RealClearScience Journal Club

Science Figures Interpreted and Analyzed by RealClearScience

Shroud of Turin DNA Comes from All over World

Alex B. Berezow - October 12, 2015

The Shroud of Turin, the supposed burial cloth of Jesus of Nazareth, has remained an object of fascination for the Christian faithful and scientists alike. Those who would suggest a supernatural origin nearly 2,000 years ago must contend with radiocarbon evidence, which dates the shroud to approximately the 13th or 14th Centuries. Those who would suggest a medieval European origin must contend with a rather large controversy over the accuracy of the sample used for dating, as well as historical evidence to the contrary. Additionally, despite extensive analysis, nobody knows how the image of a buried man was created on the shroud. In Facebook terms, the shroud's status remains "complicated."

Now, Italian researchers have added to the mystery. By sequencing the DNA of pollen and other dust particles taken from the shroud, the authors have been able to determine the types of plants and the biogeographic origin of people who have come into contact with it. Their results are depicted below:

As shown, the shroud has been contaminated with DNA from plants that can be found all over the world. Similarly, their analysis of human DNA showed haplogroups from people originating in Europe, south Asia, eastern Africa, and the Middle East. So, what does this mean?

It's hard to say. According to legend, the shroud moved around quite a bit, from Jerusalem to Turkey to France and to its final resting place in Turin, Italy. The DNA evidence confirms that many different people, from many different places, got their hands on or near the shroud.

What still remains unclear is the shroud's origin. The DNA evidence is consistent with more than one explanation: (1) The shroud really did originate in Israel and traveled extensively before making its way to Italy, or (2) The shroud was created in medieval Europe, but worshipers (and plants) from all over the world that made their way to Europe contaminated it. The authors cannot rule out either explanation. (Intriguingly, the authors suggested that the DNA evidence linked to people from India hints that the shroud may have been weaved there.)

For now, despite this rich new body of evidence, it seems the Shroud of Turin will remain shrouded in mystery.

Source: Gianni Barcaccia, Giulio Galla, Alessandro Achilli, Anna Olivieri & Antonio Torroni. "Uncovering the sources of DNA found on the Turin Shroud." Scientific Reports 5, Article number: 14484. Published online: 5-Oct-2015. doi:10.1038/srep14484

(AP photo)

The Primordial Soup Was Edible

Alex B. Berezow - October 5, 2015

Back in 2005, when I was a first-year microbiology graduate student, I enrolled in a course on bacterial physiology. One of our guest lecturers, Dr. Franklin Harold, was an esteemed researcher in bioenergetics, a field that examines how cells derive and utilize energy. One evening, outside of class, I happened upon Dr. Harold at a seminar, and I asked him a question: "What is your opinion on origin of life research?"

He responded, "It has been an abject failure."

Ten years later, it is still difficult to argue with him. A brief survey of the Wikipedia entry on abiogenesis reveals about 20 different theories and explanations for how non-living matter can evolve into metabolizing lifeforms, ranging from the plausible (RNA World) to the patently ridiculous (panspermia). Put simply, a field with so many different interpretations is wandering lost in the long grass. Any sort of hint at the truth, therefore, is a welcome discovery. Such a hint, albeit a small one, may have been uncovered by new research that has been published in Scientific Reports.

The famous Miller-Urey experiment, which showed that biological molecules can be produced by zapping water and a few gases with electricity, has been debated for some 60 years in regard to just how relevant it is to the origin of life. Yes, some biological molecules can be produced in conditions mimicking (what is thought to be) that of the early Earth, but toxic molecules, such as carbon monoxide and cyanide, are also synthesized. Additionally, it was not even known if the sludge produced by the experiment was capable of supporting life. So, a team of scientists led by Xueshu Xie and Roman Zubarev aimed to find out.

Their first results were not promising. The Miller-Urey goo blocked the growth of E. coli, a rather hardy bacterium. This was apparently due to a toxic cocktail of organic molecules present in the mixture.

So, the authors tried another approach. First, they dried the Miller-Urey gunk to eliminate the toxic, volatile compounds, and then reconstituted it in water. Second, they adapted their E. coli strain to live under harsher conditions. This can be done by growing them in media (liquid food) that the bacteria find unpleasant but tolerable. After three months, the battle-tested bacteria were once again grown in the presence of the poison-free Miller-Urey goo. This time, they did quite well. (See figure.)

