Scientists Program CRISPR to Fight Viruses in Human Cells

A common gene-editing enzyme could be used to disable RNA viruses such as flu or Ebola

By Tanya Lewis on October 23, 2019

Researchers modified the enzyme Cas13 to target and inactivate viruses such as influenza (shown here). Credit: Kateryna Kon Getty Images

CRISPR is usually thought of as a laboratory tool to edit DNA in order to fix genetic defects or enhance certain traits—but the mechanism originally evolved in bacteria as a way to fend off viruses called bacteriophages. Now scientists have found a way to adapt this ability to fight viruses in human cells.

In a recent study, Catherine Freije, Cameron Myhrvold and Pardis Sabeti at the Broad Institute of the Massachusetts Institute of Technology and Harvard University, and their colleagues programmed a CRISPR-related enzyme to target three different single-stranded RNA viruses in human embryonic kidney cells (as well as human lung cancer cells and dog kidney cells) grown in vitro and chop them up, rendering them largely unable to infect additional cells. If further experiments show this process works in living animals, it could eventually lead to new antiviral therapies for diseases such as Ebola or Zika in humans.

Viruses come in many forms, including DNA and RNA, double-stranded and single-stranded. About two thirds of the ones that infect humans are RNA viruses, and many have no approved treatment. Existing therapies often use a small molecule that interferes with viral replication—but this approach does not work for newly emerging viruses or ones that are evolving rapidly.

“CRISPR” refers to a series of DNA sequences in bacterial genomes that were left behind from previous bacteriophage infections. When the bacteria encounter these pathogens again, enzymes called CRISPR-associated (Cas) proteins recognize and bind to these sequences in the virus and destroy them. In recent years, researchers (including study co-author Feng Zhang) have reengineered one such enzyme, called Cas9, to cut and paste DNA in human cells. The enzyme binds to a short genetic tag called a guide RNA, which directs the enzyme to a particular part of the genome to make cuts. Previous studies have used Cas9 to prevent replication of double-stranded DNA viruses or of single-stranded RNA viruses that produce DNA in an intermediate step during replication. Only a small fraction of RNA viruses that infect humans produce such DNA intermediates—but another CRISPR enzyme, called Cas13, can be programmed to cleave single-stranded RNA viruses.

“The nice thing about CRISPR systems and systems like Cas13 is that their initial purpose in bacteria was to defend against viral infection of bacteria, and so we sort of wanted to bring Cas13 back to its original function—and apply this to mammalian viruses in mammalian cells,” says Freije, who is a doctoral student in virology at Harvard. “Because CRISPR systems rely on guide RNAs to specifically guide the CRISPR protein to a target, we saw this as a great opportunity to use it as a programmable antiviral.”

Freije and her colleagues programmed Cas13 to target three different viruses: lymphocytic choriomeningitis virus (LCMV), influenza A virus (IAV) and vesicular stomatitis virus (VSV). LCMV is an RNA virus that mostly infects mice—but it is in the same family as the virus that causes Lassa fever, which is found in West Africa and is much more dangerous to study in the lab. IAV is a flu virus; although some antiviral medications for flu already exist, such viruses evolve rapidly, so there is a need for better options. Finally, VSV is a model for many other single-stranded RNA viruses.

To determine how effective Cas13 was at destroying the viruses, the researchers also used it as a diagnostic tool to see how much viral RNA was being released from infected cells. They saw a twofold to 44-fold reduction in RNA, depending on which virus they were looking at and the time point. They also looked at how well the released RNA was able to go on and infect new cells. In most cases, they saw a 100-fold reduction in infectivity—and in some cases, more than 300-fold—according to Freije. The findings were published online on October 10 in Molecular Cell.

“The results are very impressive,” says Chen Liang, a professor at the Lady Davis Institute at Jewish General Hospital and the department of microbiology and immunology at McGill University in Montreal, who was not involved in the study. His own laboratory has used the Cas9 enzyme to deactivate DNA viruses. The concept is very similar, but Cas13 has a few advantages, he says. For one, Cas13 can be used to target one virus using several guide RNAs, making it difficult for the virus to “escape.” Secondly, the new study also used Cas13 to detect how much viral RNA was left over to infect cells. The amount of viral knockdown the group achieved is “very significant,” Liang says. “If you can target and inactivate all three [of these] viruses, in principle, you can inactivate any virus.

As with any approach, there are limitations. One is the question of how to deliver the Cas13 to target a virus in a living person, Liang notes, and the researchers have not yet done any animal studies. Another is the fact that viruses will eventually develop resistance. But Cas13 has an advantage here: when Cas9 cuts viral DNA, mammalian cells repair it and can cause mutations that make the virus more resistant. Yet with Cas13, these cells do not have the mechanism to repair the RNA and introduce errors that would help the virus escape being destroyed. Even if a virus does evolve resistance, or if a new virus is encountered, the method could be quickly adapted.

“One of the things that’s most exciting about this approach is the programmability,” says Myhrvold, a postdoctoral fellow at Harvard. “Once you figure out how to do this well for one virus it’s not that hard to design sequences against another virus—or another one. Furthermore, if the virus changes its own sequence—as viruses are known to do, just during an outbreak or in response to therapy—you can very easily update the CRISPR RNA sequence and keep up with the virus.”

Freije agrees. “We are definitely excited about future prospects of optimizing the system and trying it out in mouse models,” she says. Beyond therapeutics, the team hopes to understand more about how viruses operate—how they replicate and what parts of their genomes are most important. Using approaches like this, “you can really start to get a better picture of what parts of these viruses are and, most importantly, what really makes them tick.”

How do bacteria defend themselves against viruses?

The CRISPR-Cas system in some bacteria helps to form an effective barrier to invading viruses.

DIGEST Apr 3, 2019



A transmission electron microscopy image of bacteriophages taken at The University of Alabama’s Optical Analysis Facility. Image credit: Chou-Zheng and Hatoum-Aslan, 2019 (CC BY 4.0)

Just as humans are susceptible to viruses, bacteria have their own viruses to contend with. These viruses – known as phages – attach to the surface of bacterial cells, inject their genetic material, and use the cells’ enzymes to multiply while destroying their hosts.

To defend against a phage attack, bacteria have evolved a variety of immune systems. For example, when a bacterium with an immune system known as CRISPR-Cas encounters a phage, the system creates a ‘memory’ of the invader by capturing a small snippet of the phage’s genetic material. The pieces of phage DNA are copied into small molecules known as CRISPR RNAs, which then combine with one or more Cas proteins to form a group called a Cas complex. This complex patrols the inside of the cell, carrying the CRISPR RNA for comparison, similar to the way a detective uses a fingerprint to identify a criminal. Once a match is found, the Cas proteins chop up the invading genetic material and destroy the phage.

There are several different types of CRISPR-Cas systems. Type III systems are among the most widespread in nature and are unique in that they provide a nearly impenetrable barrier to phages attempting to infect bacterial cells. Medical researchers are exploring the use of phages as alternatives to conventional antibiotics and so it is important to find ways to overcome these immune responses in bacteria. However, it remains unclear precisely how Type III CRISPR-Cas systems are able to mount such an effective defense.

Chou-Zheng and Hatoum-Aslan used genetic and biochemical approaches to study the Type III CRISPR-Cas system in a bacterium called Staphylococcus epidermidis. The experiments showed that two enzymes called PNPase and RNase J2 played crucial roles in the defense response triggered by the system. PNPase helped to generate CRISPR RNAs and both enzymes were required to help to destroy genetic material from invading phages.

Previous studies have shown that PNPase and RNase J2 are part of a machine in bacterial cells that usually degrades damaged genetic material. Therefore, these findings show that the Type III CRISPR-Cas system in S. epidermidis has evolved to coordinate with another pathway to help the bacteria survive attack from phages. CRISPR-Cas immune systems have formed the basis for a variety of technologies that continue to revolutionize genetics and biomedical research. Therefore, along with aiding the search for alternatives to antibiotics, this work may potentially inspire the development of new genetic technologies in the future.

Phage-Encoded Anti-CRISPR Defenses
Annual Review of Genetics

Vol. 52:445-464 (Volume publication date November 2018)
First published as a Review in Advance on September 12, 2018
https://doi.org/10.1146/annurev-genet-120417-031321

Sabrina Y. Stanley1 and Karen L. Maxwell2
1Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
2Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada; email: karen.maxwell@utoronto.ca

Abstract

The battle for survival between bacteria and bacteriophages (phages) is an arms race where bacteria develop defenses to protect themselves from phages and phages evolve counterstrategies to bypass these defenses. CRISPR-Cas adaptive immune systems represent a widespread mechanism by which bacteria protect themselves from phage infection. In response to CRISPR-Cas, phages have evolved protein inhibitors known as anti-CRISPRs. Here, we describe the discovery and mechanisms of action of anti-CRISPR proteins. We discuss the potential impact of anti-CRISPRs on bacterial evolution, speculate on their evolutionary origins, and contemplate the possible next steps in the CRISPR-Cas evolutionary arms race. We also touch on the impact of anti-CRISPRs on the development of CRISPR-Cas-based biotechnological tools.

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Biological Sciences
RESEARCH ARTICLE
Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria
Ido Yosef, Miriam Manor, Ruth Kiro, and View ORCID Profile Udi Qimron
PNAS June 9, 2015 112 (23) 7267-7272; first published May 18, 2015 https://doi.org/10.1073/pnas.1500107112

Edited by Jennifer A. Doudna, University of California, Berkeley, CA, and approved April 28, 2015 (received for review January 25, 2015)

Significance

Antibiotic resistance of pathogens is a growing concern to human health, reviving interest in phage therapy. This therapy uses phages (natural bacterial enemies) to kill pathogens. However, it encounters many obstacles such as delivery barriers into the tissues and bacterial resistance to phages. Here, we use phages for delivering a programmable DNA nuclease, clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas), to reverse antibiotic resistance and eliminate the transfer of resistance between strains. This approach combines CRISPR-Cas delivery with lytic phage selection of antibiotic-sensitized bacteria. The strategy may reduce the prevalence of antibiotic-resistant bacteria in treated surfaces and on skin of medical personnel, as it uses phages in a unique way that overcomes many of the hurdles encountered by phage therapy.

