Tag Archives: environment

Microbiome Medicine: Scientists Harness the Body’s ‘Bugs’ to Treat Asthma, MS, and More – UCSF News Services

Plenty of probiotic yogurts, pickles, and kombuchas claim to boost our digestive health with armies of microbes, but some scientists have more ambitious therapeutic plans for the bugs that colonize us. They hope to leverage these microbes as living therapeuticsfor a range of health conditions, including ulcerative colitis, multiple sclerosis, eczema, and asthma.

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Our guts, skin, and other regions of the body harbor trillions of microbes, as many as we have cells of our own. Each of these microbes bacteria, viruses, microscopic fungi, and others that make up the human microbiome brings with it a unique genome.

The composition of our microbiome and its microbial pan-genome is shaped by diet and environment, which in turn affect its important influences on human physiology, from digestion to brain health to immune function.

One real advantage of the microbiome is that its a dynamic system, said Susan Lynch, PhD, professor of gastroenterology and director of the UCSF Benioff Center for Microbiome Medicine. What were thinking about is how we can leverage microbes in engineering that system to improve health or prevent disease.

Much of the clinical research on the microbiome revolves around its connection with autoimmune disorders, such as rheumatoid arthritis, Crohns disease, and multiple sclerosis (MS), which altogether affect 24 million Americans. While genetics factor into why some people develop autoimmune disorders, environmental triggers likely contribute, said Sergio Baranzini, PhD, a neurology professor at the UCSF Weill Institute for Neurosciences, who studies the genetics and immunology of MS.

This is where we turn to the microbiome, he said. Because it is so influenced by food and other environmental factors, its a proxy for the environment.

A decade ago, when rapid DNA sequencing techniques made it cost-effective to identify bacteria, Baranzini began studying the relationship between the gut microbiome and MS, an autoimmune disorder in which the immune system attacks the nervous system. He had been intrigued by reports of other autoimmune conditions in which patients and controls were found to have different gut microbes.

In fact, most of our immune cells reside in our gut, and they depend on short-chain fatty acids produced when gut bacteria digest dietary fiber.

Baranzini compared stool and blood samples from people with MS to those from a member of the same household without MS. He found that the two populations of gut bacteria indeed differed, and that the blood from the person with MS had considerably fewer regulatory T cells, which normally tamp down the bodys immune response.

The deficiency of these T cells, Baranzini hypothesizes, is likely tied to the microbiome and impairs the bodys ability to control inflammation. He launched the International MS Microbiome Study to seek a comprehensive picture of gut microbiota in people with MS.

B cells (green), dendritic cells (blue) and T cells (red) are immune cells that help maintain the delicate relationship between the gut microbiome and the host. Image byLauren Rodda

Weve started discovering how diverse our microbiota are and how intimately they are in contact with our own immune systems, he said. And we now know that theres a lot of back-and-forth between the immune system and cells in the intestine that were only beginning to understand.

Microbial therapies for autoimmune disorders already exist in the form of fecal microbial transplants, or FMT, which involves taking stool samples from healthy individuals, isolating the gut microbes, and giving them to patients via a pill or enema.

This past April, Najwa El-Nachef, MD, an associate professor of medicine, wrapped up a clinical trial for ulcerative colitis and found that some patients respond much better to FMT than others, with a few reporting improvements in inflammatory skin and joint conditions as well. Her next step is to identify the best patients for microbiota-based therapy and to develop more targeted treatments.

For a subset of ulcerative colitis patients, manipulating the microbiome may provide a way to treat their autoimmune disease without suppressing their immune system, she said.

Our microbiome begins to take shape early, so interventions at the start of life can set the stage for future health. Lynch has focused some of her research on the gut microbiota during a babys first months of development. Its a critical time when the composition of the babys microbiome, influenced by the mother and the environment, can affect the development of the immune system and immune memory, with lasting consequences.

Susan Lynch, PhD, is the director of the UCSF Benioff Center for Microbiome Medicine. Photo by Barbara Ries

Najwa El-Nachef, MD, is studying the role of the microbiome in treatingulcerative colitis. Photo by Barbara Ries

Weve found that the gut microbiome at one month of age really predicts the risk of developing asthma and airway disease later in childhood, she said. Lynch and her team have identified specific microbial products that drive the dysfunction of regulatory T cells, which is associated with subsequent disease.

Weve considered that engineering the gut microbiome during this key window of immune training could have a long-term beneficial impact on the health status of high-risk children, she said

Lynch has developed a live microbial intervention administered at birth to babies at high-risk for asthma, comprised of bacteria that can modulate immune response. Their bacterial genomes encode a range of functions consistently absent from high-risk infant gut microbiomes.

The idea is to shape the developing gut microbiome by providing bacteria that can train the immune system early in life with their microbial products and metabolites, ultimately influencing the microbiomes function in the long term.

Our skin harbors its own set of microbes that interact with immune cells and protect the skin from infection.

Clinical trials using skin microbiota are already showing promise for patients with eczema, an autoimmune condition that can flare up when staph bacteria proliferate, said Tiffany Scharschmidt, MD, an associate professor of dermatology. The trials involve supplementing the bacteria that ordinarily keep the staph population under control.

Tiffany Scharschmidt, MD, is studying using skin microbiota arefor patients with eczema.Photo by Barbara Ries

Sergio Baranzini, PhD, is studying he genetics and immunology of multiple sclerosis.Photo bySteve Babuljak

As we gain more understanding of the interaction between the skin microbiome and its immune system, well see other microbial-based treatments emerging, she said. In the future, therapeutic skin microbes could even be genetically engineered to produce needed compounds.

The gut microbiome is, of course, intimately tied with digestion, producing diet-derived compounds that program immune cells and produce nutrients critical for the growth of the cells that line our intestines. The basic digestive and immune functions in our gut depend on colonization by specific bacteria, said Peter Turnbaugh, PhD, an associate professor of microbiology and immunology. Our intestinal cells have evolved receptors just lying in wait to sense the chemicals produced by the gut microbiome.

Turnbaugh has found that our inner critters also play a role in metabolizing medication. A better understanding of that role, he said, could increase drug efficacy.

We think the microbiome might be second only to the liver in determining how drugs are metabolized in the body, affecting how a patient responds to an existing therapy, he said.

Some antibiotics, for example, are activated by enzymes produced by the gut microbiota. Our microbial tenants may even influence how substances move around the body or change a drugs mechanism of action, but much remains unexplored in this area, said Turnbaugh.

Deeper knowledge of how our gut microbiome interacts with drugs might enable physicians to prescribe treatments that align with or supplement our individual microbiome, a new form of precision medicine.

Lynch believes that the therapeutic advances we can make through understanding the microbiome will rival those that came with understanding the human genome, particularly on autoimmune disorders.

Though the human microbiome field is still relatively young, it has already provided exceptional insights into the dependence of human physiology on our dynamic microbial inhabitants and offers a new set of tools to elicit better health, said Lynch. Translating these early observations into new live biotherapeutics represents the next step in realizing the potential of this field.

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Microbiome Medicine: Scientists Harness the Body's 'Bugs' to Treat Asthma, MS, and More - UCSF News Services

Is riding an electric bike good exercise, or just convenient transportation? – The Irish Times

Does riding an electric bike to work count as exercise, and not just a mode of transportation?

It can, if you ride right, according to a pragmatic new study comparing the physiological effects of e-bikes and standard road bicycles during a simulated commute. The study, which involved riders new to e-cycling, found that most could complete their commutes faster and with less effort on e-bikes than standard bicycles, while elevating their breathing and heart rates enough to get a meaningful workout.

But the benefits varied and depended, to some extent, on how peoples bikes were adjusted and how they adjusted to the bikes. The findings have particular relevance at the moment, as pandemic restrictions loosen and offices reopen, and many of us consider options other than packed trains to move ourselves from our homes to elsewhere.

Few people bike to work. Asked why, many tell researchers that bike commuting requires too much time, perspiration and accident risk. Simultaneously, though, people report a growing interest in improving their health and reducing their ecological impact by driving less.

In theory, both these hopes and concerns could be met or minimised with e-bikes. An alluring technological compromise between a standard, self-powered bicycle and a scooter, e-bikes look almost like regular bikes but are fitted with battery-powered electric motors that assist pedalling, slightly juicing each stroke.

With most e-bikes, this assistance is small, similar to riding with a placid tailwind, and ceases once you reach a maximum speed of about 30km/h or stop pedalling. The motor will not turn the pedals for you.

Essentially, e-bikes are designed to make riding less taxing, which means commuters should arrive at their destinations more swiftly and with less sweat. They can also provide a psychological boost, helping riders feel capable of tackling hills they might otherwise avoid. But whether they also complete a workout while e-riding has been less clear.

So, for the new study, which was published in March in the Translational Journal of the American College of Sports Medicine, researchers at Miami University in Oxford, Ohio decided to ask inexperienced cyclists to faux-commute. To do so, they recruited 30 local men and women, aged 19 to 61, and invited them to the physiology lab to check their fitness levels, along with their current attitudes about e-bikes and commuting.

Then, they equipped each volunteer with a standard road bike and an e-bike and asked them to commute on each bike at their preferred pace for approximately 5km. The cyclists pedalled around a flat loop course, once on the road bikes and twice with the e-bike. On one of these rides, their bike was set to a low level of pedal assistance, and on the other, the oomph was upped until the motor sent more than 200 watts of power to the pedals. Throughout, the commuters wore timers, heart rate monitors and facial masks to measure their oxygen consumption.

Afterward, to no ones surprise, the scientists found that the motorised bikes were zippy. On e-bikes, at either assistance level, riders covered the 5km several minutes faster than on the standard bike about 11 or 12 minutes on an e-bike, on average, compared to about 14 minutes on a regular bike. They also reported that riding the e-bike felt easier. Even so, their heart rates and respiration generally rose enough for those commutes to qualify as moderate exercise, based on standard physiological benchmarks, the scientists decided, and should, over time, contribute to health and fitness.

But the cyclists results were not all uniform or constructive. A few riders efforts, especially when they used the higher assistance setting on the e-bikes, were too physiologically mild to count as moderate exercise. Almost everyone also burned about 30 per cent fewer calories while e-biking than while road riding 344 to 422 calories on average on an e-bike versus 505 calories on a regular bike which may be a consideration if someone is hoping to use bike commuting to help lose weight.

And several riders told the researchers they worried about safety and control on the e-bikes, although most, after the two rides, reported greater confidence in their bike-handling skills, and found the e-commutes, compared to the road biking, more fun.

This study, though, was obviously small-scale and short-term, involving only three brief pseudo-commutes. Still, the findings suggest that riding an e-bike, like other forms of active transport, can be as good for the person doing it as for the environment, says Helaine Alessio, the chair of the department of kinesiology at Miami University, who led the new study with her colleague Kyle Timmerman and others.

But to increase your potential health benefits the most, she says, keep the pedal assistance level set as low as is comfortable for you. Also, for the sake of safety, practice riding a new e-bike or any standard bike on a lightly trafficked route until you feel poised and secure with bike handling.

