Normal service may be assumed at some point – A public service announcement

In the unlikely event that anyone is following this blog, they may have noticed that updates have been somewhat erratic. At present I am very much engaged in job hunting,  this is occupying a lot of time, and obviously has to take priority over everything else.

I am hopeful that I can get things settled down into a more normal schedule at some point in the immediate future, but until that happens I’d prefer not to get too carried away with filler content to the point of drowning out the writing resources that I’m intending to be the main focus of the site. My interest in the site is not waning, and I will still be updating the site as often as possible, it’s just that the updates are unlikely to adhere to a rigid schedule.

My plan for this website has always involved the long haul, and I hope that my readers can have some patience.

I would very much welcome any feedback that people can give. It’s easier for me to justify devoting time to the site right now, if you can give me some reassurance that people are actually finding useful content here. Conversely if people aren’t finding the site helpful, then I need to know that, especially if you can offer constructive suggestions as to how to improve things.

Thanks

The Wizard

The wizard has lived in the tower for a very long time, he is old and he is weary.

 

He will not help the boy.

 

The boy is young and inexperienced, but he learns fast and works hard. He asks only to be taught how to strike against the Darkness, as the prophecies demand.

 

The wizard sets the boy to menial tasks, he sends him to gather wood in the forest, or lay another coat of paint on the towers exterior. He makes the boy clean out his stable. He sends him on long pointless errands, and offers nought but discouragement.

 

The boy perseveres and, in time, begins to see wisdom in the wizard’s demands. He believes that he sees how they make him stronger, how they test his resolve. The boy shows nought but determination.

 

Eventually the wizards acquiesces, he gives the boy a sword and tells him the secrets. He speaks of dragons, of werewolf haunted forests, of dangerous swamps, icy tundra, and treacherous ravines. Most of all, he warns about the Darkness.

 

The boy takes the sword. The sword is notched and battered, it is dented, and the binding is charred, but it is unmistakeably the sword from the prophecy. It is the sword that will slay the shadow.

 

The wizard hopes that the boy is the hero of legend, the Wolf of Autumn, a just and glorious saviour, praised by happy smiling children for millennia to come. After all, it is prophesised.

 

The boy knows that he is the one. The hero, who will right the world, and avenge his family. He will bring a light into the darkness, which will burn for millennia to come. After all, it is prophesised.

 

The wizard thinks of the other boys who found the tower. The ones he could not drive away, the ones who lie crushed and burned, drowned and frozen. He remembers children who now run with the wolves in the woods, children who now serve the Darkness.

 

The boy leaves the tower, he fears the road ahead, a little, but he is resolved. In his mind’s eye he already sees the sword shattering the Darkness. Beyond that, he sees pennants and princesses, a bright shining future stretching ahead.

 

The wizard has lived in the tower for a very long time, he is old and he is weary.

A writer’s guide to genetics

As with many of my other articles this will not be an exhaustive guide, but rather more of a conceptual roadmap of the subject. I’m going to be going through what I think are the most important concepts for the largest numbers of my readers to understand (ideally, both of you).

I’m not just going to be talking about genetics though, because I tend to the view that it can only be properly understood when viewed in a slightly wider framework

 

You’re going to feel cheated if I don’t tell you what the letters stand for, right?

DNA – Deoxyribonucleic acid. Composed of two separate polymeric chains of nucleotides, each containing one of four bases. It is the sequence of these bases, Adenine, Cytosine, Guanine, and Thymine, that encode the information.

DNA, when collected in large quantities, smells strongly of vinegar, is apparently edible, and I am informed that it tastes just as disgusting as you might expect.

Your genome is the sum total of genetic information within an organism, this term can refer to a specific individual, but is often used in reference to entire species, such as with the human genome. Much of your genome actually consists of junk DNA, this isn’t unimportant, but it doesn’t contain useful information.

 

Blueprint of what?

The word blueprint is thrown around a lot when people talk about genetics, but this is somewhat misleading. DNA actually contains information about the individual parts, not the whole.

For DNA to do anything, it must be expressed. This process involves translating the DNA first into RNA, which can be considered to be a temporary, working version, of the original master copy. This RNA is then translated into a polypeptide.

Polypeptides are chains of amino-acids, of which there are twenty different types, each of which corresponds to a three base sequence (or codon) from the original DNA (the gene).

 

Turns out our biology is largely based on origami

These polypeptides fold into proteins, which may incorporate multiple polypeptide chains, as well as non-peptide molecules.

The resulting proteins form most of the complex molecules within your body, and it is the interactions between them that actually determine most of what happens within it.

Imagine that every single item in your house was produced by squirting out chains of lego bricks that folded themselves into everything you could possibly need. I’m not just talking about your chairs and mugs here, I’m talking about your television, your fridge, your new conservatory. No assembly or planning would be required, the mechanisms that control all of this folded from the little chains too.

There is no possible way for words to do justice to the complexity of the entire system. I talked a little while ago about translation of DNA into Polypeptides. The animation linked here covers the proccesses that make this happen in more depth, and it is mind blowing.

 

The point of all this

This is the thing that you absolutely need to understand. There is nothing in your  DNA that says “arm go here” Your arm happened because some proteins fold into cells and those cells respond in specific ways to their chemical signals, neighbouring cells, pressure gradients, and a thousand other things, and that happens because of a system of interaction between proteins that has continued uninterrupted pretty much since proteins first happened.

