Earth BioGenome Project leader Harris Lewin joins ASU

To help mitigate the world biodiversity crisis, Arizona State University’s Julie Ann Wrigley Global Futures Laboratory has recruited Harris Lewin, a prominent genome scientist currently spearheading one of biology’s most ambitious moonshot goals — a complete DNA catalog of life's genetic code by the end of this decade.

Lewin leads the Earth BioGenome Project, a massive coalition of worldwide scientists and 50-plus ongoing projects that has a primary goal of completing high-quality DNA reference genomes — the gold standard of an organism’s complete DNA genetic code and sequence — for all higher organisms on Earth, an estimated 1.8 million species.

The global secretariat of the project, which was at the University of California, Davis (UC Davis), will also move to ASU in December. 

“You really have to know who's there before you can really understand biology,” Lewin said. “And right now, with only 10% of the species that exist having been named for most of life, or 80% to 90% of all life, we don't even know what’s there.”

Lewin’s appointment as professor in ASU's Global Futures Laboratory boosts its comprehensive strategy to develop solutions for our world’s planetary systems challenges, including the current biodiversity crisis. There are an estimated two-thirds of higher organisms that may face the urgent threat of a new mass extinction, primarily due to the activities of humans that impact natural ecosystems and drive climate change.

“Today, with trying to build scalable models on understanding how ecosystems function and how they might be restored and remediated, we have to have detailed understanding of the organisms in those ecosystems,” Lewin said. “We need to move as quickly as we can, because if species that comprise critical ecosystems are lost, they may never be recovered again.”

Once a species goes extinct, scientists forever lose the ability to better understand what sustained its life, or if that species might be used to improve food or medicine production. 

“As our world’s life-supporting systems continue to be stressed to levels that have never before been recorded, the significance of the Earth BioGenome Project cannot be understated,” said Peter Schlosser, vice president and vice provost of Global Futures at ASU.

“To have a pioneering scientist like Harris Lewin and his colleagues identify ASU and the Julie Ann Wrigley Global Futures Laboratory as not simply a logical home for this endeavor, but a preferred home because of our facilities and global network of partners, speaks volumes," Schlosser said. "As with all work designed to help shape options for a thriving future for our world and its inhabitants, this project is of the highest urgency and requires a deep cohort of experts from around the world.”

Sequencing life and the Earth BioGenome Project

The 19th century naturalist Charles Darwin wrote about the complexity of life on Earth — describing it as “endless forms most beautiful” — 164 years ago in his profound book on evolution, “On the Origin of Species.”

In the 20th century, the structure of DNA was discovered. The combination and exact order of DNA chemical letters — abbreviated as A, C, T or G — are responsible for the blueprints of life. To better decipher this blueprint, DNA sequencing was invented in the 1970s.

With advances in sequencing technology in the 1990s, academic, private and government labs raced to complete the genomes for the first bacterium, yeast, nematode and fruit fly. The first draft of the Human Genome Project, a Herculean effort at the time, was completed in 2003, taking an international consortium of scientists 13 years to do so and at an estimated cost of $3 billion dollars.

Fifteen years later, Lewin co-founded the Earth BioGenome Project, or EBP, and today chairs its executive council. The project was announced at the World Economic Forum in Davos, Switzerland, at the beginning of 2018 and officially launched at the Wellcome Trust in London later that year.  

He describes the EBP as a “critical biology infrastructure project” that will allow scientists to stand on the shoulder of giants to see further and better understand the world’s biodiversity — akin to how astronomers have used tools such as the Webb Space Telescope to understand the nature of the universe.

“Genomes are the infrastructure for the future of biology and the bioeconomy,” Lewin said. “Much like how the Webb Telescope allows you to peer into the cosmos to understand the origins and evolution of the universe, having all the sequence of eukaryotic life — those with a nucleus — will facilitate understanding of the origin and evolution of life on Earth.”

