Saturday, October 18, 2014

Does Literary Fiction Challenge Racial Stereotypes?

A book is a mirror: if a fool looks in, do not expect an apostle to look out.
                                                                Georg Christoph Lichtenberg (1742-1799)


Reading literary fiction can be highly pleasurable, but does it also make you a better person? Conventional wisdom and intuition lead us to believe that reading can indeed improve us. However, as the philosopher Emrys Westacott has recently pointed out in his essay for 3Quarksdaily, we may overestimate the capacity of literary fiction to foster moral improvement. A slew of scientific studies have taken on the task of studying the impact of literary fiction on our emotions and thoughts. Some of the recent research has centered on the question of whether literary fiction can increase empathy. In 2013, Bal and Veltkamp published a paper in the journal PLOS One showing that subjects who read excerpts from literary texts scored higher on an empathy scale than those who had read a nonfiction text. This increase in empathy was predominantly found in the participants who felt "transported" (emotionally and cognitively involved) into the literary narrative. Another 2013 study published in the journal Science by Kidd and Castano suggested that reading literary fiction texts increased the ability to understand and relate to the thoughts and emotions of other humans when compared to reading either non-fiction or popular fiction texts.



Scientific assessments of how fiction affects empathy are fraught with difficulties and critics raise many legitimate questions. Do "empathy scales" used in psychology studies truly capture the psychological phenomenon of "empathy"? How long does the effect of reading literary fiction last and does it translate into meaningful shifts in behavior? How does one select appropriate literary fiction texts and control texts, and conduct such studies in a heterogeneous group of participants who probably have very diverse literary tastes? Kidd and Castano, for example, used an excerpt of The Tiger's Wife by Téa Obreht as a literary fiction text because the book was a finalist for the National Book Award, whereas an excerpt of Gone Girl by Gillian Flynn was used as a ‘popular fiction' text even though it was long-listed for the prestigious Women's Prize for Fiction.
The study "Changing Race Boundary Perception by Reading Narrative Fiction" led by the psychology researcher Dan Johnson from Washington and Lee University took a somewhat different approach. Instead of assessing global changes in empathy, Johnson and colleagues focused on a more specific question. Could the reading of a fictional narrative change the perception of racial stereotypes?


Johnson and his colleagues chose an excerpt from the novel "Saffron Dreams" by the Pakistani-American author Shaila Abdullah. In this novel, the protagonist is a recently widowed pregnant Muslim woman Arissa whose husband Faizan was working in the World Trade Center on September 11, 2001 and killed when the building collapsed. The excerpt from the novel provided to the participants in Johnson's research study describes a scene in which Arissa is traveling alone late at night and is attacked by a group of male teenagers. The teenagers mock and threaten her with a knife because of her Muslim head-scarf (hijab), use racial and ethnic slurs as well as make references to the 9/11 attacks. The narrative excerpt does not specifically mention the word Caucasian, but one of the attackers is identified as blond and another one has a swastika tattoo. They do not believe her when she tries to explain that she was also a victim of the 9/11 attacks and instead refer to her as belonging to a "race of murderers".

The researchers used a second text in their experiment, a synopsis of the literary excerpt from Saffron Dreams. This allowed Johnson colleagues to distinguish between the effects of the literary narrative style with its inner monologue and description of emotions versus the effects of the content. Samples of the literary text and the synopsis used by the researchers can be found at the end of this article (scroll down) for those readers who would like to compare their own reactions to the two texts.
The researchers recruited 68 U.S. participants (mean age 36 years, roughly half were female, 81% Caucasian, reporting seven different religious affiliations but none of them were Muslim) and randomly assigned them to the full literary narrative group (33 participants) or the synopsis group (35 participants).  After the participants read the texts, they were asked to complete a number of questions about the text and its impact on them. They were also presented with 18 male faces that the researchers had designed with a special software in a manner that they appeared ambiguous in terms of Caucasian or Arab characteristics. For example, the faces combined blue eyes with darker skin tones.

The participants were asked to grade the faces as being:
1) Arab
2) mixed, more Arab than Caucasian
3) mixed, more Caucasian than Arab
4) Caucasian

The participants were also asked to estimate the genetic overlap between Caucasians and Arabs on a scale from 0% to 100%.

Participants in the narrative fiction group were more likely to choose one of the ambiguous options (mixed, more Arab than Caucasian or mixed, more Caucasian than Arab) and less likely to choose the categorical options (Arab or Caucasian) than those who read the synopsis. Even more interesting is the finding that the average percentage of genetic overlap between Caucasians and Arabs estimated by the synopsis group was 33%, whereas it was 57% in the narrative fiction group.

Both of these estimates are way off. The genetic overlap between any one human being and another human being on our planet is approximately 99.9%. Even much of the 0.1% variation in the human genome sequences is not due to 'racial' differences. As pointed out in a Nature Genetics article by Lynn Jorde and Stephen Wooding, approximately 90% of total genetic variation between humans would be present in a collection of individuals from any one continent (Asia, Europe or Africa). Only an additional 10% genetic variation would be found if the collection consisted of a mixture of Europeans, Asians and Africans.

It is surprising that both groups of study participants heavily underestimated the genetic overlap between Arabs and Caucasians, and that simply reading the fictional text changed their views of the human genome. This latter finding is also a red flag that informs us about the poor state of general knowledge of genetics, which appears to be so fragile that views can be swayed by nonscientific literary texts.