The specific system of protein interactions within an organism is termed the Proteome, the study of it is called Proteomics, and its practitioners should probably be termed Masochists. We tend to fixate on genetics, mainly because it is much easier for us to understand and influence, but it is only part of the picture.

This is a wildly complicated, emergent system that has arisen over millions of years, with no limitations to the factors that could influence it, no logic or requirement for consistency evident in its processes, and with no part of how it actually works documented anywhere, including your DNA. You probably can’t comprehend the true horror of this, unless you have worked in IT.

Essentially your DNA is just the HR filing system for the corporate entity that is your body. Every so often a Mummy corporation, and a Daddy corporation, will love each other very much, and little spin off company will be sent into the world, but they won’t succeed or fail solely on the quality of the paperwork that they inherit.

We all started out as a single cell, and that cell had DNA in it, but it also had a payload of additional biochemistry which was  important too.

I suspect that there is also joke in here about editors, but I’m worried that, if I find it, the metaphor police might actually start issuing warrants.

Anyway, this stuff has implications, even for writers.

 

Sample implications, provided for your convenience

1)      It’s very difficult to reconstruct an organism solely from genetic information – You can’t reconstruct the organism without recreating the proteomic environment that can use that information. Whilst the genome will contain the information for the pieces of that of proteome, it doesn’t tell you how it fits together, and without context you probably can’t decode the genome anyway, much less how they correspond to proteins. This is a chicken and egg situation that involves actual eggs.

Say we find some dinosaur DNA, it’s very unlikely that we can plug that DNA into the egg (in the sense of the actual ovum cell) of any modern creature to produce a dinosaur, but it’s possible that we could use our understanding of genetics and proteomics to reconstruct a viable egg, that will in turn produce a dinosaur, and then, as Hollywood teaches us, some kind of theme park and a whole bunch of lawsuits.

But if we found some Alien DNA analogue, then even if it worked in a very similar way to ours, even if we could identify patterns and codes at the genetic level, it would still be almost impossible for us to work out anything about the proteome of the organism, because the DNA doesn’t actually contain information about how proteins work.

 

2)      Complexity in biotechnology tends to scale exponentially – Say you want to turn an organisms skin green. You find a green protein somewhere, plug it into the target organisms DNA, and then try to get it expressed in a way that doesn’t interfere with anything vital. Organism is now green.

If instead you want to make an organism grow scales. You need to physically change the shape of cells, but you can’t do this without understanding the processes that govern the shape of the cell membrane, and understanding exactly how to change the peptides to achieve that. You need to be sure that changing the shape of the membrane doesn’t change the function of all of the important receptors and channels that go through that membrane, or interfere with its ability to take in nutrients, or the resources required for the cell to live.  Now, you need to consider how changing one cell affects its interactions with other cells, how to get the tissue formed by those cells to grow into new shapes, and then stop growing into new shapes. Can the organism still perspire? If it can’t how are you going to deal with that? What about circulatory changes, proprioception…? I could go on all night.

 

3)      Genetics will probably always involve experimentation, probably on living beings – Protein interactions are incredibly hard to predict. In the example given above, expressing a green protein to turn the organism green has a fair chance of working, and is relatively simple. Predicting in advance, however,  that a tiny corner of that molecule won’t interfere cataclysmically with some random cellular process, is the exact opposite of relatively simple. You could try growing the cells in a petri dish first; your first test subject could still die of liver failure because your green protein can’t be metabolized. And this is just the simplest case, the more complicated the changes, the harder it gets to predict the outcome.

 

4)      It’s not plagiarism if you are a biologist – The easiest way of dealing with the complexity issue is to find biology that has already happened and steal it. Any kind of DNA tampering is much more plausible if you can find something similar in a closely related creature or, better still, lingering in the organisms own genome. That junk DNA that I was talking about earlier contains an awful lot of old information from evolutionary history.

 

5)      Biological systems are simultaneously fragile and resilient – Related to the last point, when I described the complexity of protein interactions earlier, it’s possible that I left you with the impression that biology is entirely at the mercy of its own chaotic processes. This is not really accurate.

Biological systems tend to be highly resilient to familiar challenges but vulnerable to the totally unexpected.

Crude interactions with biology can be startlingly effective, because there are other systems that can cope with the problems that you have caused; but there  needs to be a reason for those systems to have evolved in place.

 

Using this stuff

As always, don’t let the facts get in the way of the stories, find ways to use the facts. Genetics is always going to be a subject that sees the facts get in the way of some of the fun, but temporarily getting in the way of the fun is not actually incompatible with storytelling.

Acknowledge the problems, then let your characters figure out how to overcome them, conquering the world with an army of lizard men will be so much sweeter for them if you make them really work for it.

Don’t worry too much about systematic research, but trawling wikipedia for random genetics facts can’t fail to land you plot hooks.

I do think that proteomics represents a massively under explored areas of science fiction. Anything that can be done to an organism with genetics can also be done, at least temporarily by interacting with the proteins directly.

The mainstream fixation on DNA could be a weakness to be exploited; perhaps your antagonist could develop an alternative mechanism for inheritability, his super soldiers enhancements don’t show up in the genetic screening because they aren’t in the DNA.