Wear bright, visible clothing, too, and choose your commuting route wisely, Dr Alessio says. Look for bike paths and bike lanes whenever possible, even if you need to go a little bit out of your way. New York Times

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Is riding an electric bike good exercise, or just convenient transportation? - The Irish Times

The anatomy of the health service cyber attack – RTE.ie

The National Cyber Security Agency is hoping that by next week it will be able to begin to ease the misery of the millions of sick people and their loved ones who have had their lives disrupted, their treatment delayed, their appointments cancelled and their healthcare worries exacerbated by the cruel and callous actions of an organised cyber crime gang.

The State's Cyber Security Response Team along with commercial IT contractors FireEye and international partners have been working 24 hour shifts on a decryption key supplied by the criminal gang so they can use it on the HSE systems. It is complicated and painstaking work.

Criminal gangs spend millions on designing and inserting malware into IT systems all over the world that enables them to encrypt data and steal it for ransom. They dont spend as much time or money on the decryption key, the result being that while the codes when handed over may work to some extent, they may also contain 'bugs which do more damage to the systems and the data theyre supposed to restore.

Colonial Pipeline, the company providing almost half of the fuel for the East Coast of the United States, discovered this to its cost after it was hacked by a criminal gang referred to as Darkside on 7 May last. It paid the criminals $4.4m for the key to unlock the encryption and while the code provided was of some use, it didnt immediately restore the pipelines systems.

Timeline of the attack

Six days after the US attack officials at the Department of Health here noticed suspicious activity on their computer systems and contacted the National Cyber Security Agency. Based at the Department of the Environment in Adelaide Road in Dublin and with a staff of about 30 IT specialists, its job is to manage cyber security incidents across Government and provide guidance and advice to citizens and business on these incidents.

The cyber attack first on the Department of Health and then on the HSE turned out to be the most serious ever attack on the States critical infrastructure. The health service IT systems here had avoided another ransomware attack four years ago when the WannaCry virus infected a quarter of a million machines in 150 countries including the UKs NHS.

The National Cyber Security Team activated its crisis response procedures and called in FireEye, a commercial specialist IT incident response company. Investigators found a remote access tool known as cobalt strike Beacon on the system, which hackers use to move within computer networks before launching their virus and demanding a ransom - or as its known in computer parlance "execution of a ransom payload". Unknown to anyone the hackers had already been in the IT systems before this for at least a week.

The Department of Health acted quickly enough to prevent the cyber criminals from detonating their malware, known as Conti, on its systems. The IT specialists were able to detect, through a combination of anti-virus software and the deployment of tools, an attempt to execute ransomware and stop it. The result is that the systems at the Department of Health have not been as badly damaged and should be up and running again sooner.

The HSE however was not so lucky. They first realised they were under attack in the early hours of Friday morning, 14 May, and by that time it was too late. The criminals had executed their ransom payload and the HSE systems had been disabled.

The attack has badly damaged the HSE and the health services. It has had to shut down its systems and bring in specialists to carefully go through each part of its network, step by step, find the malware, block malicious IPs and domain names, protect privileged accounts, clean, rebuild and update all infected devices, ensure antivirus is up to date on all systems, makes sure all devices are patched and ultimately restore the data.

CEO Paul Reid has admitted he fears all the HSEs data has been compromised.

A digital ransom note was also left for the HSE. Much like a kidnapper inviting someone to drop the money off, the note contained a link with an invitation to "chat" with the criminals on the darknet with a view to paying a ransom to get the data back.

The darknet is equivalent to the criminals back alley. The message stated:

"YOU SHOULD BE AWARE! Just in case, if you ignore us. Weve downloaded your data and are ready to publish."

Such a threat has been made and acted upon before. Hackers attacked a psychiatric hospital in Finland in October of last year and stole the medical records of 40,000 people. In what is known as a double extortion they not only sought a ransom from the hospital, they also emailed individual patients and threatened to publish their therapy and mental health treatment records if they werent paid.

Wizard spider

The organised cyber crime group behind the cyber attacks here is a highly technically proficient gang of criminals known as Wizard Spider. The criminal gang has been responsible for hundreds of cyber attacks all over the world; since 2019 it has carried out more than 300.

The organised crime group, according to the intelligence agencies, is based in and around St Petersburg in Russia and consists of approximately 80 employees, some of whom are unaware they are working for a criminal organisation.

It employs skilled computer programmers and hackers on a part-time and temporary basis as part of a modus operandi that involves regular changes in staff.

Wizard Spider has for many years been a target of the FBI, the UK National Crime Agency, Interpol, Europol and other international law enforcement agencies. It does not carry out attacks on systems in Russia and the groups key members do not travel outside Russia.

It specialises in inserting malware into computer systems all over the world and targets government, healthcare, aerospace, agriculture, academic, retail and commercial bodies by encrypting their data and making high ransom demands. It is known to belittle its victims.

Cyber criminals buy and sell their services and capabilities, such as fraud or hacking abilities, on underground websites, but the Wizard Spider group is very security-conscious. It does not openly advertise on the darknet and will only sell access to or work alongside trusted criminals. This has enabled it to continue to operate covertly for years.

The criminal gang first came to the attention of law enforcement seven years ago when key figures were suspected of being involved in cyber attacks in 2014 and 2015 involving malware known as Dyre.

The Dyre malware was at the time the pre-eminent virus enabling cyber criminals to steal money online.

In 2018, however, international agencies identified a significant upgrade in the criminal organisations technical ability and its primary use of three types of ransomware, Trickbot, Ryuk and Conti. These were used to target large organisations for a high value return in a criminal activity. This is known online as big game hunting.

Conti is the ransomware that was used to disable the HSE and the Department of Healths IT systems and law enforcement agencies say there is no known case of success in relation to generating a decryption key for the ransomware.

Ransom demand

A document was published online in the aftermath of the cyber attacks here claiming to show that the gang wanted $20m dollars. The figure has been dismissed by security specialists involved but they concede the gang is looking for millions to enable the HSE and the Department of Health to retrieve the data that has been stolen.

However, the Governments position from the start has remained the same - Ireland will not pay. This was repeated several times this week.

All parties involved insist that no money has changed hands and that no agency, representative, or private individual, directly or by proxy has or will pay any ransom and that none will be paid or disguised in any fees paid to a commercial company. The Government cannot be seen to capitulate to the demands or support the business model of organised crime.

The National Cyber Security Centre and the private IT specialists contractors also say they have not engaged at all with the criminal gang responsible. They are satisfied that this criminal gang knew that it had attacked a health service and that its crime would impact on sick, elderly and vulnerable people including children.

Digital notes left by the hackers were addressed to the Health Service Executive and investigators are satisfied the gang targeted the health system. "This attack," said one of the specialists working to restore the data systems, "was not an accidental discharge."

The Garda National Cyber Crime Bureau is in charge of the criminal investigation and is liaising with Europol and Interpol. While they may identify individuals within the gang responsible, these people are believed to be in countries beyond the reach of this jurisdiction. They also say that while its "probable" that personal information that appeared online this week may be from the HSEs files, that has not been verified.

The gang members may be put on no fly and international watchlists which would confine them to their own countries. They may even be liable to international financial sanctions within their own country and have their accounts and assets frozen. However, these potential sanctions are unlikely to deter them and its unlikely that any of them will be brought to justice here.

But in spite of this harsh reality, the prosecution authorities did not stand idly by this week. The State made a pre-emptive strike to limit the gangs options and devalue their stolen data. The gangsters could not keep the crime out of the Irish courts.

Super injunction

The HSE took the imaginative and proactive step of securing a High Court injunction against the hackers, referred to in the order as "persons unknown". The court order restrains any person or company from sharing, processing, selling or publishing the data stolen from the HSEs computer systems. The application is unprecedented. The courts dont usually make orders against "persons unknown".

The main purpose of the super- injunction is to put legitimate information service providers such as Google, Twitter, and Facebook on notice of a legal prohibition on the sharing and publication of the HSE information.

The hackers have threatened to publish personal and confidential HSE records if they dont get paid but the injunction severely limits the effectiveness of such a strategy. It shuts down, to them and others, the main domestic and international platforms for disseminating the stolen data.

The criminals can still put it on the darknet, the marketplace for cyber criminals, but any individual or business who subsequently circulates it on social media potentially faces a large fine and or jail for contempt of court.

Ironically, the hackers have 42 days to enter an appearance to the proceedings after which the matter will return before the court, a civil right they are unlikely to avail of. Mr Justice Kevin Cross referred to their use of blackmail as "particularly heinous" and "always the remedy of a coward".

The National Cyber Security Centre continued working to restore the healthcare systems but it came as a complete surprise to them, the Government, the Gardai, the IT specialists and the HSE that out of the blue and for no apparent reason, last Thursday afternoon, the gang posted a decryption tool online.

Decryption key

The National Cyber Security Agency and the IT specialists from Ireland and abroad immediately examined the decryption key, a complicated algorithm. They established it was "a valid decryptor", "a binary solution" which they validated by programming it into a "sandbox" which is a safe cyber environment in which to open the key.

IT specialists were then able to use the key within that safe environment on a sample of the HSEs encrypted data. They discovered that the key worked because it decrypted the data. However they also discovered that it was "highly flawed" and needed to be "debugged".

The organised cyber crime gang had spent hundreds of thousands of euro designing and placing the ransomware in the Irish health systems but far less money on the decryption tool which would solve the problem, hence the bugs.

The criminal gang had inserted "a rolling encryption" as part of its ransomware into the HSEs systems to capture the data but had also pushed the encryption down through the entire computer system. IT specialists say it is therefore a complicated task to unlock the data even with the algorithm code because the code changes or "reiterates" every time they go into the system.

They must therefore recommence at the exact same place. They say it is a complex procedure which if not done carefully could corrupt the data. And while they have the algorithm, the decryption code, they now need to build "an engine" to "house" the decryption. The "engine" must be compatible with the HSE systems to work. Only then will they be able use the code to unlock the systems and safely restore the stolen data.

"We have the cargo but we now have to build the truck" one specialist said.

The IT specialists also have to undo some of the protections that they had put into the system to protect it against further attacks. They need to take down these protections in order to use the decryption key "a long string code".

As one specialist put it, "we have had to reverse engines and take one step back to move five steps forward".

Why did the gang hand over the key?

Security specialists working to restore the systems have described the decision of the criminal gang to publicly release a decryption key as "highly unusual". It is not clear why they did this and why they did it publicly. Criminal gangs like to operate covertly, make their demands, take their money and move on quietly to the next target.

However one of the problems the gang has created for itself is that it has drawn international attention upon its criminal activities. This is now a global story. Another problem is not just the unwillingness of the Government to pay any ransom, it is the unwillingness of any agency here apart from law enforcement to engage with them.

A third problem is the fact that they have attacked a state agency which has led to the attack becoming a political and diplomatic issue. The Taoiseach has said that diplomatic channels were not used to secure the release of the encryption code but the Minister for Foreign Affairs has raised the matter with his Russian counterpart Sergei Lavrov.

In addition, the Russian Ambassador to Ireland Yuri Filatov has said that the authorities in Russia are looking for this gang, that Russian law enforcement is constantly watching for this kind of activity and that he is pretty sure that this recent incident is being investigated fully. He also disagreed with a suggestion that Russia was a safe haven for cyber criminals, pointing out that cyber crime has no borders and is not exclusively a product of Russia.

All that may have put pressure on the criminal gang but it may not be enough to stop it from dumping the data on the darknet next week to protect its reputation for ruthless extortion.

