Natural Adaptation and The Role of Humans
Tauhid Nur Azhar
Lately there has been a heated debate on social media about efforts to prevent outbreaks of dengue fever using the Wolbachia method which has been researched and tested in several areas of Yogyakarta by the FKKMK UGM team and the World Mosquito Program/WMP. In fact, in explanations on various media platforms, Prof. Adi Utarini, the main researcher of the Wolbachia method, emphasized that the use of Wolbachia is a form of non-genetic engineering preventive effort that prioritizes the function and benefits of certain symbiotic bacterial traits.
This is what she said as quoted from the official website of the Indonesian Ministry of Health:
“Neither the wolbachia bacteria nor the mosquitoes as hosts are organisms resulting from genetic modifications carried out in the laboratory. Genetically, both the mosquito and wolbachia bacteria used are identical to organisms found in nature.”
Then the information conveyed by Dr. Riris Andono Ahmad, MPH, PhD as Director of the Tropical Medicine Center, Faculty of Medicine, Public Health and Nursing (FKKMK) Universitas Gadjah Mada, provides an overview of its effectiveness when used in trial processes in the Yogyakarta area.
There was a very significant decrease in the incidence of dengue fever, which was 77%, and a decrease in the rate of hospitalization or inpatient care for dengue patients by up to 86%.
In general, referring to various available scientific references, Wolbachia is a bacterium that is commonly found in arthropods and insects, and not in mammals. Specifically in the case of Aedes Aegypti mosquitoes, Wolbachia inserted into Aedes eggs can cut dengue virus transmission, among others through an inhibitory mechanism on virus growth within the bodies of female Aedes mosquitoes as hosts, and reduces the population of female mosquitoes without Wolbachia, because non-Wolbachia mosquito eggs will not be fertilized by Wolbachia-carrying male mosquitoes.
The mechanisms for inhibiting dengue virus replication in the bodies of female Aedes mosquitoes include several of the following mechanisms:
The nature of Wolbachia as an endosymbiotic bacterium that can infect female Aedes aegypti mosquitoes will promote:
1. Competition for Space and Resources, where Wolbachia bacteria compete with dengue virus to consume resources in the mosquito’s body. These bacteria consume nutrients and spaces that may be needed by the virus to replicate.
2. Activation of the Immune Response, where Wolbachia bacteria can modulate the mosquito’s immune system by activating immune responses, such as the production of antimicrobial peptides and melanization, which in turn can inhibit virus replication.
3. Changes in Cellular Environment, where Wolbachia bacteria can modulate the cellular environment in the mosquito’s body by producing compounds that do not support virus replication or even antagonize the virus.
reference:
1. Hedges LM, Brownlie JC, O’Neill SL, Johnson KN. (2008). Wolbachia and virus protection in insects. Science, 322(5902), 702–702.
2. Moreira LA, Iturbe-Ormaetxe I, Jeffery JA, et al. (2009). A Wolbachia symbiont in Aedes aegypti limits infection with dengue, Chikungunya, and Plasmodium. Cell, 139(7), 1268–1278.
Is the concept of symbionts and endosymbionts common and naturally occurring? Or is this merely the result of human engineering and intervention? Essentially, the processes of symbiosis and endosymbiosis and the presence of symbionts are common in nature. The author himself has studied these natural mechanisms for the purpose of doctoral dissertation research in the field of edible vaccines by “entrusting” genes in Lycopersicum esculantum sp. tomatoes.
There are many symbiotic mechanisms in nature that can be referenced. In fact, there is an endosymbiotic theory related to the existence of our vital energy-producing organelle, the mitochondria, which is suspected to originate from the endosymbiosis process of prokaryotic bacteria.
The endosymbiotic theory proposed by Lynn Margulis states that mitochondria, as well as other organelles such as chloroplasts in plant cells, originate from prokaryotic bacteria that establish symbiotic relationships with eukaryotic cells. Although this concept was initially controversial, most of the scientific community now accepts this theory.