Conversely, if you someone, or something, could overcome the complexity issues, genetics and proteomics in tandem genuinely offer limitless potential to screw around with living organisms, genes can be switched on and off at will, and pretty much anything could lurk in the forgotten depths of our genomes.

I’d also suggest that that there is a lot of inspiration here for those of you who might be interested in writing about nanotechnology. Go back and watch that video again if you don’t believe me.

 

Coming attractions and matinee performances

If you like this article you might also want to check some of my earlier articles on interactions with alien biology, or plausible medical responses to weird unexpected stuff.

I’m intending to use this article as a springboard for a couple more articles, one on mutation, which is going to be taking a slightly more Saturday morning cartoon approach to this subject, as well as talking a bit more seriously about inheritance, and the other is going to talk about viruses.

Hope to see you back for them.

Horatio’s Dragon

 

Picture, if you will, a figure. Short grey hair, balding pate, thick glasses, and advancing age, no doubt dressed in a lab coat, or perhaps a waist coat with a pocket watch. This is precisely the sort of man that might be envisaged by you, the reader, in your prejudice, upon hearing the name like Horatio Pemblethwaite.

 

You would be almost completely wrong, of course.

 

Horatio was  only 28 years at the start of this narrative. He was tall and effortlessly lean, in that special kind of way that drives the effortlessly rotund to private murderous rage. His hair was short, blonde, and neatly cut. He was only moderately and unsurprisingly unattractive. He was an engineer, but he worked mainly with computers and only wore a white coat when important people were being shown round his place of work.

 

Mostly though, Horatio was obsessed.

 

Horatio’s passion was for dragons, his feelings on the subject were of similar intensity and scope to the enthusiasm Genghis Khan once felt on the subject of land ownership; they had come to define his life.

 

This had been the case for as long as anyone could remember. Even his parents could not precisely identify the precise point at which this fixation developed, but it is certainly true that dwagon was the second word that he spoke; his first utterance was burrito for reasons that will likewise forever remain opaque to logic, and which was, in any event, mistaken by his parents for gas. He was never able to articulate exactly what fascinated him so about giant flying reptiles, but that fascination was undeniable.

 

Horatio had seen almost every film ever made that featured dragons, in itself quite a feat because, as my reader may or may not be aware, most such films are quite uniformly awful, Horatio didn’t care. He greedily devoured many a poorly written novel for even a trace of draconic content.  At college he often played Dungeons and Dragons with his friends, but truth to tell he was always somewhat ambivalent about the dungeons. The small flat he lived in during his student days was plastered with posters and pictures and filled with mobiles and models, producing an unsettling visual effect, a continuous sea of scales, wings, and talons which quickly overwhelmed the eye. At any rate, the only girlfriend he invited back to the place soon developed an inexplicable headache.

 

But all these faux dragon surrogates left him wanting, a void still unfilled in his life, nay in his very soul, for Horatio’s burning ambition was, to meet in the flesh, a real live dragon.

 

This would, of course, be an unfortunate pipe dream, one of those tragic everyday quirks that bring colour to the people around you, if not for the minor detail of Horatio’s employer. For you see Horatio worked for Otherworldly Incorporated, an ambitious new start-up, who were determined to exploit what they saw as universes of  untapped potential.

 

I must take this time to explain to some of my readers, the slower ones, the essence of their business plan.

 

Many contemporary physicists believe that there is not one universe but an infinite number of them, a multiverse of dimensions, which are constantly splitting off from each other at each juncture of probability, spawning new universes for every imaginable possibility, and many more unimaginable ones. Almost uniquely for contemporary physicists they are in fact, just this once, absolutely right.

 

There exist, out there in the great void of possibility, universes ruled by super intelligent video games. There are whole galaxies which, due to the influence of bizarre otherworldly Von Neumann machines, are composed of nothing but pasta. Untold trillions of worlds exist in which Stalin was a noted humanitarian, Copernicus was wrong, David Icke was right, and in which you, the reader, are rich, successful, intelligent and the envy of all mankind. There are necessarily an infinite number of separate universes available to meet any possible specifications.

 

Contemporary physicists also love to spoil other people’s fun, and will therefore also tell you that such universes are unable to interact with each other in any substantive manner at all. In this respect, at least, they return to form and are decisively but authoritatively wrong.

 

Otherworldly Inc had found a way to reach them, they had, using a quite simple process that, alas, the narrator is unable to disclose to you for reasons of understandable pragmatism discovered a way to open the doorway to other worlds.

 

I’m sure that the less challenged of my readers understand something of the way that one can track certain entangled particles as they flit between levels of reality and perhaps use such tenuous links to forge gateways,  or how one could construct quantum computers to spy recursively on their alternate counterparts. That it might even be possible to tamper with the source code of the multiverse itself. But they would, no doubt, also appreciate that all of the aforementioned are possible only in a way described by that special kind of theoretical that is customarily invoked by physicists who harbour the secret ambition to see their work mentioned in mainstream newspapers. Otherworldly Inc did none of these things; the solution that they had found was much more elegant.

