Ancient microbes offer clues to how complex life evolved

A new study published in Science Advances reveals a surprising twist in the evolutionary history of complex life. Researchers at Queen Mary University of London have discovered that a single-celled organism, a close relative of animals, harbors the remnants of ancient giant viruses woven into its own genetic code. This finding sheds light on how complex organisms may have acquired some of their genes and highlights the dynamic interplay between viruses and their hosts.

The study focused on a microbe called Amoebidium, a unicellular parasite found in freshwater environments.

By analysing Amoebidium's genome, the researchers led by Dr Alex de Mendoza Soler, Senior Lecturer at Queen Mary's School of Biological and Behavioural Sciences, found a surprising abundance of genetic material originating from giant viruses -- some of the largest viruses known to science.

These viral sequences were heavily methylated, a chemical tag that often silences genes.

"It's like finding Trojan horses hiding inside the Amoebidium's DNA," explains Dr de Mendoza Soler.

"These viral insertions are potentially harmful, but Amoebidium seems to be keeping them in check by chemically silencing them."

The researchers then investigated how widespread this phenomenon might be. They compared the genomes of several Amoebidium isolates and found significant variation in the viral content.

This suggests that the process of viral integration and silencing is ongoing and dynamic.

"These findings challenge our understanding of the relationship between viruses and their hosts," says Dr. de Mendoza Soler.

"Traditionally, viruses are seen as invaders, but this study suggests a more complex story. Viral insertions may have played a role in the evolution of complex organisms by providing them with new genes. And this is allowed by the chemical taming of these intruders DNA."

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ProSocial World: How the principles of evolution can create lasting global change

Evolution goes beyond the genetic code and the transformation of physical form, from land-mammal to whale or dinosaur to bird.

At the core of evolutionary science is a triad: variation, selection and replication, explains Binghamton University Distinguished Professor Emeritus of Biological Sciences David Sloan Wilson, the founder of Binghamton University, State University of New York's Evolutionary Studies (EvoS) program. You can see this triad at work in culture as well, from economics and business, to engineering and the arts, and the functioning of society at all levels.

Knowing how cultural evolution happens also means we can harness it for the larger good, creating a more just and sustainable world. That's a topic of "Multilevel cultural evolution: From new theory to practical applications," a new article by Wilson recently published in Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences.

Co-authors include Binghamton alumnus Guru Madhavan, MBA '07, PhD '09, senior program director at the National Academy of Engineering; Michele J. Gelfand, professor of organizational behavior and psychology at Stanford University; University of Nevada Psychology Professor Steven C. Hayes, who developed Acceptance and Commitment Therapy (ACT); Paul W.B. Atkins, visiting associate professor of psychology with Australian National University's Crawford School of Public Policy and co-founder of the non-profit ProSocial World with Wilson; and microbiologist Rita R. Colwell, former director of the National Science Foundation.

The wide-ranging article explores the three hallmarks of cultural evolution: prosociality, or behavior oriented toward the welfare of others; social control, which enforces prosocial behavior and penalizes those who behave selfishly; and symbolic thought, which relies on a flexible inventory of symbols with shared meaning.

Humans have evolved to live in small, cooperative groups, not as disconnected individuals. To be effective, however, society also requires structure.

Otherwise, strategies that are beneficial on the individual or small-group level become maladaptive: Self-preservation becomes self-dealing, helping friends and family becomes nepotism and cronyism, and patriotism fuels international conflict, for example.

"We have to have the global good in mind and everything that we do in some sense has to be coordinated with the good of the whole," Wilson said.

A roadmap for evolution

Evolutionary concepts have been misused, however. Take social Darwinism, for example, which is often used to justify competition and harsh social inequities as "survival of the fittest," a misunderstanding and misapplication of Darwinian theory. "Social engineering" also has insidious implications, Wilson noted.

"We need to ask: Is there anything about evolutionary theory that is especially dangerous in that regard? Or is it the case that anything that can be used as a tool can also be used as a weapon?" Wilson asked. "I think it's the latter."

These concepts become weapons when they are used as means of control, with little to no input from the people they impact, he explained. When people decide to use evolutionary principles to shape their own actions and goals, however, these principles are largely benign.

Checks and balances are at the core of multilevel cultural evolution to avoid power imbalances, making it the opposite of social Darwinism, which portrayed social inequities as necessary and inevitable. Social Darwinism actually has little to do with Darwin or his theories, Wilson points out; it's a stigmatizing term associated with the moral justification for ruthless competition, and probably closer to the principles behind neoclassical economics.

But fields such as economics and business needn't define themselves with the neoclassical "greed is good" ethos of Milton Freidman. Wilson points to the work of Nobel Prize-winning economist Elinor Ostrom, who proved that groups can self-manage common-pool resources -- avoiding the proverbial "tragedy of the commons" if they implement eight "core design principles."

Wilson collaborated with Ostrom to show that the core design principles can be generalized, providing a key to successful governance for nearly all forms of cooperative activity.

"To begin, you need to have a good, strong sense of identity and purpose; that's the first core design principle," Wilson said.

Other principles involve the equitable distribution of benefits and resources, inclusive decision-making, transparent behavior, and levels of response to helpful and unhelpful behavior, as well as fast and fair conflict resolution, local autonomy and authority, and relationships with other groups.

