Komodo Dragon Christ Child

For centuries, the Christian world has marvelled at the wonder of the immaculate conception, naming it a miracle; a myth, but if we look hard enough we can see that it is a miracle that nature has created all on its own.

The Komodo dragon (Varanus komodoensis) is one of the most endangered species of lizard on the planet. With only 350 breeding females left in existence¹ it is placed on the IUCN Red List of Threatened species and considered vulnerable². These beasts are endangered mainly because of human factors like hunting and habitat loss1 and their predicament is made even worse by the fact that they live as largely solitary creatures and rarely meet appropriate mates.

However, female Komodo dragons are strong, confident lizards who don’t need any male – they can produce a clutch of eggs without being fertilised by a male³.

If a female has not encountered a male in a while she can self-fertilise her eggs and give viable offspring that are not simply clones of the mother3. The way she does this is very clever: in regular sexual reproduction, the genomes of the male and the female are combined to give offspring that are genetically different from both of the parents. This is a characteristic which is vital to natural selection as it enriches the gene pool. So how does a self-fertilising female produce genetically different children?

Well what she does is a complex shuffling of the DNA present in her egg cells which gives each one a double set of chromosomes which have mutated such that each one has a different genotype. We know that the female has definitely not mated with a male as if we consider the gene pool in her clutch alone, it displays the exact genotype of their mother³. This is called parthenogenesis.

The example of the Komodo dragon is relatively rare however, with parthenogenesis occurring in only about 0.1% or vertebrate species4, most of these being other lizards and snakes⁵. Where we see this phenomenon most is in the winged insects.

What we see in these organisms is that eggs left unfertilised (i.e. untouched by male member) develop in to male insects. We see this in all the hymenoptera, the winged insects; so that means fruit flies (the geneticist’s favourite), dragonflies and honey bees. This occurs because these insects, somewhat unusually, can develop and function with only a single set of chromosomes, unlike humans which must have two (and only two) sets. Hymenopterans have their sex determined by their number of chromosomes, in essence⁶. A single set of chromosomes makes a male and any more makes a female. Thus an egg left unfertilised will ultimately become male offspring. This is observed as an important part of the population dynamic we see in honey bees.

But what about humans doing parthenogenesis? Parthenogenesis presents a promising opportunity for the production of human stem cells. As you may know stem cells hold incredible potential in medicine, they are essentially the most basic form of cell and still hold the potential to multiply and develop in to any type of cell, or tissue or even a new organ like a heart. It is for this reason that they may in the future be used for organ transplants.

Currently, stem cells obtained for research purposes are obtained from aborted foetuses. This is a matter of some controversy. Parthenogenetic development of stem cells from a woman’s egg cells may hold the key to a more ethical method of acquiring stem cells⁷.

This may be done by taking the eggs from a consenting female donor and essentially tricking them into thinking that they had been fertilised so that they developed in to a ball of cells called the blastocyst7, the next stage in the development of the foetus. This may be seen to be more ethical as the cells are not becoming anything relatively near a developed baby, both in shape and in size.

But all we are doing in this endeavour is attempting to replicate a mechanism already seen in nature. As usual, nature is at least one step ahead of us; our technology is already rendered obsolete by nature and we are barely managing to catch up with it, and the Komodo dragon or the bumble bee’s parthenogenetic ability is only one example of that.

