the edge of a forest.

Gorse Bush, very pretty, but very prickly! Image from

This next picture is of course, the peanut (Arachis hypogaea,  hypogaea meaning underground), which, surprisingly is in the pea family!  The image afterwards is of the peanut plant in flower.

Peanuts. Image from Wikipedia

Peanut plant in flower. Image from Purdue Agriculture

The peanut is not actually a nut, it is a pod, like the pea pod, but it grows underground.  Once the flowers of the plant have been fertilised, the petals fall off, and the remaining part (the ovary, containing the seeds) develops a spike, and grows towards the ground, burying itself a few centimetres into the ground.  The picture below shows what remains of  a peanut flower after fertilisation.  The reddish brown pointy part is what will dig into the ground, and the whitish bit above it (wider than the stalk) is the ovary, and is where the peanut will develop from.

A Peanut plant after fertilisation, showing the end of the ovary growing towards the ground. Image from Wikipedia

The next picture is of the peanut just after harvesting, so you can see that the peanuts actually come up along with the roots.  It is a common idea that the peanut is part of the root, and not the fruit of the plant.  It is easy to see why people think this, because it does look exactly like that.

Peanut plant after harvesting. It is easy to see why many think the peanut is part of the roots. Image from

Other plants that you may not expect to be in the pea family are liquorice, and clover (image below is of White Clover, the most common type, Trifolium Repens (Trifolium meaning 3 leaves, and Repens meaning creeping)).

White clover, known for its 3 leaves, and the difficulty in finding 4 leaved versions of it! Also associated with leprechauns. Image from

So, I promised I would try to explain how you can tell something is in the pea family. Having just spent 5 days staring at lots of this family, when I was inserting the images for this post I thought “I cannot put these in, it is obvious that they are all in the same family”, but then I thought that it may not be so obvious if you have not just spent the best part of a week getting “pea-blindness” (Like snow-blindness, but caused by staring at various members of this family for too many hours a day with too little sleep the night before!)

So, the skeptical squirrel guide to identifying pea plants:

Firstly, hopefully it has a flower on it, this makes it very much easier!  Even with something like a clover, which does not initially look like it has the same flower, each clover head is made up of lots of small flowers, which have the same characteristics as other flowers from within this family. They look a bit like a side-on face with a sticking out tongue…..ok, maybe only a little bit, but definitely after some beers, and in the right light, they look like that!  The picture below shows the side view of a flower from this family, along with a diagram showing the parts of the flower.

Side view of a pea plant flower, and systematic diagrams. Image from Ohio State university

So, to be a bit more technical, you are looking for a flower with 5 petals, 1 large one at the top (the banner), 2 smaller ones sticking out in the middle (the wings), and 2 small ones at the bottom, forming a boat(ish) shape (the keel).  The Fabaceae  family has what are known as bilaterally symmetrical flowers, this means that if you cut them top to bottom, each half looks the same.  These flowers are very very distinctive, so once you know what they look like, if you see another one, you will recognise it immediately!

The other very distinctive feature of this family is the pods in which the seeds are held, they look like, well…., a pea pod.

Finally, if you have neither flowers nor seed pods, then it gets very annoying (and gave me a lot of headaches on the field course!), but, some plants within this family have very distinctive leaves, so can be recognised easily from those too.

Clovers, as mentioned earlier, have 3-leaves, or more correctly, a trifoliate leaf, which means it is one leaf, divided into 3 smaller leaflets, and the ones on clovers are very easy to spot.

Many Fabaceae plants have what are known as pinnate leaves, which means there are lots of small leaflets arranged along a small stalk, like in the picture below

A pinnate leaf. Image from UBC Biology 324 blog

At the end of the leaf in the picture above, there is a long curled stalky thing.  This is a tendril, and it is what the plant uses to climb. It wraps around another plant, a pole, anything it can grab onto.

