Murder Your Darling Hypotheses But Do Not Bury Them

“Whenever you feel an impulse to perpetrate a piece of exceptionally fine writing, obey it—whole-heartedly—and delete it before sending your manuscript to press. Murder your darlings.”

Sir Arthur Quiller-Couch (1863–1944). On the Art of Writing. 1916


Murder your darlings. The British writer Sir Arthur Quiller Crouch shared this piece of writerly wisdom when he gave his inaugural lecture series at Cambridge, asking writers to consider deleting words, phrases or even paragraphs that are especially dear to them. The minute writers fall in love with what they write, they are bound to lose their objectivity and may not be able to judge how their choice of words will be perceived by the reader. But writers aren’t the only ones who can fall prey to the Pygmalion syndrome. Scientists often find themselves in a similar situation when they develop “pet” or “darling” hypotheses.

Hypothesis via Shutterstock
Hypothesis via Shutterstock

How do scientists decide when it is time to murder their darling hypotheses? The simple answer is that scientists ought to give up scientific hypotheses once the experimental data is unable to support them, no matter how “darling” they are. However, the problem with scientific hypotheses is that they aren’t just generated based on subjective whims. A scientific hypothesis is usually put forward after analyzing substantial amounts of experimental data. The better a hypothesis is at explaining the existing data, the more “darling” it becomes. Therefore, scientists are reluctant to discard a hypothesis because of just one piece of experimental data that contradicts it.

In addition to experimental data, a number of additional factors can also play a major role in determining whether scientists will either discard or uphold their darling scientific hypotheses. Some scientific careers are built on specific scientific hypotheses which set apart certain scientists from competing rival groups. Research grants, which are essential to the survival of a scientific laboratory by providing salary funds for the senior researchers as well as the junior trainees and research staff, are written in a hypothesis-focused manner, outlining experiments that will lead to the acceptance or rejection of selected scientific hypotheses. Well written research grants always consider the possibility that the core hypothesis may be rejected based on the future experimental data. But if the hypothesis has to be rejected then the scientist has to explain the discrepancies between the preferred hypothesis that is now falling in disrepute and all the preliminary data that had led her to formulate the initial hypothesis. Such discrepancies could endanger the renewal of the grant funding and the future of the laboratory. Last but not least, it is very difficult to publish a scholarly paper describing a rejected scientific hypothesis without providing an in-depth mechanistic explanation for why the hypothesis was wrong and proposing alternate hypotheses.

For example, it is quite reasonable for a cell biologist to formulate the hypothesis that protein A improves the survival of neurons by activating pathway X based on prior scientific studies which have shown that protein A is an activator of pathway X in neurons and other studies which prove that pathway X improves cell survival in skin cells. If the data supports the hypothesis, publishing this result is fairly straightforward because it conforms to the general expectations. However, if the data does not support this hypothesis then the scientist has to explain why. Is it because protein A did not activate pathway X in her experiments? Is it because in pathway X functions differently in neurons than in skin cells? Is it because neurons and skin cells have a different threshold for survival? Experimental results that do not conform to the predictions have the potential to uncover exciting new scientific mechanisms but chasing down these alternate explanations requires a lot of time and resources which are becoming increasingly scarce. Therefore, it shouldn’t come as a surprise that some scientists may consciously or subconsciously ignore selected pieces of experimental data which contradict their darling hypotheses.

Let us move from these hypothetical situations to the real world of laboratories. There is surprisingly little data on how and when scientists reject hypotheses, but John Fugelsang and Kevin Dunbar at Dartmouth conducted a rather unique study “Theory and data interactions of the scientific mind: Evidence from the molecular and the cognitive laboratory” in 2004 in which they researched researchers. They sat in at scientific laboratory meetings of three renowned molecular biology laboratories at carefully recorded how scientists presented their laboratory data and how they would handle results which contradicted their predictions based on their hypotheses and models.

In their final analysis, Fugelsang and Dunbar included 417 scientific results that were presented at the meetings of which roughly half (223 out of 417) were not consistent with the predictions. Only 12% of these inconsistencies lead to change of the scientific model (and thus a revision of hypotheses). In the vast majority of the cases, the laboratories decided to follow up the studies by repeating and modifying the experimental protocols, thinking that the fault did not lie with the hypotheses but instead with the manner how the experiment was conducted. In the follow up experiments, 84 of the inconsistent findings could be replicated and this in turn resulted in a gradual modification of the underlying models and hypotheses in the majority of the cases. However, even when the inconsistent results were replicated, only 61% of the models were revised which means that 39% of the cases did not lead to any significant changes.

The study did not provide much information on the long-term fate of the hypotheses and models and we obviously cannot generalize the results of three molecular biology laboratory meetings at one university to the whole scientific enterprise. Also, Fugelsang and Dunbar’s study did not have a large enough sample size to clearly identify the reasons why some scientists were willing to revise their models and others weren’t. Was it because of varying complexity of experiments and models? Was it because of the approach of the individuals who conducted the experiments or the laboratory heads? I wish there were more studies like this because it would help us understand the scientific process better and maybe improve the quality of scientific research if we learned how different scientists handle inconsistent results.

In my own experience, I have also struggled with results which defied my scientific hypotheses. In 2002, we found that stem cells in human fat tissue could help grow new blood vessels. Yes, you could obtain fat from a liposuction performed by a plastic surgeon and inject these fat-derived stem cells into animal models of low blood flow in the legs. Within a week or two, the injected cells helped restore the blood flow to near normal levels! The simplest hypothesis was that the stem cells converted into endothelial cells, the cell type which forms the lining of blood vessels. However, after several months of experiments, I found no consistent evidence of fat-derived stem cells transforming into endothelial cells. We ended up publishing a paper which proposed an alternative explanation that the stem cells were releasing growth factors that helped grow blood vessels. But this explanation was not as satisfying as I had hoped. It did not account for the fact that the stem cells had aligned themselves alongside blood vessel structures and behaved like blood vessel cells.

Even though I “murdered” my darling hypothesis of fat –derived stem cells converting into blood vessel endothelial cells at the time, I did not “bury” the hypothesis. It kept ruminating in the back of my mind until roughly one decade later when we were again studying how stem cells were improving blood vessel growth. The difference was that this time, I had access to a live-imaging confocal laser microscope which allowed us to take images of cells labeled with red and green fluorescent dyes over long periods of time. Below, you can see a video of human bone marrow mesenchymal stem cells (labeled green) and human endothelial cells (labeled red) observed with the microscope overnight. The short movie compresses images obtained throughout the night and shows that the stem cells indeed do not convert into endothelial cells. Instead, they form a scaffold and guide the endothelial cells (red) by allowing them to move alongside the green scaffold and thus construct their network. This work was published in 2013 in the Journal of Molecular and Cellular Cardiology, roughly a decade after I had been forced to give up on the initial hypothesis. Back in 2002, I had assumed that the stem cells were turning into blood vessel endothelial cells because they aligned themselves in blood vessel like structures. I had never considered the possibility that they were scaffold for the endothelial cells.

This and other similar experiences have lead me to reformulate the “murder your darlings” commandment to “murder your darling hypotheses but do not bury them”. Instead of repeatedly trying to defend scientific hypotheses that cannot be supported by emerging experimental data, it is better to give up on them. But this does not mean that we should forget and bury those initial hypotheses. With newer technologies, resources or collaborations, we may find ways to explain inconsistent results years later that were not previously available to us. This is why I regularly peruse my cemetery of dead hypotheses on my hard drive to see if there are ways of perhaps resurrecting them, not in their original form but in a modification that I am now able to test.



Fugelsang, J., Stein, C., Green, A., & Dunbar, K. (2004). Theory and Data Interactions of the Scientific Mind: Evidence From the Molecular and the Cognitive Laboratory. Canadian Journal of Experimental Psychology/Revue canadienne de psychologie expérimentale, 58 (2), 86-95 DOI: 10.1037/h0085799


Note: An earlier version of this article first appeared on 3Quarksdaily.

Builders and Blocks – Engineering Blood Vessels with Stem Cells

Back in 2001, when we first began studying how regenerative cells (stem cells or more mature progenitor cells) enhance blood vessel growth, our group as well as many of our colleagues focused on one specific type of blood vessel: arteries. Arteries are responsible for supplying oxygen to all organs and tissues of the body and arteries are more likely to develop gradual plaque build-up (atherosclerosis) than veins or networks of smaller blood vessels (capillaries). Once the amount of plaque in an artery reaches a critical threshold, the oxygenation of the supplied tissues and organs becomes compromised. In addition to this build-up of plaque and gradual decline of organ function, arterial plaques can rupture and cause  severe sudden damage such as a heart attack. The conventional approach to treating arterial blockages in the heart was to either perform an open-heart bypass surgery in which blocked arteries were manually bypassed or to place a tube-like “stent” in the blocked artery to restore the oxygen supply. The hope was that injections of regenerative cells would ultimately replace the invasive procedures because the stem cells would convert into blood vessel cells, form healthy new arteries and naturally bypass the blockages in the existing arteries.


