Some Seriously Funny Science

The other night I was playing volleyball and, during a team huddle, made a joke that the only players working hard were those with two X chromosomes (a playful jab at the male players on my team). The only response I got was a single, delayed smile along with a bunch of blank looks. That joke certainly would have produced a better reaction among my scientific colleagues, even if that simply meant a bunch of immediate groans.

I happen to think science-minded folks like myself have a terrific sense of humor, it’s just tailored to a more niche audience since a lot of the jokes we tell may not be immediately understood by the average person. While I appreciate comedy in all forms, I delight in laughing at and making jokes related to science.

Since I don’t think I am alone, I thought I would share a few events in today’s blog that really highlight the humor that can be found in the scientific community.

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Better NGS Size Selection

One of the most critical parts of a Next Generation Sequencing (NGS) workflow is library preparation and nearly all NGS library preparation methods use some type of size-selective purification. This process involves removing unwanted fragment sizes that will interfere with downstream library preparation steps, sequencing or analysis.

Different applications may involve removing undesired enzymes and buffers or removal of nucleotides, primers and adapters for NGS library or PCR sample cleanup. In dual size selection methods, large and small DNA fragments are removed to ensure optimal library sizing prior to final sequencing. In all cases, accurate size selection is key to obtaining optimal downstream performance and NGS sequencing results.

Current methods and chemistries for the purposes listed above have been in use for several years; however, they are utilized at the cost of performance and ease-of-use. Many library preparation methods involve serial purifications which can result in a loss of DNA. Current methods can result in as much as 20-30% loss with each purification step. Ultimately this may necessitate greater starting material, which may not be possible with limited, precious samples, or the incorporation of more PCR cycles which can result in sequencing bias. Sample-to-sample reproducibility is a daily challenge that is also regularly cited as an area for improvement in size-selection.

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Lessons from My Kindergartener’s First Podcast

I am a podcast junkie. In a given week I will listen to 15-20 podcast episodes, while only watching a couple television shows. Podcasts allow me to partake in my favorite pastime, learning, while offering distraction from mundane and time-consuming activities.

Podcasts help me pass the time during my daily 1.5+ hour round trip commute, while running (including during races) and in waiting rooms or airport terminals. Not surprisingly, many of these include science podcasts.

So, I was ecstatic to hear about a new science podcast for kids, Wow in the World, that I could share with my 5-year-old daughter. I considered it an experiment, assuming that she would listen to one or two episodes and lose interest, not expecting her to stay engaged by 20 minutes of audio alone.

I couldn’t have been more wrong. Within a few seconds, she was singing along with the theme song and after a couple minutes she was fully engaged and asking questions about what was being discussed. In a world where our DVR is filled with a backlog of recorded shows for her to watch on TV, she had trouble understanding that we had to wait until next week for another episode. In the meantime, she enthusiastically listened to the same episode 3 or 4 times, picking up something new each time.

This particular podcast really honed in on topics sure to spark interest in kids, such as the velocity of poop, tooting cows and slug slime. But they also addressed more abstract subject matter like human origins, G-forces and space science, explaining complex new scientific discoveries in an entertaining and memorable way.

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Predicting the Future with Dirty Diapers

Microbiome research is booming right now, with more and more evidence that our personal health and environment are shaped and influenced by the microbes we harbor and encounter. One area of study I find particularly interesting is how the microbiome we acquire at birth affects our long-term health.

A flood of new findings have emerged related to infant microbiome research, leaving parents like me scratching their heads about whether the secrets to our children’s future health may exist in the seemingly endless stream of dirty diapers we change.

The human microbiome evolves and develops in utero and then during and after delivery is colonized by bacteria encountered during exposure to the external environment. The initial composition of microbes an infant is populated with influences their lifelong microbiome signature and can be influenced by many factors along the way, including the microbiome community of the mother, use of antibiotics or other antibacterial substances, breastfeeding, C-section birth. These variables have been correlated with disruption of the infant microbiome and associated with differences in cognitive development and the development of disease, such as asthma and allergies.

