The Gap

Still following ‘Pluribus’ but this is interesting way beyond that. First of all, an introduction. The Darién Gap is a hundred kilometre stretch of land straddling the more or less irrelevant border between Colombia and Panama, and its presence is what makes that border irrelevant. It’s inhospitable in various ways. Where to start?

Well, the longest road in the world stretches from southern Argentina to Northern Alaska and is thirty thousand kilometres long, meaning that flattened out it would go three-quarters around the planet. Except it doesn’t, because of this gap. It’s almost impossible to get between Colombia and Panama, at least for humans, even with high-tech transport methods such as ships and motor vehicles. As can be seen from this map, the roads run out either side:

As you can see, there are no railways, canals or roads between them. It is, however, occupied by people traffickers and drug smugglers, and there are two peoples, the Guna and the Emberá. Remarkably, the Guna flag looks like this:

The swastika needs some explanation. It’s a local sigil called Naa Ukuryaa symbolising the four corners of the world whence the Guna hail, so in other words it’s practically the opposite of the Nazi use. Olaf Stapledon once claimed that Homo sapiens would use this symbol with varying significance throughout our history. But a people is more than a flag. They mainly live on coastal islands and moved westward into Panama. Some of them are white and have a special role defending the Moon against a dragon. The Emberá have a larger population and like several other indigenous peoples have a tradition of FGM although they’re working to eliminate it. They traditionally live on river banks but then the same applies to the West. They’re an egalitarian society whose shamans are however revered. I just thought I’d mention these peoples because the rest of this post is going to be about other things.

Immigrants are constantly attempting to travel through the area, often ending up dead as a result. Even by the time they start, they’re not in good condition and are unlikely to have the equipment needed to survive. The situation is similar to the “small boats” plight in the Manche/English Channel, with many deaths and a lot of corruption, but the drug trade, currently illegal, makes it even worse. The transit of people from more Westernised conditions through the gap has led to economic interactions with the indigenous people which pulls them toward the money economy and there is also, quite startlingly, tourism in the region which has the same effect.

Another situation which comes to mind here is the one in the DMZ of Korea and around Chernobyl. These places deny access to most humans and consequently have gone back to a less interfered with condition, which for Chernobyl is deeply ironic. The ionising radiation in the latter also makes the situation less straightforward, with for example black frogs using it to warm their bodies and increase metabolic rate and fungi with high levels of melanin being favoured by the environment, but in the DMZ between the two Koreas the situation is more similar, since it’s human activity which has stopped the strip from being interfered with. In the Darién Gap, humans do things but not in a manner similar to the organised centres of many territories. The way international and smaller scale borders often exist, good ones at least, is that they’re placed in relatively inaccessible places. For instance, Loughborough, where I used to stay, is on the northern edge of Leicestershire and if you try to walk thence into Nottinghamshire through fields, you’re confronted not only by the unsurprising river which often forms a border but also by rather boggy, wet ground, which makes it a good place to put a border as nobody wants to argue over it. Likewise the border between Scotland and England runs through high, rocky heathland and is sparsely populated compared to, say, the Central Belt or the large cities of Yorkshire and Lancashire. The Darién Gap is the same. Humans do live there but they have difficulty doing so unless they’re hunter-gatherers. Agriculture would be hard and the heavy rainfall is the cause of frequent flooding. It’s also mountainous, like much of Central America.

The wider political structure of the region shows the relatively large territory of Mexico to the northwest becoming the increasingly fragmented area to the southeast, and in fact this already existed in pre-Columbian times. This is associated with the volcanic, mountainous and also increasingly humid nature of the isthmus as one goes south. It’s also remarkable to consider that the area is also a bottleneck for the human population, as the descendants of the humans who entered the Americas via Beringia between Siberia and Alaska to the far north and most, though possibly not all, of the population of South America before 1500 CE were descended from people who had come through the Gap. I say not all because there may have been some between Polynesians and the indigenous peoples of South America, as can be seen in the cultivation of the sweet potato, human genomes on Easter Island and chicken bones dating from the fourteenth Christian century in the Inca Empire, or at least that area. But apart from that, everyone came through the Gap.

