Back to blogging and bye bye research

Hello blog world, it’s been a while. My posts are going to change direction from now on as I have left research and am starting a PGCE. I finished my masters last September and have since worked a bit and travelled a bit. It’s been a great year, with not a lot of science, but it has given me time to reflect on my master’s year and why I decided to leave the research world… for now. Completing a masters was a really good experience and I would encourage anybody considering one to go for it (it’s tough, but worth it). But by the end of the year I’d decided that research wasn’t for me. This blog is a bit of an overview about two major problems I came across in scientific research which influenced my decision.

 breaking bad bryan cranston walter white aaron paul jesse pinkman GIFBad Science (thanks Ben (1))

I came across many examples of bad science when reading papers. I’m not going to use actual examples, mainly because this was last year and I’m not prepared to hunt through my old work, so I’m afraid you’ll have to just take my word for it, which you shouldn’t do, because that’s not good science (so maybe just stop reading now?). But here are some examples of bad research practice that I regularly came across:

  1. Conclusions would be drawn from data which didn’t relate to the results. Tenuous links were made and results were skewed to fit with hypotheses.
  2. Some experiments were simply designed badly. For example, basic requirements in an experiment, like controls and repeats (basics taught in year 7 science…) were often not evident.
  3. Using microscopic images to infer things that just weren’t there. One picture of a blurry neurone does not prove anything.
  4. Taking other papers work as given and not exploring how research was completed.

Ploughing through these papers and discussing them in journal clubs made me realise how important ‘good science’ is. But it is hard! I appreciate the inevitability of contrasting results or bizarre outcomes in science, it’s just what happens. That’s why it’s so important to not draw conclusions lightly, but encourage repeats or further experiments. However this does take time and money, which is not always on a scientist’s side. I can almost understand why research groups produce these kinds of papers. The culture in scientific research, both in industry and in universities, is designed around funding. You only have to read Ben Goldacre’s Bad Science(1) and Bad Pharma(2) for some examples of cases where results have been wrongly interpreted, or where research was rushed to meet funding body requirements. The competitiveness of research (often competing for limited funding) can lead to ill-thought out papers and possibly ill-thought out conclusions, which in turn can mislead future studies. It may even prevent progression in a whole area of science. I was lucky to be in a lab where we scrutinised everything in a paper, which meant we were very careful with the work we carried out ourselves. Yes, it was painstaking and led to long days troubleshooting experimental set ups, but it meant we could really trust what we did. However, even in my lab there was a pressure to produce results fast and in time scales that were just not realistic.

Women in Science

Having said all this, there are obviously some excellent researchers out there. I got to meet some of these people at ARUK’s conference in Manchester last year, where I was especially impressed with some of the woman scientists. But it made me realise there is still a long way to go before women in science have equal opportunities. This has already been extensively written about, but I’m going to explain a bit about my experience and perspective. I didn’t experience any sexism during my day-to-day life in research, nor have I spoken to anyone who has. That’s obviously not to say it doesn’t happen, however my experience of gender inequality is more to do with employability. A quick internet search came up with lots research in this area and repeatedly show that women really are disadvantaged when it comes to getting a job in STEM research(3).

One woman I spoke to said she found it nigh-on impossible to find a new post-doc position after having a baby. It was assumed that because of a gap in her publications, she was no longer a desirable post-doc choice as she had been out of science for a year. Now obviously this is just one perspective, but surely there is something inherently wrong when a highly qualified and intelligent woman struggles to find a position because of an assumed lack of up-to-date knowledge? The pressure to perform and have a large and up-to-date back catalogue of publications is a stress for anyone, but especially for women. Any sign of a gap in publications makes it much harder to get back into the profession. Leaving to have a family is not only a problem for women (although more likely to be). The instability of a research career can be a problem for anyone:

Short term contracts are another big problem in science, and not just for women. It is extremely hard to settle down in one place for more than a few years when projects are funded on time scales. Only after years of moving about does it become remotely possible to find a permanent position in a university. This is another reason why women in research struggle. Uprooting every few years is not the way that most people envisage bringing up a family.

This is not to say it is not possible for women. I really admire those women professors who have reached the top of their game and have made it work. Because from my position, it sure doesn’t seem easy to do. If any of you research wonder women are reading this, please let us into the secret!

