The Brave New World of Using DNA to Store Data
Netscape co-founder-turned-venture capitalist billionaire investor Marc Andreessen once posited that software was eating the world. He was right, and the takeover of software resulted in many things. One of them is data. Lots and lots and lots of data. In the previous two years, humanity created more data than it did during its entire existence combined, and the amount will only increase. Think about it: The hundreds of 50KB emails you write a day, the dozens of 10MB photos, the minute-long, 350MB 4K video you shoot on your iPhone X add up to vast quantities of information. All that information needs to be stored. And that's becoming an issue as data volume outpaces storage space.
The race is on to find another medium capable of storing massive amounts of information in as small a space as possible.
"There won't be enough silicon to store all the data we need. It's unlikely that we can make flash memory smaller. We have reached the physical limits," Victor Zhirnov, chief scientist at the Semiconductor Research Corporation, says. "We are facing a crisis that's comparable to the oil crisis in the 1970s. By 2050, we're going to need to store 10 to the 30 bits, compared to 10 to the 23 bits in 2016." That amount of storage space is equivalent to each of the world's seven billion people owning almost six trillion -- that's 10 to the 12th power -- iPhone Xs with 256GB storage space.
The race is on to find another medium capable of storing massive amounts of information in as small a space as possible. Zhirnov and other scientists are looking at the human body, looking to DNA. "Nature has nailed it," Luis Ceze, a professor in the Department of Computer Science and Engineering at the University of Washington, says. "DNA is a molecular storage medium that is remarkable. It's incredibly dense, many, many thousands of times denser than the densest technology that we have today. And DNA is remarkably general. Any information you can map in bits you can store in DNA." It's so dense -- able to store a theoretical maximum of 215 petabytes (215 million gigabytes) in a single gram -- that all the data ever produced could be stored in the back of a tractor trailer truck.
Writing DNA can be an energy-efficient process, too. Consider how the human body is constantly writing and rewriting DNA, and does so on a couple thousand calories a day. And all it needs for storage is a cool, dark place, a significant energy savings when compared to server farms that require huge amounts of energy to run and even more energy to cool.
Picture it: tiny specks of inert DNA made from silicon or another material, stored in cool, dark, dry areas, preserved for all time.
Researchers first succeeded in encoding data onto DNA in 2012, when Harvard University geneticists George Church and Sri Kosuri wrote a 52,000-word book on A, C, G, and T base pairs. Their method only produced 1.28 petabytes per gram of DNA, however, a volume exceeded the next year when a group encoded all 154 Shakespeare sonnets and a 26-second clip of Martin Luther King's "I Have A Dream" speech. In 2017, Columbia University researchers Yaniv Erlich and Dina Zielinski made the process 60 percent more efficient.
The limiting factor today is cost. Erlich said the work his team did cost $7,000 to encode and decode two megabytes of data. To become useful in a widespread way, the price per megabyte needs to plummet. Even advocates concede this point. "Of course it is expensive," Zhirnov says. "But look how much magnetic storage cost in the 1980s. What you store today in your iPhone for virtually nothing would cost many millions of dollars in 1982." There's reason to think the price will continue to fall. Genome readers are improving, getting cheaper, faster, and smaller, and genome sequencing becomes cheaper every year, too. Picture it: tiny specks of inert DNA made from silicon or another material, stored in cool, dark, dry areas, preserved for all time.
"It just takes a few minutes to double a sample. A few more minutes, you double it again. Very quickly, you have thousands or millions of new copies."
Plus, DNA has another advantage over more traditional forms of storage: It's very easy to reproduce. "If you want a second copy of a hard disk drive, you need components for a disk drive, hook both drives up to a computer, and copy. That's a pain," Nick Goldman, a researcher at the European Bioinformatics Institute, says. "DNA, once you have that first sample, it's a process that is absolutely routine in thousands of laboratories around the world to multiply that using polymerase chain reaction [which uses temperature changes or other processes]. It just takes a few minutes to double a sample. A few more minutes, you double it again. Very quickly, you have thousands or millions of new copies."
This ability to duplicate quickly and easily is a positive trait. But, of course, there's also the potential for danger. Does encoding on DNA, the very basis for life, present ethical issues? Could it get out of control and fundamentally alter life as we know it?
The chance is there, but it's remote. The first reason is that storage could be done with only two base pairs, which would serve as replacements for the 0 and 1 digits that make up all digital data. While doing so would decrease the possible density of the storage, it would virtually eliminate the risk that the sequences would be compatible with life.
But even if scientists and researchers choose to use four base pairs, other safeguards are in place that will prevent trouble. According to Ceze, the computer science professor, the snippets of DNA that they write are very short, around 150 nucleotides. This includes the title, the information that's being encoded, and tags to help organize where the snippet should fall in the larger sequence. Furthermore, they generally avoid repeated letters, which dramatically reduces the chance that a protein could be synthesized from the snippet.
"In the future, we'll know enough about someone from a sample of their DNA that we could make a specific poison. That's the danger, not those of us who want to encode DNA for storage."
