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Tag: genetics

A Biologist in Nigeria

This is the unedited version of “DNA and Nigeria: Survivor for Science Geeks” first published in the June/July 2004 edition of Maisonneuve.

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By DAVID NG

Dr. Oyekanmi Nashiri is a busy individual who exudes enthusiasm, embraces optimism, and covets high expectations. Then again, as the principle organizer of a somewhat curious scientific program, he would have to be all that and more – some would even say that his good intentions place him squarely in the category of certified nutbar. Nash (as he prefers to be called) has spent the better part of his scientific career developing and implementing the West African Biotechnology Workshops, a focused attempt on bringing scientific expertise and potential research collaborations to his homeland, Nigeria. Which is to say, he is intent on bringing the realm of high technology into an otherwise struggling country.

Ironically, I was thrown into this mix by virtue of my reputation as a university instructor, the lure of traveling to an altogether foreign place, and the somewhat naïve notion that this challenge could bring some merit into the developing world. Ironic because part of the appeal stemmed from my being guilty of harboring the same preconceptions about Africa that every other non-African seems to have. That is, the whole romantic ‘Out of Africa’ thing, where the nations that hold the continent together live in natural but primitive splendor.

“Which,” as Nash would often say “is all nonsense.” Nash is an animated speaker – his continuous gestures and movements betray his scientific patience. “You can’t think of Africa as one place, one culture. It is distinction within distinction. Every place is separate and special from the other. We are not going to Africa, David, we are going to Nigeria.” And in retrospect, he couldn’t have been more correct.

Nigeria is a country of unfathomable extremes, the kind that Meryl Streep and Robert Redford would take little comfort in. It has a population of over 100 million individuals crammed into a small wedge of land that is the coastal armpit of West Africa. Its growth rate is such that the population is expected to rise to about 300 million individuals by 2025 – a figure that would mirror that of the United States, except that it would be squished into an area half the size of Alaska. Such numbers also give rise to extreme cultural diversity, which is well exemplified by the more than 250 different ethnic groups, of which three stand out and comprise 65% of the population (Hausa in the Muslim north, Igbo in the agrcultural lands of the south-east, and Yoruba in the urban south-west.). In spite of this dominance, the remaining groups certainly do not want to be ignored. Each has its own language; each has its own way of life; and each has its own fiery brand of pride. In short, Nigeria is as close as it gets to a real cultural melting pot, African or otherwise. Quite simply, it is distinction within distinction within distinction.

It is also not a very nice place to visit. The travel advisories within the Canadian Department of Foreign Affairs and International Trade say it all rather succinctly:

The official language is English. Tourist facilities are limited. Power shortages and low water pressure are common. Telecommunications are unreliable. Those attempting to contact the police may have difficulty getting through. Violence and unrest sparked by tensions between ethnic and religious communities occur in various parts of the country and have resulted in numerous deaths. The military may intervene and curfews may be imposed. Canadians should always maintain a high level of security awareness and inquire about local conditions when travelling in the country.

To be more specific, our final destination was actually Lagos, a crowded and polluted city of some 13 million inhabitants, and a city with the dreadful reputation of having one of the highest crime rates in the world. In fact, the lonely planet guide I picked up heartily recommends it for the “truly masochistic voyager.” And upon reading through several sources of information, it really seemed like it would be wise to avoid, by all counts, practically everything.

To these information nuggets, Nash would quickly rebuttal. “This is all nonsense. Do not worry about such propaganda. Nigeria is the West African superpower. We have one of the most highly educated workforces in the continent …” And then in the middle of the blur that is his hand gesturing, he would pause and smile, “and we are going to win the World Cup.”

Still, as an educator who teaches pupils and the public alike in the nuances of biology, I wasn’t necessarily swayed by his arguments. A country’s soccer prowess holds little weight in teaching scientists the practical and theoretical aspects of molecular genetics (for instance, I have yet to witness an offside penalty in my lab). But things like reliable power and water sources do matter and, as Kate my wife would so ardently point out, it’s also nice to not worry about things like violence and riots.

* * *

The morning I left for Nigeria was a bit of a somber affair in my homestead. I would be away from my wife and my baby daughter for two and a half long weeks, the first time I was to be away from them as a new parent. This wasn’t really how it was supposed to unfold. Originally, this teaching assignment was scheduled to be held in a previous year, where Hannah would be but a twinkle in our eyes or at the very least, safe in a second trimester haven – both situations that wouldn’t have yet revealed the emotional enormity of fatherhood. It was originally to be an adventure. Even Kate had toyed with the possibility of joining me. However, adventure would now take a secondary role to family life and Kate would join me only in spirit and kind words via a bundle of letters – one for each day of my trip. It seemed that she took to heart the warnings about unreliable telecommunications.

Thankfully, I was not traveling alone. I enlisted the help of Dr. Samantha Greunheid, a post-doctorate and colleague at the University of British Columbia. Sam was a specialist in infectious diseases, which seemed to be a good fit given our destination. She was also knee deep in proteomics, a burgeoning research field that looks at proteins (what the DNA genes code for,) and, for lack of a better description, tries to look at all of them in any given circumstance. For instance, Sam was primarily interested in looking at proteins present in her bacteria, and in particular trying to observe differences between samples that were docile, and samples that were actively involved in an infection. In this respect, proteomics is a newer breed of science that relies heavily on high technology, high throughput and almost steamroller-like tendencies, all the while generating massive amounts of data such that mathematicians and statisticians are being courted into the process. This part of her research would be completely novel to the primitive state of Nigerian science. It was to be a compelling and interesting mix. Most important, however, Sam was down to earth and had an easy low maintenance attitude, which I feared was going to be necessary for this trip.

Before we had even departed on our flight, it became clear that our itinerary was a focal point of some intrigue. I remember the conversation we had in Seattle with one of the immigration officers who examined our visas. It began innocently enough:

“Where are you going?”

“Nigeria.”

Then came a short pause. “Nigeria eh? Why are you going there? Are you missionaries?”

“No, actually, we’re university teachers. We’ll be teaching a science course there.”
Another pause. “Well,.. better you than me.” A sidewise glance, “You know, you may as well say goodbye to your luggage now. Those folks down there, they just take whatever they want.”

* * *

How Lagos, and Nigeria in general came into these troubled circumstances is rather neatly if not bluntly explained in the book “The World’s Most Dangerous Places,” a Christmas gift given to me by my not so subtle parents. In it, Robert Young Pelton – who could give the Crocodile Hunter a run for his money for pure bravado – provides descriptions and anecdotes for destinations you would best avoid. My worried mother had actually folded down the pages on Nigeria, such that its 3 out of 4 ‘peril rating’ was immediately evident.

In short, Nigeria had for the better part of its 40 year history been subjected to the whims and follies of various military rules. Which together with its diverse cultural mix and its lucrative oil deposits, exacerbated into an unwieldy recipe for political chaos, ethnic tension, and rampant crime. However, even the casual follower of world politics knows that what makes Nigeria especially infamous, is its almost legendary propensity for corrupt practices. In fact, Nigeria has consistently ranked as one of the worst offenders in various Corruption Perception Indexes, and it would probably surprise no-one if its unclean borders were shown under thesaurus entries next to words like corruption, profiteering, racketeering and venality. In general, the whole messy predicament had turned Nigeria into an economic mess that to this day precariously teeters on the strength and weakness of oil prices. From this viewpoint, it is no wonder why the country has had the reputation it garners.

And yet, Nash would consistently reassure us that things were now different. That the country, and even detestable Lagos had its merits, its civility, and its comforts. That since 1999, the country had been mending albeit slowly with the first elected president residing over democratic government. He would tell us that the time was now ripe for science to return to his troubled homeland.

However, truth be told, I wasn’t sure what or who to believe anymore. Frankly, my mind was now more preoccupied with evaluating the worth of my small science workshop. Nigeria, it seemed, had problems that were much bigger than biotechnology.

