This video was created by Japanese artist Isao Hashimoto.

Kind of terrifying? Kind of eerily beautiful? A time lapse of every nuclear explosion from 1945-1998. It starts fairly slowly, but picks up at a truly alarming rate.

“Now, I am become Death, the destroyer of worlds.”

60 years ago today, Nature published an article by Francis Crick and James Watson. It was titled, “Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid”. Finally, someone had figured out the structure of DNA. That alone was a worthy achievement, after the years of work put into it. But far more importantly, the structure suggested that DNA could be the genetic material of organisms… it could be how genetic information is passed from one cell to its daughter cells, from one organism to its offspring.

After describing how the base pairs link up in a predictable way (adenine with thymine, guanine with cytosine), the authors wrote what would become the highlight of one of the most famous academic papers of all time, and possibly one of the best examples of arrogant false modesty:

“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material”.

The rest is history. The genetic code. The Human Genome Project. Blatant sexism in science. You’ll probably be reading a lot about these as we hit the 60th anniversary of the paper. It’s a story worth revisiting, or enjoying for the first time. The work by Watson and Crick is a fantastic story because it involves scientists standing on the shoulders of giants, taking the results of other scientists’ experiments and piecing them together, and answering a huge scientific question with a simple explanation. At the same time, the story of this discovery demonstrates that scientists are people, for better or worse.

Gene names can be very confusing and difficult to remember, so there are many abbreviations in biology. For example, the gene insulin-like growth factor 1 is abbreviated to Igf1. Does that make it easier to remember? Who knows. But I believe the use of abbreviations is partly responsible for the incredible confusion over homeobox and Hox genes. And I do mean incredible. It’s very obviously a confusing topic for students, or anyone new to evo-devo, developmental genetics, or gene regulation… but it’s so much worse than that. Professional publications make the mistake, academics make the mistake, and they do it often. I think the reason it keeps happening is that the word “Hox” appears to be a shortened “Homeobox”. All over the internet you will see the terms used interchangeably, and sometimes with the apparently shortened version in brackets. “Homeobox (Hox)”. This otherwise decent glossary for Epigenesys manages to dump the terms homeotic, homeobox, and Hox into one single paragraph and glossary entry, which is of little help to a confused student seeking clarity. So let’s clear this up, and I’ll keep it quick. 

First, let’s go over the facts, and the answer, before we discuss why these confusing names have been chosen. Scientists discovered that there are some genes that contain a very conserved region of DNA we now call the homeobox. When I say very conserved, I mean it. You have homeobox genes, the birds outside do, the grass outside does… even yeast does. The origin of homeobox genes is ancient, definitely pre-dating the origin of animals. This 180-base-pair homeobox codes for a 60-residue chain known as the homeobox domain (or homeodomain). So the region of the gene is known as a homeobox, the region of the protein is the homeodomain. The explanation for why it is so conserved across organisms, through hundreds of millions of years of evolution, is that its function restricts its evolution. The homeobox domain binds DNA (or RNA), allowing a protein with a homeodomain to act in gene regulation. For example, these proteins can be used to turn genes on and off. It’s an invention of evolution that’s persisted through the origin of the fungi, plants, and us animals, and the homeobox itself hasn’t changed much at all. So there’s your definition of a homeobox gene. It isn’t a specific gene, it’s a huge and ancient group of genes that all contain the homeobox, a region of DNA that codes for a domain which can bind to DNA.

Every Hox gene is a homeobox gene, but not every homeobox gene is a Hox gene. The homeobox genes have diversified so much through evolutionary history that there are now distinct classes of them. The most famous is definitely the family of Hox genes. This is also where the terms come from. When scientists first discovered the homeobox domain, they found it because they were studying animals that had mutated Hox genes. These mutants often had body parts in the wrong place, and were described as “homeotic mutants”. When they identified the genes causing the mutations, they discovered that they all shared a common motif, so they named it the homeobox. This is one of the most incredible discoveries in biology, as they quickly realised that the homeobox is found in genes from humans, flies, jellyfish, daffodils, yeast, and so on. But the actual genes they had discovered were a distinct group of homeobox genes, which we now call the Hox genes. They definitely are homeobox genes, and they regulate other genes.

Think about the confusion here. Hox genes are a distinct family of homeobox genes. Scientists discovered the homeobox motif by investigating which genes caused homeotic mutations. What they had found were the Hox genes, so calling Hox genes homeotic is fine. But they didn’t understand at the time that the homeobox motif is found in many genes that aren’t Hox genes. Many homeobox genes have absolutely nothing to do with body parts growing in the right or wrong places. But when they named the homeobox, they only knew of the Hox genes they were discovering via the homeotic mutants. This is where almost all the confusion stems from. Despite being called homeobox genes, most don’t cause homeotic mutants if modified. The Hox genes, a specific family of homeobox genes, are responsible for the homeotic mutants.

In us bilaterian animals, the main role of the Hox genes is to specify anteroposterior identity to your body. It’s a complicated system, but we’ll keep it simple. The Hox genes play a role in determining which body parts grow where on the body. So by messing with them, you can actually cause eyes to grow on arms, legs to grow where antenna should be etc. But there are plenty of other non-Hox homeobox genes, entirely different families, with entirely different roles. The Hox genes control the body plan along the anterior to posterior axis in us bilaterian animals, but there’s still some uncertainty over their precise role in non-bilaterian animals, but the Hox genes appear to be unique to animals. You do not find Hox genes in plants and fungi. They have homeobox genes, but not the Hox genes, which appear to have arisen very early in animal evolution (there is evidence that sponges had Hox genes too, but have since lost them).

