wricing about pangenomes
welcome to A Teetering Vulture! a newsletter about various science stuff as well as the life happenings of its author, Taylor.
[Note: this article contains spoilers for season two of the Star Wars series Andor]
Imagine 42,813 cups of rice—uncooked, the grains the color and size of your choice of rice variety. Jasmine, basmati, sushi, brown; short-grain, long-grain. Alternatively, imagine 8,562,600 grams (18,877 pounds) of rice—the approximate equivalent amount in weight.
If you collected them all into one receptacle, imagine how satisfying it would be to bury your hands–clean, of course–into them. The feel of one of, if not the, most important little plant for humanity’s survival and persistence on earth. Oryza sativa, Asian cultivated rice. In the Order Poales, the order of grasses, bromeliads, sedges, rushes.
42,813 cups of rice is roughly equivalent to 400,000,000 grains of rice, which is roughly equivalent to the number of nucleotide base pairs in the rice genome. Nucleotide bases, those molecular bricks that build the home of each living thing’s core self: our DNA, our genome.
(I gleaned the number 42,813 after averaging five different counts of rice grains per cup, the counts themselves courtesy of five separate TikTok bros of questionable sanity. So, imbibe my numbers alongside appropriate quantities of caution—the important thing here is envisaging 400 million grains of rice, which is indeed the true size of the rice genome.)
The genome of rice is fairly small, relatively speaking. The human genome is composed of three billion nucleotide base pairs, for instance. The coastal redwood genome is composed of twenty-six and a half billion, and the largest known genome of any living thing belongs to a small fern. The genome of Tmesipteris oblanceolata, the New Caledonian fork fern, contains 160 billion base pairs.
Genomics is the study of an organism’s complete sequence of DNA: the full compendium of a living thing’s genetic material, along with the functions of genes (functional genomics), and the structure of the entire sequence connected together in double helix-shaped molecules built primarily of these organic chemical components called nucleotides (structural genomics). Scientists working in the field of genomics must be obsessed, to one degree or another, with specificity. With teasing apart differences, identifying, sorting into specifics. Genome researchers know the importance of beholding every facet of a living thing’s DNA. To study the molecular, the invisible, in such a meticulous way, to catalogue and categorize billions of aspects of genetic material, is an exercise–perhaps more like an extreme sport–in paying attention to detail.
The human penchant to find satisfaction in specifics—in studying, collecting, storing, and archiving details of our existence. I think it’s one of our best traits. And there is also, to me, even as a writer and not a geneticist, a psychological satisfaction I feel at imagining all the DNA of one organism sequenced, assembled, analyzed. It’s all here! Look at all of this! In some ways it feels similar to the tactile satisfaction of sticking my hands into a bunch of rice. It feels very human, very intrinsically animal in the way that we are.
Words like specificity, specify, and specific originated from the Latin species: a particular kind, type, appearance—which in turn is kin to the Latin verb specere: to look, to see, to behold. When we aim to be specific, in any sense, we aim to see, or to relay accurately what, precisely, we have already seen. Specificity ensures one thing is not being mistaken for another; the concept itself seems borne by a recognition that problems could arise if things are misclassified. When something is not seen as it truly is, when its details are not gazed upon with an awareness of them, knowledge is missed out on, knowledge that could help, delight, or amaze. Specificity in this way accompanies truth. These two are inextricable. A person cannot be specific without depositing a layer of truth somewhere, a sediment composed of some kind of knowledge.
And what is science except a landscape being built layer-by-layer, sediment-by-sediment—a global, collaborative construction project intended to protect and enrich our lives, our planet?
This essay is about scientists studying the genomes of rice. Specifically, it’s about scientists’ efforts to build a rice pangenome, which is a collection of many rice genomes, one that captures much of the genetic diversity present within this single kind of plant. For, with rice as with other organisms, one individual’s genome cannot be representative of its entire species. Almost all individuals have some percentage of genetic divergence from every other living thing. Humans possess genetic differences from one another: it’s what gives us our individuality. Every other species, too, has different forms, traits, versions of genes, varying structural characteristics of their genetic architecture. These differences lead to different capacities to live and survive and reproduce in a given environment. Studying these differences can be beneficial or interesting for all sorts of reasons. The opportunities to uncover specifics are nigh on endless, in the realm of genetics. There exists billions of years worth of novel genetic details within every organic being, incalculable—and new details are birthed on our planet every day.