Their finding definitely supports the notion that the Miller-Urey gunk can support life. But, there are three major caveats:

First, the researchers still had to add inorganic salts (containing ions such as potassium, magnesium, and calcium) in order for the bacteria to grow. Second, it is debatable whether removing toxic molecules, such as cyanide, is legitimate. Finally, their experiment does nothing to solve the biggest questions of all: How did complex molecules form (e.g., DNA), and how did life evolve?

The answers to those questions remain as murky as the Miller-Urey goo.

Source: Xueshu Xie, Daniel Backman, Albert T. Lebedev, Viatcheslav B. Artaev, Liying Jiang, Leopold L. Ilag & Roman A. Zubarev. "Primordial soup was edible: abiotically produced Miller-Urey mixture supports bacterial growth." Scientific Reports 5, Article number: 14338. Published: 28-Sept-2015. doi:10.1038/srep14338

(AP photo)

Macaque Experiment Shows Vaccine Schedule Not Linked to Autism

Alex B. Berezow - September 28, 2015

During the most recent Republican presidential debate, frontrunner Donald Trump once again dragged out the still widespread myth that vaccines cause autism. This dangerous fiction was debunked as early as 2002 by the New England Journal of Medicine and has been consistently contradicted by research ever since. As a result, anti-vaxxers changed strategy: Instead of blaming thimerosal for causing autism, they now focus on the vaccine schedule itself, essentially claiming that too many shots in too short of a timespan overwhelms a child's immune system.

That is nonsense. The number of antigens (i.e., molecules that trigger an antibody response) contained within vaccines has decreased dramatically over the past several decades. In the Genetic Expert News Service, Emory University infectious disease professor Dr. Walter Orenstein says that the total number of antigens in all vaccines combined is about 150, which is practically nothing compared to the roughly 2,000-6,000 antigens children face every single day. By crawling around on the floor and sticking their hands in their mouths, children are "vaccinating" themselves all day long.

Despite the lack of scientific logic to the anti-vaxxers' argument, a team of researchers decided to address the issue of vaccine schedules head-on. Their results are reported in the journal PNAS.

The team divided 79 rhesus macaque monkeys into six experimental groups, each containing 12-16 animals. They then administered various combinations of vaccines to the animals in those groups. [Note that some vaccines contain EtHg, a metabolic derivative of thimerosal, while others do not. Also note that the vaccines used are the same as or similar to those used to vaccinate children (PDF).] The list of vaccines is shown below:

The groups were divided as follows:

Control: Saline placebos only
1990s Pediatric: The 1990s vaccine regimen for children
1990s Primate: A four-fold acceleration of the 1990s regimen
TCVs: Only thimerosal-containing vaccines, but MMR replaced with saline placebo
MMR: MMR only and saline placebos for other vaccines
2008: The 2008 vaccine regimen for children (which is similar to that used today)

After all shots were administered, the macaques' behavior was assessed and their brains were examined for signs of autism. What did they find?

Nothing. Absolutely nothing. There were neither significant differences in brain structure nor significant differences in the negative behaviors associated with autism. In other words, all the monkeys developed normally.

Critics will argue that this experiment was performed in macaques, not humans, and is therefore unreliable. Of course, it is unethical to give children placebos in place of vaccines (not to mention cutting their brains open), so this experiment cannot be performed in humans.

Because the coffin of the vaccine-autism myth has already been nailed shut, this study really should represent the flowers placed on top of the grave. Sadly, it probably won't make a dime's bit of difference to the anti-vaxxers who continue to see a conspiracy behind every corner.

Source: Bharathi S. Gadad et al. "Administration of thimerosal-containing vaccines to infant rhesus macaques does not result in autism-like behavior or neuropathology." PNAS. Published online before print: 28-Sept-2015. doi: 10.1073/pnas.1500968112

(AP photo)

Frozen in Time: 365 Million-Year-Old Fossil Shows Trilobite in the Act of Molting

Ross Pomeroy - September 21, 2015

Fossilization preserves bones -- everybody knows that. But in rare cases, fossilization does something even cooler: it preserves moments. Recently, Błażej Błażejowski, based out of the Institute of Paleobiology at the Polish Academy of Sciences, was lucky enough to stumble upon a fossil containing a very special moment frozen in time. He shared his discovery last Friday in the journal Scientific Reports.