It has the data and it can also recoup some of its expenses by selling it on to other criminals for fraud and blackmail.

In many ways the offer of the online decryption code following the theft of the data is akin to a burglar handing back the key of a house after he has ransacked it. The burglar may have lost some money because the householder wouldnt pay to get the key back but the burglar can still sell the television, the jewellery, the laptops, the mobile phones and anything else he stole from the house. Hell also keep the cash he found in the upstairs bedroom.

Its not possible to predict what the cyber crime gang will do with the valuable assets they have stolen from the HSE. But much like the burglar, while Wizard Spider may not make as much as they hoped and may have to cut their losses, its clear they have other means of making money, primarily by "fencing" the goods stolen from the HSE in the cyber crime marketplace.

Its not unusual for healthcare to be targeted by cyber crime gangs. Six hospitals in the US were attacked by ransomware last October, another in Germany in November. It is however unprecedented for a criminal gang to target the systems of a national health service.

IT specialists say once the decryption key that can be used on the HSE systems has been built they can begin rolling it out online. They can also put it on USB keys and send officials to hospitals and health clinics where they can use it to restore systems onsite. They are warning however that this will take some time and some systems will take longer to restore than others.

What systems are restored and when will be a matter for the HSE.

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The anatomy of the health service cyber attack - RTE.ie

Botany: 3 things you need to know about getting this degree – Study International News

Plant science, like plant biology or phytology, is more commonly known as botany. Its a branch within biology that studies plants. This includes their structure, properties and biochemical processes. This herb field of study also focuses on plant diseases and interactions with the environment which provides a foundation for applied sciences like agriculture, horticulture and forestry.

According to the US of Bureau Labour Statistics, the positions for soil and plant scientists are set to increase at a rate of eight to 10% which would add 6,700 jobs by 2022. With the progression of the clean energy economy, the field of botany lies on the cutting edge and is also a great profession for nature enthusiasts.

What can you work as? One job in popular demand is a plant ecologist. They help conserve endangered species and natural areas. For instance, the Rafflesia flower (the largest on the planet) that has pungent odors of decomposing flesh can be found in the forests of Borneo and Sumatra. Its also on the brink of extinction and the only way to save it, is to preserve its natural habitat. Below we take a look at the whatnots of getting a degree in botany and what jobs you can expect from it:

You must demonstrate a broad general education especially in literacy and numeracy with a minimum of a 4 in your GCSE or IGCSE. Practical skills are a must in science education and therefore youll need to pass any science A-Level taken. Usually, this includes grades AAA-ABB (two in biology), chemistry, physics and maths.

Britains Royal Botanic Gardens warned on May 10 about the threats facing the worlds plant kingdom in the first global report of its kind aimed at drawing attention to often-overlooked species. Source: Daniel Leal-Olivas/AFP

If youre submitting your International Baccalaureate, a minimum of 36-33 points is needed (including two higher level science subjects). To add to that, you must show your English Language proficiency in your GCSE/IGCSE grades or an IELTS (or equivalent) with no less than 6.5.

The undergraduate programmes in botany focuses on the growth, development, and productivity of plants. Youll be learning how to apply concepts from a wide range of biological subjects to plant science. This includes genetics, molecular biology, biochemistry and cell biology.

Depending on what institution you choose, the majority that offer this course usually have a combination of seminars and interactive events. To further add, youll most likely be getting hands-on experience in field studies where you can properly study plant environments.

A picture shows containers of Chanel creams made from camellia flowers at the Chanel fashion house camellia farm in Gaujac. Chanel uses camellias to create cosmetic products, notably creams, for the exceptional moisturising properties it can produce.Source: Gaizka Iroz/AFP

An obvious job would land you the role of a botanist whose average pay a year sums up to US$78,552. Your role would have you studying the many aspects of plants and conducting experiments to enhance the yield, disease resistance, drought resistance or the nutritional value of crops.

A biological scientist studies the living organisms and their relationship to the environment through basic and applied research. You could be doing this and earning an average of US$52,601 a year.

What about landscape design? This would be you making practical and alternative spaces that are beneficial for our health, wellbeing, and most of all protecting the environment. This could make you up to US$55,000 a year.

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Botany: 3 things you need to know about getting this degree - Study International News

How animal farming may have created ‘perfect storm’ for pandemics – Medical News Today

In the wild, parasites and their animal hosts are engaged in a dynamic cooperation comprising reciprocal, adaptive genetic changes that naturally occur when two species interact.

As a result of continuous adaptations and counter-adaptations between the parasite and its host species, neither is able to gain a sustained advantage over the other.

Evolutionary biologists liken this evolutionary standoff to the race in Lewis Carrolls Through the Looking-Glass, which, as the Red Queen describes it, takes all the running you can do, to stay in the same place.

Stay informed with live updates on the current COVID-19 outbreak and visit our coronavirus hub for more advice on prevention and treatment.

However, according to Prof. Cock Van Oosterhout, a professor of evolutionary genetics at the University of East Anglia in the United Kingdom, this is a race that humanity is losing.

In an editorial in the journal Virulence, he warns that our highly bred livestock cannot keep pace with the evolution of parasites, such as viruses, due to the animals lack of genetic diversity.

As a result, livestock act as mixing vessels for the emergence of new infectious diseases that can then make the leap from animals to humans.

In combination with habitat destruction, the illegal wildlife trade, and mass migration of both animals and people, Prof. Van Oosterhout says this has created a perfect storm for the development of pandemics, such as COVID-19.

He concludes that emerging infectious diseases are possibly the greatest existential threat to humanity.

As a result of centuries of selective breeding, livestock animals are severely inbred, writes Prof. Van Oosterhout, who is the deputy director of the Earth and Life Systems Alliance.

Despite a total biomass of livestock being 10 times that of all wildlife on Earth, research suggests that these breeds effective population size that is, a measure of a populations genetic diversity and viability is 80 times lower than that of the minimum viable population for a free-living species.

With so little genetic variation, livestock cannot evolve to meet the challenges that new pathogens pose.

Prof. Van Oosterhout writes:

Given the extraordinarily high biomass of our livestock (and us humans), the momentary fitness gains that parasites could accomplish by exploiting this plentiful resource are truly astronomical. Parasites and pathogens will continue to adapt to exploit these resources, and it is high time we recognize[d] this evolutionary inevitability.

He believes that everyone will need to make concessions to safeguard the future well-being of our species.

To minimize the threat from future pandemics and the ongoing COVID-19 pandemic, he proposes three broad strategies:

Gene flow is the mixing of different populations gene pools as a result of the movement of plants, animals, humans, and their associated pathogens.

This genetic mixing provides opportunities for the spread of disease and the emergence of new infections.

Technology that allows virtual working is a straightforward and relatively painless way to control gene flow, Prof. Van Oosterhout writes.

However, he acknowledges that other measures will involve policymakers making trade-offs between the benefits of economic growth, well-being, and education, and potential costs to human health and the environment.

He proposes that governments need to consider more controversial measures, such as compulsory vaccination and vaccine passports.

Sadly, this might be the price we have to pay for trailing in the Red Queen arms race, he writes.

Importantly, implementing these urgent changes requires us to carefully negotiate a wide range of legal and ethical issues that could inadvertently discriminate or exacerbate existing inequalities, he adds.

Prof. Van Oosterhout writes that, in order to track gene flow, governments must dedicate more resources to sequencing the viruses that make their home in wildlife and livestock.

An estimated 1.67 million viral species have yet to be discovered from mammal and bird hosts, and the costs of sequencing viruses with the highest zoonotic potential may be great (~1.2 to 7 billion US dollars), but they are dwarfed by the cost of another pandemic.

Habitat destruction is known to promote the emergence of new infectious diseases. Therefore, it will also be necessary to halt the loss of natural habitats in order to minimize the gene flow, he writes.

Prof. Van Oosterhout claims that livestock has become a sitting duck in the arms race with emerging infectious diseases as a result of extremely low genetic diversity.

Unless we act now, massive losses of crops and livestock are an evolutionary inevitability, he writes.

Fortunately, he says, much of the diversity that was once part of livestock and crops is still present in wild varieties and relatives of these animals and plants, and dispersed among different breeds.

While mass food production has underpinned our success as a species, it is unsustainable on environmental, ecological, and evolutionary grounds, he writes.

We urgently need to reduce our reliance on animal protein, in particular the consumption of other mammals, he says.

He claims that, in contrast to fish, for example, mammals pose the greatest threat for the evolution and transmission of new infectious diseases because they are the most closely related to humans.

In addition, he notes that the use of antibiotics to enhance growth and control infections has led to new, more virulent, and more resistant microorganisms.

Prof. Jonathan Stoye of the Francis Crick Institute in London, U.K., studies the evolutionary arms race between viruses, such as HIV, and their hosts. Both HIV and SARS-CoV-2 jumped from animals to humans.

While acknowledging the dangers posed by infections that originate in animals, such as COVID-19, he told Medical News Today:

I think we need to be very careful about talking of existential threats, particularly in the context of a virus that kills less than 2% of those infected. Overall, I believe that ecological changes resulting from altered land use or deforestation pose a much greater threat than the theoretical risks associated with inbreeding of potential intermediate hosts.

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How animal farming may have created 'perfect storm' for pandemics - Medical News Today

Four Penn Faculty: Election to the National Academy of Sciences – UPENN Almanac

Four Penn Faculty: Election to the National Academy of Sciences

Four members of the University of Pennsylvania faculty have been elected to the United States National Academy of Sciences (NAS). They join 120 members, 59 of whom are women, the most elected in a single year, and 30 international members, elected by their peers this year to NAS. Recognized for distinguished and continuing achievements in original research, this new class brings the total number of active members to 2,461 and of international members to 511.

Marisa Bartolomei is the Perelman Professor of Cell and Developmental Biology in the department of cell and developmental biology in the Perelman School of Medicine. She is also the co-director of the Penn Epigenetics Institute. Crossing into the disciplines of cell and molecular biology, pharmacology, and neuroscience, Dr. Bartolomei and her lab investigate genomic imprinting in mice. Specifically, they focus on the H19 gene, which is only expressed in maternal alleles, in order to better uncover the mechanisms behind imprinting and the effects of the environment, assisted reproductive technologies, and endocrine disruptors. Her lab also looks into the molecular and genetic systems behind X inactivation in mice. Her research has been published widely in journals including Nature, Nature Biotechnology, Development, and PLoS Genetics.

Michael Kearns is the National Center Professor of Management & Technology in the department of computer and information science in the School of Engineering and Applied Science. He also holds secondary appointments in the School of Arts & Sciences department of economics and the departments of statistics and operations, information and decisions at the Wharton School. He is an expert in machine learning, algorithmic game theory, and microeconomics, and applies both theoretical research and experimental techniques to better understand the social dimensions of new information technology, such as its impact on privacy and fairness. Dr. Kearns is also the founding director of Penns Warren Center for Network and Data Sciences, which draws on researchers from around the University to study some of the most pressing problems of the digital age. Dr. Kearns is also the co-author of The Ethical Algorithm, which shows how seemingly objective data science techniques can produce biased outcomes.