 

The managing directors were justifiably excited about their discovery and the spectacular implications it might have, both for humanity and their own shareholder dividends. They thought it could be used to access near infinite resources and vast cultural treasures; they did not hesitate to speculate, for the benefit of their investors, how it could provide comfortable living space for all of humanity. Like so many of history’s technological pioneers they never really considered that mostly people would find ways to exploit their invention to find new and interesting ways to have sex.

 

First however, they had a problem.

 

As any of the aforementioned spoilsport physicists will no doubt tell you, merely opening the doorway is not nearly enough. Infinity, as it turns out, is a very big place and most universes contain nothing that could be described as anything, let alone anything that might be described as interesting. If their new invention was to be useful for anything other than garbage disposal or organised crime, a means would have to be developed to sort the wheat from the cosmic chaff and indentify the incomprehensibly rare universes of narrative significance.

 

Horatio, our protagonist, was employed to resolve this problem, and he threw himself into the task with single minded intensity for, as you may already have guessed, Horatio had seen a sudden and unexpected opportunity.

 

It was an extraordinarily difficult problem, the sort of trial that is, inconveniently, overcome only by dint of many years of work, most of which involved very complicated sums and so, whilst I hate to disappoint the numerical masochists among my readership, I will skip the specifics. Suffice it to say Horatio eventually succeeded in patenting a process by which the staggering number of universes could be quickly and efficiently investigated and categorised, in the process ensuring his own unfettered access to the vast infinite reaches of potentiality.

 

Humanity had, after a brief spate of hurried press conferences, collectively rejoiced. Here at last was the means to end all wars, suffering, and tiresome weekly recycling responsibilities. Most importantly of all, here too was an opportunity to have lots and lots of sex.

 

Thousands of technicians set to work investigating and cataloguing dimensions full of interesting resources such as precious metals, oil, food, unpublished Shakespeare and J K Rowling folios, and “not unattractive young women inexplicably in need of a single virile male to repopulate their entire race”.

 

Horatio was looking for none of the above, Horatio was, as should now be blindingly obvious, was looking for dragons.

 

As most of those tiresome physicists would be able to speculate, there is a tremendous gulf in the probabilities involved between finding something of interest and finding something specific but even with this consideration in mind Horatio’s search took him far longer than he had anticipated. Nevertheless, after almost half a decade of tireless work, he suddenly and unexpectedly awoke to the insistent beeping noise telling him that his inter-dimensional search engine array had found him something that matched all the extensive specifications he had given them.

 

Horatio approached this finding with the quiet but jittery kind of calm that can only be achieved by transcending excitement; he spent several months carefully preparing for his expedition. After all, he had waited his entire life to see a dragon, he could wait a little longer if it meant he was properly prepared. No consideration went unconsidered, and no expense was spared, and that expense was considerable, but this was of little object because as you might expect Horatio’s discoveries had made him rich beyond easy reckoning.

 

Tragically however, all his efforts seemed in vain. When, finally, he stepped through the portal into the cold and unremarkable landscape, of what would otherwise have been a singularly uninteresting world, there was nothing to be seen, no majestic draconian wildlife for him to observe. All that could be found, after an extensive search, was the single gargantuan decomposing corpse of what may, or may not, have been a dragon.

 

Horatio was distraught but not discouraged, evidently dragons had been present, and obviously some freak happenstance had wiped them out while he had been preparing for his grand expedition. If he could find dragons once, then clearly he could find dragons again, and so, freshly resolute, he set back to work.

 

All this time human society progressed largely as before, with only the minor side effects of free extra dimensional travel to disturb the usual human preoccupation with war, greed, and more war. The abundance of anti-matter universes had provided cheap energy for all, as well as sharply increasing the general public’s interest in the non-local distribution of power stations.

 

There was the massive increase in emigration, all sorts of exciting new kinds of immigration for people to get upset about, the quite endearingly inept pan dimensional invasion of the treacle people from candy dimension 2672 and the subsequent bankruptcy of Tate and Lyle in the wake of the resultant drop in the wholesale price of sugar.

 

Most of these events were far less interesting than you might imagine though with the exception of the latter which, by a curious quirk of fate, was very nearly precisely as interesting as it sounded.

 

The world government had, of course, fallen to militant feminism shortly after Horatio’s great invention was first unveiled. It had all started when the women of the world had collectively complained that some of the men were using the device in ways that could possibly construed as being quite horribly sexist. The men had replied that they were sure that they could find the women plenty of dimensions full of flowers, clothing, ponies, and other girly stuff, but this had not in fact gone down terribly well and many of the men of the world had been collectively shouted at.

 

The men of the world went away and thought for a little while but not, alas, for quite long enough, and a few too many of them had then quite innocently suggested that if the women were concerned about inequality, they were quite sure that it would be straightforward to locate an abundance of dimensions full of “not unattractive young men, inexplicably in need of a single fertile female to repopulate their entire race”.

 

The coup had been relatively quick and bloodless as such things go and all things considered had probably been for the best, made far less difference to the general scheme of things than either gender would have been prepared to admit beforehand, with only the odd minor quirk, such as the fact that the trains started to run on time.

 

But I digress.

 

It took Horatio another ten years to find another dragon but, this time, he was ready. This time he didn’t wait calmly to organise an expedition, he didn’t don his custom made asbestos suit or pause to clutch his jumbo strength tranquilliser gun, this time he ran across the multidimensional control room and straight through the nearest portal.  He emerged through the portal just in time to see a grand silhouette stagger erratically through the air, crash into ground some distance away, and expire in a messy, and well distributed, fashion.

