Living and Breathing Science: The Traditional Laboratory Notebook Needs to Go Electronic

Laboratory notebooks of scientists such as Michael Faraday and Thomas Edison not only provide details of experimental methods and the day-to-day progression of their historic research, but also offer insights into how they thought and accounts of the moments of breakthrough discoveries.

For centuries, scientific recording keeping involving handwritten entries in paper notebooks has sufficed. Over the last two decades I have witnessed dramatic changes in laboratory record keeping that have stemmed from the advent of digital data. 

In academic research, it is customary for a scientist’s original laboratory notebooks to be kept by the principle investigator. So, on shelves outside my office are rows of the laboratory notebooks that have been generated by postdoctoral fellows, graduate students and technicians who have worked with me over the last 20 years.

Looking through these notebooks one can see the variety of ways in which researchers have documented their experimentation. In addition to handwritten entries there are an assortment of films, gels, photographs, graphs, spreadsheets and printouts from all kinds of instruments that have been taped, stapled or simply placed between pages. In more recent notebooks there are attached storage disks containing electronic files. It is evident these scientists have had different degrees of success dealing with problems of annotation and cross-referencing of disparate types of data, particularly digital data.

Generally, once a year I discuss with members of my lab group how to maintain a laboratory notebook and store their digital data. I stress how vital stringent record keeping is to the scientific process and that valid records preserve rights to our discoveries. Despite this, upon periodic inspection of notebooks of my personnel I am often surprised to find what actually is being recorded. Rather than adhering to the conventional format some have adopted a ‘relaxed’ style for their notebook entries. Particularly disturbing are notebooks that lack discussion of results and conclusions. I have also found it difficult and sometimes impossible to locate digital data related to particular experiments described in my people's notebooks.

These experiences not only underscore breakdowns in record keeping training and compliance, but also highlight inadequacies of current record keeping approaches generally employed by basic researchers. I am therefore a proponent of implementation of electronic laboratory notebooks (ELNs) that automate collection and recording of data. Such systems are not widely employed in academic research, but the NIH and research institutions need to take steps to see that these systems are implemented.

Southern deep-fried turkey marinades and cooking instructions

Deep-fried turkeys are delicious and have been part of our family Thanksgiving Day menu here in Charleston, South Carolina for many years. This year, I will be deep-frying two turkeys, one with a Cajun style injected marinade and the other with a Low Country-inspired marinade.

Ingredients for Cajun style marinade:

3 tablespoons Mexican hot sauce

1-teaspoon salt

1-teaspoon cayenne pepper

1 tablespoon minced garlic

1 cup lemon juice

½ cup olive oil

½ cup chicken broth

¼ cup wine vinegar

Ingredients for Low Country-inspired turkey marinade:

1 teaspoon minced garlic

3 tablespoons flat-leaf parsley

1-tablespoon sage

3 tablespoons rosemary

1-tablespoon ground thyme

½-teaspoon ground cumin

½-teaspoon ground coriander
2 tablespoons fresh oregano leaves

1-teaspoon salt

½ teaspoon freshly ground black pepper

¼ cup extra-virgin olive oil

¼ cup champagne wine vinegar

¼ cup Sauvignon Blanc

1-tablespoon soy sauce

4 tablespoons lemon juice

Determining the amount of oil needed to deep-fry your turkey:

Prior to marinading your turkey you will need to determine the amount of oil needed to fill your frying pot. To do this, place the turkey into your pot and fill the pot with water until the turkey is just covered. Leave plenty of room to avoid overflowing the pot. Remove the turkey and mark the height of the water to indicate how much oil to add.

Preparing and injecting the marinade:

Mix all ingredients in a saucepan and bring to boil. Reduce heat to low and cook for 10 minutes.

Blend and strain.

Place the thoroughly thawed turkey in a large bowl. Using paper towels remove any water from the turkey.