* * *

Murtala Mohammed International Airport in Lagos seemed to be as good a place as any to feel out the current truths on Nigeria’s reputation. This place was to be our testing ground, a microcosm of sorts, and would provide us with a visceral sense of things to come. In this respect, the airport would be a focal point of a number of things. First up was the task of transporting scientific supplies from Canada into Nigeria. Part of my responsibilities entailed the delivery of some special chemicals that were not readily available in Nigeria. An innocent enough endeavour as these chemicals included relatively obtuse things like ultra pure varieties of water and salt; as well as some more sophisticated reagents like antibodies, DNA molecules, and even live but attenuated bacteria. A few of the tubes even contained samples of fake data which were a teaching lab’s last resort should the experiments go completely awry. All of which were harmless and worthless of course, given that my work centered round educational goals rather than specific research goals. Unfortunately, all of the reagents needed to be kept cold in order to stay happy, which meant packing everything in copious amounts of dry-ice, a problematic venture given dry ice’s hazardous reputation in the transport business. This nuance caused no end of frustration especially since the reason for it being labeled dangerous wasn’t clear to me or, for that matter, to any of my chemistry colleagues.

Nevertheless, it was imperative that these supplies make it to Nigeria. For advice, I contacted Dr. Terry Pearson, a noted parasitologist at the University of Victoria, whom Nash had invited as the keynote speaker for our workshop. Terry, who specializes in Trepanoma research, the causative agent of sleeping sickness, has long had collaborations with various institutes in Kenya and was the person in my neck of the woods to consult on the ins and outs of transporting scientific goods to Africa. Although, we would later formally meet in Nigeria, he was a veritable wealth of information – a Yoda-like antidote to my ignorance.

“Don’t even bother with a courier.” he would tell me, in a gruff friendly manner that perfectly imbues someone equally at home in a state of the art biochemistry lab and in the safaris of southern Kenya. “They’re too damn expensive, and in my opinion, you’ll never see your package again.” He added, “You can try the air cargo route, but I’ve never had much luck with that myself.”
He then went on to explain that the only way to guarantee getting the materials over to Africa would be to simply bring the icebox to the airport and carry it on the airplane myself. “You’ve got to go to the airline agent and suck up big time, hope that they trust you, and let you bring it on. That’s really the best way to do it. The only way to guarantee that you actually get it to your destination. If you want, you can bring all your fancy credentials – it certainly can’t hurt. But at the end of day, it all depends on whose manning the desk, and whether they like the look of you or not.”

It boggled my mind that my best chance in all of this chaos would be to bring the reagents onto the plane myself. Reagents that included among other things, an assortment of scary sounding chemicals, kilos of dry ice, and (get this) live bacterial samples. I shuddered at the thought of trying to explain to airline staff on the harmlessness of the bacteria in the security intense world of post September 11.

Consequently, I thought it pertinent to also give the airmail route a go using either a courier or cargo service. Terry was not kidding. Although the reagent package itself was no bigger than say a stack of 5 compact discs, the process of transport itself due to flight connections, and navigation through various custom ports, meant that the trip would take a minimum of 4 days. Which translated to an awful lot of dry ice to keep things frosty throughout the whole venture. This now heavy package would subsequently amount to a small fortune in shipping costs – to the tune of about US$450 via a company like Federal Express. or a more reasonable but still expensive US$200 using an air cargo service. Still, it was an alternative worth using, and approximately a week before the workshop, I arranged to send package number one into the unknown.

Package number two was safely bundled in one of those squishy ice bags, and packaged with enough dry ice to last for a 16 hour flight. It also came with a wad of paper, large enough to look like a novella, but which actually contained MSDS or materials and safety data sheets for each and every item in the package, as well as photocopies of every official looking letter of intent. The MSDS sheets were considered to be both advantageous and detrimental in our efforts to board the plane. They were the documents required to state the relative hazard level of each chemical, but in reality they often depicted the most harmless of things as being dangerous themselves – after all, even water has a lethal dose. As I approached the airline desk with Sam, it suddenly dawned on me that my chances of getting the package on board the plane would have increased significantly if I had my baby Hannah as a token gesture of innocence. However, in one of those surreal moments where one’s expectations are flogged and hung, we experienced no problems, no lines of questioning, not even a customary look of concern. Neither Canada nor the United States seemed to care about my icebag and my package number two was therefore on its way.

The actual arrival at the airport in Lagos was our second task, and was also an exercise in tension for both Sam and I. Tense, because according to all accounts, personal and otherwise, the airport was the place for peril and quite simply, it was the one part of the trip that we were most worried about. We were repeatedly warned not to converse with anyone that we didn’t recognize, and to not take any mode of transportation without directions from someone we knew. Taxi drivers were notorious for partnering with any number of robbers and bandits, and it was reputed to be a calculated risk to interact with any stranger at the airport. Definitely not the most tourist friendly location I’ve been to. Basically, we were focused on thoughts of getting through without being detained or being robbed. In other words, we were under the uneasy impression that our lives depended on Nash showing up at the airport to be our personal escort.

Surprisingly, customs at Murtala Mohammed International Airport was brief, and my package number two caused no curiosity. In truth, the airport itself, seemed to be relatively quiet, no doubt a consequence of the armada of severe looking armed guards that manned all the key entrances. I could see through the main doors that the roadway outside was populated by a throng of locals, tidily kept behind a number of security fences. This was presumably to clear the main road of congestion, and possibly the riff raff we were told to avoid. For a fleeting moment, we sensed our folly at believing all of the tall tales, which at this point, seemed to be grossly exaggerated. Everything was going smoothly and everything seemed relatively civil.

However, as soon as we picked up our remaining luggage, we were accosted by two persons – a man and a woman – who aggressively asserted themselves as our escorts, and forcibly directed our cart towards the airport exit. Of course, this scared us out of our wits, as the very thing we had been warned about seemed to be happening before our very eyes. Even with our protestations, our new escorts were adamant on leading us into the outside throng.

Thankfully, before we ended up causing a minor scene, and likely one with the participation of armed guards, Nash appeared from the chaos to save us. It would be an understatement of monumental proportions to say that it was a relief to see him in person. We were suddenly empowered with the one criteria required for travel in Lagos – that is, a friendly face.
Boarding into a van, we soon found out that our two headstrong escorts were indeed official members of our host institution, the University of Lagos. In no small way, the whole incident clearly showed us the destructive power of heresy. Looking back, it’s still hard for me to pinpoint whether our feelings of panic were attributed to information we had been given, or to the situation itself.

As we began to move, I immediately sensed a grimness in Nash’s demeanor. He was not as animated as usual. When confronted he said, “The lab is below my expectations. The Local Organizing Committee has done a very terrible job of this.” I, ever the optimist, bounced back, “Well, at least package number two made it through.” I clutched the ice bag as if it was the most important thing in the world. “How did package number one fare?” I asked.

“It is here.” he replied curtly, “but I cannot get it without paying a customs fee.” When I explained to him that I explicitly made it clear in all the documentation that the materials were not of any worth, he just smiled at me and said, “Welcome to Nigeria.”

* * *

Bribery, or dashing, as it is affectionately called in Nigeria, is a national pastime second only perhaps to soccer. Nash would explain to me that the airport authority controlling our cargo had asked for a flat fee of 30,000 Naira, which was roughly equivalent to US$300. A tidy sum of money that is no less than a small personal fortune in Nigerian standards. Of course, Nash, ever the pragmatic individual, flatly refused to pay. Over the next two weeks, we recieved daily updates on the current amount of dash needed to relinquish the package. On the last day, the bid fell to 5,000 Naira – to which Nash responded, “Send it back to Canada.”

As predicted, our rendezvous at the airport provided a window to Nigerian life in the here and now. Sam and I both agreed that in hindsight, a lot of the apprehension we carried was a consequence of distorted information. What we saw instead, was a nation in transition, going from bad to not-so-bad (albeit slowly), and a culture that was as foreign as any other to the serious traveler.

