Tag Archives: Uppsala University

Of musical parodies, Despacito, and evolution

What great timing, I just found out about a musical science parody featuring evolution and biology and learned of the latest news about the study of evolution on one of the islands in the Galapagos (where Charles Darwin made some of his observations). Thanks to Stacey Johnson for her November 24, 2017 posting on the Signals blog for featuring Evo-Devo (Despacito Biology Parody), an A Capella Science music video from Tim Blais,

Now, for the latest regarding the Galapagos and evolution (from a November 24, 2017 news item on ScienceDaily),

The arrival 36 years ago of a strange bird to a remote island in the Galapagos archipelago has provided direct genetic evidence of a novel way in which new species arise.

In this week’s issue of the journal Science, researchers from Princeton University and Uppsala University in Sweden report that the newcomer belonging to one species mated with a member of another species resident on the island, giving rise to a new species that today consists of roughly 30 individuals.

The study comes from work conducted on Darwin’s finches, which live on the Galapagos Islands in the Pacific Ocean. The remote location has enabled researchers to study the evolution of biodiversity due to natural selection.

The direct observation of the origin of this new species occurred during field work carried out over the last four decades by B. Rosemary and Peter Grant, two scientists from Princeton, on the small island of Daphne Major.

A November 23, 2017 Princeton University news release on EurekAlert, which originated the news item, provides more detail,

“The novelty of this study is that we can follow the emergence of new species in the wild,” said B. Rosemary Grant, a senior research biologist, emeritus, and a senior biologist in the Department of Ecology and Evolutionary Biology. “Through our work on Daphne Major, we were able to observe the pairing up of two birds from different species and then follow what happened to see how speciation occurred.”

In 1981, a graduate student working with the Grants on Daphne Major noticed the newcomer, a male that sang an unusual song and was much larger in body and beak size than the three resident species of birds on the island.

“We didn’t see him fly in from over the sea, but we noticed him shortly after he arrived. He was so different from the other birds that we knew he did not hatch from an egg on Daphne Major,” said Peter Grant, the Class of 1877 Professor of Zoology, Emeritus, and a professor of ecology and evolutionary biology, emeritus.

The researchers took a blood sample and released the bird, which later bred with a resident medium ground finch of the species Geospiz fortis, initiating a new lineage. The Grants and their research team followed the new “Big Bird lineage” for six generations, taking blood samples for use in genetic analysis.

In the current study, researchers from Uppsala University analyzed DNA collected from the parent birds and their offspring over the years. The investigators discovered that the original male parent was a large cactus finch of the species Geospiza conirostris from Española island, which is more than 100 kilometers (about 62 miles) to the southeast in the archipelago.

The remarkable distance meant that the male finch was not able to return home to mate with a member of his own species and so chose a mate from among the three species already on Daphne Major. This reproductive isolation is considered a critical step in the development of a new species when two separate species interbreed.

The offspring were also reproductively isolated because their song, which is used to attract mates, was unusual and failed to attract females from the resident species. The offspring also differed from the resident species in beak size and shape, which is a major cue for mate choice. As a result, the offspring mated with members of their own lineage, strengthening the development of the new species.

Researchers previously assumed that the formation of a new species takes a very long time, but in the Big Bird lineage it happened in just two generations, according to observations made by the Grants in the field in combination with the genetic studies.

All 18 species of Darwin’s finches derived from a single ancestral species that colonized the Galápagos about one to two million years ago. The finches have since diversified into different species, and changes in beak shape and size have allowed different species to utilize different food sources on the Galápagos. A critical requirement for speciation to occur through hybridization of two distinct species is that the new lineage must be ecologically competitive — that is, good at competing for food and other resources with the other species — and this has been the case for the Big Bird lineage.

“It is very striking that when we compare the size and shape of the Big Bird beaks with the beak morphologies of the other three species inhabiting Daphne Major, the Big Birds occupy their own niche in the beak morphology space,” said Sangeet Lamichhaney, a postdoctoral fellow at Harvard University and the first author on the study. “Thus, the combination of gene variants contributed from the two interbreeding species in combination with natural selection led to the evolution of a beak morphology that was competitive and unique.”

The definition of a species has traditionally included the inability to produce fully fertile progeny from interbreeding species, as is the case for the horse and the donkey, for example. However, in recent years it has become clear that some closely related species, which normally avoid breeding with each other, do indeed produce offspring that can pass genes to subsequent generations. The authors of the study have previously reported that there has been a considerable amount of gene flow among species of Darwin’s finches over the last several thousands of years.

One of the most striking aspects of this study is that hybridization between two distinct species led to the development of a new lineage that after only two generations behaved as any other species of Darwin’s finches, explained Leif Andersson, a professor at Uppsala University who is also affiliated with the Swedish University of Agricultural Sciences and Texas A&M University. “A naturalist who came to Daphne Major without knowing that this lineage arose very recently would have recognized this lineage as one of the four species on the island. This clearly demonstrates the value of long-running field studies,” he said.

It is likely that new lineages like the Big Birds have originated many times during the evolution of Darwin’s finches, according to the authors. The majority of these lineages have gone extinct but some may have led to the evolution of contemporary species. “We have no indication about the long-term survival of the Big Bird lineage, but it has the potential to become a success, and it provides a beautiful example of one way in which speciation occurs,” said Andersson. “Charles Darwin would have been excited to read this paper.”