According to this theory, the process of forming mitochondria begins with endosymbiosis, which is when one cell engulfs another. In the context of mitochondria, aerobic prokaryotic bacteria (requiring oxygen) are referred to as the ancestors of mitochondria. Here are the steps proposed in the endosymbiotic theory :
1. Phagocytosis:
A eukaryotic cell engulfs an aerobic prokaryotic bacterium through the mechanism of phagocytosis. Phagocytosis is the process of a cell engulfing and digesting particles or other cells.
2. Initial Symbiosis Process:
The swallowed prokaryotic bacterium is not fully digested and survives within the eukaryotic cell. A symbiotic relationship is formed, where the bacterium provides energy through aerobic respiration, while the eukaryotic cell provides protection and a source of nutrients.
3. Symbiotic Evolution:
Over millions of years, this symbiotic relationship evolves. The eukaryotic cell and the prokaryotic bacterium adapt to each other, and the bacterium loses some of its original functions and structures because the eukaryotic cell provides a more stable environment.
4. Genetic Alignment:
Some genes from the mitochondrial bacteria are transferred to the nucleus of the eukaryotic cell. This causes the eukaryotic cell to have greater control over the mitochondria.
reference:
1. Margulis, L. (1967). Origin of Eukaryotic Cells. Yale University Press.
2.Sagan, L. (1967). On the origin of mitosing cells. Journal of Theoretical Biology, 14(3), 255–274.
The author himself, in the initial research documented in the research proposal submitted by L, intended to insert one of the gene segments from the Human Papilloma virus, or more commonly known as HPV, into the genome sequence of tomato plants using a carrier vector in the form of a microbe named Agrobacterium tumefaciens.
Agrobacterium tumefaciens works by attaching to wounds or cuts on plants. This process involves several steps:
1. Release of Chemical Signals, where Agrobacterium detects chemical compounds produced by injured plants, such as phenolates and cinnamic acid. This triggers changes in the bacteria.
2. Activation of Genes on the Ti Plasmid, where Agrobacterium carries a Ti (Tumor-Inducing) plasmid, which has a number of genes associated with DNA transfer (T-DNA). Signals from the plant activate these genes.
3. Formation of Transfer Structure, where Agrobacterium forms a structure called a pilus or trichome, which assists in physical contact with plant cells.
4. Transfer of DNA (T-DNA), where T-DNA is transferred from Agrobacterium into the plant cell through the pilus. This process requires special proteins that form a channel to facilitate the transfer.
5. Integration of T-DNA into the Plant Genome, where once the T-DNA is inside the plant cell, it is integrated into the plant genome by a recombination mechanism.
6. Expression of Tumor-Inducing Genes, where the genes within the T-DNA cause the formation of tumor tissue in the plant that can provide conditions favorable for the growth of Agrobacterium.
This process can be utilized to “entrust” certain genes in plants. However, it should be noted that Agrobacterium is commonly found in nature and is responsible for transferring some genes between plants in a certain biome or plant habitat. The symbiotic traits obtained usually have beneficial effects for these plants, such as weather resistance, pest resistance, or changes in stem structure, leaves, and fruit composition.
Undeniably, from the results of deep observation or observation of various natural phenomena related to the exchange of genetic material, humans with their procreative nature have begun to develop various genetic modification methods to improve species according to the demands of evolving needs. Actually, not only in plants, but modification methods can be carried out in various species that of course have genes in their nucleic acid strands (DNA).
If we talk more specifically about plants, there are several methods and techniques used to modify plant genetics. Here are some of them:
1. Agrobacterium tumefaciens Transformation:
In this method, DNA transfer (T-DNA) from the Agrobacterium plasmid is inserted into the plant genome through interaction with the bacteria.
reference:
Gelvin, S. B. (2003). Agrobacterium-mediated plant transformation: the biology behind the “gene-jockeying” tool. Microbiology and Molecular Biology Reviews, 67(1), 16–37.
