Of recrystallisation and inclusion trails

In part one we learnt about the broad background and the gap in knowledge my PhD will help to fill.

In part two we learnt about the specific samples I am looking at, where they come from and how they came to be as they are today.

In this final part, we will finally learn how my samples look now, and what sort of things I might have to do in order to say sensible (and most importantly useful) things about the processes on display inside them.

For all my big talk in part one, it’s becoming clear that we aren’t going to learn everything about mechanical-chemical feedback from this one little system. But we’ll know more than before. This step from big grand ideals to the final seemingly tiny achievements in concrete understanding is one of the hardest things about research. You always have to keep in mind why you started the project even while you are trying to understand very individual things in tiny detail.

With that in mind, let’s look at the tiny details!

At first glance, there doesn’t seem to be much shape change/deformation in my garnets. Inspection at low magnification shows that they haven’t been squeezed out of all recognition, in fact many of them show the same nice regular shape that they have had ever since they crystallised from the molten rock.

Appearances, however, can be deceiving. Under the microscope, some interesting features can be seen. Currently they are being referred to as inclusion trails, although there are other things in geology already referred to by this term, so we really ought to change it to prevent confusion. I shall present some images to show you what they are like, if you wish enlarged versions and a few extra comments, follow this link to my photo gallery.

What can we see? The most important thing to look for in any geological image is the scale. Our first picture is very zoomed out, that yellow bar is a whole millimetre! Now we know the scale, we can try and figure out what we’re looking at. This image is a microscope image of a thin section, a slice of rock 1/20 of a millimetre thick, thin enough that it is transparent to light shone through it from underneath. The whole thing is stuck to a glass microscope slide as it is obviously rather fragile otherwise! Don’t worry about that black splodge, that’s just some graphite paste on the underside of the glass plate which needs to be cleaned off.

The part of the image we are interested in is the garnet crystal itself, which is the slightly reddish-brown cracked looking stuff filling most of the image in the centre and left (this image is already zoomed in enough that you can’t fit a whole garnet into the field of view). At the far right edge of the garnet there’s a weird fragmented looking part, but that is just where during preparation of the thin section some of the material has broken away, leaving a hole through to the glass slide beneath. Several other small holes created during preparation of the sample can be spotted elsewhere in the garnet, like at the left had edge.

When we look at what’s happening inside the garnet we can straight away see that there are patches of different colours or shades. These patterns and shade changes are caused by those supremely tiny microinclusions that I previously introduced. At this scale the ‘trails’ are barely visible as a pair of very fine dotted black lines cutting diagonally SW-NE through the centre of the picture.

When we zoom in to 10 times higher magnification, we can see lots more. Note the scale in image 2 above! That yellow line now represents 0.1 millimetres (100 micrometres). Now the individual microinclusions are visible as tiny dots, and you can finally get a sense of just how tiny they are. What’s REALLY exciting though is that trail of (in comparison) HUGE inclusions going straight through the middle of the image. And either side of them there seems to be a thin pale band where the microinclusions are completely gone! Why is that? And why has it only happened in that area, and not in the bits next to it?

Well of course we don’t properly know, or I wouldn’t have a job. What we can infer (among other things) by firing electrons at the garnet is the orientation of the lines of atoms in the crystal, enough to see that near these trails the crystal structure is slightly bent. Aha! So these zones of coarser inclusions seem to a) have been made out of/ somehow used up the original tiny inclusions (otherwise we wouldn’t see a bleaching zone) and b) this change seems to be triggered in areas of the crystal where deformation is particularly strong.

The movement and recrystallisation of the tiny inclusions to form bigger ones is the chemical part of my chemical-physical interaction, and the deforming garnet is the mechanical part. It is clear that the way these trails form is intimately connected with deformation of the host crystal structure. So just by figuring out the specific mechanism that led to these strange patterns, I will be learning new things about chemical mechanical interaction and how it occurs.

