I haven't put anything up for a while, so...

Now for something a little different.

If no-one really gets why I feel that ecological studies are so important, and why I do what I do, this video clearly demonstrates why (for more background look for video 01 in the series)

This is a time-lapse of still photography taken at Koonamore Vegetation Reserve in South Australia's North-East Pastoral District. It is a project run and managed by University of Adelaide researchers, and has been ongoing since 1926.
Every year, a field trip heads up there to re-assess the original quadrats established at particular sites, to record the vegetation present. Each year the same fixed quadrats and photopoints are recorded, meaning if you've got a small tree on the left and a large one on the right, it's two photos of the same tree taken at different points in time. This allows a year-by-year insight into the vegetation changes at the station, and it's recovery from a badly over-grazed state. The original photos (taken in the 20s and 30s) can be seen on the left (or top), some of the more recent ones on the right (or bottom).
The changes are astounding.
Livestock and rabbits had completely denuded the soils in the early photos, but now the understory is coming back strongly.

How did they get this to happen? Simple. Fencing the former sheep station to exclude livestock, and beginning rabbit control programs. Larger native grazers, such as kangaroos, can still enter and exit the reserve, but livestock are excluded. Unfortunately rabbits are still present, but are now in much lower nubers than they used to be (rabbit population is indicated on individual photos by the rabbit symbol in the bottom right corner).
This project is unique and very valuable for understanding vegetation shifts in arid Australia. It is the longest running monitoring program of it's type in Australia (by quite a long way) and one of the oldest and longest-running in the world.
If there was ever a way of showing people we really can make a difference by taking some simple and relatively inexpensive steps (eg fencing and careful stock management), then this is it.

Enjoy!

https://www.youtube.com/watch?v=ACU9KCWEV6g&feature=player_embedded

Talking trees

So the long-awaited post on talking trees.

So how on earth does a tree 'talk'?
Plants have multiple ways of communicating, and the way they do it depends on what they're trying to communicate with.
For example, a flower that is long and red and tubular is a signal to birds that there is a tasty sugary treat awaiting them, similarly a rich-smelling fruit would indicate it's ripe and ready to be picked (or from the plant's point of view, dispersed), or a red one might indicate poison.
These are all fairly obvious forms of communication - we can see the flower and smell the fruit. But this isn't what is meant by a plant 'talking'. Besides, this is all communication with animals - what if the plant wanted to communicate with another plant?
There are actually a couple of ways this happens, one through the soil and the other through the air.

Many plants exude compounds from the roots in order for inaccessible nutrients in the soil to be altered to a form the plant can then use. These root 'signals' can be used by more scrupulous species as a way to block the root growth of other plants, or by parasitic plants to find their host.
But this isn't what we mean by trees 'talking' either.

Communication through the air, and hence the leaves, is known as the 'talking tree' effect. According to our anatomy 101, plants have pores called stomata on their leaves which allow the passage of oxygen and water into and out of the leaf. These molecules are able to move in the air, which as any school kid can tell you, is made up of other stuff too. This means any compounds small enough and light enough to move through the air can also enter the leaf, and can then be sensed by the recieving plant. So by releasing certain chemical signals into the air when they're attacked by herbivores, the plant being eaten can then warn other plants in the area that there is a threat around, and those surrounding plants can act accordingly.

Act accordingly?
What can a plant do about it?
Well they can't move, but they can act. Many plants synthesise toxins to discourage herbivores, but do so only when they're under attack. Because of this, most will still lose some leaf tissue before the synthesis of those toxins kicks in as they need to sense the threat first. So if they have the ability to sense other plants are under attack, they can pre-prepare themselves ready for attack, and minimise the damage done to them. Clever!

So what would be the point of this? Why would a plant bother to try to tell another plant there are herbivores in the area? Why not just make your leaves poisonous the whole time? The answers to this is: conserve your resources until they're needed. It uses resources to make toxins, as well as requiring some means of storing them, so why make them unless you need to? Many of these anti-herbivore compounds break down relatively quickly as well, so long-term storage wouldn't be a very good option. By listening in on other plants in the area, toxins can be synthesised only when they're needed, solving the resource and storage problems whilst still protecting the plant.

Cool, eh?

Taxonomy basics (part 3): Drawing a phylogentic tree

As promised, a little methodology on drawing phylogenetic trees. The process is relatively simple to understand - different organisms are grouped according to characters they share. These characters are chosen by the person doing the study, and do need to be defined reasonably carefully. I think a worked example will be best to explain here, so I'm going to go out on a limb and use one from one of my undergrad assignments. The assignment was to draw (by hand) a phylogenetic tree of anything we liked, but it needed to be things, not organisms. I used chocolate bars, and will do so again as it's really good to see how simple characters can group things together.

Basically you need a few simple things to draw a tree. The first are organisms you're studying, and from these you need to derive your characters and their 'states'. To do this, examine the 'organisms' and pick apart their appearance, internal anatomy etc, and these become your characters. You need to be able to give these characters 'states', but these need to be well defined (ie if something is blue and something else red, the character would be colour and the states would be blue and red). For example a character of size might be useful, but if you define the states as 'small, medium or large' then it's an arbitrary measurement and will be impossible for anyone else to use your characters to see how you came up with the tree you did. A better character state would be 0-1.9cm long, 2-3.9cm long, greater than 4cm long (depending of course on what organisms you're describing) as it can be exactly replicated by any other researcher. Generally the more characters you can use the better, I'll list the ones I'll use below shortly.
The other thing that is useful is one or two 'outgroup(s)'. These help root the tree, and ensure the characters you're picking will split closely related organisms rather than working because they're completely independent of everything. For example if you chose red and blue as character states for cars and you had motorbikes and ships as outgroups, it would probably show up as a bad character. Outgroups shouldn't be too far removed from what your studying (eg if your studying cuttlefish then a jellyfish would be an inappropriate outgroup, but an octopus is closely related but different enough to work well).

So for the sweets example, we'll start out with 6 chocolate bars (in this case we'll use a Milky Way bar, Mars bar, Snickers, Violet Crumble, Crunchy and a Flake) and one lolly that isn't a chocolate bar as our outgroup - say a lolly snake.
From these 7 'organisms' we need to find characters that will split them up and hopefully place closely related 'species' together.
So our characters (and their states) might be:
1. Chocolate coated (yes/no)
2. Nougat present (yes/no)
3. Caramel present (yes/no)
4. Honeycomb present (yes/no)
5. Nuts present (yes/no)

So these 5 characters would be enough to split up the chocolates, but probably not enough to completely resolve them to separate 'species'. To draw the tree from these characters, you first need to make up a character matrix. In this case it's pretty simple, as we've got a binary character set (all of the answers are no, which we'll code as a 0, or a yes, which we'll code as a 1). You can have as many states as you need - up to 4 or 5 can work well - but too many may make the character useless. Often matrices are polarized so that all the outgroup scores a 0, but in this case that happened anyway so isn't necessary.