Abstract

The increasing threat of pathogen resistance to antibiotics requires the development of novel antimicrobial strategies. Here we present a proof of concept for a genetic strategy that aims to sensitize bacteria to antibiotics and selectively kill antibiotic-resistant bacteria. We use temperate phages to deliver a functional clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) system into the genome of antibiotic-resistant bacteria. The delivered CRISPR-Cas system destroys both antibiotic resistance-conferring plasmids and genetically modified lytic phages. This linkage between antibiotic sensitization and protection from lytic phages is a key feature of the strategy. It allows programming of lytic phages to kill only antibiotic-resistant bacteria while protecting antibiotic-sensitized bacteria. Phages designed according to this strategy may be used on hospital surfaces and hand sanitizers to facilitate replacement of antibiotic-resistant pathogens with sensitive ones.

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   Genetically Engineered Phages: a Review of Advances over the Last Decade

Diana P. Pires, Sara Cleto, Sanna Sillankorva, Joana Azeredo, Timothy K. Lu

DOI: 10.1128/MMBR.00069-15

 

SUMMARY

Soon after their discovery in the early 20th century, bacteriophages were recognized to have great potential as antimicrobial agents, a potential that has yet to be fully realized. The nascent field of phage therapy was adversely affected by inadequately controlled trials and the discovery of antibiotics. Although the study of phages as anti-infective agents slowed, phages played an important role in the development of molecular biology. In recent years, the increase in multidrug-resistant bacteria has renewed interest in the use of phages as antimicrobial agents. With the wide array of possibilities offered by genetic engineering, these bacterial viruses are being modified to precisely control and detect bacteria and to serve as new sources of antibacterials. In applications that go beyond their antimicrobial activity, phages are also being developed as vehicles for drug delivery and vaccines, as well as for the assembly of new materials. This review highlights advances in techniques used to engineer phages for all of these purposes and discusses existing challenges and opportunities for future work.

INTRODUCTION

Bacteriophages (phages) are among the most abundant biological particles on earth. They are also highly versatile and adaptable to a great number of applications. Phages are viruses that infect bacteria; their self-replication depends on access to a bacterial host. Phages were discovered independently by Frederick Twort in 1915 (1) and by Félix d'Hérelle in 1917 (2), and they were used early on as antimicrobial agents. Although the initial results of phage therapy were promising (3, 4), poorly controlled trials and inconsistent results generated controversy within the scientific community about the efficacy and reproducibility of using phages to treat bacterial infections (5–7). The discovery of penicillin in 1928 and the subsequent arrival of the antibiotic era further cast a shadow on phage therapy (5, 6). As a result, phage therapy was discontinued in Western countries, even as its use continued in Eastern Europe and the former Soviet Union (8–10).

Despite the important success of antibiotics in improving human health, antibiotic resistance has emerged with steadily increasing frequency, rendering many antibiotics ineffective (11–14). Multidrug-resistant bacteria currently constitute one of the most widespread global public health concerns (15–17). More than 2 million people are sickened every year in the United States alone as a result of antibiotic-resistant infections, resulting in at least 23,000 deaths per year (16). The rising tide of antibiotic resistance coupled with the low rate of antibiotic discovery (17, 18) has revived interest in phages as antibacterial agents (19–21).

Unlike most antibiotics, phages are typically highly specific for a particular set of bacterial species or strains and are thus expected to have fewer off-target effects on commensal microflora than antibiotics do (22). The self-replicating nature of phages and the availability of simple, rapid, and low-cost phage production processes are additional advantages for their use as antimicrobials (22). Phages have been used not only to treat and prevent human bacterial infections (9, 23–25) but also to control plant diseases (26–29), detect pathogens (30–33), and assess food safety (34–37).

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REVIEW ARTICLE
Microbiol., 03 May 2019 | https://doi.org/10.3389/fmicb.2019.00954

Genetic Engineering of Bacteriophages Against Infectious Diseases

Yibao Chen1,2, Himanshu Batra3, Junhua Dong1,2, Cen Chen1,2, Venigalla B. Rao3 and Pan Tao1,2,3*

Bacteriophages (phages) are the most abundant and widely distributed organisms on Earth, constituting a virtually unlimited resource to explore the development of biomedical therapies. The therapeutic use of phages to treat bacterial infections (“phage therapy”) was conceived by Felix d’Herelle nearly a century ago. However, its power has been realized only recently, largely due to the emergence of multi-antibiotic resistant bacterial pathogens. Progress in technologies, such as high-throughput sequencing, genome editing, and synthetic biology, further opened doors to explore this vast treasure trove. Here, we review some of the emerging themes on the use of phages against infectious diseases. In addition to phage therapy, phages have also been developed as vaccine platforms to deliver antigens as part of virus-like nanoparticles that can stimulate immune responses and prevent pathogen infections. Phage engineering promises to generate phage variants with unique properties for prophylactic and therapeutic applications. These approaches have created momentum to accelerate basic as well as translational phage research and potential development of therapeutics in the near future.

Introduction

Bacteriophages (phages), discovered in the early 20th century independently by Frederick Twort and Felix d’Herelle, are the most abundant organisms on earth with up to 2.5 × 108 phages per ml in natural waters (Bergh et al., 1989). It is well accepted that phages specifically infect bacteria and, therefore, were considered for the development of natural approaches to treat bacterial infections since their discovery (Wittebole et al., 2014; Salmond and Fineran, 2015). However, due to the discovery of antibiotics that provided greater breadth and potency, phage therapy lagged behind although research continued in some Eastern European countries (Chanishvili, 2012, 2016; Wittebole et al., 2014). Therefore, in the following several decades, phages were mainly used as model organisms to explore the basic mechanisms of life and led to the birth of modern molecular biology. One classical example is the demonstration of a central biological question in the early 20th century, the nature of a gene, by “Hershey-Chase experiment” (also called “Waring blender experiment”) (Salmond and Fineran, 2015). This elegant experiment demonstrated that DNA, not protein, is the genetic material of T2 phage.

Recently, the emergence of multi-antibiotic resistant bacterial pathogens and the low rate of new antibiotic discovery brought new urgency to develop phage-based therapies (Lu and Koeris, 2011; Viertel et al., 2014; Domingo-Calap and Delgado-Martinez, 2018). A striking example is the recent San Diego patient who was infected by multi-drug resistant Acinetobacter baumannii stain during travelling to Egypt. The patient went into a coma for nearly 2 months but awoke 2 days after intravenous injection of a phage cocktail that lyses this bacterium and finally completely recovered (Schooley et al., 2017). With recent advances, particularly the genome engineering (Martel and Moineau, 2014; Ando et al., 2015; Lemay et al., 2017; Tao et al., 2017b; Kilcher et al., 2018), the applications of phages have greatly expanded. In addition to its use in antibacterial therapy, phages were used in synthetic biology (Lemire et al., 2018), material science (Cao et al., 2016), and biomedical fields (Cao et al., 2018; Tao et al., 2018c). Considering the abundance and diversity, there is vast potential to engineer phages for different applications. In this review, we will focus on the applications of phages in infectious disease, in particular, vaccine development and phage therapy. We will discuss the phage engineering strategies and how these can equip the phages with the ability to advance the vaccine and phage therapy fields.

1College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
2The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
3Department of Biology, The Catholic University of America, Washington, DC, United States

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Allosteric inhibition of CRISPR-Cas9 by bacteriophage-derived peptides
Yan-ru Cui,
Shao-jie Wang,
Jun Chen,
Jie Li,
Wenzhang Chen,
Shuyue Wang,
Bing Meng,
Wei Zhu,
Zhuhong Zhang,
Bei Yang,
Biao Jiang,
Guang Yang,
Peixiang Ma &
Jia Liu 

Genome Biology volume 21, Article number: 51 (2020) Cite this article
Research
Open Access
Published: 26 February 2020

Abstract

Background

CRISPR-Cas9 has been developed as a therapeutic agent for various infectious and genetic diseases. In many clinically relevant applications, constitutively active CRISPR-Cas9 is delivered into human cells without a temporal control system. Excessive and prolonged expression of CRISPR-Cas9 can lead to elevated off-target cleavage. The need for modulating CRISPR-Cas9 activity over time and dose has created the demand of developing CRISPR-Cas off switches. Protein and small molecule-based CRISPR-Cas inhibitors have been reported in previous studies.

ResultsWe report the discovery of Cas9-inhibiting peptides from inoviridae bacteriophages. These peptides, derived from the periplasmic domain of phage major coat protein G8P (G8PPD), can inhibit the in vitro activity of Streptococcus pyogenes Cas9 (SpCas9) proteins in an allosteric manner. Importantly, the inhibitory activity of G8PPD on SpCas9 is dependent on the order of guide RNA addition. Ectopic expression of full-length G8P (G8PFL) or G8PPD in human cells can inactivate the genome-editing activity of SpyCas9 with minimum alterations of the mutation patterns. Furthermore, unlike the anti-CRISPR protein AcrII4A that completely abolishes the cellular activity of CRISPR-Cas9, G8P co-transfection can reduce the off-target activity of co-transfected SpCas9 while retaining its on-target activity.

Conclusion

G8Ps discovered in the current study represent the first anti-CRISPR peptides that can allosterically inactivate CRISPR-Cas9. This finding may provide insights into developing next-generation CRISPR-Cas inhibitors for precision genome engineering.

