Evolution explains how all living beings, including us, came to be. It would be easy to assume evolution works by continuously adding features to organisms, constantly increasing their complexity.
Some fish evolved legs and walked onto the land. Some dinosaurs evolved wings and began to fly. Others evolved wombs and began to give birth to live young.
Yet this is one of the most predominant and frustrating misconceptions about evolution. Many successful branches of the tree of life have stayed simple, such as bacteria, or have reduced their complexity, such as parasites. And they are doing very well.
In a recent study published in Nature Ecology and Evolution, we compared the complete genomes of over 100 organisms (mostly animals), to study how the animal kingdom has evolved at the genetic level. Our results show that the origins of major groups of animals, such as the one comprising humans, are linked not to the addition of new genes but to massive gene losses.
The evolutionary biologist Stephen Jay Gould was one of the strongest opponents of "the march of progress", the idea that evolution always results in increased complexity. In his book Full House (1996), Gould uses the model of the drunkard walk. A drunkard leaves a bar in a train station and clumsily walks back and forth over the platform, swinging between the bar and the train tracks. Given enough time, the drunkard will fall in the tracks and will get stuck there.
The platform represents a scale of complexity, the pub being the lowest complexity and the tracks the maximum. Life emerged by coming out of the pub, with the minimum complexity possible. Sometimes it randomly stumbles towards the tracks (evolving in a way that increases complexity) and other times towards the pub (reducing complexity).
No option is better than the other. Staying simple or reducing complexity may be better for survival than evolving with increased complexity, depending on the environment.
But in some cases, groups of animals evolve complex features that are intrinsic to the way their bodies work, and can no longer lose those genes to become simpler - they become stuck in the train tracks. (There are no trains to worry about in this metaphor.) For example, multicellular organisms rarely go back to become unicellular.
If we only focus on the organisms trapped in the train tracks, then we have a biased perception of life evolving in a straight line from simple to complex, mistakenly believing that older lifeforms are always simple and newer ones are complex. But the real path to complexity is more tortuous.
Together with Peter Holland from the University of Oxford, we looked into how genetic complexity has evolved in animals. Previously, we have shown that the addition of new genes was key to the early evolution of the animal kingdom. The question then became whether that was the case during the later evolution of animals.
Studying the tree of life
Most animals can be grouped into major evolutionary lineages, branches on the tree of life showing how the animals alive today evolved from a series of shared ancestors. In order to answer our question, we studied every animal lineage for which a genome sequence was publicly available, and many non-animal lineages to compare them against.
One animal lineage is that of the deuterostomes, which includes humans and other vertebrates, as well as sea stars or sea urchins. Another is the ecdysozoans, comprising the arthropods (insects, lobsters, spiders, millipedes), and other moulting animals such as roundworms. Vertebrates and insects are considered some of the most complex animals. Finally, we have one lineage, the lophotrochozoans, that includes animals such as molluscs (snails, for example) or annelids (earthworms), among many others.
We took this diverse selection of organisms and looked to see how they were related on the tree of life and what genes they shared and didn't share. If a gene was present in an older branch of the tree and not in a younger one, we inferred that this gene had been lost. If a gene wasn't present in older branches but appeared in a younger branch, then we considered it a novel gene that had been gained in the younger branch.
A tree of life diagram showing the changing number of genes of different animal groups. Downward pointing orange triangles indicate gene losses. Upwards pointing green triangles indicate gene gains. The bigger the triangle, the greater the change. (Jordi Paps, Author provided)
The results showed unprecedented numbers of genes lost and gained, something never seen before in previous analyses. Two of the major lineages, the deuterostomes (including humans) and the ecdysozoans (including insects), showed the largest number of gene losses. In contrast, the lophotrochozoans show a balance between gene novelties and losses.
Our results confirm the picture given by Stephen Jay Gould by showing that, at the gene level, animal life emerged by leaving the pub and making a large leap in complexity. But after the initial enthusiasm, some lineages stumbled closer to the pub by losing genes, while other lineages drifted towards the track by gaining genes. We consider this the perfect summary of evolution, a booze-induced random choice between the bar and the train track. Or, as the internet meme says, "go home evolution, you are drunk".
Jordi Paps, Lecturer, School of Biological Sciences, University of Bristol, University of Bristol and Cristina Guijarro-Clarke, PhD Candidate in Evolution, University of Essex.
This article is republished from The Conversation under a Creative Commons license. Read the original article.
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Inside the Kalahari Desert Wonderwerk Cave
One of the oldest activities carried out by humans has been identified in a cave in South Africa. A team of geologists and archaeologists found evidence that our ancestors were making fire and tools in the Wonderwerk Cave in the country's Kalahari Desert some 1.8 million years ago.