Over half the global population depends on rice as a staple food. Our planet grows a lot of rice, and it needs to begin growing more, efficiently, sustainably. 112 million metric tons more, specifically. By 2035. On a smaller area of land than we are cultivating rice currently.
Earth’s human population is growing, our climate and environments are changing. It is important that we find ways to sustainably increase rice yields and prevent rice from succumbing to ever more present biotic and abiotic stresses, from infestations of rice pests like planthoppers, to diseases fungal and bacterial, to meteorological events like droughts and storms.
The process of domestication involves a reduction in genetic diversity. Traits favorable or desirable are chosen when animals or plants are bred, and slowly a reliable yet narrow suite of genetic varieties becomes ubiquitous. This makes domestic populations vulnerable; low genetic diversity is resoundingly a weakness. One plant felled by disease in a field of morphologically and genotypically uniform plants portends a cataclysm for the rest of them.
In the wild, rice is unfettered by the lack of human control. Rice populations are diverse; in the many regions of the world where wild rice grows, different environments favor different traits, different genes, or versions of genes. Genes are passed around via random plant reproduction and dispersal of seeds; selective pressures are changing allele frequencies within populations, working to preserve and reduce and eliminate certain mutations. Evolution is occurring, slowly, as it does. Genetic diversity is a boon to a species—it is critical to their ability to be resilient in the face of a diverse and challenging world. In this way rice and every other wild species manages travails ranging from predation and competition and disease, to severe weather events and changing climate and habitat loss.
Oryza sativa was domesticated from its wild progenitor Oryza rufipogon. Still growing and surviving in variegated conditions and environs around the world, O. rufipogon is in essence a critical genetic reservoir: the genes that help wild rice fend off pests and stress could, if harnessed in cultivated rice breeding and genetic engineering, assist human efforts to grow more cultivated rice in the coming decades, rice that is resistant against challenges for which it currently has no genetic tools to contend.
But, what are those genes? And where are they located in wild rice genomes? Which wild rice populations are likely to house them?
A team of researchers working as part of the National Center for Gene Research at the Shanghai Institute of Plant Physiology and Ecology of the Chinese Academy of Sciences, and the National Institute of Genetics in Mishima, Japan, understood that these questions might be best further investigated if they could create a pangenome. They sequenced, assembled, and analyzed the genomes of 145 genetically diverse varieties of rice, 129 O. rufipogon and 16 O. sativa, creating the first wild-cultivated rice pangenome. Along the way, they used their pangenome to answer questions about the origins of domesticated rice, as well. Their paper was published just last month, in April.
Humans weren’t capable of sequencing genomes at all until the late 1970s. Back then, we began with a small, manageable genome: that of a bacteriophage, a bacteria-infecting virus. So it makes sense that when we started trying to create pangenomes, in 2005, we also started small. Nascent pangenomics studies dealt with bacteria. Rice is one of the first plants to have a pangenome constructed. A 400 Mb (megabase) genome is, with current technologies and the cost of implementing those technologies, manageable for the task of pangenome creation. It also helps substantially that rice is already one of the best studied plants in the world.
Prior to the emergence of pangenomics, scientists were predominately (and still are, in most cases) sequencing and assembling single genomes and housing them as single, linear files, in databases such as GenBank, The National Institute of Health’s database of all publicly available DNA sequences, or the DNA Data Bank of Japan, among others. The creation of reference genomes has been the priority: the creation of high quality genomes that play the role of genetic representative for a species. Reference genomes still provide a point of comparison for scientists studying members of a species, functioning in part like a map. For example, the genome of an American chestnut tree referred to as “Ellis1” was the first American chestnut to be fully sequenced and annotated (an annotated genome is one that has had its genes and elements described), and it serves as the reference genome for American chestnut trees to this day. When scientists extract DNA from other chestnut trees, they compare those sequences with the archetype of the Ellis tree, and use the Ellis genome to help them assemble their own genomes, or regions of genomes. Imagine if you were in a plane, flying high above a coastline. You snap a picture of the coastline, and then open a maps app. The map on your phone is the reference, telling you exactly where in the world the plane is at that moment by the corresponding shape of the coastline you see below you. This is the beauty of reference genomes.