Image of mouse red blood cells flowing through an engineered human blood vessel- Image from Paul and colleagues (2013), Creative Commons license.
Image of mouse red blood cells flowing through an engineered human blood vessel implanted in a mouse- Image from Paul and colleagues (2013), Creative Commons license.

As is often the case in biomedical research, this initial approach turned out to be fraught with difficulties. The early animal studies were quite promising and the injected cells appeared to stimulate the growth of blood vessels, but the first clinical trials were less successful. It was very difficult to retain the injected cells in the desired arteries or tissues, and even harder to track the fate of the cells. Which stem cells should be injected? Where should they be injected? How many? Can one obtain enough stem cells from an individual patient so that one could use his or her own cells for the cell therapy? How does one guide the injected cells to the correct location, and then guide the cells to form functional blood vessel structures? Would the stem cells of a patient with chronic diseases such as diabetes or high blood pressure be suitable for therapies, or would such a patient have to rely on stem cells from healthier individuals and thus risk the complication of immune rejection?

The complexity of blood-vessel generation became increasingly apparent, both when studying the biology of stem cells as well as when designing and conducting clinical trials. A large clinical study published in 2013 studied the impact of bone marrow cell injections in heart attack patients and concluded that these injections did not result in any sustained benefit for heart function. Other studies using injections of patients’ own stem cells into their hearts had led to mild improvements in heart function, but none of these clinical studies came close to fulfilling the expectations of cardiovascular patients, physicians and researchers. The upside to these failed expectations was that it forced the researchers in the field of cardiovascular regeneration to rethink their goals and approaches.

One major shift in my own field of interest – the generation of new blood vessels – was to reevaluate the validity of relying on injections of cells. How likely was it that millions of injected cells could organize themselves into functional blood vessels? Injections of cells were convenient for patients because they would not require the surgical implantation of blood vessels, but was this attempt to achieve a convenient therapy undermining its success? An increasing number of laboratories began studying the engineering of blood vessels in the lab by investigating the molecular cues which regulate the assembly of blood vessel networks, identifying molecular scaffolds which would retain stem cells and blood vessel cells and combining various regenerative cell types to build functional blood vessels. This second wave of regenerative vascular medicine is engineering blood vessels which will have to be surgically implanted into patients.  This means that it will be much harder to get approval to conduct such invasive implantations in patients than the straightforward injections which were conducted in the first wave of studies, but most of us who have now moved towards a blood vessel engineering approach feel that there is a greater likelihood of long-term success even if it may take a decade or longer till we obtain our first definitive clinical results.

The second conceptual shift which has occurred in this field is the realization that blood vessel engineering is not only important for treating patients with blockages in their arteries. In fact, blood vessel engineering is critical for all forms of tissue and organ engineering. In the US, more than 120,000 people are awaiting an organ transplant but only a quarter of them will receive an organ in any given year. The number of people in need of a transplant will continue to grow but the supply of organs is limited and many patients will unfortunately die while waiting for an organ which they desperately need. The advances in stem cell biology have made it possible to envision creating organs or organoids (functional smaller parts of an organ) which could help alleviate the need for organs. One thing that most organs and tissues need is a network of tiny blood vessels that permeate the whole tissue: small capillary networks. For example, a liver built out of liver cells could never function without a network of tiny blood vessels which supply the liver cells with metabolites and oxygen. From an organ engineering point of view, microvessel engineering is just as important as the building of functional arteries.

In one of our recent projects, we engineered functional human blood vessels by combining bone marrow derived stem cells with endothelial cells (the cells which coat the inside of all blood vessels). It turns out that stem cells do not become endothelial cells but instead release a molecular signal – the protein SLIT3- which instructs the endothelial cells to assemble into networks. Using a high resolution microscope, we watched this process in real-time over a course of 72 hours in the laboratory and could observe how the endothelial cells began lining up into tube-like structures in the presence of the bone marrow stem cells. The human endothelial cells were like building blocks, the human bone marrow stem cells were the builders “overseeing” the construction. When we implanted the assembled blood vessel structures into mice, we could see that they were fully functional, allowing mouse blood to travel through them without leaking or causing any other major problems (see image, taken from reference 3).

I am sure that SLIT3 is just one of many molecular cues released by the stem cells to assemble functional networks and there are many additional mechanisms which still need to be discovered. We still need to learn much more about which “builders” and which “building blocks” are best suited for each type of blood vessel that we want to construct. The fact that human fat tissue can serve as an important resource for obtaining adult stem cells(“builders”) is quite encouraging, but we still know very little about the overall longevity of the engineered vessels, the best way to implant them into patients, and the key molecular and biomechanical mechanisms which will be required to engineer organs with functional blood vessels. It will be quite some time until the first fully engineered organs will be implanted in humans, but the dizzying rate of progress suggests that we can be quite optimistic.

(An earlier version of this article was first published on


References and links (all of them are open access, so you can read them for free, including the original paper we published):

 1. A recent longform overview article I wrote for “The Scientist” in which I describe the importance of blood vessel engineering for organ engineering:

J Rehman “Building Flesh and Blood“, The Scientist (2014), 28(5):48-53


2. An unusual and abundant source of adult stem cells which promote the formation of blood vessels: Fat tissue obtained from individuals who undergo a liposuction! 

J Rehman “The Power of Fat” Aeon Magazine (2014)


3. The study which describes how adult stem cells release a protein (SLIT3) which organizes blood vessel cells into functional networks (open access – can be read free of charge):

J.D. Paul et al., “SLIT3-ROBO4 activation promotes vascular network formation in human engineered tissue and angiogenesis in vivo” J Mol Cell Cardiol (2013), 64:124-31.

Paul JD, Coulombe KL, Toth PT, Zhang Y, Marsboom G, Bindokas VP, Smith DW, Murry CE, & Rehman J (2013). SLIT3-ROBO4 activation promotes vascular network formation in human engineered tissue and angiogenesis in vivo. Journal of molecular and cellular cardiology, 64, 124-31 PMID: 24090675

The Road to Bad Science Is Paved with Obedience and Secrecy

We often laud intellectual diversity of a scientific research group because we hope that the multitude of opinions can help point out flaws and improve the quality of research long before it is finalized and written up as a manuscript. The recent events surrounding the research in one of the world’s most famous stem cell research laboratories at Harvard shows us the disastrous effects of suppressing diverse and dissenting opinions.

Cultured cells via Shutterstock
Cultured cells via Shutterstock

The infamous “Orlic paper” was a landmark research article published in the prestigious scientific journal Nature in 2001, which showed that stem cells contained in the bone marrow could be converted into functional heart cells. After a heart attack, injections of bone marrow cells reversed much of the heart attack damage by creating new heart cells and restoring heart function. It was called the “Orlic paper” because the first author of the paper was Donald Orlic, but the lead investigator of the study was Piero Anversa, a professor and highly respected scientist at New York Medical College.

Anversa had established himself as one of the world’s leading experts on the survival and death of heart muscle cells in the 1980s and 1990s, but with the start of the new millennium, Anversa shifted his laboratory’s focus towards the emerging field of stem cell biology and its role in cardiovascular regeneration. The Orlic paper was just one of several highly influential stem cell papers to come out of Anversa’s lab at the onset of the new millenium. A 2002 Anversa paper in the New England Journal of Medicine – the world’s most highly cited academic journal –investigated the hearts of human organ transplant recipients. This study showed that up to 10% of the cells in the transplanted heart were derived from the recipient’s own body. The only conceivable explanation was that after a patient received another person’s heart, the recipient’s own cells began maintaining the health of the transplanted organ. The Orlic paper had shown the regenerative power of bone marrow cells in mouse hearts, but this new paper now offered the more tantalizing suggestion that even human hearts could be regenerated by circulating stem cells in their blood stream.

Woman having a heart attack via Shutterstock
Woman having a heart attack via Shutterstock

2003 publication in Cell by the Anversa group described another ground-breaking discovery, identifying a reservoir of stem cells contained within the heart itself. This latest coup de force found that the newly uncovered heart stem cell population resembled the bone marrow stem cells because both groups of cells bore the same stem cell protein called c-kit and both were able to make new heart muscle cells. According to Anversa, c-kit cells extracted from a heart could be re-injected back into a heart after a heart attack and regenerate more than half of the damaged heart!

These Anversa papers revolutionized cardiovascular research. Prior to 2001, most cardiovascular researchers believed that the cell turnover in the adult mammalian heart was minimal because soon after birth, heart cells stopped dividing. Some organs or tissues such as the skin contained stem cells which could divide and continuously give rise to new cells as needed. When skin is scraped during a fall from a bike, it only takes a few days for new skin cells to coat the area of injury and heal the wound. Unfortunately, the heart was not one of those self-regenerating organs. The number of heart cells was thought to be more or less fixed in adults. If heart cells were damaged by a heart attack, then the affected area was replaced by rigid scar tissue, not new heart muscle cells. If the area of damage was large, then the heart’s pump function was severely compromised and patients developed the chronic and ultimately fatal disease known as “heart failure”.