This study is the first to systematically test the impact of reading literary fiction on an individual's assessment of race boundaries and genetic similarity. It suggests that fiction can indeed blur the perception of race boundaries and challenge our stereotypes. The text chosen by the researchers is especially well-suited to defy stereotypical views held by the readers. The protagonist's Muslim husband was killed in the 9/11 attacks and she herself is being harassed by non-Muslim thugs. This may challenge assumptions held by some readers that only non-Muslims were the victims of the 9/11 attacks.

The effect of reading the narrative text seemed to have effects on the readers that went far beyond the content matter – the story of a Muslim woman who is showing significant courage while being threatened. The faces shown to the study participants were those of men, and the question of genetic overlap between Caucasians and Arabs was a rather abstract question which had little to do with Arissa's story. Perhaps Arissa's story had a broader effect on the readers. The study did not measure the impact of the narrative on additional stereotypes or assumptions held by the readers such as those regarding other races or sexual orientations, but this is a question that ought to be investigated.
One of the limitations of the study is that it assessed the impact of the story only at a single time-point, immediately after reading the text. Without measuring the effect a few days or weeks later, it is difficult to ascertain whether this was a lasting effect.  Another limitation of this study is that it purposefully chose an anti-stereotypical text, but did not test the opposite hypothesis, that some fictional narratives may potentially foster negative stereotypes.

One of my earliest memories of an English-language novel about Muslim characters is the spy novel "The Mahdi" by the British author A.J Quinnell (pen name for Philip Nicholson) written in 1981. The basic plot is that (spoiler alert) US and British intelligence agencies want to manipulate and control the Muslim world by installing a 'Mahdi', the long-awaited spiritual and political leader of Muslims foretold by Muslim tradition. The ridiculous part of the plan is that the puppet leader is accepted by the Muslim world as the true incarnation of the Mahdi because of a green laser beam emanating from a satellite. The beam incinerates a sacrificial animal in front of a crowd of millions of Muslims at the Hajj pilgrimage and convinces them (and the rest of the Muslim world) that God sent this green laser beam as a sign. This novel portrayed Muslims as gullible idiots who would simply accept the divine nature of a green laser beam. One can only wonder what impact reading an excerpt from that novel would have had on the perception of race boundaries by study participants.

The study by Johnson and colleagues is an important contribution to the research of how reading can change our perceptions of race and possibly stereotypes in general. It shows that reading fiction can blur the perception of race boundaries, but it also raises a number of additional questions about how long this effect lasts, how pervasive it is and whether fiction might also have the opposite effect. Hopefully, these questions will be addressed in future research studies.

Image Credit: Saffron Woman by N.M. Rehman (generated from an attribution-free, public domain photograph)

Reference:

Dan R. Johnson , Brandie L. Huffman & Danny M. Jasper (2014)
Changing Race Boundary Perception by Reading Narrative FictionBasic and Applied Social Psychology, 36:1, 83-90, DOI:10.1080/01973533.2013.856791


Excerpt of the literary fiction sample from "Saffron Dreams" by Shaila Abdullah
 This is just an excerpt from the narrative sample used by the researchers, which was 3,108 words in length (pages 57-64 from the book):
"I got off the northbound No. 2 IRT and found out almost immediately that I was not alone. The late October evening inside the station felt unusually weighty on my senses.
I heard heavy breathing behind me. Angry, smoky, scared. I could tell there were several of them, probably four. Not pros, perhaps in their teens. They walked closer sometimes, and other times the heavy thud of spiked boots on concrete and clanking chains receded into the distance. They walked like boys wanting to be men. They fell short. Why was there no fear in my heart? Probably because there was no more room in my heart for terror. When horror comes face-to-face with you and causes a loved one's death, fear leaves your heart. In its place, merciful God places pain. Throbbing, pulsating, oozing pus, a wound that stays fresh and raw no matter how carefully you treat it. How can you be afraid when you have no one to be fearful for? The safety of your loved ones is what breeds fear in your heart. They are the weak links in your life. Unraveled from them, you are fearless. You can dangle by a thread, hang from the rooftop, bungee jump, skydive, walk a pole, hold your hand over the flame of a candle. Burnt, scalded, crashed, lost, dead, the only loss would be to your own self. Certain things you are not allowed to say or do. Defiant as I am, I say and do them anyway.
And so I traveled with a purse that I held protectively on one side. My hijab covered my head and body as the cool breeze threatened to unveil me. I laughed inwardly as I realized I was more afraid of losing the veil than of being mugged. The funny part of it is, I desperately wanted to lose my hijab when I came to America, but Faizan had stood in my way. For generations, women in his household had worn the veil, although none of them seemed particularly devout. It's just something that was done, no questions asked, no explanations needed. My argument was that we should try to assimilate into the new culture as much as possible, not stand out. Now that he was gone, losing the hijab meant losing a portion of our time together.
It had been just 41 days. My iddat, bereavement period, was over. Technically I was a free woman, not tied to anyone, but what could I do about the skeletons in my closet that wouldn't leave me alone?"
Excerpt of the Synopsis used by the researchers as a comparator:
This is the corresponding excerpt from the synopsis used by the researchers. The full-length synopsis was 491 words long:
"The scene starts with Arissa getting off the subway train. She is being followed. Most commuters have already returned home, so it is not the safest time to be traveling alone. Four people are walking behind her. Initially confused by the lack of fear in her heart, she realizes that it is the consequence of losing someone so close to her. It is ironic that she is wearing her hijab, a Muslim veil. She wanted to get rid of it when she came to America, but her husband, Faizon, insisted she keep it. Following his death, keeping the hijab was a way of keeping some of their time together. It has been 41 days since the attack, and Arissa's iddat, bereavement period, is over. She is a free woman, but cannot put aside her grave feelings of loss."

