The hardiest bear that never was

Just over a month ago I visited the American Museum of Natural History in New York City. There I was fascinated with the phylogenetically accurate layout of fossils over the museum floorspace, showing the evolution of fish to amphibians, and then to reptiles (no Tiktaalik unfortunately) for example. During my visit I was also enraptured by an exhibition entitled; Life at the limits: Stories of Amazing Species, as one particular species stood out to me as the star of the survival show.
What if I told you there is a species of 'bear' that has existed on earth since the Cambrian period, around 500 million years ago? The word delusional would most probably spring to your mind, however I have evidence from the fossil record. Perhaps the word 'bear' was disconcerting, as I did not mean a member of the Ursidae family, but in fact a species known as the Tardigrade (me and my science word plays...). The Tardigrades have nicknames such as Water Bears or Moss Piglets, perhaps due to physical appearance (I don't see it personally, but they are kinda pudgy) and their favoured habitats; films of water that cling to mosses. Tardigrades are a large group of animals, consisting of 1,150 species, that includes some of the toughest creatures in the world. They can be found the world over; from the Himalayas 20,000 ft above sea level, to the deep sea 13,000 ft below sea level, even in the polar regions and on the equator, where the environment is hardly accommodating. Although I wouldn't hold out any hope of seeing one with the naked eye, as most individuals range from 0.3 to 0.5mm long. The Natural History Museum exhibit depicted the survival abilities of these organisms as a cycle, which I thought worked rater effectively. First, when their surroundings become intolerable, certain species of Tardigrade are able to deflate, draw in their legs and coat themselves in a waxy substance. The resulting structure is called a tun, and is barrel-like in shape with the creature's claws protruding from it. In this state tardigrades are capable of reversibly suspending their metabolism in cryptobiosis, and many members of the species can regularly survive in this state for up to 10 years. At extremely low temperatures, the Water Bear's body can go from 85% water to just 3%, ensuring they are not ripped apart by the water in their bodies expanding during freezing. When re-hydrated, it can take as little as 4 minutes for the animal to bounce back from its near-death state. Natural selection has seemingly thought of every extreme environmental condition on earth; the harshest pressure (they can survive in close to vacuums), temperature, radiation (5,000gy of gamma rays compared to the lethal dose of 5-10gy for humans), dehydration and environmental toxins. Certain species can even survive in outer space! (slight sensationalism), and in my view they truly earn their title of extremophiles. Science has so much to learn from such a tiny animal, particularly the proteins they produce to protect their cells from apoptosis during dehydration. (this seems to be a theme of my blog now), and even if humankind never make inter-planetary colonisation a reality, the Tardigrade is an excellent candidate to be our intergalactic envoy.

Pleasure, Psychoactives and a Basement...

This is a post I've been meaning to write for quite a while, but other exciting biological concepts got in the way. Story of this blog. The title is perhaps misleading, as it implies some kind of lugubrious activity, however the topic at hand is rather removed from such criminality, at least I hope. The lecture was titled; Pleasure, Novel Psychoactives  and the Brain's Basement (see, I wasn't lying about the basement) and was lead by Professor Gaetano Di Chiara of the University of Cagliari's Pharmacology department. The main body of the lecture revolved around the brain's response to psychoactive drugs, and the various experimental methods used to investigate the mechanisms behind the response. Professor Di Chiara was clearly passionate about his field of study, and so he went through the slides of the presentation at an astounding rate. This, combined with his somewhat broken English lead to my notes becoming rather scant at times, but despite this I would like to share what I was able to glean. Firstly, the definition of pleasure used by the Professor and his team; incentive to seek and accept biological incentives (food rewards for example). There are 2 distinctions of pleasure; Appetitive, which is preparatory and so comes from learned stimuli, and Consummatory, which is caused by proximal stimuli, and is unconditioned. The neurotransmitter Dopamine is widely believed to be responsible for the pleasure response of the brain, and is therefore connected to rewarding stimuli, which often aid in the survival of a species (feeding, reproduction etc). Addictive drugs also trigger dopamine release, as when a micro-dialysis tube is used to measure neurotransmission in the ventral striatum of the brain, psychoactive drugs produce a lasting spike in dopamine levels.  These ventral areas, around the amygdala of the brain, are phylogenetically the older areas of the mammalian brain, and are therefore referred to as the brain basement (just to clarify the lecture title). One fact that is, according to the lecture, contentious within the scientific community, or was contentious about 10 years ago, when most of this research was conducted, but also the last time Professor Di Chiara kept up with developments in this area of study (burn) (He referred to the archistriatum of the brain, which only exist in birds and are now called the Arcopallium; it's homologus to the amygdala im mammals essentially) is whether the biological function of dopamine is purely pleasure, or whether it has a motivatory function in survival of organisms. Rats are often the subjects of addiction experiments, and the Master/Yolked experimental paradigms are no different. The 'Master' rats were in a set-up which allowed them to actively expose themselves to the drug heroin, whereas the 'Yolked' (not quite sure about that nomenclature there) rats were passively being administered the drug. It was observed that Master rats experienced a greater dopamine output  in the shell of the nucleus accumbens (part of the ventral striatum), which is involved in the cognitive processing of wanting as well as reward and reinforcement effects. On the other hand the Yolked rats' response non-contingent drug exposure (I hope that's a thing) saw a a smaller increase in dopamine output in the core of the nucleus accumbens, dealing with new motor programs which facilitate the acquisition of a given reward in the future. This suggests that the master rats experienced a heightened euphoria on drug exposure, but why is this? I hear you mumble sleepily... I'm so glad you asked. The fact that the master rat group were self administering the drug was the key, as they were able to predict and therefore better cope with the side effects of the drug, something the passively drugged yolked rats were unable to do, thus prolonging the heroin high. The master rats would eventually have the conditioned stimulus of administering the drug completely replace the primary stimulus of the heroin itself. The drug essentially triggers no dopamine release, and so the IV self-administration becomes the main source, as the user has habituated to the drug. By extension of this paradigm researchers were able to link drugs of abuse with increased extracellular dopamine secretion in the accumbens shell particularly, clearly displaying dopamine's ability to promote expression of incentive-based motivation, in a Pavlovian manner. In my mind I have ended the debate; dopamine is a biological motivation tool, which can all too easily lead to dependance on unsavoury activities to achieve a pleasure sensation. So please, put the needle down...

