In that study, scientists compared the oldest and second-oldest HIV samples: blood (1959) and tissue (1960) from the city of Kinshasa. The HIV gene sequences differed by a whopping 12 percent. Clearly the two strains had diverged from a common ancestor long before 1959. Next, the scientists arranged decades of HIV samples into a genetic tree based on their similarities and converted the genetic distances on the tree into units of time, using the known mutation rate of HIV and some fancy computer modeling. The roots of the tree converged about one hundred years ago.
Between 1884 and 1924, AIDS was born.
Deadly virulence is the hallmark of a recently evolved disease. Deadly is not a beneficial trait, as killing the host kills the virus. More evolved diseases are less virulent, thus more successful at spreading their genes.
HIV and the Evolutionary Speed Limit
HIV has been evolving for a century, the equivalent of 100 million years of mammalian evolution, so one might expect that HIV would now be an ultra-evolved superbug, even more infectious than the original version. But, surprisingly, most of the genetic changes that have accumulated in the past century are random—driven by genetic drift rather than natural selection.
Genetic drift: genetic changes that accumulate in a species’s genome randomly, rather than through natural selection.
HIV is a retrovirus, meaning it stores its genetic information in RNA. Copying RNA back to DNA is a messy, error-prone process. The mutation rate is so high that retroviruses are said to live at the evolutionary speed limit—if they mutated any faster, they would fall apart. So HIV racks up scads of mutations that don’t confer an immediate advantage. It’s genetic drift is fast enough to be a riptide!
But don’t think that HIV doesn’t also undergo classic Darwin-style natural selection. HIV is a marvel at escaping the immune system and eluding drugs. There is no better example of natural selection in real time than its evolution within a single host: HIV can change some of its proteins by 25 percent to escape the immune system and evade drugs—and yet, amazingly, the proteins still function. The virus has made incessant random mutations work in its favor.
Protein-coding genes, the part of our DNA that is most obviously useful, makes up less than 2 percent of our genome. There are also RNA coding genes and regulatory DNA. Still, human cells contain a lot of DNA with no known purpose. For instance, the ALU sequence—a 300-nucleotide chunk that repeats ad nauseum—comprises 10 percent of our instruction manual, yet seems to be a useless accident. And a lot of DNA—more than 8 percent—is miscellaneous litter from alien retroviruses! By transferring DNA between species, retroviral infections are the Johnny Appleseed of evolution, the Wilt Chamberlain of spreading genes.
HIV tends to revert back to its old form (which is usually more stable) when transmitted to a new host, however, so these mutations aren’t preserved at the population level.
Fossils in Our Chromosomes! Prehistoric HIV
There is yet another incredible source of information about HIV evolution: Modern mammals contain clues to its ancient history embedded in their genomes.
You see, when a retrovirus infects a cell, it must insert its genetic material into a chromosome in that cell in order to reproduce. When the virus happens to infect a sex cell, and that sperm or egg becomes a baby, the viral sequence can become a permanent part of the host genome. This DNA “fossil” is called an endogenous (pronounced “en DOJ en iss”) retrovirus.
These fossils litter our chromosomes. Scientists estimate that 8.3 percent of the human genome is leftover from retroviral infections—retrovirus DNA trapped in our chromosomes. This is a huge amount of DNA, seven times more than is found in all twenty thousand protein-coding genes in the human genome! (The part of our genome that makes the building blocks of our bodies.)
In 2008, scientists discovered an endogenous lentivirus (the family to which HIV belongs) fossil in the genome of the gray mouse lemur, a small primate found in Madagascar. This discovery shows that HIV’s ancestors have been infecting primates for 14 million years. In 2009, scientists discovered a precursor of the lentivirus, an endogenous foamy virus, fossilized in the genome of the sloth. (Think Sid from the movie Ice Age.) HIV’s ancestors have been infecting mammals for 100 million years—since the age of the dinosaurs!
Startling Conclusion
We now know that our genes are full of alien DNA fossils! We now know the history of the viral scourge known as HIV. Where does it get us? Amazingly a virus that mutates at warp speed hasn’t changed much over 100 million years. And those invariant parts that cannot be changed? Good news for vaccine designers, who can exploit these to develop a shot that finally cripples HIV. This is just one of the many practical implications of understanding the evolution of HIV.
REFERENCES:
R. J. Gifford, et al., “A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution,” Proceedings of the National Academy of Sciences 105 (2008), 20362-20367.
M. T. P. Gilbert, et al., “The emergence of HIV/AIDS in the Americas and beyond,” Proceedings of the National Academy of Sciences 104 (2007), 18566-18570.
A. Katzourakis, “Macroevolution of complex retroviruses,” Science 325 (2009), 1512.
Paul Sharp and Beatrice H. Hahn, “Prehistory of HIV-1,” Nature 455 (2008), 605.