But how on earth can we go from simply describing these inclusion trails to working out how they formed? There’s no magic probe-a-tron that will tell me ‘BEEP- These inclusions recrystallised because distortion of the garnet allowed diffusion to travel faster in these areas -BOOP’. There isn’t even a magic probe-a-tron that will tell me whether or not diffusion was the only process involved. Looking at the picture it looks like lots of tiny inclusions just decided to collect into fewer, bigger inclusions. But did they also suck up some additional elements from outside the garnet crystals, or maybe chemically react with the surrounding garnet crystal? The difference between inclusions that hop around and make friends in an uncaring lump of garnet and inclusions that move around while also exchanging elements with the garnet around them is pretty big, but you can’t tell the difference if you are looking at the final result using only a normal microscope.

So the best way to start working out what things are important to our process is to start asking some very basic questions, because otherwise all we are working with are assumptions. You can probably think of some good questions yourself, but here are a few examples:

Are the types of mineral we find in inclusion trails the same type and/or chemical composition as the tiny inclusions found nearby?

Does the size of inclusions or width of bleaching zone differ depending on what types of minerals are found as inclusions in different trails?

Does the size of inclusions or width of bleaching zone differ depending on the chemical composition of the garnet the trails are in?

Is there a relationship between amount of deformation and appearance or size of trails?

You will notice that almost all of these could easily be rephrased as testable hypotheses, e.g. “Hypothesis 1: The size of inclusions in the trail is different depending on the chemical composition of the garnet the trail is in.” At that point all the theorising has been done for the moment and to get any further you need to start answering a new set of practical ‘how?’ questions, such as “How do I make sure to only measure the composition of the garnet and not accidentally measure some tiny inclusions as well?” or “What do I even mean by amount of deformation??”

That’s how even initially simple questions can lead to months of work trying to solve some technical problem before you can even start collecting the data you think you need. Of course one of the problems you are having might actually turn out to be very informative in the long run...

So what I am doing now and for the foreseeable future is using a wide variety of analytical instruments to attempt to answer hypotheses such as the ones quoted above. Only once I’ve collected lots of data will I be able to start doing any theorising, working out things that must or cannot be true considering the answers I’ve found. Naturally there will be many unexpected things along the way that will throw up more, as yet unimagined questions...

So there you have it, an overview of why I’m doing my PhD, what I’m looking at, and some of things I want to know to start answering the big questions (although these big questions are very small compared to the stated goal . I hope those that have reached this far have a better understanding of my project, my samples and also the scientific approach to observing anything you don’t understand (start by describing what you see, then set hypotheses and test them).

I also hope that by doing this you understand just why my project is really interesting and rather fun, and that I will be able to share new developments with you and you will (at the very least) understand why they are exciting!

Happy hypothesis making!

Der Tom.

(Index)

(Part One)

(Part Two)

Making the samples, the natural way

Previously I explained the very big picture of my PhD. But if you want to study a process involving deformation and chemical reaction, you need to have samples in which both of those things have occurred! This post is all about what is in my samples and (as far as we know) how it came to be there. Once again remember that lots of this geological stuff is fascinating, but it is the background to my research, not the subject itself.

It’s time to reveal at my project title. Project III.1 is called ‘The physical and chemical behaviour of solid inclusions during recrystallisation of the host mineral’. Let’s look at some parts of it. ‘Physical and chemical behaviour’ should be obvious, all it’s saying is what I told you last time, that this PhD is about a certain process. We can ignore ‘during recrystallisation’ for now, that part is being more specific about what physical and chemical interaction is going on, and I’ll deal with it in part 3. The most important thing is that to study this ‘recrystallisation’ we are clearly going to need a sample with some ‘solid inclusions’ sitting inside a ‘host mineral’, that has then experienced chemical reaction and physical deformation at the same time.