Anyway, our matrix looks like this:

(I used letters for the individual 'species' as it shortens the name and is easier to put on a tree)

So to draw a tree, we start out with whatever character is common to most species. In this case it's being chocolate coated (character 1) which splits the outgroup off immediately (diagram below - sorry for crappy quality, I don't have time to do them properly!). The character used to split the tree at that point can be indicated with a horizontal like and a number, it allows you to see exactly which characters separate species. Everything that occurs after that number has that character, so from the 1 on the tree below, we can see that A does not have any chocolate, but B, C, D, E, F and G do.

So the next step is to do the same thing again, with the remaining characters. The next one shared by most of our chocolates is character 2, which is containing nougat. So this splits off 3 species, shown below:

We keep going the same as before, looking at the next character that is common to BC and D or EF and G (as they're the biggest groups remaining). We'll use character 3 (caramel) next:

And to split the other big group, we'll use character 4 (honeycomb):

And now we'll use our last character, 5 (nuts)

So this is the final tree. It's ok, but not fantastic. We can see that A, E, B, C and D are all separate species, but we've failed to split F and G on the characters we used (both have chocolate and honeycomb, but that's as far as we got). If we were to use genetics as well, we might get further here. If we took brand to equal genus, then F and G would split nicely (VC= Nestle, Crunchy=Cadbury). I'll now colour-code branches according to brand:

Outgroup is green, Cadbury are purple, Nestle red and Mars are black. So in this case the Nestle bar was a good example of convergent evolution - that is two organisms evolving independently in similar environments that end up looking similar but are completely unrelated. It also shows that problems can arise if you use morphology alone - without the 'genetic' info here we couldn't split them at all. Just remember, things that are only one join (node) apart are most closely related (eg in this one C and D are more closely related than D and B or C and B).

This was a reasonably simple example, with only 5 characters across 7 'species' and realistically only one option for the best tree. However if you throw a few more species and a few more characters into the mix, there become multiple options as to what the tree could look like, and because of this it is easiest to use computer programs to try re-combinations hundreds of times rather than doing it by hand.

So that is how you draw a phylogenetic tree. Hopefully it helps in understanding how they come about, and how to read them. You'll come across terms like monophyly and paraphyly, which I might go through in a future post (for a definition right now, google a taxonomic dictionary ;) ), but it should hopefully be easier to understand relationships between species by looking at these diagrams.


One final note: if anyone has any questions or comments, feel free to ask away. I'll try to answer as best I can ;) Also if you've something you're interested in for a post about, let me know and I'll see what I can do... Perhaps next time for something different I'll write about the long-awaited 'talking' trees ;)

Plant of the week #5

Leptospermum myrsinoides
(heath tea-tree)

A brief description: A common shrubby species throughout it's range, the heath tea-tree grows to about 1-2 meters in height. However it is often found as an understory shrub in Eucalyptus woodlands and is much smaller. The 5-petal flowers are white (sometimes pink) and appear in spring.

Taxonomy: From the same family as the Eucalyptus genus, Myrtaceae, it is one of about 85 species. Most species are endemic to South-Eastern Australia, with one found in New Zealand and another in Malaysia.

Distribution: SA, VIC, rare but reported in NSW (mostly in the SE).

Conservation status: Locally common in SA and VIC, not considered at risk in the wild.

Interesting things about tea-tree: Various species in this genus are commercially important for the garden industry and also for honey producers. Dense plantings of tea-trees are popular as hedges and there are many cultivars that are common garden plants (particularly due to the drought-tolerance of older plants). Honey made from the nectar of some species has been found to have antibacterial and antifungal properties.

Taxonomy basics (part 2): How do you decide what is a species?

The underlying question all taxonomists ask is what exactly is a species?
Perhaps slightly surprisingly, this is a question still without a strict answer. Generally it's thought to be if two groups of organisms can't interbreed, then you have separate species, but this doesn't always work (bacteria, for example, screw up this definition by reproducing asexually).
So aside from a definition debate, how do we work out whether or not something should be named as a new species, and also where it fits in with other currently known species?

There are 2 ways to go about this, and depending on the field you're in, you can use one or the other or (preferably) both.

The first method used is the traditional morphological method. This involves picking apart what the organism looks like and using those traits to group it with things that are similar. It's the method that has been used since the first ancient attempts were made to classify things, and realistically humans have been doing it for centuries. How did we determine that a mouse and a worm are different species? Because they look like they are.
Thankfully methods in morphological study are more advanced than that now. Traits studied might be form and function, as well as internal structures of that plant/animal. However different traits are also given different weighting, according to their importance, as not all characteristics are necessarily useful for classifying animals/plants/fungi. For example red hair in Orangutans and humans would certainly be a trait that would be largely ignored, as there are so many others that are far more important for determining whether or not they're different species.

However it is exactly this sort of uninformative characteristic that makes a purely morphological study potentially unreliable (although good systemics know this and choose better characters/leave out really dubious ones). It is important to recognise this, and make sure your characteristics are reliable, for example colour is usually a bad character for animal species (but is often ok for plants), as it can be really variable within a species.

Let's make a case-study of two similar species, say... the plant I'm working on, Cassytha pubescens (Lauraceae), and a dodder species, Cuscuta australis (Convolvulaceae). The reason I'll use these two is that they're frequently confused, and are a good example of the pros and cons of using morphology alone to describe species.

(Cuscuta image from http://www.natureloveyou.sg/Cuscuta%20australis/Main.html; Cassytha photo is my own) 

Cuscuta australis

Cassytha pubescens

             

So you can see from the above photos that the two plants are superficially similar. They're both rootless, twining parasitic vines that can spread quite rapidly. Single plants can cover rather large areas, with dense mats forming over the host vegetation. Their leaves are so reduced they appear like scales, and they both attach to host plants using haustoria. These traits, without looking at any others, would immediately create an idea that they should be grouped together.

However an immediate difference we can see is the colour - the Cassytha is green, whereas the Cuscuta is yellow. This is due to their different modes of parasitism - Cassytha is a hemiparasite (takes water and the associated dissolved nutrients from its host) and Cuscuta is a holoparasite (takes photosynthates from it's host, which is why it's orange - it doesn't typically photosynthesise much). In addition to this, Cassytha is a perennial plant and Cuscuta is an annual. So on outward appearance we might group them together, but we can already see that their physiology is very different.