Using a syringe and a large gauge needle, inject the marinade at a dozen more sites in the turkey.

Pour any remaining marinade over the turkey.

Lightly dust the turkey with cayenne pepper.

Place your turkey onto the deep frying rack in a large bowl. Allow all of the marinade liquid to thoroughly drain.

Deep-frying the marinaded turkey:

Set up your fryer outdoors in a flat, uncovered area free of foot traffic. Have a fire extinguisher handy.

Add oil (I use a peanut/soy bean oil blend) making sure to add no more than needed to cover the submerged turkey without over flowing the pot. The volume of oil needed should be determined beforehand as described above.

Heat oil to 390 degrees, allowing approximately 1 hour for the oil to reach temperature.

Put on oven gloves and an apron.

Turn the flame off and carefully and slowly lower your marinaded and unstuffed turkey into the oil.

Cover and turn on the flame.

Cook 3-3.5 minutes per pound.

Turn the flame off and carefully remove the turkey from the oil and place the racked bird on a large cookie sheet to drain and cool.

Let the turkey cool for 30 minutes prior to carving.

Living and Breathing Science: Advancing Basic Scientific Research Despite The Will Of The Skeptics

Today on Face The Nation, CBS News’ Chief Washington correspondent, Bob Schieffer, articulated a passionate and effectual argument in support of basic research (http://www.cbsnews.com/stories/2010/08/29/ftn/main6816315.shtml). Aware that basic research has led to therapies that offer hope of recovery to his friends that have recently been diagnosed with cancer, Mr. Schieffer commented on the restraints being placed on stem cell research. He likened the inability of many to recognize that there is knowledge to be gained from embryonic stem cell research to those that refused to look through Galileo's telescope, convinced that they already knew what they would see based on their doctrines and traditions. Where would we be now if the will of such skeptics had prevailed?

Cleaning Oil Contaminated Beaches with Fertilizer-Bacteria Technology

Numerous studies describe the necessity of adding nitrogen and phosphorus to facilitate microbial degradation of hydrocarbons. For example, a field trial of a controlled-release, hydrophobic fertilizer together with crude oil degrading bacteria was conducted in 1992 on an oil contaminated sandy beach in Israel (1). The results of the study showed an approximately 86% degradation of pentane compounds as compared to only a 15% decrease in a control plot of beach. Later that year the entire beach, containing approximately 200 tons of crude oil, was cleaned using the fertilizer-bacteria technology.

1. Petroleum bioremediation - a multiphase problem. Rosenberg E, Legmann R, Kushmaro A, Taube R, Adler E and Ron EZ. Biodegradation, Volume 3, Numbers 2-3, 337-350 1992

Give Companies Marketing Oil Eating Bacteria a Chance in Gulf Oil Spill Clean Up

There are a number of companies that specialize in production of hydrocarbon-eating microbes for use in bioremediation of oil spills. For example, Clift Industries, Inc. markets a blend of a dozen microbial strains, enzymes and nutrients designed to digest hydrocarbons. Similarly, Alabaster Corp. also sells a blend of naturally occurring, non-pathogenic oil degrading microbes. A number of other companies offer products that accelerate biodegradation by providing the necessary support and stimulation for native microbes to multiply and produce enzymes to speed up the metabolic process of biodegradation. For example, Universal Remediation Inc. sells miniature spheres comprised of bee’s wax and soy wax, which encapsulate oil and allow bacteria to break it down. BioNutraTech markets a biostimulant composite particle that can accelerate biodegradation by providing the necessary nutrients for native microbes.