Here’s a link to and a citation for the paper,

Rapid hybrid speciation in Darwin’s finches by Sangeet Lamichhaney, Fan Han, Matthew T. Webster, Leif Andersson, B. Rosemary Grant, Peter R. Grant. Science 23 Nov 2017: eaao4593 DOI: 10.1126/science.aao4593

This paper is behind a paywall.

Happy weekend! And for those who love their Despacito, there’s this parody featuring three Italians in a small car (thanks again to Stacey Johnson’s blog posting),

Macchiarini controversy and synthetic trachea transplants (part 2 of 2)

For some bizarre frosting on this disturbing cake (see part 1 of the Macchiarini controversy and synthetic trachea transplants for the medical science aspects), a January 5, 2016 Vanity Fair article by Adam Ciralsky documents Macchiarini’s courtship of an NBC ([US] National Broadcasting Corporation) news producer who was preparing a documentary about him and his work,

Macchiarini, 57, is a magnet for superlatives. He is commonly referred to as “world-renowned” and a “super-surgeon.” He is credited with medical miracles, including the world’s first synthetic organ transplant, which involved fashioning a trachea, or windpipe, out of plastic and then coating it with a patient’s own stem cells. That feat, in 2011, appeared to solve two of medicine’s more intractable problems—organ rejection and the lack of donor organs—and brought with it major media exposure for Macchiarini and his employer, Stockholm’s Karolinska Institute, home of the Nobel Prize in Physiology or Medicine. Macchiarini was now planning another first: a synthetic-trachea transplant on a child, a two-year-old Korean-Canadian girl named Hannah Warren, who had spent her entire life in a Seoul hospital. …

Macchiarini had come to Vieira’s [Meredith Vieira, American journalist] attention in September 2012, when she read a front-page New York Times story about the doctor. She turned to [Benita] Alexander, one of her most seasoned and levelheaded producers, to look into a regenerative-medicine story for television.

When Alexander and Macchiarini found themselves together in Illinois for a period of weeks in the spring of 2013—brought there by the NBC special—they met frequently for quiet dinners. The trachea transplant on Hannah Warren, the Korean-Canadian girl, was being performed at Children’s Hospital of Illinois, in Peoria, and the procedure was fraught with risks, not least because Macchiarini’s technique was still a work in progress even for adults. (Christopher Lyles, an American who became the second person to receive an artificial trachea, died less than four months after his surgery at Karolinska.) “He’s a brilliant scientist and a great technical surgeon,” said Dr. Richard Pearl, who operated alongside Macchiarini in Illinois. Like others, Pearl described his Italian colleague as a Renaissance man, fluent in half a dozen languages. Another person, who would get to know him through Alexander, compared Macchiarini to “the Most Interesting Man in the World,” the character made famous in Dos Equis beer commercials.

In Peoria, Macchiarini’s medical magic appeared to have its limitations. Hannah Warren died from post-surgical complications less than three months after the transplant. Her anatomy “was much more challenging than we realized,” Pearl recounted. “Scientifically, the operation itself worked. It was just a shame what happened. When you’re doing something for the first time, you don’t have a textbook. It was the hardest operation I’ve ever scrubbed on.”

Then, there was the romance (from the Ciralsky article),

The personal relationship between Alexander and Macchiarini continued to blossom. In June 2013, they flew to Venice for what Alexander called “an incredibly romantic weekend.” Macchiarini bought her red roses and Venetian-glass earrings and took her on a gondola ride under the Bridge of Sighs. Like a pair of teenagers, they attached love locks to the Ponte dell’Accademia bridge, one of them bearing the inscription “B—P 23/6/13, 4 Ever.” Alexander told me that, “when he took me to Venice, we were still shooting the story … He always paid for everything … gifts, expensive dinners, flowers—the works. When it came to money, he was incredibly generous.”

It is a bedrock principle at NBC and every other news organization that journalists must avoid conflicts of interest, real or apparent. Alexander was not oblivious to this. “I knew that I was crossing the line in the sense that it’s a basic and well-understood rule of journalism that you don’t become involved with one of the subjects of your story, because your objectivity could clearly become compromised,” she told me. “I never once thought about him paying for the trip as him ‘buying’ me in some fashion, or potentially using money to influence me, because, from my perspective anyway … that just wasn’t the case. We were just crazy about each other, and I was falling in love.”

Alexander made her way to Stockholm at a later date (from the Ciralsky article),

Macchiarini was in Stockholm to attend to Yesim Cetir, a 25-year-old Turkish woman whose artificial trachea had failed. As Swedish television later reported, “It has taken nearly 100 surgeries to support the cell tissue around the airpipes. Her breathing is bad, and to avoid suffocation, her respiratory tract must be cleansed from mucus every fourth hour. She has now been lying in the hospital for nearly 1,000 days.” NBC’s special would come to include skeptical commentary from Dr. Joseph Vacanti, who questioned the sufficiency of Macchiarini’s research, but Cetir’s post-operative complications were not mentioned.