Other differences can be easily found in the flowers and fruits of the plants. Typically when classifying plants by their morphology any characters you can find that are not reliant on flowers and fruits are good. This is because vegetative characteristics (eg veins in leaves, or leaf arrangement etc) are there the whole year around (ok, excluding deciduous trees!) but flowers and fruits are only on the plant at certain times of the year. Having said that, flowers and fruits are really important for classifying plants. It can just makes it a pain to identify them in the field if they're not in flower/fruit!

The above examples both have leaves that are so tiny they're called scales - they're only a few mm long and sit flush with the stem at the nodes where the vine branches. So while they can be used for taxonomic purposes, flower and fruit characters are also really useful here.

In the photo of Cassytha, you can see the flowers are yellow, whereas in Cuscuta they're white. Cassytha flowers are tiny, and open about half-way in comparison to Cuscuta flowers. They're anatomically different (which can get complicated, so I won't explain that in detail) and you can also see the distribution of the flowers is different - the position of flowers along the stem bearing them and also the structure of the inflorescence is different - in Cassytha they're borne on spikes and have about 3-5 flowers in a cluster, in Cuscuta they're closer to the stem and have many in tight clusters. The fruits are really different too (although you can't see them in the photos), with Cassytha having fleshy fruits that are vertebrate dispersed, and Cuscuta having light, dry papery fruits.
So all the physiology and flower/fruit characters are pointing to them being very different species, from different families.

There are many other differences between these two plants, I've just picked out a few obvious ones. So you can see how once you start to look closely, sufficient characters can be found to place them into different families.
This is why morphological studies work. For some areas of taxonomy, this is essential - for example palaentology. Morphological studies are  the only method they have to determine which ancient organisms belong together. But for those lucky enough to be working on living things, we can also use the newer, shinier methods created by our new(ish) knowledge of genetics.

So, to explain how we can do this, we turn to genetics 101, dot-point style:
- All living things have DNA (we won't go into the 'is a virus a living thing' debate here)
- This DNA is made up of 4 amino acid bases, Adenine, Guanine, Thymine, Cytosine, known as A, G, T and C.
- These pair up with each other (A with T, G with C)
- These pairs of bases run in sequence and create a double-helix of DNA.
- A specific region of DNA sequence makes up a 'gene' and is responsible for a certain function; ie it might be for blue eyes.
- Because all members of a species must have compatible genes, you tend to get subtle changes between species that allow us to tell them apart if we look at their DNA (if we can figure out which genes are best to look for this in).
- If the DNA can be extracted and sequenced, you end up with a string of A, T, G and Cs. By comparing these between your samples, you can determine if there are large enough differences to call them different species.
- Usually more than one gene is used - the more the better - as there is some variability within species as well as between them.

So from genetics combined with morphology we could, theoretically, end up with two different answers to whether or not our Cassytha and Cuscuta are in fact different species. However usually the two methods complement each other, and neither are without their own problems. The morphology results can be influenced by which characters you choose, or even how you score them, and the genetics could be influenced by how many genes you used, whether you took them from chloroplasts (which are like our mitochondria and only inherited from the 'female' plant) or the nucleus of the cells, or even which genes you picked. However with good experimentation and care these problems can be easily minimised.

Taxonomy isn't really that complicated. Both of these methods rely on the same principle - detecting differences between species based on the characters you chose to use (whether they be genetic or mophological ones). There also ways to represent the relationships between species visually, and these are typically known as phylogenetic trees. The process for making these is simple, but because you need so many characters to justify splits bewteen species, it can get mindbogglingly complicated with all the recombining and maths that becomes involved. This is why we let computers do the legwork for us now.
Having said that, I might make a post on how to construct a phylogenetic tree to finish up the taxonomy thread, as it's a concept that I think is way better understood if you actually make one from scratch, by hand. It's so easy to just plug in numbers and have a computer spit out an answer without actually understanding any of the processes involved.
So that's what I'll talk about next time :)

Taxonomy basics (part 1): What is it, and why do it?

Metaphorically speaking, people like to put things in boxes. It's human nature to catagorize things, and plants, animals and fungi are no different. Besides being human nature, it's also a useful tool to help describe something to anyone from any background - for example you might want to describe a leopard on the African savannah. You could try to tell someone that it's a large cat with spots, but a general description such as that won't tell them exactly what it was. If you gave them a species name, in this case Panthera pardus, they would then be able to look up exactly what you meant. This is because of the way species names (often called 'latin' or scientific names) work, with each two-part (binomial) name unique to the species you're trying to describe.

The naming system we currently use was created by Carl Linneus in 1735. Names are typically written in two parts (although there is a whole set of different levels which I'll run through later), with the first word describing the group that species belongs to, and the second the actual species it is. The first part is known as the genus name, and in the case of the leopard it is Panthera, along with jaguars, tigers and lions. So the information you get from the genus is the sort of species it is, and what it is closely related to. Once it's been used the first time the genus name is often abbreviated to the first letter, which abbreviated or written in full, is always capitalised. The whole name should also be written in italics or underlined (it's just the convention that is followed, so it's clear exactly what is the species name).

The second part of the name is the unique name of the species itself. This tells you exactly what your species is, in the case of the leopard it is pardus, which distinguishes it from the jaguars, tigers and lions that make up the rest of the Panthera genus. So in full its binomial name is Panthera pardus, telling you it's a big cat with spots that lives in Africa.
Or is it?

There are other levels of classification in addition to the genus and species levels. There are broader groups, such as family, or even kingdom, and there are also some other lower levels that might include subspecies, breed, or in plants variety or cultivar. These last few are all the same species, they're just different forms of the same species, and they should be able to reproduce with eachother to produce viable offspring. For example going back to the leopard, there are a couple of sub-species you might have. P. pardus sub. pardus is the African leopard, however the International Union for the Conservation of Nature (ICUN, the big-boys in validating species internationally) currently recognise 9 subspecies of leopard, with another 2 possible subspecies described from skulls. These include subspecies from South-East Asia, China, India, Russia and the Middle-East. However in theory as they're only subspecies and may look a little different, if you stuck a Javanese and an African leopard together, they should still be able to breed and create fertile offspring.

Confused? I'll put in the heirachy now then, and use a plant-based example this time, we'll make it the... Sunflower (Helianthus annuus) :)

Kingdom: Is it a plant, animal, fungi, or bacteria? Plant
Phylum: If it's a plant, is it a flowering plant? Seed plant? Seedless vascular plant? Flowering plant (angiosperm)
Class: Be more speciefic? it belongs to the Asterids, a very species-rich group of plants.