It was when our van took us through the harrowed and crowded streets of downtown Lagos, that the full brunt of culture shock finally hit. Peering through the windows of our vehicle, we saw a completely different way of life – primitive, at times decrepid, and altogether frightening. The heat of the night seemed to mix well with the incessant dust and ramshackle nature of each and every building we saw. These sights made us instinctively think of home and so our first order of business was to look for an internet cafe. This was to qualm the fears of our loved ones with a friendly and reassuring message of “I’m in Lagos and go figure, I’m safe and sound.” Then a welcome stop for food. I think Nash was trying his best to make us feel comfortable since he took us to a ‘Mr. Biggs’, which was more or less a clone of the MacDonald’s variety, except with burly armed guards. As I ate, I found it decidedly ironic that the first meal I had on this exotic adventure was a hamburger and fries.

Nash then took us to our accommodations. We were staying at the University of Lagos Guest House which was more a hotel than a student residence and was considered luxurious at a cost of about US$40 a night. Although my own room was fairly large, this did little to obscure its general disheveled state. Despite this first impression, I counted my blessings since the room actually had reliable power in the form of a back-up generator, working air conditioning, a toilet (sort of), and a television with 5 channels (curiously, three of which were set to MTV). It even had malarial pest control in the form of staff spraying the room each night with a can of Raid, and it also came with a comforting set of door locks. In any event, it would more than suffice and I gladly dropped off my backpack, and then queried Nash for a good place to stash the contents of my ice bag.

Although we were very tired, Nash said that the best place would be in a scientific freezer, and that we should see the lab facilities immediately. The sense of urgency and the fact that he continued to look sullen was troubling to say the least. Here was the eternal optimist reduced to a stoic figure. I was thinking, “how bad could it be?” We had, after all, been corresponding with the Local Organizing Committee for several months, and according to all the pertinent check lists everything appeared to be sound. Everything should have been ready and waiting, and the only possible shortfalls we had to worry about, were the chemicals and reagents in my package number two.

* * *

The Local Organizing Committee or the L.O.C. for short was a group of scientists, and university representatives who were responsible for providing us the necessary facilities and equipment required for the laboratory workshop. However, it was clear upon first glance of our adopted lab space that the L.O.C. really had no apparent skill in organizing anything. To begin with, our allotted space was not even in the university campus but was instead situated several kilometres away at the Nigerian Institute of Medical Research (N.I.M.R.). Although this distance itself didn’t sound so bad, the additional need to travel by car was very awkward given that the streets of Lagos consistently imbued a state of pandemonium. There was even a colloquial term for the act of driving – a very appropriate “go slow.”

When we approached the iron gates of the N.I.M.R. compound, it was evident that the entire area was caught in the grips of a power outage. In the somber light of our vehicle’s headlights, we drove further into the maze of buildings and stopped in front of a rather unpresuming looking wall. Then following flashlight beams, we were guided like airplanes up a flight of stairs and into a room that looked gutted, disorderly, and plain filthy. “This is our space,” Nash said matter of factly.

In short, the space was horrendous, and dirty to the point that sterility would be pure fiction. In addition, the emergency generator backing our area was ranked somewhere between sub-par and non-existent, which meant that loss of power was a real consideration. However, this concern was soon countered with the realization that we were given next to no equipment to run our experiments anyway.

As we blew off the dust from the one solitary bench in the room, I was drawn to one of three conclusions. One, that Nigerian science had deteriorated to such an extreme that even a campus that boasted a student population of 30,000 students and connections with over 100 other Nigerian Universities, could not muster up enough basic equipment for 12 experimental stations. Two, perhaps Nash had been misleading us all along with respect to his country’s resources. Or three, maybe all of those tall tales were not so tall after all.

The following morning was spent contemplating the Guest House breakfast menu, which basically consisted of eggs and toast, toast and eggs, eggs alone, or toast alone. The poor selection of items mirrored our facility and equipment status. Consequently, our second day in Nigeria would primarily concern itself with sorting these problems out and we would try to do this at the opening ceremony. Here, we would have the opportunity to meet face to face with some of the members of the L.O.C.. and voice our concerns. Unfortunately, it soon became very clear that the L.O.C. were largely indifferent. Instead, most of the members were more interested in garnering attention by using the ceremony as a chance to exhibit their skills in speech making. We did, however, have a few sympathetic ears – individuals who were quite apologetic about the whole situation and tried to explain that the lack of resources was a pressing reflection of the financial hardships within the research community. Not so much that the equipment didn’t exist, but rather that the equipment was such a precious commodity that the distinction between the haves and the have nots was zealously guarded. In Nigeria, the notion of collaboration was swept under rugs, in favour of concealment and selfishness.

In retrospect, this reality was already evident, given our experience with transporting reagents. If securing a small shipment of chemicals had cost me several hundred dollars in transportation and “custom” fees, then what hope was there for the average Nigerian biologist. This was beginning to look less and less like a workshop on molecular techniques, and more and more like a Survivor episode for science geeks.

Fortunately, due to my background as a Boy Scout and an inbred predisposition to being prepared, I had taken every tall tale I heard in Canada to heart and had pretty much prepared for any and all contingencies. So after the opening ceremony, Sam and I immediately went to work assessing the general status of the workshop. To begin with, the sparse supply of equipment necessitated a change in how the students would work together. Nash had originally arranged for enough chemicals so that a class of 24 students could be split into 12 working pairs. However, the equipment that was given to us by the L.O.C. would limit us to only 3 working groups – each with 8 students, which was hardly optimal. Nash was especially angry with this nuance and even went so far as to accuse the L.O.C. of arranging this on purpose so that the excess reagents could be scavenged for personal use.

Even the equipment we did have was suspect at best. For example, the lab was supplied with one centrifuge that worked in a quirky fashion. This machine to the uninitiated is a device that contains a rotor capable of spinning around at high speeds. The net effect of this action is the creation of centrifugal force – the type of force that makes water stay within a swinging bucket. In essence, this machine speeds up the ability to separate constituents within a mixture according to density. For instance, a mixture of sand and water would result in a sand pellet at the bottom of a tube with the fluid on top. Anyhow, our centrifuge worked like a charm except that the lid wouldn’t open unless you turned the machine upside down, which was a really aggravating feature since our separated samples would simply become mixed up again.

We were also in dire need of a Polymerase Chain Reaction machine or P.C.R. machine for short. This device essentially allows an experimenter to amplify DNA molecules such that you can have a billion fold increase of material to work with. In short, this makes it easier to observe and characterize DNA molecules, especially when the initial amount is very small. To the layman, P.C.R. was the token technique described in Jurassic Park. Although, not actually powerful enough to clone dinosaurs, its overall utility is such that this is the machine of choice for a number of key experiments such as DNA fingerprinting, DNA sequencing and any technique devised to look for specific genes. All in all, about a quarter of the procedures in the workshop syllabus would rely on this one piece of machinery. Frustratingly, the L.O.C. had actually provided us with a machine to use, but only after politely telling us that it was broken.

We had heard through the grapevine that the N.I.M.R. compound actually had a brand new P.C.R. machine, and soon found out that the device itself was only a few hundred feet away from our own disordered facilities. This adjacent building turned out to be a newly built structure with the explicit purpose of conducting research on the human immunodeficiency virus, the causative agent of AIDS. Funded by the Bill Gates Foundation, it was exactly the sort of space that our workshop should’ve been offered in that it was clean, it was fully equipped, it had reliable power, and from first sight, it even appeared to be underutilized. I immediately cursed my luck for it being a centre for HIV research since this would imply strict procedural rules that would make it next to impossible to borrow the entire facility itself – HIV is after all a hazardous organism. However, I saw no problem with the use of its PCR machine given that our samples were essentially benign and had no chance of jeopardizing any of the HIV work.

So all in all, pressing on with the workshop presented itself as a formidable task, and it was decided that clear objectives needed to be tackled. I would begin by assessing a general flowchart of how the lab would run, taking into account all of the possible shortfalls along the way. Sam would visit working internet to see if she could find information on ways we could cheat or MacGyver our way through certain procedures – essentially finding procedural tricks that would enable us to perform the experiments without the luxury of certain scientific supplies. And Nash would see about getting us permission and access to the Bill Gates’ PCR apparatus. Taken together, it was clear that we would need some extra time before the lab was ready, so in order to stall, we announced that the first day of the workshop would be limited to a full day of lectures.