I’m aware this has been a bit of a rant and perhaps slightly one-sided. Yet after speaking to many people in research, these views are widely shared and are some of the reasons I decided not to pursue a research career. Instead, I’m about to start a PGCE, to teach secondary school biology. Aside from the issues I have with research, I found that the part of my masters I enjoyed the most was outreach and communicating the joys of science to others. But going into a profession where I hope to inspire young women and men to consider a career in science, I am very keen for some of these issues to be addressed. What the answer is, I am not quite sure (another post maybe). Because getting people excited about science is only the first step, keeping them in science is another matter.

  1. Goldacre B. Bad Science. Tantor Media Inc; 2012.
  2. Goldacre B. Bad pharma. London: Fourth Estate; 2013.
  3. http://gender.stanford.edu/news/2014/why-does-john-get-stem-job-rather-jennifer
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A link between neurodegenerative diseases?

I have talked a lot about Alzheimer’s Disease and how we think it progresses as a neurodegenerative disease etc. This time I’m going to talk about another neurodegenerative disease – Parkinson’s disease. Like in Alzheimer’s, Parkinson’s Disease has worsening symptoms as it progresses because of increasing levels of neuronal damage. It is mainly a motor disorder where control over movement is lost.

Parkinson’s is also caused by the build-up of a misfolded protein called α-synuclein. This protein can stick (or aggregate) together to form build-ups called Lewy Bodies. In Alzheimer’s, Tau and amyloid β first build up in the hippocampus, causing memory loss. In a similar way, Lewy Bodies form in the substantia nigra, where they destroy dopamine signalling neurones required for controlling movement.

That’s a brief overview of Parkinson’s disease (aren’t my blog posts up beat?!), but what I really want to talk to you about is an interesting link between these two neurodegenerative diseases. In a surprising number of dementia cases, signs that are normally associated with Parkinson’s disease have been found. The presence of α-synuclein appears to occur alongside tau. Not only this, but it appears that the two proteins somehow interact to cause a more severe form of the disease. Structures in the brain are damaged more when both of the misfolded proteins are present. But, as per usual, this is about all that is known. There are some theories about how α-synuclein causes an increase in tau’s affects:
Tau normally helps to ‘stabilise’ structures called microtubules in our neurones. These microtubules act like trains to transport goods from one end of the cell to the other. In Alzheimer’s, the tau can no longer do this because of modifications to its structure, in part caused by a particular enzyme. A possible theory is that when α-synuclein is present, it activates this enzyme into further modifying tau, causing the ‘trains’ in our cells to stop transporting. As you might expect, if proteins aren’t reaching the areas of the cell where they are needed, there is going to be a nasty knock-on effect on how the neurone will function.

A project in our lab has recently shown that over-expressing both tau and α-synuclein in flies (poor flies) causes a larger change in the animal’s behaviour. Casey Morris, a PhD student in our lab, spent her undergrad project creating genetically modified cell lines expressing both Alzheimer’s related and Parkinson’s related proteins. The flies were put through all sorts of experiments to determine changes in their behaviour. Over 3 months, she monitored the flies and was able to calculate any differences in their average life span. She found that when both tau and α-synuclein were expressed in the brain, the life span of the flies was significantly decreased compared to when just tau was expressed. She also used a technique to monitor the climbing ability of the flies. If you tap a fly to the bottom of a tube, it pretty quickly runs back up. With age and in disease, this climbing ability decreases. When the two proteins acted together, the fly’s climbing ability decreased at a faster rate than with just tau alone.
These simple behavioural studies prove that when the protein normally associated with Parkinson’s disease is also present in the brain of someone with Alzheimer’s Disease (or some tested animals at least), causes more dramatic effects.

Parkinson’s like symptoms have been linked to Alzheimer’s disease and this mixed bunch of disrupted protein might provide a reason why. There has also been some cases where tau has accumulated in the neurons affected in Parkinson’s disease (in the substantia nigra), possibly another reason for the overlapping symptoms.

More work is needed to determine exactly how this worsening of symptoms is caused. The link leads us to interesting questions within the field of neurodegeneration. If you have a neurodegenerative disease, are you more prone to develop another? Are certain brains generally more susceptible to neurodegenerative disease or are they just unlucky random occurrences?

