Revealed: the chameleon's disguise

Who hasn't dreamed of having a chameleon as a pet? Just me? Oh, ok then. Anyway, I've never understood the the biology that allows them to change colour dependant on mood or surroundings, so I thought I'd do a little research... I discovered that chameleons have a transparent outer skin, below which there are 3 layers of specialised chromatophore cells with chemical pigments in their cytoplasm. In the top layer, the chromatophores used are known as xanthophores and erythrophores, which contain yellow and red pigments. The second layer contains iridophores and guanophores, which contain guanine and contain the blue/white pigments. The 3rd and deepest layer of chromatophores, known as melanophores, have a slightly different and all together more interesting function. They are the cells which control how much light is reflected back from these 3 layers, to adjust for light intensity. The intensity of the colours given off is determined by the distribution of pigment molecules within the cells- if these molecules are spread all over the cytoplasm, the colour given off is more vibrant. But the chameleon can also make these cells transparent by concentrating the pigment in the centre of the cell. The reptile is able to rapidly reallocate the pigment molecules, allowing the colours to shift wildly like a bad LSD trip. But why go to all this trouble to develop such a mechanism? Many believe that it is so chameleons can blend in with their environment, however for the majority of chameleons this is not the case. Most species use their colour change ability to signal to other chameleons their physiological condition and their emotions; for example they show darker colours when angry, to intimidate foes. The Namaqua chameleon species even uses the ability to help regulate its body temperature (homeostasis yo!), turing a light grey colour during the heat of the day to reflect infra red radiation from the scorching desert sun. As Adam Savage might say: MYTH BUSTED! Woa Woa Woa, hold your horses there! Why do chameleons bother with such a complicated mechanism, which could be almost entirely replaced by simple body language to portray emotions? Most of the animal kingdom uses body language for intraspecies communication. However I have a theory: because chameleons rely on an element of stealth and patience to catch prey and evade predation, they cannot afford superfluous motion which may give them away to other species. Therefore they use colour changes which not all predators/prey have the optic capability to see, in order to communicate. That is their ecological niche. It all fits rather well doesn't it? Although I can't prove this hypothesis without data...this isn't Philosophy! (joking).

Is evolution lazy?

I've always thought the motto of evolution and natural selection to be: 'If it ain't broke, don't fix it'. Take plants for example, their chlorophyll has a green pigment meaning it reflects all green light, and it can't be used in photosynthesis (plants only absorb 3% of light that hits their leaves). Why isn't the chlorophyll red, or yellow, or colour that excludes less light though? Well the explanation for that is simpler than you might expect; because during the trial and error phase of the chlorophyll development in evolution, green was probably tested, it worked well enough for plants up to a certain size to meet their sunlight absorption needs, so it was kept. The plants weren't exactly capable of testing the best pigment colours in a longitudinal study; once they found one that worked, they kept it, and 'if it ain't broke, don't fix it'. This may be the reason that plants don't have a central nervous system like animals do. For animals the CNS is vital, as we need brains capable of problem solving, fast impulse conduction from sensory organs via neurones, co-ordinated movements, and the ability to feel pain, in order to survive as omnivores, in finding food, remembering the best places to find said food, evading predation, reproducing and to find suitable habitats. Whereas plants can survive perfectly well using photosynthesis to produce sugars, relying on insects and the wind for pollination, and using plant growth chemicals like auxins to respond to environmental stimuli in like sunlight (phototropism) by promoting cell division or elongation, because plants don't have an endocrine system like animals do. But it's because they don't need one to survive, that they don't have one. Plants have never needed to evolve a CNS by natural selection to survive, as they can produce all they need as stationary entities, without the need for complex thought or electrical impulses, ergo they don't have a spinal cord or brain. Because 'if it ain't broke, don't fix it'...

I am Groot?

We've all seen the wonder of science fiction that is, Guardians of the Galaxy, right? Well it contains some outstanding scientific achievements, like a cybernetic and overly narcissistic racoon, a vacuum repelling face mask, a black hole grenade, space shuttles capable of time dilation and, what I found most fascinating, a sentient, mobile tree-like organism. That got me thinking, why are there no such life forms on this planet? What stopped plants from developing a CNS + receptors, and becoming as developed as we are? It may be an ambitious aim, but I'm going to try an find out why we are not Groot... so to speak.