In general, these correlations are discovered by taking a fecal sample from an infant and analyzing the DNA sequences of the bacteria present. The microbiome composition of the individual is then compared against different individual characteristics (such as presence or absence of a disease) at the time of the sample and/or at later points in time. Finally researchers look for statistically significant patterns among individuals with similar characteristics or microbiome communities. This type of study can reveal associations between the microbiome and individual traits, but further experiments are needed to show causation. Continue reading

Searching for Secrets in Single Cells

There has been a lot of effort recently to perform whole genome sequencing, for humans and other species. The results yield new frontiers of data analysis that offer a lot of promise for groundbreaking scientific discoveries.

One objective of human genome sequencing has been to identify sources of disease and new therapeutic targets. This movement has opened the door to create personalized medicine for cancer, whereby the genetic makeup of an individual’s tumors can be used to determine the most effective drug intervention to administer.

Interest in studying the characteristics unique to individual cells seems obvious when considering the function of healthy cells versus tumor cells, or brain cells compared to heart cells. What has surprised scientists is the realization that two cells in the same tissue can be more different from each other, genetically, than from a cell in another organ.

For example, a small number of brain cells with a specific mutation can lead to some forms of epilepsy while healthy people may also carry cells with these mutations, but too few to cause disease. The lineage of a cell, where it came from and what events shaped its development, ultimately determines what diseases can exist.

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Creating ART from 3D Printed Ovaries

It is remarkable to me how quickly in vitro fertilization has gone from an experimental, controversial and prohibitively expensive procedure to becoming a mainstream option for those struggling with fertility issues. What was unheard of in my parents’ generation is nothing extraordinary among my friends who are having children.

My personal observations are supported by the CDC, which reported that 1.6% of all infants born in the U.S. in 2015 were the result of assisted reproductive technology (ART). This is a 33% increase since 2006, which can be attributed to rapid advances and refinements of the various technologies available to those seeking reproductive assistance.

It challenges the mind to imagine what reproductive technologies might be widespread when my children and their friends are adults. When experts speculate about the future of human reproduction, there always seems to be a lot of focus on provocative scenarios that portend a dystopian future, such as designer babies. What gets lost are some of the more general scientific advances that are being applied to ART in fascinating ways.

While improvements in reproductive technologies serve many, one group that remains underserved are pediatric cancer patients. As a result of treatment, these patients are often faced with impaired ovarian function that can prevent puberty and result in infertility. In vitro fertilization and ovarian transplants are currently used, but do not provide lasting solutions for all individuals.

In response to this need, researchers are working to develop an organ replacement that can provide long-term hormone function and fertility for all patients.  A recent study in Nature Communications presented encouraging results in mice using bioprosthetic ovaries that may further revolutionize the field of ART. Continue reading

Knots: Friend or Foe?

Knots affect our lives in perplexing ways. They can perform life-saving assistance, such as during rock climbing, or provide Sisyphean puzzles of entanglement. Often, knots seem to have the contrarian personality of an adolescent. They loosen and unwind when you want them to stay fastened, and inevitably form tangles of confounding complexity when you seek to avoid them. These puzzling characteristics of knots were brought to mind when I read two recent articles about the scientific investigation of knots.37190697-May-5-Darcia---Option-2

Why Knots Fail

The explanation of how shoelaces come untied, published in Proceedings of the Royal Society A, was quite prevalent in the news cycle recently. After observing slow-motion video footage of the shoelaces of a runner on a treadmill, researchers were able to explain how motion affects knots and results in untied shoelaces.

First, they observed that the failure of a knot is not a gradual process, but happens abruptly over the course of only one or two strides. This is possible due to the surprising amount of force generated by the impact of one step, which this study calculated to be an average of 7 g—more than twice the g-force experienced by the Space Shuttle upon reentry into the Earth’s atmosphere. Continue reading

Making a Case for Basic Research Funding

The value of public funding for “basic” versus “applied” research has long been questioned. To address this debate, the authors of a recent report in Science performed a large-scale evaluation of the value of public investment in biomedical research. After analyzing the relationship between the U.S. National Institutes of Health (NIH) grants and private patents, they found that distinguishing research as basic or applied is not useful in determining the productivity of grant funding.