References

Substantia Nigra in Alzheimer’s disease: Burns, J., Galvin, J., Roe, C., Morris, J. and McKeel, D. (2005). The pathology of the substantia nigra in Alzheimer disease with extrapyramidal signs. Neurology, 64(8), pp.1397-1403.

α-synuclein in Alzheimer’s: Arai, Y., Yamazaki, M., Mori, O., Muramatsu, H., Asano, G. and Katayama, Y. (2001). α-Synuclein-positive structures in cases with sporadic Alzheimer’s disease: morphology and its relationship to tau aggregation. Brain Research, 888(2), pp.287-296.

Casey Morris PhD student, University of Southampton

Back to basics: DNA – deoxyribo-whaaat

I seem to have a big mix of people reading my blog which is exciting, but I’ve realised it means that some things I talk about might seem straightforward to more scientific readers but pretty confusing for the non-sciencey bunch (i.e. my science noob dad). I’m starting to realise this is one of the biggest difficulties in talking about science, so as well as the current research posts, I’m going to start doing some ‘back to basic’ blogs to help with some of the basic concepts which are fundamental for understanding how our body works.

The first one is going to be DNA (or deoxyribonucleic acid if you’re feeling fancy). As you know, DNA is the mole
cule that determines just about everything about us, from our hair colour to the things that are common to all living organisms like how we reproduce. But how does it do this? This post will try to unpick what it means when we say that DNA ‘codes’ for things and how this links in with genetics.

You’ve probably heard that our DNA is 99% the same as a plant’s DNA. That’s because most of it “codes” for proteins that carry out tasks in our cells that we’re not even aware are being done. It does this by encoding for proteins. When scientists talk about the proteins in our diet that turn us into muscle men, that’s just one tiny portion of the protein in our body. It is the small percentage our body needs that can’t be encoded for by our DNA. Proteins are required for virtually all functions in our cells. I could do hundreds of blogs on proteins, so will leave it at that for now – all we need to remember for this post is that proteins are at the heart of just about everything that happens in our bodies.

Structure
DNA is made up of two strands which wrap together to form the famous double helix. These strands contain 3 main parts – phosphate groups, forming the backbone

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DNA structure (Image created by Madeleine Price Ball)

of the strands, bases which do the all-important coding (I’ll explain this in a minute) and deoxyribose sugar groups that join the base and the backbone together.

There are four types of bases – adenine, thymine, cytosine and guanine, or A, T, C and G. These pair up with each other to join two strands together to form the double helix.
Each strand is ‘complementary’ to the other, meaning they pair up neatly. A can only join to T while C can only join to G. The order in which these bases appear determines what that particular strand of DNA encodes for.

How does this code fit into genes and chromosomes?
DNA is found in every cell, coiled up into chromosomes. As you probably know, there are 23 pairs of chromosomes (so 46 all together) in humans. Each is made up of around 2000 genes and because there are two copies of each chromosome, there are two copies of every single gene (there is one long strand of DNA in each chromosome and sections of this strand make up the genes – the picture shows this a bit more clearly). I’ll talk in a future post about how these genes are inherited and why certain genes are expressed rather than others.

Now, every cell has the identical full set of chromosomes, but not every cell needs all the DNA to code for every single protein all the time. For example, you don’t need the DNA for the pigment that causes a specific eye colour to be expressed in your big toe. Whole genes (i.e. – whole segments of DNA) are either switched on or off. These switches are controlled by a set of proteins called ‘transcription factors’ – the regulators of DNA expression.

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DNA to chromosome (from BBC Bitesize)

DNA to protein
So how does DNA ‘code’ for a protein? DNA is found in the nucleus, whereas proteins are generally required in the rest of the cell – the cytoplasm. The problem is, DNA is too big and bulky to get out of the nucleus to code for proteins directly. That is one of the reasons why there is a step in between. This is where the molecule RNA, or ribonucleic acid, comes in. RNA is very like DNA, but with a couple of differences. For example RNA only has a single strand and uses ribose sugars rather than deoxyribose sugars to bond the bases to the backbone.

So when a certain protein is required, transcription factors (mentioned above) activate the DNA in a specific gene. This DNA undergoes a process called ‘transcription’ – the formation of a new strand of RNA, using the DNA as a template. The RNA contains the exact ‘complimentary’ sequence to DNA. So for example if the DNA sequence was CTGGTC, then the corresponding RNA would be GACCAG (remember how the bases match up). But chromosomes have anywhere between 50,000,000 to 300,000,000 base pairs each, so the strand being sequenced would be a lot longer than 6 letters!

