LUCA: The global mega-organism What is referred to as LUCA; the primary ancesteral gene pool that is present in every organism on the planet. LUCA consisted of three types of micro-organisms that eventually gave rise to animals and plants. These are known as; bacteria, archaea and eukaryotes.
WORDS: Ian Sample ILLUSTRATIONS: Tommings
ONCE upon a time, 3 billion years ago, there lived a single organism called LUCA. It was enormous: a mega-organism like none seen since,
it filled the planet’s oceans before splitting into three and giving birth to the ancestors of all living things on Earth today. This strange picture is emerging from efforts to pin down the last universal common ancestor - not the first life that emerged on Earth but the life form that gave rise to all others. The latest results suggest LUCA was the result of early life’s fight to survive, attempts at which turned the ocean into aglobal genetic swap shop for hundreds of millions of years. Cells struggling to survive on their own exchanged useful parts with each other without competition - effectively creating a
Bacteria Bacteria are present in most habitats on Earth, growing in soil, acidic hot springs, radioactive waste, water, and deep in the Earth's crust, as well as in organic matter and the live bodies of plants and animals, providing outstanding examples of mutualism in the digestive tracts of humans, termites and cockroaches. There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water; in all, there are approximately five nonillion (5×1030) bacteria on Earth, forming a biomass that exceeds that of all plants and animals. Bacteria are vital in recycling nutrients, with many steps in nutrient cycles depending on these organisms, such as the fixation of nitrogen from the atmosphere and putrefaction. In the biological communities surrounding hydrothermal vents and cold seeps, bacteria provide the nutrients needed to sustain life by converting dissolved compounds such as hydrogen sulphide and methane. Most bacteria have not been characterised, and only about half of the phyla of bacteria have species that can be grown in the laboratory.
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Modern Virosphere Archaea Initially, archaea were seen as extremophiles that lived in harsh environments, such as hot springs and salt lakes, but they have since been found in a broad range of habitats, including soils, oceans, marshlands and the human colon. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are now recognized as a major part of Earth’s life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, but they are often mutualists or commensals. One example is the methanogens that inhabit the gut of humans and ruminants, where their vast numbers aid digestion. Methanogens are used in biogas production and sewage treatment, and enzymes from extremophile archaea that can endure high temperatures and organic solvents are exploited in biotechnology.
Eukaryotes Cell division in eukaryotes is different from that in organisms without a nucleus (Prokaryote). It involves separating the duplicated chromosomes, through movements directed by microtubules. There are two types of division processes. In mitosis, one cell divides to produce two genetically identical cells. In meiosis, which is required in sexual reproduction, one diploid cell (having two instances of each chromosome, one from each parent) undergoes recombination of each pair of parental chromosomes, and then two stages of cell division, resulting in four haploid cells (gametes). Each gamete has just one complement of chromosomes, each a unique mix of the corresponding pair of parental chromosomes.
March 2012 | Neuroscience | Eureka | THE TIMES | 30
A brief history of life Earth bombarded with meteorites carrying water and minerals. Earliest chemical evidence of fossils recorded. Earliest fossils of cells. LUCA splits into ancestors of bacteria, eukaryotes and archaea. First multicellular life appears.
“LUCA was a clumsy guy trying to solve the complexities of living on primitive Earth” global mega-organism. It was around 2.9 billion years ago that LUCA split into the three domains of life: the single-celled bacteria and archaea, and the more complex eukaryotes that gave rise to animals and plants (see timeline). It’s hard to know what happened before the split. Hardly any fossil evidence remains from this time, and any genes that date that far back are likely to have mutated beyond recognition. That isn’t an insuperable obstacle to painting LUCA’s portrait, says Gustavo Caetano-Anollés of the University of Illinois at UrbanaChampaign. While the sequence of genes changes quickly, the threedimensional structure of the proteins they code for is more resistant to the test of time. So if all organisms today make a protein with the
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Anollés of the University of Illinois at UrbanaChampaign. While the sequence of genes changes quickly, the three-dimensional structure of the proteins they code for is more resistant to the test of time. So if all organisms today make a protein with the same overall structure, he says, it’s a good bet that the structure was present in LUCA. He calls such structures living fossils, and points out that since the function of a protein is highly dependent on its structure, they could tell us what LUCA could do. “Structure is known to be conserved when sequences aren’t,” agrees Anthony Poole of the University of Canterbury in Christchurch, New Zealand, though he cautions that two very similar structures could conceivably have evolved independently after LUCA. To reconstruct the set of proteins LUCA could make, Caetano-Anollés searched a database of proteins from 420 modern organisms, looking for structures that were common to all. Of the structures he found, just 5 to 11 per cent were universal, meaning they were conserved enough to have originated in LUCA. By looking at their function, he concludes that LUCA had enzymes to break down and extract energy from nutrients, and some protein-making equipment, but it lacked the enzymes for making and reading DNA molecules. This is in line with unpublished work by Wolfgang Nitschke of the Mediterranean Institute of Microbiology in Marseille, France. He reconstructed the history of enzymes crucial to metabolism and found that LUCA could use both nitrate and carbon as energy sources. Nitschke presented his work at the UCL Symposium on the Origin of Life in London on 11 November. If LUCA was made of cells it must have had membranes, and Armen Mulkidjanian of the University of Osnabrück in Germany thinks he knows what kind. He traced the history of membrane proteins and concluded that LUCA could only make simple isoprenoid membranes, which were leaky compared with more modern designs (Proceedings of the International Moscow Conference on Computational Molecular Biology, 2011, p 92).