But, as I mentioned, wild populations are often wealthy with genetic diversity. There is, in reality, no archetype—no single genome upon which all the rest of individual members of a species are based. Our genetic coastlines are all unique, even if within one species they usually follow the same general pattern of metaphorical bays, points, deltas, peninsulas and so on. The cultivated rice reference genome is named “Nipponbare,” and was for years the only high quality sequenced monocot genome in existence—but it is only one genome. From one organism. In research, this can lead to what is referred to as a reference allele bias: all subsequent genetic material that is sequenced, mapped, and studied using a reference genome as a guide risks missing, overlooking, or mischaracterizing alleles, structural aspects of a genome, or entire genes because the reference doesn’t contain an analog.
Pangenomes, in contrast, are naturally much more complex. They are constructed not as linear files but often as phased, integrated assemblies of multiple genomes, typically represented as a graph—or sometimes as a set of variants against a single reference (though this latter construction is less dynamic, less useful, for similar reasons as discussed in the paragraph above). In the former, DNA from different organisms are sequenced, and computational technologies–software, algorithms–are used to build a multilayered genome, a representative of all the vast variation between multiple genomes. That way, when scientists use the pangenome as a reference, they are able to map and compare their samples not to one reference genome, but many—sometimes hundreds—at a time. It’s a type of map that’s nearly impossible for a person (especially a person who isn’t a geneticist or a computer scientist) to visualize, but it’s a much more comprehensive and powerful way to study genomes; at its crux a pangenome is about taking diversity into account. They help us see the genetic makeup of a population or species in an entirely new light. It’s a genomic gestalt. Together, many genomes give us more than a single, separate genome ever could—they give us something entirely new.
Dongling Guo, Yan Li, and their colleagues sequenced the genomes of rice from approximately 20 countries, obtaining their choice varieties from those that have been studied previously and therefore have information housed about them in places like the China National Rice Research Insitute in Hangzhou, China, and the National Institute of Genetics in Mishima, Japan. The researchers grew all of the rice for their study in one location in Lingshui county, in Hainan, and extracted genomic DNA from fresh leaves that had been flash frozen in liquid nitrogen. They sequenced DNA using a combination of PacBio HiFi Technology, Oxford Nanopore Technology, and Illumina technology. There are only a few major sequencing companies that offer high throughput, highly accurate, and affordable sequencing technology, of which PacBio, Oxford Nanopore, and Illumina represent the biggest names. Next generation sequencing (NGS) is the name given to the sequencing techniques employed by these companies, techniques that have innovatively built upon and been inspired by humanity’s first method of sequencing, Sanger Sequencing.
PacBio’s HiFi (or High Fidelity) technology utilizes, in part, fluorescently tagged nucleotides. Specifically, four tags of different colors, one for each of the nucleotide bases (adenine (A), guanine (G), Cytosine (C), and Thymine(T)). An overview is as follows: a purified DNA sample from an organism is sheared into pieces, and specially designed oligonucleotides—small chains of DNA with a known sequence—are ligated (attached) to the pieces. Another oligonucleotide, a primer, which is a specific sequence that allows for the binding of the DNA-synthesizing enzyme polymerase, is then attached to these adaptor oligonucleotides. Once polymerases have bound to primers, each of these modified DNA pieces are fixed into place inside their own microscopic well on a microchip. Polymerase synthesizes new DNA, using the sample strand as a template. Every time the polymerase adds a new base to the growing strand, the tag is detected by a sensor. These sequenced strands are then computationally arranged and assembled into a genome, de novo. This is known as single-molecule, real-time sequencing.