Prior to the NBC documentary’s (A Leap of Faith) airing, the romance became an engagement (from the Ciralsky article),

Macchiarini proposed to Benita Alexander on Christmas Day 2013, Alexander said. In the months leading up to the airing of A Leap of Faith, in June 2014, Macchiarini and Alexander went on trips to the Bahamas, Turkey, Mexico, Greece, and Italy. They went on shopping sprees and ate their way through Michelin-starred restaurants. Macchiarini even took Alexander and her daughter to meet his mother at her home, in Lucca. “She cooked homemade gnocchi,” Alexander recalled. Macchiarini’s mother shared pictures from the family photo album while her son translated. Emanuela Pecchia, the woman whom Macchiarini had married years earlier, lived only a short distance away. When Macchiarini informed Alexander, during a dinner cruise later that summer, that his divorce had finally come through, she recounted, he gave her an engagement ring.

In the months that followed, the doctor and his fiancée began planning their wedding in earnest. They set a date for July 11, 2015, in Rome. But their desire to marry in the Catholic Church was complicated by the fact that she is Episcopalian and divorced. Divorce would have been an issue for Macchiarini as well. However, Alexander said, Macchiarini insisted that he would fix things by visiting his friend and patient in the Vatican.

In October 2014, Alexander recalled, Macchiarini told her that he had met with Pope Francis for four hours and that the Pontiff consented to the couple’s marriage and, in yet another sign of his progressive tenure, vowed to officiate. Alexander said Macchiarini referred to himself as Pope Francis’s “personal doctor” and maintained that in subsequent meetings his patient offered to host the wedding at his summer residence, the Apostolic Palace of Castel Gandolfo.

Shortly after quitting her job in anticipation of her July 2015 wedding to Macchiarini, Alexander learned that Pope Francis who was supposed to officiate was in fact scheduled to be in South America during that time.  From the Ciralsky article,

As Alexander would discover with the help of a private investigator named Frank Murphy, virtually every detail Macchiarini provided about the wedding was false. A review of public records in Italy would also seem to indicate that Macchiarini remains married to Emanuela Pecchia, his wife of nearly 30 years. Murphy, who spent 15 years as a Pennsylvania State Police detective, told me, “I’ve never in my experience witnessed a fraud like this, with this level of international flair…. The fact that he could keep all the details straight and compartmentalize these different lives and lies is really amazing.

Ciralsky broaches the question of why someone with Macchiarini’s accomplishments would jeopardize his position in such a way,

To understand why someone of considerable stature could construct such elaborate tales and how he could seemingly make others believe them, I turned to Dr. Ronald Schouten, a Harvard professor who directs the Law and Psychiatry Service at Massachusetts General Hospital. “We’re taught from an early age that when something is too good to be true, it’s not true,” he said. “And yet we ignore the signals. People’s critical judgment gets suspended. In this case, that happened at both the personal and institutional level.” Though he will not diagnose from a distance, Schouten, who is one of the nation’s foremost authorities on psychopathy, observed, “Macchiarini is the extreme form of a con man. He’s clearly bright and has accomplishments, but he can’t contain himself. There’s a void in his personality that he seems to want to fill by conning more and more people.” When I asked how Macchiarini stacks up to, say, Bernie Madoff, he laughed and said, “Madoff was an ordinary con man with a Ponzi scheme. He never claimed to be the chairman of the Federal Reserve. He didn’t suggest he was part of a secret international society of bankers. This guy is really good.”

In addition to the romance, Ciralsky and Vanity Fair checked out Macchiarini’s résumé,

Vanity Fair contacted many of the schools at which Macchiarini claimed to have either earned a degree or held an academic post. While the University of Pisa confirmed that he indeed received an M.D. and had specialized in surgery, the University of Alabama at Birmingham denied that Macchiarini earned a master’s in biostatistics or that he participated in a two-year fellowship in thoracic surgery. In fact, according to U.A.B. spokesman Bob Shepard, the only record the school has for Macchiarini indicates that he did a six-month non-surgical fellowship in hematology/oncology—which according to the current Accreditation Council for Graduate Medical Education guidelines is 30 months shy of what is required for a clinical fellowship in that field. The University of Paris—Sud never responded to repeated requests for comment, but Hannover Medical School wrote to say that Macchiarini had been neither a full nor an associate professor there, merely an adjunct.


As I noted in part 1, there are medical science and ethical issues to be considered. As well, Macchiarini’s romantic behaviour certainly seems fraudulent as do parts of his curriculum vitae (CV) and there’s more about Macchiarini’s professional accomplishments (read Ciralsky’s entire January 5, 2016 Vanity Fair article for details).

The romantic and CV chicanery may or may not suggest serious problems with Macchiarini’s revolutionary procedure and ethics. History is littered with stories of people who achieved extraordinary advances and were not the most exemplary human beings. Paracelsus, founder of the field of toxicology and an important contributor in the fields of medicine and science, was reputedly a sketchy character. Caravaggio now remembered for his art, killed someone (accidentally or not) and was known for his violent behaviour even in a time when there was higher tolerance for it.

What I’m saying is that Macchiarini may be pioneering something important regardless of how you view his romantic chicanery and falsified CV. Medical research can be high risk and there is no way to avoid that sad fact. However, criticisms of the work from Macchiarini’s colleagues need to be addressed and the charge that a Russian patient who was not in imminent danger and not properly advised of the extremely high risk must also be addressed.

It should also be remembered that Macchiarini did not pull this off by himself. Institutions such as the Karolinska Institute failed to respond appropriately in the initial stages. As well, the venerable medical journal, The Lancet seems reluctant to address the situation even now.