2. Protoplast Transformation:
This method involves removing the cell wall of the plant to produce a protoplast that can accept foreign DNA through transfection.
reference:
Davey, M. R., & Anthony, P. (2010). Plant protoplasts: status and biotechnological perspectives. Biotechnology Advances, 28(3), 219–234.
3. Gene Insertion with Gene Gun:
This method involves using gold or tungsten particles coated with DNA, which are shot into plant cells to deliver genetic material.
reference:
Sanford, J. C., Smith, F. D., & Russell, J. A. (1993). Optimizing the biolistic process for different biological applications. Methods in Enzymology, 217, 483–509.
4. Electroporation:
This method involves the application of an electric field to open the pores of plant cells, allowing the absorption of DNA.
reference:
Fromm, M., Taylor, L. P., & Walbot, V. (1985). Stable transformation of maize after gene transfer by electroporation. Nature, 317(6034), 741–744.
5. CRISPR-Cas9:
This method is a current system for editing genomes with high precision using the Cas9 enzyme and guide RNA.
reference:
Doudna, J. A., & Charpentier, E. (2014). The new frontier of genome engineering with CRISPR-Cas9. Science, 346(6213), 1258096.
6. Virus-Mediated Gene Transduction:
This method involves using viral vectors to deliver and insert genetic material into plants.
reference:
Chapman, S., Kavanagh, T., & Baulcombe, D. (1992). Potato virus X as a vector for gene expression in plants. The Plant Journal, 2(4), 549–557.
7. RNA Interference (RNAi):
This method involves the use of small RNAs to suppress or stop the expression of certain genes.
reference :
Baulcombe, D. (2004). RNA silencing in plants. Nature, 431(7006), 356–363.
The development of science and technology today has also brought us to the dimension of cognitive augmentation that has entered the phase of Artificial General Intelligence or AGI, which is classified into several levels, where at level 5, known as the Super Human level, various analysis capacities and cognitive functions have been developed up to procreation competencies that fall into the category of Super Human Narrow Artificial Intelligence, which among other things has given birth to Alpha Fold that can design the construction of molecular structures with very specific functions.
The next stage is the achievement of Artificial Super Intelligence or ASI, which seems to be achieved in the not too distant future with the increase in data processing capacity supported by discoveries in new material aspects and methods such as quantum computing.
The implementation of AI that is relevant to the development of biodesign, synthetic biology, and genetic modification includes subsets of machine learning such as deep learning, and it seems that the Knowledge Growing System developed by Dr. Arwin Sumari has great potential to be applied in this realm as well.
Several artificial intelligence (AI) methods used in supporting the process of plant genetic engineering involve complex data analysis, molecular design, and a deeper understanding of gene interactions. Here are some relevant AI methods.
1. Genomic Data Processing with Machine Learning:
This method involves using machine learning algorithms such as RNN to analyze large genomic data, identify patterns, and understand the relationship between genes and plant traits.
Reference:
Ching, T., Himmelstein, D. S., Beaulieu-Jones, B. K., Kalinin, A. A., Do, B. T., Way, G. P., … & Xie, W. (2018). Opportunities and obstacles for deep learning in biology and medicine. Journal of The Royal Society Interface, 15(141), 20170387.
2. Gene Function Prediction and Functional Genomics:
This method involves using machine learning algorithms such as DL to predict gene functions and identify important genomic elements.
Reference:
Angermueller, C., Pärnamaa, T., Parts, L., & Stegle, O. (2016). Deep learning for computational biology. Molecular Systems Biology, 12(7), 878.
3. Molecular Design with ML:
This method involves using machine learning algorithms, particularly Deep Learning and CNN, to design DNA molecules with specific properties, supporting genetic engineering design.
Reference: Nielsen, A. A., & Voigt, C. A. (2014). Deep learning to predict the lab-of-origin of engineered DNA. Nature Communications, 5, 5701.