Anversa’s work challenged this dogma by putting forward a bold new theory: the adult heart was highly regenerative, its regeneration was driven by c-kit stem cells, which could be isolated and used to treat injured hearts. All one had to do was harness the regenerative potential of c-kit cells in the bone marrow and the heart, and millions of patients all over the world suffering from heart failure might be cured. Not only did Anversa publish a slew of supportive papers in highly prestigious scientific journals to challenge the dogma of the quiescent heart, he also happened to publish them at a unique time in history which maximized their impact.

In the year 2001, there were few innovative treatments available to treat patients with heart failure. The standard approach was to use medications that would delay the progression of heart failure. But even the best medications could not prevent the gradual decline of heart function. Organ transplants were a cure, but transplantable hearts were rare and only a small fraction of heart failure patients would be fortunate enough to receive a new heart. Hopes for a definitive heart failure cure were buoyed when researchers isolated human embryonic stem cells in 1998. This discovery paved the way for using highly pliable embryonic stem cells to create new heart muscle cells, which might one day be used to restore the heart’s pump function without  resorting to a heart transplant.


Human heart jigsaw puzzle via Shutterstock
Human heart jigsaw puzzle via Shutterstock

The dreams of using embryonic stem cells to regenerate human hearts were soon squashed when the Bush administration banned the generation of new human embryonic stem cells in 2001, citing ethical concerns. These federal regulations and the lobbying of religious and political groups against human embryonic stem cells were a major blow to research on cardiovascular regeneration. Amidst this looming hiatus in cardiovascular regeneration, Anversa’s papers appeared and showed that one could steer clear of the ethical controversies surrounding embryonic stem cells by using an adult patient’s own stem cells. The Anversa group re-energized the field of cardiovascular stem cell research and cleared the path for the first human stem cell treatments in heart disease.

Instead of having to wait for the US government to reverse its restrictive policy on human embryonic stem cells, one could now initiate clinical trials with adult stem cells, treating heart attack patients with their own cells and without having to worry about an ethical quagmire. Heart failure might soon become a disease of the past. The excitement at all major national and international cardiovascular conferences was palpable whenever the Anversa group, their collaborators or other scientists working on bone marrow and cardiac stem cells presented their dizzyingly successful results. Anversa received numerous accolades for his discoveries and research grants from the NIH (National Institutes of Health) to further develop his research program. He was so successful that some researchers believed Anversa might receive the Nobel Prize for his iconoclastic work which had redefined the regenerative potential of the heart. Many of the world’s top universities were vying to recruit Anversa and his group, and he decided to relocate his research group to Harvard Medical School and Brigham and Women’s Hospital 2008.

There were naysayers and skeptics who had resisted the adult stem cell euphoria. Some researchers had spent decades studying the heart and found little to no evidence for regeneration in the adult heart. They were having difficulties reconciling their own results with those of the Anversa group. A number of practicing cardiologists who treated heart failure patients were also skeptical because they did not see the near-miraculous regenerative power of the heart in their patients. One Anversa paper went as far as suggesting that the whole heart would completely regenerate itself roughly every 8-9 years, a claim that was at odds with the clinical experience of practicing cardiologists.  Other researchers pointed out serious flaws in the Anversa papers. For example, the 2002 paper on stem cells in human heart transplant patients claimed that the hearts were coated with the recipient’s regenerative cells, including cells which contained the stem cell marker Sca-1. Within days of the paper’s publication, many researchers were puzzled by this finding because Sca-1 was a marker of mouse and rat cells – not human cells! If Anversa’s group was finding rat or mouse proteins in human hearts, it was most likely due to an artifact. And if they had mistakenly found rodent cells in human hearts, so these critics surmised, perhaps other aspects of Anversa’s research were similarly flawed or riddled with artifacts.

At national and international meetings, one could observe heated debates between members of the Anversa camp and their critics. The critics then decided to change their tactics. Instead of just debating Anversa and commenting about errors in the Anversa papers, they invested substantial funds and efforts to replicate Anversa’s findings. One of the most important and rigorous attempts to assess the validity of the Orlic paper was published in 2004, by the research teams of Chuck Murry and Loren Field. Murry and Field found no evidence of bone marrow cells converting into heart muscle cells. This was a major scientific blow to the burgeoning adult stem cell movement, but even this paper could not deter the bone marrow cell champions.

Despite the fact that the refutation of the Orlic paper was published in 2004, the Orlic paper continues to carry the dubious distinction of being one of the most cited papers in the history of stem cell research. At first, Anversa and his colleagues would shrug off their critics’ findings or publish refutations of refutations – but over time, an increasing number of research groups all over the world began to realize that many of the central tenets of Anversa’s work could not be replicated and the number of critics and skeptics increased. As the signs of irreplicability and other concerns about Anversa’s work mounted, Harvard and Brigham and Women’s Hospital were forced to initiate an internal investigation which resulted in the retraction of one Anversa paper and an expression of concern about another major paper. Finally, a research group published a paper in May 2014 using mice in which c-kit cells were genetically labeled so that one could track their fate and found that c-kit cells have a minimal – if any – contribution to the formation of new heart cells: a fraction of a percent!

The skeptics who had doubted Anversa’s claims all along may now feel vindicated, but this is not the time to gloat. Instead, the discipline of cardiovascular stem cell biology is now undergoing a process of soul-searching. How was it possible that some of the most widely read and cited papers were based on heavily flawed observations and assumptions? Why did it take more than a decade since the first refutation was published in 2004 for scientists to finally accept that the near-magical regenerative power of the heart turned out to be a pipe dream.

One reason for this lag time is pretty straightforward: It takes a tremendous amount of time to refute papers. Funding to conduct the experiments is difficult to obtain because grant funding agencies are not easily convinced to invest in studies replicating existing research. For a refutation to be accepted by the scientific community, it has to be at least as rigorous as the original, but in practice, refutations are subject to even greater scrutiny. Scientists trying to disprove another group’s claim may be asked to develop even better research tools and technologies so that their results can be seen as more definitive than those of the original group. Instead of relying on antibodies to identify c-kit cells, the 2014 refutation developed a transgenic mouse in which all c-kit cells could be genetically traced to yield more definitive results – but developing new models and tools can take years.

The scientific peer review process by external researchers is a central pillar of the quality control process in modern scientific research, but one has to be cognizant of its limitations. Peer review of a scientific manuscript is routinely performed by experts for all the major academic journals which publish original scientific results. However, peer review only involves a “review”, i.e. a general evaluation of major strengths and flaws, and peer reviewers do not see the original raw data nor are they provided with the resources to replicate the studies and confirm the veracity of the submitted results. Peer reviewers rely on the honor system, assuming that the scientists are submitting accurate representations of their data and that the data has been thoroughly scrutinized and critiqued by all the involved researchers before it is even submitted to a journal for publication. If peer reviewers were asked to actually wade through all the original data generated by the scientists and even perform confirmatory studies, then the peer review of every single manuscript could take years and one would have to find the money to pay for the replication or confirmation experiments conducted by peer reviewers. Publication of experiments would come to a grinding halt because thousands of manuscripts would be stuck in the purgatory of peer review. Relying on the integrity of the scientists submitting the data and their internal review processes may seem naïve, but it has always been the bedrock of scientific peer review. And it is precisely the internal review process which may have gone awry in the Anversa group.

Just like Pygmalion fell in love with Galatea, researchers fall in love with the hypotheses and theories that they have constructed. To minimize the effects of these personal biases, scientists regularly present their results to colleagues within their own groups at internal lab meetings and seminars or at external institutions and conferences long before they submit their data to a peer-reviewed journal. The preliminary presentations are intended to spark discussions, inviting the audience to challenge the veracity of the hypotheses and the data while the work is still in progress. Sometimes fellow group members are truly skeptical of the results, at other times they take on the devil’s advocate role to see if they can find holes in their group’s own research. The larger a group, the greater the chance that one will find colleagues within a group with dissenting views. This type of feedback is a necessary internal review process which provides valuable insights that can steer the direction of the research.

Considering the size of the Anversa group – consisting of 20, 30 or even more PhD students, postdoctoral fellows and senior scientists – it is puzzling why the discussions among the group members did not already internally challenge their hypotheses and findings, especially in light of the fact that they knew extramural scientists were having difficulties replicating the work.

Retraction Watch is one of the most widely read scientific watchdogs which tracks scientific misconduct and retractions of published scientific papers. Recently, Retraction Watch published the account of an anonymous whistleblower who had worked as a research fellow in Anversa’s group and provided some unprecedented insights into the inner workings of the group, which explain why the internal review process had failed:

“I think that most scientists, perhaps with the exception of the most lucky or most dishonest, have personal experience with failure in science—experiments that are unreproducible, hypotheses that are fundamentally incorrect. Generally, we sigh, we alter hypotheses, we develop new methods, we move on. It is the data that should guide the science.

 In the Anversa group, a model with much less intellectual flexibility was applied. The “Hypothesis” was that c-kit (cd117) positive cells in the heart (or bone marrow if you read their earlier studies) were cardiac progenitors that could: 1) repair a scarred heart post-myocardial infarction, and: 2) supply the cells necessary for cardiomyocyte turnover in the normal heart.