The piece of shale, excavated from the Kowala Quarry in Poland's Holy Cross Mountains, held what appeared to be a trilobite -- an ancient ocean-dwelling animal resembling a large armored bug -- in the act of shedding its exoskeleton. Subsequent X-ray modeling both confirmed the discovery and revealed the fossilized animal's identity. It was Trimerocephalus, an eyeless trilobite roughly 6.3 inches long and 3 inches wide.

In shedding it's armored exoskeleton, the fossilized creature was molting. Molting is without a doubt one of nature's most incredible acts. Every so often, certain creatures cast off parts of their bodies in a process of biological renewal. Cats and dogs do it with their fur (often shedding hair all over your sofa). Chickens do it with their feathers. Snakes do it with their skin. Most remarkably, many arthropods, including spiders, crabs, and insects, discard their entire exoskeleton! Ripping themselves out of their bodies in an unnerving and alien manner, they emerge revitalized and renewed, leaving behind a near-complete husk of their former selves.

But this particular ancient bug did not emerge renewed. Quite the opposite. It appears to have died in the process.

"The animal died within the sediment shortly after extricating itself from the old exoskeleton," Błażejowski and his co-authors write. "The cause of mortality is, of course, not known but might be due to stress of molting or possibly, given the context, death by hypoxia or hydrogen sulfide toxicity within the sediment."

Scientists always assumed that ancient arthropods like trilobites molted in similar manners to modern arthropods, but Błażejowski says that this discovery is the oldest to directly confirm that educated hunch.

Source: Błażejowski, B. et al. A moment from before 365 Ma frozen in time and space. Sci. Rep. 5, 14191; doi: 10.1038/srep14191 (2015).

Women See Job Advancement as Less Desirable

Alex B. Berezow - September 21, 2015

Quite rightly, our society identifies sources of disparity and works to eliminate them. One such disparity is the relative lack of women in top jobs, such as CEOs and professorships. There are multiple reasons for this, but the only politically correct one is discrimination. The data, however, often point to different conclusions. For instance, in April of this year, PNAS released a study that showed that women were preferred 2-to-1 in academic science jobs.

To be sure, discrimination plays some role. Tribalism -- which can manifest itself in our tendency to associate with or favor others based upon gender, race, ethnicity, religion, or a whole host of other traits -- appears to be an inherent part of the human condition. Additionally, women are often viewed as less competent than men. Fortunately, we have made great strides in overcoming such weaknesses, and a growing base of evidence suggests that factors other than discrimination may play a bigger role in women's professional outcomes.

More evidence in support of this viewpoint has just been published in PNAS. The researchers, all of whom were women from Harvard, conducted a series of studies whose aim was to determine how men and women viewed the desirability of professional advancement. They discovered that women found job promotions to be less desirable than men did. (See chart.)

Probing deeper, the researchers found that women had a greater expectation of negative consequences from a job promotion, such as more stress or conflict with other life goals. Furthermore, women craved power less than men did.

The authors admit that the cause of these gender differences remain complex and unknown. Biology, cultural norms, and discrimination all play a role in shaping the preferences of men and women. Yet, their research does seem to suggest that while job advancement opportunities are being made available to women, many choose not to pursue them. The authors conclude:

"[C]ompared to men, women have more life goals that make achieving high-power positions at work seem less desirable (but equally attainable). Therefore, women may not assume high-level positions in organizations — at least in part — because they desire other things as well."

While the researchers' findings are certainly interesting, there isn't much news here. Indeed, the team merely seems to have confirmed the mundane observations of everyday life. Yet, in our politically charged environment, stating the obvious can be a career-ending mistake. So, cheers to the authors for having the courage to publish it.

Source: Francesca Gino, Caroline Ashley Wilmuth, and Alison Wood Brooks. "Compared to men, women view professional advancement as equally attainable, but less desirable." PNAS. Published online before print: 21-Sept-2015. doi: 10.1073/pnas.1502567112

(AP photo)

What Penis Size Do Women Prefer?

Ross Pomeroy - September 8, 2015

Good news, normally-endowed men of the world! When it comes to penis size, bigger isn't always better! But it doesn't hurt to be slightly above average...

