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Who first buried the dead?

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Paige Madison, a PhD candidate in the history and philosophy of science at Arizona State University, writes in Aeon:

A mysterious cache of bones, recovered from a deep chamber in a South African cave, is challenging long-held beliefs about how a group of bipedal apes developed into the abstract-thinking creatures that we call ‘human’. The fossils were discovered in 2013 and were quickly recognised as the remains of a new species unlike anything seen before. Named Homo naledi, it has an unexpected mix of modern features and primitive ones, including a fairly small brain. Arguably the most shocking aspect of Homo naledi, though, concerned not the remains themselves but rather their resting place.

The chamber where the bones were found is far from the cave entrance, accessible only through a narrow, difficult passage that is completely shrouded in darkness. Scientists believe the chamber has long been difficult to access, requiring a journey of vertical climbing, crawling and tight squeezing through spaces only 20 cm across. It would be an impossible place to live, and a highly unlikely location for many individuals to have ended up by accident. Those details pushed the research team toward a shocking hypothesis: despite its puny brain, Homo naledi purposefully interred its dead. The cave chamber was a graveyard, they concluded.

For anthropologists, mortuary rituals carry an outsize importance in tracing the emergence of human uniqueness – especially the capacity to think symbolically. Symbolic thought gives us the ability to transcend the present, remember the past, and visualise the future. It allows us to imagine, to create, and to alter our environment in ways that have significant consequences for the planet. Use of language is the quintessential embodiment of such mental abstractions, but studying its history is difficult because language doesn’t fossilise. Burials do.

Burials provide a hard, material record of a behaviour that is deeply spiritual and meaningful. It allows scientists to trace the emergence of beliefs, values and other complex ideas that appear to be uniquely human. Homo sapiens is unquestionably unlike any other species alive today. Pinpointing what separates us from the rest of nature is surprisingly difficult, however.

The paradox is that humans are also unquestionably a part of nature, having evolved alongside with all the rest of life. Anthropologists have narrowed in on one singular human feature in particular: the capacity to think in the abstract. Our ability to imagine and communicate ideas about things that are not immediately in front of us is a complex cognitive process, scientists argue, one that is remarkably different from simple, primitive communication about nearby food or imminent danger.

Humans use symbols to communicate and convey these abstract thoughts and ideas. We imbue non-practical things with meaning. Art and jewellery, for example, communicate concepts about beliefs, values and social status. Mortuary rituals, too, have been put forward as a key example of symbolic thought, with the idea that deliberate treatment of the dead represents a whole web of ideas. Mourning the dead involves remembering the past and imagining a future in which we too will die – abstractions believed to be complex enough to be contemplated only by our species.

The assumption, then, was that death rituals were practised only by modern humans, or perhaps also by their very closest relatives. The possibility that primitive, small-brained Homo naledi could have engaged in the deliberate disposal of dead bodies not only challenges the timeline about when such behaviours appeared; it disrupts the whole conventional thinking about the distinction between modern humans and earlier species and, by extension, the distinction between us and the rest of nature.

For humans, death is an enormously culturally meaningful process. Cultures around the world honour the deceased with rituals and ceremonies that communicate a variety of values and abstract ideas. Since the 19th century, anthropologists have examined these mortuary practices to learn about the religions and beliefs of other cultures. During this time, it never occurred to anyone that other creatures, even other hominins (the primate group encompassing the genus Homo, along with the genus Australopithecus and other close relatives) could have engaged in similar behaviour. Surely, the thinking went, humans alone operate in such an abstract world as to assign deep meaning to death.

Yet this behaviour must have appeared at some point in our evolutionary history. Since mortuary rituals such as song and dance are invisible in the archaeological record, scientists focused on material aspects such as burial to trace the history of the practice. The discoveries soon prompted tough questions about the conventional viewpoint, suggesting that mortuary rituals might not have been uniquely human after all.

The first debate over non-humans burying their dead arose in 1908 with the discovery of a fairly complete Neanderthal skeleton near La Chapelle-aux-Saints in France. After excavating their find, the discoverers argued that the skeleton had clearly been deliberately buried. To them, it looked as though a grave had been dug, the body purposefully laid inside in the foetal position, and safely covered up from the elements. Many contemporary scientists remained dubious of this interpretation or dismissed the evidence outright. Later skeptics suggested that early 20th-century excavation techniques were too sloppy to prove such a sweeping conclusion. Debate over the burial of the La Chappelle Neanderthal continues to this day.