If you go a bit further west from Darien, nowadays you’ll come across the Panama Canal. This is of course economically very important and necessary due to the closure of the Isthmus of Panama, which I’ll mention again. Of course, this does depend on long-distance trade being considered important, which is probably not ecologically sound. There was a time before it was practically to dig canals of that scale, and in the late seventeenth century, before the Union, Scotland attempted to exploit this with the Darien Scheme, the establishment of the colony of New Caledonia, where the idea was to transport goods across the Gap from the Pacific to the Atlantic, and charge for each transaction there. Apart from the obvious colonialism (“A big boy did it and ran away”, but this is before the big boy), this might sound like a good idea, particularly when you consider that it’s a mountainous and rain-soaked area like a certain other country thousands of kilometres to the northeast, but it didn’t work. Scotland invested a heap of money in the scheme, taken from the purses of Scots of fairly limited means who invested their life savings. I’m going to try to summarise what happened.

William Paterson, Scottish founder of the Bank of England, began a company known as The Company of Scotland Trading To Africa And The Indies. Lionel Wafer talked Darien up to him and he decided to found a unique type of colony which would neither exploit the land or people on it nor produce goods for international trade, but simply move items between the oceans for a fee. The East India company unsuccessfully lobbied the English parliament to impeach the new company and then threatened to boycott anyone who traded with Paterson, who raised £400 000 from the Scottish people for the colony, to be called New Edinburgh. He took five ships which carried various items useful for the colony but also three carriages without horses to transport them, a large quantity of garments and also many combs and mirrors which he planned to use to trade with the Guna. Leaving without telling the settlers or anyone else where they were going until they were well on the way to avoid word getting to the East India company, they arrived having lost a remarkably small number of the initial 1200 settlers. Their initial attempt to build a settlement was hampered by the unsuitability of the land and the recalcitrant nature of the jungle, whose trees would need to be felled and cleared for it to work, so they moved to another site and tried again. In Spring 1699, torrential rain and tropical diseases killed two hundred within a month and they were losing ten a day at one point. The Guna were also not interested in the mirrors and combs and the land was unsuitable for farming, so they were forced to eat less than a pound of mouldy flour boiled in water each per week, skimming off the infesting maggots and worms in the process. They then attempted to trade with other nearby English colonies but William of Orange, English king at that point, forbade trade with them, and they also got wind of an imminent Spanish attack so they abandoned the colony and went back to Scotland. Only two hundred of them made it there. In August 1699, Paterson tried again with two thousand settlers who hadn’t heard about the disastrous first attempt. They once again suffered disease and malnutrition, accompanied by rebellion against the leaders and a local pastor blamed their misfortune on their revolt, which was seen as deeply sinful by the leaders. However, they then united with the Guna in an alliance against another threatened attack by the Spanish, who blockaded them by land and sea with cannons and ships until they surrendered in March 1700. The Spanish were gracious enough to let them leave for Scotland, but by the time they got back everyone hated them, they’d lost everyone’s life savings, they got disowned and ostracised and Scotland had lost all of its money. And of course a lot of them died. As a result, the English parliament agreed to bail the Company out to the tune of £398000 in return for the Union, which became known as the Price Of Scotland, because although they had enough money to pursue the ongoing War of the Spanish Succession, they also needed bodies and there were more men available as cannon fodder in Scotland than in England, so that’s what they did. Scots were also soon involved in running the Empire and keep the British economy going. Many Scots saw the money as a bribe and the Union as the result of corruption and incompetence. So that’s a rough sketch of the role of the Darien Gap in the downfall of Scotland and the Act of Union’s success, which as well as everything else was partly the result of the inhospitality of the region to European-style human settlement, and it also means that Scotland is morally compromised to some extent by being instrumental in keeping the British Empire going. Had this not happened, it isn’t clear that the Empire would’ve been as victorious as it turned out to be, so whereas Scotland has every right to gripe about its position, the rich and powerful of this nation played their part in putting it in that predicament although the relatively modestly off also had a role. The likes of crofters and fishing families, of course, got the short straw and can’t be blamed at all for it, as usual.