* * *

Meeting the students changed everything. In contrast to the wallowing apathy of the organizing committee, these young faces were a breath of fresh air. Although, it was a grueling first day of work where my time was spent rooted in front of a small blackboard, it was enlightening due to the enthusiasm of the young crowd. In light of all the hardships that this country faced, it was evident that the Nigerian youth took its education seriously. This was further espoused by the country’s willingness to grant access to university level education based on free will alone. Despite this positive outlook, it was discouraging to ponder the future of bright individuals who appeared focused, willing to learn, and yet realistic in what outcome this workshop could bring. You also had students who naively embraced the hope that the workshop would literally change their views on science, and unquestionably lead to a better life. And of course, in a society such as this, we were not surprised by personalities who were desperate to leave the country, and simply viewed Sam and I with the ambitious and tenacious intent of a possible ticket out.

I paid careful attention to each of the student’s attributes, because Nash had vested in me the responsibility of selecting the four most promising individuals. These four would then benefit from Nash’s personal attention in mentoring and guidance. I took this decision very seriously because I really felt that being one of the chosen would result in a dramatic improvement in life itself.

All told, the practical sessions ran for two weeks and constituted a flash pan of memories. It was a session like no other, where each day brought a different obstacle to the mix, and like any challenge, there were notable ups and downs. The lab began in an interesting enough fashion with a brief visit from Dr. Emmanuel Denenu – a messenger from the Federal government and an unfortunate scapegoat for the frustration that must greet these students day in and day out. Although he came to discuss the future, opinions about the present took centre stage and the fire in the student’s voices during this confrontation would continue to ring in my ears for the rest of the workshop.

On many occasions, my heart sank as I began to second guess the value of the workshop. Sometimes, it seemed all too silly to be coming to a place such as this, to teach something as absurd as molecular biology. These pangs of doubt were constantly highlighted by the looks of disappointment on the student’s faces whenever it became all too clear that the chemicals and reagents that I lectured about, were simply not feasible in a country with corrupt shipping practices and freezers that were forcibly useless. How could one talk of delicate molecules, when we even had difficulty getting something as benign as chalk! (At one point, Nash would have to purchase some himself since the L.O.C. would refuse to help).

There was also a disturbing sense of innocence and a dangerous level of ignorance about the science in general. The students were often unrealistic in their assessment on what these genetic techniques could accomplish and how fast they could be performed. There were many instances where the idea of genetic modification was nonchalantly chosen as the be all and end all to experimental design. Many of the student presentations we heard would conclude with a simple “I would make this and that better by genetically modifying it.” This eagerness to so readily adopt the use of molecular biology was troubling to say the least. In our own developed society, there is a general theme of caution applied to any scientific endeavour, and it was important that these students understood the possible ramifications and considered the ethical arguments behind the use of such technology.

We spent a fair amount of time deliberating these issues, and it was interesting to hear the musings and opinions of Nigerian students. Suffice to say, opinion was mixed in that whilst all agreed with the general intention of being ethically sound, several suggested that the barrage of ethical polemic was a western luxury – that only for countries as rich as Canada or the United States, which reflected a high degree of stability, was wasting valuable time and money arguing over the pros and cons of a technology acceptable. This was certainly food for thought.

As a whole, teaching conditions remained pretty primitive in that the equipment and facility dilemma never really sorted itself out. Still, we could boast a few tangible victories. For instance, we were able to secure access to the Bill Gates PCR machine, although this achievement took a little maneuvering and involved a fortuitous meeting with the director of the N.I.M.R. facility over coffee, crackers, and (presumably for public relation reasons) several photographs. We were extremely lucky with our power situation, in that it never directly affected our experimental procedures. Rather, the loss of power tended to conveniently coincide with the lecture components of the course – it was almost uncanny. Most astonishly, we managed to tease success from about two thirds of our experiments, an almost unbelievable statistic that hopefully reflected our skills as instructors, our knowledge of the material, and of course, searing blind luck. In truth, we did have to resort to our “fake” data stash, but only once. It’s also safe to assume that there are now 24 Nigerian students who are quietly pondering the identity of this MacGyver fellow that Sam and I kept talking about.

The intangible victories were a little harder to ascertain. Apart from the empirical act of teaching new material, I hope we were able to leave the students with a strong sense of what we thought was wrong with Nigerian science. That is the prevailing acceptance of the harsh but understandable ‘every man for himself’ attitude. For us, this philosophy was painfully evident from the very beginning in the effort required to get any help whatsoever. In our minds, this selfishness was shattering any hope of allowing Nigerian science to flourish. In simple terms, here we had a well educated society that was stifling under limited resources – it simply made more sense to us to foster collaboration, to rely and build on each other strengths, and to share valuable resources.

We also left behind a small legacy of embarrassment. Our negative experience with the Local Organizing Committee and with the University of Lagos, in general, bequeathed a lasting impression on the Federal Ministry of Science and Technology. Dr. Denenu was obviously disappointed with the behaviour of the L.O.C. In the interim, it seemed that more than a few eyebrows were raised during our workshop, and Nash consequently earned the right to formally interact with the government in all future programs. One can only hope that this will lead to better things.

Fittingly, the last day presented itself with two dominant and opposing memories. In an amusing turn of events, Nash and I were presented with a bill for various charges. It was stunning to us that the L.O.C. would have the audacity to ply us for even more money. The bill itself was a mockery with money attributed to items like extringencies, which, to this day, is one of the great mysteries of the workshop. To be perfectly honest, no-one was even sure what the word meant. Nash took care of the bill in his own special way, which is to say that he probably threw it away.

The other memory was that of the students huddled together in a welcoming circle, holding hands and saying a small prayer.

“Thank you lord for your generosity in life, that you hold together our faith in you, and that you provide what you can in our lives. Thank you for the opportunity in allowing us to attend this molecular biology workshop, that we might take what we have learnt to help our people and country in need. That we use it responsibly and with respect to our land. We ask that you guide us in shaping a better future. That you guide us in the spirit of collaboration. That you help us all of us stay true to this aim and to deny the spirit of selfishness. We asked this in the name of the Father, the Son and the Holy Spirit, Amen.”

This is going to sound cliched but the workshop, and I suppose the whole experience itself, made me reflect on my own lot in life. I would be fooling everyone if I didn’t comment that during each day of our laboratory and lecturing sessions, I felt a strong sense of relief and gratitude. Relief in that at the end of it all, I actually had the option of leaving it all behind. Gratitude because through some cosmic roll of the die, I was born in a country where food, shelter, and indeed a decent way of life were readily available. We really take too much for granted.

Today, Nigeria like most of my memories is slowly fading from my mind, in this case buried by the security of my own family and kept alive only in souvenir status by the occasion headlines that skim my consciousness. Where indeed does science fit in a country that is on the one hand dogged by controversy over Amina Lawal, a woman sentenced to lethal stoning by a Sharia judge; whilst on the other hand prepares for the Miss World pageant? Next time I talk to Nash, I’m going to have to ask him. Turns out, Nigeria didn’t win the World Cup that year, but then again I suppose there’s always next time.

The Von Trapp Children Speak to a Geneticist

By DAVID NG

von-trapp-family11

LIESL: Why is it that we can all sing very well?

GENETICIST: Liesl, that is an excellent question! And essentially one that boils down to the classic debate of nature versus nurture. Are your genes responsible for this particular talent, or has it more to do with your upbringing? Looking at this scenario objectively, I would have to say that it is both. There have been reports that the ability to have perfect pitch—that is the ability to distinguish musical notes without points of reference—is a hereditary phenomenon, thereby strongly suggesting a genetic basis. This would seem to be supported by your father’s musical talent as well. Of course, you’ve also had the benefit of being tutored by your wayward novice governess with all-world pipes, Maria.