A new study published in the journal Quaternary Science Reviews from researchers at the Hebrew University of Jerusalem and the University of Toronto proposes that Wonderwerk — which means "miracle" in Afrikaans — contains the oldest evidence of human activity discovered.
"We can now say with confidence that our human ancestors were making simple Oldowan stone tools inside the Wonderwerk Cave 1.8 million years ago," shared the study's lead author Professor Ron Shaar from Hebrew University.
Oldowan stone tools are the earliest type of tools that date as far back as 2.6 million years ago. An Oldowan tool, which was useful for chopping, was made by chipping flakes off of one stone by hitting it with another stone.
An Oldowan stone toolCredit: Wikimedia / Public domain
Professor Shaar explained that Wonderwerk is different from other ancient sites where tool shards have been found because it is a cave and not in the open air, where sample origins are harder to pinpoint and contamination is possible.
Studying the cave, the researchers were able to pinpoint the time over one million years ago when a shift from Oldowan tools to the earliest handaxes could be observed. Investigating deeper in the cave, the scientists also established that a purposeful use of fire could be dated to one million years back.
This is significant because examples of early fire use usually come from sites in the open air, where there is the possibility that they resulted from wildfires. The remnants of ancient fires in a cave — including burned bones, ash, and tools — contain clear clues as to their purpose.
To precisely date their discovery, the researchers relied on paleomagnetism and burial dating to measure magnetic signals from the remains hidden within a sedimentary rock layer that was 2.5 meters thick. Prehistoric clay particles that settled on the cave floor exhibit magnetization and can show the direction of the ancient earth's magnetic field. Knowing the dates of magnetic field reversals allowed the scientists to narrow down the date range of the cave layers.
The Kalahari desert Wonderwerk CaveCredit: Michael Chazan / Hebrew University of Jerusalem
Professor Ari Matmon of Hebrew University used another dating method to solidify their conclusions, focusing on isotopes within quartz particles in the sand that "have a built-in geological clock that starts ticking when they enter a cave." He elaborated that in their lab, the scientists were "able to measure the concentrations of specific isotopes in those particles and deduce how much time had passed since those grains of sand entered the cave."
Finding the exact dates of human activity in the Wonderwerk Cave could lead to a better understanding of human evolution in Africa as well as the way of life of our early ancestors.
Excerpt from a 19th century map of the Paris Catacombs, showing the labyrinthine layout underground (in color) beneath the straight-lined structures on the surface (in grey).
Ancient mining areas below Paris for limestone (red) and gypsum (green).Credit: Émile Gérards (1859–1920) / Public domain
"If you're brave enough to try, you might be able to catch a train from UnLondon to Parisn't, or No York, or Helsunki, or Lost Angeles, or Sans Francisco, or Hong Gone, or Romeless."
China Miéville's fantasy novel Un Lun Dun is set in an eerie mirror version of London. In it, he hints that other cities have similar doubles. On the list that he offhandedly rattles off, Paris stands out. Because the City of Light really does have a twisted sister. Below Paris Overground is Paris Underground, the City of Darkness.
Most people will have heard of the Catacombs of Paris: subterranean charnel houses for the bones of around six million dead Parisians. They are one of the French capital's most famous tourist attractions – and undoubtedly its grisliest.
But they constitute only a small fragment of what the locals themselves call les carrières de Paris ("the mines of Paris"), a collection of tunnels and galleries up to 300 km (185 miles) long, most of which are off-limits to the public, yet eagerly explored by so-called cataphiles.
The Grand Réseau Sud ("Great Southern Network") takes up around 200 km beneath the 5th, 6th, 14th, and 15th arrondissements (administrative districts), all south of the river Seine. Smaller networks run beneath the 12th, 13th, and 16th arrondissements. How did they get there?
Paris stone and plaster of Paris
It all starts with geology. Sediments left behind by ancient seas created large deposits of limestone in the south of the city, mostly south of the Seine; and gypsum in the north, particularly in the hills of Montmartre and Ménilmontant. Highly sought after as building materials, both have been mined since Roman times.
The limestone is also known as Lutetian limestone (Lutetia is the Latin name for ancient Paris) or simply "Paris stone." It has been used for many famous Paris landmarks, including the Louvre and the grand buildings erected during Georges-Eugène Haussmann's large-scale remodelling of the city in the mid-19th century. The stone's warm, yellowish color provides visual unity and a bright elegance to the city.