Lets start at the beginning, with LUCA (Last Universal Common Ancestor), a bacteria-like organism that lived deep below the earths surface around geothermal hotspots. So it obviously didn't contain chloroplasts for photosynthesis, it in fact used chemiosis, the generation of ATP by the movement of hydrogen ions across a membrane, for its energy. It contained DNA and RNA, with a genetic code composed of 3 base codons, and 80s ribosomes like all eukaryotic life on earth today. Just by looking at the phylogenic tree of life, derived from ribosomal RNA sequence data, you can see that animals and plants only branched from each other relatively recently on the eukaryota arm of the tree. What caused this divide between plant cells and animal cells you may be asking? Well, what could have happened was that during the eukaryotic cell's evolution, it ingested a smaller prokaryotic cell via endocytosis, and the prokaryote just happened to contain the organelles required for photosynthesis. This new combination thrived and became an entirely new brach of our phylogenic history, the plants. They use a complex electron transport chain between 2 photosystems and photolysis to generate NADPH and ATP, which then goes on to produce glucose in a light independent reaction. Whereas animals get their glucose from what they consume, and their ATP is produced via the Krebs cycle and another electron transfer system.

There are definitely other factors that led to this separation, however the key principle to understand here is that plants and animals are fundamentally different organisms, with little overlap in their phenotypes at least. The mechanisms they use to produce ATP , are different enough to warrant such different forms for these organisms, developed through evolution, a topic I will discuss further in my next post...

The mechanism of bruising

Over the weekend, whilst I was being pelted by a firing squad of my friends with the dangerous, high velocity weapon that is a football, I asked myself 2 things. One, why do I play as a goalkeeper? Two, what causes the myriad bruises that bloom across my arms and legs in the aftermath of my exploits defending a string netting and metal frame from a rubber ball? Well, I discovered that the discolouration under the skin is caused by cells bursting open and spilling their contents; the organelles and everything else in the cytoplasm. This happens due to trauma induced premature autolysis- basically the force of the ball hitting my limbs, causes cells to digest their membranes with their own hydrolytic enzymes, in a process known as necrosis. Who knew such an everyday thing like bruising could be so interesting? However, I also discovered a second type of cell death, known as apoptosis. Apoptosis is altogether more natural and controlled carefully by the body, also known as programmed cell death (PCD). Apoptitic proteins target the mitochondria of cells, and can effect them in different ways, for example by the formation of membrane pores, or an increase in the permeability of the mitochondrial membrane, which in turn causes apoptotic effectors to leak out. Either way the mitochondria is destroyed, and the cell cannot respire aerobically, so it dies. There is also a pretty complicated process involving direct initiation of apoptotic mechanisms, and there are seemingly 2 rival theories: the Tumour Necrosis Factor model, and the First Apoptosis Signal model. Anyway, unlike necrosis, apoptosis produces cell fragments called apoptotic bodies that phagocytic white blood cells are able to engulf and quickly remove before the contents of the cell can spill out onto surrounding cells and cause damage. Pretty neat huh?  And in an average human adult, around 60 billion cells die each day due to PCD, which seems like a lot until you consider there are around 37 trillion cells in our body. How all these cells organise themselves into complex structures, and work together in near perfect unity, is part of the reason I never ceased to be amazed by the field of Biology.

The fantastic four

Before I launch lead long into the field of epigenetics, I would just like to explain what a stem cell is. The pluripotent stem cells, generally thought of as the gold standard of stem cells as they can become any cell type other than placental tissue, we can harvest from a blastocyst early in development. The inner cell mass, that would become the embryo later on, is removed from the trophoblast (the developing placenta) and specially cultured to form pluripotent Embryonic stem cells (ES cells). They may be difficult to produce, but these ES cells can divide an infinite number of times, and if you have the right culture conditions, you can make almost any cell type. For example ES cells can differentiate into autorhythmic cardiomyocytes that beat, if you can imitate the conditions of the heart in a culture.