More powerful than Aquaman? Impossible.

Fancy seeing me here, on my own blog... Anyway, of late I have been enraptured by the Reckoners series of novels by a hero of mine, Brandon Sanderson. The series thus far tells of ordinary humans being transformed into super-humans, with an immense spectrum of powers, by a deity/celestial body known as Calamity. In the Reckoners universe such super-humans are known as Epics, and their powers corrupt them to such a degree that they have fractured society and created a nightmarish dystopia. This got me thinking, if Epics had dominion over ultra-specific biological processes, would they be stronger than the fictional  superheroes we have bombarded at our retinas every time we go to the cinema? Thor may have Mjolnir, and Bruce Banner may be able to turn into a green thug when his heart rate spikes, but those powers have nothing over the total control of AXOPLASMIC STREAMING (long context is very long). Axoplasmic streaming is the process responsible for the movement of proteins, lipids, mitochondria and other organelles to and from the cell body of a neurone. An example of when this mechanism is relevant is in the synthesis of neurotransmitters and synaptic vesicles in the cell body of motor or sensory neurones, which must then be transported to the synaptic knob (eloquent I know) for the propagation of action potentials across the synaptic cleft. Microtubules, much akin to those that construct the cytoskeleton in your average Joe body cell (all cells are amazing I merely jest), made of the globular subunit tubulin, create the pathways for movement along the axon to the synapse, and 2 vital motor proteins; dynein and kinesin, are used as haulage vehicles for everything synthesised by the Nissl's granules in neuronal cell bodies. The speed of axoplasmic streaming is variable, something I found particularly interesting with regard to my super-human powers investigation. The speed is dependant on the cargo of the motor proteins, with vesicular cargo moving far faster at up to 400mm/day, than other proteins; for example cytoskeleton proteins move as slow as 8mm/day. To clarify, the Epic with this power over Axoplasmic streaming would not manipulate his/her own process.  That would have no biological benefits as the mechanism has been optimised by millions of years of evolution. The Epic would manipulate the streaming in other people, making it a weapon of sorts. By slowing down the streaming of synaptic vesicles and the neurotransmitters within them along the axon to the synaptic knob, less neurotransmitter (acetylcholine for example) would be available for release into the synaptic cleft when an impulse reaches the pre-synaptic membrane, essentially halting the progress of the action potential, due to the reduced permeability of the post synaptic membrane to sodium and potassium ions (acetylcholine binding there increases permeability to ions). This would  create a kind of rapidly induced accommodation effect in the neurone, causing paralysis of muscles comparable to that induced by the botulinum toxin, which inhibits the binding of acetylcholine. So my hypothetical Epic power would allow the wielder to kill a person with spectacular efficacy, just by having dominion over one relatively esoteric, yet vital biological process. In fact, if the wielder could create a wave of axoplasmic manipulation, they could kill in vast volumes over a minuscule time period. Who needs a high-tech suit or the powers of a Norse God, when you can disrupt the highly complex interplay of biological molecules in the nervous system? This Biologist certainly doesn't (therein lies my bias...).

