The Science Sleuth Holding Fraudulent Research Accountable
Kira Peikoff was the editor-in-chief of Leaps.org from 2017 to 2021. As a journalist, her work has appeared in The New York Times, Newsweek, Nautilus, Popular Mechanics, The New York Academy of Sciences, and other outlets. She is also the author of four suspense novels that explore controversial issues arising from scientific innovation: Living Proof, No Time to Die, Die Again Tomorrow, and Mother Knows Best. Peikoff holds a B.A. in Journalism from New York University and an M.S. in Bioethics from Columbia University. She lives in New Jersey with her husband and two young sons. Follow her on Twitter @KiraPeikoff.
Introduction by Mary Inman, Whistleblower Attorney
For most people, when they see the word "whistleblower," the image that leaps to mind is a lone individual bravely stepping forward to shine a light on misconduct she has witnessed first-hand. Meryl Streep as Karen Silkwood exposing safety violations observed while working the line at the Kerr-McGee plutonium plant. Matt Damon as Mark Whitacre in The Informant!, capturing on his pocket recorder clandestine meetings between his employer and its competitors to fix the price of lysine. However, a new breed of whistleblower is emerging who isn't at the scene of the crime but instead figures it out after the fact through laborious review of publicly available information and expert analysis. Elisabeth Bik belongs to this new class of whistleblower.
"There's this delicate balance where on one hand we want to spread results really fast as scientists, but on the other hand, we know it's incomplete, it's rushed and it's not great."
Using her expertise as a microbiologist and her trained eye, Bik studies publicly available scientific papers to sniff out potential irregularities in the images that suggest research fraud, later seeking retraction of the offending paper from the journal's publisher. There's no smoking gun, no first-hand account of any kind. Just countless hours spent reviewing scores of scientific papers and Bik's skills and dedication as a science fraud sleuth.
While Bik's story may not as readily lend itself to the big screen, her work is nonetheless equally heroic. By tirelessly combing scientific papers to expose research fraud, Bik is playing a vital role in holding the scientific publishing process accountable and ensuring that misleading information does not spread unchecked. This is important work in any age, but particularly so in the time of COVID, where we can ill afford the setbacks and delays of scientists building on false science. In the present climate, where science is politicized and scientific principles are under attack, strong voices like Bik's must rise above the din to ensure the scientific information we receive, and our governments act upon, is accurate. Our health and wellbeing depend on it.
Whistleblower outsiders like Bik are challenging the traditional concept of what it means to be a whistleblower. Fortunately for us, the whistleblower community is a broad church. As with most ecosystems, we all benefit from a diversity of voices —whistleblower insiders and outsiders alike. What follows is an illuminating conversation between Bik, and Ivan Oransky, the co-founder of Retraction Watch, an influential blog that reports on retractions of scientific papers and related topics. (Conversation facilitated by LeapsMag Editor-in-Chief Kira Peikoff)
Elisabeth Bik and Ivan Oransky.
(Photo credits Michel & Co Photography, San Jose, CA and Elizabeth Solaka)
Ivan
I'd like to hear your thoughts, Elisabeth, on an L.A. Times story, which was picking up a preprint about mutations and the novel coronavirus, alleging that the virus is mutating to become more infectious – even though this conclusion wasn't actually warranted.
Elisabeth
A lot of the news around it is picking up on one particular side of the story that is maybe not that much exaggerated by the scientists. I don't think this paper really showed that the mutations were causing the virus to be more virulent. Some of these viruses continuously mutate and mutate and mutate, and that doesn't necessarily make a strain more virulent. I think in many cases, a lot of people want to read something in a paper that is not actually there.
Ivan
The tone level, everything that's being published now, it's problematic. It's being rushed, here it wasn't even peer-reviewed. But even when they are peer-reviewed, they're being peer-reviewed by people who often aren't really an expert in that particular area.
Elisabeth
That's right.
Ivan
To me, it's all problematic. At the same time, it's all really good that it's all getting out there. I think that five or 10 years ago, or if we weren't in a pandemic, maybe that paper wouldn't have appeared at all. It would have maybe been submitted to a top-ranked journal and not have been accepted, or maybe it would have been improved during peer review and bounced down the ladder a bit to a lower-level journal.
