Due to federal regulations, access to abortion medications is restricted, despite their record of safety and efficacy.
A few days before Christmas 2015, Paige Alexandria, a 28-year-old counselor at the Austin Women's Health Center in Texas, found out she was pregnant.
Alexandria had missed the cutoff for a medication abortion by three days.
"It was an unplanned pregnancy, and instantaneously I knew I needed an abortion," Alexandria recalls. Already a mother of two children, one with special needs, a third child was not something Alexandria and her husband felt prepared to take on. "Mentally, I knew my limit. I wasn't prepared for a third and I didn't want one," she says.
At an ultrasound appointment one week later, scans showed she was a little over eight weeks pregnant. Alexandria opted to have an abortion as soon as possible, and preferably with medication. "I really wanted to avoid a surgical abortion," she says. "It sounded a lot more invasive, and I'm already uncomfortable with pap smears and pelvic exams, so I initially went in wanting to do the pill."
But at the time, medication guidelines stipulated that one of the pills, called Mifepristone, could only be prescribed to end a pregnancy at eight weeks gestation or earlier – Alexandria had missed the cutoff by three days. If she wanted to end the pregnancy, she would need to undergo a surgical abortion, otherwise known as a vacuum aspiration abortion.
With a vacuum aspiration abortion, doctors dilate the cervix and manually aspirate out the contents of the uterus. Medication abortion, on the other hand, consists of the patient taking two pills – Mifepristone, which blocks the hormones that help the pregnancy develop, and Misoprostol, which empties the uterus over a period of days, identical to a miscarriage.
Alexandria was upset about the change of plans but resolute in her decision to end the pregnancy. "The fact that I didn't really have a choice in how my procedure was performed has made the experience just a little more sensitive for me," she says. She scheduled the earliest available appointment for a surgical abortion.
Paige Alexandria would have chosen to terminate her pregnancy with medication if the regulations were less stringent.
(Photo courtesy of Alexandria)
Like Alexandria, many people looking to terminate a pregnancy opt to do so with medication. According to research from the Guttmacher Institute, medication abortions accounted for nearly 40 percent of all abortions in the year 2017 – a marked increase from 2001, when medication abortions only accounted for roughly five percent of terminations. Taken 24-48 hours apart, Mifepristone and Misoprostol have a 95-99 percent success rate in terminating pregnancies up to 63 days – or nine weeks – of gestation, according to the American College of Obstetrics and Gynecology (ACOG).
But even though the World Health Organization (WHO) considers medical abortion to be highly safe and effective, the medication is still carefully guarded in the United States: Mifepristone is only available for terminating pregnancies up to 10 weeks gestation, per the FDA, even though limited research suggests that both are safe and effective at terminating pregnancies between 12 and 20 weeks.
Additionally, a separate set of regulations known as a Risk Evaluation and Mitigation Strategy (REMS) means that patients can only take Mifepristone under specific circumstances. Mifepristone must be distributed in person by a healthcare provider – usually interpreted in most states as a doctor or nurse practitioner – who has registered with the drug's manufacturer. The medication cannot be distributed through a pharmacy, so doctors who wish to provide the drug must stock the medication in-office, and both the provider and the patient must sign a form that warns them of the "risk of serious complications associated with Mifepristone," according to the FDA.
"REMS is a set of restrictions that the FDA puts on the distribution of drugs it considers dangerous or risky in some way," says Dr. Elizabeth Raymond, an OB-GYN and senior medical associate at Gynuity Health Projects. Although not always called REMS, these restrictions have been imposed on Mifepristone since the medication was approved by the FDA in 2000, Raymond says.
Raymond is part of a growing number of physicians and researchers who want to eliminate the REMS requirements for Mifepristone, also known by its brand name Mifeprex. In 2017, Raymond and several other physicians authored a paper in the New England Journal of Medicine (NEJM) arguing that Mifepristone is extremely safe and needlessly over-regulated.
"When the FDA first approved [Mifepristone] and imposed these requirements, they might have made sense 19 years ago when there was limited information about the use of this treatment in the United States," says Dr. Daniel Grossman, director at Advancing New Standards in Reproductive Health at UCSF and co-author of the 2017 report in the NEJM. "Now, after 19 years, it's clear that this medication is very safe, and safer than a lot of others available in a pharmacy."
Since 2000, Mifepristone has been implicated in 19 deaths, making its mortality rate 0.00063 percent.
According to their research, over three million people have taken Mifepristone since it was approved in 2000. Since then, Mifepristone has been implicated in 19 deaths, making its mortality rate 0.00063 percent. Even then, the risk is inflated, Grossman says.