M. Worobey, et al., “Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960,” Nature 455 (2008), 661- 664.
CHAPTER 9
WORKING NINE TO FIVE
If you find yourself thinking, “This tricky shortcut will save a little time . . .” then you might be headed for a Darwin Award.
Construction, demolition, and all things in between. Whether you’re a professional or a do-it-yourselfer, even a seemingly safe, sane, straightforward job can turn into a hazard in the hands of a Darwin Award wannabe. From seasonal ski-lift operator to career safety inspector, working for a living takes on a startling new meaning!
Wheel of Fortune • Pillar of Strength • A Screw Loose • Bricks in the Head • Down in the Dumps • Duct Don’t
Darwin Award Winner: Wheel of Fortune
Unconfirmed
Featuring work and machismo
WINTER 1995, MICHIGAN | During the ski season at Sugarloaf Resort, a new lift operator assigned to the bottom of Lift 2 was greatly impressed by the bull wheel that turned slowly above his head. The giant spokes on the wheel were impossible to resist. He grabbed a spoke and did a few pull-ups while the wheel turned.
After entertaining himself in this manner for a while, he decided to try this trick on the outer rim of the wheel. His timing was off—he did not drop down in time. Caught between the wheel and the lift cable, he was sliced in twain during his fateful final trip around the bull wheel.
Reference: Anonymous eyewitness
Darwin Award Winner: Pillar of Strength
Confirmed by Darwin
Featuring work, vehicles, and gravity
9 OCTOBER 2008, SOUTH AFRICA | For days, Johannesburg office workers watched a demolition worker slowly chip away at a pillar supporting the concrete slab above him. One said, “I wondered how they would drop that section.” The walls were gone, and only the support pillars remained.
Dozens of observers watched the slow and senseless demolition proceed. Finally the only possible outcome concluded this epic battle. The besieged support collapsed, crushing man and machine beneath a pile of rubble.
The worker, fifty-two, was killed instantly inside the cab of his mini-excavator.
Observers said they had been concerned about the workers’ safety for several days. “I cannot believe they did not foresee this,” said a shocked witness who did not foresee this. “There was no common sense!”
Reference: thetimes.co.za
Darwin Award Winner: A Screw Loose
Confirmed by Darwin
Featuring work and falling!
14 APRIL 2008, TEXAS | A contract worker was hired to install reinforcement bars on
a communi- cations tower near Camp Bullis. He was wielding power tools high above the ground, when two other workers saw him lean back and fall 225 feet to his death. Turns out, the man had wrenched loose the bolts on the bar to which he was attached. Police are calling it a tragic accident.
“Pride goeth before a fall.”
—Proverbs 16:18
Team Darwin is calling it a “wrenching” accident.
Reference: woai.com
Darwin Award Winner: Bricks in the Head
Confirmed by Darwin
Featuring work, gravity, and do-it-yourself
30 APRIL 2009, YORK, UNITED KINGDOM | In another do-it-yourself project gone wrong, a forty-one-year-old homeowner attempting to demolish a large brick garden shed succeeded in his primary objective, but suffered collateral damage when the cement-slab roof demolished him.
The unfortunate chap was alone on his property at the time. While one has to question the wisdom of undertaking a demolition project with no one on hand in the event of a mishap, a neighbor happened to witness this “mishap” and immediately summoned help. Hydraulic rams and high-pressure air bags were employed, but it was too late to stop fate. Paramedics pronounced the homeowner dead at the scene.
Speaking to the press, a neighbor described the accident as unspeakable.
In the unequal contest between flesh and stone, the stone always wins.
Reference: York Evening Press, thepress.co.uk
Reader Comment
“This could have been on Renovation Realities Gone Wrong: the Don’t DIY TV show.”
At-Risk Survivor: Down in the Dumps
Confirmed by Reliable Eyewitness
Featuring work, insurance, and feces!
2006, UK | During the scrape and resurface of a large residential street in Edinburgh, it was noticed that a large foul sewer ran down the street. As it was believed to be quite shallow, it was necessary to determine its exact route in order to avoid damage by the resurfacing works. Working in a sewer can be dangerous, so three men were sent to an expensive two-week training course, and another six thousand pounds went into the purchase of appropriate equipment: masks, suits, and gas monitors.
Once the project was under way, the supervising engineer decided to pop along one afternoon and see how work was commencing. The tent covering the sewer was shaking and bulging oddly. He threw open the flaps and was presented with the unsavory sight of three men wrestling over the open manhole, covered in waste matter! Two were shouting at a third, who was unconscious, drenched in waste, and not breathing.
What was going on?
The civil engineer, trained in resuscitation techniques, began the unappealing process of clearing the unconscious man’s airway. Fortunately at that point the man started breathing again and immediately vomited a stream of waste. The ambulance was summoned—and then it was time for ’splaining.
Remember the training course? Remember the expensive new gear? Dumb, Dumber, and Dumbest decided that that was all too much effort. The sewer was so close to the surface, they figured that it would be easier to simply hang one of them head first with a torch to see the lay of the line. They held an arm-wrestling contest, and the loser was flipped upside down and lowered into the narrow manhole.
