Tuesday, December 29, 2015

The Moral Permissibility of Harm and The Doctrine of Double Effect

One of the most well-known and descriptive illustrations of the moral conflict of doing harm versus allowing harm is the classic trolley problem, introduced by Philippa Foot in the 1960s. There is a trolley that has run out of control and is heading down a railway track with five people tied up to it. Youre standing in front of a lever that can switch the trolleys direction onto an alternative track. However, one person is tied up on the alternative track. Do you pull the lever and save five people at the cost of killing one person, or do you not do anything and allow five people to die while one survives?

A consequentialist would without a question argue that pulling the lever is the only morally acceptable thing to do. Consequentialists do not consider doing harm to have intrinsic moral significance, because the only thing that matters for them is the goodness of the outcome, not the act itself. On the other hand, a deontologist would argue that the distinction between doing and allowing harm does have intrinsic moral significance. An absolute deontologist would claim that although by allowing the harm more people will die, killing is worse than letting die, therefore not pulling the lever would be the right thing to do. This doesnt mean that the deontologist believes that allowing harm is morally insignificant, but it simply has less moral weight than doing harm does.

In her paper discussing the trolley problem, Judith Thomson introduces an interesting additional normative factor; claim. Lets change the scenario just slightly. What if the five people on the first track are workers that have been promised their safety as part of their work contract, while the one person on the second track just got stuck while aimlessly wondering. In this case, Thomson would argue that the lever must be pulled, for the workers have more claim against the trolley. According to Thomson, the normative factor of claim holds more weight than the distinction between doing and allowing. However, although this normative factor may apply to this specific scenario, it might not always be applicable to the broader context of harm.

Now in discussing harm in a broader context, I will introduce a normative factor that neither consequentialists nor absolute deontologists acknowledge; intending harm. Certainly, there is a notable distinction between doing harm, allowing harm and intending harm. In scenarios like that of the trolley problem, there will inevitably be both a positive and negative outcome. In this sense, since the outcomes will be similar regardless of which act is performed, its questionable whether the distinction between doing and allowing is really the only additional morally significant factor that should be considered. Here it is appropriate to introduce the idea of the intention of harm. Once this normative factor comes into the picture, the moral permissibility of the act gains some more clarity. However it is still important that we analyze the significance of different ways of intending harm. This brings us to the “doctrine of double effect.”

The doctrine of double effect defines an action that intends harm as an end or as a means to be morally forbidden, but permits an action that causes harm as a foreseen byproduct of the action. Lets say youre indefinitely trapped in the basement of an abandoned building with your sister. Its been 48 hours, and there is nothing but a single slice of bread that is equally accessible to both you and your sister. In scenario A, your sister eats the slice of bread. You get extremely angry, and you strangle her to death. In scenario B, you strangle her to death with the means of eating the bread yourself. In scenario C, rather than killing your sister, you decide to eat the bread, which causes her to die from starvation. Here we have a case where no matter what scenario, you are playing a role in your sisters death. How can we determine which act is morally permissible?

According to the doctrine of double effect, only scenario C is morally permissible. In scenario A you are intending the death (harm) of your sister as your end goal, and in scenario B you are intending the death of your sister as a means for the end goal of eating the bread yourself. On the other hand, in scenario C, although you can foresee that your sister will die from starvation, you do not intend her death in any way; her death is simply a side effect of your action of eating the bread.

Perhaps one of the most interesting things about this case is that within the doctrine of double effect we are able to observe the same outcome being produced by two scenarios where the harm is done directly, and one where the harm is done indirectly. Although the absolute deontologist would not label the action in scenario C to be morally permissible, they would consider it to be more morally permissible than the actions in scenarios A and B. Furthermore, the act in scenario C would even be the preferable act for a consequentialist; the goodness of the outcome is the highest out of all scenarios because you get to eat the bread without dealing with the guilt of directly causing the death of your sister. If we are ending up with the same conclusion regardless of which ethical approach were taking, are the additional moral factors weve analyzed truly morally significant?


I believe that intention has high moral significance in the context of evaluating harm. In the absence of intention, an individual should not be held morally responsible for their act of harm, because although they physically performed the act that caused the harm, they cannot be faulty for a negative outcome that they in no way anticipated or desired. Along the same lines, I also believe that the doctrine of double effect does not necessarily lead us to the correct evaluation of the harm that has been done. Even if the harm is an unintentional byproduct of an action, I dont agree that the action can be morally permissible if the harm is foreseeable. Lets go back to scenario C. This is not the same case of allowing harm as not pulling the lever in the trolley problem, because after eating the bread I dont have the means of saving my sister, therefore rather than allowing her to die, I am a mere observer of her death. However, I did at some point have the option of not eating the bread, and I always had the knowledge that if I were to eat the bread, she would starve to death. In this case, how different is my role in causing her harm in scenario C compared to scenario B? Am I not causing the harm as a means of achieving the goal of my survival in both scenarios? Is it really any more morally permissible for me to cause the harm indirectly even though I am aware that the harm will be caused? Does this awareness not indicate that the harm is a direct causation of my act? It does. Therefore, unless the harm is an unforeseeable byproduct of an act, it is not morally permissible in the context of the normative factor of intending harm.