It is fitting that the controversy over mortuary ritual in hominins began with the Neanderthals, now known as the species Homo neanderthalensis. Ever since the first discovery of Neanderthal fossils in 1856 in the Neandertal valley in Germany, the species has occupied an ambiguous relationship to humans. Neanderthals are the closest species to humans, and their location on the spectrum between humans and other animals has constantly been contested.

For the first century after their discovery, they were typically imagined as highly non-human creatures, their primitive aspects emphasised to such an extent that they became known as brutes who couldn’t even stand up straight. More recently, the pendulum has swung the other way, with some scientists arguing that the creatures were so close to humans that a Neanderthal wearing a suit and a hat on a subway would go largely unnoticed. The debate over Neanderthal burials has similarly wavered back and forth. At some times, . . .

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Written by LeisureGuy

14 November 2017 at 2:37 pm

Posted in Evolution, Religion, Science

Seeing the Beautiful Intelligence of Microbes

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John Rennie and Lucy Redding-Ikkanda have a very interesting article in Quanta, from which I quote the text below, but you really should click the link to see the stunning photos and gifs. They write:

Intelligence is not a quality to attribute lightly to microbes. There is no reason to think that bacteria, slime molds and similar single-cell forms of life have awareness, understanding or other capacities implicit in real intellect. But particularly when these cells commune in great numbers, their startling collective talents for solving problemsand controlling their environment emerge. Those behaviors may be genetically encoded into these cells by billions of years of evolution, but in that sense the cells are not so different from robots programmed to respond in sophisticated ways to their environment. If we can speak of artificial intelligence for the latter, perhaps it’s not too outrageous to refer to the underappreciated cellular intelligence of the former.

Under the microscope, the incredible exercise of the cells’ collective intelligence reveals itself with spectacular beauty. Since 1983, Roberto Kolter, a professor of microbiology and immunobiology at Harvard Medical School and co-director of the Microbial Sciences Initiative, has led a laboratory that has studied these phenomena. In more recent years, it has also developed techniques for visualizing them. In the photographic essay book Life at the Edge of Sight: A Photographic Exploration of the Microbial World (Harvard University Press), released in September, Kolter and his co-author, Scott Chimileski, a research fellow and imaging specialist in his lab, offer an appreciation of microorganisms that is both scientific and artistic, and that gives a glimpse of the cellular wonders that are literally underfoot. Imagery from the lab is also on display in the exhibition World in a Drop at the Harvard Museum of Natural History. That display will close in early January but will be followed by a broader exhibition, Microbial Life, scheduled to open in February.

The slime mold Physarum polycephalum sometimes barely qualifies as a microorganism at all: When it oozes across the leaf litter of a forest floor during the active, amoeboid stage of its life cycle, it can look like a puddle of yellowish goo between an inch and a meter across. Yet despite its size, Physarum is a huge single cell, with tens of thousands of nuclei floating in an uninterrupted mass of cytoplasm. In this form, Physarum is a superbly efficient hunter. When sensors on its cell membrane detect good sources of nutrients, contractile networks of proteins (closely related to the ones found in human muscle) start pumping streams of cytoplasm in that direction, advancing the slime mold toward what it needs.

But Physarum is not just reflexively surging toward food. As it moves in one direction, signals transmitted throughout the cell discourage it from pushing counterproductively along less promising routes. Moreover, slime molds have evolved a system for essentially mapping their terrain and memorizing where not to go: As they move, they leave a translucent chemical trail behind that tells them which areas are not worth revisiting. . .

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Written by LeisureGuy

14 November 2017 at 12:30 pm

Posted in Evolution, Science

Deriving design from evolution’s results: Biomimicry

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Written by LeisureGuy

9 November 2017 at 3:49 pm

A Zombie Gene Protects Elephants From Cancer

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Viviane Callier writes in Quanta:

Elephants and other large animals have a lower incidence of cancer than would be expected statistically, suggesting that they have evolved ways to protect themselves against the disease. A new study reveals how elephants do it: An old gene that was no longer functional was recycled from the vast “genome junkyard” to increase the sensitivity of elephant cells to DNA damage, enabling them to cull potentially cancerous cells early.