Order: Asterales - they have many little flowers clustered together to produce one large 'flower' like inflorescence
Family: Now we're getting to the other closely-related species, it belongs to the Asteraceae family, a group of plants with daisy-like flowers.
Genus: Helianthus - this tells us what it's closest relatives are :)
Species: annuus - tells us exactly what it is

(then there might be subspecies and cultivars or even hybrids listed here)


The other useful thing about two part names is that it allows the actual species name to be re-used. For example people like to name species after other people, so if you get someone famous like Sir Joseph Banks, you end up with a bunch of species named after/in honour of him. So you might have a plant with the species name banksii (for example Banks' Grevillia, Grevillia banksii) but also animal species like the Red-tailed Black Cockatoo (Calyptorhynchus banksii) and the binomial name allows you to differentiate the two because the plant and the cockatoo will have different genus names. Clever eh? It also means our imaginations are not taxed as heavily, as I suspect the number of species in the world would far outweigh our creativeness at naming them ;)

Usually the names you'll see written down will be from Family level down (you can tell it's a family name in botany if it ends in 'ceae', or in zoology if it ends in 'idae'), and in botany at least you should mention who named the species the first time you write the name out in full as well (it allows people to look it up/refer to it etc). Often with plants you'll find the genus and species name, followed by the family name in brackets e.g. Helianthus annuus (Asteraceae). The use of family level ID is good, as it allows you to either see how weird your species is (such as the one that is the subject of my PhD, Cassytha pubescens (Lauraceae) as it is the only Lauraceae that looks and behaves like that) or to look up what it is related to quickly and easily.

So now we know how to write out a descriptive species name and why to do it, the remaining obvious question is how? How do you decide what is a species? And as that's a question with a rather chunky answer, I'll put that in a fresh post later ;)

Plant of the week #4

Cassytha pubescens
(Downy Snotty-Gobble) 

A brief description: Also known as dodder-laurel, devil's twine, jungle string or love vine, this interesting plant is actually a parasite. All species in the genus are hemiparasites, meaning they still photosynthesise and tap into the host plant's xylem (taking water and the associated dissolved nutrients) but not sugars. It is rootless as an adult (although the seedlings have roots) and is completely dependent on its host for survival. Flowering and fruiting in summer, the picture above shows some flowers in bud and opening, as well as some immature fruit. The host in this case is an Acacia pycnantha, although it is a generalist parasite and will grow on pretty much anything (even barbed-wire fences!).


Taxonomy: The taxonomy of this genus is not well researched. There are approximately 23 species, 16 of which are endemic to Australia. The genus is placed within Lauraceae, often within it's own subfamily as it's so weird. *It is unrelated to the Dodder species in the Cuscuta genus. They're a completely different family (Convolvulaceae) and are an excellent example of convergent evolution as they look very similar but are completely unrelated, and physiologically very different*

 Distribution: Eastern states; Coastal SA, Vic, Tas, NSW and QLD. Also found in New Zealand and Japan (introduced).

Conservation status: Locally common, not considered at risk in the wild. Distribution is typically patchy


Interesting things about downy snotty-gobble: There are many, where should I start?! (this is the plant I'm studying for my PhD, so I'm perhaps a bit biased :P). It has been seen to damage some weedy species in South Australia, even killing Gorse (Ulex europaeus) and Scotch Broom (Cytisus scoparius) but not the native species. This is thought to be due to the native species co-evolving with Snotty-Gobble.
The other thing I find rather interesting, is the seedling stages of this parasite. It germinates and grows for the first 6-8 weeks with a short root (usually no more than a couple of cm long) which dies back after it's found a host and wrapped itself securely around it. This means if there's a disturbance such as a fire, the adults are all toasted and it's up to the seeds left in the soil to re-establish the population. Interesting, yes?

How does photosynthesis work? (part 3): Photorespiration, C4 and CAM

So the final installment of this thread of posts is about one of the big problems of C3 photosynthesis, and also how alternative methods of photosynthesis help plants overcome this problem.

As previously mentioned, the enzyme responsible for the whole shebang is Rubisco - it captures CO2 in the first place, and allows the chloroplasts to do their thing. The problem with this system is that Rubisco also has an affinity to Oxygen (particularly at higher temperatures or low CO2 levels), meaning when the temperature of a leaf increases less photosynthesis is achieved. The process of Rubisco fixing O2, rather than CO2, is called photorespiration and can slow plant growth by reducing the rate of photosynthesis by a significant amount.

Photorespiration is a particular problem in the tropics, as the temperature is usually high (and this also causes problems with waterloss). This has lead to the evolution of a different form of photosynthesis, that allows the plant to separate the absorption of CO2 either temporally or spatially, hence reducing photorespiration by limiting Rubisco's access to O2.

The first alternative to C3 photosynthesis is called C4. This is because it involves the CO2 being fixed into a 4-Carbon sugar at the first stage. For the initial absorption of CO2, C4 plants use a different enzyme called PEP Carboxylase. This then delivers the CO2 to the photosynthetic part of the leaf by the 4-C sugar breaking down and releasing the CO2 directly to the Rubisco.
The whole process works well because C4 plants have a slightly different leaf anatomy to C3 - they have specialised cells that surround the veins in the leaves, called bundle-sheath cells (this is known as Kranz anatomy). These are packed with chloroplasts, and photosynthesis takes place here rather than in the mesophyll. So by spatially separating the initial capture of CO2 and the Rubisco, photorespiration is significantly reduced. However this form of photosynthesis is also more energetically costly, requiring more ATP than C3. This means it is less efficient that C3, and only occurs in areas where the benefit of reducing photoresipration and waterloss outweigh the larger energy cost, such as the tropics and some arid zones.

The second alternative to C3 photosynthesis is CAM photosynthesis. CAM photosynthesis (Crassulacean Acid Metabolism photosynthesis) was named after the family of plants in which it was first discovered, Crassulaceae (a family of succulents). It tends to occur in arid plants, like cacti, and works by separating the CO2 capture and photosynthesis temporally. This again reduces photorspiration, however perhaps more substantially reduces waterloss. It works in two stages, at night when it is cooler and waterloss is less severe, the plant opens its stomata. It stores the captured CO2 as a 4-Carbon acid, Malate, and then breaks this down back to CO2 during the day to feed back to the Rubisco so photosynthesis can occur. This allows the plant to keep its stomata closed during the day, when it is hot and dry, helping it avoid waterloss and photorespiration.
I also have a healthy admiration for CAM plants, as they can also use this system to do what other plants cannot. During times of extreme stress, such as a severe drought, they can 'CAM-idle'. This means they can keep their stomata closed during the day and the night, and use the CO2 released through respiration at night for photosynthesis during the day and the O2 released from the photosynthesis during the day for respiration at night. Which is pretty cool. But they can't do this indefinitely, and will eventually need to open their stomata to start the photosynthetic process up again. It does, however, allow them to survive long periods of water stress, and also to recover quickly when water again becomes available.