There’s one further aspect to the Darien Gap I want to cover, which is connected to climatic and other changes which led to the ice ages and also, in my opinion, the Biblical Fall of Man. You can ignore the last bit for now if you find it too off-putting, but this is how things went. Right now the Southern and Arctic Oceans alone stretch all the way around the world and in the case of the latter it isn’t bordered by land on both north and south, since there is by definition nothing north of the North Pole. The Southern Ocean, however, provides a vast swirl of current all the way round the planet. There also used to be another such ocean in prehistoric times, known today as the Tethys, which separated the northern and southern continents, and like the Southern Ocean it had an uninterrupted current passing all the way round Earth flowing east to west. Its remnants today are present as the Caribbean, parts of the Atlantic and Pacific, the Med, Black Sea, Caspian and certain other lakes through central Eurasia. Three million years ago, this ocean finally closed for the time being at least when the Americas collided. This had immediate effects on the wildlife of the two continents, with exchanges such as camels, armadillos, opossums and the extinction of much of the life on the southern continent in particular. It also caused the current passing across what was now the Atlantic to be blocked by the Gulf of MEXICO and the warm water to be redirected north, where it increased precipitation and warmed the lands around the North Atlantic. Snowfall also increased due to the humidity, which did two things: it increased the reflectivity of the planet overall, bouncing heat and light back into space, and it locked up a lot of the planet’s water in ice, making it drier and increasing the spread of grassland and desert while causing the rain forests to shrink. It also lowered sea levels, exposing continental shelves, ultimately making it possible for fauna, including humans in the end, to move between North America and Eurasia. However, all of this was less significant than Milankovitch cycles, which are beyond the scope of this post.

It’s also possible that the shrinkage of rain forests led to our ancestors having to leave them for harsher environments such as the savannah, where less food was available, threat from predators was greater and water was harder to come across. This is where the “Fall Of Man” comes in. I believe it’s possible that this harshness led to different, for instance more aggressive, behaviour in and between our communities due to having to compete for fewer resources and various deficiencies in our diets and the ability to deal with health problems, which led to two things: stressed out malnourished pregnant people giving birth to babies who were less than optimally behaved, and parenting and other activities which tended to traumatise them and lead to poor behaviour. In other words, the Fall. We’re all the victims of this and it’s handed down by the rather dystopian flavour of society. The fruit of the tree of knowledge is actually the absence of fruit, not its presence, and the serpent is our base desires and impulses being brought to the surface by these harsh conditions. I realise this sounds nuts, and the questions of free will and a benevolent God are compromised by this line of thought.

I want to end with Keats’s ‘On First Looking Into Chapman’s Homer’:
Much have I travell’d in the realms of gold,
And many goodly states and kingdoms seen;
Round many western islands have I been
Which bards in fealty to Apollo hold.
Oft of one wide expanse had I been told
That deep-brow’d Homer ruled as his demesne;
Yet did I never breathe its pure serene
Till I heard Chapman speak out loud and bold:
Then felt I like some watcher of the skies
When a new planet swims into his ken;
Or like stout Cortez when with eagle eyes
He star’d at the Pacific—and all his men
Look’d at each other with a wild surmise—
Silent, upon a peak in Darien.

I realise there’s a lot going on in this poem, but there’s one thing which I don’t think is at all and want to mention the unfairness of the criticism. I think Keats was fully aware that Cortez never went to Darien (which is not surprising since he had a successful career destroying the Aztec Empire and so on before going back to Spain to end his life in his early sixties as opposed to being bitten and killed by a puff adder or dying of dysentery) and was attempting to convey that he had vision enough to “see” the Pacific. It’s not erroneous at all to my mind. I just wanted to get that in.

In the meantime, this has given me a Thompson Twins earworm even though that song has nothing at all to do with Panama, and I haven’t thought about the fashion chain at all.

DNA – The Only Way?

I’ve been struggling to write a post about the new TV show ‘Pluribus’ but it’s actually huge and therefore hard to talk about in a single piece, so for now, and possibly instead of that, I’ll just be talking about a scientific point it raises and it isn’t really about the series. There’ll be spoilers for about the first ten minutes of the first episode and then I’ll be moving off the subject. Here goes.

At the start of the first episode of ‘Pluribus’, astronomers detect a signal from the TRAPPIST-1 system around 600 light years away in the constellation of Cygnus. It repeats every seventy-eight seconds and consists of a series of four types of signal which they quickly realise represent the four bases of RNA, cytosine, guanine, adenine and uracil. This makes sense, in a way, as RNA is used to send messages from DNA for transcription into proteins, and it’s doing the same job here. This made me wonder a couple of things. How did they know it was uracil and not thymine, and RNA but not DNA? Also, does this mean that RNA and DNA are universal codes for genetic information, everywhere there’s life, or is it individually customised for different recipients, in which case how did they know terrestrial life used that code? Seems like insider information is involved somewhere.