In conclusion, like most things pertaining to our individuality, we are influenced by both our biology and our surroundings.

GRETL: I think Liesl is very beautiful. Why am I not as pretty?

GENETICIST: Assuming no mutational errors occur during the production of sperm and egg cells, there was approximately a 1-in-70,000,000,000,000 chance that you would have been an identical clone of your sister. If you included the multitude of mutational and regulatory events that ensue during this process, that statistic would escalate to an even smaller chance that is, quite frankly, unfathomable to calculate. How did I get to this absurd number? Well, one must realize that your genetic instructions are housed as a collection of 23 pairs of chromosomes (i.e., 46 in all). In other words, it is correct to say that each human has two sets of instructions—one given to you by your father, and one by your mother. If you keep in mind that your parents themselves also have 23 pairs of chromosomes, and you realize that the child may receive only one from each pair, the likelihood of siblings having the same 46 chromosomes is the fantastic number mentioned above.

However, Gretl, do not fret. You are the youngest of the lot and still have a good chance to blossom into a stunning flower like your sister Liesel. Furthermore, cosmetic surgery these days I hear is quite impressive. And then there is always the chance of Liesl having a disfiguring accident—I hear she may be a Nazi sympathizer, which is never a good thing.

FRIEDRICH: Yes, Liesl is hot. Sometimes, even I have feelings for her. Why is it bad for me to feel that way?

GENETICIST: Incestuous relationships, as well as being frowned upon by most of society, are also disadvantageous from a biological point of view. In the genetic world, diversity breeds fitness. One example is to imagine the following. You have a set of genes that determine the ability of your immune system to recognize and combat various pathogens. Your sister Liesl also has a set of genes that do the same thing. And because you and your sister come from the same genetic pool (you have the same parents), Liesl’s immunity is quite likely to be similar to yours. Do you not see that the net effect of this is that you would create offspring with a limited repertoire of immune-system genes? Compare that to your having a child with, say, Marcia from The Brady Bunch, and you will note that this union will create offspring that have the benefit of a wider genetic pool (your parents and Marcia’s parents), thereby allowing your children to acquire a more diverse and fitter immune system.

Also, dude, she’s your sister.

BRIGITTA: Why do all of our siblings have blondish hair and blue eyes, whereas Marta and I have dark hair and dark eyes?

GENETICIST: You are thinking, perhaps, that your mother was a whore? It is true that the disparity in your outward appearances is a mite unusual. However, there is no reason to believe that any adultery has occurred. Here is the reason why. Although it is generally thought—though not confirmed—that extreme blondness (as in the case of Louisa and Friedrich) has a recessive distribution, there are numerous factors that can account for your instances of dark hair and dark eyes. First, hair and eye color are very subjective terms. Is Greta or Kurt blond, dirty blond, or strawberry blond? Genetic characterization is very difficult when the observational characterization is less than strict. Second, the pigmentation of hair is normally attributed to melanin levels, which have been shown to vary greatly during different stages of a person’s life. You may have noticed, for example, that a person’s childhood hair color tends to be lighter than their adult hair color. Third, the amount of melanin that an individual produces is influenced in part by their environment. For instance, melanin acts to protect the person from the damaging effects of the sun’s radiation. In conclusion, I do not feel that there is anything to worry about. Besides, you did not mention Liesl, who herself has dark hair. Did you omit her because you are secretly jealous of her hotness?

KURT: I think I might want to be with another boy. Is this to do with my DNA?

GENETICIST: Unfortunately, the answer is currently unknown. There have been numerous reports that have tried to implicate specific genetic regions to homosexual behavior, but presently those studies, although titillating, are at best only an indication that there is a hereditary factor for this type of sexual orientation. However, there is an abundance of ongoing research in this area, particularly with homosexual men. If you are interested, perhaps you could participate in the scientific process. Of course, it is important to remember that the Nazis do not dig gay people.

LOUISA: Why doesn’t anybody remember who I am?

GENETICIST: Alas, it appears that this is because you are the second child. I would not be surprised if there are very few pictures of you. It is not, I assume, because your parents did not love you, but simply a facet of being born after the initial excitement and newness of parenthood has passed. This, of course, has nothing to do with genetics. In order to be taken more notice of, you could try different fashions, or perhaps a new haircut. In truth, Liesl could probably give you better advice, as I am, sadly, only a geneticist.

- – -

Originally published at McSweeney’s

Looks like we can’t run the ethanol precipitation today. #funny

lookslikewecantruntheethanolppttoday

From Saturday Morning Breakfast Cereal.

Preliminary Data from the Unicorn Genome: First Possible Indication in History of Mammalian Evolution of Hybridization Across Orders.

From the Science Creative Quarterly. Could this signal the return of the SCQ?

Hope so… (send in some submissions if you hope so too)

unicornpaper

Full paper available here (pdf)

Journal of Fantastic Phylogenetics 2012 8(9): 42-49

Abstract: In this study we present the preliminary finding of what could be the first record in history of hybridization between mammalian Orders (Perissodactyla and Cetacea). Phylogenetic analyses from the unicorn (Equus unicornus) mitochondrial genes (protein-coding Cytochrome b, Cytb) show a matriline belonging to the Narwhal (Monodon monceros) while nuclear (V-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homologKit) clearly show a sister relationship of the unicorn-pegasus (Equus alatus) clade with the rest of the Perissodactyl family Equidae. Our preliminary study strongly suggests the need for further investigation because this finding could completely revolutionise our understanding of the processes of hybridization in mammals.

From the Introduction:

Hybridization is widely known from the plant kingdom (Rieseberg & Carney 1998) and horizontal gene transfer has been repeatedly reported in prokaryotes (Jain et al. 1999). However, these forms of genetic exchange have never been prevalent (or even recorded in the case of horizontal gene transfer) in the Mammalia and never been recorded at such an evolutionary distance between organisms (Equidae and Cetacea).

Here are presented the incongruent results from two phylogenies built with mitochondrial and nuclear genes of E. unicornus showing relatedness to two different orders of the Mammalia.

unicornfig1

unicornfig2

This awesome fake paper by Anna Bazzicalupo, via the Science Creative Quarterly

Sciencegeek Advent Calendar Extravaganza! – Day 5

day5

SNOWMAN SCIENCE
Courtesy of Calvin and Hobbes, by Bill Watterson

Evolution

Paleosnowman
Sharks
anatomicallycorrect

snowflake

(see more of Popperfont’s Sciencegeek Advent Calendar Extravanganza here)

One doozy of a genetic test. Kind of nasty too.

From Esquire, July 2000.

Angry Words From a Gnome Who to This Day Continues to Think The Human Genome Project was Actually The Human Gnome Project

By DAVID NG

It’s hard to believe that the Human Gnome Project formally began in 1990s. It was quite frankly a great time for all of us gnomes as we thought we had finally gained the attention and respect we deserved as a community. But decades later, we as a community are disappointed, angry, full of resentment, and still addicted to nicotine.

To our knowledge, of the billions of research funds given to human gnome initiatives, none of it ever actually went to fund “gnome” research. Instead, a sizable portion went to human human research, and in an apparent slap in the face to my kindred, significant amounts also went towards research looking at bacterial, yeast, worm, fugu, fly, and mouse genetics. Suffice to say, that with the exception of humans, these are all organisms that do not smoke pipes. To say that this has been hard on my community is an understatement of vast proportions. Apart from the soaring lung-cancer rates, I find I am continually aware of other lost opportunities the money could have been used towards.

For instance, for whatever reason, we as a race are forever doomed by our incessant need to wear pointy hats. I hate my stupid hat—loath it with a passion. And yet I have to wear it. We all do. Why this is so has been mystery for many an age. Maybe that’s why I go through 70 grams of tobacco each day. And whilst pointy hats are fine for garden work (one of our main sources of economic recovery), they are hardly advantageous in the current global market—especially when first impressions play a key role. Surely, there is an underlying neurological basis for this behavior—a basis that science could have elucidated.