 

“Egad” exclaimed Horatio, for it is impossible to do something quite as sadistic as to name a child Horatio Pemblethwaite without it having some lingering effect on them.   Horatio had finally realised what was happening to his dragons.

 

Obviously the majority of my readership, the smart ones, will be well ahead of Horatio at this point and there is no real need to clarify things, but I suppose I can spell things out explicitly for the incorrigibly slow. Horatio had realised just how intrinsically improbable dragons actually are. He had realised that for a dragon to fly it must be buoyed up by millions of air molecules, that, for it to breathe flame, a million molecules worth of dragon must collectively decide not to catch on fire. In order for dragons to exist in any dimension which the laws of physics would actually allow Horatio to visit, these preposterous impossibilities had to occur every time any single dragon actually did anything.

 

While our friendly contemporary physicist would tell you that they couldn’t even begin to quantify how ridiculously and stupendously unlikely that this would be, they would also have to grudgingly concede that logically a nearly infinite number of such dimensions would still exist. They would also point out with a trace of satisfaction that whilst effectively infinite in number and constantly appearing, the laws of reason would ruthlessly expunge the vast majority of these errant dimensions of dragons on a moment to moment basis in a constant churning genocide of possibilities.

 

So it was not just that Horatio’s objective required a dragon to exist in the specified dimension, a dragon, let us not forget, which had evolved and live out its life entirely against the current of chance. He had also to accept that, as soon as his dragon hunting equipment had detected, the great universal dice would roll again and his newly discovered dragons would, with overwhelming certainty, become extinct. In order for Horatio to find his dragon, he not only had to find a dimension where dragons existed, he had to find a dimension in which they would continue to exist, at least for the foreseeable future.

 

This is the point at which the pedants among my readership, you know who you are, might feel inclined to object. They would probably begin by complaining that the degree of improbability involved in finding even a single dragon renders this whole tale completely implausible. They would be wrong of course and I can forgive their ignorance. They would then, no doubt, continue to suggest, their voices brimming with whining nasal smugness, that the only way of predicting the future of any given dimension, whilst remaining comfortably in the present, requires charting the course and state of every single atom within it. This, they would contend, would be very nearly totally impossible, and on this single, but significant, point they would be correct.

 

Horatio realised this almost immediately, his calculations soon told him that running the calculations required, even the limited extent that he required, would require a computer the size of a galaxy, of complexity orders of magnitude greater than any that have ever, or will ever, exist in this universe.

It took Horatio’s machine a quarter of a century to find one.

 

The air was crisp and cold on his skin as he stepped through the threshold; he ignored the nagging pain in his limbs and squinted against the light of the sun as it rose over an unfamiliar horizon. Above him shapes danced through the air as the dragons sang in a hauntingly beautiful, and utterly alien, song.

 

That song quickly became a lament, however, as the shapes began to stagger in the air and then spin slowly and gracelessly towards the ground.

 

If Horatio had observed this sight, he would most likely to have been struck by a final terrible realisation, that his very presence on this world would disturb the fragile cobwebs of whimsy which would have kept his beast’s alive, that this was not a factor that he could correct for and avoid, that he had in fact brought premature destruction to the very wonders he so appreciated, that he could never enjoy the living company of his icons, and that any further attempt to do so would result only in further disappointment, genocide, and possible canonization on account of dedicated service in the field of dragon slaying.

 

This final truth would most likely have destroyed him utterly and, so, it was probably a small mercy that he was distracted by the shadow descending over him, in the final span of seconds before he was crushed utterly by a confused and rapidly expiring dragon.

 

You could speculate dear reader, that this is a morality play, a cautionary tale, meant to impress upon you the dangers of pursuing a hollow dream at the expense of the other things that life may promise. This may indeed be the case, although it is perhaps worth noting that reality seldom provides a moral to its stories more worthy than that evil often prevails, greed can provide its own rewards, and that few good deeds go completely unpunished.

 

It is also possible that this is nothing of the sort, that this tale ignored the normal and average components of Horatio’s life. It is possible that the tragedy of the story is projected by you the reader and that our Horatio in fact lived a relatively long and happy life filled with purpose, unrelated hobbies, and happy smiling grandchildren, that you have conjured a tortured and empty existence to meet your own twisted expectations of truth.

 

It is would be possible for the most cynical of readers to realise the necessary existence of an infinity of Horatio’s, the lives of whom, even when constrained to fit precisely within the details of this narrative, plot a wide and bizarre plot on some universal tragedy curve, rendering any scientific attempt to extract trite revelation a futile endeavour for those unwilling to spend an eternity studying exceedingly large and complicated graphs.

 

Whilst the statisticians amongst you are thus engaged, the more sentimental of you can therefore be reassured, that in at least one universe of an unfathomable infinity, as at least one Horatio looked up for the final time, that the expression that crossed his elderly face was not in fact terror, horrified comprehension, or even resignation. That it was one of fulfilment and contentment and true happiness, that rarest of all emotions, and that in his final seconds he spread his arms wide open as he prepared to embrace in a tangle of limbs, scales and claws, his very first dragon.