Diana Mutz is the Samuel A. Stouffer Professor of Political Science and Communication in the Annenberg School for Communication. She also serves as director of the Institute for the Study of Citizens and Politics; she is also an affiliate of the Warren Center. She studies political communication, political psychology, and public opinion, and her research focuses on how the American mass public relates to the political world and how people form opinions on issues and candidates. She received a 2017 Carnegie Fellowship and a 2016 Guggenheim Fellowship to pursue research on globalization and public opinion, and in 2011 received the Lifetime Career Achievement Award in Political Communication from the American Political Science Association. In addition to many journal articles, Dr. Mutz is the author of Impersonal Influence: How Perceptions of Mass Collectives Affect Political Attitudes, Hearing the Other Side: Deliberative Versus Participatory Democracy, and In-Your-Face Politics: The Consequences of Uncivil Media.

M. Celeste Simon is the Arthur H. Rubenstein, MB BCh, Professor in the department of cell and developmental biology in the Perelman School of Medicine and the scientific director of The Abramson Family Cancer Research Institute. She and her lab research the metabolism of cancer cells, tumor immunology, metastasis, and how healthy cells and cancer cells respond to a lack of oxygen and nutrients. Her work uses both animal models and cancer patient samples, and her goal is to create techniques to treat various tumors like kidney cancer, soft tissue sarcoma, liver cancer, and pancreatic cancer. Dr. Simon was the recipient of a National Cancer Institute Outstanding Investigator Award in 2017, and she has authored more than 275 articles in journals including Cell, Science, Nature, Cancer Discovery, Nature Genetics, and Cancer Cell.

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Four Penn Faculty: Election to the National Academy of Sciences - UPENN Almanac

Early human impacts and ecosystem reorganization in southern-central Africa – Science Advances

Abstract

Modern Homo sapiens engage in substantial ecosystem modification, but it is difficult to detect the origins or early consequences of these behaviors. Archaeological, geochronological, geomorphological, and paleoenvironmental data from northern Malawi document a changing relationship between forager presence, ecosystem organization, and alluvial fan formation in the Late Pleistocene. Dense concentrations of Middle Stone Age artifacts and alluvial fan systems formed after ca. 92 thousand years ago, within a paleoecological context with no analog in the preceding half-million-year record. Archaeological data and principal coordinates analysis indicate that early anthropogenic fire relaxed seasonal constraints on ignitions, influencing vegetation composition and erosion. This operated in tandem with climate-driven changes in precipitation to culminate in an ecological transition to an early, pre-agricultural anthropogenic landscape.

Modern humans act as powerful agents of ecosystem transformation. They have extensively and intentionally modified their environments for tens of millennia, leading to much debate about when and how the first human-dominated ecosystems arose (1). A growing body of archaeological and ethnographic evidence shows substantial, recursive interactions between foragers and their environments that suggest that these behaviors were fundamental to the evolution of our species (24). Fossil and genetic data indicate that Homo sapiens were present in Africa by ~315 thousand years (ka) ago, and archaeological data show notable increases in the complexity of behavior that took place across the continent within the past ~300- to 200-ka span at the end of the Middle Pleistocene (Chibanian) (5). Since our emergence as a species, humans have come to rely on technological innovation, seasonal scheduling, and complex social cooperation to thrive. These attributes have enabled us to exploit previously uninhabited or extreme environments and resources, so that today humans are the only pan-global animal species (6). Fire has played a key role in this transformation (7).

Biological models suggest that adaptations for cooked food extend back at least 2 million years, but regular archaeological evidence for controlled use of fire does not appear until the end of the Middle Pleistocene (8). A marine core with a dust record drawn from a wide swath of the African continent shows that over the past million years, peaks in elemental carbon occurred after ~400 ka, predominately during shifts from interglacial to glacial conditions, but also during the Holocene (9). This suggests that fire was less common in sub-Saharan Africa before ~400 ka and that by the Holocene, there was a substantial anthropogenic contribution (9). Fire is a tool that has been used by pastoralists to open and maintain grasslands throughout the Holocene (10). However, detecting the contexts and ecological impacts of fire use by Pleistocene early hunter-gatherers is more complex (11).

Fire is known both ethnographically and archaeologically as an engineering tool for resource manipulation, including improvement of subsistence returns or modification of raw materials, with these activities often associated with communal planning and requiring substantial ecological knowledge (2, 12, 13). Landscape-scale fires allow hunter-gatherers to drive game, control pests, and enhance productivity of habitat (2). On-site fire facilitates cooking, warmth, predator defense, and social cohesion (14). However, there is substantial ambiguity regarding the extent to which fires by hunter-gatherers can reconfigure components of a landscape, such as ecological community structure and geomorphology (15, 16).

Understanding the development of human-induced ecological change is problematic without well-dated archaeological and geomorphic data from multiple sites, paired with continuous environmental records. Long lacustrine sedimentary records from the southern African Rift Valley, coupled with the antiquity of the archaeological record in this region, make it a place where anthropogenically induced ecological impacts may be investigated into the Pleistocene. Here, we report the archaeology and geomorphology of an extensively dated Stone Age landscape in southern-central Africa. We then link it to paleoenvironmental data spanning >600 ka to identify the earliest coupled evidence for human behavior and ecosystem transformation in the context of anthropogenic fire.

We provide previously unreported age constraints for the Chitimwe Beds of the Karonga District that lie at the northern end of Lake Malawi in the southern portion of the African Rift Valley (Fig. 1) (17). These beds are composed of lateritic alluvial fan and stream deposits that cover ~83 km2, containing millions of stone artifacts, but do not have preserved organic remains such as bone (Supplementary Text) (18). Our optically stimulated luminescence (OSL) data from terrestrial records (Fig. 2 and tables S1 to S3) revise the age of the Chitimwe Beds to the Late Pleistocene, with the oldest age for both alluvial fan activation and burial of Stone Age sites ca. 92 ka (18, 19). The alluvial and fluvial Chitimwe Beds overlie Plio-Pleistocene Chiwondo Beds of lacustrine and fluvial origin in a low, angular unconformity (17). These sedimentary packages are in fault-bounded wedges along the lake margin. Their configuration indicates interactions between lake level fluctuations and active faulting extending into the Pliocene (17). Although tectonism may have affected regional relief and piedmont slopes over an extended time, fault activity in this region likely slowed since the Middle Pleistocene (20). After ~800 ka until shortly after 100 ka, the hydrology of Lake Malawi became primarily climate driven (21). Therefore, neither is likely the sole explanation for Late Pleistocene alluvial fan formation (22).

(A) Location of sites in Africa (star) relative to modern precipitation; blue is wetter and red is more arid (73); boxed area at left shows location of the MAL05-2A and MAL05-1B/1C cores (purple dots) in Lake Malawi and surrounding region, with the Karonga District highlighted as a green outline and location of Luchamange Beds as a white box. (B) Northern basin of Lake Malawi showing the hillshaded topography, remnant Chitimwe Beds (brown patches), and Malawi Earlier-Middle Stone Age Project (MEMSAP) excavation locations (yellow dots), relative to the MAL05-2A core; CHA, Chaminade; MGD, Mwangandas Village; NGA, Ngara; SS, Sadala South; VIN, Vinthukutu; WW, White Whale.

OSL central age (red lines) and error ranges at 1- (25% gray) for all OSL ages associated with in situ artifact occurrences in Karonga. Ages are shown against the past 125 ka of data for (A) Kernel density estimate of all OSL ages from alluvial fan deposits indicating sedimentation/alluvial fan accumulation (teal), and lake level reconstructions based on eigenvalues of a principal components analysis (PCA) of aquatic fossils and authigenic minerals from the MAL05-1B/1C core (21) (blue). (B) Counts of macrocharcoal per gram normalized by sedimentation rate, from the MAL05-1B/1C core (black, one value near 7000 off scale with asterisk) and MAL05-2A core (gray). (C) Margalefs index of species richness (Dmg) from fossil pollen of the MAL05-1B/1C core. (D) Percentages of fossil pollen from Asteraceae, miombo woodland, and Olea, and (E) percentages of fossil pollen from Poaceae and Podocarpus. All pollen data are from the MAL05-1B/1C core. Numbers at the top refer to individual OSL samples detailed in tables S1 to S3. Differences in data availability and resolution are due to different sampling intervals and material availability in the core. Figure S9 shows the two macrocharcoal records converted to z scores.

Landscape stability after (Chitimwe) fan formation is indicated by formation of laterites and pedogenic carbonates, which cap fan deposits across the study region (Supplementary Text and table S4). The formation of alluvial fans in the Late Pleistocene of the Lake Malawi basin is not restricted to the Karonga region. About 320 km to the southeast in Mozambique, terrestrial cosmogenic nuclide depth profiles of 26Al and 10Be constrain formation of the alluvial, lateritic Luchamange Beds to 119 to 27 ka (23). This broad age constraint is consistent with our OSL chronology for the western Lake Malawi basin and indicates regional alluvial fan expansion in the Late Pleistocene. This is supported by data from lake core records, which suggest a higher sedimentation rate accompanied by increased terrigenous input after ca. 240 ka, with particularly high values at ca. 130 and 85 ka (Supplementary Text) (21).

The earliest evidence for human occupation in the region is tied to the Chitimwe sedimentary deposits identified at ~92 7 ka. This result is based on 605 m3 of excavated sediment from 14 archaeological excavations with subcentimeter spatial control, and 147 m3 of sediment from 46 archaeological test pits with 20-cm vertical and 2-m horizontal control (Supplementary Text and figs. S1 to S3). In addition, we have surveyed 147.5 linear km, emplaced 40 geological test pits, and analyzed over 38,000 artifacts from 60 of these localities (tables S5 and S6) (18). These extensive surveys and excavations show that while hominins, including early modern humans, may have inhabited the region before ~92 ka, depositional aggradation associated with rising and then stabilized Lake Malawi levels did not preserve archaeological evidence until formation of the Chitimwe Beds.

The archaeological data support the inference that during the Late Quaternary, fan expansion and human activities in northern Malawi were substantial, and artifacts were of a type associated elsewhere in Africa with early modern humans. The majority of artifacts were created from quartzite or quartz river cobbles and featured radial, Levallois, platform, and casual core reduction (fig. S4). Morphologically diagnostic artifacts can be predominantly attributable to Levallois-type technologies characteristic of the Middle Stone Age (MSA), known to date from at least ~315 ka in Africa (24). The uppermost Chitimwe Beds, which continue into the Early Holocene, contain sparsely distributed Later Stone Age occurrences, found in association with terminal Pleistocene and Holocene hunter-gatherers across Africa. In contrast, stone tool traditions typically associated with the Early and Middle Pleistocene, such as large cutting tools, are rare. Where these do occur, they are found within MSA-bearing deposits dated to the Late Pleistocene, not an earlier phase of sedimentation (table S4) (18). Although sites are present from ~92 ka, the most well-represented period of both human activity and alluvial fan deposition occurs after ~70 ka, well defined by a cluster of OSL ages (Fig. 2). We confirm this pattern with 25 published and 50 previously unpublished OSL ages (Fig. 2 and tables S1 to S3). These show that of a total of 75 age determinations, 70 were recovered from sediment that postdates ~70 ka. The 40 ages associated with in situ MSA artifacts are shown in Fig. 2, relative to major paleoenvironmental indicators published from the MAL05-1B/1C central basin lake core (25) and previously unpublished charcoal from the MAL05-2A northern basin lake core (adjacent to the fans that produced the OSL ages).

