biology, evolution, Miscellaneous, Science, SF and science, Sunday Science Stories

Sunday Science 08/10/17

Welcome to today’s Sunday Science, with some weird and wonderful animals, some human quirks, and future life on the oceans..

How did the weevil get its shell? Well, they have bacterial symbionts who live inside them with severely reduced genomes. These bacteria do not much more than churn out the amino acid tyrosine, needed to harden the shells. I love how nature is so weird sometimes. Link is to the full scientific paper, so fairly technical.

A fascinating account of the changes in the onset and duration of puberty, which has changed significantly over the years.

Seasteading, which means living on permanent floating artificial habitats, outside the jurisdiction of any government, seems to be taking a step forward. This long thoughtful piece examines the progress and implications of what was, until now, an idea confined to science fiction and libertarian dreamers.

And finally…did you ever collect tadpoles as a child and try and grow them to frogs? Well, toad tadpoles are less cute than they look: they contain potent heart poisons. The researchers thought this was to ward off competition from frogs, but it seems actually to be do with each other – the more toad tadpoles there are, the more toxic they get.

Credit: This week’s featured image via Nature, by Bert Willaert/NPL.

biology, Developmental biology, evolution, genetic modification, Miscellaneous, Science, Science and society, science news, SF and science, Sunday Science Stories

Sunday Science 01/10/17

Here is the this week’s Sunday Science, including truly wearable tech, tsunami-borne sea creatures and duck penises.

Do you have one of those smartwatches which measures your heart rate when you exercise? Does your smartphone automatically keep track of how many steps you take each day. Well, the future both for this and for medical monitoring may lie more in flexible, wearable sensors, or the bodynet, as this fascinating piece in Nature of the latest merging of scifi with science fact explores.

Male ruddy ducks regenerate their penis every year, apparently, one of those glorious facts you never knew you needed in your life. However, they may grow an extra-long (as in, 18cm!) or an extra-short one (only 0.5cm), due to fierce sexual competition.

Salmon have returned to a river in Derbyshire for the first time since the Industrial Revolution.

Continuing the CRISPR revolution, it has been used to genetically engineer human embryos to study early embryo development, revealing an important role for a gene in embryo implantation and miscarriage risk.

This week’s featured image is of marine sea slugs from a Japanese vessel from Iwate Prefecture, washed ashore in Oregon in April 2015 [Image credit Mark Chapman via Science Daily]. Thousands of creatures were washed across the ocean as a consequence of the Japanese tsunami, a study published in Science magazine discovered. Such “rafting” events are natural, of course, but what’s not natural is the extent of this migration, much of which was enabled by animals riding along on our non-degradable plastic waste. Nearly 300 species have appeared on the west coast of the US and Hawaii. This is potentially setting in motion a radical ecological experiment.

biology, Climate change, News, Science, science news, SF and science

Sunday Science 24/09/17

Here are today’s Sunday Science links, for stories you may have missed in the mainstream media.

Today’s featured image is that iconic mammal the snow leopard, which has been downgraded from “endangered” to “vulnerable” on the IUCN Red List of endangered species. Its fellow mammal, the Christmas island pipistrelle bat, was not so fortunate: it is the first Australian mammal in 50 years to be declared extinct. [Leopard photo Vincent J Musi/NGC, from Nature.]

Defects in next generation solar cells, made of perovskite, can be repaired using light. Perovskite is abundant and cheap, but tends to have flaws which affect its efficiency in solar cells, so this is an important step forward.

A new analysis indicates that achieving the target of limiting global warming to 1.5C set by the Paris Agreement might be more feasible than thought (if still tough going). For a far less technical report on this, there’s a decent news article here.

A dinosaur called Chilesaurus may be the missing link between the plant eaters and theropod dinosaurs, which includes the famous carnivorous ones such as T. rex.