Yet, now, because it's about coronavirus, it's in a major newspaper and, in fact, it's getting critiqued immediately.
Maybe it's too Pollyanna-ish, but I actually think that quick uploading is a good thing. The fear people have about preprint servers is based on this idea that the peer-reviewed literature is perfect. Once it is in a peer-reviewed journal, they think it must have gone through this incredible process. You're laughing because-
Elisabeth
I am laughing.
Ivan
You know it's not true.
Elisabeth
Yes, we both know that. I agree and I think in this particular situation, a pandemic that is unlike something our generation has seen before, there is a great, great need for fast dissemination of science.
If you have new findings, it is great that there is a thing called a preprint server where scientists can quickly share their results, with, of course, the caveat that it's not peer-reviewed yet.
It's unlike the traditional way of publishing papers, which can take months or years. Preprint publishing is a very fast way of spreading your results in a good way so that is what the world needs right now.
On the other hand, of course, there's the caveat that these are brand new results and a good scientist usually thinks about their results to really interpret it well. You have to look at it from all sides and I think with the rushed publication of preprint papers, there is no such thing as carefully thinking about what results might mean.
So there's this delicate balance where on one hand we want to spread results really fast as scientists, but on the other hand, we know it's incomplete, it's rushed and it's not great. This might be hard for the general audience to understand.
Ivan
I still think the benefits of that dissemination are more positive than negative.
Elisabeth
Right. But there's also so many papers that come out now on preprint servers and most of them are not that great, but there are some really good studies in there. It's hard to find those nuggets of really great papers. There's just a lot of papers that come out now.
Ivan
Well, you've made more than a habit of finding problems in papers. These are mostly, of course, until now published papers that you examined, but what is this time like for you? How is it different?
Elisabeth
It's different because in the beginning I looked at several COVID-19-related papers that came out and wrote some critiques about it. I did experience a lot of backlash because of that. So I felt I had to take a break from social media and from writing about COVID-19.
I focused a little bit more on other work because I just felt that a lot of these papers on COVID-19 became so politically divisive that if you tried to be a scientist and think critically about a paper, you were actually assigned to a particular political party or to be against other political parties. It's hard for me to be sucked into the political discussion and to the way that our society now is so completely divided into two camps that seem to be not listening to each other.
Ivan
I was curious about that because I've followed your work for a number of years, as you know, and certainly you have had critics before. I'm thinking of the case in China that you uncovered, the leading figure in the Chinese Academy who was really a powerful political figure in addition to being a scientist.
Elisabeth
So that was a case in which I found a couple of papers at first from a particular group in China, and I was just posting on a website called PubPeer, where you can post comments, concerns about papers. And in this case, these were image duplication issues, which is my specialty.
I did not realize that the group I was looking at at that moment was led by one of the highest ranked scientists in China. If I had known that, I would probably not have posted that under my full name, but under a pseudonym. Since I had already posted, some people were starting to send me direct messages on Twitter like, "OMG, the guy you're posting about now is the top scientist in China so you're going to have a lot of backlash."
Then I decided I'll just continue doing this. I found a total of around 50 papers from this group and posted all of them on PubPeer. That story quickly became a very popular story in China: number two on Sina Weibo, a social media site in China.
I was surprised it wasn't suppressed by the Chinese government, it was actually allowed by journalists that were writing about it, and I didn't experience a lot of backlash because of that.
Actually the Chinese doctor wrote me an email saying that he appreciated my feedback and that he would look into these cases. He sent a very polite email so I sent him back that I appreciated that he would look into these cases and left it there.
Ivan
There are certain subjects that I know when we write about them in Retraction Watch, they have tended in the past to really draw a lot of ire. I'm thinking anything about vaccines and autism, anything about climate change, stem cell research.
For a while that last subject has sort of died down. But now it's become a highly politically charged atmosphere. Do you feel that this pandemic has raised the profile of people such as yourself who we refer to as scientific sleuths, people who look critically and analytically at new research?