“While the sequence of genes changes quickly, the three-dimensional structure of the proteins they code for is more resistant to the test of time. So if all organisms today make a protein with the same overall structure, it’s a good bet that the structure was present in LUCA.” LUCA probably also had an organelle, a cell compartment with a specific function. Organelles were thought to be the preserve of eukaryotes, but in 2003 researchers found an organelle called the acidocalcisome in bacteria. CaetanoAnollés has now found that tiny granules in some archaea are also acidocalcisomes, or at least their precursors. That means acidocalcisomes are found in all three domains of life, and date back to LUCA. So LUCA had a rich metabolism that used different food sources, and it had internal organelles. So far, so familiar. But its genetics are a different story altogether. For starters, LUCA may not have used DNA. Poole has studied the history of enzymes called ribonucleotide reductases, which create the building blocks of DNA, and found no evidence that LUCA had them. Instead, it may have used RNA: many biologists think RNA came first because it can store information and control chemical reactions (New Scientist, 13 August, p 32). The crucial point is that LUCA was a “progenote”, with poor control over the proteins that it made, says Massimo Di Giulio of the Institute of Genetics and Biophysics in Naples, Italy. Progenotes can make proteins using genes as a template, but the process is so error-prone that the proteins can be quite unlike what the gene specified. Both Di Giulio and Caetano-
Anollés have found evidence that systems that make protein synthesis accurate appear long after LUCA. “LUCA was a clumsy guy trying to solve the complexities of living on primitive Earth,” says Caetano-Anollés. He thinks that in order to cope, the early cells must have shared their genes and proteins with each other. New and useful molecules would have been passed from cell to cell without competition, and eventually gone global. Any cells that dropped out of the swap shop were doomed. “It was more important to keep the living system in place than to compete with other systems,” says Caetano-Anollés. He says the free exchange and lack of competition mean this living primordial ocean essentially functioned as a single mega-organism. “There is a solid argument in favour of sharing genes, enzymes and metabolites,” says Mulkidjanian. Remnants of this geneswapping system are seen in communities of microorganisms that can only survive in mixed
March 2012 | Early Life | Eureka | THE TIMES | 30
Animals demonstrate a much higher level of cognitive ability than previous studies, but does it make them intelligent?
WORDS: Ian Sample ILLUSTRATIONS: Tommings
It is common knowledge that we are not the only species on the planet who are capable of cognitive tasks and various feats of adapting to the environment to survive. But recent studies have shown that there is a lot more going on in the animal kingdom in regards to developing skills that are considered or close to accumulated knowledge. Here are a few examples of animal studies that prove them to be sterling examples of nature, nuture and evolution.
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Mathematical Pigeons Pigeons have now shown that they can learn abstract rules about numbers, an ability that until now had been demonstrated only in primates. The pigeons had learned an abstract rule: peck images on a screen in order, lower numbers to higher. It may have taken a year of training, with different shapes, sizes and colors of items, always in groups of one, two or three, but all that work paid off when it was time for higher math. pick, or peck, the images in the right order. This is one more bit of evidence of how smart birds really are, and it is intriguing because the pigeons’ performance was so similar to the monkeys’. “I was surprised,” Dr. Scarf said. He and his colleagues wrote that the common ability to learn rules about numbers is an example either of different groups — birds and primates, in this case — evolving these abilities separately, or of both pigeons and primates using an ability that was already present in their last common ancestor.