In what may be the most titillating use of 3D printing to date, researchers primarily based out of the University of California Los Angeles manufactured 33 phallic objects of various sizes (pictured above) and asked a diverse group of 75 women attracted to men (average age 25) to analyze the collection and select which would be their preferred penis size for sexual intercourse. The results were published last week to PLoS ONE.

According to the researchers:

"Women preferred a penis of slightly larger circumference and length for one-time (length = 6.4 inches/16.3 cm, circumference = 5.0 inches/12.7 cm) versus long-term (length = 6.3 inches/16.0 cm, circumference = 4.8 inches/12.2 cm) sexual partners."

Those values are slightly larger than the average American penis size: roughly 5.6 inches in length and 4.8 inches in circumference when fully erect.

The researchers noted that women might not prefer even larger penises because of their potential to tear or damage the sensitive structures inside the vagina.

"Anything that increases friction during intercourse may promote genital injury, indirectly increasing infection risk. A larger phallus would increase friction relative to a smaller phallus. These potential complications of a larger penis suggest why the human penis has not evolved to be larger," the researchers noted

Other interesting tidbits from the study: 27% of the subjects reported that they had ended a relationship partly due to a mismatch in their preferred penis size and their partner's genitalia. However, 83% of the respondents said that they were about as concerned with penis size as other women or not very concerned about it at all.

A key strength of the study was its use of three dimensional reference objects and a study design in which subjects actually answered questions in the lab. However, these methodological strengths limited the size and scope of the participant group. Subjects tended to be younger and were recruited around the UCLA campus. Who knows if their preferences will match those of women across the country?

A past study showed that around two-thirds of men agonize at some point about the size of their member, and many even attempt methods to enhance the size of their phallus. But rather than popping penis enlargement pills that don't work, men would be better off not worrying about their genitalia, being confident in who they are, and learning to use the complete repertoire of tools at their disposal for sexual pleasure.

Citation: Prause N, Park J, Leung S, Miller G (2015) Women's Preferences for Penis Size: A New Research Method Using Selection among 3D Models. PLoS ONE 10(9): e0133079. doi:10.1371/journal.pone.0133079

Scratched Moles Could Lead to Cancer

Alex B. Berezow - September 8, 2015

"Keep an eye on that mole," doctors are fond of reminding us. Any changes in size, shape, or color might indicate that skin cancer, specifically a melanoma, is forming. Now, a new review article in Trends in Immunology suggests that doctors may also want to tell us, "Don't scratch that mole, either."

Moles, more formally known as nevi, are benign skin imperfections or beauty marks. But, they may not be completely harmless. Moles possess a few activated cancer-causing genes, called oncogenes, which arise through DNA mutations. Because it takes several different mutations in various oncogenes for cancer to form, moles generally do not become malignant. However, anything that provokes mutations can, in theory, cause cancer. And since the pigment-producing cells, called melanocytes, that make up a mole already contain a few worrisome oncogenes, it may be wise to avoid damaging them.

That, essentially, is the possibility put forth by researchers at Memorial Sloan Kettering Cancer Center in New York City. Their idea largely draws upon new zebrafish research in the journal EMBO that showed that zebrafish, which were predisposed to developing cancer due to their possession of a particular oncogene, tended to develop melanomas at body sites that were frequently damaged.

How exactly this occurs may involve a particular type of immune cell called a neutrophil. These "tiny hand grenades," as my graduate school mentor liked to refer to them, are mostly known for protecting the body against infectious microbes. When tissue is damaged, neutrophils are among the first immune cells arriving at the scene. They release toxic compounds to kill any invaders. Though this is a necessary part of the innate immune response, it may be problematic if there are precancerous cells nearby.

The toxic compounds released by neutrophils can damage host cells, too, including their DNA. Furthermore, neutrophils also release a chemical, called prostaglandin E2, that can trigger cell proliferation, including that of cancerous cells. This is asking for trouble. Provoking the growth of precancerous cells in a highly toxic, mutation-causing environment may just be the perfect storm necessary to cause the cells to transform into full-blown cancer.