Before dissecting the Alexander situation, it should be said that she showed courage in admitting her professional transgression and discussing a painful and humiliating romantic failure. All of us are capable of misjudgments and wishful thinking, unfortunately for her, this became an international affair.

More critically, Alexander, a journalist, set aside her ethics for a romance and what seems to be surprisingly poor research by Alexander’s team.  (Even I had a little something about this in 2013.) How did a crack NBC research team miss the problems? (For the curious, this Bryan Burrough April 30, 2015 article for Vanity Fair highlighting scandals plaguing NBC News may help to answer the question about NBC research.)

Finally, there’s an enormous amount of pressure on stem cell scientists due to the amounts of money and the degree of prestige involved. Ciralsky’s story notes the pressure when he describes how Macchiarini got one of this positions at an Italian facility in Florence through political machinations. (The situation is a little more complicated than I’ve described here but an accommodation in Macchiarini’s favour was made.) Laura Margottini’s Oct. 7, 2014 article for Science magazine provides a synopsis of another stem cell controversy in Italy.

Stem cell controversies have not been confined to Italy or Europe for that matter. There was the South Korean scandal in 2006 (see a Sept. 19, 2011 BBC [British Broadcasting Corporation] news online post for an update and synopsis) when a respected scientist was found to have falsified research results. Up to that  point, South Korea was considered the world leader in the field.

Finally,  if there are two survivors, is there a possibility that this procedure could be made successful for more patients or that some patients are better candidates than others?

Additional notes

Macchiarini is mounting a defence for himself according to a March 30, 2016 news item on phys.org and a Swedish survey indicates that the average Swede’s trust in researchers still remains high despite the Macchiarini imbroglio according to an April 15, 2016 news item on phys.org.

For anyone interested in the timeline and updates for this scandal, Retraction Watch offers this: http://retractionwatch.com/2016/02/12/reading-about-embattled-trachea-surgeon-paolo-macchiarini-heres-what-you-need-to-know/

Macchiarini controversy and synthetic trachea transplants (part 1 of 2)

Having featured Paolo Macchiarini and his work on transplanting synthetic tracheas into humans when it was lauded (in an Aug. 2, 2011 post titled: Body parts nanostyle), it seems obligatory to provide an update now that he and his work are under a very large cloud. Some of this is not new, there were indications as early as this Dec. 27, 2013 post titled: Trachea transplants: an update which featured an article by Gretchen Vogel in Science magazine hinting at problems.

Now, a Feb. 4, 2016 article by Gretchen Vogel for Science magazine provides a more current update and opens with this (Note: Links have been removed),

The Karolinska Institute (KI) in Stockholm “has lost its confidence” in surgeon Paolo Macchiarini, a senior researcher at the institute, and will end its ties with him. In a statement issued today, KI said that it won’t renew Macchiarini’s contract after it expires on 30 November 2016.

The move comes in the wake of a chilling three-part TV documentary about Macchiarini, a former media darling who was cleared of scientific misconduct charges by KI vice-chancellor Anders Hamsten last summer. Among other things, The Experiments, broadcast in January by Swedish public television channel SVT, suggests that Macchiarini didn’t fully inform his patients about the risks of his pioneering trachea implants. Most of the patients died, including at least one—a woman treated in Krasnodar, Russia—who was not seriously ill before the surgery.

For a profession that has “do no harm” as one of its universal tenets, the hint that a patient not in dire need agreed to a very risky procedure without being properly apprised of the risks is chilling.

Macchiarini’s behavriour is not the only concern, the Karolinska Institute is also being held to account (from the Vogel article),

The film has also raised questions about the way Hamsten and other administrators at KI, Sweden’s most prestigious university and home of the selection committee for the Nobel Prize in Physiology or Medicine, have handled the scandal. Today [Feb. 4, 2016], the Institute’s Board decided to launch an independent review, to be led by an experienced lawyer, into KI’s 5-year relationship with Macchiarini. Among the things the inquiry should address is whether any errors were made or laws were broken when Macchiarini was hired; whether misconduct charges against him were handled properly; and why, given the controversy, he was given a new 1-year contract  as a senior researcher after his appointment as a visiting professor at KI ended in October 2015.

Getting back to Macchiarini (from the Vogel article),

In 2014, colleagues at KI alleged that Macchiarini’s papers made his transplants seem more successful than they were, omitting serious complications. Two patients treated at Karolinska died, and a third has been in intensive care since receiving a trachea in 2012. The Illinois patient also died, as did three patients in Russia. Bengt Gerdin, a professor emeritus of surgery at Uppsala University in Sweden who investigated the charges at KI’s request, concluded in May 2015 that differences between published papers and lab records constituted scientific misconduct. But Hamsten rejected that conclusion in August, based on additional material Macchiarini submitted later.

The documentary shows footage of a patient who says Macchiarini reassured him before the surgery that experiments had been done on pigs, when in fact none had taken place. It also follows the wrenching story of the first patient in Krasnodar. A 33-year-old woman, she was living with a tracheostomy that she said caused her pain, but her condition was not life-threatening. The film suggests that she wasn’t fully aware of the risks of the operation, and that Macchiarini and his colleagues knew about problems with the implant before the surgery. The patient’s first implant failed, and she received a second one in 2013. She died in 2014.