References

1. Federation, W. W. Komodo Dragon, King of the Lizards, URL:http://wwf.panda.org/about_our_earth/teacher_resources/best_place_species/current_top_10/komodo_dragon.cfm, 2012
2. List, I. R. Varanus komodoensis, URL:http://www.iucnredlist.org/details/22884/0 (2012).
3. Watts, P., C., Buley, Kevin, R., Sanderson, Stephanie, Boardman, Wayne, Ciofi, Claudio, Gibson, Rischard,. Parthenogenesis in Komodo Dragons. Nature 444, 1021-1022, doi:http://dx.doi.org/10.1038/4441021a (2006).
4. White, M. J. D. Animal Cytology and Evolution. (Cambridge University Press, 1973).
5. W. Booth, L. M., R. G. Reynolds, G. M. Burghardt, E. L. Vargo, C. Schal, A. C. Tzika, G. W. Schuett. Consecutive virgin births in the new world boid snake, the Colombian rainbow boa, Epicrates maurus. Journal of Heredity 102, 759-763 (2011).
6. D. P. Cowan, J. K. S. Functionally reproductive diploid and haploid males in an inbreeding hymenopteran with complementary sex determination. Proceedings of the National Academy of Sciences of the United States of America 101, 10374-10379 (2004).
7. Ester Polak de Fried, M. D., Pablo Ross, M.Sc., Gisela Zang, M.Sc., Andrea Divita, M.D., & Kerrianne Cunniff, M. S., Flavia Denaday, M.D., Daniel Salamone, M.Sc., Ann Kiessling, Ph.D., and Josie Cibelli, Ph.D. Parthenogenetic blastocysts from frozen oocytes. Fertility and Sterility 89, 943-947 (2008).

Martian DNA

Genomics maverick Craig Venter, life synthesiser and human genome cracker has conquered all Earthly summits and has set his sights on the next frontier: Mars.

Last week Venter revealed that he plans to send a DNA sequencer to Mars in his “biological teleporter” which will sequence any DNA it can find in the Martian soil and beam the data back to Earth. This eliminates the risky and potentially costly procedure of returning any physical samples to us in a useful form.

We’ve been searching for life on Mars for the past thirty odd years though, why haven’t we found it? And what makes Venter so sure he can succeed?

Venter is looking for something we’ve not looked for before, specifically DNA, what we know as the basis of all life on Earth. One thing we’ve learned recently about the building blocks of DNA is that the sugar that forms its backbone has been found floating around in space. Maybe they were thrown out from the fallout of asteroid collision that created our moon from primordial microbes on the Earth that was. Maybe they weren’t, but however they got there, there’s reason that they couldn’t settle on Mars and start making machines – life!

In the past, searches for organic chemistry on Mars have turned up nothing but ambiguity, most famously the Viking landers. These crafts found evidence of metabolic chemical reactions like those we see on Earth however the unusual content of the Martian soil may have corrupted the results of the experiments and any conclusions in favour of life have been more or less thrown out of the window. What Venter is looking for now is not simply reactions indicative of life but the chemical makeup of it itself.

Venter is not alone however in his search for DNA on Mars. A group at Massachusetts Institute of Technology called Search of Extraterrestrial Genomes (SETG) is working on building their own genome sequencer aimed at use on the red planet. SETG has divulged significantly more information than Venter has however. They are looking at identifying and sequencing both DNA and RNA (DNA’s older brother) using a next generation sequencing machine on a computer chip called Ion Torrent. SETG is seven years in the making and will search for genomic material made by something still living to anything synthesised up to a million years ago.

All of these plans are well meaning and incredibly exciting, but there’s every chance that if there is life on Mars, it’s still going to elude us because it’s not DNA based. Nevertheless if we do find DNA on Mars yet more weight is added to the hypothesis that life was seeded here and on Mars by passing asteroids. This would suggest that there might also be life in innumerable other locations throughout space, and how awesome would that be?

Living up to his reputation for arrogance and audacity, Venter has put forward that he has no doubt that there is life to be found on Mars. He says “there will be DNA life forms there”, this author for one hopes he is correct.

Bird Flu Redux?

In the past couple of months the story of the creation of a hyper-virulent strain of bird flu by Dutch virologists has caught the attention of many in the scientific establishment as well as those in government. Yes, these results and conclusions has sparked a row over the scientist’s right to publish and has forced us even to question the purpose of the scientific endeavour itself. The US authorities, quite rightly so, raised the issue that publication and possession of this knowledge is a potential target for nefarious exploitation and could usher in a new era of bioterrorism.