 This central theme was that which supplied the lab with upwards of $50 million worth of public funding over a decade, a number which would be much higher if one considers collaborating labs that worked on related subjects.

 In theory, this hypothesis would be elegant in its simplicity and amenable to testing in current model systems. In practice, all data that did not point to the “truth” of the hypothesis were considered wrong, and experiments which would definitively show if this hypothesis was incorrect were never performed (lineage tracing e.g.).”

Discarding data that might have challenged the central hypothesis appears to have been a central principle.


Hood over screen - via Shutterstock
Hood over screen – via Shutterstock

According to the whistleblower, Anversa’s group did not just discard undesirable data, they actually punished group members who would question the group’s hypotheses:

In essence, to Dr. Anversa all investigators who questioned the hypothesis were “morons,” a word he used frequently at lab meetings. For one within the group to dare question the central hypothesis, or the methods used to support it, was a quick ticket to dismissal from your position.

The group also created an environment of strict information hierarchy and secrecy which is antithetical to the spirit of science:

“The day to day operation of the lab was conducted under a severe information embargo. The lab had Piero Anversa at the head with group leaders Annarosa Leri, Jan Kajstura and Marcello Rota immediately supervising experimentation. Below that was a group of around 25 instructors, research fellows, graduate students and technicians. Information flowed one way, which was up, and conversation between working groups was generally discouraged and often forbidden.

 Raw data left one’s hands, went to the immediate superior (one of the three named above) and the next time it was seen would be in a manuscript or grant. What happened to that data in the intervening period is unclear.

 A side effect of this information embargo was the limitation of the average worker to determine what was really going on in a research project. It would also effectively limit the ability of an average worker to make allegations regarding specific data/experiments, a requirement for a formal investigation.

This segregation of information is a powerful method to maintain an authoritarian rule and is more typical for terrorist cells or intelligence agencies than for a scientific lab, but it would definitely explain how the Anversa group was able to mass produce numerous irreproducible papers without any major dissent from within the group.

In addition to the secrecy and segregation of information, the group also created an atmosphere of fear to ensure obedience:

“Although individually-tailored stated and unstated threats were present for lab members, the plight of many of us who were international fellows was especially harrowing. Many were technically and educationally underqualified compared to what might be considered average research fellows in the United States. Many also originated in Italy where Dr. Anversa continues to wield considerable influence over biomedical research.

 This combination of being undesirable to many other labs should they leave their position due to lack of experience/training, dependent upon employment for U.S. visa status, and under constant threat of career suicide in your home country should you leave, was enough to make many people play along.

 Even so, I witnessed several people question the findings during their time in the lab. These people and working groups were subsequently fired or resigned. I would like to note that this lab is not unique in this type of exploitative practice, but that does not make it ethically sound and certainly does not create an environment for creative, collaborative, or honest science.”

Foreign researchers are particularly dependent on their employment to maintain their visa status and the prospect of being fired from one’s job can be terrifying for anyone.

This is an anonymous account of a whistleblower and as such, it is problematic. The use of anonymous sources in science journalism could open the doors for all sorts of unfounded and malicious accusations, which is why the ethics of using anonymous sources was heavily debated at the recent ScienceOnline conference. But the claims of the whistleblower are not made in a vacuum – they have to be evaluated in the context of known facts. The whistleblower’s claim that the Anversa group and their collaborators received more than $50 million to study bone marrow cell and c-kit cell regeneration of the heart can be easily verified at the public NIH grant funding RePORTer website. The whistleblower’s claim that many of the Anversa group’s findings could not be replicated is also a verifiable fact. It may seem unfair to condemn Anversa and his group for creating an atmosphere of secrecy and obedience which undermined the scientific enterprise, caused torment among trainees and wasted millions of dollars of tax payer money simply based on one whistleblower’s account. However, if one looks at the entire picture of the amazing rise and decline of the Anversa group’s foray into cardiac regeneration, then the whistleblower’s description of the atmosphere of secrecy and hierarchy seems very plausible.

The investigation of Harvard into the Anversa group is not open to the public and therefore it is difficult to know whether the university is primarily investigating scientific errors or whether it is also looking into such claims of egregious scientific misconduct and abuse of scientific trainees. It is unlikely that Anversa’s group is the only group that might have engaged in such forms of misconduct. Threatening dissenting junior researchers with a loss of employment or visa status may be far more common than we think. The gravity of the problem requires that the NIH – the major funding agency for biomedical research in the US – should look into the prevalence of such practices in research labs and develop safeguards to prevent the abuse of science and scientists.


Note: An earlier version of this article was first published on

Does Human Fat Contain Stem Cells?

Aeon Magazine recently published my longform essay on our research with human liposuction samples and our attempts to use fat for regenerative and therapeutic purposes. Many research groups, including our own group, have been able to isolate stem cells from human fat. However, when it came to using this cells for treating cardiovascular disease, the cells behaved in a manner that we had not anticipated.

Undifferentiated mesenchymal stem cells (left) and their fat neighbors (right)
Undifferentiated mesenchymal stem cells (left) and their fat neighbors (right) – From our PLOS One paper

We were unable to convert them into heart muscle cells or blood vessel endothelial cells, but we found that they could help build large networks of blood vessels by releasing important growth factors. Within a few years of our initial publication, clinical trials with patients with blocked arteries or legs were already being planned, and are currently underway.

We decided to call the cells “adipose stromal cells” because we wanted to emphasize that they were acting as a “stroma” (i.e. supportive environment for blood vessels) and not necessarily as stem cells (i.e. cells that convert from an undifferentiated state into mature cell types). In other contexts, these same cells were indeed able to act like “stem cells”, because they could be converted into bone-forming or cartilage-forming cells, thus showing the enormous versatility and value of the cells that reside within our fat tissues.

The answer to the question “Does Human Fat Contain Stem Cells?” is Yes, but these cells cannot be converted into all desired tissues. Instead, they have important supportive functions that can be used to engineer new blood vessels, which is a critical step in organ engineering.

In addition to describing our scientific work, the essay also mentions the vagaries of research, the frustrations I had as a postdoctoral fellow when my results were not turning out as I had expected, and how some predatory private clinics are already marketing “fat-derived stem cell therapies” to paying customers, even though the clinical results are still rather preliminary.


For the readers who want to dig a bit deeper, here are some references and links:


1. The original paper by Patricia Zuk and colleagues which described the presence of stem cells in human liposuction fat:

Zuk, P et al (2001) “Multilineage Cells from Human Adipose Tissue: Implications for Cell-Based Therapies


2. Our work on how the cells can help grow blood vessels by releasing proteins:

Rehman, J et al (2004) “Secretion of Angiogenic and Antiapoptotic Factors by Human Adipose Stromal Cells


3. Preliminary findings from ongoing clinical studies in which heart attack patients receive infusions of fat derived cells into their hearts to improve heart function and blood flow to the heart:

Houtgraf, J et al (2012) “First Experience in Humans Using Adipose Tissue–Derived Regenerative Cells in the Treatment of Patients With ST-Segment Elevation Myocardial Infarction


4. Preliminary results from an ongoing trial using the fat-derived cells in patients with severe blockages of leg arteries:

Bura, A et al (2014) “Phase I trial: the use of autologous cultured adipose-derived stroma/stem cells to treat patients with non-revascularizable critical limb ischemia


5. Example of how “cell therapies” (in this case bone marrow cells) are sometimes marketed as “stem cells” but hardly contain any stem cells:

The Largest Cell Therapy Trial in Heart Attack Patients Uses Hardly Any Stem Cells


6. The major scientific society devoted to studying the science of fat and its cells as novel therapies is called International Federation for Adipose Therapeutics and Science (IFATS).

I am not kidding, it is I-FATS!

Explore their website if you want to learn about all the exciting new research with fat derived cells.


7. Some of our newer work on how bone marrow mesenchymal stem cells turn into fat cells and what role their metabolism plays during this process:

Zhang, Y et al (2013) “Mitochondrial Respiration Regulates Adipogenic Differentiation of Human Mesenchymal Stem Cells

Zuk PA, Zhu M, Mizuno H, Huang J, Futrell JW, Katz AJ, Benhaim P, Lorenz HP, & Hedrick MH (2001). Multilineage cells from human adipose tissue: implications for cell-based therapies. Tissue engineering, 7 (2), 211-28 PMID: 11304456

Rehman J, Traktuev D, Li J, Merfeld-Clauss S, Temm-Grove CJ, Bovenkerk JE, Pell CL, Johnstone BH, Considine RV, & March KL (2004). Secretion of angiogenic and antiapoptotic factors by human adipose stromal cells. Circulation, 109 (10), 1292-8 PMID: 14993122

Lab Grown Organs and Artistic Computers in Fifty Years?

The Pew Research Center released the 2014 survey of U.S. adults (1,001 participants, surveyed by land-line or cell phone interviews) regarding their views on technological advancements in the next 50 years.

Robot – via Shutterstock

Over eighty percent of the participants said that “People in need of an organ transplant will have new organs custom made for them in a lab” and roughly half of the participants felt that “Computers will be as effective as people at creating important works of art such as music, novels, movies, or paintings” within the next 50 years. The vast majority did not think that humans will be able to control the weather during the next few decades.