Inevitably, some DNA will get spilt. "But it's so unlikely that anything that gets created for storage would have a biological interpretation that could interfere with the mechanisms going on in a living organism that it doesn't worry me in the slightest," Goldman says. "We're not of concern for the people who are worried about the ethical issues of synthetic DNA. They are much more concerned about people deliberately engineering anthrax. In the future, we'll know enough about someone from a sample of their DNA that we could make a specific poison. That's the danger, not those of us who want to encode DNA for storage."
In the end, the reality of and risks surrounding encoding on DNA are the same as any scientific advancement: It's another system that is vulnerable to people with bad intentions but not one that is inherently unethical.
"Every human action has some ethical implications," Zhirnov says. "I can use a hammer to build a house or I can use it to harm another person. I don't see why DNA is in any way more or less ethical."
If that house can store all the knowledge in human history, it's worth learning how to build it.
Editor's Note: In response to readers' comments that silicon is one of the earth's most abundant materials, we reached back out to our source, Dr. Victor Zhirnov. He stands by his statement about a coming shortage of silicon, citing this research. The silicon oxide found in beach sand is unsuitable for semiconductors, he says, because the cost of purifying it would be prohibitive. For use in circuit-making, silicon must be refined to a purity of 99.9999999 percent. So the process begins by mining for pure quartz, which can only be found in relatively few places around the world.
Time to visit your TikTok doc? The good and bad of doctors on social media
Rakhi Patel has carved a hobby out of reviewing pizza — her favorite food — on Instagram. In a nod to her preferred topping, she calls herself thepepperoniqueen. Photos and videos show her savoring slices from scores of pizzerias. In some of them, she’s wearing scrubs — her attire as an inpatient neurology physician associate at Tufts Medical Center in Boston.
“Depending on how you dress your pizza, it can be more nutritious,” said Patel, who suggests a thin crust, sugarless tomato sauce and vegetables galore as healthier alternatives. “There are no boundaries for a health care professional to enjoy pizza.”
Beyond that, “pizza fuels my mental health and makes me happy, especially when loaded with pepperoni,” she said. “If I’m going to be a pizza connoisseur, then I also need to take care of my physical health by ensuring that I get at least three days of exercise per week and eat nutritiously when I’m not eating pizza.”
She’s among an increasing number of health care professionals, including doctors and nurses, who maintain an active persona on social media, according to bioethics researchers. They share their hobbies and interests with people inside and outside the world of medicine, helping patients and the public become acquainted with the humans behind the scrubs or white coats. Other health care experts limit their posts to medical topics, while some opt for a combination of personal and professional commentaries. Depending on the posts, ethical issues may come into play.
“Health care professionals are quite prevalent on social media,” said Mercer Gary, a postdoctoral researcher at The Hastings Center, an independent bioethics research institute in Garrison, New York. “They’ve been posting on #medTwitter for many years, mainly to communicate with one another, but, of course, anyone can see the threads. Most recently, doctors and nurses have become a presence on TikTok.”
On social media, many health care providers perceive themselves to be “humanizing” their profession by coming across as more approachable — “reminding patients that providers are people and workers, as well as repositories of medical expertise,” Gary said. As a result, she noted that patients who are often intimidated by clinicians may feel comfortable enough to overcome barriers to scheduling health care appointments. The use of TikTok in particular may help doctors and nurses connect with younger followers.
When health care providers post on social media, they must bear in mind that they have legal and ethical duties to their patients, profession and society, said Elizabeth Levy, founder and director of Physicians for Justice.
While enduring three years of pandemic conditions, many health care professionals have struggled with burnout, exhaustion and moral distress. “Much health care provider content on social media seeks to expose the difficulties of the work,” Gary added. “TikTok and Instagram reels have shown health care providers crying after losing a patient or exhausted after a night shift in the emergency department.”
A study conducted in Beijing, China and published last year found that TikTok is the world’s most rapidly growing video application, amassing 1.6 billion users in 2021. “More and more patients are searching for information on genitourinary cancers via TikTok,” the study’s authors wrote in Frontiers in Oncology, referring to cancers of the urinary tracts and male reproductive organs. Among the 61 sample videos examined by the researchers, health care practitioners contributed the content in 29, or 47 percent, of them. Yet, 22 posts, 36 percent, were misinformative, mostly due to outdated information.
More than half of the videos offered good content on disease symptoms and examinations. The authors concluded that “most videos on genitourinary cancers on TikTok are of poor to medium quality and reliability. However, videos posted by media agencies enjoyed great public attention and interaction. Medical practitioners could improve the video quality by cooperating with media agencies and avoiding unexplained terminologies.”
When health care providers post on social media, they must bear in mind that they have legal and ethical duties to their patients, profession and society, said Elizabeth Levy, founder and director of Physicians for Justice in Irvine, Calif., a nonprofit network of volunteer physicians partnering with public interest lawyers to address the social determinants of health.
“Providers are also responsible for understanding the mechanics of their posts,” such as who can see these messages and how long they stay up, Levy said. As a starting point for figuring what’s acceptable, providers could look at social media guidelines put out by their professional associations. Even beyond that, though, they must exercise prudent judgment. “As social media continues to evolve, providers will also need to stay updated with the changing risks and benefits of participation.”