In September of 2011, it was reported that Ron Fouchier at the Erasmus Medical Centre in Rotterdam had successfully made a H5N1 virus - which causes bird flu - able to spread between mammals in his lab. This was a feat that had not before been achieved and many virologists had postulated that it was not even possible.

Fouchier’s H5N1 is also miles more infectious than traditional bird flu and was seen to be at least so infectious as seasonal flu. This is the factor that has previously prevented a bird flu pandemic, it's deadly enough but simply too poorly infectious for a deadly killer virus outbreak like in the movies as hyped by the media, and likely never would be.

However, Fouchier and his team have proved this to be wrong. They showed that only five specific mutations were sufficient to transform the virus in to a potential Hollywood style killer.

Initially the virus was given three mutations which before had shown that the virus could be transferred to a mammal. This allowed the virus to infect Fouchier’s mammal of choice - the ferret chosen for its similar response to viral infection to humans - and kill them but not infect fresh healthy subjects. So far business as usual.

The three mutation virus which killed these ferrets then was isolated from dead ferrets and reinfected in to healthy ones in a contained and stringent procedure. This is a common method for making a virus adapt to a new host and was iterated ten times, with virus shed from the tenth test group becoming infectious enough to infect a healthy ferret and kill them.

Fast forward to November and the US National Science Advisory Board for Biosecurity (USNSABB) decides to delay the publication of the work of Fouchier et al on H5N1 on grounds that it could in the wrong hands become a weapon or further work on the so-called “armageddon virus” could allow it to escape the lab and enter the population.

As the story stands at this point, things appear to be being hideously sensationalised and misrepresented. Some articles on the subject appeared to imply that Fouchier et al “DELIBERATELY [sic] creat[ed] armageddon bird flu virus” as though their work had been funded by the Lex Luthor Institute for Evil. All Fouchier et al were trying to do was find out if it was possible for H5N1 strains like this to evolve and how it could be prevented, better monitored, treated and cured.

Eventually, Fouchier was allowed to publish by the USNSABB, initially with certain data redacted from the finished paper and made available only to accredited researchers, although this decision was soon overturned and the USNSABB came out in favour of publication.

It was the Dutch authorities who next threatened Fouchier’s right to publish. Since Fouchier’s base at the Erasmus Medical Centre is in the Netherlands he is subject to Dutch law which prohibits the export of weaponisable technology, and they say that potentially this is what Fouchier is hawking. Apparently fed up with the red tape, Fouchier now plans to submit his article to the American journal Science who are protected under to US law to publish any article which has been formally submitted to them, however as of seventh of March 2012, Science are yet to receive correspondence from Fouchier.

This story highlights important issues in science and its relationship with world governments and the apparently rising issue of censorship in science. As I see it, science should never be censored, as the second we begin to put limitations on our knowledge we bolt these limits also to our capabilities as individuals and societies.

Censorship is antithetical to the nature of the scientific endeavour. When we observe phenomena we experiment with them to find out what’s really going on and once we have conclusions we tell everyone about it and welcome their criticism. Censorship could put the clamps on that altogether, then where would be?

In saying this though, science is dangerous, that’s part of what makes it so exciting, so correct measures should be made in order to ensure that dangerous science is used safely and appropriately - by which I mean no weaponisation at all - a task which some might say can be entrusted to no individual government or inter-governmental organisation...

Sources New Scientist Science Nature Discover Magazine

Synthesising Sight

Corneal blindness is the fourth most common cause of blindness worldwide, causing 5.1% of all blindness. It is caused by damage and scarring to the cornea, the transparent covering of the eye which protects the pupil and iris and so the only real treatment for this kind of blindness has been a transplant of the cornea. This sounds simple enough, but donors are sparse and the procedure is risky and expensive, making treatment implausible in many developing countries.

For years, this has been the general prognosis for corneal blindness: either to live with it or patiently await a donor and even a transplant is only a temporary fix. However this week Sylvia Paton in Edinburgh became the first person to receive a stem cell transplant in the cornea to reverse the damage causing the disease.