In multicellular animals, cells go through many cycles of growth and division. At each division, cells copy their entire genome, and inevitably a few mistakes creep in. Some of those mutations can lead to cancer. One might think that animals with larger bodies and longer lives would therefore have a greater risk of developing cancer. But that’s not what researchers see when they compare species across a wide range of body sizes: The incidence of cancer does not appear to correlate with the number of cells in an organism or its lifespan. In fact, researchers find that larger, longer-lived mammals have fewer cases of cancer. In the 1970s, the cancer epidemiologist Richard Peto, now a professor of medical statistics and epidemiology at the University of Oxford, articulated this surprising phenomenon, which has come to be known as Peto’s paradox.

The fact that larger animals like elephants do not have high rates of cancer suggests that they have evolved special cancer suppression mechanisms. In 2015, Joshua Schiffman at the University of Utah School of Medicine and Carlo Maley at Arizona State University headed a team of researchers who showed that the elephant genome has about 20 extra duplicates of p53, a canonical tumor suppressor gene. They went on to suggest that these extra copies of p53 could account, at least in part, for the elephants’ enhanced cancer suppression capabilities. Currently, Lisa M. Abegglen, a cell biologist at the Utah School of Medicine who contributed to the study, is leading a project to find out whether the copies of p53 have different functions.

Yet extra copies of p53 are not the elephants’ only source of protection. New work led by Vincent Lynch, a geneticist at the University of Chicago, shows that elephants and their smaller-bodied relatives (such as hyraxes, armadillos and aardvarks) also have duplicate copies of the LIF gene, which encodes for leukemia inhibitory factor. This signaling protein is normally involved in fertility and reproduction and also stimulates the growth of embryonic stem cells. Lynch presented his work at the Pan-American Society for Evolutionary Developmental Biology meeting in Calgary in August 2017, and it is currently posted on biorxiv.org.

Lynch found that the 11 duplicates of LIF differ from one another but are all incomplete: At a minimum they all lack the initial block of protein-encoding information as well as a promoter sequence to regulate the activity of the gene. These deficiencies suggested to Lynch that none of the duplicates should be able to perform the normal functions of a LIF gene, or even be expressed by cells.

But when Lynch looked in cells, he found RNA transcripts from at least one of the duplicates, LIF6, which indicated that it must have a promoter sequence somewhere to turn it on. Indeed, a few thousand bases upstream of LIF6 in the genome, Lynch and his collaborators discovered a sequence of DNA that looked like a binding site for p53 protein. It suggested to them that p53 (but not any of the p53 duplicates) might be regulating the expression of LIF6. Subsequent experiments on elephant cells confirmed this hunch.

To discover what LIF6 was doing, the researchers blocked the gene’s activity and subjected the cells to DNA-damaging conditions. The result was that the cells became less likely to destroy themselves through a process called apoptosis (programmed cell death), which organisms often use as a kind of quality control system for eliminating defective tissue. LIF6 therefore seems to help eradicate potentially malignant cells. Further experiments indicated that LIF6 triggers cell death by creating leaks in the membranes around mitochondria, the vital energy-producing organelles of cells.

To find out more about the evolutionary history of LIF and its duplicates, Lynch found their counterparts in the genomes of closely related species: manatees, hyraxes and extinct mammoths and mastodons. His analysis suggested that . . .

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Written by LeisureGuy

7 November 2017 at 3:47 pm

Posted in Evolution, Health, Science

How to Build a Robot That Wants to Change the World

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John Pavlus writes in Quanta:

Isaac Asimov’s famous Three Laws of Robotics — constraints on the behavior of androids and automatons meant to ensure the safety of humans — were also famously incomplete. The laws, which first appeared in his 1942 short story “Runaround” and again in classic works like I, Robot, sound airtight at first:

1. A robot may not injure a human being or, through inaction, allow a human being to come to harm.
2. A robot must obey the orders given it by human beings, except where such orders would conflict with the First Law.
3. A robot must protect its own existence as long as such protection does not conflict with the First or Second Law.