Key facets of a bio-driven economy from genome science include renewable biofuels from algae, food crops like corn and soybeans, threats like agricultural pests, model scientific organisms for drug and medicine development, and biodefense and biosecurity issues, such as the recent worldwide COVID-19 pandemic. Other products of the bioeconomy will involve new industrial catalysts, biomaterials and drugs. 

Working together, to date, the EBP has completed a pilot phase of about 2,000 genomes. Among the EBP are 55 genome projects underway, the largest led by the U.K.’s Wellcome Sanger Institute, Rockefeller University, the European Union, Genome Canada, China, a pan-African consortium and Australia. In the U.S., Rockefeller University leads the Vertebrate Genomes Project, which has now completed over 300 genomes, and the California Conservation Genomics Project has finished over 150 genomes.

With rapid advances in DNA sequencing technology and computing power, Lewin thinks the EBP can sequence the rest of all 1.8 million named eukaryotic species for around the same cost as the human genome draft within the next 10 years. 

Funding for the EBP will come from a variety of worldwide endeavors.

“There’s no central funding,” Lewin said. “It's a distributed model. Each of these projects raises their own money, but they're all agreeing to coordinate and work together with common standards towards the goal of sequencing all eukaryotes in 10 years. The limitation these days is really not the sequencing technology, the limitation is acquiring taxonomically well-identified, vouchered and ethically sourced samples from all over the world.”

The next goal is to complete 10,000 genomes by the end of 2025. When fully up to speed, the affiliated projects of the EBP will need to sequence an estimated 1,500 genomes per day to meet its ambitious goal.

“This also includes a very aggressive set of standards for a collection of samples, all the metadata that gets collected with them, and how the sequencing is to be done and to what specifications in terms of quality,” Lewin said.

Arizona focus

With the move to ASU, there will now be abundant opportunities to develop an “EBP at ASU” program to sequence and better understand iconic life found in desert climates — from the mighty arms of the saguaro cactus to Gila monsters to Gimbal quail to the diamondback rattlesnake.

The EBP at ASU will be greatly strengthened by the National Science Foundation NEON (National Ecological Observatory Network) Biorepository, directed by Nico Franz, Virginia M. Ullman Professor of Ecology and Biocollections director.

“Our team is thrilled to have the opportunity to work with Harris Lewin,” Franz said. “We have a shared, inclusive vision to advance EBP at ASU and beyond. This model is based on sound biodiversity sampling design, ethical data governance and broadly impacting education in the computational life sciences."

From the world’s coral reefs to rainforests — which together account for an estimated 75% of worldwide biodiversity — to temperate land climates, ASU has been at the forefront of developing innovative solutions for understanding and conserving biodiversity.

“ASU will be one of the global centers for Earth BioGenome Project, not just on the sample provision side, but all the way through sequencing, assembly and analysis,” Lewin said. “We certainly have early plans to try and understand desert ecosystems and to reveal the impacts of climate change on those critical ecosystems, including aquatic ecosystems.” 

The Earth BioGenome Project now joins the new School of Ocean Futures, NeoBio, Bermuda Institute of Ocean Science, Center for Global Discovery and Conservation Science, and Center for Biodiversity Outcomes as ASU’s academic lead initiatives to help solve the world biodiversity crisis.

“We are excited to see how this work integrates with programs like the Bermuda Institute of Ocean Sciences and Nico Franz’s research with the Biodiversity Knowledge Integration Center and NEON,” Schlosser said. “These collaborations can help repair, preserve and protect our world’s ecosystems.”

Lewin’s official ASU appointment began Nov. 1. For the past 12 years, Lewin served as distinguished professor of evolution and ecology and former vice chancellor for research at UC Davis. He is a member of the National Academy of Sciences and won the Wolf Prize in Agriculture for his research into cattle genomics. He has been a leader in the field of mammalian comparative genomics and has made major contributions to our understanding of chromosome evolution and its relationship to adaptation, speciation and the origins of cancers. Previously, Lewin worked at the University of Illinois for 27 years and, in 2003, served as the founding director of the Carl R. Woese Institute for Genomic Biology.