User:LOTY Pierre Jean Daniel

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Designing Biological Machines


             By LOTY Pierre Jean-Daniel

Introduction Designing a biosoftware interfacing with man-made software through a bioprotocol is for sure an exciting project. It entails the convergence of various scientific domains (mainly Biology and Computer Science) in order to achieve a given goal. I once worked on a similar study in the area of social sciences. (For further information, see the entry: Sociotelecom: Social Optimization of Networks (SON), by LOTY Pierre Jean-Daniel). In that case, I had to face the need of a new protocol in order to apply digital network model to social network model (a social network here is a purposeful simplification of specific social interactions). I came to the conclusion that theoretical efforts to establish the principles governing the new field of study (sociotelecom), should run parallel with a more practical process aiming at identifying examples of social networks needing optimization (computerNetwotklike abilities). When various examples are found, a common thread would come out with the name sociotelecom. In the present instance, I equally believe in a twofold process. As researchers put theoretical efforts to tackle interdisciplinary challenges (for instance, the creation of a comprehensive bioprotocol model); engineers permeated by the overall reality of a particular experiment start developing workable, specific technologies that in turn will guide theoretical efforts. The present study, as a complete example, gives a conceptual overview of the programmable bacteria system.

I. DEFINING THE BIOPROTOCOL I do not believe in bioprotocols trying to mimic network protocols. The superiority of the evident design in nature stands as a compelling reason to design a protocol inspired from nature itself. Therefore, I design here a specific bioprotocol embedded in bacteria world.

1. The law of adaptation with subsequent loss of life This newly discovered law comes as a death stroke to evolution theory. We have the guarantee from the nature of the underlying philosophy (Intelligent Design) that the resulting application (programmable bacteria) is free of eugenics. First of all; let us recall the fundamental reasoning in evolutionism: natural selection coupled with mutations can transform a species S1 into a totally new species S2. Then, let us assume an individual S1 is under difficult conditions and undergoes modifications. What evolutionism did not consider is that at the same time, another process comes into play: difficult conditions cause S1 to enter into a resistant form, with a subsequent loss of life. What if conditions improve? As shown with the 1970’s research led by Peter and Rosemary Grant, “in the years following the drought, previous finches (with smaller beaks) again dominated the population. There was a reversal in the direction of the selection; the population subjected to selection oscillating back and forth each time the climate changed.” Thus, modifications tend to reduce if difficult conditions do not persist. However, there is absolute need of a directional, steady line of changes, should the species cross over to a new form of life. Now, in case difficult conditions do persist, two processes admittedly would run parallel. As modifications would increase, the “quantity of life” would decrease downward limits of tolerance. Modifications would at best help the species to cope, though with a subsequent loss of life. Surprisingly, the species S2 that admittedly evolved from S1 is found with high “quantity of life”. But S2, which is assumed to have undergone the full amount of modifications, should have undergone accordingly the full amount of adverse conditions. Thus, S2 would have been found with a lowest “quantity of life”. Indeed, natural selection, coupled with mutations leads necessarily toward the extinction of the species. As evidenced by the law of recurrent variation, the range of possible adaptations is preprogrammed in DNA, thus imposing inherent boundaries between kinds (groups of species defined only through lineage criteria).

2. Application The law of adaptation with subsequent loss of life, applied to bacteria world, results in fruitful applications. If conditions imposed upon bacteria (such as exposure to a given “quantity of oxygen”) are gradually harder, we observe various adaptations with subsequent loss of life. (Adaptation; Quantity of life) pairs are used to determine qualitative dosage. Each adaptation would be able to tackle a specific abnormality, or a given intensity of abnormality. From this reasoning springs the following protocol.

bioprotocol for programmable bacteria



1. Which bacteria? Recycling urine is the basic idea. In Africa, urine proved to be effective in combating several pains. Sadly, urine being highly toxic for the body led to administrative ban of urine as medicine (in Cameroon). Nevertheless, I came to the conclusion that the element responsible for treatment and the element responsible for toxicity were different, thus leading to designing a process to isolate useful bacteria from urine. 2. The recycling process We could get efficient bacteria from human body by recycling urine. The bacteria being from the body ensure that there is no side effect. Therefore, the applications derived will meet biosolutions standards. I even realized urine become more toxic outside human body, when coming in contact with oxygen. Therefore, our bacteria should be isolated under anaerobic conditions. The recycling process uses electricity to separate useful deposit from urine.


The population of bacteria is viewed as a complete, integrated system. Therefore, there is no need to modify or reproduce its elements separately. The design therein is superior and any attempt to manipulate the elements of the system without the system would prove environmentally damaging. The present approach is therefore about a clean, sustainable system. Consistently with the above comments, I design communication between man-made software and biosoftware (DNA program). Variable results are requested from DNA by imposing gradually harder conditions over the bacteria population, in order to provoke adaptation with subsequent loss of life. The needed adaptation is performed by the biomachine (the bacteria population itself) as it executes instructions from DNA (the biosoftware). MMS to biosphere communication is implemented through a man-made machine (Hardware made of electronic devices). The man-made machine (MMM) controls the environment, receiving commands from the user and forwading them to the MMS, which in turn gives lower level instructions to the MMM. The MMM, in charge of controlling the mixture of chemicals within the same architecture, will cause to modify conditions over bacteria (presence of oxygen), thus challenging DNA into a given adaptation. After a calculated time period (quantum), the MMM will verify adaptations have been made and give back an output to the user. The following chart describes the execution sequence. Biomachine system


           1: User commands to MMM
           2: MMM forwarding User command to MMS
           3: MMS giving instruction to MMM
           4: MMM translating instructions to biomachine
           5: Biosoftware giving instructions to biomachine
           6: MMM verifying adaptations after time quantum
           7: MMM issuing the final product


I hope you have been built up by the brief presentation of my biomachine. If you have any comment, do not hesitate to post. I also welcome any biological engineer that would like to work in the project. Any structure, company or state entity interested in funding the project will be given careful consideration.