Now onto the main course, the Japanese doctor-turned-geneticist Shinya Yamanaka. Yamanaka spent a huge amount of time and resources trying to identify the genes expressed in ES cells, which allow them divide infinitely and differentiate into almost any other cell, but which are silenced after the cell has differentiated. He started his investigation with a list of 24 genes, knowns as 'pluripotency genes', which were thought to be vital in ES cells.  Yamanaka tested combinations of these genes, to see if they would cause a differentiated cell to move back up Waddington's epigenetic landscape(picture on right) and become pluripotent again, a huge risk to take - putting his career on the line for scientific progress; that's what I call dedication. He tested the combinations of his 24 genes in mouse embryonic fibroblasts (connective tissue cells) (MEFs). These cells were taken from embryos, as the name implies, and Yamanaka was hopeful that they would retain some of their capacity to convert into early cell types in the right culture. However, the mice cells used were special, they contained an extra gene known as the neomycin resistance gene, giving the cells resistance to the normally deadly compound neomycin. The gene was inserted into the genome in a way that meant cells would only express it, and survive neomycin if they became pluripotent. When all 24 genes were inserted in vectors simultaneously, only a tiny fraction of cells became pluripotent and survived the neomycin. However, the winning combination, of only 4 genes in fact, was;Oct4, Sox2, Klf4 and c-Myc. These 4 genes allowed cells to survive neomycin poisoning, and even change their appearance to look like ES cells. Yamanaka christened his discovery 'induced pluripotent stem cells', and the 4 genes are forever known as the 'Yamanaka factors'. What I find most incredible about this breakthrough is, that despite the fact our cells contain around 20,000 genes, only 4 are required to produce a pluripotent cell. It just goes to show the immense power even individual genes wield within the human body...

Toadspawn: the making of a Biology legend

John Gurdon. Does that name mean anything to you? If it doesn't, and you call yourself a biologist, stop now. I saw a job vacancy at the local Tesco Metro. Anyway, John Gurdon is a legend in the world of biology. He started his research on the African clawed toad, Xenopus laevis, to determine whether tissue cells from an adult toad still contained all the genetic material they started with as a blastocyst, or whether they had 'lost' some of this DNA as the cells became more specialised. He did this using the SCNT process (Somatic Cell Nuclear Transfer for the uninitiated), where he transplanted a nucleus from a somatic cell of an adult toad into an enucleated egg cell, which is then given an electric shock, to stimulate mitosis, and the cells are transplanted into a surrogate mother. Gurdon then kept the resulting eggs in a suitably controlled environment. The nucleus from the adult toad somatic cell was relatively unsuccessful at producing tadpoles, however this was irrelevant. He had proved that, genes are not permanently lost during cell differentiation, they were just deactivated. Putting the nucleus in the right environment, like an egg cell, allowed the cell to move back up Waddington's landscape of differentiation and, if not entirely successfully, reactivate the genes required for blastocyst development. This means the cell was essentially made pluripotent, and whatever was 'silencing' the genes in a differentiated cell, was 'wiped off' in the enucleated egg's cytoplasm. Although he was oblivious to it at the time, Gurdon's work was the dawn of a new age for genetics. The age of Epigenetics.

To be continued... (the suspense though!)

Entropy: the chemistry of chaos

Entropy was an idea first conceived by Ludwig Boltzmann, an Austrian physicist credited as the father of statistical mathematics: which explains and predicts how the properties of atoms, like mass or charge, determine the physical properties of matter, like viscosity or diffusion rate. He called it the H-theorem (S=K logW - the inscription on his gravestone too interestingly), which basically boils down to the 2nd law of thermodynamics; the entropy of a closed system always tends towards a maximum. So the universe essentially wants to be as chaotic and disordered as possible, at least, that's how I understand it. That's why a dissolved substance remains in suspension I guess, because a liquid has more entropy than a solid, as it's particles are sort of random and can flow-they don't just vibrate around fixed points like in a solid, and the closest the dissolved solid can come to maximum entropy is being in an aqueous solution. That's all well and good, but how does that link to biology?, I don't hear anyone scream. Good question, and here's where entropy gets interesting (for me at least). 


As Erwin Schrödinger so eloquently put it, living creatures 'drink orderliness' from their environment. Take any tree-dwelling Arboreal Gecko for example, they eat insects, and those insects are broken down into their constituent elements by enzymes and acids etc in digestion, and mostly assimilated into the Gecko's flesh. In a world that tends toward disorder, these Gecko's are performing an amazing feat. A gecko may be an open system, with inputs and outputs, which means it does not violate the 2nd law of thermodynamics, which assumes a closed system, but what they actual do seems so obvious on the surface, but is still truly incredible if you open your eyes. They have bodies. These bodies are vessels for order, allowing the Geckos, or any other organism for that matter, to become more complex, without the disorder of the universe driving them backwards, and they expend a lot of energy doing so. So there you have it; never take your body for granted, as not only is it a biological wonder the like of which earth has never seen before, it is a rare piece of tranquility in the calamity that is the universe.