Oxford Nanopore Sequencing, in contrast, uses flow cells: special membranes containing an array of tiny holes–nanopores–through which single-stranded DNA fragments can flow. The nanopores are each equipped with electrodes and sensors that measure electrical currents flowing through them. When one of the four bases travels through the pore, an identifiable disruption to the current allows determination, base by base, current disruption by current disruption, of the order of bases along a strand of DNA. This is also a form of real-time sequencing.
Scientists typically have access to a veritable trove of assembly and assembly assessment methods, methods for piecing together the files of sequencing data and determining the quality and accuracy of those puzzled together, de novo assembled genomes. Merely one of many of the evaluation tools used by Guo et al. is called BUSCO, which stands for benchmarking universal single-copy orthologs. It’s a software package developed by the Swiss Institute of Bioinformatics—and its mechanism is beyond the scope of this writing (as is, if we’re honest, most of this process; if I could study and explain particulars all day, I would. Alas, I am restrained by 1. my self-imposed word count and 2. My severe lack of expertise in software engineering and computer programming).
Only after genomes have been assembled can functional annotation begin. The process, also largely computational and predictive, identifies protein-coding genes. Defining structural components of genetic architecture like centromeres, telomeres, transposable elements, and non-coding and repetitive regions accompanies functional annotation. Then, differences between each individual genome are characterized, which is another challenge in and of itself. Deciding which differences might be significant enough to constitute different genes is tricky; decoding the genetic spectrum formed by slow evolutionary change requires punctilious effort at every turn. These differences can include mutations like single nucleotide polymorphisms, in which one nucleotide has mutated into another, and small regions (50 base pairs or less, typically) of inserted or deleted nucleotides. Then larger mutations that have resulted in marked structural variations between genomes–mutations like inversions of segments of DNA, translocations of one segment from one area to another, copy number variations in which sections of DNA are doubled, or tripled, and so on. Presence-absence variations are yet another, in which some genomes contain sections of DNA that others do not.
Pangenome construction entails representing all of this information—in this case, 400 million base pairs times 145 (the number of genomes assembled in this study)–in an accessible format. Guo et al. used a pangenome-creation computing pipeline called Minigraph-Cactus, which involves five steps and a selection of tools, taking as inputs genome assemblies and outputting them as a pangenome graph.
And at last, we’ve reached their findings.
In total, across all of the genomes, they found 69,531 genes. These genes are referred to as pan-genes, and of them, 28,907 (41.57%) are core genes, or genes shared among all the rice samples sequenced, 13,728 (19.74%) were found to be specific to O. rufipogon, wild rice, and 5,181 (7.45%) were found to be private, or only present in one sample. Private genes reveal the extent of presence-absence variation within rice. One individual or one population may not have all the genes of its species. It may only have a percentage of them.
All-in-all, they unearthed 3.87 billion bases missing from the Nipponbare reference genome.
When analyzed, many of the genes unique to wild rice were found to align closely with the shape and structure of resistance genes and defense genes, those genes that help a wild organism survive in the face of hardship, specifically the hardships of a sessile organism incapable of moving to avoid potential peril. They asserted that O. rufipogon genomes contained both a greater abundance and greater diversity of these sorts of genes, in comparison with O. sativa.
As an example of one of these resistance genes: another group of researchers, Yang et al., characterized a gene called Bph38, several years ago. Its gene product helps rice fight against brown planthoppers and white-backed planthoppers. These two insects cause the most damage to rice worldwide, and their outbreaks have worsened over the past several decades. Brown planthoppers feed exclusively on rice, and so selective pressures have established Bph38 in wild rice populations because it grants plants the ability to roll out a chemical response that both repels the insects and has negative effects on their survival and reproduction.