Of course, hidden conflicts and loopholes abound (which was Asimov’s point). In our current age of advanced machine-learning software and autonomous robotics, defining and implementing an airtight set of ethics for artificial intelligence has become a pressing concern for organizations like the Machine Intelligence Research Institute and OpenAI.

Christoph Salge, a computer scientist currently at New York University, is taking a different approach. Instead of pursuing top-down philosophical definitions of how artificial agents should or shouldn’t behave, Salge and his colleague Daniel Polani are investigating a bottom-up path, or “what a robot should do in the first place,” as they write in their recent paper, “Empowerment as Replacement for the Three Laws of Robotics.” Empowerment, a concept inspired in part by cybernetics and psychology, describes an agent’s intrinsic motivation to both persist within and operate upon its environment. “Like an organism, it wants to survive. It wants to be able to affect the world,” Salge explained. A Roomba programmed to seek its charging station when its batteries are getting low could be said to have an extremely rudimentary form of empowerment: To continue acting on the world, it must take action to preserve its own survival by maintaining a charge.

Empowerment might sound like a recipe for producing the very outcome that safe-AI thinkers like Nick Bostrom fear: powerful autonomous systems concerned only with maximizing their own interests and running amok as a result. But Salge, who has studied human-machine social interactions, wondered what might happen if an empowered agent “also looked out for the empowerment of another. You don’t just want your robot to stay operational — you also want it to maintain that for the human partner.”

Salge and Polani realized that information theory offers a way to translate this mutual empowerment into a mathematical framework that a non-philosophizing artificial agent could put into action. “One of the shortcomings of the Three Laws of Robotics is that they are language-based, and language has a high degree of ambiguity,” Salge said. “We’re trying to find something that is actually operationizable.”

Quanta spoke with Salge about information theory, nihilist AI and the canine model of human-robot interaction. An edited and condensed version of the conversation follows.

Some technologists believe that AI is a major, even existential threat. Does the prospect of runaway AI worry you?

I’m a bit on the fence. I mean, I do think there are currently genuine concerns with robots and the growing influence of AI. But I think in the short term we’re probably more concerned about maybe job replacement, decision making, possibly a loss of democracy, a loss of privacy. I’m unsure how likely it is that this kind of runaway AI will happen anytime soon. But even an AI controlling your health care system or what treatment options you’re getting — we should start to be concerned about the kind of ethical questions that arise from this.

How does the concept of empowerment help us deal with these issues? . . .

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Written by LeisureGuy

1 November 2017 at 8:13 pm

Posted in Evolution, Law, Memes, Technology

Insects Conquered a Watery Realm With Just Two New Genes

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Viviane Callier writes in Quanta:

Ever since Darwin articulated his theory of natural selection, the question of evolutionary novelties has intrigued biologists. It’s relatively easy to understand how natural selection can reshape an existing trait — to make antlers bigger, legs longer or wings more colorful. But sometimes a fully formed trait appears seemingly out of the blue, without any apparent antecedent. Where did it come from?

Part of the answer can be found in a new study appearing today inScience that shows how the sudden emergence of just one or two new genes can profoundly transform organisms’ appearance, behavior and ecological niche. Using developmental genetics, evolutionary analysis, biomechanics and ecology, the researchers paint a picture of how a vital novelty evolved within one group of aquatic insects. But the significance of the discovery as a model for evolutionary innovation could extend throughout the animal kingdom.

“People have shown with comparative genomics that novel genes can be involved in novel structures. But this is the first time, to my knowledge, that the direct link is established from a novel gene to a novel structure to the invasion of a completely new ecological opportunity,” said Abderrahman Khila, an evolutionary and developmental genomicist at the Institute of Functional Genomics of Lyon, who led the study on the delicate insects called water striders.

Water striders are adept at navigating the surface of still water; they glide across ponds and lakes around the world. Those in the tropical genus Rhagovelia, however, have also figured out how to walk across fast-flowing streams and turbulent whitewater. Their secret asset is a special extendable structure on their middle leg resembling a Japanese fan, which no other water striders have. By deploying the fan, the insects can increase their leg’s contact with the water surface and can push against the water more forcefully. It’s a clever adaptation, but how did Rhagovelia acquire it when it has no precursors in other water striders?