So that, in 3 long posts, is how photosynthesis works. Perhaps next time I'll discuss talking trees, or some other thing that isn't physiology related ;)

How does photosynthesis work? (part 2): Light and dark reactions and the Calvin cycle

The basic reaction of water + CO2  (catalyze with sunlight) ------> H2O + O2 is explained in more depth below, mostly because I get sick of the 'add CO2 and water and sunlight and.... magic happens!' explanation ;)
Photosynthesis is a rather complicated process, and I'll try to keep this simple.

Within a leaf there are cells that specialise and become functionally different from each other. As previously discussed, in leaves one of the major cell types are known as mesophyll, and this again differentiates into 2 types with different functions.
However it's not just plant tissues that specialise, they do it at the cellular level too, and even the sub-cellular level! (I told you it gets complicated).
Within the cells that make up mesophyll tissue, there are organelles that are called chloroplasts (these are what make leaves appear green). This is where the photosynthetic process actually happens.

So the mechanisms of photosynthesis are best discussed if you split them along the conventional lines and talk about them in two parts. The first part is known as the 'Light reactions' as it takes place in direct sunlight, and the second part is the 'Dark reactions' which do not need direct sunlight (although they usually take place during the day).

Light reactions occur in the membrane of the chloroplasts (which remember are within the plant cells). When light is available, it causes a chain reaction that converts chemicals in the chloroplast to ATP (adenosine triphosphate) and NADPH (Nicotinamide adenine dinucleotide phosphate), two molecules that are basically the universal fuels of cells. The ATP acts to move energy to where it's needed, and the NADPH allows phosphorous and more importantly Hydrogen ions to move to where they're needed for photosynthetic reactions.
So once these molecules are generated in light reactions the ATP and NADPH can be used to make sugars in the Dark reactions.

The Dark reactions are where the carbon dioxide is converted into sugars by the plant, in a process known as the Calvin cycle (because it was discovered by Melvin Calvin, James Bassham, and Andrew Benson). For a diagram of this cycle, use your favourite search engine - wikipedia is more than a little complex for this one. Or for a written explanation, keep reading below ;)
So the ATP and NADPH generated in the Light reactions are essential to the turning of this cycle, which is a rather complicated piece of molecular-energy transfer. It occurs in 3 stages, known as Carbon fixation, Reduction and Regeneration.

In Carbon fixation, CO2 is incorporated into a 5-carbon sugar, called ribulose biphosphate, via the enzyme Ribulose-1,5-bisphosphate carboxylase oxygenase (aka Rubisco). Rubsico is an important enzyme, not only as it allows CO2 to be captured and converted into a sugar, but also as it has an affinity to Oxygen, which can cause problems with something called photorespiration (I'll discuss why photorespiration is a problem and how plants deal with it in the next post). So at this point if the Rubisco has fixed CO2 as it should (and not O2), the sugar has 6 Carbon units in it. However this is only an intermediate product and it is then split into two 3-carbon sugars.

The next stage, Reduction, uses the ATP and NADPH from the light reactions to alter the structure of the 3-carbon sugars (this is where the chemistry will take over this post, so I'm keeping it simple here!) and turns them into the precursor to glucose. This can then be used to generate the 6-carbon sugars for the plant. The remaining 3-C sugars continue within the cycle, and enters the next stage, Regeneration. For this, more ATP is used to convert the 3-C sugar from this pool back into the original 5-C sugar that is used to capture the CO2, and the cycle can begin again.

So in summary, while a complicated process, each turn of the Calvin cycle will actually only capture just a single additional Carbon, so for a 6-C glucose molecule to be generated it will require 6 turns of the cycle. This involves 12 photons hitting the chloroplasts and generating 18 ATP and 12 NADPH molecules in the light reactions, which can then be used for 6 turns of the Calvin cycle in the Dark reactions to fix 6 CO2 molecules to end up with a single 6-Carbon sugar. In a nutshell, the light reactions provide the energy required for the dark reactions to fix carbon, and this is how basic C3 photosynthesis works (so called C3 as it's based on 3-Carbon sugars).

However some plants run into trouble with maintaining water balance, or with excessive light or temperatures. As such they've evolved to cope with this by photosynthesising in a different way. There are 2 main alternatives to C3 photosynthesis: C4 or CAM photosythesis, and I'll discuss these (along with photorespiration) in the next post...

How does photosynthesis work? (part 1): Leaf anatomy

Ok, so I took a week off - ah the hassles of PhD life!
I also sort of lied, as upon reflection perhaps it is better to discuss basic leaf anatomy before going on to how the process of photosynthesis actually works. But I'll make it a long post to make up for it ;)

So there are a few basic components to leaves, that are common to all no matter what species of plant we're talking about. I'll list these, along with their function below:

Cuticle - A waxy layer that sits on the surface of the leaf, it's main role is protecting the leaf from attack from pathogens and to prevent water loss.

Epidermis - This is a single cell layer that surrounds the outside of the leaf (cuticle sits on this layer). It functions much like our skin, in the sense that it prevents nasties from getting in, and water and the insides of the leaf from escaping. There are openings called stomata within this layer, that allow gases to move in and out of the leaf. These pores are controlled by the plant, which can open and close them as it needs. Some plants also have hairs arising from their epidermis, and these have multiple functions (protect from predation, reflects excess light, help reduce water loss through the creation of cool and humid microclimates around the stomata) although which function they perform varies with species.

Vascular tissue - Much like our veins and arteries, this is made up of Xylem tissue, which conducts water and it's associated dissolved nutrients, and Phloem tissue which carries photosynthates (ie the sugary products of photosynthesis) around the plant.

Mesophyll tissue - This is where it gets interesting. Mesophyll is a tissue that is usually found in 2 forms in leaves (although to be fair some leaves only have one type).
The first is Palisade mesophyll (also known as palisade parenchyma), and is composed of elongated, block-like cells that are usually stacked along the sun-side of the leaf. These cells collect light and are full of chloroplasts. You guessed it, they're the photosythetic cells in the leaf. However CO2 is also needed for photosynthesis, and that's where the second type of mesophyll comes in.
Spongy mesophyll (or spongy parenchyma) is (surprise surprise) called such because it is full of air-spaces and so looks like a sponge. The airspaces allow gases to pass in and out of the leaf easily whilst minimizing water loss.

