Biological therapy, biology, genetic modification, medicine, News, Science, science news

A successful first for gene therapy

Who would like to hear some really good news? Thought so. One of the promises of the molecular biology and genomics revolutions was that gene therapy – replacing defective, disease-causing genes with functioning ones, or otherwise treating these diseases by genetic means – would become a reality. Even, optimistically, something commonplace. Like so many things, however, it has proved more complicated than hoped, and those longed-for treatments elusive. There has never been a therapy of any kind that alters the disease progress of a neurodegenerative disease – until now. Continue reading

biology, Science

Human embryo development in 3D

Well, December proved to be rather more busy than anticipated, what with moving house and getting tonsillitis etc….and whilst I’m on the excuses, this is going to be a very busy term for me. So let’s start the New Year with a very short little post about my own favourite subject, developmental biology.

Researchers have compiled a 3D atlas of human embryology by making interactive three-dimensional digital reconstructions based on microscopically sectioned human embryos. It covers the first two months of gestation, in which the major organ systems and body plan are established, and it’s well worth a look and free to access. You can download interactive PDFs. I’ve spent ages playing with them. From the related Science paper:

We created a three-dimensional digital atlas and database spanning the first 2 months of human development, based on analysis of nearly 15,000 histological sections of the renowned Carnegie Collection of human embryonic specimens. We identified and labeled up to 150 organs and structures per specimen and made three-dimensional models to quantify growth, establish changes in the position of organs, and clarify current ambiguities. The atlas provides an educational and reference resource for studies on early human development, growth, and congenital malformations.

Even if you have no real clue about the biology it will give you an appreciation of the complexity of the early embryo and is frankly quite beautiful in places; don’t be surprised how little like a human it looks like in the early stages (it does in fact look very like the chick embryos I used to work on; evolutionary conservation in action). If you are a developmental biologist, it’s a useful resource and quite fascinating.

There are still huge amounts we don’t know about human development in particular (as compared to model organisms such as mice). One of the things that can be surprisingly hard to work out is what embryonic tissue an adult organ is derived from, not to mention the complex process of, say, making a kidney from a little tube. Studies like this are really illuminating these processes and advancing our understanding of ourselves.

biology, genetic modification, Science, science news

Artificial carbon fixation

Probably most of us are aware that plants take sunlight and use it to “fix” carbon from carbon dioxide (CO2) in the atmosphere into sugar compounds by the process of photosynthesis. In fact, natural photosynthesis removes about 100 billion tonnes of CO2 from the atmosphere every year. The natural release and absorption of CO2 is balanced – but humans are releasing over 30 billion tonnes per year on top of that, which is increasing the CO2 in the atmosphere and causing global warming; this exceeds the ability of plants to remove it. But what if we could find a way to make carbon fixation more efficient? Now, a team of researchers have done just that. Continue reading

biology, evolution, Science, Science and society

The (evolutionary) roots of lethal human violence

How much of human violence is innate, and how much of it is shaped by our environments? Are we a uniquely violent species? These are questions philosophers and social scientists have tried to answer for centuries. Now researchers have done an evolutionary comparison – and conclude that the rate of lethal human violence is six times that of the average mammal…but about average for a great ape.

Continue reading

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