One chapter reviews – John dies at the end – chapter 14

 

A new series of articles, highlighting outstanding individual chapters from the books that I’ve read.

Starting off with – John dies at the end, by David Wong

 

Cover © Macmillan

Chapter 14 – John Investigates

“Two steps in, John found himself standing on a faded pink stain on the snow, as wide as a car. He deduced that this was blood, though the truck driver’s body was gone. He stood over this large bloodstain and said, out loud and in the presence of several by-standers, “This is blood! David must have been here””

There’s the unreliable narrator, and then there’s this.

This chapter sees the protagonist relate, with some justifiable skepticism, a parallel series of events as described to him by the titular John. At this point in the story we have already established that John is a pathological liar, a borderline sociopath, and, frankly, not terribly bright. Nevertheless, the book’s main narrative is one of bizarre, reality warping, horror.

So not only does the author get to have tremendous fun writing a riotously funny, Munchausen style, mini narrative, he still gets to keep most of it credible within the framework of the book, something that can continue to pay off within the rest of the story.

This is incredibly funny writing, and magnificent story construction, especially as it’s interweaved to soften some of the heavier components of the main story.

 

The Rest of the book –

This is not a very mature book, at least, not on first examination. There is plenty here that will offend some of my readers.

But it also has to be said that it’s very genuinely immature. This is the voice of the twenty to thirty year old, with nothing apparent to aim for, and with no obvious reason to engage their intellect. It is a voice that, distressingly, is becoming more and more common online. But it’s one that very rarely gets as widely heard as it should, mainly, it has to be said, because of the politically incorrect epithets and the bodily fluids, and the references to genitalia.

Anyone who is already familiar with this book is probably about to accuse me of over sensitivity here. And in the specific context and market in which it has already been incredibly successful, they are probably right. I’m sure the author is happy with the book’s success, and comfortable with the audience that he does have. But this is a book that deserves a wider audience, and I’d like to think that at least some of that audience deserves it.

This is an assured story, especially for a first effort. It’s clever and observant. It can transition effortlessly and instantly between real humor and genuine horror in both directions. It makes a lot of very valid observations, often about things that don’t get talked about nearly enough. It is painfully honest.

It isn’t a perfect book. It loses steam towards the end, and never really delivers on some of the conceptual promises delivered in the blurb. But I’ve never read a perfect book.

You will not get many opportunities to read a story like this, in a voice like this, delivered so assuredly. Frankly, it’s not a story that could survive being sanitized, even if the author was inclined to try.

I’m not trying to sound all literary here; I wouldn’t know where to start. All I’m trying to say is, if you are reading this review, and you sound like the kind of person who would never read a book like this, then this is a good opportunity to try something different.

Stats 5 – Power to the people, why large groups are just better

Welcome back to An astonishingly useful guide to data analysis for people that don’t like maths in last week’s exciting episode you learned how to evaluate your data before you start doing maths with it. This week I’m sure you’ll be thrilled to discover that I’m going to be introducing you to some more important concepts.

This is because they are important.

 

Random facts –

Random data is random. People forget this, a lot.

This is especially important when you are using Mean values, simply because nothing about a sample mean offers any useful information about its reliability as an estimation of the population mean. It’s very easy for them to mislead.

 

The above chart illustrates the mean values of 5 separate groups of data. The data in each set was comprised of ten entirely random numbers between 1 and 10. The final bar indicates the mean of all 50 values.

In this case you can treat the population mean as 5, and each set as a separate sample group the mean of which is obviously the sample mean. The final bar treats all 5 sets as one single group of 50 values, and indicates the sample mean for that case.

As you can see, even with ten data-points in a group, some of the the sample mean values differ substantially from the expected population mean of 5.

Conventional wisdom suggests a minimum of three samples in each group before you start to work with data, but even with 10 samples a deviation of up to 20% from the expected sample means is apparent. If we treat all 50 values as a single sample, the sample mean almost exactly matches the population mean.

 

This is another set of mean values. There are 20 values here, representing the deviation from the expected population mean (50), of the sample mean of a set of 20 groups, each containing between 5 and 100 values. Each individual value was randomly generated between 1 and 100.

In other words, the graph does not show the sample means, it shows the extent to which they deviate from the expected population mean.

There are a couple of important things to take on board here.

  • A small group is not always associated with a high deviation.
  • The larger the group is, the less likely it is that the results will be skewed significantly by chance.

It is important to realise that it is still possible for a large group of  samples to return a mean that deviates substantially from the true population mean, it just becomes less likely as the sample size is increased. The issue is one of variance, which is one of the next concepts that I’m going to discuss. But before I do that we need to discuss something else.

 

Striving to be normal

You may have noticed that the examples of random data that I gave in the previous example seemed to result in more variability in the sample means than seemed intuitive. This is because of how it was distributed.

It’s probably worth taking the time here to be clear on the difference between random distribution and random generation. Randomly generated numbers are those produced as a result of an ostensibly random process, in this case Excel’s number generation function. The randomly generated values that I showed you before, are of uniform distribution, that is to say, the numbers have an equal chance to fall anywhere in the specified range.

One of the reasons that people are so bad at dealing with randomness is that it is not a common occurrence in real life. In reality, data tends to cluster around the sample mean. In fact, a lot of statistical procedures assume that data will follow what is called a normal distribution.