Elisabeth
Yeah, some people. But I'm also worried that some people who are great scientists and have shown a lot of critical thinking are being attacked because of that. If you just look at what happened to Dr. Fauci, I think that's a prime example. Where somebody who actually is very knowledgeable and very cautious of new science has not been widely accepted as a great leader, in our country at least. It's sad to see that. I'm just worried how long he will be at his position, to be honest.
Ivan
We noticed a big uptick in our traffic in the last few days to Retraction Watch and it turns out it was because someone we wrote about a number of years ago has really hopped on the bandwagon to try and discredit and even try to have Dr. Fauci fired.
It's one of these reminders that the way people think about scientists has, in many cases, far more to do with their own history or their own perspective going in than with any reality or anything about the science. It's pretty disturbing, but it's not a new thing. This has been happening for a while.
You can go back and read sociologists of science from 50-60 years ago and see the same thing, but I just don't think that it's in the same way that it is now, maybe in part because of social media.
Elisabeth
I've been personally very critical about several studies, but this is the first time I've experienced being attacked by trolls and having some nasty websites written about me. It is very disturbing to read.
"I don't think that something that's been peer-reviewed is perfect and something that hasn't been peer reviewed, you should never bother reading it."
Ivan
It is. Yet you have been a fearless and vocal critic of some very high-profile papers, like the infamous French study about hydroxychloroquine.
Elisabeth
Right, the paper that came out was immediately tweeted by the President of the United States. At first I thought it was great that our President tweeted about science! I thought that was a major breakthrough. I took a look at this paper.
It had just come out that day, I believe. The first thing I noticed is that it was accepted within 24 hours of being submitted to the journal. It was actually published in a journal where one of the authors is the editor-in-chief, which is a huge conflict of interest, but it happens.
But in this particular case, there were also a lot of flaws with the study and that, I think, should have been caught during peer review. The paper was first published on a preprint server and then within 24 hours or so it was published in that paper, supposedly after peer review.
There were very few changes between the preprint version and the peer review paper. There were just a couple of extra lines, extra sentences added here and there, but it wasn't really, I think, critically looked at. Because there were a lot of things that I thought were flaws.
Just to go over a couple of them. This paper showed supposedly that people who were treated with hydroxychloroquine and azithromycin were doing much better by clearing their virus much faster than people who were not treated with these drugs.
But if you look carefully at the paper there were a couple of people who were left out of the study. So they were treated with hydroxychloroquine, but they were not shown in the end results of the paper. All six people who were treated with the drug combination were clearing the virus within six days, but there were a couple of others who were left out of the study. They also started the drug combination, but they stopped taking the drugs for several reasons and three of them were admitted to the intensive care, one died, one had some side effects and one apparently walked out of the hospital.
They were left out of the study but they were actually not doing very well with the drug combination. It's not very good science if you leave out people who don't do very well with your drug combination in your study. That was one of my biggest critiques of the paper.
Ivan
What struck us about that case was, in addition to what you, of course, mentioned, the fact that Trump tweeted it and was talking about hydroxychloroquine, was that it seemed to be a perfect example of, "well, it was in a peer review journal." Yeah, it was a preprint first, but, well, it's a peer review journal. And yet, as you point out, when you look at the history of the paper, it was accepted in 24 hours.
If you talk to most scientists, the actual act of a peer review, once you sit down to do it and can concentrate, a good one takes, again, these are averages, but four hours, a half a day is not unreasonable. So you had to find three people who could suddenly review this paper. As you pointed out, it was in a journal where one of the authors was editor.
Then some strange things also happened, right? The society that actually publishes the journal, they came out with a statement saying this wasn't up to our standards, which is odd. Then Elsevier came in, they're the ones who are actually contracted to publish the journal for the society. They said, basically, "Oh, we're going to look into this now too."
It just makes you wonder what happened before the paper was actually published. All the people who were supposed to have been involved in doing the peer review or checking on it are clearly very distraught about what actually happened. It's that scene from Casablanca, "I'm shocked, shocked there's gambling going on here." And then, "Your winnings, sir."
Elisabeth
Yes.
Ivan
And I don't actually blame the public, I don't blame reporters for getting a bit confused about what it all means and what they should trust. I don't think trust is a binary any more than anything else is a binary. I don't think that something that's been peer-reviewed is perfect and something that hasn't been peer reviewed, you should never bother reading it. I think everything is much more gray.