So, crystallising that thought, this is the situation. All known life here on Earth uses one of two complex types of molecules, deoxyribonucleic acid and ribonucleic acid, DNA and RNA. At this point I’m stuck because I have no idea how much is common knowledge. If I get this wrong, I’m going to lose a lot of people. So I’m going to assume that everyone knows the remarkable general double helix with rungs structure of DNA, how its coils are themselves in coils so that it’s packed together very closely most of the time, that most of it doesn’t carry genetic information but has other functions related to it, that it has sides made of alternating sugar molecules and phosphate groups and four types of bases which link up in specific pairs, adenine with thymine and cytosine with guanine. RNA is generated from DNA and has a different, simpler structure, again with a sugar molecule alternating with phosphate groups and again four bases, except that instead of thymine it has a base called uracil. RNA is used to transfer information to ribosomes, which are like playback heads except that instead of sound they produce proteins, one amino acid at a time. Although most species of animal, plant and other organisms use DNA to store their genes, many viruses use RNA instead. RNA is less stable than DNA, so for example whereas animal or plant remains from many millennia in the past can have their DNA information extracted in a form increasingly corrupted with their age, RNA is not the same and doesn’t last long.

This is important. Please tell me if I’m assuming too much and if I’m not writing clearly. I really struggle with brevity, clarity and trying to work out what people do and don’t know about things, and one way of addressing this might be to get some feedback. In a sense, this entire blog post is a test of my ability to communicate clearly and well at least as much as it is about DNA.

So, I have questions, some of which I know some of the answers to but most I don’t. DNA can be considered to have the following components: deoxyribose, phosphate, adenine, thymine, guanine and cytosine. RNA has ribose instead of deoxyribose and uracil instead of thymine. The question is, are any or all of these essential for any molecule carrying genetic information within an organic life form, or are there other possibilities? How rigidly restrained is this aspect of biochemistry? This could be framed as a question about alien life but in fact it’s as relevant to biochemistry as it’s actually known to be on this planet as it is to that possibility.

First of all, the bases. There are two types of these: purines and pyrimidines. Purines have two rings in their molecule and pyrimidines only one. I remember this by thinking that the long name describes the short molecules and vice versa. Purines include some other familiar compounds including caffeine and the related stimulants often found with it. A particularly prominent purine is guanine, which forms the reflective layer at the back of many vertebrate retinae such as dogs and owls and increases their visual sensitivity in low-light conditions, and also the white cross on the back of garden spiders. They tend to be broken down into uric acid, so a diet high in DNA can contribute to gout and kidney stones and also conditions involving a high turnover of DNA such as leukaemia can also have these effects. Pyrimidines strike me as more obscure. Vitamin B1, thiamine, is a pyrimidine, as the name of thymine suggests, but as I understand it, although they’re widespread most of them are not well-known. However, similar pyrimidines to the ones found in nucleic acids are used as anti-cancer and anti-viral drugs.

Hence we have a system with four bases of particular kinds which can pair up with each other and consecutive groups of three bases are known as codons, each encoding for a particular amino acid, which are the blocks of proteins, as well as acting as “punctuation” such as full stops marking the end of a protein synthesis sequence. That’s sixty-four possibilities. However, since other bases can exist, it’s hypothetically feasible that these data can be stored more densely and efficiently. In particular it seems odd that uracil occurs in RNA but not DNA, but the reason for this is that it’s less stable and therefore can’t reliably encode for a long period of time, so it’s not so much that it’s used in RNA as that it isn’t used in DNA, and maybe at some stage it was but wasn’t selected for. This, then, is the first identifiable factor in the structure of DNA which determines its nature. I think there are probably at least four more usable bases, and this would double their data density. What it might not do, however, is enable evolution, as it might be that these bases are less amenable to mutation. For all I know, the first life forms in our lineage may have had different bases but couldn’t evolve as fast and therefore wasn’t able to compete with other organisms and aren’t our ancestors, even though there was nothing wrong with the basis of their genomes.

The next issue is sugar. Two sugars are involved and give their initials to the first letter of DNA and RNA. They’re pentoses, like fructose, rather than hexoses like dextrose or disaccharides like sucrose. Again, the explanation for the difference is durability and stability. The hydroxyl group on the second carbon which is absent on the deoxyribose molecule means it’s more stable than ribose and less likely to be altered by water. The presence of this hydroxyl group on the ribose molecule makes it easier to break down, ensuring that protein synthesis stops when it needs to. However, three- and four-carbon sugars could form the basis of the backbone instead of ribose or deoxyribose. Any more than five carbons stops double helix working: it gets in the way of the shape, making packing into the coils and supercoils unfeasible, and also makes it more reactive and also encourages branching. The double helix arrangement isn’t just pretty. It makes it possible to pack it into a small space, such as in chromosomes. It is possible for hexose nucleic acids to form but they don’t become double helices. Fructose is of course another pentose but the position on its molecule at which nitrogens from the bases can form are in the wrong place and the arrangement would be too crowded. Inulin, which is the daisy family’s alternative to starch which tastes like Jerusalem artichokes because those are in that family too, and sucrose itself both contain fructose but it’s not used in nucleic acids for this reason. It’s also thought that the processes which led to living processes preferred pentoses over other types of sugar, so life built on what was available.