My samples come from south-eastern Austria. They are garnet crystals. Garnets form large, symmetrical almost spherical crystals in many rocks. They have a reasonably simple chemical formula as minerals go (good for me!) and are also quite tough, not usually letting much in or out of them after they form. My garnets are unusual, because they crystallised straight from molten rock (or ‘magma’, hence why we call these ‘magmatic’ garnets). Most garnets grow gradually in metamorphic rocks, but metamorphism is slow and messy and it is rarely possible to understand everything that happened to a garnet or in what order, so these magmatic garnets are much better as a starting material for the experiment that nature is going to carry out for us. All natural samples have lots more unknown factors than experiments done in the lab, but we still try to choose samples that start out as simple as possible.

The magma that the garnets crystallised from wasn’t blasted out of a volcano, instead it sat underground in a nearly vertical sheet of rock called a ‘dyke’, cutting through the layering of older rocks around it. From radioactive dating, we know this all happened around 250 million years ago (that’s just under 4x as old as T-Rex, dino-fans). The magma in the dyke was of quite a rare composition. It is what is called a pegmatite, the last little bit of a granite to solidify. All the unusual elements that hate to sit in crystals are in this liquid, so some very unusual minerals can be found, made from elements like titanium, yttrium, phosphorous, boron, fluorine, chlorine and others.

These ‘unhappy’ elements that don’t fit so nicely into crystal structures are the key to making the next thing we require in our sample, the inclusions. When the garnets formed, they probably incorporated some of the elements mentioned above in various places in their crystal structure (crystal structure is the regular repeating 3D pattern of atoms that makes up a crystal, the simplest would be salt, with alternating Cl and Na in a cube structure). At high temperatures when atoms are wobbling around a lot, you can more easily wedge atoms of many different sizes into a crystal structure, but when the crystal cools it can be more stable to throw out the badly fitting atoms, which are more stable forming their own crystals in new minerals.

In my garnets, this process (called ‘exsolution’, which just means ‘unmixing’) means that after cooling instead of lovely clear garnet crystals, we end up with garnet crystals clouded with literally billions of extremely tiny ‘inclusions’ of other mineral types. So tiny are the inclusions that happened to form in these garnets that individual inclusions (less than 1/1000^th of a millimetre across) are impossible to see even in a microscope unless you use a really big magnification. Some pictures to illustrate this are here!

So we have a host mineral, filled with inclusions. Now all we need is to deform this host mineral (causing it to ‘recrystallise’) and reactions can happen involving the garnet host and the tiny inclusions. Then we’ll have our natural, deformed sample where we can try and pin down some hard facts about this feedback stuff!

The force that will take and deform our inclusion filled garnets sitting minding their own business in their pegmatite dykes is one that most will recognise: the Alps. 90 million years ago proto Italy was busy crashing into mainland Europe. This collision first caused the rocks in which our garnets sat to be forced deep under the earth’s surface, but by a fluke of interacting forces (that we still can’t 100% perfectly model), these rocks were squeezed out again (geologically) soon afterwards, a bit like toothpaste*.

All you really need to take from this is that the rocks in which our garnets sit were rather badly tortured during formation of the Alps, and that’s the cause of the deformation (remember, all I mean by that is distortion/shape change) in our samples. Deformation is good, because without deformation, we can’t study the chemical reactions and feedbacks that might have occurred during it!

So now we’ve made and squashed our samples, all that remains is to tell you about the structures that all this squashing and reacting produced. It’s my job to understand in great detail what controls the formation of these structures, so we can come to some general conclusions about the processes of mechanical deformation and chemical reaction in this special system.

Join me in part 3!

(Index)

* How do we know all this? New minerals can be formed during this process, which we can radioactively date. Some of the minerals only form if a rock is at extremely high pressure and temperature, they tell us how deep the rock went. Others formed later when the rock cooled down a bit, and the difference in times and the pressures that we think the minerals formed at can give us a rough estimate of how fast the rocks were moving upwards.

A process, not an area.