So that’s transcription – the conversion of DNA to RNA in the nucleus of cells. This RNA is smaller and more transportable, so it then moves out of the nucleus through nuclear pores into the cytoplasm, where it can finally start making proteins.

The conversion of RNA to protein is called ‘translation’ – you can think of it as being converted into a whole new ‘language’. This process occurs on a piece of machinery called the ribosome. The ribosome feeds the RNA strand through its ‘reading apparatus’ and ‘reads’ the code. The ribosome can then recruit the correct amino acids required, depending on what it has read on the RNA. Every three bases code for a particular amino acid, depending on the order that they appear. For example, AGT codes for serine while AGA codes for arginine. These 3 letter codes are called codons. As there are only 20 biological amino acids used to make up all proteins, but 64 possible codons (different combinations of the 4 bases to produce a 3 letter code), there is more than one codon that can code for a particular amino acid. And not all 64 codons actually code for an amino acid, some code for a ‘stop’, which signals to the ribosome that the amino acid strand is complete.

Once the amino acid strand has been made, it is transported to various other structures in the cell to be processed into a correctly folded and complete protein.

Things can go wrong at any stage of the process I’ve just described. It requires so many things to go right that it’s not surprising that problems occur from time to time. For example, cancer is often caused by mutated genes, i.e. – mutated DNA sequences. UV light or carcinogens may cause a base pair to be deleted or swapped for another, causing a whole different amino acid to be coded for. Luckily, as you may have realised, our bodies are extremely clever and well adapted to deal with these problems. There are various repair mechanisms to ensure that mutated DNA doesn’t produce misfolded proteins. Often, it is only when these repair mechanisms themselves are mutated that disease occur.

So hopefully, if you’ve made it to the end of this long post, you understand why DNA is so important. It’s quite hard to get your head around how complicated all these tiny processes are. Plus they’re taking place every second in all the billions of cells in your body.

Alzheimer’s Disease – taking over the brain

My first blog was about a transmissible form of cancer in dogs, Tasmanian devils and clams (Transmissible Cancer). This time I’m going to explain about the transmission of Alzheimer’s Disease but don’t worry, I don’t mean the transmission between people, that can’t happen. I mean the progression and spread of the disease to different parts of the brain. In my last post (Alzheimer’s Disease), I talked about the basic pathology of the disease and how it is thought the build-up of misfolded proteins (tau and amyloid β) cause the nasty memory loss symptoms. This build-up first occurs in areas important for short-term learning and memory, thinking and planning, namely the hippocampus, and it often happens before any symptoms are detected. In mild Alzheimer’s Disease, the damage spreads to other regions of the brain including areas important for spatial awareness and speech. In late stages of the disease, the pathology can be found in many areas. The associated cell death causes significant shrinkage in brain size.

But how do these misfolded proteins spread? Well… this has puzzled scientists for a while. Recently, I went to an Alzheimer’s Research UK day with really interesting talks from top researchers in this area. Dr Amy Pooler, who worked at King’s College London, explained about some of her research into how tau protein ‘jumps’ between neurons.

As you might already know, neurons signal to each other using chemicals called neurotransmitters, which are released from the end of one neuron, pass across a tiny gap (called a synapse) and are taken up by specific receptors on another neurone. Dr Pooler and her colleagues found that tau is released from neurons when they signal to each other. This tau is then somehow taken up by other cells. They discovered this when they stopped one neuron’s ability to produce its own tau. They then stimulated a signal from another neuron and found that, lo and behold, the first neuron contained tau even though it couldn’t produce its own. The mechanism is still unclear, but it does seem that the transmission of tau requires a functioning synapse. This might not seem significant, but it proves that a functioning neural connection is required for the disease to spread and it is not simply cell death and the bursting of cells. This is an important finding as it gets us one step closer to understanding how the pathology spreads to other brain regions.