That leaves the phosphate groups. These keep the molecule regular in shape and enable the DNA to bind to histones, which are the proteins making up much of the chromosomes around which it winds. Obviously this doesn’t apply to RNA because it isn’t wound round anything. Actually, it doesn’t apply to prokaryotic organisms such as bacteria either because they don’t have histones, but they do have nucleoid-associated proteins which do similar jobs. Bacterial DNA is in loops called plasmids. Plastids (not plasmids) have less DNA than free-living prokaryotes because many of their genes have been transferred to the nucleus.

Surprisingly, phosphate groups are not essential to the structure of nucleic acids and are in fact weaker than other options. For instance, glycine, the simplest, and the only non-chiral amino acid, can bond the sugar molecules together. Amide bonds are an option. There are also some different arrangements with phosphorus itself. These stronger bonds, though, can’t cross membranes as easily. Now I’ve previously mentioned how phosphorus may be the dog in the manger which explains the Fermi Paradox, but this is clearly not to do with DNA or RNA as it’s entirely feasible for an adequate alternative to DNA to exist without phosphorus, but with glycolysis and the Krebs Cycle where so far as I can tell it really cannot be replaced. This does however open up the possibility of life existing in the Universe in places with rather less phosphorus than this solar system. Incidentally, a decade or so ago organisms were found in a lake which were thought to be able to substitute arsenic for phosphorus in their DNA, but it turned out they were just really good at finding phosphorus.

It does seem, then, that fairly dramatically different but still perfectly functional analogues to DNA and RNA could exist, and even that they might be more likely than those two to form in an environment with less phosphorus. Getting back to ‘Pluribus’, it’s exceedingly unlikely that it’s the kind of series for this to matter. It’s known that there’s a gene for the receptor which detects the odour of Convallaria majalis in the genome received, which is lily of the valley, and this is probably a throwaway reference to that storyline in ‘Breaking Bad’, and this receptor is also found in sperm cells and attracts them towards the ovum, although it’s thought nowadays that the ovum chooses the sperm rather than the other way around. But it leads to two organisms joining. I very much doubt whether any of this matters to the show. However, it is possible to push this further for the sheer scienciness of it all. Yeah, science!

OK, so here are two alternate scenarios regarding the origin of life on Earth. One is that life as we know it originated somewhere in the Universe before the birth of the solar system and spread through the Galaxy, including this solar system. The other is that life arose many times, in this solar system and elsewhere. In the first scenario, for which there’s actually quite a bit of evidence, it’s feasible for many worlds to have life with identical biochemistry, since all of it would have the same ancestry. In such a situation, the transmission of the RNA from TRAPPIST-1 makes sense and isn’t customised for life here, at least as far as genetic code is concerned. However, the fact that it uses the code for this receptor would seem to mean a remarkable degree of convergent evolution, the presence of the gene in the last universal common ancestor with the life in that system or detailed knowledge about life here. Another is that there are various different ways of storing and transferring genetic information, in which case it’s a mild coincidence that the signal happens to be RNA base-pairs. Given what I’ve suggested here, there seems to be no particular reason why the chemical basis of the genome should be the same. There are more complex possibilities, such as there being various different independent empires of life throughout the Galaxy, and this one happens to be the same as ours.

All of this is most unlikely to have much to do with the plot of the series. I don’t know how ‘The Walking Dead’ ended but there was initially speculation about the origin and a possible cure for the Wildfire virus, but later on it seemed to become clear that these questions were irrelevant to the story. If this later changed, to my mind this would detract from the quality of the series. Whether the same is true of the ‘Pluribus’ virus remains to be seen but it doesn’t feel like treating it as a central mystery would add to the quality of the series, which is currently very high indeed of course because it’s Vince Gilligan. What’s occupying everyone’s minds right now, just after episode 5, ‘Got Milk’, is of course whether “Soylent Green is people”.