Note: An earlier version of this article was first published on the 3Quarksdaily blog.


ResearchBlogging.org Johnson, D., Huffman, B., & Jasper, D. (2014). Changing Race Boundary Perception by Reading Narrative Fiction Basic and Applied Social Psychology, 36 (1), 83-90 DOI: 10.1080/01973533.2013.856791

Buddhist Musings in Ramadan

Ramadan is the month of fasting and a time for spiritual growth among Muslims. The traditionalist approach to "spiritual growth" is for Muslims to complement their fasting with performing additional prayers at night and regular reading of the Quran throughout the month. My own approach is somewhat different, I tend to complement my fasting with the reading of writings and scriptures from other philosophies or faith traditions, including atheist and humanist teachings. This year, I decided to study the Dhammapada (in the translation of Gil Fronsdal), one of the most widely read and revered writings in the Buddhist faith.

Buddha Statue from the Takht-i-Bahi monastery in Pakistan

I was inspired to learn more about Buddhism because I was reading the remarkable novel "A Tale for the Time Being" by Ruth Ozeki, who is not only a brilliant author but also an ordained Zen Buddhist priest. The first person narrator in the novel is a 16-year old Japanese girl Nao who is bullied by her classmates. Nao's parents moved from Japan to Silicon Valley but were forced to return to Japan when the Dotcom bubble burst. Nao's father loses his job and the family is forced to live in poverty. The family's poverty and the fact that Nao is seen as an alien "transfer student" lead to her being ostracized at school. But her classmates go even further and begin psychologically and physically torturing her, leaving scars and scabs all over her body.


A photo of the Takht-i-Bahi monastery, the most complete ancient Buddhist monastic center in Pakistan and a UNESCO World heritage site



Nao is invited to spend the summer with her 104-year old great-grandmother Jiko who is a Buddhist nun. In the following scene, Jiko takes a bath with Nao and notices the scars:

"I waited. Old Jiko liked to take her time, and she was really good at it because she'd been practicing for so many years, so as a result, I was always waiting for her, and you'd think that waiting would be annoying for a young person like me, but for some reason I didn't mind. It wasn't like I had anything better to do that summer. I sat there on my little wooden stool, naked and hugging my knees and shivering, not from the cold but in anticipation of the scalding heat of the water, so when, instead, I felt her fingertip touch a small scar in the middle of my back, I was startled. My body stiffened. The light was so dim, how could she see my scars with her bad eyes? I figured she couldn't, but then I felt her finger move across my skin in a pattern, hesitant, pausing here and there to connect the dots."You must be very angry," she said. She spoke so quietly, it was like she was talking to herself, and maybe she was. Or maybe she hadn't said anything at all, and I'd just imagined it. Either way, my throat squeezed shut and I couldn't answer, so I shook my head. I was so ashamed, but at the same time, this enormous feeling of sadness brimmed up inside me, and I had to hold my breath to stop from crying.
She didn't say anything else. She washed me gently, and for the first time I just wanted her to hurry up and finish. After we were done, I got dressed quickly and said good night and left her there. I thought I was going to throw up. I didn't want to go back to my room, so I ran halfway down the mountainside and hid in the bamboo forest until it got dark and the fireflies came out. When Muji rang the big bell at the end of her fire watch to signal the end of the day, I snuck back into the temple and crawled into bed.
The next morning I went looking for old Jiko and found her in her room. She was sitting on the floor with her back to the door, bent over her low table. She was reading. I stood in the doorway and didn't even bother to go in. "Yes," I told her. "I'm angry, so what?"

(excerpted from novel "A Tale for the Time Being" by Ruth Ozeki)

Once Nao is able to speak about her anger to Jiko, Nao's healing process can begin. The story makes frequent references to Buddhist teachings, quoting from Buddhist texts as well as allowing the reader to gradually imbibe important spiritual concepts. To better understand these concepts, I decided to read the Dhammapada

I first began with the chapter on "Anger" where I was struck by the following verses:

"The one who keeps anger in check as it arises,
            As one would a careening chariot,
I call a charioteer.
            Others are merely rein-holders."

How often do we let our anger chariot determine our paths? I can remember countless times when I have been passively holding the reins but rarely take control of this chariot.
I will just leave you with one more excerpt from the Dhammapada, but I advise you to read it (and, of course, Ozeki's novel!) in its entirety:

From the chapter "The Sage":

"As a solid mass of rock,
            Is not moved by the wind,
So a sage is not moved
            By praise or blame."

***************
Image credit: 1) Buddha statue now housed in Berlin, image by Gryffindor via Wikimedia, 2) Takht-i-Bahi monastery ruins in Northern Pakistan, image by Ziegler175 via Wikimedia.

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.
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.


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.

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.


Pygmalion and Glatea by Louis Gauffier (via Wikimedia - Public Domain)


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.


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.