From all of this genetic data, the scientists were also able to construct a phylogenetic tree. Their tree provided support for the long-standing hypothesis that a population of rice in China called Or-IIIa is the likely monophyletic (single lineage) origin of Asian cultivated rice. Their phylogenetic analyses moreover identified many of the genes that were desirable early on in the history of rice breeding and domestication, and the alleles that so rapidly came to dominate rice populations. This selective sweep occurred for genes that contribute to traits like rice hull color, tiller angle, leaf sheath color, nitrogen-use efficiency, panicle shape, awn length, and pericarp color.
Again as an example, a mutation in the gene that affects tiller angle, PROG1 (Prostrate Growth 1), gives a plant the ability to stand erect throughout its entire growth phase of life. Wild rice, contrastingly, only grows erectly during its reproductive phase. In the vegetative period, it lays upon the ground prostrate, which is thought to be an adaptation to prevent the growth of weeds, to confer the plant a tolerance to trampling, and to avoid grazing by certain animals. But humans found a use for mutated PROG1. A rice plant that grows straight its entire life takes up less space, thus increasing both plant density and rice yield per unit of area. It also increases a plant’s ability to photosynthesize.
Thus, agronomically valuable variants of genes like PROG1 have been conserved and propagated at the expense of others, such as disease resistance genes. Despite the existence of thousands of variegated cultivars of O. sativa that produce rice grains of difference colors, shapes, flavors, and textures, which make them appear quite diverse, their genomes aren’t as robust as wild rice in some ways.
The researchers who discovered the PROG1 gene, it should be noted, conducted their work over four years. They mapped it to a location in the rice genome, characterized it. They grew and bred thousands of rice plants, engineered plants to express different forms of PROG1 and measured the phenotypic effect. Even with the invention of increasingly refined, accurate, and powerful technologies, it’s not at all a novel thing for scientists to dedicate years of their lives to studying the specifics of one tiny little thing. One plant, one species’ (pan)genome, one gene, one molecular process—seeing the world as it is takes a lot of time, patience, discipline. Even the putatively beneficial wild rice genes uncovered by Guo et al. will need to be studied in greater detail before they may be chosen to be applied to existing rice agricultural systems. Some of them undoubtedly contribute to quantitative traits, as well—traits that arise from multiple genes working together. Rice yield is a good example of a quantitative trait. Many regions of a genome must work in concert to craft a plant that produces a certain quantity of grain. There are many different quantitative traits important to rice cultivation, and so not always can one locus (a region on a chromosome where a gene is located) be studied in isolation.
When I encounter scientific research like this, I often find myself slightly affronted by the realization that I will die without knowing and experiencing the great majority of what there is to know and experience. What do you mean I will never do hands-on laboratory work to study rice, most likely? What do you mean I may never even grow rice myself? I’ve thought this about basically every other topic this newsletter has covered. Never mind that I lean severely towards the ways of a reclusive introvert and may not even enjoy the particulars of rice genomics research, if I were given the chance to do it. It’s not about that. It’s about my curiosity and enthusiasm for humans doing specific, niche things; it’s about the excitement I feel towards people who are working to feed the planet. I think they’re immensely cool.
I encountered the topic of rice pangenomes in an article published in Genetic Engineering and Biotechnology News (GEN). It caught my eye after I’d recently had a conversation with Dasha about cooking rice. We talked about how best to cook it so it wasn’t too moist or too dry, too sticky or clumped. Also about cooking rice with a rice cooker, shaping cooked rice into delectable onigiri filled with egg or seaweed, preparing it the way a friend from Peru had once taught me, with oil and garlic. After I finished reading more about the topic and once I began writing this, I would text Dasha updates such as:
05/19: I need to sleep now so that I can be powered to do rice writing. Wricing.
05/20: I was wricing today as planned btw. Wrote (Wroce?) 2500 words of a draft. It’s going well I think.
05/21: Right now I need to wrice.
05/22: Wricing is literally killing me.
But writing about rice–wricing–hasn’t killed me. It’s overall been nice, and fun, and incredibly interesting.
And so it sort of sucks that there is a second GEN article this essay needs to contend with. One published a day before “Pangenome Reference Incorporates 145 Wild and Cultivated Rice Genomes.” This one is not about genetics or biotechnology at all. It’s titled, “How Did Scientists Become the Enemy?”