The Gulf Coast Restoration Plan Needs To Support Health and Environmental Research

The American Recovery & Reinvestment Act of 2009 (ARRA) provided an unprecedented level of funding to the National Institutes of Health (NIH) ($8.2 billion) and the National Science Foundation (NSF) ($3 billion) to help stimulate the US economy through the support and advancement of scientific research. A similar boost to NIH and NSF funding should be part of the Gulf Coast Restoration Plan proposed by President Obama on June 15, 2010. Funds provided to NIH could be used to support meritorious research programs that will study expected deleterious impacts of petroleum contamination on the health of Gulf coast residents. NSF funds could be used to support high-return, innovative research related to bioremediation, habitat restoration and comprehensive studies of the impact of the oil leak on wildlife. Special priorities must be given to those research projects that will stimulate the economy of the Gulf coast region, create or retain jobs, and have the potential for making rapid scientific progress.

Bioremediation by Application of Fertilizers to Oil-Soaked Gulf Coast Shorelines

Bioremediation approaches based on the application of fertilizers to oil-soaked shorelines have been shown to stimulate the rate of oil biodegradation by ubiquitous oil-degrading microorganisms (1). Weeks after the Exxon Valdez oil spill in March of 1989, a bioremediation approach was employed on a number of oil contaminated sites in Prince William Sound. Fertilizer was applied to these sites in order to promote growth of naturally occurring bacteria capable of degrading polycyclic aromatic hydrocarbon compounds present in the oil. Follow-up studies of the impact of this U.S. Environmental Protection Agency-approved approach showed that the levels of polycyclic aromatic hydrocarbons were significantly lower in treated sites as compared to untreated sites.

1. Swannell RP, Lee K, McDonagh M. Field evaluations of marine oil spill bioremediation. Microbiol Rev. 1996 Jun;60(2):342-65.

Old Grand-Dad Whiskey Bottles and Leaking Gulf Oil

Bobby Thompson is a Texan, a scientist, and a man rich in life experiences. In the early 1960’s he participated in a research project in which thousands of Old Grand-Dad Whiskey Bottles with return mail addresses sealed inside were tossed into the Gulf Sea at sites around Pass a la Outre, Louisiana. The results not only mapped currents within the Gulf, but also demonstrated that many of the bottles floated on currents that ultimately carried them to Ireland. The findings of this simple experiment highlight the potential for the oil now spewing into the Gulf to contaminate beaches all along the path of the Gulf Stream, which originates in the Gulf of Mexico and passes along the eastern coast of the United States and Newfoundland before crossing the Atlantic Ocean.

Why Isn't Bioremediation Being Employed on the Gulf Oil Leak?

Dispersants, skimmers, absorbents, containment booms, and shovels are all that the public hears about as being used to clean up the oil that is currently fouling the tidal marshes, rivers and beaches of the Gulf coast. These primitive technologies are proving to be largely ineffective. What about bioremediation? Naturally occurring, hydrocarbon-degrading, microbes are available that can be employed to degrade the oil. A major objection that is raised with respect to use of oil degrading microbes is that oxygen deprivation will result from their use. This is true, but the environmental impact of transient oxygen deprivation versus the persistent effects of harmful petroleum compounds on Gulf habitats has not been discussed. Forty years after the Exxon Valdez oil spill, oil can still be found just beneath the surface of the shoreline of the rocky coves of Prince William Sound. Despite the extensive cleanup attempts employed in Alaska Oil Spill (which used the same techniques currently being used in the Gulf Sea), less than ten percent of the oil was recovered.

Balloon Approaches to Stem the Gulf Oil Leak

Brainstorming with my brother Gary we came up with several plausible approaches to stem the flow of oil gushing from the broken pipe in the Gulf Sea floor. Both approaches involve the use of balloons. One method is to capture the oil in an enormous balloon anchored over the pipe. This balloon would have vent pipes that would allow oil and gas to be removed to the surface for collection. Another approach would be to insert an inflatable balloon into the pipe to act as a valve/plug. The inflatable devise might allow cement to be piped through the balloon to seal the pipe.

If you have proposals they can be submitted to BP via the Louisiana Business Emergency Operations Center (LABEOC).