Thursday, July 24, 2014

FC Bayern Munich: Too Jewish for the Nazis

Konrad Heitkamp was taken aback by the extraordinary ordinariness present in the lobby of the Zurich hotel. In November of 1943, life in Zurich seemed unperturbed by the fact that the countries surrounding Switzerland were embroiled in one of the most devastating wars in the history of the world. Heitkamp realized that as the coach of the FC Bayern München soccer team, he was one of the privileged few who could bask in this oasis of normalcy for a few days before he would have to head back home to Munich. He surveyed the lobby and began waving his hand at some of his players standing across the vestibule. Hopefully, the Gestapo men watching him thought of this as an innocuous gesture, a soccer team coach acknowledging the arrival of his players and performing a headcount. But he could not bank on it.


The Gestapo must have known that for the past weeks, Heitkamp and his players were forward to the friendly match against the Swiss national soccer team because it would give them a chance to finally see their friend Kurt Landauer again. Before the team embarked on their trip to Zurich, the Gestapo had ordered all Bayern München players to attend a special "education" session in Gestapo headquarters of Munich. The team was informed that the Gestapo would accompany the team on their brief trip to Switzerland. The Gestapo explicitly forbade the team members to have any contact with German emigrants in Switzerland.

The Nazis were always weary of any potential contacts between Germans and German emigrants who were seen as traitors and collaborators of the Allied forces. But FC Bayern München was a special thorn in the flesh of the Nazi machinery. Nazis routinely referred to FC Bayern München as a "Judenclub" ("Jew Club"), because German Jews had held some of the key leadership positions. The club won its first German national soccer championship in 1932 under the leadership of the Jewish club president Kurt Landauer and the coach Richard Dombi, an Austrian Jew. Only a few months later in January 1933, Hitler came to power and soon all leaders of Jewish origin were forced to give up their leadership positions.

Kurt Landauer was one of the first to resign from the club presidency. He even lost his job as the manager of a Munich newspaper's advertising department, and was only able to find work in a textile shop owned by a Jewish family. In the wake of the anti-semitic pogroms in the night of the 9th November 1938 (Kristallnacht oder Reichspogromnacht), this shop was attacked and devastated. Landauer was arrested and sent to the Dachau concentration camp. After a brief period of internment, he was released and he used this opportunity to emigrate to Switzerland and survived the Holocaust. Most of his siblings were less fortunate and were murdered by the Nazis.



Konrad Heitkamp and his wife Magdalena are about to walk towards their hotel room, when a bellhop appears in front of them and hands Heitkamp a note. It is a message from Kurt Landauer. Heitkamp tries to suppress his excitement , but it is already too late. Before he can even read the note, a man taps him on the shoulder and says "Gestapo. Give me the note. We know who it is from and we absolutely forbid you to have any contact with that man. We are watching you!"

For the remainder of the trip, the Gestapo closely walls off Heitkamp and his players, making it impossible for them to have any contact with Landauer. But the players still manage to embarrass the Nazis and the Gestapo. Immediately after the whistle is blown to start the game, the FC Bayern München players run up to the area of the soccer field in front of Kurt Landauer and greet their former president from afar.

The book "Der FC Bayern und seine Juden: Aufstieg und Zerschlagung einer liberalen Fußballkultur" (FC Bayern and its Jews: The Rise and Destruction of a Liberal Soccer Culture) by the German soccer historian Dietrich Schulze-Marmeling describes the prevalent culture of tolerance at FC Bayern München in the years prior to the Nazi takeover of Germany. Many members, players and leaders of the club were Jewish, but the question of ethnicity or religion was not even a real issue for the club. All that really mattered was whether or not you were a member of the club. Once the Nazis came to power in 1933, they tried to install their henchmen at leadership positions of all institutions, including sport clubs. TSV 1860, the other big Munich soccer club, immediately acquiesced to the new Nazi masters, allowing  SA men to take control of the club from 1934 onwards. Players and members of FC Bayern München, on the other hand, staving off Nazi leadership up until 1943. The Nazis were often frustrated by the recalcitrant "Judenclub" which resisted and delayed the implementation of Nazi ordinances.

I have been an FC Bayern München fan all my life. My childhood home in Munich was just a ten minute walk away from the club's headquarters at the Säbener Strasse. It is not difficult to be proud of its achievements. In 2013, the club won every major trophy that it was eligible for - Bundesliga champions, the German soccer federation cup (DFB-Pokal), the European Champions League and the 2013 FIFA Club World Cup – thus underscoring its dominance as the world's best soccer club. But none of these victories made me as proud of my club as finding out about how my club defied anti-semitism and the Nazis.

Image: The headquarters of FC Bayern München in the Säbener Strasse (photo by J. Rehman)


Note: An earlier version of this article was first published on 3Quarksdaily.com.

Reference: Schulze-Marmeling, D. (2011). "Der FC Bayern und seine Juden: Aufstieg und Zerschlagung einer liberalen Fußballkultur". Werkstatt GmbH

Is Internet-Centrism a Religion?

On the evening of March 3 in 1514, Steven is sitting next to Friar Clay in a Nottingham pub, covering his face with his hands.

"I am losing the will to live", Steven sobs, "Death may be sweeter than life in this world of poverty, injustice and war."

"Do not despair, my friend", Clay says, "for the printing press will change everything."

*******

Let us now fast-forward 500 years and re-enact this hypothetical scene with some tiny modifications.

On the evening of March 3 in 2014, Steven is sitting next to TED-Talker Clay in a Nottingham pub, covering his face with his hands.

"I am losing the will to live", Steven sobs, "Death may be sweeter than life in this world of poverty, injustice and war."

"Do not despair, my friend", Clay says, "for the internet will change everything."