Wednesday, November 25, 2015

Cleaning Up Pollution With Fungi

It’s no news that rapid industrialization has caused numerous environmental problems. Our most densely populated areas are cities of concrete and glass, where the sky is coated gray from car exhaust, and man-made lights replace stars for miles. In rural areas, drugs used in farming to treat diseases in the livestock leak into the water and soil, contaminating and negatively affecting all surrounding ecosystems, including the microbial communities (1). Furthermore, our water and soil are becoming increasingly contaminated with toxic metals, which are also detrimental to their respective ecosystems, as well as a high risk to human health (2).

Environmental contamination caused by industrial waste reduces the quality of the environment, and therefore the quality of life for all organisms. Traditionally, the issue of contamination has been approached by moving the contamination elsewhere, generally to landfills. Of course this does not actually fix the problem, it just gets rid of it in its original setting. Another method that has been used is destroying or transforming the contaminants to a harmless form via chemical decomposition (3). It isn’t hard to see how this method isn’t a great approach either; adding more chemicals to the mix causes further contamination.

The best alternative is bioremediation, and particularly mycoremediation. Bioremediation uses microorganisms that are already part of their environments to clean up pollution. Mycoremediation more specifically uses fungi. These fungi eat organic pollutants. Through the use of fertilizers and enhanced conditions, they grow more rapidly, and therefore breakdown the pollutants at a faster rate. This is a considerably better approach to solve the problem of environmental contamination.

Unfortunately, the field of mycoremediation has not been able to expand enough to be applied in practice. This is mainly due to the lack of funding for the field. The few studies that have been conducted on mycoremediation have all yielded successful results, which indicates that this is indeed a promising field of study. Funding for research in mycoremediation is crucial, for it is potentially one of the most preferable solutions to environmental contamination.

Fungi achieve the digestion of the contaminants by secreting extracellular enzymes that breakdown organic waste (4). A good example of the success of mycoremediation is seen in a study by Migliore et al. on the biodegradation of oxytetracycline by Pleurotus ostreatus. Oxytetracycline (OTC) is a drug that is heavily used on livestocks in intensive farming to treat diseases. Due to animal waste disposal, OTC contaminates water, sediments and soil, negatively affecting microbial community structures and natural systems. They cultured Pleurotus ostreatus with exposure to varying concentrations of OTC, and measured mycelial growth, extracellular enzyme secretion, and the degradation of OTC. Their results demonstrated that P. ostreatus survived and successfully grew even when exposed to high concentrations of the drug. While no OTC degradation was observed in the controls, P. ostreatus almost completely degraded the drug in a few days (1).

Valentin et al. conducted a study on the mycoremediation of contaminated wood and soil samples that was similarly successful. In order to really reflect the conditions of the setting their results would have potential use in, they used non-sterile conditions in their experiment. With the intentions of investigating white-rot and litter-decomposing fungi to treat contamination by chlorinated phenols present in sawmills, they inoculated non-sterile soil and wood — meaning the soil and wood had native microbial communities along with contamination — with nine fungi. The litter-decomposing fungus, Stropharia rugosoannulata, mineralized and degraded multiple contaminants at a significantly faster rate than indigenous microbes in soil. Therefore, S. rugosoannulata is a suitable fungus for mycoremediation of soil contaminated with chlorophenols. In wood, white-rot fungi grew and degraded contaminants faster than both indigenous degraders (which were barely present), and litter-decomposing fungi. These results show that S. rugosoannulata has particularly high potential to be used in mycoremediation of specifically sawmills containing chlorophenols (5). This study displays successful fungal growth as well as high degradation success in realistic conditions. It also pushes to further investigate the understudied litter-decomposing fungi for mycoremediation. Funding for more studies of this kind are necessary to improve our understanding of specific fungal interactions with contaminated environments.

Both these studies indicate successful usage of fungi in cleaning pollutants. Because this is a field that leans towards experimentation in rather specific contexts, thorough research must be done in a variety of contexts in order to ensure its applicability to real-life scenarios. However, the experimentation that has been done clearly shows the potential of mycoremediation. Even studies that have been done indicate the necessity for further research in the field in order to start applying their results in real life. Environmental contamination decreases the life quality of all organisms, and using fungi as remedies for our environment is a sustainable, natural, and affordable solution. With sufficient funding, this field could grow and become the number one cure for environmental pollution.