Yet we've turned things into a binary. Even if you go back before coronavirus, coffee is good for you, coffee is bad for you, red wine, chocolate, all the rest of it. A lot of that is because of this sort of binary construct of the world for journalists, frankly, for scientists that need to get their next grants. And certainly for the general public, they want answers.
On the one hand, if I had to choose what group of experts, or what field of human endeavor would I trust with finding the answer to a pandemic like this, or to any crisis, it would absolutely be scientists. Hands down. This is coming from someone who writes about scientific fraud.
But on the other hand, that means that if scientists aren't clear about what they don't know and about the nuances and about what the scientific method actually allows us to do and learn, that just sets them up for failure. It sets people like Dr. Fauci up for failure.
Elisabeth
Right.
Ivan
It sets up any public health official who has a discussion about models. There's a famous saying: "All models are wrong, but some are useful."
Just because the projections change, it's not proof of wrongness, it's not proof that the model is fatally flawed. In fact, I'd be really concerned if the projections didn't change based on new information. I would love it if this whole episode did lead to a better understanding of the scientific process and how scientific publishing fits into that — and doesn't fit into it.
Elisabeth
Yes, I'm with you. I'm very worried that the general audience's perspective is based on maybe watching too many movies where the scientist comes up with a conclusion one hour into the movie when everything is about to fail. Like that scene in Contagion where somebody injects, I think, eight monkeys, and one of the monkeys survives and boom we have the vaccine. That's not really how science works. Everything takes many, many years and many, many applications where usually your first ideas and your first hypothesis turn out to be completely wrong.
Then you go back to the drawing board, you develop another hypothesis and this is a very reiterative process that usually takes years. Most of the people who watch the movie might have a very wrong idea and wrong expectations about how science works. We're living in the movie Contagion and by September, we'll all be vaccinated and we can go on and live our lives. But that's not what is going to happen. It's going to take much, much longer and we're going to have to change the models every time and change our expectations. Just because we don't know all the numbers and all the facts yet.
Ivan
Generally it takes a fairly long time to change medical practice. A lot of times people see that as a bad thing. What I think that ignores, or at least doesn't take into as much account as I would, is that you don't want doctors and other health care professionals to turn on a dime and suddenly switch. Unless, of course, it turns out there was no evidence for what you were looking at.
It's a complicated situation.
Everybody wants scientists to be engineers, right?
Elisabeth
Right.
Ivan
I'm not saying engineering isn't scientific, nor am I saying that science is just completely whimsical, but there's a different process. It's a different way of looking at things and you can't just throw all the data into a big supercomputer, which is what I think a lot of people seem to want us to do, and then the obvious answer will come out on the other side.
Elisabeth
No. It's true and a lot of engineers suddenly feel their inherent need to solve this as a problem. They're not scientists and it's not building a bridge over a big river. But we're dealing with something that is very hard to solve because we don't understand the problem yet. I think scientists are usually first analyzing the problem and trying to understand what the problem actually is before you can even think about a solution.
Ivan
I think we're still at the understanding the problem phase.
Elisabeth
Exactly. And going back to the French group paper, that promised such a result and that was interpreted as such by a lot of people including presidents, but it's a very rare thing to find a medication that will have a 100% curation rate. That's something that I wish the people would understand better. We all want that to happen, but it's very unlikely and very unprecedented in the best of times.
Ivan
I would second that and also say that the world needs to better value the work that people like Elisabeth and others are doing. Because we're not going to get to a better answer if we're not rigorous about scrutinizing the literature and scrutinizing the methodology and scrutinizing the results.
"I quit my job to be able to do this work."
It's a relatively new phenomenon that you're able to do this at any scale at all, and even now it's at a very small scale. Elisabeth mentioned PubPeer and I'm a big fan — also full disclosure, I'm on their board of directors as a volunteer — it's a very powerful engine for readers and journal editors and other scientists to discuss issues.
And Elisabeth has used it really, really well. I think we need to start giving credit to people like that. And, also creating incentives for that kind of work in a way that science hasn't yet.
Elisabeth
Yeah. I quit my job to be able to do this work. It's really hard to combine it with a job either in academia or industry because we're looking for or criticizing papers and it's hard when you are still employed to do that.