The first thing I want to explain is the very broad theme of my PhD, what the final goal is and what it is not. I want to start by talking about my research group, 10 PhD students who are all united by a common theme of study. That theme is ‘Deformation of geological materials’. What is the most important thing that we all have in common? ‘Geological materials’ is a pretty broad category. Into that category falls almost everything on and in the earth that isn’t currently alive or man-made! What unites us all is ‘deformation’, changing something’s form. We can do that in a number of ways, squashing, pulling, twisting, or a combination of all three, but the process, the way a particular material manages to deform, stays pretty much the same. The most important thing to remember about my PhD is that I am studying a process. While I am in fact studying actual rocks to do so, the most important goal is NOT to understand the geology of a specific area. If that happens, that’s great, but it isn’t the only or the ultimate goal.

So I’m trying to understand more about a process. What kind of process? Perhaps the subtitle of our research group will give us a clue. It reads: ‘Mechanical-chemical feedback and the coupling across scales’. That second part is really only there to remind you of the fact that geologists can study things as small as atoms or as big as continents, for much less than a second to much more than a billion years. Sometimes stuff we find out at one scale might be useful for studying another! The much more important part is the first bit, ‘mechanical-chemical feedback’. That’s the process we want to know more about, but it’s not very clear what we mean. ‘Mechanical’ and ‘chemical’ on their own make sense, and it is possible to see that they apply to rocks. Rocks can get squashed (mechanical) and they can take part in chemical reactions (chemical). When rocks get squashed and heated they can change their shape and, and the amount and type of minerals that they consist of. Rocks which have been changed by pressure and heat are metamorphic rocks, a name that you might have heard.

But why should there be ‘feedback’, why should these two separate things affect each other? Here we have to use some imagination. Imagine I have a cube of rock, which is made of a bunch of different minerals. I start to squash the rock (one kind of deformation). Just like some chemical reactions only happen after you reach a certain temperature (burning!), there are also reactions that only happen once you reach a certain pressure (for example the melting of ice when you press on it with the blade of an ice skate, allowing you to slide easily along). Imagine I press hard enough on the rock that a reaction happens. I don’t add or take away anything from the rock, but the mineral that is the product of the reaction won’t take up exactly the same amount of space, it will either be denser or less dense (different volume, same mass).

Imagine I make a reaction happen by squashing the rock cube. Let’s say the minerals I form take up more space than the minerals used up. That means they need to make space for themselves, by pushing outwards. They are pushing against the pressure from outside. That means that pressure on the rock is reduced. If the pressure goes down, the reaction can’t carry on (recall it needs a certain pressure to happen). So we have a negative feedback loop. The reaction stops itself!

If the product of the reaction takes up less space in the rock, less stuff is pushing outwards to resist the squashing, so the pressure inside the rock increases. That encourages even more of the product to form, which causes the pressure to increase... In that case you have a runaway reaction that would carry on until there was nothing more to react, positive feedback!

That does sound a bit complicated. You’ll be glad to know, geologists agree! We know a lot about how rocks behave when they get deformed and there are no chemical reactions, and we know a lot about chemical reactions in rocks when there is no deformation. Normally people studying a rock spend a long time proving that only one of the two processes happened, so they can understand it. Perhaps you see then why we need some PhD students to look at both at once!

Hopefully it’s clear by now that:

1) My PhD is about understanding a process, not the geological history of an area.

And:

2) The process I’m trying to understand is the way physical deformation and chemical reactions affect each other.

Onwards to part 2...

(Index)

So, what is it that you’re studying for your PhD then? (Index)

All PhD students hear this question a lot. In this series of posts, I am going to attempt to explain the ‘what?’ AND the ‘why?’ of my PhD, without using any complicated words I haven’t explained beforehand. I hope that if you stick around to the end you will understand what I am doing and why someone asked me to do it. More importantly however, I hope you will see that ‘doing research’ is an activity which can easily be understood by anybody, because everything that is done has to be logically justified. Scientists are not the white coated oracles of a mysterious god!

I start off with ‘why’, because there’s nothing worse than reading someone describing something that seems pointless!

Part 1: A process, not an area.

Part 2: Making the samples, the natural way

Part 3: Of recrystallisation and inclusion trails