As someone working in the field of vascular and tissue engineering, I think that the perception of scientists being able to engineer transplantable organs within 50 years is realistic. We have made quite a bit of progress in the past decade when it comes to deriving functional tissues from stem cells, but we still need more research before we will be able to build functional organs. It may take a decade or two before we can reliably generate these organs, and even longer to teat and optimize them for therapeutic purposes, and to ensure their long-term survival in transplant recipients.

50 year predictions

The reason to be optimistic about engineering organs is that we have already seen examples of engineered tissues and small organoids being implanted into animal models. There are also ongoing early clinical trials with patches of engineered tissues and engineered blood vessels. Scaling up these successes to whole organ engineering in humans will be challenging but sounds feasible.

I am surprised by the fact that half of the U.S. adults believe computers will be “effective” at creating works of art within the next 50 years. Do we have preliminary evidence – even at a small scale – that computers can currently “create” art? Perhaps this comes down to our definitions of what constitutes “creativity”. One could envision computers generating paintings, music and novels based on existing art created by humans. But is that true creativity? Then again, when humans “create” art, they also base their new product on their experiences and prior art created by other humans. Maybe computer-created art in fifty years isn’t  far-fetched after all.


Attitudes towards changes

Not everyone is enthusiastic about new technologies.


When asked whether it would be a change for the better or a change for the worse……


1) “If most people wear implants or other devices that constantly show them information about the world around them”

2) “If lifelike robots become the primary caregivers for the elderly and people in poor health”

3) “If personal and commercial drones are given permission to fly through most U.S. airspace”

4) “If prospective parents can alter the DNA of their children to produce smarter, healthier, or more athletic offspring”


…the majority of participants felt they would be worse off with these changes.

The way the questions were phrased did not leave room for a more nuanced response. For example, would it be ok to change DNA to “produce” healthier children (i.e. correct lethal genetic defects using genome editing) without necessarily “producing” smarter and more athletic children?

Conflating health, intelligence and athleticism into one question makes it difficult to ascertain how the public feels about using genome editing to help children survive versus using it to make kids run faster.

Most participants did not think they would want to eat lab grown meat or use brain implants to improve their mental capacity but roughly half of them seemed fine with using driverless cars.


Lab grown meat


When asked about what futuristic invention they would like to own, younger participants seemed most excited about time travel and other travel gadgets (flying cars, bikes and space crafts), whereas older participants wanted to inventions to prolong life or cure diseases.

What do people want

I was a bit surprised that this final question did not elicit responses such as inventions that would help reduce or reverse global warming and pollution or inventions that could remedy world hunger and the global scarcity of resources. Maybe it has to also do with how the question was phrased. Here is the actual question:

Science fiction writers have always imagined new inventions that change the world of the future. How about you? If there was one futuristic invention that you could own, what would it be?


Here is the actual data (PDF) of the responses people gave:


Improved health and longevity/Cure for diseases                        9%

Time machine/Time travel                                                           9%

Flying car/Flying bike                                                                6%

Personal robot/Robot servants                                                 4%

Personal space craft                                                                 4%

Self-driving car                                                                         3%

Teleporter/Teleportation/Transporter                                           3%

World peace/Stop wars/Improved understanding/Better planet     2%

New energy source/efficient cars/other environment                    2%

Invention to make household tasks easier                                   1%

Ability to live forever/Immortality                                                  1%

Jetpack                                                                                    1%

Money/Scheme to get rich/Ability to read future                         1%

Brain implant/Improve memory                                                   1%

Hovercar/Hoverboard                                                                1%

Hologram/Holodeck                                                                  *

Remote communications (via device or ESP)                              *

Other                                                                                        9%

None/Nothing/Not interested in futuristic inventions                     11%


The science fiction reference in the question may have prompted participants to think of technologies described in sci-fi novels and movies. Perhaps the majority of respondents did not think that world peace or climate-control could be achieved with specific sci-fi style inventions. Or perhaps the participants did not realize that climate change, global scarcity of food or other resources and violent conflicts are some of the biggest threats that humankind has ever faced.

Many of the responses to this final question tend to fall into the category of “how could my life become more convenient“, such as using personal robots and flying cars. But will these conveniences even matter if we cannot curb the major threats that our planet faces?

The Largest Cell Therapy Trial in Heart Attack Patients Uses Hardly Any Stem Cells

One of the world’s largest clinical cell therapy trials has begun to enroll 3,000 heart attack patients, some of whom will have bone marrow cells extracted with a needle from their hip and fed into their heart using a catheter in their coronary arteries.


The BAMI trial has €5.9m in funding from the European Commission and will be conducted in ten European countries. Enlisted patients will be randomly assigned into two groups: one group will receive the standard care given to heart attack patients while the other will get an added infusion of bone marrow cells.

A number of studies, including one in the New England Journal of Medicine and another in the European Heart Journal, have suggested that bone marrow cells could be beneficial to patients with heart disease. However, because these studies were too small to work out whether cell infusions affected patients’ survival, they instead focused on the extent of scar formation after a heart attack or the ability of the heart muscle to contract after cell infusion.

One commonly used surrogate measure is the cardiac ejection fraction, which measures the fraction of blood squeezed out by the heart during a contraction. A healthy rate ranges from 55% to 65%. Bone marrow cell infusion has been associated with a modest but statistically significant improvement in heart function. In 2012, a comprehensive analysis of 50 major studies with a combined total of 2,625 heart disease patients showed that cardiac ejection fraction in patients receiving these infusions was 4% higher than in control patients.

While the results were encouraging, the study was a retrospective analysis with patients who had varying treatments and endpoints. There also remain questions over 400 patients included in the analysis from trials showing benefits of bone marrow cell infusions that were conducted by controversial German cardiologist Bodo Strauer, who some scientists have accused of errors in research.

The new large-scale BAMI trial will be able to provide a more definitive answer to the efficacy of bone marrow cell infusions and address the even more important question: does this experimental treatment prolong the lives of heart attack patients?

A hard cell

Despite the impressive target of enrolling 3,000 patients, there is a problem with how the trial is being framed. The underlying premise of why bone marrow cells are thought to improve heart function is that the bone marrow contains stem cells which could potentially regenerate the heart. In media reports, the BAMI trial is portrayed as a study which will test whether stem cells can heal broken hearts, and a press release by Barts Health NHS Trust, which is leading on the trial, described the study as “the largest ever adult stem cell heart attack trial”. But the scientific value of the BAMI trial for stem cell research is questionable.

In 2013, a Swiss study reported the results of treating heart attack patients with bone marrow cells. Not only did the study find no significant improvement of heart function with cell therapy, the researchers also reported that only 1% of the infused cells had clearly defined stem cell characteristics. The vast majority of the infused bone marrow cells were a broad mixture of various cell types, including immune cells such as lymphocytes and monocytes.

Scientific studies have even cast doubts about whether any of the scarce stem cells in bone marrow can convert into beating heart muscle cells. A study published in 2001 suggested bone marrow cells injected into mouse hearts could differentiate into heart muscle cells, but the finding could not be replicated in a subsequent study published in 2004.

If there are so few stem cells in the bone marrow and if the stem cells do not become cardiac cells, then how does one explain the improvements observed in the smaller studies? Researchers have proposed a variety of potential explanations, including the release of growth factors or proteins by bone marrow cells that are independent of their stem cell activity.

The disease machine

The success of modern medicine lies in its ability to isolate causal mechanisms of disease and design therapies which specifically target these mechanisms using rigorous scientific methods. Instead of using nebulous “fever tinctures” or willow bark, physicians now prescribe therapies with well-defined active ingredients such as paracetamol (acetaminophen) or aspirin.

Infusing heterogeneous bone marrow cell mixtures into the hearts of patients seems like a throwback to the era of mysterious herbal extracts containing a variety of active and inactive ingredients.

Even if the BAMI trial succeeds in demonstrating that infusion of bone marrow cell mixtures can prolong lives, then the scientific value of the results will still remain doubtful. We will not know whether the tiny fraction of stem cells contained in the bone marrow was responsible for the improvement or whether this effect was due to one of the many other cell types contained in the cell mixtures.

One could argue that it is irrelevant to know the mechanism of action as long as the infusions can prolong patient survival. But for any evidence-based therapy to succeed, it is essential for physicians to know how to dose or modify the therapy according to the needs of an individual patient. This won’t be possible if we don’t even understand how the treatment works.

We should also consider the impact of a negative result. If the BAMI trial fails to show improved survival, will the lack of efficacy be interpreted as a failure of stem cell therapy for heart disease? An alternate explanation would be that a negative result was due to infusing numerous cell types, most of which were not stem cells.

The ultimate test of a treatment’s efficacy is how it fares in controlled, large-scale trials. And these trials need to be grounded in solid scientific data and provide answers that can be interpreted in the context of scientifically sound mechanisms. The BAMI trial might provide an answer to the question of whether or not bone marrow cell infusions are efficacious in heart disease, but it will not teach us much about stem cells.