I try to make it about the papers and do it in a polite way, but still it's a very hard job to do if you have a daytime job and a position and a career to worry about. Because if you're critical of other academics, that could actually mean the end of your career and that's sad. They should be more open to polite criticism.
Ivan
And for the general public, if you're reading a newspaper story or something online about a single study and it doesn't mention any other studies that have said the same thing or similar, or frankly, if it doesn't say anything about any studies that contradicted it, that's probably also telling you something.
Say you're looking at a huge painting of a shoreline, a beach, and a forest. Any single study is just a one-centimeter-by-one-centimeter square of any part of that canvas. If you just look at that, you would either think it was a painting of the sea, of a beach, or of the forest. It's actually all three of those things.
We just need to be patient, and that's very challenging to us as human beings, but we need to take the time to look at the whole picture.
DISCLAIMER: Neither Elisabeth Bik nor Ivan Oransky was compensated for participation in The Pandemic Issue. While the magazine's editors suggested broad topics for discussion, consistent with Bik's and Oransky's work, neither they nor the magazine's underwriters had any influence on their conversation.
[Editor's Note: This article was originally published on June 8th, 2020 as part of a standalone magazine called GOOD10: The Pandemic Issue. Produced as a partnership among LeapsMag, The Aspen Institute, and GOOD, the magazine is available for free online.]
Kira Peikoff was the editor-in-chief of Leaps.org from 2017 to 2021. As a journalist, her work has appeared in The New York Times, Newsweek, Nautilus, Popular Mechanics, The New York Academy of Sciences, and other outlets. She is also the author of four suspense novels that explore controversial issues arising from scientific innovation: Living Proof, No Time to Die, Die Again Tomorrow, and Mother Knows Best. Peikoff holds a B.A. in Journalism from New York University and an M.S. in Bioethics from Columbia University. She lives in New Jersey with her husband and two young sons. Follow her on Twitter @KiraPeikoff.
Genomics has begun its golden age. Just 20 years ago, sequencing a single genome cost nearly $3 billion and took over a decade. Today, the same feat can be achieved for a few hundred dollars and the better part of a day . Suddenly, the prospect of sequencing not just individuals, but whole populations, has become feasible.
The genetic differences between humans may seem meager, only around 0.1 percent of the genome on average, but this variation can have profound effects on an individual's risk of disease, responsiveness to medication, and even the dosage level that would work best.
Already, initiatives like the U.K.'s 100,000 Genomes Project - now expanding to 1 million genomes - and other similarly massive sequencing projects in Iceland and the U.S., have begun collecting population-scale data in order to capture and study this variation.
The resulting data sets are immensely valuable to researchers and drug developers working to design new 'precision' medicines and diagnostics, and to gain insights that may benefit patients. Yet, because the majority of this data comes from developed countries with well-established scientific and medical infrastructure, the data collected so far is heavily biased towards Western populations with largely European ancestry.
This presents a startling and fast-emerging problem: groups that are under-represented in these datasets are likely to benefit less from the new wave of therapeutics, diagnostics, and insights, simply because they were tailored for the genetic profiles of people with European ancestry.
We may indeed be approaching a golden age of genomics-enabled precision medicine. But if the data bias persists then there is a risk, as with most golden ages throughout history, that the benefits will not be equally accessible to all, and existing inequalities will only be exacerbated.
To remedy the situation, a number of initiatives have sprung up to sequence genomes of under-represented groups, adding them to the datasets and ensuring that they too will benefit from the rapidly unfolding genomic revolution.
Global Gene Corp
The idea behind Global Gene Corp was born eight years ago in Harvard when Sumit Jamuar, co-founder and CEO, met up with his two other co-founders, both experienced geneticists, for a coffee.
"They were discussing the limitless applications of understanding your genetic code," said Jamuar, a business executive from New Delhi.
"And so, being a technology enthusiast type, I was excited and I turned to them and said hey, this is incredible! Could you sequence me and give me some insights? And they actually just turned around and said no, because it's not going to be useful for you - there's not enough reference for what a good Sumit looks like."
What started as a curiosity-driven conversation on the power of genomics ended with a commitment to tackle one of the field's biggest roadblocks - its lack of global representation.