To understand where the leg fan came from, Khila and his postdoctoral fellow Emília Santos, along with a couple of students, first had to figure out how to rear the water striders in the lab — a non-trivial task with what turned out to be a finicky species. It took about three years to figure out how to maintain the insects throughout the entire life cycle, from egg to adult. Once the colony was established, the team was ready for experiments.

Khila and Santos ground up the developing legs of the Rhagoveliawater striders and sequenced the transcriptome — the complete suite of genes active in those tissues. The fan is only present on the second pair of legs, so the researchers compared the gene activity in the second pair to that of the first and third pairs. They discovered about 80-90 genes that were overexpressed only in the second legs.

Next, they used a method called in situ hybridization to pin down where in the leg those 80-90 genes were active. Khila and Santos identified five genes from that group that were expressed specifically in the tip of the second leg, where the fan develops. Three of the five were related to the structure of the cuticle, the protective outer layer of the insect’s exoskeleton. The other two genes appeared to be paralogs — genes that are the result of a duplication event in the DNA. The function of the paralogs was unknown.

In search of clues about the function of the two paralogs, the researchers looked for the genes across many water strider species. By looking at the evolutionary history of genes in the lineage of water striders, the researchers uncovered the ancestral copy of the gene (distinguished from the more recent duplicate) and nailed down the moment in evolutionary time when the duplicate appeared: at the origin of the Rhagovelia genus. Only water striders in the Rhagoveliagenus have the duplicate gene, and they are also the only ones to have a leg fan.

“The evolution of the fan coincides with the duplication of that gene,” Khila said, also noting that the expression of the gene in the tip of the leg is significant. “It’s a big smoking gun.”

Because the leg fan reminded the researchers of a Japanese fan, they decided to call the newer gene geisha and its ancestral version mother of geisha. To learn what the genes were doing, they used a method called RNA interference to “knock down” (or turn off) the expression of those genes. Knockdown of geisha and mother of geisha caused the resulting insects to make only small, rudimentary fans. (Because of the strong sequence similarities between the two genes, the scientists have not yet been able to turn off one without the other, so differences between their functions are still unclear.) . . .

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Written by LeisureGuy

19 October 2017 at 7:27 pm

Simple Bacteria Offer Clues to the Origins of Photosynthesis

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Jordana Cepelewicz writes in Quanta:

Researchers have caught their best glimpse yet into the origins of photosynthesis, one of nature’s most momentous innovations. By taking near-atomic, high-resolution X-ray images of proteins from primitive bacteria, investigators at Arizona State University and Pennsylvania State University have extrapolated what the earliest version of photosynthesis might have looked like nearly 3.5 billion years ago. If they are right, their findings could rewrite the evolutionary history of the process that life uses to convert sunlight into chemical energy.

Photosynthesis directly or indirectly powers and sustains almost every organism on Earth. It is responsible for the composition of our atmosphere and forms the foundation of the planet’s many interwoven ecosystems. Moreover, as Wolfgang Nitschke, a biologist at the French National Center for Scientific Research (CNRS) in Paris, noted, photosynthesis liberated cells to grow and evolve boundlessly by letting them derive energy from a new, inexhaustible, nonterrestrial source. “When photosynthesis entered the picture, life connected up to the cosmos,” he said.

Scientists want to figure out what made that possible. In its current form, the machinery that converts light energy to chemical energy in photosynthesis — a protein complex called a reaction center — is incredibly sophisticated. The evidence suggests, however, that its design, which stretches back almost to the root of the tree of life, was once very simple. Researchers have been trying for decades to fill that enormous gap in their understanding of how (and why) photosynthesis evolved.

To that end, they have turned their attention to existing organisms. By studying the molecular details of the reactions that green plants, algae and some bacteria use to photosynthesize, and by analyzing the evolutionary relationships among them, scientists are trying to piece together a cogent historical narrative for the process.