*******

Clay's advice in the first scene sounds ludicrous to us because we know that the printing press did not usher in an era of wealth, justice and peace. Being retrospectators, we realize that the printing press revolutionized how we disseminate information, but even the most efficient dissemination tool is just a means and not the ends.


It is more difficult for us to dismiss Clay's advice in the second scene because it echoes the familiar Silicon Valley slogans which inundate us with such persistence that some of us have begun to believe them. Clay's response is an example of what Evgeny Morozov refers to as "Internet-centrism", the unwavering belief that the Internet is not just an information dissemination tool but that it constitutes the path to salvation for humankind. In his book "To Save Everything, Click Here: The Folly of Technological Solutionism", Morozov suggests that "Internet-centrism" is taking on religion-like qualities:
"If the public debate is any indication, the finality of "the Internet"— the belief that it's the ultimate technology and the ultimate network— has been widely accepted. It's Silicon Valley's own version of the end of history: just as capitalism-driven liberal democracy in Francis Fukuyama's controversial account remains the only game in town, so does the capitalism-driven "Internet." It, the logic goes, is a precious gift from the gods that humanity should never abandon or tinker with. Thus, while "the Internet" might disrupt everything, it itself should never be disrupted. It's here to stay— and we'd better work around it, discover its real nature, accept its features as given, learn its lessons, and refurbish our world accordingly. If it sounds like a religion, it's because it is."
Morozov does not equate mere internet usage with "Internet-centrism". People  routinely use the internet for work or leisure without ascribing mythical powers to it, but it is when the latter occurs that internet usage transforms into "Internet-centrism".


Does Morozov's portrayal of "Internet-centrism" as a religion correspond to our current understanding of religions? "Internet-centrism" does not involve deities, sacred scripture or traditional prayers, but social scientists and scholars of religion do not require deism, scriptures or prayers to categorize a body of beliefs and practices as a religion.

The German theologian Friedrich Schleiermacher (1768-1834) thought that the feeling of "absolute dependence" ("das schlechthinnige Abhängigkeitsgefühl") was one of the defining characteristics of a religion. In a January 2014 Pew Internet survey, 53% of adult internet users in said that it would be "very hard" to give up the internet, whereas only 38% felt this way in 2006.  This does not necessarily meet the Schleiermacher threshold of "absolute dependence" but it indicates a growing perception of dependence among internet users, who are struggling to envision a life without the internet or a life beyond the internet.
Absolute dependence is  not unique to religion, therefore it may be more helpful to turn to religion-specific definitions if we want to understand the religionesque characteristics of Internet-centrism. In his classic essay "Religion as a cultural system" (published in "The Interpretation of Cultures"), the anthropologist Clifford Geertz (1926-2006) defined religion as:
" (1) a system of symbols which acts to (2) establish powerful, persuasive, and long-lasting moods and motivations in men by (3) formulating conceptions of a general order of existence and (4) clothing these conceptions with such an aura of factuality that (5) the moods and motivations seem uniquely realistic."
 Today's Silicon Valley pundits (incidentally a Sanskrit term originally used for learned Hindu scholars well-versed in Vedic scriptures) excel at establishing "powerful, persuasive, and long-lasting moods and motivations" and endowing "conceptions of general order of existence" with an "aura of factuality". Morozov does not specifically reference the Geertz definition of religion, but he provides extensive internet pundit quotes which fit the bill. Here is one such example:
"To be a peer progressive, then, is to live with the conviction that Wikipedia is just the beginning, that we can learn from its success to build new systems that solve problems in education, governance, health, local communities, and countless other regions of human experience." 
—Steven Johnson in "Future Perfect: The Case For Progress In A Networked Age"
One problem with abstract definitions of religion is that they do not encompass the practice of religion and its mythical or supernatural aspects, which are often essential parts of most religions. In "The Religious Experience", the religion scholar Ninian Smart (1927-2001) does not provide a handy definition for religions but instead offers six "dimensions" that are present in most major religions: 1) The Ritual Dimension, 2) The Mythological Dimension, 3) The Doctrinal Dimension, 4) The Ethical Dimension, 5) The Social Dimension and 6) The Experiential Dimension.

How do these dimensions of religion apply to Internet-centrism?

1) The Ritual Dimension: The need to continuously seek connectivity by accessing computers or seeking out wireless connectivity, checking emails or social media updates so frequently that this connectivity exceeds one's pragmatic needs could be considered a ritual of Internet-centrism. If one feels the need to check emails and Facebook or Twitter updates every one to two minutes, despite the fact that it is unlikely one would have received a message that required urgent action, it may be an indicator of the important role that this ritual plays in the life of an Internet-centrist. Worshippers of traditional religions feel uncomfortable if they miss out on regular prayers or lose their rosaries that allow them to commune with their God, and it appears that for some humans, the ritual of Internet-connectivity may play a similar role.

2) The Mythological Dimension: There is the physical internet, which consists of billions of physical components such as computers, servers, routers or cables that are connected to each other. Prophets and pundits of Internet-centrism also describe a mythical "Internet" which goes for beyond the physical internet, because it involves mythical narratives about the power of the internet as a higher force that is shaping human destiny. Just like "Scientism" attributes a certain mystique to real-world science, Internet-centrism adorns the physical internet with a similar mythological dimension.   
Ideas of "cognitive surplus", crowdsourcing knowledge to improve the human condition, internet-based political revolutions that will put an end to injustice, oppression and poverty and other powerful metaphors are used to describe this poorly defined mythical entity that has little to do with the physical internet. The myth of egalitarianism is commonly perpetuated, yet the internet is anything but egalitarian. Social media hubs have millions of followers and certain corporations or organizations are experts at building filters and algorithms to control the information seen by consumers who have minimal power and control over the flow of information.