The fine-powdered gypsum of northern Paris, used for making quick-setting plaster, was so famed for its quality that "plaster of Paris" is still used as a term of distinction. However, as gypsum is very soluble in water, the underground cavities left by its extraction were extremely vulnerable to collapse.
Like living on top of a rotting tooth: subsidence starts far below the surface, but it can destroy your house.Credit : Delavanne Avocats
In previous centuries, a road would occasionally open up to swallow a chariot, or even a whole house would disappear down a sinkhole. In 1778, a catastrophic subsidence in Ménilmontant killed seven. That's why the Montmartre gypsum quarries were dynamited rather than just left as they were. The remaining gypsum caves were to be filled up with concrete.
The official body governing Paris down below is the Inspection Générale des Carrières (IGC), founded in the late 1770s by King Louis XVI. The IGC was tasked with mapping and, where needed, propping up the current and ancient (and sometimes forgotten) mining corridors and galleries hiding beneath Paris.
A delightful hiding place
Also around that time, the dead of Paris were getting in the way of the living. At the end of the 18th century, their final destination consisted of about 200 small cemeteries, scattered throughout the city — all bursting at the seams, so to speak. There was no room to bury the newly dead, and the previously departed were fouling up both the water and air around their respective churchyards.
Something radical had to happen. And it did. From 1785 until 1814, the smaller cemeteries were emptied of their bones, which were transported with full funerary pomp to their final resting place in the ancient limestone quarries at Tombe-Issoire. Three large and modern cemeteries were opened to receive the remains of subsequent generations of Parisians: Montparnasse, Père-Lachaise, and Passy.
Who says stacking skulls and bones can't be fun?Credit: Rijin via Wikimedia and licensed under CC BY-SA 4.0
The six million dead Parisians in the Catacombs, from all corners of the capital and across many centuries, together form the world's largest necropolis — their now anonymized skulls and bones methodically stacked, occasionally into whimsical patterns. The Catacombs are fashioned into a memorial to the brevity of life. The message above the entrance reads: Arrête! C'est ici l'empire de la Mort. ("Halt! This is the empire of Death.")
That has not stopped the Catacombs, accessible via a side door to a classicist building on the Avenue du Colonel Henri Rol-Tanguy, making just about every Top 20 list of things to see in Paris.
An underground economy
However, while the Catacombs certainly are the most famous part of the centuries-old network beneath Paris, and in non-pandemic times draw thousands of tourists each day, they constitute just 1.7 km (1 mile) of the 300-km (185-mile) tunneling total.
Subterranean Paris wasn't just used for mining and storing dead people. In the 17th century, Carthusian monks converted the ancient quarries under their monastery into distilleries for the green or yellow liqueur that still carries their name, chartreuse.
Because the mines generally keep a constant cool temperature of around 15° C (60° F), they were also ideal for brewing beer, as happened on a large scale from the end of the 17th century until well into the 20th century. Several caves were dug especially for establishing breweries, and not just because of the ambient temperature: going underground allowed brewers to remain close to their customers without having to pay a premium for real estate up top.
Overview of the Paris Catacombs.Credit: Inspection Générale des Carrières, 1857 / Public domain.
At the end of the 19th century, the underground breweries of the 14th arrondissement alone produced more than a million hectoliters (22 million gallons) per year. One of the most famous of Paris' underground breweries, Dumesnil, stayed in operation until the late 1960s.
In that decade, the network of corridors and galleries south of the Seine, long since abandoned by miners, became the unofficial playground for the young people of Paris. They explored the fantastical world beneath their feet, in some cases via entry points located in their very schools. Fascinated, these cataphiles ("catacomb lovers") read up on old books, explored the subterranean labyrinth, and drew up schematics that were passed around among fellow initiates as reverently as treasure maps.
As Robert Macfarlane writes in Underland, Paris-beneath-their-feet became "a place where people might slip into different identities, assume new ways of being and relating, become fluid and wild in ways that are constrained on the surface."
Some larger caves turned into notorious party zones: a 7-meter-tall gallery below the Val-de-Grâce hospital is widely known as "Salle Z." Over the last few decades, various other locations in subterranean Paris have hosted jazz and rock concerts and rave parties — like no other city, Paris really has an "underground music scene."
Hokusai's Great Wave as the backdrop to the "beach" under Paris.Credit: Reddit
Cataphiles vs. cataphobes
With popularity came increased reports of nuisance and crime — the tunnels provided easy access to telephone cables, which were stolen for the resale value of their copper.
The general public's "discovery" of the underground network led the city of Paris to officially interdict all access by non-authorized persons. That decree dates back to 1955, but the "underground police" have an understanding with seasoned cataphiles. Their main targets are so-called tourists, who by their lack of knowledge expose themselves to risk of injuries or worse, and degrade their surroundings, often leaving loads of litter in their wake.
