Summary
Highlights
The speaker, Dr. Ian Kenrich Pontanilla, a UP scientist and head of the DNA Barcoding Laboratory, is introduced. He specializes in evolutionary biology, molecular phylogenetics, and wildlife forensics. His lab partners with the Department of Environment and Natural Resources to develop DNA barcodes for Philippine endemic species and assist in cases of illegal wildlife trade. He also uses environmental DNA (eDNA) for detecting pathogens and introduced species. The session will cover bioinformatics and digital science information in the Philippine context, starting with the basics of DNA.
DNA is the genetic material containing instructions for all living organisms. Prokaryotic cells have DNA in their cytoplasm, while eukaryotic cells have DNA in the nucleus, mitochondria, and chloroplasts. DNA and RNA are nucleic acids, differing in their sugar backbone. Nucleotides, composed of a sugar, phosphate group, and a nitrogenous base (adenine, guanine, cytosine, thymine, uracil), form chains. These sequences, reaching billions in length, carry genetic information determining traits. DNA is double-stranded, connected by hydrogen bonds between complementary bases (adenine with thymine, cytosine with guanine).
The Central Dogma describes the flow of genetic information: DNA replicates itself, is transcribed into RNA, and RNA is translated into proteins. Reverse transcription also occurs, where RNA is used to produce DNA, as seen in some viruses. Proteins, essential for various bodily functions, are formed from amino acid sequences dictated by triplet codes (codons) on mRNA. The complete set of an organism's DNA is its genome, its RNA is the transcriptome, and its proteins make up the proteome. This information is considered digital, translatable between different 'languages' of biomolecules.
Genetic resources (living organisms) provide nucleotide sequence data from DNA and RNA, and protein sequences. These can be stored in digital repositories like GenBank for analysis. DNA sequences can be annotated for gene function, RNA sequences for gene expression, and protein sequences for structural and functional predictions. This information is crucial for industrial biotechnology, pharmaceutical development, synthetic biology, precision medicine, environmental research, and conservation efforts. A global collaboration maintains extensive databases of annotated sequences, utilized by millions of users annually.
DNA barcoding uses specific DNA sequences to identify species from unknown samples, useful in contexts like food authentication (e.g., halal meat, fish content in fish balls) and wildlife forensics to protect endangered species. Researchers collect DNA sequences of Philippine endemic species to populate databases for conservation and law enforcement. Genetic information also aids in developing testing kits (e.g., RT-PCR for COVID-19) and creating genetically modified organisms (GMOs) like BT corn and BT eggplant that produce their own pesticides. Additionally, synthetic biology, like developing a more effective painkiller from the conotoxin toxin, showcases the potential of understanding protein structures.
Countries have sovereign rights to regulate access to their genetic resources, requiring 'prior informed consent' and 'mutually agreed terms' for 'benefit sharing.' This means that the providing country or community should share in the advantages and profits derived from the use of their genetic resources. In the Philippines, collecting samples is guided by Republic Act 9147 (Wildlife Resources Conservation and Protection Act). Researchers must obtain permits from relevant government agencies (DENR, DA-BFAR, Palawan Council for Sustainable Development) and local government units.
The Philippines faces several challenges: limited capital and support for the local biotechnology industry, high costs of imported reagents and equipment, and a scarcity of bioinformaticians. Research and development in this field often have a long gestation period for returns on investment. Many endemic species, which are potential sources of genetic information, are threatened, making it difficult to extract and study their genetic data. The country lacks a comprehensive database of Philippine digital sequence information, relying on global databases. Some DSI from the Philippines is embargoed due to patent applications, often exploited by foreign companies without local benefit sharing. Countries with fewer restrictions on DSI benefit disproportionately.
Dr. Pontanilla addresses questions, stating that a starting bioinformatician in the Philippines can earn around 50,000 PHP per month. He explains that fully resurrecting extinct species is difficult because defining a species involves its interaction with the environment, which is hard to replicate. He emphasizes the need for government investment in science and technology to foster innovation and leadership in biotechnology, highlighting that the Philippines' investment is less than 1% of its GDP compared to 5-10% in other countries. He also discusses the current educational crisis, recommending curriculum review and integration of science and technology, and the ethical considerations of genetic screening and personal genetic information.
Dr. Pontanilla explains that inbreeding, or breeding between closely related individuals, increases the probability of offspring inheriting defective recessive genes. This is because closely related parents are more likely to share similar genetic defects. He also clarifies that genetic screening, such as the newborn screening required in the Philippines, involves extracting DNA from biological samples (like blood) to identify potential predispositions to certain diseases. He warns about the ethical implications of commercial genetic screening, where personal genetic information could be used for discriminatory purposes in the future.