Addendum: Monsters Screaming
Spoiler: I’m using the rice pangenome as a metaphor. If you haven’t already been mulling over its glaring figurative potential, you may start now.
Specificity and truth, those concepts I disclosed my adoration for, several thousand words ago. These days I often feel like I’m holding each of them tightly in my grasp, concerned that someone might try and take them away from me, try to convince me that they are not as essential as I know them to be to my happiness and my pleasure here on this planet.
This protectiveness that I feel. It was articulated recently by Mon Mothma.
And so the rice essay becomes an essay about Star Wars, too.
Recently, as of this writing, the Star Wars prequel series Andor has just finished airing its second season. The narrative, which is more solemn, serious, and focused on themes of rebellion, fascism, and politics than some of the other stories in the Star Wars canon, follows myriad characters fighting in the early days of the Rebellion (the Rebellion being an organized effort to carry out a revolution that overthrows the oppressive and galaxy-terrorizing Empire, which is led by tyrannical Emperor Palpatine).
In a speech given to the imperial senate following the Empire’s cover-up of a planet-wide genocide, Senator and soon-to-be Rebel-leader Mon Mothma says:
“The distance between what is said and what is known to be true has become an abyss. Of all the things at risk, the loss of an objective reality is perhaps the most dangerous. The death of truth is the ultimate victory of evil. When truth leaves us, when we let it slip away, when it is ripped from our hands, we become vulnerable to whatever monster screams the loudest."
It is a relevant speech.
Many of the heroes and rebel characters of Andor die without being widely known or recognized. They are largely not famous or renowned. The only reason they succeed is because of each other. The rebellion is empathetic, collaborative, and works tirelessly in pursuit of truth and freedom. Its members understand that they’re part of something much bigger than themselves. Many sacrifice their lives in the hope that a future they’ll never see will be one liberated from the Empire’s cruelty. In the first scene of the season, titular Cassian Andor escapes an Empire-controlled facility only because of the help of a newly recruited, undercover rebel:
“I’m so nervous,” she–Niya–says.
“Nervous is good,” Cassian tells her. “Nervous keeps us awake.”
Here on Earth, tucked in our infinitesimal corner of the Milky Way, we often don’t know the people saving our lives, either. Those working to help us are often more-or-less invisible. Relatively speaking, a few individuals’ faces and voices tend to dominate the news and online spaces. Many of the people working for change are more interested in working, and the work itself, than talking or being popular and recognizable. They are the multitudes working every day to ensure half the global population is still able to eat rice, and millions of others in all manner of roles thought of only by the people in them, or surrounding those who are in them. This is hardly news to anyone reading this, I’m sure; but we still must be reminded of this, and reminded that other people know this.
In this age where the ability to perform, to scream to large audiences is within reach for all of us at all hours of the day, where some people seek fame and power and carelessly discard specificity and truth, we must remember that communities of kind, attentive people are what is good. The world becomes better and more people live longer, healthier lives, when our focus is on working together. Ecosystems remain diverse and healthy as well, when we stay awake because we are anxious and compelled to do what is right, when we are obsessed with doing what is good.
When we sink our efforts into seeing what is around us, what is truly around us, and using that knowledge to help our collective home, our collective body—Earth—that is when we thrive. We don’t thrive in influencer-manufactured upheaval, or when we grow erroneously convinced we must uphold merely one or a few loud, relatable voices. Anyone studying a topic or working in a field the majority of us never even think about deserves to be listened to, deserves safety and security and freedom. I want to pay attention to these people much more than I feel compelled to pay attention to others. To monsters screaming loudly.
Hana El-Samad and Martin Borch Jensen, the authors of “How Did Science Become the Enemy?” say:
Science, as a process of finding out how things work and making things possible, is perhaps the most powerful source of freedoms–freedom from famine, freedom to see our children triumph over childhood diseases, freedom to live after developing cancer.
But the question they pose is this: “Why isn’t the public rising en masse in defense of science?”