Steve the telomere

Hello fellow biologists and apparently Zach too! I'm back after what seems like an eternal sabbatical, and it must have seemed longer for you guys, because I know how much you love reading my random and often overly opinionated thoughts on biological processes. Doing 4 A-levels is tough ok, and the majority of the school Biology syllabus is so dull. More epidemiology or epigenetic mechanisms are required please Edexcel. Anyways, today I'm going to tell you guys a story, with a biological twist. Once upon a time, in a nucleus far, far away there lived a chromosome. This chromosome was young and healthy, no mutations or replication errors, just enjoying life in the nucleolus, surrounded by friendly histones and its other chromosomal buddies. But what keeps our young chromosome friend mutation free? you may ask. Telomeres, my dear Wattson (I know that doesn't work, just humor me). Telomeres are areas of repeated nucleotide sequences, TTAGGG repeated 2,500 times in humans, at the the end of each chromatid on a chromosome, which protect the chromosome from potential mutations, as well as stopping neighboring chromosomes or fragments from randomly fusing with each other (they're such a friendly bunch). Due to the nature of semi-conservative DNA replication in eukaryotic organisms, the ends of the chromatids cannot be copied by DNA polymerase, and so instead of the base sequence being ruined by this flaw in our DNA replication mechanism, the telomeres are there to valiantly defend the chromosome from damage. I may be romanticising slightly here, but I can't stress enough how valuable telomeres are to our genome. After 'taking one for the team' so to speak, an enzyme called telomerase, a reverse transcriptase kind of enzyme, synthesises new repeating sequences to replenish the telomere 'cap' on the chromatids, so they can continue to protect the chromosome from damage. At this point you would be forgiven for thinking that, if we could maintain the telomeres in our multipotent bone marrow (hematopoietic if you're a sucker for the biological terminology like me) stem cells for example, we could extend our lifespans. But actually, telomere shortening in cellular senescence (biological word for aging) is an essential process in the reduction of cancer risk, we think. Telomere shortening in humans can induce replicative senescence, a mechanism which prevents instability within our genetic material and thus the development of cancer in the older body cells produced, by limiting the number of cell divisions they can undergo before apoptosis. However, shortened telomeres can also impair the immune system, and that might increase cancer susceptibility. The telomere shortening process is the very definition of a double edged sword, as it may protect our most vital genetic information from the corruption of cancer, but it is also the root of just about every age-related disease you can think of. So next time you're having an existential crisis about your place in the universe, remember that Steve the telomere has always got your back.

The biological supercomputer? (The Brain A-level notes)

The human brain:

• Brain is part of the CNS-information processed and coordinated response results.
• Spinal chord (CNS) contains grey matter; made up of neurone cell bodies, and white matter; made up of nerve fibres. 
• Brain has 3 distinct areas: forebrain (olfactory lobes+cerebral hemispheres), midbrain (optic lobes) and hindbrain (cerebellum+medulla).
• In vertebrate embryos: anterior end of tube swells and folds back on itself forming a brain. 
• Cerebral cortex folded back over the entire brain. 
• Human brain contains around one hundred thousand million neurones, each synaspsed to 10,000 other neurones-complex. 

Cerebral hemispheres: 

• Higher functions of brain; learning, feeling emotions, thought.
• Grey matter-nerve cell bodies, dendrites and synapses. 
• Deeply folded to give larger surface area. 
• Corpus callosum: band of axons (white matter) connecting hemispheres. 
• Frontal lobe: emotion, reasoning, personality. Idea+association development. Contains primary motor cortex involved in control of body movements via motor neurones in spinal chord. 
• Temporal lobe: auditory information, memory. 
• Occipital lobe: visual information (input from optic nerves). 
• Parietal lobe: varied functions; recognition, calculation, movement, sensation, spatial orientation. 

Other areas of the brain:

• Hypothalamus: coordinates autonomic nervous system, thermoregulation, monitors chemistry of blood (hormones from pituitary glands) and basic feelings; hunger, aggression, reproduction. 
• Cerebellum: coordinates smooth muscle movements, uses info from muscles+ears for balance.
• Medulla oblongata: primitive, contains reflex centres controlling heart rate, peristalsis etc. Maintains basic life responses even if higher areas destroyed. 

Animal studies:

• Removing/damaging areas of the brain (cerebral hemispheres) of an animal to observe effect on behaviour. 
• Implanting electrodes and artificially stimulating areas of the brain to see behaviour change.
• Normal behaviour compared with post mortem changes to brain. 
• Anthropomorphism is a problem.

