Soup recipe

Here is a Big Island holiday soup recipe: local fusion cuisine, with Filipino, old Hawaiian, Thai, and Indian influences in the ingredients. Serves about 10 as a main dish.

Kupa Chicken Masala me papaia maka


3 lbs (optionally de-boned) roasting chicken, cut up (boneless breast or thigh meat works well)

3 tablespoons olive oil

2 tablespoons sesame oil

6 cloves garlic, finely chopped

1 large onion, coarsely chopped

1 large green or orange sweet pepper, coarsely chopped

2 tablespoons finely chopped (paper matchstick sized) or grated fresh ginger

6 cups green papayas, peeled, seeded, and cut into medium to large pieces

4 cups chopped raw lu'au (kalo taro leaves) (deveined; may substitute other fresh green herb to taste)

1 cup Thai basil leaves (may substitute or combine other fresh green herb such as sweet basil or oregano)

3 tablespoons tikka masala “Simply Asia” brand (or other curry type spice mix) powder

6 tablespoons patios (fish sauce)

1 cup coconut milk (can also use yoghurt or sour cream if desired)

Juice of 4 limes

6 to 8 cups water

1 to 2 teaspoons white pepper (optional)


Heat olive and sesame oil in a large soup kettle or similar large 2+ gallon capacity pan.

Cook garlic, onion, ginger, and sweet pepper in oils. Remove onion and pepper from pan temporarily. Add chicken and brown lightly, then turn chicken over in pan and lightly brown chicken on the other side.

Return cooked onion and sweet pepper to pan. Add patois, tikka masala type curry powder, Thai basil, chopped lu'au, and cubed green papaya. Cover with the water, lime juice, and coconut milk and bring to a boil, simmering on low for about an hour or until papaya is semitransparent.

Add pepper to taste as desired. Allow to sit for at least one hour, then serve.

Phenotypic Plasticity: Mixing Darwinian and Lamarckian Adaptation in our bioRxiv Weekend Preprint Review

In a paper that is bound to raise the expectations of trolls in the debate on the role of adaptation in natural selection, the paper below analyzes genome changes in a microbial population exposed to the stress of a toxic environment. Darwinian selection leads to shifts in the average genome of the population towards those that can better induce the enzymes needed to detoxify the stressed cells.

How is this Lamarckian? Actually, it isn't. Lamarck's typical example would be one in which later generations of giraffes had longer necks as a shift in the population toward a better reach to the greenery of the tops of leafy trees induced by the animals straining upward. Even when shifted to a plains environment without trees, the offspring of giraffes that stretched their necks would keep their long necks, in Lamarck's theory. But the paper below's version of Lamarckian adaptation (not really Lamarck's) would rather be one in which the giraffes could grow longer necks if they were in an environment where stretching upwards was needed, but in an environment where the giraffe had no need to stretch upwards, the offspring of long-necked giraffes would only have short necks, and the long necks would never be seen. In biology, this is termed phenotypic plasticity. I would reframe the paper's reference to Lamark, calling the makeup of the host organism's bacterial flora a part of the host's phenotype. In humans, where we surely consider our commensal bacteria part of phenotype (or even just part of our environment) and not genotype, another common, minor example of phenotypic plasticity is the ability to tan the skin under sunlight exposure.

Is phenotypic plasticity where Lamarck was right? I think not. That honor belongs to epigenetics.

One interesting feature of the paper is that its "Holobiont" organism is partially composed of microbial elements all of which could be germ plasm for another holobiont, unlike mammals which have separate populations of haploid cells. This emphasizes a key difference in natural selection of animals versus some plants and most bacteria.