We know so much about homeobox genes, especially the Hox cluster, that we could discuss it all day. The evolution of the Hox, ParaHox, and NK clusters is quite fascinating, as are the roles of these gene families in a developing animal. I’ll save these for future entries. Today’s point is mostly just an early-morning rant. Hox genes are homeobox genes as they contain the homeobox, but homeobox genes include Hox genes, ParaHox genes etc. The terms are not interchangeable. It’s such an easy mistake to make, that it appears in books, academic websites, and helpful videos on YouTube. Just keep it in mind and focus on what it is exactly that they’re talking about. It’s not necessarily wrong to describe a mobile phone as technology, but the terms aren’t interchangeable. You can’t go around describing technology as mobile phones. It makes no sense to say, “the electron microscope is a wonderful mobile phone”. You can describe a Hox gene as a homeobox gene, because that’s exactly what it is. But note that the terms aren’t interchangeable.

Here’s a video of the happy part. This footage is from last year, when eight blue iguanas were released into the Salina Reserve. You can see they are left in little wooden structures. These provide shelter and security for the animal as it makes the transition from captivity to life in the Salina Reserve.

This is a message for all the amazing people who have come to the brilliant Edinburgh International Science Festival. If you’re up for some shenanigans, and don’t have a weak stomach, come along to see us at the Ugly Animal Preservation Society! If comedy and nasty ugly are your things, you’ll be in a disgusting heaven!

As well as myself, you’ll see performers including Helen Arney (Uncaged Monkeys, Festival of the Spoken Nerd), Simon Watt (Inside Nature’s Giants), Steve Cross (Science Showoff), the guys from Punk Science, and more! It will be funny, interesting, and horrific in equal measure.

It’s on Wednesday night, 9pm-11pm. You can get all the details here!

With such success as a scientist and science-communicator, and with such controversial views, he seems a prime target for memorable quotes. It would be quite easy to find a great creationism-bashing quote from Huxley, or a controversial view on race. But the whole point of this series of posts is to go over weirder quotes, the types that might not appear in a quick biography of a person. I’ve chosen to avoid the controversy altogether. The following quote is taken directly from a scientific paper, yet would seem quite out of place in modern papers. While others were slaving away in labs with mice pressing levers, Huxley was contributing to behavioural biology while having what seems to be a rather pleasant time outdoors.

“A good glass, a notebook, some patience, and a spare fortnight in the spring – with these I not only managed to discover many unknown facts about the crested grebe, but also had one of the pleasantest of holidays. Go thou and do likewise.”

- Julian S Huxley (1914). The Courtship habits of the Great Crested Grebe (Podiceps cristatus); with an addition to the Theory of Sexual Selection. Proceedings of the Zoological Society of London, 84(3), pp. 491–562.

“I never received any encouragement from my family to continue my academic career; in fact my determination to attend the University met with derision. At home, scolding and fault-finding were my daily portion”

Hyman wrote an incredibly successful textbook, A Laboratory Manual for Elementary Zoology (1919), which generated enough income that it allowed her to become an unpaid research assistant at the American Museum of Natural History. There, with no assistance, she accomplished a truly epic piece of work that has been of great use to zoologists since. She wrote and illustrated her six-volume treatise on The Invertebrates, a comprehensive work expertly analysing invertebrate animals. Unfortunately she never covered the entire topic due to ill health, but the first six volumes were an incredible accomplishment for an individual. As well as being the go-to source for invertebrates, Hyman also developed several important theories that had big impacts on modern biology (e.g. she argued, correctly, that echinoderms were more closely related to us chordates than the annelids etc they had often been grouped with).

Despite the incredible impact her work had, I don’t see her name that often. I’d like to give her a mention here on the blog as I’ve always found her workload, her accomplishments, and her background very interesting. I have a couple of quotes that hopefully get across her character, or what I believe her character to be, from everything I’ve read.

“I was brought up in a home devoid of affection and consideration. My father, an ageing man constantly worried about his declining fortunes, took practically no notice of his four children. My mother regarded children as property to be ordered about as she liked and to be used for her benefit. She seemed incapable of feelings of affection. She was also thoroughly infiltrated with the European worship of the male sex. My three brothers were brought up in idleness and irresponsibility, with the result that two of them never earned more than a bare living, whereas I, as a mere child, was required to participate in the endless work of the big ten-room house. For this reason I have violently hated housework all my life.”

“By about 1930 I perceived that I could live on the royalties of my books. About this time, also, Professor Child came to the retiring age. Therefore I resigned my position as research assistant in the zoology department and have had no paid position since. I am amply supported by the royalties of my books, and so was left free to write a treatise on the invertebrates.”

- Libbie Hyman, Biographical Memoirs. National Academy of Science.

In my own experience with other people, this video has changed opinions on the intelligence of non-human animals more than any other. It also highlights the fact that “intelligence” is clearly an ambiguous term. We’re more intelligent than chimps if we consider our use of language. But this video demonstrates that if we were to measure intelligence differently, say with working memory, then chimps beat us. And with spatial memory, plenty of other animals beat us. And so on.

This is one of my favourite videos on the internet. Enjoy!