"The requirement is that practitioners need to report any deaths that occur after taking these medications, and so you'll see deaths included in that figure which are homicides or suicides or something unrelated to taking Mifepristone," says Grossman. In contrast, Acetaminophen – better known as Tylenol – was associated with 458 overdose deaths between 1990 and 1998, as well as 56,000 emergency room visits and 26,000 hospitalizations. Sildenafil, better known as Viagra, was linked to 762 deaths in the first twenty months after it was approved by the FDA. Yet neither Tylenol nor Viagra have been burdened with the same REMS restrictions as Mifepristone.
"It's clearly about more than just the safety of the medication at this point," says Grossman. "It's more about stigma related to abortion and politics."
For people who want a medication abortion, the REMS requirements mean they often need to take off work to schedule a doctor's appointment, arrange for transportation and childcare, and then arrange an additional doctor's appointment days afterward to take the second dose of medication. While surgical abortion procedures are quicker (usually a one-day outpatient procedure, depending on gestation), many people prefer having the abortion in the comfort of their home or surrounded by family instead.
Paige Alexandria, who counsels people seeking abortions at her job, says that survivors of sexual violence often prefer medical abortions to surgical ones. "A lot of time survivors have a trauma associated with medical instruments or having pelvic exams, and so they're more comfortable taking a pill," she says.
But REMS also creates a barrier for healthcare providers, Grossman says. Stocking the medication in-office is "a hassle" and "expensive," while others are reluctant to register their name with the drug manufacturer, fearing harassment or violence from anti-choice protestors. As a result, the number of practitioners willing to provide medical abortions nationwide is severely limited. According to Grossman's own research published in the journal Obstetrics and Gynecology, 28 percent of OBGYNs admitted they would administer medication abortions if it were possible to write a prescription for Mifepristone rather than stock it in-office.
Amazingly, the restrictions on Mifepristone have loosened since it first came on the market. In 2016, the FDA updated the guidelines on Mifepristone to allow its use until 10 weeks gestation, up from eight weeks. But doctors say the REMS restrictions should be eliminated completely so that people can obtain abortions as early as possible.
"REMS restrictions inhibit people from being able to get a timely abortion," says Raymond, who stresses that abortion is generally more comfortable, more affordable, and safer for women the earlier it's done. "Abortion is very safe no matter when you get it, but it's also easier because there's less risk for bleeding, infections, or other complications," Raymond says. Abortions that occur earlier than eight weeks of gestation have a complication rate of less than one percent, while an abortion done at 12 or 13 weeks has a three to six percent chance of complications.
And even for people who want a medication abortion early on in their pregnancy, REMS restrictions make it so that they may not have time to obtain it before the 10-week period lapses, Raymond says.
"If you're seven weeks pregnant but it takes you three weeks to figure out travel and childcare arrangements to go into the doctor and take this medication, now you're at the cutoff date," she says. "Even if you manage to get an abortion at nine weeks, that's still a later gestational age, and so the risks are increased."
In 2016, at a little over nine weeks gestation, Alexandria completed her abortion by having a D&E. But because she didn't have anyone to drive her home after the procedure, she wasn't able to have sedation throughout, something she describes as "traumatic."
"I had the abortion completely aware and coherent, and paired with the fact that I hadn't even wanted a surgical abortion in the first place made it harder to deal with," Alexandria says.
"When you're just a day or two past eight weeks and you want an abortion – why is medication not immediately available?"
Today, Alexandria shares her story publicly to advocate for abortion care. Although she doesn't regret her surgical abortion and acknowledges that not everyone experiences surgical abortion the same way she did, she does wish that she could have gone a different route.
"If I had to do it over, I would still try to do the pill, because [the surgical abortion] was such a terrifying experience," she says. "When you're just a day or two past eight weeks and you want an abortion – why is medication not immediately available? It just doesn't make sense."
Basecamp Research is using portable labs like this one to gather samples from ecosystems around the world.
Clark works for Basecamp Research, a biotech company headquartered in London, and his job is to collect samples from ecosystems around the world. By extracting DNA from soil, water, plants, microbes and other organisms, Basecamp is building an extensive database of the Earth’s proteins. While DNA itself isn’t a protein, the information stored in DNA is used to create proteins, so extracting, sequencing, and annotating DNA allows for the discovery of unique protein sequences.
Using what they’re finding in the middle of the Atlantic and beyond, Basecamp’s detailed database is constantly growing. The outputs could be essential for cleaning up the damage done by toxic chemicals and finding alternatives to these chemicals.
Catalysts for change
Proteins provide structure and function in all living organisms. Some of these functional proteins are enzymes, which quite literally make things happen.