As science spending plummets in the United States, as people in science lose their jobs or their research funding, and many around the world lose access to life-saving medical treatments or preventative care, why isn’t the public rising en masse in defense of science?
They offer seven proposed contributing factors, and ultimately aver that “a commission of scientists, universities, public and private organizations and, prominently, members of the general public, [is needed] to examine this question.”
Those seven factors are associated in one way or another with questions such as: who still has faith in science? What do we think of science today and the role it plays in our lives? What effects did the COVID pandemic have on our perceptions of our scientists, our medical providers? What happens when politics and science become entangled, or become perceived as entangled? What is thought about the relationships between universities and science, government organizations and science, private organizations and science? In a world where we have only been sequencing genomes for fifty-something years, where the universe of science has expanded explosively in the last several decades, how do we adapt? Science is answering so many questions at so rapid a rate, and we have access to all of it, and anyone's thoughts about it, in our pockets.
It is imperative that we find ways to handle all of this change and discuss all of our concerns. We should aim to do it not with a primary focus on productivity, efficiency, or profit for individuals, but with a focus on compassion, curiosity, a hope that society–all of humanity–can become healthier, more peaceful, more free. Many of the stories that humans love, stories like Star Wars, are beloved because they showcase that goodness lies in teamwork and honesty and kindness. We are taught from the time we are young, from the very first time we open a children’s book, often, that valuing one another and our world, all the beautiful, colorful creatures that inhabit it—is the coolest, most exciting thing we can do.
The proposed, best way to further examine El-Samad and Jensen’s question is by looking at the perspectives of a diverse array of people. A commission representing as many of us as possible. So many stressors in the world right now, and an inability to defend against it—to survive free from the peril created by uniformity, lack of input from many voices, domination of space by the few.
Our solutions will come from cooperation amongst us all. We destroy ourselves in isolation. We destroy ourselves when we lie to one another, when we don’t accept the world in all its complexities and nuances. We destroy ourselves when we treat each other like competitors and customers and consumers, rather than infinitely complicated beings, genetically, personally, culturally, each of us with manifold uniqueness never before seen on the earth, each of us able to help and contribute to our well-being.
I don’t overly care about how productive a person is, or how efficient, or how popular. I care about creating a world where as many people as possible are free to pursue whatever they want, as slowly, diligently, and carefully as they want—so as to generate knowledge and truth that is helpful, amazing, delightful. This is our solution. This is how we can truly serve one another. Specificity, truth, diversity. These things will help us resist pain and suffering and oppression. They will.
Information for this article was obtained from:
✼ A pangenome reference of wild and cultivated rice ✼ Pangenome Reference Incorporates 145 Wild and Cultivated Rice Genomes ✼ How Did Scientists Become the Enemy? ✼ 100 Days that Shook Science ✼ Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics ✼ Plant Pan-Genomics Comes of Age ✼ Genomic variation in 3,010 diverse accessions of Asian cultivated rice ✼ Identification of a novel planthopper resistance gene from wild rice (Oryza rufipogon Griff.) ✼ Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes ✼ Control of a key transition from prostrate to erect growth in rice domestication ✼ ✼ Pangenome graph construction from genome alignments with Minigraph-Cactus ✼ Pangenomics enables genotyping of known structural variants in 5202 diverse genomes ✼ Ellis1 ✼ Nipponbare reference genome ✼ How HiFi sequencing works - PacBio ✼ Overview of PacBio SMRT sequencing ✼ 2025 Trends: NGS ✼ How nanopore sequencing works ✼ Reference Genome: Wikipedia ✼ 3000 Rice Genomes Project ✼ What Will 2024 Mean for NGS and Genomics? ✼ User Guide BUSCO ✼ Oryza sativa: a Resume of Rice ✼ International Rice Genebank ✼ Merriam-Webster: Species & Specific ✼ Crop Genomics Goes Beyond a Single Reference Genome ✼ NextPolish: a fast and efficient genome polishing tool for long-read assembly ✼ Wookiepedia ✼