Jamuar set out to begin with India, which has about 20 percent of the world's population, including over 4000 different ethnicities, but contributes less than 2 percent of genomic data, he told Leaps.org.
Eight years later, Global Gene Corp's sequencing initiative is well underway, and is the largest in the history of the Indian subcontinent. The program is being carried out in collaboration with biotech giant Regeneron, with support from the Indian government, local communities, and the Indian healthcare ecosystem. In August 2020, Global Gene Corp's work was recognized through the $1 million 2020 Roddenberry award for organizations that advance the vision of 'Star Trek' creator Gene Roddenberry to better humanity.
This problem has already begun to manifest itself in, for example, much higher levels of genetic misdiagnosis among non-Europeans tested for their risk of certain diseases, such as hypertrophic cardiomyopathy - an inherited disease of the heart muscle.
Global Gene Corp also focuses on developing and implementing AI and machine learning tools to make sense of the deluge of genomic data. These tools are increasingly used by both industry and academia to guide future research by identifying particularly promising or clinically interesting genetic variants. But if the underlying data is skewed European, then the effectiveness of the computational analysis - along with the future advances and avenues of research that emerge from it - will be skewed towards Europeans too.
This problem has already begun to manifest itself in, for example, much higher levels of genetic misdiagnosis among non-Europeans tested for their risk of certain diseases, such as hypertrophic cardiomyopathy - an inherited disease of the heart muscle. Most of the genetic variants used in these tests were identified as being causal for the disease from studies of European genomes. However, many of these variants differ both in their distribution and clinical significance across populations, leading to many patients of non-European ancestry receiving false-positive test results - as their benign genetic variants were misclassified as pathogenic. Had even a small number of genomes from other ethnicities been included in the initial studies, these misdiagnoses could have been avoided.
"Unless we have a data set which is unbiased and representative, we're never going to achieve the success that we want," Jamuar says.
"When Siri was first launched, she could hardly recognize an accent which was not of a certain type, so if I was trying to speak to Siri, I would have to repeat myself multiple times and try to mimic an accent which wasn't my accent so that she could understand it.
"But over time the voice recognition technology improved tremendously because the training data was expanded to include people of very diverse backgrounds and their accents, so the algorithms were trained to be able to pick that up and it dramatically improved the technology. That's the way we have to think about it - without that good-quality diverse data, we will never be able to achieve the full potential of the computational tools."
While mapping India's rich genetic diversity has been the organization's primary focus so far, they plan, in time, to expand their work to other under-represented groups in Asia, the Middle East, Africa, and Latin America.
"As other like-minded people and partners join the mission, it just accelerates the achievement of what we have set out to do, which is to map out and organize the world's genomic diversity so that we can enable high-quality life and longevity benefits for everyone, everywhere," Jamuar says.
Empowering African Genomics
Africa is the birthplace of our species, and today still retains an inordinate amount of total human genetic diversity. Groups that left Africa and went on to populate the rest of the world, some 50 to 100,000 years ago, were likely small in number and only took a fraction of the total genetic diversity with them. This ancient bottleneck means that no other group in the world can match the level of genetic diversity seen in modern African populations.
Despite Africa's central importance in understanding the history and extent of human genetic diversity, the genomics of African populations remains wildly understudied. Addressing this disparity has become a central focus of the H3Africa Consortium, an initiative formally launched in 2012 with support from the African Academy of Sciences, the U.S. National Institutes of Health, and the UK's Wellcome Trust. Today, H3Africa supports over 50 projects across the continent, on an array of different research areas in genetics relevant to the health and heredity of Africans.
"Africa is the cradle of Humankind. So what that really means is that the populations that are currently living in Africa are among some of the oldest populations on the globe, and we know that the longer populations have had to go through evolutionary phases, the more variation there is in the genomes of people who live presently," says Zane Lombard, a principal investigator at H3Africa and Associate Professor of Human Genetics at the University of the Witwatersrand in Johannesburg, South Africa.
"So for that reason, African populations carry a huge amount of genetic variation and diversity, which is pretty much uncaptured. There's still a lot to learn as far as novel variation is concerned by looking at and studying African genomes."