Climate and environmental conditions coeval with MSA human occupation at Lake Malawi were reconstructed using freshly generated data from phytoliths and soil micromorphology from archaeological excavations and published data from fossil pollen, macrocharcoal, aquatic fossils, and authigenic minerals from the Lake Malawi Drilling Project cores (21). The latter two proxies are the primary basis of the reconstruction of relative lake depth dating back over 1200 ka (21) and are matched to pollen and macrocharcoal samples taken from the same places in the core that span the past ~636 ka (25). The longest cores (MAL05-1B and MAL05-1C; 381 and 90 m, respectively) were collected ~100 km southeast of the archaeological project area. A shorter core (MAL05-2A; 41 m) was collected ~25 km east, offshore from the North Rukuru River (Fig. 1). The MAL05-2A core reflects terrigenous paleoenvironmental conditions of the Karonga region, whereas the MAL05-1B/1C cores did not receive direct riverine input from Karonga and thus are more reflective of regional conditions.

Sedimentation rates recorded in the MAL05-1B/1C composite drill core began to increase starting ~240 ka from a long-term average of 0.24 to 0.88 m/ka (fig. S5). The initial increase is associated with changes in orbitally modulated insolation, which drive high amplitude changes in lake level during this interval (25). However, when orbital eccentricity decreased and climate stabilized after 85 ka, sedimentation rates remained high (0.68 m/ka). This is concurrent with the terrestrial OSL record, which shows extensive evidence for alluvial fan expansion after ~92 ka, and congruent with magnetic susceptibility data that show a positive relationship between erosion and fire after 85 ka (Supplementary Text and table S7). Given the error ranges of available geochronological controls, it is not possible to tell whether this set of relationships evolved slowly from a progression of recursive processes or occurred in rapid bursts as tipping points were reached. On the basis of geophysical models of basin evolution, rift extension and associated subsidence have slowed since the Middle Pleistocene (20) and, therefore, are not the primary cause of extensive fan formation processes we have dated to mainly after 92 ka.

Climate has been the dominant control of lake level since the Middle Pleistocene (26). Specifically, uplift in the northern basin closed an existing outlet ca. 800 ka, allowing the lake to deepen until reaching the sill elevation of the modern outlet (21). This outlet, located at the southern end of the lake, provides an upper limit on lake levels during wet intervals (including the present day), but allows the basin to close as lake levels drop during periods of aridity (27). Lake level reconstructions show alternating wet-dry cycles over the past 636 ka. On the basis of evidence from fossil pollen, periods of extreme aridity (>95% decrease in total water volume) linked to lows in summer insolation resulted in the expansion of semidesert vegetation with trees restricted to permanent waterways (27). These (lake) lowstands were associated with pollen spectra showing high proportions of grass (80% or more) and xerophytic herbs (Amaranthaceae) at the expense of tree taxa and low overall species richness (25). In contrast, when the lake was near the modern level, vegetation with strong affinities to Afromontane forest typically expanded to the lakeshore [~500 m above sea level (masl)]. Today, Afromontane forests only occur in small, discontinuous patches above ~1500 masl (25, 28).

The most recent period of extreme aridity occurred from 104 to 86 ka, after which open miombo woodland with substantial grass and herbaceous components became widespread, despite recovery of the lake level to high-stand conditions (27, 28). Afromontane forest taxa, most notably Podocarpus, never recovered after 85 ka to values similar to previous periods of high lake levels (10.7 7.6% after 85 ka versus 29.8 11.8% during analogous lake level before 85 ka). Margalefs index (Dmg) also shows that the past 85 ka has been marked by species richness 43% lower than during previous sustained periods of high lake level (2.3 0.20 versus 4.6 1.21, respectively), for example, in the high lake period between ca. 420 and 345 ka (Supplementary Text and figs. S5 and S6) (25). Pollen samples from the period ca. 88 to 78 ka also contain high percentages of Asteraceae pollen, which can be indicative of vegetation disturbance and is within the error range of the oldest date for human occupation of the area.

We use a climate anomaly approach (29) to analyze paleoecological and paleoclimatic data from the drill cores before and after 85 ka and test the hypothesis that the ecological relations among vegetation, species richness, and precipitation became decoupled from predictions derived from the presumably purely climate-driven baseline pattern of the preceding ~550 ka. This transformed ecological system was influenced by both lake infilling precipitation conditions and fire occurrence, as reflected in a species-poor and novel vegetation assemblage. Only some forest elements recovered after the last arid period, and these included fire-tolerant components of the Afromontane forest such as Olea, and hardy components of tropical seasonal forest such as Celtis (Supplementary Text and fig. S5) (25). To test this hypothesis, we model lake level derived from ostracode and authigenic mineral proxies as the independent variable (21) versus dependent variables such as charcoal and pollen that could have been affected by increased fire frequency (25).

To examine how similar or dissimilar the assemblages were to one another at different times, we conducted a principal coordinates analysis (PCoA) using pollen from Podocarpus (evergreen tree), Poaceae (grasses), Olea (a fire-tolerant component of Afromontane forest), and miombo (the dominant woodland component today). By mapping the PCoA on top of an interpolated surface that represents lake level at the time each assemblage was formed, we examine how pollen assemblages changed relative to precipitation and how this relationship changed after 85 ka (Fig. 3 and fig. S7). Before 85 ka, samples dominated by Poaceae cluster toward drier conditions, while samples dominated by Podocarpus cluster toward wetter conditions. In contrast, samples dating to after 85 ka cluster away from the majority of pre-85-ka samples and have a different average value, showing that their composition is unusual for similar precipitation conditions. Their position in the PCoA reflects the influence of Olea and miombo, both of which are favored under more fire-prone conditions. Of the post-85-ka samples, Podocarpus is only abundant in three successive samples, which occurred just after the onset of this interval between 78 and 79 ka. This suggests that after initial rainfall increase, forests appear to make a brief recovery before eventual collapse.

Each dot represents a single pollen sample at a given point in time, using the age model in the Supplementary Text and fig. S8. Vectors show the direction and gradient of change, with longer vectors representing a stronger trend. The underlying surface represents lake levels as a proxy for precipitation; darker blue is higher. A mean value for the PCoA eigenvalues is provided for the post-85-ka data (red diamond) and all pre-85-ka data from analogous lake levels (yellow diamond). Analogous lake levels are between 0.130- and 0.198- around the mean eigenvalue of the lake level PCA using the entire 636 ka of data.

To investigate the relations among the pollen, lake levels, and charcoal, we used a nonparametric multivariate analysis of variance (NP-MANOVA) to compare the total environment (represented by a data matrix of pollen, lake levels, and charcoal), before and after the transition at 85 ka. We found that variation and covariation found in this data matrix are statistically significantly different before and after 85 ka (Table 1).

DF, degrees of freedom.

Our terrestrial paleoenvironmental data from phytoliths and soils on the western lake margins agree with interpretations based on proxies from the lake. These show that despite high lake levels, the landscape had transitioned to one dominated by open canopy woodland and wooded grassland, much as today (25). All localities analyzed for phytoliths on the western margin of the basin date to after ~45 ka and show substantial arboreal cover that reflect wet conditions. However, they suggest that much of that cover is in the form of open woodlands in cohort with bambusoid and panicoid grasses. On the basis of phytolith data, fire-intolerant palms (Arecaceae) were present exclusively by the lake shoreline and rare or absent from inland archaeological sites (table S8) (30).

In general, wet but open conditions in the later part of the Pleistocene are also inferred from terrestrial paleosols (19). Lagoonal clay and palustrine-pedogenic carbonates from the vicinity of the Mwangandas Village archaeological site date between 40 and 28 cal ka BP (calibrated kiloanni before present) (table S4). Carbonate soil horizons within the Chitimwe Beds are typically nodular calcretes (Bkm) and argillic and carbonate (Btk) horizons, which indicate locations of relative landform stability with slow sedimentation derived from distal alluvial fan progradation by ca. 29 cal ka BP (Supplementary Text). Eroded, indurated laterite soils (petroplinthites) formed on remnants of paleofans are indicative of open landscape conditions (31) with strongly seasonal precipitation (32), illustrating the ongoing legacy of these conditions on the landscape.

Support for the role of fire in this transformation comes from the paired macrocharcoal records from the drill cores, which from the central basin (MAL05-1B/1C) show an overall increase in charcoal influx starting ca. 175 ka. Substantial peaks follow between ca. 135 and 175 ka and 85 and 100 ka, after which time lake levels recover but forest trees and species richness do not (Supplementary Text, Fig. 2, and fig. S5). The relationship between charcoal influx and magnetic susceptibility of lake sediments can also show patterns in long-term fire history (33). Using data from Lyons et al. (34), ongoing erosion of burned landscapes after 85 ka is implied at Lake Malawi by a positive correlation (Spearmans Rs = 0.2542 and P = 0.0002; table S7), whereas older sediments show an inverse relationship (Rs = 0.2509 and P < 0.0001). In the northern basin, the shorter MAL05-2A core has its deepest chronological anchor point with the Youngest Toba Tuff at ~74 to 75 ka (35). Although it lacks the longer-term perspective, it receives input directly from the catchment from which the archaeological data derive. The north basin charcoal record shows a steady increase in terrigenous charcoal input since the Toba crypto-tephra marker, over the period where archaeological evidence is most prevalent (Fig. 2B).

Evidence for anthropogenic fire may reflect intentional use at the landscape scale, widespread populations creating more or larger on-site ignitions, alteration of fuel availability through harvesting of the understory, or a combination of these activities. Modern hunter-gatherers use fire to actively modify foraging returns (2). Their activities increase prey abundances, maintain mosaic landscapes, and increase pyrodiversity and succession stage heterogeneity (13). Fire is also important for on-site activities such as heat, cooking, defense, and socialization (14). Even small differences in the deployment of fire outside of natural lightning strikes can alter patterns of forest succession, fuel availability, and seasonality of ignitions. Reductions in arboreal cover and woody understory have the most potential to enhance erosion, while loss of species diversity in this region is tightly tied to loss of Afromontane forest communities (25).

Human control of fire is well established in the archaeological record from before the start of the MSA (15), but its use as a landscape management tool has only so far been documented in a few Paleolithic contexts. These include in Australia ca. 40 ka (36), Highland New Guinea ca. 45 ka (37), and ca. 50 ka at Niah Cave in lowland Borneo (38). In the Americas, anthropogenic ignitions have been implicated as major factors in the reconfiguration of faunal and floral communities as humans first entered these ecosystems, especially within the past 20 ka (16). These conclusions are necessarily based on correlative evidence, but the argument for a cause-and-effect relationship is strengthened where there is direct overlap of archaeological, geochronological, geomorphic, and paleoenvironmental data. Although marine core data offshore of Africa have previously provided evidence of altered fire regimes over the past ~400 ka (9), here, we provide evidence of anthropogenic impacts that draw from correlated archaeological, paleoenvironmental, and geomorphic datasets.