(Credit: Antonio et al., EMBO, 2015)

There are at least two major caveats to this hypothesis. First, the zebrafish model used a particular oncogene that is not common in human moles. Second, cells that contain oncogenes often preemptively shut themselves down in a process called senescence. Thus, it may be that damaged human moles are no likelier than any other damaged tissue to become cancerous.

Still, it may be wise to take the precaution of protecting your moles from physical injury, just in case.

Source: Mark Jelcic & Philipp Niethammer. "Do not scratch that mole!" Trends Immunol 36 (9): 503–504. Published: September 2015. doi: 10.1016/

Source: Nicole Antonio, Marie Louise Bønnelykke‐Behrndtz, Laura Chloe Ward, John Collin, Ib Jarle Christensen, Torben Steiniche, Henrik Schmidt, Yi Feng, Paul Martin. "The wound inflammatory response exacerbates growth of pre‐neoplastic cells and progression to cancer." EMBO J 34: 2219-2236. Published online: 1-Jul-2015. doi: 10.15252/embj.201490147

(AP photo)

Could Wealth Inequality Lead to Homosexuality?

Ross Pomeroy - September 2, 2015

Male homosexuality has stumped evolutionary biologists and psychologists for decades. According to evolutionary theory, the highest goal is to pass on one's genes, yet homosexual males will father no direct offspring without the help of surrogates. Moreover, homosexuality seems to be at least partially heritable and is relatively common in developed societies. Why would such an evolutionarily costly trait be so prevalent?

Past studies have suggested that genes related to homosexuality might confer a mating advantage to heterosexuals expressing them, and that female relatives of homosexual males may receive a boost to fecundity. Evidence supporting those notions remains sparse, however.

A study published in August to PLoS ONE provides support for the former contention. Lead author Julien Barthes, along with his counterparts Pierre-André Crochet and Michel Raymond, suggest that a sexually-transmitted gene on the X chromosome may yield higher femininity or attractiveness in women, and thus signal increased levels of fertility. But, as a side effect, when this gene is expressed in a male on his single X chromosome, it can increase the odds that he will be homosexual. The researchers further suggest that social stratification in societies exacerbates the expression of this gene, as women expressing it may be able to rise to a higher social class, possibly by attracting powerful or affluent mates.

To test their hypothesis, the authors conducted an exhaustive review of the archaeological record for evidence of homosexuality in human prehistory. They also perused anthropological accounts to determine how widespread homosexuality is across societies worldwide. They then assessed levels of social stratification in 92 societies (shown below) across the globe and examined how that stratification correlated to the probability that male homosexuality is present.

The researchers could find no conclusive evidence that homosexual behavior was present in human prehistory, before the rise of organized societies. Moreover, their anthropological search revealed that homosexuality does not appear to be a universal trait. In some societies, particularly those that are smaller and more isolated, homosexuality is entirely absent. For example, the Aka people of the Central African Republic don't even have a word to describe same-sex sexual interaction. It is literally unheard of. Finally, the authors did indeed find a link between social stratification and homosexuality. The more highly stratified a society was -- by rank, wealth, or power, for example -- the greater the chance that male homosexuality was present.

The authors' hypothesis is an intriguing one, and would seem to suggest that wealth inequality, which is a key driver of social stratification, may indirectly contribute to male homosexuality. The theory is a fairly novel notion, however, and will need much more evidential support before it can be taken too seriously.

To that end, Barthes and his co-authors invite others to analyze their work.

"Each step toward a better understanding of the evolution and spread of male homosexual preference among humans would contribute to a constructive social debate."

Source: Barthes J, Crochet P-A, Raymond M (2015) Male Homosexual Preference: Where, When, Why? PLoS ONE 10(8): e0134817. doi:10.1371/journal.pone.0134817

(Image: AP)

Sugar-Based Computer Plays Tic-Tac-Toe

Ross Pomeroy - August 25, 2015

Last year, Professor Alex Schiller of Friedrich Schiller University and two of his students, Martin Elstner and Jörg Axthelm, announced that they had created a sugar-based molecular computer. Admittedly not as complex as your average desktop, the "sugar computer" was still just as cool. It was even able to calculate the correct answer to a simple math problem (10 +15), although the task took roughly forty minutes to complete.

There was one thing the computer was missing, however: games. Well, now Schiller and his associates have programmed their sugar computer to play tic-tac-toe. They revealed their success August 7th in the Journal of Chemical Information and Modeling.