So those are the basic tissue types (there are sometimes others, such as fibers for structural support or other specialized cells in various different plants), however their arrangement within a leaf can vary dramatically.
Basically the aim of any leaf is to photosynthesise, whilst not losing too much water, so the tissues within the leaf will be arranged to best accomplish this in the environment that the plant grows in.
For example, a plant that grows in a hot, dry climate is more likely to have a thick cuticle and less spongy mesophyll than a plant that grows in cooler wetter environments, as it will need to conserve water whereas the cool climate plant won't.

Perhaps the best example of changing the arrangement of tissues within a leaf to suit the environment, is to compare a typical European plant, such as a privet leaf, to an Australian plant adapted for hot dry environments, such as a Eucalyptus leaf.
Pictures below (I don't have access to a camera that I can take micrographs on at the moment, so the sources were: http://sols.unlv.edu/Schulte/Anatomy/Leaves/PrivetLeaf.jpg for the privet and http://www.sciencephoto.com/media/98433/enlarge for the Eucalyptus)

 Here (left) we have the typical leaf. Along the top is that palisade mesophyll, and this is the side of the leaf that would be in the sun. The leaf is held parallel to the ground (known as a dorsoventral leaf), meaning the sun always hits the upper surface of the leaf no matter what time of day it is. So to sum up it makes sense to pack that side with the light-collecting palisade mesophyll, and have the spongy on the cooler side of the leaf that is   permanently shaded.

And this one (right) is of the Eucalyptus leaf. You can see there is lots of palisade mesophyll, but hardly any spongy. The big red bit in the middle is a vascular bundle - the reason it's so huge is that it's the central vein in the leaf - and the white holes are actually oil glands. But the mesophyll is what we're interested in here ;)
It's arranged like this (ie palisade is packed on both sides of the leaf) because Eucalyptus species have their leaves hanging downwards, perpendicular to the ground. This is known as an isobilateral orientation, and helps reduce waterloss and photodamage during the hot part of the day. Because the leaf hangs downwards, during the morning and afternoon (when the sun is cooler) the light hits one side of the leaf. As it moves overhead at midday and becomes hotter, there is very very little leaf exposed to the sun (sort of like a person - in the morning and afternoon the sun will strike your whole body when you're standing up, but at midday only the top of your head will be hit by the sun). And in the afternoon the other side of the leaf is in the sun. This system helps keep the leaf cool, but means that stomata and palisade mesophyll are needed on both sides of the leaf.

So that, in a nutshell, is basic leaf anatomy. There are minor differences between monocotyledon and dicotyledons (for definitions of those types of plants, see wikipedia), and of course different types of plant may have different specialisations, but for your general C3 plant, that's what it looks like. C4 are slightly different, but for a proper explanation of what the hell C3 and C4 even mean, and how they're different, you'll have to wait for the next post ;)

Plant of the week #3

Corybas diemenicus
(veined helmet orchid) 

A brief description:
A winter flowering orchid, this species prefers cool damp Eucalyptus woodlands. Being small (about a centimeter or two in height) they are easily missed - look for the heart-shaped leaves with prominent veins appearing in May-July. The flowers, like all orchids, are insect pollinated, and appear in late winter.

Taxonomy:
The veined helmet orchid is one species of about 100 that belongs to the genus Corybas (Family: Orchidaceae). This genus is found throughout Oceania, with about 20 Australian endemic species.

Distribution: Eastern states; eastern SA, Vic, Tas, and NSW (south-eastern coast).

Conservation status: Locally common in Eastern Australia, less common in SA; not considered at risk in the wild

Interesting things about the veined helmet orchid: 
Veined helmet orchids like cool, moist environments. They're often found on the underside of logs and around cool, rocky streams. Even in large patches all the flowers tend to face south, and produce quite a spectacular display in large quantities.

Problems with photosynthesis (part 2): Photodamage and the xanthophyll cycle

Right, so again a slightly late post (whatever happened to Monday updates?!) regarding more problems with photosynthesis.
Last time we dealt with problems arising from water stress, and how plants can deal with them. This time it's light, again an essential part of the photosynthetic process, but also one that if taken in excess will cause damage to the plant.

Photodamage occurs in the photosynthetic tissues of plants when light and/or heat is in excess and damages these delicate organs. Basically plants use a chain reaction to transfer energy from sunlight into carbohydrates (through an electron transport chain - a series of proteins that can pass on electrons and hence form a chain - a process known as the Calvin cycle - will discuss the exact mechanisms in a later post), however an excess of this energy can begin to damage the proteins that are used to convert this energy. If the amount of sunlight doesn't decrease (ie it's a hot summer day), the plants do need some way of releasing or absorbing this energy before they become photodamaged.
Luckily for them, they've evolved such a system.

A nifty piece of evolution known as Xanthophyll pigments evolved to deal with this problem. These are a series of 3 pigments that have the capacity to absorb some of this excess energy before it can damage the photosynthetic parts of the leaf, and these are found in the thylakoid membrane that makes up the surface of the chloroplast (where photosynthesis occurs - more on this next week). To explain how the system works, a little chemistry is needed (sorry).

The first pigment in the cycle is violaxanthin, and this contains two double-bonded Oxygen (for a good image of the pigments and their conversion process, go to wikipedia). When violaxanthin absorbs some of this excess energy, one of the oxygen atoms breaks away to form a water molecule, and the pigment becomes known as antheraxanthin. The same process can then occur again, and once the pigment has lost it's second Oxygen, it becomes known as Zeaxanthin. The whole process is reversible, which means during the day each violaxanthin molecule can absorb two excess electrons, and by loading the thylakoid membrane of each chloroplast with these pigments, the plant can prevent quite a lot of photodamage.
However there is a limit, and if excess light continues to fall on the leaf, photodamage will eventually result (and is more often than not  irreversible).
During the night is when these pigments usually convert back to the lowest energy state (violaxanthin), and the plant can prepare it's defenses for the next day.

The xanthophyll cycle is just one way plants can deal with light stress, but it is I think by far the coolest ;) Other ways can be to preferentially grow in shadier areas (although the plant will acclimatise and produce fewer xanthophyll pigments - afterall, why produce them if you grow in the shade and won't need them?) and also via leaf alignment (as in the Eucalyptus example in the previous post). Why this protective mechanism is so important will be the subject of the next post - how does photosynthesis work?

Plant of the week #2

Stylidium graminifolium
(grass trigger-plant)

A brief description:
The grass trigger-plant is a spring flowering plant found predominantly in moist to dry eucalypt woodlands throughout south-eastern Australia. Emerging in late winter, leaves are up to mid-shin height, with the flower-spike up to knee height. Flowers vary from hot pink to white with pink streaks (as above), with the inflorescence covered in small black hairs.