Genetic research at the laboratoryThe $30 billion annual budget of the NIH makes it the largest source of life science funding in the world and provides a third of all US biomedical research and development. Although there has long been a strong argument for public investment in scientific research, attacks on the tangible benefits of this research persist. In particular, some opponents argue that “basic” research is too far removed from practical applications to be worthy of investment.

To quantify the effects of NIH funding for basic versus applied research, the authors looked at data from 365,380 grants awarded between 1980–2007 and compared their direct and indirect influence on patent filed. In particular, they decided to use patent-article citations as a measure of the influence of publicly funded science on commercial developments.

The researchers determined two ways in which research funded by the NIH could impact patenting; patents could be filed by the NIH-funded scientists or by private entities that cited research funded by NIH grants. This study found that roughly 10% of NIH grants were directly responsible for a patent while nearly a third of NIH grants had an indirect influence on patents. This indirect influence was attributed to articles associated with grant research that were later cited by a patent.

Delving deeper into the data, the authors found a similar pattern when looking at drugs brought to market that were associated with NIH grants; less than 1% of grants were directly linked to a patent associated with a drug, while 5% resulted in a publication cited by a patent for a drug. Despite public policies like the Bayh-Dole Act, that encourage academic researchers to file their own patents, the traditional route of applying public research to private patents continues to predominate.

For those that question the value of basic research and aim to steer public policy toward supporting applied research, this report makes a strong case against this way of thinking. The findings also suggest that using direct generation of patents as a metric for the return on investment of publicly funded biomedical research is not very useful since most of the effects of NIH research appear to be indirect.

In fact, the authors posit that basic research is just as productive as applied research in terms of patenting since the amount of grant research cited by private patents is much greater than the number of grants directly associated with patents. Perhaps it is time policy makers consider studies like this and forgo disseminating grant funds based on whether research is basic or applied.

So NASA Found Some New Exoplanets…Now What?

34412848-March-8-Planets-600x600-WEBYou have probably heard a lot of excitement over NASA’s recent announcement about the discovery of seven earth-size planets found orbiting around the star TRAPPIST-1, which is part of the constellation Aquarius.

These exoplanets are notable because they exist within the habitable zone of the star (nicknamed Goldilocks planets because this area is not too hot and not too cold) and are probably rocky with the potential to contain water on their surface.

A lot of the enthusiasm revolves around the hope that one of these planets might harbor extraterrestrial life or could be suitable for human inhabitants. Of course, many further observations must be made to determine if these scenarios are plausible, not to mention the huge advances in technology that would need to occur so we could actually verify the planetary conditions or send humans 40 light-years away. Continue reading

Familial Searching Solves Cold Cases—At What Cost?

A cold case that had stumped investigators for nearly 41 years was solved last month. The 1976 sexual assault and murder of Karen Klass, ex-wife of Righteous Brother’s singer Bill Medley, shocked her Hermosa Beach, CA community and captured the public interest. Failing to make any arrests for decades, detectives were able to use DNA evidence to eliminate suspects in 1999 but were unable to find a database match. In 2011, investigators decided to try a new technique called a familial search and, after a few attempts, successfully identified the perpetrator.

Familial searching (FS) involves taking a DNA profile obtained from a crime scene and comparing it to profiles in CODIS and other databases to identify male relatives. The DNA profile of an immediate family member, such as a sibling, parent or child, can provide a match that generates new leads for law enforcement. Detectives can then collect additional evidence to narrow down that new pool of individuals to a single suspect.DNA-Handcuffs-double-exposure-R2

Last May I wrote a blog featuring a Q & A about FS provided by Mr. Rockne Harmon, a respected member of the forensic community and passionate advocate for FS. Supporters, like Harmon, and opponents agree that this method of obtaining matches to DNA evidence has demonstrated scientific precision and successful outcomes, as in the Klass case. However, it is still considered controversial and most states have not implemented specific policies regarding the application of FS to criminal investigations. So why isn’t the use of FS more widespread?

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