Finally, a sweet little piece on the science in Conan Doyle’s Sherlock Holmes stories, including a couple of neat examples of fiction predicting scientific advances (although the psychology stuff I think is a bit unconvincing). Trivia: Holmes is the only fictional character to be made an honorary Fellow of the Royal Society of Chemistry.


biology, medicine, Organ transplantation, Robotics, Science, SF and science

The future of artificial limbs

I’ve written on this blog before about how advances in our understanding and application of genetic engineering and stem cell technology is raising the realistic possibility of growing replacement human organs. What I haven’t really covered is replacing limbs. This is a somewhat different proposition: if we grew human organs in a dish (so to speak), we’d transplant them into the people that needed them. These kinds of transplant operations now have a substantial surgical history and practice behind them, so it wouldn’t require the development of new techniques. Replacing limbs, however, does not: people have instead relied on artificial prostheses. These are a staple of science fiction too: from Luke Skywalker to the 6 million dollar man to Robocop, prosthetics and – at the extreme end – full human “cyborgs” are everywhere. Replacing limbs with actual biological limbs, however, well…the first thing that springs to mind is Frankenstein, which is unfortunate. There are a few scifi societies where regrowing replacement limbs is the norm (notably lain M Banks’ Culture) but scifi seems to think prostheses are the future, as they are our present. But are they?

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biology, Developmental biology, Explainer, Opinion piece, Science, Science and society, SF and science

Will we ever have artificial wombs?

A few years back I attended the annual conference of the British Society for Developmental Biology. There was a discussion session towards the end of the day concerning future developments and directions in our field of research, namely how one goes from the early embryo to, ultimately, the adult human (or other organism). Into a lull in the conversation, my then-boss, who was heavily pregnant with twins and very uncomfortable, interjected the following question: “I only want to know one thing right now: when are we going to be able to grow babies in artificial wombs?” Good question…

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biology, Opinion piece, Science, science fiction, SF and science

Of wasps and aliens

I remember as a child I liked to watch a lot of nature programmes that my mother would record for me off the television (recorded on VCR, anyone under about 30 will be bemused to know!). One of the ones that fascinated and horrified me featured the tale of a parasitic wasp that captured a caterpillar, paralysing it with its sting. It then laid eggs in the body of the caterpillar which hatched and ate their hapless victim alive. Gruesome!

wasps caterpillar
Caterpillar chestbursters, i.e. wasp larvae

Of course, this is the obvious reason why a lot of SF (particularly films) like to feature alien biology as being parasitic. They suck you in (pun intended) with that element of horrified fascination – and you can get a lot of mileage out of that (if not necessarily high-quality drama). It’s not like there aren’t plenty of horrible examples of parasites – here’s a relatively cute cartoon video, with only some nasty pictures, but there’s plenty worse to search for if you have the stomach for it. I still recall that parasitology practical in my second year pathology module with horror…not least because the entire room smelt of, well, poo.

The gruesome wasps were of course one of the inspirations behind Alien, one of my all-time favourite films. The film is stuffed with metaphors for sex, rape and birth (although probably anyone who has given birth probably notices the birth thing more…), but interestingly the director, Ridley Scott, said that:

“It has absolutely no message…it works on a very visceral level and its only point is terror, and more terror.”

Ah, visceral, such a great word – and a key one. This is pure Body Horror – as, indeed, a lot of horror is. These bad aliens don’t just invade, blow up your cities and kill you – they take over your body. Being bodily creatures, that squicks us. Badly.

The infamous “facehugger”. 20th century fox.

What’s even worse is when some of them take over your mind. Again, this isn’t without precedent – a lot of parasites change the behaviour of their host organisms. Mice infected with Toxoplasma, for example, lose their fear of cats, because the parasite’s goal is to infect a cat, it’s next host. Stargate’s Goa’uld are snake-like parasites that completely take over the body and the mind – the personality “running” the body is that of the alien. This might have been more horrifying if most of the Goa’uld weren’t pantomime villains often played for laughs as well.

From Stargate SG-1, MGM studios.

Far more interesting were the rebel Tok’ra – still Goa’uld, but ones that did not suppress their host and shared the body equally, meaning that you effectively got two people for the price of one. Symbiosis, in other words, as was also seen in Star Trek’s Trill, although here the personalities merged. Unfortunately the series under-utilised these rather interesting characters, and favoured the hugely boring Jaffa, which carried the larval Goa’uld, and were a frankly cliched noble warrior race. I don’t know about you, but I could definitely do with fewer noble warrior races in my fandoms.