And what about our facial hair? Believe me, it is not because we are particularly fond of our beards. It’s not even because tobacco pipes look cooler in this context. Our beards just happen to grow at amazingly fast rates! This is not such a huge issue with me and the other male gnomes, but my poor wife actually has to shave every 45 minutes or else deal with social harassment. This is also compounded by the fact that services, like laser hair removal or electrolysis, are just too expensive, especially on a gardener’s income. Ironically, the only gnomes who could possibly afford these high tech solutions are the few who have made it into Hollywood where maintaining the typecast “bearded” look is required anyway. Furthermore, even when a hairless gnome is needed on a movie set (e.g., Mini Me in the Austin Powers franchise), we still get passed over because of our goddamn pointy hats! I bet billions could have sorted this problem out a long time ago.

But if there was ever a strong case for gnome research, you only need to look at my poor Uncle Bill. This unlucky bastard of a gnome must have some bladder problem or something, since he is (no exaggeration) urinating constantly. Seriously, I don’t think he’s even had a chance to put his penis away since he started 14 years ago! And the truth of the matter is that this particular problem is relatively rampant in my circles. Most start off fishing, and then they feel the urge and then whammo! It’s like a disease. I don’t think it’s too difficult to appreciate the magnitude of this medical condition. Aside from the psychological pain endured, imagine how uncomfortable it must be to leave it “out” constantly in all manner of weather conditions. I don’t care if you are the gardener type— when it’s cold, it’s cold! Plus, it makes smoking a pipe tricky.

Anyway, I’m not here to preach endlessly about our problems. I just here to say I want a fair piece of the action. If the project is called the Human Gnome Project, then it only makes sense that at least some of the money should go towards gnome research—right?

O.K., I’ve said my piece. I really have to go outside now to smoke my pipe—stupid human nicotine patch, piece-of-crap waste of money …

(This is very old and originally published at Yankee Pot Roast, inspired by this)

Quite possibly the most complicated (and therefore awesome) Venn Diagram ever!

The figure legend reads:

Figure 4: Six-way Venn diagram showing the distribution of shared gene families (sequence clusters) among M. acuminata, P. dactylifera, Arabidopsis thaliana, Oryza sativa, Sorghum bicolor and Brachypodium distachyon genomes.

In case it wasn’t obvious, M. acuminata is the banana plant.

Full paper on the draft genomic sequence of the banana, and the info this divulged regarding its evolution is available for free downloading at Nature.

REF: The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Angélique D’Hont, France Denoeud, et al. Nature (2012) doi:10.1038 / nature11241 (published online July 11, 2012)

Embroidered Science!

By The Floss Box, via Flickr.

On Radiohead, genetics, and bringing up children.

By DAVID NG


(This is the type of Father’s Day certificate you get
when you’ve been playing too much Radiohead.)

- – -

Lately, I’ve been listening to a lot of Radiohead.

This might be because there is an anniversary of sorts – the epic O.K. Computer was released just over 15 years ago, and so is finding a renewed presence in various media outlets. But it’s also because I’m simply a fan: I find their musical compositions, instrumentations, and Thom Yorke’s heart wrenching vocals a compelling mix; although admittedly, I do sometimes miss the days when some of their material was a little less challenging to radio ears.

Truth be told, I’m such an admirer that I sometimes bring up Radiohead in my role as a science educator. Here, I might play a specific song of theirs and then project the below statement on the screen:

“The song you are listening to is the title track of a Billboard number one CD. The song and CD appear to have been specifically written and dedicated to the first putative human clone.”

Then I ask my students, “Is this true or false?”

Inevitably, the students will concentrate on the song coming over the speakers, and they will note that what they are hearing, sounds somewhat unconventional. It’s distorted in many places, and doesn’t adhere to any semblance of common chord progressions. It definitely does not sound like an obvious reflection of a Billboard number one CD.

And then the reveal: yes, the statement is true. The song is the title track of the CD Kid A, and on October 21st, 2000, it did chart at number one. Not on the Alternative Billboard chart, or the Electronic Billboard chart, but on the whole-freaking-thing Billboard chart. Furthermore, it does apparently connect with the topic of cloning. At least, that is what you might surmise when you read what Thom once said on the subject:

POSTED BY Thom ON JULY 30, 2000 AT 23.39:21:
IN REPLY TO: Thom, why Kid A?

dedicated to the first human clone.
i bet it has already happened.

In any event, I tend to use this little activity as an excuse to talk about science perceptions, and how topics like genetics can be quite pervasive in popular culture. Not only pervasive, but often with a negative connotation. Think of all the movies where genetics plays an integral part of the conflict in the plot; be it biological warfare in spy franchises, clone armies in science fiction sagas, or even battle scenes between Pokemon characters and their angry identical copies (Yes, there is a central cloning plot to the movie, Mewtwo Strikes Back). In its own way, the song Kid A also presents a certain kind of tone that is both foreign sounding and haunting. Maybe Radiohead did this to add their own criticism of technology to the mix, or maybe it’s more to do with simple representation. Think of how strange an episode of human cloning might be in the here and now, to the clone in particular. Of course, maybe the song just came out that way because the band thought it sounded cool.

Interestingly, the idea of coolness also brings up a strange thought I’ve been considering.

That is: let us assume that Radiohead were right – that they were right about the first putative human clone being produced, or say, conceived roughly in the year 2000. This would mean that their sonic ode would be temporally, fittingly, and perhaps even devastatingly relevant. Furthermore, it would mean that somewhere out there, on our busy little planet, is a child who is technically the song’s point of inspiration, and also a child who is now probably around 11 years old.

What if this child found out? What would it think when it learns that an iconic British band wrote a song for him/her. Would the child write a letter? What would the letter say?

Perhaps, he/she would comment on the science?

“To be honest, I’m not even sure what “human cloning” means, since right now, the science I’m learning at school, is mainly to do with habitats, and food chains and why the sun is super important. Someone did once try to explain the cloning thing to me, but I just got confused.”

Or maybe there would be mention of Radiohead’s popularity

“My parents tell me that you are famous. In fact, they tell me that you are very famous. I have to admit that this is surprising to me, since I have never even heard of you, or even seen you on TV. As well, I tried to listen to the song Kid A, but I think the song was broken since it sounded strange…”

Which, not surprisingly, might culminate in a request to meet, or possibly something more selfish:

“I’m wondering that since you are super famous musicians, that maybe you can introduce me to some of your friends. For instance, have you heard of One Direction? My friends keep playing their CD – it’s really good. It would also be cool to meet Katy Perry or Jay-Z. Even chatting with Justin Bieber might be interesting…”

Which leaves us with an idea that is so deliciously meta. What kind of music would the real Kid A actually listen to? Here, having kids of my own (and despite my best attempts at steering them away from the Disneyfied pop that fills the current musical landscape), I’m pretty sure that this Kid A is not going to be listening to Radiohead. Which is actually very sad – although the glimmer of hope is that maybe it’s sad enough for Radiohead to write a song about.

You know that’s not how genetics works, right?

I wish I had this comic for my genomics 101 workshop!

By Saturday Morning Breakfast Cereal.

Gorilla with Deoxyribose Nucleic Acid #whoa #illustration

By Ricardo Martinez.

In which I tell a story about the pervasiveness of my name (with a little genetics thrown in for good measure)

By DAVID NG

Just told this story at the Pathology Arts Gala last night, and I thought that maybe others would like to hear it. This is based on a piece I wrote for the Believer, and it’s about a time when I was a bit obsessed with my name.


Recorded by The Monti at ScienceOnline 2012, January 20th, 2012.

His genetic make-up only allows him to be alive for one day.

I find this strangely poignant, as well as a possible visual aid if I need to talk about senescence.

By Matt Forsythe over at Supermutant Magic Academy, via Drawn.