These principles not only build better workplaces, neighborhoods and nations, they can also heal the mind. As social mammals, our minds interpret social isolation as an emergency situation, the authors note, and social support is key for the treatment of such conditions as anxiety and depression.

The tools used in therapy -- particularly mindfulness -- are also applicable on a societal level, encouraging adaptability and cognitive flexibility, which helps individuals recover from adverse life events. That's true of groups as well, Wilson said.

Planting the seed

Creating a more prosocial world grounded in equity and cooperation isn't some unreachable pipe dream.

"There are practical applications," said Wilson, who established the nonprofit ProSocial World to plant these ideas outside of academia. "Right now, not in some far, distant future, we could be using these ideas to accomplish positive change."

It's important to avoid what Wilson calls the archipelago of knowledge and practice, consisting of "many islands with little communication." Otherwise, ideas and solutions may become trapped in separate silos.

In essence, the EvoS' speaker series functions that way for students, mingling lectures on bacteria with Neanderthals, morality, the arts and more. Students are exposed to ideas they may not have otherwise encountered, which introduces new paths and possibilities. The same can happen in the larger society, too.

While technological changes can spread from one culture to another over decades or centuries, Wilson hopes to spark societal change more quickly. He draws upon the concept of catalysis in chemistry: Added in small amounts, a catalytic molecule hastens the rate of change, he explains.

As catalytic agents, individuals may inspire changes that would otherwise take decades or not happen at all. And this catalysis can happen in ordinary ways, by leaning into the small-group community mindset that fuels our humanity.

Consider a community garden, for example: Reaching out to different community gardens and sharing knowledge can only benefit everyone involved, Wilson said. And those connections don't need to consist of dull meetings; they can involve social interactions such as parties and potlucks, which bring people together and encourage them to make connections.

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Viruses can steal our genetic code to create new human-virus genes

Like a scene out of "Invasion of the Body Snatchers," a virus infects a host and converts it into a factory for making more copies of itself. Now researchers have shown that a large group of viruses, including the influenza viruses and other serious pathogens, steal genetic signals from their hosts to expand their own genomes.

This finding is presented in a study published online today and in print June 25 in Cell. The cross-disciplinary collaborative study was led by researchers at the Global Health and Emerging Pathogens Institute at Icahn School of Medicine at Mount Sinai in New York, and at the MRC-University of Glasgow Centre for Virus Research in the UK.

The cross-disciplinary team of virologists looked at a large group of viruses known as segmented negative-strand RNA viruses (sNSVs), which include widespread and serious pathogens of humans, domesticated animals and plants, including the influenza viruses and Lassa virus (the cause of Lassa fever). They showed that, by stealing genetic signals from their hosts, viruses can produce a wealth of previously undetected proteins. The researchers labeled them as UFO (Upstream Frankenstein Open reading frame) proteins, as they are encoded by stitching together the host and viral sequences. There was no knowledge of the existence of these kinds of proteins prior to this study.

These UFO proteins can alter the course of viral infection and could be exploited for vaccine purposes.

"The capacity of a pathogen to overcome host barriers and establish infection is based on the expression of pathogen-derived proteins," said Ivan Marazzi, PhD, Associate Professor of Microbiology at Icahn School of Medicine and corresponding author on the study. "To understand how a pathogen antagonizes the host and establishes infection, we need to have a clear understanding of what proteins a pathogen encodes, how they function, and the manner in which they contribute to virulence."

Viruses cannot build their own proteins, so they need to feed suitable instructions to the machinery that builds proteins in their host's cells. Viruses are known to do this through a process called "cap-snatching," in which they cut the end from one of the cell's own protein-encoding messages (a messenger RNA, or mRNA) and then extend that sequence with a copy of one of their own genes. This gives a hybrid message to be read.

"For decades we thought that by the time the body encounters the signal to start translating that message into protein (a 'start codon') it is reading a message provided to it solely by the virus. Our work shows that the host sequence is not silent," said Dr. Marazzi.

The researchers show that, because they make hybrids of host mRNAs with their own genes, viruses (sNSVs) can produce messages with extra, host-derived start codons, a process they called "start snatching." This makes it possible to translate previously unsuspected proteins from the hybrid host-virus sequences. They further show that these novel genes are expressed by influenza viruses and potentially a vast number of other viruses. The product of these hybrid genes can be visible to the immune system, and they can modulate virulence. Further studies are needed to understand this new class of proteins and what the implications are of their pervasive expression by many of the RNA viruses that cause epidemics and pandemics.

Ed Hutchinson, PhD, corresponding author and a research fellow at MRC-University of Glasgow Centre for Virus Research, said, "Viruses take over their host at the molecular level, and this work identifies a new way in which some viruses can wring every last bit of potential out of the molecular machinery they are exploiting. While the work done here focusses on influenza viruses, it implies that a huge number of viral species can make previously unsuspected genes."

Researchers say the next part of their work is to understand the distinct roles the unsuspected genes play. "Now we know they exist, we can study them and use the knowledge to help disease eradication," said Dr. Marazzi. "A large global effort is required to stop viral epidemics and pandemics, and these new insights may lead to identifying novel ways to stop infection."

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