Living and Breathing Science: Microbial Approach to Clean up of the Gulf Oil Spill

Naturally occurring, hydrocarbon-degrading, microbes are perhaps the best tools in our arsenal to clean up the oil that is currently polluting the tidal marshes, rivers and beaches of Louisiana. I am dismayed by the apparent lack of attention being paid to employing microbial agents in the fight to save the gulf coast from the devastating effects of the oil spill. One such microbial product called Biorem-2000 Oil Digester (produced in South Carolina) has been approved in several US states for use in oil clean up operations. For example, in the states of Utah and Georgia, Biorem is being injected into the ground at multiple sites where oil has contaminated ground water.

Please contact Dennis Woods of Industrial Fluids Management at DWoods@IndustrialFluidsManagement.com to discuss details of Biorem 2000 Oil Digester and approaches to employ it on the oil that is currently polluting the beaches and pristine wetlands of Louisiana. Bioremediation must be made a major component of the strategy.

A Tree More Than Any Other

A magnificent tree, estimated to be one thousand years old, grows on Johns Island, South Carolina. The Angel Oak is truly awe inspiring, having a trunk of enormous girth with furrowed bark and great limbs that reach down to enter the earth and rise up again. The grand oak draws countless visitors each year down a dusty dirt road to its home nestled among trees that are a tiny fraction of its age. If estimates are correct, the Angel Oak was beginning its life before the Crusades, before the Aztec and Inca civilizations existed and before the Vikings came to North America. It has endured earthquakes, hurricanes, floods, fires, disease and escaped the axe. Over the decades it has enthralled all who have stood beneath its enormous canopy. This weekend we took my friend Bridget de Socio to Angel Oak. Seeing the tree she told my daughter Livia, “This tree wanted to be a tree more than any other”.

Living and Breathing Science: Competiveness is Perseverance

Receiving a poor score on a grant application can be a very discouraging experience for a scientist. In my view, the worst thing that can happen is to let this disappointment turn to fear that failure cannot be a path to successful funding. One of the greatest baseball players, Babe Ruth, struck out more than any player of his era. Nonetheless, Ruth was an outstanding hitter, batting .342 for his career. By analogy, in addition to having quality science we need to know that a major aspect of competiveness is perseverance. Perseverance not only means to be responsive to the criticisms of reviewers on a grant application that received a poor score, but also to increase ones chances of success by devising and submitting new applications.

Living and Breathing Science: Nature’s mystery revealed through testing countless hypotheses

A hypothesis is a tentative explanation for a phenomena or a prediction as to a possible outcome of an experiment. The hypothesis is the stock in trade of the scientist. Hypotheses can be simplistic or intricate and formulated from the tiniest bits of data. What any experienced scientist knows all too well is that most of her or his hypotheses will inevitably be proven wrong. But this does not stop us from generating hypotheses by the thousands in our efforts to solve nature’s mysteries. Indeed Mark Twain remarked that, “There is something fascinating about science. One gets such wholesome returns of conjecture out of such a trifling investment of fact.” His point is well taken, we must resist over interpreting our data and placing too much weight on our hypotheses. There may be few precious instances when findings from rigorous experimentation prove our hypotheses to be correct and a bit of nature's mystery is revealed.

Living and Breathing Science: A Milestone in Fibulin Research

In the 1980s, while working as a postdoctoral fellow with Erkki Ruoslahti in La Jolla, California, I discovered a protein that I later named fibulin from the Latin fibula for clasp. This year marked the twentieth year since my first publication on fibulin (which I pronounce FY-beau-lin). Over these two decades, many other investigators and I have built on the initial discovery. As a result, findings reported in nearly 400 manuscripts have revealed that fibulin (now called fibulin-1) is a member of family of eight extracellular matrix proteins having a variety of critical functions. One of the most significant roles to emerge for members of the fibulin family as a group is their ability to coordinate the assembly of elastic extracellular matrix fibers such as those that provide elasticity to blood vessels, lungs and skin.

