2015 Top 10 in Science


Raşit Gürdilek

They herald edited genomes, Solar System picture...

At the end of a year rich in scientific and technological breakthroughs, the ones which especially stood out were chosen by the editors of Science in the  magazine’s traditional poll.

“T-model” of genetic engineering: CRISPR

As the “breakthrough of the year”,  Science editors put the genetic manipulation technique CRISPR, which had also made the lists in 2012 and 2013 but whose popularity in the realm  of genetics  peaked in 2015, at the top of the list of 10 exceptional  feats.

Developed from a bacterial defense system fiirst discovered by a yoghurt company in 2007, the method takes its name from the bacterium’s  mechanism of defending itself against a group of viruses called bacteriophages which carry their genetic material as DNA and prey on bacteria. Having formed a collection of DNA segments of viruses which have infected before, when the bacterium is invaded by one of these viruses, it sends the stored DNA segment to the DNA of theinvading virus by a guide RNA which, with an attached enzyme cuts out the matching DNA section and debilitates the virus. CRISPR takes its name from  the  strange DNA sequences in which it stores the viral DNA samples and uses as its defense mechanism. These are called “Clustered Regularly Interspaced Short Palindromic  Repeats.” The bacterium launches CRISPR at the target usually linked with a cutting enzyme called Cas9. 

After deciphering the secrets of the CRISPR, genetic engineers  discovered that it was a perfect tool of manipulation that can be used both for the silencing and activation of the target genes, resulting in a chain of experiments and applications throughout the world.  The CRISPR-Cas9 combination saw its star rise in recent years  with the role it played in the cancer treatments based on the reinforcement of the immune system.  But with the rapid spread of its use, it entered both the realm of novel experimental treatments , and the “forbidden zone” of editing  gonad cells and even human embryos, avoided  until now due to  potentially adverse results and ethical concerns.

One of the developments which most excited the scientists in recent years, stimulating new research and the foundation of commercial companies, is a technique which opens the door to the  treatment of the diagnosed or potential diseases by correcting a flawed gene or silencing it. Called the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), the technology derives its name from repeating DNA sequences which form a part of the defense mechanism bacteria have developed against  group of viruses called “bacteriophage” (bacteria eaters).  The bacterium ties a protein named Cas9 to a RNA strand which matches the genome of the virus and this hybrid structure inactivates the virus by slashing its DNA. RNA, is a molecule easier to synthesize in a laboratory compared to a piece of protein. Hence, replacing the RNA which locks onto the target DNA,  CRISPR outperforms other gene manipulation techniques developed in recent years. Now, as some researchers are trying to modify CAS9 structures to make it “prune” the DNA instead of cutting it, biochemists are engaged in studies directed at determining their structures to produce them artificially. Some other labs, meanwhile, are searching for other Cas proteins which may be more efficient than Cas9.

In the past year, a research group using CRISPR-Cas9 eliminated a virus group in pig kidneys, opening the doors for pig organ transplants to humans. Experiments targeting the “improvement” of  genes in human embryos and gonad cells had already triggered a call for a moratorium from leading geneticists. But the successful altering of genes by a Chinese group in an experiment with unviable embryos caused a more forceful  repetition of the warning

Attaching a nonalive form of Cas9  to CRISPR , geneticists  can also use the combo as a guide which seeks out the target genes, as well as a vehicle unerringly transporting  the attached molecules to its target. In a recent demonstration of the method, CRISPR-Cas9 technique used on mouse models with Duchenne syndrome, destroyed the faulty genes  which cause the ailment, enabling for the first time the treatment of a  genetic disease  in a mature mammal.

The method  is so successful and easy, that according to the geneticists who have pioneered the gene manipulation techniques, CRISPR, “which can now be used in any biology laboratory,” has “democtaticized” the gene editing studies. And in a fitting analogy, another geneticist likens the technique to the T-Model  first marketed in 1908 by Ford, which, with the ease of its production,  dependability and cheapness  transformed the U.S. society.

Pluto basking in late glory

Although Science editors do not rank the other nine scientific and technological breakthroughs, the undisputed runner up was dwarf planet Pluto which took its place at the center of a months-long media storm unleashed by the July flyby of the New Horizons spacecraft. Adding to its glory, Pluto came far ahead in the standings of a poll  by Science readers.