A recent landmark H3Africa study, led by Lombard and published in Nature in October, sequenced the genomes of over 400 African individuals from 50 ethno-linguistic groups - many of which had never been sampled before.
Despite the relatively modest number of individuals sequenced in the study, over three million previously undescribed genetic variants were found, and complex patterns of ancestral migration were uncovered.
"In some of these ethno-linguistic groups they don't have a word for DNA, so we've had to really think about how to make sure that we communicate the purposes of different studies to participants so that you have true informed consent," says Lombard.
"The objective," she explained, "was to try and fill some of the gaps for many of these populations for which we didn't have any whole genome sequences or any genetic variation data...because if we're thinking about the future of precision medicine, if the patient is a member of a specific group where we don't know a lot about the genomic variation that exists in that group, it makes it really difficult to start thinking about clinical interpretation of their data."
From H3Africa's conception, the consortium's goal has not only been to better represent Africa's staggering genetic diversity in genomic data sets, but also to build Africa's domestic genomics capabilities and empower a new generation of African researchers. By doing so, the hope is that Africans will be able to set their own genomics agenda, and leapfrog to new and better ways of doing the work.
"The training that has happened on the continent and the number of new scientists, new students, and fellows that have come through the process and are now enabled to start their own research groups, to grow their own research in their countries, to be a spokesperson for genomics research in their countries, and to build that political will to do these larger types of sequencing initiatives - that is really a significant outcome from H3Africa as well. Over and above all the science that's coming out," Lombard says.
"What has been created through H3Africa is just this locus of researchers and scientists and bioethicists who have the same goal at heart - to work towards adjusting the data bias and making sure that all global populations are represented in genomics."
Jurassic Park Without the Scary Parts: How Stem Cells May Rescue the Near-Extinct Rhinoceros
I am a stem cell scientist. In my day job I work on developing ways to use stem cells to treat neurological disease – human disease. This is the story about how I became part of a group dedicated to rescuing the northern white rhinoceros from extinction.
The earth is now in an era that is called the "sixth mass extinction." The first extinction, 400 million years ago, put an end to 86 percent of the existing species, including most of the trilobites. When the earth grew hotter, dustier, or darker, it lost fish, amphibians, reptiles, plants, dinosaurs, mammals and birds. Each extinction event wiped out 80 to 90 percent of the life on the planet at the time. The first 5 mass extinctions were caused by natural disasters: volcanoes, fires, a meteor. But humans can take credit for the 6th.
Because of human activities that destroy habitats, creatures are now becoming extinct at a rate that is higher than any previously experienced. Some animals, like the giant panda and the California condor, have been pulled back from the brink of extinction by conserving their habitats, breeding in captivity, and educating the public about their plight.
But not the northern white rhino. This gentle giant is a vegetarian that can weigh up to 5,000 pounds. The rhino's weakness is its horn, which has become a valuable commodity because of the mistaken idea that it grants power and has medicinal value. Horns are not medicine; the horns are made of keratin, the same protein that is in fingernails. But as recently as 2017 more than 1,000 rhinos were slaughtered each year to harvest their horns.
All 6 rhino species are endangered. But the northern white has been devastated. Only two members of this species are alive now: Najin, age 32, and her daughter Fatu, 21, live in a protected park in Kenya. They are social animals and would prefer the company of other rhinos of their kind; but they can't know that they are the last two survivors of their entire species. No males exist anymore. The last male, Sudan, died in 2018 at age 45.
We are celebrating a huge milestone in the efforts to use stem cells to rescue the rhino.
I became involved in the rhino rescue project on a sunny day in February, 2008 at the San Diego Wild Animal Park in Escondido, about 30 miles north of my lab in La Jolla. My lab had relocated a couple of months earlier to Scripps Research Institute to start the Center for Regenerative Medicine for human stem cell research. To thank my staff for their hard work, I wanted to arrange a special treat. I contacted my friend Oliver Ryder, who is director of the Institute for Conservation Research at the zoo, to see if I could take them on a safari, a tour in a truck through the savanna habitat at the park.