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Heterogeneous Diversity of Spacers within CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)
Article (PDF Available) in Physical Review Letters 105(12):128102 · September 2010 with 231
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DOI: 10.1103/PhysRevLett.105.128102 · Source: PubMedCite this publication

Jiankui he
Southern University of Science and Technology


Michael Deem
Rice University

Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of antiviral immune system in these organisms. We here study the diversity of spacers in CRISPR under selective pressure. We propose a population dynamics model that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is more conserved. This result is shown to be in agreement with recent experiments. Our results show that the CRISPR spacer structure is influenced by and provides a record of the viral challenges that bacteria face.
https://www.researchgate.net/publication/46424214_Heterogeneous_Diversity_of_Spacers_within_CRISPR_Clustered_Regularly_Interspaced_Short_Palindromic_Repeats

Volume 366
Issue 9
May 2019

Article Contents
ABSTRACT
INTRODUCTION
BIOLOGICAL RELEVANCE OF ANTI-CRISPR PROTEINS
MECHANISMS AND STRUCTURES OF ANTI-CRISPR PROTEINS
APPLICATIONS OF ANTI-CRISPR PROTEINS
OUTLOOK
FUNDING
REFERENCES


MINI REVIEW

Keeping CRISPR in check: diverse mechanisms of phage-encoded anti-CRISPRS 
Despoina Trasanidou, Ana Sousa Gerós, Prarthana Mohanraju, Anna Cornelia Nieuwenweg, Franklin L Nobrega, Raymond H J Staals

FEMS Microbiology Letters, Volume 366, Issue 9, May 2019, fnz098, https://doi.org/10.1093/femsle/fnz098

Published: 11 May 2019

ABSTRACT

CRISPR-Cas represents the only adaptive immune system of prokaryotes known to date. These immune systems are widespread among bacteria and archaea, and provide protection against invasion of mobile genetic elements, such as bacteriophages and plasmids. As a result of the arms-race between phages and their prokaryotic hosts, phages have evolved inhibitors known as anti-CRISPR (Acr) proteins to evade CRISPR immunity. In the recent years, several Acr proteins have been described in both temperate and virulent phages targeting diverse CRISPR-Cas systems. Here, we describe the strategies of Acr discovery and the multiple molecular mechanisms by which these proteins operate to inhibit CRISPR immunity. We discuss the biological relevance of Acr proteins and speculate on the implications of their activity for the development of improved CRISPR-based research and biotechnological tools.

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The physicist's guide to one of biotechnology's hottest new topics: CRISPR-Cas

Melia E Bonomo1,3 and Michael W Deem1,2,3,4

Published 30 April 2018 • © 2018 IOP Publishing Ltd
Physical Biology, Volume 15, Number 4

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Article information

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) constitute a multi-functional, constantly evolving immune system in bacteria and archaea cells. A heritable, molecular memory is generated of phage, plasmids, or other mobile genetic elements that attempt to attack the cell. This memory is used to recognize and interfere with subsequent invasions from the same genetic elements. This versatile prokaryotic tool has also been used to advance applications in biotechnology. Here we review a large body of CRISPR-Cas research to explore themes of evolution and selection, population dynamics, horizontal gene transfer, specific and cross-reactive interactions, cost and regulation, non-immunological CRISPR functions that boost host cell robustness, as well as applicable mechanisms for efficient and specific genetic engineering. We offer future directions that can be addressed by the physics community. Physical understanding of the CRISPR-Cas system will advance uses in biotechnology, such as developing cell lines and animal models, cell labeling and information storage, combatting antibiotic resistance, and human therapeutics.

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Original content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI.


1. Introduction


In 1987, Ishino and colleagues had set out to identify the encoded protein and primary structure of a particular gene in Escherichia coli by analyzing its chromosomal DNA segment and flanking regions [1]. They found an interesting sequence structure at the gene's 3'-end flanking region, in which five homologous sequences of 29 nucleotides were arranged as direct repeats with 32-nucleotide sequences spaced between them. Little did they know that their discovery would prove to have critical immunological significance. It was not until 2000 that these mysterious repeated genomic elements were revisited when Mojica and colleagues searched the available microbial genome database and found many organisms that contained partially palindromic sequences of 24–40 basepairs with 20–58 basepair sequences spaced between them [2]. These were found in almost all archaea, about half of bacteria, no viruses, and no eukaryotes. Related and unrelated species had nearly identical structure in these repeat sequence units. The sequences in between, called 'spacers', were unique to an individual locus and were not found in other genomes [3]. After many suggested abbreviations, including SRSRs, short regularly spaced repeats, and SPIDR, spacers interspersed direct repeats, the scientific community settled on calling these elements clustered regularly interspaced short palindromic repeats, or CRISPR.

SEE 
https://plawiuk.blogspot.com/search?q=BACTERIOPHAGES

https://plawiuk.blogspot.com/search?q=PHAGES

From Pleistocene to trophic rewilding: A wolf in sheep’s clothing


Dustin R. Rubenstein and Daniel I. Rubenstein

PNAS January 5, 2016 https://doi.org/10.1073/pnas.1521757113

This Letter has a Reply and related content. Please see:
Reply to Rubenstein and Rubenstein: Time to move on from ideological debates on rewilding - December 16, 2015
Science for a wilder Anthropocene: Synthesis and future directions for trophic rewilding research - October 26, 2015

Nearly 10 y ago, we (1) critiqued the idea of Pleistocene rewilding (2), a misguided attempt to resurrect bygone ecosystems. Much has happened to the Earth’s biodiversity over the decade since the term “Pleistocene rewilding” was coined, most of it bad. More than half a billion people have been added to the world’s population, and ecosystems continue to be degraded at an alarming rate. A sixth mass extinction is underway, and poaching of megafauna has increased across sub-Saharan Africa. Unfortunately, one thing that has not happened is any serious attempt to scientifically study Pleistocene rewilding. Despite a number of publicized Pleistocene rewilding projects (Oostvaardersplassen in The Netherlands and Pleistocene Park in Siberia), we have yet to see any quantitative data concerning the impacts of megafauna reintroductions.

Svenning et al. (3) again revive the Pleistocene rewilding debate. No longer calling it Pleistocene rewilding, they repackage the sensational into something more palatable: “trophic rewilding.” “Trophic” refers to a “trophic cascade”—when the removal of a top predator or herbivore has indirect and cascading effects on lower tropic levels. Over the past decade, there has been much scientific study of trophic cascades, including those created by the removal of megafauna. However, even these studies recognize that ecosystems are no longer pristine, especially those harboring large mammals. Today’s reality is that wildlife and people must coexist. Setting aside large tracts to bring back communities of disrupted cascades is a luxury.

As the metaanalysis of Svenning et al. (3) shows, rewilding—especially when trophic cascades are reinstated—can alter ecosystem function, often for the better, even if the mechanism is incompletely understood. However, using proxy species when mechanisms are uncertain to recreate ancient ecosystems could have many unintended consequences (1). Simply repackaging Pleistocene rewilding as trophic rewilding does nothing to change this fact. Without good science, such large-scale reintroductions could be as untested as dumping iron into the sea, or placing particles in the sky to attenuate the effects of climate change. We cannot afford to co-opt good science (research on trophic cascades) to justify bad science (Pleistocene rewilding) at a time when species are in peril.

There is no doubt that today’s ecosystems are different from those of 10,000 y ago. However, they are also quite different from the ecosystems of just 10 y ago, when rhinoceros and elephant poaching in Africa seemed under control. In another 10 y, there may be no rhinoceros left. Rather than continuing to promote the sensational by repackaging a failed conservation strategy in shiny new clothing, we should direct our efforts toward preserving the ecosystems and wildlife that remain. We should focus on ways to feed the millions of new mouths appearing each year without destroying more biodiversity (4). We should stop talking about trophic or Pleistocene rewilding, or its next rebadging. We were criticized (5) for drawing the analogy to Jurasssic Park (1). However, Svenning et al. (3) argue for “a framework for integrating synthetic biology and trophic rewilding science.” It is time to be practical, not sensational. It is time to move on.

Footnotes
↵1To whom correspondence should be addressed. Email: dr2497@columbia.edu.


Author contributions: D.R.R. and D.I.R. wrote the paper.


The authors declare no conflict of interest, though they are related.

References
↵

Rubenstein DR,
Rubenstein DI,
Sherman PW,
Gavin TA

(2006) Pleistocene park: Does re-wilding North America represent sound conservation for the 21st century? Biol Conserv 132:232–238

CrossRefGoogle Scholar
↵

Donlan J, et al.

(2005) Re-wilding North America. Nature 436(7053):913–914

.


CrossRefPubMedGoogle Scholar
↵

Svenning J-C, et al.

(2015) Science for a wilder Anthropocene: Synthesis and future directions for trophic rewilding research. Proc Natl Acad Sci USA doi:10.1073/pnas.1502556112

.


Abstract/FREE Full TextGoogle Scholar
↵

Searchinger TD, et al.

(2015) High carbon and biodiversity costs from converting Africa’s wet savannahs to cropland. Nat Clim Change 5:481–486

.


CrossRefGoogle Scholar
↵

Donlan CJ

(2007) Restoring America’s big, wild animals. Sci Am 296(6):70–77

.


PubMedGoogle Scholar

Elaborately decorated eggs predate Easter by thousands of years

JONONMAC46 (CC BY-SA 3.0)

By Michael Price Apr. 8, 2020

If you wanted to make an impression on a high-ranking Bronze or Iron Age chieftain, mere jewelry or gems wouldn’t cut it. Instead, you’d present them with an egg—an elaborately carved and embellished ostrich eggshell, to be exact. Such oologic offerings have been found inside the tombs of Mediterranean and Middle Eastern elites who lived from about 2500 to 500 B.C.E., equally thrilling and perplexing archaeologists. Who made them, and how did they wind up in the hands of ancient nobility?