1.     Migliore, L. et al., “Biodegradation of oxytetracycline by Pleurotus ostreatus mycelium: a mycoremediation technique.” Journal of Hazardous Materials. 215-216, 227-232, 2012.
2.     Sharma, A., Sharma, H., “Role Of Vesicular Arbuscular Mycorrhiza In The Mycoremediation of Heavy Toxic Metals From Soil.” International Journal of Life Sciences Biotechnology and Pharma Research. 2, no. 3, 418-427, 2013.
3.    Vidali, M. "Bioremediation. An Overview*." Pure Applied Chemistry 73, no. 7, 1163-172. IUPAC, 2001.
4.     Adenipekun, C. O., Lawal, R. “Uses of mushrooms in bioremediation: A review.” Biotechnology and Molecular Biololgy Review, 7, no. 3, 62-68. Academic Journals, 2012.

5.     Valentin, L. et al., “Mycoremediation of wood and soil from an old sawmill area contaminated for decades.” Journal of Hazardous Materials. 260, 668-675, 2013

Sunday, November 1, 2015

The Human Mycobiome ;)

MYCOBIOME
Fungal diversity in the human skin microbiome
A discussion of the importance of fungi in microbial community composition and stability.


by Doğa Tekin

We used to associate bacteria with disease and disease only. In recent years, we’ve been becoming more comfortable with the idea of commensal bacterial presence in different microbial communities throughout our bodies. However, in this effort to accept friendly bacteria, we’ve completely ignored the same role played by fungi. Most of us still think of fungal interactions with humans to be solely pathogenic. Recent research within the up and coming field of the human microbiome has revealed that fungi play just as significant a role in microbial community composition and stability as bacteria do. 

Although most studies on the human microbiome have focused solely on bacteria, a new study performed by Findley et al. showed that our skin microbiome exhibits a vast amount of fungal diversity as well (1). The term ‘microbiota,’ which we are quite familiar with, is primarily used to describe bacterial communities, whereas ‘mycobiota’ can be used to describe the fungal component of our microbiome (2).  

Mycobiota on our skin consist of much more than toenail infections and athlete’s foot. Findley et al. demonstrated that the diversity and composition of microbial communities on our skin depends highly on the topography of the inhabited region. They analyzed 14 regions of the skin in 10 healthy adults to determine the genera and species composition of the mycobiota. Their results indicated the highest level of fungal diversity in the plantar heel, toenail and toe web. All other regions were primarily dominated by the genus Malassezia, which also displayed a higher level of species diversity in the three foot regions (see Fig. 1). This genus contains yeasts that have been known to be part of the natural human flora for over a century. Malassezia yeasts depend on lipids for survival, which is why they are commonly found in skin microbiomes. (3)
To test temporal stability, Findley et al. sampled six of the healthy volunteers one to three months later. Their results showed consistency in topography-based diversity, which indicates structural and temporal stability of the mycobiota. (1)
Furthermore, they investigated the bacterial profile of the same region using genomic sequencing. Their results indicated lower bacterial diversity compared to fungal diversity in foot regions, and higher bacterial diversity compared to fungal diversity in arm regions. This entails a high level of complexity in the composition of the skin microbiome, and suggests that the microbiota and mycobiota form based on different characteristics (1).
While Findley et al. focus on the skin, other studies reveal similar fungal diversity mycobiotic composition in different parts of the human body. For example, in a study of the oral mycobiota, Ghannoum et al. identified a total of 101 species in the oral cavities of 20 healthy individuals (4). This was the first study that identified the oral mycobiota. Although they did not include bacterial communities, the level of fungal diversity alone is sufficient to indicate a highly delicate ecosystem.
 The human microbiome is just like all ecosystems; organisms are linked through multiple layers and networks of interactions. In this sense, to understand changes in our microbiotic ecosystem especially those with the potential of causing us harm we must familiarize ourselves with all of the organisms that partake in it. Exploring the diversity of our fungal inhabitants is key to understanding our microbiome, and has potential applications to treat microbial infections. Research in this field has indicated a high level of complexity in fungal and bacterial interactions. The two communities influence each other directly and indirectly (5). Therefore, future implications of these studies are huge. Understanding the commensal inhabitants of our microbiomes and their interactions with each other and the environment can enable us to develop new and more successful therapies for fungal and bacterial pathogenicity. (6) 

REFERENCES

1. K. Findley et al., Nature 498, 367 (2013).
2. D. M. Underhill, I. D. Iliev, Nature Reviews Immunology 14, 405 (2014)
3. A. J. Kindo, J. Kalyani, S. Anandan, Indian Journal of Medical Microbiology, 22, 179 (2004)
4. M. A. Ghannoum et al., PLoS Pathog. 6.1, (2010)
5. A. Y. Peleg, D. A. Hogan, E. Mylonakis, Nature Reviews Microbiology 8, 340 (2010)

6. E. A. Grice et al., Genome Res. 18, 1043 (2008)