Jaffa v Tok'ra
Stargate SG1, MGM studios

Of course, both these examples are hugely unrealistic. Parasites are highly specialised, usually adapted to infect either only one species, or a few at different stages of their lifecycle (e.g. the malarial parasite infecting both us and mosquitoes).  It’s vastly unlikely that an alien species would ever successfully manage to parasitise something from another planet, like us, so rest easy in your beds. (I grant you the Alien xenomorphs were implied to be engineered biological weapons). One of the key problems a parasite has is to evade the host’s immune system from attacking it. Another is reproduction – how are you supposed to meet parasites of the opposite sex when they are stuck somewhere inside another host body? For this reason, many are hermaphrodite, and self-fertilise. Why then does the Alien xenomorph have a queen, only one individual in a colony capable of reproducing (and whose job it is to do little else)?

The whole xenomorph “biology” setup is a weird mash-up of ideas. You have the facehuggers, which hatch from eggs and have to find hosts, which lay another kind of egg down the (human) host’s throat. That then hatches as a chestburster which grows into a bigger adult version of itself that attacks and often kills future hosts, but is supposed to bring them back to the queen so they can be cocooned, ready for the eggs that the queen has laid. It’s taken the idea of the parasitic wasp and the idea of a beehive and produced something completely biologically implausible. Again, I think this is for maximum squick factor. You don’t just get the parasites, you get big monsters stalking you (bringing out a lot of primal childhood fears of something big and scary eating you), and finally one huge and terrifying dragon at the centre of it. You have to love it. I can only think that Stargate adopted the queen system because of Alien, and not because, well, they thought it through at all.

Only here to freak you out further: the Alien queen. 20th century fox.

It’s not the only type of parasitism you can encounter of course. John Wyndham’s Midwich Cuckoos exhibited a form of brood parasitism in which human women became pregnant with and later raised as their own children, non-human aliens (very like cuckoos, which lay their eggs in other birds’ nests). It’s a more insidious form of societal takeover in this case, not so much a biological one, although it is possible that the humans would later be supplanted by the aliens if they do not necessarily require human hosts.

Cuckoo egg
Cuckoo egg in reed warbler’s nest

This starts treading into the territory of aliens altering our society, as opposed to our bodies. Here, the concept of organisms being interlinked and inter-dependent in ecologies, inspired by the Gaia hypothesis, and the rise of environmentalism, led to parasitism and symbiosis being used as tools to explore human relationships with other species in general. Indeed, the Encyclopedia of Science Fiction notes that:

…Exotic biological relationships are transformed into metaphors applicable to social relationships (or vice versa), relationships between humans and other intelligent beings or even, in a psychological sense, relationships between humans and their environment. This is, of course, a totally unscientific use of scientific ideas, but it can be very effective as a literary device….Thus, for example, the hive-mind becomes in SF not so much a mode of social organization pertaining to insect species as a metaphor for considering possible states of human society. Similarly, symbiosis becomes symbolic of an idealized relationship between humans, or between human and other beings.

Indeed, if you don’t get body horror, you get a kind of social horror, like the hive mind of the Borg. Yes, I know this isn’t strictly parasitism, but it is essentially being invaded and taken over by an alien, and it manages to work in that other type of “other” to fear, machine-based life, in a creepily effective amalgam of the two. Oh, and they have a queen as well. Why do they have a queen? Maybe it’s something to do with the linking of fears about communism and “mindless worker drones” (although communist societies shouldn’t, theoretically, have a monarch at the top). Maybe, at the end of the day, modern humans just have to believe that somebody has to be in charge. Or that lots of aliens evolved from something like bees and wasps.

Those nature programmes have a lot to answer for.

biology, genetic modification, Science, science fiction

Alternative biochemistries…on Earth

Firstly, sincere apologies for the reduced frequency of posting. New job, and new term in full swing (not to mention a lot of baby illness), has meant very little spare time. Things will be slow for a while, but I hope to pick up again more in November.