“Industrial chemistry is heavily polluting, especially the chemistry done in pharmaceutical drug development. Biocatalysis is providing advantages, both to make more complex drugs and to be more sustainable, reducing the pollution and toxicity of conventional chemistry," says Ahir Pushpanath, who heads partnerships for Basecamp.
“Enzymes are perfectly evolved catalysts,” says Ahir Pushpanath, a partnerships lead at Basecamp. ”Enzymes are essentially just a polymer, and polymers are made up of amino acids, which are nature’s building blocks.” He suggests thinking about it like Legos — if you have a bunch of Lego pieces and use them to build a structure that performs a function, “that’s basically how an enzyme works. In nature, these monuments have evolved to do life’s chemistry. If we didn’t have enzymes, we wouldn’t be alive.”
In our own bodies, enzymes catalyze everything from vision to digesting food to regrowing muscles, and these same types of enzymes are necessary in the pharmaceutical, agrochemical and fine chemical industries. But industrial conditions differ from those inside our bodies. So, when scientists need certain chemical reactions to create a particular product or substance, they make their own catalysts in their labs — generally through the use of petroleum and heavy metals.
These petrochemicals are effective and cost-efficient, but they’re wasteful and often hazardous. With growing concerns around sustainability and long-term public health, it's essential to find alternative solutions to toxic chemicals. “Industrial chemistry is heavily polluting, especially the chemistry done in pharmaceutical drug development,” Pushpanath says.
Basecamp is trying to replace lab-created catalysts with enzymes found in the wild. This concept is called biocatalysis, and in theory, all scientists have to do is find the right enzymes for their specific need. Yet, historically, researchers have struggled to find enzymes to replace petrochemicals. When they can’t identify a suitable match, they turn to what Pushpanath describes as “long, iterative, resource-intensive, directed evolution” in the laboratory to coax a protein into industrial adaptation. But the latest scientific advances have enabled these discoveries in nature instead.
Marlon Clark, a research scientist at Basecamp Research, looks for novel biochemistries in the Azores.
Glen Gowers
Enzyme hunters
Whether it’s Clark and a colleague setting off on an expedition, or a local, on-the-ground partner gathering and processing samples, there’s a lot to be learned from each collection. “Microbial genomes contain complete sets of information that define an organism — much like how letters are a code allowing us to form words, sentences, pages, and books that contain complex but digestible knowledge,” Clark says. He thinks of the environmental samples as biological libraries, filled with thousands of species, strains, and sequence variants. “It’s our job to glean genetic information from these samples.”
“We can actually dream up new proteins using generative AI," Pushpanath says.
Basecamp researchers manage this feat by sequencing the DNA and then assembling the information into a comprehensible structure. “We’re building the ‘stories’ of the biota,” Clark says. The more varied the samples, the more valuable insights his team gains into the characteristics of different organisms and their interactions with the environment. Sequencing allows scientists to examine the order of nucleotides — the organic molecules that form DNA — to identify genetic makeups and find changes within genomes. The process used to be too expensive, but the cost of sequencing has dropped from $10,000 a decade ago to as low as $100. Notably, biocatalysis isn’t a new concept — there have been waves of interest in using natural enzymes in catalysis for over a century, Pushpanath says. “But the technology just wasn’t there to make it cost effective,” he explains. “Sequencing has been the biggest boon.”
AI is probably the second biggest boon.
“We can actually dream up new proteins using generative AI,” Pushpanath says, which means that biocataylsis now has real potential to scale.
Glen Gowers, the co-founder of Basecamp, compares the company’s AI approach to that of social networks and streaming services. Consider how these platforms suggest connecting with the friends of your friends, or how watching one comedy film from the 1990s leads to a suggestion of three more.
“They’re thinking about data as networks of relationships as opposed to lists of items,” says Gowers. “By doing the same, we’re able to link the metadata of the proteins — by their relationships to each other, the environments in which they’re found, the way those proteins might look similar in sequence and structure, their surrounding genome context — really, this just comes down to creating a searchable network of proteins.”
On an Azores island, this volcanic opening may harbor organisms that can help scientists identify enzymes for biocatalysis to replace toxic chemicals.
Emma Bolton
Uwe Bornscheuer, professor at the Institute of Biochemistry at the University of Greifswald, and co-founder of Enzymicals, another biocatalysis company, says that the development of machine learning is a critical component of this work. “It’s a very hot topic, because the challenge in protein engineering is to predict which mutation at which position in the protein will make an enzyme suitable for certain applications,” Bornscheuer explains. These predictions are difficult for humans to make at all, let alone quickly. “It is clear that machine learning is a key technology.”