A member of the Fabaceae family (Vicia sativa, or Common Vetch), the tendril is visible on the far right of the picture, extending from the leaf stalk. Image from wikimedia

This is just a very rough guide to how to spot a Fabaceae plant, but hopefully it is a bit helpful.  Tomorrow will be back to Cnidaria, plants will be in later posts, but, the land plants come along a whole lot later in our journey through evolution.

Eukaryotes – Or, why we love bacteria part II

Ok, so following on from the post on photosynthesis, this post will be about eukaryotes and endosymbiosis.  As with photosynthesis, this is a HUGE topic that I could happily write 5 posts on, but will try to keep it to one, shortish post.

The next 10 or so posts will be inspired by the series which led me into Biology.  David Attenborough’s “Life on Earth” (Which is what inspired me to get up at 1am to write the photosynthesis post), basically I will take particularly awesome organisms and moments from the series, and go into greater depth on them, with diagrams, links to videos etc.  The aim of this will be to a) get people to watch the awesome series as I will mention the episode each post is inspired by, and link to the video, and b) to give more detail on each one, and hopefully show why I am so excited by the natural world.   By the way, David Attenborough got me into university, and through the first 2 years! I did not go to college, but got into university with a letter of motivation, and what I learned from Attenborough, and the research online that it led me to do, got me through the first 2 years of courses, without it, I would have felt more lost than I did, with having a 16 year gap between school and university, all the maths, physics and chemistry can seem scary!

Finally, before we jump into endosymbiosis, I would like to share two thoughts for the day that have occupied my mind on my 1 hour train journey each way to uni and back today to pick up my essay exam question:

1) Never mind made of star stuff….There are atoms in your body which have most likely been part of the sort of animals you see in fossils…there may be part of me that was once part of a carnivore, and another which was part of an animal which it preyed on, and another which was part of a plant eaten by that animal!….part of me may once have been one of the sulfur bacteria I wrote about last time!  Thinking about the journey that molecules and atoms made to go into me sitting here today just blows my mind.

2) I am more closely related to some archaea than they are to bacteria, despite them both being prokaryotes, and often thought of as one group, and I am more related to fungi than some bacteria are to each other!

Bacteria are blue, Archaea are green, Eukaryotes are red

Ok, so, onto todays post: How eukaryotes arose, and a bit about endosymbiotic theory.

First we need to define some terms which will be used constantly through this post:

Prokaryotes are organisms which do not have a nucleus in their cell. These are found today in bacteria, and single-celled organisms known as Archaea.

Eukaryotes are organisms with nuclei, that is, a membrane surrounds the centre of the cell, containing the genetic material.  This is found in all organisms apart from archaea and bacteria.  We are eukaryotes.

Comparison of Eukaryote and Prokaryote cells

Image is from  which also has a nice comparison of eukaryotes and prokaryotes.

Mitochondria: These are organelles, which exist outside of the nucleus of the cell.  They perform some important functions in the cell, including providing ATP which is vital to the processes within the cell. They also control things such as cell growth.  The important thing to note is that although I just wrote that the genetic material is inside the nucleus, mitochondria have their own DNA.  You may be familiar with the term Mitochondrial DNA, which is used for tracing genetic heritage, this is only inherited from your mother, as the mtDNA from sperm is destroyed during fertilization of the egg.

Chloroplasts: This is the region in a plant cell where photosynthesis occurs.  As with mitochondria, these exist outside of the nucleus, but contain their own DNA.

Structure of a plant cell. The mitochondria and chloroplast can be seen outside of the nucleus

Endosymbiosis: When one organism lives within another without damaging the host, and becomes incorporated into it.  The most well-known type of endosymbiosis for most people is the algae which live inside corals, where they provide through photosynthesis, the energy required for the coral.  They become surrounded by a membrane, and thus become part of the coral itself.