4. Gene Expression Analysis with Deep Learning:
This method involves using artificial neural networks (deep neural networks) to analyze gene expression data and understand genetic regulation.
Reference:
Alipanahi, B., Delong, A., Weirauch, M. T., & Frey, B. J. (2015). Predicting the sequence specificities of DNA-and RNA-binding proteins by deep learning. Nature Biotechnology, 33(8), 831–838.
5. Genetic Optimization with Genetic Algorithms:
This method involves using genetic algorithms to optimize genetic design, considering various parameters and constraints.
Reference:
Marchisio, M. A., & Stelling, J. (2008). Computational design tools for synthetic biology. Current Opinion in Biotechnology, 19(6), 563–570.
6. Metabolomic Analysis with Data Mining Methods:
This method involves using data mining techniques to analyze metabolomic data, aiding understanding of plant metabolic pathways that can be genetically modified.
Reference:
Oliver, S. G., Winson, M. K., Kell, D. B., & Baganz, F. (1998). Systematic functional analysis of the yeast genome. Trends in Biotechnology, 16(9), 373–378.
From the various explanations above, we can see that the rapid development of science after the Sapiens brain revolution has brought us to a new era in understanding various processes and mechanisms of how the universe works around us. Some of these have been used as a basis of knowledge to create various breakthroughs that become part of the development of science and its utilization, which falls into the realm of technology as part of the foundation of civilization construction.
A simple example is building construction technology, which is a human need to adapt to their environment. To withstand the weather, and rest peacefully because they are protected from threats.
The buildings we know today are mostly made of concrete, cement, and bricks as well as various materials that make up their roofs. Cement itself has been known since ancient Egyptian times around the 5th century. At that time, cement was made from calcination or burning limestone used to build pyramids and other large buildings. Meanwhile, the ancient Romans and Greeks made cement using volcanic slag from volcanoes. Volcanic slag was mixed with quicklime and gypsum, which was then called Pozzolan Cement (Rahadja, 1990).
From the perspective of inorganic chemistry, the main ingredients contained in cement are lime (CaO), silicate (SiO2), alumina (Al2O3), ferrous oxide (Fe2O3), magnesite (MgO), and other oxides in small amounts (Rahadja, 1990).
Let’s imagine, the discovery of elements that eventually led us to placement based on chemical properties on Mendeleev’s periodic table. The first periodic system of elements was proposed by Antoine Lavoisier in 1789 by grouping elements based on their properties.
Research on the regularity of chemical elements continues to be carried out by many scientists such as Johann Wolfgang Dobreiner, Alexandre-Emile Beguyer de Chancourtois, John Newland, and Julius Lothar Meyes.
Actually, the idea of basic elements of nature has been going on since the early days of human civilization. The idea that there are a small number of initial elements of the universe began around 330 BC, when the Greek philosopher Aristotle proposed that everything is made from a mixture of one or more roots, an idea previously put forward by the Sicilian philosopher Empedocles. The four roots, which were later named elements by Plato, are earth, water, air, and fire.
Scientists or the Alchemists in the next generation who conducted a search through various continuous experimental processes, eventually began to discover the concept of elements as we know today.
One milestone that needs to be appreciated is the effort of a German merchant named Hennig Brand who in 1649, conducted an experiment to distill human urine and was able to produce a glowing white material, which was then named phosphorus. The discovery of the phosphorus element triggered the search for other elements and the definition and criteria related to chemical elements developed.
In 1661, Robert Boyle defined an element as “a substance that cannot be broken down into simpler substances through chemical reactions”.
From a series of search and discovery processes, we can make cement, as well as many other inventions, including fuel and packaging plastics, right?
So, if ASI has hybridized with communal cognitive intelligence integrated with social and industrial interaction processes, what will happen is a form of neocultural adaptation that will bring human civilization to become one of the hybrid species that might voluntarily undergo endosymbiosis processes with various biosynthesis devices as we can now see happening in nature like Agrobacterium or also Wolbachia, right?
