MOLEKÜLER BİYOLOJİ AÇISINDAN İNSANDA İNCE AYAR ARGÜMANI

Yıl 2023, Sayı: 36, 347 - 368, 27.11.2023

Selcen Çelik Uzuner

https://doi.org/10.53844/flsf.1301688

Öz

İnce ayar argümanı, yaşam için en uygun şartları sağlayan bir evrenin varlığını açıklamak için fizik ve felsefenin ilgisini çekmiştir; ancak, özellikle moleküler biyoloji olmak üzere biyolojik bilimlerde kapsamlı bir şekilde tartışılmamıştır. Moleküler biyoloji, rasgele olaylara ve sınırlı yasalara sahip olduğu için fizik ve matematikten farklıdır. Bu bağlamda, biyolojik bilimler, sabitler ve yasalar için yeniden gözden geçirilmelidir. Oysa hücrelerdeki sistematik olaylar, moleküler biyolojide ince ayar argümanının tartışılabilme imkanını da beraberinde getirmektedir. Hücreler sistematik olarak molekül, gen ve genom düzeylerinde birçok moleküler mekanizmayı gerçekleştirir. Bu çalışma, hücrelerde ve genomdaki ince ayarların varlığını tartışmayı hedeflemektedir. Bu çalışma kapsamında molekül, gen, genom ve/veya organizma seviyelerinde meydana gelen 1) konum, 2) etkileşim, 3) miktar ve 4) zaman olmak üzere dört grup ince ayar parametresi önerilmektedir. Bu ince ayar parametreleri birbiriyle ilişkilendirilerek hayatı birlikte yönetmektedir. Dolayısıyla sistematik hücresel aktiviteler, bu karmaşıklığın insanın moleküler sistemindeki ince ayar ile yönetildiğine işaret etmektedir.

Anahtar Kelimeler

İnce ayar argümanı, moleküler biyoloji, felsefe, rastgelelik, akıllı tasarım

FINE-TUNING ARGUMENT FROM THE PERSPECTIVE OF MOLECULAR BIOLOGY IN HUMAN

Öz

Fine tuning argument has been of interest in physics and philosophy to answer the existence of the universe which is best fit for life; however, it has not been extensively applied to biological sciences in particular molecular biology. Molecular biology is different from physics and mathematics as it has stochastic events and limited laws. Biological sciences should be revisited for constants and laws. Though, the systematic events in the cells bring on the possibility of fine-tuning in molecular biology. Cells systematically perform many molecular mechanisms at molecule, gene and genome levels. This work focuses on the fine-tuning argument in the cells and the genome, and suggests four fine-tuning parameters 1) position, 2) interaction, 3) amount, and 4) time which occur at molecule, gene, genome and/or organism levels. These fine-tuning parameters are associated with each other and manage life together. Systematic cellular activities suggest that this complexity is managed by fine-tuning in human’s molecular system.

Anahtar Kelimeler

Fine tuning argument, molecular biology, philosophy, randomness, intelligent design