Immediately he was overcome by the fumes and passed out. With no shout to stop, Dumb and Dumber continued to lower Dumbest until he was immersed up to his shoulders in the pooling waste. After a minute or so with no response, they pulled him up and realized what had happened. They were both fighting to administer CPR when their supervisor arrived.
All four men received injections to ward off infection. Dumbest was kept in the hospital for further treatment. He developed a nasty mouth infection that caused him to lose teeth, but he survived. Denied Darwin Awards, the three men subsequently decided to try for a Stella Award3: Dumb, Dumber, and Dumbest filed an insurance claim against their company for injury and trauma, as their shortcut was not specifically forbidden in the method statement! The company settled out of court.
Reference: Disillusioned engineer
Reader Comments
“Shitty job.”
“Even the best-trained people do stupid things.”
“Pass this along to your crews, this is not the correct way to inspect a sewage leakage!”
“See what happens when you have an employee manual?”
“An unsavory example of sue-age.”
DARWIN AWARD WINNER: MAN MEETS MANURE
At least the Dunkin’ Donut man survived his disgusting dip. In a case of man-meets-manure, twenty-three-year-old Benjamin lost his life in 1999 in one of the most unappetizing manners possible when he careened into a 400,000-gallon tank of raw sewage. He was apparently driving too fast to make the sharp turn in front of the wastewater treatment plant, as his momentum carried him through a chain link fence, across an easement, and past a low post-and-rail fence surrounding the tank of decomposing sewage. Divers located his body beside his Mazda pickup, at the bottom of the sixteen-foot-deep tank.
Reference: Darwin Awards: Evolution in Action (Plume, 2001)
At-Risk Survivor: Duct Don’t
Confirmed by Reliable Eyewitness
Featuring work and gravity!
DECEMBER 2009, CANADA | Lester4, a career fire-safety inspector, entered a building in downtown Alberta for its annual fire inspection. Although new to the building, Lester is not new to his job. With several degrees in Fire and Health Safety, and fluent in three languages, this all-around nice guy has expertly inspected buildings around the world for many years.
The structure he entered has a mechanical room in the bowels of the building, a “boiler room” with a vast air duct that feeds into the air filters. The duct itself is more than strong enough to support the weight of a man. Indeed, inspectors are required to climb onto the duct from a cat-walk on the floor above, in order to inspect one of the fire extinguishers.
Oh, the Darwin Awards that have resulted from time-saving shortcuts.
Lester had just inspected that very safety device and was standing on top of the air duct when he decided to save himself a few minutes of time. Oh, the Darwin Awards that have resulted from time-saving shortcuts. The nearby fire device was almost in range if he stretched!
A highly trained Fire and Safety Inspector—well, it’s his or her job to know how to inspect a building safely. But sometimes the safe route is inconvenient. Instead of traveling all the way back down to the basement and climbing a ladder, Lester decided toA. climb down the side of the air duct,
B. in nearly complete darkness,
C. despite being warned by his senior partner an hour earlier that he definitely should not climb on the ductwork.
Halfway down, he misjudged his footing . . . and gravity performed its civic duty. Lester plummeted ten feet to the cement ground, landing in the carpentry shop adjacent to the boiler room and punching a hole through a tile ceiling in the process.
Sometimes the safe route is inconvenient.
Lester survived with two broken ankles, but easily could have impaled himself had he landed to either side—on the table saw or the tool bench.
Reference: D. Gustafson, First Aid Responder
Reader Comment
“An Inconvenient Truth Route.”
SCIENCE INTERLUDE RNAI: INTERFERENCE BY MOTHER NATURE
By Alison Davis
When was the last time you were happy about a flub-up?
In the unvarnished world of science, a wrong result can be the best thing that ever happened, but that success isn’t always immediately obvious. Thus is the case for the discovery of the game-changing, paradigm-busting, gene-silencing process called RNA interference, or RNAi.
To be fair, RNAi isn’t exactly new, and it wasn’t just discovered. Like so many stories in science, the epic tale of RNAi is one of hard work, some blind luck, and a careful eye for the unexpected.
RNA Rules
Thanks to the Human Genome Project and subsequent discoveries, DNA is a househo
ld name. Less famous, but also part of our genetic material, is RNA. You can’t see either of these stringy molecules, even with a very powerful scope, but both consist of long chains of four molecular “letters” (GATC or GAUC) hooked together by sugar molecules.
The notion that RNA is as important as DNA contradicts the traditional paradigm we are taught in school. But it’s true! RNA is headed for Warhol’s fifteen minutes of fame.
New types of RNA seem to appear monthly: snRNA, piRNA, and many more; microRNAs are the powerful “transcription factors” of eighties’ fame. Noncoding RNAs are about to turn the definition of a gene on its head!
The Darwin Awards Countdown to Extinction Page 4