The modern theory of endosymbiosis suggests that mitochondria and chloroplasts originated by the joining of two individual organisms. This is similar to the way that coral and zooxanthellae have a symbiotic relationship, although zooanxthelles are able to be ejected from their host if the conditions become unfavourable. (As an aside, zooxanthellae are a form of algae known as Dinoflagellates…and are totally awesome in their own right, their shapes are almost as amazing as diatoms)

This modern theory was put forward by Lynn Margulis in 1967, and is based on the structure of eukaryotic cells, as well as genetic studies of chloroplasts and mitochondria.

It is thought that the original endosymbionts for the chloroplast were cyanobacteria, and the host was a protist.  The cyanobacteria provided sugar to the host from photosynthesis, and the host provided carbon dioxide and nutrients for the cyanobacteria to perform photosynthesis.  As part of this union, chloroplasts (and mitochondria) lost some of their own genetic material, and proteins known as chaperone proteins transport material from the nucleus across to the chloroplast.  This made some of the genetic material in the chloroplast redundant, and it became more dependent on the hosts own genetic material. Chloroplasts today have less than 10% of the genetic material of free-living cyanobacteria.

The exact origin of endosymbiosis to form eukaryotes is still debated (This does not mean scientists do not agree whether it happened, they are discussing the HOW), some think that it was predation that led to the first endosymbiont.  This does happen in nature today, there is a species of comb jelly which preys on jellyfish and incorporates their stings into its own body for defenses, and there is one organism which “eats” photosynthetic green algae, but does not digest them, but uses their photosynthesis to form sugars. (Paramecium bursaria)

For more information on the origins of eukaryotes, this site has good descriptions

There is further evidence for this endosymbiosis in the way that mitochondria reproduce.  Mitochondria reproduce in the same way as bacteria, by a process of binary fission. This differs from the way eukaryote cells usually divide, which is a process called mitosis (This process in itself is fascinating, especially now we have microscopes to show it)

Mitochondria, and chloroplasts both exist outside of the nucleus, in membranes of their own.  Chloroplasts have two membranes surrounding them, reflecting the inner and outer membrane of prokaryotes, some chloroplasts have 3 or 4 membranes surrounding them, suggesting a secondary endosymbiosis of an organism which already contained a chloroplast.

Which happened first? Mitochondria or Chloroplasts? All eukaryotes have mitochondria, but only plants have chloroplasts, so the incorporation of the mitochondria must have happened before the divergence into plants, fungi and animals.

How many times did this occur? phylogenetics suggests that this occurred at least 6 separate times (phylogenetics is the study of relationships between organisms based on molecular data and physical similarities) for chloroplasts.  The initial cyanobacteria endosymbiosis was then repeated with chloroplasts from later organisms, such as red algae.

So, once again, we have those little microscopic organisms we spend so much time trying to eradicate to thank for me sitting here rambling, and you being patient and reading this.

Suggested sites: There are numerous websites which go into detail on this, as well as a large number of scientific papers. If you want to read about the early life on earth, I recommend “Life on a Young Planet” by Andrew Knoll, it covers the first 3 billion years of life on the planet in an easy to read format. For websites, the ones I have linked (including Wikipedia) are good places to start, but also see:

Oxygenation of the atmosphere – or why we love bacteria, part I

One of the critical steps in the development of life as we know it today was the evolution of cyanobacteria (also called blue-green algae).  These single-celled organisms are responsible for adding oxygen to the atmosphere, and paving the way for the higher life forms that we have today.

They were not the first autotrophs (organisms that generate their food directly from sunlight, or inorganic chemicals, as opposed to heterotrophs (like us), who get their carbohydrates second-hand by consuming other organisms),  one view is that organisms similar to purple sulfur bacteria existed first, and it is the transition from these to cyanobacteria that today’s post is about.

Purple sulfur bacteria are only able to grow under anaerobic conditions (that is, conditions without oxygen present), because the synthesis of pigments in the cell is suppressed if oxygen is present. The early atmosphere of the earth was not oxygenated as it is today (as evidenced by sulfur isotopes in rocks over 2.45 billion years old, among other indicators), although there is some debate about the exact timing of the first atmospheric oxygen (NB: This does not mean I am saying “Science does not know what happened”….the time period in discussion is a few million years, and the discussions are about whether any atmospheric oxygen was immediately reacted with iron or other chemicals in the oceans).