However, this isn’t the full story. Professor Goedert from the University of Cambridge hypothesises that the spread is ‘prion like’. Let me explain what that means: a prion is basically an infectious protein. When an abnormal protein moves from one cell to another cell, the abnormal protein becomes the dominant force in the new cell. It seems to take over the normal version of the same protein, disrupting normal cell processes. There are still a lot of unknowns about why this happens. Is normal protein being converted into abnormal, or is abnormal protein being produced from scratch?

image
The dark purple clumps are tau tangles, in the brain of a patient with Alzheimer’s Disease.(By Patho – own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=20016547 )

We already know about prion neurodegenerative diseases like Kuru and Creutzfeldt-Jakob disease which are ‘transmissible’ through the brain. Prof Goedert suspects that Alzheimer’s Disease and abnormal, bad tau spreads like this too (remember normal tau is still required for proper neuronal signalling, it’s the abnormal tau that is so destructive). He backed up this theory by injecting a misfolded tau protein into a mouse. It was found that the mouse began to develop tau pathology of its own in the injected brain region. Not only this, but over time the disease pathology spread to other parts of the brain. More needs to be learned about how this process occurs, but cracking the mechanisms could provide a great area for new treatments. Being able to stop the spread of the disease early on could mean vital areas of the brain are saved.

As per usual with most biology, the bottom line is that nobody knowwwwsss – yet! People have good ideas about the spread of Alzheimer’s around the brain, but a lot more firm evidence is required before we can understand how, why and where this happens. And also why only certain neurones are affected. But maybe I’ll leave that for the next post!

Alzheimer’s Disease

Alzheimer’s disease is a horrible, degenerative disease of the brain where neurones become dysfunctional and eventually die. The biggest risk factor for the disease is clearly age – nearly half of everyone over 85 has Alzheimer’s and your risk increases greatly after the age of 65. People still don’t really understand why age is such a big factor, but I think that cracking this could reveal a whole range of new treatments.
Age isn’t the only risk factor. In a genetic, inherited form of the disease, symptoms can appear as early as 30.

In this post I’m going to try and explain some of the changes that occur at a cellular level in the brain when Alzheimer’s Disease is present. But you’ll realise that largely, the real cause of the changes that occur in the brain have only been guessed at.

The first sign of the disease is the presence of two abnormal proteins aggregating. Monomers (individual molecules) of a protein called Amyloid beta bind together to form larger oligomers and eventually aggregate into plaques in the extracellular space (outside of the neurones). It is not known what amyloid beta’s normal function in the body is, but plaques are a common pathological marker for AD.
The other protein is tau and is what our lab mainly focusses on. Normally, tau is found bound to microtubules – the structures in cells involved in transport. Microtubules act as a kind of conveyer belt, transporting proteins from one end of the cell to the other. This is especially important in long neurones where the cell body (where proteins are generally made) could be meters away from the synapses (where most of the signalling occurs). Tau stabilizes these microtubule structures to allow for normal axonal transport – the transportation of proteins along the cell. In Alzheimer’s disease, the protein is modified and can no longer perform this function, meaning transport is disrupted and neurones can no longer properly signal. Tau also aggregates, but into ‘tangles’ inside the cell.

The disruption of normal cellular function – probably because of these two proteins causing trouble – can eventually lead to cell death and the grim symptoms that come with Alzheimer’s disease.
An example of a group of drugs on the market for treatment at the moment are ‘cholinesterase inhibitors’. They work by increasing the levels of signalling between neurones.
Another novel drug, undergoing clinical trials at the moment (which was also researched in our lab) works by re-stabilizing the microtubules to try and re-establish axonal transport.

Although current treatments are semi-successful at reducing symptoms, there is still an urgent need for a cure, especially with the rising older population. This is not a simple task, seeing as we still don’t have a deep understanding of the exact causes of the disease.
But this isn’t the only issue: it is now believed that pathological signs of the disease may actually appear up to 20 years before any symptoms even arise. This adds another level of complexity to curing the disease as it would require identification of changes in the brain when a seemingly healthy person is quite young.

Research groups around the world are working hard towards the common goal of finding a cure, but first the mysteries of what exactly causes this disease, as well as early risk factor markers, must be fully uncovered!

I wrote this post, then found a video, so just watch this if you can’t be bothered to read, it’s very good:

 

Flying Around

When I tell people about the research we’re doing in my lab, everyone’s first question is always how do you give flies Alzheimer’s disease? Followed by how can you find out anything useful from a fly? They’re both valid questions which I didn’t understand for a long time, so I’ll try and briefly explain the answers here.