3) The Doctrinal Dimension: The doctrine of Internet-centrism is the relentless pursuit of sharedom through the internet. The idea is that the more we share, the more we collaborate and the more transparent we are via the internet, the easier it will be for us humans to conquer the challenges that face us. Challenging this basic doctrine that is promoted by Silicon Valley corporations can be perceived as heretical. It is a remarkable testimony to the proselytizing power of the prophets and pundits in Silicon Valley that people were outraged at the government institution NSA for violating our privacy. There was comparatively little concern about the fact that the primary benefactors of the growing culture of sharedom are the for-profit internet corporations that make money off our willingness to sacrifice our privacy.

4) The Ethical Dimension: In many religions, one is asked to follow aspects of a religious doctrine which have no direct ethical context. For example, seeking salvation by praying alone to a god on a mountain-top does not necessarily require adherence to ethical standards. On the other hand, most religions have developed moral imperatives that govern how adherents of a religion interact with fellow believers or non-believers. In Internet-centrism, the doctrinal dimension is conflated with the ethical dimension. Sharedom is not only a doctrinal imperative, it is also a moral imperative. We are told that sharing and collaborating is an ethical duty.
This may be unique to Internet-centrism since the internet (both in its physical or its mythical form) presupposes the existence of fellow beings with whom one can connect. If a catastrophe wiped out all humans but one, who happened to adhere to a traditional religion, she could still pray to a god (ritual), believe in salvation by a supernatural entity (mythological) and abide by the the religious laws (doctrinal). However, if she were an Internet-centrist, all her rituals, beliefs and doctrines would become meaningless.

5) The Social Dimension: Congregating in groups and social interactions are key for many religions, but Internet-centrism provides more tools than any other ideology, cultural movement or religion for us to interact with others. Whether we engage in this social activity by using social media such as Facebook or Twitter, by reading or writing blog posts, or by playing multi-player games online, Internet-centrism encourages us to fulfill our social needs by using the tools of the internet.   

6) The Experiential Dimension: Most religions offer their adherents opportunities for highly personal, spiritual experiences. Internet-centrism avoids any talk of "spirituality", but the idea of a personalized experience is very much a part of Internet-centrism. One of its goals is to provide opportunities for self-actualization. We all may be connected via the internet, but Internet-centrists also want us to believe that this connectivity provides a path for self-actualization. We can modify settings to customize our web browsing experience, we can pick and choose from millions of options of what online courses we want to take, videos we want to watch or music we want to listen to. The sense of connectedness and omnipotentiality is what provides the adherent of Internet-centrism with a feeling of personal empowerment that comes close to a spiritual experience of traditional religions.   

When one reviews the definitions by Schleiermacher or Geertz, or the multi-dimensional analysis by Ninian Smart, it does indeed seem that Morozov is right and that Internet-centrism is taking on many religion-like characteristics. There is probably still a big disconnect between the Silicon valley prophets or pundits who proselytize and the vast majority of internet users who primarily act as "consumers" but do not yet buy into the tenets of Internet-centrism. But it is likely that at least in the short-term, Internet-centrism will continue to grow, especially if Internet-centrist ideas are introduced to children in schools and they grow up believing that these ideas are both essential and sufficient for our intellectual and social wellbeing. Perhaps the pundits of Internet-centrism could discuss the future of this emerging religion with adherents of other faiths at a TEDxInterfaith conference.

Image Credits: Photo of Gutenberg Bible (Creative Commons license, via NYC Wanderer at Flickr)

Monday, June 16, 2014

Synthetic Biology: Engineering Life To Examine It

Two scientific papers that were published in the journal Nature in the year 2000 marked the beginning of engineering biological circuits in cells. The paper "Construction of a genetic toggle switch in Escherichia coli" by Timothy Gardner, Charles Cantor and James Collins created a genetic toggle switch by simultaneously introducing an artificial DNA plasmid into a bacterial cell. This DNA plasmid contained two promoters (DNA sequences which regulate the expression of genes) and two repressors (genes that encode for proteins which suppress the expression of genes) as well as a gene encoding for green fluorescent protein that served as a read-out for the system. The repressors used were sensitive to either selected chemicals or temperature. In one of the experiments, the system was turned ON by adding the chemical IPTG (a modified sugar) and nearly all the cells became green fluorescent within five to six hours. Upon raising the temperature to activate the temperature-sensitive repressor, the cells began losing their green fluorescence within an hour and returned to the OFF state. Many labs had used chemical or temperature switches to turn gene expression on in the past, but this paper was the first to assemble multiple genes together and construct a switch which allowed switching cells back and forth between stable ON and OFF states.


The same issue of Nature contained a second land-mark paper which also described the engineering of gene circuits. The researchers Michael Elowitz and Stanislas Leibler describe the generation of an engineered gene oscillator in their article "A synthetic oscillatory network of transcriptional regulators". By introducing three repressor genes which constituted a negative feedback loop and a green fluorescent protein as a marker of the oscillation, the researchers created a molecular clock in bacteria with an oscillation period of roughly 150 minutes. The genes and proteins encoded by the genes were not part of any natural biological clock and none of them would have oscillated if they had been introduced into the bacteria on their own. The beauty of the design lay in the combination of three serially repressing genes and the periodicity of this engineered clock reflected the half-life of the protein encoded by each gene as well as the time it took for the protein to act on the subsequent member of the gene loop.