To crack the case, a team of archaeologists and museum curators took a closer look at decorated eggshells in the collection of the British Museum, which includes five prized eggs in outstanding condition. The intact eggs were all discovered in a burial site known as the Isis Tomb in Vulci, Italy, that was uncovered in 1839 by Napoleon Bonaparte’s brother, Prince Lucien. The tomb dates to about 600 B.C.E. and was filled with other luxury items, including gold jewelry and bronze dinnerware. All five of the ostrich eggs were painted, and four were engraved with repeating geometric patterns (as seen above), animal motifs, and chariots and soldiers.

On other, fragmented pieces found in about a dozen other burial sites around the Mediterranean and Middle East, the researchers used stable isotope analysis—a technique that matches chemical markers in bones and teeth to specific regions—to trace the eggs’ origins. Researchers already suspected they were made by Assyrian and Phoenician craftworkers, and the isotope analysis bore that out. But they found that even within the same tomb, eggshells came from several different regions, indicating a more complex supply chain than previously thought, the researchers report today in Antiquity. A scanning electron microscope also revealed the engravers used a multitude of tools and techniques, underlining the intense effort and skill that went into making these ovular ornaments.

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The Rich Meals That Keep Wild Animals on the Menu

Samoa’s population of “little dodos” is dwindling down to nothing, but the appetites of wealthy people keep putting these rare birds at risk.

Melanie Lambrick

Story by J. B. MacKinnon

MARCH 19, 2020 SCIENCE

The biggest bird-hunting day of the year in the island nation of Samoa, it turns out, is not a great day to start searching for one of the world’s rarest birds. It is the eve of White Sunday, a national holiday during which many wild birds are eaten as a favorite traditional food, and 12-gauge shotguns have been ringing out in the forests for days. Even the most common birds are in hiding.

I have joined Gianluca Serra, an Italian ecologist and conservationist who specializes in creatures at the furthest edge of extinction, on a week-long quest for a bird that probably numbers no more than 200. We begin on an airy jungle ridge above a village called Uafato, in a hut designed to conceal us in shadows. Uafato is remote by the standards of Upolu, the more heavily populated of Samoa’s two main islands, and it has turned its communal forest into a no-hunting zone. The birds don’t appear to be aware of this fact. Apart from the ocean winds, which periodically drag in a squall so heavy that it triggers instant symptoms of the common cold, the landscape is remarkably still and silent.

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I would like to tell you the name of the bird we are pursuing, but even that is not easy. In Samoan, it is called either manumea (which can mean “red bird” or “precious bird”) or manuma (“shy bird”). The first scientific report on the species was published in 1845, and the bird soon became known to English speakers as the tooth-billed pigeon, because its lower bill features bizarre sawlike serrations. Early naturalists also tossed around names such as “dodo pigeon” and “dodlet,” because it resembles a miniature version of the dodo, that famously flightless bird driven extinct in the 1600s. Because genetic testing has now shown that the tooth-billed pigeon really is related to the dodo, and because it, too, may be facing extinction, some are again calling it the “little dodo.”

Let us agree, here, to call it the manumea. By any name, it is a dark blue-green and chestnut pigeon, large enough to be mistaken for a chicken, with a hooked, outsize, sunset-colored beak, as though it had ambitions of becoming a parrot. It lives only in Samoa, where it is the national bird, found on the nation’s currency and in murals throughout the capital city of Apia. Hardly any Samoans have seen the living bird.

Ironically, on those rare occasions when a manumea reveals itself, the bird has presence. Since the 19th century, observers have described it as beautiful, dignified, special. Serra has had one clear sighting and sketched his impression immediately afterward. His drawing shows an electric-blue phantasm on the wing, more like an angel or a pegasus than any earthly being. He saw it from the same hiding spot we are using above Uafato.

After five and a half hours, we are still, with apologies to Samuel Beckett, waiting for dodo. “It’s a ghost species,” says Serra, whose swept-back silver hair and perpetually sunburned face give him the look of a European consul gone tropical. “How can we conserve something we can’t see?”

Giving up for the day, we descend to Uafato, whose white sand and palm trees are overseen by a tall, tumbling waterfall. Cooking for the White Sunday feast has begun, and the air smells like burning coconut husks.

“Where are the manumea?” Serra asks one giggling 10-year-old. He pats the boy’s stomach. “Are they all in Samoan bellies?”

It’s a joke, but a dark-humored one: When a species is reduced to very low numbers, hunters can easily pick off the last individuals. For decades, everyone from conservationists and economists to much of the general public has assumed that the culprits are the world’s desperate, hungry poor, for whom filling an empty stomach is a higher priority than biodiversity. But in Samoa, a more complicated story has emerged, one that doesn’t so easily let the rich world off the hook. We human beings aren’t just eating endangered species any more. We’re consuming them.


Aday later, Serra and I are standing on an ancient structure in the jungle of Savai’i, the larger and wilder of Samoa’s main islands. It is a place of endings. We are just inland from the nation’s western limit, a point of black rock that seems to descend, stepwise, into the sea. In Polynesian tradition, this is O Le Fāfā, entrance to the underwater world of the dead.

The pyramidal edifice we have clambered to the top of is one of dozens in Samoa’s forests. The mound is not small: It’s wider than a basketball court and as tall as a one-story building. The jungle has nearly taken it over, but eight rounded lobes stemming off a central platform are still discernible. The mysterious structure is known as a “star mound,” and it was used, at least at times, to hunt pigeons.

When the ancestors of today’s Samoans arrived by boat about 3,000 years ago, the islands were home only to creatures that could swim, fly, or drift to their shores. Among these, pigeons, including the manumea, were the largest and tastiest wildlife on hand. Under Samoa’s strongly hierarchical social system, hunting them was reserved for chiefs, in the same way that deer hunting in England was once the preserve of aristocrats.

When a village hosted a pigeon hunt, invited chiefs, or matai, are thought to have been assigned to the lobes on the star mound, and would then compete to capture the most wild pigeons using long-handled nets. The hunts were a divine ritual, a spectator sport, a reason for communities to gather and feast, and they disappeared rapidly under the influence of European missionaries in the early 19th century. Or rather, they were transmuted.


In 2014, Samoa’s statistics bureau wrapped up a survey of what Samoans were eating and drinking. The nation has the third-highest prevalence of obesity in the world, and the research, carried out in partnership with the Food and Agriculture Organization of the United Nations, was comprehensive. Nearly 10 percent of households turned in detailed accounts of their daily diet.

Read: Is it safe to eat bushmeat?

Rebecca Stirnemann, an ecologist from New Zealand who was living in Samoa, saw an opportunity to sort out who, exactly, was eating Samoan wildlife. She didn’t expect to catch people eating manumea. Hunters who specialized in manumea could still be found as late as the 1980s, but soon afterward the bird became too rare to target. Instead, Stirnemann worried that hunters pursuing the more common Pacific pigeon, or lupe (pronounced loop-ay), were killing manumea opportunistically or by accident. Interviews with Samoan hunters carried out by Stirnemann and Samoa’s environment ministry indicated that more than a quarter of them had shot multiple manumea by mistake. In later interviews with a smaller group of highly experienced hunters, Serra learned that 41 percent had shot at least one manumea.

“If you hear a pigeon-like call and shoot up in the air, you could get either of them,” Stirnemann told me. She hoped the dietary survey would reveal how many lupe Samoans were eating, as a measure of the threat that hunting posed to manumea. In keeping with prevailing wisdom, she assumed that many of the hunted pigeons were ending up in the pots of the poorest people—a consequence of the subsistence hunting that endangers wildlife worldwide.


Analyzing the results of the household survey, Stirnemann found that Samoans were collectively eating more pigeon than anyone had anticipated: at least 22,000 birds each year. That’s 22,000 chances to accidentally shoot a manumea. But the poor weren’t eating the most: Nearly 45 percent of those pigeons had been eaten in the homes of the richest 10 percent. Expand that to the wealthiest 40 percent of households, and the share climbed to a stunning 80 percent.

“We were all surprised by the results,” Stirnemann said. “People didn’t realize they were having such a big impact on the population of pigeons, let alone manumea. And they also didn’t realize who was predominantly eating them.”

As stirnemann soon learned, her findings added to a growing body of research that is shattering assumptions about who eats threatened species, and why. In the same year as the Samoan survey, pioneering research from the Brazilian Amazon showed that people may be eating more wildlife, not less, as they escape rural poverty for the cities. Poorer households were still hunting wild animals to put food on the table, but also to sell to richer people. The wealthy were the greatest consumers of threatened and “prestige” species—including a monkey, a large rodent called the lowland paca, and a fish that can weigh as much as a German shepherd.

Because mainly poor, rural people had killed wild animals in the past for food or medicine, conservationists and development experts alike had predicted that people raised out of poverty would buy industrial food and pharmaceuticals at the store, the way most of us do in the West. Presto chango, the world’s wildlife would be saved.


But worrying studies kept trickling in. In Peru’s rain-forest cities, some of the heaviest consumers of wild meat proved to be visiting military personnel, industry executives, and tourists. In Vietnam, rhinoceros horn is still used as medicine, but the illness might best be described as affluenza: Almost half of users were treating hangovers, and another third were attempting to detoxify their body, in some cases mixing the powdered horn directly into wine to make a cocktail described in news articles as “the alcoholic drink of millionaires.” The story is much the same in China, where officials suspect that the coronavirus first passed to humans through an as-yet-unidentified wild animal. If you picture impoverished Chinese people eating any living thing they can get their hands on, think again. In today’s China, wild meat is frequently a delicacy and other animal products, like fur and traditional medicine, are luxuries; the trade has sharply increased, rather than decreased, with the nation’s rising wealth. (In February, China banned the sale of wild meat, with a loophole for medicinal products, but a lot of the trade was already underground.) Even in a country as impoverished as Zimbabwe, researchers found that hunters ate only a quarter of the meat they harvested, selling the rest to “people with cash incomes” who were “generally older and wealthier.”