This was the first of the "stem cell safaris" that the lab would enjoy over the next few years. On the safari we saw elands and cape buffalo, and fed giraffes and rhinos. And we talked about stem cells; in particular, we discussed a surprising technological breakthrough recently reported by the Japanese scientist Shinya Yamanaka that enabled conversion of ordinary skin cells into pluripotent stem cells.
Pluripotent stem cells can develop into virtually any cell type in the body. They exist when we are very young embryos; five days after we were just fertilized eggs, we became blastocysts, invisible tiny balls of a few hundred cells packed with the power to develop into an entire human being. Long before we are born, these cells of vast potential transform into highly specialized cells that generate our brains, our hearts, and everything else.
Human pluripotent stem cells from blastocysts can be cultured in the lab, and are called embryonic stem cells. But thanks to Dr. Yamanaka, anyone can have their skin cells reprogrammed into pluripotent stem cells, just like the ones we had when we were embryos. Dr. Yamanaka won the Nobel Prize for these cells, called "induced pluripotent stem cells" (iPSCs) several years later.
On our safari we realized that if we could make these reprogrammed stem cells from human skin cells, why couldn't we make them from animals' cells? How about endangered animals? Could such stem cells be made from animals whose skin cells had been being preserved since the 1970s in the San Diego Zoo's Frozen Zoo®? Our safari leader, Oliver Ryder, was the curator of the Frozen Zoo and knew what animal cells were stored in its giant liquid nitrogen tanks at −196°C (-320° F). The Frozen Zoo was established by Dr. Kurt Benirschke in 1975 in the hope that someday the collection would aid in rescue of animals that were on the brink of extinction. The frozen collection reached 10,000 cell lines this year.
We returned to the lab after the safari, and I asked my scientists if any of them would like to take on the challenge of making reprogrammed stem cells from endangered species. My new postdoctoral fellow, Inbar Friedrich Ben-Nun, raised her hand. Inbar had arrived only a few weeks earlier from Israel, and she was excited about doing something that had never been done before. Oliver picked the animals we would use. He chose his favorite animal, the critically endangered northern white rhinoceros, and the drill, which is an endangered primate related to the mandrill monkey,
When Inbar started work on reprogramming cells from the Frozen Zoo, there were 8 living northern rhinoceros around the world: Nola, Angalifu, Nesari, Nabire, Suni, Sudan, Najin, and Fatu. We chose to reprogram Fatu, the youngest of the remaining animals.
Through sheer determination and trial and error, Inbar got the reprogramming technique to work, and in 2011 we published the first report of iPSCs from endangered species in the scientific journal Nature Methods. The cover of the journal featured a drawing of an ark packed with animals that might someday be rescued through iPSC technology. By 2011, one of the 8 rhinos, Nesari, had died.
This kernel of hope for using iPSCs to rescue rhinos grew over the next 10 years. The zoo built the Rhino Rescue Center, and brought in 6 females of the closely related species, the southern white rhinoceros, from Africa. Southern white rhino populations are on the rise, and it appears that this species will survive, at least in captivity. The females are destined to be surrogate mothers for embryos made from northern white rhino cells, when eventually we hope to generate sperm and eggs from the reprogrammed stem cells, and fertilize the eggs in vitro, much the same as human IVF.
The author, Jeanne Loring, at the Rhino Rescue Center with one of the southern white rhino surrogates.
David Barker
As this project has progressed, we've been saddened by the loss of all but the last two remaining members of the species. Nola, the last northern white rhino in the U.S., who was at the San Diego Zoo, died in 2015.
But we are celebrating a huge milestone in the efforts to use stem cells to rescue the rhino. Just over a month ago, we reported that by reprogramming cells preserved in the Frozen Zoo, we produced iPSCs from stored cells of 9 northern white rhinos: Fatu, Najin, Nola, Suni, Nadi, Dinka, Nasima, Saut, and Angalifu. We also reprogrammed cells from two of the southern white females, Amani and Wallis.
We don't know when it will be possible to make a northern white rhino embryo; we have to figure out how to use methods already developed for laboratory mice to generate sperm and eggs from these cells. The male rhino Angalifu died in 2014, but ever since I saw beating heart cells derived from his very own cells in a culture dish, I've felt hope that he will one day have children who will seed a thriving new herd of northern white rhinos.