So in May 2015, an investigator concluded there had been scientific misconduct and, yet, Macchiarini’s contract is renewed in the fall of 2015.

Kerry Grens in a March 7, 2016 article for The Scientist provides information about the consequences of the latest investigation into Macchiarini’s work (Note: Links have been removed),

Karl-Henrik Grinnemo, a surgeon at the Karolinska Institute and one of a number of colleagues who voiced concerns about the conduct of fellow surgeon Paolo Macchiarini, is no longer a coauthor on a 2011 The Lancet study led by Macchiarini that described an artificial windpipe. Grinnemo asked to be removed from the paper, and the journal complied last week (March 3).

Grinnemo’s removal from the study is the latest in a string of repercussions related to an investigation of Macchiarini’s work. Last month, the head of the Karolinska Institute, Anders Hamsten, resigned because the institution’s initial investigation concluded no wrongdoing. Hamsten said he and his colleagues were probably wrong about Macchiarini; the institute has launched another investigation into the surgeon’s work.

A March 23, 2016 news item on phys.org announces Macchiarini’s firing from the Karolinska Institute and provides a brief description of his work with synthetic tracheas (Note: A link has been removed),

Sweden’s Karolinska Institute (KI), which awards the Nobel Prize for Medicine, on Wednesday [March 23, 2016] dismissed a Italian transplant surgeon suspected of research fraud and ethical breaches, in an affair that has plunged the renowned institution into crisis.

“It is impossible for KI to continue to have any cooperation with Paolo Macchiarini. He has acted in a way that has had very tragic consequences for the people affected and their families. His conduct has seriously damaged confidence in KI,” human resource director Mats Engelbrektson said in a statement.

Macchiarini, a 57-year-old visiting professor at Karolinska since 2010, rose to fame for carrying out the first synthetic trachea, or windpipe, transplant in 2011.

It was a plastic structure seeded with the patient’s own stem cells—immature cells that grow into specialised cells of the body’s organs.

The surgeon performed three such operations in Stockholm and five others around the world, and the exploit was initially hailed as a game-changer for transplant medicine.

But six of the eight patients reportedly died, and allegations ensued that the risky procedure had been carried out on at least one individual who had not been life-threateningly ill.

Macchiarini is also suspected of lying about his scientific research and his past experience with prestigious medical research centres.

“Paolo Macchiarini supplied false or misleading information in the CV he submitted to KI” and “demonstrated scientific negligence” in his research, said the institute.

H/t to Don Bright, a reader who informed me about this April 2, 2016 posting by Pierre Delaere (a long time Macchiarini critic), published in Leonid Schneider’s blog, For Better Science,

I have written this overview as a trachea surgeon working at KU Leuven and privileged witness of the “Tracheal regeneration scandal” from the very start.

Because of its immense scale, the scandal is difficult to grasp and explain. Fortunately, we have recently been provided with an excellent overview in the 3 x 1-hour documentary by Bosse Lindquist on Swedish national TV. Due to Paolo Macchiarini’s appetite for the spotlights and thanks to the professional standards of the Swedish top producer this is probably the very first case of a medical crime played out in the media. Anyone who has seen this brilliant investigative documentary cannot help but wonder why there are still people who doubt that this is a case of gross medical misconduct.

The story began in Barcelona in 2008 with the publication in The Lancet of a report on a regenerated windpipe, featuring Paolo Macchiarini (PM) as its first author (Macchiarini et al. Lancet 2008). This ground-breaking achievement consisted of bringing to life a dead windpipe from a donor, by putting it in a plastic box, a so-called ‘bioreactor’ together with bone marrow fluid (stem cells). A few weeks later, I wrote a letter to The Lancet, pointing out:

    “The main drawback of the proposed reconstruction is the lack of an intrinsic blood supply to the trachea. We know that a good blood supply is the first requirement in all other tissue and organ transplantations. Therefore, the reported success of this technique is questionable” (correspondence by Delaere and Hermans, Lancet 2009).

Delaere goes on to recount and critique the story of the first synthetic trachea,

…  PM had mounted bone marrow extract (‘stem cells’) on a plastic tube (‘bioartificial trachea’) in a plastic box (‘bioreactor’). After a day or two this creation was ‘successfully’ transplanted in a patient with a trachea defect. This occurred in the Karolinska hospital in July 2011 and was reported on in The Lancet shortly afterwards . Biologically speaking, the procedure is absolutely implausible.

In reality an important part of the windpipe had been replaced by a synthetic tube, and the presence of stem cells made no difference to this whatsoever.

For those not in the field, this procedure may still seem acceptable. A blood vessel can also be replaced by synthetic material because the material can grow into the sterile environment of the blood stream. However, this is completely impossible if the synthetic material is exposed to an environment of inhaled air full of bacteria. The laws of biology allow us to predict accurately what will happen after part of the windpipe has been replaced by a synthetic tube. After some time, the suturing between the synthetic tube and the surrounding tissue will come loose, leading to a number of serious complications. These complications inevitably lead to death in the short (months) or in the mid-long term (a few years). How long the patient will survive also depends on the options still left to treat complications. In most cases so far, a metal stent had to be implanted to keep the airway open in the sutured area.It is entirely predictable that additional complications after placement of the metal stent will ultimately lead to the patient’s death, usually by asphyxiation or by bleeding out after complete rupture of the sutures. This gruesome fate awaiting patients was clearly shown in the documentary. Replacing a part of the trachea by a synthetic tube can therefore be compared to death by medical torture. The amount of suffering it induces is directly proportional to the duration between implantation and the patient’s death.