Asian elephants have passed a test of cooperation with flying colors, one that cognitive psychologists say demonstrates an ape-level awareness and sense of teamwork. Their collaboration isn’t just the product of rote learning, but the result of careful thought. In the wild, of course, elephants routinely work together. But that doesn’t pass laboratory muster, said University of Cambridge psychologist Joshua Plotkin. “It’s anecdotal evidence. These animals are empathetic, they’re cooperative,” he said. “But how empathetic? How cooperative? The best we can do is institute controls, do experiments like this, and figure out how what they do is unique from learning.” In 2006, they showed that elephants could recognize themselves in a mirror, a benchmark feat believed to indicate an especially sophisticated level of selfawareness, on par with that of young humans. Though important, mirror selfrecognition is just one test, and doesn’t address the sort of cooperative behavior for which elephants are famed in the wild. They’re known to help individuals in distress, cooperate in rearing children and may even mourn their dead. From a behavioral perspective, they clearly demonstrate empathy.
Dolphins have large, sophisticated brains, elaborately developed in the areas linked to higher-order thinking. They have a complex social structure, form alliances, share duties and display personalities. Put a mirror in their tank and they can recognize themselves, indicating a sense of self. When trained, they have a remarkable capacity to pick up language. At the Dolphin Institute in Hawaii, Louis Herman and his team taught dolphins hundreds of words using gestures and symbols. Dolphins, they found, could understand the difference between statements and questions, concepts like “none” or “absent,” and that changing word order changes the meaning of a sentence. Essentially, they get syntax. Herzing created an open-ended framework for communication, using sounds, symbols and props to interact with the dolphins. The goal was to create a shared, primitive language that would allow dolphins and humans to ask for props, such as balls or scarves. Divers demonstrated the system by pressing keys on a large submerged keyboard. Other humans would throw them the corresponding prop. In addition to being labeled with a symbol, each key was paired with a whistle that dolphins could mimic. A dolphin could ask for a toy either by pushing the key with her nose, or whistling.
Emotional Honeybees Honeybees have become the first invertebrates to exhibit pessimism, a benchmark cognitive trait supposedly limited to “higher” animals. Bateson and Wright tested their bees with a type of experiment designed to show whether animals are, like humans, capable of experiencing cognitive states in which ambiguous information is interpreted in negative fashion. Researchers must first train them to associate one stimulus — a sound, a shape, or for honeybees, a smell — with a positive reward, and a second with a punishment. Bateson and Wright trained their honeybees to associate one scent with a sugary reward and another scent with bitterness. Then they shook half their beehives, mimicking a predator attack. Afterwards, shaken bees still responded to the sugary scent, but were more reluctant than their unshaken brethren to investigate the in-between smell. Further analysis of the shaken bees’ brains found altered levels of dopamine, serotonin and octopamine, three neurotransmitters implicated in depression. In short, the bees acted like they felt pessimistic, and their brains looked like it, too.
With a few liberating swipes of their paws, a group of research rats freed trapped labmates and raised anew the possibility that empathy isn’t unique to humans and a few extra-smart animals, but is widespread in the animal world. Though more studies are needed on the rats’ motivations, it’s at least plausible they demonstrated “empathically motivated pro-social behavior.” People would generally call that helpfulness, or even kindness. “Rats help other rats in distress. That means it’s a biological inheritance,” said neurobiologist Peggy Mason of the University of Chicago. “That’s the biological program we have.” In a study published Dec. 7 in Science, Mason and University of Chicago psychologists Jean Decety and Inbal Ben-Ami Bartal describe their rat empathy-testing apparatus: An enclosure into which pairs of rats were placed, with one roaming free and the other restrained inside a plastic tube. It could only be opened from the outside, which is exactly what the free rats did — again and again and again, seemingly in response to their trapped companions’ distress. Once rats learned to free their trapped and agitated partners, they did so almost immediately in trial after trial. The behavior was clearly deliberate. When the restrainer was empty, rats ignored it. When stuffed rats were restrained, the rats ignored them. “It’s compelling evidence that it’s the distress of the trapped cagemate motivating this helping behavior,” said Mason. “It is a huge leap up to use emotional contagion to actually do something, to actually help another individual.”