Though very different in design, Schiller's sugar computer runs on essentially the same idea that allows normal computers to function.

“The binary logic which makes a conventional computer chip work is based on simple yes/no-decisions,” Professor Schiller explained. “There is either electricity flowing between both poles of an electric conductor or there isn’t.”

In the sugar computer, the poles are replaced by tiny wells interconnected on a rectangular grid. Each well is filled with sugar solution. Two chemicals either make the solution in a well fluoresce or not. This fluorescence is read by logic gates. Computations begin with a basic, wired algorithm.

"If a fluorescence signal is registered, the algorithm determines what goes into the reaction vessel next. In this way signals are not translated and processed in a current flow, like in a computer but in a flow of matter," Schiller's student, Martin Elstner, explained.

Tic-tac-toe is essentially a game of if _____ then ____. When one player makes a move, the other responds based on the data available. This is something that computers can do very well; that's why tic-tac-toe was the first graphical computer game ever created all the way back in 1952.

With their sugar computer, Schiller and his co-author Elstner set up a 3 x 3 grid of wells connected by logic gates that can measure fluorescence. When a human player pipettes a blue nanoparticle solution into one of the wells, the computer responds by making another well fluoresce red.

"Moves from the human player (marked with blue luminescent nanoparticles) are read out and the gaming strategy determines where to move next. The computer move is finally marked with red luminescent nanoparticles and the turn goes again to the human player," Schiller wrote.

For the game to work on their sugar computer, Schiller and Elstner had to simplify it. The human player is only allowed to make a move on corners or edges, and the computer always gets to go first with a move in the middle well.

Unfortunately, that means the human player can never win, but one has to assume that playing a sugar computer in a rousing game of tic-tac-toe is a reward in its own right.

Source: M. Elstner and A. Schiller. Playing Tic-Tac-Toe with a Sugar-Based Molecular Computer. J. Chem. Inf. Model. DOI: 10.1021/acs.jcim.5b00324

Did Jupiter Form From Pebbles?

Ross Pomeroy - August 19, 2015

Jupiter is gargantuan. With a mass two and a half times greater than all of the other planets combined and a volume equivalent to 1,321 Earths, the gas giant commands respect. There are some who even credit Jupiter with shaping the Solar System as we know it, altering the orbits of the lesser planets and cajoling careening asteroids.

Incredibly, despite Jupiter's massive influence and impressive resumé, the planet may have formed from mere pebbles just centimeters in size.

The pebble accretion model, as the idea is called, suggests that tiny objects first coalesce together due to drag then gravitationally collapse and form larger objects one hundred to one thousand kilometers in size. These larger objects, now referred to as planetesimals, than draw in all the remaining pebbles and become the cores of larger planets.

Simulations completed last year cast doubt on this interesting theory. They suggested that -- in the context of our solar system -- too many planetesimals would form -- as many as one hundred objects the size of Earth! Since our Solar System only contains eight planets and five recognized dwarf planets, this theory was mostly ruled out.

However, a new simulation carried out primarily by researchers at the Southwest Research Institute and published to the journal Nature suggests that if these pebbles form slowly enough, fewer large planetesimals will emerge. 

But what's slow is still pretty fast on cosmic terms. According to the simulation, an object with one Earth-mass would grow in just 400,000 years. This object would then become the core of a gas giant, and start to accumulate dust and gas circulating throughout the nascent solar system.

The research fills in the blanks of how our neighborhood gas giants, Jupiter and Saturn, formed. Roughly 4.6 billion years ago, the Solar System was just a hot cloud of dust and gas. Eventually, some of the gas became so concentrated that it collapsed in on itself, forming the Sun. The rest of the material began to swirl and spin around the growing star, forming what's called a protoplanetary disc. In this roiling environment, pebbles joined together to form Jupiter's core, which then captured hydrogen and helium escaping the protoplanetary disc. Saturn's core likely formed a little bit later. When it did, it too began to snatch up the escaping gases. The rest is cosmic history.

(Image: AP)

Source: Harold F. Levison, Katherine A. Kretke & Martin J. Duncan. "Growing the gas-giant planets by the gradual accumulation of pebbles." Nature. 20 Aug 2015. doi:10.1038/nature14675

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