Jalees Rehman has received research funding from the National Institutes of Health (NIH).

The Conversation

This article was originally published on The Conversation.
Read the original article.





Rehman, J. (2013). Bone Marrow Tinctures for Cardiovascular Disease: Lost in Translation Circulation, 127 (19), 1935-1937 DOI: 10.1161/CIRCULATIONAHA.113.002775


Surder, D., Manka, R., Lo Cicero, V., Moccetti, T., Rufibach, K., Soncin, S., Turchetto, L., Radrizzani, M., Astori, G., Schwitter, J., Erne, P., Zuber, M., Auf der Maur, C., Jamshidi, P., Gaemperli, O., Windecker, S., Moschovitis, A., Wahl, A., Buhler, I., Wyss, C., Kozerke, S., Landmesser, U., Luscher, T., & Corti, R. (2013). Intracoronary Injection of Bone Marrow-Derived Mononuclear Cells Early or Late After Acute Myocardial Infarction: Effects on Global Left Ventricular Function Circulation, 127 (19), 1968-1979 DOI: 10.1161/CIRCULATIONAHA.112.001035

Growing Skepticism about the Stem Cell Acid Trip

In January 2014, the two papers “Stimulus-triggered fate conversion of somatic cells into pluripotency” and “Bidirectional developmental potential in reprogrammed cells with acquired pluripotency” published in the journal Nature by Haruko Obokata and colleagues took the world of stem cell research by surprise.

Since Shinya Yamanaka’s landmark discovery that adult skin cells could be reprogrammed into embryonic-like induced pluripotent stem cells (iPSCs) by introducing selected embryonic genes into adult cells, laboratories all over the world have been using modifications of the “Yamanaka method” to create their own stem cell lines. The original Yamanaka method published in 2006 used a virus which integrated into the genome of the adult cell to introduce the necessary genes. Any introduction of genetic material into a cell carries the risk of causing genetic aberrancies that could lead to complications, especially if the newly generated stem cells are intended for therapeutic usage in patients.


Researchers have therefore tried to modify the “Yamanaka method” and reduce the risk of genetic aberrations by either using genetic tools to remove the introduced genes once the cells are fully reprogrammed to a stem cell state, introducing genes without non-integrating viruses or by using complex cocktails of chemicals and growth factors in order to generate stem cells without the introduction of any genes into the adult cells.

The papers by Obokata and colleagues at the RIKEN center in Kobe, Japan use a far more simple method to reprogram adult cells. Instead of introducing foreign genes, they suggest that one can expose adult mouse cells to a severe stress such as an acidic solution. The cells which survive acid-dipping adventure (25 minutes in a solution with pH 5.7) activate their endogenous dormant embryonic genes by an unknown mechanism. The researchers then show that these activated cells take on properties of embryonic stem cells or iPSCs if they are maintained in a stem cell culture medium and treated with the necessary growth factors. Once the cells reach the stem cell state, they can then be converted into cells of any desired tissue, both in a culture dish as well as in a developing mouse embryo. Many of the experiments in the papers were performed by starting out with adult mouse lymphocytes, but the researchers also found that mouse skin fibroblasts and other cells could also be successfully converted into an embryonic-like state using the acid stress.

My first reaction was incredulity. How could such a simple and yet noxious stress such as exposing cells to acid be sufficient to initiate a complex “stemness” program? Research labs have spent years fine-tuning the introduction of the embryonic genes, trying to figure out the optimal combination of genes and timing of when the genes are essential during the reprogramming process. These two papers propose that the whole business of introducing stem cell genes into adult cells was unnecessary – All You Need Is Acid.


This sounds too good to be true. The recent history in stem cell research has taught us that we need to be skeptical. Some of the most widely cited stem cell papers cannot be replicated. This problem is not unique to stem cell research, because other biomedical research areas such as cancer biology are also struggling with issues of replicability, but the high scientific impact of burgeoning stem cell research has forced its replicability issues into the limelight. Nowadays, whenever stem cell researchers hear about a ground-breaking new stem cell discovery, they often tend to respond with some degree of skepticism until multiple independent laboratories can confirm the results.

My second reaction was that I really liked the idea. Maybe we had never tried something as straightforward as an acid stress because we were too narrow-minded, always looking for complex ways to create stem cells instead of trying simple approaches. The stress-induction of stem cell behavior may also represent a regenerative mechanism that has been conserved by evolution. When our amphibian cousins regenerate limbs following an injury, adult tissue cells are also reprogrammed to a premature state by the stress of the injury before they start building a new limb.

The idea of stress-induced reprogramming of adult cells to an embryonic-like state also has a powerful poetic appeal, which inspired me to write the following haiku:


The old warrior

plunges into an acid lake

to emerge reborn.


(Read more about science-related haikus here)

Just because the idea of acid-induced reprogramming is so attractive does not mean that it is scientifically accurate or replicable.

A number of concerns about potential scientific misconduct in the context of the two papers have been raised and it appears that the RIKEN center is investigating these concerns. Specifically, anonymous bloggers have pointed out irregularities in the figures of the papers and that some of the images may be duplicated. We will have to wait for the results of the investigation, but even if image errors or duplications are found, this does not necessarily mean that this was intentional misconduct or fraud. Assembling manuscripts with so many images is no easy task and unintentional errors do occur. These errors are probably far more common than we think. High profile papers undergo much more scrutiny than the average peer-reviewed paper, and this is probably why we tend to uncover them more readily in such papers. For example, image duplication errors were discovered in the 2013 Cell paper on human cloning, but many researchers agreed that the errors in the 2013 Cell paper were likely due to sloppiness during the assembly of the submitted manuscript and did not constitute intentional fraud.

Irrespective of the investigation into the irregularities of figures in the two Nature papers, the key question that stem cell researchers have to now address is whether the core findings of the Obokata papers are replicable. Can adult cells – lymphocytes, skin fibroblasts or other cells – be converted into embryonic-like stem cells by an acid stress? If yes, then this will make stem cell generation far easier and it will open up a whole new field of inquiry, leading to many new exciting questions. Do human cells also respond to acid stress in the same manner as the mouse cells? How does acid stress reprogram the adult cells? Is there an acid-stress signal that directly acts on stem cell transcription factors or does the stress merely activate global epigenetic switches? Are other stressors equally effective? Does this kind of reprogramming occur in our bodies in response to an injury such as low oxygen or inflammation because these kinds of injuries can transiently create an acidic environment in our tissues?

Researchers all around the world are currently attempting to test the effect of acid exposure on the activation of stem cell genes. Paul Knoepfler’s stem cell blog is currently soliciting input from researchers trying to replicate the work. Paul makes it very clear that this is an informal exchange of ideas so that researchers can learn from each other on a “real-time” basis. It is an opportunity to find out about how colleagues are progressing without having to wait for 6-12 months for the next big stem cell meeting or the publication of a paper confirming or denying the replication of acid-induced reprogramming. Posting one’s summary of results on a blog is not as rigorous as publishing a peer-reviewed paper with all the necessary methodological details, but it can at least provide some clues as to whether some or all of the results in the controversial Obokata papers can be replicated.

If the preliminary findings of multiple labs posted on the blog indicate that lymphocytes or skin cells begin to activate their stem cell gene signature after acid stress, then we at least know that this is a project which merits further investigation and researchers will be more willing to invest valuable time and resources to conduct additional replication experiments. On the other hand, if nearly all the researchers post negative results on the blog, then it is probably not a good investment of resources to spend the next year or so trying to replicate the results.

It does not hurt to have one’s paradigms or ideas challenged by new scientific papers as long as we realize that paradigm-challenging papers need to be replicated. The Nature papers must have undergone rigorous peer review before their publication, but scientific peer review does not involve checking replicability of the results. Peer reviewers focus on assessing the internal logic, experimental design, novelty, significance and validity of the conclusions based on the presented data. The crucial step of replicability testing occurs in the post-publication phase. The post-publication exchange of results on scientific blogs by independent research labs is an opportunity to crowd-source replicability testing and thus accelerate the scientific authentication process. Irrespective of whether or not the attempts to replicate acid-induced reprogramming succeed, the willingness of the stem cell community to engage in a dialogue using scientific blogs and evaluate replicability is an important step forward.
Obokata H, Wakayama T, Sasai Y, Kojima K, Vacanti MP, Niwa H, Yamato M, & Vacanti CA (2014). Stimulus-triggered fate conversion of somatic cells into pluripotency. Nature, 505 (7485), 641-7 PMID: 24476887

Stem Cells and Their Fat Neighbors

We recently published a PLOS ONE paper (Mitochondrial respiration regulates adipogenic differentiation of human mesenchymal stem cells) in which we studied how the metabolism of an adult stem cell can influence its ability to differentiate. Human bone marrow mesenchymal stem cells (also known as marrow stromal cells, marrow progenitor cells or MSCs) can be converted into fat (adipocytes), cartilage (chondrocytes) or bone (osteoblasts). The work performed by Yanmin Zhang and Glenn Marsboom in my lab showed that MSCs undergo a major metabolic shift towards increased mitochondrial oxidation when they become fat cells and that suppressing mitochondrial respiration can prevent their differentiation. The metabolic state of the adult stem cells is therefore not only an indicator of their “stemness”, it can be used to either promote or suppress their differentiation.