Read: The price of protecting rhinos


CITES, the treaty body that governs international trade in wild plants and animals, first picked up on the trend in 2014. “We are seeing a disturbing shift in demand for some species from health to wealth,” John Scanlon, the secretary-general of the organization at the time, said. Wild meat, which had long been a dietary staple for many of the world’s poorer people, was morphing into a modern consumer luxury—a “positional good” that, like a Louis Vuitton handbag or Cartier watch, is used far less for its functional purpose than to signal identity, social belonging, and status. Threatened species were being eaten as a flash of conspicuous consumption by businessmen bonding on drunken sprees, by wealthy families showing respect to visitors, by urbanites hoping to reconnect with their rural roots.

Part of the reason Western conservationists expect countries with rising incomes to go easier on threatened species is that they believe their own countries did so in the past. But in the late 19th and early 20th centuries, commercial “market hunters” were still supplying mainly upper-class Americans with wild delicacies such as diamondback terrapin and canvasback duck even as—especially as—those species’ populations were being decimated. The trade slowed only with the advent of strictly enforced conservation laws. Rosaleen Duffy, a political ecologist at the University of Sheffield, argues that, again, the consumption of wildlife didn’t stop; it was transmuted. The United States and the United Kingdom are major importers of wildlife products; a study of eBay purchases found that the U.S. is the end destination for more than two-thirds of the traffic in protected species.


Even legal wild foods reflect a shift from strictly caloric to “elite” consumption. A 2018 study by an international team of fishery scientists looked at where fish caught in the world’s high seas—outside any nation’s jurisdiction—were going to market. Conservationists are concerned that the high seas are being overfished; fishery defenders reply that their fishing helps feed the hungry. In the end, the researchers found that the catch ranged from big-game species like tuna and swordfish (some of which have been reduced to 10 percent or less of their historical abundance) to an assortment of smaller fish, squid, and other sea creatures. The majority was feeding upscale consumers in places such as the United States, the European Union, and Japan. Several species were used almost entirely as feed for fish farms or pets (again, mainly in rich nations), while others were turned into nutraceuticals aimed not at combatting hunger or disease, but at optimizing the performance of already healthy people—to make us, as we say today, “better than well.”Melanie Lambrick

“All of us are consumers of wildlife in one way or another,” Duffy says. “We eat wildlife, we wear it as clothing and accessories, we consume it as medicine, and we buy ornaments made from it.”

The reasons for the manumea’s disappearance in Samoa are less rapacious: The bird is no longer deliberately hunted, but killed unintentionally. Yet it, too, is entangled in matters of prestige and identity. And the little dodo is on the verge—the very brink of the cusp—of extinction.


“Let me paint a picture of why it is so hard for people to say no to pigeon dishes,” Jesse Lee, a young chef with an interest in Samoan foodways, told me. “It’s a memory food; it’s the peak of all dishes. It’s the ultimate chicken soup.”

We were seated in his restaurant, Mi Amor, a farm-to-table joint in Apia that smells of lime leaves, coconut, tuna, and fresh lemongrass. Lee has eaten pigeon only a few times. In every case, it has been because his parents—his father is a matai—have received them as gifts. “It’s a mark of respect.”

Nearly every Samoan I spoke with had eaten pigeon, but a clear pattern emerged: How often and how recently they had eaten it tended to correlate with their wealth, power, and status. Fiame Naomi Mata’afa is about as prestigious as a figure can be in Samoa: Besides being the deputy prime minister and minister of natural resources and environment, Fiame holds a high matai title and is the daughter of the man whose hands literally lowered the flag of colonial rule to launch Samoa’s independence. (Note that in Samoa, matai titles are used in place of individuals’ surnames.) Fiame is also a spokesperson for a new campaign to save the manumea led by the Samoa Conservation Society and her ministry; in the campaign’s strategy document, she publicly applauds “all Samoans who have made the voluntary decision to forego the purchase, gifting, or eating of all pigeon until we can ensure that our Manumea is out of danger.” Yet when I asked where and when she had last eaten pigeon, she replied with candor. “Probably in cabinet. Probably last month,” she said. “The minister who usually brings it, he has a restaurant, so usually it arrives cooked.” The minister in question is Sala Fata Pinati, the minister of tourism.


Similarly, Seumaloisalafai Afele Faiilagi, who oversees manumea conservation at the environment ministry, acknowledges that he used to receive “a lot of lupe” because his father is the high matai of Uafato—the village where Serra and I first searched for manumea. “Because it is rare, people recognize that it is for the high chief,” Seumaloisalafai said. In Samoa, that can add up to a lot of pigeons: The country has 18,000 matai. Church leaders, too, often receive pigeon as gifts, or even request it as a favorite food. As Stirnemann put it, the well-to-do consumers in Samoa are typically a far cry from the global elite. “It’s not like wealthy-with-swimming-pools wealthy. It would just be your richer people in the average population.”

By comparison, Tu Alauni, a young woman raised in Apia, said that the only time she had tasted pigeon was when her mother, very ill, had arranged to buy a single bird, hoping it might improve her health. “It was the most important food in their times,” Alauni told me. She expected that the small piece of pigeon her mother shared with her would be a “once in a lifetime” experience—all the more so now that Alauni has actually seen a live manumea. In 2017, one perched alongside the terrace of her workplace, the Forest Cafe, which overlooks a jungle ravine in the mountains above the city. Alauni now feels personally invested in the fate of the manumea, and the café’s owners, who also saw the bird, are reforesting the area with native trees. Still, hunting takes place so close to the property that bird shot once fell out of the sky onto the café’s roof.


Poor people in Samoa have practical reasons for eating less pigeon. A single bird costs 15 Samoan tālā—enough money to buy a week’s worth of meals for a family. A box of shotgun shells costs 65 tālā, which could otherwise purchase four dress shirts, three backpacks for schoolchildren, or 13 whole chickens. Hunters I spoke with said that even their shells are now often paid for by wealthy buyers.

To be clear, hunting pigeons has been against the law in Samoa for more than 25 years. The law has not been enforced, however, and most Samoans consider it inoperative to the point that hunting and eating pigeon are spoken of freely. I encountered secrecy only once: After a professor told me he had dined on lupe the previous week at a resort, the hotel’s staff insisted they had never served the bird.

Wild pigeon is food in Samoa, but no one needs to eat pigeon. Sitting at Mi Amor, its doors and windows open in the evening heat, Lee said the perception of wild pigeon as something consumed, not merely eaten, could one day be the manumea’s salvation. “The next generation is not as interested in food, actually. They’re more interested in the next iPhone or the next Samsung—whatever the new technology is going to be,” Lee said. “If the next generation will prefer to get a gift of an iPhone instead, or some shoes, the pigeons probably won’t be too bothered.”

Of course, the manumea has to survive that long—which is anything but a sure bet.


Serra tells me that searching for the rarest of rare creatures takes not only perseverance, but faith. After days of fruitless trekking through Samoa’s wildest forests, I understand what he means. The idea that a manumea might appear just around the next corner begins to seem ridiculous, as though we were watching for shooting stars in the tiny clear patch of a night sky otherwise obscured by clouds. Every second seems essential—you can’t step off the trail to relieve yourself without keeping your eyes peeled—but at the same time hopeless. Carrying on, then, takes faith, or obsession. Serra’s favorite book, he tells me, is Moby-Dick.

So we ascend for hours into the clouds above the village of A’opo, on the north slope of Savai’i. The jungle is alive, teeming with birds, and in that single day we see or hear nearly all of the forest species in Samoa’s slim birdwatching guide. “All except one,” says Serra, as we finally descend in drenching, blood-warm rain. “Maybe we are documenting the extinction.”

The extinction. Most of us understand those words only in the abstract. To Serra, they’re personal. Serra, who currently lives in Florence, Italy, moved to Samoa in 2012 to run conservation projects with the United Nations’ Environment Programme and Global Environment Facility across the South Pacific. After four years, he returned to the field as a freelance manumea researcher, working for Samoa’s ministry of the environment, among others. But his immersion in critically endangered species began nearly 20 years ago with the northern bald ibis, when he traced ghostly sightings by Bedouin nomads and local hunters to a small colony in Syria. At the time, the black, cranelike bird—once widespread across North Africa, southeastern Europe, and the Middle East—was known to nest only in Morocco; there hadn’t been a verified sighting in Syria since the 1930s. Serra and his Syrian and Bedouin colleagues found seven birds. He then watched as all these remaining ibises were lost in subsequent years, mainly to hunting.


The idea that Serra may witness another disappearance—the global extinction of the manumea—weighs on him. Yet he doesn’t even know, really, where to look for the bird. Contradictory reports have been the norm since the earliest written accounts. Sometimes the manumea is described as a bird of the high cloud forests, sometimes of the coastal lowlands; the last known photograph of the species was taken in 2013, in the parking lot of a resort near the busiest town on Savai’i. Some have said the manumea prefers, like its cousin the dodo, to peck about on the ground; others, that it never leaves the treetops. “Who knows?” Serra says. “Total speculations.”

Because manumea are hard to see, estimates of how many remain have depended in part on where they’ve been heard. But when Serra tested 10 expert bird hunters, he found that even most of them could not consistently identify the bird by its recorded call. (The manumea’s only known call is a softly rising and falling sound—mmmMMMmmm—like a cow on a foggy morning; it is thought to be slightly lower in pitch and subtly different in rhythm than a similar call made by the lupe.) The idea that 200 birds remain is, Serra says, little more than a guess. The number could be higher, or much, much lower. “We may be searching for the last 10, or 15.”

If the manumea does go extinct, the last one could die something like this: On a hunt when he was 17 years old, a man named Norman Paul saw the silhouette of a pigeon on a telephone wire, and shot at it. He was startled to discover that what he had gunned down was not a lupe, but a bird he had never seen before. Immediately, he regretted the kill—something special had died by his hand. Today, some 45 years later, he runs a hotel on the mountainside where he shot the bird. It is called Le Manumea, in memoriam, and tourists there gather in an atmosphere of thatch and tiki, unaware of the lingering sadness captured by the resort’s name. A sign at the entrance promises happy hour all day.