April 2012 | Animal Magic | Eureka | THE TIMES | 30
Breakthrough in neuroscience could allow troops to use mind control WORDS: Ian Sample ILLUSTRATIONS: Tommings
oldiers could have their minds plugged directly into weapons systems, undergo brain scans during recruitment and take courses of neural stimulation to boost their learning, if the armed forces embrace the latest developments in neuroscience to hone the performance of their troops. These scenarios are described in a report into the military and law enforcement uses of neuroscience, published on Tuesday, which also highlights a raft of legal and ethical concerns that innovations in the field may bring. The report by the Royal Society, the UK’s national academy of science, says that while the rapid advance of neuroscience is expected to benefit society and improve treatments for brain disease and mental illness, it also has substantial security applications that should be carefully analysed. “Neuroscience will have more of an impact in the future,” said Rod Flower, chair of the report’s working group. “People can see a lot of possibilities, but so far very few have made their way through to actual use. “All leaps forward start out this way. You have a groundswell of ideas and suddenly you get a step change.” The report calls for a fresh effort to educate neuroscientists about such uses of the work early in their careers. Some techniques used widely in neuroscience are on the brink of being adopted by the military to improve the training of soldiers, pilots and other personnel. A growing body of research suggests that passing weak electrical signals through the skull, using transcranial direct current stimulation (tDCS), can improve people’s
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performance in some tasks. One study cited by the report described how US neuroscientists employed tDCS to improve people’s ability to spot roadside bombs, snipers and other hidden threats in a virtual reality training programme used by US troops bound for the Middle East. “Those who had tDCS learned to spot the targets much quicker,” said Vince Clark, a cognitive neuroscientist and lead author on the study at the University of New Mexico. “Their accuracy increased twice as fast as those who had minimal brain stimulation. I was shocked that the effect was so large.” Clark, whose wider research on tDCS could lead to radical therapies for those with dementia, psychiatric disorders and learning difficulties, admits to a tension in knowing that neuroscience will be used by the military. “As a scientist I dislike that someone might be hurt by my work. I want to reduce suffering, to make the world a better place, but there are people in the world with different intentions, and I don’t know how to deal with that. “If I stop my work, the people who might be helped won’t be helped. Almost any technology has a defence application.” Research with tDCS is in its infancy, but work so far suggests it might help people by boosting their attention and memory. According to the Royal Society report, when used with brain imaging systems, tDCS “may prove to be the much soughtafter tool to enhance learning in a military context”. One of the report’s most striking scenarios involves the use of devices called brainmachine interfaces (BMIs) to connect people’s brains directly to military technology, including drones and other weapons systems. The work builds on research that has enabled people to control cursors and artificial limbs through BMIs that read their brain signals. “Since the human brain can process images, such as targets, much faster than the subject is consciously aware of, a neurally interfaced weapons system could provide significant
advantages over other system control methods in terms of speed and accuracy,” the report states. The authors go on to stress the ethical and legal concerns that surround the use of BMIs by the military. Flower, a professor of pharmacology at the William Harvey Research Institute at Barts and the London hospital, said: “If you are controlling a drone and you shoot the wrong target or bomb a wedding party, who is responsible for that action? Is it you or the BMI? “There’s a blurring of the line between individual responsibility and the functioning of the machine. Where do you stop and the machine begin?” Another tool expected to enter military use is the EEG (electroencephalogram), which uses a hairnet of electrodes to record brainwaves through the skull. Used with a system called “neurofeedback”, people can learn to control their brainwaves and improve their skills. According to the report, the technique has been shown to improve training in golfers and archers. The EEG traces revealed that the brain sometimes noticed targets but failed to make them conscious thoughts. Staff used the EEG traces to select a group of images for closer inspection and improved their target detection threefold, the report notes. Work on brain connectivity has already raised the prospect of using scans to select fast learners during recruitment drives. Research last year by Scott Grafton at the University of California, Santa Barbara, drew on functional magnetic resonance imaging (fMRI) scans to measure the flexibility of brain networks. They found that a person’s flexibility helped predict how quickly they would learn a new task. Other studies suggest neuroscience could help distinguish risk-takers from more conservative decision-makers, and so help with assessments of whether they are better suited to peacekeeping missions or special forces, the report states. “Informal assessment occurs routinely throughout the military community. The issue is whether adopting more formal techniques based on the results of research in neuroeconomics, neuropsychology and other neuroscience disciplines confers an advantage in decision- making.”
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Archaea Eukaryotes Bacteria LUCA LUCA WORDS: Ian Sample ILLUSTRATIONS: Tommings ONCE upon a time, 3 billion years ago, there lived a single...