The answer to the first question – how do you give flies Alzheimer’s disease – is that actually, you can’t. There is no one cause of Alzheimer’s disease. It appears to be caused by multiple cell mishaps which I’ll talk about in another post. This complexity and the fact it isn’t completely understood means you can’t replicate the full disease in any model. But you can replicate certain features. By over-expressing or under-expressing certain genes in the fly, you can induce changes in the ‘phenotype’ i.e.- a behavioural or physiological change (or both). Not only that, it is also possible to express human versions of genes (in true ‘Cramps’ style) in the fly to give a more accurate depiction of what happens in the human disease.

You don’t often associate flies as having behavioural traits like learning and memory, but actually they do. Flies are capable of long term and short term memory which has found to be altered with age, just like in humans. Now obviously, humans have a much more sophisticated and complex neuroanatomy to allow more complex memories, but the underlying basic circuitry in the brain is very similar between us and the flies. This means we can train them to remember and we can track differences in the animals with Alzheimer’s like symptoms. We can use cheap and simple experiments to measure these behaviours. For example, my work uses an experiment where we teach the flies to evade their normal response to go towards light. We can train them to associate light with a chemical called quinine which they don’t like the taste of. Later on, we can then assess whether they have remembered to associate light with something they would normally avoid.

There are many other behavioural experiments to examine changes in flies with different genotypes, but there is also biochemical data that can be found. For example, you can look at fly brains under the microscope and image certain neuronal tracts using fluorescent staining. This is a pretty cool technique and lets you see changes that occur to neurons in Alzheimer’s brains. Not only this, but you can also use live larvae to image axonal transport (transport of molecules up and down neurones). Because fly larvae have clear cuticles, you can see right into their bodies and when a fluorescent dye is added, you can actually video the neurones doing their thing!

Now you may still be wondering why you would choose a fly to do these assays, but there is a very straight forward answer – flies are cheap and much easier to look after. Plus you can get very convincing results with a large number of flies very quickly. A fly also has a maximum lifespan of about 3 months meaning that experiments involved in ageing (a very important factor in Alzheimer’s research) can be done easily. A mouse, for example, has a lifespan of a couple of years so ageing experiments are much harder and more expensive.

So yeah, flies are pretty good for lots of reasons. Just not when they eat your fruit.

 

 

Transmissible Cancer.. a scary thought!

First blog post – exciting!

Last week I went to a seminar about transmissible cancer.. yes, it is a thing..

In virtually all human cases of cancer, the disease is not transmissible from person to person. The cancer’s cell line dies off when the host dies. But in some rare circumstances in the animal kingdom, cancers can spread from one host to another. There are three separate cases of transmissible cancer known – in dogs, Tasmanian devils and clams, it’s an odd mix but they’re the only 3 known species where this occurs. Dogs transmit the cancer through sex while Tasmanian devils transmit the cancer through biting and it is thought that clams transmit the cancer through diffusion of cells in water.

The talk was by Dr Elizabeth Murchison from the University of Cambridge. She mainly talked about her work on the canine form of transmissible cancer – CTVT.

CTVT is found all around the world, but, get this – through genetic studies it has been shown that every single case of the cancer, wherever it is from in the world, originated from one single dog! Using fluorescent tags to mark certain genes in chromosomes, Dr Murchison and her team showed that the cancer’s genomes were almost identical from tumours found on opposite sides of the world. And that’s not the only thing they found.

 

 

 

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CTVT cells taken from a dog during a biopsy. Photo by Joel Mills

 

Looking at the genetic variation found in the DNA of the cancer, they even managed to sketch what the dog might have looked like. Also by counting and tracking the mutations in the DNA, a rough estimate of the age of the dog has also been made. It is thought this founder dog was around 11,000 years ago -that’s quite old for one cancer cell line to survive!

So the question that a lot of people are thinking is why this obviously very successful transmissible form of cancer isn’t found in more animals and how likely is it to develop in humans? Well the answer isn’t exactly clear, but our immune systems are always underestimated in their ability to prevent the body from catching all sorts of diseases. There are also not actually many opportunities where a cancer can be transplanted into another organism. It would require the exchange of cancer cells between individuals which in theory is possible, but very unlikely.