On the basis of confirmed sightings, Serra now estimates that a person looking for the manumea could expect to spot one only every three to five years. “There is a Tasmanian-tiger aspect to the manumea,” he says, referring to the wolflike marsupial that probably went extinct in Tasmania in 1936, but is still regularly, if unreliably, reported to exist in the wild. “As people become aware of the manumea, they desire to see it.” A radio station once contacted the environment ministry to report that a listener had brought a manumea into the studio. It proved to be the fiaui, or white-throated pigeon, a bird often mistaken for the manumea. Serra and I have seen plenty of them.

The first campaign to save the manumea was launched in 1993. It was funded by Rare, an American organization that promotes local pride in endangered species, but otherwise took a grassroots approach—including school puppet shows and a manumea-friendly sermon for Samoa’s many, many churches—led by government environmental staff. Fourteen years passed before the next big conservation drive, followed again by a long lapse.

Today’s effort to save the manumea, then, is beginning almost from scratch. Samoa has dedicated conservationists (the head parks and reserves officer, Moeumu Uili, teared up as she recounted capturing the manumea on film in 2013), but money and resources are hard to come by in a nation with the same population as Yonkers, New York—and in a world replete with endangered species that need help. This time, international partners include BirdLife, the Auckland Zoo, and the New Zealand government.


Hunting is certainly not the only threat facing the bird. Most evidence points to manumea preferring lowland forests, 80 percent of which have been logged, built over, or cleared for the family farms that Samoans call plantations. Then there are invasive species such as rats and cats, which count the manumea among their prey. The first documented observations of manumea in the wild, written in gorgeously hurried cursive by the naturalist and explorer Titian Peale in the late 1840s, were also the first to predict the bird’s extinction:


A few years since a passion arose for cats, and they were obtained by all possible means from the whale ships visiting the islands … Pussy (a name generally adopted by the Polynesians for cats), not liking yams and taro, the principal food of the islanders, preferred Manu-mea, and took to the mountains in pursuit of them. There the cats have multiplied and become wild, and live upon our Didunculus, or Little Dodo, the Manu-mea of the natives, which, it is believed, will, in a very few years, cease to be known.

The manumea has outlived expectations by more than 170 years—but barely. In 2014, its global conservation status was downgraded from endangered to critically endangered, meaning “intensive conservation actions” are needed to prevent its extinction.

Read: The quiet disappearance of birds in North America

The international team met in Samoa in October 2019 to decide on those actions, all of which were abruptly postponed when a deadly measles outbreak was declared a national emergency in November. The Samoan government’s top priority for the manumea’s recovery, according to Seumaloisalafai, will be to pursue Serra’s research into the bird’s call. If the manumea’s vocal imprint can be distinguished from the lupe’s through digital analysis, scientists could distribute sensors throughout the islands and collect the best data yet on where the birds are and how many remain.


Also key to the recovery plan is developing and supporting a network of manumea-friendly villages (there are already six) that commit to protecting their forests and banning hunting. The Auckland Zoo, meanwhile, is prepared to provide training and support for rat-killing programs in village forests. The zoo will also study the feasibility of a captive-breeding facility in Samoa, its first great challenge being the fact that, as one manumea researcher put it, “the difficulty throughout the present century has been to find even single representatives of the species.”

Pigeon hunting is a practice that can be addressed cheaply and immediately—at least in theory. With Samoa’s measles crisis now over, a marketing campaign starting in April will first draw attention to the manumea’s plight before calling on Samoans to ban the shooting, trading, and eating of pigeon. The goal is to reduce pigeon consumption by a quarter this year. “I don’t think the bird will be saved by the hunting issue alone,” said James Atherton, who is of British and Samoan descent and helped found the Samoa Conservation Society seven years ago, “but it’s the one thing that every Samoan can do to save the manumea.”

Still, asking Samoans to stop eating pigeon is as fraught with complexity as asking the world’s wealthy consumers to give up their favorite seafood. Seiuli Vaifou Aloalii Temese, head of the Centre for Samoan Studies at the National University of Samoa, pulled back the layers of meaning associated with pigeons. She told me about memories of her father hunting for lupe before White Sunday when she was a girl, and always giving one bird to the pastor before preparing the rest. They would share those meals with neighbors who had no lupe to eat, dishing out the best portions to the chiefs. Pigeon hunting has even been woven into the language. A meeting might open with a phrase like Ua malumaunu le fogatia, which translates as “The star mound is made sacred by the lupe that gather there,” or an attractive woman might be described in casual conversation as a “lupe.”


“They feel very Samoan when they eat the lupe. It is also nice to eat the lupe. They will think of those proverbs when they eat the lupe,” Seiuli Vaifou said. “This is why the lupe hunting is so important.”

I heard another story that put it more bluntly. After a workshop for the save-the-manumea campaign, one visiting conservationist, feeling buoyant about the bird’s future, went to a nearby market and told a vendor about the plan to discourage people from eating pigeon. “But,” the vendor said in disbelief, “it’s like cocaine to some people!”

Serra and i may have possibly, finally, caught a glimpse of the manumea. We had traveled to Tafua-tai, a brightly painted village laid out beneath the emerald saddle of a volcanic crater. As one story would have it, the entire village was won by the ancestors of its current inhabitants—in a pigeon-catching contest.

Tafua-tai offers reasons for optimism. For one, it is a manumea-friendly village. For another, the famous 2013 photo of the bird was taken nearby. Also, we are guided by Tuluiga Ulu Anoa’i, whose grandfather, as a high matai in the late 1980s, convinced the community to protect its forest from development. Ulu Anoa’i, who has a keen eye for forest wildlife, might be the person to have most recently sighted a manumea—just two months ago, at the crater’s edge. Because she had never seen one before, however, she can’t be absolutely certain.


During an extended trip to the volcano, we see wonderful things—the many-colored fruit dove is as beautiful as its name suggests—but not our little dodo. Then Ulu Anoa’i takes us to hear the remarkable claims of her uncle, Tiaalii Matauaina. He is a barrel of a man, with the dramatic, wide-eyed facial expressions of a mustachioed Rodney Dangerfield. Sitting in a yellow lavalava sarong and polo shirt in front of his home, he tells us he sees manumea in the forest frequently—sometimes even in his garden. His most recent sighting was three or four days ago. “If I kill a manumea, we can give it to you,” he says. It’s hard to tell whether he’s joking.

Tiaalii agrees to take us to the places where he sees manumea most often. First, though, we have to wait out the heat of the afternoon. “In the morning, the light here is magnificent; it is like the dawn of creation,” Serra says. “At midday, it is hostile. It is hell.” At last, with the lowering sun, the birding hour arrives: As we set out, patches of forest are trilling and cooing with pigeons and doves. Once, Tiaalii thinks he hears the manumea’s call, but he isn’t sure. At last, we turn up a narrow path through a green delirium.

“One day, here—four, five manumea,” Tiaalii says, gesturing as though his hands were birds bursting from the bush. We carry on toward a towering tree.

“Manumea!” Tiaalii cries. His powerful right hand seizes me by the scruff of my neck and directs my head to a spot in the sky. There, a pigeon-size bird hurtles overhead, a black silhouette against the blue. A moment later it’s gone.


Serra, coming up from behind, caught only the briefest glimpse. “What a difficult bird,” he says, and proceeds to ask Tiaalii for details about what he had seen.

“The color!” says Tiaalii, eyes bulging. “Blue, red, and bit of black!” With his hands he makes a large, hooked beak, opening and closing. “Psh psh psh.”

So there you have it: An experienced local with an eye for birds has found us our manumea. Also possible, though, is that he wants rather badly to be the one to help us find the bird, or that he feels our longing, and the fast approach of twilight, and wants us to go home happy. It is hard to imagine that there had been time, in the brief moment when the bird flushed from the tree and crossed overhead, for Tiaalii to see the color and detail he claimed. Even he, ultimately, seems unconvinced.

To see a manumea, or to save one, is bound up in memory and desire. “My left brain doesn’t believe him, but my right brain wants to believe him,” Serra says. He is not prepared to add this to his list of probable sightings in the field.

A few days later, our search over, we sit at the edge of Apia’s harbor with James Atherton, of the Samoa Conservation Society. Reviewing our efforts, Serra concludes they had been “quite representative” and “quite depressing.”

“This bird,” Serra says, “it’s impossible to see.”

“Well, that’s why we’re working so hard to save this very rare bird,” Atherton replies.

Serra looks out to where the waves break over the twilight reef with a dull and constant roar, like the engine of the world. “I think we’d better hurry up a little,” he says.

J. B. MACKINNON is a writer based in Vancouver, Canada. His work has appeared in The New Yorker, National Geographic, and Nautilus. He is the author of The Once and Future World.

Discovery challenges nuclear theory

Researchers test the way we understand forces in the universe

Date:April 1, 2020

Source:University of Massachusetts Lowell

A discovery by a team of researchers led by UMass Lowell nuclear physicists could change how atoms are understood by scientists and help explain extreme phenomena in outer space.

The breakthrough by the researchers revealed that a symmetry that exists within the core of the atom is not as fundamental as scientists have believed. The discovery sheds light on the forces at work within the atoms' nucleus, opening the door to a greater understanding of the universe. The findings were published today in Nature, one of the world's premier scientific journals.

The discovery was made when the UMass Lowell-led team was working to determine how atomic nuclei are created in X-ray bursts -- explosions that happen on the surface of neutron stars, which are the remnants of massive stars at the end of their life.

"We are studying what happens inside the nuclei of these atoms to better understand these cosmic phenomena and, ultimately, to answer one of the biggest questions in science -- how the chemical elements are created in the universe," said Andrew Rogers, UMass Lowell assistant professor of physics, who heads the research team.