Identifying anthropogenic fire in the paleoenvironmental record requires evidence of temporal or spatial changes in fire activity and vegetation, demonstration that these changes are not predicted by climate parameters alone, and temporal/spatial coincidence between fire regime changes and changes in the human record (29). Here, the first evidence for extensive MSA occupation and alluvial fan formation in the Lake Malawi basin occurred alongside a major reorganization of regional vegetation that began ca. 85 ka. Charcoal abundances in the MAL05-1B/1C core are reflective of regional trends in charcoal production and sedimentation that show substantial differences after ca. 150 ka when compared to the rest of the 636-ka record (figs. S5, S9, and S10). This transition shows an important contribution of fire for shaping ecosystem composition that cannot be explained by climate alone. In natural fire regimes, lightning ignitions typically occur at the end of the dry season (39). Anthropogenic fires, however, may be ignited at any time if fuels are sufficiently dry. On a site scale, humans can alter fire regimes continuously through collection of firewood from the understory. The net result of anthropogenic fire of any kind is that it has the potential to result in more consumption of woody vegetation, continuously throughout the year, and at a variety of scales.

In South Africa, fire was used in the heat treatment of stone for tool manufacture as early as 164 ka (12) and as a tool for cooking starchy tubers as early as 170 ka (40), taking advantage of resources that thrived in ancient fire-prone landscapes (41). Landscape fires reduce arboreal cover and are crucial tools in maintaining grassland and forest patch environments, which are defining elements of anthropogenically mediated ecosystems (13). If modification of vegetation or prey behavior was the intent of increased anthropogenic burning, then this behavior represents an increase in the complexity with which early modern humans controlled and deployed fire in comparison to earlier hominins and shows a transformed interdependency in our relationship with fire (7). Our analysis offers an additional avenue for understanding how human use of fire changed in the Late Pleistocene and what impacts these changes had on their landscapes and environments.

The expansion of alluvial fans during the Late Quaternary in the Karonga region may be attributable to changes in seasonal burning cycles under higher-than-average rainfall conditions, which resulted in enhanced hillslope erosion. The mechanism through which this occurred was likely by driving watershed-scale responses from fire-induced disturbance with enhanced and sustained denudation in the upper portions of the watersheds, and alluvial fan expansion in the piedmont environments adjacent to Lake Malawi. These responses likely included changes in soil properties to decrease infiltration rates, diminished surface roughness, and enhanced runoff as high precipitation conditions combined with reduced arboreal cover (42). Sediment availability is enhanced initially by the stripping of cover material and over longer time scales potentially by loss of soil strength from heating and from decreased root strength. The stripping of topsoil increased sediment flux, which was accommodated by fan aggradation downstream and accelerated laterite formation on the fans.

Many factors can control the landscape response to changing fire regime, and most of them operate at short time scales (4244). The signal we associate here is manifest at the thousand-year time scale. Analytical and landscape evolution models have shown notable denudation rate changes over thousand-year time scales with recurrent wildfire-induced vegetation disturbances (45, 46). A lack of regional fossil records contemporaneous with the observed changes in charcoal and vegetation records impedes reconstruction of the impacts of human behavior and environmental change on herbivore community composition. However, large grazing herbivores that inhabit landscapes that are more open play a role in maintaining them and in keeping woody vegetation from encroaching (47). Evidence of change across different components of the environment should not be expected to be simultaneous, but rather viewed as a series of cumulative effects that may have occurred over a prolonged period (11). Using a climate anomaly approach (29), we attribute human activity as a key driver in shaping the landscape of northern Malawi over the course of the Late Pleistocene. However, these impacts may be built on an earlier, less visible legacy of human-environment interactions. Charcoal peaks that appear in the paleoenvironmental record before the earliest archaeological dates may include an anthropogenic component that did not result in the same ecological regime change that is documented later in time and that did not involve sedimentation sufficient to confidently indicate human occupation.

Short sediment cores, such as that from the adjacent Lake Masoko basin in Tanzania, or shorter cores within Lake Malawi itself, show changes in the relative pollen abundances of grass to woodland taxa that have been attributed to natural climate variability over the past 45 ka (4850). However, it is only with the longer perspective of the >600-ka pollen record of Lake Malawi, accompanied by the extensively dated archaeological landscape next to it, that it is possible to understand the longer-term associations between climate, vegetation, charcoal, and human activity. Although humans were likely present in the northern Lake Malawi basin before 85 ka, the density of archaeological sites after ca. 85 ka, and especially after 70 ka, indicates that the region was attractive for human occupation after the last major arid period ended. At this time, novel or more intensive/frequent usage of fire by humans apparently combined with natural climate shifts to restructure a >550-ka ecological relationship, ultimately generating an early preagricultural anthropogenic landscape (Fig. 4). Unlike during earlier time periods, the depositional nature of this landscape preserved MSA sites as a function of the recursive relationship between environment (resource distributions), human behavior (activity patterns), and fan activation (sedimentation/site burial).

(A) ca. 400 ka: No detectable human presence. Wet conditions similar to today with high lake level. Diverse, nonfire-tolerant arboreal cover. (B) ca. 100 ka: No archaeological record, but human presence possibly detected by charcoal influx. Extremely arid conditions occur in a desiccated watershed. Commonly exposed bedrock, limited surface sediment. (C) ca. 85 to 60 ka: Lake level is increasing with higher precipitation. Human presence archaeologically detectable after 92 ka and concentrated after 70 ka. Burning of uplands and alluvial fan expansion ensue. Less diverse, fire-tolerant vegetation regime emerges. (D) ca. 40 to 20 ka: Ambient charcoal input in the northern basin increases. Alluvial fan formation continues but begins to abate toward the end of this period. Lake levels remain high and stable relative to the preceding 636-ka record.

The Anthropocene represents the accumulation of niche construction behaviors that have developed over millennia, at a scale unique to modern H. sapiens (1, 51). In the modern context, anthropogenic landscapes persist and have intensified following the introduction of agriculture, but they are extensions, not disconnections, of patterns established during the Pleistocene (52). Data from northern Malawi show that periods of ecological transition can be prolonged, complex, and iterative. Transformations of this scale reflect complex ecological knowledge by early modern humans and illustrate their transition to the globally dominant species we are today.

Site survey and recording of artifact and cobble characteristics on survey tracts followed protocols described in Thompson et al. (53). Test pit emplacement and main site excavation, including micromorphology and phytolith sampling, followed protocols described in Thompson et al. (18) and Wright et al. (19). Our Geographic Information System (GIS) maps based on Malawi geological survey maps of the region show a clear association between the Chitimwe Beds and archaeological sites (fig. S1). Placement of geologic and archaeological test pits in the Karonga region was spaced to capture the broadest representative sample possible (fig. S2). Geomorphic, geochronometric, and archaeological investigations of Karonga involved four main field approaches: pedestrian survey, archaeological test pitting, geological test pitting, and detailed site excavations. Together, these techniques allowed major exposures of the Chitimwe Beds to be sampled in the northern, central, and southern parts of Karonga (fig. S3).

Site survey and recording of artifact and cobble characteristics on pedestrian survey tracts followed protocols described in Thompson et al. (53). This approach had two main goals. The first was to identify localities where artifacts were actively eroding, and then place archaeological test pits upslope at those localities to recover artifacts in situ from buried contexts. The second goal was to formally document the distribution of artifacts, their characteristics, and their relationship to nearby sources of lithic raw material (53). For this work, a crew comprising three people walked at 2- to 3-m spacing for a combined total of 147.5 linear km, transecting across most of the mapped Chitimwe Beds (table S6).

Work concentrated first on the Chitimwe Beds to maximize the sample of observed artifacts, and second on long linear transects from the lakeshore to the uplands that crosscut different sedimentary units. This confirmed the key observation that artifacts located between the western highlands and the lakeshore are exclusively associated with the Chitimwe Beds or more recent Late Pleistocene and Holocene deposits. Artifacts found in other deposits are ex situ and have been relocated from elsewhere on the landscape, as revealed by their abundances, sizes, and degree of weathering.

Archaeological test pit emplacement and main site excavation, including micromorphology and phytolith sampling, followed protocols described in Thompson et al. (18, 54) and Wright et al. (19, 55). The primary aim was to understand the subsurface distribution of artifacts and fan deposits across the larger landscape. Artifacts are typically deeply buried within the Chitimwe Beds in all places except at the margins, where erosion has begun to remove the top part of the deposit. During informal survey, two people walked across Chitimwe Beds that appear as mapped features on Government of Malawi geological maps. As these people encountered the shoulders of Chitimwe Bed deposits, they began to walk along the margins where they could observe artifacts eroding from the deposits. By placing excavations slightly (3 to 8 m) upslope from actively eroding artifacts, excavations could reveal their in situ locations relative to their containing sediments, without the necessity of laterally extensive excavations. Test pits were emplaced so that they would be 200- to 300-m distant from the next-nearest pit and thus capture the variation across Chitimwe Bed deposits and the artifacts they contained. In some cases, test pits revealed localities that later became the sites of full excavations.

All test pits began as 1 2 m squares, oriented north-south, and excavated in 20-cm arbitrary units, unless there was a noticeable change in sediment color, texture, or inclusions. Sedimentologic and pedologic attributes were recorded for all excavated sediment, which was passed uniformly through a 5-mm dry sieve. If deposit depth continued beyond 0.8 to 1 m, then excavation ceased in one of the two square meters and continued in the other, thus creating a step so that the deeper layers could be safely accessed. Excavation then continued until bedrock was reached, at least 40 cm of archaeologically sterile sediment had been reached below a concentration of artifacts, or excavation became too unsafe (deep) to proceed. In some cases, deposit depth required extension of the test pit into a third square meter, with two steps into the trench.

Geologic test pits had previously revealed that the Chitimwe Beds often appear on geologic maps because of a distinctive reddish color, when they include a wide range of stream and river deposits, alluvial fan deposits, and do not always present as red in color (19). Geologic test pits were excavated as simple pits designed to clean off mixed upper sediments to reveal the subsurface stratigraphy of deposits. This was necessary because the Chitimwe Beds erode as parabolic hillslopes with slumped sediments coating the slope and do not typically form clear natural sections or cuts. These excavations thus occurred either at the tops of Chitimwe Beds, where there was an inferred subsurface contact between the Chitimwe Beds and the underlying Pliocene Chiwondo Beds, or where river terrace deposits required dating (55).

Full archaeological excavations proceeded at localities that promised large assemblages of in situ stone artifacts, typically based on test pits or where artifacts could be seen eroding in large quantities from a slope. Artifacts from the main excavations were recovered from sedimentary units that were excavated separately in 1 1 m squares. Units were excavated as spits of either 10 or 5 cm if artifact densities were high. All stone artifacts, fossil bone, and ochre were piece plotted at each main excavation, with no size cutoff. The sieve size was 5 mm. Artifacts were assigned unique barcoded plotted find numbers if they were recovered during excavation, and find numbers within the same series were assigned to sieved finds. Artifacts were labeled with permanent ink, placed in a bag with their specimen label, and bagged together with other artifacts from the same context. After analysis, all artifacts were stored at the Cultural and Museum Centre, Karonga.

All excavation was conducted according to natural layers. These were subdivided into spits, with spit thickness dependent on artifact density (e.g., spit thickness would be high if artifact density was low). Context data (e.g., sediment attributes, context relationships, and observations about disturbances and artifact densities) were recorded in an Access database. All coordinate data (e.g., piece-plotted finds, context elevations, square corners, and samples) are based on Universal Transverse Mercator (UTM) coordinates (WGS 1984, Zone 36S). At main sites, all points were recorded using a Nikon Nivo C-series 5 total station that was established within a local grid oriented as closely as possible to UTM north. The location of the northwest corner of each excavated site and the volume of sediment removed for each are given in table S5.