Reptiles and facultative parthenogenesis

If you understand the title of this post, you have my undying respect. Most people wrongly assume  that asexual reproduction only occurs in prokaryotes and plants, by binary fission or runners for example, however animals can also reproduce in this manner, and not via divine impregnation. Seriously, if you are a devout catholic I suggest you leave this page and maybe read the Bible instead. In parthenogenesis an embryo develops from an unfertilised egg and the process occurs perfectly naturally in invertebrates like scorpions, and also in a select few vertebrates, like the Komodo Dragon (yes, it deserves capital letters). A normal egg cell produced by meiosis has the haploid number of chromosomes, as the other half of the offspring's genome is made up by the father's haploid sperm cell. However in parthenogenesis such haploid individuals are non-viable (may die during embryonic development or have a low zygote hybrid vigour) , and the parthenogenic offspring must often be diploid. Therefore full clones produced by parthenogenesis develop without the need for meiosis to manufacture haploid gametes in parents. But how is an embryo produced without without fertilisation? I hear you scream. Well, a mature egg cell is produced from mitotic oogenesis, which then develops directly into an embryo. This process is known as apomitic parthenogenesis, and is the less complex branch of the phenomenon. When parthenogenesis does occur with meiosis, offspring may be haploid, like the male ant, however there is often a complicated chain of processes which occur to restore diploidy to the offspring, in order to make them viable. However these offspring are only half clones of the parent organism, so they are genetically in-identical. But what I really want to talk about are the facultatively parthenogenic Komodo Dragons, which usually reproduce sexually, but can occasionally reproduce asexually. Therefore, when no viable males are present in a habitat, a female can ensure the survival of the species via parthenogenesis, making them more resistant to extinction than most species. What I particularly like about the Komodo Dragon, apart from its totally awesome name, is its ZW-sex determination, in which ZZ genotypes create males, ZW creates females, and in rare cases the WW genotype creates a female, however it is mostly unviable. Komodo Dragons are just too awesome for the XY sex determination system, although that may be a rather subjective analysis. In conclusion, the fact that an intelligent organism can clone itself in a pinch, to ensure the continued evolution of its species, is an incredible feat of mother nature. Imagine if we could induce parthenogenesis in humans? I mean, we've done it in fish...Actually, I don't like what I'm imagining. Bye!

Is this the Matrix?

Have you ever had a sudden panicked moment when you believe you've experienced something before? A conversation, a person or anything really. I know I certainly have, but thanks to science, I'm pretty sure that we are not all living in a computer generated world whilst robots harvest our body heat for energy. Deja Vu is not a glitch in the Matrix. The simplest, memory based, definition of Deja Vu is that a stimulus that triggers the feeling is linked to a similar memory that is already stored within the hippocampus, but which the person cannot remember. So if an event in the present has strong associations to a forgotten event in the past, then the feeling of Deja Vu is triggered. In 1941 researchers attempted to recreate the feeling in a laboratory, using hypnosis to induce post-hypnotic amnesia on volunteers. They were then shown a stimulus they had encountered before the hypnosis, yet only 3/10 people experienced Deja Vu. Spooky right? Although this test is of limited reliability given it's small sample size... so I wouldn't trust it implicitly. Recent virtual reality studies indicate that Deja Vu is more often triggered by the degree of familiarity felt in a certain situation, and so when a similar, familiar situation is encountered again, a person believes they have already lived through it. Location also appears to be important in this effect, as the degree of similarity between the spatial layouts of the previously experienced scene (which the person has forgotten) and the present scene increased the instance of Deja Vu in the VR test subjects. Cryptomnesia is another possible explanation for the phenomenon. I would like to take this moment to apologise to my readers who look down in haughty derision at the social sciences. Whilst I often do that myself, I thought this was too interesting a concept to pass up. Anyway brace yourselves, more unsupported conjecture coming your way. Cryptomnesia is essentially when information learnt is 'forgotten', but is still stored somewhere in the depths of the hippocampus, and is vaguely recalled based on more established concepts. The original memory is therefore distorted, and parts are omitted entirely. When this 'butchered' memory matches a current situation, Deja Vu is triggered. Each time we recall that 'memory' we are recalling our last construction of it. Deja Vu could therefore be a means of reconstructing and repurposing forgotten information to suit current needs. Although that theory does sound rather frivolous given its lack of scientific grounding. In truth, we don't fully understand the human brain, and researchers aren't really sure why Deja Vu like events are so different from person to person. Personally I think social conditioning has a part to play, as the populous are so aware of the phenomenon that they assume every half formed memory is Deja Vu. But then again, who doesn't want a little supernatural in their life?