The research is supported by a $1.2 million grant from the U.S. Department of Energy to UMass Lowell and was conducted at the National Superconducting Cyclotron Laboratory (NSCL) at Michigan State University. At the lab, scientists create exotic atomic nuclei to measure their properties in order to understand their role as the building blocks of matter, the cosmos and of life itself.

Atoms are some of the smallest units of matter. Each atom includes electrons orbiting around a tiny nucleus deep within its core, which contains almost all its mass and energy. Atomic nuclei are composed of two nearly identical particles: charged protons and uncharged neutrons. The number of protons in a nucleus determines which element the atom belongs to on the periodic table and thus its chemistry. Isotopes of an element have the same number of protons but a different number of neutrons.

At the NSCL, nuclei were accelerated to near the speed of light and smashed apart into fragments creating strontium-73 -- a rare isotope that is not found naturally on Earth but can exist for short periods of time during violent thermonuclear X-ray bursts on the surface of neutron stars. This isotope of strontium contains 38 protons and 35 neutrons and only lives for a fraction of a second.

Working around the clock over eight days, the team created more than 400 strontium-73 nuclei and compared them to the known properties of bromine-73, an isotope that contains 35 protons and 38 neutrons. With interchanged number of protons and neutrons, bromine-73 nuclei are considered "mirror partners" to strontium-73 nuclei. Mirror symmetry in nuclei exists because of the similarities between protons and neutrons and underlies scientists' understanding of nuclear physics.

Roughly every half-hour, the researchers created one strontium-73 nucleus, transported it through the NSCL's isotope separator and then brought the nucleus to a stop at the center of a complex detector array where they could observe its behavior. By studying the radioactive decay of these nuclei, the scientists found that strontium-73 behaved entirely differently from bromine-73. The discovery raises new questions about nuclear forces, according to Rogers.

"Strontium-73 and bromine-73 should appear identical in structure, but surprisingly do not, we found. Probing symmetries that exist in nature is a very powerful tool for physicists. When symmetries break down, that tells us something's wrong in our understanding, and we need to take a closer look," Rogers said.

What the scientists saw will challenge nuclear theory, according to Daniel Hoff, a UMass Lowell research associate who was the lead author of the article published in Nature.

"Comparing strontium-73 and bromine-73 nuclei was like looking in a mirror and not recognizing yourself. Once we convinced ourselves that what we were seeing was real, we were very excited," Hoff said.

Along with Rogers, a Somerville resident, and Hoff of Medford, the UMass Lowell team included Physics Department faculty members Assistant Prof. Peter Bender, Emeritus Prof. C.J. Lister and former UMass Lowell research associate Chris Morse. Physics graduate students Emery Doucet of Mason, N.H., and Sanjanee Waniganeththi of Lowell also contributed to the project.

As part of the team's study, state-of-the-art theoretical calculations were carried out by Simin Wang, a research associate at Michigan State, and directed by Witold Nazarewicz, MSU's John A. Hannah Distinguished Professor of Physics and chief scientist at the Facility for Rare Isotope Beams (FRIB), which will open next year.

The researchers' work "offers unique insights into the structure of rare isotopes," Nazarewicz said. "But much still remains to be done. New facilities coming online, such as FRIB at MSU, will provide missing clues into a deeper understanding of the mirror symmetry puzzle. I am glad that the exotic beams delivered by our facility, unique instrumentation and theoretical calculations could contribute to this magnificent work."

Plans for more experiments are already underway, as the researchers seek to refine and confirm their observations and study these isotopes further.

Story Source:
Materials provided by University of Massachusetts Lowell.

Journal Reference:
D. E. M. Hoff, A. M. Rogers, S. M. Wang, P. C. Bender, K. Brandenburg, K. Childers, J. A. Clark, A. C. Dombos, E. R. Doucet, S. Jin, R. Lewis, S. N. Liddick, C. J. Lister, Z. Meisel, C. Morse, W. Nazarewicz, H. Schatz, K. Schmidt, D. Soltesz, S. K. Subedi, S. Waniganeththi. Mirror-symmetry violation in bound nuclear ground states. Nature, 2020; 580 (7801): 52 DOI: 10.1038/s41586-020-2123-1


Cite This Page:
University of Massachusetts Lowell. "Discovery challenges nuclear theory: Researchers test the way we understand forces in the universe." ScienceDaily. ScienceDaily, 1 April 2020. .

MUTUAL AID
Black rhinos eavesdrop on the alarm calls of hitchhiking oxpeckers to avoid humans

Date:April 9, 2020

Source:Cell Press

In Swahili, red-billed oxpeckers are called Askari wa kifaru, or "the rhino's guard." Now, a paper appearing April 9 in the journal Current Biology suggests that this indigenous name rings true: red-billed oxpeckers may act as a first line of defense against poachers by behaving like sentinels, sounding an alarm to potential danger. By tracking wild black rhinos, researchers found that those carrying oxpeckers were far better at sensing and avoiding humans than those without the hitchhiking bird.

While conservation efforts have rebounded the critically endangered black rhino's numbers, poaching remains a major threat. "Although black rhinos have large, rapier-like horns and a thick hide, they are as blind as a bat. If the conditions are right, a hunter could walk within five meters of one, as long as they are downwind," says Roan Plotz (@RoanPlotz), a lecturer and behavioral ecologist at Victoria University, Australia., who co-authored the paper with ecological scientist Wayne Linklater (@PolitEcol) of California State University -- Sacramento. Oxpeckers, which are known to feed on the ticks and lesions found on the rhino's body, may make up for the rhino's poor eyesight by calling out if they detect an approaching human.

To study the role that oxpeckers might play, Plotz and his team recorded the number of oxpeckers on two groups of the rhinos they encountered. Rhinos tagged with radio transmitters -- which allowed researchers to track them while evading detection from oxpeckers -- carried the bird on their backs more than half the time. The untagged black rhinos they found, on the other hand, carried no oxpeckers most of the time -- suggesting that other untagged rhinos that carried the birds might have avoided encountering the researchers altogether. "Using the differences we observed between oxpeckers on the tagged versus untagged rhinos, we estimated that between 40% and 50% of all possible black rhino encounters were thwarted by the presence of oxpeckers," says Plotz.


Even when the researchers were able to locate the tagged rhinos, the oxpeckers' alarm calls still appeared to play a role in predator defense. The field team ran a "human approach" experiment, where one researcher would walk towards the rhino from crosswind while a colleague recorded the rhino's behavior. The field team recorded the number of oxpecker carried, the rhinos' behavior upon approach, and the distance of the researcher when either the rhinos became vigilant or, if undetected, it became unsafe to get any closer.

"Our experiment found that rhinos without oxpeckers detected a human approaching only 23% of the time. Due to the bird's alarm call, those with oxpeckers detected the approaching human in 100% of our trials and at an average distance of 61 meters -- nearly four times further than when rhinos were alone. In fact, the more oxpeckers the rhino carried, the greater the distance at which a human was detected," he says. He adds that these improved detection and distance estimates may even be conservative, because they don't take into account the untagged rhinos carrying oxpeckers that the team could not detect.

When a rhino perceived the oxpecker alarm call, it nearly always re-oriented itself to face downwind -- their sensory blind spot. "Rhinos cannot smell predators from downwind, making it their most vulnerable position. This is particularly true from humans, who primarily hunt game from that direction," says Plotz.

Taken together, these results suggest that oxpeckers are effective companions that enable black rhinos to evade encounters with people and facilitate effective anti-predator strategies once found. Some scientists even hypothesize that oxpeckers evolved this adaptive behaviour as a way to protect their source of food: the rhinos.

"Rhinos have been hunted by humans for tens of thousands of years, but the species was driven to the brink of extinction over the last 150 years. One hypothesis is that oxpeckers have evolved this cooperative relationship with rhinos relatively recently to protect their food source from human overkill," says Plotz.

Despite this closely tied relationship, oxpecker populations have significantly declined, even becoming locally extinct in some areas. As a result, most wild black rhino populations now live without oxpeckers in their environment. But based on the findings in this study, reintroducing the bird back into rhino populations may bolster conservation efforts. "While we do not know that reintroducing the birds would significantly reduce hunting impacts, we do know oxpeckers would help rhinos evade detection, which on its own is a great benefit," says Plotz.

Plotz says that these findings, inspired by a Swahili name, also highlight the importance of local knowledge. "We too often dismiss the importance of indigenous people and their observations. While western science has been incredibly useful, there are many insights we can learn from indigenous communities."

Story Source:
Materials provided by Cell Press. 

Journal Reference:
Roan D. Plotz, Wayne L. Linklater. Oxpeckers Help Rhinos Evade Humans. Current Biology, 2020; DOI: 10.1016/j.cub.2020.03.015

Cite This Page:
Cell Press. "Black rhinos eavesdrop on the alarm calls of hitchhiking oxpeckers to avoid humans." ScienceDaily. ScienceDaily, 9 April 2020. .

New fossil from Brazil hints at the origins of the mysterious tanystropheid reptiles

New species named after Tolkien's Aragorn hints at early southern evolution for these reptiles

A new species of Triassic reptile from Brazil is a close cousin of a mysterious group called tanystropheids

Date:April 8, 2020

Source:PLOS

A new species of Triassic reptile from Brazil is a close cousin of a mysterious group called tanystropheids, according to a study published April 8, 2020 in the open-access journal PLOS ONE by Tiane De-Oliviera of the Federal University of Santa Maria, Brazil and colleagues.

After the Permian mass extinction, 250 million years ago, reptiles took over global ecosystems. Among the early groups to appear after this extinction event were the tanystropheids, a group of long-necked animals whose lifestyles are still mysterious, but who were nonetheless successful in the Triassic Period. However, the early evolution of this group is poorly understood, as their remains are very rare from the Early Triassic.