Dr. Peter Toth, one of the co-authors on the paper, helped us acquire some really beautiful images of the cells that I would like to share with the readers of the blog. The image below shows undifferentiated adult human bone marrow mesenchymal stem cells (MSCs) that were exposed to an adipogenic differentiation medium, i.e a combination of factors which induces the formation of fat cells (adipocytes). However, as with many stem cell differentiation protocols, not all stem cells turned into fat cells. The cells on the right have a typical fat-like structure in which cells are full of round lipid droplets. The neighboring cells on the left are MSCs that have not (yet?) become fat cells. We stained the cells with the fluorescent mitochondrial dye JC-1. Depolarized mitochondria appear green and hyperpolarized mitochondria red. As you can see, the cells on the left have a much higher mitochondrial membrane potential (significant amount of red among the green mitochondria) than their fat neighbors on the right (mostly green mitochondria, all of them located between lipid droplets). By capturing both cell types next to each other, we could show an illustrative example of how entwined metabolism and stem cell differentiation are. The morphology and metabolic state of neighboring cells in this image were quite different, despite the fact that all cells were subjected to the same cocktail of differentiation factors. The blue-appearing dye is DAPI and stains nuclei of cells so one can tell the cells apart. Each cell in this image has one blue nucleus.



The image was published with a PLoS ONE CC-BY license. Feel free to use it as an example of adult stem cell differentiation or how mitochondrial morphology and function can vary between stem cell and its differentiated progeny, as long as you attribute the original PLoS One paper. The image in the paper also has a scale bar and asterisks/arrows pointing out the specific cells.

Zhang Y, Marsboom G, Toth PT, & Rehman J (2013). Mitochondrial respiration regulates adipogenic differentiation of human mesenchymal stem cells. PLoS ONE 8(10): e77077;  PMID: 24204740; DOI: 10.1371/journal.pone.0077077

Replicability of High-Impact Papers in Stem Cell Research

I recently used the Web of Science database to generate a list of the most highly cited papers in stem cell research. As of July 2013, the search for original research articles which use the key word “stem cells” resulted in the following list of the ten most widely cited papers to date:


Human ESC colony – Wikimedia

1. Pittenger M et al. (1999) Multilineage potential of adult human mesenchymal stem cells. Science 284(5411):143-147

Citations: 8,157


2.  Thomson JA et al. (1998) Embryonic stem cell lines derived from human blastocysts. Science 282(5391):1145-1147

Citations: 5,565


3. Takahashi K and Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126(4): 663-676

Citations: 5,034


4. Takahashi K et al. (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131(5):861-872

Citations: 4,061


5. Donehower LA et al  (1992) Mice deficient for p53 are developmentally normal but susceptible to spontaneous tumours. Nature 356(6366): 215-221

Citations: 3,279


6. Al-Hajj M et al (2003) Prospective identification of tumorigenic breast cancer cells. Proceedings of the National Academy of Sciences 100(7): 3983-3988

Citations: 3,183


7. Yu J et al (2007) Induced pluripotent stem cell lines derived from human somatic cells. Science 318(5858): 1917-1920

Citations: 3,086


8. Jiang YH et al (2002) Pluripotency of mesenchymal stem cells derived from adult marrow. Nature 418(6893):41-49

Citations: 2,983


9. Orlic D et al (2001) Bone marrow cells regenerate infarcted myocardium. Nature 410 (6829):701-705

Citations: 2,961


10. Lu J et al (2005) MicroRNA expression profiles classify human cancers. Nature 435(7043): 834-838

Citations: 2,917


Three of the articles (Donehower et al, Al-Hajj et al and Lu et al) in this “top ten list” do not focus on stem cells but are actually cancer research papers. They were probably identified by the search because the authors may have made comparisons to stem cells or used stem cells as tools.The remaining seven articles are indeed widely known in the stem cell field.


The Science paper by Pittenger and colleagues in 1999 provided a very comprehensive description of mesenchymal stem cells (MSCs), a type of adult stem cell which is found in the bone marrow alongside hematopoietic stem cells (HSCs). Despite the fact that MSCs and HSCs are both adult stem cells in the bone marrow, they have very different functions. HSCs give rise to circulating blood cells, whereas MSCs primarily form bone, fat and cartilage as was nicely demonstrated by Pittenger and colleagues.

The article by Thomson and colleagues was published in 1998 in the journal Science described the derivation of human embryonic stem cells (ESCs) and revolutionized the field of stem cell research. While adult stem cells have a very limited capacity in terms of lineages they can turn into, ESCs are derived from the early blastocyst stage of embryonic development (within the first 1-2 weeks following fertilization) and thus retain the capacity to turn into a very wide range of tissues, such as neurons, heart cells, blood vessel cells or liver cells. This paper not only identified the methods for isolating human ESCs, but also how to keep them in culture and expand them as undifferentiated stem cells.

The Cell paper by Takahashi and Yamanaka in 2006 represented another major advancement in the field of stem cell biology, because it showed for the first time that a mouse adult skin cell (fibroblast) could be reprogrammed and converted into a truly pluripotent stem cell (an induced pluripotent stem cell or iPSC) which exhibited all the major characteristics of an embryonic stem cell (ESC). It was as if the adult skin cell was traveling back in time, erasing its identity of having been a skin cell and returning to primordial, embryonic-like stem cell. Only one year later, Dr. Yamanaka’s group was able to demonstrate the same phenomena for adult human skin cells in the 2007 Cell paper (Takahashi et al), and in the same year a different group independently confirmed that adult human cells could be reprogrammed to the iPSC state (Science paper by Yu et al in 2007). The generation of iPSCs described in these three papers is probably the most remarkable discovery in stem cell biology during the past decade. It is no wonder that each of these three papers have been cited several thousand times even though they were published only six or seven years ago, and that Dr. Yamanaka was awarded the 2012 Nobel prize for this pioneering work.

All five of the above-mentioned stem cell papers have one thing in common: the results have been repeated and confirmed by numerous independent laboratories all over the world. However, this does not necessarily hold true for the other two highly cited stem cell papers on this list.

The 2002 Nature paper by Jiang and colleagues from Dr. Verfaillie’s laboratory at the University of Minnesota proposed that the bone marrow contained a rather special subset of adult MSCs which had a much broader differentiation potential than had been previously recognized. While adult MSCs were thought to primarily turn into bone, cartilage or fat when given the appropriate cues, this rare new cell type – referred to as MAPCs (multipotent adult progenitor cells) – appeared to differentiate into a much broader range of tissues. The paper even showed data from an experiment in which these adult mouse bone marrow stem cells were combined with embryonic cells and gave rise to a chimeric mouse. i.e. a mouse in which the tissues were in part derived from standard embryonic cells and in part from the newly discovered adult MAPCs. Such chimerism suggested that the MAPCs were embryonic-like, contributing to the formation of all the tissues in the mice. At the time of its publication, this paper was met with great enthusiasm because it proved that the adult body contained embryonic-like cells, hidden away in the bone marrow, and that these MAPCs could be used to regenerate ailing organs and tissues without having to use ethically problematic human embryonic stem cells.

There was just one major catch. Many laboratories around the world tried to replicate the results and were unable to identify the MAPCs, and even when they found cells that were MAPCs, they were unable to confirm the embryonic-like nature of the cells. In a remarkable example of investigative journalism, the science journalists Peter Aldhous and Eugenie Reich identified multiple irregularities in the publications involving MAPCs and documented the inability of researchers to replicate the findings by publishing the results of their investigation in the New Scientist (PDF).

The second high profile stem cell paper which was also plagued by an inability to replicate the results was the 2001 Nature paper by Orlic and colleagues. In this paper from Dr. Anversa’s laboratory, the authors suggested that adult hematopoietic (blood-forming) stem cells from the bone marrow could regenerate an infarcted heart by becoming heart cells (cardiomyocytes). It was a rather bold claim, because simply injecting these blood-forming stem cells into the heart seemed to be sufficient to redirect their fate. Instead of giving rise to red and white blood cells, these bone marrow cells were generating functional heart cells. If this were the case, then every patient could be potentially treated with their own bone marrow and grow back damaged heart tissue after a heart attack. Unfortunately, it was too good to be true. Two leading stem cell laboratories partnered up to confirm the results, but even after years of experiments, they were unable to find any evidence of adult bone marrow stem cells converting into functional heart cells. They published their findings three years later, also in the journal Nature:

Murry CE et al (2004) Haematopoietic stem cells do not transdifferentiate into cardiac myocytes in myocardial infarcts. Nature 428(6983): 664-668

Citations: 1,150


Interestingly, the original paper which had made the claim that bone marrow cells can become functional heart cells has been cited nearly 3,000 times, whereas the refutation by Murry and colleagues, published in the same high-profile journal has been cited only 1,150 times. The vast majority of the nearly 3,000 citations of the 2001 paper by Orlic and colleagues occurred after it had been refuted in 2004! The 2001 Orlic et al paper has even been used to justify clinical trials in which bone marrow was obtained from heart attack patients and injected into their hearts. As expected after the refutation by Murry and colleagues, the success of these clinical trials was rather limited One of the largest bone marrow infusion trials in heart attack patients was recently published, showing no success of the therapy.