In the above chart each line of points represents a separate set of randomly generated data. The first line consists of 50 values that are uniformly distributed, the second, 50 normally distributed values. You can see that the first set spread out fairly evenly between 1-100, whereas the second set tend to cluster nearer the expected mean of 50, although they still represent a considerable range of values.

The pattern is not as neat as you might expect, because the values are still generated randomly. Which means that any pattern of data could have occurred. Excel could have delivered me 50 identical values of 100, for example, in both cases, it’s just (very) unlikely.

Most statistics programs will inform you if your data is not normally distributed, although they will often allow you to proceed anyway.

You need to be aware if your data is not normal. It may prevent the test from working properly, but it may also reveal problems with your data that you are not aware of.

 

Possible reasons why your data does not follow a normal distribution –

  • There is a genuine and reasonable expectation that data would be randomly distributed – For example, you are looking for evidence of bias in what should be a random system such as a roulette wheel.
  • Subgroups within your data – If your data shows distinct clusters of normality it suggests that the factor that you are investigating is not consistent across the sample group or target population. It might also imply that the data was collected or processed inconsistently or conglomerated from separate sets.
  • Exponential growth – A good example of this would be the way a story or joke is shared by Twitter users. Because each retweet increases the pool of people who can make further re-tweets, the most successful Twitter posts will tend to be dramatically more shared than the least. You can expect to see this pattern a lot with social media data.
  • Fraud – You need to be careful here, but it is not uncommon for people who are falsifying data, but who do not have an in depth knowledge of statistics to do this by generating a uniformly random number series within a specified range, rather than a normally distributed one. You should be suspicious of truly uniform distributions within a large set or subset of numbers unless there is a very good explanation. The scarcity of uniform distributions within nature means that, with large groups of data, it is difficult for them to happen by accident or as a result of innocent mistakes that don’t happen to involve random number generators. but…
  • It can still happen by chance – As previously stated, you will never be able to be absolutely certain about data unless you have all of it, and if you have all of it, you don’t need to make predictions about it.

Statistics  = Confidence not certainty

You can never get away from chance when you are working with samples. Statistics does not allow you to make definitive statements about what is happening, but it allows you to determine how confident that you can be in your predictions.

“My data is not normally distributed, what do I do?

Start by figuring out why your data isn’t normally distributed.

If your data is showing clusters of data, the best approach is going to involve trying to untangle the subgroups from each other, obviously this may reduce the sample size below the level required for good quality data.

In some cases, especially with data associated with exponential growth, data that isn’t normally distributed can be “transformed” to meet a normal distribution, however this is very context specific.

 

Variance

As you should now realise, the problems associated with small data-sets are a function of their increased exposure to chance.

You should also understand that representing data from a group of samples, just by indicating the mean values,  provides no information about the level of variability within that group.

Variance describes the extent to which individual values fall close to the sample mean.

How random happens

With the examples of random numbers given above, the numbers come from a machine, and because machines suck at random, these will result from a natural process of some type, which while not random either, will in turn be influenced by other processes, and so on until we have split enough hairs that quantum processes, that may actually be random, are involved, and at any rate it’s long since become impossible to keep track.

Remember that variance doesn’t spring into existence just because the universe hates you (although that’s my go-to explanation for a lot of other stuff). It come from those aforementioned external influence, which we call factors.

Generally if you are doing statistics, it’s because you wish to investigate one or more of these factors, but trying to do this doesn’t make all the other factors go away and stop influencing your samples, because even if the universe doesn’t hate you, it’s not about to start doing you any favours

 

Fitting it together

So..

Normality describes the pattern that data most often falls in, and variance describes how precisely this actually occured. The variance is determined by all of the factors acting on your sample values other than the one that you using to define your target population.

Considering the assumptions that you have made will often allow you to identify some of the most important factors ahead of time, understand their interaction with the one you wish to investigate and help you to assemble sample data that is more representative of the target population.

Variance reduces your ability to make accurate predictions about the target population from your sample values, and this in turn decreases your confidence in those predictions.

If you can’t identify or correct for the influence of additional factors your data, you can oppose the resulting variance by increasing the number of samples that you take.

 

Next time on Stats – Practical stuff will happen

So how do we indicate variance and quantify confidence?

Come back for the next article in this series, in which I will finally start to talk about the actual process of data manipulation, starting with calculation and appropriate use of standard deviation and standard error.

Interactions between terrestrial and alien biology

Can this space virus make my character sick? Can my captain sleep with the alien Princess?

This article is going to talk about the implications of mixing alien and earth biology.

The science here is going to start off fairly strict, but this is a subject in which a hard science framework is going to seriously limit what you can do, so I will progress to talking about ways in which you can justify softening things up a bit.

 

The important bit – chemistry and biochemistry

This is where the problems start. As you will probably know, biochemistry involves the subset of chemical reactions associated with living organisms. Whilst you can expect alien life to be made from the same basic elemental building blocks and react in somewhat predictable way to straightforward chemistry, biochemical reactions are often very very specific.

An acid for example, is always going to be an acid. If it is corrosive, this is usually the result of a very straightforward hydrogen exchange reaction, and you can reasonably justify any alien with even the remotest biological similarity to us being burned by it.