Stem cells are the poster child of the tomorrow’s medicine and are at the core of the dynamic field of regenerative medicine. A stem cell is one which can generate a complete tissue of any kind in the body, herein lies their usefulness. A very small sample of stem cells could in the future be used to generate an entirely new lung or kidney or any other organ imaginable.

This procedure involved formation of new corneal tissue formed from stem cells which was replaced the damaged scarred tissue which caused the blindness.

It will be months before a the effect (if any) of this treatment may be seen but Professor Baljean Dhillon, a consultant ophthalmic surgeon at Murrayfield Hosptial in Edinburgh and the study’s principle investigator, is hopeful and says that such treatment “could bring sight to many people around the world who currently live in darkness”.

As pioneering as this treatment is, it is not the first of its kind. In July of last year, the first ever synthetic organ transplant was performed in Sweden, where a synthetic trachea coated in the patient’s own stem cells was transplanted in to a woman who had lost hers to cancer, while a surgeon in the USA has been performing transplants of synthetic bladders made from stem cells since the late ‘90s.

Professor Dhillon’s procedure potentially gives thousands of people around the world their sight back, however for patients with a genetic predisposition to corneal blindness – as this patient was – the stem cells must be obtained from the eyes of another adult donor. This does not really solve much for patients in this predicament since donations of eye tissue appears to be a source of distaste among the public and donors are of eye tissue are rare.

Engineering Slime

In the shadows, beneath decaying logs and leaves, shying away from the light lurks an unlikely civil engineer. The slime mould Physarum polycephalum (the “many headed slime”) is the most intelligent of scum. It can navigate a maze and anticipate a natural disaster – and now it can create a road network.

Unconventional computer scientists Andy Adamatzky and Jeff Jones of the University of West England have been using P. polycephalum as an unconventional computing tool to solve various problems, one of the most intriguing of which being the mapping of road networks across the world.

They did this by inoculating an area of agar gel representing the capital city of the country with the slime mould and using oat flakes as other major cities. Once inoculated, the Physarum will extend tendrils (the “roads”) in the direction of the oat flakes in search of nutrition, finding the shortest routes from the “capital” to the nearest oat flake city and between that and other cities. This creates the Physarum’s road map of the country.

From the videos above you can see the Physarum extending its gloopy tendrils across the land. This is called amoeboid movement, where the cell will move by extending its gooey self in the direction of a stimulus. And therein lies Physarum polycephalum’s smarts.

It collects information from its environment and makes an informed decision in its actions – just like you do (or should do at least). In detecting a “good” stimulus (i.e. the oat flakes) it will move towards it and in detecting a “bad” one (e.g. a poison) it will avoid it. This phenomenon is called chemotaxis and is displayed by almost all microbes to some extent. P. polycephalum will also respond to a lack of stimulus by retracting tendrils which are proving to be fruitless in their search.

The researchers also used bad stimuli (chemorepellents) to mimic a disaster which would make a route non-traversable. Adamatzky and Jones’s disaster was a grain of salt placed in a simulated urban area. This caused diffusion of sodium chloride throughout the medium which repels the Physarum. The slime mould responds by reconfiguring its road network to avoid the salt disaster.

As shown, the slime mould makes a road network which matches the one already present in the UK and in the USA. Adamatzky and Jones speculate that our road networks are similar to the slime mould’s as ours were initially forged by migrating animals.

Japanese scientists led by Prof. Atsushi Tero of Hokkaido University have also used similar experiments using Physarum polycephalum to create a rail network to compare the efficiency of the slime mould to that of Japanese civil engineers – using the Tokyo rail network as their model, naturally. They concluded that Physarum polycephalum is at least "comparably efficient" in this role.

This draws an interesting parallel with what we see as the uniquely human concept of engineering things to our own ends. How human is it really when the many headed slime can do it just as well?