Profiles of sedimentologic and pedologic features were documented from all excavation units using the U.S. Department of Agriculture classification scheme (56). Sedimentologic units were designated on the basis of grain sizes, angularity, and bedding features. Anomalous inclusions and disturbances relative to the sediment unit were noted. Soil development was determined on the basis of subsurface accumulation of sesquioxides or carbonates in the subsoils. Subaerial weathering (e.g., redox, residual Mn nodule formation) was also commonly documented.

Collection points for OSL samples were determined on the basis of an estimation of which facies were likely to yield the most reliable estimation of sediment burial age. At sample locations, trenches were made to expose authigenic sediment layers. All samples for OSL dating were collected by inserting light-tight steel tubes (approximately 4 cm in diameter and 25 cm in length) into the sediment profiles.

OSL dating measures the size of the population of trapped electrons within crystals such as quartz or feldspar arising from exposure to ionizing radiation. The bulk of this radiation originates from the decay of radioactive isotopes within the environment with a minor additional component in the tropical latitudes coming in the form of cosmic radiation. Trapped electrons are released upon exposure of the crystals to light, which occurs either during transport (the zeroing event) or in the laboratory, where illumination occurs beneath a sensor (for example, a photomuliplier tube or charged couple device camera) that can detect photons emitted when the electrons return to their ground state. Quartz grains measuring between 150 and 250 m were isolated through sieving, acid treatments and density separations, and analyzed either as small aliquots (<100 grains) mounted to the surface of aluminum disks or as single grains held within 300 by 300 mm wells drilled into an aluminum disc. Burial doses were typically estimated using single aliquot regeneration methods (57). In addition to assessment of the radiation dose received by grains, OSL dating also requires estimation of the dose rate through measurements using gamma spectrometry or neutron activation analysis of radionuclide concentrations within the sediments from which the sample was collected, along with determination of a cosmic dose rate by reference to the sample location and burial depth. Final age determination is achieved by dividing the burial dose by the dose rate. However, statistical modeling is required to determine an appropriate burial dose to use when there is a variation in the doses measured for individual grains or groups of grains. Burial doses were calculated here using the Central Age Model, in the case of single aliquot dating, or the finite mixture model in the case of single grain dating (58).

Three separate laboratories performed OSL analysis for this study. Detailed individual methods for each laboratory are presented below. In general, we applied OSL dating using regenerative-dose methods to small aliquots (tens of grains) rather than using single grain analysis. This is because small aliquots of samples had low recuperation ratios (<2%) during regenerative growth experiments and the OSL signals were not saturated at the levels of natural signals. Interlaboratory consistency of age determinations, consistent harmony of results within and between stratigraphic sections tested, and parity with geomorphic interpretations of 14C ages from carbonates were the primary basis of this assessment. Single grain protocols were evaluated or performed at each laboratory, but independently determined to be inappropriate for use in this study. Detailed methods and analytical protocols followed by individual laboratories are provided in Supplementary Materials and Methods.

Lithic artifacts recovered from controlled excavations (BRU-I; CHA-I, CHA-II, and CHA-III; MGD-I, MGD-II, and MGD-III; and SS-I) were analyzed and described according to metric and qualitative characteristics. Weight and maximum dimension were measured for each artifact (weight was measured to 0.1 g using a digital scale; all dimensions measured to 0.01 mm with Mitutoyo digital calipers). All artifacts were also classified according to raw material (quartz, quartzite, chert, and other), grain size (fine, medium, and coarse), grain size homogeneity, color, cortex type and coverage, weathering/edge rounding, and technological class (complete or fragmentary core or flake, flake piece/angular shatter, hammerstone, manuport, and other).

Cores were measured along their maximum length; maximum width; width at 15, 50, and 85% of length; maximum thickness; and thickness at 15, 50, and 85% of length. Measurements were also taken to assess the volumetric attributes of hemispherically organized (radial and Levallois) cores. Both complete and broken cores were classified according to reduction method (single or multiplatform, radial, Levallois, and other), and flake scars were counted at both 15 mm and at 20% of core length. Cores with five or fewer scars 15 mm were classified as casual. Cortex coverage was recorded for the total core surface, and on hemispherically organized cores, the relative cortex coverage was recorded for each side.

Flakes were measured along their maximum length; maximum width; width at 15, 50, and 85% of length; maximum thickness; and thickness at 15, 50, and 85% of length. Fragmentary flakes were described according to the portion preserved (proximal, medial, distal, split right, and split left). Elongation was calculated by dividing maximum length by maximum width. Platform width, thickness, and exterior platform angle were measured on complete flakes and proximal flake fragments, and platforms were classified according to degree of preparation. Cortex coverage and location were recorded on all flakes and fragments. Distal edges were classified according to termination type (feather, hinge, and overshot). On complete flakes, the number and orientation of prior flake scars were recorded. When encountered, retouch location and invasiveness were recorded following the protocol established by Clarkson (59). Refitting programs were initiated for most of the excavated assemblages to assess reduction methods and site depositional integrity.

Lithic artifacts recovered from test pits (CS-TP1-21, SS-TP1-16, and NGA-TP1-8) were described according to a simpler scheme than those from controlled excavations. For each artifact, the following characteristics were recorded: raw material, grain size, cortex coverage, size class, weathering/edge damage, technological component, and preserved portion of fragmentary pieces. Descriptive notes were recorded for diagnostic features of flakes and cores.

Intact blocks of sediment were cut from profiles exposed in excavations and geological trenches. These blocks were stabilized in the field, using either plaster-of-Paris bandages or toilet paper and packaging tape, and transported to the Geoarchaeology Laboratory at the University of Tbingen, Germany. There, the samples were dried at 40C for at least 24 hours. They were then indurated under vacuum, using a mixture of unpromoted polyester resin and styrene at a ratio of 7:3. Methyethylketone peroxide was used as the catalyst, with resin-styrene mixture (3 to 5 ml/liter). Once the resin mixture had gelled, the samples were heated at 40C for at least 24 hours to completely harden the mixture. The hardened samples were cut with a tile saw into chips measuring 6 9 cm, which were glued to a glass slide and ground to a thickness of 30 m. The resulting thin sections were scanned using a flatbed scanner and analyzed under the naked eye and under magnification (50 to 200) using plane-polarized light, cross-polarized light, oblique incident light, and blue-light fluorescence. Terminology and descriptions of the thin sections follow guidelines published by Stoops (60) and Courty et al. (61). Pedogenic carbonate nodules, collected from a depth of >80 cm, were sliced in half so that one half could be impregnated and studied in thin section (4.5 2.6 cm), using standard stereoscopic and petrographic microscopes, as well as cathodoluminescence (CL) microscopy. Control on the type of carbonate was given much care, as pedogenic carbonates form in connection to a stable ground surface, while groundwater carbonates form independently from a ground surface or soil.

Samples were drilled from the cut faces of pedogenic carbonate nodules, which were halved to be used for various analyses. The thin sections were studied by F.S. with standard stereo and petrographic microscopes of the working group for geoarchaeology and with a CL microscope at the working group for experimental mineralogy, both in Tbingen, Germany. Subsamples for radiocarbon dating were drilled with a precision drill from designated areas of ca. 3 mm in diameter in the opposing half of the nodule, avoiding zones with late recrystallization, abundant mineral inclusions, or great variability in calcite crystal sizes. The same protocol could not be followed for samples MEM-5038, MEM-5035, and MEM-5055 A, which were selected from loose sediment samples and too small to be cut in half for thin sectioning. However, corresponding micromorphological samples of the adjacent sediment, including carbonate nodules, were studied in thin section.

We submitted samples for 14C dating to the Center for Applied Isotope Studies (CAIS), at the University of Georgia, Athens, USA. The carbonate samples were reacted with 100% phosphoric acid in evacuated reaction vessels to produce CO2. CO2 samples were cryogenically purified from the other reaction products and catalytically converted to graphite. Graphite 14C/13C ratios were measured using a 0.5-MeV accelerator mass spectrometer. The sample ratios were compared to the ratio measured from the oxalic acid I standard (NBS SRM 4990). Carrara marble (IAEA C1) was used as the background, and travertine (IAEA C2) was used as a secondary standard. The results are presented as percent modern carbon, and the quoted uncalibrated dates are given in radiocarbon years before 1950 (years BP), using the 14C half-life of 5568 years. The error is quoted as 1- and reflects both statistical and experimental errors. The dates have been corrected for isotope fractionation based on the isotope-ratio mass spectrometrymeasured 13C values reported by C. Wissing at the laboratory for Biogeology in Tbingen, Germany, except in the case of UGAMS-35944r, which was measured at CAIS. Sample 6887B was analyzed in duplicate. A second subsample was drilled from the nodule for this purpose (UGAMS-35944r) from the sampling region indicated on the cut surface. All samples were corrected for atmospheric fractionation of 14C to 2- using the southern hemisphere application of the INTCAL20 calibration curve (table S4) (62).

Sample (sediment, 0.7 g) was mixed with 0.1% preboiled solution of sodium hexametaphosphate Na6[(PO3)6] and sonicated (5 min). Orbital shaking took place overnight at 200 rpm. After clay dispersal, 3 N hydrochloric and nitric acids (HCl) (HNO3) plus hydrogen peroxide (H2O2) were added. Then, sodium polytungstate (3Na2WO49WO3H2O) (Poly-Gee) at specific gravity 2.4 (preboiled) separated out phytoliths. This was followed by rinsing and centrifugation of samples at 3000 rpm for 5 min. Aliquots (15 l) were mounted on boiled microscope slides with Entellan New (cover, 20 40 mm = inspected area). System microscopy was performed at 40 (Olympus BX41, Motic BA410E). Classification nomenclature followed the International Code for Phytolith Nomenclature (63). The referential baseline included modern plants from several African ecoregions (64) and local soils (65), as well as archaeological localities in the Malawi basin (19, 66).

The OSL data from the landscape and paleoecological data from the Lake Malawi 1B/1C core were subjected to statistical analyses to examine how they changed before and after ~85 ka. Kernel density estimates (KDEs) of sedimentation were constructed following protocols developed in Vermeesch (67) and Kappler et al. (68) from 72 luminescence ages interpreted as originating from alluvial fan deposits (tables S1 to S3). KDEs provide reliable distributions of age occurrences when standard errors (SEs) overlap or the analytical imprecision of the true age is high (67). For the present analysis, each age was replotted 10,000 times along a normal distribution using the rnorm command in R based on the laboratory generated mean and 1- SE. The KDE was created in the kde1d package in R (69). Bandwidth was set to default, with data-derived parameters developed by Sheather and Jones (70).

To characterize the biotic environment, we used proportions of pollen from Poaceae, Podocarpus, miombo, and Olea. We used lake levels to characterize the abiotic environment. Over the ~636 ka span of the MAL05-1B/1C core for which pollen data are available, there have been several periods when lake level was equivalent to modern conditions. We have defined these analogous conditions by downsampling the published lake level data (21) to fit the pollen sample intervals (25), and then calculating the statistical mean of the principal components analysis (PCA) eigenvalue for all lake level proxies over the past 74 ka to represent modern-like lake conditions. The pollen sampling intervals effectively make this the statistical mean of lake levels between 21.4 and 56.2 ka [0.130- and 0.198- (25)] and enable us to compare recent vegetation composition to its composition during older, analogous precipitation regimes.