These claims of the two papers (Orlic et al and Jiang et al) were quite innovative and exciting, and they were also published in a high-profile, peer-reviewed journal, just like the other five stem cell papers. The crucial difference was the fact that their findings could not be replicated by other laboratories. Despite their lack of replicability, both papers had an enormous impact on the field of stem cell research. Senior scientists, postdocs and graduate students may have devoted a substantial amount of time and resources to developing projects that built on the findings of these two papers, only to find out that they could not be replicated. If there is a lesson to be learned, it is that we need to be rather cautious in terms of our enthusiasm for new claims in stem cell biology until they have been appropriately confirmed by other researchers. Furthermore, we need to streamline the replicability testing process so that we do not have to wait years before we find out that one of the most highly prized discoveries cannot be independently confirmed.


Update 7/24/2013: Peter Aldhous reminded me that the superb job of investigative journalism into the question of MAPCs was performed in partnership with the science writer Eugenie Reich, the author of a book on scientific fraud. I have updated the blog post to reflect this.

Cellular Alchemy: Converting Fibroblasts Into Heart Cells

Medieval alchemists devoted their lives to the pursuit of the infamous Philosopher’s Stone, an elusive substance that was thought to convert base metals into valuable gold. Needless to say, nobody ever discovered the Philosopher’s Stone. Well, perhaps some alchemist did get lucky but was wise enough to keep the discovery secret. Instead of publishing the discovery and receiving the Nobel Prize for Alchemy, the lucky alchemist probably just walked around in junkyards, surreptitiously collected scraps of metal and brought them to home to create a Scrooge-McDuck-style money bin.  Today, we view the Philosopher’s Stone as just a myth that occasionally resurfaces in the titles of popular fantasy novels, but cell biologists have discovered their own version of the Philosopher’s Stone: The conversion of fibroblast cells into precious heart cells (cardiomyocytes) or brain cells (neurons).


Fibroblasts are an abundant cell type, found in many organs such as the heart, liver and the skin. One of their main functions is to repair wounds and form scars in this process. They are fairly easy to grow or to expand, both in the body as well as in a culture dish. The easy access to large quantities of fibroblasts makes them analogous to the “base metals” of the alchemist. Adult cardiomyocytes, on the other hand, are not able to grow, which is why a heart attack which causes death of cardiomyocytes can be so devastating. There is a tiny fraction of regenerative stem-cell like cells in the heart that are activated after a heart attack and regenerate some cardiomyocytes, but most of the damaged and dying heart cells are replaced by a scar – formed by the fibroblasts in the heart. This scar keeps the heart intact so that the wall of the heart does not rupture, but it is unable to contract or beat, thus weakening the overall pump function of the heart. In a large heart attack, a substantial portion of cardiomycoytes are replaced with scar tissue, which can result in heart failure and heart failure.

A few years back, a research group at the Gladstone Institute of Cardiovascular Disease (University of California, San Francisco) headed by Deepak Srivastava pioneered a very interesting new approach to rescuing heart function after a heart attack.  In a 2010 paper published in the journal Cell, the researchers were able to show that plain-old fibroblasts from the heart or from the tail of a mouse could be converted into beating cardiomyocytes! The key to this cellular alchemy was the introduction of three genes – Gata4, Mef2C and Tbx5 also known as the GMT cocktail– into the fibroblasts. These genes encode for developmental cardiac transcription factors, i.e. proteins that regulate the expression of genes which direct the formation of heart cells. The basic idea was that by introducing these regulatory factors, they would act as switches that turn on the whole heart gene program machinery. Unlike the approach of the Nobel Prize laureate Shinya Yamanaka, who had developed a method to generate stem cells (induced pluripotent stem cells or iPSCs) from fibroblasts, Srivastava’s group bypassed the whole stem cell generation process and directly created heart cells from fibroblasts. In a follow-up paper published in the journal Nature in 2012, the Srivastava group took this research to the next level by introducing the GMT cocktail directly into the heart of mice and showing that this substantially improved heart function after a heart attack. Instead of merely forming scars, the fibroblasts in the heart were being converted into functional, beating heart cells – cellular alchemy with great promise for new cardiovascular therapies.

As exciting as these discoveries were, many researchers remained skeptical because the cardiac stem cell field has so often seen paradigm-shifting discoveries appear on the horizon, only to later on find out that they cannot be replicated by other laboratories. Fortunately, Eric Olson’s group at the University of Texas, Southwestern Medical Center also published a paper in Nature in 2012, independently confirming that cardiac fibroblasts could indeed be converted into cardiomyocytes. They added on a fourth factor to the GMT cocktail because it appeared to increase the success of conversion. Olson’s group was also able to confirm Srivastava’s finding that directly treating the mouse hearts with these genes helped convert cardiac fibroblasts into heart cells. They also noticed an interesting oddity. Their success of creating heart cells from fibroblasts in the living mouse was far better than what they would have expected from their experiments in a dish. They attributed this to the special cardiac environment and the presence of other cells in the heart that may have helped the fibroblasts convert to beating heart cells. However, another group of scientists attempted to replicate the findings of the 2010 Cell paper and found that their success rate was far lower than that of the Srivastava group. In the paper entitled “Inefficient Reprogramming of Fibroblasts into Cardiomyocytes Using Gata4, Mef2c, and Tbx5” published in the journal Circulation Research in 2012, Chen and colleagues found that very few fibroblasts could be converted into cardiomyocytes and that the electrical properties of the newly generated heart cells did not match up to those of adult heart cells. One of the key differences between this Circulation Research paper and the 2010 paper of the Srivastava group was that Chen and colleagues used fibroblasts from older mice, whereas the Srivastava group had used fibroblasts from newly born mice. Arguably, the use of older cells by Chen and colleagues might be a closer approximation to the cells one would use in patients. Most patients with heart attacks are older than 40 years and not newborns.

These studies were all performed on mouse fibroblasts being converted into heart cells, but they did not address the question whether human fibroblasts would behave the same way. A recent paper in the Proceedings of the National Academy of Sciences by Eric Olson’s laboratory (published online before print on March 4, 2013 by Nam and colleagues) has now attempted to answer this question. Their findings confirm that human fibroblasts can also be converted into beating heart cells, however the group of genes required to coax the fibroblasts into converting is slightly different and also requires the introduction of microRNAs – tiny RNA molecules that can also regulate the expression of a whole group of genes. Their paper also points out an important caveat.  The generated heart-like cells were not uniform and showed a broad range of function, with only some of the spontaneously contracting and with an electrical activity pattern that was not the same as in adult heart cells.

Where does this whole body of work leave us? One major finding seems to be fairly solid. Fibroblasts can be converted into beating heart cells. The efficiency of conversion and the quality of the generated heart cells – from mouse or human fibroblasts – still needs to be optimized. Even though the idea of cellular alchemy sounds fascinating, there are many additional obstacles that need to be overcome before such therapies could ever be tested in humans. The method to introduce these genes into the fibroblasts used viruses which permanently integrate into the DNA of the fibroblast and could cause genetic anomalies in the fibroblasts. It is unlikely that such viruses could be used in patients. The fact that the generated heart cells show heterogeneity in their electrical activity could become a major problem for patients because patches of newly generated heart cells in one portion of the heart might be beating at a different rate of rhythm than other patches. Such electrical dyssynchony can cause life threatening heart rhythm problems, which means that the electrical properties of the generated cells need to be carefully understood and standardized. We also know little about the long-term survival of these converted cells in the heart and whether the converted cells maintain their heart-cell-like activity for months or years. The idea of directly converting fibroblasts by introducing the genes into the heart instead of first obtaining the fibroblasts, then converting them in a dish and lastly implanting the converted cells back into the heart sounds very convenient. But this convenience comes at a price. It requires human gene therapy which has its own risks and it is very difficult to control the cell conversion process in an intact heart of a patient. On the other hand, if cells are converted in a dish, one can easily test and discard the suboptimal cells and only implant the most mature or functional heart cells.

This process of cellular alchemy is still in its infancy. It is one of the most exciting new areas in the field of regenerative medicine, because it shows how plastic cells are. Hopefully, as more and more labs begin to investigate the direct reprogramming of cells, we will be able to address the obstacles and challenges posed by this emerging field.


Image credit: Painting in 1771 by Joseph Wright of Derby – The Alchymist, In Search of the Philosopher’s Stone via Wikimedia Commons
Nam, Y., Song, K., Luo, X., Daniel, E., Lambeth, K., West, K., Hill, J., DiMaio, J., Baker, L., Bassel-Duby, R., & Olson, E. (2013). Reprogramming of human fibroblasts toward a cardiac fate Proceedings of the National Academy of Sciences, 110 (14), 5588-5593 DOI: 10.1073/pnas.1301019110