Delaere describes his own and others’ efforts to bring these issues to light,

Since 2011, I have contacted both the President of KI and the Editors of The Lancet with well-documented information to clarify that what had happened was completely unacceptable. These alerts were repeated in 2013 and 2014. Since 2014, four doctors from KI, who had seen it all happen, have been collecting evidence to show the extent of misconduct [Matthias Corbascio, Thomas Fux, Karl-Henrik Grinnemo and Oscar Simonsson, their letter to Vice-Chancellor Hamsten from June 22, 2015, and its attachments available here; -LS]. Not only did KI not react to the doctors’ complaint, these doctors were in fact intimidated and threatened with dismissal. KI’s Ethical Commission came to a verdict of ‘no misconduct’ in April 2015 following an inquiry based on a series of complaints filed by myself [verdict available from SVT here, -LS]. The Lancet Editor did not even bother to reply to my complaints.

In the reports, eight patients were given synthetic tracheas with six now dead and, allegedly, two still living. Delaere comments,

… To prove that this transplantation technique is effective, reports about the long-term success of this technique in the first 2 patients in Barcelona and London is still being spread. What the real situation of the two patients is at the moment is very difficult to establish. For some time now, reports about these two cases seem to have disappeared from the face of the earth. After the air has been cleared in Sweden, the same will probably happen in London and Barcelona.


Sometimes medical research can be very dangerous. While, a 25% chance of success (two of Macchiarini’s eight patients undergoing the synthetic trachea transplant have allegedly survived) is not encouraging, it’s understandable that people in dire circumstances and with no other options might want to take a chance.

It’s troubling that the woman in Russia was not in dire straights and that she may not have known how dangerous the procedure is. It would have been unethical of Macchiarini to knowingly perform the procedure under those circumstances.

I am wrestling with some questions about the composite used to create the synthetic trachea and the surviving patients. My understanding is that the composite was designed for eventual deterioration as the patient’s own harvested stem cells fully formed the trachea. Whether the trachea is the one I imagined or he plastic one described by Delaere, how did two patients survive and what is their condition now? The first patient Andemariam Teklesenbet Beyene in 2011 had apparently completed his PhD studies by 2013 (my Dec. 27, 2013 posting). Assuming Beyene is one of the two survivors, what has happened to him and the other one?

As for Delaere’s comments, he certainly raises some red flags not only regarding the procedure but the behaviour of the Lancet editorial team and the Karolinska Institute (they seem to be addressing the issues by firing Macchiarini and with the  resignations of the staff and board).

There are two more twists to this story, which carries on in part 2.

Natural nanoparticles and perfluorinated compounds in soil

The claim in a Sept. 9, 2015 news item on Nanowerk is that ‘natural’ nanoparticles are being used to remove perfluorinated compounds (PFC) from soil,

Perfluorinated compounds (PFC) are a new type of pollutants found in contaminated soils from industrial sites, airports and other sites worldwide.

In Norway, The Environment Agency has published a plan to eliminate PFOS [perfluorooctanesulfonic acid or perfluorooctane sulfonate] from the environment by 2020. In other countries such as China and the United States, the levels are far higher, and several studies show accumulation of PFOS in fish and animals, however no concrete measures have been taken.

The Norwegian company, Fjordforsk AS, which specializes in nanosciences and environmental methods, has developed a method to remove PFOS from soil by binding them to natural minerals. This method can be used to extract PFOS from contaminated soil and prevent leakage of PFOS to the groundwater.

Electron microscopy images show that the minerals have the ability to bind PFOS on the surface of the natural nanoparticles. [emphasis mine] The proprietary method does not contaminate the treated grounds with chemicals or other parts from remediation process and uses only natural components.

Electron microscopy images and more detail can be found in the Nanowerk news item.

I can’t find the press release, which originated the news item but there is a little additional information about Fjoorkforsk’s remediation efforts on the company’s “Purification of perfluorinated compounds from soil samples” project page,

Project duration: 2014 –

Project leader: Manzetti S.

Collaborators: Prof Lutz Ahrens. Swedish Agricultural University. Prof David van der Spoel, Uppsala University.

Project description:

Perfluorinated compounds (PFCs) are emerging pollutants used in flame retardants on a large scale on airports and other sites of heavy industrial activity. Perfluroinated compounds are toxic and represent an ultra-persistent class of chemicals which can accumulate in animals and humans and have been found to remain in the body for over 5 years after uptake. Perfluorinated compounds can also affect the nerve-system and have recently been associated with high- priority pollutants to be discontinued and to be removed from the environment. Using non-toxic methods, this project develops an approach to sediment perfluorinated compounds from contaminated soil samples using nanoparticles, in order to remove the ecotoxic and ground-water contaminating potential of PFCs from afflicted sites and environments.

The only mineral that I know is used for soil remediation is nano zero-valent iron (nZVI). A very fast search for more information yielded a 2010 EMPA [Swiss Federal Laboratories for Materials Science and Technology] report titled “Nano zero valent iron – THE solution for water and soil remediation? ” (32 pp. pdf) published by ObservatoryNANO.