Passing  just 12.500 kilometers   above Pluto’s surface on July 14 following a 10-year, 5 billion kiilometer voyage, the spacecraft  sent stunning images which exposed the unsuspected features of this oft-neglected member of the Solar system which remained in shadows for 85 years and suffered the humiliation  of being demoted to dwarf planet status, leaving the astronomical community in disbelieving awe.

At the head of the surprises were ample evidence showing Pluto was being shaped by  still active geological processes despite its small mass and the billions of years it spent in  the frigid cold of space far from the Sun. Images show in incredibe detail the mountain ranges of water ice rising 3500 meters at  the rim of  vast plains of frozen methane and nitrogen  and evidence of ice volcanism at some of the peaks.

Another surprise from Pluto was its blue skies. Besides the images of the  “Sputnik Planum” in the shape of a big heart which warmed  the hearts of astronomy fans, New Horizons also provided detailed  data on Pluto’s largest companion, Charon, as well as four smaller moons. 

Pluton

New evidence for Asian origin of New World natives 

The famous “Kennewick Man”, whose origin was the object of scientific and political controversies ever since his 8500-year-old bones were discovered on the shore of a river in the state of Washington in western U.S.,  had his genetic code sequenced at last. What his nuclear genome has revealed is his kinship with the native tribes in the area,  long engaged in a legal battle for the possession of the remains of the “ancient one”. The findings also confirmed that the first inhabitants of the New World were Asians who crossed a land bridge which in the past joined the opposing sides of today’s Bering Strait.  Thus, some new theories proposing European origins for America’s first settlers were proven incorrect. 

Shot in the arm for experimental psychology

How trustworthy are psychology experiments? In  other  words, how  far can they be reproduced? These questions were stemming from aroused suspicions about their reliability due to  usually limited number of  participants and the fact that  studies  often related to conditions not very widespread. The answers to the these questions should have  been the harvest of same results in replicated experiments. But although 10 of the 13 experiments replicated in 2013 confirmed the findings of the original experiment,  in about 100 tests throughout the world of  27 published experiments, a third failed to obtain the original results. The field fared even worse in 2015, with only 39 of the 100 studies published in  three prestigious journals passing the replication test. But despite the bad news about the reliability of original results, a new method introduced in replication test called “preregistration” , or publishing of the methods and the rationale of the tests in advance and report of the results afterwards to prevent the manipulation of data, came as a confidence building measure that would benefit not only psychology, but other fields of science as well. 

Yet another human species

Some 1500 fossil bones, unearthed by  an international team of anthropologists at a deep cave system in South Africa, added another species to our family tree.  Researchers determined that  bones found at the Rising Star cave belonged to at least 15 individuals of the same species. The hominin species named “Naledi”  which means star in  native language, is thought to be relatively tall and able to walk erect. But its small brain and hands with elongated fingers which it likely used to climb trees to avoid predators show that Homo naledi was a primitive human species.

Since the researchers could not date the fossils as yet, it is not clear whether H. naledi was a species who lived about 2 million years ago when the Homo genus to which our ancestors belong was emerging, or one that arose later.

Down to the bottom

The existence of  columns of  molten rock called “plumes” rising from hot points at the depths of Earth towards the surface was known for long. Also known is the formation of island chains (e.g. Hawaiis) from the ejecta of  volcanoes which sprout as tectonic plates slide past these plumes. What was unknown, however, was whether the base of these plumes extend  all the way down to the boundary of the Earth’s hot core 3000 kilometers below the surface, or to more shallow depths.  Analyses by researchers using a novel technique called “whole waveform tomography”,  based on the monitoring of the progress of all the tremors caused by an earthquake instead of the initial waves as was done until now, put an end to the controversy:  At least 28 plumes descend through the mantle to the  core’s boundary. Furthermore, thickness of the plumes reach 800 kilometers, which is three times what was believed so far. Researchers hope that the technique will shed light on  other details of  the planet which have remained in the dark, like, for instance, how far deep lies the “graveyard” of ocean crust slabs which dive into the mantle in the process of plate tectonics. 

An Effective vaccine against Ebola

The fight against the deadly Ebola disease which scoured Africa and threatened to spread to the world had remained largely ineffective in recent years.  But  in 2015, a vaccine developed by researchers at the Public Health Agency of Canada and began to be produced by pharmaceutics company Merck after positive data were obtained from tests on monkeys, yielded encouraging results in a clinical study conducted by the World Health Organisation in Guinea. 