Taxonomy:
The grass trigger-plant is one species of about 130 that belongs to the genus Stylidium (Family: Stylidiaceae). Most species are Australian, however there are some found throughout south-east Asia.

Distribution: Eastern states; eastern SA, Vic, Tas, NSW (eastern coast) and QLD (south-east).

Conservation status: Locally common; not considered at risk in the wild

Interesting things about trigger-plants:
The flowers of trigger-plants are insect pollinated, and it is from the flowers that the plant derives both it's common and genus names. The flower consists of 5 petals (4 clearly visible, one tucked back up behind the trigger) and fused stamens (2) and style that form a trigger. This trigger is pulled backwards (like cocking a gun), and when an insect lands on the flower it is released, swinging forward and stamping pollen onto the back of the insect's head. You can see this trigger clearly locked-and-loaded in the photo below. Unfortunately I wasn't smart enough to trigger it and take a before/after photo. Perhaps next time? ;)

Problems with photosynthesis (part 1): Maintaining water balance

As promised, a (slightly late) post about photosynthesis, and some of the problems that plants face when they try to do it. Because these can get complicated, I'll split it into 3 posts. Firstly we'll deal with maintaining water balance, and then photodamage caused by excess light (including the xanthophyll cycle - a really cool bit of evolution involving photosynthetic pigments). The last post will be an introduction to the actual process of photosynthesis at a molecular level, and the development of different kinds of photosynthesis to suit different environments (known as C3, C4 and CAM photosynthesis), and subsequently why higher CO2 levels are not necessarily a useful thing for most plants.

So, as every year 7 student can tell you, plants take up carbon dioxide from the atmosphere, water from the soil and absorb sunlight to magically produce sugars. The process is really a marvel of evolution, and involves complex chain-reactions at a molecular level. However for this to even begin, the basic ingredients (CO2, sunlight and water) need to be collected. Most plants use their leaves to obtain the first two, and roots to gather water (by the mechanisms discussed in the previous post!), although of course there are exceptions to this rule (some plants photosynthesise in only their stems, others are parasitic and get water from their hosts rather than root systems, but you get what I mean).
However one of the biggest problems plants have while trying to photosynthesise is maintaining a balance of all 3 requirements, and particularly maintaining enough water to survive (how well they do this is known as their Water Use Efficiency - WUE).

The means by which plants take-up CO2 is through the pores in their leaves known as stomata (singular: stoma). Plants have direct control over these pores, and can open and close them when they need. Opening stomata to uptake CO2 allows the absorption of carbon necessary for photosynthesis to occur, however it also allows water (and oxygen) to escape the leaf, and the plants have little control over this. Consequently in times of water-stress, plants must close their stomata and cease photosynthesis or they will lose valuable water. However allowing water to evaporate from the leaf in hot weather can also assist in cooling the leaf down, as excess light can heat the leaf and damage the photosynthetic organs within it (the other mechanisms to deal with this problem will be discussed in the next post).

Because this is a big problem, many adaptations to low-water environments have evolved (although usually perennial plants in low-water systems are deep-rooted as well). Three of the most common dry-climate adaptations include:

1. Reduced leaf area: This allows for fewer stomata to lose water per unit leaf area, and consequently a greater WUE, although as it does decrease the rate of absorption of CO2 these plants are usually slower-growing than plants without this adaptation. Often leaves are fleshy and succulent as well, and store fluids even in dry times. In some plants, such as cacti, the leaves are so reduced they became spines, and photosynthesis occurs in the stem, while the spines protect the valuable photosynthetic stem from herbivores.

2. Light colouring/hairs on leaves: Many species have a woolly coating on their leaves, intended to reflect excess light. If a leaf remains cooler, less water will be driven from it through evaporation, and the chances of damaging photosynthetic structures is lower. Saltbush and many other arid species are examples of plants that use this protective mechanism.

3. Sunken/hairy stomata: This is really quite cool - many plants have pits and/or hairs in the leaf surface that create a cooler, more moist microclimate around each stoma, reducing water loss but still allowing CO2 to enter the leaf. Banksia species often show this sort of adaptation, particularly those found in the drier regions of Western Australia.

Other plants have more simple mechanisms to deal with waterloss, such as members of the Eucalyptus genus that have leaves that hang downwards, rather than holding them horizontally. This ensures that during the morning and afternoon when the sunlight is cooler the leaves are exposed to it, but when it is overhead and hot at midday the thin edge of the leaf is the only part exposed. This simple anatomical re-arrangement dramatically reduces water loss and allows the trees to grow easily in hot, dry environments (now go find a gumtree and see what I mean!)

So to sum up, plants (like all living things) need to maintain their internal water levels to survive, but also have to balance collecting the ingredients required for photosynthesise. They have evolved many different ways to achieve this, while maintaining a capacity to collect sunlight for photosynthesis. Stay tuned for the next post on the nifty mechanisms used to deal with excess (hence potentially damaging) sunlight.

A word on water potential

So it's time for the first of the physiology posts.

Water is essential for all life on earth. Without a plentiful supply of it, we certainly wouldn't be here. Plants originated in aquatic environments, and one of the many challenges they had to overcome when they made their move onto dry land was how to obtain water. They cannot actively drink it like we can, so a way to passively move water from their roots to the stems evolved.

In order to regulate the water within their tissues, plants use pressure gradients. Because water will always flow from an area of high pressure to low pressure, by creating a pressure gradient in the tissues of the leaves water will be drawn into them from the stem, and into the stem from the roots. In this way, the whole plant becomes a pressure gradient - the roots always have the highest water potential, followed by the stems and finally the leaves. By opening and closing their stomata (pores on the leaf surface), water can leave the plant, and the gradient can continually function (otherwise the water would build up in the leaves, the pressure would increase and the gradient would eventually stop).
During drought of course the plant conserves it's water by closing the stomata, and usually the water potential of the whole plant decreases. If it continues without water for too long, leaves wilt and the plant eventually dies.

So, the underlying question about all this is how does the plant create different pressures in its tissues? There are two basic ways to achieve this. Firstly, you can change the volume of the plant cell, without altering it's size (think of a bottle of fizzy drink - if you shake it and the gas leaves the drink but you've not opened the bottletop, the bottle becomes highly pressurised), or you can pack the interior of the cell with solutes such as salt, and water will be drawn into it. Typically plants use solute loading to decrease and increase their water potential, taking up salts such as potassium from the soil and ground water.