As for the claim that the company is using ‘natural’ nanoparticles for their remediation efforts, it’s not clear what they mean by that. I suspect they’re using the term ‘natural’ to mean that engineered nanoparticles are being derived from a naturally occurring material, e.g. iron.

Archimedes as in nano-archimedes and graphene nanoscrolls

Over the last 10 days or so, I’ve stumbled across two references to Archimedes in my constant search for information on nanotechnology. Not remembering my ancient Greeks very well, I found this about him on Wikipedia (Note: Links and footnotes have been removed),

Archimedes of Syracuse (Greek: Ἀρχιμήδης; c. 287 BC – c. 212 BC) was a Greek mathematician, physicist, engineer, inventor, and astronomer. Although few details of his life are known, he is regarded as one of the leading scientists in classical antiquity. Among his advances in physics are the foundations of hydrostatics, statics and an explanation of the principle of the lever. He is credited with designing innovative machines, including siege engines and the screw pump that bears his name. Modern experiments have tested claims that Archimedes designed machines capable of lifting attacking ships out of the water and setting ships on fire using an array of mirrors.

Archimedes is generally considered to be the greatest mathematician of antiquity and one of the greatest of all time.

His influence lives on as he’s referenced in an Aug. 15, 2013 news item on Nanowerk concerning graphene nanoscrolls,

Researchers at Umeå University, together with researchers at Uppsala University and Stockholm University, show in a new study how nitrogen doped graphene can be rolled into perfect Archimedean nano scrolls by adhering magnetic iron oxide nanoparticles on the surface of the graphene sheets. The new material may have very good properties for application as electrodes in for example Li-ion batteries.

The Aug. 15, 2013 Umeå University press release,which originated the news item, provides technical details,

In the study the researchers have modified the graphene by replacing some of the carbon atoms by nitrogen atoms. By this method they obtain anchoring sites for the iron oxide nanoparticles that are decorated onto the graphene sheets in a solution process. In the decoration process one can control the type of iron oxide nanoparticles that are formed on the graphene surface, so that they either form so called hematite (the reddish form of iron oxide that often is found in nature) or maghemite, a less stable and more magnetic form of iron oxide.

“Interestingly we observed that when the graphene is decorated by maghemite, the graphene sheets spontaneously start to roll into perfect Archimedean nano scrolls, while when decorated by the less magnetic hematite nanoparticles the graphene remain as open sheets, says Thomas Wågberg, Senior lecturer at the Department of Physics at Umeå University.

The nanoscrolls can be visualized as traditional “Swiss rolls” where the sponge-cake represents the graphene, and the creamy filling is the iron oxide nanoparticles. The graphene nanoscrolls are however around one million times thinner.

The results that now have been published in Nature Communications are conceptually interesting for several reasons. It shows that the magnetic interaction between the iron oxide nanoparticles is one of the main effects behind the scroll formation. It also shows that the nitrogen defects in the graphene lattice are necessary for both stabilizing a sufficiently high number of maghemite nanoparticles, and also responsible for “buckling” the graphene sheets and thereby lowering the formation energy of the nanoscrolls.

The process is extraordinary efficient. Almost 100 percent of the graphene sheets are scrolled. After the decoration with maghemite particles the research team could not find any open graphene sheets.

Moreover, they showed that by removing the iron oxide nanoparticles by acid treatment the nanoscrolls again open up and go back to single graphene sheets

The researchers have an image showing a partially reopened scroll (despite references to Archimedes and swiss rolls, I see a plant leaf or flower unfurling),

Caption: Snapshot of a partially re-opened nanoscroll. The atomic layer thick graphene resembles a thin foil with some few wrinkles. [Courtesy of  Umeå University]

Caption: Snapshot of a partially re-opened nanoscroll. The atomic layer thick graphene resembles a thin foil with some few wrinkles. [Courtesy of Umeå University]

Here’s a link to and a citation for the published paper,

Tiva Sharifi, Eduardo Gracia-Espino, Hamid Reza Barzegar, Xueen Jia, Florian Nitze, Guangzhi Hu, Per Nordblad, Cheuk-Wai Tai, and Thomas Wågberg: Formation of nitrogen-doped graphene nanoscrolls by adsorption of magnetic γ-Fe2O3 nanoparticles, Nature Communications (2013), DOI:10.1038/ncomms3319.

The article is behind a paywall.

The other Archimedes reference is regarding a new website, nano-archimedes, mentioned in an Aug. 10, 2013 news item on Nanowerk,

Nano-archimedes is a Technology Computer Aided Design tool (TCAD) for the simulation of electron transport in nanometer scale semiconductor devices (nanodevices). It is based on the Wigner equation, a convenient reformulation of the Schrödinger equation in terms of a phase-space, which allows the application of stochastic particles methods and the extension towards mixed state kinetic descriptions such as the Wigner-Boltzmann equation.

There’s more on the nano-archimedes homepage,

It is an experimental code for validation and analysis of the compatibility of existing quantum particle concepts in algorithmic schemes. Our preliminary results have clearly shown that time-dependent, full quantum and multi-dimensional simulations of electron transport can be achieved with no special computational requirements. The code is already able to simulate time dependent phenomena such as two-dimensional wave phase breaking and single electron ballistic transport with open boundary conditions aiming to have, very soon, full quantum self-consistent calculations for nanodevices.

nano-archimedes runs both on serial and parallel machines and the parallelization scheme is based on OpenMP – a standard library for parallel calculations. The code is entirely written in C and can compile on a huge variety of machines without any particular effort. The only external dependence is OpenMP, everything else is embedded in the code to make it truly cross-platform.