The understanding does not extend to the IGC. Unlike in the 19th century, when weak cavities were shored up by purpose-built pillars, the policy now is to inject concrete to fill up endangered spaces — thus progressively blocking off parts of the network. That procedure has also been used to separate the Catacombs to prevent "infiltration" of the site by cataphiles.
Many subterranean streets have their own names, signs and all. This is the Rue des Bourguignons (Street of the Burgundians) below the Champs des Capucins (Capuchin Field), neither of which exists on the surface.Credit: Jean-François Gornet via Wikimedia and licensed under
The cataphiles, however, are fighting back. In a game of cat and mouse with the authorities, they are reopening blocked passages and creating chatières ("cat flaps") through which they can squeeze into chambers no longer accessible via other underground corridors.
Catacomb climate control
Alone against the unstoppable tide of concrete, the amateurs of Underground Paris would be helpless. But the fight against climate change may turn the subterranean labyrinths from a liability into an asset — and the City of Paris into an ally.
The UN's 2015 Climate Plan — concluded in Paris, by the way — requires the world to reduce greenhouse gas emissions by 75 percent by 2050. And Paris itself wants to be Europe's greenest city by 2030. More sustainable climate control of our living spaces would be a great help toward both targets. A lot of energy is spent heating houses in winter and cooling them in summer.
This is where the constant temperature of the Parisian tunnels comes in. It's not just good for brewing beer; it's a source of geothermal energy, says Fieldwork, an architectural firm based in Paris. It can be used to temper temperatures, helping to cool houses in summer and warming them in winter.
One catch for the cataphiles: it also works when the underground cavities are filled up with concrete. So perhaps one day, Paris Underground, fully filled up with concrete, will completely fall off the map, reducing the city's formerly real doppelgänger into an air conditioning unit.
Cool in summer, warm in winter: Paris Underground could become Paris A/C.Credit: Fieldwork
Strange Maps #1083
Got a strange map? Let me know at strangemaps@gmail.com.
The prevalence of allergies arising in childhood has increased over the last 50 years, with 30 percent of the human population now having some kind of atopic disease such as eczema, food allergies, or asthma. The cause of this increase is still subject to debate, though it has been associated with a number of factors, including changes to the gut microbiomes of infants.
A new study by Canadian researchers published in Cell Reports Medicine may shed further light on how these allergies develop in children by examining the contents of their first diaper.
The things you do for science
The research team examined the first stool of 100 infants from the CHILD Cohort Study. The first stool of an infant is a thick, green, horrid-looking substance called meconium. It consists of various things that the infant ingests during the second half of gestation. Additionally, it provides not only a snapshot of what the infant was exposed to during that time, but it also reveals what the food sources will be for the initial gut bacteria that colonize the baby's digestive tract.
The content of the meconium was examined and found to contain such varied elements as amino acids, lipids, carbohydrates, and myriad other substances.
A graph of the comparative, summed abundance of different elements in a metabolic pathway after scaling to median abundance of each metabolite. The blue figures are those children without atopy, the yellow ones show the data for those with an atopic condition. Petersen et al.
The authors fed this information into an algorithm that used this data, along with the identities of the bacteria present as well as the baby's overall health, to predict which infants would go on to develop allergies within one year. The algorithm got it right 76 percent of the time.
A way to prevent childhood allergies?
Infants whose meconium had a less diverse metabolic niche the initial microbes to settle in the gut were at the highest risk of developing allergies a year later. Many of these elements were associated with the presence or absence of different bacterial groups in the digestive system of the child, which play an increasingly appreciated role in our overall health and development. The findings were summarized by senior co-author Dr. Brett Finlay:
"Our analysis revealed that newborns who developed allergic sensitization by one year of age had significantly less 'rich' meconium at birth, compared to those who didn't develop allergic sensitization."
The findings could be used to help understand how allergies form and even how to prevent them. Co-author Dr. Stuart Turvey commented on this possibility:
"We know that children with allergies are at the highest risk of also developing asthma. Now we have an opportunity to identify at-risk infants who could benefit from early interventions before they even begin to show signs and symptoms of allergies or asthma later in life."
A model for early childhood allergies
Petersen et al.
As shown above, the authors constructed a model of how they believe metabolites and bacterial diversity help prevent allergies. Increased diversity of metabolic products in the meconium encourage the development of "healthy" families of bacteria, like Peptostreptococcaceae, which in turn promote the development of a healthy and diverse gut microbiome. Ultimately, such diversity decreases the likelihood that a child will develop allergies.