The latest important clue comes from Heliobacterium modesticaldum, which has the distinction of being the simplest known photosynthetic bacterium. Its reaction center, researchers think, is the closest thing available to the original complex. Ever since the biologists Kevin ReddingRaimund Fromme and Christopher Gisrielof Arizona State University, in collaboration with their colleagues at Penn State, published the crystallographic structure of that protein complex in a July edition of Science, experts have been unpacking exactly what it means for the evolution of photosynthesis. “It’s really a window into the past,” Gisriel said.

“This is something we’ve been waiting for for 15 years,” Nitschke said.

In Search of a Common Ancestor

At first, most scientists did not believe that all the reaction centers found in photosynthetic organisms today could possibly have a single common ancestor. True, all reaction centers harvest energy from light and lock it into compounds in a form that’s chemically useful to cells. To do this, the proteins pass electrons along a transfer chain of molecules in a membrane, as though skipping along a series of stepping stones. Each step releases energy that’s ultimately used down the line to make energy-carrier molecules for the cell.

But in terms of function and structure, the photosystem reaction centers fall into two categories that differ in almost every way. Photosystem I serves mainly to produce the energy carrier NADPH, whereas photosystem II makes ATP and splits water molecules. Their reaction centers use different light-absorbing pigments and soak up different portions of the spectrum. Electrons flow through their reaction centers differently. And the protein sequences for the reaction centers don’t seem to bear any relation to each other.

Both types of photosystem come together in green plants, algae and cyanobacteria to perform a particularly complex form of photosynthesis — oxygenic photosynthesis — that produces energy (in the form of ATP and carbohydrates) as well as oxygen, a byproduct toxic to many cells. The remaining photosynthetic organisms, all of which are bacteria, use only one type of reaction center or the other.

So it seemed as though there were two evolutionary trees to follow — that was, until the crystal structures of these reaction centers began to emerge in the early 1990s. Researchers then saw undeniable evidence that the reaction centers for photosystems I and II had a common origin. Specific working components of the centers seemed to have undergone some substitutions during evolution, but the overall structural motif at their cores was conserved. “It turned out that big structural features were retained, but sequence similarities were lost in the mists of time,” said Bill Rutherford, the chairman in biochemistry of solar energy at Imperial College London.

“Nature has played small games to change some of the functions of the reaction center, to change the mechanisms by which it works,” Redding added. “But it hasn’t rewritten the playbook. It’s like having a cookie-cutter design for a house, building that same house over and over again, and then changing how the rooms are arranged, how the furniture is positioned. It’s the same house, but the functions inside are different.”

Researchers began to make more detailed comparisons between the reaction centers, searching for clues about their relationship and how they diverged. Heliobacteria have brought them a few steps closer to that goal.

Harkening Back to an Earlier Time

Since it was discovered in the soil around Iceland’s hot springs in the mid-1990s, H. modesticaldum has presented researchers with an interesting piece of the photosynthesis puzzle. The only photosynthetic bacterium in a family with hundreds of species and genera, heliobacteria’s photosynthetic equipment is very simple — something that became even more apparent when it was sequenced in 2008. “Its genetics are very streamlined,” said Tanai Cardona, a biochemist at Imperial College London.

Heliobacteria have perfectly symmetrical reaction centers, use a form of bacteriochlorophyll that’s different from the chlorophyll found in most bacteria, and cannot perform all the functions that other photosynthetic organisms can. For instance, they cannot use carbon dioxide as a source of carbon, and they die when exposed to oxygen. In fact, their structure took nearly seven years to obtain, partly because of the technical difficulties in keeping the heliobacteria insulated from oxygen. “When we first started working on it,” Redding said, “we killed it more than once.”

Taken together, “heliobacteria have a simplicity in their organization that’s surprising compared to the very sophisticated systems you have in plants and other organisms,” said Robert Blankenship, a leading figure in photosynthesis research at Washington University in St. Louis. “It harkens back to an earlier evolutionary time.”

Its symmetry and other features “represent something quite stripped down,” Redding added, “something we think is closer to what that ancestral reaction center would have looked like three billion years ago.”

A Glimpse of the Past

After carefully taking images of the crystallized reaction centers, the team found that although the reaction center is officially classified as type I, it seemed to be more of a . . .

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Written by LeisureGuy

17 October 2017 at 11:25 am

Posted in Evolution, Science

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