Ok, so about these cute little purple sulfur bacteria, they are photosynthetic, so this means they use sunlight to obtain their carbohydrates.  Unlike plants today which use chlorophyll (the reason they have a green colour, but more on that later), these purple bacteria use a compound called bacteriochlorophyll, which uses different wavelengths of light, and does not produce oxygen as a waste product – This is kind of handy, since, as we saw in the previous paragraph, sulfur bacteria do not function so well in the presence of oxygen.

So, I have just mentioned photosynthesis, which is the method that plants use to obtain sugars from sunlight.  The equation for this in sulfur bacteria is as follows (Simplified version).

CO2 + 2H2S → CH2O + H2O + 2S, (or carbon dioxide + 2 lots of hydrogen sulfide is converted using light to carbohydrate + water + 2 sulfur molecules.)

Hydrogen sulfide is the rotten egg smell, and is emitted by volcanos.  The early earth was very geologically active, and volcanic activity was much higher than it is today, providing plenty of hydrogen sulfur for these bacteria to use.

This equation is important, because it was the discovery of this method of photosynthesis which demonstrated that it is water, and not carbon dioxide which is used for producing oxygen.  Prior to that, it was thought that the carbon dioxide was split to produce the waste product of oxygen.

So, back on the early earth, there were these bacteria pumping out sulfur, and using up the CO2 and H2S from volcanos.  Because they were purple, they used light in a different wavelength to the  plants of today, which reflect back the green portion of the incoming light, and thus we see them as various shades of green.  These purple sulfur bacteria reflected light back at both the higher end of the spectrum (red) and the lower end (blue), giving them their colour.

Absorption of light for purple and green chlorophyll pigments.

(Image from )

So, now we have oceans filled with reddish purple bacteria! I always try imagining how our planet would have looked back then, not so much a pale blue dot with green patches, but more likely a vivid colour like we see today when we get blooms of purple sulfur bacteria in places like Yellowstone park and other oxygen low, sulfur rich hot springs.

The next development was for some bacteria to evolve to use the light that was not being used by these organisms.

As you can see from the image, the purple bacteria would have used the light at in the centre of the spectrum, leaving light at the ends available for use, so any organisms which evolved to utilise this would have had a competitive advantage. If you want to know more about the evolution of cyanobacteria, without getting overly heavy on technical stuff, there are two systems within plants which do the conversion of light, these are called Photosystem I and Photosystem II. Green sulfur bacteria have Photosystem I only, and purple bacteria have Photosystem II only, so it is currently thought that the evolution of an organism which had both, either by endosymbiosis, or by sexual reproduction (yes, bacteria get it on too!) led to the cyanobacteria. (This is not my main area of interest, so please feel free to correct me if I got that wrong).

Ok, so now we have bacteria that reflect light in the green region, and use it from the ends of the spectrum, and have two photosystems…so what?

Well, it so happens that chlorophyll (the pigment involved), when using electrons to generate energy, gets electrons by splitting water, instead of hydrogen sulfide.  (This happens in photosystem II, in case you were wondering) So, now we have a new equation for photosynthesis, which is more familiar:

CO2 + 2H2O → CH2O + H2O + O2

By using water (which was in abundance), and producing oxygen (which the sulfur bacteria could not tolerate), the cyanobacteria gained a large evolutionary advantage.  In addition, due to the release of oxygen into the atmosphere, ozone was formed by the reaction of sunlight with oxygen to form O3

Ozone is what is primarily responsible for filtering out the UV from the sun, so once atmospheric oxygen, and ozone were in place, the stage was set for the long evolutionary road which would eventually lead to me sitting here typing, and you sitting somewhere else in the world reading these words.