In a nutshell, plants can use water thanks to basic physics. They can regulate their water use through a variety of mechanisms, all of which are vitally important for the plants photosynthesis and survival. An important component of why plants water regulate the way they do is a need to balance water loss with the uptake of the carbon dioxide necessary for photosynthesis (which occurs when stomata are open). So this will be the subject of the next post :)

Plant of the Week #1

Amyema miquilii
(common box mistletoe)

A brief description:
Common box, or drooping, mistletoe is a hemiparasitic plant. This means it takes water and the associated dissolved nutrients (such as nitrogen) from it's host, through a structure called a haustorium. Mistletoes are stem parasites, and as such depend on their hosts for survival. Because of this, contrary to popular belief, they rarely kill their hosts. The red flowers appear in late summer and throughout autumn, and the fleshy fruits develop soon after flowering. Pollination and fruit dispersal is bird assisted, with the seeds leaving the birds gut encased in a sticky, glue-like substance. The birds then wipe this against a branch (to remove it), and the seed sticks to the branch. If it has been deposited on a suitable host, the seed will quickly germinate, and forms a strong attachment to the host.

Common hosts for this species include members of the Eucalyptus and Acacia genera.

Taxonomy:
The common box mistletoe is one species of about 100 that belongs to the genus Amyema (Family: Loranthaceae). There are about 35 species found throughout Australia.

Distribution:
A. miquilii is present in all mainland states of Australia

Conservation status: Common; widespread (throughout Australia)

Interesting things about mistletoes
Mistletoes are key food sources for birds (both pollinators and fruit eaters), as well as insects such as butterfly larvae. Mistletoes can also be nutrient accumulators. Being hemiparasitic, they are not water limited during droughts, as their hosts provide a reliable water source. Because they can rapidly use water without drying out, the nutrients carried by that water are deposited in the leaves and nutrients can accumulate. Mistletoes have been known to directly affect the distribution of nutrients in the landscape, with their leaves releasing patches of nutrients back into the soil as they decay.

Firstly, to science!

The inspiration for this particular post is two-fold. I'd been intending to write something along these lines for a while, but hadn't so far gotten around to it. Considering Easter has just come and gone, and there was, shall we say an 'enthusiastic', debate on a particular TV show last night it has prompted me to actually do it.
Writing about the scientific process, and science as a 'new religion' I think is a good starting point for this particular blog. So here we go!

First and foremost, science is a process. It is a methodology used to uncover information about the world around us, and to discover how the systems within that world function and interact with one another. It is not about proving things to be true, or about dogma (usually - although in some disciplines it does sneak in with some theories) but instead is about experimentation and discovery of the most plausible explanation available at the time, and the ability to switch to an alternative and better explanation should one ever arise.
In this, is the core of the power of science.
Because of the way science functions, better explanations for phenomena are always sought. Dogma rarely takes hold, and if there is insufficient evidence to support them, theories do not progress very far. Even widely accepted theories, even those strongly supported over such a long period of time as to be called the 'laws' of science, are continually being put to the test. E=MC(squared), Einstein's famous equation used to explain the relationship between mass, energy and the speed of light (in a vacuum at least) is now again under scrutiny, as are the theories of gravity (well, talk to any quantum physicist about that one), evolution by natural selection (microbiologists, geneticists etc) and Netwon's Laws (those quantum physicists again). That is not to say those laws are now seen as 'untrue' and will be scrapped - far from it. The beauty of science is to continually progress such laws, adjusting them accordingly as new knowledge is gained.
Those who state science is the new religion have no understanding of what either 'science' or 'religion' actually mean, nor what they stand for. Equally, those who boldly state that 'science will eventually answer all our questions' also do not understand the scientific process, nor how it functions within our society. These are two reasons I refuse to give science the capital S that many do (aside of course, from when it is at the beginning of the sentence).

Take, for example, a simple experiment. We're growing tomatoes, and want to know if we add fertiliser twice as often, if they'll grow better/produce more fruit (bear with me, I am a botanist and this is the first appearance of plants in this blog!).
The scientifically designed experiment you'd use, would be to have two 'treatments'. One you could give lots of fertiliser to, and the other none (or much less - termed a 'control'). Then, once they have fruited for whatever length of time you choose, count or weigh the produce and compare the two. It might be expected that the one with more plant-food did better, and for the sake of this example let us say that this is indeed the case.
The purpose of science, however, is not to simply find out whether things are 'true' or not, but also to attempt to explain why they are so. In the case of the tomatoes, the first thought you would have would be that they extra nutrients allowed the plants to produce more fruit. However this may not be the actual effect the nutrients had. There could be many other factors that accounted for this extra fruit, and these are known as variables.
Perhaps the pots the tomatoes were planted in were placed in patchy light? If those with the higher nutrient treatment happened to have more light (due to chance) than the others, this, rather than the nutrient levels, may explain their increased fruit set. If they had more light, they'd also have likely been exposed to higher temperatures, as it gets hot in the sun. Or it could be something else - perhaps the extra nutrients allowed them to grow more roots, take up more water and then produce more fruit? Or perhaps it was some other chemical or biological process, such as the particular blend of those extra nutrients allowing a particular beneficial microbe to grow in the soil with the plant, and hence increase the fruit production. Or the presence of the fertiliser may have changed the pH level of the soil, and allowed previously inaccessible nutrient sources to be 'unlocked' for the plant by changing them to a different form. Any one of these explanations could tell us why higher nutrients caused a greater fruit set, and each could have it's own experiment set up to investigate it. Or, better yet, the scientist would have had some ideas as to why nutrients would work before they started, and would have built tests for some of these factors into the original experiment (known as 'controlled' variables).

So from this terrifically simple example, you can see how complicated science can get. Without the question of 'why' as well as 'does', we could easily conclude that the additional fertiliser works because fertiliser is magic, and our knowledge of the system would barely increase at all. The point of this example is to illustrate one of my favourite aspects of science. Think of it, if you will, as the mythical beast, a hydra.
Chop off one head, or answer one question, and another two will appear in it's place.
This is the fundamental reason that science can never answer all our questions. But in the past few centuries, and certainly within the last one, our scientific endeavour has brought us so very far. Our knowledge base is rapidly increasing, and the rate of new advancements in science is also accelerating. Having said all of this, I don't see our hydra situation as a problem. As our knowledge increases, so does our want to learn. Learning is good for us, if we didn't learn we would still be monkeys sitting around in trees in Africa (well, there is another contested theory - the 'out of Africa' theory). And yes, I know monkeys can and do learn but you know what I mean.


In a nutshell, science is a remarkable process by which we learn about the world around us. It is not some god worthy of worship, nor does it attempt to be. It is a tool we use to understand the universe we live in, and hopefully one that will allow us to improve our lives and the lives of those to come.