I found the background of the team members behind this effort rather interesting, from the Team page,

Main developer and principal maintainer of the code:
Jean Michel Sellier, IICT, Bulgarian Academy of Sciences, Bulgaria, supported by the AComIn project.

Main developer, theory and physical analysis:
Mihail Nedjalkov, Institute for Microelectronics, TU Wien, Austria.

Advisory board:
Ivan Dimov, Bulgarian Academy of Sciences, Bulgaria.
Siegfried Selberherr, Institute for Microelectronics, TU Wien, Austria.

Website Master:
Marc Sellier, working at Selliweb, Italy.

I don’t often have a chance to mention Bulgaria and I expect that’s due to the fact that my linguistic skills are largely English with a little French flavour thrown into the mix. The consequence is that I’m confined and while  I realize English is the dominant language in science there’s still a lot of scientific materials that never finds its way into English and I don’t trust machine translations.

Upsalite, an impossible material from Uppsala University (Sweden) and Disruptive Materials

You can feel the researchers’ excitement crackling from the July 18, 2013 news release (English language version available at Uppsala University [Sweden]) about a new material that shares properties with zeolite, mesoporous silica, and carbon nanotubes and has some special properties all its own,

A novel material with world record breaking surface area and water adsorption abilities has been synthesized by researchers from Uppsala University, Sweden. The results are published today in PLOS ONE.

The magnesium carbonate material that has been given the name Upsalite is foreseen to reduce the amount of energy needed to control environmental moisture in the electronics and drug formulation industry as well as in hockey rinks and warehouses. It can also be used for collection of toxic waste, chemicals or oil spill and in drug delivery systems, for odor control and sanitation after fire.

Apparently this work represents a break with orthodoxy, from the news release,

-In contrast to what has been claimed for more than 100 years in the scientific literature, we have found that amorphous magnesium carbonate can be made in a very simple, low-temperature process, says Johan Forsgren, researcher at the Nanotechnology and Functional Materials Division

While ordered forms of magnesium carbonate, both with and without water in the structure, are abundant in nature, water-free disordered forms have been proven extremely difficult to make. In 1908, German researchers claimed that the material could indeed not be made in the same way as other disordered carbonates, by bubbling CO2 through an alcoholic suspension. Subsequent studies in 1926 and 1961 came to the same conclusion.

-A Thursday afternoon in 2011, we slightly changed the synthesis parameters of the earlier employed unsuccessful attempts, and by mistake left the material in the reaction chamber over the weekend. Back at work on Monday morning we discovered that a rigid gel had formed and after drying this gel we started to get excited, says Johan Forsgren.

A year of detailed materials analysis and fine tuning of the experiment followed.

-One of the researchers got to take advantage of his Russian skill since some of the chemistry details necessary for understanding the reaction mechanism was only available in an old Russian PhD thesis.

-After having gone through a number of state of the art materials characterization techniques it became clear that we had indeed synthesized the material that previously had been claimed impossible to make, says Maria Strømme, professor of nanotechnology and head of the nanotechnology and functional materials division. The most striking discovery was, however, not that we had produced a new material but it was instead the striking properties we found that this novel material possessed. It turned out that Upsalite had the highest surface area measured for an alkali earth metal carbonate; 800 square meters per gram. This places the new material in the exclusive class of porous, high surface area materials including mesoporous silica, zeolites, metal organic frameworks, and carbon nanotubes, says Strømme.

In addition we found that the material was filled with empty pores all having a diameter smaller than 10 nano meters. This pore structure gives the material a totally unique way of interacting with the environment leading to a number of properties important for application of the material. Upsalite is for example found to absorb more water at low relative humidities than the best materials presently available; the hydroscopic zeolites, a property that can be regenerated with less energy consumption than is used in similar processes today.

This, together with other unique properties of the discovered impossible material is expected to pave the way for new sustainable products in a number of industrial applications, says Maria Strømme.

The discovery will be commercialized though the University spin-out company Disruptive Materials (www.disruptivematerials.com) that has been formed by the researchers together with the holding company of Uppsala University

Here’s a link to and a citation for the researchers’ published paper,

A Template-Free, Ultra-Adsorbing, High Surface Area Carbonate Nanostructure by Johan Forsgren, Sara Frykstrand, Kathryn Grandfield, Albert Mihranyan, and Maria Strømme. PLoS ONE, 2013; 8 (7): e68486 DOI: 10.1371/journal.pone.0068486

Here’s a little more abut Upsalite from the university’s spin-off company, Disruptive Materials homepage,

A new material with world record breaking surface area and water adsorption abilities

It was supposed to be impossible, but… We did it! Disruptive Materials has succeeded to manufacture micro-porous magnesium carbonate and the properties are mind blowing. Over 800 m2/g in surface area, better water adsorbtion ability than the former champion Zeolite Y and a very low manufacturing cost. We have been testing the material for a long time, and we see new applications every week for this new and true super-material.

Finally for those with Swedish language skills, here’s the July 18, 2013 news release from Disruptive Materials.