Benefiting from nature’s bounty
Biodiversity commonly refers to plants and animals, but the term extends to all life, including microbial life, and some regions of the world are more biodiverse than others. Building relationships with global partners is another key element to Basecamp’s success. Doing so in accordance with the access and benefit sharing principles set forth by the Nagoya Protocol — an international agreement that seeks to ensure the benefits of using genetic resources are distributed in a fair and equitable way — is part of the company's ethos. “There's a lot of potential for us, and there’s a lot of potential for our partners to have exactly the same impact in building and discovering commercially relevant proteins and biochemistries from nature,” Clark says.
Bornscheuer points out that Basecamp is not the first company of its kind. A former San Diego company called Diversa went public in 2000 with similar work. “At that time, the Nagoya Protocol was not around, but Diversa also wanted to ensure that if a certain enzyme or microorganism from Costa Rica, for example, were used in an industrial process, then people in Costa Rica would somehow profit from this.”
An eventual merger turned Diversa into Verenium Corporation, which is now a part of the chemical producer BASF, but it laid important groundwork for modern companies like Basecamp to continue to scale with today’s technologies.
“To collect natural diversity is the key to identifying new catalysts for use in new applications,” Bornscheuer says. “Natural diversity is immense, and over the past 20 years we have gained the advantages that sequencing is no longer a cost or time factor.”
This has allowed Basecamp to rapidly grow its database, outperforming Universal Protein Resource or UniProt, which is the public repository of protein sequences most commonly used by researchers. Basecamp’s database is three times larger, totaling about 900 million sequences. (UniProt isn’t compliant with the Nagoya Protocol, because, as a public database, it doesn’t provide traceability of protein sequences. Some scientists, however, argue that Nagoya compliance hinders progress.)
“Eventually, this work will reduce chemical processes. We’ll have cleaner processes, more sustainable processes," says Uwe Bornscheuer, a professor at the University of Greifswald.
With so much information available, Basecamp’s AI has been trained on “the true dictionary of protein sequence life,” Pushpanath says, which makes it possible to design sequences for particular applications. “Through deep learning approaches, we’re able to find protein sequences directly from our database, without the need for further laboratory-directed evolution.”
Recently, a major chemical company was searching for a specific transaminase — an enzyme that catalyzes a transfer of amino groups. “They had already spent a year-and-a-half and nearly two million dollars to evolve a public-database enzyme, and still had not reached their goal,” Pushpanath says. “We used our AI approaches on our novel database to yield 10 candidates within a week, which, when validated by the client, achieved the desired target even better than their best-evolved candidate.”
Basecamp’s other huge potential is in bioremediation, where natural enzymes can help to undo the damage caused by toxic chemicals. “Biocatalysis impacts both sides,” says Gowers. “It reduces the usage of chemicals to make products, and at the same time, where contamination sites do exist from chemical spills, enzymes are also there to kind of mop those up.”
So far, Basecamp's round-the-world sampling has covered 50 percent of the 14 major biomes, or regions of the planet that can be distinguished by their flora, fauna, and climate, as defined by the World Wildlife Fund. The other half remains to be catalogued — a key milestone for understanding our planet’s protein diversity, Pushpanath notes.
There’s still a long road ahead to fully replace petrochemicals with natural enzymes, but biocatalysis is on an upward trajectory. "Eventually, this work will reduce chemical processes,” Bornscheuer says. “We’ll have cleaner processes, more sustainable processes.”
In an initial study, Canary analyzed speech recordings with AI and identified early stage Alzheimer’s with 96 percent accuracy.
Arnold was diagnosed sooner than many others. It's important to find out early, when interventions can make the most difference. One promising avenue is looking at how people talk. Research has shown that Alzheimer’s affects a part of the brain that controls speech, resulting in small changes before people show other signs of the disease.
Now, Canary Speech, a company based in Utah, is using AI to examine elements like the pitch of a person’s voice and their pauses. In an initial study, Canary analyzed speech recordings with AI and identified early stage Alzheimer’s with 96 percent accuracy.
Developing the AI model
Canary Speech’s CEO, Henry O’Connell, met cofounder Jeff Adams about 40 years before they started the company. Back when they first crossed paths, they were both living in Bethesda, Maryland; O’Connell was a research fellow at the National Institutes of Health studying rare neurological diseases, while Adams was working to decode spy messages. Later on, Adams would specialize in building mathematical models to analyze speech and sound as a team leader in developing Amazon's Alexa.
It wasn't until 2015 that they decided to make use of the fit between their backgrounds. ““We established Canary Speech in 2017 to build a product that could be used in multiple languages in clinical environments,” O'Connell says.