The Nude Mouse: An Exclusive Interview

Ben Cohen and I wrote this one a few years back. The Nude mouse (image from wiki) has always been one of those things that is almost always misunderstood by the general public. Consequently, we decided to write something that could also work as a pinup. Hey, these mice also need some validation – they have feelings too…

(CLICK HERE FOR PIN-UP POSTER - pdf file ~250k)
- We suggest photocopying at 129% – LTR to 11×17 -

Earlier this week, we had the chance to sit down with a member of a growing army of naked bubble mice. In thousands of biology labs around the globe, these lab mice quietly do their part in the pursuit of science and medicine. Called Nude Mice, these striking creatures are a result of spontaneous inbreeding, natural genetic freak shows if you will. More importantly, they are bereft of both hair and immunity – things that would normally protect them from the elements of the sky and the cooties of the world. And lucky for us, traits that not only afford some big advantages in the research arena but make for a great interview. The nude mouse we interviewed was just finished with a talk biopsy, so we met in his lab while he worked through his lunch.

- – -I want to shoot straight from the hip here: On having no hair. How is it?
It can get cold sometimes, but generally it doesn’t bother me. Besides, most females prefer it that way.

Okay, okay. Then I’ll stay on this pattern: On having no immune system. Your thoughts?
Well, I have to say that as bad as it sounds, I love it. I mean – it’s who I am. If anything, the part I hate is having to explain what having no immune system actually means. If you go into B cells, T cells, antibodies and the like, people just glaze over. It can really kill a conversation.

I’m with you on that.
In the past, I’d talk about being like the bubble boy. Nowadays, I usually just say rent the movie Fantastic Voyage – yes, that Fantastic Voyage, with Raquel Welch in the tight suit – and watch out for those bad ass white cells eating the spaceship. I tell them that not having an immune system means stuff like not having any of those bad ass white cells.

Sort of After-School Special-ish, no?
Don’t judge me, ‘kay?

Of course not. How about, Give us your reflections on the media.
You’re asking me?

Yep.
The media I can live without. We’re fairly private creatures, so the whole publicity thing is not cool. Besides, they almost never get it right. One time, my uncle had a human ear prosthetic grow on his back, and well, Christ, with all the press that ensued, you’d think he was sleeping with Jennifer Anniston. Not only that, but if you picked up a newspaper, you’d see this picture of poor naked Uncle Orv with a huge human ear on his back, and you’d be totally thinking that he could hear out of this thing. Which, of course, is not at all true. A shame really – that experiment was pretty elegant in my view.

You’re kidding me, right?
Not at all. Engraft a hollow polymer scaffold (shaped like an ear) on Uncle Orv’s back, infiltrate it with tissue cells from a burn victim needing an ear prosthetic, and wait for growth. Unky Orv ends up doing good because he has no hair, and he also doesn’t have the biology to reject the foreign ear tissue. How brilliant is that?

Point taken. Let’s move on. On stem cell research. React.
Basically, and to quote a GREAT movie, “bring it on!” Although to be honest, my opinion is pretty biased. They do a lot of bone marrow research on types like me, since having no immune system means I’m great as a clean slate. Just put some stem cells in my spleen and hey, you just might reconstitute my immune system. That’s awesome when it happens, because then I can actually leave my bubble for a while. I hate living in a fucking bubble.

On scientists playing God, creationism and intelligent design.
Seriously, do I look like something that is a result of intelligent design? And I don’t care much for those creationism types either. Did you know that only humans get to enter the gates of heaven? What’s up with that?

I have no problem with that, if you’re asking. But let’s keep this one-way. On the ethical treatment of animals. Everyone’s always bitching about that.
Look, it’s really not so bad. I get nice living quarters, and plenty of food. And every once in a while, they bring in a wheel or a bunch of females, sometimes both. Plus, I know I’m doing some good in this world – the experiments they carry out can actually help people. Really, what more could you ask for?

The Evolutionary Biology of the Unicorn.

By DAVID NG

Unicorns are great. Seriously.

And here I’m going to think out loud and think of them in a conventional biology sort of way. You know – have a little fun evolution wise.

In many respects (except for the magical powers bit) I don’t think this is necessarily too hard to do. i.e. you have something that looks like a horse, but hey what’s this – there’s also a horn there.

I guess the question I’m pondering is whether a unicorn could occur from a realistic evolutionary biology point of view – you know, given the right circumstances and the right timescale. And if so, exactly what sort of things, biologically and genetically, would need to happen?

Anyway, here’s a couple options to sift through.

One possible way to get the whole horn thing started on a poor horse is through a condition known as “cutaneous horn” formation. In this situation, you essentially have an abnormal, sometimes cancerous growth, that results in a keratin structure protruding from the skin.

(Here’s a picture of a cutaneous horn – it’s kind of ugly)

“Cutaneous horns usually arise on sun-exposed skin but can occur even in sun-protected areas. The hyperkeratosis that results in horn formation develops over the surface of a hyperproliferative lesion. Most often, this is a benign verruca or seborrheic keratosis; or it could be a premalignant actinic keratosis. A malignancy has been reported at the base of a cutaneous horn in up to 20% of lesions. More than half of all cutaneous horns are benign.Benign lesions associated with cutaneous horns include angiokeratoma, angioma, benign lichenoid keratosis, cutaneous leishmaniasis, dermatofibroma, discoid lupus, infundibular cyst, epidermal nevus, epidermolytic acanthoma, fibroma, granular cell tumor, inverted follicular keratosis, keratotic and micaceous pseudoepitheliomatous balanitis, organoid nevus, prurigo nodularis, pyogenic granuloma, sebaceous adenoma, seborrheic keratosis, trichilemmoma, and verruca vulgaris. Lesions with premalignant or malignant potential that may give rise to cutaneous horns include adenoacanthoma, actinic keratosis, arsenical keratosis, basal cell carcinoma, Bowen’s disease, Kaposi sarcoma, keratoacanthoma, Paget’s disease, renal cell carcinoma, sebaceous carcinoma, solar keratosis, and squamous cell carcinoma.” (From eMedicine)

So you have something producing horn-like features, and whilst not exactly common, is still within the realm of possibility.

However, this possibility of unicorn evolution is kind of weak, because often the base of the “horn” structure is not at all stable, and in fact it looks like these horn structures can often be quite easily removed surgically. As well, this is not really a heritable trait in the usual sense – i.e. normally these structures are formed due to abnormal growth coming from a one cell, possibly mutated from exposure to a some mutagen (the sun is often sited for example). In other words, whilst susceptibility to the abnormal growth is likely genetic, the act of it always occuring on the horses head is less so (or something like that).

In other words, let’s move on.

One thing I can say is that it’s interesting to note that both the horse ((Equus ferus caballus) and the rhino (Rhinocerotidae) both belong to the Perissodactyla order, also often termed the odd-toed ungulates. This suggests that in the grand scheme of things, these two types of creatures are not so far apart. Whilst obviously interbreeding isn’t an option (since the species barrier would presumably be more than sufficient to disallow the formation, as well as the propagation, of hybrids unicorn like rhino-horses), it does present the idea that however the horn formed on the rhino, this could still be in the realm of reality with something like a horse.

Which actually makes all the more sense when you look through a paper published in the Journal of Morphology in 2006, which did CT scanning of rhinoceros’ horns to get a better sense of their anatomy. Here, the suggestion is that the horn of rhinos are markedly different from a horn of, say, a sheep. Specifically:

“The horns of most animals have a bony core covered by a thin sheath of keratin, the same substance as hair and nails. Rhino horns are unique, however, because they are composed entirely of keratin.”

This might fit a little with the “cutaneous horn” angle, but then another observation came about from the CT scans. The lead authors goes on to say that:

“The horns most closely resemble the structure of horses’ hoofs, turtle beaks and cockatoo bills. This might be related to the strength of these materials, although more research is needed in this area.”

And this nugget of information brings up a delicious possibility.

That is – maybe a unicorn could develop initially from a mutation within a hox gene, resulting in a hoof like structure coming out of the animal’s head. And in case, you’re wondering what a hox gene is all about, it’s essentially:

(From wiki) “A group of related genes that specify the anterior-posterior axis and segment identity of metazoan organisms during early embryonic development. These genes are critical for the proper number and placement of embryonic segment structures (such as legs, antennae, and eyes).”