In this study, De-Oliviera and colleagues describe a new specimen of reptile from Early Triassic rocks of the Sanga do Cabral Formation in southern Brazil. Skeletal comparison indicates this specimen, known from remains of the hind leg, pelvis, and tail, is the closest known relative of tanystropheids. The researchers identified these remains as belonging to a new species, which they named Elessaurus gondwanoccidens. The name derives in part from the Elvish name (Elessar) of a character from Lord of the Rings also known as Aragorn or Strider, chosen as a reference to the fossil animal's long legs.

Most tanystropheid fossils are found in Middle to Late Triassic rocks of Europe, Asia, and North America, and often in marine sediments. The presence of Elessaurus in continental deposits of Early Triassic South America suggests that the origins of this group may lie in the southern continents, and that their ancestors may have lived on land before later species adapted to aquatic life. A clearer view of the group's origins will rely on more rare fossils from this early time in their evolution.


Story Source:
Materials provided by PLOS. Note: Content may be edited for style and length.

Journal Reference:
Tiane M. De-Oliveira, Felipe L. Pinheiro, Átila Augusto Stock Da-Rosa, Sérgio Dias-Da-Silva, Leonardo Kerber. A new archosauromorph from South America provides insights on the early diversification of tanystropheids. PLOS ONE, 2020; 15 (4): e0230890 DOI: 10.1371/journal.pone.0230890


Cite This Page:
PLOS. "New fossil from Brazil hints at the origins of the mysterious tanystropheid reptiles: New species named after Tolkien's Aragorn hints at early southern evolution for these reptiles." ScienceDaily. ScienceDaily, 8 April 2020. .

Smartphone videos produce highly realistic 3D face reconstructions

Method foregoes expensive scanners, camera setups, studios

Date:April 1, 2020

Source:Carnegie Mellon University

Normally, it takes pricey equipment and expertise to create an accurate 3D reconstruction of someone's face that's realistic and doesn't look creepy. Now, Carnegie Mellon University researchers have pulled off the feat using video recorded on an ordinary smartphone.

Using a smartphone to shoot a continuous video of the front and sides of the face generates a dense cloud of data. A two-step process developed by CMU's Robotics Institute uses that data, with some help from deep learning algorithms, to build a digital reconstruction of the face. The team's experiments show that their method can achieve sub-millimeter accuracy, outperforming other camera-based processes.

A digital face might be used to build an avatar for gaming or for virtual or augmented reality, and could also be used in animation, biometric identification and even medical procedures. An accurate 3D rendering of the face might also be useful in building customized surgical masks or respirators.

"Building a 3D reconstruction of the face has been an open problem in computer vision and graphics because people are very sensitive to the look of facial features," said Simon Lucey, an associate research professor in the Robotics Institute. "Even slight anomalies in the reconstructions can make the end result look unrealistic."

Laser scanners, structured light and multicamera studio setups can produce highly accurate scans of the face, but these specialized sensors are prohibitively expensive for most applications. CMU's newly developed method, however, requires only a smartphone.

The method, which Lucey developed with master's students Shubham Agrawal and Anuj Pahuja, was presented in early March at the IEEE Winter Conference on Applications of Computer Vision (WACV) in Snowmass, Colorado. It begins with shooting 15-20 seconds of video. In this case, the researchers used an iPhone X in the slow-motion setting.

"The high frame rate of slow motion is one of the key things for our method because it generates a dense point cloud," Lucey said.

The researchers then employ a commonly used technique called visual simultaneous localization and mapping (SLAM). Visual SLAM triangulates points on a surface to calculate its shape, while at the same time using that information to determine the position of the camera. This creates an initial geometry of the face, but missing data leave gaps in the model.

In the second step of this process, the researchers work to fill in those gaps, first by using deep learning algorithms. Deep learning is used in a limited way, however: it identifies the person's profile and landmarks such as ears, eyes and nose. Classical computer vision techniques are then used to fill in the gaps.

"Deep learning is a powerful tool that we use every day," Lucey said. "But deep learning has a tendency to memorize solutions," which works against efforts to include distinguishing details of the face. "If you use these algorithms just to find the landmarks, you can use classical methods to fill in the gaps much more easily."

The method isn't necessarily quick; it took 30-40 minutes of processing time. But the entire process can be performed on a smartphone.

In addition to face reconstructions, the CMU team's methods might also be employed to capture the geometry of almost any object, Lucey said. Digital reconstructions of those objects can then be incorporated into animations or perhaps transmitted across the internet to sites where the objects could be duplicated with 3D printers.


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Carnegie Mellon University. "Smartphone videos produce highly realistic 3D face reconstructions: Method foregoes expensive scanners, camera setups, studios." ScienceDaily. ScienceDaily, 1 April 2020. .

Astronomers use slime mould to map the universe's largest structures

The behaviour of one of nature's humblest creatures and archival data from the NASA/ESA Hubble Space Telescope are helping astronomers probe the largest structures in the Universe

Date:March 26, 2020

Source: ESA/Hubble Information Centre

The single-cell organism known as slime mould (Physarum polycephalum) builds complex web-like filamentary networks in search of food, always finding near-optimal pathways to connect different locations.

In shaping the Universe, gravity builds a vast cobweb-like structure of filaments tying galaxies and clusters of galaxies together along invisible bridges of gas and dark matter hundreds of millions of light-years long. There is an uncanny resemblance between the two networks, one crafted by biological evolution, the other by the primordial force of gravity.

The cosmic web is the large-scale backbone of the cosmos, consisting primarily of dark matter and laced with gas, upon which galaxies are built. Even though dark matter cannot be seen, it makes up the bulk of the Universe's material. Astronomers have had a difficult time finding these elusive strands, because the gas within them is too dim to be detected.

The existence of a web-like structure to the Universe was first hinted at in galaxy surveys in the 1980s. Since those studies, the grand scale of this filamentary structure has been revealed by subsequent sky surveys. The filaments form the boundaries between large voids in the Universe. Now a team of researchers has turned to slime mould to help them build a map of the filaments in the local Universe (within 100 million light-years of Earth) and find the gas within them.

They designed a computer algorithm, inspired by the behaviour of slime mould, and tested it against a computer simulation of the growth of dark matter filaments in the Universe. A computer algorithm is essentially a recipe that tells a computer precisely what steps to take to solve a problem.

The researchers then applied the slime mould algorithm to data containing the locations of over 37,000 galaxies mapped by the Sloan Digital Sky Survey. The algorithm produced a three-dimensional map of the underlying cosmic web structure.

They then analysed the light from 350 faraway quasars catalogued in the Hubble Spectroscopic Legacy Archive. These distant cosmic flashlights are the brilliant black-hole-powered cores of active galaxies, whose light shines across space and through the foreground cosmic web. Imprinted on that light was the telltale signature of otherwise invisible hydrogen gas that the team analysed at specific points along the filaments. These target locations are far from the galaxies, which allowed the research team to link the gas to the Universe's large-scale structure.

"It's really fascinating that one of the simplest forms of life actually enables insights into the very largest-scale structures in the Universe," said lead researcher Joseph Burchett of the University of California (UC), U.S.A. "By using the slime mould simulation to find the location of the cosmic web filaments, including those far from galaxies, we could then use the Hubble Space Telescope's archival data to detect and determine the density of the cool gas on the very outskirts of those invisible filaments. Scientists have detected signatures of this gas for over half a century, and we have now proven the theoretical expectation that this gas comprises the cosmic web."

The survey further validates research that indicates intergalactic gas is organised into filaments and also reveals how far away gas is detected from the galaxies. Team members were surprised to find gas associated with the cosmic web filaments more than 10 million light-years away from the galaxies.

But that wasn't the only surprise. They also discovered that the ultraviolet signature of the gas gets stronger in the filaments' denser regions, but then disappears. "We think this discovery is telling us about the violent interactions that galaxies have in dense pockets of the intergalactic medium, where the gas becomes too hot to detect," Burchett said.

The researchers turned to slime mould simulations when they were searching for a way to visualise the theorised connection between the cosmic web structure and the cool gas, detected in previous Hubble spectroscopic studies.

Then team member Oskar Elek, a computer scientist at UC Santa Cruz, discovered online the work of Sage Jenson, a Berlin-based media artist. Among Jenson's works were mesmerizing artistic visualisations showing the growth of a slime mould's tentacle-like network of structures moving from one food source to another. Jenson's art was based on scientific work from 2010 by Jeff Jones of the University of the West of England in Bristol, which detailed an algorithm for simulating the growth of slime mould.

The research team was inspired by how the slime mould builds complex filaments to capture new food, and how this mapping could be applied to how gravity shapes the Universe, as the cosmic web constructs the strands between galaxies and galaxy clusters. Based on the simulation outlined in Jones's paper, Elek developed a three-dimensional computer model of the buildup of slime mould to estimate the location of the cosmic web's filamentary structure.

This analysis of the cosmic web in the local Universe also dovetails with observations published last autumn in the journal Science of the Universe's filamentary structure much farther away, about 12 billion light-years from Earth, near the Universe's beginning. In that study, astronomers analysed the energetic light from a young galaxy cluster illuminating the filaments of hydrogen gas connecting it.

The team's paper will appear in the Astrophysical Journal Letters.

Story Source:
Materials provided by ESA/Hubble Information Centre. Note: Content may be edited for style and length.

Journal Reference:
Joseph N. Burchett, Oskar Elek, Nicolas Tejos, J. Xavier Prochaska, Todd M. Tripp, Rongmon Bordoloi, Angus G. Forbes. Revealing the Dark Threads of the Cosmic Web. The Astrophysical Journal, 2020; 891 (2): L35 DOI: 10.3847/2041-8213/ab700c
ESA/Hubble Information Centre. "Astronomers use slime mould to map the universe's largest structures." ScienceDaily. ScienceDaily, 26 March 2020. .