The need is growing. About 55 million people worldwide currently live with Alzheimer’s, a number that is expected to double by 2050. Some scientists think the disease results from a buildup of plaque in the brain. It causes mild memory loss at first and, over time, this issue get worse while other symptoms, such as disorientation and hallucinations, can develop. Treatment to manage the disease is more effective in the earlier stages, but detection is difficult since mild symptoms are often attributed to the normal aging process.
O’Connell and Adams specialize in the complex ways that Alzheimer’s effects how people speak. Using AI, their mathematical model analyzes 15 million data points every minute, focusing on certain features of speech such as pitch, pauses and elongation of words. It also pays attention to how the vibrations of vocal cords change in different stages of the disease.
To create their model, the team used a type of machine learning called deep neural nets, which looks at multiple layers of data - in this case, the multiple features of a person’s speech patterns.
“Deep neural nets allow us to look at much, much larger data sets built out of millions of elements,” O’Connell explained. “Through machine learning and AI, we’ve identified features that are very sensitive to an Alzheimer’s patient versus [people without the disease] and also very sensitive to mild cognitive impairment, early stage and moderate Alzheimer's.” Based on their learnings, Canary is able to classify the disease stage very quickly, O’Connell said.
“When we’re listening to sublanguage elements, we’re really analyzing the direct result of changes in the brain in the physical body,” O’Connell said. “The brain controls your vocal cords: how fast they vibrate, the expansion of them, the contraction.” These factors, along with where people put their tongues when talking, function subconsciously and result in subtle changes in the sounds of speech.
Further testing is needed
In an initial trial, Canary analyzed speech recordings from phone calls to a large U.S. health insurer. They looked at the audio recordings of 651 policyholders who had early stage Alzheimer’s and 1018 who did not have the condition, aiming for a representative sample of age, gender and race. They used this data to create their first diagnostic model and found that it was 96 percent accurate in identifying Alzheimer’s.
Christian Herff, an assistant professor of neuroscience at Maastricht University in the Netherlands, praised this approach while adding that further testing is needed to assess its effectiveness.
“I think the general idea of identifying increased risk for cognitive impairment based on speech characteristics is very feasible, particularly when change in a user’s voice is monitored, for example, by recording speech every year,” Herff said. He noted that this can only be a first indication, not a full diagnosis. The accuracy still needs to be validated in studies that follows individuals over a period of time, he said.
Toby Walsh, a professor of artificial intelligence at the University of New South Wales, also thinks Canary’s tool has potential but highlights that Canary could diagnose some people who don’t really have the disease. “This is an interesting and promising application of AI,” he said, “but these tools need to be used carefully. Imagine the anxiety of being misdiagnosed with Alzheimer’s.”
As with many other AI tools, privacy and bias are additional issues to monitor closely, Walsh said.
Other languages
A related issue is that not everyone is fluent in English. Mahnaz Arvaneh, a senior lecturer in automatic control and systems engineering at the University of Sheffield, said this could be a blind spot.
“The system may not be very accurate for those who have English as their second language as their speaking patterns would be different, and any issue might be because of language deficiency rather than cognitive issues,” Arvaneh said.
The team is expanding to multiple languages starting with Japanese and Spanish. The elements of the model that make up the algorithm are very similar, but they need to be validated and retrained in a different language, which will require access to more data.
Recently, Canary analyzed the phone calls of 233 Japanese patients who had mild cognitive impairment and 704 healthy people. Using an English model they were able to identify the Japanese patients who had mild cognitive impairment with 78 percent accuracy. They also developed a model in Japanese that was 45 percent accurate, and they’re continuing to train it with more data.
The future
Canary is using their model to look at other diseases like Huntington’s and Parkinson’s. They’re also collaborating with pharmaceuticals to validate potential therapies for Alzheimer’s. By looking at speech patterns over time, Canary can get an indication of how well these drugs are working.
Dave Arnold and his wife dance at his nephew’s wedding in Rochester, New York, ten years ago, before his Alzheimer's diagnosis.
Dave Arnold
Ultimately, they want to integrate their tool into everyday life. “We want it to be used in a smartphone, or a teleconference call so that individuals could be examined in their home,” O’Connell said. “We could follow them over time and work with clinical teams and hospitals to improve the evaluation of patients and contribute towards an accurate diagnosis.”
Arnold, the patient with early stage Alzheimer’s, sees great promise. “The process of getting a diagnosis is already filled with so much anxiety,” he said. “Anything that can be done to make it easier and less stressful would be a good thing, as long as it’s proven accurate.”