In plain speak, this simply means that the hox family of genes are the grand controllers of body architecture – as in your arms go here, your head here, and this is about right for your big toes.  In other words, for our unicorn, we really just need a mutational event where something meant to be coming out at the limbs is inadvertently coming out of the wrong part of the general body plan.

Classic examples of hox mutants occur in fly embryogenesis, and here are two of many examples of mutations that result in something along the lines of a foot/leg like structure coming out of the head area.

This is an image of a fly with a mutated proboscipedia gene: basically the labium develops into a pair of legs (image link)

Here’s another:

(Image link)

All to say that I’m wondering if the hox idea might actually have some (pardon the pun) legs to it.

Of course, even so, the hox idea would only be part of the story. Natural selection and the whole epic time scale stuff would still need to do its thing. Here, I must admit that I am curious to see what readers would think are the best environmental conditions (serious and funny ones) to produce the right selecting pressures for unicorn morphology. Maybe a few suggestions in the comments section would be cool?

And what about those magical powers? Well, how about we let the Intelligent Design folks debate over that one…

Science posters by Christian Petersen

By Christian Petersen, via io9.

After winning the Nobel Prize, Francis Crick would send out this card to anybody trying to contact him

From Futility Closet.

Deluged with mail after his discovery of the double helix, Francis Crick began sending a printed card in response to invitations:

The “cure your disease” part is priceless.

When Celebrities, Who Have Been Cloned in the Movies, Get Together For a Coffee

I wrote this waay back in 2005. Could do with a bit of an update (I’m sure there’s a lot more in the cloning genre now…)

- – -

By DAVID NG

SETTING: A Starbucks in L.A. – three celebrities are sitting at a table with their coffees and sharing a newspaper, a fourth is walking towards the table with his coffee.

FADE IN

MICHAEL KEATON
(Approaching the table)
Man, I really need this now.

(Sits down, whilst the others nod or wave).
Is there a free section of paper?

ARNOLD SCHWARZENEGGER
You vant the sports section?

MICHAEL KEATON
Sure.
(Takes the paper and starts looking at the front page)

(A few minutes of silence as everyone reads their newspaper)

HITLER
(Slams his paper down and stands up).
Dis ist terrible! As Fuehrer of the German people and Chancellor of the Reich, I cannot agree with dis. Vee must fight. Neither force of arms nor lapse of time vill conquer Germany. It ist infantile to hope for the disintegration of our people. Mr. Bush may be convinced that America vill win. I do not doubt for a single moment that Germany vill be victorious. Destiny vill decide who is right. One thing only ist certain. In the course of world history, there have never been two victors, but very often only losers.

MICHAEL KEATON
Whoa easy there Adolf. Is that de-caf you’re drinking there buddy?

PIKACHU:
Pikachu! Pikachu!

MICHAEL KEATON:
Hey, look at this, Governor Arnold. Looks like you’re in the paper today.

ARNOLD SCHWARZENEGGER
I know, isn’t it swell? My biceps looked especially good on that day.

MICHAEL KEATON
(sipping his coffee)
Yeah, pretty cool, pretty cool. I’ve got to ask though, what’s it like being a Governor of California anyway?

ARNOLD SCHWARZENEGGER
Oh, you know, nothing special really. Besides, what makes you so sure that it is me and not my clone.
(Everyone chuckles).

HITLER
Hey, I saw Spider Man 2 yesterday – it vas really good. Hey Michael, do dat funny thing I like.

MICHAEL KEATON
You mean this.
(Grabs Arnold by the shirt lapels and pulls him close to his face)

I’m Batman!

ARNOLD SCHWARZENEGGER
(Laughing)
Ya, that kills me too.

PIKACHU
Weeeeeeeeeeeeeeeeeee!

(Darth Vader, the Lord of Sith then approaches the table)

DARTH VADER
Hello Arnold, may I join you?

HITLER
(Standing up and cutting in)
I’m sorry Mr Vader, but dis table ist reserved only for celebrities who have been cloned in zee movies.

DARTH VADER
(Facing Arnold)
Your destiny lies with me Schwarzenegger. Obi-Wan knew this to be true.

(Turning to Hitler, with two raised fingers and speaking very deliberately)
I am welcome to join you for coffee.

HITLER
(In a sort of trance)
You are velcome to join us for coffee.

DARTH VADER
Here, please have my seat.

HITLER
Here, please have my seat.

ARNOLD SCHWARZENEGGER
Darth! Stop that now!
(Hitler shakes his head)

The ‘cyborg’ coffee group doesn’t meet until tomorrow morning.

DARTH VADER
(Turning to Arnold)
Impressive. Most impressive. Obi-Wan has taught you well. You have controlled your fear. Now, release your anger. Only your hatred can destroy me.

MICHAEL KEATON
(Tapping his finger on Darth Vader’s arm)
Umm, buddy, I think Arnold told you to get lost.

DARTH VADER
(Looking at everyone)
Hmmmpph, very well.

(Turns away and leaves)

MICHAEL KEATON
(Quietly)
Loser.

PIKACHU
Pffffsssstttt!

FADE OUT
.

* Michael Keaton was in “Multiplicity,” Arnold Schwarzenegger was in “The Sixth Day,” Hitler was in “The Boys of Brazil,” and Pikachu was in “Pokemon, the First Movie: Mew vs MewTwo”

Notes from Mattel’s “Future of Barbie®” Brainstorming Session (including Stem Cell Barbie and others…)

I always thought the Stem Cell Barbie’s slogan would make an interesting t-shirt. Note that this was originally published at Yankee Pot Raost.

By DAVID NG

ConceptStem-Cell Barbie®

Description: Produce a plastic mesh form in the shape of a Barbie doll. Seed this mesh with embryonic stem cells. Culture in bio-chambers until cells infiltrate and coat the plastic form.
Pro: This Barbie might get pregnant.
Con: This Barbie might get cancer
Potential slogan: “Feels like real skin because it is real skin.”

ConceptHybrid Barbie®

Description: Barbie doll powered by both conventional gasoline engine, as well as an electric motor.
Pro: Barbie is emissions-compliant.
Con: No one can figure out a good place for the gas nozzle to go in. It always ends up looking dirty.
Potential slogan: “This baby gets up to 40 miles per gallon.”

ConceptSchrödinger’s Barbie®

Description: Interactive Barbie doll placed inside a thick lead box, containing a mock cyanide canister, and mock Geiger counter. The Geiger counter may or may not release one decaying mock atom, which in turn, may or may not break the canister releasing the cyanide. Therefore, child would be uncertain as to the fate of the Barbie doll (who could be pretend-dead or pretend-alive) until the lead box is actually opened.
Pro: This is fun way to illustrate an aspect of quantum law, which suggests that due to the superposition of states, Barbie is both dead and alive until the box is opened.
Con: Huh?
Potential slogan: “Schrödinger’s Barbie—be the first to give a shit.”

ConceptSuper Malleable Barbie®

Description: Produce Barbie dolls using the Dow Corning 3179 dilatant compound (a mixture containing silicone oil and boric acid, commonly known as Silly Putty).
Pro: Barbie can bounce.
Con: When Barbie pretend-falls asleep whilst pretend-reading a newspaper, the newsprint will show up on her face.
Potential slogan: “Ken will thank you.”

ConceptFlame-Retardant Barbie®

Description: Coat existing doll product with copious amounts of the common flame retardant, polybrominated diphenyl ether.
Pro: Excellent opportunity for accessories (fireworks, matches, flame throwers, etc).
Con: Excellent opportunity for accessories (fireworks, matches, flame throwers, etc).
Potential slogan: “Throw the Barbie on the barbie!”

ConceptSupercomputer Artificial-Intelligence Robot Barbie®

Description: Multiple clusters of high-powered processors networked to a Barbie doll mainframe. 2 USB ports standard. CD/DVD burner drive optional.
Pro: No more stupid brainstorming sessions—send Barbie instead.
Con: Small chance of total world domination and destruction of the human race as we know it.
Potential slogan: “Kicks ass at chess!”

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