Patients often research their providers online, so finding them on social media can help inform about values and approaches to care, said M. Sara Rosenthal, a professor and founding director of the program for bioethics and chair of the hospital ethics committee at the University of Kentucky College of Medicine.
Health care providers’ posts on social media also could promote patient education. They can advance informed consent and help patients navigate the risks and benefits of various treatments or preventive options. However, providers could violate ethical principles if they espouse “harmful, risky or questionable therapies or medical advice that is contrary to clinical practice guidelines or accepted standards of care,” Rosenthal said.
Inappropriate self-disclosure also can affect a provider’s reputation, said Kelly Michelson, a professor of pediatrics and director of the Center for Bioethics and Medical Humanities at Northwestern University’s Feinberg School of Medicine. A clinician’s obligations to professionalism extend beyond those moments when they are directly taking care of their patients, she said. “Many experts recommend against clinicians ‘friending’ patients or the families on social media because it blurs the patient-clinician boundary.”
Meanwhile, clinicians need to adhere closely to confidentiality. In sharing a patient’s case online for educational purposes, safeguarding identity becomes paramount. Removing names and changing minor details is insufficient, Michelson said.
“The patient-clinician relationship is sacred, and it can only be effective if patients have 100 percent confidence that all that happens with their clinician is kept in the strictest of confidence,” she said, adding that health care providers also should avoid obtaining information about their patients from social media because it can lead to bias and risk jeopardizing objectivity.
Academic clinicians can use social media as a recruitment tool to expand the pool of research participants for their studies, Michelson said. Because the majority of clinical research is conducted at academic medical centers, large segments of the population are excluded. “This affects the quality of the data and knowledge we gain from research,” she said.
Don S. Dizon, a professor of medicine and surgery at the Warren Alpert Medical School of Brown University in Providence, Rhode Island, uses LinkedIn and Doximity, as well as Twitter, Instagram, TikTok, Facebook, and most recently, YouTube and Post. He’s on Twitter nearly every day, where he interacts with the oncology community and his medical colleagues.
Also, he said, “I really like Instagram. It’s where you will see a hybrid of who I am professionally and personally. I’ve become comfortable sharing both up to a limit, but where else can I combine my appreciation of clothes with my professional life?” On that site, he’s seen sporting shirts with polka dots or stripes and an occasional bow-tie. He also posts photos of his cats.
Don S. Dizon, a professor of medicine and surgery at Brown, started using TikTok several years ago, telling medical stories in short-form videos.
Don S. Dizon
Dizon started using TikTok several years ago, telling medical stories in short-form videos. He may talk about an inspirational patient, his views on end-of-life care and death, or memories of people who have passed. But he is careful not to divulge any details that would identify anyone.
Recently, some people have become his patients after viewing his content on social media or on the Internet in general, which he clearly states isn’t a forum for medical advice. “In both situations, they are so much more relaxed when we meet, because it’s as if they have a sense of who I am as a person,” Dizon said. “I think that has helped so much in talking through a cancer diagnosis and a treatment plan, and yes, even discussions about prognosis.”
He also posts about equity and diversity. “I have found myself more likely to repost or react to issues that are inherently political, including racism, homophobia, transphobia and lack-of-access issues, because medicine is not isolated from society, and I truly believe that medicine is a social justice issue,” said Dizon, who is vice chair of diversity, equity, inclusion and professional integrity at the SWOG Cancer Research Network.
Through it all, Dizon likes “to break through the notion of doctor as infallible and all-knowing, the doctor as deity,” he said. “Humanizing what I do, especially in oncology, is something that challenges me on social media, and I appreciate the opportunities to do it on TikTok.”
Could this habit related to eating slow down rates of aging?
Last Thursday, scientists at Columbia University published a new study finding that cutting down on calories could lead to longer, healthier lives. In the phase 2 trial, 220 healthy people without obesity dropped their calories significantly and, at least according to one test, their rate of biological aging slowed by 2 to 3 percent in over a couple of years. Small though that may seem, the researchers estimate that it would translate into a decline of about 10 percent in the risk of death as people get older. That's basically the same as quitting smoking.
Previous research has shown that restricting calories results in longer lives for mice, worms and flies. This research is unique because it applies those findings to people. It was published in Nature Aging.
But what did the researchers actually show? Why did two other tests indicate that the biological age of the research participants didn't budge? Does the new paper point to anything people should be doing for more years of healthy living? Spoiler alert: Maybe, but don't try anything before talking with a medical expert about it. I had the chance to chat with someone with inside knowledge of the research -- Dr. Evan Hadley, director of the National Institute of Aging's Division of Geriatrics and Clinical Gerontology, which funded the study. Dr. Hadley describes how the research participants went about reducing their calories, as well as the risks and benefits involved. He also explains the "aging clock" used to measure the benefits.
Evan Hadley, Director of the Division of Geriatrics and Clinical Gerontology at the National Institute of Aging
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