Darwinian Selection Induces Lamarckian Adaptation in a Holobiont Model

Dino Osmanovic, David A Kessler, Yitzhak Rabin, Yoav Soen



Current models of animal evolution focus on selection of individuals, ignoring the much faster selection of symbiotic bacteria. Here we take host-symbiont interactions into account by introducing a Population Genetics-like model of holobionts exposed to toxic stress. The stress can be alleviated by selection of resistant individuals (host and bacteria) and by secretion of a detoxification agent (“detox”). By defining a new measure, termed the ‘Lamarckian’, we show that selection of resistant bacteria over one generation of hosts leads to stress-dependent increase in the tolerance of the hosts' offspring. This benefit is mediated by co-alleviation of toxic and physiologic stress. Prolonged exposure leads to further adaptation by ‘group selection’ of bacterial communities with higher detox per bacterium. These findings show that Lamarckian adaptation can arise via interactions between two levels of Darwinian selection within a holobiont system. The conclusions and modelling framework are applicable to diverse types of holobiont systems.

Electronic Prescribing Improves Compliance

...and in other news, if some of us had a dime for every time we had to write a prescription twice because the first was (genuinely) lost, there'd be some extra money for presents this year.



Association Between Method of Prescribing and Primary Nonadherence to Dermatologic Medication in an Urban Hospital Population

Adewole S. Adamson, MD, MPP1,2; Elizabeth A. Suarez, MPH3; April R. Gorman, MS4

JAMA Dermatol. Published online October 26, 2016. doi:10.1001/jamadermatol.2016.3491


Importance Prescription underuse is associated with poorer clinical outcomes. A significant proportion of underuse is owing to primary nonadherence, defined as the rate at which patients fail to fill and pick up new prescriptions. Although electronic prescribing increases coordination of care and decreases errors, its effect on primary nonadherence is less certain.

Objectives To analyze factors associated with primary nonadherence to dermatologic medications and study whether electronic prescribing affects rates of primary nonadherence.

Design, Setting, and Participants A retrospective review of medical records was conducted from January 1, 2011, to December 31, 2013, among a cohort of new patients prescribed dermatologic medications at a single, urban, safety-net hospital outpatient dermatology clinic.

Main Outcomes and Measures The primary outcome was the overall rate of primary nonadherence, defined as filling and picking up all prescribed medications within a 1-year period, and the difference in primary nonadherence between patients who received electronic prescriptions and those who received paper prescriptions. Secondary outcomes included the association of primary nonadherence with sex, age, relationship status, primary language, race/ethnicity, and number of prescriptions.

Results A total of 4318 prescriptions were written for 2496 patients (mean [SD] age, 47.7 [13.2] years; 849 men and 1647 women). The overall rate of primary nonadherence was 31.6% (n = 788). Based on multivariable analysis, the risk of primary nonadherence was 16 percentage points lower among patients given an electronic prescription (15.2%) than patients given a paper prescription (31.5%). Primary nonadherence decreased with age (<30 y, 38.9%; 30-49 y, 35.3%; and 50-69 y, 26.3%), and then increased in elderly patients 70 years and older (31.9%). Of patients who were given 1, 2, 3, 4, or 5 prescriptions, rates of primary nonadherence were 33.1%, 28.8%, 26.4%, 39.8%, and 38.1%, respectively. Primary nonadherence decreased with age but then increased in elderly patients. Patients identifying English as their primary language had the highest rate of primary nonadherence (33.9%) compared with Spanish (29%) or other speakers (20.4%).

Conclusions and Relevance Compared with paper prescriptions, electronic prescriptions were associated with less primary nonadherence. Number of prescriptions, language, race/ethnicity, and age were associated with increased rates of primary nonadherence. Efforts must be made to understand why primary nonadherence occurs, identify patients prone to primary nonadherence, and simplify medication regimens to maximize adherence and quality of care.

No to Echo Chambers

Political independents just say no to those social media-generated, politically-insulated safe spaces :)

Here are the political characteristics of my news feeds, as characterized by PolitEcho:

Winter in Hawaii

An ice and snow conditions winter storm warning with almost three feet of snow atop Mauna Kea. At the house here in makai Paukaa, over four inches of rain in 24 hours. Yes, winter has come to the Big Island.

An alternative to Kim's physicalism

In his book Physicalism, or Something Near Enough , Jaegwon Kim says: The final picture that has emerged is this: P is a cause of P*, wi...