Kaynakça

• Barnes, L. A. ‘The Fine-Tuning of the Universe for Intelligent Life’. Publications of the Astronomical Society of Australia. Cambridge University Press, 2012. https://doi.org/10.1071/AS12015.
• Boice, Ashley, and Lisa Bouchier-Hayes. ‘Targeting Apoptotic Caspases in Cancer’. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier, 1 June 2020. https://doi.org/10.1016/j.bbamcr.2020.118688.
• Brooks, Christopher L., and Wei Gu. ‘P53 Ubiquitination: Mdm2 and Beyond’. Molecular Cell. Cell Press, 3 February 2006. https://doi.org/10.1016/j.molcel.2006.01.020.
• Çalışkan, Mehmet Ali. Rastlanti Bi̇li̇m ve Felsefeni̇n Ortasi. İstanbul: Küre Yayınları, 2018.
• Collins, Robin. ‘God, Design, and Fine-Tuning’. In God Matters: Readings in the Philosophy of Religion. Longman Publications, 2003.
• Colyvan, Mark, Jay L. Garfield, and Graham Priest. ‘Problems with the Argument from Fine Tuning’. Synthese 145, no. 3 (July 2005): 325–38. https://doi.org/10.1007/s11229-005-6195-0.
• Dhar, Pawan K., and Alessandro Giuliani. ‘Laws of Biology: Why so Few?’ Systems and Synthetic Biology 4, no. 1 (February 2010): 7–13. https://doi.org/10.1007/s11693-009-9049-0.
• Doko, Enis. ‘Does Fine-Tuning Need an Explanation?’ Kader 17, no. 1 (30 June 2019): 1–14. https://doi.org/10.18317/kaderdergi.552749.
• Fabregat, Antonio, Konstantinos Sidiropoulos, Guilherme Viteri, Pablo Marin-Garcia, Peipei Ping, Lincoln Stein, Peter D’Eustachio, and Henning Hermjakob. ‘Reactome Diagram Viewer: Data Structures and Strategies to Boost Performance.’ Bioinformatics (Oxford, England) 34, no. 7 (2018): 1208–14. https://doi.org/10.1093/bioinformatics/btx752.
• Friederich, Simon. ‘A New Fine-Tuning Argument for the Multiverse’. Foundations of Physics 49, no. 9 (20 March 2019): 1011–21. https://doi.org/10.1007/s10701-019-00246-2.
• Goeman, Jelle J. ‘Randomness and the Games of Science’. In The Challenge of Chance, 91–109. Springer, Cham, 2016. https://doi.org/10.1007/978-3-319-26300-7_5.
• Han, Na, Fang Yuan, Peng Xian, Nan Liu, Jianmin Liu, Haiyan Zhang, Huayong Zhang, Kai Yao, and Gangjun Yuan. ‘GADD45a Mediated Cell Cycle Inhibition Is Regulated by P53 in Bladder Cancer’. OncoTargets and Therapy 12 (2019): 7591–99. https://doi.org/10.2147/OTT.S222223.
• Han, Yuyan, Lixian Chen, Leonardo Baiocchi, Ludovica Ceci, Shannon Glaser, Heather Francis, Gianfranco Alpini, and Lindsey Kennedy. ‘Circadian Rhythm and Melatonin in Liver Carcinogenesis: Updates on Current Findings’. Critical ReviewsTM in Oncogenesis 26, no. 3 (2021): 69–85. https://doi.org/10.1615/critrevoncog.2021039881.
• Jjingo, Daudi, Andrew B Conley, Soojin V Yi, Victoria V Lunyak, and I King Jordan. ‘On the Presence and Role of Human Gene-Body DNA Methylation’. Oncotarget 3, no. 4 (2012): 462–74. https://doi.org/10.18632/oncotarget.497.
• Khare, Tarang, Shraddha Pai, Karolis Koncevicius, Mrinal Pal, Edita Kriukiene, Zita Liutkeviciute, Manuel Irimia, et al. ‘5-HmC in the Brain Is Abundant in Synaptic Genes and Shows Differences at the Exon-Intron Boundary’. Nature Structural and Molecular Biology 19, no. 10 (2012): 1037–44. https://doi.org/10.1038/nsmb.2372.
• Kitsera, Nataliya, Julia Allgayer, Edris Parsa, Nadine Geier, Martin Rossa, Thomas Carell, and Andriy Khobta. ‘Functional Impacts of 5-Hydroxymethylcytosine, 5-Formylcytosine, and 5-Carboxycytosine at a Single Hemi-Modified CpG Dinucleotide in a Gene Promoter’. Nucleic Acids Research 45, no. 19 (2 November 2017): 11033–42. https://doi.org/10.1093/nar/gkx718.
