Posts tagged: xenobiology

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.

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-


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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