Both papers described the introduction of plasmids encoding for multiple genes into bacteria but this itself was not novel. In fact, this has been a routine practice since the 1970s for many molecular biology laboratories. The panache of the work lay in the construction of functional biological modules consisting of multiple genes which interacted with each other in a controlled and predictable manner. Since the publication of these two articles, hundreds of scientific papers have been published which describe even more intricate engineered gene circuits. These newer studies take advantage of the large number of molecular tools that have become available to query the genome as well as newer DNA plasmids which encode for novel biosensors and regulators.

Synthetic biology is an area of science devoted to engineering novel biological circuits, devices, systems, genomes or even whole organisms. This rather broad description of what "synthetic biology" encompasses reflects the multidisciplinary nature of this field which integrates ideas derived from biology, engineering, chemistry and mathematical modeling as well as a vast arsenal of experimental tools developed in each of these disciplines. Specific examples of "synthetic biology" include the engineering of microbial organisms that are able to mass produce fuels or other valuable raw materials, synthesizing large chunks of DNA to replace whole chromosomes or even the complete genome in certain cells, assembling synthetic cells or introducing groups of genes into cells so that these genes can form functional circuits by interacting with each other. Synthesis in the context of synthetic biology can signify the engineering of artificial genes or biological systems that do not exist in nature (i.e. synthetic = artificial or unnatural), but synthesis can also stand for integration and composition, a meaning which is closer to the Greek origin of the word.  It is this latter aspect of synthetic biology which makes it an attractive area for basic scientists who are trying to understand the complexity of biological organisms. Instead of the traditional molecular biology focus on studying just one single gene and its function, synthetic biology is engineering biological composites that consist of multiple genes and regulatory elements of each gene. This enables scientists to interrogate the interactions of these genes, their regulatory elements and the proteins encoded by the genes with each other. Synthesis serves as a path to analysis.

One goal of synthetic biologists is to create complex circuits in cells to facilitate biocomputing, building biological computers that are as powerful or even more powerful that traditional computers. While such gene circuits and cells that have been engineered have some degree of memory and computing power, they are no match for the comparatively gigantic computing power of even small digital computers. Nevertheless, we have to keep in mind that the field is very young and advances are progressing at a rapid pace.
One of the major recent advances in synthetic biology occurred in 2013 when an MIT research team led by Rahul Sarpeshkar and Timothy Lu at MIT created analog computing circuits in cells.

Most synthetic biology groups that engineer gene circuits in cells to create biological computers have taken their cues from contemporary computer technology. Nearly all of the computers we use are digital computers, which process data using discrete values such as 0's and 1's. Analog data processing on the other hand uses a continuous range of values instead of 0's and 1's. Digital computers have supplanted analog computing in nearly all areas of life because they are easy to program, highly efficient and process analog signals by converting them into digital data. Nature, on the other hand, processes data and information using both analog and digital approaches. Some biological states are indeed discrete, such as heart cells which are electrically depolarized and then repolarized in periodical intervals in order to keep the heart beating. Such discrete states of cells (polarized / depolarized) can be modeled using the ON and OFF states in the biological circuit described earlier. However, many biological processes, such as inflammation, occur on a continuous scale. Cells do not just exist in uninflamed and inflamed states; instead there is a continuum of inflammation from minimal inflammatory activation of cells to massive inflammation. Environmental signals that are critical for cell behavior such as temperature, tension or shear stress occur on a continuous scale and there is little evidence to indicate that cells convert these analog signals into digital data.

Most of the attempts to create synthetic gene circuits and study information processing in cells have been based on a digital computing paradigm. Sarpeshkar and Lu instead wondered whether one could construct analog computation circuits and take advantage of the analog information processing systems that may be intrinsic to cells. The researchers created an analog synthetic gene circuit using only three proteins that regulate gene expression and the fluorescent protein mCherry as a read-out. This synthetic circuit was able to perform additions or ratiometric calculations in which the cumulative fluorescence of the mCherry was either the sum or the ratio of selected chemical input concentrations. Constructing a digital circuit with similar computational power would have required a much larger number of components.

The design of analog gene circuits represents a major turning point in synthetic biology and will likely spark a wave of new research which combines analog and digital computing when trying to engineer biological computers. In our day-to-day lives, analog computers have become more-or-less obsolete. However, the recent call for unconventional computing research by the US Defense Advanced Research Projects Agency (DARPA) is seen by some as one indicator of a possible paradigm shift towards re-examining the value of analog computing. If other synthetic biology groups can replicate the work of Sarpeshkar and Lu and construct even more powerful analog or analog-digital hybrid circuits, then the renaissance of analog computing could be driven by biology.  It is difficult to make any predictions regarding the construction of biological computing machines which rival or surpass the computing power of contemporary digital computers. What we can say is that synthetic biology is becoming one of the most exciting areas of research that will provide amazing insights into the complexity of biological systems and may provide a path to revolutionize biotechnology.

An earlier version of this article was first published at 3Quarksdaily.