• Landsman, Klaas. ‘The Fine-Tuning Argument: Exploring the Improbability of Our Existence’. In The Challenge of Chance: A Multidisciplinary Approach from Science and the Humanities, 111–29. Springer, Cham, 2016. https://doi.org/10.1007/978-3-319-26300-7_6.
• Li, Xun, Matthias Wilmanns, Janet Thornton, and Maja Köhn. ‘Elucidating Human Phosphatase-Substrate Networks’. Science Signaling 6, no. 275 (14 May 2013). https://doi.org/10.1126/scisignal.2003203.
• Liu, Yansheng, Andreas Beyer, and Ruedi Aebersold. ‘On the Dependency of Cellular Protein Levels on MRNA Abundance’. Cell. Cell Press, 21 April 2016. https://doi.org/10.1016/j.cell.2016.03.014.
• Manson, Neil A. ‘The Fine-Tuning Argument’. Philosophy Compass 4, no. 1 (January 2009): 271–86. https://doi.org/10.1111/j.1747-9991.2008.00188.x.
• Meek, David W. ‘The P53 Response to DNA Damage’. DNA Repair. Elsevier, 1 August 2004. https://doi.org/10.1016/j.dnarep.2004.03.027.
• Michaels, Yale S., Mike B. Barnkob, Hector Barbosa, Toni A. Baeumler, Mary K. Thompson, Violaine Andre, Huw Colin-York, et al. ‘Precise Tuning of Gene Expression Levels in Mammalian Cells’. Nature Communications 10, no. 1 (18 February 2019): 1–12. https://doi.org/10.1038/s41467-019-08777-y.
• Mohtat, Davoud, and Katalin Susztak. ‘Fine Tuning Gene Expression: The Epigenome’. Seminars in Nephrology 30, no. 5 (September 2010): 468–76. https://doi.org/10.1016/j.semnephrol.2010.07.004.
• Pray, Leslie A. ‘Errors in DNA Replication’. Nature, 2008, 4–6.
• Rijo-Ferreira, Filipa, and Joseph S. Takahashi. ‘Genomics of Circadian Rhythms in Health and Disease’. Genome Medicine. BioMed Central, 17 December 2019. https://doi.org/10.1186/s13073-019-0704-0.
• Siu, Wai-Kwan. ‘Genetics of Monoamine Neurotransmitter Disorders.’ Translational Pediatrics 4, no. 2 (April 2015): 175–80. https://doi.org/10.3978/J.ISSN.2224-4336.2015.03.01.
• Tang, Qiaosi, Zhenyi Su, Wei Gu, and Anil K. Rustgi. ‘Mutant P53 on the Path to Metastasis’. Trends in Cancer. Cell Press, 1 January 2020. https://doi.org/10.1016/j.trecan.2019.11.004.
• Tegmark, Max. ‘Parallel Universes’. Scientific American 288, no. 5 (2003): 40–51.
• Terwijn, Sebastiaan A. ‘The Mathematical Foundations of Randomness’. In The Challenge of Chance: A Multidisciplinary Approach from Science and the Humanities, edited by Klass Landsman and Ellen van Wolde, 49–66. Springer, Cham, 2016. https://doi.org/10.1007/978-3-319-26300-7_3.
• Thorvaldsen, Steinar, and Ola Hössjer. ‘Using Statistical Methods to Model the Fine-Tuning of Molecular Machines and Systems’. Journal of Theoretical Biology 501 (21 September 2020): 110352. https://doi.org/10.1016/J.JTBI.2020.110352.
• Trevors, J. T., and M. H. Saier. ‘Three Laws of Biology’. Water, Air, and Soil Pollution. Springer, 2 December 2010. https://doi.org/10.1007/s11270-008-9925-3.
• Trott, Alexandra J., and Jerome S. Menet. ‘Regulation of Circadian Clock Transcriptional Output by CLOCK:BMAL1’. PLoS Genetics 14, no. 1 (1 January 2018): e1007156. https://doi.org/10.1371/journal.pgen.1007156.
• Wang, Jin, Kun Zhang, Li Xu, and Erkang Wang. ‘Quantifying the Waddington Landscape and Biological Paths for Development and Differentiation’. Proceedings of the National Academy of Sciences of the United States of America 108, no. 20 (17 May 2011): 8257–62. https://doi.org/10.1073/pnas.1017017108.
• Zhou, Jie, Shantao Li, Kevin K. Leung, Brian O’Donovan, James Y. Zou, Joseph L. DeRisi, and James A. Wells. ‘Deep Profiling of Protease Substrate Specificity Enabled by Dual Random and Scanned Human Proteome Substrate Phage Libraries’. Proceedings of the National Academy of Sciences of the United States of America 117, no. 41 (13 October 2020): 25464–75. https://doi.org/10.1073/pnas.2009279117.