Lifeforms based on biochemistries other than that found on Earth are a small but firm favourite in science fiction, which is interesting given that so many aliens found in science fiction fall into the “Rubber-Forehead alien” trope beloved of Star Trek. Some of these exotic organisms are just microorganisms, which makes it a bit easier – like the infectious agent in Wyndham’s The Andromeda Strain. I would love to create a truly alien world with fully-fledged thinking aliens based on a unique biochemistry…but I have to say to do so properly would require an enormous amount of research and work (which is to say it would take far more time than I feel I will ever possess!)

The classic is probably the “silicon based lifeform”, perhaps most recognisably in the Horta, the, er, rock beast thing that Spock communed with in Star Trek (after they’d finished zapping it, anyway)

From “The Devil in the Dark”, copyright Paramount/Viacom, via MemoryAlpha

The X-files went one further and had a silicon-based fungus that sent you slightly bonkers (of course). Our life is, famously, “carbon-based” – this is actually referring to the vast majority of organic compounds that are built around carbon and its remarkable talent for bonding with other elements. Silicon, a similar element, is often argued as an alternative, but there are problems with this: silicon is a much larger atom, and it doesn’t form bonds with other elements nearly so readily as carbon does. Moreover, carbon is far more abundant in the galaxy. In fact, on our planet, silicon is the more abundant element, but life arose from carbon anyway.

As an interesting aside, a thermophilic bacterium that lives in hot springs has been found to have a fundamental metabolic enzyme, cytochrome c, that can incorporate silicon into organic molecules, really as an accidental byproduct. Researchers have recently artificially selected this enzyme so that is several thousand times more efficient at this process; not that useful, at the moment, but very interesting nonetheless (and yes, they thought of the Horta too!).

Now researchers are trying to make an organism with a modified genetic code. The genetic code is how the information in DNA is converted into a protein. Three nucleotide bases of a DNA (that sequence of A,T,G and C you’ve all seen) codes (via a “messenger” RNA intermediate) for one amino acid, the building block of a protein. A few encode “start” and “stop” signals for the synthetic machinery. There are about 20 commonly used amino acids in living organims (on this planet), although the code allows for more – there are 64 of these “codons” in fact, and some of them are redundant; that is, they can code for more than one amino acid (you will notice from the table below that it is the last base in the triplet that tends to vary). This reduces the possibility of a mutation in the DNA sequence actually causing a potentially damaging change in the protein.


What these researchers have now done is eliminate 7 of the redundant codons in the bacterium E.coli, to leave 57, reasoning that since they were redundant this was unlikely to do the cell any harm. This may sound a little underwhelming, but it is no mean technical feat: they would have to remove every instance of these codons (all 62,214 of them) in the nearly 4 million bases of DNA in the bacterium. Removing them piecemeal would have taken too long, so they essentially re-sequenced the entire genome from scratch.

From Ostrov et al, 2016

Figure 2A: Codons AGA, AGG, AGC, AGU, UUA, UUG, and UAG were computationally replaced by synonymous alternatives (center). Other codons (e.g.,UGC) remain unchanged. Color-coded histograms represent the abundance of the seven forbidden codons in each segment.

Why bother? Like a lot of speculative science, it’s a little hard to tell how useful it will be, but there are a lot of potential uses. E.coli is used to synthesise a lot of proteins useful to us, like a little bioreactor, and this could render it immune to infection by viruses that depend on the codons it no longer uses. Additionally, these seven removed codons could now be used to code for a new synthetic amino acid not normally found in nature, potentially opening up a world of novel proteins. (Oh, and yes, they did build in a failsafe). This is still a work in progress; the genome hasn’t been completely assembled yet, but it’s an interesting and conceptually radical idea. It’s not a non-carbon based biochemistry, to be sure, but, if it were taken a few steps further, it could mean we could create an entirely synthetic organism with an entirely different genetic code to our own. And that’s pretty science fiction, if you ask me.


Ostrov et al, 2016: Design, synthesis and testing toward a 57-codon genome, Science Vol. 353, Issue 6301, pp. 819-822 DOI: 10.1126/science.aaf3639