Yeast put on drugs job!

Adding new genes to yeast, biologists in the U.S. succeded in making it produce opioids, the opium based painkillers, the product of a biosynthesis which could only be done by the opium poppy until now.

Employing genetic engineering methods, the biologists added 21 genes taken from three different opium plants, goldthread (a plant , with  a three-lobed leaf resembling that of a clover and a thin gold-colored root – hence the name – which the natives munch to suppress the pain of mouth sores), bacteria and a rat to the yeast’s original genome. The reserchers hope the control of this biosynthesis pathway could lead to more effective drugs. On the other side of the coin, there is the theoretical possibility of the recruitment of yeast to home production by drug addicts or dealers. But the task exceeds the limits of home economy, the researchers assure. Pointing out that thousands of liters of culture are required for a dose of painkiller, they say they’ve checked and found that a detectable amount of opioids cannot be produced at home setups.

Secret lymphatic vessel in the brain

Contrary to what Italian physician Paolo Mascagni had said more than two centuries ago, it was assumed that the lymphatic system, made of a network of vessels helping the cleanup of cellular waste and transportation of immune cells in the body, was extending upto the neck without passing into the brain. Therefore the brain was believed to have an immune system  of its own. In 2015, however, a lymphatic vesssel  system discovered in the outermost brain layer called meninges was found to  be connected with the system in the body. Researchers hope the discovery could open a new pathway for treatments of Alzheimer, MS and meningitis.

Towards a quantum Internet

The rules of quantum mechanics which studies the particles, forces and their interactions in the subatomic world, defy our logic conditioned to our experiences in the large-scale “classical” world we are accustomed to. One of the weirdest of  these is the possibility of a hidden link called entanglement between two particles. Thanks to this phenomenon which was unacceptable even for a logic as Einstein’s, we can, for instance make a measurement on  one of the two entangled electrons and determine the direction of a quantum mechanical property called “spin”, and know that its partner had “collapsed” to the opposite spin direction at the same instant no matter how far away it is. Rejecting the uncertainties which are the hallmark of quantum mechanics with his famous quote “God doesn’t throw dice,” Einstein had proposed that each of the entangled particles could carry “local hidden variables” which would eliminate the need for “spooky action at a distance”. But in 2015, the result of an experiment meticulously designed by researchers at the Delft University of The Netherlands and the  Institute of Photonic Research  (ICFO) of the University of Barcelona made the latest and most solid confirmation of the quantum mechanical effect from a distance, thus putting the final nail in the coffin of  local hidden variables.

To describe the experiment in simple terms, two electrons put in an entangled state were encapsulated in two diamond crystals set 1.3 kilometers apart. When the spin direction of  one of the electrons were determined with an extremely rapid measurement,  it was seen that its partner had the opposite spin. For this to happen, there has to be a communication between the two electrons. But according to Einstein, no message can travel faster than the light. In the experiment, the distance the light could travel in the time taken by the measurenet was calculated to be 30 meters. Since, the distance between the electrons were 1.3 kilometers, the effect on the pair cannot be done by the light. This means that action at a distance (which can be faster than light) predicted  by quantum mechanics is true. But according to physicists, even if the action can be instantenous independent of the distance, it cannot be used to send messages faster than light. Although the outcome has come as no surprise for physicists, the precision method ussed therein is thought capable of opening the door for exotic technologies like the quantum Internet. 

REFERENCES

  • 1. “Science’s 2015 Breakthrough of the Year: CRISPR”, American Association for the Advancement of Science, 17 Decembre 2015
  • 2. http://news.sciencemag.org/scientific-community/2015/12/and-science-s-breakthrough-year?utm_source=general_public&utm_medium=magazine&utm_campaign=Breakthrough15-1427
  • 3. “Genome-wide inactivation of porcine endogenous retroviruses (PERVs)”, Sciencexpress, 11 Octobre 2015
  • 4. “Late harvest from Pluto reveals aa complex world”, Science, 16 Octobre 2015
  • 5. “Historic Delft Experiments tests Einstein's 'God does not play dice' using quantum 'dice' made in Barcelona”, ICFO-The Institute of Photonic Sciences, 21 Octobre 2015