ResearchBlogging.org Daniel R, Rubens JR, Sarpeshkar R, & Lu TK (2013). Synthetic analog computation in living cells. Nature, 497 (7451), 619-23 PMID: 23676681

Tuesday, June 3, 2014

Sharing Our Sorrow Via Facebook

Geteiltes Leid ist halbes Leid ("Shared sorrow is half the sorrow") is a popular German proverb which refers to the importance of sharing bad news and troubling experiences with others. The therapeutic process of sharing takes on many different forms: we may take comfort in the fact that others have experienced similar forms of sorrow, we are often reassured by the empathy and encouragement we receive from friends, and even the mere process of narrating the details of what is troubling us can be beneficial. Finding an attentive audience that is willing to listen to our troubles is not always easy. In a highly mobile, globalized world, some of our best friends may be located thousands of kilometers away, unable to meet face-to-face. The omnipresence of social media networks may provide a solution. We are now able to stay in touch with hundreds of friends and family members, and commiserate with them. But are people as receptive to sorrow shared via Facebook as they are in face-to-face contacts?



A team of researchers headed by Dr. Andrew High at the University of Iowa recently investigated this question and published their findings in the article "Misery rarely gets company: The influence of emotional bandwidth on supportive communication on Facebook". The researchers created three distinct Facebook profiles of a fictitious person named Sara Thomas who had just experienced a break-up. The three profiles were identical in all respects except for how much information was conveyed about the recent (fictitious) break-up. In their article, High and colleagues use the expression "emotional bandwidth" to describe the extent of emotions conveyed in the Facebook profile.
In the low bandwidth scenario, the profile contained the following status update:

"sad and depressed:("


The medium bandwidth profile included a change in relationship status to "single" in the timeline, in addition to the  low bandwidth profile update "sad and depressed:(".




Finally, the high emotional bandwidth profile not only contained the updates of the low and medium bandwidth profiles, but also included a picture of a crying woman (the other two profiles had no photo, just the standard Facebook shadow image).



The researchers then surveyed 84 undergraduate students (enrolled in communications courses, average age 20, 53% female) and presented them with screenshots of one of the three profiles.


They asked the students to imagine that the person in the profile was a member of their Facebook network. After reviewing the assigned profile, each student completed a questionnaire asking about their willingness to provide support for Sara Thomas using a 9-point scale (1 = strongly disagree; 9 = strongly agree). The survey contained questions that evaluated the willingness to provide emotional support (e.g.  "Express sorrow or regret for her situation") and network support (e.g. "Connect her with people whom she may turn to for help''). In addition to being queried about their willingness to provide distinct forms of support, the students were also asked about their sense of community engendered by Facebook (e.g., "Facebook makes me feel I am a part of a community'') and their preference for online interactions over face-to-face interactions  (e.g., "I prefer communicating with other people online rather than face-to-face'').

High and colleagues hypothesized that the high emotional bandwidth profiles would elicit greater support from the students. In face-to-face interactions, it is quite common for us to provide greater support to a person – friend or stranger – if we see them overtly crying and therefore the researchers' hypothesis was quite reasonable. To their surprise, the researchers found the opposite. The willingness to provide emotional or network support was significantly lower among students who viewed the high emotional bandwidth profile! For example, average emotional support scores were 7.8 among students who saw Sara entering the "sad and depressed:(" update (low bandwidth) but the scores were only 6.5 among students who also saw the image of Sara crying and updating her relationship status to single (high bandwidth). Interestingly, students who preferred online interactions over face-to-face interactions or those who felt that Facebook created a strong sense of community responded positively to the high bandwidth profile.

There are some important limitations of the study. The students were asked to evaluate whether they would provide support to a fictitious person by imagining that she was part of their Facebook friends network. This is a rather artificial situation because actual supportive Facebook interactions occur among people who know each other. It is not easy to envision support for a fictitious person whose profile one sees for the first time. Furthermore, "emotional bandwidth" is a broad concept and it is difficult to draw general conclusions about "emotional bandwidth" from the limited differences between the three profiles. Increasing the sample size of the study subjects as well as creating a broader continuum of emotional bandwidth differences (e.g. including profiles which include pictures of a fictitious Sara Thomas who is not crying, using other status updates, etc.), and also considering scenarios that are not just related to break-ups (e.g. creating profiles of a fictitious grieving person who has lost a loved one) would be useful for an in-depth analysis of "emotional bandwidth".

The study by High and colleagues is an intriguing and important foray into the cyberpsychology of emotional self-disclosure and supportive communication on Facebook. This study raises important questions about how cyberbehavior differs from real world face-to-face behavior, and the even more interesting question of why these behaviors are different. Online interactions omit the dynamic gestures, nuanced intonations and other cues which play a critical role in determining our face-to-face behavior. When we share emotions via Facebook, our communication partners are often spatially and temporally displaced. This allows us to carefully "edit" what we disclose about ourselves, but it also allows our audience to edit their responses, unlike the comparatively spontaneous responses of a person sitting next to us. Facebook invites us to use the "Share" button, but we need to remember that online "sharing" is a sharing between heavily edited and crafted selves that is very different from traditional forms of "sharing".     

********************************

Acknowledgments: An earlier version of this article was first published at 3Quarksdaily. The images from the study profiles were provided by Dr. Andrew High, copyright of the images - Dr. Andrew High. 

Reference: Misery rarely gets company: The influence of emotional bandwidth on supportive communication on Facebook, AC High, A Oeldorf-Hirsch, S BellurComputers in Human Behavior (2014) 34, 79-88





ResearchBlogging.org High, A., Oeldorf-Hirsch, A., & Bellur, S. (2014). Misery rarely gets company: The influence of emotional bandwidth on supportive communication on Facebook Computers in Human Behavior, 34, 79-88 DOI: 10.1016/j.chb.2014.01.037