Living and Breathing Science

As a boy growing up in Connecticut, when I wasn’t playing baseball, I was exploring the woods, ponds and streams in the forest behind my home, looking under rocks and logs and wading in the creeks and finding frogs, fish, tadpoles and insects. Little did I know that these were the formative experiences in my path to becoming a scientist. It has been a long journey to get where I am today as a scientist. As a result I have learned many lessons that I can impart to students and early stage researchers. In my blog series 'Living and breathing science' I will share my experiences in science and reveal my scientific credo.

NIH Funded Research is One Public Investment that Yields Enormous Returns

As a researcher who has been supported by grants from the National Institutes of Health (NIH) for over 20 years I am keenly aware of the largely prudent and accountable ways in which grant monies are spent by academic researchers. Dollar for dollar, the biomedical research enterprise may be one of the most cost effective of federally subsidized programs. I see first hand the enormous returns being paid on the taxpayer investment in biomedical research in the form of advancements in our understanding of disease mechanisms and new therapeutic approaches. In addition, federally funding of biomedical research directly and substantially benefits the American biotechnology industry. The days of biologists making their own reagents and gizmos to conduct experiments are long gone. Researchers now depend on a huge array of commercially available reagents, chemicals, consumables, kits and advanced instrumentation to conduct their investigations. Furthermore, a rising trend is to contract companies to provide highly specialized research services. In effect, this means that a large, and growing fraction of federal grant dollars are being funneled to U.S. companies that produce these goods and services. Therefore, an argument can be made that augmenting the NIH budget will stimulate the American biotechnology industry. I believe that this is indeed true and is only one of the reasons why I advocate doubling the NIH budget.

Shared Resource Facilities: Discovery Engines for Biomedical Research Institutions

In most academic biomedical research institutions, shared resource facilities exist to provide researchers access to state-of-the-art technologies. The services offered through these facilities are extremely valuable to advancing the research programs of investigators either by generating data for testing or developing scientific hypotheses. At the 2009 Southeast Institutional Development Award (IDeA) Regional Meeting held in Charleston, South Carolina on November 10th, I was a panelist in a session focusing on shared resource facilities. Based on my 13 years of experience as a director of shared resource facilities at the Medical University of South Carolina (http://proteogenomics.musc.edu/), I talked about issues related to sustaining financial support for shared resource facilities and incentivizing their use.

DiGeorge Syndrome Seminar at Medical College of Georgia

On October 23rd I presented a Grand Rounds seminar in the Department of Pediatrics at the Medical College of Georgia. In my lecture I conveyed evidence for the extracellular matrix protein fibulin-1 playing a critical role in the formation of the thymus, thyroid, cranial nerves, bones of the skull, blood vessels of the head, aortic arch arteries and outflow tract of the heart. The morphogenesis of all of these tissues involves contributions from a population of cells known as neural crest cells. Disorders of neural crest cells lead to congenital malformations referred to as neurocristopathies. The disorder, DiGeorge syndrome, is a human neurocristopathy having a range of clinical features including hypoparathyroidism, hypoplastic thymus or absent thymus, conotruncal heart defects (e.g., tetralogy of Fallot, interrupted aortic arch, ventricular septal defects, vascular rings) cleft lip and/or palate.
Our research shows that mice deficient in fibulin-1 display many of the abnormalities associated with DiGeorge syndrome. While 90% of individuals with DiGeorge syndrome have a deletion is a region of chromosome 22, specifically the q11.2 region, 10% of DiGeorge patients do not have this deletion. The fibulin-1 gene maps outside of the 22q11.2 region, located at 22q13.2. Ongoing research in my lab has implicated fibulin-1 a regulator of neural crest cell survival and migration during embryonic development. Furthermore, we have evidence that fibulin-1 regulates the expression of several genes previously implicated as being dysregulated in the pathogenesis of DiGeorge syndrome.