Many substances which have a major effect on earth biology do so because they are inherently reactive molecules. Hydrogen cyanide poisons humans because of its ability to interrupt an incredibly specific set of reactions that our cells use to produce energy, and although this is unlikely to happen with alien life, it would be plausible for it to have some other effect instead. It is a simplistic molecule, which is relevant to the organic (carbon based) chemistry that alien life would probably be based upon.

Why Carbon?

It’s versatile and relatively common.

Carbon is one of the most common elements in the universe and forms strong, stable, bonds with a wide variety of other elements. This allows it to form the extremely wide range of different molecules critical to life’s diversity and complexity.

Silicon has similar, if more limited properties, and there are a handful of other chemical systems that it is speculated might produce life within specific niche environments, but the chances that alien life would share a common carbon heritage is very high.

Silicon is actually more abundant than carbon within a terrestrial environment, but it’s probably less available for the formation of life, as it is mostly tied up in none water-soluble silicate materials such as sand, whilst analogous carbon molecules dissolve readily. However, carbon’s real advantage comes from its incredible ability to form compounds, and it is this versatility that renders the compatibility of different biological systems problematic.

It’s complicated

Biology is built on complex reactions built on complex reactions. The proteins that your biochemistry is based around are exceedingly complicated molecules that are reliant on, and which evolved in association with, other complicated systems.

Whilst it is certainly probable that alien life will involve similar levels of complexity, it becomes completely implausible that they will evolve identical complexity, which is what would often be required for such systems to interact.

There are certainly grey areas here. There may be some complicated systems that are necessarily similar just because there are only so many ways for them to arise within nature. It could be that the metabolic reactions that an alien uses to create energy within their cells could be disconcertingly similar to our own, for example. But this can only go so far.

 

So what does this mean?

The more straightforward the chemistry, the more likely systems will interact. Highly complicated molecules such as DNA and other proteins will simply be incapable of making complex interactions with alien biology. Some particular sticking points-

Viruses

Alien viruses are straight out. I’m going to talk a lot more about viruses and bacteria and DNA elsewhere in this blog, but the problem is as follows.

Viruses have arisen as an artifact of the way DNA works; they are not so much living organisms as much as rogue instruction manuals for our cellular machinery.

While it’s possible that something similar could arise in alien environments, they would not be viruses as we define them, and they could not harm us in the same way as terrestrial viruses. It is utterly implausible for alien life to interact with terrestrial viruses or vice versa.

To make an analogy, it would be like trying to get a specific book published by posting random strings of gibberish text to someone at the building containing the printing press.

Other bugs

Other micro-organisms are more complex. They aren’t going to be able to interact with us in all of the ways that a terrestrial bacteria might, by releasing complex toxins, or forming symbiotic interactions with our biochemistry. However, they could be similar enough to us that they could try to eat us, and some of the chemicals that they might release in the attempt could be simplistic enough to damage our tissues.

Likewise, our immune system could plausibly provide some degree of protection to such attack. Antibodies released by our cells would have problems with alien biochemistry, but immune cells that envelop and digest foreign molecules through crude oxidative reactions might have more success although it’s possible that they would not be able to fully digest the alien molecules, which could lead to more complications.

Poisons and toxins

As I already mentioned, complicated biological toxins are not going to influence alien biology. But, if anything, it may even be more likely for alien life to contain simpler chemical hazards.

Take the aforementioned Hydrogen Cyanide. The extreme sensitivity of terrestrial life to this substance severely limits the extent to which it is incorporated into earth biology (excepting those parts of it that are attempting to produce it to kill other creatures), an alien life form could use it far more ubiquitously in their own biological processes and therefore be inherently toxic to terrestrial life.

DNA and mutations

Yeah, sorry, you’ve probably figured out by now, but mutation by alien DNA is definitely off the table, as is pretty much anything else cinematic involved with reproduction.

So the question a lot of people probably want to ask, at this point is…

 

How do I get away with ignoring this?

Honestly, this is one of those subjects where ignoring the facts is sometimes going to be your best option, but there are a few possible get out clauses.

Chariots of the Gods

First option is to try and explain why alien and terrestrial life is so implausibly similar. Random chance isn’t a great option here, because of the magnitude of unlikeliness we are talking about, but the idea of life in different parts of space sharing common progenitors has a long science fiction tradition (even if a lot of it was been published as non-fiction). This can come across as pretty weak if introduced as a random plot point, but it’s obviously much easier to work into other types of story.

We’ve seen your type here before

Biology evolves; an alien ecosystem that has been exposed to terrestrial biology at some time in the past could eventually evolve to interact with it at a more complex level. The more complicated the interaction, the longer this is likely to take.

Alien life from a planet that was contaminated with terrestrial bacteria from a crashed space probe could plausibly evolve to produce terrestrial specific toxins within a relatively short period of time. Incorporating DNA into alien reproduction however would be a much bigger deal (I can think of a few ways it could happen, but it’s a massive shift in complexity, plausibility, and likely time frame).

An alien overlord did it

These are obviously issues that can be overcome by intelligent beings. There is nothing stopping Alien invaders deliberately creating viral weapons that can infect us, or creating organisms that are compatible with our biochemistry and ecosystem.

 

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