To evaluate whether there were differences in the regional environmental structure before and after 85 ka, we conducted a NP-MANOVA (71). However, vegetation and lake level proxies are inherently different data types [pollen proportions (25) and the first principal component of all lake level proxies (21), respectively]. To conduct the MANOVA, these data must be the same type. Pollen, lake level proxies, and macrocharcoal were also sampled at different densities and intervals in the cores. To properly adjust the data so that once a single pollen sample and its age are matched to a single charcoal and lake level sample, we conducted a series of transformations. Because the pollen data were the most sparsely sampled, we used a spline to fit and downsample the lake level and charcoal data to match them. To make the pollen and lake level data equivalent, we conducted a PCoA using R software (72). PCoA is similar to the widely known PCA in that PCoA conducts a decomposition of a data matrix to obtain eigenvalues and their corresponding eigenvectors. The difference is that while PCA decomposes the variance-covariance matrix, PCoA solves for the eigenvalues of a distance matrix of the original data. To create the distance matrix, we used the 2 distance, which is appropriate for proportion data, like pollen. The PCoA results in a set of scores, representing the original data, which can be plotted similar to PCA. In our case, these scores are not only useful for graphic illustration, but as they are normalized and Euclidean, they are identical to the lake level data and maintain all information contained by the original pollen dataset. This procedure allowed us to use the PCoA pollen scores in conjunction with lake level variable in the NP-MANOVA to test whether there was a difference in environment before and after 85 ka. For the Supplementary Materials statistics, biplots of species richness and lake level were constructed using the ggplot2 package of R. Box and whiskers quartiles used the boxplot command in base R.

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Early human impacts and ecosystem reorganization in southern-central Africa - Science Advances

Newest American Academy of Arts and Sciences members – Stanford Today – Stanford University News

Ten Stanford faculty members are among the 252 new members elected to the American Academy of Arts and Sciences, which honors exceptional scholars, leaders, artists and innovators engaged in advancing the public good.

From left to right starting from the top: Axel Brunger, Tirin Moore, Chang-rae Lee, Robert Byer, Fei-Fei Li, John Etchemendy, Zhenan Bao, Yakov Eliashberg, Teresa Meng and James Mattis. (Image credit: Andrew Brodhead)

The new Stanford members to join the Class of 2021 are as follows:

Zhenan Bao, the K.K. Lee Professor in Chemical Engineering, is the department chair of Chemical Engineering. She is also a member of Stanford Bio-X and the Wu Tsai Neurosciences Institute, senior fellow at the Precourt Institute for Energy, a fellow at Stanford ChEM-H, an affiliate of the Stanford Woods Institute for the Environment and a principal investigator with the Stanford Institute for Materials and Energy Sciences at SLAC National Accelerator Laboratory. Research areas in the Bao Group include synthesis of functional organic and polymer materials, organic electronic device design and fabrication and applications development for organic electronics.

Axel Brunger is a professor of molecular and cellular physiology and of neurology in the Stanford School of Medicine and professor of photon science at Stanford and SLAC. He is also a member of Stanford Bio-X and the Wu Tsai Neurosciences Institute. Brungers research focuses on studying the molecular mechanisms of neurotransmitter release and how these mechanisms relate to physiological function.

Robert Byer, the William R. Kenan, Jr. Professor, is a professor of photon science at Stanford and SLAC and of applied physics in the School of Humanities and Sciences. He is also a member of Stanford Bio-X. Byer has conducted research and taught classes in lasers and nonlinear optics at Stanford since 1969. His current research includes precision laser measurements in support of the detection of gravitational waves and laser accelerator on a chip technology.

Yakov Eliashberg, the Herald L. and Caroline L. Ritch Professor in the School of Humanities and Sciences, is a professor of mathematics. He is one of the founders of symplectic and contact topology, a field that arose in part from the study of various classical phenomena in physics that involve the evolution of mechanical systems, such as springs and planetary systems.

John Etchemendy is the Denning Co-Director of the Stanford Institute for Human-Centered Artificial Intelligence and the Patrick Suppes Family Professor in the School of Humanities and Sciences. As a philosopher, Etchemendys scholarship research interests include logic, semantics and the philosophy of language. Etchemendy also served as Stanfords 12th provost.

Chang-rae Lee, the Ward W. and Priscilla B. Woods Professor in the Department of English, is the author of six novels. His most recent book, My Year Abroad (Riverhead Books) was published earlier this year and has received much critical acclaim. Lees novels have won numerous awards and citations, including the Hemingway Foundation/PEN Award, the American Book Award and the American Library Association Notable Book of the Year Award. He has also written stories and articles for the New Yorker, the New York Times, Time (Asia), Conde Nast Traveler and many other publications.

Fei-Fei Li is the Sequoia Capital Professor in the Department of Computer Science and co-director of the Stanford Institute For Human-Centered Artificial Intelligence (HAI). She is also a member of Stanford Bio-X and the Wu Tsai Neurosciences Institute. Her current research interests include cognitively inspired AI, machine learning, deep learning, computer vision and the intersection of AI and healthcare. In the past, Li has also worked on cognitive and computational neuroscience.

General Jim Mattis, U.S. Marine Corps (Ret.), is the Davies Family Distinguished Fellow at the Hoover Institution, after having served as the nations 26th Secretary of Defense. His expertise is in national security, military history, military strategy, Iran and the Middle East. At Hoover, he is a participant in two research teams: Military History/Contemporary Conflict Working Group and the National Security Task Force.

Teresa Meng is the Reid Weaver Dennis Professor of Electrical Engineering, emerita, and a member of Stanford Bio-X. Her research has focused on low-power circuit and system design, video signal processing, wireless communications, and applying signal processing and integrated circuit design to biomedical engineering. Meng retired from Stanford in 2013.

Tirin Moore, a professor of neurobiology in the Stanford School of Medicine, is also a member of Bio-X, the Maternal & Child Health Research Institute (MCHRI) and the Wu Tsai Neurosciences Institute. The Moore lab studies the activity of single neurons and populations of neurons in areas of the brain that relate to visual and motor functions. They explore the consequences of changes in that activity and aim to develop innovative approaches to fundamental problems in systems and circuit-level neuroscience.

The American Academy of Arts and Sciences serves the nation as a champion of scholarship, civil dialogue and useful knowledge. The academy is committed to interdisciplinary, nonpartisan research that provides pragmatic solutions for complex challenges.

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Newest American Academy of Arts and Sciences members - Stanford Today - Stanford University News

Butterflies and moths look at the world differently: Blame it on evolution – Research Matters

Image by Jeremy Zero via Unsplash

The genetic makeup of butterflies and moths is similar. However, while most butterflies, which are a kind of moth, fly by the day, other moths are active at night. They possess different eyes that adapt to the surrounding lights, ranging from dazzling light to complete darkness. While the butterflies eyes enhance the clarity of images in bright light conditions, other moths eyes have evolved to help them see clearly in dim light settings. Hence, butterflies are unable to see clearly in the dark, while moths end up viewing the world a bit blurred.

All moths engage in swift flight manoeuvres, and their eyes can sense the slightest change in their environment. What causes their eyes to perform the same functions under different light conditions is not clear to scientists. Recently, researchers have studied whether the butterflies and moths activity patterns at different times of the day can explain the difference in how their eyes function. The study, by researchers from the National Centre of Biological Sciences (NCBS), Tata Institute of Fundamental Research, Bengaluru and Indian Institute of Science Education and Research Pune (IISER-Pune), was published in the Journal of Comparative Physiology A. It was supported by the Air Force Office of Scientific Research (AFOSR) and the Department of Science and Technology (DST), the Government of India.

To facilitate seeing, light-detecting cells in the retina send a signal to the brain about the ambient visual environment. An object appears to flicker when the eyes light-detecting cells can register the dark and light periods from an irregular light source. Sometimes, the interval between the dark and light periods is so small that eyes fail to detect it, and an individual perceives even a flickering object as a regular light source. Scientists refer to the frequency at which eyes fail to detect an actual flicker as the Flicker Fusion Frequency or the FFF. As the FFF can vary across species, researchers often use it to compare the visual abilities of animals. The scientists compared the FFF of the butterflies and the moths.

To do so, the researchers collected live butterflies and moths from the gardens of the NCBS campus. Their sample comprised day-flying, evening-flying, and night-flying species of these insects.

We initially measured flicker fusion frequencies just as a quick fun activity, says Sanjay Sane, a Professor at NCBS and an author of the study. In due course, as many of these insects fly past our backyards, we developed this study, he adds. The researchers, however, depended on an opportunistic sampling of butterflies and moths in the NCBS backyard.

The researchers studied how the eyes of butterflies and other moths perceive a light source at various rates of flicker. They observed that the FFF is significantly different for the two groups. Butterflies eyes are better at detecting objects with a higher rate of flickering than moths eyes. Additionally, evening-flying butterflies can detect flickering in an even broader range of frequency.

Although their eyes are not as good as ours, their ability to sense changes in their environment is superior, and hence their reactions much faster, says Sanjay.

The scientists found that the ability to detect a flicker did not depend upon whether they are day-flying or night-flying, but whether they are butterflies or other moth species. The study suggests that as the butterflies and other moth species have diverged from their common ancestors during evolution, their eyes evolved differently. As butterflies adapted to day-light lifestyles, their eyes got more sensitive to change in ambient light. If a moth has evolved a diurnal lifestyle, it still has to function with a sensitivity of eyes that is best under low light levels, explains Sanjay. It points out that evolution happens continuously and has not yet optimised every organ for its current role.

The researchers were able to compare the different groups by studying them simultaneously. Fossil records or comparisons of genes would be insufficient to make such a comparison because physiological or behavioural differences are often not captured when animals are not alive.

Our study highlights the importance of comparative work across all levels including physiological to assess how evolutionary processes work, Sanjay signs off.

This article has been run past the researchers, whose work is covered, to ensure accuracy.

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Butterflies and moths look at the world differently: Blame it on evolution - Research Matters

Wound healing, infection can be determined by genetics – Times of India

TEXAS: Researchers from Texas Tech's Department of Biological Sciences and Natural Science Research Laboratory recently determined that some genes have an association with the pathogens that infect chronic wounds and hinder the healing process.

In a first-of-its-kind study, researchers have determined that genetics may play a role in how wounds heal. Caleb Phillips, an assistant professor at Texas Tech University and director of the Phillips Laboratory in the Department of Biological Sciences, and doctoral student Craig Tipton led the study, "Patient genetics is linked to chronic wound microbiome composition and healing," according to a study published in the open-access, peer-reviewed medical journal PLOS Pathogens.

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"We showed that there are identifiable locations in people's genome where, depending on their genotype, they tend to get infections by specific bacteria," Phillips said. "The different genomic locations identified tend to be related in terms of the types of genes they are close to and may regulate. A working hypothesis emerging from the research is that genetic differences influencing genes encoding the way our cells interact with the environment and each other are important for infection differences."

Though there is still work to be done before the research directly benefits patients, Tipton said the study is an important and promising step in that direction.

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Wound healing, infection can be determined by genetics - Times of India